diff --git a/CHANGES/Unreleased.txt b/CHANGES/Unreleased.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e8cb2db3ef28cab59760b7ace38009cdce93a60
--- /dev/null
+++ b/CHANGES/Unreleased.txt
@@ -0,0 +1,45 @@
+/**
+
+@page CHANGES-UNRELEASED Unreleased changes
+
+Include all fixes in branch 2.0 indicated in \ref CHANGES-2-0 .
+
+Changes from version 2.0 which are relevant for users:
+- Root-mean-square devations with align weights different from displace weights
+ are now considerably faster. This will affect \ref RMSD calculations plus
+ other variables based on RMSD.
+- Added WALKERS_MPI to \ref METAD, allowing to run multiple walkers in a mpi-based multi-replica framework.
+- Added ACCELERATION to \ref METAD, allowing to calculate on the fly the Metadynamics acceleration factor.
+- Added option PRECISION to set number of digits in \ref DUMPATOMS.
+- Added NDX_FILE and NDX_GROUP to action \ref GROUP, allowing to import atom lists from ndx files.
+- Small optimization in \ref WHOLEMOLECULES
+- Small optimization in \ref COORDINATION when NN and MM are even and D_0=0
+- Faster atom scattering with domain decomposition.
+- \ref SPRINT topological collective variables.
+- \ref CH3SHIFTS collective variable.
+- Improved multicolvar neighbor lists.
+- Maximum colvar as well as minimum colvar is now possible.
+- \ref COMMITTOR analysis.
+- Added possibility to use negative strides in atom ranges (e.g. 10-1:-3).
+- Added possibility to use \ref COORDINATION or \ref DHENERGY with NLIST in replica exchange simulations.
+- Added STRETCH flag to \ref switchingfunction.
+- Added possibility to read trajectories from \ref driver using VMD molfile
+ plugin (requires VMD plugins to be compiled and installed)
+
+Changes from version 2.0 which are relevant for developers:
+- Added regtests for plumed as a library (e.g. basic/rt-make-0). plumed command has an additional
+ flag (--is-installed) to probe if running from a compilation directory or from a fully installed copy
+ (this is needed for regtests to work properly).
+- Improved class Communicator. Many operations can now be done directly on Vectors, Tensors, std::vector and PLMD::Matrix.
+- Patches for GPL codes (QuantumEspresso and Gromacs) now also include
+ original code so as to simplify their modification.
+- Fixed dependencies among actions such that it is now possible (and reliable)
+ to use MPI calls inside Action::prepare()
+- colvar/CoordinationBase.cpp has been changed to make it faster. If you devised a class which inherits from here,
+ consider that CoordinationBase::pairing now needs _squared_ distance instead of distance
+- It is possible to run "make install" from subdirectories (e.g. from src/colvar)
+- There is a small script which disables/enables all optional modules (make mod-light/mod-heavy/mod-reset)
+- Added "-q" option to plumed patch
+
+
+*/
diff --git a/CHANGES/v2.0.txt b/CHANGES/v2.0.txt
index f0845dd334fda5718dd1767ea2343e703a332090..650b8360faa8b3fd281dfcb59492b20e8e092aba 100644
--- a/CHANGES/v2.0.txt
+++ b/CHANGES/v2.0.txt
@@ -6,19 +6,43 @@ Version 2.0.0
-------------
Version 2.0 is a complete rewrite, so there is no way to write a complete set of difference
-with respect to plumed 1.3. Here is a summary of the difference:
-- The input is simpler and more error proof. Many checks are now performed and in this way common errors are avoided.
+with respect to plumed 1.3. Here is a possibly incomplete summary of the difference:
+- The input is simpler, more flexible, and more error proof. Many checks are now performed and in this way common errors are avoided.
- The units are now the same for all MD codes. If you want to use a different unit than the default you set it in the input file.
- The analysis tools are now much more flexible. As an example of this it is now possible to write different collective variables with different frequencies
- Many complex collective variables are considerably faster than they were in plumed1. In particular, all variables based on RMSD distances.
- Centers of mass can be used as if they were atoms. Hence, unlike plumed 1.3, you can use center of mass positions in ALL collective variables.
- The virial contribution is now computed and passed to the MD code. Plumed can thus now be used to perform biased NPT simulations
+- Variables can be dumped on different files and with different files, and are
+ computed only when this is necessary.
+- PLUMED is now compiled as a separate library. This simplifies the patching
+ procedure, but might require some extra work to configure PLUMED properly.
+ Since PLUMED can be loaded as a shared library, it is possible to setup
+ everything such that PLUMED and MD codes can be updated independently from each
+ other.
In addition, it is now much easier to contribute new functionality to the code because:
- There is a much simpler interface between plumed and the base MD codes. This makes it much easier to add plumed to a new MD code.
- There is C++ object oriented programming and full compatibility with the C++ standard library
-- A modular structure
-- Developer and user documentation
+- A modular structure
+- New collective variables and methods can be released independently
+- There is an extensive developer documentation
+- User documentation is provided together inside the implementation files
+- Interfacing with MD codes is simpler. Hopefully, in the future, these
+ interface will be maitained by the developers of the MD codes
+ independently from PLUMED developers. This will allow more MD codes
+ to be compatible with PLUMED.
+
+Caveats:
+- PLUMED 2 input file (plumed.dat) has a syntax which is not
+ compatible with PLUMED 1.
+ Transition should be easy, but cannot
+ be done just using the new version with the old input file.
+- PLUMED 2 is written in C++, thus requires a C++ compiler
+- PLUMED 2 may not include all the features that were available
+ in PLUMED 1.
+
+A tutorial explaining how to move from PLUMED 1 to PLUMED 2 is available (see \ref moving).
Version 2.0.1
-------------
@@ -45,7 +69,14 @@ Unreleased changes
-------------
See <a href="http://github.com/plumed/plumed2/tree/v2.0">branch v2.0 on git repository</a>.
-There are currently no unreleased changes.
+For users:
+- Added full reference (page/number) to published paper in doc and log.
+- Fixed a bug in file backups (only affecting Windows version - thanks to T. Giorgino).
+- Several small fixes in documentation and log file.
+
+For developers:
+- Fixed makefile dependencies in some auxiliary files in src/lib (src/lib/*cmake and src/lib/*inc).
+- Several small fixes in documentation.
*/
diff --git a/Makefile b/Makefile
index 43fd254694a61e3a9759ed29aa9fb26dbcec6778..1f6a0c49e044db24e42e57a8f2a655d6868b941a 100644
--- a/Makefile
+++ b/Makefile
@@ -1,10 +1,10 @@
-include Makefile.conf
-SRCDIRS = src test
-SUBDIRS = $(SRCDIRS) user-doc developer-doc regtest
+SRCDIRS := src test
+SUBDIRS := $(SRCDIRS) user-doc developer-doc regtest
-SUBDIRSCLEAN=$(addsuffix .clean,$(SUBDIRS))
+SUBDIRSCLEAN:=$(addsuffix .clean,$(SUBDIRS))
.PHONY: all lib clean $(SRCDIRS) doc docclean check
diff --git a/patches/gromacs-4.5.5.config b/patches/gromacs-4.5.5.config
index c4c96cc70c23ae5ce30c003563e8c5e5a23acc93..8529732bb2d56c68645d017d87ec94464e22f7e3 100644
--- a/patches/gromacs-4.5.5.config
+++ b/patches/gromacs-4.5.5.config
@@ -18,3 +18,10 @@ function plumed_after_revert(){
mv src/kernel/Makefile.plumedbck src/kernel/Makefile
}
+function plumed_patch_info(){
+ echo ""
+ echo "PLUMED can be incorporated into gromacs using a simple patching procedure."
+ echo "Patching must be done _after_ gromacs has been configured but _before_ gromacs is compiled"
+ echo
+ echo "For more information on gromacs you should visit http://www.gromacs.org"
+}
diff --git a/patches/gromacs-4.6.3.config b/patches/gromacs-4.6.3.config
index a5d00fcea22295d52544fcd345e60947ff7553ef..b5d89332bfd90c7da73c33769c3f5ff3e8529642 100644
--- a/patches/gromacs-4.6.3.config
+++ b/patches/gromacs-4.6.3.config
@@ -4,3 +4,11 @@ function plumed_preliminary_test(){
# check if the README contains the word GROMACS and if gromacs has been already configured
grep -q GROMACS README 1>/dev/null 2>/dev/null
}
+
+function plumed_patch_info(){
+ echo ""
+ echo "PLUMED can be incorporated into gromacs using a simple patching procedure."
+ echo "Patching must be done _before_ the cmake command is invoked"
+ echo
+ echo "For more information on gromacs you should visit http://www.gromacs.org"
+}
diff --git a/patches/gromacs-4.6.3.diff b/patches/gromacs-4.6.3.diff
deleted file mode 100644
index 652e9523a19e005a57da4c9bb6bb98ed6e9adaac..0000000000000000000000000000000000000000
--- a/patches/gromacs-4.6.3.diff
+++ /dev/null
@@ -1,490 +0,0 @@
-patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/CMakeLists.txt" << \EOF_EOF
---- ./src/kernel/CMakeLists.txt.preplumed
-+++ ./src/kernel/CMakeLists.txt
-@@ -31,10 +31,12 @@
- #
- # To help us fund GROMACS development, we humbly ask that you cite
- # the research papers on the package. Check out http://www.gromacs.org.
- #
-
-+include(${CMAKE_SOURCE_DIR}/Plumed.cmake)
-+
- set(GMXPREPROCESS_SOURCES
- add_par.c
- calc_verletbuf.c
- compute_io.c
- convparm.c
-@@ -121,11 +123,11 @@
- set_target_properties(${PROGRAM} PROPERTIES OUTPUT_NAME "${PROGRAM}${GMX_BINARY_SUFFIX}")
- endforeach()
-
- add_executable(mdrun ${MDRUN_SOURCES} main.c)
- gmx_add_man_page(mdrun)
--target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
-+target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS} ${PLUMED_LOAD})
- set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}" COMPILE_FLAGS "${OpenMP_C_FLAGS}")
-
- if(GMX_OPENMM)
- target_link_libraries(mdrun openmm_api_wrapper)
- endif()
-EOF_EOF
-patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF
---- ./src/kernel/md.c.preplumed
-+++ ./src/kernel/md.c
-@@ -91,10 +91,16 @@
- #include "membed.h"
- #include "types/nlistheuristics.h"
- #include "types/iteratedconstraints.h"
- #include "nbnxn_cuda_data_mgmt.h"
-
-+/* PLUMED */
-+#include "../../Plumed.h"
-+extern int plumedswitch;
-+extern plumed plumedmain;
-+/* END PLUMED */
-+
- #ifdef GMX_LIB_MPI
- #include <mpi.h>
- #endif
- #ifdef GMX_THREAD_MPI
- #include "tmpi.h"
-@@ -235,10 +241,14 @@
- /* PME load balancing data for GPU kernels */
- pme_load_balancing_t pme_loadbal = NULL;
- double cycles_pmes;
- gmx_bool bPMETuneTry = FALSE, bPMETuneRunning = FALSE;
-
-+/* PLUMED */
-+ int plumedNeedsEnergy;
-+/* END PLUMED */
-+
- #ifdef GMX_FAHCORE
- /* Temporary addition for FAHCORE checkpointing */
- int chkpt_ret;
- #endif
-
-@@ -715,10 +725,50 @@
- }
- }
- fprintf(fplog, "\n");
- }
-
-+ /* PLUMED */
-+ if(plumedswitch){
-+ if(cr->ms && cr->ms->nsim>1) {
-+ if(MASTER(cr)) plumed_cmd(plumedmain,"GREX setMPIIntercomm",&cr->ms->mpi_comm_masters);
-+ if(PAR(cr)){
-+ if(DOMAINDECOMP(cr)) {
-+ plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->dd->mpi_comm_all);
-+ }else{
-+ plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->mpi_comm_mysim);
-+ }
-+ }
-+ plumed_cmd(plumedmain,"GREX init",NULL);
-+ }
-+ if(PAR(cr)){
-+ if(DOMAINDECOMP(cr)) {
-+ plumed_cmd(plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
-+ }else{
-+ plumed_cmd(plumedmain,"setMPIComm",&cr->mpi_comm_mysim);
-+ }
-+ }
-+ plumed_cmd(plumedmain,"setNatoms",&top_global->natoms);
-+ plumed_cmd(plumedmain,"setMDEngine","gromacs");
-+ plumed_cmd(plumedmain,"setLog",fplog);
-+ real real_delta_t;
-+ real_delta_t=ir->delta_t;
-+ plumed_cmd(plumedmain,"setTimestep",&real_delta_t);
-+ plumed_cmd(plumedmain,"init",NULL);
-+
-+ if(PAR(cr)){
-+ if(DOMAINDECOMP(cr)) {
-+ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
-+ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
-+ }else{
-+ plumed_cmd(plumedmain,"setAtomsNlocal",&mdatoms->homenr);
-+ plumed_cmd(plumedmain,"setAtomsContiguous",&mdatoms->start);
-+ }
-+ }
-+ }
-+ /* END PLUMED */
-+
- /* Set and write start time */
- runtime_start(runtime);
- print_date_and_time(fplog, cr->nodeid, "Started mdrun", runtime);
- wallcycle_start(wcycle, ewcRUN);
- if (fplog)
-@@ -1031,10 +1081,17 @@
- vsite, shellfc, constr,
- nrnb, wcycle,
- do_verbose && !bPMETuneRunning);
- wallcycle_stop(wcycle, ewcDOMDEC);
- /* If using an iterative integrator, reallocate space to match the decomposition */
-+
-+ /* PLUMED */
-+ if(plumedswitch){
-+ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
-+ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
-+ }
-+ /* END PLUMED */
- }
- }
-
- if (MASTER(cr) && do_log && !bFFscan)
- {
-@@ -1176,16 +1233,39 @@
- /* The coordinates (x) are shifted (to get whole molecules)
- * in do_force.
- * This is parallellized as well, and does communication too.
- * Check comments in sim_util.c
- */
-+
-+ /* PLUMED */
-+ plumedNeedsEnergy=0;
-+ if(plumedswitch){
-+ long int lstep=step; plumed_cmd(plumedmain,"setStepLong",&lstep);
-+ plumed_cmd(plumedmain,"setPositions",&state->x[mdatoms->start][0]);
-+ plumed_cmd(plumedmain,"setMasses",&mdatoms->massT[mdatoms->start]);
-+ plumed_cmd(plumedmain,"setCharges",&mdatoms->chargeA[mdatoms->start]);
-+ plumed_cmd(plumedmain,"setBox",&state->box[0][0]);
-+ plumed_cmd(plumedmain,"prepareCalc",NULL);
-+ plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
-+ }
-+ /* END PLUMED */
- do_force(fplog, cr, ir, step, nrnb, wcycle, top, top_global, groups,
- state->box, state->x, &state->hist,
- f, force_vir, mdatoms, enerd, fcd,
- state->lambda, graph,
- fr, vsite, mu_tot, t, outf->fp_field, ed, bBornRadii,
-- (bNS ? GMX_FORCE_NS : 0) | force_flags);
-+ (plumedNeedsEnergy? GMX_FORCE_ENERGY : 0) |(bNS ? GMX_FORCE_NS : 0) | force_flags);
-+ /* PLUMED */
-+ if(plumedswitch){
-+ if(plumedNeedsEnergy) plumed_cmd(plumedmain,"setEnergy",&enerd->term[F_EPOT]);
-+ plumed_cmd(plumedmain,"setForces",&f[mdatoms->start][0]);
-+ plumed_cmd(plumedmain,"setVirial",&force_vir[0][0]);
-+ plumed_cmd(plumedmain,"performCalc",NULL);
-+ if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
-+ do_per_step(step,repl_ex_nst)) plumed_cmd(plumedmain,"GREX savePositions",NULL);
-+ }
-+ /* END PLUMED */
- }
-
- GMX_BARRIER(cr->mpi_comm_mygroup);
-
- if (bTCR)
-EOF_EOF
-patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/mdrun.c" << \EOF_EOF
---- ./src/kernel/mdrun.c.preplumed
-+++ ./src/kernel/mdrun.c
-@@ -56,10 +56,16 @@
- #endif
-
- /* afm stuf */
- #include "pull.h"
-
-+/* PLUMED */
-+#include "../../Plumed.h"
-+int plumedswitch;
-+plumed plumedmain;
-+/* END PLUMED */
-+
- int cmain(int argc, char *argv[])
- {
- const char *desc[] = {
- "The [TT]mdrun[tt] program is the main computational chemistry engine",
- "within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
-@@ -399,10 +405,11 @@
- { efLOG, "-rs", "rotslabs", ffOPTWR },
- { efLOG, "-rt", "rottorque", ffOPTWR },
- { efMTX, "-mtx", "nm", ffOPTWR },
- { efNDX, "-dn", "dipole", ffOPTWR },
- { efRND, "-multidir", NULL, ffOPTRDMULT},
-+ { efDAT, "-plumed", "plumed", ffOPTRD }, /* PLUMED */
- { efDAT, "-membed", "membed", ffOPTRD },
- { efTOP, "-mp", "membed", ffOPTRD },
- { efNDX, "-mn", "membed", ffOPTRD }
- };
- #define NFILE asize(fnm)
-@@ -731,19 +738,50 @@
- }
-
- ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
- ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
- ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
-+ /* PLUMED */
-+ plumedswitch=0;
-+ if (opt2bSet("-plumed",NFILE,fnm)) plumedswitch=1;
-+ if(plumedswitch){
-+ int plumed_is_there=0;
-+ int real_precision=sizeof(real);
-+ real energyUnits=1.0;
-+ real lengthUnits=1.0;
-+ real timeUnits=1.0;
-+
-+
-+ if(!plumed_installed()){
-+ gmx_fatal(FARGS,"Plumed is not available. Check your PLUMED_KERNEL variable.");
-+ }
-+ plumedmain=plumed_create();
-+ plumed_cmd(plumedmain,"setRealPrecision",&real_precision);
-+ // this is not necessary for gromacs units:
-+ plumed_cmd(plumedmain,"setMDEnergyUnits",&energyUnits);
-+ plumed_cmd(plumedmain,"setMDLengthUnits",&lengthUnits);
-+ plumed_cmd(plumedmain,"setMDTimeUnits",&timeUnits);
-+ //
-+ plumed_cmd(plumedmain,"setPlumedDat",ftp2fn(efDAT,NFILE,fnm));
-+ plumedswitch=1;
-+ }
-+ /* END PLUMED */
-
- rc = mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose, bCompact,
- nstglobalcomm, ddxyz, dd_node_order, rdd, rconstr,
- dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
- nbpu_opt[0],
- nsteps, nstepout, resetstep,
- nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
- pforce, cpt_period, max_hours, deviceOptions, Flags);
-
-+ /* PLUMED */
-+ if(plumedswitch){
-+ plumed_finalize(plumedmain);
-+ }
-+ /* END PLUMED */
-+
- gmx_finalize_par();
-
- if (MULTIMASTER(cr))
- {
- thanx(stderr);
-EOF_EOF
-patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/repl_ex.c" << \EOF_EOF
---- ./src/kernel/repl_ex.c.preplumed
-+++ ./src/kernel/repl_ex.c
-@@ -51,10 +51,16 @@
- #include "names.h"
- #include "mvdata.h"
- #include "domdec.h"
- #include "partdec.h"
-
-+/* PLUMED */
-+#include "../../Plumed.h"
-+extern int plumedswitch;
-+extern plumed plumedmain;
-+/* END PLUMED */
-+
- #define PROBABILITYCUTOFF 100
- /* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
-
- enum {
- ereTEMP, ereLAMBDA, ereENDSINGLE, ereTL, ereNR
-@@ -111,18 +117,20 @@
-
- snew(qall, ms->nsim);
- qall[re->repl] = q;
- gmx_sum_sim(ms->nsim, qall, ms);
-
-- bDiff = FALSE;
-- for (s = 1; s < ms->nsim; s++)
-- {
-- if (qall[s] != qall[0])
-- {
-+ /* PLUMED */
-+ //bDiff = FALSE;
-+ //for (s = 1; s < ms->nsim; s++)
-+ //{
-+ // if (qall[s] != qall[0])
-+ // {
- bDiff = TRUE;
-- }
-- }
-+ // }
-+ //}
-+ /* END PLUMED */
-
- if (bDiff)
- {
- /* Set the replica exchange type and quantities */
- re->type = ere;
-@@ -255,10 +263,14 @@
- for (i = 0; i < re->nrepl; i++)
- {
- re->ind[i] = i;
- }
-
-+ /* PLUMED */
-+ // plumed2: check if we want alternative patterns (i.e. for bias-exchange metaD)
-+ // in those cases replicas can share the same temperature.
-+ /*
- if (re->type < ereENDSINGLE)
- {
-
- for (i = 0; i < re->nrepl; i++)
- {
-@@ -275,10 +287,12 @@
- gmx_fatal(FARGS, "Two replicas have identical %ss", erename[re->type]);
- }
- }
- }
- }
-+ */
-+ /* END PLUMED */
-
- /* keep track of all the swaps, starting with the initial placement. */
- snew(re->allswaps, re->nrepl);
- for (i = 0; i < re->nrepl; i++)
- {
-@@ -976,10 +990,14 @@
- for (i = 0; i < re->nrepl; i++)
- {
- pind[i] = re->ind[i];
- }
-
-+ /* PLUMED */
-+ int plumed_test_exchange_pattern=0;
-+ /* END PLUMED */
-+
- if (bMultiEx)
- {
- /* multiple random switch exchange */
- for (i = 0; i < re->nex; i++)
- {
-@@ -1045,19 +1063,56 @@
- }
- else
- {
- /* standard nearest neighbor replica exchange */
- m = (step / re->nst) % 2;
-+ /* PLUMED */
-+ if(plumedswitch){
-+ int partner=re->repl;
-+ plumed_cmd(plumedmain,"getExchangesFlag",&plumed_test_exchange_pattern);
-+ if(plumed_test_exchange_pattern>0){
-+ int *list;
-+ snew(list,re->nrepl);
-+ plumed_cmd(plumedmain,"setNumberOfReplicas",&(re->nrepl));
-+ plumed_cmd(plumedmain,"getExchangesList",list);
-+ for(i=0; i<re->nrepl; i++) re->ind[i]=list[i];
-+ sfree(list);
-+ }
-+
-+ for(i=1; i<re->nrepl; i++) {
-+ if (i % 2 != m) continue;
-+ a = re->ind[i-1];
-+ b = re->ind[i];
-+ if(re->repl==a) partner=b;
-+ if(re->repl==b) partner=a;
-+ }
-+ plumed_cmd(plumedmain,"GREX setPartner",&partner);
-+ plumed_cmd(plumedmain,"GREX calculate",NULL);
-+ plumed_cmd(plumedmain,"GREX shareAllDeltaBias",NULL);
-+ }
-+ /* END PLUMED */
- for (i = 1; i < re->nrepl; i++)
- {
- a = re->ind[i-1];
- b = re->ind[i];
-
- bPrint = (re->repl == a || re->repl == b);
- if (i % 2 == m)
- {
- delta = calc_delta(fplog, bPrint, re, a, b, a, b);
-+ /* PLUMED */
-+ if(plumedswitch){
-+ real adb,bdb,dplumed;
-+ char buf[300];
-+ sprintf(buf,"GREX getDeltaBias %d",a); plumed_cmd(plumedmain,buf,&adb);
-+ sprintf(buf,"GREX getDeltaBias %d",b); plumed_cmd(plumedmain,buf,&bdb);
-+ dplumed=adb*re->beta[a]+bdb*re->beta[b];
-+ delta+=dplumed;
-+ if (bPrint)
-+ fprintf(fplog,"dplumed = %10.3e dE_Term = %10.3e (kT)\n",dplumed,delta);
-+ }
-+ /* END PLUMED */
- if (delta <= 0)
- {
- /* accepted */
- prob[i] = 1;
- bEx[i] = TRUE;
-@@ -1077,15 +1132,26 @@
- }
- re->prob_sum[i] += prob[i];
-
- if (bEx[i])
- {
-+ /* PLUMED */
-+ if(!plumed_test_exchange_pattern) {
-+ /* standard neighbour swapping */
- /* swap these two */
- tmp = pind[i-1];
- pind[i-1] = pind[i];
- pind[i] = tmp;
- re->nexchange[i]++; /* statistics for back compatibility */
-+ } else {
-+ /* alternative swapping patterns */
-+ tmp = pind[a];
-+ pind[a] = pind[b];
-+ pind[b] = tmp;
-+ re->nexchange[i]++; /* statistics for back compatibility */
-+ }
-+ /* END PLUMED */
- }
- }
- else
- {
- prob[i] = -1;
-@@ -1097,10 +1163,19 @@
- print_prob(fplog, "pr", re->nrepl, prob);
- fprintf(fplog, "\n");
- re->nattempt[m]++;
- }
-
-+ /* PLUMED */
-+ if(plumed_test_exchange_pattern>0) {
-+ for (i = 0; i < re->nrepl; i++)
-+ {
-+ re->ind[i] = i;
-+ }
-+ }
-+ /* END PLUMED */
-+
- /* record which moves were made and accepted */
- for (i = 0; i < re->nrepl; i++)
- {
- re->nmoves[re->ind[i]][pind[i]] += 1;
- re->nmoves[pind[i]][re->ind[i]] += 1;
-@@ -1306,10 +1381,14 @@
- * exchanges. */
- /* Where each replica ends up after the exchange attempt(s). */
- /* The order in which multiple exchanges will occur. */
- gmx_bool bThisReplicaExchanged = FALSE;
-
-+ /* PLUMED */
-+ if(plumedswitch)plumed_cmd(plumedmain,"GREX prepare",NULL);
-+ /* END PLUMED */
-+
- if (MASTER(cr))
- {
- replica_id = re->repl;
- test_for_replica_exchange(fplog, cr->ms, re, enerd, det(state_local->box), step, time);
- prepare_to_do_exchange(fplog, re->destinations, replica_id, re->nrepl, &maxswap,
-@@ -1355,14 +1434,14 @@
- exchange_partner = re->order[replica_id][j];
-
- if (exchange_partner != replica_id)
- {
- /* Exchange the global states between the master nodes */
-- if (debug)
-- {
-- fprintf(debug, "Exchanging %d with %d\n", replica_id, exchange_partner);
-- }
-+ //if (debug)
-+ //{
-+ fprintf(fplog, "Exchanging %d with %d\n", replica_id, exchange_partner);
-+ //}
- exchange_state(cr->ms, exchange_partner, state);
- }
- }
- /* For temperature-type replica exchange, we need to scale
- * the velocities. */
-EOF_EOF
diff --git a/patches/gromacs-4.6.3.diff/src/kernel/CMakeLists.txt b/patches/gromacs-4.6.3.diff/src/kernel/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ed862a7cab99b767626ee93d3b2fdf298f0abf4
--- /dev/null
+++ b/patches/gromacs-4.6.3.diff/src/kernel/CMakeLists.txt
@@ -0,0 +1,197 @@
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# David van der Spoel, Berk Hess, Erik Lindahl, and including many
+# others, as listed in the AUTHORS file in the top-level source
+# directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+#
+
+include(${CMAKE_SOURCE_DIR}/Plumed.cmake)
+
+set(GMXPREPROCESS_SOURCES
+ add_par.c
+ calc_verletbuf.c
+ compute_io.c
+ convparm.c
+ gen_ad.c
+ gen_vsite.c
+ genhydro.c
+ gpp_atomtype.c
+ gpp_bond_atomtype.c
+ h_db.c
+ hackblock.c
+ hizzie.c
+ nm2type.c
+ pdb2top.c
+ pgutil.c
+ readir.c
+ readpull.c
+ readadress.c
+ readrot.c
+ resall.c
+ sorting.c
+ specbond.c
+ ter_db.c
+ tomorse.c
+ topdirs.c
+ topexcl.c
+ topio.c
+ toppush.c
+ topshake.c
+ toputil.c
+ tpbcmp.c
+ vsite_parm.c
+ fflibutil.c
+ xlate.c)
+
+set(MDRUN_SOURCES
+ gctio.c ionize.c runner.c
+ do_gct.c repl_ex.c xutils.c pme_loadbal.c
+ md.c mdrun.c genalg.c membed.c)
+
+add_library(gmxpreprocess ${GMXPREPROCESS_SOURCES})
+target_link_libraries(gmxpreprocess md)
+set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME "gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
+ COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+
+if(GMX_GPU)
+ include_directories(${CMAKE_SOURCE_DIR}/src/gmxlib/gpu_utils)
+endif()
+
+if(GMX_OPENMM)
+ # Even though the OpenMM build has "moved to contrib", many things
+ # have be be done from within the scope of the CMakeLists.txt that
+ # builds its mdrun, and that is here
+ list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/src/contrib)
+ find_package(OpenMM)
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+ include(${CMAKE_SOURCE_DIR}/src/contrib/BuildMdrunOpenMM.cmake)
+endif(GMX_OPENMM)
+
+if(GMX_GPU OR GMX_FORCE_CXX)
+ set_source_files_properties(main.c PROPERTIES LANGUAGE CXX)
+ if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+ set_source_files_properties(main.c PROPERTIES COMPILE_FLAGS "-x c++")
+ endif()
+endif()
+
+if(GMX_FAHCORE)
+ add_library(fahcore ${MDRUN_SOURCES})
+else(GMX_FAHCORE)
+
+set(GMX_KERNEL_PROGRAMS
+ grompp tpbconv pdb2gmx g_protonate gmxdump g_x2top gmxcheck)
+if (NOT GMX_NO_QUOTES)
+ set(GMX_KERNEL_PROGRAMS ${GMX_KERNEL_PROGRAMS} g_luck)
+endif (NOT GMX_NO_QUOTES)
+
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+ add_executable(${PROGRAM} ${PROGRAM}.c main.c)
+ if (NOT ${PROGRAM} STREQUAL "g_luck")
+ gmx_add_man_page(${PROGRAM})
+ endif()
+ target_link_libraries(${PROGRAM} gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
+ set_target_properties(${PROGRAM} PROPERTIES OUTPUT_NAME "${PROGRAM}${GMX_BINARY_SUFFIX}")
+endforeach()
+
+add_executable(mdrun ${MDRUN_SOURCES} main.c)
+gmx_add_man_page(mdrun)
+target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS} ${PLUMED_LOAD})
+set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}" COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+if(GMX_OPENMM)
+ target_link_libraries(mdrun openmm_api_wrapper)
+endif()
+
+# Construct component groups for installation; note that a component may
+# belong to only one group
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+ set(CPACK_COMPONENT_${PROGRAM}_GROUP tools)
+endforeach()
+set(CPACK_COMPONENT_MDRUN_GROUP mdrun)
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS} mdrun)
+ # Manage CPack component dependencies
+ set(CPACK_COMPONENT_${PROGRAM}_DEPENDS libraries libraries-gmxpreprocess)
+
+ # Create custom install-xxxx target
+ if (BUILD_SHARED_LIBS)
+ # If shared libraries are used, we need to install the libraries in
+ # addition to the mdrun binary.
+ add_custom_target(install-${PROGRAM}
+ COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries
+ -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+ COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries-gmxpreprocess
+ -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+ COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+ -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+ COMMENT "Installing ${PROGRAM}")
+ else()
+ add_custom_target(install-${PROGRAM}
+ COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+ -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+ COMMENT "Installing ${PROGRAM}")
+ endif()
+ add_dependencies(install-${PROGRAM} ${PROGRAM})
+
+ # Finally, trigger installation
+ install(
+ TARGETS ${PROGRAM}
+ COMPONENT ${PROGRAM}
+ DESTINATION ${BIN_INSTALL_DIR}
+ )
+endforeach()
+
+install(TARGETS gmxpreprocess DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries-gmxpreprocess)
+
+if (INSTALL_CUDART_LIB) #can be set manual by user
+ if (GMX_GPU)
+ foreach(CUDA_LIB ${CUDA_LIBRARIES})
+ string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
+ if(IS_CUDART) #libcuda should not be installed
+ #install also name-links (linker uses those)
+ file(GLOB CUDA_LIBS ${CUDA_LIB}*)
+ install(FILES ${CUDA_LIBS} DESTINATION
+ ${LIB_INSTALL_DIR} COMPONENT libraries)
+ endif()
+ endforeach()
+ else()
+ message(WARNING "INSTALL_CUDART_LIB only makes sense with GMX_GPU")
+ endif()
+endif ()
+endif(GMX_FAHCORE)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgmxpreprocess.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc @ONLY)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc
+ DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+ RENAME "libgmxpreprocess${GMX_LIBS_SUFFIX}.pc"
+ COMPONENT development)
diff --git a/patches/gromacs-4.6.3.diff/src/kernel/CMakeLists.txt.preplumed b/patches/gromacs-4.6.3.diff/src/kernel/CMakeLists.txt.preplumed
new file mode 100644
index 0000000000000000000000000000000000000000..e2125333387440d266eb0e6e77f23e8adb635511
--- /dev/null
+++ b/patches/gromacs-4.6.3.diff/src/kernel/CMakeLists.txt.preplumed
@@ -0,0 +1,195 @@
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# David van der Spoel, Berk Hess, Erik Lindahl, and including many
+# others, as listed in the AUTHORS file in the top-level source
+# directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+#
+
+set(GMXPREPROCESS_SOURCES
+ add_par.c
+ calc_verletbuf.c
+ compute_io.c
+ convparm.c
+ gen_ad.c
+ gen_vsite.c
+ genhydro.c
+ gpp_atomtype.c
+ gpp_bond_atomtype.c
+ h_db.c
+ hackblock.c
+ hizzie.c
+ nm2type.c
+ pdb2top.c
+ pgutil.c
+ readir.c
+ readpull.c
+ readadress.c
+ readrot.c
+ resall.c
+ sorting.c
+ specbond.c
+ ter_db.c
+ tomorse.c
+ topdirs.c
+ topexcl.c
+ topio.c
+ toppush.c
+ topshake.c
+ toputil.c
+ tpbcmp.c
+ vsite_parm.c
+ fflibutil.c
+ xlate.c)
+
+set(MDRUN_SOURCES
+ gctio.c ionize.c runner.c
+ do_gct.c repl_ex.c xutils.c pme_loadbal.c
+ md.c mdrun.c genalg.c membed.c)
+
+add_library(gmxpreprocess ${GMXPREPROCESS_SOURCES})
+target_link_libraries(gmxpreprocess md)
+set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME "gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
+ COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+
+if(GMX_GPU)
+ include_directories(${CMAKE_SOURCE_DIR}/src/gmxlib/gpu_utils)
+endif()
+
+if(GMX_OPENMM)
+ # Even though the OpenMM build has "moved to contrib", many things
+ # have be be done from within the scope of the CMakeLists.txt that
+ # builds its mdrun, and that is here
+ list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/src/contrib)
+ find_package(OpenMM)
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+ include(${CMAKE_SOURCE_DIR}/src/contrib/BuildMdrunOpenMM.cmake)
+endif(GMX_OPENMM)
+
+if(GMX_GPU OR GMX_FORCE_CXX)
+ set_source_files_properties(main.c PROPERTIES LANGUAGE CXX)
+ if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+ set_source_files_properties(main.c PROPERTIES COMPILE_FLAGS "-x c++")
+ endif()
+endif()
+
+if(GMX_FAHCORE)
+ add_library(fahcore ${MDRUN_SOURCES})
+else(GMX_FAHCORE)
+
+set(GMX_KERNEL_PROGRAMS
+ grompp tpbconv pdb2gmx g_protonate gmxdump g_x2top gmxcheck)
+if (NOT GMX_NO_QUOTES)
+ set(GMX_KERNEL_PROGRAMS ${GMX_KERNEL_PROGRAMS} g_luck)
+endif (NOT GMX_NO_QUOTES)
+
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+ add_executable(${PROGRAM} ${PROGRAM}.c main.c)
+ if (NOT ${PROGRAM} STREQUAL "g_luck")
+ gmx_add_man_page(${PROGRAM})
+ endif()
+ target_link_libraries(${PROGRAM} gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
+ set_target_properties(${PROGRAM} PROPERTIES OUTPUT_NAME "${PROGRAM}${GMX_BINARY_SUFFIX}")
+endforeach()
+
+add_executable(mdrun ${MDRUN_SOURCES} main.c)
+gmx_add_man_page(mdrun)
+target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
+set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}" COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+if(GMX_OPENMM)
+ target_link_libraries(mdrun openmm_api_wrapper)
+endif()
+
+# Construct component groups for installation; note that a component may
+# belong to only one group
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+ set(CPACK_COMPONENT_${PROGRAM}_GROUP tools)
+endforeach()
+set(CPACK_COMPONENT_MDRUN_GROUP mdrun)
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS} mdrun)
+ # Manage CPack component dependencies
+ set(CPACK_COMPONENT_${PROGRAM}_DEPENDS libraries libraries-gmxpreprocess)
+
+ # Create custom install-xxxx target
+ if (BUILD_SHARED_LIBS)
+ # If shared libraries are used, we need to install the libraries in
+ # addition to the mdrun binary.
+ add_custom_target(install-${PROGRAM}
+ COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries
+ -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+ COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries-gmxpreprocess
+ -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+ COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+ -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+ COMMENT "Installing ${PROGRAM}")
+ else()
+ add_custom_target(install-${PROGRAM}
+ COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+ -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+ COMMENT "Installing ${PROGRAM}")
+ endif()
+ add_dependencies(install-${PROGRAM} ${PROGRAM})
+
+ # Finally, trigger installation
+ install(
+ TARGETS ${PROGRAM}
+ COMPONENT ${PROGRAM}
+ DESTINATION ${BIN_INSTALL_DIR}
+ )
+endforeach()
+
+install(TARGETS gmxpreprocess DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries-gmxpreprocess)
+
+if (INSTALL_CUDART_LIB) #can be set manual by user
+ if (GMX_GPU)
+ foreach(CUDA_LIB ${CUDA_LIBRARIES})
+ string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
+ if(IS_CUDART) #libcuda should not be installed
+ #install also name-links (linker uses those)
+ file(GLOB CUDA_LIBS ${CUDA_LIB}*)
+ install(FILES ${CUDA_LIBS} DESTINATION
+ ${LIB_INSTALL_DIR} COMPONENT libraries)
+ endif()
+ endforeach()
+ else()
+ message(WARNING "INSTALL_CUDART_LIB only makes sense with GMX_GPU")
+ endif()
+endif ()
+endif(GMX_FAHCORE)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgmxpreprocess.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc @ONLY)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc
+ DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+ RENAME "libgmxpreprocess${GMX_LIBS_SUFFIX}.pc"
+ COMPONENT development)
diff --git a/patches/gromacs-4.6.3.diff/src/kernel/md.c b/patches/gromacs-4.6.3.diff/src/kernel/md.c
new file mode 100644
index 0000000000000000000000000000000000000000..3d639fd33651057fbbdfc26782e79af0bdad2b5f
--- /dev/null
+++ b/patches/gromacs-4.6.3.diff/src/kernel/md.c
@@ -0,0 +1,2343 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "typedefs.h"
+#include "smalloc.h"
+#include "sysstuff.h"
+#include "vec.h"
+#include "statutil.h"
+#include "vcm.h"
+#include "mdebin.h"
+#include "nrnb.h"
+#include "calcmu.h"
+#include "index.h"
+#include "vsite.h"
+#include "update.h"
+#include "ns.h"
+#include "trnio.h"
+#include "xtcio.h"
+#include "mdrun.h"
+#include "md_support.h"
+#include "md_logging.h"
+#include "confio.h"
+#include "network.h"
+#include "pull.h"
+#include "xvgr.h"
+#include "physics.h"
+#include "names.h"
+#include "xmdrun.h"
+#include "ionize.h"
+#include "disre.h"
+#include "orires.h"
+#include "pme.h"
+#include "mdatoms.h"
+#include "repl_ex.h"
+#include "qmmm.h"
+#include "mpelogging.h"
+#include "domdec.h"
+#include "domdec_network.h"
+#include "partdec.h"
+#include "topsort.h"
+#include "coulomb.h"
+#include "constr.h"
+#include "shellfc.h"
+#include "compute_io.h"
+#include "mvdata.h"
+#include "checkpoint.h"
+#include "mtop_util.h"
+#include "sighandler.h"
+#include "txtdump.h"
+#include "string2.h"
+#include "pme_loadbal.h"
+#include "bondf.h"
+#include "membed.h"
+#include "types/nlistheuristics.h"
+#include "types/iteratedconstraints.h"
+#include "nbnxn_cuda_data_mgmt.h"
+
+/* PLUMED */
+#include "../../Plumed.h"
+extern int plumedswitch;
+extern plumed plumedmain;
+/* END PLUMED */
+
+#ifdef GMX_LIB_MPI
+#include <mpi.h>
+#endif
+#ifdef GMX_THREAD_MPI
+#include "tmpi.h"
+#endif
+
+#ifdef GMX_FAHCORE
+#include "corewrap.h"
+#endif
+
+static void reset_all_counters(FILE *fplog, t_commrec *cr,
+ gmx_large_int_t step,
+ gmx_large_int_t *step_rel, t_inputrec *ir,
+ gmx_wallcycle_t wcycle, t_nrnb *nrnb,
+ gmx_runtime_t *runtime,
+ nbnxn_cuda_ptr_t cu_nbv)
+{
+ char sbuf[STEPSTRSIZE];
+
+ /* Reset all the counters related to performance over the run */
+ md_print_warn(cr, fplog, "step %s: resetting all time and cycle counters\n",
+ gmx_step_str(step, sbuf));
+
+ if (cu_nbv)
+ {
+ nbnxn_cuda_reset_timings(cu_nbv);
+ }
+
+ wallcycle_stop(wcycle, ewcRUN);
+ wallcycle_reset_all(wcycle);
+ if (DOMAINDECOMP(cr))
+ {
+ reset_dd_statistics_counters(cr->dd);
+ }
+ init_nrnb(nrnb);
+ ir->init_step += *step_rel;
+ ir->nsteps -= *step_rel;
+ *step_rel = 0;
+ wallcycle_start(wcycle, ewcRUN);
+ runtime_start(runtime);
+ print_date_and_time(fplog, cr->nodeid, "Restarted time", runtime);
+}
+
+double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
+ const output_env_t oenv, gmx_bool bVerbose, gmx_bool bCompact,
+ int nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int stepout, t_inputrec *ir,
+ gmx_mtop_t *top_global,
+ t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed, t_forcerec *fr,
+ int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t membed,
+ real cpt_period, real max_hours,
+ const char *deviceOptions,
+ unsigned long Flags,
+ gmx_runtime_t *runtime)
+{
+ gmx_mdoutf_t *outf;
+ gmx_large_int_t step, step_rel;
+ double run_time;
+ double t, t0, lam0[efptNR];
+ gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEner;
+ gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD, bNotLastFrame = FALSE,
+ bFirstStep, bStateFromCP, bStateFromTPX, bInitStep, bLastStep,
+ bBornRadii, bStartingFromCpt;
+ gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
+ gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
+ bForceUpdate = FALSE, bCPT;
+ int mdof_flags;
+ gmx_bool bMasterState;
+ int force_flags, cglo_flags;
+ tensor force_vir, shake_vir, total_vir, tmp_vir, pres;
+ int i, m;
+ t_trxstatus *status;
+ rvec mu_tot;
+ t_vcm *vcm;
+ t_state *bufstate = NULL;
+ matrix *scale_tot, pcoupl_mu, M, ebox;
+ gmx_nlheur_t nlh;
+ t_trxframe rerun_fr;
+ gmx_repl_ex_t repl_ex = NULL;
+ int nchkpt = 1;
+ gmx_localtop_t *top;
+ t_mdebin *mdebin = NULL;
+ df_history_t df_history;
+ t_state *state = NULL;
+ rvec *f_global = NULL;
+ int n_xtc = -1;
+ rvec *x_xtc = NULL;
+ gmx_enerdata_t *enerd;
+ rvec *f = NULL;
+ gmx_global_stat_t gstat;
+ gmx_update_t upd = NULL;
+ t_graph *graph = NULL;
+ globsig_t gs;
+ gmx_rng_t mcrng = NULL;
+ gmx_bool bFFscan;
+ gmx_groups_t *groups;
+ gmx_ekindata_t *ekind, *ekind_save;
+ gmx_shellfc_t shellfc;
+ int count, nconverged = 0;
+ real timestep = 0;
+ double tcount = 0;
+ gmx_bool bIonize = FALSE;
+ gmx_bool bTCR = FALSE, bConverged = TRUE, bOK, bSumEkinhOld, bExchanged;
+ gmx_bool bAppend;
+ gmx_bool bResetCountersHalfMaxH = FALSE;
+ gmx_bool bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
+ gmx_bool bUpdateDoLR;
+ real mu_aver = 0, dvdl_constr;
+ int a0, a1, gnx = 0, ii;
+ atom_id *grpindex = NULL;
+ char *grpname;
+ t_coupl_rec *tcr = NULL;
+ rvec *xcopy = NULL, *vcopy = NULL, *cbuf = NULL;
+ matrix boxcopy = {{0}}, lastbox;
+ tensor tmpvir;
+ real fom, oldfom, veta_save, pcurr, scalevir, tracevir;
+ real vetanew = 0;
+ int lamnew = 0;
+ /* for FEP */
+ int nstfep;
+ real rate;
+ double cycles;
+ real saved_conserved_quantity = 0;
+ real last_ekin = 0;
+ int iter_i;
+ t_extmass MassQ;
+ int **trotter_seq;
+ char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
+ int handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
+ gmx_iterate_t iterate;
+ gmx_large_int_t multisim_nsteps = -1; /* number of steps to do before first multisim
+ simulation stops. If equal to zero, don't
+ communicate any more between multisims.*/
+ /* PME load balancing data for GPU kernels */
+ pme_load_balancing_t pme_loadbal = NULL;
+ double cycles_pmes;
+ gmx_bool bPMETuneTry = FALSE, bPMETuneRunning = FALSE;
+
+/* PLUMED */
+ int plumedNeedsEnergy=0;
+ int plumedWantsToStop=0;
+/* END PLUMED */
+
+#ifdef GMX_FAHCORE
+ /* Temporary addition for FAHCORE checkpointing */
+ int chkpt_ret;
+#endif
+
+ /* Check for special mdrun options */
+ bRerunMD = (Flags & MD_RERUN);
+ bIonize = (Flags & MD_IONIZE);
+ bFFscan = (Flags & MD_FFSCAN);
+ bAppend = (Flags & MD_APPENDFILES);
+ if (Flags & MD_RESETCOUNTERSHALFWAY)
+ {
+ if (ir->nsteps > 0)
+ {
+ /* Signal to reset the counters half the simulation steps. */
+ wcycle_set_reset_counters(wcycle, ir->nsteps/2);
+ }
+ /* Signal to reset the counters halfway the simulation time. */
+ bResetCountersHalfMaxH = (max_hours > 0);
+ }
+
+ /* md-vv uses averaged full step velocities for T-control
+ md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
+ md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
+ bVV = EI_VV(ir->eI);
+ if (bVV) /* to store the initial velocities while computing virial */
+ {
+ snew(cbuf, top_global->natoms);
+ }
+ /* all the iteratative cases - only if there are constraints */
+ bIterativeCase = ((IR_NPH_TROTTER(ir) || IR_NPT_TROTTER(ir)) && (constr) && (!bRerunMD));
+ gmx_iterate_init(&iterate, FALSE); /* The default value of iterate->bIterationActive is set to
+ false in this step. The correct value, true or false,
+ is set at each step, as it depends on the frequency of temperature
+ and pressure control.*/
+ bTrotter = (bVV && (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir)));
+
+ if (bRerunMD)
+ {
+ /* Since we don't know if the frames read are related in any way,
+ * rebuild the neighborlist at every step.
+ */
+ ir->nstlist = 1;
+ ir->nstcalcenergy = 1;
+ nstglobalcomm = 1;
+ }
+
+ check_ir_old_tpx_versions(cr, fplog, ir, top_global);
+
+ nstglobalcomm = check_nstglobalcomm(fplog, cr, nstglobalcomm, ir);
+ bGStatEveryStep = (nstglobalcomm == 1);
+
+ if (!bGStatEveryStep && ir->nstlist == -1 && fplog != NULL)
+ {
+ fprintf(fplog,
+ "To reduce the energy communication with nstlist = -1\n"
+ "the neighbor list validity should not be checked at every step,\n"
+ "this means that exact integration is not guaranteed.\n"
+ "The neighbor list validity is checked after:\n"
+ " <n.list life time> - 2*std.dev.(n.list life time) steps.\n"
+ "In most cases this will result in exact integration.\n"
+ "This reduces the energy communication by a factor of 2 to 3.\n"
+ "If you want less energy communication, set nstlist > 3.\n\n");
+ }
+
+ if (bRerunMD || bFFscan)
+ {
+ ir->nstxtcout = 0;
+ }
+ groups = &top_global->groups;
+
+ /* Initial values */
+ init_md(fplog, cr, ir, oenv, &t, &t0, state_global->lambda,
+ &(state_global->fep_state), lam0,
+ nrnb, top_global, &upd,
+ nfile, fnm, &outf, &mdebin,
+ force_vir, shake_vir, mu_tot, &bSimAnn, &vcm, state_global, Flags);
+
+ clear_mat(total_vir);
+ clear_mat(pres);
+ /* Energy terms and groups */
+ snew(enerd, 1);
+ init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
+ enerd);
+ if (DOMAINDECOMP(cr))
+ {
+ f = NULL;
+ }
+ else
+ {
+ snew(f, top_global->natoms);
+ }
+
+ /* lambda Monte carlo random number generator */
+ if (ir->bExpanded)
+ {
+ mcrng = gmx_rng_init(ir->expandedvals->lmc_seed);
+ }
+ /* copy the state into df_history */
+ copy_df_history(&df_history, &state_global->dfhist);
+
+ /* Kinetic energy data */
+ snew(ekind, 1);
+ init_ekindata(fplog, top_global, &(ir->opts), ekind);
+ /* needed for iteration of constraints */
+ snew(ekind_save, 1);
+ init_ekindata(fplog, top_global, &(ir->opts), ekind_save);
+ /* Copy the cos acceleration to the groups struct */
+ ekind->cosacc.cos_accel = ir->cos_accel;
+
+ gstat = global_stat_init(ir);
+ debug_gmx();
+
+ /* Check for polarizable models and flexible constraints */
+ shellfc = init_shell_flexcon(fplog,
+ top_global, n_flexible_constraints(constr),
+ (ir->bContinuation ||
+ (DOMAINDECOMP(cr) && !MASTER(cr))) ?
+ NULL : state_global->x);
+
+ if (DEFORM(*ir))
+ {
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_lock(&deform_init_box_mutex);
+#endif
+ set_deform_reference_box(upd,
+ deform_init_init_step_tpx,
+ deform_init_box_tpx);
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
+#endif
+ }
+
+ {
+ double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
+ if ((io > 2000) && MASTER(cr))
+ {
+ fprintf(stderr,
+ "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
+ io);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ top = dd_init_local_top(top_global);
+
+ snew(state, 1);
+ dd_init_local_state(cr->dd, state_global, state);
+
+ if (DDMASTER(cr->dd) && ir->nstfout)
+ {
+ snew(f_global, state_global->natoms);
+ }
+ }
+ else
+ {
+ if (PAR(cr))
+ {
+ /* Initialize the particle decomposition and split the topology */
+ top = split_system(fplog, top_global, ir, cr);
+
+ pd_cg_range(cr, &fr->cg0, &fr->hcg);
+ pd_at_range(cr, &a0, &a1);
+ }
+ else
+ {
+ top = gmx_mtop_generate_local_top(top_global, ir);
+
+ a0 = 0;
+ a1 = top_global->natoms;
+ }
+
+ forcerec_set_excl_load(fr, top, cr);
+
+ state = partdec_init_local_state(cr, state_global);
+ f_global = f;
+
+ atoms2md(top_global, ir, 0, NULL, a0, a1-a0, mdatoms);
+
+ if (vsite)
+ {
+ set_vsite_top(vsite, top, mdatoms, cr);
+ }
+
+ if (ir->ePBC != epbcNONE && !fr->bMolPBC)
+ {
+ graph = mk_graph(fplog, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
+ }
+
+ if (shellfc)
+ {
+ make_local_shells(cr, mdatoms, shellfc);
+ }
+
+ init_bonded_thread_force_reduction(fr, &top->idef);
+
+ if (ir->pull && PAR(cr))
+ {
+ dd_make_local_pull_groups(NULL, ir->pull, mdatoms);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* Distribute the charge groups over the nodes from the master node */
+ dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle, FALSE);
+
+ }
+
+ update_mdatoms(mdatoms, state->lambda[efptMASS]);
+
+ if (opt2bSet("-cpi", nfile, fnm))
+ {
+ bStateFromCP = gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr);
+ }
+ else
+ {
+ bStateFromCP = FALSE;
+ }
+
+ if (MASTER(cr))
+ {
+ if (bStateFromCP)
+ {
+ /* Update mdebin with energy history if appending to output files */
+ if (Flags & MD_APPENDFILES)
+ {
+ restore_energyhistory_from_state(mdebin, &state_global->enerhist);
+ }
+ else
+ {
+ /* We might have read an energy history from checkpoint,
+ * free the allocated memory and reset the counts.
+ */
+ done_energyhistory(&state_global->enerhist);
+ init_energyhistory(&state_global->enerhist);
+ }
+ }
+ /* Set the initial energy history in state by updating once */
+ update_energyhistory(&state_global->enerhist, mdebin);
+ }
+
+ if ((state->flags & (1<<estLD_RNG)) && (Flags & MD_READ_RNG))
+ {
+ /* Set the random state if we read a checkpoint file */
+ set_stochd_state(upd, state);
+ }
+
+ if (state->flags & (1<<estMC_RNG))
+ {
+ set_mc_state(mcrng, state);
+ }
+
+ /* Initialize constraints */
+ if (constr)
+ {
+ if (!DOMAINDECOMP(cr))
+ {
+ set_constraints(constr, top, ir, mdatoms, cr);
+ }
+ }
+
+ /* Check whether we have to GCT stuff */
+ bTCR = ftp2bSet(efGCT, nfile, fnm);
+ if (bTCR)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "Will do General Coupling Theory!\n");
+ }
+ gnx = top_global->mols.nr;
+ snew(grpindex, gnx);
+ for (i = 0; (i < gnx); i++)
+ {
+ grpindex[i] = i;
+ }
+ }
+
+ if (repl_ex_nst > 0)
+ {
+ /* We need to be sure replica exchange can only occur
+ * when the energies are current */
+ check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
+ "repl_ex_nst", &repl_ex_nst);
+ /* This check needs to happen before inter-simulation
+ * signals are initialized, too */
+ }
+ if (repl_ex_nst > 0 && MASTER(cr))
+ {
+ repl_ex = init_replica_exchange(fplog, cr->ms, state_global, ir,
+ repl_ex_nst, repl_ex_nex, repl_ex_seed);
+ }
+
+ /* PME tuning is only supported with GPUs or PME nodes and not with rerun.
+ * With perturbed charges with soft-core we should not change the cut-off.
+ */
+ if ((Flags & MD_TUNEPME) &&
+ EEL_PME(fr->eeltype) &&
+ ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME)) &&
+ !(ir->efep != efepNO && mdatoms->nChargePerturbed > 0 && ir->fepvals->bScCoul) &&
+ !bRerunMD)
+ {
+ pme_loadbal_init(&pme_loadbal, ir, state->box, fr->ic, fr->pmedata);
+ cycles_pmes = 0;
+ if (cr->duty & DUTY_PME)
+ {
+ /* Start tuning right away, as we can't measure the load */
+ bPMETuneRunning = TRUE;
+ }
+ else
+ {
+ /* Separate PME nodes, we can measure the PP/PME load balance */
+ bPMETuneTry = TRUE;
+ }
+ }
+
+ if (!ir->bContinuation && !bRerunMD)
+ {
+ if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
+ {
+ /* Set the velocities of frozen particles to zero */
+ for (i = mdatoms->start; i < mdatoms->start+mdatoms->homenr; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
+ {
+ state->v[i][m] = 0;
+ }
+ }
+ }
+ }
+
+ if (constr)
+ {
+ /* Constrain the initial coordinates and velocities */
+ do_constrain_first(fplog, constr, ir, mdatoms, state, f,
+ graph, cr, nrnb, fr, top, shake_vir);
+ }
+ if (vsite)
+ {
+ /* Construct the virtual sites for the initial configuration */
+ construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, NULL,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, graph, cr, state->box);
+ }
+ }
+
+ debug_gmx();
+
+ /* set free energy calculation frequency as the minimum
+ greatest common denominator of nstdhdl, nstexpanded, and repl_ex_nst*/
+ nstfep = ir->fepvals->nstdhdl;
+ if (ir->bExpanded)
+ {
+ nstfep = gmx_greatest_common_divisor(ir->fepvals->nstdhdl,nstfep);
+ }
+ if (repl_ex_nst > 0)
+ {
+ nstfep = gmx_greatest_common_divisor(repl_ex_nst,nstfep);
+ }
+
+ /* I'm assuming we need global communication the first time! MRS */
+ cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
+ | ((ir->comm_mode != ecmNO) ? CGLO_STOPCM : 0)
+ | (bVV ? CGLO_PRESSURE : 0)
+ | (bVV ? CGLO_CONSTRAINT : 0)
+ | (bRerunMD ? CGLO_RERUNMD : 0)
+ | ((Flags & MD_READ_EKIN) ? CGLO_READEKIN : 0));
+
+ bSumEkinhOld = FALSE;
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld, cglo_flags);
+ if (ir->eI == eiVVAK)
+ {
+ /* a second call to get the half step temperature initialized as well */
+ /* we do the same call as above, but turn the pressure off -- internally to
+ compute_globals, this is recognized as a velocity verlet half-step
+ kinetic energy calculation. This minimized excess variables, but
+ perhaps loses some logic?*/
+
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags &~(CGLO_STOPCM | CGLO_PRESSURE));
+ }
+
+ /* Calculate the initial half step temperature, and save the ekinh_old */
+ if (!(Flags & MD_STARTFROMCPT))
+ {
+ for (i = 0; (i < ir->opts.ngtc); i++)
+ {
+ copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
+ }
+ }
+ if (ir->eI != eiVV)
+ {
+ enerd->term[F_TEMP] *= 2; /* result of averages being done over previous and current step,
+ and there is no previous step */
+ }
+
+ /* if using an iterative algorithm, we need to create a working directory for the state. */
+ if (bIterativeCase)
+ {
+ bufstate = init_bufstate(state);
+ }
+ if (bFFscan)
+ {
+ snew(xcopy, state->natoms);
+ snew(vcopy, state->natoms);
+ copy_rvecn(state->x, xcopy, 0, state->natoms);
+ copy_rvecn(state->v, vcopy, 0, state->natoms);
+ copy_mat(state->box, boxcopy);
+ }
+
+ /* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
+ temperature control */
+ trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
+
+ if (MASTER(cr))
+ {
+ if (constr && !ir->bContinuation && ir->eConstrAlg == econtLINCS)
+ {
+ fprintf(fplog,
+ "RMS relative constraint deviation after constraining: %.2e\n",
+ constr_rmsd(constr, FALSE));
+ }
+ if (EI_STATE_VELOCITY(ir->eI))
+ {
+ fprintf(fplog, "Initial temperature: %g K\n", enerd->term[F_TEMP]);
+ }
+ if (bRerunMD)
+ {
+ fprintf(stderr, "starting md rerun '%s', reading coordinates from"
+ " input trajectory '%s'\n\n",
+ *(top_global->name), opt2fn("-rerun", nfile, fnm));
+ if (bVerbose)
+ {
+ fprintf(stderr, "Calculated time to finish depends on nsteps from "
+ "run input file,\nwhich may not correspond to the time "
+ "needed to process input trajectory.\n\n");
+ }
+ }
+ else
+ {
+ char tbuf[20];
+ fprintf(stderr, "starting mdrun '%s'\n",
+ *(top_global->name));
+ if (ir->nsteps >= 0)
+ {
+ sprintf(tbuf, "%8.1f", (ir->init_step+ir->nsteps)*ir->delta_t);
+ }
+ else
+ {
+ sprintf(tbuf, "%s", "infinite");
+ }
+ if (ir->init_step > 0)
+ {
+ fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
+ gmx_step_str(ir->init_step+ir->nsteps, sbuf), tbuf,
+ gmx_step_str(ir->init_step, sbuf2),
+ ir->init_step*ir->delta_t);
+ }
+ else
+ {
+ fprintf(stderr, "%s steps, %s ps.\n",
+ gmx_step_str(ir->nsteps, sbuf), tbuf);
+ }
+ }
+ fprintf(fplog, "\n");
+ }
+
+ /* PLUMED */
+ if(plumedswitch){
+ if(cr->ms && cr->ms->nsim>1) {
+ if(MASTER(cr)) plumed_cmd(plumedmain,"GREX setMPIIntercomm",&cr->ms->mpi_comm_masters);
+ if(PAR(cr)){
+ if(DOMAINDECOMP(cr)) {
+ plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->dd->mpi_comm_all);
+ }else{
+ plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->mpi_comm_mysim);
+ }
+ }
+ plumed_cmd(plumedmain,"GREX init",NULL);
+ }
+ if(PAR(cr)){
+ if(DOMAINDECOMP(cr)) {
+ plumed_cmd(plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
+ }else{
+ plumed_cmd(plumedmain,"setMPIComm",&cr->mpi_comm_mysim);
+ }
+ }
+ plumed_cmd(plumedmain,"setNatoms",&top_global->natoms);
+ plumed_cmd(plumedmain,"setMDEngine","gromacs");
+ plumed_cmd(plumedmain,"setLog",fplog);
+ real real_delta_t;
+ real_delta_t=ir->delta_t;
+ plumed_cmd(plumedmain,"setTimestep",&real_delta_t);
+ plumed_cmd(plumedmain,"init",NULL);
+
+ if(PAR(cr)){
+ if(DOMAINDECOMP(cr)) {
+ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
+ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
+ }else{
+ plumed_cmd(plumedmain,"setAtomsNlocal",&mdatoms->homenr);
+ plumed_cmd(plumedmain,"setAtomsContiguous",&mdatoms->start);
+ }
+ }
+ }
+ /* END PLUMED */
+
+ /* Set and write start time */
+ runtime_start(runtime);
+ print_date_and_time(fplog, cr->nodeid, "Started mdrun", runtime);
+ wallcycle_start(wcycle, ewcRUN);
+ if (fplog)
+ {
+ fprintf(fplog, "\n");
+ }
+
+ /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
+#ifdef GMX_FAHCORE
+ chkpt_ret = fcCheckPointParallel( cr->nodeid,
+ NULL, 0);
+ if (chkpt_ret == 0)
+ {
+ gmx_fatal( 3, __FILE__, __LINE__, "Checkpoint error on step %d\n", 0 );
+ }
+#endif
+
+ debug_gmx();
+ /***********************************************************
+ *
+ * Loop over MD steps
+ *
+ ************************************************************/
+
+ /* if rerunMD then read coordinates and velocities from input trajectory */
+ if (bRerunMD)
+ {
+ if (getenv("GMX_FORCE_UPDATE"))
+ {
+ bForceUpdate = TRUE;
+ }
+
+ rerun_fr.natoms = 0;
+ if (MASTER(cr))
+ {
+ bNotLastFrame = read_first_frame(oenv, &status,
+ opt2fn("-rerun", nfile, fnm),
+ &rerun_fr, TRX_NEED_X | TRX_READ_V);
+ if (rerun_fr.natoms != top_global->natoms)
+ {
+ gmx_fatal(FARGS,
+ "Number of atoms in trajectory (%d) does not match the "
+ "run input file (%d)\n",
+ rerun_fr.natoms, top_global->natoms);
+ }
+ if (ir->ePBC != epbcNONE)
+ {
+ if (!rerun_fr.bBox)
+ {
+ gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f does not contain a box, while pbc is used", rerun_fr.step, rerun_fr.time);
+ }
+ if (max_cutoff2(ir->ePBC, rerun_fr.box) < sqr(fr->rlistlong))
+ {
+ gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f has too small box dimensions", rerun_fr.step, rerun_fr.time);
+ }
+ }
+ }
+
+ if (PAR(cr))
+ {
+ rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
+ }
+
+ if (ir->ePBC != epbcNONE)
+ {
+ /* Set the shift vectors.
+ * Necessary here when have a static box different from the tpr box.
+ */
+ calc_shifts(rerun_fr.box, fr->shift_vec);
+ }
+ }
+
+ /* loop over MD steps or if rerunMD to end of input trajectory */
+ bFirstStep = TRUE;
+ /* Skip the first Nose-Hoover integration when we get the state from tpx */
+ bStateFromTPX = !bStateFromCP;
+ bInitStep = bFirstStep && (bStateFromTPX || bVV);
+ bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
+ bLastStep = FALSE;
+ bSumEkinhOld = FALSE;
+ bExchanged = FALSE;
+
+ init_global_signals(&gs, cr, ir, repl_ex_nst);
+
+ step = ir->init_step;
+ step_rel = 0;
+
+ if (ir->nstlist == -1)
+ {
+ init_nlistheuristics(&nlh, bGStatEveryStep, step);
+ }
+
+ if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
+ {
+ /* check how many steps are left in other sims */
+ multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
+ }
+
+
+ /* and stop now if we should */
+ bLastStep = (bRerunMD || (ir->nsteps >= 0 && step_rel > ir->nsteps) ||
+ ((multisim_nsteps >= 0) && (step_rel >= multisim_nsteps )));
+ while (!bLastStep || (bRerunMD && bNotLastFrame))
+ {
+
+ wallcycle_start(wcycle, ewcSTEP);
+
+ GMX_MPE_LOG(ev_timestep1);
+
+ if (bRerunMD)
+ {
+ if (rerun_fr.bStep)
+ {
+ step = rerun_fr.step;
+ step_rel = step - ir->init_step;
+ }
+ if (rerun_fr.bTime)
+ {
+ t = rerun_fr.time;
+ }
+ else
+ {
+ t = step;
+ }
+ }
+ else
+ {
+ bLastStep = (step_rel == ir->nsteps);
+ t = t0 + step*ir->delta_t;
+ }
+
+ if (ir->efep != efepNO || ir->bSimTemp)
+ {
+ /* find and set the current lambdas. If rerunning, we either read in a state, or a lambda value,
+ requiring different logic. */
+
+ set_current_lambdas(step, ir->fepvals, bRerunMD, &rerun_fr, state_global, state, lam0);
+ bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
+ bDoFEP = (do_per_step(step, nstfep) && (ir->efep != efepNO));
+ bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded) && (ir->bExpanded) && (step > 0));
+ }
+
+ if (bSimAnn)
+ {
+ update_annealing_target_temp(&(ir->opts), t);
+ }
+
+ if (bRerunMD)
+ {
+ if (!(DOMAINDECOMP(cr) && !MASTER(cr)))
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ copy_rvec(rerun_fr.x[i], state_global->x[i]);
+ }
+ if (rerun_fr.bV)
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ copy_rvec(rerun_fr.v[i], state_global->v[i]);
+ }
+ }
+ else
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ clear_rvec(state_global->v[i]);
+ }
+ if (bRerunWarnNoV)
+ {
+ fprintf(stderr, "\nWARNING: Some frames do not contain velocities.\n"
+ " Ekin, temperature and pressure are incorrect,\n"
+ " the virial will be incorrect when constraints are present.\n"
+ "\n");
+ bRerunWarnNoV = FALSE;
+ }
+ }
+ }
+ copy_mat(rerun_fr.box, state_global->box);
+ copy_mat(state_global->box, state->box);
+
+ if (vsite && (Flags & MD_RERUN_VSITE))
+ {
+ if (DOMAINDECOMP(cr))
+ {
+ gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented for domain decomposition, use particle decomposition");
+ }
+ if (graph)
+ {
+ /* Following is necessary because the graph may get out of sync
+ * with the coordinates if we only have every N'th coordinate set
+ */
+ mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
+ shift_self(graph, state->box, state->x);
+ }
+ construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, state->v,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, graph, cr, state->box);
+ if (graph)
+ {
+ unshift_self(graph, state->box, state->x);
+ }
+ }
+ }
+
+ /* Stop Center of Mass motion */
+ bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
+
+ /* Copy back starting coordinates in case we're doing a forcefield scan */
+ if (bFFscan)
+ {
+ for (ii = 0; (ii < state->natoms); ii++)
+ {
+ copy_rvec(xcopy[ii], state->x[ii]);
+ copy_rvec(vcopy[ii], state->v[ii]);
+ }
+ copy_mat(boxcopy, state->box);
+ }
+
+ if (bRerunMD)
+ {
+ /* for rerun MD always do Neighbour Searching */
+ bNS = (bFirstStep || ir->nstlist != 0);
+ bNStList = bNS;
+ }
+ else
+ {
+ /* Determine whether or not to do Neighbour Searching and LR */
+ bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
+
+ bNS = (bFirstStep || bExchanged || bNStList || bDoFEP ||
+ (ir->nstlist == -1 && nlh.nabnsb > 0));
+
+ if (bNS && ir->nstlist == -1)
+ {
+ set_nlistheuristics(&nlh, bFirstStep || bExchanged || bDoFEP, step);
+ }
+ }
+
+ /* check whether we should stop because another simulation has
+ stopped. */
+ if (MULTISIM(cr))
+ {
+ if ( (multisim_nsteps >= 0) && (step_rel >= multisim_nsteps) &&
+ (multisim_nsteps != ir->nsteps) )
+ {
+ if (bNS)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr,
+ "Stopping simulation %d because another one has finished\n",
+ cr->ms->sim);
+ }
+ bLastStep = TRUE;
+ gs.sig[eglsCHKPT] = 1;
+ }
+ }
+ }
+
+ /* < 0 means stop at next step, > 0 means stop at next NS step */
+ if ( (gs.set[eglsSTOPCOND] < 0) ||
+ ( (gs.set[eglsSTOPCOND] > 0) && (bNStList || ir->nstlist == 0) ) )
+ {
+ bLastStep = TRUE;
+ }
+
+ /* Determine whether or not to update the Born radii if doing GB */
+ bBornRadii = bFirstStep;
+ if (ir->implicit_solvent && (step % ir->nstgbradii == 0))
+ {
+ bBornRadii = TRUE;
+ }
+
+ do_log = do_per_step(step, ir->nstlog) || bFirstStep || bLastStep;
+ do_verbose = bVerbose &&
+ (step % stepout == 0 || bFirstStep || bLastStep);
+
+ if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
+ {
+ if (bRerunMD)
+ {
+ bMasterState = TRUE;
+ }
+ else
+ {
+ bMasterState = FALSE;
+ /* Correct the new box if it is too skewed */
+ if (DYNAMIC_BOX(*ir))
+ {
+ if (correct_box(fplog, step, state->box, graph))
+ {
+ bMasterState = TRUE;
+ }
+ }
+ if (DOMAINDECOMP(cr) && bMasterState)
+ {
+ dd_collect_state(cr->dd, state, state_global);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* Repartition the domain decomposition */
+ wallcycle_start(wcycle, ewcDOMDEC);
+ dd_partition_system(fplog, step, cr,
+ bMasterState, nstglobalcomm,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle,
+ do_verbose && !bPMETuneRunning);
+ wallcycle_stop(wcycle, ewcDOMDEC);
+ /* If using an iterative integrator, reallocate space to match the decomposition */
+
+ /* PLUMED */
+ if(plumedswitch){
+ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
+ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
+ }
+ /* END PLUMED */
+ }
+ }
+
+ if (MASTER(cr) && do_log && !bFFscan)
+ {
+ print_ebin_header(fplog, step, t, state->lambda[efptFEP]); /* can we improve the information printed here? */
+ }
+
+ if (ir->efep != efepNO)
+ {
+ update_mdatoms(mdatoms, state->lambda[efptMASS]);
+ }
+
+ if ((bRerunMD && rerun_fr.bV) || bExchanged)
+ {
+
+ /* We need the kinetic energy at minus the half step for determining
+ * the full step kinetic energy and possibly for T-coupling.*/
+ /* This may not be quite working correctly yet . . . . */
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
+ }
+ clear_mat(force_vir);
+
+ /* Ionize the atoms if necessary */
+ if (bIonize)
+ {
+ ionize(fplog, oenv, mdatoms, top_global, t, ir, state->x, state->v,
+ mdatoms->start, mdatoms->start+mdatoms->homenr, state->box, cr);
+ }
+
+ /* Update force field in ffscan program */
+ if (bFFscan)
+ {
+ if (update_forcefield(fplog,
+ nfile, fnm, fr,
+ mdatoms->nr, state->x, state->box))
+ {
+ gmx_finalize_par();
+
+ exit(0);
+ }
+ }
+
+ GMX_MPE_LOG(ev_timestep2);
+
+ /* We write a checkpoint at this MD step when:
+ * either at an NS step when we signalled through gs,
+ * or at the last step (but not when we do not want confout),
+ * but never at the first step or with rerun.
+ */
+ bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
+ (bLastStep && (Flags & MD_CONFOUT))) &&
+ step > ir->init_step && !bRerunMD);
+ if (bCPT)
+ {
+ gs.set[eglsCHKPT] = 0;
+ }
+
+ /* Determine the energy and pressure:
+ * at nstcalcenergy steps and at energy output steps (set below).
+ */
+ if (EI_VV(ir->eI) && (!bInitStep))
+ {
+ /* for vv, the first half of the integration actually corresponds
+ to the previous step. bCalcEner is only required to be evaluated on the 'next' step,
+ but the virial needs to be calculated on both the current step and the 'next' step. Future
+ reorganization may be able to get rid of one of the bCalcVir=TRUE steps. */
+
+ bCalcEner = do_per_step(step-1, ir->nstcalcenergy);
+ bCalcVir = bCalcEner ||
+ (ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
+ }
+ else
+ {
+ bCalcEner = do_per_step(step, ir->nstcalcenergy);
+ bCalcVir = bCalcEner ||
+ (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
+ }
+
+ /* Do we need global communication ? */
+ bGStat = (bCalcVir || bCalcEner || bStopCM ||
+ do_per_step(step, nstglobalcomm) || (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)) ||
+ (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));
+
+ do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
+
+ if (do_ene || do_log)
+ {
+ bCalcVir = TRUE;
+ bCalcEner = TRUE;
+ bGStat = TRUE;
+ }
+
+ /* these CGLO_ options remain the same throughout the iteration */
+ cglo_flags = ((bRerunMD ? CGLO_RERUNMD : 0) |
+ (bGStat ? CGLO_GSTAT : 0)
+ );
+
+ force_flags = (GMX_FORCE_STATECHANGED |
+ ((DYNAMIC_BOX(*ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
+ GMX_FORCE_ALLFORCES |
+ GMX_FORCE_SEPLRF |
+ (bCalcVir ? GMX_FORCE_VIRIAL : 0) |
+ (bCalcEner ? GMX_FORCE_ENERGY : 0) |
+ (bDoFEP ? GMX_FORCE_DHDL : 0)
+ );
+
+ if (fr->bTwinRange)
+ {
+ if (do_per_step(step, ir->nstcalclr))
+ {
+ force_flags |= GMX_FORCE_DO_LR;
+ }
+ }
+
+ if (shellfc)
+ {
+ /* Now is the time to relax the shells */
+ count = relax_shell_flexcon(fplog, cr, bVerbose, bFFscan ? step+1 : step,
+ ir, bNS, force_flags,
+ bStopCM, top, top_global,
+ constr, enerd, fcd,
+ state, f, force_vir, mdatoms,
+ nrnb, wcycle, graph, groups,
+ shellfc, fr, bBornRadii, t, mu_tot,
+ state->natoms, &bConverged, vsite,
+ outf->fp_field);
+ tcount += count;
+
+ if (bConverged)
+ {
+ nconverged++;
+ }
+ }
+ else
+ {
+ /* The coordinates (x) are shifted (to get whole molecules)
+ * in do_force.
+ * This is parallellized as well, and does communication too.
+ * Check comments in sim_util.c
+ */
+
+ /* PLUMED */
+ plumedNeedsEnergy=0;
+ if(plumedswitch){
+ long int lstep=step; plumed_cmd(plumedmain,"setStepLong",&lstep);
+ plumed_cmd(plumedmain,"setPositions",&state->x[mdatoms->start][0]);
+ plumed_cmd(plumedmain,"setMasses",&mdatoms->massT[mdatoms->start]);
+ plumed_cmd(plumedmain,"setCharges",&mdatoms->chargeA[mdatoms->start]);
+ plumed_cmd(plumedmain,"setBox",&state->box[0][0]);
+ plumed_cmd(plumedmain,"prepareCalc",NULL);
+ plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+ }
+ /* END PLUMED */
+ do_force(fplog, cr, ir, step, nrnb, wcycle, top, top_global, groups,
+ state->box, state->x, &state->hist,
+ f, force_vir, mdatoms, enerd, fcd,
+ state->lambda, graph,
+ fr, vsite, mu_tot, t, outf->fp_field, ed, bBornRadii,
+ (plumedNeedsEnergy? GMX_FORCE_ENERGY : 0) |(bNS ? GMX_FORCE_NS : 0) | force_flags);
+ /* PLUMED */
+ if(plumedswitch){
+ if(plumedNeedsEnergy) plumed_cmd(plumedmain,"setEnergy",&enerd->term[F_EPOT]);
+ plumed_cmd(plumedmain,"setStopFlag",&plumedWantsToStop);
+ plumed_cmd(plumedmain,"setForces",&f[mdatoms->start][0]);
+ plumed_cmd(plumedmain,"setVirial",&force_vir[0][0]);
+ plumed_cmd(plumedmain,"performCalc",NULL);
+ if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
+ do_per_step(step,repl_ex_nst)) plumed_cmd(plumedmain,"GREX savePositions",NULL);
+ if(plumedWantsToStop) ir->nsteps=step_rel+1;
+ }
+ /* END PLUMED */
+ }
+
+ GMX_BARRIER(cr->mpi_comm_mygroup);
+
+ if (bTCR)
+ {
+ mu_aver = calc_mu_aver(cr, state->x, mdatoms->chargeA,
+ mu_tot, &top_global->mols, mdatoms, gnx, grpindex);
+ }
+
+ if (bTCR && bFirstStep)
+ {
+ tcr = init_coupling(fplog, nfile, fnm, cr, fr, mdatoms, &(top->idef));
+ fprintf(fplog, "Done init_coupling\n");
+ fflush(fplog);
+ }
+
+ if (bVV && !bStartingFromCpt && !bRerunMD)
+ /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
+ {
+ if (ir->eI == eiVV && bInitStep)
+ {
+ /* if using velocity verlet with full time step Ekin,
+ * take the first half step only to compute the
+ * virial for the first step. From there,
+ * revert back to the initial coordinates
+ * so that the input is actually the initial step.
+ */
+ copy_rvecn(state->v, cbuf, 0, state->natoms); /* should make this better for parallelizing? */
+ }
+ else
+ {
+ /* this is for NHC in the Ekin(t+dt/2) version of vv */
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ1);
+ }
+
+ /* If we are using twin-range interactions where the long-range component
+ * is only evaluated every nstcalclr>1 steps, we should do a special update
+ * step to combine the long-range forces on these steps.
+ * For nstcalclr=1 this is not done, since the forces would have been added
+ * directly to the short-range forces already.
+ */
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
+ f, bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, upd, bInitStep, etrtVELOCITY1,
+ cr, nrnb, constr, &top->idef);
+
+ if (bIterativeCase && do_per_step(step-1, ir->nstpcouple) && !bInitStep)
+ {
+ gmx_iterate_init(&iterate, TRUE);
+ }
+ /* for iterations, we save these vectors, as we will be self-consistently iterating
+ the calculations */
+
+ /*#### UPDATE EXTENDED VARIABLES IN TROTTER FORMULATION */
+
+ /* save the state */
+ if (iterate.bIterationActive)
+ {
+ copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
+ }
+
+ bFirstIterate = TRUE;
+ while (bFirstIterate || iterate.bIterationActive)
+ {
+ if (iterate.bIterationActive)
+ {
+ copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
+ if (bFirstIterate && bTrotter)
+ {
+ /* The first time through, we need a decent first estimate
+ of veta(t+dt) to compute the constraints. Do
+ this by computing the box volume part of the
+ trotter integration at this time. Nothing else
+ should be changed by this routine here. If
+ !(first time), we start with the previous value
+ of veta. */
+
+ veta_save = state->veta;
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ0);
+ vetanew = state->veta;
+ state->veta = veta_save;
+ }
+ }
+
+ bOK = TRUE;
+ if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
+ {
+ update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, shake_vir, NULL,
+ cr, nrnb, wcycle, upd, constr,
+ bInitStep, TRUE, bCalcVir, vetanew);
+
+ if (!bOK && !bFFscan)
+ {
+ gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
+ }
+
+ }
+ else if (graph)
+ {
+ /* Need to unshift here if a do_force has been
+ called in the previous step */
+ unshift_self(graph, state->box, state->x);
+ }
+
+ /* if VV, compute the pressure and constraints */
+ /* For VV2, we strictly only need this if using pressure
+ * control, but we really would like to have accurate pressures
+ * printed out.
+ * Think about ways around this in the future?
+ * For now, keep this choice in comments.
+ */
+ /*bPres = (ir->eI==eiVV || IR_NPT_TROTTER(ir)); */
+ /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir)));*/
+ bPres = TRUE;
+ bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
+ if (bCalcEner && ir->eI == eiVVAK) /*MRS: 7/9/2010 -- this still doesn't fix it?*/
+ {
+ bSumEkinhOld = TRUE;
+ }
+ /* for vv, the first half of the integration actually corresponds to the previous step.
+ So we need information from the last step in the first half of the integration */
+ if (bGStat || do_per_step(step-1, nstglobalcomm))
+ {
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags
+ | CGLO_ENERGY
+ | (bTemp ? CGLO_TEMPERATURE : 0)
+ | (bPres ? CGLO_PRESSURE : 0)
+ | (bPres ? CGLO_CONSTRAINT : 0)
+ | ((iterate.bIterationActive) ? CGLO_ITERATE : 0)
+ | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
+ | CGLO_SCALEEKIN
+ );
+ /* explanation of above:
+ a) We compute Ekin at the full time step
+ if 1) we are using the AveVel Ekin, and it's not the
+ initial step, or 2) if we are using AveEkin, but need the full
+ time step kinetic energy for the pressure (always true now, since we want accurate statistics).
+ b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
+ EkinAveVel because it's needed for the pressure */
+ }
+ /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
+ if (!bInitStep)
+ {
+ if (bTrotter)
+ {
+ m_add(force_vir, shake_vir, total_vir); /* we need the un-dispersion corrected total vir here */
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ2);
+ }
+ else
+ {
+ if (bExchanged)
+ {
+
+ /* We need the kinetic energy at minus the half step for determining
+ * the full step kinetic energy and possibly for T-coupling.*/
+ /* This may not be quite working correctly yet . . . . */
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
+ }
+ }
+ }
+
+ if (iterate.bIterationActive &&
+ done_iterating(cr, fplog, step, &iterate, bFirstIterate,
+ state->veta, &vetanew))
+ {
+ break;
+ }
+ bFirstIterate = FALSE;
+ }
+
+ if (bTrotter && !bInitStep)
+ {
+ copy_mat(shake_vir, state->svir_prev);
+ copy_mat(force_vir, state->fvir_prev);
+ if (IR_NVT_TROTTER(ir) && ir->eI == eiVV)
+ {
+ /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
+ enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, NULL, (ir->eI == eiVV), FALSE, FALSE);
+ enerd->term[F_EKIN] = trace(ekind->ekin);
+ }
+ }
+ /* if it's the initial step, we performed this first step just to get the constraint virial */
+ if (bInitStep && ir->eI == eiVV)
+ {
+ copy_rvecn(cbuf, state->v, 0, state->natoms);
+ }
+
+ GMX_MPE_LOG(ev_timestep1);
+ }
+
+ /* MRS -- now done iterating -- compute the conserved quantity */
+ if (bVV)
+ {
+ saved_conserved_quantity = compute_conserved_from_auxiliary(ir, state, &MassQ);
+ if (ir->eI == eiVV)
+ {
+ last_ekin = enerd->term[F_EKIN];
+ }
+ if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
+ {
+ saved_conserved_quantity -= enerd->term[F_DISPCORR];
+ }
+ /* sum up the foreign energy and dhdl terms for vv. currently done every step so that dhdl is correct in the .edr */
+ if (!bRerunMD)
+ {
+ sum_dhdl(enerd, state->lambda, ir->fepvals);
+ }
+ }
+
+ /* ######## END FIRST UPDATE STEP ############## */
+ /* ######## If doing VV, we now have v(dt) ###### */
+ if (bDoExpanded)
+ {
+ /* perform extended ensemble sampling in lambda - we don't
+ actually move to the new state before outputting
+ statistics, but if performing simulated tempering, we
+ do update the velocities and the tau_t. */
+
+ lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, &df_history, step, mcrng, state->v, mdatoms);
+ }
+ /* ################## START TRAJECTORY OUTPUT ################# */
+
+ /* Now we have the energies and forces corresponding to the
+ * coordinates at time t. We must output all of this before
+ * the update.
+ * for RerunMD t is read from input trajectory
+ */
+ GMX_MPE_LOG(ev_output_start);
+
+ mdof_flags = 0;
+ if (do_per_step(step, ir->nstxout))
+ {
+ mdof_flags |= MDOF_X;
+ }
+ if (do_per_step(step, ir->nstvout))
+ {
+ mdof_flags |= MDOF_V;
+ }
+ if (do_per_step(step, ir->nstfout))
+ {
+ mdof_flags |= MDOF_F;
+ }
+ if (do_per_step(step, ir->nstxtcout))
+ {
+ mdof_flags |= MDOF_XTC;
+ }
+ if (bCPT)
+ {
+ mdof_flags |= MDOF_CPT;
+ }
+ ;
+
+#if defined(GMX_FAHCORE) || defined(GMX_WRITELASTSTEP)
+ if (bLastStep)
+ {
+ /* Enforce writing positions and velocities at end of run */
+ mdof_flags |= (MDOF_X | MDOF_V);
+ }
+#endif
+#ifdef GMX_FAHCORE
+ if (MASTER(cr))
+ {
+ fcReportProgress( ir->nsteps, step );
+ }
+
+ /* sync bCPT and fc record-keeping */
+ if (bCPT && MASTER(cr))
+ {
+ fcRequestCheckPoint();
+ }
+#endif
+
+ if (mdof_flags != 0)
+ {
+ wallcycle_start(wcycle, ewcTRAJ);
+ if (bCPT)
+ {
+ if (state->flags & (1<<estLD_RNG))
+ {
+ get_stochd_state(upd, state);
+ }
+ if (state->flags & (1<<estMC_RNG))
+ {
+ get_mc_state(mcrng, state);
+ }
+ if (MASTER(cr))
+ {
+ if (bSumEkinhOld)
+ {
+ state_global->ekinstate.bUpToDate = FALSE;
+ }
+ else
+ {
+ update_ekinstate(&state_global->ekinstate, ekind);
+ state_global->ekinstate.bUpToDate = TRUE;
+ }
+ update_energyhistory(&state_global->enerhist, mdebin);
+ if (ir->efep != efepNO || ir->bSimTemp)
+ {
+ state_global->fep_state = state->fep_state; /* MRS: seems kludgy. The code should be
+ structured so this isn't necessary.
+ Note this reassignment is only necessary
+ for single threads.*/
+ copy_df_history(&state_global->dfhist, &df_history);
+ }
+ }
+ }
+ write_traj(fplog, cr, outf, mdof_flags, top_global,
+ step, t, state, state_global, f, f_global, &n_xtc, &x_xtc);
+ if (bCPT)
+ {
+ nchkpt++;
+ bCPT = FALSE;
+ }
+ debug_gmx();
+ if (bLastStep && step_rel == ir->nsteps &&
+ (Flags & MD_CONFOUT) && MASTER(cr) &&
+ !bRerunMD && !bFFscan)
+ {
+ /* x and v have been collected in write_traj,
+ * because a checkpoint file will always be written
+ * at the last step.
+ */
+ fprintf(stderr, "\nWriting final coordinates.\n");
+ if (fr->bMolPBC)
+ {
+ /* Make molecules whole only for confout writing */
+ do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, state_global->x);
+ }
+ write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
+ *top_global->name, top_global,
+ state_global->x, state_global->v,
+ ir->ePBC, state->box);
+ debug_gmx();
+ }
+ wallcycle_stop(wcycle, ewcTRAJ);
+ }
+ GMX_MPE_LOG(ev_output_finish);
+
+ /* kludge -- virial is lost with restart for NPT control. Must restart */
+ if (bStartingFromCpt && bVV)
+ {
+ copy_mat(state->svir_prev, shake_vir);
+ copy_mat(state->fvir_prev, force_vir);
+ }
+ /* ################## END TRAJECTORY OUTPUT ################ */
+
+ /* Determine the wallclock run time up till now */
+ run_time = gmx_gettime() - (double)runtime->real;
+
+ /* Check whether everything is still allright */
+ if (((int)gmx_get_stop_condition() > handled_stop_condition)
+#ifdef GMX_THREAD_MPI
+ && MASTER(cr)
+#endif
+ )
+ {
+ /* this is just make gs.sig compatible with the hack
+ of sending signals around by MPI_Reduce with together with
+ other floats */
+ if (gmx_get_stop_condition() == gmx_stop_cond_next_ns)
+ {
+ gs.sig[eglsSTOPCOND] = 1;
+ }
+ if (gmx_get_stop_condition() == gmx_stop_cond_next)
+ {
+ gs.sig[eglsSTOPCOND] = -1;
+ }
+ /* < 0 means stop at next step, > 0 means stop at next NS step */
+ if (fplog)
+ {
+ fprintf(fplog,
+ "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
+ gmx_get_signal_name(),
+ gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
+ fflush(fplog);
+ }
+ fprintf(stderr,
+ "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
+ gmx_get_signal_name(),
+ gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
+ fflush(stderr);
+ handled_stop_condition = (int)gmx_get_stop_condition();
+ }
+ else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
+ (max_hours > 0 && run_time > max_hours*60.0*60.0*0.99) &&
+ gs.sig[eglsSTOPCOND] == 0 && gs.set[eglsSTOPCOND] == 0)
+ {
+ /* Signal to terminate the run */
+ gs.sig[eglsSTOPCOND] = 1;
+ if (fplog)
+ {
+ fprintf(fplog, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
+ }
+ fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
+ }
+
+ if (bResetCountersHalfMaxH && MASTER(cr) &&
+ run_time > max_hours*60.0*60.0*0.495)
+ {
+ gs.sig[eglsRESETCOUNTERS] = 1;
+ }
+
+ if (ir->nstlist == -1 && !bRerunMD)
+ {
+ /* When bGStatEveryStep=FALSE, global_stat is only called
+ * when we check the atom displacements, not at NS steps.
+ * This means that also the bonded interaction count check is not
+ * performed immediately after NS. Therefore a few MD steps could
+ * be performed with missing interactions.
+ * But wrong energies are never written to file,
+ * since energies are only written after global_stat
+ * has been called.
+ */
+ if (step >= nlh.step_nscheck)
+ {
+ nlh.nabnsb = natoms_beyond_ns_buffer(ir, fr, &top->cgs,
+ nlh.scale_tot, state->x);
+ }
+ else
+ {
+ /* This is not necessarily true,
+ * but step_nscheck is determined quite conservatively.
+ */
+ nlh.nabnsb = 0;
+ }
+ }
+
+ /* In parallel we only have to check for checkpointing in steps
+ * where we do global communication,
+ * otherwise the other nodes don't know.
+ */
+ if (MASTER(cr) && ((bGStat || !PAR(cr)) &&
+ cpt_period >= 0 &&
+ (cpt_period == 0 ||
+ run_time >= nchkpt*cpt_period*60.0)) &&
+ gs.set[eglsCHKPT] == 0)
+ {
+ gs.sig[eglsCHKPT] = 1;
+ }
+
+ /* at the start of step, randomize or scale the velocities (trotter done elsewhere) */
+ if (EI_VV(ir->eI))
+ {
+ if (!bInitStep)
+ {
+ update_tcouple(fplog, step, ir, state, ekind, wcycle, upd, &MassQ, mdatoms);
+ }
+ if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
+ {
+ gmx_bool bIfRandomize;
+ bIfRandomize = update_randomize_velocities(ir, step, mdatoms, state, upd, &top->idef, constr);
+ /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
+ if (constr && bIfRandomize)
+ {
+ update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, tmp_vir, NULL,
+ cr, nrnb, wcycle, upd, constr,
+ bInitStep, TRUE, bCalcVir, vetanew);
+ }
+ }
+ }
+
+ if (bIterativeCase && do_per_step(step, ir->nstpcouple))
+ {
+ gmx_iterate_init(&iterate, TRUE);
+ /* for iterations, we save these vectors, as we will be redoing the calculations */
+ copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
+ }
+
+ bFirstIterate = TRUE;
+ while (bFirstIterate || iterate.bIterationActive)
+ {
+ /* We now restore these vectors to redo the calculation with improved extended variables */
+ if (iterate.bIterationActive)
+ {
+ copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
+ }
+
+ /* We make the decision to break or not -after- the calculation of Ekin and Pressure,
+ so scroll down for that logic */
+
+ /* ######### START SECOND UPDATE STEP ################# */
+ GMX_MPE_LOG(ev_update_start);
+ /* Box is changed in update() when we do pressure coupling,
+ * but we should still use the old box for energy corrections and when
+ * writing it to the energy file, so it matches the trajectory files for
+ * the same timestep above. Make a copy in a separate array.
+ */
+ copy_mat(state->box, lastbox);
+
+ bOK = TRUE;
+ dvdl_constr = 0;
+
+ if (!(bRerunMD && !rerun_fr.bV && !bForceUpdate))
+ {
+ wallcycle_start(wcycle, ewcUPDATE);
+ /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
+ if (bTrotter)
+ {
+ if (iterate.bIterationActive)
+ {
+ if (bFirstIterate)
+ {
+ scalevir = 1;
+ }
+ else
+ {
+ /* we use a new value of scalevir to converge the iterations faster */
+ scalevir = tracevir/trace(shake_vir);
+ }
+ msmul(shake_vir, scalevir, shake_vir);
+ m_add(force_vir, shake_vir, total_vir);
+ clear_mat(shake_vir);
+ }
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
+ /* We can only do Berendsen coupling after we have summed
+ * the kinetic energy or virial. Since the happens
+ * in global_state after update, we should only do it at
+ * step % nstlist = 1 with bGStatEveryStep=FALSE.
+ */
+ }
+ else
+ {
+ update_tcouple(fplog, step, ir, state, ekind, wcycle, upd, &MassQ, mdatoms);
+ update_pcouple(fplog, step, ir, state, pcoupl_mu, M, wcycle,
+ upd, bInitStep);
+ }
+
+ if (bVV)
+ {
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ /* velocity half-step update */
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, upd, FALSE, etrtVELOCITY2,
+ cr, nrnb, constr, &top->idef);
+ }
+
+ /* Above, initialize just copies ekinh into ekin,
+ * it doesn't copy position (for VV),
+ * and entire integrator for MD.
+ */
+
+ if (ir->eI == eiVVAK)
+ {
+ copy_rvecn(state->x, cbuf, 0, state->natoms);
+ }
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+ wallcycle_stop(wcycle, ewcUPDATE);
+
+ update_constraints(fplog, step, &dvdl_constr, ir, ekind, mdatoms, state,
+ fr->bMolPBC, graph, f,
+ &top->idef, shake_vir, force_vir,
+ cr, nrnb, wcycle, upd, constr,
+ bInitStep, FALSE, bCalcVir, state->veta);
+
+ if (ir->eI == eiVVAK)
+ {
+ /* erase F_EKIN and F_TEMP here? */
+ /* just compute the kinetic energy at the half step to perform a trotter step */
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, lastbox,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags | CGLO_TEMPERATURE
+ );
+ wallcycle_start(wcycle, ewcUPDATE);
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
+ /* now we know the scaling, we can compute the positions again again */
+ copy_rvecn(cbuf, state->x, 0, state->natoms);
+
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+ wallcycle_stop(wcycle, ewcUPDATE);
+
+ /* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
+ /* are the small terms in the shake_vir here due
+ * to numerical errors, or are they important
+ * physically? I'm thinking they are just errors, but not completely sure.
+ * For now, will call without actually constraining, constr=NULL*/
+ update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, tmp_vir, force_vir,
+ cr, nrnb, wcycle, upd, NULL,
+ bInitStep, FALSE, bCalcVir,
+ state->veta);
+ }
+ if (!bOK && !bFFscan)
+ {
+ gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
+ }
+
+ if (fr->bSepDVDL && fplog && do_log)
+ {
+ fprintf(fplog, sepdvdlformat, "Constraint dV/dl", 0.0, dvdl_constr);
+ }
+ if (bVV)
+ {
+ /* this factor or 2 correction is necessary
+ because half of the constraint force is removed
+ in the vv step, so we have to double it. See
+ the Redmine issue #1255. It is not yet clear
+ if the factor of 2 is exact, or just a very
+ good approximation, and this will be
+ investigated. The next step is to see if this
+ can be done adding a dhdl contribution from the
+ rattle step, but this is somewhat more
+ complicated with the current code. Will be
+ investigated, hopefully for 4.6.3. However,
+ this current solution is much better than
+ having it completely wrong.
+ */
+ enerd->term[F_DVDL_CONSTR] += 2*dvdl_constr;
+ }
+ else
+ {
+ enerd->term[F_DVDL_CONSTR] += dvdl_constr;
+ }
+ }
+ else if (graph)
+ {
+ /* Need to unshift here */
+ unshift_self(graph, state->box, state->x);
+ }
+
+ GMX_BARRIER(cr->mpi_comm_mygroup);
+ GMX_MPE_LOG(ev_update_finish);
+
+ if (vsite != NULL)
+ {
+ wallcycle_start(wcycle, ewcVSITECONSTR);
+ if (graph != NULL)
+ {
+ shift_self(graph, state->box, state->x);
+ }
+ construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, state->v,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, graph, cr, state->box);
+
+ if (graph != NULL)
+ {
+ unshift_self(graph, state->box, state->x);
+ }
+ wallcycle_stop(wcycle, ewcVSITECONSTR);
+ }
+
+ /* ############## IF NOT VV, Calculate globals HERE, also iterate constraints ############ */
+ /* With Leap-Frog we can skip compute_globals at
+ * non-communication steps, but we need to calculate
+ * the kinetic energy one step before communication.
+ */
+ if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)))
+ {
+ if (ir->nstlist == -1 && bFirstIterate)
+ {
+ gs.sig[eglsNABNSB] = nlh.nabnsb;
+ }
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr,
+ bFirstIterate ? &gs : NULL,
+ (step_rel % gs.nstms == 0) &&
+ (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
+ lastbox,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags
+ | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
+ | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
+ | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
+ | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
+ | (iterate.bIterationActive ? CGLO_ITERATE : 0)
+ | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
+ | CGLO_CONSTRAINT
+ );
+ if (ir->nstlist == -1 && bFirstIterate)
+ {
+ nlh.nabnsb = gs.set[eglsNABNSB];
+ gs.set[eglsNABNSB] = 0;
+ }
+ }
+ /* bIterate is set to keep it from eliminating the old ekin kinetic energy terms */
+ /* ############# END CALC EKIN AND PRESSURE ################# */
+
+ /* Note: this is OK, but there are some numerical precision issues with using the convergence of
+ the virial that should probably be addressed eventually. state->veta has better properies,
+ but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
+ generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
+
+ if (iterate.bIterationActive &&
+ done_iterating(cr, fplog, step, &iterate, bFirstIterate,
+ trace(shake_vir), &tracevir))
+ {
+ break;
+ }
+ bFirstIterate = FALSE;
+ }
+
+ if (!bVV || bRerunMD)
+ {
+ /* sum up the foreign energy and dhdl terms for md and sd. currently done every step so that dhdl is correct in the .edr */
+ sum_dhdl(enerd, state->lambda, ir->fepvals);
+ }
+ update_box(fplog, step, ir, mdatoms, state, graph, f,
+ ir->nstlist == -1 ? &nlh.scale_tot : NULL, pcoupl_mu, nrnb, wcycle, upd, bInitStep, FALSE);
+
+ /* ################# END UPDATE STEP 2 ################# */
+ /* #### We now have r(t+dt) and v(t+dt/2) ############# */
+
+ /* The coordinates (x) were unshifted in update */
+ if (bFFscan && (shellfc == NULL || bConverged))
+ {
+ if (print_forcefield(fplog, enerd->term, mdatoms->homenr,
+ f, NULL, xcopy,
+ &(top_global->mols), mdatoms->massT, pres))
+ {
+ gmx_finalize_par();
+
+ fprintf(stderr, "\n");
+ exit(0);
+ }
+ }
+ if (!bGStat)
+ {
+ /* We will not sum ekinh_old,
+ * so signal that we still have to do it.
+ */
+ bSumEkinhOld = TRUE;
+ }
+
+ if (bTCR)
+ {
+ /* Only do GCT when the relaxation of shells (minimization) has converged,
+ * otherwise we might be coupling to bogus energies.
+ * In parallel we must always do this, because the other sims might
+ * update the FF.
+ */
+
+ /* Since this is called with the new coordinates state->x, I assume
+ * we want the new box state->box too. / EL 20040121
+ */
+ do_coupling(fplog, oenv, nfile, fnm, tcr, t, step, enerd->term, fr,
+ ir, MASTER(cr),
+ mdatoms, &(top->idef), mu_aver,
+ top_global->mols.nr, cr,
+ state->box, total_vir, pres,
+ mu_tot, state->x, f, bConverged);
+ debug_gmx();
+ }
+
+ /* ######### BEGIN PREPARING EDR OUTPUT ########### */
+
+ /* use the directly determined last velocity, not actually the averaged half steps */
+ if (bTrotter && ir->eI == eiVV)
+ {
+ enerd->term[F_EKIN] = last_ekin;
+ }
+ enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
+
+ if (bVV)
+ {
+ enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
+ }
+ else
+ {
+ enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + compute_conserved_from_auxiliary(ir, state, &MassQ);
+ }
+ /* Check for excessively large energies */
+ if (bIonize)
+ {
+#ifdef GMX_DOUBLE
+ real etot_max = 1e200;
+#else
+ real etot_max = 1e30;
+#endif
+ if (fabs(enerd->term[F_ETOT]) > etot_max)
+ {
+ fprintf(stderr, "Energy too large (%g), giving up\n",
+ enerd->term[F_ETOT]);
+ }
+ }
+ /* ######### END PREPARING EDR OUTPUT ########### */
+
+ /* Time for performance */
+ if (((step % stepout) == 0) || bLastStep)
+ {
+ runtime_upd_proc(runtime);
+ }
+
+ /* Output stuff */
+ if (MASTER(cr))
+ {
+ gmx_bool do_dr, do_or;
+
+ if (fplog && do_log && bDoExpanded)
+ {
+ /* only needed if doing expanded ensemble */
+ PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
+ &df_history, state->fep_state, ir->nstlog, step);
+ }
+ if (!(bStartingFromCpt && (EI_VV(ir->eI))))
+ {
+ if (bCalcEner)
+ {
+ upd_mdebin(mdebin, bDoDHDL, TRUE,
+ t, mdatoms->tmass, enerd, state,
+ ir->fepvals, ir->expandedvals, lastbox,
+ shake_vir, force_vir, total_vir, pres,
+ ekind, mu_tot, constr);
+ }
+ else
+ {
+ upd_mdebin_step(mdebin);
+ }
+
+ do_dr = do_per_step(step, ir->nstdisreout);
+ do_or = do_per_step(step, ir->nstorireout);
+
+ print_ebin(outf->fp_ene, do_ene, do_dr, do_or, do_log ? fplog : NULL,
+ step, t,
+ eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
+ }
+ if (ir->ePull != epullNO)
+ {
+ pull_print_output(ir->pull, step, t);
+ }
+
+ if (do_per_step(step, ir->nstlog))
+ {
+ if (fflush(fplog) != 0)
+ {
+ gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
+ }
+ }
+ }
+ if (bDoExpanded)
+ {
+ /* Have to do this part after outputting the logfile and the edr file */
+ state->fep_state = lamnew;
+ for (i = 0; i < efptNR; i++)
+ {
+ state_global->lambda[i] = ir->fepvals->all_lambda[i][lamnew];
+ }
+ }
+ /* Remaining runtime */
+ if (MULTIMASTER(cr) && (do_verbose || gmx_got_usr_signal()) && !bPMETuneRunning)
+ {
+ if (shellfc)
+ {
+ fprintf(stderr, "\n");
+ }
+ print_time(stderr, runtime, step, ir, cr);
+ }
+
+ /* Replica exchange */
+ bExchanged = FALSE;
+ if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
+ do_per_step(step, repl_ex_nst))
+ {
+ bExchanged = replica_exchange(fplog, cr, repl_ex,
+ state_global, enerd,
+ state, step, t);
+
+ if (bExchanged && DOMAINDECOMP(cr))
+ {
+ dd_partition_system(fplog, step, cr, TRUE, 1,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle, FALSE);
+ }
+ }
+
+ bFirstStep = FALSE;
+ bInitStep = FALSE;
+ bStartingFromCpt = FALSE;
+
+ /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
+ /* With all integrators, except VV, we need to retain the pressure
+ * at the current step for coupling at the next step.
+ */
+ if ((state->flags & (1<<estPRES_PREV)) &&
+ (bGStatEveryStep ||
+ (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
+ {
+ /* Store the pressure in t_state for pressure coupling
+ * at the next MD step.
+ */
+ copy_mat(pres, state->pres_prev);
+ }
+
+ /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
+
+ if ( (membed != NULL) && (!bLastStep) )
+ {
+ rescale_membed(step_rel, membed, state_global->x);
+ }
+
+ if (bRerunMD)
+ {
+ if (MASTER(cr))
+ {
+ /* read next frame from input trajectory */
+ bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
+ }
+
+ if (PAR(cr))
+ {
+ rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
+ }
+ }
+
+ if (!bRerunMD || !rerun_fr.bStep)
+ {
+ /* increase the MD step number */
+ step++;
+ step_rel++;
+ }
+
+ cycles = wallcycle_stop(wcycle, ewcSTEP);
+ if (DOMAINDECOMP(cr) && wcycle)
+ {
+ dd_cycles_add(cr->dd, cycles, ddCyclStep);
+ }
+
+ if (bPMETuneRunning || bPMETuneTry)
+ {
+ /* PME grid + cut-off optimization with GPUs or PME nodes */
+
+ /* Count the total cycles over the last steps */
+ cycles_pmes += cycles;
+
+ /* We can only switch cut-off at NS steps */
+ if (step % ir->nstlist == 0)
+ {
+ /* PME grid + cut-off optimization with GPUs or PME nodes */
+ if (bPMETuneTry)
+ {
+ if (DDMASTER(cr->dd))
+ {
+ /* PME node load is too high, start tuning */
+ bPMETuneRunning = (dd_pme_f_ratio(cr->dd) >= 1.05);
+ }
+ dd_bcast(cr->dd, sizeof(gmx_bool), &bPMETuneRunning);
+
+ if (bPMETuneRunning || step_rel > ir->nstlist*50)
+ {
+ bPMETuneTry = FALSE;
+ }
+ }
+ if (bPMETuneRunning)
+ {
+ /* init_step might not be a multiple of nstlist,
+ * but the first cycle is always skipped anyhow.
+ */
+ bPMETuneRunning =
+ pme_load_balance(pme_loadbal, cr,
+ (bVerbose && MASTER(cr)) ? stderr : NULL,
+ fplog,
+ ir, state, cycles_pmes,
+ fr->ic, fr->nbv, &fr->pmedata,
+ step);
+
+ /* Update constants in forcerec/inputrec to keep them in sync with fr->ic */
+ fr->ewaldcoeff = fr->ic->ewaldcoeff;
+ fr->rlist = fr->ic->rlist;
+ fr->rlistlong = fr->ic->rlistlong;
+ fr->rcoulomb = fr->ic->rcoulomb;
+ fr->rvdw = fr->ic->rvdw;
+ }
+ cycles_pmes = 0;
+ }
+ }
+
+ if (step_rel == wcycle_get_reset_counters(wcycle) ||
+ gs.set[eglsRESETCOUNTERS] != 0)
+ {
+ /* Reset all the counters related to performance over the run */
+ reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, runtime,
+ fr->nbv != NULL && fr->nbv->bUseGPU ? fr->nbv->cu_nbv : NULL);
+ wcycle_set_reset_counters(wcycle, -1);
+ if (!(cr->duty & DUTY_PME))
+ {
+ /* Tell our PME node to reset its counters */
+ gmx_pme_send_resetcounters(cr, step);
+ }
+ /* Correct max_hours for the elapsed time */
+ max_hours -= run_time/(60.0*60.0);
+ bResetCountersHalfMaxH = FALSE;
+ gs.set[eglsRESETCOUNTERS] = 0;
+ }
+
+ }
+ /* End of main MD loop */
+ debug_gmx();
+
+ /* Stop the time */
+ runtime_end(runtime);
+
+ if (bRerunMD && MASTER(cr))
+ {
+ close_trj(status);
+ }
+
+ if (!(cr->duty & DUTY_PME))
+ {
+ /* Tell the PME only node to finish */
+ gmx_pme_send_finish(cr);
+ }
+
+ if (MASTER(cr))
+ {
+ if (ir->nstcalcenergy > 0 && !bRerunMD)
+ {
+ print_ebin(outf->fp_ene, FALSE, FALSE, FALSE, fplog, step, t,
+ eprAVER, FALSE, mdebin, fcd, groups, &(ir->opts));
+ }
+ }
+
+ done_mdoutf(outf);
+
+ debug_gmx();
+
+ if (ir->nstlist == -1 && nlh.nns > 0 && fplog)
+ {
+ fprintf(fplog, "Average neighborlist lifetime: %.1f steps, std.dev.: %.1f steps\n", nlh.s1/nlh.nns, sqrt(nlh.s2/nlh.nns - sqr(nlh.s1/nlh.nns)));
+ fprintf(fplog, "Average number of atoms that crossed the half buffer length: %.1f\n\n", nlh.ab/nlh.nns);
+ }
+
+ if (pme_loadbal != NULL)
+ {
+ pme_loadbal_done(pme_loadbal, cr, fplog,
+ fr->nbv != NULL && fr->nbv->bUseGPU);
+ }
+
+ if (shellfc && fplog)
+ {
+ fprintf(fplog, "Fraction of iterations that converged: %.2f %%\n",
+ (nconverged*100.0)/step_rel);
+ fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
+ tcount/step_rel);
+ }
+
+ if (repl_ex_nst > 0 && MASTER(cr))
+ {
+ print_replica_exchange_statistics(fplog, repl_ex);
+ }
+
+ runtime->nsteps_done = step_rel;
+
+ return 0;
+}
diff --git a/patches/gromacs-4.6.3.diff/src/kernel/md.c.preplumed b/patches/gromacs-4.6.3.diff/src/kernel/md.c.preplumed
new file mode 100644
index 0000000000000000000000000000000000000000..f82e6974ca5095ff0eb4b7268ddf9b63798ca64d
--- /dev/null
+++ b/patches/gromacs-4.6.3.diff/src/kernel/md.c.preplumed
@@ -0,0 +1,2260 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "typedefs.h"
+#include "smalloc.h"
+#include "sysstuff.h"
+#include "vec.h"
+#include "statutil.h"
+#include "vcm.h"
+#include "mdebin.h"
+#include "nrnb.h"
+#include "calcmu.h"
+#include "index.h"
+#include "vsite.h"
+#include "update.h"
+#include "ns.h"
+#include "trnio.h"
+#include "xtcio.h"
+#include "mdrun.h"
+#include "md_support.h"
+#include "md_logging.h"
+#include "confio.h"
+#include "network.h"
+#include "pull.h"
+#include "xvgr.h"
+#include "physics.h"
+#include "names.h"
+#include "xmdrun.h"
+#include "ionize.h"
+#include "disre.h"
+#include "orires.h"
+#include "pme.h"
+#include "mdatoms.h"
+#include "repl_ex.h"
+#include "qmmm.h"
+#include "mpelogging.h"
+#include "domdec.h"
+#include "domdec_network.h"
+#include "partdec.h"
+#include "topsort.h"
+#include "coulomb.h"
+#include "constr.h"
+#include "shellfc.h"
+#include "compute_io.h"
+#include "mvdata.h"
+#include "checkpoint.h"
+#include "mtop_util.h"
+#include "sighandler.h"
+#include "txtdump.h"
+#include "string2.h"
+#include "pme_loadbal.h"
+#include "bondf.h"
+#include "membed.h"
+#include "types/nlistheuristics.h"
+#include "types/iteratedconstraints.h"
+#include "nbnxn_cuda_data_mgmt.h"
+
+#ifdef GMX_LIB_MPI
+#include <mpi.h>
+#endif
+#ifdef GMX_THREAD_MPI
+#include "tmpi.h"
+#endif
+
+#ifdef GMX_FAHCORE
+#include "corewrap.h"
+#endif
+
+static void reset_all_counters(FILE *fplog, t_commrec *cr,
+ gmx_large_int_t step,
+ gmx_large_int_t *step_rel, t_inputrec *ir,
+ gmx_wallcycle_t wcycle, t_nrnb *nrnb,
+ gmx_runtime_t *runtime,
+ nbnxn_cuda_ptr_t cu_nbv)
+{
+ char sbuf[STEPSTRSIZE];
+
+ /* Reset all the counters related to performance over the run */
+ md_print_warn(cr, fplog, "step %s: resetting all time and cycle counters\n",
+ gmx_step_str(step, sbuf));
+
+ if (cu_nbv)
+ {
+ nbnxn_cuda_reset_timings(cu_nbv);
+ }
+
+ wallcycle_stop(wcycle, ewcRUN);
+ wallcycle_reset_all(wcycle);
+ if (DOMAINDECOMP(cr))
+ {
+ reset_dd_statistics_counters(cr->dd);
+ }
+ init_nrnb(nrnb);
+ ir->init_step += *step_rel;
+ ir->nsteps -= *step_rel;
+ *step_rel = 0;
+ wallcycle_start(wcycle, ewcRUN);
+ runtime_start(runtime);
+ print_date_and_time(fplog, cr->nodeid, "Restarted time", runtime);
+}
+
+double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
+ const output_env_t oenv, gmx_bool bVerbose, gmx_bool bCompact,
+ int nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int stepout, t_inputrec *ir,
+ gmx_mtop_t *top_global,
+ t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed, t_forcerec *fr,
+ int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t membed,
+ real cpt_period, real max_hours,
+ const char *deviceOptions,
+ unsigned long Flags,
+ gmx_runtime_t *runtime)
+{
+ gmx_mdoutf_t *outf;
+ gmx_large_int_t step, step_rel;
+ double run_time;
+ double t, t0, lam0[efptNR];
+ gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEner;
+ gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD, bNotLastFrame = FALSE,
+ bFirstStep, bStateFromCP, bStateFromTPX, bInitStep, bLastStep,
+ bBornRadii, bStartingFromCpt;
+ gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
+ gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
+ bForceUpdate = FALSE, bCPT;
+ int mdof_flags;
+ gmx_bool bMasterState;
+ int force_flags, cglo_flags;
+ tensor force_vir, shake_vir, total_vir, tmp_vir, pres;
+ int i, m;
+ t_trxstatus *status;
+ rvec mu_tot;
+ t_vcm *vcm;
+ t_state *bufstate = NULL;
+ matrix *scale_tot, pcoupl_mu, M, ebox;
+ gmx_nlheur_t nlh;
+ t_trxframe rerun_fr;
+ gmx_repl_ex_t repl_ex = NULL;
+ int nchkpt = 1;
+ gmx_localtop_t *top;
+ t_mdebin *mdebin = NULL;
+ df_history_t df_history;
+ t_state *state = NULL;
+ rvec *f_global = NULL;
+ int n_xtc = -1;
+ rvec *x_xtc = NULL;
+ gmx_enerdata_t *enerd;
+ rvec *f = NULL;
+ gmx_global_stat_t gstat;
+ gmx_update_t upd = NULL;
+ t_graph *graph = NULL;
+ globsig_t gs;
+ gmx_rng_t mcrng = NULL;
+ gmx_bool bFFscan;
+ gmx_groups_t *groups;
+ gmx_ekindata_t *ekind, *ekind_save;
+ gmx_shellfc_t shellfc;
+ int count, nconverged = 0;
+ real timestep = 0;
+ double tcount = 0;
+ gmx_bool bIonize = FALSE;
+ gmx_bool bTCR = FALSE, bConverged = TRUE, bOK, bSumEkinhOld, bExchanged;
+ gmx_bool bAppend;
+ gmx_bool bResetCountersHalfMaxH = FALSE;
+ gmx_bool bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
+ gmx_bool bUpdateDoLR;
+ real mu_aver = 0, dvdl_constr;
+ int a0, a1, gnx = 0, ii;
+ atom_id *grpindex = NULL;
+ char *grpname;
+ t_coupl_rec *tcr = NULL;
+ rvec *xcopy = NULL, *vcopy = NULL, *cbuf = NULL;
+ matrix boxcopy = {{0}}, lastbox;
+ tensor tmpvir;
+ real fom, oldfom, veta_save, pcurr, scalevir, tracevir;
+ real vetanew = 0;
+ int lamnew = 0;
+ /* for FEP */
+ int nstfep;
+ real rate;
+ double cycles;
+ real saved_conserved_quantity = 0;
+ real last_ekin = 0;
+ int iter_i;
+ t_extmass MassQ;
+ int **trotter_seq;
+ char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
+ int handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
+ gmx_iterate_t iterate;
+ gmx_large_int_t multisim_nsteps = -1; /* number of steps to do before first multisim
+ simulation stops. If equal to zero, don't
+ communicate any more between multisims.*/
+ /* PME load balancing data for GPU kernels */
+ pme_load_balancing_t pme_loadbal = NULL;
+ double cycles_pmes;
+ gmx_bool bPMETuneTry = FALSE, bPMETuneRunning = FALSE;
+
+#ifdef GMX_FAHCORE
+ /* Temporary addition for FAHCORE checkpointing */
+ int chkpt_ret;
+#endif
+
+ /* Check for special mdrun options */
+ bRerunMD = (Flags & MD_RERUN);
+ bIonize = (Flags & MD_IONIZE);
+ bFFscan = (Flags & MD_FFSCAN);
+ bAppend = (Flags & MD_APPENDFILES);
+ if (Flags & MD_RESETCOUNTERSHALFWAY)
+ {
+ if (ir->nsteps > 0)
+ {
+ /* Signal to reset the counters half the simulation steps. */
+ wcycle_set_reset_counters(wcycle, ir->nsteps/2);
+ }
+ /* Signal to reset the counters halfway the simulation time. */
+ bResetCountersHalfMaxH = (max_hours > 0);
+ }
+
+ /* md-vv uses averaged full step velocities for T-control
+ md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
+ md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
+ bVV = EI_VV(ir->eI);
+ if (bVV) /* to store the initial velocities while computing virial */
+ {
+ snew(cbuf, top_global->natoms);
+ }
+ /* all the iteratative cases - only if there are constraints */
+ bIterativeCase = ((IR_NPH_TROTTER(ir) || IR_NPT_TROTTER(ir)) && (constr) && (!bRerunMD));
+ gmx_iterate_init(&iterate, FALSE); /* The default value of iterate->bIterationActive is set to
+ false in this step. The correct value, true or false,
+ is set at each step, as it depends on the frequency of temperature
+ and pressure control.*/
+ bTrotter = (bVV && (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir)));
+
+ if (bRerunMD)
+ {
+ /* Since we don't know if the frames read are related in any way,
+ * rebuild the neighborlist at every step.
+ */
+ ir->nstlist = 1;
+ ir->nstcalcenergy = 1;
+ nstglobalcomm = 1;
+ }
+
+ check_ir_old_tpx_versions(cr, fplog, ir, top_global);
+
+ nstglobalcomm = check_nstglobalcomm(fplog, cr, nstglobalcomm, ir);
+ bGStatEveryStep = (nstglobalcomm == 1);
+
+ if (!bGStatEveryStep && ir->nstlist == -1 && fplog != NULL)
+ {
+ fprintf(fplog,
+ "To reduce the energy communication with nstlist = -1\n"
+ "the neighbor list validity should not be checked at every step,\n"
+ "this means that exact integration is not guaranteed.\n"
+ "The neighbor list validity is checked after:\n"
+ " <n.list life time> - 2*std.dev.(n.list life time) steps.\n"
+ "In most cases this will result in exact integration.\n"
+ "This reduces the energy communication by a factor of 2 to 3.\n"
+ "If you want less energy communication, set nstlist > 3.\n\n");
+ }
+
+ if (bRerunMD || bFFscan)
+ {
+ ir->nstxtcout = 0;
+ }
+ groups = &top_global->groups;
+
+ /* Initial values */
+ init_md(fplog, cr, ir, oenv, &t, &t0, state_global->lambda,
+ &(state_global->fep_state), lam0,
+ nrnb, top_global, &upd,
+ nfile, fnm, &outf, &mdebin,
+ force_vir, shake_vir, mu_tot, &bSimAnn, &vcm, state_global, Flags);
+
+ clear_mat(total_vir);
+ clear_mat(pres);
+ /* Energy terms and groups */
+ snew(enerd, 1);
+ init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
+ enerd);
+ if (DOMAINDECOMP(cr))
+ {
+ f = NULL;
+ }
+ else
+ {
+ snew(f, top_global->natoms);
+ }
+
+ /* lambda Monte carlo random number generator */
+ if (ir->bExpanded)
+ {
+ mcrng = gmx_rng_init(ir->expandedvals->lmc_seed);
+ }
+ /* copy the state into df_history */
+ copy_df_history(&df_history, &state_global->dfhist);
+
+ /* Kinetic energy data */
+ snew(ekind, 1);
+ init_ekindata(fplog, top_global, &(ir->opts), ekind);
+ /* needed for iteration of constraints */
+ snew(ekind_save, 1);
+ init_ekindata(fplog, top_global, &(ir->opts), ekind_save);
+ /* Copy the cos acceleration to the groups struct */
+ ekind->cosacc.cos_accel = ir->cos_accel;
+
+ gstat = global_stat_init(ir);
+ debug_gmx();
+
+ /* Check for polarizable models and flexible constraints */
+ shellfc = init_shell_flexcon(fplog,
+ top_global, n_flexible_constraints(constr),
+ (ir->bContinuation ||
+ (DOMAINDECOMP(cr) && !MASTER(cr))) ?
+ NULL : state_global->x);
+
+ if (DEFORM(*ir))
+ {
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_lock(&deform_init_box_mutex);
+#endif
+ set_deform_reference_box(upd,
+ deform_init_init_step_tpx,
+ deform_init_box_tpx);
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
+#endif
+ }
+
+ {
+ double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
+ if ((io > 2000) && MASTER(cr))
+ {
+ fprintf(stderr,
+ "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
+ io);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ top = dd_init_local_top(top_global);
+
+ snew(state, 1);
+ dd_init_local_state(cr->dd, state_global, state);
+
+ if (DDMASTER(cr->dd) && ir->nstfout)
+ {
+ snew(f_global, state_global->natoms);
+ }
+ }
+ else
+ {
+ if (PAR(cr))
+ {
+ /* Initialize the particle decomposition and split the topology */
+ top = split_system(fplog, top_global, ir, cr);
+
+ pd_cg_range(cr, &fr->cg0, &fr->hcg);
+ pd_at_range(cr, &a0, &a1);
+ }
+ else
+ {
+ top = gmx_mtop_generate_local_top(top_global, ir);
+
+ a0 = 0;
+ a1 = top_global->natoms;
+ }
+
+ forcerec_set_excl_load(fr, top, cr);
+
+ state = partdec_init_local_state(cr, state_global);
+ f_global = f;
+
+ atoms2md(top_global, ir, 0, NULL, a0, a1-a0, mdatoms);
+
+ if (vsite)
+ {
+ set_vsite_top(vsite, top, mdatoms, cr);
+ }
+
+ if (ir->ePBC != epbcNONE && !fr->bMolPBC)
+ {
+ graph = mk_graph(fplog, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
+ }
+
+ if (shellfc)
+ {
+ make_local_shells(cr, mdatoms, shellfc);
+ }
+
+ init_bonded_thread_force_reduction(fr, &top->idef);
+
+ if (ir->pull && PAR(cr))
+ {
+ dd_make_local_pull_groups(NULL, ir->pull, mdatoms);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* Distribute the charge groups over the nodes from the master node */
+ dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle, FALSE);
+
+ }
+
+ update_mdatoms(mdatoms, state->lambda[efptMASS]);
+
+ if (opt2bSet("-cpi", nfile, fnm))
+ {
+ bStateFromCP = gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr);
+ }
+ else
+ {
+ bStateFromCP = FALSE;
+ }
+
+ if (MASTER(cr))
+ {
+ if (bStateFromCP)
+ {
+ /* Update mdebin with energy history if appending to output files */
+ if (Flags & MD_APPENDFILES)
+ {
+ restore_energyhistory_from_state(mdebin, &state_global->enerhist);
+ }
+ else
+ {
+ /* We might have read an energy history from checkpoint,
+ * free the allocated memory and reset the counts.
+ */
+ done_energyhistory(&state_global->enerhist);
+ init_energyhistory(&state_global->enerhist);
+ }
+ }
+ /* Set the initial energy history in state by updating once */
+ update_energyhistory(&state_global->enerhist, mdebin);
+ }
+
+ if ((state->flags & (1<<estLD_RNG)) && (Flags & MD_READ_RNG))
+ {
+ /* Set the random state if we read a checkpoint file */
+ set_stochd_state(upd, state);
+ }
+
+ if (state->flags & (1<<estMC_RNG))
+ {
+ set_mc_state(mcrng, state);
+ }
+
+ /* Initialize constraints */
+ if (constr)
+ {
+ if (!DOMAINDECOMP(cr))
+ {
+ set_constraints(constr, top, ir, mdatoms, cr);
+ }
+ }
+
+ /* Check whether we have to GCT stuff */
+ bTCR = ftp2bSet(efGCT, nfile, fnm);
+ if (bTCR)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "Will do General Coupling Theory!\n");
+ }
+ gnx = top_global->mols.nr;
+ snew(grpindex, gnx);
+ for (i = 0; (i < gnx); i++)
+ {
+ grpindex[i] = i;
+ }
+ }
+
+ if (repl_ex_nst > 0)
+ {
+ /* We need to be sure replica exchange can only occur
+ * when the energies are current */
+ check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
+ "repl_ex_nst", &repl_ex_nst);
+ /* This check needs to happen before inter-simulation
+ * signals are initialized, too */
+ }
+ if (repl_ex_nst > 0 && MASTER(cr))
+ {
+ repl_ex = init_replica_exchange(fplog, cr->ms, state_global, ir,
+ repl_ex_nst, repl_ex_nex, repl_ex_seed);
+ }
+
+ /* PME tuning is only supported with GPUs or PME nodes and not with rerun.
+ * With perturbed charges with soft-core we should not change the cut-off.
+ */
+ if ((Flags & MD_TUNEPME) &&
+ EEL_PME(fr->eeltype) &&
+ ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME)) &&
+ !(ir->efep != efepNO && mdatoms->nChargePerturbed > 0 && ir->fepvals->bScCoul) &&
+ !bRerunMD)
+ {
+ pme_loadbal_init(&pme_loadbal, ir, state->box, fr->ic, fr->pmedata);
+ cycles_pmes = 0;
+ if (cr->duty & DUTY_PME)
+ {
+ /* Start tuning right away, as we can't measure the load */
+ bPMETuneRunning = TRUE;
+ }
+ else
+ {
+ /* Separate PME nodes, we can measure the PP/PME load balance */
+ bPMETuneTry = TRUE;
+ }
+ }
+
+ if (!ir->bContinuation && !bRerunMD)
+ {
+ if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
+ {
+ /* Set the velocities of frozen particles to zero */
+ for (i = mdatoms->start; i < mdatoms->start+mdatoms->homenr; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
+ {
+ state->v[i][m] = 0;
+ }
+ }
+ }
+ }
+
+ if (constr)
+ {
+ /* Constrain the initial coordinates and velocities */
+ do_constrain_first(fplog, constr, ir, mdatoms, state, f,
+ graph, cr, nrnb, fr, top, shake_vir);
+ }
+ if (vsite)
+ {
+ /* Construct the virtual sites for the initial configuration */
+ construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, NULL,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, graph, cr, state->box);
+ }
+ }
+
+ debug_gmx();
+
+ /* set free energy calculation frequency as the minimum
+ greatest common denominator of nstdhdl, nstexpanded, and repl_ex_nst*/
+ nstfep = ir->fepvals->nstdhdl;
+ if (ir->bExpanded)
+ {
+ nstfep = gmx_greatest_common_divisor(ir->fepvals->nstdhdl,nstfep);
+ }
+ if (repl_ex_nst > 0)
+ {
+ nstfep = gmx_greatest_common_divisor(repl_ex_nst,nstfep);
+ }
+
+ /* I'm assuming we need global communication the first time! MRS */
+ cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
+ | ((ir->comm_mode != ecmNO) ? CGLO_STOPCM : 0)
+ | (bVV ? CGLO_PRESSURE : 0)
+ | (bVV ? CGLO_CONSTRAINT : 0)
+ | (bRerunMD ? CGLO_RERUNMD : 0)
+ | ((Flags & MD_READ_EKIN) ? CGLO_READEKIN : 0));
+
+ bSumEkinhOld = FALSE;
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld, cglo_flags);
+ if (ir->eI == eiVVAK)
+ {
+ /* a second call to get the half step temperature initialized as well */
+ /* we do the same call as above, but turn the pressure off -- internally to
+ compute_globals, this is recognized as a velocity verlet half-step
+ kinetic energy calculation. This minimized excess variables, but
+ perhaps loses some logic?*/
+
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags &~(CGLO_STOPCM | CGLO_PRESSURE));
+ }
+
+ /* Calculate the initial half step temperature, and save the ekinh_old */
+ if (!(Flags & MD_STARTFROMCPT))
+ {
+ for (i = 0; (i < ir->opts.ngtc); i++)
+ {
+ copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
+ }
+ }
+ if (ir->eI != eiVV)
+ {
+ enerd->term[F_TEMP] *= 2; /* result of averages being done over previous and current step,
+ and there is no previous step */
+ }
+
+ /* if using an iterative algorithm, we need to create a working directory for the state. */
+ if (bIterativeCase)
+ {
+ bufstate = init_bufstate(state);
+ }
+ if (bFFscan)
+ {
+ snew(xcopy, state->natoms);
+ snew(vcopy, state->natoms);
+ copy_rvecn(state->x, xcopy, 0, state->natoms);
+ copy_rvecn(state->v, vcopy, 0, state->natoms);
+ copy_mat(state->box, boxcopy);
+ }
+
+ /* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
+ temperature control */
+ trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
+
+ if (MASTER(cr))
+ {
+ if (constr && !ir->bContinuation && ir->eConstrAlg == econtLINCS)
+ {
+ fprintf(fplog,
+ "RMS relative constraint deviation after constraining: %.2e\n",
+ constr_rmsd(constr, FALSE));
+ }
+ if (EI_STATE_VELOCITY(ir->eI))
+ {
+ fprintf(fplog, "Initial temperature: %g K\n", enerd->term[F_TEMP]);
+ }
+ if (bRerunMD)
+ {
+ fprintf(stderr, "starting md rerun '%s', reading coordinates from"
+ " input trajectory '%s'\n\n",
+ *(top_global->name), opt2fn("-rerun", nfile, fnm));
+ if (bVerbose)
+ {
+ fprintf(stderr, "Calculated time to finish depends on nsteps from "
+ "run input file,\nwhich may not correspond to the time "
+ "needed to process input trajectory.\n\n");
+ }
+ }
+ else
+ {
+ char tbuf[20];
+ fprintf(stderr, "starting mdrun '%s'\n",
+ *(top_global->name));
+ if (ir->nsteps >= 0)
+ {
+ sprintf(tbuf, "%8.1f", (ir->init_step+ir->nsteps)*ir->delta_t);
+ }
+ else
+ {
+ sprintf(tbuf, "%s", "infinite");
+ }
+ if (ir->init_step > 0)
+ {
+ fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
+ gmx_step_str(ir->init_step+ir->nsteps, sbuf), tbuf,
+ gmx_step_str(ir->init_step, sbuf2),
+ ir->init_step*ir->delta_t);
+ }
+ else
+ {
+ fprintf(stderr, "%s steps, %s ps.\n",
+ gmx_step_str(ir->nsteps, sbuf), tbuf);
+ }
+ }
+ fprintf(fplog, "\n");
+ }
+
+ /* Set and write start time */
+ runtime_start(runtime);
+ print_date_and_time(fplog, cr->nodeid, "Started mdrun", runtime);
+ wallcycle_start(wcycle, ewcRUN);
+ if (fplog)
+ {
+ fprintf(fplog, "\n");
+ }
+
+ /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
+#ifdef GMX_FAHCORE
+ chkpt_ret = fcCheckPointParallel( cr->nodeid,
+ NULL, 0);
+ if (chkpt_ret == 0)
+ {
+ gmx_fatal( 3, __FILE__, __LINE__, "Checkpoint error on step %d\n", 0 );
+ }
+#endif
+
+ debug_gmx();
+ /***********************************************************
+ *
+ * Loop over MD steps
+ *
+ ************************************************************/
+
+ /* if rerunMD then read coordinates and velocities from input trajectory */
+ if (bRerunMD)
+ {
+ if (getenv("GMX_FORCE_UPDATE"))
+ {
+ bForceUpdate = TRUE;
+ }
+
+ rerun_fr.natoms = 0;
+ if (MASTER(cr))
+ {
+ bNotLastFrame = read_first_frame(oenv, &status,
+ opt2fn("-rerun", nfile, fnm),
+ &rerun_fr, TRX_NEED_X | TRX_READ_V);
+ if (rerun_fr.natoms != top_global->natoms)
+ {
+ gmx_fatal(FARGS,
+ "Number of atoms in trajectory (%d) does not match the "
+ "run input file (%d)\n",
+ rerun_fr.natoms, top_global->natoms);
+ }
+ if (ir->ePBC != epbcNONE)
+ {
+ if (!rerun_fr.bBox)
+ {
+ gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f does not contain a box, while pbc is used", rerun_fr.step, rerun_fr.time);
+ }
+ if (max_cutoff2(ir->ePBC, rerun_fr.box) < sqr(fr->rlistlong))
+ {
+ gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f has too small box dimensions", rerun_fr.step, rerun_fr.time);
+ }
+ }
+ }
+
+ if (PAR(cr))
+ {
+ rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
+ }
+
+ if (ir->ePBC != epbcNONE)
+ {
+ /* Set the shift vectors.
+ * Necessary here when have a static box different from the tpr box.
+ */
+ calc_shifts(rerun_fr.box, fr->shift_vec);
+ }
+ }
+
+ /* loop over MD steps or if rerunMD to end of input trajectory */
+ bFirstStep = TRUE;
+ /* Skip the first Nose-Hoover integration when we get the state from tpx */
+ bStateFromTPX = !bStateFromCP;
+ bInitStep = bFirstStep && (bStateFromTPX || bVV);
+ bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
+ bLastStep = FALSE;
+ bSumEkinhOld = FALSE;
+ bExchanged = FALSE;
+
+ init_global_signals(&gs, cr, ir, repl_ex_nst);
+
+ step = ir->init_step;
+ step_rel = 0;
+
+ if (ir->nstlist == -1)
+ {
+ init_nlistheuristics(&nlh, bGStatEveryStep, step);
+ }
+
+ if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
+ {
+ /* check how many steps are left in other sims */
+ multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
+ }
+
+
+ /* and stop now if we should */
+ bLastStep = (bRerunMD || (ir->nsteps >= 0 && step_rel > ir->nsteps) ||
+ ((multisim_nsteps >= 0) && (step_rel >= multisim_nsteps )));
+ while (!bLastStep || (bRerunMD && bNotLastFrame))
+ {
+
+ wallcycle_start(wcycle, ewcSTEP);
+
+ GMX_MPE_LOG(ev_timestep1);
+
+ if (bRerunMD)
+ {
+ if (rerun_fr.bStep)
+ {
+ step = rerun_fr.step;
+ step_rel = step - ir->init_step;
+ }
+ if (rerun_fr.bTime)
+ {
+ t = rerun_fr.time;
+ }
+ else
+ {
+ t = step;
+ }
+ }
+ else
+ {
+ bLastStep = (step_rel == ir->nsteps);
+ t = t0 + step*ir->delta_t;
+ }
+
+ if (ir->efep != efepNO || ir->bSimTemp)
+ {
+ /* find and set the current lambdas. If rerunning, we either read in a state, or a lambda value,
+ requiring different logic. */
+
+ set_current_lambdas(step, ir->fepvals, bRerunMD, &rerun_fr, state_global, state, lam0);
+ bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
+ bDoFEP = (do_per_step(step, nstfep) && (ir->efep != efepNO));
+ bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded) && (ir->bExpanded) && (step > 0));
+ }
+
+ if (bSimAnn)
+ {
+ update_annealing_target_temp(&(ir->opts), t);
+ }
+
+ if (bRerunMD)
+ {
+ if (!(DOMAINDECOMP(cr) && !MASTER(cr)))
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ copy_rvec(rerun_fr.x[i], state_global->x[i]);
+ }
+ if (rerun_fr.bV)
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ copy_rvec(rerun_fr.v[i], state_global->v[i]);
+ }
+ }
+ else
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ clear_rvec(state_global->v[i]);
+ }
+ if (bRerunWarnNoV)
+ {
+ fprintf(stderr, "\nWARNING: Some frames do not contain velocities.\n"
+ " Ekin, temperature and pressure are incorrect,\n"
+ " the virial will be incorrect when constraints are present.\n"
+ "\n");
+ bRerunWarnNoV = FALSE;
+ }
+ }
+ }
+ copy_mat(rerun_fr.box, state_global->box);
+ copy_mat(state_global->box, state->box);
+
+ if (vsite && (Flags & MD_RERUN_VSITE))
+ {
+ if (DOMAINDECOMP(cr))
+ {
+ gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented for domain decomposition, use particle decomposition");
+ }
+ if (graph)
+ {
+ /* Following is necessary because the graph may get out of sync
+ * with the coordinates if we only have every N'th coordinate set
+ */
+ mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
+ shift_self(graph, state->box, state->x);
+ }
+ construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, state->v,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, graph, cr, state->box);
+ if (graph)
+ {
+ unshift_self(graph, state->box, state->x);
+ }
+ }
+ }
+
+ /* Stop Center of Mass motion */
+ bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
+
+ /* Copy back starting coordinates in case we're doing a forcefield scan */
+ if (bFFscan)
+ {
+ for (ii = 0; (ii < state->natoms); ii++)
+ {
+ copy_rvec(xcopy[ii], state->x[ii]);
+ copy_rvec(vcopy[ii], state->v[ii]);
+ }
+ copy_mat(boxcopy, state->box);
+ }
+
+ if (bRerunMD)
+ {
+ /* for rerun MD always do Neighbour Searching */
+ bNS = (bFirstStep || ir->nstlist != 0);
+ bNStList = bNS;
+ }
+ else
+ {
+ /* Determine whether or not to do Neighbour Searching and LR */
+ bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
+
+ bNS = (bFirstStep || bExchanged || bNStList || bDoFEP ||
+ (ir->nstlist == -1 && nlh.nabnsb > 0));
+
+ if (bNS && ir->nstlist == -1)
+ {
+ set_nlistheuristics(&nlh, bFirstStep || bExchanged || bDoFEP, step);
+ }
+ }
+
+ /* check whether we should stop because another simulation has
+ stopped. */
+ if (MULTISIM(cr))
+ {
+ if ( (multisim_nsteps >= 0) && (step_rel >= multisim_nsteps) &&
+ (multisim_nsteps != ir->nsteps) )
+ {
+ if (bNS)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr,
+ "Stopping simulation %d because another one has finished\n",
+ cr->ms->sim);
+ }
+ bLastStep = TRUE;
+ gs.sig[eglsCHKPT] = 1;
+ }
+ }
+ }
+
+ /* < 0 means stop at next step, > 0 means stop at next NS step */
+ if ( (gs.set[eglsSTOPCOND] < 0) ||
+ ( (gs.set[eglsSTOPCOND] > 0) && (bNStList || ir->nstlist == 0) ) )
+ {
+ bLastStep = TRUE;
+ }
+
+ /* Determine whether or not to update the Born radii if doing GB */
+ bBornRadii = bFirstStep;
+ if (ir->implicit_solvent && (step % ir->nstgbradii == 0))
+ {
+ bBornRadii = TRUE;
+ }
+
+ do_log = do_per_step(step, ir->nstlog) || bFirstStep || bLastStep;
+ do_verbose = bVerbose &&
+ (step % stepout == 0 || bFirstStep || bLastStep);
+
+ if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
+ {
+ if (bRerunMD)
+ {
+ bMasterState = TRUE;
+ }
+ else
+ {
+ bMasterState = FALSE;
+ /* Correct the new box if it is too skewed */
+ if (DYNAMIC_BOX(*ir))
+ {
+ if (correct_box(fplog, step, state->box, graph))
+ {
+ bMasterState = TRUE;
+ }
+ }
+ if (DOMAINDECOMP(cr) && bMasterState)
+ {
+ dd_collect_state(cr->dd, state, state_global);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* Repartition the domain decomposition */
+ wallcycle_start(wcycle, ewcDOMDEC);
+ dd_partition_system(fplog, step, cr,
+ bMasterState, nstglobalcomm,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle,
+ do_verbose && !bPMETuneRunning);
+ wallcycle_stop(wcycle, ewcDOMDEC);
+ /* If using an iterative integrator, reallocate space to match the decomposition */
+ }
+ }
+
+ if (MASTER(cr) && do_log && !bFFscan)
+ {
+ print_ebin_header(fplog, step, t, state->lambda[efptFEP]); /* can we improve the information printed here? */
+ }
+
+ if (ir->efep != efepNO)
+ {
+ update_mdatoms(mdatoms, state->lambda[efptMASS]);
+ }
+
+ if ((bRerunMD && rerun_fr.bV) || bExchanged)
+ {
+
+ /* We need the kinetic energy at minus the half step for determining
+ * the full step kinetic energy and possibly for T-coupling.*/
+ /* This may not be quite working correctly yet . . . . */
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
+ }
+ clear_mat(force_vir);
+
+ /* Ionize the atoms if necessary */
+ if (bIonize)
+ {
+ ionize(fplog, oenv, mdatoms, top_global, t, ir, state->x, state->v,
+ mdatoms->start, mdatoms->start+mdatoms->homenr, state->box, cr);
+ }
+
+ /* Update force field in ffscan program */
+ if (bFFscan)
+ {
+ if (update_forcefield(fplog,
+ nfile, fnm, fr,
+ mdatoms->nr, state->x, state->box))
+ {
+ gmx_finalize_par();
+
+ exit(0);
+ }
+ }
+
+ GMX_MPE_LOG(ev_timestep2);
+
+ /* We write a checkpoint at this MD step when:
+ * either at an NS step when we signalled through gs,
+ * or at the last step (but not when we do not want confout),
+ * but never at the first step or with rerun.
+ */
+ bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
+ (bLastStep && (Flags & MD_CONFOUT))) &&
+ step > ir->init_step && !bRerunMD);
+ if (bCPT)
+ {
+ gs.set[eglsCHKPT] = 0;
+ }
+
+ /* Determine the energy and pressure:
+ * at nstcalcenergy steps and at energy output steps (set below).
+ */
+ if (EI_VV(ir->eI) && (!bInitStep))
+ {
+ /* for vv, the first half of the integration actually corresponds
+ to the previous step. bCalcEner is only required to be evaluated on the 'next' step,
+ but the virial needs to be calculated on both the current step and the 'next' step. Future
+ reorganization may be able to get rid of one of the bCalcVir=TRUE steps. */
+
+ bCalcEner = do_per_step(step-1, ir->nstcalcenergy);
+ bCalcVir = bCalcEner ||
+ (ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
+ }
+ else
+ {
+ bCalcEner = do_per_step(step, ir->nstcalcenergy);
+ bCalcVir = bCalcEner ||
+ (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
+ }
+
+ /* Do we need global communication ? */
+ bGStat = (bCalcVir || bCalcEner || bStopCM ||
+ do_per_step(step, nstglobalcomm) || (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)) ||
+ (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));
+
+ do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
+
+ if (do_ene || do_log)
+ {
+ bCalcVir = TRUE;
+ bCalcEner = TRUE;
+ bGStat = TRUE;
+ }
+
+ /* these CGLO_ options remain the same throughout the iteration */
+ cglo_flags = ((bRerunMD ? CGLO_RERUNMD : 0) |
+ (bGStat ? CGLO_GSTAT : 0)
+ );
+
+ force_flags = (GMX_FORCE_STATECHANGED |
+ ((DYNAMIC_BOX(*ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
+ GMX_FORCE_ALLFORCES |
+ GMX_FORCE_SEPLRF |
+ (bCalcVir ? GMX_FORCE_VIRIAL : 0) |
+ (bCalcEner ? GMX_FORCE_ENERGY : 0) |
+ (bDoFEP ? GMX_FORCE_DHDL : 0)
+ );
+
+ if (fr->bTwinRange)
+ {
+ if (do_per_step(step, ir->nstcalclr))
+ {
+ force_flags |= GMX_FORCE_DO_LR;
+ }
+ }
+
+ if (shellfc)
+ {
+ /* Now is the time to relax the shells */
+ count = relax_shell_flexcon(fplog, cr, bVerbose, bFFscan ? step+1 : step,
+ ir, bNS, force_flags,
+ bStopCM, top, top_global,
+ constr, enerd, fcd,
+ state, f, force_vir, mdatoms,
+ nrnb, wcycle, graph, groups,
+ shellfc, fr, bBornRadii, t, mu_tot,
+ state->natoms, &bConverged, vsite,
+ outf->fp_field);
+ tcount += count;
+
+ if (bConverged)
+ {
+ nconverged++;
+ }
+ }
+ else
+ {
+ /* The coordinates (x) are shifted (to get whole molecules)
+ * in do_force.
+ * This is parallellized as well, and does communication too.
+ * Check comments in sim_util.c
+ */
+ do_force(fplog, cr, ir, step, nrnb, wcycle, top, top_global, groups,
+ state->box, state->x, &state->hist,
+ f, force_vir, mdatoms, enerd, fcd,
+ state->lambda, graph,
+ fr, vsite, mu_tot, t, outf->fp_field, ed, bBornRadii,
+ (bNS ? GMX_FORCE_NS : 0) | force_flags);
+ }
+
+ GMX_BARRIER(cr->mpi_comm_mygroup);
+
+ if (bTCR)
+ {
+ mu_aver = calc_mu_aver(cr, state->x, mdatoms->chargeA,
+ mu_tot, &top_global->mols, mdatoms, gnx, grpindex);
+ }
+
+ if (bTCR && bFirstStep)
+ {
+ tcr = init_coupling(fplog, nfile, fnm, cr, fr, mdatoms, &(top->idef));
+ fprintf(fplog, "Done init_coupling\n");
+ fflush(fplog);
+ }
+
+ if (bVV && !bStartingFromCpt && !bRerunMD)
+ /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
+ {
+ if (ir->eI == eiVV && bInitStep)
+ {
+ /* if using velocity verlet with full time step Ekin,
+ * take the first half step only to compute the
+ * virial for the first step. From there,
+ * revert back to the initial coordinates
+ * so that the input is actually the initial step.
+ */
+ copy_rvecn(state->v, cbuf, 0, state->natoms); /* should make this better for parallelizing? */
+ }
+ else
+ {
+ /* this is for NHC in the Ekin(t+dt/2) version of vv */
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ1);
+ }
+
+ /* If we are using twin-range interactions where the long-range component
+ * is only evaluated every nstcalclr>1 steps, we should do a special update
+ * step to combine the long-range forces on these steps.
+ * For nstcalclr=1 this is not done, since the forces would have been added
+ * directly to the short-range forces already.
+ */
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
+ f, bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, upd, bInitStep, etrtVELOCITY1,
+ cr, nrnb, constr, &top->idef);
+
+ if (bIterativeCase && do_per_step(step-1, ir->nstpcouple) && !bInitStep)
+ {
+ gmx_iterate_init(&iterate, TRUE);
+ }
+ /* for iterations, we save these vectors, as we will be self-consistently iterating
+ the calculations */
+
+ /*#### UPDATE EXTENDED VARIABLES IN TROTTER FORMULATION */
+
+ /* save the state */
+ if (iterate.bIterationActive)
+ {
+ copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
+ }
+
+ bFirstIterate = TRUE;
+ while (bFirstIterate || iterate.bIterationActive)
+ {
+ if (iterate.bIterationActive)
+ {
+ copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
+ if (bFirstIterate && bTrotter)
+ {
+ /* The first time through, we need a decent first estimate
+ of veta(t+dt) to compute the constraints. Do
+ this by computing the box volume part of the
+ trotter integration at this time. Nothing else
+ should be changed by this routine here. If
+ !(first time), we start with the previous value
+ of veta. */
+
+ veta_save = state->veta;
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ0);
+ vetanew = state->veta;
+ state->veta = veta_save;
+ }
+ }
+
+ bOK = TRUE;
+ if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
+ {
+ update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, shake_vir, NULL,
+ cr, nrnb, wcycle, upd, constr,
+ bInitStep, TRUE, bCalcVir, vetanew);
+
+ if (!bOK && !bFFscan)
+ {
+ gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
+ }
+
+ }
+ else if (graph)
+ {
+ /* Need to unshift here if a do_force has been
+ called in the previous step */
+ unshift_self(graph, state->box, state->x);
+ }
+
+ /* if VV, compute the pressure and constraints */
+ /* For VV2, we strictly only need this if using pressure
+ * control, but we really would like to have accurate pressures
+ * printed out.
+ * Think about ways around this in the future?
+ * For now, keep this choice in comments.
+ */
+ /*bPres = (ir->eI==eiVV || IR_NPT_TROTTER(ir)); */
+ /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir)));*/
+ bPres = TRUE;
+ bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
+ if (bCalcEner && ir->eI == eiVVAK) /*MRS: 7/9/2010 -- this still doesn't fix it?*/
+ {
+ bSumEkinhOld = TRUE;
+ }
+ /* for vv, the first half of the integration actually corresponds to the previous step.
+ So we need information from the last step in the first half of the integration */
+ if (bGStat || do_per_step(step-1, nstglobalcomm))
+ {
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags
+ | CGLO_ENERGY
+ | (bTemp ? CGLO_TEMPERATURE : 0)
+ | (bPres ? CGLO_PRESSURE : 0)
+ | (bPres ? CGLO_CONSTRAINT : 0)
+ | ((iterate.bIterationActive) ? CGLO_ITERATE : 0)
+ | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
+ | CGLO_SCALEEKIN
+ );
+ /* explanation of above:
+ a) We compute Ekin at the full time step
+ if 1) we are using the AveVel Ekin, and it's not the
+ initial step, or 2) if we are using AveEkin, but need the full
+ time step kinetic energy for the pressure (always true now, since we want accurate statistics).
+ b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
+ EkinAveVel because it's needed for the pressure */
+ }
+ /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
+ if (!bInitStep)
+ {
+ if (bTrotter)
+ {
+ m_add(force_vir, shake_vir, total_vir); /* we need the un-dispersion corrected total vir here */
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ2);
+ }
+ else
+ {
+ if (bExchanged)
+ {
+
+ /* We need the kinetic energy at minus the half step for determining
+ * the full step kinetic energy and possibly for T-coupling.*/
+ /* This may not be quite working correctly yet . . . . */
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
+ }
+ }
+ }
+
+ if (iterate.bIterationActive &&
+ done_iterating(cr, fplog, step, &iterate, bFirstIterate,
+ state->veta, &vetanew))
+ {
+ break;
+ }
+ bFirstIterate = FALSE;
+ }
+
+ if (bTrotter && !bInitStep)
+ {
+ copy_mat(shake_vir, state->svir_prev);
+ copy_mat(force_vir, state->fvir_prev);
+ if (IR_NVT_TROTTER(ir) && ir->eI == eiVV)
+ {
+ /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
+ enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, NULL, (ir->eI == eiVV), FALSE, FALSE);
+ enerd->term[F_EKIN] = trace(ekind->ekin);
+ }
+ }
+ /* if it's the initial step, we performed this first step just to get the constraint virial */
+ if (bInitStep && ir->eI == eiVV)
+ {
+ copy_rvecn(cbuf, state->v, 0, state->natoms);
+ }
+
+ GMX_MPE_LOG(ev_timestep1);
+ }
+
+ /* MRS -- now done iterating -- compute the conserved quantity */
+ if (bVV)
+ {
+ saved_conserved_quantity = compute_conserved_from_auxiliary(ir, state, &MassQ);
+ if (ir->eI == eiVV)
+ {
+ last_ekin = enerd->term[F_EKIN];
+ }
+ if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
+ {
+ saved_conserved_quantity -= enerd->term[F_DISPCORR];
+ }
+ /* sum up the foreign energy and dhdl terms for vv. currently done every step so that dhdl is correct in the .edr */
+ if (!bRerunMD)
+ {
+ sum_dhdl(enerd, state->lambda, ir->fepvals);
+ }
+ }
+
+ /* ######## END FIRST UPDATE STEP ############## */
+ /* ######## If doing VV, we now have v(dt) ###### */
+ if (bDoExpanded)
+ {
+ /* perform extended ensemble sampling in lambda - we don't
+ actually move to the new state before outputting
+ statistics, but if performing simulated tempering, we
+ do update the velocities and the tau_t. */
+
+ lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, &df_history, step, mcrng, state->v, mdatoms);
+ }
+ /* ################## START TRAJECTORY OUTPUT ################# */
+
+ /* Now we have the energies and forces corresponding to the
+ * coordinates at time t. We must output all of this before
+ * the update.
+ * for RerunMD t is read from input trajectory
+ */
+ GMX_MPE_LOG(ev_output_start);
+
+ mdof_flags = 0;
+ if (do_per_step(step, ir->nstxout))
+ {
+ mdof_flags |= MDOF_X;
+ }
+ if (do_per_step(step, ir->nstvout))
+ {
+ mdof_flags |= MDOF_V;
+ }
+ if (do_per_step(step, ir->nstfout))
+ {
+ mdof_flags |= MDOF_F;
+ }
+ if (do_per_step(step, ir->nstxtcout))
+ {
+ mdof_flags |= MDOF_XTC;
+ }
+ if (bCPT)
+ {
+ mdof_flags |= MDOF_CPT;
+ }
+ ;
+
+#if defined(GMX_FAHCORE) || defined(GMX_WRITELASTSTEP)
+ if (bLastStep)
+ {
+ /* Enforce writing positions and velocities at end of run */
+ mdof_flags |= (MDOF_X | MDOF_V);
+ }
+#endif
+#ifdef GMX_FAHCORE
+ if (MASTER(cr))
+ {
+ fcReportProgress( ir->nsteps, step );
+ }
+
+ /* sync bCPT and fc record-keeping */
+ if (bCPT && MASTER(cr))
+ {
+ fcRequestCheckPoint();
+ }
+#endif
+
+ if (mdof_flags != 0)
+ {
+ wallcycle_start(wcycle, ewcTRAJ);
+ if (bCPT)
+ {
+ if (state->flags & (1<<estLD_RNG))
+ {
+ get_stochd_state(upd, state);
+ }
+ if (state->flags & (1<<estMC_RNG))
+ {
+ get_mc_state(mcrng, state);
+ }
+ if (MASTER(cr))
+ {
+ if (bSumEkinhOld)
+ {
+ state_global->ekinstate.bUpToDate = FALSE;
+ }
+ else
+ {
+ update_ekinstate(&state_global->ekinstate, ekind);
+ state_global->ekinstate.bUpToDate = TRUE;
+ }
+ update_energyhistory(&state_global->enerhist, mdebin);
+ if (ir->efep != efepNO || ir->bSimTemp)
+ {
+ state_global->fep_state = state->fep_state; /* MRS: seems kludgy. The code should be
+ structured so this isn't necessary.
+ Note this reassignment is only necessary
+ for single threads.*/
+ copy_df_history(&state_global->dfhist, &df_history);
+ }
+ }
+ }
+ write_traj(fplog, cr, outf, mdof_flags, top_global,
+ step, t, state, state_global, f, f_global, &n_xtc, &x_xtc);
+ if (bCPT)
+ {
+ nchkpt++;
+ bCPT = FALSE;
+ }
+ debug_gmx();
+ if (bLastStep && step_rel == ir->nsteps &&
+ (Flags & MD_CONFOUT) && MASTER(cr) &&
+ !bRerunMD && !bFFscan)
+ {
+ /* x and v have been collected in write_traj,
+ * because a checkpoint file will always be written
+ * at the last step.
+ */
+ fprintf(stderr, "\nWriting final coordinates.\n");
+ if (fr->bMolPBC)
+ {
+ /* Make molecules whole only for confout writing */
+ do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, state_global->x);
+ }
+ write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
+ *top_global->name, top_global,
+ state_global->x, state_global->v,
+ ir->ePBC, state->box);
+ debug_gmx();
+ }
+ wallcycle_stop(wcycle, ewcTRAJ);
+ }
+ GMX_MPE_LOG(ev_output_finish);
+
+ /* kludge -- virial is lost with restart for NPT control. Must restart */
+ if (bStartingFromCpt && bVV)
+ {
+ copy_mat(state->svir_prev, shake_vir);
+ copy_mat(state->fvir_prev, force_vir);
+ }
+ /* ################## END TRAJECTORY OUTPUT ################ */
+
+ /* Determine the wallclock run time up till now */
+ run_time = gmx_gettime() - (double)runtime->real;
+
+ /* Check whether everything is still allright */
+ if (((int)gmx_get_stop_condition() > handled_stop_condition)
+#ifdef GMX_THREAD_MPI
+ && MASTER(cr)
+#endif
+ )
+ {
+ /* this is just make gs.sig compatible with the hack
+ of sending signals around by MPI_Reduce with together with
+ other floats */
+ if (gmx_get_stop_condition() == gmx_stop_cond_next_ns)
+ {
+ gs.sig[eglsSTOPCOND] = 1;
+ }
+ if (gmx_get_stop_condition() == gmx_stop_cond_next)
+ {
+ gs.sig[eglsSTOPCOND] = -1;
+ }
+ /* < 0 means stop at next step, > 0 means stop at next NS step */
+ if (fplog)
+ {
+ fprintf(fplog,
+ "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
+ gmx_get_signal_name(),
+ gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
+ fflush(fplog);
+ }
+ fprintf(stderr,
+ "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
+ gmx_get_signal_name(),
+ gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
+ fflush(stderr);
+ handled_stop_condition = (int)gmx_get_stop_condition();
+ }
+ else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
+ (max_hours > 0 && run_time > max_hours*60.0*60.0*0.99) &&
+ gs.sig[eglsSTOPCOND] == 0 && gs.set[eglsSTOPCOND] == 0)
+ {
+ /* Signal to terminate the run */
+ gs.sig[eglsSTOPCOND] = 1;
+ if (fplog)
+ {
+ fprintf(fplog, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
+ }
+ fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
+ }
+
+ if (bResetCountersHalfMaxH && MASTER(cr) &&
+ run_time > max_hours*60.0*60.0*0.495)
+ {
+ gs.sig[eglsRESETCOUNTERS] = 1;
+ }
+
+ if (ir->nstlist == -1 && !bRerunMD)
+ {
+ /* When bGStatEveryStep=FALSE, global_stat is only called
+ * when we check the atom displacements, not at NS steps.
+ * This means that also the bonded interaction count check is not
+ * performed immediately after NS. Therefore a few MD steps could
+ * be performed with missing interactions.
+ * But wrong energies are never written to file,
+ * since energies are only written after global_stat
+ * has been called.
+ */
+ if (step >= nlh.step_nscheck)
+ {
+ nlh.nabnsb = natoms_beyond_ns_buffer(ir, fr, &top->cgs,
+ nlh.scale_tot, state->x);
+ }
+ else
+ {
+ /* This is not necessarily true,
+ * but step_nscheck is determined quite conservatively.
+ */
+ nlh.nabnsb = 0;
+ }
+ }
+
+ /* In parallel we only have to check for checkpointing in steps
+ * where we do global communication,
+ * otherwise the other nodes don't know.
+ */
+ if (MASTER(cr) && ((bGStat || !PAR(cr)) &&
+ cpt_period >= 0 &&
+ (cpt_period == 0 ||
+ run_time >= nchkpt*cpt_period*60.0)) &&
+ gs.set[eglsCHKPT] == 0)
+ {
+ gs.sig[eglsCHKPT] = 1;
+ }
+
+ /* at the start of step, randomize or scale the velocities (trotter done elsewhere) */
+ if (EI_VV(ir->eI))
+ {
+ if (!bInitStep)
+ {
+ update_tcouple(fplog, step, ir, state, ekind, wcycle, upd, &MassQ, mdatoms);
+ }
+ if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
+ {
+ gmx_bool bIfRandomize;
+ bIfRandomize = update_randomize_velocities(ir, step, mdatoms, state, upd, &top->idef, constr);
+ /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
+ if (constr && bIfRandomize)
+ {
+ update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, tmp_vir, NULL,
+ cr, nrnb, wcycle, upd, constr,
+ bInitStep, TRUE, bCalcVir, vetanew);
+ }
+ }
+ }
+
+ if (bIterativeCase && do_per_step(step, ir->nstpcouple))
+ {
+ gmx_iterate_init(&iterate, TRUE);
+ /* for iterations, we save these vectors, as we will be redoing the calculations */
+ copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
+ }
+
+ bFirstIterate = TRUE;
+ while (bFirstIterate || iterate.bIterationActive)
+ {
+ /* We now restore these vectors to redo the calculation with improved extended variables */
+ if (iterate.bIterationActive)
+ {
+ copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
+ }
+
+ /* We make the decision to break or not -after- the calculation of Ekin and Pressure,
+ so scroll down for that logic */
+
+ /* ######### START SECOND UPDATE STEP ################# */
+ GMX_MPE_LOG(ev_update_start);
+ /* Box is changed in update() when we do pressure coupling,
+ * but we should still use the old box for energy corrections and when
+ * writing it to the energy file, so it matches the trajectory files for
+ * the same timestep above. Make a copy in a separate array.
+ */
+ copy_mat(state->box, lastbox);
+
+ bOK = TRUE;
+ dvdl_constr = 0;
+
+ if (!(bRerunMD && !rerun_fr.bV && !bForceUpdate))
+ {
+ wallcycle_start(wcycle, ewcUPDATE);
+ /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
+ if (bTrotter)
+ {
+ if (iterate.bIterationActive)
+ {
+ if (bFirstIterate)
+ {
+ scalevir = 1;
+ }
+ else
+ {
+ /* we use a new value of scalevir to converge the iterations faster */
+ scalevir = tracevir/trace(shake_vir);
+ }
+ msmul(shake_vir, scalevir, shake_vir);
+ m_add(force_vir, shake_vir, total_vir);
+ clear_mat(shake_vir);
+ }
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
+ /* We can only do Berendsen coupling after we have summed
+ * the kinetic energy or virial. Since the happens
+ * in global_state after update, we should only do it at
+ * step % nstlist = 1 with bGStatEveryStep=FALSE.
+ */
+ }
+ else
+ {
+ update_tcouple(fplog, step, ir, state, ekind, wcycle, upd, &MassQ, mdatoms);
+ update_pcouple(fplog, step, ir, state, pcoupl_mu, M, wcycle,
+ upd, bInitStep);
+ }
+
+ if (bVV)
+ {
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ /* velocity half-step update */
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, upd, FALSE, etrtVELOCITY2,
+ cr, nrnb, constr, &top->idef);
+ }
+
+ /* Above, initialize just copies ekinh into ekin,
+ * it doesn't copy position (for VV),
+ * and entire integrator for MD.
+ */
+
+ if (ir->eI == eiVVAK)
+ {
+ copy_rvecn(state->x, cbuf, 0, state->natoms);
+ }
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+ wallcycle_stop(wcycle, ewcUPDATE);
+
+ update_constraints(fplog, step, &dvdl_constr, ir, ekind, mdatoms, state,
+ fr->bMolPBC, graph, f,
+ &top->idef, shake_vir, force_vir,
+ cr, nrnb, wcycle, upd, constr,
+ bInitStep, FALSE, bCalcVir, state->veta);
+
+ if (ir->eI == eiVVAK)
+ {
+ /* erase F_EKIN and F_TEMP here? */
+ /* just compute the kinetic energy at the half step to perform a trotter step */
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, lastbox,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags | CGLO_TEMPERATURE
+ );
+ wallcycle_start(wcycle, ewcUPDATE);
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
+ /* now we know the scaling, we can compute the positions again again */
+ copy_rvecn(cbuf, state->x, 0, state->natoms);
+
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+ wallcycle_stop(wcycle, ewcUPDATE);
+
+ /* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
+ /* are the small terms in the shake_vir here due
+ * to numerical errors, or are they important
+ * physically? I'm thinking they are just errors, but not completely sure.
+ * For now, will call without actually constraining, constr=NULL*/
+ update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, tmp_vir, force_vir,
+ cr, nrnb, wcycle, upd, NULL,
+ bInitStep, FALSE, bCalcVir,
+ state->veta);
+ }
+ if (!bOK && !bFFscan)
+ {
+ gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
+ }
+
+ if (fr->bSepDVDL && fplog && do_log)
+ {
+ fprintf(fplog, sepdvdlformat, "Constraint dV/dl", 0.0, dvdl_constr);
+ }
+ if (bVV)
+ {
+ /* this factor or 2 correction is necessary
+ because half of the constraint force is removed
+ in the vv step, so we have to double it. See
+ the Redmine issue #1255. It is not yet clear
+ if the factor of 2 is exact, or just a very
+ good approximation, and this will be
+ investigated. The next step is to see if this
+ can be done adding a dhdl contribution from the
+ rattle step, but this is somewhat more
+ complicated with the current code. Will be
+ investigated, hopefully for 4.6.3. However,
+ this current solution is much better than
+ having it completely wrong.
+ */
+ enerd->term[F_DVDL_CONSTR] += 2*dvdl_constr;
+ }
+ else
+ {
+ enerd->term[F_DVDL_CONSTR] += dvdl_constr;
+ }
+ }
+ else if (graph)
+ {
+ /* Need to unshift here */
+ unshift_self(graph, state->box, state->x);
+ }
+
+ GMX_BARRIER(cr->mpi_comm_mygroup);
+ GMX_MPE_LOG(ev_update_finish);
+
+ if (vsite != NULL)
+ {
+ wallcycle_start(wcycle, ewcVSITECONSTR);
+ if (graph != NULL)
+ {
+ shift_self(graph, state->box, state->x);
+ }
+ construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, state->v,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, graph, cr, state->box);
+
+ if (graph != NULL)
+ {
+ unshift_self(graph, state->box, state->x);
+ }
+ wallcycle_stop(wcycle, ewcVSITECONSTR);
+ }
+
+ /* ############## IF NOT VV, Calculate globals HERE, also iterate constraints ############ */
+ /* With Leap-Frog we can skip compute_globals at
+ * non-communication steps, but we need to calculate
+ * the kinetic energy one step before communication.
+ */
+ if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)))
+ {
+ if (ir->nstlist == -1 && bFirstIterate)
+ {
+ gs.sig[eglsNABNSB] = nlh.nabnsb;
+ }
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr,
+ bFirstIterate ? &gs : NULL,
+ (step_rel % gs.nstms == 0) &&
+ (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
+ lastbox,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags
+ | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
+ | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
+ | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
+ | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
+ | (iterate.bIterationActive ? CGLO_ITERATE : 0)
+ | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
+ | CGLO_CONSTRAINT
+ );
+ if (ir->nstlist == -1 && bFirstIterate)
+ {
+ nlh.nabnsb = gs.set[eglsNABNSB];
+ gs.set[eglsNABNSB] = 0;
+ }
+ }
+ /* bIterate is set to keep it from eliminating the old ekin kinetic energy terms */
+ /* ############# END CALC EKIN AND PRESSURE ################# */
+
+ /* Note: this is OK, but there are some numerical precision issues with using the convergence of
+ the virial that should probably be addressed eventually. state->veta has better properies,
+ but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
+ generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
+
+ if (iterate.bIterationActive &&
+ done_iterating(cr, fplog, step, &iterate, bFirstIterate,
+ trace(shake_vir), &tracevir))
+ {
+ break;
+ }
+ bFirstIterate = FALSE;
+ }
+
+ if (!bVV || bRerunMD)
+ {
+ /* sum up the foreign energy and dhdl terms for md and sd. currently done every step so that dhdl is correct in the .edr */
+ sum_dhdl(enerd, state->lambda, ir->fepvals);
+ }
+ update_box(fplog, step, ir, mdatoms, state, graph, f,
+ ir->nstlist == -1 ? &nlh.scale_tot : NULL, pcoupl_mu, nrnb, wcycle, upd, bInitStep, FALSE);
+
+ /* ################# END UPDATE STEP 2 ################# */
+ /* #### We now have r(t+dt) and v(t+dt/2) ############# */
+
+ /* The coordinates (x) were unshifted in update */
+ if (bFFscan && (shellfc == NULL || bConverged))
+ {
+ if (print_forcefield(fplog, enerd->term, mdatoms->homenr,
+ f, NULL, xcopy,
+ &(top_global->mols), mdatoms->massT, pres))
+ {
+ gmx_finalize_par();
+
+ fprintf(stderr, "\n");
+ exit(0);
+ }
+ }
+ if (!bGStat)
+ {
+ /* We will not sum ekinh_old,
+ * so signal that we still have to do it.
+ */
+ bSumEkinhOld = TRUE;
+ }
+
+ if (bTCR)
+ {
+ /* Only do GCT when the relaxation of shells (minimization) has converged,
+ * otherwise we might be coupling to bogus energies.
+ * In parallel we must always do this, because the other sims might
+ * update the FF.
+ */
+
+ /* Since this is called with the new coordinates state->x, I assume
+ * we want the new box state->box too. / EL 20040121
+ */
+ do_coupling(fplog, oenv, nfile, fnm, tcr, t, step, enerd->term, fr,
+ ir, MASTER(cr),
+ mdatoms, &(top->idef), mu_aver,
+ top_global->mols.nr, cr,
+ state->box, total_vir, pres,
+ mu_tot, state->x, f, bConverged);
+ debug_gmx();
+ }
+
+ /* ######### BEGIN PREPARING EDR OUTPUT ########### */
+
+ /* use the directly determined last velocity, not actually the averaged half steps */
+ if (bTrotter && ir->eI == eiVV)
+ {
+ enerd->term[F_EKIN] = last_ekin;
+ }
+ enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
+
+ if (bVV)
+ {
+ enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
+ }
+ else
+ {
+ enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + compute_conserved_from_auxiliary(ir, state, &MassQ);
+ }
+ /* Check for excessively large energies */
+ if (bIonize)
+ {
+#ifdef GMX_DOUBLE
+ real etot_max = 1e200;
+#else
+ real etot_max = 1e30;
+#endif
+ if (fabs(enerd->term[F_ETOT]) > etot_max)
+ {
+ fprintf(stderr, "Energy too large (%g), giving up\n",
+ enerd->term[F_ETOT]);
+ }
+ }
+ /* ######### END PREPARING EDR OUTPUT ########### */
+
+ /* Time for performance */
+ if (((step % stepout) == 0) || bLastStep)
+ {
+ runtime_upd_proc(runtime);
+ }
+
+ /* Output stuff */
+ if (MASTER(cr))
+ {
+ gmx_bool do_dr, do_or;
+
+ if (fplog && do_log && bDoExpanded)
+ {
+ /* only needed if doing expanded ensemble */
+ PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
+ &df_history, state->fep_state, ir->nstlog, step);
+ }
+ if (!(bStartingFromCpt && (EI_VV(ir->eI))))
+ {
+ if (bCalcEner)
+ {
+ upd_mdebin(mdebin, bDoDHDL, TRUE,
+ t, mdatoms->tmass, enerd, state,
+ ir->fepvals, ir->expandedvals, lastbox,
+ shake_vir, force_vir, total_vir, pres,
+ ekind, mu_tot, constr);
+ }
+ else
+ {
+ upd_mdebin_step(mdebin);
+ }
+
+ do_dr = do_per_step(step, ir->nstdisreout);
+ do_or = do_per_step(step, ir->nstorireout);
+
+ print_ebin(outf->fp_ene, do_ene, do_dr, do_or, do_log ? fplog : NULL,
+ step, t,
+ eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
+ }
+ if (ir->ePull != epullNO)
+ {
+ pull_print_output(ir->pull, step, t);
+ }
+
+ if (do_per_step(step, ir->nstlog))
+ {
+ if (fflush(fplog) != 0)
+ {
+ gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
+ }
+ }
+ }
+ if (bDoExpanded)
+ {
+ /* Have to do this part after outputting the logfile and the edr file */
+ state->fep_state = lamnew;
+ for (i = 0; i < efptNR; i++)
+ {
+ state_global->lambda[i] = ir->fepvals->all_lambda[i][lamnew];
+ }
+ }
+ /* Remaining runtime */
+ if (MULTIMASTER(cr) && (do_verbose || gmx_got_usr_signal()) && !bPMETuneRunning)
+ {
+ if (shellfc)
+ {
+ fprintf(stderr, "\n");
+ }
+ print_time(stderr, runtime, step, ir, cr);
+ }
+
+ /* Replica exchange */
+ bExchanged = FALSE;
+ if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
+ do_per_step(step, repl_ex_nst))
+ {
+ bExchanged = replica_exchange(fplog, cr, repl_ex,
+ state_global, enerd,
+ state, step, t);
+
+ if (bExchanged && DOMAINDECOMP(cr))
+ {
+ dd_partition_system(fplog, step, cr, TRUE, 1,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle, FALSE);
+ }
+ }
+
+ bFirstStep = FALSE;
+ bInitStep = FALSE;
+ bStartingFromCpt = FALSE;
+
+ /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
+ /* With all integrators, except VV, we need to retain the pressure
+ * at the current step for coupling at the next step.
+ */
+ if ((state->flags & (1<<estPRES_PREV)) &&
+ (bGStatEveryStep ||
+ (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
+ {
+ /* Store the pressure in t_state for pressure coupling
+ * at the next MD step.
+ */
+ copy_mat(pres, state->pres_prev);
+ }
+
+ /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
+
+ if ( (membed != NULL) && (!bLastStep) )
+ {
+ rescale_membed(step_rel, membed, state_global->x);
+ }
+
+ if (bRerunMD)
+ {
+ if (MASTER(cr))
+ {
+ /* read next frame from input trajectory */
+ bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
+ }
+
+ if (PAR(cr))
+ {
+ rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
+ }
+ }
+
+ if (!bRerunMD || !rerun_fr.bStep)
+ {
+ /* increase the MD step number */
+ step++;
+ step_rel++;
+ }
+
+ cycles = wallcycle_stop(wcycle, ewcSTEP);
+ if (DOMAINDECOMP(cr) && wcycle)
+ {
+ dd_cycles_add(cr->dd, cycles, ddCyclStep);
+ }
+
+ if (bPMETuneRunning || bPMETuneTry)
+ {
+ /* PME grid + cut-off optimization with GPUs or PME nodes */
+
+ /* Count the total cycles over the last steps */
+ cycles_pmes += cycles;
+
+ /* We can only switch cut-off at NS steps */
+ if (step % ir->nstlist == 0)
+ {
+ /* PME grid + cut-off optimization with GPUs or PME nodes */
+ if (bPMETuneTry)
+ {
+ if (DDMASTER(cr->dd))
+ {
+ /* PME node load is too high, start tuning */
+ bPMETuneRunning = (dd_pme_f_ratio(cr->dd) >= 1.05);
+ }
+ dd_bcast(cr->dd, sizeof(gmx_bool), &bPMETuneRunning);
+
+ if (bPMETuneRunning || step_rel > ir->nstlist*50)
+ {
+ bPMETuneTry = FALSE;
+ }
+ }
+ if (bPMETuneRunning)
+ {
+ /* init_step might not be a multiple of nstlist,
+ * but the first cycle is always skipped anyhow.
+ */
+ bPMETuneRunning =
+ pme_load_balance(pme_loadbal, cr,
+ (bVerbose && MASTER(cr)) ? stderr : NULL,
+ fplog,
+ ir, state, cycles_pmes,
+ fr->ic, fr->nbv, &fr->pmedata,
+ step);
+
+ /* Update constants in forcerec/inputrec to keep them in sync with fr->ic */
+ fr->ewaldcoeff = fr->ic->ewaldcoeff;
+ fr->rlist = fr->ic->rlist;
+ fr->rlistlong = fr->ic->rlistlong;
+ fr->rcoulomb = fr->ic->rcoulomb;
+ fr->rvdw = fr->ic->rvdw;
+ }
+ cycles_pmes = 0;
+ }
+ }
+
+ if (step_rel == wcycle_get_reset_counters(wcycle) ||
+ gs.set[eglsRESETCOUNTERS] != 0)
+ {
+ /* Reset all the counters related to performance over the run */
+ reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, runtime,
+ fr->nbv != NULL && fr->nbv->bUseGPU ? fr->nbv->cu_nbv : NULL);
+ wcycle_set_reset_counters(wcycle, -1);
+ if (!(cr->duty & DUTY_PME))
+ {
+ /* Tell our PME node to reset its counters */
+ gmx_pme_send_resetcounters(cr, step);
+ }
+ /* Correct max_hours for the elapsed time */
+ max_hours -= run_time/(60.0*60.0);
+ bResetCountersHalfMaxH = FALSE;
+ gs.set[eglsRESETCOUNTERS] = 0;
+ }
+
+ }
+ /* End of main MD loop */
+ debug_gmx();
+
+ /* Stop the time */
+ runtime_end(runtime);
+
+ if (bRerunMD && MASTER(cr))
+ {
+ close_trj(status);
+ }
+
+ if (!(cr->duty & DUTY_PME))
+ {
+ /* Tell the PME only node to finish */
+ gmx_pme_send_finish(cr);
+ }
+
+ if (MASTER(cr))
+ {
+ if (ir->nstcalcenergy > 0 && !bRerunMD)
+ {
+ print_ebin(outf->fp_ene, FALSE, FALSE, FALSE, fplog, step, t,
+ eprAVER, FALSE, mdebin, fcd, groups, &(ir->opts));
+ }
+ }
+
+ done_mdoutf(outf);
+
+ debug_gmx();
+
+ if (ir->nstlist == -1 && nlh.nns > 0 && fplog)
+ {
+ fprintf(fplog, "Average neighborlist lifetime: %.1f steps, std.dev.: %.1f steps\n", nlh.s1/nlh.nns, sqrt(nlh.s2/nlh.nns - sqr(nlh.s1/nlh.nns)));
+ fprintf(fplog, "Average number of atoms that crossed the half buffer length: %.1f\n\n", nlh.ab/nlh.nns);
+ }
+
+ if (pme_loadbal != NULL)
+ {
+ pme_loadbal_done(pme_loadbal, cr, fplog,
+ fr->nbv != NULL && fr->nbv->bUseGPU);
+ }
+
+ if (shellfc && fplog)
+ {
+ fprintf(fplog, "Fraction of iterations that converged: %.2f %%\n",
+ (nconverged*100.0)/step_rel);
+ fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
+ tcount/step_rel);
+ }
+
+ if (repl_ex_nst > 0 && MASTER(cr))
+ {
+ print_replica_exchange_statistics(fplog, repl_ex);
+ }
+
+ runtime->nsteps_done = step_rel;
+
+ return 0;
+}
diff --git a/patches/gromacs-4.6.3.diff/src/kernel/mdrun.c b/patches/gromacs-4.6.3.diff/src/kernel/mdrun.c
new file mode 100644
index 0000000000000000000000000000000000000000..ba301007d08d9dcc0eeef4d656fb31b686e40b46
--- /dev/null
+++ b/patches/gromacs-4.6.3.diff/src/kernel/mdrun.c
@@ -0,0 +1,798 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "typedefs.h"
+#include "macros.h"
+#include "copyrite.h"
+#include "main.h"
+#include "statutil.h"
+#include "smalloc.h"
+#include "futil.h"
+#include "smalloc.h"
+#include "edsam.h"
+#include "mdrun.h"
+#include "xmdrun.h"
+#include "checkpoint.h"
+#ifdef GMX_THREAD_MPI
+#include "thread_mpi.h"
+#endif
+
+/* afm stuf */
+#include "pull.h"
+
+/* PLUMED */
+#include "../../Plumed.h"
+int plumedswitch;
+plumed plumedmain;
+/* END PLUMED */
+
+int cmain(int argc, char *argv[])
+{
+ const char *desc[] = {
+ "The [TT]mdrun[tt] program is the main computational chemistry engine",
+ "within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
+ "but it can also perform Stochastic Dynamics, Energy Minimization,",
+ "test particle insertion or (re)calculation of energies.",
+ "Normal mode analysis is another option. In this case [TT]mdrun[tt]",
+ "builds a Hessian matrix from single conformation.",
+ "For usual Normal Modes-like calculations, make sure that",
+ "the structure provided is properly energy-minimized.",
+ "The generated matrix can be diagonalized by [TT]g_nmeig[tt].[PAR]",
+ "The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
+ "and distributes the topology over nodes if needed.",
+ "[TT]mdrun[tt] produces at least four output files.",
+ "A single log file ([TT]-g[tt]) is written, unless the option",
+ "[TT]-seppot[tt] is used, in which case each node writes a log file.",
+ "The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
+ "optionally forces.",
+ "The structure file ([TT]-c[tt]) contains the coordinates and",
+ "velocities of the last step.",
+ "The energy file ([TT]-e[tt]) contains energies, the temperature,",
+ "pressure, etc, a lot of these things are also printed in the log file.",
+ "Optionally coordinates can be written to a compressed trajectory file",
+ "([TT]-x[tt]).[PAR]",
+ "The option [TT]-dhdl[tt] is only used when free energy calculation is",
+ "turned on.[PAR]",
+ "A simulation can be run in parallel using two different parallelization",
+ "schemes: MPI parallelization and/or OpenMP thread parallelization.",
+ "The MPI parallelization uses multiple processes when [TT]mdrun[tt] is",
+ "compiled with a normal MPI library or threads when [TT]mdrun[tt] is",
+ "compiled with the GROMACS built-in thread-MPI library. OpenMP threads",
+ "are supported when mdrun is compiled with OpenMP. Full OpenMP support",
+ "is only available with the Verlet cut-off scheme, with the (older)",
+ "group scheme only PME-only processes can use OpenMP parallelization.",
+ "In all cases [TT]mdrun[tt] will by default try to use all the available",
+ "hardware resources. With a normal MPI library only the options",
+ "[TT]-ntomp[tt] (with the Verlet cut-off scheme) and [TT]-ntomp_pme[tt],",
+ "for PME-only processes, can be used to control the number of threads.",
+ "With thread-MPI there are additional options [TT]-nt[tt], which sets",
+ "the total number of threads, and [TT]-ntmpi[tt], which sets the number",
+ "of thread-MPI threads.",
+ "Note that using combined MPI+OpenMP parallelization is almost always",
+ "slower than single parallelization, except at the scaling limit, where",
+ "especially OpenMP parallelization of PME reduces the communication cost.",
+ "OpenMP-only parallelization is much faster than MPI-only parallelization",
+ "on a single CPU(-die). Since we currently don't have proper hardware",
+ "topology detection, [TT]mdrun[tt] compiled with thread-MPI will only",
+ "automatically use OpenMP-only parallelization when you use up to 4",
+ "threads, up to 12 threads with Intel Nehalem/Westmere, or up to 16",
+ "threads with Intel Sandy Bridge or newer CPUs. Otherwise MPI-only",
+ "parallelization is used (except with GPUs, see below).",
+ "[PAR]",
+ "To quickly test the performance of the new Verlet cut-off scheme",
+ "with old [TT].tpr[tt] files, either on CPUs or CPUs+GPUs, you can use",
+ "the [TT]-testverlet[tt] option. This should not be used for production,",
+ "since it can slightly modify potentials and it will remove charge groups",
+ "making analysis difficult, as the [TT].tpr[tt] file will still contain",
+ "charge groups. For production simulations it is highly recommended",
+ "to specify [TT]cutoff-scheme = Verlet[tt] in the [TT].mdp[tt] file.",
+ "[PAR]",
+ "With GPUs (only supported with the Verlet cut-off scheme), the number",
+ "of GPUs should match the number of MPI processes or MPI threads,",
+ "excluding PME-only processes/threads. With thread-MPI the number",
+ "of MPI threads will automatically be set to the number of GPUs detected.",
+ "When you want to use a subset of the available GPUs, you can use",
+ "the [TT]-gpu_id[tt] option, where GPU id's are passed as a string,",
+ "e.g. 02 for using GPUs 0 and 2. When you want different GPU id's",
+ "on different nodes of a compute cluster, use the GMX_GPU_ID environment",
+ "variable instead. The format for GMX_GPU_ID is identical to ",
+ "[TT]-gpu_id[tt], but an environment variable can have different values",
+ "on different nodes of a cluster.",
+ "[PAR]",
+ "When using PME with separate PME nodes or with a GPU, the two major",
+ "compute tasks, the non-bonded force calculation and the PME calculation",
+ "run on different compute resources. If this load is not balanced,",
+ "some of the resources will be idle part of time. With the Verlet",
+ "cut-off scheme this load is automatically balanced when the PME load",
+ "is too high (but not when it is too low). This is done by scaling",
+ "the Coulomb cut-off and PME grid spacing by the same amount. In the first",
+ "few hundred steps different settings are tried and the fastest is chosen",
+ "for the rest of the simulation. This does not affect the accuracy of",
+ "the results, but it does affect the decomposition of the Coulomb energy",
+ "into particle and mesh contributions. The auto-tuning can be turned off",
+ "with the option [TT]-notunepme[tt].",
+ "[PAR]",
+ "[TT]mdrun[tt] pins (sets affinity of) threads to specific cores,",
+ "when all (logical) cores on a compute node are used by [TT]mdrun[tt],",
+ "even when no multi-threading is used,",
+ "as this usually results in significantly better performance.",
+ "If the queuing systems or the OpenMP library pinned threads, we honor",
+ "this and don't pin again, even though the layout may be sub-optimal.",
+ "If you want to have [TT]mdrun[tt] override an already set thread affinity",
+ "or pin threads when using less cores, use [TT]-pin on[tt].",
+ "With SMT (simultaneous multithreading), e.g. Intel Hyper-Threading,",
+ "there are multiple logical cores per physical core.",
+ "The option [TT]-pinstride[tt] sets the stride in logical cores for",
+ "pinning consecutive threads. Without SMT, 1 is usually the best choice.",
+ "With Intel Hyper-Threading 2 is best when using half or less of the",
+ "logical cores, 1 otherwise. The default value of 0 do exactly that:",
+ "it minimizes the threads per logical core, to optimize performance.",
+ "If you want to run multiple mdrun jobs on the same physical node,"
+ "you should set [TT]-pinstride[tt] to 1 when using all logical cores.",
+ "When running multiple mdrun (or other) simulations on the same physical",
+ "node, some simulations need to start pinning from a non-zero core",
+ "to avoid overloading cores; with [TT]-pinoffset[tt] you can specify",
+ "the offset in logical cores for pinning.",
+ "[PAR]",
+ "When [TT]mdrun[tt] is started using MPI with more than 1 process",
+ "or with thread-MPI with more than 1 thread, MPI parallelization is used.",
+ "By default domain decomposition is used, unless the [TT]-pd[tt]",
+ "option is set, which selects particle decomposition.",
+ "[PAR]",
+ "With domain decomposition, the spatial decomposition can be set",
+ "with option [TT]-dd[tt]. By default [TT]mdrun[tt] selects a good decomposition.",
+ "The user only needs to change this when the system is very inhomogeneous.",
+ "Dynamic load balancing is set with the option [TT]-dlb[tt],",
+ "which can give a significant performance improvement,",
+ "especially for inhomogeneous systems. The only disadvantage of",
+ "dynamic load balancing is that runs are no longer binary reproducible,",
+ "but in most cases this is not important.",
+ "By default the dynamic load balancing is automatically turned on",
+ "when the measured performance loss due to load imbalance is 5% or more.",
+ "At low parallelization these are the only important options",
+ "for domain decomposition.",
+ "At high parallelization the options in the next two sections",
+ "could be important for increasing the performace.",
+ "[PAR]",
+ "When PME is used with domain decomposition, separate nodes can",
+ "be assigned to do only the PME mesh calculation;",
+ "this is computationally more efficient starting at about 12 nodes.",
+ "The number of PME nodes is set with option [TT]-npme[tt],",
+ "this can not be more than half of the nodes.",
+ "By default [TT]mdrun[tt] makes a guess for the number of PME",
+ "nodes when the number of nodes is larger than 11 or performance wise",
+ "not compatible with the PME grid x dimension.",
+ "But the user should optimize npme. Performance statistics on this issue",
+ "are written at the end of the log file.",
+ "For good load balancing at high parallelization, the PME grid x and y",
+ "dimensions should be divisible by the number of PME nodes",
+ "(the simulation will run correctly also when this is not the case).",
+ "[PAR]",
+ "This section lists all options that affect the domain decomposition.",
+ "[PAR]",
+ "Option [TT]-rdd[tt] can be used to set the required maximum distance",
+ "for inter charge-group bonded interactions.",
+ "Communication for two-body bonded interactions below the non-bonded",
+ "cut-off distance always comes for free with the non-bonded communication.",
+ "Atoms beyond the non-bonded cut-off are only communicated when they have",
+ "missing bonded interactions; this means that the extra cost is minor",
+ "and nearly indepedent of the value of [TT]-rdd[tt].",
+ "With dynamic load balancing option [TT]-rdd[tt] also sets",
+ "the lower limit for the domain decomposition cell sizes.",
+ "By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
+ "the initial coordinates. The chosen value will be a balance",
+ "between interaction range and communication cost.",
+ "[PAR]",
+ "When inter charge-group bonded interactions are beyond",
+ "the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
+ "For pair interactions and tabulated bonds",
+ "that do not generate exclusions, this check can be turned off",
+ "with the option [TT]-noddcheck[tt].",
+ "[PAR]",
+ "When constraints are present, option [TT]-rcon[tt] influences",
+ "the cell size limit as well.",
+ "Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
+ "should not be beyond the smallest cell size. A error message is",
+ "generated when this happens and the user should change the decomposition",
+ "or decrease the LINCS order and increase the number of LINCS iterations.",
+ "By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
+ "in a conservative fashion. For high parallelization it can be useful",
+ "to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
+ "[PAR]",
+ "The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
+ "of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
+ "the cells can scale down by at least this factor. This option is used",
+ "for the automated spatial decomposition (when not using [TT]-dd[tt])",
+ "as well as for determining the number of grid pulses, which in turn",
+ "sets the minimum allowed cell size. Under certain circumstances",
+ "the value of [TT]-dds[tt] might need to be adjusted to account for",
+ "high or low spatial inhomogeneity of the system.",
+ "[PAR]",
+ "The option [TT]-gcom[tt] can be used to only do global communication",
+ "every n steps.",
+ "This can improve performance for highly parallel simulations",
+ "where this global communication step becomes the bottleneck.",
+ "For a global thermostat and/or barostat the temperature",
+ "and/or pressure will also only be updated every [TT]-gcom[tt] steps.",
+ "By default it is set to the minimum of nstcalcenergy and nstlist.[PAR]",
+ "With [TT]-rerun[tt] an input trajectory can be given for which ",
+ "forces and energies will be (re)calculated. Neighbor searching will be",
+ "performed for every frame, unless [TT]nstlist[tt] is zero",
+ "(see the [TT].mdp[tt] file).[PAR]",
+ "ED (essential dynamics) sampling and/or additional flooding potentials",
+ "are switched on by using the [TT]-ei[tt] flag followed by an [TT].edi[tt]",
+ "file. The [TT].edi[tt] file can be produced with the [TT]make_edi[tt] tool",
+ "or by using options in the essdyn menu of the WHAT IF program.",
+ "[TT]mdrun[tt] produces a [TT].xvg[tt] output file that",
+ "contains projections of positions, velocities and forces onto selected",
+ "eigenvectors.[PAR]",
+ "When user-defined potential functions have been selected in the",
+ "[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
+ "a formatted table with potential functions. The file is read from",
+ "either the current directory or from the [TT]GMXLIB[tt] directory.",
+ "A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
+ "for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
+ "normal Coulomb.",
+ "When pair interactions are present, a separate table for pair interaction",
+ "functions is read using the [TT]-tablep[tt] option.[PAR]",
+ "When tabulated bonded functions are present in the topology,",
+ "interaction functions are read using the [TT]-tableb[tt] option.",
+ "For each different tabulated interaction type the table file name is",
+ "modified in a different way: before the file extension an underscore is",
+ "appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
+ "and finally the table number of the interaction type.[PAR]",
+ "The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
+ "coordinates and forces when pulling is selected",
+ "in the [TT].mdp[tt] file.[PAR]",
+ "With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ",
+ "simulated in parallel.",
+ "As many input files/directories are required as the number of systems. ",
+ "The [TT]-multidir[tt] option takes a list of directories (one for each ",
+ "system) and runs in each of them, using the input/output file names, ",
+ "such as specified by e.g. the [TT]-s[tt] option, relative to these ",
+ "directories.",
+ "With [TT]-multi[tt], the system number is appended to the run input ",
+ "and each output filename, for instance [TT]topol.tpr[tt] becomes",
+ "[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.",
+ "The number of nodes per system is the total number of nodes",
+ "divided by the number of systems.",
+ "One use of this option is for NMR refinement: when distance",
+ "or orientation restraints are present these can be ensemble averaged",
+ "over all the systems.[PAR]",
+ "With [TT]-replex[tt] replica exchange is attempted every given number",
+ "of steps. The number of replicas is set with the [TT]-multi[tt] or ",
+ "[TT]-multidir[tt] option, described above.",
+ "All run input files should use a different coupling temperature,",
+ "the order of the files is not important. The random seed is set with",
+ "[TT]-reseed[tt]. The velocities are scaled and neighbor searching",
+ "is performed after every exchange.[PAR]",
+ "Finally some experimental algorithms can be tested when the",
+ "appropriate options have been given. Currently under",
+ "investigation are: polarizability and X-ray bombardments.",
+ "[PAR]",
+ "The option [TT]-membed[tt] does what used to be g_membed, i.e. embed",
+ "a protein into a membrane. The data file should contain the options",
+ "that where passed to g_membed before. The [TT]-mn[tt] and [TT]-mp[tt]",
+ "both apply to this as well.",
+ "[PAR]",
+ "The option [TT]-pforce[tt] is useful when you suspect a simulation",
+ "crashes due to too large forces. With this option coordinates and",
+ "forces of atoms with a force larger than a certain value will",
+ "be printed to stderr.",
+ "[PAR]",
+ "Checkpoints containing the complete state of the system are written",
+ "at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
+ "unless option [TT]-cpt[tt] is set to -1.",
+ "The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
+ "make sure that a recent state of the system is always available,",
+ "even when the simulation is terminated while writing a checkpoint.",
+ "With [TT]-cpnum[tt] all checkpoint files are kept and appended",
+ "with the step number.",
+ "A simulation can be continued by reading the full state from file",
+ "with option [TT]-cpi[tt]. This option is intelligent in the way that",
+ "if no checkpoint file is found, Gromacs just assumes a normal run and",
+ "starts from the first step of the [TT].tpr[tt] file. By default the output",
+ "will be appending to the existing output files. The checkpoint file",
+ "contains checksums of all output files, such that you will never",
+ "loose data when some output files are modified, corrupt or removed.",
+ "There are three scenarios with [TT]-cpi[tt]:[PAR]",
+ "[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
+ "[TT]*[tt] all files are present with names and checksums matching those stored",
+ "in the checkpoint file: files are appended[PAR]",
+ "[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
+ "With [TT]-noappend[tt] new output files are opened and the simulation",
+ "part number is added to all output file names.",
+ "Note that in all cases the checkpoint file itself is not renamed",
+ "and will be overwritten, unless its name does not match",
+ "the [TT]-cpo[tt] option.",
+ "[PAR]",
+ "With checkpointing the output is appended to previously written",
+ "output files, unless [TT]-noappend[tt] is used or none of the previous",
+ "output files are present (except for the checkpoint file).",
+ "The integrity of the files to be appended is verified using checksums",
+ "which are stored in the checkpoint file. This ensures that output can",
+ "not be mixed up or corrupted due to file appending. When only some",
+ "of the previous output files are present, a fatal error is generated",
+ "and no old output files are modified and no new output files are opened.",
+ "The result with appending will be the same as from a single run.",
+ "The contents will be binary identical, unless you use a different number",
+ "of nodes or dynamic load balancing or the FFT library uses optimizations",
+ "through timing.",
+ "[PAR]",
+ "With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
+ "file is written at the first neighbor search step where the run time",
+ "exceeds [TT]-maxh[tt]*0.99 hours.",
+ "[PAR]",
+ "When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
+ "step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
+ "pressed), it will stop after the next neighbor search step ",
+ "(with nstlist=0 at the next step).",
+ "In both cases all the usual output will be written to file.",
+ "When running with MPI, a signal to one of the [TT]mdrun[tt] processes",
+ "is sufficient, this signal should not be sent to mpirun or",
+ "the [TT]mdrun[tt] process that is the parent of the others.",
+ "[PAR]",
+ "When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
+ };
+ t_commrec *cr;
+ t_filenm fnm[] = {
+ { efTPX, NULL, NULL, ffREAD },
+ { efTRN, "-o", NULL, ffWRITE },
+ { efXTC, "-x", NULL, ffOPTWR },
+ { efCPT, "-cpi", NULL, ffOPTRD },
+ { efCPT, "-cpo", NULL, ffOPTWR },
+ { efSTO, "-c", "confout", ffWRITE },
+ { efEDR, "-e", "ener", ffWRITE },
+ { efLOG, "-g", "md", ffWRITE },
+ { efXVG, "-dhdl", "dhdl", ffOPTWR },
+ { efXVG, "-field", "field", ffOPTWR },
+ { efXVG, "-table", "table", ffOPTRD },
+ { efXVG, "-tabletf", "tabletf", ffOPTRD },
+ { efXVG, "-tablep", "tablep", ffOPTRD },
+ { efXVG, "-tableb", "table", ffOPTRD },
+ { efTRX, "-rerun", "rerun", ffOPTRD },
+ { efXVG, "-tpi", "tpi", ffOPTWR },
+ { efXVG, "-tpid", "tpidist", ffOPTWR },
+ { efEDI, "-ei", "sam", ffOPTRD },
+ { efXVG, "-eo", "edsam", ffOPTWR },
+ { efGCT, "-j", "wham", ffOPTRD },
+ { efGCT, "-jo", "bam", ffOPTWR },
+ { efXVG, "-ffout", "gct", ffOPTWR },
+ { efXVG, "-devout", "deviatie", ffOPTWR },
+ { efXVG, "-runav", "runaver", ffOPTWR },
+ { efXVG, "-px", "pullx", ffOPTWR },
+ { efXVG, "-pf", "pullf", ffOPTWR },
+ { efXVG, "-ro", "rotation", ffOPTWR },
+ { efLOG, "-ra", "rotangles", ffOPTWR },
+ { efLOG, "-rs", "rotslabs", ffOPTWR },
+ { efLOG, "-rt", "rottorque", ffOPTWR },
+ { efMTX, "-mtx", "nm", ffOPTWR },
+ { efNDX, "-dn", "dipole", ffOPTWR },
+ { efRND, "-multidir", NULL, ffOPTRDMULT},
+ { efDAT, "-plumed", "plumed", ffOPTRD }, /* PLUMED */
+ { efDAT, "-membed", "membed", ffOPTRD },
+ { efTOP, "-mp", "membed", ffOPTRD },
+ { efNDX, "-mn", "membed", ffOPTRD }
+ };
+#define NFILE asize(fnm)
+
+ /* Command line options ! */
+ gmx_bool bCart = FALSE;
+ gmx_bool bPPPME = FALSE;
+ gmx_bool bPartDec = FALSE;
+ gmx_bool bDDBondCheck = TRUE;
+ gmx_bool bDDBondComm = TRUE;
+ gmx_bool bTunePME = TRUE;
+ gmx_bool bTestVerlet = FALSE;
+ gmx_bool bVerbose = FALSE;
+ gmx_bool bCompact = TRUE;
+ gmx_bool bSepPot = FALSE;
+ gmx_bool bRerunVSite = FALSE;
+ gmx_bool bIonize = FALSE;
+ gmx_bool bConfout = TRUE;
+ gmx_bool bReproducible = FALSE;
+
+ int npme = -1;
+ int nmultisim = 0;
+ int nstglobalcomm = -1;
+ int repl_ex_nst = 0;
+ int repl_ex_seed = -1;
+ int repl_ex_nex = 0;
+ int nstepout = 100;
+ int resetstep = -1;
+ gmx_large_int_t nsteps = -2; /* the value -2 means that the mdp option will be used */
+
+ rvec realddxyz = {0, 0, 0};
+ const char *ddno_opt[ddnoNR+1] =
+ { NULL, "interleave", "pp_pme", "cartesian", NULL };
+ const char *dddlb_opt[] =
+ { NULL, "auto", "no", "yes", NULL };
+ const char *thread_aff_opt[threadaffNR+1] =
+ { NULL, "auto", "on", "off", NULL };
+ const char *nbpu_opt[] =
+ { NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
+ real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
+ char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
+ real cpt_period = 15.0, max_hours = -1;
+ gmx_bool bAppendFiles = TRUE;
+ gmx_bool bKeepAndNumCPT = FALSE;
+ gmx_bool bResetCountersHalfWay = FALSE;
+ output_env_t oenv = NULL;
+ const char *deviceOptions = "";
+
+ gmx_hw_opt_t hw_opt = {0, 0, 0, 0, threadaffSEL, 0, 0, NULL};
+
+ t_pargs pa[] = {
+
+ { "-pd", FALSE, etBOOL, {&bPartDec},
+ "Use particle decompostion" },
+ { "-dd", FALSE, etRVEC, {&realddxyz},
+ "Domain decomposition grid, 0 is optimize" },
+ { "-ddorder", FALSE, etENUM, {ddno_opt},
+ "DD node order" },
+ { "-npme", FALSE, etINT, {&npme},
+ "Number of separate nodes to be used for PME, -1 is guess" },
+ { "-nt", FALSE, etINT, {&hw_opt.nthreads_tot},
+ "Total number of threads to start (0 is guess)" },
+ { "-ntmpi", FALSE, etINT, {&hw_opt.nthreads_tmpi},
+ "Number of thread-MPI threads to start (0 is guess)" },
+ { "-ntomp", FALSE, etINT, {&hw_opt.nthreads_omp},
+ "Number of OpenMP threads per MPI process/thread to start (0 is guess)" },
+ { "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
+ "Number of OpenMP threads per MPI process/thread to start (0 is -ntomp)" },
+ { "-pin", FALSE, etENUM, {thread_aff_opt},
+ "Fix threads (or processes) to specific cores" },
+ { "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
+ "The starting logical core number for pinning to cores; used to avoid pinning threads from different mdrun instances to the same core" },
+ { "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
+ "Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
+ { "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_id},
+ "List of GPU id's to use" },
+ { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
+ "Check for all bonded interactions with DD" },
+ { "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
+ "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
+ { "-rdd", FALSE, etREAL, {&rdd},
+ "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
+ { "-rcon", FALSE, etREAL, {&rconstr},
+ "Maximum distance for P-LINCS (nm), 0 is estimate" },
+ { "-dlb", FALSE, etENUM, {dddlb_opt},
+ "Dynamic load balancing (with DD)" },
+ { "-dds", FALSE, etREAL, {&dlb_scale},
+ "Minimum allowed dlb scaling of the DD cell size" },
+ { "-ddcsx", FALSE, etSTR, {&ddcsx},
+ "HIDDENThe DD cell sizes in x" },
+ { "-ddcsy", FALSE, etSTR, {&ddcsy},
+ "HIDDENThe DD cell sizes in y" },
+ { "-ddcsz", FALSE, etSTR, {&ddcsz},
+ "HIDDENThe DD cell sizes in z" },
+ { "-gcom", FALSE, etINT, {&nstglobalcomm},
+ "Global communication frequency" },
+ { "-nb", FALSE, etENUM, {&nbpu_opt},
+ "Calculate non-bonded interactions on" },
+ { "-tunepme", FALSE, etBOOL, {&bTunePME},
+ "Optimize PME load between PP/PME nodes or GPU/CPU" },
+ { "-testverlet", FALSE, etBOOL, {&bTestVerlet},
+ "Test the Verlet non-bonded scheme" },
+ { "-v", FALSE, etBOOL, {&bVerbose},
+ "Be loud and noisy" },
+ { "-compact", FALSE, etBOOL, {&bCompact},
+ "Write a compact log file" },
+ { "-seppot", FALSE, etBOOL, {&bSepPot},
+ "Write separate V and dVdl terms for each interaction type and node to the log file(s)" },
+ { "-pforce", FALSE, etREAL, {&pforce},
+ "Print all forces larger than this (kJ/mol nm)" },
+ { "-reprod", FALSE, etBOOL, {&bReproducible},
+ "Try to avoid optimizations that affect binary reproducibility" },
+ { "-cpt", FALSE, etREAL, {&cpt_period},
+ "Checkpoint interval (minutes)" },
+ { "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
+ "Keep and number checkpoint files" },
+ { "-append", FALSE, etBOOL, {&bAppendFiles},
+ "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
+ { "-nsteps", FALSE, etGMX_LARGE_INT, {&nsteps},
+ "Run this number of steps, overrides .mdp file option" },
+ { "-maxh", FALSE, etREAL, {&max_hours},
+ "Terminate after 0.99 times this time (hours)" },
+ { "-multi", FALSE, etINT, {&nmultisim},
+ "Do multiple simulations in parallel" },
+ { "-replex", FALSE, etINT, {&repl_ex_nst},
+ "Attempt replica exchange periodically with this period (steps)" },
+ { "-nex", FALSE, etINT, {&repl_ex_nex},
+ "Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
+ { "-reseed", FALSE, etINT, {&repl_ex_seed},
+ "Seed for replica exchange, -1 is generate a seed" },
+ { "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
+ "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
+ { "-ionize", FALSE, etBOOL, {&bIonize},
+ "Do a simulation including the effect of an X-Ray bombardment on your system" },
+ { "-confout", FALSE, etBOOL, {&bConfout},
+ "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
+ { "-stepout", FALSE, etINT, {&nstepout},
+ "HIDDENFrequency of writing the remaining runtime" },
+ { "-resetstep", FALSE, etINT, {&resetstep},
+ "HIDDENReset cycle counters after these many time steps" },
+ { "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
+ "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
+ };
+ gmx_edsam_t ed;
+ unsigned long Flags, PCA_Flags;
+ ivec ddxyz;
+ int dd_node_order;
+ gmx_bool bAddPart;
+ FILE *fplog, *fpmulti;
+ int sim_part, sim_part_fn;
+ const char *part_suffix = ".part";
+ char suffix[STRLEN];
+ int rc;
+ char **multidir = NULL;
+
+
+ cr = init_par(&argc, &argv);
+
+ if (MASTER(cr))
+ {
+ CopyRight(stderr, argv[0]);
+ }
+
+ PCA_Flags = (PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET));
+
+ /* Comment this in to do fexist calls only on master
+ * works not with rerun or tables at the moment
+ * also comment out the version of init_forcerec in md.c
+ * with NULL instead of opt2fn
+ */
+ /*
+ if (!MASTER(cr))
+ {
+ PCA_Flags |= PCA_NOT_READ_NODE;
+ }
+ */
+
+ parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv);
+
+
+ /* we set these early because they might be used in init_multisystem()
+ Note that there is the potential for npme>nnodes until the number of
+ threads is set later on, if there's thread parallelization. That shouldn't
+ lead to problems. */
+ dd_node_order = nenum(ddno_opt);
+ cr->npmenodes = npme;
+
+ hw_opt.thread_affinity = nenum(thread_aff_opt);
+
+ /* now check the -multi and -multidir option */
+ if (opt2bSet("-multidir", NFILE, fnm))
+ {
+ int i;
+ if (nmultisim > 0)
+ {
+ gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
+ }
+ nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
+ }
+
+
+ if (repl_ex_nst != 0 && nmultisim < 2)
+ {
+ gmx_fatal(FARGS, "Need at least two replicas for replica exchange (option -multi)");
+ }
+
+ if (repl_ex_nex < 0)
+ {
+ gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
+ }
+
+ if (nmultisim > 1)
+ {
+#ifndef GMX_THREAD_MPI
+ gmx_bool bParFn = (multidir == NULL);
+ init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
+#else
+ gmx_fatal(FARGS, "mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support");
+#endif
+ }
+
+ bAddPart = !bAppendFiles;
+
+ /* Check if there is ANY checkpoint file available */
+ sim_part = 1;
+ sim_part_fn = sim_part;
+ if (opt2bSet("-cpi", NFILE, fnm))
+ {
+ if (bSepPot && bAppendFiles)
+ {
+ gmx_fatal(FARGS, "Output file appending is not supported with -seppot");
+ }
+
+ bAppendFiles =
+ read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
+ fnm, cr),
+ &sim_part_fn, NULL, cr,
+ bAppendFiles, NFILE, fnm,
+ part_suffix, &bAddPart);
+ if (sim_part_fn == 0 && MULTIMASTER(cr))
+ {
+ fprintf(stdout, "No previous checkpoint file present, assuming this is a new run.\n");
+ }
+ else
+ {
+ sim_part = sim_part_fn + 1;
+ }
+
+ if (MULTISIM(cr) && MASTER(cr))
+ {
+ if (MULTIMASTER(cr))
+ {
+ /* Log file is not yet available, so if there's a
+ * problem we can only write to stderr. */
+ fpmulti = stderr;
+ }
+ else
+ {
+ fpmulti = NULL;
+ }
+ check_multi_int(fpmulti, cr->ms, sim_part, "simulation part", TRUE);
+ }
+ }
+ else
+ {
+ bAppendFiles = FALSE;
+ }
+
+ if (!bAppendFiles)
+ {
+ sim_part_fn = sim_part;
+ }
+
+ if (bAddPart)
+ {
+ /* Rename all output files (except checkpoint files) */
+ /* create new part name first (zero-filled) */
+ sprintf(suffix, "%s%04d", part_suffix, sim_part_fn);
+
+ add_suffix_to_output_names(fnm, NFILE, suffix);
+ if (MULTIMASTER(cr))
+ {
+ fprintf(stdout, "Checkpoint file is from part %d, new output files will be suffixed '%s'.\n", sim_part-1, suffix);
+ }
+ }
+
+ Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
+ Flags = Flags | (bSepPot ? MD_SEPPOT : 0);
+ Flags = Flags | (bIonize ? MD_IONIZE : 0);
+ Flags = Flags | (bPartDec ? MD_PARTDEC : 0);
+ Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
+ Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
+ Flags = Flags | (bTunePME ? MD_TUNEPME : 0);
+ Flags = Flags | (bTestVerlet ? MD_TESTVERLET : 0);
+ Flags = Flags | (bConfout ? MD_CONFOUT : 0);
+ Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
+ Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
+ Flags = Flags | (bAppendFiles ? MD_APPENDFILES : 0);
+ Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
+ Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
+ Flags = Flags | (sim_part > 1 ? MD_STARTFROMCPT : 0);
+ Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
+
+
+ /* We postpone opening the log file if we are appending, so we can
+ first truncate the old log file and append to the correct position
+ there instead. */
+ if ((MASTER(cr) || bSepPot) && !bAppendFiles)
+ {
+ gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
+ !bSepPot, Flags & MD_APPENDFILES, &fplog);
+ CopyRight(fplog, argv[0]);
+ please_cite(fplog, "Hess2008b");
+ please_cite(fplog, "Spoel2005a");
+ please_cite(fplog, "Lindahl2001a");
+ please_cite(fplog, "Berendsen95a");
+ }
+ else if (!MASTER(cr) && bSepPot)
+ {
+ gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr, !bSepPot, Flags, &fplog);
+ }
+ else
+ {
+ fplog = NULL;
+ }
+
+ ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
+ ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
+ ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
+ /* PLUMED */
+ plumedswitch=0;
+ if (opt2bSet("-plumed",NFILE,fnm)) plumedswitch=1;
+ if(plumedswitch){
+ int plumed_is_there=0;
+ int real_precision=sizeof(real);
+ real energyUnits=1.0;
+ real lengthUnits=1.0;
+ real timeUnits=1.0;
+
+
+ if(!plumed_installed()){
+ gmx_fatal(FARGS,"Plumed is not available. Check your PLUMED_KERNEL variable.");
+ }
+ plumedmain=plumed_create();
+ plumed_cmd(plumedmain,"setRealPrecision",&real_precision);
+ // this is not necessary for gromacs units:
+ plumed_cmd(plumedmain,"setMDEnergyUnits",&energyUnits);
+ plumed_cmd(plumedmain,"setMDLengthUnits",&lengthUnits);
+ plumed_cmd(plumedmain,"setMDTimeUnits",&timeUnits);
+ //
+ plumed_cmd(plumedmain,"setPlumedDat",ftp2fn(efDAT,NFILE,fnm));
+ plumedswitch=1;
+ }
+ /* END PLUMED */
+
+ rc = mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose, bCompact,
+ nstglobalcomm, ddxyz, dd_node_order, rdd, rconstr,
+ dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
+ nbpu_opt[0],
+ nsteps, nstepout, resetstep,
+ nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
+ pforce, cpt_period, max_hours, deviceOptions, Flags);
+
+ /* PLUMED */
+ if(plumedswitch){
+ plumed_finalize(plumedmain);
+ }
+ /* END PLUMED */
+
+ gmx_finalize_par();
+
+ if (MULTIMASTER(cr))
+ {
+ thanx(stderr);
+ }
+
+ /* Log file has to be closed in mdrunner if we are appending to it
+ (fplog not set here) */
+ if (MASTER(cr) && !bAppendFiles)
+ {
+ gmx_log_close(fplog);
+ }
+
+ return rc;
+}
diff --git a/patches/gromacs-4.6.3.diff/src/kernel/mdrun.c.preplumed b/patches/gromacs-4.6.3.diff/src/kernel/mdrun.c.preplumed
new file mode 100644
index 0000000000000000000000000000000000000000..a5c0e6a6256def6a24b6b0bb702c5eef114b58c5
--- /dev/null
+++ b/patches/gromacs-4.6.3.diff/src/kernel/mdrun.c.preplumed
@@ -0,0 +1,760 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "typedefs.h"
+#include "macros.h"
+#include "copyrite.h"
+#include "main.h"
+#include "statutil.h"
+#include "smalloc.h"
+#include "futil.h"
+#include "smalloc.h"
+#include "edsam.h"
+#include "mdrun.h"
+#include "xmdrun.h"
+#include "checkpoint.h"
+#ifdef GMX_THREAD_MPI
+#include "thread_mpi.h"
+#endif
+
+/* afm stuf */
+#include "pull.h"
+
+int cmain(int argc, char *argv[])
+{
+ const char *desc[] = {
+ "The [TT]mdrun[tt] program is the main computational chemistry engine",
+ "within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
+ "but it can also perform Stochastic Dynamics, Energy Minimization,",
+ "test particle insertion or (re)calculation of energies.",
+ "Normal mode analysis is another option. In this case [TT]mdrun[tt]",
+ "builds a Hessian matrix from single conformation.",
+ "For usual Normal Modes-like calculations, make sure that",
+ "the structure provided is properly energy-minimized.",
+ "The generated matrix can be diagonalized by [TT]g_nmeig[tt].[PAR]",
+ "The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
+ "and distributes the topology over nodes if needed.",
+ "[TT]mdrun[tt] produces at least four output files.",
+ "A single log file ([TT]-g[tt]) is written, unless the option",
+ "[TT]-seppot[tt] is used, in which case each node writes a log file.",
+ "The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
+ "optionally forces.",
+ "The structure file ([TT]-c[tt]) contains the coordinates and",
+ "velocities of the last step.",
+ "The energy file ([TT]-e[tt]) contains energies, the temperature,",
+ "pressure, etc, a lot of these things are also printed in the log file.",
+ "Optionally coordinates can be written to a compressed trajectory file",
+ "([TT]-x[tt]).[PAR]",
+ "The option [TT]-dhdl[tt] is only used when free energy calculation is",
+ "turned on.[PAR]",
+ "A simulation can be run in parallel using two different parallelization",
+ "schemes: MPI parallelization and/or OpenMP thread parallelization.",
+ "The MPI parallelization uses multiple processes when [TT]mdrun[tt] is",
+ "compiled with a normal MPI library or threads when [TT]mdrun[tt] is",
+ "compiled with the GROMACS built-in thread-MPI library. OpenMP threads",
+ "are supported when mdrun is compiled with OpenMP. Full OpenMP support",
+ "is only available with the Verlet cut-off scheme, with the (older)",
+ "group scheme only PME-only processes can use OpenMP parallelization.",
+ "In all cases [TT]mdrun[tt] will by default try to use all the available",
+ "hardware resources. With a normal MPI library only the options",
+ "[TT]-ntomp[tt] (with the Verlet cut-off scheme) and [TT]-ntomp_pme[tt],",
+ "for PME-only processes, can be used to control the number of threads.",
+ "With thread-MPI there are additional options [TT]-nt[tt], which sets",
+ "the total number of threads, and [TT]-ntmpi[tt], which sets the number",
+ "of thread-MPI threads.",
+ "Note that using combined MPI+OpenMP parallelization is almost always",
+ "slower than single parallelization, except at the scaling limit, where",
+ "especially OpenMP parallelization of PME reduces the communication cost.",
+ "OpenMP-only parallelization is much faster than MPI-only parallelization",
+ "on a single CPU(-die). Since we currently don't have proper hardware",
+ "topology detection, [TT]mdrun[tt] compiled with thread-MPI will only",
+ "automatically use OpenMP-only parallelization when you use up to 4",
+ "threads, up to 12 threads with Intel Nehalem/Westmere, or up to 16",
+ "threads with Intel Sandy Bridge or newer CPUs. Otherwise MPI-only",
+ "parallelization is used (except with GPUs, see below).",
+ "[PAR]",
+ "To quickly test the performance of the new Verlet cut-off scheme",
+ "with old [TT].tpr[tt] files, either on CPUs or CPUs+GPUs, you can use",
+ "the [TT]-testverlet[tt] option. This should not be used for production,",
+ "since it can slightly modify potentials and it will remove charge groups",
+ "making analysis difficult, as the [TT].tpr[tt] file will still contain",
+ "charge groups. For production simulations it is highly recommended",
+ "to specify [TT]cutoff-scheme = Verlet[tt] in the [TT].mdp[tt] file.",
+ "[PAR]",
+ "With GPUs (only supported with the Verlet cut-off scheme), the number",
+ "of GPUs should match the number of MPI processes or MPI threads,",
+ "excluding PME-only processes/threads. With thread-MPI the number",
+ "of MPI threads will automatically be set to the number of GPUs detected.",
+ "When you want to use a subset of the available GPUs, you can use",
+ "the [TT]-gpu_id[tt] option, where GPU id's are passed as a string,",
+ "e.g. 02 for using GPUs 0 and 2. When you want different GPU id's",
+ "on different nodes of a compute cluster, use the GMX_GPU_ID environment",
+ "variable instead. The format for GMX_GPU_ID is identical to ",
+ "[TT]-gpu_id[tt], but an environment variable can have different values",
+ "on different nodes of a cluster.",
+ "[PAR]",
+ "When using PME with separate PME nodes or with a GPU, the two major",
+ "compute tasks, the non-bonded force calculation and the PME calculation",
+ "run on different compute resources. If this load is not balanced,",
+ "some of the resources will be idle part of time. With the Verlet",
+ "cut-off scheme this load is automatically balanced when the PME load",
+ "is too high (but not when it is too low). This is done by scaling",
+ "the Coulomb cut-off and PME grid spacing by the same amount. In the first",
+ "few hundred steps different settings are tried and the fastest is chosen",
+ "for the rest of the simulation. This does not affect the accuracy of",
+ "the results, but it does affect the decomposition of the Coulomb energy",
+ "into particle and mesh contributions. The auto-tuning can be turned off",
+ "with the option [TT]-notunepme[tt].",
+ "[PAR]",
+ "[TT]mdrun[tt] pins (sets affinity of) threads to specific cores,",
+ "when all (logical) cores on a compute node are used by [TT]mdrun[tt],",
+ "even when no multi-threading is used,",
+ "as this usually results in significantly better performance.",
+ "If the queuing systems or the OpenMP library pinned threads, we honor",
+ "this and don't pin again, even though the layout may be sub-optimal.",
+ "If you want to have [TT]mdrun[tt] override an already set thread affinity",
+ "or pin threads when using less cores, use [TT]-pin on[tt].",
+ "With SMT (simultaneous multithreading), e.g. Intel Hyper-Threading,",
+ "there are multiple logical cores per physical core.",
+ "The option [TT]-pinstride[tt] sets the stride in logical cores for",
+ "pinning consecutive threads. Without SMT, 1 is usually the best choice.",
+ "With Intel Hyper-Threading 2 is best when using half or less of the",
+ "logical cores, 1 otherwise. The default value of 0 do exactly that:",
+ "it minimizes the threads per logical core, to optimize performance.",
+ "If you want to run multiple mdrun jobs on the same physical node,"
+ "you should set [TT]-pinstride[tt] to 1 when using all logical cores.",
+ "When running multiple mdrun (or other) simulations on the same physical",
+ "node, some simulations need to start pinning from a non-zero core",
+ "to avoid overloading cores; with [TT]-pinoffset[tt] you can specify",
+ "the offset in logical cores for pinning.",
+ "[PAR]",
+ "When [TT]mdrun[tt] is started using MPI with more than 1 process",
+ "or with thread-MPI with more than 1 thread, MPI parallelization is used.",
+ "By default domain decomposition is used, unless the [TT]-pd[tt]",
+ "option is set, which selects particle decomposition.",
+ "[PAR]",
+ "With domain decomposition, the spatial decomposition can be set",
+ "with option [TT]-dd[tt]. By default [TT]mdrun[tt] selects a good decomposition.",
+ "The user only needs to change this when the system is very inhomogeneous.",
+ "Dynamic load balancing is set with the option [TT]-dlb[tt],",
+ "which can give a significant performance improvement,",
+ "especially for inhomogeneous systems. The only disadvantage of",
+ "dynamic load balancing is that runs are no longer binary reproducible,",
+ "but in most cases this is not important.",
+ "By default the dynamic load balancing is automatically turned on",
+ "when the measured performance loss due to load imbalance is 5% or more.",
+ "At low parallelization these are the only important options",
+ "for domain decomposition.",
+ "At high parallelization the options in the next two sections",
+ "could be important for increasing the performace.",
+ "[PAR]",
+ "When PME is used with domain decomposition, separate nodes can",
+ "be assigned to do only the PME mesh calculation;",
+ "this is computationally more efficient starting at about 12 nodes.",
+ "The number of PME nodes is set with option [TT]-npme[tt],",
+ "this can not be more than half of the nodes.",
+ "By default [TT]mdrun[tt] makes a guess for the number of PME",
+ "nodes when the number of nodes is larger than 11 or performance wise",
+ "not compatible with the PME grid x dimension.",
+ "But the user should optimize npme. Performance statistics on this issue",
+ "are written at the end of the log file.",
+ "For good load balancing at high parallelization, the PME grid x and y",
+ "dimensions should be divisible by the number of PME nodes",
+ "(the simulation will run correctly also when this is not the case).",
+ "[PAR]",
+ "This section lists all options that affect the domain decomposition.",
+ "[PAR]",
+ "Option [TT]-rdd[tt] can be used to set the required maximum distance",
+ "for inter charge-group bonded interactions.",
+ "Communication for two-body bonded interactions below the non-bonded",
+ "cut-off distance always comes for free with the non-bonded communication.",
+ "Atoms beyond the non-bonded cut-off are only communicated when they have",
+ "missing bonded interactions; this means that the extra cost is minor",
+ "and nearly indepedent of the value of [TT]-rdd[tt].",
+ "With dynamic load balancing option [TT]-rdd[tt] also sets",
+ "the lower limit for the domain decomposition cell sizes.",
+ "By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
+ "the initial coordinates. The chosen value will be a balance",
+ "between interaction range and communication cost.",
+ "[PAR]",
+ "When inter charge-group bonded interactions are beyond",
+ "the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
+ "For pair interactions and tabulated bonds",
+ "that do not generate exclusions, this check can be turned off",
+ "with the option [TT]-noddcheck[tt].",
+ "[PAR]",
+ "When constraints are present, option [TT]-rcon[tt] influences",
+ "the cell size limit as well.",
+ "Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
+ "should not be beyond the smallest cell size. A error message is",
+ "generated when this happens and the user should change the decomposition",
+ "or decrease the LINCS order and increase the number of LINCS iterations.",
+ "By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
+ "in a conservative fashion. For high parallelization it can be useful",
+ "to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
+ "[PAR]",
+ "The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
+ "of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
+ "the cells can scale down by at least this factor. This option is used",
+ "for the automated spatial decomposition (when not using [TT]-dd[tt])",
+ "as well as for determining the number of grid pulses, which in turn",
+ "sets the minimum allowed cell size. Under certain circumstances",
+ "the value of [TT]-dds[tt] might need to be adjusted to account for",
+ "high or low spatial inhomogeneity of the system.",
+ "[PAR]",
+ "The option [TT]-gcom[tt] can be used to only do global communication",
+ "every n steps.",
+ "This can improve performance for highly parallel simulations",
+ "where this global communication step becomes the bottleneck.",
+ "For a global thermostat and/or barostat the temperature",
+ "and/or pressure will also only be updated every [TT]-gcom[tt] steps.",
+ "By default it is set to the minimum of nstcalcenergy and nstlist.[PAR]",
+ "With [TT]-rerun[tt] an input trajectory can be given for which ",
+ "forces and energies will be (re)calculated. Neighbor searching will be",
+ "performed for every frame, unless [TT]nstlist[tt] is zero",
+ "(see the [TT].mdp[tt] file).[PAR]",
+ "ED (essential dynamics) sampling and/or additional flooding potentials",
+ "are switched on by using the [TT]-ei[tt] flag followed by an [TT].edi[tt]",
+ "file. The [TT].edi[tt] file can be produced with the [TT]make_edi[tt] tool",
+ "or by using options in the essdyn menu of the WHAT IF program.",
+ "[TT]mdrun[tt] produces a [TT].xvg[tt] output file that",
+ "contains projections of positions, velocities and forces onto selected",
+ "eigenvectors.[PAR]",
+ "When user-defined potential functions have been selected in the",
+ "[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
+ "a formatted table with potential functions. The file is read from",
+ "either the current directory or from the [TT]GMXLIB[tt] directory.",
+ "A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
+ "for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
+ "normal Coulomb.",
+ "When pair interactions are present, a separate table for pair interaction",
+ "functions is read using the [TT]-tablep[tt] option.[PAR]",
+ "When tabulated bonded functions are present in the topology,",
+ "interaction functions are read using the [TT]-tableb[tt] option.",
+ "For each different tabulated interaction type the table file name is",
+ "modified in a different way: before the file extension an underscore is",
+ "appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
+ "and finally the table number of the interaction type.[PAR]",
+ "The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
+ "coordinates and forces when pulling is selected",
+ "in the [TT].mdp[tt] file.[PAR]",
+ "With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ",
+ "simulated in parallel.",
+ "As many input files/directories are required as the number of systems. ",
+ "The [TT]-multidir[tt] option takes a list of directories (one for each ",
+ "system) and runs in each of them, using the input/output file names, ",
+ "such as specified by e.g. the [TT]-s[tt] option, relative to these ",
+ "directories.",
+ "With [TT]-multi[tt], the system number is appended to the run input ",
+ "and each output filename, for instance [TT]topol.tpr[tt] becomes",
+ "[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.",
+ "The number of nodes per system is the total number of nodes",
+ "divided by the number of systems.",
+ "One use of this option is for NMR refinement: when distance",
+ "or orientation restraints are present these can be ensemble averaged",
+ "over all the systems.[PAR]",
+ "With [TT]-replex[tt] replica exchange is attempted every given number",
+ "of steps. The number of replicas is set with the [TT]-multi[tt] or ",
+ "[TT]-multidir[tt] option, described above.",
+ "All run input files should use a different coupling temperature,",
+ "the order of the files is not important. The random seed is set with",
+ "[TT]-reseed[tt]. The velocities are scaled and neighbor searching",
+ "is performed after every exchange.[PAR]",
+ "Finally some experimental algorithms can be tested when the",
+ "appropriate options have been given. Currently under",
+ "investigation are: polarizability and X-ray bombardments.",
+ "[PAR]",
+ "The option [TT]-membed[tt] does what used to be g_membed, i.e. embed",
+ "a protein into a membrane. The data file should contain the options",
+ "that where passed to g_membed before. The [TT]-mn[tt] and [TT]-mp[tt]",
+ "both apply to this as well.",
+ "[PAR]",
+ "The option [TT]-pforce[tt] is useful when you suspect a simulation",
+ "crashes due to too large forces. With this option coordinates and",
+ "forces of atoms with a force larger than a certain value will",
+ "be printed to stderr.",
+ "[PAR]",
+ "Checkpoints containing the complete state of the system are written",
+ "at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
+ "unless option [TT]-cpt[tt] is set to -1.",
+ "The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
+ "make sure that a recent state of the system is always available,",
+ "even when the simulation is terminated while writing a checkpoint.",
+ "With [TT]-cpnum[tt] all checkpoint files are kept and appended",
+ "with the step number.",
+ "A simulation can be continued by reading the full state from file",
+ "with option [TT]-cpi[tt]. This option is intelligent in the way that",
+ "if no checkpoint file is found, Gromacs just assumes a normal run and",
+ "starts from the first step of the [TT].tpr[tt] file. By default the output",
+ "will be appending to the existing output files. The checkpoint file",
+ "contains checksums of all output files, such that you will never",
+ "loose data when some output files are modified, corrupt or removed.",
+ "There are three scenarios with [TT]-cpi[tt]:[PAR]",
+ "[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
+ "[TT]*[tt] all files are present with names and checksums matching those stored",
+ "in the checkpoint file: files are appended[PAR]",
+ "[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
+ "With [TT]-noappend[tt] new output files are opened and the simulation",
+ "part number is added to all output file names.",
+ "Note that in all cases the checkpoint file itself is not renamed",
+ "and will be overwritten, unless its name does not match",
+ "the [TT]-cpo[tt] option.",
+ "[PAR]",
+ "With checkpointing the output is appended to previously written",
+ "output files, unless [TT]-noappend[tt] is used or none of the previous",
+ "output files are present (except for the checkpoint file).",
+ "The integrity of the files to be appended is verified using checksums",
+ "which are stored in the checkpoint file. This ensures that output can",
+ "not be mixed up or corrupted due to file appending. When only some",
+ "of the previous output files are present, a fatal error is generated",
+ "and no old output files are modified and no new output files are opened.",
+ "The result with appending will be the same as from a single run.",
+ "The contents will be binary identical, unless you use a different number",
+ "of nodes or dynamic load balancing or the FFT library uses optimizations",
+ "through timing.",
+ "[PAR]",
+ "With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
+ "file is written at the first neighbor search step where the run time",
+ "exceeds [TT]-maxh[tt]*0.99 hours.",
+ "[PAR]",
+ "When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
+ "step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
+ "pressed), it will stop after the next neighbor search step ",
+ "(with nstlist=0 at the next step).",
+ "In both cases all the usual output will be written to file.",
+ "When running with MPI, a signal to one of the [TT]mdrun[tt] processes",
+ "is sufficient, this signal should not be sent to mpirun or",
+ "the [TT]mdrun[tt] process that is the parent of the others.",
+ "[PAR]",
+ "When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
+ };
+ t_commrec *cr;
+ t_filenm fnm[] = {
+ { efTPX, NULL, NULL, ffREAD },
+ { efTRN, "-o", NULL, ffWRITE },
+ { efXTC, "-x", NULL, ffOPTWR },
+ { efCPT, "-cpi", NULL, ffOPTRD },
+ { efCPT, "-cpo", NULL, ffOPTWR },
+ { efSTO, "-c", "confout", ffWRITE },
+ { efEDR, "-e", "ener", ffWRITE },
+ { efLOG, "-g", "md", ffWRITE },
+ { efXVG, "-dhdl", "dhdl", ffOPTWR },
+ { efXVG, "-field", "field", ffOPTWR },
+ { efXVG, "-table", "table", ffOPTRD },
+ { efXVG, "-tabletf", "tabletf", ffOPTRD },
+ { efXVG, "-tablep", "tablep", ffOPTRD },
+ { efXVG, "-tableb", "table", ffOPTRD },
+ { efTRX, "-rerun", "rerun", ffOPTRD },
+ { efXVG, "-tpi", "tpi", ffOPTWR },
+ { efXVG, "-tpid", "tpidist", ffOPTWR },
+ { efEDI, "-ei", "sam", ffOPTRD },
+ { efXVG, "-eo", "edsam", ffOPTWR },
+ { efGCT, "-j", "wham", ffOPTRD },
+ { efGCT, "-jo", "bam", ffOPTWR },
+ { efXVG, "-ffout", "gct", ffOPTWR },
+ { efXVG, "-devout", "deviatie", ffOPTWR },
+ { efXVG, "-runav", "runaver", ffOPTWR },
+ { efXVG, "-px", "pullx", ffOPTWR },
+ { efXVG, "-pf", "pullf", ffOPTWR },
+ { efXVG, "-ro", "rotation", ffOPTWR },
+ { efLOG, "-ra", "rotangles", ffOPTWR },
+ { efLOG, "-rs", "rotslabs", ffOPTWR },
+ { efLOG, "-rt", "rottorque", ffOPTWR },
+ { efMTX, "-mtx", "nm", ffOPTWR },
+ { efNDX, "-dn", "dipole", ffOPTWR },
+ { efRND, "-multidir", NULL, ffOPTRDMULT},
+ { efDAT, "-membed", "membed", ffOPTRD },
+ { efTOP, "-mp", "membed", ffOPTRD },
+ { efNDX, "-mn", "membed", ffOPTRD }
+ };
+#define NFILE asize(fnm)
+
+ /* Command line options ! */
+ gmx_bool bCart = FALSE;
+ gmx_bool bPPPME = FALSE;
+ gmx_bool bPartDec = FALSE;
+ gmx_bool bDDBondCheck = TRUE;
+ gmx_bool bDDBondComm = TRUE;
+ gmx_bool bTunePME = TRUE;
+ gmx_bool bTestVerlet = FALSE;
+ gmx_bool bVerbose = FALSE;
+ gmx_bool bCompact = TRUE;
+ gmx_bool bSepPot = FALSE;
+ gmx_bool bRerunVSite = FALSE;
+ gmx_bool bIonize = FALSE;
+ gmx_bool bConfout = TRUE;
+ gmx_bool bReproducible = FALSE;
+
+ int npme = -1;
+ int nmultisim = 0;
+ int nstglobalcomm = -1;
+ int repl_ex_nst = 0;
+ int repl_ex_seed = -1;
+ int repl_ex_nex = 0;
+ int nstepout = 100;
+ int resetstep = -1;
+ gmx_large_int_t nsteps = -2; /* the value -2 means that the mdp option will be used */
+
+ rvec realddxyz = {0, 0, 0};
+ const char *ddno_opt[ddnoNR+1] =
+ { NULL, "interleave", "pp_pme", "cartesian", NULL };
+ const char *dddlb_opt[] =
+ { NULL, "auto", "no", "yes", NULL };
+ const char *thread_aff_opt[threadaffNR+1] =
+ { NULL, "auto", "on", "off", NULL };
+ const char *nbpu_opt[] =
+ { NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
+ real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
+ char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
+ real cpt_period = 15.0, max_hours = -1;
+ gmx_bool bAppendFiles = TRUE;
+ gmx_bool bKeepAndNumCPT = FALSE;
+ gmx_bool bResetCountersHalfWay = FALSE;
+ output_env_t oenv = NULL;
+ const char *deviceOptions = "";
+
+ gmx_hw_opt_t hw_opt = {0, 0, 0, 0, threadaffSEL, 0, 0, NULL};
+
+ t_pargs pa[] = {
+
+ { "-pd", FALSE, etBOOL, {&bPartDec},
+ "Use particle decompostion" },
+ { "-dd", FALSE, etRVEC, {&realddxyz},
+ "Domain decomposition grid, 0 is optimize" },
+ { "-ddorder", FALSE, etENUM, {ddno_opt},
+ "DD node order" },
+ { "-npme", FALSE, etINT, {&npme},
+ "Number of separate nodes to be used for PME, -1 is guess" },
+ { "-nt", FALSE, etINT, {&hw_opt.nthreads_tot},
+ "Total number of threads to start (0 is guess)" },
+ { "-ntmpi", FALSE, etINT, {&hw_opt.nthreads_tmpi},
+ "Number of thread-MPI threads to start (0 is guess)" },
+ { "-ntomp", FALSE, etINT, {&hw_opt.nthreads_omp},
+ "Number of OpenMP threads per MPI process/thread to start (0 is guess)" },
+ { "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
+ "Number of OpenMP threads per MPI process/thread to start (0 is -ntomp)" },
+ { "-pin", FALSE, etENUM, {thread_aff_opt},
+ "Fix threads (or processes) to specific cores" },
+ { "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
+ "The starting logical core number for pinning to cores; used to avoid pinning threads from different mdrun instances to the same core" },
+ { "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
+ "Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
+ { "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_id},
+ "List of GPU id's to use" },
+ { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
+ "Check for all bonded interactions with DD" },
+ { "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
+ "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
+ { "-rdd", FALSE, etREAL, {&rdd},
+ "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
+ { "-rcon", FALSE, etREAL, {&rconstr},
+ "Maximum distance for P-LINCS (nm), 0 is estimate" },
+ { "-dlb", FALSE, etENUM, {dddlb_opt},
+ "Dynamic load balancing (with DD)" },
+ { "-dds", FALSE, etREAL, {&dlb_scale},
+ "Minimum allowed dlb scaling of the DD cell size" },
+ { "-ddcsx", FALSE, etSTR, {&ddcsx},
+ "HIDDENThe DD cell sizes in x" },
+ { "-ddcsy", FALSE, etSTR, {&ddcsy},
+ "HIDDENThe DD cell sizes in y" },
+ { "-ddcsz", FALSE, etSTR, {&ddcsz},
+ "HIDDENThe DD cell sizes in z" },
+ { "-gcom", FALSE, etINT, {&nstglobalcomm},
+ "Global communication frequency" },
+ { "-nb", FALSE, etENUM, {&nbpu_opt},
+ "Calculate non-bonded interactions on" },
+ { "-tunepme", FALSE, etBOOL, {&bTunePME},
+ "Optimize PME load between PP/PME nodes or GPU/CPU" },
+ { "-testverlet", FALSE, etBOOL, {&bTestVerlet},
+ "Test the Verlet non-bonded scheme" },
+ { "-v", FALSE, etBOOL, {&bVerbose},
+ "Be loud and noisy" },
+ { "-compact", FALSE, etBOOL, {&bCompact},
+ "Write a compact log file" },
+ { "-seppot", FALSE, etBOOL, {&bSepPot},
+ "Write separate V and dVdl terms for each interaction type and node to the log file(s)" },
+ { "-pforce", FALSE, etREAL, {&pforce},
+ "Print all forces larger than this (kJ/mol nm)" },
+ { "-reprod", FALSE, etBOOL, {&bReproducible},
+ "Try to avoid optimizations that affect binary reproducibility" },
+ { "-cpt", FALSE, etREAL, {&cpt_period},
+ "Checkpoint interval (minutes)" },
+ { "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
+ "Keep and number checkpoint files" },
+ { "-append", FALSE, etBOOL, {&bAppendFiles},
+ "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
+ { "-nsteps", FALSE, etGMX_LARGE_INT, {&nsteps},
+ "Run this number of steps, overrides .mdp file option" },
+ { "-maxh", FALSE, etREAL, {&max_hours},
+ "Terminate after 0.99 times this time (hours)" },
+ { "-multi", FALSE, etINT, {&nmultisim},
+ "Do multiple simulations in parallel" },
+ { "-replex", FALSE, etINT, {&repl_ex_nst},
+ "Attempt replica exchange periodically with this period (steps)" },
+ { "-nex", FALSE, etINT, {&repl_ex_nex},
+ "Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
+ { "-reseed", FALSE, etINT, {&repl_ex_seed},
+ "Seed for replica exchange, -1 is generate a seed" },
+ { "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
+ "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
+ { "-ionize", FALSE, etBOOL, {&bIonize},
+ "Do a simulation including the effect of an X-Ray bombardment on your system" },
+ { "-confout", FALSE, etBOOL, {&bConfout},
+ "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
+ { "-stepout", FALSE, etINT, {&nstepout},
+ "HIDDENFrequency of writing the remaining runtime" },
+ { "-resetstep", FALSE, etINT, {&resetstep},
+ "HIDDENReset cycle counters after these many time steps" },
+ { "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
+ "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
+ };
+ gmx_edsam_t ed;
+ unsigned long Flags, PCA_Flags;
+ ivec ddxyz;
+ int dd_node_order;
+ gmx_bool bAddPart;
+ FILE *fplog, *fpmulti;
+ int sim_part, sim_part_fn;
+ const char *part_suffix = ".part";
+ char suffix[STRLEN];
+ int rc;
+ char **multidir = NULL;
+
+
+ cr = init_par(&argc, &argv);
+
+ if (MASTER(cr))
+ {
+ CopyRight(stderr, argv[0]);
+ }
+
+ PCA_Flags = (PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET));
+
+ /* Comment this in to do fexist calls only on master
+ * works not with rerun or tables at the moment
+ * also comment out the version of init_forcerec in md.c
+ * with NULL instead of opt2fn
+ */
+ /*
+ if (!MASTER(cr))
+ {
+ PCA_Flags |= PCA_NOT_READ_NODE;
+ }
+ */
+
+ parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv);
+
+
+ /* we set these early because they might be used in init_multisystem()
+ Note that there is the potential for npme>nnodes until the number of
+ threads is set later on, if there's thread parallelization. That shouldn't
+ lead to problems. */
+ dd_node_order = nenum(ddno_opt);
+ cr->npmenodes = npme;
+
+ hw_opt.thread_affinity = nenum(thread_aff_opt);
+
+ /* now check the -multi and -multidir option */
+ if (opt2bSet("-multidir", NFILE, fnm))
+ {
+ int i;
+ if (nmultisim > 0)
+ {
+ gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
+ }
+ nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
+ }
+
+
+ if (repl_ex_nst != 0 && nmultisim < 2)
+ {
+ gmx_fatal(FARGS, "Need at least two replicas for replica exchange (option -multi)");
+ }
+
+ if (repl_ex_nex < 0)
+ {
+ gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
+ }
+
+ if (nmultisim > 1)
+ {
+#ifndef GMX_THREAD_MPI
+ gmx_bool bParFn = (multidir == NULL);
+ init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
+#else
+ gmx_fatal(FARGS, "mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support");
+#endif
+ }
+
+ bAddPart = !bAppendFiles;
+
+ /* Check if there is ANY checkpoint file available */
+ sim_part = 1;
+ sim_part_fn = sim_part;
+ if (opt2bSet("-cpi", NFILE, fnm))
+ {
+ if (bSepPot && bAppendFiles)
+ {
+ gmx_fatal(FARGS, "Output file appending is not supported with -seppot");
+ }
+
+ bAppendFiles =
+ read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
+ fnm, cr),
+ &sim_part_fn, NULL, cr,
+ bAppendFiles, NFILE, fnm,
+ part_suffix, &bAddPart);
+ if (sim_part_fn == 0 && MULTIMASTER(cr))
+ {
+ fprintf(stdout, "No previous checkpoint file present, assuming this is a new run.\n");
+ }
+ else
+ {
+ sim_part = sim_part_fn + 1;
+ }
+
+ if (MULTISIM(cr) && MASTER(cr))
+ {
+ if (MULTIMASTER(cr))
+ {
+ /* Log file is not yet available, so if there's a
+ * problem we can only write to stderr. */
+ fpmulti = stderr;
+ }
+ else
+ {
+ fpmulti = NULL;
+ }
+ check_multi_int(fpmulti, cr->ms, sim_part, "simulation part", TRUE);
+ }
+ }
+ else
+ {
+ bAppendFiles = FALSE;
+ }
+
+ if (!bAppendFiles)
+ {
+ sim_part_fn = sim_part;
+ }
+
+ if (bAddPart)
+ {
+ /* Rename all output files (except checkpoint files) */
+ /* create new part name first (zero-filled) */
+ sprintf(suffix, "%s%04d", part_suffix, sim_part_fn);
+
+ add_suffix_to_output_names(fnm, NFILE, suffix);
+ if (MULTIMASTER(cr))
+ {
+ fprintf(stdout, "Checkpoint file is from part %d, new output files will be suffixed '%s'.\n", sim_part-1, suffix);
+ }
+ }
+
+ Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
+ Flags = Flags | (bSepPot ? MD_SEPPOT : 0);
+ Flags = Flags | (bIonize ? MD_IONIZE : 0);
+ Flags = Flags | (bPartDec ? MD_PARTDEC : 0);
+ Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
+ Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
+ Flags = Flags | (bTunePME ? MD_TUNEPME : 0);
+ Flags = Flags | (bTestVerlet ? MD_TESTVERLET : 0);
+ Flags = Flags | (bConfout ? MD_CONFOUT : 0);
+ Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
+ Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
+ Flags = Flags | (bAppendFiles ? MD_APPENDFILES : 0);
+ Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
+ Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
+ Flags = Flags | (sim_part > 1 ? MD_STARTFROMCPT : 0);
+ Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
+
+
+ /* We postpone opening the log file if we are appending, so we can
+ first truncate the old log file and append to the correct position
+ there instead. */
+ if ((MASTER(cr) || bSepPot) && !bAppendFiles)
+ {
+ gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
+ !bSepPot, Flags & MD_APPENDFILES, &fplog);
+ CopyRight(fplog, argv[0]);
+ please_cite(fplog, "Hess2008b");
+ please_cite(fplog, "Spoel2005a");
+ please_cite(fplog, "Lindahl2001a");
+ please_cite(fplog, "Berendsen95a");
+ }
+ else if (!MASTER(cr) && bSepPot)
+ {
+ gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr, !bSepPot, Flags, &fplog);
+ }
+ else
+ {
+ fplog = NULL;
+ }
+
+ ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
+ ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
+ ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
+
+ rc = mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose, bCompact,
+ nstglobalcomm, ddxyz, dd_node_order, rdd, rconstr,
+ dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
+ nbpu_opt[0],
+ nsteps, nstepout, resetstep,
+ nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
+ pforce, cpt_period, max_hours, deviceOptions, Flags);
+
+ gmx_finalize_par();
+
+ if (MULTIMASTER(cr))
+ {
+ thanx(stderr);
+ }
+
+ /* Log file has to be closed in mdrunner if we are appending to it
+ (fplog not set here) */
+ if (MASTER(cr) && !bAppendFiles)
+ {
+ gmx_log_close(fplog);
+ }
+
+ return rc;
+}
diff --git a/patches/gromacs-4.6.3.diff/src/kernel/repl_ex.c b/patches/gromacs-4.6.3.diff/src/kernel/repl_ex.c
new file mode 100644
index 0000000000000000000000000000000000000000..2e79c67ad53769d9b8df84b99b66ca2bfa18de30
--- /dev/null
+++ b/patches/gromacs-4.6.3.diff/src/kernel/repl_ex.c
@@ -0,0 +1,1520 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include "repl_ex.h"
+#include "network.h"
+#include "random.h"
+#include "smalloc.h"
+#include "physics.h"
+#include "copyrite.h"
+#include "macros.h"
+#include "vec.h"
+#include "names.h"
+#include "mvdata.h"
+#include "domdec.h"
+#include "partdec.h"
+
+/* PLUMED */
+#include "../../Plumed.h"
+extern int plumedswitch;
+extern plumed plumedmain;
+/* END PLUMED */
+
+#define PROBABILITYCUTOFF 100
+/* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
+
+enum {
+ ereTEMP, ereLAMBDA, ereENDSINGLE, ereTL, ereNR
+};
+const char *erename[ereNR] = { "temperature", "lambda", "end_single_marker", "temperature and lambda"};
+/* end_single_marker merely notes the end of single variable replica exchange. All types higher than
+ it are multiple replica exchange methods */
+/* Eventually, should add 'pressure', 'temperature and pressure', 'lambda_and_pressure', 'temperature_lambda_pressure'?;
+ Let's wait until we feel better about the pressure control methods giving exact ensembles. Right now, we assume constant pressure */
+
+typedef struct gmx_repl_ex
+{
+ int repl;
+ int nrepl;
+ real temp;
+ int type;
+ real **q;
+ gmx_bool bNPT;
+ real *pres;
+ int *ind;
+ int *allswaps;
+ int nst;
+ int nex;
+ int seed;
+ int nattempt[2];
+ real *prob_sum;
+ int **nmoves;
+ int *nexchange;
+
+ /* these are helper arrays for replica exchange; allocated here so they
+ don't have to be allocated each time */
+ int *destinations;
+ int **cyclic;
+ int **order;
+ int *tmpswap;
+ gmx_bool *incycle;
+ gmx_bool *bEx;
+
+ /* helper arrays to hold the quantities that are exchanged */
+ real *prob;
+ real *Epot;
+ real *beta;
+ real *Vol;
+ real **de;
+
+} t_gmx_repl_ex;
+
+static gmx_bool repl_quantity(FILE *fplog, const gmx_multisim_t *ms,
+ struct gmx_repl_ex *re, int ere, real q)
+{
+ real *qall;
+ gmx_bool bDiff;
+ int i, s;
+
+ snew(qall, ms->nsim);
+ qall[re->repl] = q;
+ gmx_sum_sim(ms->nsim, qall, ms);
+
+ /* PLUMED */
+ //bDiff = FALSE;
+ //for (s = 1; s < ms->nsim; s++)
+ //{
+ // if (qall[s] != qall[0])
+ // {
+ bDiff = TRUE;
+ // }
+ //}
+ /* END PLUMED */
+
+ if (bDiff)
+ {
+ /* Set the replica exchange type and quantities */
+ re->type = ere;
+
+ snew(re->q[ere], re->nrepl);
+ for (s = 0; s < ms->nsim; s++)
+ {
+ re->q[ere][s] = qall[s];
+ }
+ }
+ sfree(qall);
+ return bDiff;
+}
+
+gmx_repl_ex_t init_replica_exchange(FILE *fplog,
+ const gmx_multisim_t *ms,
+ const t_state *state,
+ const t_inputrec *ir,
+ int nst, int nex, int init_seed)
+{
+ real temp, pres;
+ int i, j, k;
+ struct gmx_repl_ex *re;
+ gmx_bool bTemp;
+ gmx_bool bLambda = FALSE;
+
+ fprintf(fplog, "\nInitializing Replica Exchange\n");
+
+ if (ms == NULL || ms->nsim == 1)
+ {
+ gmx_fatal(FARGS, "Nothing to exchange with only one replica, maybe you forgot to set the -multi option of mdrun?");
+ }
+
+ snew(re, 1);
+
+ re->repl = ms->sim;
+ re->nrepl = ms->nsim;
+ snew(re->q, ereENDSINGLE);
+
+ fprintf(fplog, "Repl There are %d replicas:\n", re->nrepl);
+
+ check_multi_int(fplog, ms, state->natoms, "the number of atoms", FALSE);
+ check_multi_int(fplog, ms, ir->eI, "the integrator", FALSE);
+ check_multi_large_int(fplog, ms, ir->init_step+ir->nsteps, "init_step+nsteps", FALSE);
+ check_multi_large_int(fplog, ms, (ir->init_step+nst-1)/nst,
+ "first exchange step: init_step/-replex", FALSE);
+ check_multi_int(fplog, ms, ir->etc, "the temperature coupling", FALSE);
+ check_multi_int(fplog, ms, ir->opts.ngtc,
+ "the number of temperature coupling groups", FALSE);
+ check_multi_int(fplog, ms, ir->epc, "the pressure coupling", FALSE);
+ check_multi_int(fplog, ms, ir->efep, "free energy", FALSE);
+ check_multi_int(fplog, ms, ir->fepvals->n_lambda, "number of lambda states", FALSE);
+
+ re->temp = ir->opts.ref_t[0];
+ for (i = 1; (i < ir->opts.ngtc); i++)
+ {
+ if (ir->opts.ref_t[i] != re->temp)
+ {
+ fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
+ fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
+ }
+ }
+
+ re->type = -1;
+ bTemp = repl_quantity(fplog, ms, re, ereTEMP, re->temp);
+ if (ir->efep != efepNO)
+ {
+ bLambda = repl_quantity(fplog, ms, re, ereLAMBDA, (real)ir->fepvals->init_fep_state);
+ }
+ if (re->type == -1) /* nothing was assigned */
+ {
+ gmx_fatal(FARGS, "The properties of the %d systems are all the same, there is nothing to exchange", re->nrepl);
+ }
+ if (bLambda && bTemp)
+ {
+ re->type = ereTL;
+ }
+
+ if (bTemp)
+ {
+ please_cite(fplog, "Sugita1999a");
+ if (ir->epc != epcNO)
+ {
+ re->bNPT = TRUE;
+ fprintf(fplog, "Repl Using Constant Pressure REMD.\n");
+ please_cite(fplog, "Okabe2001a");
+ }
+ if (ir->etc == etcBERENDSEN)
+ {
+ gmx_fatal(FARGS, "REMD with the %s thermostat does not produce correct potential energy distributions, consider using the %s thermostat instead",
+ ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
+ }
+ }
+ if (bLambda)
+ {
+ if (ir->fepvals->delta_lambda != 0) /* check this? */
+ {
+ gmx_fatal(FARGS, "delta_lambda is not zero");
+ }
+ }
+ if (re->bNPT)
+ {
+ snew(re->pres, re->nrepl);
+ if (ir->epct == epctSURFACETENSION)
+ {
+ pres = ir->ref_p[ZZ][ZZ];
+ }
+ else
+ {
+ pres = 0;
+ j = 0;
+ for (i = 0; i < DIM; i++)
+ {
+ if (ir->compress[i][i] != 0)
+ {
+ pres += ir->ref_p[i][i];
+ j++;
+ }
+ }
+ pres /= j;
+ }
+ re->pres[re->repl] = pres;
+ gmx_sum_sim(re->nrepl, re->pres, ms);
+ }
+
+ /* Make an index for increasing replica order */
+ /* only makes sense if one or the other is varying, not both!
+ if both are varying, we trust the order the person gave. */
+ snew(re->ind, re->nrepl);
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->ind[i] = i;
+ }
+
+ /* PLUMED */
+ // plumed2: check if we want alternative patterns (i.e. for bias-exchange metaD)
+ // in those cases replicas can share the same temperature.
+ /*
+ if (re->type < ereENDSINGLE)
+ {
+
+ for (i = 0; i < re->nrepl; i++)
+ {
+ for (j = i+1; j < re->nrepl; j++)
+ {
+ if (re->q[re->type][re->ind[j]] < re->q[re->type][re->ind[i]])
+ {
+ k = re->ind[i];
+ re->ind[i] = re->ind[j];
+ re->ind[j] = k;
+ }
+ else if (re->q[re->type][re->ind[j]] == re->q[re->type][re->ind[i]])
+ {
+ gmx_fatal(FARGS, "Two replicas have identical %ss", erename[re->type]);
+ }
+ }
+ }
+ }
+ */
+ /* END PLUMED */
+
+ /* keep track of all the swaps, starting with the initial placement. */
+ snew(re->allswaps, re->nrepl);
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->allswaps[i] = re->ind[i];
+ }
+
+ switch (re->type)
+ {
+ case ereTEMP:
+ fprintf(fplog, "\nReplica exchange in temperature\n");
+ for (i = 0; i < re->nrepl; i++)
+ {
+ fprintf(fplog, " %5.1f", re->q[re->type][re->ind[i]]);
+ }
+ fprintf(fplog, "\n");
+ break;
+ case ereLAMBDA:
+ fprintf(fplog, "\nReplica exchange in lambda\n");
+ for (i = 0; i < re->nrepl; i++)
+ {
+ fprintf(fplog, " %3d", (int)re->q[re->type][re->ind[i]]);
+ }
+ fprintf(fplog, "\n");
+ break;
+ case ereTL:
+ fprintf(fplog, "\nReplica exchange in temperature and lambda state\n");
+ for (i = 0; i < re->nrepl; i++)
+ {
+ fprintf(fplog, " %5.1f", re->q[ereTEMP][re->ind[i]]);
+ }
+ fprintf(fplog, "\n");
+ for (i = 0; i < re->nrepl; i++)
+ {
+ fprintf(fplog, " %5d", (int)re->q[ereLAMBDA][re->ind[i]]);
+ }
+ fprintf(fplog, "\n");
+ break;
+ default:
+ gmx_incons("Unknown replica exchange quantity");
+ }
+ if (re->bNPT)
+ {
+ fprintf(fplog, "\nRepl p");
+ for (i = 0; i < re->nrepl; i++)
+ {
+ fprintf(fplog, " %5.2f", re->pres[re->ind[i]]);
+ }
+
+ for (i = 0; i < re->nrepl; i++)
+ {
+ if ((i > 0) && (re->pres[re->ind[i]] < re->pres[re->ind[i-1]]))
+ {
+ fprintf(fplog, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
+ fprintf(stderr, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
+ }
+ }
+ }
+ re->nst = nst;
+ if (init_seed == -1)
+ {
+ if (MASTERSIM(ms))
+ {
+ re->seed = make_seed();
+ }
+ else
+ {
+ re->seed = 0;
+ }
+ gmx_sumi_sim(1, &(re->seed), ms);
+ }
+ else
+ {
+ re->seed = init_seed;
+ }
+ fprintf(fplog, "\nReplica exchange interval: %d\n", re->nst);
+ fprintf(fplog, "\nReplica random seed: %d\n", re->seed);
+
+ re->nattempt[0] = 0;
+ re->nattempt[1] = 0;
+
+ snew(re->prob_sum, re->nrepl);
+ snew(re->nexchange, re->nrepl);
+ snew(re->nmoves, re->nrepl);
+ for (i = 0; i < re->nrepl; i++)
+ {
+ snew(re->nmoves[i], re->nrepl);
+ }
+ fprintf(fplog, "Replica exchange information below: x=exchange, pr=probability\n");
+
+ /* generate space for the helper functions so we don't have to snew each time */
+
+ snew(re->destinations, re->nrepl);
+ snew(re->incycle, re->nrepl);
+ snew(re->tmpswap, re->nrepl);
+ snew(re->cyclic, re->nrepl);
+ snew(re->order, re->nrepl);
+ for (i = 0; i < re->nrepl; i++)
+ {
+ snew(re->cyclic[i], re->nrepl);
+ snew(re->order[i], re->nrepl);
+ }
+ /* allocate space for the functions storing the data for the replicas */
+ /* not all of these arrays needed in all cases, but they don't take
+ up much space, since the max size is nrepl**2 */
+ snew(re->prob, re->nrepl);
+ snew(re->bEx, re->nrepl);
+ snew(re->beta, re->nrepl);
+ snew(re->Vol, re->nrepl);
+ snew(re->Epot, re->nrepl);
+ snew(re->de, re->nrepl);
+ for (i = 0; i < re->nrepl; i++)
+ {
+ snew(re->de[i], re->nrepl);
+ }
+ re->nex = nex;
+ return re;
+}
+
+static void exchange_reals(const gmx_multisim_t *ms, int b, real *v, int n)
+{
+ real *buf;
+ int i;
+
+ if (v)
+ {
+ snew(buf, n);
+#ifdef GMX_MPI
+ /*
+ MPI_Sendrecv(v, n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
+ buf,n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
+ ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+ */
+ {
+ MPI_Request mpi_req;
+
+ MPI_Isend(v, n*sizeof(real), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, &mpi_req);
+ MPI_Recv(buf, n*sizeof(real), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+ MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+ }
+#endif
+ for (i = 0; i < n; i++)
+ {
+ v[i] = buf[i];
+ }
+ sfree(buf);
+ }
+}
+
+
+static void exchange_ints(const gmx_multisim_t *ms, int b, int *v, int n)
+{
+ int *buf;
+ int i;
+
+ if (v)
+ {
+ snew(buf, n);
+#ifdef GMX_MPI
+ /*
+ MPI_Sendrecv(v, n*sizeof(int),MPI_BYTE,MSRANK(ms,b),0,
+ buf,n*sizeof(int),MPI_BYTE,MSRANK(ms,b),0,
+ ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+ */
+ {
+ MPI_Request mpi_req;
+
+ MPI_Isend(v, n*sizeof(int), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, &mpi_req);
+ MPI_Recv(buf, n*sizeof(int), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+ MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+ }
+#endif
+ for (i = 0; i < n; i++)
+ {
+ v[i] = buf[i];
+ }
+ sfree(buf);
+ }
+}
+
+static void exchange_doubles(const gmx_multisim_t *ms, int b, double *v, int n)
+{
+ double *buf;
+ int i;
+
+ if (v)
+ {
+ snew(buf, n);
+#ifdef GMX_MPI
+ /*
+ MPI_Sendrecv(v, n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
+ buf,n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
+ ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+ */
+ {
+ MPI_Request mpi_req;
+
+ MPI_Isend(v, n*sizeof(double), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, &mpi_req);
+ MPI_Recv(buf, n*sizeof(double), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+ MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+ }
+#endif
+ for (i = 0; i < n; i++)
+ {
+ v[i] = buf[i];
+ }
+ sfree(buf);
+ }
+}
+
+static void exchange_rvecs(const gmx_multisim_t *ms, int b, rvec *v, int n)
+{
+ rvec *buf;
+ int i;
+
+ if (v)
+ {
+ snew(buf, n);
+#ifdef GMX_MPI
+ /*
+ MPI_Sendrecv(v[0], n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
+ buf[0],n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
+ ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+ */
+ {
+ MPI_Request mpi_req;
+
+ MPI_Isend(v[0], n*sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, &mpi_req);
+ MPI_Recv(buf[0], n*sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+ MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+ }
+#endif
+ for (i = 0; i < n; i++)
+ {
+ copy_rvec(buf[i], v[i]);
+ }
+ sfree(buf);
+ }
+}
+
+static void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
+{
+ /* When t_state changes, this code should be updated. */
+ int ngtc, nnhpres;
+ ngtc = state->ngtc * state->nhchainlength;
+ nnhpres = state->nnhpres* state->nhchainlength;
+ exchange_rvecs(ms, b, state->box, DIM);
+ exchange_rvecs(ms, b, state->box_rel, DIM);
+ exchange_rvecs(ms, b, state->boxv, DIM);
+ exchange_reals(ms, b, &(state->veta), 1);
+ exchange_reals(ms, b, &(state->vol0), 1);
+ exchange_rvecs(ms, b, state->svir_prev, DIM);
+ exchange_rvecs(ms, b, state->fvir_prev, DIM);
+ exchange_rvecs(ms, b, state->pres_prev, DIM);
+ exchange_doubles(ms, b, state->nosehoover_xi, ngtc);
+ exchange_doubles(ms, b, state->nosehoover_vxi, ngtc);
+ exchange_doubles(ms, b, state->nhpres_xi, nnhpres);
+ exchange_doubles(ms, b, state->nhpres_vxi, nnhpres);
+ exchange_doubles(ms, b, state->therm_integral, state->ngtc);
+ exchange_rvecs(ms, b, state->x, state->natoms);
+ exchange_rvecs(ms, b, state->v, state->natoms);
+ exchange_rvecs(ms, b, state->sd_X, state->natoms);
+}
+
+static void copy_rvecs(rvec *s, rvec *d, int n)
+{
+ int i;
+
+ if (d != NULL)
+ {
+ for (i = 0; i < n; i++)
+ {
+ copy_rvec(s[i], d[i]);
+ }
+ }
+}
+
+static void copy_doubles(const double *s, double *d, int n)
+{
+ int i;
+
+ if (d != NULL)
+ {
+ for (i = 0; i < n; i++)
+ {
+ d[i] = s[i];
+ }
+ }
+}
+
+static void copy_reals(const real *s, real *d, int n)
+{
+ int i;
+
+ if (d != NULL)
+ {
+ for (i = 0; i < n; i++)
+ {
+ d[i] = s[i];
+ }
+ }
+}
+
+static void copy_ints(const int *s, int *d, int n)
+{
+ int i;
+
+ if (d != NULL)
+ {
+ for (i = 0; i < n; i++)
+ {
+ d[i] = s[i];
+ }
+ }
+}
+
+#define scopy_rvecs(v, n) copy_rvecs(state->v, state_local->v, n);
+#define scopy_doubles(v, n) copy_doubles(state->v, state_local->v, n);
+#define scopy_reals(v, n) copy_reals(state->v, state_local->v, n);
+#define scopy_ints(v, n) copy_ints(state->v, state_local->v, n);
+
+static void copy_state_nonatomdata(t_state *state, t_state *state_local)
+{
+ /* When t_state changes, this code should be updated. */
+ int ngtc, nnhpres;
+ ngtc = state->ngtc * state->nhchainlength;
+ nnhpres = state->nnhpres* state->nhchainlength;
+ scopy_rvecs(box, DIM);
+ scopy_rvecs(box_rel, DIM);
+ scopy_rvecs(boxv, DIM);
+ state_local->veta = state->veta;
+ state_local->vol0 = state->vol0;
+ scopy_rvecs(svir_prev, DIM);
+ scopy_rvecs(fvir_prev, DIM);
+ scopy_rvecs(pres_prev, DIM);
+ scopy_doubles(nosehoover_xi, ngtc);
+ scopy_doubles(nosehoover_vxi, ngtc);
+ scopy_doubles(nhpres_xi, nnhpres);
+ scopy_doubles(nhpres_vxi, nnhpres);
+ scopy_doubles(therm_integral, state->ngtc);
+ scopy_rvecs(x, state->natoms);
+ scopy_rvecs(v, state->natoms);
+ scopy_rvecs(sd_X, state->natoms);
+ copy_ints(&(state->fep_state), &(state_local->fep_state), 1);
+ scopy_reals(lambda, efptNR);
+}
+
+static void scale_velocities(t_state *state, real fac)
+{
+ int i;
+
+ if (state->v)
+ {
+ for (i = 0; i < state->natoms; i++)
+ {
+ svmul(fac, state->v[i], state->v[i]);
+ }
+ }
+}
+
+static void pd_collect_state(const t_commrec *cr, t_state *state)
+{
+ int shift;
+
+ if (debug)
+ {
+ fprintf(debug, "Collecting state before exchange\n");
+ }
+ shift = cr->nnodes - cr->npmenodes - 1;
+ move_rvecs(cr, FALSE, FALSE, GMX_LEFT, GMX_RIGHT, state->x, NULL, shift, NULL);
+ if (state->v)
+ {
+ move_rvecs(cr, FALSE, FALSE, GMX_LEFT, GMX_RIGHT, state->v, NULL, shift, NULL);
+ }
+ if (state->sd_X)
+ {
+ move_rvecs(cr, FALSE, FALSE, GMX_LEFT, GMX_RIGHT, state->sd_X, NULL, shift, NULL);
+ }
+}
+
+static void print_transition_matrix(FILE *fplog, const char *leg, int n, int **nmoves, int *nattempt)
+{
+ int i, j, ntot;
+ float Tprint;
+
+ ntot = nattempt[0] + nattempt[1];
+ fprintf(fplog, "\n");
+ fprintf(fplog, "Repl");
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fplog, " "); /* put the title closer to the center */
+ }
+ fprintf(fplog, "Empirical Transition Matrix\n");
+
+ fprintf(fplog, "Repl");
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fplog, "%8d", (i+1));
+ }
+ fprintf(fplog, "\n");
+
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fplog, "Repl");
+ for (j = 0; j < n; j++)
+ {
+ Tprint = 0.0;
+ if (nmoves[i][j] > 0)
+ {
+ Tprint = nmoves[i][j]/(2.0*ntot);
+ }
+ fprintf(fplog, "%8.4f", Tprint);
+ }
+ fprintf(fplog, "%3d\n", i);
+ }
+}
+
+static void print_ind(FILE *fplog, const char *leg, int n, int *ind, gmx_bool *bEx)
+{
+ int i;
+
+ fprintf(fplog, "Repl %2s %2d", leg, ind[0]);
+ for (i = 1; i < n; i++)
+ {
+ fprintf(fplog, " %c %2d", (bEx != 0 && bEx[i]) ? 'x' : ' ', ind[i]);
+ }
+ fprintf(fplog, "\n");
+}
+
+static void print_allswitchind(FILE *fplog, int n, int *ind, int *pind, int *allswaps, int *tmpswap)
+{
+ int i;
+
+ for (i = 0; i < n; i++)
+ {
+ tmpswap[i] = allswaps[i];
+ }
+ for (i = 0; i < n; i++)
+ {
+ allswaps[i] = tmpswap[pind[i]];
+ }
+
+ fprintf(fplog, "\nAccepted Exchanges: ");
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fplog, "%d ", pind[i]);
+ }
+ fprintf(fplog, "\n");
+
+ /* the "Order After Exchange" is the state label corresponding to the configuration that
+ started in state listed in order, i.e.
+
+ 3 0 1 2
+
+ means that the:
+ configuration starting in simulation 3 is now in simulation 0,
+ configuration starting in simulation 0 is now in simulation 1,
+ configuration starting in simulation 1 is now in simulation 2,
+ configuration starting in simulation 2 is now in simulation 3
+ */
+ fprintf(fplog, "Order After Exchange: ");
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fplog, "%d ", allswaps[i]);
+ }
+ fprintf(fplog, "\n\n");
+}
+
+static void print_prob(FILE *fplog, const char *leg, int n, real *prob)
+{
+ int i;
+ char buf[8];
+
+ fprintf(fplog, "Repl %2s ", leg);
+ for (i = 1; i < n; i++)
+ {
+ if (prob[i] >= 0)
+ {
+ sprintf(buf, "%4.2f", prob[i]);
+ fprintf(fplog, " %3s", buf[0] == '1' ? "1.0" : buf+1);
+ }
+ else
+ {
+ fprintf(fplog, " ");
+ }
+ }
+ fprintf(fplog, "\n");
+}
+
+static void print_count(FILE *fplog, const char *leg, int n, int *count)
+{
+ int i;
+
+ fprintf(fplog, "Repl %2s ", leg);
+ for (i = 1; i < n; i++)
+ {
+ fprintf(fplog, " %4d", count[i]);
+ }
+ fprintf(fplog, "\n");
+}
+
+static real calc_delta(FILE *fplog, gmx_bool bPrint, struct gmx_repl_ex *re, int a, int b, int ap, int bp)
+{
+
+ real ediff, dpV, delta = 0;
+ real *Epot = re->Epot;
+ real *Vol = re->Vol;
+ real **de = re->de;
+ real *beta = re->beta;
+
+ /* Two cases; we are permuted and not. In all cases, setting ap = a and bp = b will reduce
+ to the non permuted case */
+
+ switch (re->type)
+ {
+ case ereTEMP:
+ /*
+ * Okabe et. al. Chem. Phys. Lett. 335 (2001) 435-439
+ */
+ ediff = Epot[b] - Epot[a];
+ delta = -(beta[bp] - beta[ap])*ediff;
+ break;
+ case ereLAMBDA:
+ /* two cases: when we are permuted, and not. */
+ /* non-permuted:
+ ediff = E_new - E_old
+ = [H_b(x_a) + H_a(x_b)] - [H_b(x_b) + H_a(x_a)]
+ = [H_b(x_a) - H_a(x_a)] + [H_a(x_b) - H_b(x_b)]
+ = de[b][a] + de[a][b] */
+
+ /* permuted:
+ ediff = E_new - E_old
+ = [H_bp(x_a) + H_ap(x_b)] - [H_bp(x_b) + H_ap(x_a)]
+ = [H_bp(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_bp(x_b)]
+ = [H_bp(x_a) - H_a(x_a) + H_a(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_b(x_b) + H_b(x_b) - H_bp(x_b)]
+ = [H_bp(x_a) - H_a(x_a)] - [H_ap(x_a) - H_a(x_a)] + [H_ap(x_b) - H_b(x_b)] - H_bp(x_b) - H_b(x_b)]
+ = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]) */
+ /* but, in the current code implementation, we flip configurations, not indices . . .
+ So let's examine that.
+ = [H_b(x_ap) - H_a(x_a)] - [H_a(x_ap) - H_a(x_a)] + [H_a(x_bp) - H_b(x_b)] - H_b(x_bp) - H_b(x_b)]
+ = [H_b(x_ap) - H_a(x_ap)] + [H_a(x_bp) - H_b(x_pb)]
+ = (de[b][ap] - de[a][ap]) + (de[a][bp] - de[b][bp]
+ So, if we exchange b<=> bp and a<=> ap, we return to the same result.
+ So the simple solution is to flip the
+ position of perturbed and original indices in the tests.
+ */
+
+ ediff = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]);
+ delta = ediff*beta[a]; /* assume all same temperature in this case */
+ break;
+ case ereTL:
+ /* not permuted: */
+ /* delta = reduced E_new - reduced E_old
+ = [beta_b H_b(x_a) + beta_a H_a(x_b)] - [beta_b H_b(x_b) + beta_a H_a(x_a)]
+ = [beta_b H_b(x_a) - beta_a H_a(x_a)] + [beta_a H_a(x_b) - beta_b H_b(x_b)]
+ = [beta_b dH_b(x_a) + beta_b H_a(x_a) - beta_a H_a(x_a)] +
+ [beta_a dH_a(x_b) + beta_a H_b(x_b) - beta_b H_b(x_b)]
+ = [beta_b dH_b(x_a) + [beta_a dH_a(x_b) +
+ beta_b (H_a(x_a) - H_b(x_b)]) - beta_a (H_a(x_a) - H_b(x_b))
+ = beta_b dH_b(x_a) + beta_a dH_a(x_b) - (beta_b - beta_a)(H_b(x_b) - H_a(x_a) */
+ /* delta = beta[b]*de[b][a] + beta[a]*de[a][b] - (beta[b] - beta[a])*(Epot[b] - Epot[a]; */
+ /* permuted (big breath!) */
+ /* delta = reduced E_new - reduced E_old
+ = [beta_bp H_bp(x_a) + beta_ap H_ap(x_b)] - [beta_bp H_bp(x_b) + beta_ap H_ap(x_a)]
+ = [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
+ = [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
+ - beta_pb H_a(x_a) + beta_ap H_a(x_a) + beta_pb H_a(x_a) - beta_ap H_a(x_a)
+ - beta_ap H_b(x_b) + beta_bp H_b(x_b) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
+ = [(beta_bp H_bp(x_a) - beta_bp H_a(x_a)) - (beta_ap H_ap(x_a) - beta_ap H_a(x_a))] +
+ [(beta_ap H_ap(x_b) - beta_ap H_b(x_b)) - (beta_bp H_bp(x_b) - beta_bp H_b(x_b))]
+ + beta_pb H_a(x_a) - beta_ap H_a(x_a) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
+ = [beta_bp (H_bp(x_a) - H_a(x_a)) - beta_ap (H_ap(x_a) - H_a(x_a))] +
+ [beta_ap (H_ap(x_b) - H_b(x_b)) - beta_bp (H_bp(x_b) - H_b(x_b))]
+ + beta_pb (H_a(x_a) - H_b(x_b)) - beta_ap (H_a(x_a) - H_b(x_b))
+ = ([beta_bp de[bp][a] - beta_ap de[ap][a]) + beta_ap de[ap][b] - beta_bp de[bp][b])
+ + (beta_pb-beta_ap)(H_a(x_a) - H_b(x_b)) */
+ delta = beta[bp]*(de[bp][a] - de[bp][b]) + beta[ap]*(de[ap][b] - de[ap][a]) - (beta[bp]-beta[ap])*(Epot[b]-Epot[a]);
+ break;
+ default:
+ gmx_incons("Unknown replica exchange quantity");
+ }
+ if (bPrint)
+ {
+ fprintf(fplog, "Repl %d <-> %d dE_term = %10.3e (kT)\n", a, b, delta);
+ }
+ if (re->bNPT)
+ {
+ /* revist the calculation for 5.0. Might be some improvements. */
+ dpV = (beta[ap]*re->pres[ap]-beta[bp]*re->pres[bp])*(Vol[b]-Vol[a])/PRESFAC;
+ if (bPrint)
+ {
+ fprintf(fplog, " dpV = %10.3e d = %10.3e\nb", dpV, delta + dpV);
+ }
+ delta += dpV;
+ }
+ return delta;
+}
+
+static void
+test_for_replica_exchange(FILE *fplog,
+ const gmx_multisim_t *ms,
+ struct gmx_repl_ex *re,
+ gmx_enerdata_t *enerd,
+ real vol,
+ gmx_large_int_t step,
+ real time)
+{
+ int m, i, j, a, b, ap, bp, i0, i1, tmp;
+ real ediff = 0, delta = 0, dpV = 0;
+ gmx_bool bPrint, bMultiEx;
+ gmx_bool *bEx = re->bEx;
+ real *prob = re->prob;
+ int *pind = re->destinations; /* permuted index */
+ gmx_bool bEpot = FALSE;
+ gmx_bool bDLambda = FALSE;
+ gmx_bool bVol = FALSE;
+
+ bMultiEx = (re->nex > 1); /* multiple exchanges at each state */
+ fprintf(fplog, "Replica exchange at step " gmx_large_int_pfmt " time %g\n", step, time);
+
+ if (re->bNPT)
+ {
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->Vol[i] = 0;
+ }
+ bVol = TRUE;
+ re->Vol[re->repl] = vol;
+ }
+ if ((re->type == ereTEMP || re->type == ereTL))
+ {
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->Epot[i] = 0;
+ }
+ bEpot = TRUE;
+ re->Epot[re->repl] = enerd->term[F_EPOT];
+ /* temperatures of different states*/
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->beta[i] = 1.0/(re->q[ereTEMP][i]*BOLTZ);
+ }
+ }
+ else
+ {
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->beta[i] = 1.0/(re->temp*BOLTZ); /* we have a single temperature */
+ }
+ }
+ if (re->type == ereLAMBDA || re->type == ereTL)
+ {
+ bDLambda = TRUE;
+ /* lambda differences. */
+ /* de[i][j] is the energy of the jth simulation in the ith Hamiltonian
+ minus the energy of the jth simulation in the jth Hamiltonian */
+ for (i = 0; i < re->nrepl; i++)
+ {
+ for (j = 0; j < re->nrepl; j++)
+ {
+ re->de[i][j] = 0;
+ }
+ }
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->de[i][re->repl] = (enerd->enerpart_lambda[(int)re->q[ereLAMBDA][i]+1]-enerd->enerpart_lambda[0]);
+ }
+ }
+
+ /* now actually do the communication */
+ if (bVol)
+ {
+ gmx_sum_sim(re->nrepl, re->Vol, ms);
+ }
+ if (bEpot)
+ {
+ gmx_sum_sim(re->nrepl, re->Epot, ms);
+ }
+ if (bDLambda)
+ {
+ for (i = 0; i < re->nrepl; i++)
+ {
+ gmx_sum_sim(re->nrepl, re->de[i], ms);
+ }
+ }
+
+ /* make a duplicate set of indices for shuffling */
+ for (i = 0; i < re->nrepl; i++)
+ {
+ pind[i] = re->ind[i];
+ }
+
+ /* PLUMED */
+ int plumed_test_exchange_pattern=0;
+ /* END PLUMED */
+
+ if (bMultiEx)
+ {
+ /* multiple random switch exchange */
+ for (i = 0; i < re->nex; i++)
+ {
+ /* randomly select a pair */
+ /* in theory, could reduce this by identifying only which switches had a nonneglibible
+ probability of occurring (log p > -100) and only operate on those switches */
+ /* find out which state it is from, and what label that state currently has. Likely
+ more work that useful. */
+ i0 = (int)(re->nrepl*rando(&(re->seed)));
+ i1 = (int)(re->nrepl*rando(&(re->seed)));
+ if (i0 == i1)
+ {
+ i--;
+ continue; /* self-exchange, back up and do it again */
+ }
+
+ a = re->ind[i0]; /* what are the indices of these states? */
+ b = re->ind[i1];
+ ap = pind[i0];
+ bp = pind[i1];
+
+ bPrint = FALSE; /* too noisy */
+ /* calculate the energy difference */
+ /* if the code changes to flip the STATES, rather than the configurations,
+ use the commented version of the code */
+ /* delta = calc_delta(fplog,bPrint,re,a,b,ap,bp); */
+ delta = calc_delta(fplog, bPrint, re, ap, bp, a, b);
+
+ /* we actually only use the first space in the prob and bEx array,
+ since there are actually many switches between pairs. */
+
+ if (delta <= 0)
+ {
+ /* accepted */
+ prob[0] = 1;
+ bEx[0] = TRUE;
+ }
+ else
+ {
+ if (delta > PROBABILITYCUTOFF)
+ {
+ prob[0] = 0;
+ }
+ else
+ {
+ prob[0] = exp(-delta);
+ }
+ /* roll a number to determine if accepted */
+ bEx[0] = (rando(&(re->seed)) < prob[0]);
+ }
+ re->prob_sum[0] += prob[0];
+
+ if (bEx[0])
+ {
+ /* swap the states */
+ tmp = pind[i0];
+ pind[i0] = pind[i1];
+ pind[i1] = tmp;
+ }
+ }
+ re->nattempt[0]++; /* keep track of total permutation trials here */
+ print_allswitchind(fplog, re->nrepl, re->ind, pind, re->allswaps, re->tmpswap);
+ }
+ else
+ {
+ /* standard nearest neighbor replica exchange */
+ m = (step / re->nst) % 2;
+ /* PLUMED */
+ if(plumedswitch){
+ int partner=re->repl;
+ plumed_cmd(plumedmain,"getExchangesFlag",&plumed_test_exchange_pattern);
+ if(plumed_test_exchange_pattern>0){
+ int *list;
+ snew(list,re->nrepl);
+ plumed_cmd(plumedmain,"setNumberOfReplicas",&(re->nrepl));
+ plumed_cmd(plumedmain,"getExchangesList",list);
+ for(i=0; i<re->nrepl; i++) re->ind[i]=list[i];
+ sfree(list);
+ }
+
+ for(i=1; i<re->nrepl; i++) {
+ if (i % 2 != m) continue;
+ a = re->ind[i-1];
+ b = re->ind[i];
+ if(re->repl==a) partner=b;
+ if(re->repl==b) partner=a;
+ }
+ plumed_cmd(plumedmain,"GREX setPartner",&partner);
+ plumed_cmd(plumedmain,"GREX calculate",NULL);
+ plumed_cmd(plumedmain,"GREX shareAllDeltaBias",NULL);
+ }
+ /* END PLUMED */
+ for (i = 1; i < re->nrepl; i++)
+ {
+ a = re->ind[i-1];
+ b = re->ind[i];
+
+ bPrint = (re->repl == a || re->repl == b);
+ if (i % 2 == m)
+ {
+ delta = calc_delta(fplog, bPrint, re, a, b, a, b);
+ /* PLUMED */
+ if(plumedswitch){
+ real adb,bdb,dplumed;
+ char buf[300];
+ sprintf(buf,"GREX getDeltaBias %d",a); plumed_cmd(plumedmain,buf,&adb);
+ sprintf(buf,"GREX getDeltaBias %d",b); plumed_cmd(plumedmain,buf,&bdb);
+ dplumed=adb*re->beta[a]+bdb*re->beta[b];
+ delta+=dplumed;
+ if (bPrint)
+ fprintf(fplog,"dplumed = %10.3e dE_Term = %10.3e (kT)\n",dplumed,delta);
+ }
+ /* END PLUMED */
+ if (delta <= 0)
+ {
+ /* accepted */
+ prob[i] = 1;
+ bEx[i] = TRUE;
+ }
+ else
+ {
+ if (delta > PROBABILITYCUTOFF)
+ {
+ prob[i] = 0;
+ }
+ else
+ {
+ prob[i] = exp(-delta);
+ }
+ /* roll a number to determine if accepted */
+ bEx[i] = (rando(&(re->seed)) < prob[i]);
+ }
+ re->prob_sum[i] += prob[i];
+
+ if (bEx[i])
+ {
+ /* PLUMED */
+ if(!plumed_test_exchange_pattern) {
+ /* standard neighbour swapping */
+ /* swap these two */
+ tmp = pind[i-1];
+ pind[i-1] = pind[i];
+ pind[i] = tmp;
+ re->nexchange[i]++; /* statistics for back compatibility */
+ } else {
+ /* alternative swapping patterns */
+ tmp = pind[a];
+ pind[a] = pind[b];
+ pind[b] = tmp;
+ re->nexchange[i]++; /* statistics for back compatibility */
+ }
+ /* END PLUMED */
+ }
+ }
+ else
+ {
+ prob[i] = -1;
+ bEx[i] = FALSE;
+ }
+ }
+ /* print some statistics */
+ print_ind(fplog, "ex", re->nrepl, re->ind, bEx);
+ print_prob(fplog, "pr", re->nrepl, prob);
+ fprintf(fplog, "\n");
+ re->nattempt[m]++;
+ }
+
+ /* PLUMED */
+ if(plumed_test_exchange_pattern>0) {
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->ind[i] = i;
+ }
+ }
+ /* END PLUMED */
+
+ /* record which moves were made and accepted */
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->nmoves[re->ind[i]][pind[i]] += 1;
+ re->nmoves[pind[i]][re->ind[i]] += 1;
+ }
+ fflush(fplog); /* make sure we can see what the last exchange was */
+}
+
+static void write_debug_x(t_state *state)
+{
+ int i;
+
+ if (debug)
+ {
+ for (i = 0; i < state->natoms; i += 10)
+ {
+ fprintf(debug, "dx %5d %10.5f %10.5f %10.5f\n", i, state->x[i][XX], state->x[i][YY], state->x[i][ZZ]);
+ }
+ }
+}
+
+static void
+cyclic_decomposition(FILE *fplog,
+ const int *destinations,
+ int **cyclic,
+ gmx_bool *incycle,
+ const int nrepl,
+ int *nswap)
+{
+
+ int i, j, c, p;
+ int maxlen = 1;
+ for (i = 0; i < nrepl; i++)
+ {
+ incycle[i] = FALSE;
+ }
+ for (i = 0; i < nrepl; i++) /* one cycle for each replica */
+ {
+ if (incycle[i])
+ {
+ cyclic[i][0] = -1;
+ continue;
+ }
+ cyclic[i][0] = i;
+ incycle[i] = TRUE;
+ c = 1;
+ p = i;
+ for (j = 0; j < nrepl; j++) /* potentially all cycles are part, but we will break first */
+ {
+ p = destinations[p]; /* start permuting */
+ if (p == i)
+ {
+ cyclic[i][c] = -1;
+ if (c > maxlen)
+ {
+ maxlen = c;
+ }
+ break; /* we've reached the original element, the cycle is complete, and we marked the end. */
+ }
+ else
+ {
+ cyclic[i][c] = p; /* each permutation gives a new member of the cycle */
+ incycle[p] = TRUE;
+ c++;
+ }
+ }
+ }
+ *nswap = maxlen - 1;
+
+ if (debug)
+ {
+ for (i = 0; i < nrepl; i++)
+ {
+ fprintf(debug, "Cycle %d:", i);
+ for (j = 0; j < nrepl; j++)
+ {
+ if (cyclic[i][j] < 0)
+ {
+ break;
+ }
+ fprintf(debug, "%2d", cyclic[i][j]);
+ }
+ fprintf(debug, "\n");
+ }
+ fflush(debug);
+ }
+}
+
+static void
+compute_exchange_order(FILE *fplog,
+ int **cyclic,
+ int **order,
+ const int nrepl,
+ const int maxswap)
+{
+ int i, j;
+
+ for (j = 0; j < maxswap; j++)
+ {
+ for (i = 0; i < nrepl; i++)
+ {
+ if (cyclic[i][j+1] >= 0)
+ {
+ order[cyclic[i][j+1]][j] = cyclic[i][j];
+ order[cyclic[i][j]][j] = cyclic[i][j+1];
+ }
+ }
+ for (i = 0; i < nrepl; i++)
+ {
+ if (order[i][j] < 0)
+ {
+ order[i][j] = i; /* if it's not exchanging, it should stay this round*/
+ }
+ }
+ }
+
+ if (debug)
+ {
+ fprintf(fplog, "Replica Exchange Order\n");
+ for (i = 0; i < nrepl; i++)
+ {
+ fprintf(fplog, "Replica %d:", i);
+ for (j = 0; j < maxswap; j++)
+ {
+ if (order[i][j] < 0)
+ {
+ break;
+ }
+ fprintf(debug, "%2d", order[i][j]);
+ }
+ fprintf(fplog, "\n");
+ }
+ fflush(fplog);
+ }
+}
+
+static void
+prepare_to_do_exchange(FILE *fplog,
+ const int *destinations,
+ const int replica_id,
+ const int nrepl,
+ int *maxswap,
+ int **order,
+ int **cyclic,
+ int *incycle,
+ gmx_bool *bThisReplicaExchanged)
+{
+ int i, j;
+ /* Hold the cyclic decomposition of the (multiple) replica
+ * exchange. */
+ gmx_bool bAnyReplicaExchanged = FALSE;
+ *bThisReplicaExchanged = FALSE;
+
+ for (i = 0; i < nrepl; i++)
+ {
+ if (destinations[i] != i)
+ {
+ /* only mark as exchanged if the index has been shuffled */
+ bAnyReplicaExchanged = TRUE;
+ break;
+ }
+ }
+ if (bAnyReplicaExchanged)
+ {
+ /* reinitialize the placeholder arrays */
+ for (i = 0; i < nrepl; i++)
+ {
+ for (j = 0; j < nrepl; j++)
+ {
+ cyclic[i][j] = -1;
+ order[i][j] = -1;
+ }
+ }
+
+ /* Identify the cyclic decomposition of the permutation (very
+ * fast if neighbor replica exchange). */
+ cyclic_decomposition(fplog, destinations, cyclic, incycle, nrepl, maxswap);
+
+ /* Now translate the decomposition into a replica exchange
+ * order at each step. */
+ compute_exchange_order(fplog, cyclic, order, nrepl, *maxswap);
+
+ /* Did this replica do any exchange at any point? */
+ for (j = 0; j < *maxswap; j++)
+ {
+ if (replica_id != order[replica_id][j])
+ {
+ *bThisReplicaExchanged = TRUE;
+ break;
+ }
+ }
+ }
+}
+
+gmx_bool replica_exchange(FILE *fplog, const t_commrec *cr, struct gmx_repl_ex *re,
+ t_state *state, gmx_enerdata_t *enerd,
+ t_state *state_local, gmx_large_int_t step, real time)
+{
+ int i, j;
+ int replica_id = 0;
+ int exchange_partner;
+ int maxswap = 0;
+ /* Number of rounds of exchanges needed to deal with any multiple
+ * exchanges. */
+ /* Where each replica ends up after the exchange attempt(s). */
+ /* The order in which multiple exchanges will occur. */
+ gmx_bool bThisReplicaExchanged = FALSE;
+
+ /* PLUMED */
+ if(plumedswitch)plumed_cmd(plumedmain,"GREX prepare",NULL);
+ /* END PLUMED */
+
+ if (MASTER(cr))
+ {
+ replica_id = re->repl;
+ test_for_replica_exchange(fplog, cr->ms, re, enerd, det(state_local->box), step, time);
+ prepare_to_do_exchange(fplog, re->destinations, replica_id, re->nrepl, &maxswap,
+ re->order, re->cyclic, re->incycle, &bThisReplicaExchanged);
+ }
+ /* Do intra-simulation broadcast so all processors belonging to
+ * each simulation know whether they need to participate in
+ * collecting the state. Otherwise, they might as well get on with
+ * the next thing to do. */
+ if (PAR(cr))
+ {
+#ifdef GMX_MPI
+ MPI_Bcast(&bThisReplicaExchanged, sizeof(gmx_bool), MPI_BYTE, MASTERRANK(cr),
+ cr->mpi_comm_mygroup);
+#endif
+ }
+
+ if (bThisReplicaExchanged)
+ {
+ /* Exchange the states */
+
+ if (PAR(cr))
+ {
+ /* Collect the global state on the master node */
+ if (DOMAINDECOMP(cr))
+ {
+ dd_collect_state(cr->dd, state_local, state);
+ }
+ else
+ {
+ pd_collect_state(cr, state);
+ }
+ }
+
+ if (MASTER(cr))
+ {
+ /* There will be only one swap cycle with standard replica
+ * exchange, but there may be multiple swap cycles if we
+ * allow multiple swaps. */
+
+ for (j = 0; j < maxswap; j++)
+ {
+ exchange_partner = re->order[replica_id][j];
+
+ if (exchange_partner != replica_id)
+ {
+ /* Exchange the global states between the master nodes */
+ //if (debug)
+ //{
+ fprintf(fplog, "Exchanging %d with %d\n", replica_id, exchange_partner);
+ //}
+ exchange_state(cr->ms, exchange_partner, state);
+ }
+ }
+ /* For temperature-type replica exchange, we need to scale
+ * the velocities. */
+ if (re->type == ereTEMP || re->type == ereTL)
+ {
+ scale_velocities(state, sqrt(re->q[ereTEMP][replica_id]/re->q[ereTEMP][re->destinations[replica_id]]));
+ }
+
+ }
+
+ /* With domain decomposition the global state is distributed later */
+ if (!DOMAINDECOMP(cr))
+ {
+ /* Copy the global state to the local state data structure */
+ copy_state_nonatomdata(state, state_local);
+
+ if (PAR(cr))
+ {
+ bcast_state(cr, state, FALSE);
+ }
+ }
+ }
+
+ return bThisReplicaExchanged;
+}
+
+void print_replica_exchange_statistics(FILE *fplog, struct gmx_repl_ex *re)
+{
+ int i;
+
+ fprintf(fplog, "\nReplica exchange statistics\n");
+
+ if (re->nex == 0)
+ {
+ fprintf(fplog, "Repl %d attempts, %d odd, %d even\n",
+ re->nattempt[0]+re->nattempt[1], re->nattempt[1], re->nattempt[0]);
+
+ fprintf(fplog, "Repl average probabilities:\n");
+ for (i = 1; i < re->nrepl; i++)
+ {
+ if (re->nattempt[i%2] == 0)
+ {
+ re->prob[i] = 0;
+ }
+ else
+ {
+ re->prob[i] = re->prob_sum[i]/re->nattempt[i%2];
+ }
+ }
+ print_ind(fplog, "", re->nrepl, re->ind, NULL);
+ print_prob(fplog, "", re->nrepl, re->prob);
+
+ fprintf(fplog, "Repl number of exchanges:\n");
+ print_ind(fplog, "", re->nrepl, re->ind, NULL);
+ print_count(fplog, "", re->nrepl, re->nexchange);
+
+ fprintf(fplog, "Repl average number of exchanges:\n");
+ for (i = 1; i < re->nrepl; i++)
+ {
+ if (re->nattempt[i%2] == 0)
+ {
+ re->prob[i] = 0;
+ }
+ else
+ {
+ re->prob[i] = ((real)re->nexchange[i])/re->nattempt[i%2];
+ }
+ }
+ print_ind(fplog, "", re->nrepl, re->ind, NULL);
+ print_prob(fplog, "", re->nrepl, re->prob);
+
+ fprintf(fplog, "\n");
+ }
+ /* print the transition matrix */
+ print_transition_matrix(fplog, "", re->nrepl, re->nmoves, re->nattempt);
+}
diff --git a/patches/gromacs-4.6.3.diff/src/kernel/repl_ex.c.preplumed b/patches/gromacs-4.6.3.diff/src/kernel/repl_ex.c.preplumed
new file mode 100644
index 0000000000000000000000000000000000000000..60cd71848a783e2395493ef9bd3b75d3fdfd9a95
--- /dev/null
+++ b/patches/gromacs-4.6.3.diff/src/kernel/repl_ex.c.preplumed
@@ -0,0 +1,1441 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, Erik Lindahl, and including many
+ * others, as listed in the AUTHORS file in the top-level source
+ * directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include "repl_ex.h"
+#include "network.h"
+#include "random.h"
+#include "smalloc.h"
+#include "physics.h"
+#include "copyrite.h"
+#include "macros.h"
+#include "vec.h"
+#include "names.h"
+#include "mvdata.h"
+#include "domdec.h"
+#include "partdec.h"
+
+#define PROBABILITYCUTOFF 100
+/* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
+
+enum {
+ ereTEMP, ereLAMBDA, ereENDSINGLE, ereTL, ereNR
+};
+const char *erename[ereNR] = { "temperature", "lambda", "end_single_marker", "temperature and lambda"};
+/* end_single_marker merely notes the end of single variable replica exchange. All types higher than
+ it are multiple replica exchange methods */
+/* Eventually, should add 'pressure', 'temperature and pressure', 'lambda_and_pressure', 'temperature_lambda_pressure'?;
+ Let's wait until we feel better about the pressure control methods giving exact ensembles. Right now, we assume constant pressure */
+
+typedef struct gmx_repl_ex
+{
+ int repl;
+ int nrepl;
+ real temp;
+ int type;
+ real **q;
+ gmx_bool bNPT;
+ real *pres;
+ int *ind;
+ int *allswaps;
+ int nst;
+ int nex;
+ int seed;
+ int nattempt[2];
+ real *prob_sum;
+ int **nmoves;
+ int *nexchange;
+
+ /* these are helper arrays for replica exchange; allocated here so they
+ don't have to be allocated each time */
+ int *destinations;
+ int **cyclic;
+ int **order;
+ int *tmpswap;
+ gmx_bool *incycle;
+ gmx_bool *bEx;
+
+ /* helper arrays to hold the quantities that are exchanged */
+ real *prob;
+ real *Epot;
+ real *beta;
+ real *Vol;
+ real **de;
+
+} t_gmx_repl_ex;
+
+static gmx_bool repl_quantity(FILE *fplog, const gmx_multisim_t *ms,
+ struct gmx_repl_ex *re, int ere, real q)
+{
+ real *qall;
+ gmx_bool bDiff;
+ int i, s;
+
+ snew(qall, ms->nsim);
+ qall[re->repl] = q;
+ gmx_sum_sim(ms->nsim, qall, ms);
+
+ bDiff = FALSE;
+ for (s = 1; s < ms->nsim; s++)
+ {
+ if (qall[s] != qall[0])
+ {
+ bDiff = TRUE;
+ }
+ }
+
+ if (bDiff)
+ {
+ /* Set the replica exchange type and quantities */
+ re->type = ere;
+
+ snew(re->q[ere], re->nrepl);
+ for (s = 0; s < ms->nsim; s++)
+ {
+ re->q[ere][s] = qall[s];
+ }
+ }
+ sfree(qall);
+ return bDiff;
+}
+
+gmx_repl_ex_t init_replica_exchange(FILE *fplog,
+ const gmx_multisim_t *ms,
+ const t_state *state,
+ const t_inputrec *ir,
+ int nst, int nex, int init_seed)
+{
+ real temp, pres;
+ int i, j, k;
+ struct gmx_repl_ex *re;
+ gmx_bool bTemp;
+ gmx_bool bLambda = FALSE;
+
+ fprintf(fplog, "\nInitializing Replica Exchange\n");
+
+ if (ms == NULL || ms->nsim == 1)
+ {
+ gmx_fatal(FARGS, "Nothing to exchange with only one replica, maybe you forgot to set the -multi option of mdrun?");
+ }
+
+ snew(re, 1);
+
+ re->repl = ms->sim;
+ re->nrepl = ms->nsim;
+ snew(re->q, ereENDSINGLE);
+
+ fprintf(fplog, "Repl There are %d replicas:\n", re->nrepl);
+
+ check_multi_int(fplog, ms, state->natoms, "the number of atoms", FALSE);
+ check_multi_int(fplog, ms, ir->eI, "the integrator", FALSE);
+ check_multi_large_int(fplog, ms, ir->init_step+ir->nsteps, "init_step+nsteps", FALSE);
+ check_multi_large_int(fplog, ms, (ir->init_step+nst-1)/nst,
+ "first exchange step: init_step/-replex", FALSE);
+ check_multi_int(fplog, ms, ir->etc, "the temperature coupling", FALSE);
+ check_multi_int(fplog, ms, ir->opts.ngtc,
+ "the number of temperature coupling groups", FALSE);
+ check_multi_int(fplog, ms, ir->epc, "the pressure coupling", FALSE);
+ check_multi_int(fplog, ms, ir->efep, "free energy", FALSE);
+ check_multi_int(fplog, ms, ir->fepvals->n_lambda, "number of lambda states", FALSE);
+
+ re->temp = ir->opts.ref_t[0];
+ for (i = 1; (i < ir->opts.ngtc); i++)
+ {
+ if (ir->opts.ref_t[i] != re->temp)
+ {
+ fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
+ fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
+ }
+ }
+
+ re->type = -1;
+ bTemp = repl_quantity(fplog, ms, re, ereTEMP, re->temp);
+ if (ir->efep != efepNO)
+ {
+ bLambda = repl_quantity(fplog, ms, re, ereLAMBDA, (real)ir->fepvals->init_fep_state);
+ }
+ if (re->type == -1) /* nothing was assigned */
+ {
+ gmx_fatal(FARGS, "The properties of the %d systems are all the same, there is nothing to exchange", re->nrepl);
+ }
+ if (bLambda && bTemp)
+ {
+ re->type = ereTL;
+ }
+
+ if (bTemp)
+ {
+ please_cite(fplog, "Sugita1999a");
+ if (ir->epc != epcNO)
+ {
+ re->bNPT = TRUE;
+ fprintf(fplog, "Repl Using Constant Pressure REMD.\n");
+ please_cite(fplog, "Okabe2001a");
+ }
+ if (ir->etc == etcBERENDSEN)
+ {
+ gmx_fatal(FARGS, "REMD with the %s thermostat does not produce correct potential energy distributions, consider using the %s thermostat instead",
+ ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
+ }
+ }
+ if (bLambda)
+ {
+ if (ir->fepvals->delta_lambda != 0) /* check this? */
+ {
+ gmx_fatal(FARGS, "delta_lambda is not zero");
+ }
+ }
+ if (re->bNPT)
+ {
+ snew(re->pres, re->nrepl);
+ if (ir->epct == epctSURFACETENSION)
+ {
+ pres = ir->ref_p[ZZ][ZZ];
+ }
+ else
+ {
+ pres = 0;
+ j = 0;
+ for (i = 0; i < DIM; i++)
+ {
+ if (ir->compress[i][i] != 0)
+ {
+ pres += ir->ref_p[i][i];
+ j++;
+ }
+ }
+ pres /= j;
+ }
+ re->pres[re->repl] = pres;
+ gmx_sum_sim(re->nrepl, re->pres, ms);
+ }
+
+ /* Make an index for increasing replica order */
+ /* only makes sense if one or the other is varying, not both!
+ if both are varying, we trust the order the person gave. */
+ snew(re->ind, re->nrepl);
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->ind[i] = i;
+ }
+
+ if (re->type < ereENDSINGLE)
+ {
+
+ for (i = 0; i < re->nrepl; i++)
+ {
+ for (j = i+1; j < re->nrepl; j++)
+ {
+ if (re->q[re->type][re->ind[j]] < re->q[re->type][re->ind[i]])
+ {
+ k = re->ind[i];
+ re->ind[i] = re->ind[j];
+ re->ind[j] = k;
+ }
+ else if (re->q[re->type][re->ind[j]] == re->q[re->type][re->ind[i]])
+ {
+ gmx_fatal(FARGS, "Two replicas have identical %ss", erename[re->type]);
+ }
+ }
+ }
+ }
+
+ /* keep track of all the swaps, starting with the initial placement. */
+ snew(re->allswaps, re->nrepl);
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->allswaps[i] = re->ind[i];
+ }
+
+ switch (re->type)
+ {
+ case ereTEMP:
+ fprintf(fplog, "\nReplica exchange in temperature\n");
+ for (i = 0; i < re->nrepl; i++)
+ {
+ fprintf(fplog, " %5.1f", re->q[re->type][re->ind[i]]);
+ }
+ fprintf(fplog, "\n");
+ break;
+ case ereLAMBDA:
+ fprintf(fplog, "\nReplica exchange in lambda\n");
+ for (i = 0; i < re->nrepl; i++)
+ {
+ fprintf(fplog, " %3d", (int)re->q[re->type][re->ind[i]]);
+ }
+ fprintf(fplog, "\n");
+ break;
+ case ereTL:
+ fprintf(fplog, "\nReplica exchange in temperature and lambda state\n");
+ for (i = 0; i < re->nrepl; i++)
+ {
+ fprintf(fplog, " %5.1f", re->q[ereTEMP][re->ind[i]]);
+ }
+ fprintf(fplog, "\n");
+ for (i = 0; i < re->nrepl; i++)
+ {
+ fprintf(fplog, " %5d", (int)re->q[ereLAMBDA][re->ind[i]]);
+ }
+ fprintf(fplog, "\n");
+ break;
+ default:
+ gmx_incons("Unknown replica exchange quantity");
+ }
+ if (re->bNPT)
+ {
+ fprintf(fplog, "\nRepl p");
+ for (i = 0; i < re->nrepl; i++)
+ {
+ fprintf(fplog, " %5.2f", re->pres[re->ind[i]]);
+ }
+
+ for (i = 0; i < re->nrepl; i++)
+ {
+ if ((i > 0) && (re->pres[re->ind[i]] < re->pres[re->ind[i-1]]))
+ {
+ fprintf(fplog, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
+ fprintf(stderr, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
+ }
+ }
+ }
+ re->nst = nst;
+ if (init_seed == -1)
+ {
+ if (MASTERSIM(ms))
+ {
+ re->seed = make_seed();
+ }
+ else
+ {
+ re->seed = 0;
+ }
+ gmx_sumi_sim(1, &(re->seed), ms);
+ }
+ else
+ {
+ re->seed = init_seed;
+ }
+ fprintf(fplog, "\nReplica exchange interval: %d\n", re->nst);
+ fprintf(fplog, "\nReplica random seed: %d\n", re->seed);
+
+ re->nattempt[0] = 0;
+ re->nattempt[1] = 0;
+
+ snew(re->prob_sum, re->nrepl);
+ snew(re->nexchange, re->nrepl);
+ snew(re->nmoves, re->nrepl);
+ for (i = 0; i < re->nrepl; i++)
+ {
+ snew(re->nmoves[i], re->nrepl);
+ }
+ fprintf(fplog, "Replica exchange information below: x=exchange, pr=probability\n");
+
+ /* generate space for the helper functions so we don't have to snew each time */
+
+ snew(re->destinations, re->nrepl);
+ snew(re->incycle, re->nrepl);
+ snew(re->tmpswap, re->nrepl);
+ snew(re->cyclic, re->nrepl);
+ snew(re->order, re->nrepl);
+ for (i = 0; i < re->nrepl; i++)
+ {
+ snew(re->cyclic[i], re->nrepl);
+ snew(re->order[i], re->nrepl);
+ }
+ /* allocate space for the functions storing the data for the replicas */
+ /* not all of these arrays needed in all cases, but they don't take
+ up much space, since the max size is nrepl**2 */
+ snew(re->prob, re->nrepl);
+ snew(re->bEx, re->nrepl);
+ snew(re->beta, re->nrepl);
+ snew(re->Vol, re->nrepl);
+ snew(re->Epot, re->nrepl);
+ snew(re->de, re->nrepl);
+ for (i = 0; i < re->nrepl; i++)
+ {
+ snew(re->de[i], re->nrepl);
+ }
+ re->nex = nex;
+ return re;
+}
+
+static void exchange_reals(const gmx_multisim_t *ms, int b, real *v, int n)
+{
+ real *buf;
+ int i;
+
+ if (v)
+ {
+ snew(buf, n);
+#ifdef GMX_MPI
+ /*
+ MPI_Sendrecv(v, n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
+ buf,n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
+ ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+ */
+ {
+ MPI_Request mpi_req;
+
+ MPI_Isend(v, n*sizeof(real), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, &mpi_req);
+ MPI_Recv(buf, n*sizeof(real), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+ MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+ }
+#endif
+ for (i = 0; i < n; i++)
+ {
+ v[i] = buf[i];
+ }
+ sfree(buf);
+ }
+}
+
+
+static void exchange_ints(const gmx_multisim_t *ms, int b, int *v, int n)
+{
+ int *buf;
+ int i;
+
+ if (v)
+ {
+ snew(buf, n);
+#ifdef GMX_MPI
+ /*
+ MPI_Sendrecv(v, n*sizeof(int),MPI_BYTE,MSRANK(ms,b),0,
+ buf,n*sizeof(int),MPI_BYTE,MSRANK(ms,b),0,
+ ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+ */
+ {
+ MPI_Request mpi_req;
+
+ MPI_Isend(v, n*sizeof(int), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, &mpi_req);
+ MPI_Recv(buf, n*sizeof(int), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+ MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+ }
+#endif
+ for (i = 0; i < n; i++)
+ {
+ v[i] = buf[i];
+ }
+ sfree(buf);
+ }
+}
+
+static void exchange_doubles(const gmx_multisim_t *ms, int b, double *v, int n)
+{
+ double *buf;
+ int i;
+
+ if (v)
+ {
+ snew(buf, n);
+#ifdef GMX_MPI
+ /*
+ MPI_Sendrecv(v, n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
+ buf,n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
+ ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+ */
+ {
+ MPI_Request mpi_req;
+
+ MPI_Isend(v, n*sizeof(double), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, &mpi_req);
+ MPI_Recv(buf, n*sizeof(double), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+ MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+ }
+#endif
+ for (i = 0; i < n; i++)
+ {
+ v[i] = buf[i];
+ }
+ sfree(buf);
+ }
+}
+
+static void exchange_rvecs(const gmx_multisim_t *ms, int b, rvec *v, int n)
+{
+ rvec *buf;
+ int i;
+
+ if (v)
+ {
+ snew(buf, n);
+#ifdef GMX_MPI
+ /*
+ MPI_Sendrecv(v[0], n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
+ buf[0],n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
+ ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+ */
+ {
+ MPI_Request mpi_req;
+
+ MPI_Isend(v[0], n*sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, &mpi_req);
+ MPI_Recv(buf[0], n*sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0,
+ ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+ MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+ }
+#endif
+ for (i = 0; i < n; i++)
+ {
+ copy_rvec(buf[i], v[i]);
+ }
+ sfree(buf);
+ }
+}
+
+static void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
+{
+ /* When t_state changes, this code should be updated. */
+ int ngtc, nnhpres;
+ ngtc = state->ngtc * state->nhchainlength;
+ nnhpres = state->nnhpres* state->nhchainlength;
+ exchange_rvecs(ms, b, state->box, DIM);
+ exchange_rvecs(ms, b, state->box_rel, DIM);
+ exchange_rvecs(ms, b, state->boxv, DIM);
+ exchange_reals(ms, b, &(state->veta), 1);
+ exchange_reals(ms, b, &(state->vol0), 1);
+ exchange_rvecs(ms, b, state->svir_prev, DIM);
+ exchange_rvecs(ms, b, state->fvir_prev, DIM);
+ exchange_rvecs(ms, b, state->pres_prev, DIM);
+ exchange_doubles(ms, b, state->nosehoover_xi, ngtc);
+ exchange_doubles(ms, b, state->nosehoover_vxi, ngtc);
+ exchange_doubles(ms, b, state->nhpres_xi, nnhpres);
+ exchange_doubles(ms, b, state->nhpres_vxi, nnhpres);
+ exchange_doubles(ms, b, state->therm_integral, state->ngtc);
+ exchange_rvecs(ms, b, state->x, state->natoms);
+ exchange_rvecs(ms, b, state->v, state->natoms);
+ exchange_rvecs(ms, b, state->sd_X, state->natoms);
+}
+
+static void copy_rvecs(rvec *s, rvec *d, int n)
+{
+ int i;
+
+ if (d != NULL)
+ {
+ for (i = 0; i < n; i++)
+ {
+ copy_rvec(s[i], d[i]);
+ }
+ }
+}
+
+static void copy_doubles(const double *s, double *d, int n)
+{
+ int i;
+
+ if (d != NULL)
+ {
+ for (i = 0; i < n; i++)
+ {
+ d[i] = s[i];
+ }
+ }
+}
+
+static void copy_reals(const real *s, real *d, int n)
+{
+ int i;
+
+ if (d != NULL)
+ {
+ for (i = 0; i < n; i++)
+ {
+ d[i] = s[i];
+ }
+ }
+}
+
+static void copy_ints(const int *s, int *d, int n)
+{
+ int i;
+
+ if (d != NULL)
+ {
+ for (i = 0; i < n; i++)
+ {
+ d[i] = s[i];
+ }
+ }
+}
+
+#define scopy_rvecs(v, n) copy_rvecs(state->v, state_local->v, n);
+#define scopy_doubles(v, n) copy_doubles(state->v, state_local->v, n);
+#define scopy_reals(v, n) copy_reals(state->v, state_local->v, n);
+#define scopy_ints(v, n) copy_ints(state->v, state_local->v, n);
+
+static void copy_state_nonatomdata(t_state *state, t_state *state_local)
+{
+ /* When t_state changes, this code should be updated. */
+ int ngtc, nnhpres;
+ ngtc = state->ngtc * state->nhchainlength;
+ nnhpres = state->nnhpres* state->nhchainlength;
+ scopy_rvecs(box, DIM);
+ scopy_rvecs(box_rel, DIM);
+ scopy_rvecs(boxv, DIM);
+ state_local->veta = state->veta;
+ state_local->vol0 = state->vol0;
+ scopy_rvecs(svir_prev, DIM);
+ scopy_rvecs(fvir_prev, DIM);
+ scopy_rvecs(pres_prev, DIM);
+ scopy_doubles(nosehoover_xi, ngtc);
+ scopy_doubles(nosehoover_vxi, ngtc);
+ scopy_doubles(nhpres_xi, nnhpres);
+ scopy_doubles(nhpres_vxi, nnhpres);
+ scopy_doubles(therm_integral, state->ngtc);
+ scopy_rvecs(x, state->natoms);
+ scopy_rvecs(v, state->natoms);
+ scopy_rvecs(sd_X, state->natoms);
+ copy_ints(&(state->fep_state), &(state_local->fep_state), 1);
+ scopy_reals(lambda, efptNR);
+}
+
+static void scale_velocities(t_state *state, real fac)
+{
+ int i;
+
+ if (state->v)
+ {
+ for (i = 0; i < state->natoms; i++)
+ {
+ svmul(fac, state->v[i], state->v[i]);
+ }
+ }
+}
+
+static void pd_collect_state(const t_commrec *cr, t_state *state)
+{
+ int shift;
+
+ if (debug)
+ {
+ fprintf(debug, "Collecting state before exchange\n");
+ }
+ shift = cr->nnodes - cr->npmenodes - 1;
+ move_rvecs(cr, FALSE, FALSE, GMX_LEFT, GMX_RIGHT, state->x, NULL, shift, NULL);
+ if (state->v)
+ {
+ move_rvecs(cr, FALSE, FALSE, GMX_LEFT, GMX_RIGHT, state->v, NULL, shift, NULL);
+ }
+ if (state->sd_X)
+ {
+ move_rvecs(cr, FALSE, FALSE, GMX_LEFT, GMX_RIGHT, state->sd_X, NULL, shift, NULL);
+ }
+}
+
+static void print_transition_matrix(FILE *fplog, const char *leg, int n, int **nmoves, int *nattempt)
+{
+ int i, j, ntot;
+ float Tprint;
+
+ ntot = nattempt[0] + nattempt[1];
+ fprintf(fplog, "\n");
+ fprintf(fplog, "Repl");
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fplog, " "); /* put the title closer to the center */
+ }
+ fprintf(fplog, "Empirical Transition Matrix\n");
+
+ fprintf(fplog, "Repl");
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fplog, "%8d", (i+1));
+ }
+ fprintf(fplog, "\n");
+
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fplog, "Repl");
+ for (j = 0; j < n; j++)
+ {
+ Tprint = 0.0;
+ if (nmoves[i][j] > 0)
+ {
+ Tprint = nmoves[i][j]/(2.0*ntot);
+ }
+ fprintf(fplog, "%8.4f", Tprint);
+ }
+ fprintf(fplog, "%3d\n", i);
+ }
+}
+
+static void print_ind(FILE *fplog, const char *leg, int n, int *ind, gmx_bool *bEx)
+{
+ int i;
+
+ fprintf(fplog, "Repl %2s %2d", leg, ind[0]);
+ for (i = 1; i < n; i++)
+ {
+ fprintf(fplog, " %c %2d", (bEx != 0 && bEx[i]) ? 'x' : ' ', ind[i]);
+ }
+ fprintf(fplog, "\n");
+}
+
+static void print_allswitchind(FILE *fplog, int n, int *ind, int *pind, int *allswaps, int *tmpswap)
+{
+ int i;
+
+ for (i = 0; i < n; i++)
+ {
+ tmpswap[i] = allswaps[i];
+ }
+ for (i = 0; i < n; i++)
+ {
+ allswaps[i] = tmpswap[pind[i]];
+ }
+
+ fprintf(fplog, "\nAccepted Exchanges: ");
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fplog, "%d ", pind[i]);
+ }
+ fprintf(fplog, "\n");
+
+ /* the "Order After Exchange" is the state label corresponding to the configuration that
+ started in state listed in order, i.e.
+
+ 3 0 1 2
+
+ means that the:
+ configuration starting in simulation 3 is now in simulation 0,
+ configuration starting in simulation 0 is now in simulation 1,
+ configuration starting in simulation 1 is now in simulation 2,
+ configuration starting in simulation 2 is now in simulation 3
+ */
+ fprintf(fplog, "Order After Exchange: ");
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fplog, "%d ", allswaps[i]);
+ }
+ fprintf(fplog, "\n\n");
+}
+
+static void print_prob(FILE *fplog, const char *leg, int n, real *prob)
+{
+ int i;
+ char buf[8];
+
+ fprintf(fplog, "Repl %2s ", leg);
+ for (i = 1; i < n; i++)
+ {
+ if (prob[i] >= 0)
+ {
+ sprintf(buf, "%4.2f", prob[i]);
+ fprintf(fplog, " %3s", buf[0] == '1' ? "1.0" : buf+1);
+ }
+ else
+ {
+ fprintf(fplog, " ");
+ }
+ }
+ fprintf(fplog, "\n");
+}
+
+static void print_count(FILE *fplog, const char *leg, int n, int *count)
+{
+ int i;
+
+ fprintf(fplog, "Repl %2s ", leg);
+ for (i = 1; i < n; i++)
+ {
+ fprintf(fplog, " %4d", count[i]);
+ }
+ fprintf(fplog, "\n");
+}
+
+static real calc_delta(FILE *fplog, gmx_bool bPrint, struct gmx_repl_ex *re, int a, int b, int ap, int bp)
+{
+
+ real ediff, dpV, delta = 0;
+ real *Epot = re->Epot;
+ real *Vol = re->Vol;
+ real **de = re->de;
+ real *beta = re->beta;
+
+ /* Two cases; we are permuted and not. In all cases, setting ap = a and bp = b will reduce
+ to the non permuted case */
+
+ switch (re->type)
+ {
+ case ereTEMP:
+ /*
+ * Okabe et. al. Chem. Phys. Lett. 335 (2001) 435-439
+ */
+ ediff = Epot[b] - Epot[a];
+ delta = -(beta[bp] - beta[ap])*ediff;
+ break;
+ case ereLAMBDA:
+ /* two cases: when we are permuted, and not. */
+ /* non-permuted:
+ ediff = E_new - E_old
+ = [H_b(x_a) + H_a(x_b)] - [H_b(x_b) + H_a(x_a)]
+ = [H_b(x_a) - H_a(x_a)] + [H_a(x_b) - H_b(x_b)]
+ = de[b][a] + de[a][b] */
+
+ /* permuted:
+ ediff = E_new - E_old
+ = [H_bp(x_a) + H_ap(x_b)] - [H_bp(x_b) + H_ap(x_a)]
+ = [H_bp(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_bp(x_b)]
+ = [H_bp(x_a) - H_a(x_a) + H_a(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_b(x_b) + H_b(x_b) - H_bp(x_b)]
+ = [H_bp(x_a) - H_a(x_a)] - [H_ap(x_a) - H_a(x_a)] + [H_ap(x_b) - H_b(x_b)] - H_bp(x_b) - H_b(x_b)]
+ = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]) */
+ /* but, in the current code implementation, we flip configurations, not indices . . .
+ So let's examine that.
+ = [H_b(x_ap) - H_a(x_a)] - [H_a(x_ap) - H_a(x_a)] + [H_a(x_bp) - H_b(x_b)] - H_b(x_bp) - H_b(x_b)]
+ = [H_b(x_ap) - H_a(x_ap)] + [H_a(x_bp) - H_b(x_pb)]
+ = (de[b][ap] - de[a][ap]) + (de[a][bp] - de[b][bp]
+ So, if we exchange b<=> bp and a<=> ap, we return to the same result.
+ So the simple solution is to flip the
+ position of perturbed and original indices in the tests.
+ */
+
+ ediff = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]);
+ delta = ediff*beta[a]; /* assume all same temperature in this case */
+ break;
+ case ereTL:
+ /* not permuted: */
+ /* delta = reduced E_new - reduced E_old
+ = [beta_b H_b(x_a) + beta_a H_a(x_b)] - [beta_b H_b(x_b) + beta_a H_a(x_a)]
+ = [beta_b H_b(x_a) - beta_a H_a(x_a)] + [beta_a H_a(x_b) - beta_b H_b(x_b)]
+ = [beta_b dH_b(x_a) + beta_b H_a(x_a) - beta_a H_a(x_a)] +
+ [beta_a dH_a(x_b) + beta_a H_b(x_b) - beta_b H_b(x_b)]
+ = [beta_b dH_b(x_a) + [beta_a dH_a(x_b) +
+ beta_b (H_a(x_a) - H_b(x_b)]) - beta_a (H_a(x_a) - H_b(x_b))
+ = beta_b dH_b(x_a) + beta_a dH_a(x_b) - (beta_b - beta_a)(H_b(x_b) - H_a(x_a) */
+ /* delta = beta[b]*de[b][a] + beta[a]*de[a][b] - (beta[b] - beta[a])*(Epot[b] - Epot[a]; */
+ /* permuted (big breath!) */
+ /* delta = reduced E_new - reduced E_old
+ = [beta_bp H_bp(x_a) + beta_ap H_ap(x_b)] - [beta_bp H_bp(x_b) + beta_ap H_ap(x_a)]
+ = [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
+ = [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
+ - beta_pb H_a(x_a) + beta_ap H_a(x_a) + beta_pb H_a(x_a) - beta_ap H_a(x_a)
+ - beta_ap H_b(x_b) + beta_bp H_b(x_b) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
+ = [(beta_bp H_bp(x_a) - beta_bp H_a(x_a)) - (beta_ap H_ap(x_a) - beta_ap H_a(x_a))] +
+ [(beta_ap H_ap(x_b) - beta_ap H_b(x_b)) - (beta_bp H_bp(x_b) - beta_bp H_b(x_b))]
+ + beta_pb H_a(x_a) - beta_ap H_a(x_a) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
+ = [beta_bp (H_bp(x_a) - H_a(x_a)) - beta_ap (H_ap(x_a) - H_a(x_a))] +
+ [beta_ap (H_ap(x_b) - H_b(x_b)) - beta_bp (H_bp(x_b) - H_b(x_b))]
+ + beta_pb (H_a(x_a) - H_b(x_b)) - beta_ap (H_a(x_a) - H_b(x_b))
+ = ([beta_bp de[bp][a] - beta_ap de[ap][a]) + beta_ap de[ap][b] - beta_bp de[bp][b])
+ + (beta_pb-beta_ap)(H_a(x_a) - H_b(x_b)) */
+ delta = beta[bp]*(de[bp][a] - de[bp][b]) + beta[ap]*(de[ap][b] - de[ap][a]) - (beta[bp]-beta[ap])*(Epot[b]-Epot[a]);
+ break;
+ default:
+ gmx_incons("Unknown replica exchange quantity");
+ }
+ if (bPrint)
+ {
+ fprintf(fplog, "Repl %d <-> %d dE_term = %10.3e (kT)\n", a, b, delta);
+ }
+ if (re->bNPT)
+ {
+ /* revist the calculation for 5.0. Might be some improvements. */
+ dpV = (beta[ap]*re->pres[ap]-beta[bp]*re->pres[bp])*(Vol[b]-Vol[a])/PRESFAC;
+ if (bPrint)
+ {
+ fprintf(fplog, " dpV = %10.3e d = %10.3e\nb", dpV, delta + dpV);
+ }
+ delta += dpV;
+ }
+ return delta;
+}
+
+static void
+test_for_replica_exchange(FILE *fplog,
+ const gmx_multisim_t *ms,
+ struct gmx_repl_ex *re,
+ gmx_enerdata_t *enerd,
+ real vol,
+ gmx_large_int_t step,
+ real time)
+{
+ int m, i, j, a, b, ap, bp, i0, i1, tmp;
+ real ediff = 0, delta = 0, dpV = 0;
+ gmx_bool bPrint, bMultiEx;
+ gmx_bool *bEx = re->bEx;
+ real *prob = re->prob;
+ int *pind = re->destinations; /* permuted index */
+ gmx_bool bEpot = FALSE;
+ gmx_bool bDLambda = FALSE;
+ gmx_bool bVol = FALSE;
+
+ bMultiEx = (re->nex > 1); /* multiple exchanges at each state */
+ fprintf(fplog, "Replica exchange at step " gmx_large_int_pfmt " time %g\n", step, time);
+
+ if (re->bNPT)
+ {
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->Vol[i] = 0;
+ }
+ bVol = TRUE;
+ re->Vol[re->repl] = vol;
+ }
+ if ((re->type == ereTEMP || re->type == ereTL))
+ {
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->Epot[i] = 0;
+ }
+ bEpot = TRUE;
+ re->Epot[re->repl] = enerd->term[F_EPOT];
+ /* temperatures of different states*/
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->beta[i] = 1.0/(re->q[ereTEMP][i]*BOLTZ);
+ }
+ }
+ else
+ {
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->beta[i] = 1.0/(re->temp*BOLTZ); /* we have a single temperature */
+ }
+ }
+ if (re->type == ereLAMBDA || re->type == ereTL)
+ {
+ bDLambda = TRUE;
+ /* lambda differences. */
+ /* de[i][j] is the energy of the jth simulation in the ith Hamiltonian
+ minus the energy of the jth simulation in the jth Hamiltonian */
+ for (i = 0; i < re->nrepl; i++)
+ {
+ for (j = 0; j < re->nrepl; j++)
+ {
+ re->de[i][j] = 0;
+ }
+ }
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->de[i][re->repl] = (enerd->enerpart_lambda[(int)re->q[ereLAMBDA][i]+1]-enerd->enerpart_lambda[0]);
+ }
+ }
+
+ /* now actually do the communication */
+ if (bVol)
+ {
+ gmx_sum_sim(re->nrepl, re->Vol, ms);
+ }
+ if (bEpot)
+ {
+ gmx_sum_sim(re->nrepl, re->Epot, ms);
+ }
+ if (bDLambda)
+ {
+ for (i = 0; i < re->nrepl; i++)
+ {
+ gmx_sum_sim(re->nrepl, re->de[i], ms);
+ }
+ }
+
+ /* make a duplicate set of indices for shuffling */
+ for (i = 0; i < re->nrepl; i++)
+ {
+ pind[i] = re->ind[i];
+ }
+
+ if (bMultiEx)
+ {
+ /* multiple random switch exchange */
+ for (i = 0; i < re->nex; i++)
+ {
+ /* randomly select a pair */
+ /* in theory, could reduce this by identifying only which switches had a nonneglibible
+ probability of occurring (log p > -100) and only operate on those switches */
+ /* find out which state it is from, and what label that state currently has. Likely
+ more work that useful. */
+ i0 = (int)(re->nrepl*rando(&(re->seed)));
+ i1 = (int)(re->nrepl*rando(&(re->seed)));
+ if (i0 == i1)
+ {
+ i--;
+ continue; /* self-exchange, back up and do it again */
+ }
+
+ a = re->ind[i0]; /* what are the indices of these states? */
+ b = re->ind[i1];
+ ap = pind[i0];
+ bp = pind[i1];
+
+ bPrint = FALSE; /* too noisy */
+ /* calculate the energy difference */
+ /* if the code changes to flip the STATES, rather than the configurations,
+ use the commented version of the code */
+ /* delta = calc_delta(fplog,bPrint,re,a,b,ap,bp); */
+ delta = calc_delta(fplog, bPrint, re, ap, bp, a, b);
+
+ /* we actually only use the first space in the prob and bEx array,
+ since there are actually many switches between pairs. */
+
+ if (delta <= 0)
+ {
+ /* accepted */
+ prob[0] = 1;
+ bEx[0] = TRUE;
+ }
+ else
+ {
+ if (delta > PROBABILITYCUTOFF)
+ {
+ prob[0] = 0;
+ }
+ else
+ {
+ prob[0] = exp(-delta);
+ }
+ /* roll a number to determine if accepted */
+ bEx[0] = (rando(&(re->seed)) < prob[0]);
+ }
+ re->prob_sum[0] += prob[0];
+
+ if (bEx[0])
+ {
+ /* swap the states */
+ tmp = pind[i0];
+ pind[i0] = pind[i1];
+ pind[i1] = tmp;
+ }
+ }
+ re->nattempt[0]++; /* keep track of total permutation trials here */
+ print_allswitchind(fplog, re->nrepl, re->ind, pind, re->allswaps, re->tmpswap);
+ }
+ else
+ {
+ /* standard nearest neighbor replica exchange */
+ m = (step / re->nst) % 2;
+ for (i = 1; i < re->nrepl; i++)
+ {
+ a = re->ind[i-1];
+ b = re->ind[i];
+
+ bPrint = (re->repl == a || re->repl == b);
+ if (i % 2 == m)
+ {
+ delta = calc_delta(fplog, bPrint, re, a, b, a, b);
+ if (delta <= 0)
+ {
+ /* accepted */
+ prob[i] = 1;
+ bEx[i] = TRUE;
+ }
+ else
+ {
+ if (delta > PROBABILITYCUTOFF)
+ {
+ prob[i] = 0;
+ }
+ else
+ {
+ prob[i] = exp(-delta);
+ }
+ /* roll a number to determine if accepted */
+ bEx[i] = (rando(&(re->seed)) < prob[i]);
+ }
+ re->prob_sum[i] += prob[i];
+
+ if (bEx[i])
+ {
+ /* swap these two */
+ tmp = pind[i-1];
+ pind[i-1] = pind[i];
+ pind[i] = tmp;
+ re->nexchange[i]++; /* statistics for back compatibility */
+ }
+ }
+ else
+ {
+ prob[i] = -1;
+ bEx[i] = FALSE;
+ }
+ }
+ /* print some statistics */
+ print_ind(fplog, "ex", re->nrepl, re->ind, bEx);
+ print_prob(fplog, "pr", re->nrepl, prob);
+ fprintf(fplog, "\n");
+ re->nattempt[m]++;
+ }
+
+ /* record which moves were made and accepted */
+ for (i = 0; i < re->nrepl; i++)
+ {
+ re->nmoves[re->ind[i]][pind[i]] += 1;
+ re->nmoves[pind[i]][re->ind[i]] += 1;
+ }
+ fflush(fplog); /* make sure we can see what the last exchange was */
+}
+
+static void write_debug_x(t_state *state)
+{
+ int i;
+
+ if (debug)
+ {
+ for (i = 0; i < state->natoms; i += 10)
+ {
+ fprintf(debug, "dx %5d %10.5f %10.5f %10.5f\n", i, state->x[i][XX], state->x[i][YY], state->x[i][ZZ]);
+ }
+ }
+}
+
+static void
+cyclic_decomposition(FILE *fplog,
+ const int *destinations,
+ int **cyclic,
+ gmx_bool *incycle,
+ const int nrepl,
+ int *nswap)
+{
+
+ int i, j, c, p;
+ int maxlen = 1;
+ for (i = 0; i < nrepl; i++)
+ {
+ incycle[i] = FALSE;
+ }
+ for (i = 0; i < nrepl; i++) /* one cycle for each replica */
+ {
+ if (incycle[i])
+ {
+ cyclic[i][0] = -1;
+ continue;
+ }
+ cyclic[i][0] = i;
+ incycle[i] = TRUE;
+ c = 1;
+ p = i;
+ for (j = 0; j < nrepl; j++) /* potentially all cycles are part, but we will break first */
+ {
+ p = destinations[p]; /* start permuting */
+ if (p == i)
+ {
+ cyclic[i][c] = -1;
+ if (c > maxlen)
+ {
+ maxlen = c;
+ }
+ break; /* we've reached the original element, the cycle is complete, and we marked the end. */
+ }
+ else
+ {
+ cyclic[i][c] = p; /* each permutation gives a new member of the cycle */
+ incycle[p] = TRUE;
+ c++;
+ }
+ }
+ }
+ *nswap = maxlen - 1;
+
+ if (debug)
+ {
+ for (i = 0; i < nrepl; i++)
+ {
+ fprintf(debug, "Cycle %d:", i);
+ for (j = 0; j < nrepl; j++)
+ {
+ if (cyclic[i][j] < 0)
+ {
+ break;
+ }
+ fprintf(debug, "%2d", cyclic[i][j]);
+ }
+ fprintf(debug, "\n");
+ }
+ fflush(debug);
+ }
+}
+
+static void
+compute_exchange_order(FILE *fplog,
+ int **cyclic,
+ int **order,
+ const int nrepl,
+ const int maxswap)
+{
+ int i, j;
+
+ for (j = 0; j < maxswap; j++)
+ {
+ for (i = 0; i < nrepl; i++)
+ {
+ if (cyclic[i][j+1] >= 0)
+ {
+ order[cyclic[i][j+1]][j] = cyclic[i][j];
+ order[cyclic[i][j]][j] = cyclic[i][j+1];
+ }
+ }
+ for (i = 0; i < nrepl; i++)
+ {
+ if (order[i][j] < 0)
+ {
+ order[i][j] = i; /* if it's not exchanging, it should stay this round*/
+ }
+ }
+ }
+
+ if (debug)
+ {
+ fprintf(fplog, "Replica Exchange Order\n");
+ for (i = 0; i < nrepl; i++)
+ {
+ fprintf(fplog, "Replica %d:", i);
+ for (j = 0; j < maxswap; j++)
+ {
+ if (order[i][j] < 0)
+ {
+ break;
+ }
+ fprintf(debug, "%2d", order[i][j]);
+ }
+ fprintf(fplog, "\n");
+ }
+ fflush(fplog);
+ }
+}
+
+static void
+prepare_to_do_exchange(FILE *fplog,
+ const int *destinations,
+ const int replica_id,
+ const int nrepl,
+ int *maxswap,
+ int **order,
+ int **cyclic,
+ int *incycle,
+ gmx_bool *bThisReplicaExchanged)
+{
+ int i, j;
+ /* Hold the cyclic decomposition of the (multiple) replica
+ * exchange. */
+ gmx_bool bAnyReplicaExchanged = FALSE;
+ *bThisReplicaExchanged = FALSE;
+
+ for (i = 0; i < nrepl; i++)
+ {
+ if (destinations[i] != i)
+ {
+ /* only mark as exchanged if the index has been shuffled */
+ bAnyReplicaExchanged = TRUE;
+ break;
+ }
+ }
+ if (bAnyReplicaExchanged)
+ {
+ /* reinitialize the placeholder arrays */
+ for (i = 0; i < nrepl; i++)
+ {
+ for (j = 0; j < nrepl; j++)
+ {
+ cyclic[i][j] = -1;
+ order[i][j] = -1;
+ }
+ }
+
+ /* Identify the cyclic decomposition of the permutation (very
+ * fast if neighbor replica exchange). */
+ cyclic_decomposition(fplog, destinations, cyclic, incycle, nrepl, maxswap);
+
+ /* Now translate the decomposition into a replica exchange
+ * order at each step. */
+ compute_exchange_order(fplog, cyclic, order, nrepl, *maxswap);
+
+ /* Did this replica do any exchange at any point? */
+ for (j = 0; j < *maxswap; j++)
+ {
+ if (replica_id != order[replica_id][j])
+ {
+ *bThisReplicaExchanged = TRUE;
+ break;
+ }
+ }
+ }
+}
+
+gmx_bool replica_exchange(FILE *fplog, const t_commrec *cr, struct gmx_repl_ex *re,
+ t_state *state, gmx_enerdata_t *enerd,
+ t_state *state_local, gmx_large_int_t step, real time)
+{
+ int i, j;
+ int replica_id = 0;
+ int exchange_partner;
+ int maxswap = 0;
+ /* Number of rounds of exchanges needed to deal with any multiple
+ * exchanges. */
+ /* Where each replica ends up after the exchange attempt(s). */
+ /* The order in which multiple exchanges will occur. */
+ gmx_bool bThisReplicaExchanged = FALSE;
+
+ if (MASTER(cr))
+ {
+ replica_id = re->repl;
+ test_for_replica_exchange(fplog, cr->ms, re, enerd, det(state_local->box), step, time);
+ prepare_to_do_exchange(fplog, re->destinations, replica_id, re->nrepl, &maxswap,
+ re->order, re->cyclic, re->incycle, &bThisReplicaExchanged);
+ }
+ /* Do intra-simulation broadcast so all processors belonging to
+ * each simulation know whether they need to participate in
+ * collecting the state. Otherwise, they might as well get on with
+ * the next thing to do. */
+ if (PAR(cr))
+ {
+#ifdef GMX_MPI
+ MPI_Bcast(&bThisReplicaExchanged, sizeof(gmx_bool), MPI_BYTE, MASTERRANK(cr),
+ cr->mpi_comm_mygroup);
+#endif
+ }
+
+ if (bThisReplicaExchanged)
+ {
+ /* Exchange the states */
+
+ if (PAR(cr))
+ {
+ /* Collect the global state on the master node */
+ if (DOMAINDECOMP(cr))
+ {
+ dd_collect_state(cr->dd, state_local, state);
+ }
+ else
+ {
+ pd_collect_state(cr, state);
+ }
+ }
+
+ if (MASTER(cr))
+ {
+ /* There will be only one swap cycle with standard replica
+ * exchange, but there may be multiple swap cycles if we
+ * allow multiple swaps. */
+
+ for (j = 0; j < maxswap; j++)
+ {
+ exchange_partner = re->order[replica_id][j];
+
+ if (exchange_partner != replica_id)
+ {
+ /* Exchange the global states between the master nodes */
+ if (debug)
+ {
+ fprintf(debug, "Exchanging %d with %d\n", replica_id, exchange_partner);
+ }
+ exchange_state(cr->ms, exchange_partner, state);
+ }
+ }
+ /* For temperature-type replica exchange, we need to scale
+ * the velocities. */
+ if (re->type == ereTEMP || re->type == ereTL)
+ {
+ scale_velocities(state, sqrt(re->q[ereTEMP][replica_id]/re->q[ereTEMP][re->destinations[replica_id]]));
+ }
+
+ }
+
+ /* With domain decomposition the global state is distributed later */
+ if (!DOMAINDECOMP(cr))
+ {
+ /* Copy the global state to the local state data structure */
+ copy_state_nonatomdata(state, state_local);
+
+ if (PAR(cr))
+ {
+ bcast_state(cr, state, FALSE);
+ }
+ }
+ }
+
+ return bThisReplicaExchanged;
+}
+
+void print_replica_exchange_statistics(FILE *fplog, struct gmx_repl_ex *re)
+{
+ int i;
+
+ fprintf(fplog, "\nReplica exchange statistics\n");
+
+ if (re->nex == 0)
+ {
+ fprintf(fplog, "Repl %d attempts, %d odd, %d even\n",
+ re->nattempt[0]+re->nattempt[1], re->nattempt[1], re->nattempt[0]);
+
+ fprintf(fplog, "Repl average probabilities:\n");
+ for (i = 1; i < re->nrepl; i++)
+ {
+ if (re->nattempt[i%2] == 0)
+ {
+ re->prob[i] = 0;
+ }
+ else
+ {
+ re->prob[i] = re->prob_sum[i]/re->nattempt[i%2];
+ }
+ }
+ print_ind(fplog, "", re->nrepl, re->ind, NULL);
+ print_prob(fplog, "", re->nrepl, re->prob);
+
+ fprintf(fplog, "Repl number of exchanges:\n");
+ print_ind(fplog, "", re->nrepl, re->ind, NULL);
+ print_count(fplog, "", re->nrepl, re->nexchange);
+
+ fprintf(fplog, "Repl average number of exchanges:\n");
+ for (i = 1; i < re->nrepl; i++)
+ {
+ if (re->nattempt[i%2] == 0)
+ {
+ re->prob[i] = 0;
+ }
+ else
+ {
+ re->prob[i] = ((real)re->nexchange[i])/re->nattempt[i%2];
+ }
+ }
+ print_ind(fplog, "", re->nrepl, re->ind, NULL);
+ print_prob(fplog, "", re->nrepl, re->prob);
+
+ fprintf(fplog, "\n");
+ }
+ /* print the transition matrix */
+ print_transition_matrix(fplog, "", re->nrepl, re->nmoves, re->nattempt);
+}
diff --git a/patches/lammps-6Apr13.config b/patches/lammps-6Apr13.config
index 7aa1e453acc89b3e771728925a4620caa2836edd..a83ff65c1a8e63d7f15d7d5aae0e6bdcafcc0f35 100644
--- a/patches/lammps-6Apr13.config
+++ b/patches/lammps-6Apr13.config
@@ -14,3 +14,14 @@ function plumed_after_revert(){
rm -fr src/USER-PLUMED/
}
+function plumed_patch_info(){
+ echo ""
+ echo "PLUMED can be incorporated into LAMMPS using a simple patching procedure."
+ echo "Patching must be done _before_ LAMMPS is configured."
+ echo "After patching, one should enable PLUMED using the command"
+ echo "make yes-user-plumed"
+ echo "In the same way, before reverting one should disable PLUMED using the command"
+ echo "make no-user-plumed"
+ echo
+ echo "For more information on LAMMPS you should visit http://lammps.sandia.gov/"
+}
diff --git a/patches/namd-2.8.config b/patches/namd-2.8.config
index 3eff738a2fc6ae97add7a847e49352c15fcbe335..991290087a4827c57884b42ffb6e5702961f2eed 100644
--- a/patches/namd-2.8.config
+++ b/patches/namd-2.8.config
@@ -4,3 +4,10 @@ function plumed_preliminary_test(){
# check if the README.txt contains the word NAMD
grep -q NAMD README.txt 1>/dev/null 2>/dev/null && test -f */Make.config
}
+
+function plumed_patch_info(){
+ echo "WARNING: NAMD does not currently take into account virial contributions"
+ echo "from PLUMED. Please use constant volume simulations only"
+ echo ""
+ echo "For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/"
+}
diff --git a/patches/namd-2.9.config b/patches/namd-2.9.config
new file mode 100644
index 0000000000000000000000000000000000000000..991290087a4827c57884b42ffb6e5702961f2eed
--- /dev/null
+++ b/patches/namd-2.9.config
@@ -0,0 +1,13 @@
+
+
+function plumed_preliminary_test(){
+# check if the README.txt contains the word NAMD
+ grep -q NAMD README.txt 1>/dev/null 2>/dev/null && test -f */Make.config
+}
+
+function plumed_patch_info(){
+ echo "WARNING: NAMD does not currently take into account virial contributions"
+ echo "from PLUMED. Please use constant volume simulations only"
+ echo ""
+ echo "For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/"
+}
diff --git a/patches/patch.sh b/patches/patch.sh
index 082026b24f091509b1cc3c49d7fde72897bbdb64..6ee52c5af150b5a0fa557119189d4d6203d9b605 100755
--- a/patches/patch.sh
+++ b/patches/patch.sh
@@ -13,8 +13,12 @@ Actions (choose one):
print a list of available MD engines
-s, --save
save, this needs *.preplumed files (*)
+ --save-originals
+ same as save, but save also original files
-n NEWENGINE, --new NEWENGINE
create a new patch named NEWENGINE (*)
+ -i, --info
+ output information on the patching procedure for a particular code
Options:
-e ENGINE, --engine ENGINE
set MD engine to ENGINE (default: choose interactively)
@@ -28,6 +32,9 @@ Options:
same as --mode runtime
-d FILE, --diff FILE
set the path to diff file (default: ROOT/patches/ENGINE.diff) (*)
+ -q, --quiet
+ do not write loggin information; useful with -i to print just
+ the patching information
-f, --force
force patching (*)
@@ -45,6 +52,10 @@ newpatch=
multiple_actions=
+otherfiles=
+save_originals=
+quiet=
+
for option
do
@@ -55,8 +66,10 @@ do
(--help|-h) echo "$MANUAL" ; exit ;;
(--patch|-p) test -n "$action" && multiple_actions=yes ; action=patch ;;
(--save|-s) test -n "$action" && multiple_actions=yes ; action=save ;;
+ (--save-originals) test -n "$action" && multiple_actions=yes ; action=save ; save_originals=yes ;;
(--revert|-R|-r) test -n "$action" && multiple_actions=yes ; action=revert ;;
(--list-engines|-l) test -n "$action" && multiple_actions=yes ; action=list ;;
+ (--info|-i) test -n "$action" && multiple_actions=yes ; action=info ;;
(--new=*) test -n "$action" && multiple_actions=yes ; action=new ; newpatch="${prefix_option#--new=}" ;;
(--description) echo "patch an MD engine" ; exit ;;
(--engine=*) engine="${prefix_option#--engine=}" ;;
@@ -71,6 +84,7 @@ do
(--shared) mode=shared ;;
(--runtime) mode=runtime ;;
(--force|-f) force=yes ;;
+ (--quiet|-q) quiet=yes ;;
(*)
echo "ERROR: Unknown option $prefix_option. Use -h for help."
exit
@@ -87,8 +101,8 @@ if [ -z "$action" ] ; then
exit
fi
-echo "PLUMED patching tool"
-echo
+test -n "$quiet" || echo "PLUMED patching tool"
+test -n "$quiet" || echo
if [ -z "$PLUMED_ROOT" ]
then
echo "ERROR: I cannot find PLUMED"
@@ -126,14 +140,14 @@ fi
if [ "$action" == new ]
then
- echo "Creating a new patch"
+ test -n "$quiet" || echo "Creating a new patch"
if [[ -e "$PLUMED_ROOT"/patches/"$newpatch".diff ]] ; then
echo "ERROR: patch $newpatch is already defined"
exit
fi
touch "$PLUMED_ROOT"/patches/"$newpatch".diff
- echo "Created file $PLUMED_ROOT/patches/$newpatch.diff"
- echo "Also consider the possibility of adding a $PLUMED_ROOT/patches/$newpatch.config file"
+ test -n "$quiet" || echo "Created file $PLUMED_ROOT/patches/$newpatch.diff"
+ test -n "$quiet" || echo "Also consider the possibility of adding a $PLUMED_ROOT/patches/$newpatch.config file"
exit
fi
@@ -162,19 +176,19 @@ then
test -d "$PLUMED_ROOT/patches/${engine}" && otherfiles="$PLUMED_ROOT/patches/${engine}/"
fi
-echo "MD engine: $engine"
-echo "PLUMED location: $PLUMED_ROOT"
-echo "diff file: $diff"
+test -n "$quiet" || echo "MD engine: $engine"
+test -n "$quiet" || echo "PLUMED location: $PLUMED_ROOT"
+test -n "$quiet" || echo "diff file: $diff"
if [ -f "$config" ]
then
- echo "sourcing config file: $config"
+ test -n "$quiet" || echo "sourcing config file: $config"
source "$config"
fi
if [ -d "$otherfiles" ]
then
- echo "extra files located in: $otherfiles"
+ test -n "$quiet" || echo "extra files located in: $otherfiles"
fi
case "$mode" in
@@ -187,7 +201,7 @@ esac
case "$action" in
(patch)
- if [ ! -f "$diff" ] ; then
+ if [ ! -e "$diff" ] ; then
echo "ERROR: MD engine not supported (or mispelled)"
exit
fi
@@ -213,19 +227,44 @@ case "$action" in
exit
fi
if type -t plumed_before_patch 1>/dev/null ; then
- echo "Executing plumed_before_patch function"
+ test -n "$quiet" || echo "Executing plumed_before_patch function"
plumed_before_patch
fi
- echo "Linking Plumed.h and Plumed.inc ($mode mode)"
+ test -n "$quiet" || echo "Linking Plumed.h and Plumed.inc ($mode mode)"
ln -s "$PLUMED_ROOT/src/wrapper/Plumed.h"
ln -s "$PLUMED_ROOT/src/lib/Plumed.inc.$mode" Plumed.inc
ln -s "$PLUMED_ROOT/src/lib/Plumed.cmake.$mode" Plumed.cmake
- bash "$diff"
+
+ if [ -d "$diff" ]; then
+ test -n "$quiet" || echo "Patching with on-the-fly diff from stored originals"
+ PREPLUMED=$(cd $diff ; find . -name "*.preplumed" | sort)
+ for bckfile in $PREPLUMED ; do
+ file="${bckfile%.preplumed}"
+ if test -e "$file" ; then
+ diff -U 5 "$diff/$bckfile" "$diff/$file" --label="$bckfile" --label="$file" |
+ patch -u -l -b -F 5 --suffix=.preplumed "$file"
+ else
+ echo "ERROR: File $file is missing"
+ fi
+ done
+ else
+ test -n "$quiet" || echo "Patching with stored diff"
+ bash "$diff"
+ fi
+
if type -t plumed_after_patch 1>/dev/null ; then
- echo "Executing plumed_after_patch function"
+ test -n "$quiet" || echo "Executing plumed_after_patch function"
plumed_after_patch
fi
;;
+ (info)
+ if type -t plumed_patch_info 1>/dev/null ; then
+ test -n "$quiet" || echo "Executing plumed_patch_info function"
+ plumed_patch_info
+ else
+ echo "No special info for this MD engine"
+ fi
+ ;;
(save)
if [ ! -L Plumed.h -o ! -L Plumed.inc ]
then
@@ -247,16 +286,45 @@ case "$action" in
exit
fi
fi
- echo "Saving your changes to $diff"
- echo "Preplumed files:"
- echo "$PREPLUMED"
- test -e "$diff" && rm "$diff"
+ test -n "$quiet" || echo "Saving your changes to $diff"
+ test -n "$quiet" || echo "Preplumed files:"
+ test -n "$quiet" || echo "$PREPLUMED"
+ if [ -d "$diff" ] && [ -z "$save_originals" ]; then
+ echo "This patch uses the dir format (originals are saved)"
+ echo "Are you sure you want to save the single diff?"
+ echo "Possible reasons to do it are:"
+ echo "* because of licence you do not want to store originals in plumed"
+ echo "* you do not want to do a big change on the diff files now"
+ answer=
+ PS3="Choose:"
+ select answer in single-diff originals ; do
+ if [[ -n "$answer" ]] ; then
+ break
+ else
+ echo "ERROR: choose in the list above or interrupt (^c)"
+ fi
+ done
+ if [ "$answer" = originals ] ; then
+ test -n "$quiet" || echo "saving originals"
+ save_originals=yes
+ else
+ test -n "$quiet" || echo "saving single diff file"
+ fi
+ fi
+ test -e "$diff" && rm -r "$diff"
for bckfile in $PREPLUMED ; do
file="${bckfile%.preplumed}"
if test -e "$file" ; then
- echo "patch -u -l -b -F 5 --suffix=.preplumed \"${file}\" << \\EOF_EOF" >> "$diff"
- diff -U 5 "${bckfile}" "$file" --label="$bckfile" --label="$file" >> "$diff"
- echo "EOF_EOF" >> "$diff"
+ if [ -n "$save_originals" ] ; then
+ xx="$diff/$file"
+ mkdir -p "${xx%/*}"
+ cp "$file" "$diff/$file"
+ cp "$bckfile" "$diff/$bckfile"
+ else
+ echo "patch -u -l -b -F 5 --suffix=.preplumed \"${file}\" << \\EOF_EOF" >> "$diff"
+ diff -U 5 "${bckfile}" "$file" --label="$bckfile" --label="$file" >> "$diff"
+ echo "EOF_EOF" >> "$diff"
+ fi
else
echo "ERROR: File $file is missing"
fi
@@ -270,26 +338,26 @@ cat <<EOF
EOF
;;
(revert)
- if [ ! -f "$diff" ] ; then
+ if [ ! -e "$diff" ] ; then
echo "ERROR: MD engine not supported (or mispelled)"
exit
fi
if type -t plumed_before_revert 1>/dev/null ; then
- echo "Executing plumed_before_revert function"
+ test -n "$quiet" || echo "Executing plumed_before_revert function"
plumed_before_revert
fi
if [ ! -L Plumed.h -o ! -L Plumed.inc ]
then
echo "WARNING: I cannot find Plumed.h and Plumed.inc files. You have likely not patched yet."
else
- echo "Removing Plumed.h and Plumed.inc"
+ test -n "$quiet" || echo "Removing Plumed.h and Plumed.inc"
rm Plumed.h Plumed.inc Plumed.cmake
fi
PREPLUMED=$(find . -name "*.preplumed")
if ! test "$PREPLUMED" ; then
echo "No .preplumed file found, nothing to restore."
else
- echo "Reverting changes and touching reverted files"
+ test -n "$quiet" || echo "Reverting changes and touching reverted files"
for bckfile in $PREPLUMED ; do
file="${bckfile%.preplumed}"
mv "$bckfile" "$file"
@@ -297,7 +365,7 @@ EOF
done
fi
if type -t plumed_after_revert 1>/dev/null ; then
- echo "Executing plumed_after_revert function"
+ test -n "$quiet" || echo "Executing plumed_after_revert function"
plumed_after_revert
fi
esac
diff --git a/patches/qespresso-5.0.2.config b/patches/qespresso-5.0.2.config
index 84c8e48453a9c74b3998ecf58c1ef6fe42d95a5d..f7c7b6ff5255426bf2178facfc72cc428d32e120 100644
--- a/patches/qespresso-5.0.2.config
+++ b/patches/qespresso-5.0.2.config
@@ -15,3 +15,9 @@ awk '{if($1=="LIBS" && $2=="="){print $0" $(PLUMED_LOAD) "}else{print }}' make.s
function plumed_after_revert(){
mv make.sys.old make.sys
}
+
+function plumed_patch_info(){
+ echo ""
+ echo "For more information on Quantum Espresso you should visit http://www.quantum-espresso.org"
+}
+
diff --git a/patches/qespresso-5.0.2.diff b/patches/qespresso-5.0.2.diff
deleted file mode 100644
index e260c8849860bdcf5ad1aab0c938123713fc5358..0000000000000000000000000000000000000000
--- a/patches/qespresso-5.0.2.diff
+++ /dev/null
@@ -1,149 +0,0 @@
-patch -u -l -b -F 5 --suffix=.preplumed "./PW/src/forces.f90" << \EOF_EOF
---- ./PW/src/forces.f90.preplumed
-+++ ./PW/src/forces.f90
-@@ -247,11 +247,13 @@
- !
- IF( textfor ) force(:,:) = force(:,:) + extfor(:,:)
- !
- ! ... call void routine for user define/ plugin patches on forces
- !
-- CALL plugin_forces()
-+ ! plugin should be called after stress has been computed
-+ ! Look in pwscf.f90
-+ ! CALL plugin_forces()
- !
- ! ... write on output the forces
- !
- DO na = 1, nat
- !
-EOF_EOF
-patch -u -l -b -F 5 --suffix=.preplumed "./PW/src/plugin_forces.f90" << \EOF_EOF
---- ./PW/src/plugin_forces.f90.preplumed
-+++ ./PW/src/plugin_forces.f90
-@@ -16,9 +16,51 @@
- USE kinds, ONLY : DP
- USE io_files, ONLY : outdir
- !
- USE plugin_flags
- !
-+ USE cell_base, ONLY : alat, at
-+ USE ions_base, ONLY : tau, nat,amass
-+ USE force_mod, ONLY : force,sigma
-+ USE control_flags, ONLY : istep
-+ USE ener, ONLY : etot
-+ !
- IMPLICIT NONE
- !
-+ INTEGER:: i,j
-+ REAL(DP) :: at_plumed(3,3)
-+ REAL(DP) :: virial(3,3)
-+ REAL(DP) :: volume
-+ REAL(DP), ALLOCATABLE :: tau_plumed(:,:)
-+ !
-+ IF(use_plumed) then
-+ IF(ionode)THEN
-+ at_plumed=alat*at; ! the cell, rescaled properly
-+ allocate(tau_plumed(3,nat))
-+ tau_plumed=alat*tau
-+ volume=+at_plumed(1,1)*at_plumed(2,2)*at_plumed(3,3) &
-+ +at_plumed(1,2)*at_plumed(2,3)*at_plumed(3,1) &
-+ +at_plumed(1,3)*at_plumed(2,1)*at_plumed(3,2) &
-+ -at_plumed(1,1)*at_plumed(3,2)*at_plumed(2,3) &
-+ -at_plumed(1,2)*at_plumed(3,3)*at_plumed(2,1) &
-+ -at_plumed(1,3)*at_plumed(3,1)*at_plumed(2,2)
-+ virial=-sigma*volume
-+
-+ CALL plumed_f_gcmd("setStep"//char(0),istep)
-+ CALL plumed_f_gcmd("setMasses"//char(0),amass)
-+ CALL plumed_f_gcmd("setForces"//char(0),force)
-+ CALL plumed_f_gcmd("setPositions"//char(0),tau_plumed)
-+ CALL plumed_f_gcmd("setBox"//char(0),at_plumed)
-+ CALL plumed_f_gcmd("setVirial"//char(0),virial)
-+ CALL plumed_f_gcmd("setEnergy"//char(0),etot)
-+ CALL plumed_f_gcmd("calc"//char(0),0)
-+
-+ sigma=-virial/volume
-+
-+ deallocate(tau_plumed)
-+ ENDIF
-+ CALL mp_bcast(force, ionode_id, intra_image_comm)
-+ CALL mp_bcast(sigma, ionode_id, intra_image_comm)
-+ ENDIF
-+ !
- !
- END SUBROUTINE plugin_forces
-EOF_EOF
-patch -u -l -b -F 5 --suffix=.preplumed "./PW/src/plugin_initialization.f90" << \EOF_EOF
---- ./PW/src/plugin_initialization.f90.preplumed
-+++ ./PW/src/plugin_initialization.f90
-@@ -13,9 +13,50 @@
- USE kinds, ONLY : DP
- USE io_files, ONLY : tmp_dir
- !
- USE plugin_flags
- !
-+ USE ions_base, ONLY : amass, ityp, nat
-+ !
-+ USE dynamics_module, ONLY : dt
-+ USE constants, ONLY : au_ps
-+ !
-+ !
- IMPLICIT NONE
- !
-+ INTEGER :: na
-+ INTEGER :: plumedavailable
-+ REAL*8 :: energyUnits,lengthUnits,timeUnits
-+ !
-+ IF(use_plumed) then
-+
-+ CALL plumed_f_installed(plumedavailable)
-+
-+ IF(plumedavailable<=0)THEN
-+ write(stdout,*)"YOU ARE LOOKING FOR PLUMED BUT LOOKS LIKE IT IS NOT AVAILABLE: DO YOU HAVE IT IN YOUR LD_LIBRARY_PATH?"
-+ STOP
-+ ELSE
-+ IF (ionode) THEN
-+
-+ write(stdout,*)" CREATING PLUMED FROM THE PROGRAM"
-+ call plumed_f_gcreate()
-+ CALL plumed_f_gcmd("setRealPrecision"//char(0),8)
-+ energyUnits=1312.75 ! Ry to kjoule mol
-+ lengthUnits=0.0529177249 ! bohr to nm
-+ timeUnits=2*au_ps ! internal time to ps
-+ call plumed_f_gcmd("setMDEnergyUnits"//char(0),energyUnits)
-+ call plumed_f_gcmd("setMDLengthUnits"//char(0),lengthUnits)
-+ call plumed_f_gcmd("setMDTimeUnits"//char(0),timeUnits)
-+ call plumed_f_gcmd("setPlumedDat"//char(0),"plumed.dat"//char(0))
-+ call plumed_f_gcmd("setLogFile"//char(0),"PLUMED.OUT"//char(0))
-+ call plumed_f_gcmd("setNatoms"//char(0),nat)
-+ call plumed_f_gcmd("setMDEngine"//char(0),"qespresso");
-+ call plumed_f_gcmd("setTimestep"//char(0),dt);
-+ call plumed_f_gcmd("init"//char(0),0);
-+
-+
-+ ENDIF
-+ ENDIF
-+ ENDIF
-+ !
- !
- END SUBROUTINE plugin_initialization
-EOF_EOF
-patch -u -l -b -F 5 --suffix=.preplumed "./PW/src/pwscf.f90" << \EOF_EOF
---- ./PW/src/pwscf.f90.preplumed
-+++ ./PW/src/pwscf.f90
-@@ -126,10 +126,14 @@
- !
- ! ... stress calculation
- !
- IF ( lstres ) CALL stress ( sigma )
- !
-+ ! ... this is the right place for plugin forces:
-+ !
-+ CALL plugin_forces()
-+ !
- IF ( lmd .OR. lbfgs ) THEN
- !
- if (fix_volume) CALL impose_deviatoric_stress(sigma)
- !
- if (fix_area) CALL impose_deviatoric_stress_2d(sigma)
-EOF_EOF
diff --git a/patches/qespresso-5.0.2.diff/PW/src/forces.f90 b/patches/qespresso-5.0.2.diff/PW/src/forces.f90
new file mode 100644
index 0000000000000000000000000000000000000000..6f37122b9371019fcbc7e3f307c9c8356ddb8396
--- /dev/null
+++ b/patches/qespresso-5.0.2.diff/PW/src/forces.f90
@@ -0,0 +1,368 @@
+!
+! Copyright (C) 2001-2011 Quantum ESPRESSO group
+! This file is distributed under the terms of the
+! GNU General Public License. See the file `License'
+! in the root directory of the present distribution,
+! or http://www.gnu.org/copyleft/gpl.txt .
+!
+!
+!----------------------------------------------------------------------------
+SUBROUTINE forces()
+ !----------------------------------------------------------------------------
+ !
+ ! ... This routine is a driver routine which computes the forces
+ ! ... acting on the atoms. The complete expression of the forces
+ ! ... contains four parts which are computed by different routines:
+ !
+ ! ... a) force_lc, local contribution to the forces
+ ! ... b) force_cc, contribution due to NLCC
+ ! ... c) force_ew, contribution due to the electrostatic ewald term
+ ! ... d) force_us, contribution due to the non-local potential
+ ! ... e) force_corr, correction term for incomplete self-consistency
+ ! ... f) force_hub, contribution due to the Hubbard term
+ ! ... g) force_london, semi-empirical correction for dispersion forces
+ !
+ !
+ USE kinds, ONLY : DP
+ USE io_global, ONLY : stdout
+ USE cell_base, ONLY : at, bg, alat, omega
+ USE ions_base, ONLY : nat, ntyp => nsp, ityp, tau, zv, amass, extfor
+ USE fft_base, ONLY : dfftp
+ USE gvect, ONLY : ngm, gstart, ngl, nl, igtongl, g, gg, gcutm
+ USE lsda_mod, ONLY : nspin
+ USE symme, ONLY : symvector
+ USE vlocal, ONLY : strf, vloc
+ USE force_mod, ONLY : force, lforce
+ USE scf, ONLY : rho
+ USE ions_base, ONLY : if_pos
+ USE ldaU, ONLY : lda_plus_u, U_projection
+ USE extfield, ONLY : tefield, forcefield
+ USE control_flags, ONLY : gamma_only, remove_rigid_rot, textfor, &
+ iverbosity, llondon
+#ifdef __ENVIRON
+ USE environ_base, ONLY : do_environ, env_static_permittivity, rhopol
+ USE fft_interfaces, ONLY : fwfft
+#endif
+ USE bp, ONLY : lelfield, gdir, l3dstring, efield_cart, &
+ efield_cry,efield
+ USE uspp, ONLY : okvan
+ USE martyna_tuckerman, ONLY: do_comp_mt, wg_corr_force
+ USE london_module, ONLY : force_london
+ !
+ IMPLICIT NONE
+ !
+ REAL(DP), ALLOCATABLE :: forcenl(:,:), &
+ forcelc(:,:), &
+ forcecc(:,:), &
+ forceion(:,:), &
+ force_disp(:,:),&
+ force_mt(:,:), &
+ forcescc(:,:), &
+ forces_bp_efield(:,:), &
+ forceh(:,:)
+ ! nonlocal, local, core-correction, ewald, scf correction terms, and hubbard
+#ifdef __ENVIRON
+ REAL(DP), ALLOCATABLE :: force_environ(:,:)
+ COMPLEX(DP), ALLOCATABLE :: aux(:)
+#endif
+
+ REAL(DP) :: sumfor, sumscf, sum_mm
+ REAL(DP),PARAMETER :: eps = 1.e-12_dp
+ INTEGER :: ipol, na
+ ! counter on polarization
+ ! counter on atoms
+ !
+ !
+ CALL start_clock( 'forces' )
+ !
+ ALLOCATE( forcenl( 3, nat ), forcelc( 3, nat ), forcecc( 3, nat ), &
+ forceh( 3, nat ), forceion( 3, nat ), forcescc( 3, nat ) )
+ !
+ forcescc(:,:) = 0.D0
+ forceh(:,:) = 0.D0
+ !
+ WRITE( stdout, '(/,5x,"Forces acting on atoms (Ry/au):", / )')
+ !
+ ! ... The nonlocal contribution is computed here
+ !
+ CALL force_us( forcenl )
+ !
+ ! ... The local contribution
+ !
+ CALL force_lc( nat, tau, ityp, alat, omega, ngm, ngl, igtongl, &
+ g, rho%of_r, nl, nspin, gstart, gamma_only, vloc, &
+ forcelc )
+ !
+ ! ... The NLCC contribution
+ !
+ CALL force_cc( forcecc )
+ !
+ ! ... The Hubbard contribution
+ ! (included by force_us if using beta as local projectors)
+ !
+ IF ( lda_plus_u .AND. U_projection.NE.'pseudo' ) CALL force_hub( forceh )
+ !
+ ! ... The ionic contribution is computed here
+ !
+ CALL force_ew( alat, nat, ntyp, ityp, zv, at, bg, tau, omega, g, &
+ gg, ngm, gstart, gamma_only, gcutm, strf, forceion )
+ !
+ ! ... the semi-empirical dispersion correction
+ !
+ IF ( llondon ) THEN
+ !
+ ALLOCATE ( force_disp ( 3 , nat ) )
+ force_disp ( : , : ) = 0.0_DP
+ force_disp = force_london( alat , nat , ityp , at , bg , tau )
+ !
+ END IF
+
+ !
+ ! ... The SCF contribution
+ !
+ CALL force_corr( forcescc )
+ !
+ IF (do_comp_mt) THEN
+ !
+ ALLOCATE ( force_mt ( 3 , nat ) )
+#ifdef __ENVIRON
+ IF ( do_environ .AND. env_static_permittivity .GT. 1.D0 ) THEN
+ ALLOCATE( aux( dfftp%nnr ) )
+ aux(:) = CMPLX(rhopol( : ),0.D0,kind=dp)
+ CALL fwfft ('Dense', aux, dfftp)
+ rho%of_g(:,1) = rho%of_g(:,1) + aux(nl(:))
+ ENDIF
+#endif
+ CALL wg_corr_force( omega, nat, ntyp, ityp, ngm, g, tau, zv, strf, &
+ nspin, rho%of_g, force_mt )
+#ifdef __ENVIRON
+ IF ( do_environ .AND. env_static_permittivity .GT. 1.D0 ) THEN
+ rho%of_g(:,1) = rho%of_g(:,1) - aux(nl(:))
+ DEALLOCATE(aux)
+ ENDIF
+#endif
+
+ END IF
+#ifdef __ENVIRON
+ IF (do_environ) THEN
+ !
+ ! ... The external environment contribution
+ !
+ ALLOCATE ( force_environ ( 3 , nat ) )
+ force_environ = 0.0_DP
+ !
+ ! ... Computes here the solvent contribution
+ !
+ IF ( env_static_permittivity .GT. 1.D0 ) &
+ CALL force_lc( nat, tau, ityp, alat, omega, ngm, ngl, igtongl, &
+ g, rhopol, nl, 1, gstart, gamma_only, vloc, &
+ force_environ )
+ !
+ ! ... Add the other environment contributions
+ !
+ CALL calc_fenviron( dfftp%nnr, nat, force_environ )
+ !
+ END IF
+ !
+#endif
+ !
+ ! Berry's phase electric field terms
+ !
+ if(lelfield) then
+ ALLOCATE ( forces_bp_efield (3,nat) )
+ forces_bp_efield(:,:)=0.d0
+ if(.not.l3dstring) then
+ if(okvan) call forces_us_efield(forces_bp_efield,gdir,efield)
+ call forces_ion_efield(forces_bp_efield,gdir,efield)
+ else
+ if(okvan)then
+ do ipol=1,3
+ call forces_us_efield(forces_bp_efield,ipol,efield_cry(ipol))
+ enddo
+ endif
+ do ipol=1,3
+ call forces_ion_efield(forces_bp_efield,ipol,efield_cart(ipol))
+ enddo
+ endif
+ endif
+ !
+ ! ... here we sum all the contributions and compute the total force acting
+ ! ... on the crstal
+ !
+ DO ipol = 1, 3
+ !
+ sumfor = 0.D0
+ !
+ DO na = 1, nat
+ !
+ force(ipol,na) = forcenl(ipol,na) + &
+ forceion(ipol,na) + &
+ forcelc(ipol,na) + &
+ forcecc(ipol,na) + &
+ forceh(ipol,na) + &
+ forcescc(ipol,na)
+ !
+ IF ( llondon ) force(ipol,na) = force(ipol,na) + force_disp(ipol,na)
+ IF ( tefield ) force(ipol,na) = force(ipol,na) + forcefield(ipol,na)
+ IF (lelfield) force(ipol,na) = force(ipol,na) + forces_bp_efield(ipol,na)
+ IF (do_comp_mt)force(ipol,na) = force(ipol,na) + force_mt(ipol,na)
+! DCC
+! IF (do_comp) force(ipol,na) = force(ipol,na) + force_vcorr(ipol,na)
+#ifdef __ENVIRON
+ IF (do_environ) force(ipol,na) = force(ipol,na) + force_environ(ipol,na)
+#endif
+
+ sumfor = sumfor + force(ipol,na)
+ !
+ END DO
+ !
+ ! ... impose total force = 0
+ !
+ DO na = 1, nat
+ !
+ force(ipol,na) = force(ipol,na) - sumfor / DBLE( nat )
+ !
+ END DO
+ !
+#ifdef __MS2
+ !
+ ! ... impose total force of the quantum subsystem /= 0
+ !
+ DO na = 1, nat
+ !
+ force(ipol,na) = force(ipol,na) + sumfor / DBLE( nat )
+ !
+ END DO
+ !
+#endif
+ !
+ END DO
+ !
+ ! ... resymmetrize (should not be needed, but ...)
+ !
+ CALL symvector ( nat, force )
+ !
+ IF ( remove_rigid_rot ) &
+ CALL remove_tot_torque( nat, tau, amass(ityp(:)), force )
+ !
+ IF( textfor ) force(:,:) = force(:,:) + extfor(:,:)
+ !
+ ! ... call void routine for user define/ plugin patches on forces
+ !
+ ! plugin should be called after stress has been computed
+ ! Look in pwscf.f90
+ ! CALL plugin_forces()
+ !
+ ! ... write on output the forces
+ !
+ DO na = 1, nat
+ !
+ WRITE( stdout, 9035) na, ityp(na), force(:,na)
+ !
+ END DO
+ !
+ ! ... forces on fixed coordinates are set to zero ( C.S. 15/10/2003 )
+ !
+ force(:,:) = force(:,:) * DBLE( if_pos )
+ forcescc(:,:) = forcescc(:,:) * DBLE( if_pos )
+ !
+ IF ( iverbosity > 0 ) THEN
+ IF ( do_comp_mt ) THEN
+ WRITE( stdout, '(5x,"The Martyna-Tuckerman correction term to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( force_mt(ipol,na), ipol = 1, 3 )
+ END DO
+ END IF
+ !
+ WRITE( stdout, '(5x,"The non-local contrib. to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forcenl(ipol,na), ipol = 1, 3 )
+ END DO
+ WRITE( stdout, '(5x,"The ionic contribution to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forceion(ipol,na), ipol = 1, 3 )
+ END DO
+ WRITE( stdout, '(5x,"The local contribution to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forcelc(ipol,na), ipol = 1, 3 )
+ END DO
+ WRITE( stdout, '(5x,"The core correction contribution to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forcecc(ipol,na), ipol = 1, 3 )
+ END DO
+ WRITE( stdout, '(5x,"The Hubbard contrib. to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forceh(ipol,na), ipol = 1, 3 )
+ END DO
+ WRITE( stdout, '(5x,"The SCF correction term to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forcescc(ipol,na), ipol = 1, 3 )
+ END DO
+#ifdef __ENVIRON
+ IF ( do_environ ) THEN
+ WRITE( stdout, '(5x,"The external environment correction to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( force_environ(ipol,na), ipol = 1, 3 )
+ END DO
+ END IF
+#endif
+ !
+ IF ( llondon) THEN
+ WRITE( stdout, '(/,5x,"Dispersion contribution to forces:")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), (force_disp(ipol,na), ipol = 1, 3)
+ END DO
+ END IF
+ !
+ END IF
+ !
+ sumfor = 0.D0
+ sumscf = 0.D0
+ !
+ DO na = 1, nat
+ !
+ sumfor = sumfor + force(1,na)**2 + force(2,na)**2 + force(3,na)**2
+ sumscf = sumscf + forcescc(1,na)**2 + forcescc(2,na)**2+ forcescc(3,na)**2
+ !
+ END DO
+ !
+ sumfor = SQRT( sumfor )
+ sumscf = SQRT( sumscf )
+ !
+ WRITE( stdout, '(/5x,"Total force = ",F12.6,5X, &
+ & "Total SCF correction = ",F12.6)') sumfor, sumscf
+ !
+ IF ( llondon .AND. iverbosity > 0 ) THEN
+ !
+ sum_mm = 0.D0
+ DO na = 1, nat
+ sum_mm = sum_mm + &
+ force_disp(1,na)**2 + force_disp(2,na)**2 + force_disp(3,na)**2
+ END DO
+ sum_mm = SQRT( sum_mm )
+ WRITE ( stdout, '(/,5x, "Total Dispersion Force = ",F12.6)') sum_mm
+ !
+ END IF
+ !
+ DEALLOCATE( forcenl, forcelc, forcecc, forceh, forceion, forcescc )
+ IF ( llondon ) DEALLOCATE ( force_disp )
+ IF ( lelfield ) DEALLOCATE ( forces_bp_efield )
+ !
+ lforce = .TRUE.
+ !
+ CALL stop_clock( 'forces' )
+ !
+ IF ( ( sumfor < 10.D0*sumscf ) .AND. ( sumfor > eps ) ) &
+ WRITE( stdout,'(5x,"SCF correction compared to forces is large: ", &
+ & "reduce conv_thr to get better values")')
+ !
+ IF(ALLOCATED(force_mt)) DEALLOCATE( force_mt )
+#ifdef __ENVIRON
+ IF(ALLOCATED(force_environ)) DEALLOCATE( force_environ )
+#endif
+
+ RETURN
+ !
+9035 FORMAT(5X,'atom ',I4,' type ',I2,' force = ',3F14.8)
+ !
+END SUBROUTINE forces
diff --git a/patches/qespresso-5.0.2.diff/PW/src/forces.f90.preplumed b/patches/qespresso-5.0.2.diff/PW/src/forces.f90.preplumed
new file mode 100644
index 0000000000000000000000000000000000000000..e51fad41de8fc4fadfe904fecde3fcf84d579ac0
--- /dev/null
+++ b/patches/qespresso-5.0.2.diff/PW/src/forces.f90.preplumed
@@ -0,0 +1,366 @@
+!
+! Copyright (C) 2001-2011 Quantum ESPRESSO group
+! This file is distributed under the terms of the
+! GNU General Public License. See the file `License'
+! in the root directory of the present distribution,
+! or http://www.gnu.org/copyleft/gpl.txt .
+!
+!
+!----------------------------------------------------------------------------
+SUBROUTINE forces()
+ !----------------------------------------------------------------------------
+ !
+ ! ... This routine is a driver routine which computes the forces
+ ! ... acting on the atoms. The complete expression of the forces
+ ! ... contains four parts which are computed by different routines:
+ !
+ ! ... a) force_lc, local contribution to the forces
+ ! ... b) force_cc, contribution due to NLCC
+ ! ... c) force_ew, contribution due to the electrostatic ewald term
+ ! ... d) force_us, contribution due to the non-local potential
+ ! ... e) force_corr, correction term for incomplete self-consistency
+ ! ... f) force_hub, contribution due to the Hubbard term
+ ! ... g) force_london, semi-empirical correction for dispersion forces
+ !
+ !
+ USE kinds, ONLY : DP
+ USE io_global, ONLY : stdout
+ USE cell_base, ONLY : at, bg, alat, omega
+ USE ions_base, ONLY : nat, ntyp => nsp, ityp, tau, zv, amass, extfor
+ USE fft_base, ONLY : dfftp
+ USE gvect, ONLY : ngm, gstart, ngl, nl, igtongl, g, gg, gcutm
+ USE lsda_mod, ONLY : nspin
+ USE symme, ONLY : symvector
+ USE vlocal, ONLY : strf, vloc
+ USE force_mod, ONLY : force, lforce
+ USE scf, ONLY : rho
+ USE ions_base, ONLY : if_pos
+ USE ldaU, ONLY : lda_plus_u, U_projection
+ USE extfield, ONLY : tefield, forcefield
+ USE control_flags, ONLY : gamma_only, remove_rigid_rot, textfor, &
+ iverbosity, llondon
+#ifdef __ENVIRON
+ USE environ_base, ONLY : do_environ, env_static_permittivity, rhopol
+ USE fft_interfaces, ONLY : fwfft
+#endif
+ USE bp, ONLY : lelfield, gdir, l3dstring, efield_cart, &
+ efield_cry,efield
+ USE uspp, ONLY : okvan
+ USE martyna_tuckerman, ONLY: do_comp_mt, wg_corr_force
+ USE london_module, ONLY : force_london
+ !
+ IMPLICIT NONE
+ !
+ REAL(DP), ALLOCATABLE :: forcenl(:,:), &
+ forcelc(:,:), &
+ forcecc(:,:), &
+ forceion(:,:), &
+ force_disp(:,:),&
+ force_mt(:,:), &
+ forcescc(:,:), &
+ forces_bp_efield(:,:), &
+ forceh(:,:)
+ ! nonlocal, local, core-correction, ewald, scf correction terms, and hubbard
+#ifdef __ENVIRON
+ REAL(DP), ALLOCATABLE :: force_environ(:,:)
+ COMPLEX(DP), ALLOCATABLE :: aux(:)
+#endif
+
+ REAL(DP) :: sumfor, sumscf, sum_mm
+ REAL(DP),PARAMETER :: eps = 1.e-12_dp
+ INTEGER :: ipol, na
+ ! counter on polarization
+ ! counter on atoms
+ !
+ !
+ CALL start_clock( 'forces' )
+ !
+ ALLOCATE( forcenl( 3, nat ), forcelc( 3, nat ), forcecc( 3, nat ), &
+ forceh( 3, nat ), forceion( 3, nat ), forcescc( 3, nat ) )
+ !
+ forcescc(:,:) = 0.D0
+ forceh(:,:) = 0.D0
+ !
+ WRITE( stdout, '(/,5x,"Forces acting on atoms (Ry/au):", / )')
+ !
+ ! ... The nonlocal contribution is computed here
+ !
+ CALL force_us( forcenl )
+ !
+ ! ... The local contribution
+ !
+ CALL force_lc( nat, tau, ityp, alat, omega, ngm, ngl, igtongl, &
+ g, rho%of_r, nl, nspin, gstart, gamma_only, vloc, &
+ forcelc )
+ !
+ ! ... The NLCC contribution
+ !
+ CALL force_cc( forcecc )
+ !
+ ! ... The Hubbard contribution
+ ! (included by force_us if using beta as local projectors)
+ !
+ IF ( lda_plus_u .AND. U_projection.NE.'pseudo' ) CALL force_hub( forceh )
+ !
+ ! ... The ionic contribution is computed here
+ !
+ CALL force_ew( alat, nat, ntyp, ityp, zv, at, bg, tau, omega, g, &
+ gg, ngm, gstart, gamma_only, gcutm, strf, forceion )
+ !
+ ! ... the semi-empirical dispersion correction
+ !
+ IF ( llondon ) THEN
+ !
+ ALLOCATE ( force_disp ( 3 , nat ) )
+ force_disp ( : , : ) = 0.0_DP
+ force_disp = force_london( alat , nat , ityp , at , bg , tau )
+ !
+ END IF
+
+ !
+ ! ... The SCF contribution
+ !
+ CALL force_corr( forcescc )
+ !
+ IF (do_comp_mt) THEN
+ !
+ ALLOCATE ( force_mt ( 3 , nat ) )
+#ifdef __ENVIRON
+ IF ( do_environ .AND. env_static_permittivity .GT. 1.D0 ) THEN
+ ALLOCATE( aux( dfftp%nnr ) )
+ aux(:) = CMPLX(rhopol( : ),0.D0,kind=dp)
+ CALL fwfft ('Dense', aux, dfftp)
+ rho%of_g(:,1) = rho%of_g(:,1) + aux(nl(:))
+ ENDIF
+#endif
+ CALL wg_corr_force( omega, nat, ntyp, ityp, ngm, g, tau, zv, strf, &
+ nspin, rho%of_g, force_mt )
+#ifdef __ENVIRON
+ IF ( do_environ .AND. env_static_permittivity .GT. 1.D0 ) THEN
+ rho%of_g(:,1) = rho%of_g(:,1) - aux(nl(:))
+ DEALLOCATE(aux)
+ ENDIF
+#endif
+
+ END IF
+#ifdef __ENVIRON
+ IF (do_environ) THEN
+ !
+ ! ... The external environment contribution
+ !
+ ALLOCATE ( force_environ ( 3 , nat ) )
+ force_environ = 0.0_DP
+ !
+ ! ... Computes here the solvent contribution
+ !
+ IF ( env_static_permittivity .GT. 1.D0 ) &
+ CALL force_lc( nat, tau, ityp, alat, omega, ngm, ngl, igtongl, &
+ g, rhopol, nl, 1, gstart, gamma_only, vloc, &
+ force_environ )
+ !
+ ! ... Add the other environment contributions
+ !
+ CALL calc_fenviron( dfftp%nnr, nat, force_environ )
+ !
+ END IF
+ !
+#endif
+ !
+ ! Berry's phase electric field terms
+ !
+ if(lelfield) then
+ ALLOCATE ( forces_bp_efield (3,nat) )
+ forces_bp_efield(:,:)=0.d0
+ if(.not.l3dstring) then
+ if(okvan) call forces_us_efield(forces_bp_efield,gdir,efield)
+ call forces_ion_efield(forces_bp_efield,gdir,efield)
+ else
+ if(okvan)then
+ do ipol=1,3
+ call forces_us_efield(forces_bp_efield,ipol,efield_cry(ipol))
+ enddo
+ endif
+ do ipol=1,3
+ call forces_ion_efield(forces_bp_efield,ipol,efield_cart(ipol))
+ enddo
+ endif
+ endif
+ !
+ ! ... here we sum all the contributions and compute the total force acting
+ ! ... on the crstal
+ !
+ DO ipol = 1, 3
+ !
+ sumfor = 0.D0
+ !
+ DO na = 1, nat
+ !
+ force(ipol,na) = forcenl(ipol,na) + &
+ forceion(ipol,na) + &
+ forcelc(ipol,na) + &
+ forcecc(ipol,na) + &
+ forceh(ipol,na) + &
+ forcescc(ipol,na)
+ !
+ IF ( llondon ) force(ipol,na) = force(ipol,na) + force_disp(ipol,na)
+ IF ( tefield ) force(ipol,na) = force(ipol,na) + forcefield(ipol,na)
+ IF (lelfield) force(ipol,na) = force(ipol,na) + forces_bp_efield(ipol,na)
+ IF (do_comp_mt)force(ipol,na) = force(ipol,na) + force_mt(ipol,na)
+! DCC
+! IF (do_comp) force(ipol,na) = force(ipol,na) + force_vcorr(ipol,na)
+#ifdef __ENVIRON
+ IF (do_environ) force(ipol,na) = force(ipol,na) + force_environ(ipol,na)
+#endif
+
+ sumfor = sumfor + force(ipol,na)
+ !
+ END DO
+ !
+ ! ... impose total force = 0
+ !
+ DO na = 1, nat
+ !
+ force(ipol,na) = force(ipol,na) - sumfor / DBLE( nat )
+ !
+ END DO
+ !
+#ifdef __MS2
+ !
+ ! ... impose total force of the quantum subsystem /= 0
+ !
+ DO na = 1, nat
+ !
+ force(ipol,na) = force(ipol,na) + sumfor / DBLE( nat )
+ !
+ END DO
+ !
+#endif
+ !
+ END DO
+ !
+ ! ... resymmetrize (should not be needed, but ...)
+ !
+ CALL symvector ( nat, force )
+ !
+ IF ( remove_rigid_rot ) &
+ CALL remove_tot_torque( nat, tau, amass(ityp(:)), force )
+ !
+ IF( textfor ) force(:,:) = force(:,:) + extfor(:,:)
+ !
+ ! ... call void routine for user define/ plugin patches on forces
+ !
+ CALL plugin_forces()
+ !
+ ! ... write on output the forces
+ !
+ DO na = 1, nat
+ !
+ WRITE( stdout, 9035) na, ityp(na), force(:,na)
+ !
+ END DO
+ !
+ ! ... forces on fixed coordinates are set to zero ( C.S. 15/10/2003 )
+ !
+ force(:,:) = force(:,:) * DBLE( if_pos )
+ forcescc(:,:) = forcescc(:,:) * DBLE( if_pos )
+ !
+ IF ( iverbosity > 0 ) THEN
+ IF ( do_comp_mt ) THEN
+ WRITE( stdout, '(5x,"The Martyna-Tuckerman correction term to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( force_mt(ipol,na), ipol = 1, 3 )
+ END DO
+ END IF
+ !
+ WRITE( stdout, '(5x,"The non-local contrib. to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forcenl(ipol,na), ipol = 1, 3 )
+ END DO
+ WRITE( stdout, '(5x,"The ionic contribution to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forceion(ipol,na), ipol = 1, 3 )
+ END DO
+ WRITE( stdout, '(5x,"The local contribution to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forcelc(ipol,na), ipol = 1, 3 )
+ END DO
+ WRITE( stdout, '(5x,"The core correction contribution to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forcecc(ipol,na), ipol = 1, 3 )
+ END DO
+ WRITE( stdout, '(5x,"The Hubbard contrib. to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forceh(ipol,na), ipol = 1, 3 )
+ END DO
+ WRITE( stdout, '(5x,"The SCF correction term to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( forcescc(ipol,na), ipol = 1, 3 )
+ END DO
+#ifdef __ENVIRON
+ IF ( do_environ ) THEN
+ WRITE( stdout, '(5x,"The external environment correction to forces")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), ( force_environ(ipol,na), ipol = 1, 3 )
+ END DO
+ END IF
+#endif
+ !
+ IF ( llondon) THEN
+ WRITE( stdout, '(/,5x,"Dispersion contribution to forces:")')
+ DO na = 1, nat
+ WRITE( stdout, 9035) na, ityp(na), (force_disp(ipol,na), ipol = 1, 3)
+ END DO
+ END IF
+ !
+ END IF
+ !
+ sumfor = 0.D0
+ sumscf = 0.D0
+ !
+ DO na = 1, nat
+ !
+ sumfor = sumfor + force(1,na)**2 + force(2,na)**2 + force(3,na)**2
+ sumscf = sumscf + forcescc(1,na)**2 + forcescc(2,na)**2+ forcescc(3,na)**2
+ !
+ END DO
+ !
+ sumfor = SQRT( sumfor )
+ sumscf = SQRT( sumscf )
+ !
+ WRITE( stdout, '(/5x,"Total force = ",F12.6,5X, &
+ & "Total SCF correction = ",F12.6)') sumfor, sumscf
+ !
+ IF ( llondon .AND. iverbosity > 0 ) THEN
+ !
+ sum_mm = 0.D0
+ DO na = 1, nat
+ sum_mm = sum_mm + &
+ force_disp(1,na)**2 + force_disp(2,na)**2 + force_disp(3,na)**2
+ END DO
+ sum_mm = SQRT( sum_mm )
+ WRITE ( stdout, '(/,5x, "Total Dispersion Force = ",F12.6)') sum_mm
+ !
+ END IF
+ !
+ DEALLOCATE( forcenl, forcelc, forcecc, forceh, forceion, forcescc )
+ IF ( llondon ) DEALLOCATE ( force_disp )
+ IF ( lelfield ) DEALLOCATE ( forces_bp_efield )
+ !
+ lforce = .TRUE.
+ !
+ CALL stop_clock( 'forces' )
+ !
+ IF ( ( sumfor < 10.D0*sumscf ) .AND. ( sumfor > eps ) ) &
+ WRITE( stdout,'(5x,"SCF correction compared to forces is large: ", &
+ & "reduce conv_thr to get better values")')
+ !
+ IF(ALLOCATED(force_mt)) DEALLOCATE( force_mt )
+#ifdef __ENVIRON
+ IF(ALLOCATED(force_environ)) DEALLOCATE( force_environ )
+#endif
+
+ RETURN
+ !
+9035 FORMAT(5X,'atom ',I4,' type ',I2,' force = ',3F14.8)
+ !
+END SUBROUTINE forces
diff --git a/patches/qespresso-5.0.2.diff/PW/src/plugin_forces.f90 b/patches/qespresso-5.0.2.diff/PW/src/plugin_forces.f90
new file mode 100644
index 0000000000000000000000000000000000000000..2eb91290e44d369cea7187950d8f1e142d7241e2
--- /dev/null
+++ b/patches/qespresso-5.0.2.diff/PW/src/plugin_forces.f90
@@ -0,0 +1,66 @@
+!
+! Copyright (C) 2001-2009 Quantum ESPRESSO group
+! This file is distributed under the terms of the
+! GNU General Public License. See the file `License'
+! in the root directory of the present distribution,
+! or http://www.gnu.org/copyleft/gpl.txt .
+!
+!----------------------------------------------------------------------------
+SUBROUTINE plugin_forces()
+ !----------------------------------------------------------------------------
+ !
+ !
+ USE mp_global, ONLY : intra_image_comm
+ USE mp, ONLY : mp_bcast
+ USE io_global, ONLY : stdout, ionode, ionode_id
+ USE kinds, ONLY : DP
+ USE io_files, ONLY : outdir
+ !
+ USE plugin_flags
+ !
+ USE cell_base, ONLY : alat, at
+ USE ions_base, ONLY : tau, nat,amass
+ USE force_mod, ONLY : force,sigma
+ USE control_flags, ONLY : istep
+ USE ener, ONLY : etot
+ !
+ IMPLICIT NONE
+ !
+ INTEGER:: i,j
+ REAL(DP) :: at_plumed(3,3)
+ REAL(DP) :: virial(3,3)
+ REAL(DP) :: volume
+ REAL(DP), ALLOCATABLE :: tau_plumed(:,:)
+ !
+ IF(use_plumed) then
+ IF(ionode)THEN
+ at_plumed=alat*at; ! the cell, rescaled properly
+ allocate(tau_plumed(3,nat))
+ tau_plumed=alat*tau
+ volume=+at_plumed(1,1)*at_plumed(2,2)*at_plumed(3,3) &
+ +at_plumed(1,2)*at_plumed(2,3)*at_plumed(3,1) &
+ +at_plumed(1,3)*at_plumed(2,1)*at_plumed(3,2) &
+ -at_plumed(1,1)*at_plumed(3,2)*at_plumed(2,3) &
+ -at_plumed(1,2)*at_plumed(3,3)*at_plumed(2,1) &
+ -at_plumed(1,3)*at_plumed(3,1)*at_plumed(2,2)
+ virial=-sigma*volume
+
+ CALL plumed_f_gcmd("setStep"//char(0),istep)
+ CALL plumed_f_gcmd("setMasses"//char(0),amass)
+ CALL plumed_f_gcmd("setForces"//char(0),force)
+ CALL plumed_f_gcmd("setPositions"//char(0),tau_plumed)
+ CALL plumed_f_gcmd("setBox"//char(0),at_plumed)
+ CALL plumed_f_gcmd("setVirial"//char(0),virial)
+ CALL plumed_f_gcmd("setEnergy"//char(0),etot)
+ CALL plumed_f_gcmd("calc"//char(0),0)
+
+ sigma=-virial/volume
+
+ deallocate(tau_plumed)
+ ENDIF
+ CALL mp_bcast(force, ionode_id, intra_image_comm)
+ CALL mp_bcast(sigma, ionode_id, intra_image_comm)
+ ENDIF
+ !
+ !
+END SUBROUTINE plugin_forces
diff --git a/patches/qespresso-5.0.2.diff/PW/src/plugin_forces.f90.preplumed b/patches/qespresso-5.0.2.diff/PW/src/plugin_forces.f90.preplumed
new file mode 100644
index 0000000000000000000000000000000000000000..52fdbecc2765f6b627dbe7948efba0757d5ab49a
--- /dev/null
+++ b/patches/qespresso-5.0.2.diff/PW/src/plugin_forces.f90.preplumed
@@ -0,0 +1,24 @@
+!
+! Copyright (C) 2001-2009 Quantum ESPRESSO group
+! This file is distributed under the terms of the
+! GNU General Public License. See the file `License'
+! in the root directory of the present distribution,
+! or http://www.gnu.org/copyleft/gpl.txt .
+!
+!----------------------------------------------------------------------------
+SUBROUTINE plugin_forces()
+ !----------------------------------------------------------------------------
+ !
+ !
+ USE mp_global, ONLY : intra_image_comm
+ USE mp, ONLY : mp_bcast
+ USE io_global, ONLY : stdout, ionode, ionode_id
+ USE kinds, ONLY : DP
+ USE io_files, ONLY : outdir
+ !
+ USE plugin_flags
+ !
+ IMPLICIT NONE
+ !
+ !
+END SUBROUTINE plugin_forces
diff --git a/patches/qespresso-5.0.2.diff/PW/src/plugin_initialization.f90 b/patches/qespresso-5.0.2.diff/PW/src/plugin_initialization.f90
new file mode 100644
index 0000000000000000000000000000000000000000..c0c40d69fc033f5269ecaf8f8d103a0dd0e40660
--- /dev/null
+++ b/patches/qespresso-5.0.2.diff/PW/src/plugin_initialization.f90
@@ -0,0 +1,62 @@
+!
+! Copyright (C) 2010 Quantum ESPRESSO group
+! This file is distributed under the terms of the
+! GNU General Public License. See the file `License'
+! in the root directory of the present distribution,
+! or http://www.gnu.org/copyleft/gpl.txt .
+!
+!----------------------------------------------------------------------------
+SUBROUTINE plugin_initialization()
+ !----------------------------------------------------------------------------
+ !
+ USE io_global, ONLY : stdout, ionode
+ USE kinds, ONLY : DP
+ USE io_files, ONLY : tmp_dir
+ !
+ USE plugin_flags
+ !
+ USE ions_base, ONLY : amass, ityp, nat
+ !
+ USE dynamics_module, ONLY : dt
+ USE constants, ONLY : au_ps
+ !
+ !
+ IMPLICIT NONE
+ !
+ INTEGER :: na
+ INTEGER :: plumedavailable
+ REAL*8 :: energyUnits,lengthUnits,timeUnits
+ !
+ IF(use_plumed) then
+
+ CALL plumed_f_installed(plumedavailable)
+
+ IF(plumedavailable<=0)THEN
+ write(stdout,*)"YOU ARE LOOKING FOR PLUMED BUT LOOKS LIKE IT IS NOT AVAILABLE: DO YOU HAVE IT IN YOUR LD_LIBRARY_PATH?"
+ STOP
+ ELSE
+ IF (ionode) THEN
+
+ write(stdout,*)" CREATING PLUMED FROM THE PROGRAM"
+ call plumed_f_gcreate()
+ CALL plumed_f_gcmd("setRealPrecision"//char(0),8)
+ energyUnits=1312.75 ! Ry to kjoule mol
+ lengthUnits=0.0529177249 ! bohr to nm
+ timeUnits=2*au_ps ! internal time to ps
+ call plumed_f_gcmd("setMDEnergyUnits"//char(0),energyUnits)
+ call plumed_f_gcmd("setMDLengthUnits"//char(0),lengthUnits)
+ call plumed_f_gcmd("setMDTimeUnits"//char(0),timeUnits)
+ call plumed_f_gcmd("setPlumedDat"//char(0),"plumed.dat"//char(0))
+ call plumed_f_gcmd("setLogFile"//char(0),"PLUMED.OUT"//char(0))
+ call plumed_f_gcmd("setNatoms"//char(0),nat)
+ call plumed_f_gcmd("setMDEngine"//char(0),"qespresso");
+ call plumed_f_gcmd("setTimestep"//char(0),dt);
+ call plumed_f_gcmd("init"//char(0),0);
+
+
+ ENDIF
+ ENDIF
+ ENDIF
+ !
+ !
+END SUBROUTINE plugin_initialization
diff --git a/patches/qespresso-5.0.2.diff/PW/src/plugin_initialization.f90.preplumed b/patches/qespresso-5.0.2.diff/PW/src/plugin_initialization.f90.preplumed
new file mode 100644
index 0000000000000000000000000000000000000000..f2c9c0097f7c6232cab5b63ddff934f7c3dee1ae
--- /dev/null
+++ b/patches/qespresso-5.0.2.diff/PW/src/plugin_initialization.f90.preplumed
@@ -0,0 +1,21 @@
+!
+! Copyright (C) 2010 Quantum ESPRESSO group
+! This file is distributed under the terms of the
+! GNU General Public License. See the file `License'
+! in the root directory of the present distribution,
+! or http://www.gnu.org/copyleft/gpl.txt .
+!
+!----------------------------------------------------------------------------
+SUBROUTINE plugin_initialization()
+ !----------------------------------------------------------------------------
+ !
+ USE io_global, ONLY : stdout, ionode
+ USE kinds, ONLY : DP
+ USE io_files, ONLY : tmp_dir
+ !
+ USE plugin_flags
+ !
+ IMPLICIT NONE
+ !
+ !
+END SUBROUTINE plugin_initialization
diff --git a/patches/qespresso-5.0.2.diff/PW/src/pwscf.f90 b/patches/qespresso-5.0.2.diff/PW/src/pwscf.f90
new file mode 100644
index 0000000000000000000000000000000000000000..d656dac6f36946cfe2d7199d043dca782a9984bc
--- /dev/null
+++ b/patches/qespresso-5.0.2.diff/PW/src/pwscf.f90
@@ -0,0 +1,189 @@
+!
+! Copyright (C) 2001-2011 Quantum ESPRESSO group
+! This file is distributed under the terms of the
+! GNU General Public License. See the file `License'
+! in the root directory of the present distribution,
+! or http://www.gnu.org/copyleft/gpl.txt .
+!
+!----------------------------------------------------------------------------
+PROGRAM pwscf
+ !----------------------------------------------------------------------------
+ !
+ ! ... Plane Wave Self-Consistent Field code
+ !
+ USE io_global, ONLY : stdout, ionode, ionode_id
+ USE parameters, ONLY : ntypx, npk, lmaxx
+ USE cell_base, ONLY : fix_volume, fix_area
+ USE control_flags, ONLY : conv_elec, gamma_only, lscf
+ USE control_flags, ONLY : conv_ions, istep, nstep, restart, lmd, lbfgs
+ USE force_mod, ONLY : lforce, lstres, sigma
+ USE environment, ONLY : environment_start
+ USE check_stop, ONLY : check_stop_init, check_stop_now
+ USE mp_global, ONLY : mp_startup, mp_global_end, intra_image_comm
+ USE mp_global, ONLY : nimage, me_image, root_image, my_image_id
+#if defined(__MS2)
+ USE ms2, ONLY : MS2_enabled, &
+ ms2_initialization, &
+ set_positions, return_forces
+#endif
+ USE io_files, ONLY : tmp_dir
+ USE image_io_routines, ONLY : io_image_start
+ USE xml_io_base, ONLY : create_directory, change_directory
+ USE read_input, ONLY : read_input_file
+ !
+ IMPLICIT NONE
+ !
+ !
+ CHARACTER(len=256) :: dirname
+ !
+#ifdef __MPI
+ !
+ CALL mp_startup ( )
+ ! reset IO nodes
+ ! (do this to make each "image head node" an ionode)
+ ! Has to be used ONLY to run nimage copies of pwscf
+ !
+ IF ( nimage > 1 ) CALL io_image_start( )
+#endif
+ CALL environment_start ( 'PWSCF' )
+ !
+ IF ( ionode ) WRITE( unit = stdout, FMT = 9010 ) &
+ ntypx, npk, lmaxx
+ !
+ IF (ionode) CALL plugin_arguments()
+ CALL plugin_arguments_bcast( ionode_id, intra_image_comm )
+ !
+ ! ... open, read, close input file
+ !
+ CALL read_input_file ('PW')
+ !
+ ! ... convert to internal variables
+ !
+ CALL iosys()
+ !
+ IF ( gamma_only ) WRITE( UNIT = stdout, &
+ & FMT = '(/,5X,"gamma-point specific algorithms are used")' )
+ !
+ IF( nimage > 1 ) THEN
+ !
+ ! ... When nimage are used, open a directory for each one
+ ! ...It has to be done here in order not to disturb NEB like calculations
+ !
+ WRITE( dirname, FMT = '( I5.5 )' ) my_image_id
+ tmp_dir = TRIM( tmp_dir )//TRIM( dirname )//'/'
+ CALL create_directory( tmp_dir )
+ CALL change_directory( tmp_dir )
+ !
+ END IF
+ !
+ ! call to void routine for user defined / plugin patches initializations
+ !
+ CALL plugin_initialization()
+ !
+ CALL check_stop_init()
+ !
+#if defined(__MS2)
+ CALL ms2_initialization()
+#endif
+ !
+ CALL setup ()
+ !
+#if defined(__MS2)
+ CALL set_positions()
+#endif
+ !
+ CALL init_run()
+ !
+ IF ( check_stop_now() ) CALL stop_run( .TRUE. )
+ !
+ main_loop: DO
+ !
+ ! ... electronic self-consistency
+ !
+ CALL electrons()
+ !
+ IF ( .NOT. conv_elec ) THEN
+ CALL punch( 'all' )
+ CALL stop_run( conv_elec )
+ ENDIF
+ !
+ ! ... ionic section starts here
+ !
+ CALL start_clock( 'ions' )
+ conv_ions = .TRUE.
+ !
+ ! ... recover from a previous run, if appropriate
+ !
+ IF ( restart .AND. lscf ) CALL restart_in_ions()
+ !
+ ! ... file in CASINO format written here if required
+ !
+ CALL pw2casino()
+ !
+ ! ... force calculation
+ !
+ IF ( lforce ) CALL forces()
+ !
+ ! ... stress calculation
+ !
+ IF ( lstres ) CALL stress ( sigma )
+ !
+ ! ... this is the right place for plugin forces:
+ !
+ CALL plugin_forces()
+ !
+ IF ( lmd .OR. lbfgs ) THEN
+ !
+ if (fix_volume) CALL impose_deviatoric_stress(sigma)
+ !
+ if (fix_area) CALL impose_deviatoric_stress_2d(sigma)
+ !
+ ! ... ionic step (for molecular dynamics or optimization)
+ !
+ CALL move_ions()
+ !
+ ! ... then we save restart information for the new configuration
+ !
+ IF ( istep < nstep .AND. .NOT. conv_ions ) THEN
+ !
+ CALL punch( 'config' )
+ CALL save_in_ions()
+ !
+ END IF
+ !
+ END IF
+ !
+ CALL stop_clock( 'ions' )
+ !
+#if defined(__MS2)
+ CALL return_forces()
+#endif
+ ! ... exit condition (ionic convergence) is checked here
+ !
+ IF ( conv_ions ) EXIT main_loop
+ !
+ ! ... terms of the hamiltonian depending upon nuclear positions
+ ! ... are reinitialized here
+ !
+#if defined(__MS2)
+ CALL set_positions()
+#endif
+ IF ( lmd .OR. lbfgs ) CALL hinit1()
+ !
+ END DO main_loop
+ !
+ ! ... save final data file
+ !
+ CALL punch('all')
+ CALL stop_run( conv_ions )
+ !
+ ! END IF
+ !
+ STOP
+ !
+9010 FORMAT( /,5X,'Current dimensions of program PWSCF are:', &
+ & /,5X,'Max number of different atomic species (ntypx) = ',I2,&
+ & /,5X,'Max number of k-points (npk) = ',I6,&
+ & /,5X,'Max angular momentum in pseudopotentials (lmaxx) = ',i2)
+ !
+END PROGRAM pwscf
diff --git a/patches/qespresso-5.0.2.diff/PW/src/pwscf.f90.preplumed b/patches/qespresso-5.0.2.diff/PW/src/pwscf.f90.preplumed
new file mode 100644
index 0000000000000000000000000000000000000000..aef5e9fce1b9aefb3287b6f825289b3d50599cf4
--- /dev/null
+++ b/patches/qespresso-5.0.2.diff/PW/src/pwscf.f90.preplumed
@@ -0,0 +1,185 @@
+!
+! Copyright (C) 2001-2011 Quantum ESPRESSO group
+! This file is distributed under the terms of the
+! GNU General Public License. See the file `License'
+! in the root directory of the present distribution,
+! or http://www.gnu.org/copyleft/gpl.txt .
+!
+!----------------------------------------------------------------------------
+PROGRAM pwscf
+ !----------------------------------------------------------------------------
+ !
+ ! ... Plane Wave Self-Consistent Field code
+ !
+ USE io_global, ONLY : stdout, ionode, ionode_id
+ USE parameters, ONLY : ntypx, npk, lmaxx
+ USE cell_base, ONLY : fix_volume, fix_area
+ USE control_flags, ONLY : conv_elec, gamma_only, lscf
+ USE control_flags, ONLY : conv_ions, istep, nstep, restart, lmd, lbfgs
+ USE force_mod, ONLY : lforce, lstres, sigma
+ USE environment, ONLY : environment_start
+ USE check_stop, ONLY : check_stop_init, check_stop_now
+ USE mp_global, ONLY : mp_startup, mp_global_end, intra_image_comm
+ USE mp_global, ONLY : nimage, me_image, root_image, my_image_id
+#if defined(__MS2)
+ USE ms2, ONLY : MS2_enabled, &
+ ms2_initialization, &
+ set_positions, return_forces
+#endif
+ USE io_files, ONLY : tmp_dir
+ USE image_io_routines, ONLY : io_image_start
+ USE xml_io_base, ONLY : create_directory, change_directory
+ USE read_input, ONLY : read_input_file
+ !
+ IMPLICIT NONE
+ !
+ !
+ CHARACTER(len=256) :: dirname
+ !
+#ifdef __MPI
+ !
+ CALL mp_startup ( )
+ ! reset IO nodes
+ ! (do this to make each "image head node" an ionode)
+ ! Has to be used ONLY to run nimage copies of pwscf
+ !
+ IF ( nimage > 1 ) CALL io_image_start( )
+#endif
+ CALL environment_start ( 'PWSCF' )
+ !
+ IF ( ionode ) WRITE( unit = stdout, FMT = 9010 ) &
+ ntypx, npk, lmaxx
+ !
+ IF (ionode) CALL plugin_arguments()
+ CALL plugin_arguments_bcast( ionode_id, intra_image_comm )
+ !
+ ! ... open, read, close input file
+ !
+ CALL read_input_file ('PW')
+ !
+ ! ... convert to internal variables
+ !
+ CALL iosys()
+ !
+ IF ( gamma_only ) WRITE( UNIT = stdout, &
+ & FMT = '(/,5X,"gamma-point specific algorithms are used")' )
+ !
+ IF( nimage > 1 ) THEN
+ !
+ ! ... When nimage are used, open a directory for each one
+ ! ...It has to be done here in order not to disturb NEB like calculations
+ !
+ WRITE( dirname, FMT = '( I5.5 )' ) my_image_id
+ tmp_dir = TRIM( tmp_dir )//TRIM( dirname )//'/'
+ CALL create_directory( tmp_dir )
+ CALL change_directory( tmp_dir )
+ !
+ END IF
+ !
+ ! call to void routine for user defined / plugin patches initializations
+ !
+ CALL plugin_initialization()
+ !
+ CALL check_stop_init()
+ !
+#if defined(__MS2)
+ CALL ms2_initialization()
+#endif
+ !
+ CALL setup ()
+ !
+#if defined(__MS2)
+ CALL set_positions()
+#endif
+ !
+ CALL init_run()
+ !
+ IF ( check_stop_now() ) CALL stop_run( .TRUE. )
+ !
+ main_loop: DO
+ !
+ ! ... electronic self-consistency
+ !
+ CALL electrons()
+ !
+ IF ( .NOT. conv_elec ) THEN
+ CALL punch( 'all' )
+ CALL stop_run( conv_elec )
+ ENDIF
+ !
+ ! ... ionic section starts here
+ !
+ CALL start_clock( 'ions' )
+ conv_ions = .TRUE.
+ !
+ ! ... recover from a previous run, if appropriate
+ !
+ IF ( restart .AND. lscf ) CALL restart_in_ions()
+ !
+ ! ... file in CASINO format written here if required
+ !
+ CALL pw2casino()
+ !
+ ! ... force calculation
+ !
+ IF ( lforce ) CALL forces()
+ !
+ ! ... stress calculation
+ !
+ IF ( lstres ) CALL stress ( sigma )
+ !
+ IF ( lmd .OR. lbfgs ) THEN
+ !
+ if (fix_volume) CALL impose_deviatoric_stress(sigma)
+ !
+ if (fix_area) CALL impose_deviatoric_stress_2d(sigma)
+ !
+ ! ... ionic step (for molecular dynamics or optimization)
+ !
+ CALL move_ions()
+ !
+ ! ... then we save restart information for the new configuration
+ !
+ IF ( istep < nstep .AND. .NOT. conv_ions ) THEN
+ !
+ CALL punch( 'config' )
+ CALL save_in_ions()
+ !
+ END IF
+ !
+ END IF
+ !
+ CALL stop_clock( 'ions' )
+ !
+#if defined(__MS2)
+ CALL return_forces()
+#endif
+ ! ... exit condition (ionic convergence) is checked here
+ !
+ IF ( conv_ions ) EXIT main_loop
+ !
+ ! ... terms of the hamiltonian depending upon nuclear positions
+ ! ... are reinitialized here
+ !
+#if defined(__MS2)
+ CALL set_positions()
+#endif
+ IF ( lmd .OR. lbfgs ) CALL hinit1()
+ !
+ END DO main_loop
+ !
+ ! ... save final data file
+ !
+ CALL punch('all')
+ CALL stop_run( conv_ions )
+ !
+ ! END IF
+ !
+ STOP
+ !
+9010 FORMAT( /,5X,'Current dimensions of program PWSCF are:', &
+ & /,5X,'Max number of different atomic species (ntypx) = ',I2,&
+ & /,5X,'Max number of k-points (npk) = ',I6,&
+ & /,5X,'Max angular momentum in pseudopotentials (lmaxx) = ',i2)
+ !
+END PROGRAM pwscf
diff --git a/regtest/.gitignore b/regtest/.gitignore
index e0fa2957c0eedf46e72c27c6c848909bf4306297..87e790cd82d1089b0238778eb236b48d0c168c66 100644
--- a/regtest/.gitignore
+++ b/regtest/.gitignore
@@ -6,14 +6,14 @@
!/function
!/analysis
!/basic
+!/crystallization
!/multicolvar
!/secondarystructure
!/trajectories
!/scripts
!/manyrestraints
+!/molfile_plugin
!/has-almost
-
# These files we just want to ignore completely
tmp
report.txt
-crystallization
diff --git a/regtest/Makefile b/regtest/Makefile
index 2a38c7884c59520d92d557f4ce216d749b2c9a8b..e13f12d5ed1e67a4f1cebf74acc164d981185f75 100644
--- a/regtest/Makefile
+++ b/regtest/Makefile
@@ -1,8 +1,6 @@
-ACTIVE_MODULES = $(shell ./scripts/find_modules.sh) basic
-#SUBDIRS = $(subst /Makefile,,$(wildcard rt*/Makefile))
-SUBDIRS = $(shell for dir in $(ACTIVE_MODULES) ; do ls $$dir/rt*/Makefile | sed 's/\Makefile//' 2>/dev/null; done)
-SUBDIRSCLEAN = $(addsuffix .clean,$(SUBDIRS))
-SUBDIRSVALGRIND = $(addsuffix .valgrind,$(SUBDIRS))
+SUBDIRS := basic $(shell ./scripts/find_modules.sh)
+SUBDIRSCLEAN := $(addsuffix .clean,$(SUBDIRS))
+SUBDIRSVALGRIND := $(addsuffix .valgrind,$(SUBDIRS))
.PHONY: all clean valgrind $(SUBDIRS) $(SUBDIRSCLEAN) $(SUBDIRSVALGRIND)
diff --git a/regtest/analysis/Makefile b/regtest/analysis/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..42480767ae852294cf2d7269ac5a1c16064d1849
--- /dev/null
+++ b/regtest/analysis/Makefile
@@ -0,0 +1,2 @@
+include ../scripts/module.make
+
diff --git a/regtest/basic/Makefile b/regtest/basic/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..42480767ae852294cf2d7269ac5a1c16064d1849
--- /dev/null
+++ b/regtest/basic/Makefile
@@ -0,0 +1,2 @@
+include ../scripts/module.make
+
diff --git a/regtest/basic/rt-make-0/Makefile b/regtest/basic/rt-make-0/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt-make-0/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-make-0/config b/regtest/basic/rt-make-0/config
new file mode 100644
index 0000000000000000000000000000000000000000..df1f95bf3ee289aa8367431334c00cf144754ddf
--- /dev/null
+++ b/regtest/basic/rt-make-0/config
@@ -0,0 +1 @@
+type=make
diff --git a/regtest/basic/rt-make-0/main.cpp b/regtest/basic/rt-make-0/main.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..916928a9362f5f69fd341249da2b8f8c699e8cd4
--- /dev/null
+++ b/regtest/basic/rt-make-0/main.cpp
@@ -0,0 +1,31 @@
+#include "plumed/tools/Vector.h"
+#include "plumed/tools/Tensor.h"
+#include "plumed/tools/Stopwatch.h"
+#include <fstream>
+#include <iostream>
+
+using namespace PLMD;
+
+int main(){
+ Stopwatch sw;
+ sw.start();
+ Vector a(1.0,2.0,3.0);
+ Tensor A(Tensor::identity());
+ std::ofstream ofs("output");
+ Vector b=(matmul(A,a));
+
+ Tensor B(1.0,2.0,3.0,5.0,4.0,3.0,10.0,8.0,2.0);
+ Vector c=(matmul(a,matmul(B,inverse(B))));
+
+ ofs<<a[0]<<" "<<a[1]<<" "<<a[2]<<"\n";
+ ofs<<b[0]<<" "<<b[1]<<" "<<b[2]<<"\n";
+ ofs<<c[0]<<" "<<c[1]<<" "<<c[2]<<"\n";
+
+ B-=A;
+ ofs<<determinant(B)<<"\n";
+
+ sw.stop();
+ std::cout<<sw;
+
+ return 0;
+}
diff --git a/regtest/basic/rt-make-0/output.reference b/regtest/basic/rt-make-0/output.reference
new file mode 100644
index 0000000000000000000000000000000000000000..cb1abba6fb95cc2813f7ada326a1d8c6cba5b70a
--- /dev/null
+++ b/regtest/basic/rt-make-0/output.reference
@@ -0,0 +1,4 @@
+1 2 3
+1 2 3
+1 2 3
+80
diff --git a/regtest/basic/rt-make-1/Makefile b/regtest/basic/rt-make-1/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt-make-1/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-make-1/config b/regtest/basic/rt-make-1/config
new file mode 100644
index 0000000000000000000000000000000000000000..df1f95bf3ee289aa8367431334c00cf144754ddf
--- /dev/null
+++ b/regtest/basic/rt-make-1/config
@@ -0,0 +1 @@
+type=make
diff --git a/regtest/basic/rt-make-1/logfile.reference b/regtest/basic/rt-make-1/logfile.reference
new file mode 100644
index 0000000000000000000000000000000000000000..cb27ff833010239d8b58cc9f0dd6e492666bbe1d
--- /dev/null
+++ b/regtest/basic/rt-make-1/logfile.reference
@@ -0,0 +1,24 @@
+Box type 0
+Failures 0
+Shifts 0.00
+
+Box type 1
+Failures 0
+Shifts 0.00
+
+Box type 2
+Failures 0
+Shifts 0.40
+
+Box type 3
+Failures 0
+Shifts 0.68
+
+Box type 4
+Failures 0
+Shifts 1.04
+
+Box type 5
+Failures 0
+Shifts 1.21
+
diff --git a/regtest/basic/rt-make-1/main.cpp b/regtest/basic/rt-make-1/main.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..37914f52da4be643a222715d0dddd080dff59a03
--- /dev/null
+++ b/regtest/basic/rt-make-1/main.cpp
@@ -0,0 +1,116 @@
+#include "plumed/tools/Pbc.h"
+#include "plumed/tools/Random.h"
+#include "plumed/tools/Exception.h"
+#include "plumed/tools/Stopwatch.h"
+#include <iostream>
+#include <fstream>
+
+using namespace PLMD;
+
+int run(int boxtype,double* av_nshifts=NULL){
+ Random r;
+ int failures=0;
+ r.setSeed(-20);
+ int nshifts=0;
+ int nbox=1000;
+ int nvec=100;
+ for(int i=0;i<nbox;i++){
+// random matrix with some zero element
+ Tensor box;
+ for(int j=0;j<3;j++) for(int k=0;k<3;k++) if(r.U01()>0.2){
+ box[j][k]=2.0*r.U01()-1.0;
+ }
+ switch(boxtype){
+ case 0:
+// cubic
+ for(int j=0;j<3;j++) for(int k=0;k<3;k++) if(j!=k) box[j][k]=0.0;
+ for(int j=1;j<3;j++) box[j][j]=box[0][0];
+ break;
+ case 1:
+// orthorombic
+ for(int j=0;j<3;j++) for(int k=0;k<3;k++) if(j!=k) box[j][k]=0.0;
+ break;
+ case 2:
+// hexagonal
+ {
+ int perm=r.U01()*100;
+ Vector a;
+ a(0)=r.U01()*2-2; a(1)=0.0;a(2)=0.0;
+ double d=r.U01()*2-2;
+ Vector b(0.0,d,0.0);
+ Vector c(0.0,0.5*d,sqrt(3.0)*d*0.5);
+ box.setRow((perm+0)%3,a);
+ box.setRow((perm+1)%3,b);
+ box.setRow((perm+2)%3,c);
+ }
+ break;
+ case 3:
+// bcc
+ {
+ int perm=r.U01()*100;
+ double d=r.U01()*2-2;
+ Vector a(d,d,d);
+ Vector b(d,-d,d);
+ Vector c(d,d,-d);
+ box.setRow((perm+0)%3,a);
+ box.setRow((perm+1)%3,b);
+ box.setRow((perm+2)%3,c);
+ }
+ break;
+ case 4:
+// fcc
+ {
+ int perm=r.U01()*100;
+ double d=r.U01()*2-2;
+ Vector a(d,d,0);
+ Vector b(d,0,d);
+ Vector c(0,d,d);
+ box.setRow((perm+0)%3,a);
+ box.setRow((perm+1)%3,b);
+ box.setRow((perm+2)%3,c);
+ }
+ break;
+ default:
+// triclinic
+ break;
+ }
+
+ Pbc pbc;
+ pbc.setBox(box);
+ for(int j=0;j<nvec;j++){
+// random vector
+ Vector v(r.U01()-0.5,r.U01()-0.5,r.U01()-0.5);
+ v*=5;
+// set some component to zero
+ for(int j=0;j<3;j++) if(r.U01()>0.2) v(j)=0.0;
+// fast version
+ Vector fast=pbc.distance(Vector(0,0,0),v,&nshifts);
+// full search around that
+ Vector full(fast);
+ pbc.fullSearch(full);
+// compare
+ if(std::fabs(modulo2(fast)-modulo2(full))>1e-15) failures++;
+ }
+ }
+ if(av_nshifts) *av_nshifts=double(nshifts)/double(nbox*nvec);
+ return failures;
+}
+
+
+int main(){
+ Stopwatch sw;
+ sw.start();
+ std::ofstream ofs("logfile");
+ ofs.precision(2);
+ ofs<<std::fixed;
+ for(unsigned type=0;type<6;type++){
+ double nsh;
+ int err=run(type,&nsh);
+ ofs<<"Box type "<<type<<"\n";
+ ofs<<"Failures "<<err<<"\n";
+ ofs<<"Shifts "<<nsh<<"\n\n";
+ }
+ sw.stop();
+ std::cout<<sw;
+ return 0;
+}
diff --git a/regtest/basic/rt-make-2/Makefile b/regtest/basic/rt-make-2/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt-make-2/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-make-2/config b/regtest/basic/rt-make-2/config
new file mode 100644
index 0000000000000000000000000000000000000000..e0a0313a44661a53e6324a85dd96a14c86403894
--- /dev/null
+++ b/regtest/basic/rt-make-2/config
@@ -0,0 +1,2 @@
+mpiprocs=3
+type=make
diff --git a/regtest/basic/rt-make-2/main.cpp b/regtest/basic/rt-make-2/main.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..5f51966a05bb6261853d18ee5e14a3995950e046
--- /dev/null
+++ b/regtest/basic/rt-make-2/main.cpp
@@ -0,0 +1,142 @@
+#include "mpi.h"
+#include "plumed/tools/Communicator.h"
+#include "plumed/tools/Tools.h"
+#include <fstream>
+#include <string>
+#include "plumed/tools/Vector.h"
+#include "plumed/tools/Tensor.h"
+
+using namespace PLMD;
+
+template<typename T>
+void reset(Communicator& comm,std::vector<T> & v){
+ for(unsigned i=0;i<v.size();i++) v[i]=(i+1)*(comm.Get_rank()+1);
+}
+
+template<typename T>
+void dump(Communicator& comm,std::ostream&ofs,const std::vector<T> & v){
+ for(unsigned i=0;i<v.size();i++) ofs<<" "<<v[i]; ofs<<"\n";
+}
+
+void run(Communicator& comm){
+ std::string ff;
+ Tools::convert(comm.Get_rank(),ff);
+ ff="output"+ff;
+ std::ofstream ofs(ff.c_str());
+ std::vector<int> a(4*comm.Get_size());
+ std::vector<int> b(a);
+ std::vector<int> collect;
+ Communicator::Request req;
+
+ double pippo=0;
+
+ pippo=comm.Get_rank()+1;
+ comm.Bcast(pippo,0);
+ ofs<<pippo<<"\n";
+
+ reset(comm,a);
+ comm.Sum(&a[0],a.size());
+ dump(comm,ofs,a);
+
+ reset(comm,a);
+ comm.Bcast(&a[0],a.size(),0);
+ dump(comm,ofs,a);
+
+ reset(comm,a);
+ comm.Bcast(&a[0],a.size(),2);
+ dump(comm,ofs,a);
+
+ reset(comm,a);
+ Communicator::Status status;
+ if(comm.Get_rank()==0) req=comm.Isend(&a[0],a.size(),1,77);
+ if(comm.Get_rank()==1) req=comm.Isend(a,2,77);
+ if(comm.Get_rank()==2) req=comm.Isend(a,0,77);
+ if(comm.Get_rank()==0) comm.Recv(&b[0],b.size(),2,77,status);
+ if(comm.Get_rank()==1) comm.Recv(b,0,77);
+ if(comm.Get_rank()==2) comm.Recv(b,1,77);
+ if(comm.Get_rank()==0) req.wait();
+ if(comm.Get_rank()==1) req.wait(status);
+ if(comm.Get_rank()==2) req.wait();
+ dump(comm,ofs,a);
+ if(comm.Get_rank()==0) ofs<<"status "<<status.Get_count<int>()<<"\n";
+ if(comm.Get_rank()==1) ofs<<"status "<<status.Get_count<int>()<<"\n";
+
+ reset(comm,a);
+ collect.assign(a.size()*comm.Get_size(),0.0);
+ comm.Allgather(&a[0],a.size(),&collect[0],a.size());
+ dump(comm,ofs,collect);
+
+ reset(comm,a);
+ std::vector<int> displace(comm.Get_size());
+ std::vector<int> count(comm.Get_size());
+ for(int l=0;l<comm.Get_size();l++) count[l]=1+l;
+ displace[0]=0;
+ for(int l=0;l<comm.Get_size()-1;l++) displace[l+1]=displace[l]+count[l];
+ collect.assign(displace[comm.Get_size()-1]+count[comm.Get_size()-1],0.0);
+ comm.Allgatherv(&a[0],count[comm.Get_rank()],&collect[0],&count[0],&displace[0]);
+ dump(comm,ofs,collect);
+
+ std::vector<Vector> vec(comm.Get_size());
+ std::vector<Vector> newvec(comm.Get_size());
+ for(unsigned i=0;i<vec.size();i++) vec[i]=Vector((i+1)*(comm.Get_rank()+1),(i+1)*(comm.Get_rank()+1)+100,(i+1)*(comm.Get_rank()+1)+200);
+ if(comm.Get_rank()==0) req=comm.Isend(&vec[0][0],3*vec.size(),1,78);
+ if(comm.Get_rank()==1) req=comm.Isend(&vec[0],vec.size(),2,78);
+ if(comm.Get_rank()==2) req=comm.Isend(vec,0,78);
+ if(comm.Get_rank()==0) comm.Recv(&newvec[0][0],3*newvec.size(),2,78);
+ if(comm.Get_rank()==1) comm.Recv(&newvec[0],newvec.size(),0,78);
+ if(comm.Get_rank()==2) comm.Recv(newvec,1,78);
+ req.wait();
+ for(unsigned i=0;i<vec.size();i++) ofs<<" "<<newvec[i][0]<<" "<<newvec[i][1]<<" "<<newvec[i][2]<<"\n";
+
+ std::vector<Tensor> ten(comm.Get_size());
+ std::vector<Tensor> newten(comm.Get_size());
+ for(unsigned i=0;i<ten.size();i++)
+ ten[i]=Tensor((i+1)*(comm.Get_rank()+1),(i+1)*(comm.Get_rank()+1)+100,(i+1)*(comm.Get_rank()+1)+200,
+ (i+1)*(comm.Get_rank()+1)+300,(i+1)*(comm.Get_rank()+1)+400,(i+1)*(comm.Get_rank()+1)+500,
+ (i+1)*(comm.Get_rank()+1)+600,(i+1)*(comm.Get_rank()+1)+700,(i+1)*(comm.Get_rank()+1)+800);
+ if(comm.Get_rank()==0) req=comm.Isend(&ten[0][0][0],9*ten.size(),1,78);
+ if(comm.Get_rank()==1) req=comm.Isend(&ten[0][0][0],9*ten.size(),2,78);
+ if(comm.Get_rank()==2) req=comm.Isend(&ten[0][0][0],9*ten.size(),0,78);
+ if(comm.Get_rank()==0) comm.Recv(&newten[0][0][0],9*newten.size(),2,78);
+ if(comm.Get_rank()==1) comm.Recv(&newten[0][0][0],9*newten.size(),0,78);
+ if(comm.Get_rank()==2) comm.Recv(&newten[0][0][0],9*newten.size(),1,78);
+ req.wait();
+ for(unsigned i=0;i<ten.size();i++) ofs<<" "<<newten[i][0][0]<<" "<<newten[i][0][1]<<" "<<newten[i][0][2]<<"\n"
+ <<" "<<newten[i][1][0]<<" "<<newten[i][1][1]<<" "<<newten[i][1][2]<<"\n"
+ <<" "<<newten[i][2][0]<<" "<<newten[i][2][1]<<" "<<newten[i][2][2]<<"\n";
+
+ std::string stringsend;
+ std::string stringrecv;
+ if(comm.Get_rank()==0){
+ stringsend="uno";
+ stringrecv="uno";
+ req=comm.Isend(stringsend,1,80);
+ comm.Recv(stringrecv,2,80);
+ }
+ if(comm.Get_rank()==1){
+ stringsend="due";
+ stringrecv="due";
+ req=comm.Isend(stringsend,2,80);
+ comm.Recv(stringrecv,0,80);
+ }
+ if(comm.Get_rank()==2){
+ stringsend="tre";
+ stringrecv="tre";
+ req=comm.Isend(stringsend,0,80);
+ comm.Recv(stringrecv,1,80);
+ }
+ req.wait();
+ ofs<<stringsend<<" "<<stringrecv<<"\n";
+}
+
+int main(int argc,char**argv){
+ MPI_Init(&argc,&argv);
+ {
+ MPI_Comm c;
+ MPI_Comm_dup(MPI_COMM_WORLD,&c);
+ PLMD::Communicator comm;
+ comm.Set_comm(&c);
+ run(comm);
+ }
+ MPI_Finalize();
+}
diff --git a/regtest/basic/rt-make-2/output0.reference b/regtest/basic/rt-make-2/output0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..daae14a3eea8e58fbe1844852502ee164aa21380
--- /dev/null
+++ b/regtest/basic/rt-make-2/output0.reference
@@ -0,0 +1,21 @@
+1
+ 6 12 18 24 30 36 42 48 54 60 66 72
+ 1 2 3 4 5 6 7 8 9 10 11 12
+ 3 6 9 12 15 18 21 24 27 30 33 36
+ 1 2 3 4 5 6 7 8 9 10 11 12
+status 12
+ 1 2 3 4 5 6 7 8 9 10 11 12 2 4 6 8 10 12 14 16 18 20 22 24 3 6 9 12 15 18 21 24 27 30 33 36
+ 1 2 4 3 6 9
+ 3 103 203
+ 6 106 206
+ 9 109 209
+ 3 103 203
+ 303 403 503
+ 603 703 803
+ 6 106 206
+ 306 406 506
+ 606 706 806
+ 9 109 209
+ 309 409 509
+ 609 709 809
+uno tre
diff --git a/regtest/basic/rt-make-2/output1.reference b/regtest/basic/rt-make-2/output1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..e073a6943b6536dc79cf0045f7f86f3cfeaa65e2
--- /dev/null
+++ b/regtest/basic/rt-make-2/output1.reference
@@ -0,0 +1,21 @@
+1
+ 6 12 18 24 30 36 42 48 54 60 66 72
+ 1 2 3 4 5 6 7 8 9 10 11 12
+ 3 6 9 12 15 18 21 24 27 30 33 36
+ 2 4 6 8 10 12 14 16 18 20 22 24
+status 12
+ 1 2 3 4 5 6 7 8 9 10 11 12 2 4 6 8 10 12 14 16 18 20 22 24 3 6 9 12 15 18 21 24 27 30 33 36
+ 1 2 4 3 6 9
+ 1 101 201
+ 2 102 202
+ 3 103 203
+ 1 101 201
+ 301 401 501
+ 601 701 801
+ 2 102 202
+ 302 402 502
+ 602 702 802
+ 3 103 203
+ 303 403 503
+ 603 703 803
+due uno
diff --git a/regtest/basic/rt-make-2/output2.reference b/regtest/basic/rt-make-2/output2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2baff966c4c5f4d61fe78156eef45d9057e4ec7d
--- /dev/null
+++ b/regtest/basic/rt-make-2/output2.reference
@@ -0,0 +1,20 @@
+1
+ 6 12 18 24 30 36 42 48 54 60 66 72
+ 1 2 3 4 5 6 7 8 9 10 11 12
+ 3 6 9 12 15 18 21 24 27 30 33 36
+ 3 6 9 12 15 18 21 24 27 30 33 36
+ 1 2 3 4 5 6 7 8 9 10 11 12 2 4 6 8 10 12 14 16 18 20 22 24 3 6 9 12 15 18 21 24 27 30 33 36
+ 1 2 4 3 6 9
+ 2 102 202
+ 4 104 204
+ 6 106 206
+ 2 102 202
+ 302 402 502
+ 602 702 802
+ 4 104 204
+ 304 404 504
+ 604 704 804
+ 6 106 206
+ 306 406 506
+ 606 706 806
+tre due
diff --git a/regtest/basic/rt-molfile-1/COLVAR.reference b/regtest/basic/rt-molfile-1/COLVAR.reference
new file mode 100644
index 0000000000000000000000000000000000000000..9bfeb7ab606f5abb5ac61fed80b0279ca8e46b51
--- /dev/null
+++ b/regtest/basic/rt-molfile-1/COLVAR.reference
@@ -0,0 +1,22 @@
+#! FIELDS time rmsd0 rmsd1 sum @3.bias @3.force2
+ 0.000000 0.000 0.149 0.149 197.034 394.068
+ 0.005000 0.072 0.160 0.231 195.399 390.797
+ 0.010000 0.032 0.147 0.178 196.450 392.899
+ 0.015000 0.051 0.144 0.195 196.121 392.242
+ 0.020000 0.090 0.144 0.235 195.331 390.662
+ 0.025000 0.070 0.142 0.212 195.776 391.552
+ 0.030000 0.068 0.119 0.187 196.271 392.542
+ 0.035000 0.100 0.137 0.237 195.289 390.578
+ 0.040000 0.070 0.125 0.196 196.106 392.212
+ 0.045000 0.088 0.102 0.190 196.211 392.422
+ 0.050000 0.109 0.130 0.240 195.235 390.470
+ 0.055000 0.133 0.086 0.219 195.641 391.283
+ 0.060000 0.121 0.112 0.233 195.358 390.715
+ 0.065000 0.126 0.110 0.236 195.313 390.627
+ 0.070000 0.125 0.113 0.238 195.272 390.544
+ 0.075000 0.120 0.105 0.224 195.536 391.072
+ 0.080000 0.128 0.105 0.233 195.363 390.726
+ 0.085000 0.157 0.117 0.274 194.558 389.117
+ 0.090000 0.168 0.107 0.275 194.538 389.076
+ 0.095000 0.169 0.101 0.270 194.635 389.270
+ 0.100000 0.149 0.000 0.149 197.034 394.068
diff --git a/regtest/basic/rt-molfile-1/Makefile b/regtest/basic/rt-molfile-1/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt-molfile-1/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-molfile-1/config b/regtest/basic/rt-molfile-1/config
new file mode 100644
index 0000000000000000000000000000000000000000..78d2fd2c116d46e4273ad7d4dc67c48f8948cc5a
--- /dev/null
+++ b/regtest/basic/rt-molfile-1/config
@@ -0,0 +1,4 @@
+type=driver
+plumed_needs=molfile
+arg="--plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --pdb diala.pdb --mf_xtc traj.xtc --dump-forces forces --dump-forces-fmt=%10.6f"
+extra_files="../../trajectories/molfile_plugin/traj.xtc ../../trajectories/molfile_plugin/test0.pdb ../../trajectories/molfile_plugin/test1.pdb ../../trajectories/molfile_plugin/diala.pdb "
diff --git a/regtest/basic/rt-molfile-1/plumed.dat b/regtest/basic/rt-molfile-1/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..4cb1673e7c34dd9176b72565a5c3e75344d35b6b
--- /dev/null
+++ b/regtest/basic/rt-molfile-1/plumed.dat
@@ -0,0 +1,16 @@
+rmsd0: RMSD TYPE=OPTIMAL REFERENCE=test0.pdb
+rmsd1: RMSD TYPE=OPTIMAL REFERENCE=test1.pdb
+
+sum: COMBINE ARG=* PERIODIC=NO
+
+RESTRAINT ARG=sum AT=20.0 KAPPA=1.0
+
+PRINT ...
+ STRIDE=1
+ ARG=*
+ FILE=COLVAR FMT=%6.3f
+... PRINT
+
+ENDPLUMED
+
+text here should be ignored
diff --git a/regtest/basic/rt-molfile-2/COLVAR.reference b/regtest/basic/rt-molfile-2/COLVAR.reference
new file mode 100644
index 0000000000000000000000000000000000000000..9bfeb7ab606f5abb5ac61fed80b0279ca8e46b51
--- /dev/null
+++ b/regtest/basic/rt-molfile-2/COLVAR.reference
@@ -0,0 +1,22 @@
+#! FIELDS time rmsd0 rmsd1 sum @3.bias @3.force2
+ 0.000000 0.000 0.149 0.149 197.034 394.068
+ 0.005000 0.072 0.160 0.231 195.399 390.797
+ 0.010000 0.032 0.147 0.178 196.450 392.899
+ 0.015000 0.051 0.144 0.195 196.121 392.242
+ 0.020000 0.090 0.144 0.235 195.331 390.662
+ 0.025000 0.070 0.142 0.212 195.776 391.552
+ 0.030000 0.068 0.119 0.187 196.271 392.542
+ 0.035000 0.100 0.137 0.237 195.289 390.578
+ 0.040000 0.070 0.125 0.196 196.106 392.212
+ 0.045000 0.088 0.102 0.190 196.211 392.422
+ 0.050000 0.109 0.130 0.240 195.235 390.470
+ 0.055000 0.133 0.086 0.219 195.641 391.283
+ 0.060000 0.121 0.112 0.233 195.358 390.715
+ 0.065000 0.126 0.110 0.236 195.313 390.627
+ 0.070000 0.125 0.113 0.238 195.272 390.544
+ 0.075000 0.120 0.105 0.224 195.536 391.072
+ 0.080000 0.128 0.105 0.233 195.363 390.726
+ 0.085000 0.157 0.117 0.274 194.558 389.117
+ 0.090000 0.168 0.107 0.275 194.538 389.076
+ 0.095000 0.169 0.101 0.270 194.635 389.270
+ 0.100000 0.149 0.000 0.149 197.034 394.068
diff --git a/regtest/basic/rt-molfile-2/Makefile b/regtest/basic/rt-molfile-2/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt-molfile-2/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-molfile-2/config b/regtest/basic/rt-molfile-2/config
new file mode 100644
index 0000000000000000000000000000000000000000..7e67c1ed5f0b71c49e06ba2a8dc8b6fc19856d85
--- /dev/null
+++ b/regtest/basic/rt-molfile-2/config
@@ -0,0 +1,4 @@
+type=driver
+plumed_needs=molfile
+arg="--plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --pdb diala.pdb --mf_dcd traj.dcd --dump-forces forces --dump-forces-fmt=%10.6f"
+extra_files="../../trajectories/molfile_plugin/traj.dcd ../../trajectories/molfile_plugin/test0.pdb ../../trajectories/molfile_plugin/test1.pdb ../../trajectories/molfile_plugin/diala.pdb "
diff --git a/regtest/basic/rt-molfile-2/plumed.dat b/regtest/basic/rt-molfile-2/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..4cb1673e7c34dd9176b72565a5c3e75344d35b6b
--- /dev/null
+++ b/regtest/basic/rt-molfile-2/plumed.dat
@@ -0,0 +1,16 @@
+rmsd0: RMSD TYPE=OPTIMAL REFERENCE=test0.pdb
+rmsd1: RMSD TYPE=OPTIMAL REFERENCE=test1.pdb
+
+sum: COMBINE ARG=* PERIODIC=NO
+
+RESTRAINT ARG=sum AT=20.0 KAPPA=1.0
+
+PRINT ...
+ STRIDE=1
+ ARG=*
+ FILE=COLVAR FMT=%6.3f
+... PRINT
+
+ENDPLUMED
+
+text here should be ignored
diff --git a/regtest/basic/rt-molfile-3/Makefile b/regtest/basic/rt-molfile-3/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt-molfile-3/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-molfile-3/config b/regtest/basic/rt-molfile-3/config
new file mode 100644
index 0000000000000000000000000000000000000000..3777da90c335d6b6563e538b40ed66936ca6801f
--- /dev/null
+++ b/regtest/basic/rt-molfile-3/config
@@ -0,0 +1,3 @@
+type=driver
+plumed_needs=molfile
+arg="--plumed plumed.dat --mf_xtc test.xtc"
diff --git a/regtest/basic/rt-molfile-3/plumed.dat b/regtest/basic/rt-molfile-3/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..0a7ba6d22af7780c8a4ffa8704fd37647c57c22b
--- /dev/null
+++ b/regtest/basic/rt-molfile-3/plumed.dat
@@ -0,0 +1 @@
+DUMPATOMS ATOMS=1 FILE=test.gro PRECISION=6
diff --git a/regtest/basic/rt-molfile-3/test.gro.reference b/regtest/basic/rt-molfile-3/test.gro.reference
new file mode 100644
index 0000000000000000000000000000000000000000..94f5425eb39072bbab35debbf734cd89cf190f1d
--- /dev/null
+++ b/regtest/basic/rt-molfile-3/test.gro.reference
@@ -0,0 +1,4 @@
+Made with PLUMED t=0.000000
+1
+ 0 X 1 1.369000 3.074000 1.368000
+ 4.178910 3.939910 3.412060 0.000000 0.000000 1.392970 0.000000 -1.392970 1.969960
diff --git a/regtest/basic/rt-molfile-3/test.xtc b/regtest/basic/rt-molfile-3/test.xtc
new file mode 100644
index 0000000000000000000000000000000000000000..c41854d53ca8412883771b5703615613fc4ec9c4
Binary files /dev/null and b/regtest/basic/rt-molfile-3/test.xtc differ
diff --git a/regtest/basic/rt-mpi6/HILLS_multi.0.reference b/regtest/basic/rt-mpi6/HILLS_multi.0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2092e8760aec70f3093c8996de206a96f6927a09
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_multi.0.reference
@@ -0,0 +1,14 @@
+#! FIELDS time c d sigma_c sigma_d height biasf
+#! SET multivariate false
+ 0.100000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.100000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.100000 116.675711 1.162646 0.100000 0.200000 0.100000 1.000000
+ 0.200000 117.327813 1.086855 0.100000 0.200000 0.100000 1.000000
+ 0.200000 116.675711 1.162646 0.100000 0.200000 0.100000 1.000000
+ 0.200000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.157418 1.130546 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.157418 1.130546 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.327813 1.086855 0.100000 0.200000 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/HILLS_multi.1.reference b/regtest/basic/rt-mpi6/HILLS_multi.1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2092e8760aec70f3093c8996de206a96f6927a09
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_multi.1.reference
@@ -0,0 +1,14 @@
+#! FIELDS time c d sigma_c sigma_d height biasf
+#! SET multivariate false
+ 0.100000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.100000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.100000 116.675711 1.162646 0.100000 0.200000 0.100000 1.000000
+ 0.200000 117.327813 1.086855 0.100000 0.200000 0.100000 1.000000
+ 0.200000 116.675711 1.162646 0.100000 0.200000 0.100000 1.000000
+ 0.200000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.157418 1.130546 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.157418 1.130546 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.327813 1.086855 0.100000 0.200000 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/HILLS_multi.2.reference b/regtest/basic/rt-mpi6/HILLS_multi.2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2092e8760aec70f3093c8996de206a96f6927a09
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_multi.2.reference
@@ -0,0 +1,14 @@
+#! FIELDS time c d sigma_c sigma_d height biasf
+#! SET multivariate false
+ 0.100000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.100000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.100000 116.675711 1.162646 0.100000 0.200000 0.100000 1.000000
+ 0.200000 117.327813 1.086855 0.100000 0.200000 0.100000 1.000000
+ 0.200000 116.675711 1.162646 0.100000 0.200000 0.100000 1.000000
+ 0.200000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.157418 1.130546 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.157418 1.130546 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.327813 1.086855 0.100000 0.200000 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/HILLS_multi_a.0.reference b/regtest/basic/rt-mpi6/HILLS_multi_a.0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..98ae5effb63bbd3e65c2ffbdee401959e1205731
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_multi_a.0.reference
@@ -0,0 +1,14 @@
+#! FIELDS time c d sigma_c_c sigma_d_d sigma_d_c height biasf
+#! SET multivariate true
+ 0.100000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.100000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.100000 116.675711 1.162646 0.092485 0.141408 -0.001954 0.100000 1.000000
+ 0.200000 117.327813 1.086855 0.138834 0.141221 -0.007521 0.100000 1.000000
+ 0.200000 116.675711 1.162646 0.092485 0.141408 -0.001954 0.100000 1.000000
+ 0.200000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
+ 0.300000 117.157418 1.130546 0.152456 0.141400 -0.002453 0.100000 1.000000
+ 0.300000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
+ 0.300000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.400000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
+ 0.400000 117.157418 1.130546 0.152456 0.141400 -0.002453 0.100000 1.000000
+ 0.400000 117.327813 1.086855 0.138834 0.141221 -0.007521 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/HILLS_multi_a.1.reference b/regtest/basic/rt-mpi6/HILLS_multi_a.1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..98ae5effb63bbd3e65c2ffbdee401959e1205731
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_multi_a.1.reference
@@ -0,0 +1,14 @@
+#! FIELDS time c d sigma_c_c sigma_d_d sigma_d_c height biasf
+#! SET multivariate true
+ 0.100000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.100000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.100000 116.675711 1.162646 0.092485 0.141408 -0.001954 0.100000 1.000000
+ 0.200000 117.327813 1.086855 0.138834 0.141221 -0.007521 0.100000 1.000000
+ 0.200000 116.675711 1.162646 0.092485 0.141408 -0.001954 0.100000 1.000000
+ 0.200000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
+ 0.300000 117.157418 1.130546 0.152456 0.141400 -0.002453 0.100000 1.000000
+ 0.300000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
+ 0.300000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.400000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
+ 0.400000 117.157418 1.130546 0.152456 0.141400 -0.002453 0.100000 1.000000
+ 0.400000 117.327813 1.086855 0.138834 0.141221 -0.007521 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/HILLS_multi_a.2.reference b/regtest/basic/rt-mpi6/HILLS_multi_a.2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..98ae5effb63bbd3e65c2ffbdee401959e1205731
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_multi_a.2.reference
@@ -0,0 +1,14 @@
+#! FIELDS time c d sigma_c_c sigma_d_d sigma_d_c height biasf
+#! SET multivariate true
+ 0.100000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.100000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.100000 116.675711 1.162646 0.092485 0.141408 -0.001954 0.100000 1.000000
+ 0.200000 117.327813 1.086855 0.138834 0.141221 -0.007521 0.100000 1.000000
+ 0.200000 116.675711 1.162646 0.092485 0.141408 -0.001954 0.100000 1.000000
+ 0.200000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
+ 0.300000 117.157418 1.130546 0.152456 0.141400 -0.002453 0.100000 1.000000
+ 0.300000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
+ 0.300000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.400000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
+ 0.400000 117.157418 1.130546 0.152456 0.141400 -0.002453 0.100000 1.000000
+ 0.400000 117.327813 1.086855 0.138834 0.141221 -0.007521 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/HILLS_single.0.reference b/regtest/basic/rt-mpi6/HILLS_single.0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..ab4025be912600b787479febd5ec01f34f07f9c3
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_single.0.reference
@@ -0,0 +1,6 @@
+#! FIELDS time c d sigma_c sigma_d height biasf
+#! SET multivariate false
+ 0.100000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.200000 117.327813 1.086855 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.157418 1.130546 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/HILLS_single.1.reference b/regtest/basic/rt-mpi6/HILLS_single.1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..f0fcd361e41759bc8a04198949ffac62e8d895be
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_single.1.reference
@@ -0,0 +1,6 @@
+#! FIELDS time c d sigma_c sigma_d height biasf
+#! SET multivariate false
+ 0.100000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.200000 116.675711 1.162646 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.157418 1.130546 0.100000 0.200000 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/HILLS_single.2.reference b/regtest/basic/rt-mpi6/HILLS_single.2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..46d469f849837305ac198fa2b28c5b75f721c116
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_single.2.reference
@@ -0,0 +1,6 @@
+#! FIELDS time c d sigma_c sigma_d height biasf
+#! SET multivariate false
+ 0.100000 116.675711 1.162646 0.100000 0.200000 0.100000 1.000000
+ 0.200000 117.282739 1.080244 0.100000 0.200000 0.100000 1.000000
+ 0.300000 117.237723 1.097928 0.100000 0.200000 0.100000 1.000000
+ 0.400000 117.327813 1.086855 0.100000 0.200000 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/HILLS_single_a.0.reference b/regtest/basic/rt-mpi6/HILLS_single_a.0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..3f0a76a5a19d85d6d25740493c50d23832801574
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_single_a.0.reference
@@ -0,0 +1,6 @@
+#! FIELDS time c d sigma_c_c sigma_d_d sigma_d_c height biasf
+#! SET multivariate true
+ 0.100000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.200000 117.327813 1.086855 0.138834 0.141221 -0.007521 0.100000 1.000000
+ 0.300000 117.157418 1.130546 0.152456 0.141400 -0.002453 0.100000 1.000000
+ 0.400000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/HILLS_single_a.1.reference b/regtest/basic/rt-mpi6/HILLS_single_a.1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..4bae414f06390fd76aeb656f6c034e546fe1774c
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_single_a.1.reference
@@ -0,0 +1,6 @@
+#! FIELDS time c d sigma_c_c sigma_d_d sigma_d_c height biasf
+#! SET multivariate true
+ 0.100000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.200000 116.675711 1.162646 0.092485 0.141408 -0.001954 0.100000 1.000000
+ 0.300000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
+ 0.400000 117.157418 1.130546 0.152456 0.141400 -0.002453 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/HILLS_single_a.2.reference b/regtest/basic/rt-mpi6/HILLS_single_a.2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..73d6c6137cb94e1b4b938b3e7584475441b7c287
--- /dev/null
+++ b/regtest/basic/rt-mpi6/HILLS_single_a.2.reference
@@ -0,0 +1,6 @@
+#! FIELDS time c d sigma_c_c sigma_d_d sigma_d_c height biasf
+#! SET multivariate true
+ 0.100000 116.675711 1.162646 0.092485 0.141408 -0.001954 0.100000 1.000000
+ 0.200000 117.282739 1.080244 0.129745 0.141143 -0.008874 0.100000 1.000000
+ 0.300000 117.237723 1.097928 0.131552 0.141292 -0.006049 0.100000 1.000000
+ 0.400000 117.327813 1.086855 0.138834 0.141221 -0.007521 0.100000 1.000000
diff --git a/regtest/basic/rt-mpi6/Makefile b/regtest/basic/rt-mpi6/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt-mpi6/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-mpi6/colvar.0.reference b/regtest/basic/rt-mpi6/colvar.0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..1c21ab2c45921972042a6a37aabf1ccbb95eaf45
--- /dev/null
+++ b/regtest/basic/rt-mpi6/colvar.0.reference
@@ -0,0 +1,11 @@
+#! FIELDS time single.bias multi.bias single_a.bias multi_a.bias
+ 0.000000 0.000000 0.000000 0.000000 0.000000
+ 0.050000 0.000000 0.000000 0.000000 0.000000
+ 0.100000 0.000000 0.000000 0.000000 0.000000
+ 0.150000 0.090012 0.180024 0.093739 0.187479
+ 0.200000 0.066541 0.133083 0.079002 0.158004
+ 0.250000 0.000000 0.200000 0.000000 0.200000
+ 0.300000 0.094345 0.210006 0.126986 0.268304
+ 0.350000 0.238022 0.618046 0.265873 0.653185
+ 0.400000 0.224483 0.604507 0.255701 0.643180
+ 0.450000 0.279697 0.716226 0.324273 0.821471
diff --git a/regtest/basic/rt-mpi6/colvar.1.reference b/regtest/basic/rt-mpi6/colvar.1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..dae263b7355de83801a606e5b538cb6152129695
--- /dev/null
+++ b/regtest/basic/rt-mpi6/colvar.1.reference
@@ -0,0 +1,11 @@
+#! FIELDS time single.bias multi.bias single_a.bias multi_a.bias
+ 0.000000 0.000000 0.000000 0.000000 0.000000
+ 0.050000 0.000000 0.000000 0.000000 0.000000
+ 0.100000 0.000000 0.000000 0.000000 0.000000
+ 0.150000 0.071481 0.142961 0.081280 0.162559
+ 0.200000 0.000000 0.100000 0.000000 0.100000
+ 0.250000 0.066541 0.323374 0.079002 0.351926
+ 0.300000 0.090012 0.370315 0.093739 0.382150
+ 0.350000 0.190012 0.618046 0.193656 0.653185
+ 0.400000 0.115661 0.425667 0.141318 0.509622
+ 0.450000 0.100000 0.200000 0.100669 0.201339
diff --git a/regtest/basic/rt-mpi6/colvar.2.reference b/regtest/basic/rt-mpi6/colvar.2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..adcd5baf5312d317a5917e079a4d8ebc7559eee7
--- /dev/null
+++ b/regtest/basic/rt-mpi6/colvar.2.reference
@@ -0,0 +1,11 @@
+#! FIELDS time single.bias multi.bias single_a.bias multi_a.bias
+ 0.000000 0.000000 0.000000 0.000000 0.000000
+ 0.050000 0.000000 0.000000 0.000000 0.000000
+ 0.100000 0.000000 0.000000 0.000000 0.000000
+ 0.150000 0.000000 0.133083 0.000000 0.158004
+ 0.200000 0.000000 0.180024 0.000000 0.187479
+ 0.250000 0.044180 0.210006 0.060038 0.268304
+ 0.300000 0.090012 0.356553 0.093656 0.374593
+ 0.350000 0.100000 0.200000 0.100000 0.200669
+ 0.400000 0.156832 0.503071 0.172924 0.576200
+ 0.450000 0.280303 0.838978 0.288411 0.905141
diff --git a/regtest/basic/rt-mpi6/config b/regtest/basic/rt-mpi6/config
new file mode 100644
index 0000000000000000000000000000000000000000..87bae6c4d2525c92b4711c4945a287fc5358d24a
--- /dev/null
+++ b/regtest/basic/rt-mpi6/config
@@ -0,0 +1,4 @@
+mpiprocs=6
+type=driver
+# this is to test a different name
+arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --multi 3"
diff --git a/regtest/basic/rt-mpi6/ff.0.reference b/regtest/basic/rt-mpi6/ff.0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..0e95b3aa984604506f00ad066f062dbbfc6bda9c
--- /dev/null
+++ b/regtest/basic/rt-mpi6/ff.0.reference
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diff --git a/regtest/basic/rt-mpi6/plumed.dat b/regtest/basic/rt-mpi6/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..bc47f67fe9b2d7c9e507ef8c6a54612635fac4f0
--- /dev/null
+++ b/regtest/basic/rt-mpi6/plumed.dat
@@ -0,0 +1,11 @@
+d: DISTANCE ATOMS=1,10
+c: COORDINATION GROUPA=1-108 GROUPB=1-108 R_0=0.5
+
+single: METAD ARG=c,d SIGMA=0.1,0.2 HEIGHT=0.1 PACE=2 FMT=%14.6f FILE=HILLS_single
+multi: METAD ARG=c,d SIGMA=0.1,0.2 HEIGHT=0.1 PACE=2 FMT=%14.6f WALKERS_MPI FILE=HILLS_multi
+
+single_a: METAD ARG=c,d ADAPTIVE=GEOM SIGMA=0.1 HEIGHT=0.1 PACE=2 FMT=%14.6f FILE=HILLS_single_a
+multi_a: METAD ARG=c,d ADAPTIVE=GEOM SIGMA=0.1 HEIGHT=0.1 PACE=2 FMT=%14.6f WALKERS_MPI FILE=HILLS_multi_a
+
+PRINT ARG=single.bias,multi.bias,single_a.bias,multi_a.bias FILE=colvar
+
diff --git a/regtest/basic/rt-mpi6/test.pdb b/regtest/basic/rt-mpi6/test.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..32c805761fdf9285aa92786672bdf49d6e2bc632
--- /dev/null
+++ b/regtest/basic/rt-mpi6/test.pdb
@@ -0,0 +1,108 @@
+ATOM 1 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 2 Ar 0.000 0.000 0.000 2.00 0.00
+ATOM 3 Ar 0.000 0.000 0.000 3.00 1.00
+ATOM 4 Ar 0.000 0.000 0.000 2.00 0.00
+ATOM 5 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 6 Ar 0.000 0.000 0.000 2.00 0.00
+ATOM 7 Ar 0.000 0.000 0.000 3.00 1.00
+ATOM 8 Ar 0.000 0.000 0.000 2.00 0.00
+ATOM 9 Ar 0.000 0.000 0.000 1.00 10.00
+ATOM 10 Ar 0.000 0.000 0.000 2.00 0.00
+ATOM 11 Ar 0.000 0.000 0.000 3.00 20.00
+ATOM 12 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 13 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 14 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 15 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 16 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 17 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 18 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 19 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 20 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 21 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 22 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 23 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 24 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 25 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 26 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 27 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 28 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 29 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 30 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 31 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 32 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 33 Ar 0.000 0.000 0.000 1.00 1.00
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diff --git a/regtest/basic/rt-mpi6/trajectory.xyz.0 b/regtest/basic/rt-mpi6/trajectory.xyz.0
new file mode 100644
index 0000000000000000000000000000000000000000..e9766a03312bd6580f19bf1a8e6242940a4cc7bf
--- /dev/null
+++ b/regtest/basic/rt-mpi6/trajectory.xyz.0
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diff --git a/regtest/basic/rt-mpi6/trajectory.xyz.1 b/regtest/basic/rt-mpi6/trajectory.xyz.1
new file mode 100644
index 0000000000000000000000000000000000000000..a33fb0241bc304e573b5ca30e71b85e974e0a192
--- /dev/null
+++ b/regtest/basic/rt-mpi6/trajectory.xyz.1
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diff --git a/regtest/basic/rt-mpi6/trajectory.xyz.2 b/regtest/basic/rt-mpi6/trajectory.xyz.2
new file mode 100644
index 0000000000000000000000000000000000000000..be99d48b46b6aea5beb4d96a7766e30ecc74659d
--- /dev/null
+++ b/regtest/basic/rt-mpi6/trajectory.xyz.2
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+ Ar 2.50158282360438 2.54754885618802 3.44787548939131
+ Ar 1.67148086080540 2.64773782567095 4.14328399099856
+ Ar 1.55856067665018 3.33914886257725 -7.882223611267573E-002
+ Ar 2.61401897649377 3.42323653514337 0.805744343409354
+ Ar 2.68199978871527 4.20249660577513 2.401513187003788E-003
+ Ar 1.70131148235919 4.11224625852237 0.734798642838649
+ Ar 1.50744011367944 3.33746989638913 1.66359162278271
+ Ar 2.68317527355494 3.40543551523704 2.49105937409657
+ Ar 2.30865993097341 3.96454642231613 1.71404351796603
+ Ar 1.69073020869972 4.20351567358475 2.49105320830998
+ Ar 1.79104324256645 3.40488120714126 3.29374799997469
+ Ar 2.52268012820315 3.37663615600579 4.40544846289852
+ Ar 2.52690275226929 4.18061141469645 3.42056328195702
+ Ar 1.59690054599501 4.19084593585540 4.07988898024915
+ Ar 3.38837032905679 -0.106719050973078 -4.044580819091372E-002
+ Ar 4.20574882005637 -0.127340558861311 0.824241728638394
+ Ar 4.21064834970282 0.859143843346849 -3.048607191605546E-002
+ Ar 3.52714128903246 0.891515712949772 0.811294570666182
+ Ar 3.29829365298609 9.678824809121567E-002 1.64970824790893
+ Ar 4.24779258165091 -8.060095250857245E-002 2.42137863318697
+ Ar 4.08628662225109 0.841487343553101 1.73222389512198
+ Ar 3.05004747602194 0.907631966281553 2.58964371713587
+ Ar 3.38958079865663 0.199058381418399 3.50477081239431
+ Ar 4.24808745031262 -0.147777592146594 4.28248268311284
+ Ar 4.28344245386949 1.01013663146064 3.44469553501090
+ Ar 3.43321954653266 1.05244431874078 4.10034911394721
+ Ar 3.31763727211403 1.73521335486417 2.006500916657193E-002
+ Ar 4.20268695212408 1.79841295223325 0.745579809104725
+ Ar 4.34156837483850 2.69960210790029 0.112246200494744
+ Ar 3.33057921681367 2.51995980580015 0.910925609209384
+ Ar 3.42369773618588 1.73041116938367 1.79530781722495
+ Ar 4.23124644947798 1.69432699031619 2.71118773546222
+ Ar 4.18398923911985 2.44681180741616 1.68621090884286
+ Ar 3.37454046721136 2.51793386685518 2.56953949733156
+ Ar 3.30048333616920 1.83682309426927 3.47314845619438
+ Ar 4.30325743099893 1.77079150059311 4.40618089109385
+ Ar 4.21675502976708 2.42263013811371 3.43242056200395
+ Ar 3.26889408783612 2.52152574924775 4.38400652761676
+ Ar 3.35166589609703 3.29461545705247 2.199556782777175E-002
+ Ar 4.27375962177807 3.21707865035780 0.951813096355821
+ Ar 4.08939395943035 4.05846281502895 9.459333352382746E-002
+ Ar 3.30072279587725 4.22606475976981 1.00197308516514
+ Ar 3.49578477491527 3.32102036930211 1.54043986519850
+ Ar 4.17767771645916 3.34557125587935 2.42029079445840
+ Ar 4.11107971070805 4.20427308709450 1.66847390720948
+ Ar 3.20825153540620 4.36732876704832 2.39490914474285
+ Ar 3.28498236284964 3.26964325452891 3.37491549727801
+ Ar 4.31661446993803 3.25360215079398 4.20376952300048
+ Ar 4.15434425381581 3.88712049196740 3.36153925845236
+ Ar 3.41917467863288 4.08991256559258 4.15013804937161
diff --git a/regtest/basic/rt-mpi8/COLVAR.0.reference b/regtest/basic/rt-mpi8/COLVAR.0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..74c3f8050f084afef5faffcd3f6c26928aa19277
--- /dev/null
+++ b/regtest/basic/rt-mpi8/COLVAR.0.reference
@@ -0,0 +1,5 @@
+#! FIELDS time c c2
+ 0.000000 1.000 1.000
+ 0.050000 1.000 1.000
+ 0.100000 0.000 0.000
+ 0.150000 0.000 0.000
diff --git a/regtest/basic/rt-mpi8/COLVAR.1.reference b/regtest/basic/rt-mpi8/COLVAR.1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..f6a33d1f3c2b536abf4392cb84d8d01fd644d82f
--- /dev/null
+++ b/regtest/basic/rt-mpi8/COLVAR.1.reference
@@ -0,0 +1,5 @@
+#! FIELDS time c c2
+ 0.000000 0.000 0.000
+ 0.050000 0.000 0.000
+ 0.100000 1.000 1.000
+ 0.150000 1.000 1.000
diff --git a/regtest/basic/rt-mpi8/COLVAR.2.reference b/regtest/basic/rt-mpi8/COLVAR.2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..74c3f8050f084afef5faffcd3f6c26928aa19277
--- /dev/null
+++ b/regtest/basic/rt-mpi8/COLVAR.2.reference
@@ -0,0 +1,5 @@
+#! FIELDS time c c2
+ 0.000000 1.000 1.000
+ 0.050000 1.000 1.000
+ 0.100000 0.000 0.000
+ 0.150000 0.000 0.000
diff --git a/regtest/basic/rt-mpi8/Makefile b/regtest/basic/rt-mpi8/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt-mpi8/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-mpi8/config b/regtest/basic/rt-mpi8/config
new file mode 100644
index 0000000000000000000000000000000000000000..e77c2576345c9305a71239a01e56a9c9673d1ddb
--- /dev/null
+++ b/regtest/basic/rt-mpi8/config
@@ -0,0 +1,5 @@
+mpiprocs=6
+type=driver
+# this is to test a different name
+arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --multi 3
+ --debug-dd --debug-grex 2 --debug-grex-log log.grex"
diff --git a/regtest/basic/rt-mpi8/log.grex.0.reference b/regtest/basic/rt-mpi8/log.grex.0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..d688c5dd35c79b98765bbb7e391dbc46bf140d87
--- /dev/null
+++ b/regtest/basic/rt-mpi8/log.grex.0.reference
@@ -0,0 +1,2 @@
+ 0.000000 1.000000 -1.000000
+ 1.000000 -1.000000 0.000000
diff --git a/regtest/basic/rt-mpi8/log.grex.1.reference b/regtest/basic/rt-mpi8/log.grex.1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..d688c5dd35c79b98765bbb7e391dbc46bf140d87
--- /dev/null
+++ b/regtest/basic/rt-mpi8/log.grex.1.reference
@@ -0,0 +1,2 @@
+ 0.000000 1.000000 -1.000000
+ 1.000000 -1.000000 0.000000
diff --git a/regtest/basic/rt-mpi8/log.grex.2.reference b/regtest/basic/rt-mpi8/log.grex.2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..d688c5dd35c79b98765bbb7e391dbc46bf140d87
--- /dev/null
+++ b/regtest/basic/rt-mpi8/log.grex.2.reference
@@ -0,0 +1,2 @@
+ 0.000000 1.000000 -1.000000
+ 1.000000 -1.000000 0.000000
diff --git a/regtest/basic/rt-mpi8/plumed.dat b/regtest/basic/rt-mpi8/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..9e0ea71de614815f263c6e05a8a44f53b75a598f
--- /dev/null
+++ b/regtest/basic/rt-mpi8/plumed.dat
@@ -0,0 +1,14 @@
+# NOTICE: this test will not work with neighbor lists because they are not compatible with repl ex
+c: COORDINATION GROUPA=1 GROUPB=2 NLIST NL_STRIDE=2 NL_CUTOFF=2.0 SWITCH={RATIONAL R_0=0.5 D_0=1.5 D_MAX=2.0}
+c2: COORDINATION GROUPA=1 GROUPB=2 SWITCH={RATIONAL R_0=0.5 D_0=1.5 D_MAX=2.0}
+
+RESTRAINT ARG=c AT=0 SLOPE=1
+
+PRINT ...
+ STRIDE=1
+ ARG=c,c2
+ FILE=COLVAR FMT=%6.3f
+... PRINT
+
+ENDPLUMED
+
diff --git a/regtest/basic/rt-mpi8/test.pdb b/regtest/basic/rt-mpi8/test.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..32c805761fdf9285aa92786672bdf49d6e2bc632
--- /dev/null
+++ b/regtest/basic/rt-mpi8/test.pdb
@@ -0,0 +1,108 @@
+ATOM 1 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 2 Ar 0.000 0.000 0.000 2.00 0.00
+ATOM 3 Ar 0.000 0.000 0.000 3.00 1.00
+ATOM 4 Ar 0.000 0.000 0.000 2.00 0.00
+ATOM 5 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 6 Ar 0.000 0.000 0.000 2.00 0.00
+ATOM 7 Ar 0.000 0.000 0.000 3.00 1.00
+ATOM 8 Ar 0.000 0.000 0.000 2.00 0.00
+ATOM 9 Ar 0.000 0.000 0.000 1.00 10.00
+ATOM 10 Ar 0.000 0.000 0.000 2.00 0.00
+ATOM 11 Ar 0.000 0.000 0.000 3.00 20.00
+ATOM 12 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 13 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 14 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 15 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 16 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 17 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 18 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 19 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 20 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 21 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 22 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 23 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 24 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 25 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 26 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 27 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 28 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 29 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 30 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 31 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 32 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 33 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 34 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 35 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 36 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 37 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 38 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 39 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 40 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 41 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 42 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 43 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 44 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 45 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 46 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 47 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 48 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 49 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 50 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 51 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 52 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 53 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 54 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 55 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 56 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 57 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 58 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 59 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 60 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 61 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 62 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 63 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 64 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 65 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 66 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 67 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 68 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 69 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 70 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 71 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 72 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 73 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 74 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 75 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 76 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 77 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 78 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 79 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 80 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 81 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 82 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 83 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 84 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 85 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 86 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 87 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 88 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 89 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 90 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 91 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 92 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 93 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 94 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 95 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 96 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 97 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 98 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 99 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 100 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 101 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 102 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 103 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 104 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 105 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 106 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 107 Ar 0.000 0.000 0.000 1.00 1.00
+ATOM 108 Ar 0.000 0.000 0.000 1.00 10.00
diff --git a/regtest/basic/rt-mpi8/trajectory.xyz.0 b/regtest/basic/rt-mpi8/trajectory.xyz.0
new file mode 100644
index 0000000000000000000000000000000000000000..0f5bfe76e60278cbe357a5b11b9647df4e46e637
--- /dev/null
+++ b/regtest/basic/rt-mpi8/trajectory.xyz.0
@@ -0,0 +1,20 @@
+3
+0 0 0
+X 0 0 0
+X 0 0 1
+X 0 0 10
+3
+0 0 0
+X 0 0 0
+X 0 0 1
+X 0 0 10
+3
+0 0 0
+X 0 0 0
+X 0 0 9
+X 0 0 10
+3
+0 0 0
+X 0 0 0
+X 0 0 9
+X 0 0 10
diff --git a/regtest/basic/rt-mpi8/trajectory.xyz.1 b/regtest/basic/rt-mpi8/trajectory.xyz.1
new file mode 100644
index 0000000000000000000000000000000000000000..404802509a80ce3ec0d18ae3a1730fadaac574d2
--- /dev/null
+++ b/regtest/basic/rt-mpi8/trajectory.xyz.1
@@ -0,0 +1,20 @@
+3
+0 0 0
+X 0 0 0
+X 0 0 9
+X 0 0 10
+3
+0 0 0
+X 0 0 0
+X 0 0 9
+X 0 0 10
+3
+0 0 0
+X 0 0 0
+X 0 0 1
+X 0 0 10
+3
+0 0 0
+X 0 0 0
+X 0 0 1
+X 0 0 10
diff --git a/regtest/basic/rt-mpi8/trajectory.xyz.2 b/regtest/basic/rt-mpi8/trajectory.xyz.2
new file mode 100644
index 0000000000000000000000000000000000000000..0f5bfe76e60278cbe357a5b11b9647df4e46e637
--- /dev/null
+++ b/regtest/basic/rt-mpi8/trajectory.xyz.2
@@ -0,0 +1,20 @@
+3
+0 0 0
+X 0 0 0
+X 0 0 1
+X 0 0 10
+3
+0 0 0
+X 0 0 0
+X 0 0 1
+X 0 0 10
+3
+0 0 0
+X 0 0 0
+X 0 0 9
+X 0 0 10
+3
+0 0 0
+X 0 0 0
+X 0 0 9
+X 0 0 10
diff --git a/regtest/basic/rt0/forces.reference b/regtest/basic/rt0/forces.reference
index 534c25e86448f154af0a1e0f27218dc5dc2e74a3..844853373cfc43a87c6003799556bce2e0bc512e 100644
--- a/regtest/basic/rt0/forces.reference
+++ b/regtest/basic/rt0/forces.reference
@@ -1,5 +1,5 @@
108
- -3.6537 -23.9554 -30.6234
+ -3.6537 -23.9554 -30.6233
X 0.0000 0.0000 0.0000
X 0.8129 -2.0125 -1.8501
X 0.0000 0.0000 0.0000
@@ -109,7 +109,7 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
108
- -3.6096 -23.4265 -30.3767
+ -3.6097 -23.4265 -30.3767
X 0.0000 0.0000 0.0000
X 0.8263 -1.9997 -1.8213
X 0.0000 0.0000 0.0000
@@ -117,9 +117,9 @@ X -0.5079 -0.8670 -2.0396
X 0.0000 0.0000 0.0000
X 0.5076 -1.7401 0.1283
X 0.5236 -0.8420 -0.9629
-X -0.9937 -1.2450 0.2600
+X -0.9936 -1.2450 0.2600
X -0.5684 -2.1038 1.0153
-X 0.3844 -2.1673 1.9982
+X 0.3845 -2.1673 1.9982
X 0.0000 0.0000 0.0000
X -0.3383 -1.0899 2.0200
X 0.0000 0.0000 0.0000
@@ -240,7 +240,7 @@ X 0.0000 0.0000 0.0000
X 0.3006 0.7210 0.0988
X 0.5727 2.5586 -0.9302
X -0.7280 2.6416 0.3691
-X -0.4723 1.2371 1.4881
+X -0.4722 1.2371 1.4881
X 0.7497 1.4802 3.0089
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
@@ -439,15 +439,15 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
108
- -4.6839 -23.2396 -30.7391
+ -4.6840 -23.2396 -30.7391
X 0.0000 0.0000 0.0000
X 1.0667 -2.0511 -1.7927
X 0.0000 0.0000 0.0000
X -0.6627 -0.8873 -2.1631
X 0.0000 0.0000 0.0000
-X 0.5741 -1.6315 0.2008
+X 0.5742 -1.6315 0.2008
X 0.6715 -0.8239 -1.0595
-X -1.2004 -1.2170 0.2710
+X -1.2003 -1.2170 0.2710
X -0.7572 -2.2573 1.0986
X 0.1630 -2.2602 2.0289
X 0.0000 0.0000 0.0000
diff --git a/regtest/basic/rt0/plumed.dat b/regtest/basic/rt0/plumed.dat
index 9e985d1dc036c8f7eb1aaa16096c074b878dfe43..3d4a96a34919a9c000eb5357c4dfc56d0e695b79 100644
--- a/regtest/basic/rt0/plumed.dat
+++ b/regtest/basic/rt0/plumed.dat
@@ -19,6 +19,18 @@ PRINT ...
FILE=COLVAR FMT=%6.3f
... PRINT
+## # This is to check numerical derivatives:
+## rmsd0n: RMSD TYPE=OPTIMAL REFERENCE=test0.pdb NUMERICAL_DERIVATIVES
+## rmsd1n: RMSD TYPE=OPTIMAL REFERENCE=test1.pdb NUMERICAL_DERIVATIVES
+## rmsd2n: RMSD TYPE=OPTIMAL REFERENCE=test2.pdb NUMERICAL_DERIVATIVES
+## rmsd3n: RMSD TYPE=OPTIMAL REFERENCE=test3.pdb NUMERICAL_DERIVATIVES
+## rmsd4n: RMSD TYPE=OPTIMAL REFERENCE=test4.pdb NUMERICAL_DERIVATIVES
+## DUMPDERIVATIVES ARG=rmsd0,rmsd0n FILE=check0
+## DUMPDERIVATIVES ARG=rmsd1,rmsd1n FILE=check1
+## DUMPDERIVATIVES ARG=rmsd2,rmsd2n FILE=check2
+## DUMPDERIVATIVES ARG=rmsd3,rmsd3n FILE=check3
+## DUMPDERIVATIVES ARG=rmsd4,rmsd4n FILE=check4
+
ENDPLUMED
text here should be ignored
diff --git a/regtest/basic/rt10/plumed.dat b/regtest/basic/rt10/plumed.dat
index ebde2b3ad545381b2ec56d5450d712200623fa1f..5fb2053e4efaf8bfe59c7a37ab429b4acdb840f9 100644
--- a/regtest/basic/rt10/plumed.dat
+++ b/regtest/basic/rt10/plumed.dat
@@ -11,5 +11,14 @@ PRINT ...
FLUSH STRIDE=100
+# this is to test ranges:
+# should expand to 10,12,14,16:
+t1: TORSION ATOMS=10-17:2
+# these two should give two opposite vectors
+d1: DISTANCE ATOMS=10-15:5 COMPONENTS
+d2: DISTANCE ATOMS=15-10:-5 COMPONENTS
+
+PRINT ARG=t1,d1.x,d2.x FILE=ranges
+
ENDPLUMED
diff --git a/regtest/basic/rt10/ranges.reference b/regtest/basic/rt10/ranges.reference
new file mode 100644
index 0000000000000000000000000000000000000000..51dfbeaa1fecca522054497fe885da03a7946f72
--- /dev/null
+++ b/regtest/basic/rt10/ranges.reference
@@ -0,0 +1,8 @@
+#! FIELDS time t1 d1.x d2.x
+#! SET min_t1 -pi
+#! SET max_t1 pi
+ 0.000000 3.137405 0.078081 -0.078081
+ 0.050000 -3.119466 0.156540 -0.156540
+ 0.100000 -3.059250 0.253655 -0.253655
+ 0.150000 -2.976120 0.337881 -0.337881
+ 0.200000 -2.910732 0.409918 -0.409918
diff --git a/regtest/basic/rt2/plumed.dat b/regtest/basic/rt2/plumed.dat
index 1ac8927aaac61c94c134ec82283fc607b66b8b5f..d504175d4dc752d49b0e71c33a99666cb12e0cbb 100644
--- a/regtest/basic/rt2/plumed.dat
+++ b/regtest/basic/rt2/plumed.dat
@@ -1,12 +1,21 @@
g1: GROUP ATOMS=1-9:2,2-10:2
g2: GROUP ATOMS=30-40,5
-c1: COM ATOMS=g1
-c2: COM ATOMS=g2
+ndx1: GROUP NDX_FILE=test.ndx
+ndx2: GROUP NDX_FILE=test.ndx NDX_GROUP=second
+
+c1: COM ATOMS=g1
+c2: COM ATOMS=g2
+c1n: COM ATOMS=ndx1
+c2n: COM ATOMS=ndx2
d1: DISTANCE ATOMS=1,10
d2: DISTANCE ATOMS=c1,50
d3: DISTANCE ATOMS=50,c2
+d1n: DISTANCE ATOMS=1,10
+d2n: DISTANCE ATOMS=c1n,50
+d3n: DISTANCE ATOMS=50,c2n
+
RESTRAINT ARG=d2 AT=0.9 KAPPA=3.0
PRINT ...
@@ -15,5 +24,12 @@ PRINT ...
FILE=COLVAR FMT=%6.3f
... PRINT
+PRINT ...
+ STRIDE=1
+ ARG=d1n,d2n,d3n
+ FILE=COLVARN FMT=%6.3f
+... PRINT
+
+
ENDPLUMED
diff --git a/regtest/basic/rt2/test.ndx b/regtest/basic/rt2/test.ndx
new file mode 100644
index 0000000000000000000000000000000000000000..510d0f972096b1ecb27454819cf888d0457d0113
--- /dev/null
+++ b/regtest/basic/rt2/test.ndx
@@ -0,0 +1,6 @@
+[ first ]
+1 3 5 7 9
+2 4 6 8 10
+[ second ]
+30 31 32 33 34 35 36 37 38 39 40
+5
diff --git a/regtest/basic/rt20/COLVAR.reference b/regtest/basic/rt20/COLVAR.reference
new file mode 100644
index 0000000000000000000000000000000000000000..1d260e359cf6f4dc5fcf19a5abedf1c312d6d36d
--- /dev/null
+++ b/regtest/basic/rt20/COLVAR.reference
@@ -0,0 +1,31 @@
+#! FIELDS time c cs
+ 0.000000 1.000000 1.000000
+ 1.000000 1.000000 1.000000
+ 2.000000 0.999987 0.999987
+ 3.000000 0.999849 0.999847
+ 4.000000 0.999152 0.999139
+ 5.000000 0.996773 0.996723
+ 6.000000 0.990427 0.990277
+ 7.000000 0.976206 0.975834
+ 8.000000 0.948488 0.947683
+ 9.000000 0.900818 0.899268
+ 10.000000 0.828379 0.825698
+ 11.000000 0.731515 0.727320
+ 12.000000 0.617808 0.611837
+ 13.000000 0.500000 0.492188
+ 14.000000 0.390634 0.381113
+ 15.000000 0.297631 0.286656
+ 16.000000 0.223422 0.211288
+ 17.000000 0.166646 0.153625
+ 18.000000 0.124277 0.110594
+ 19.000000 0.093051 0.078880
+ 20.000000 0.070130 0.055601
+ 21.000000 0.053280 0.038488
+ 22.000000 0.040834 0.025847
+ 23.000000 0.031576 0.016444
+ 24.000000 0.024635 0.009395
+ 25.000000 0.019387 0.004065
+ 26.000000 0.000000 0.000000
+ 27.000000 0.000000 0.000000
+ 28.000000 0.000000 0.000000
+ 29.000000 0.000000 0.000000
diff --git a/regtest/basic/rt20/Makefile b/regtest/basic/rt20/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt20/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt20/config b/regtest/basic/rt20/config
new file mode 100644
index 0000000000000000000000000000000000000000..f93ec1a97465724691bf162d4735f5ea3648bbb4
--- /dev/null
+++ b/regtest/basic/rt20/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz trajectory.xyz"
diff --git a/regtest/basic/rt20/deriv.reference b/regtest/basic/rt20/deriv.reference
new file mode 100644
index 0000000000000000000000000000000000000000..40c11ea6e26329b213e16aad5cccd70c550ab8a7
--- /dev/null
+++ b/regtest/basic/rt20/deriv.reference
@@ -0,0 +1,451 @@
+#! FIELDS time parameter c cs
+ 0.000000 0 0.0000 0.0000
+ 0.000000 1 0.0000 0.0000
+ 0.000000 2 0.0000 0.0000
+ 0.000000 3 0.0000 0.0000
+ 0.000000 4 0.0000 0.0000
+ 0.000000 5 0.0000 0.0000
+ 0.000000 6 0.0000 0.0000
+ 0.000000 7 0.0000 0.0000
+ 0.000000 8 0.0000 0.0000
+ 0.000000 9 0.0000 0.0000
+ 0.000000 10 0.0000 0.0000
+ 0.000000 11 0.0000 0.0000
+ 0.000000 12 0.0000 0.0000
+ 0.000000 13 0.0000 0.0000
+ 0.000000 14 0.0000 0.0000
+ 1.000000 0 0.0000 0.0000
+ 1.000000 1 0.0000 0.0000
+ 1.000000 2 0.0000 0.0000
+ 1.000000 3 0.0000 0.0000
+ 1.000000 4 0.0000 0.0000
+ 1.000000 5 -0.0000 -0.0000
+ 1.000000 6 0.0000 0.0000
+ 1.000000 7 0.0000 0.0000
+ 1.000000 8 0.0000 0.0000
+ 1.000000 9 0.0000 0.0000
+ 1.000000 10 0.0000 0.0000
+ 1.000000 11 0.0000 0.0000
+ 1.000000 12 0.0000 0.0000
+ 1.000000 13 0.0000 0.0000
+ 1.000000 14 0.0000 0.0000
+ 2.000000 0 0.0000 0.0000
+ 2.000000 1 0.0000 0.0000
+ 2.000000 2 0.0004 0.0004
+ 2.000000 3 0.0000 0.0000
+ 2.000000 4 0.0000 0.0000
+ 2.000000 5 -0.0004 -0.0004
+ 2.000000 6 0.0000 0.0000
+ 2.000000 7 0.0000 0.0000
+ 2.000000 8 0.0000 0.0000
+ 2.000000 9 0.0000 0.0000
+ 2.000000 10 0.0000 0.0000
+ 2.000000 11 0.0000 0.0000
+ 2.000000 12 0.0000 0.0000
+ 2.000000 13 0.0000 0.0000
+ 2.000000 14 0.0001 0.0001
+ 3.000000 0 0.0000 0.0000
+ 3.000000 1 0.0000 0.0000
+ 3.000000 2 0.0030 0.0031
+ 3.000000 3 0.0000 0.0000
+ 3.000000 4 0.0000 0.0000
+ 3.000000 5 -0.0030 -0.0031
+ 3.000000 6 0.0000 0.0000
+ 3.000000 7 0.0000 0.0000
+ 3.000000 8 0.0000 0.0000
+ 3.000000 9 0.0000 0.0000
+ 3.000000 10 0.0000 0.0000
+ 3.000000 11 0.0000 0.0000
+ 3.000000 12 0.0000 0.0000
+ 3.000000 13 0.0000 0.0000
+ 3.000000 14 0.0009 0.0009
+ 4.000000 0 0.0000 0.0000
+ 4.000000 1 0.0000 0.0000
+ 4.000000 2 0.0127 0.0129
+ 4.000000 3 0.0000 0.0000
+ 4.000000 4 0.0000 0.0000
+ 4.000000 5 -0.0127 -0.0129
+ 4.000000 6 0.0000 0.0000
+ 4.000000 7 0.0000 0.0000
+ 4.000000 8 0.0000 0.0000
+ 4.000000 9 0.0000 0.0000
+ 4.000000 10 0.0000 0.0000
+ 4.000000 11 0.0000 0.0000
+ 4.000000 12 0.0000 0.0000
+ 4.000000 13 0.0000 0.0000
+ 4.000000 14 0.0051 0.0052
+ 5.000000 0 0.0000 0.0000
+ 5.000000 1 0.0000 0.0000
+ 5.000000 2 0.0386 0.0392
+ 5.000000 3 0.0000 0.0000
+ 5.000000 4 0.0000 0.0000
+ 5.000000 5 -0.0386 -0.0392
+ 5.000000 6 0.0000 0.0000
+ 5.000000 7 0.0000 0.0000
+ 5.000000 8 0.0000 0.0000
+ 5.000000 9 0.0000 0.0000
+ 5.000000 10 0.0000 0.0000
+ 5.000000 11 0.0000 0.0000
+ 5.000000 12 0.0000 0.0000
+ 5.000000 13 0.0000 0.0000
+ 5.000000 14 0.0193 0.0196
+ 6.000000 0 0.0000 0.0000
+ 6.000000 1 0.0000 0.0000
+ 6.000000 2 0.0948 0.0963
+ 6.000000 3 0.0000 0.0000
+ 6.000000 4 0.0000 0.0000
+ 6.000000 5 -0.0948 -0.0963
+ 6.000000 6 0.0000 0.0000
+ 6.000000 7 0.0000 0.0000
+ 6.000000 8 0.0000 0.0000
+ 6.000000 9 0.0000 0.0000
+ 6.000000 10 0.0000 0.0000
+ 6.000000 11 0.0000 0.0000
+ 6.000000 12 0.0000 0.0000
+ 6.000000 13 0.0000 0.0000
+ 6.000000 14 0.0569 0.0578
+ 7.000000 0 0.0000 0.0000
+ 7.000000 1 0.0000 0.0000
+ 7.000000 2 0.1991 0.2022
+ 7.000000 3 0.0000 0.0000
+ 7.000000 4 0.0000 0.0000
+ 7.000000 5 -0.1991 -0.2022
+ 7.000000 6 0.0000 0.0000
+ 7.000000 7 0.0000 0.0000
+ 7.000000 8 0.0000 0.0000
+ 7.000000 9 0.0000 0.0000
+ 7.000000 10 0.0000 0.0000
+ 7.000000 11 0.0000 0.0000
+ 7.000000 12 0.0000 0.0000
+ 7.000000 13 0.0000 0.0000
+ 7.000000 14 0.1394 0.1415
+ 8.000000 0 0.0000 0.0000
+ 8.000000 1 0.0000 0.0000
+ 8.000000 2 0.3664 0.3722
+ 8.000000 3 0.0000 0.0000
+ 8.000000 4 0.0000 0.0000
+ 8.000000 5 -0.3664 -0.3722
+ 8.000000 6 0.0000 0.0000
+ 8.000000 7 0.0000 0.0000
+ 8.000000 8 0.0000 0.0000
+ 8.000000 9 0.0000 0.0000
+ 8.000000 10 0.0000 0.0000
+ 8.000000 11 0.0000 0.0000
+ 8.000000 12 0.0000 0.0000
+ 8.000000 13 0.0000 0.0000
+ 8.000000 14 0.2932 0.2977
+ 9.000000 0 0.0000 0.0000
+ 9.000000 1 0.0000 0.0000
+ 9.000000 2 0.5956 0.6049
+ 9.000000 3 0.0000 0.0000
+ 9.000000 4 0.0000 0.0000
+ 9.000000 5 -0.5956 -0.6049
+ 9.000000 6 0.0000 0.0000
+ 9.000000 7 0.0000 0.0000
+ 9.000000 8 0.0000 0.0000
+ 9.000000 9 0.0000 0.0000
+ 9.000000 10 0.0000 0.0000
+ 9.000000 11 0.0000 0.0000
+ 9.000000 12 0.0000 0.0000
+ 9.000000 13 0.0000 0.0000
+ 9.000000 14 0.5361 0.5444
+ 10.000000 0 0.0000 0.0000
+ 10.000000 1 0.0000 0.0000
+ 10.000000 2 0.8530 0.8663
+ 10.000000 3 0.0000 0.0000
+ 10.000000 4 0.0000 0.0000
+ 10.000000 5 -0.8530 -0.8663
+ 10.000000 6 0.0000 0.0000
+ 10.000000 7 0.0000 0.0000
+ 10.000000 8 0.0000 0.0000
+ 10.000000 9 0.0000 0.0000
+ 10.000000 10 0.0000 0.0000
+ 10.000000 11 0.0000 0.0000
+ 10.000000 12 0.0000 0.0000
+ 10.000000 13 0.0000 0.0000
+ 10.000000 14 0.8530 0.8663
+ 11.000000 0 0.0000 0.0000
+ 11.000000 1 0.0000 0.0000
+ 11.000000 2 1.0713 1.0880
+ 11.000000 3 0.0000 0.0000
+ 11.000000 4 0.0000 0.0000
+ 11.000000 5 -1.0713 -1.0880
+ 11.000000 6 0.0000 0.0000
+ 11.000000 7 0.0000 0.0000
+ 11.000000 8 0.0000 0.0000
+ 11.000000 9 0.0000 0.0000
+ 11.000000 10 0.0000 0.0000
+ 11.000000 11 0.0000 0.0000
+ 11.000000 12 0.0000 0.0000
+ 11.000000 13 0.0000 0.0000
+ 11.000000 14 1.1784 1.1968
+ 12.000000 0 0.0000 0.0000
+ 12.000000 1 0.0000 0.0000
+ 12.000000 2 1.1806 1.1991
+ 12.000000 3 0.0000 0.0000
+ 12.000000 4 0.0000 0.0000
+ 12.000000 5 -1.1806 -1.1991
+ 12.000000 6 0.0000 0.0000
+ 12.000000 7 0.0000 0.0000
+ 12.000000 8 0.0000 0.0000
+ 12.000000 9 0.0000 0.0000
+ 12.000000 10 0.0000 0.0000
+ 12.000000 11 0.0000 0.0000
+ 12.000000 12 0.0000 0.0000
+ 12.000000 13 0.0000 0.0000
+ 12.000000 14 1.4167 1.4389
+ 13.000000 0 0.0000 0.0000
+ 13.000000 1 0.0000 0.0000
+ 13.000000 2 1.1538 1.1719
+ 13.000000 3 0.0000 0.0000
+ 13.000000 4 0.0000 0.0000
+ 13.000000 5 -1.1538 -1.1719
+ 13.000000 6 0.0000 0.0000
+ 13.000000 7 0.0000 0.0000
+ 13.000000 8 0.0000 0.0000
+ 13.000000 9 0.0000 0.0000
+ 13.000000 10 0.0000 0.0000
+ 13.000000 11 0.0000 0.0000
+ 13.000000 12 0.0000 0.0000
+ 13.000000 13 0.0000 0.0000
+ 13.000000 14 1.5000 1.5234
+ 14.000000 0 0.0000 0.0000
+ 14.000000 1 0.0000 0.0000
+ 14.000000 2 1.0202 1.0361
+ 14.000000 3 0.0000 0.0000
+ 14.000000 4 0.0000 0.0000
+ 14.000000 5 -1.0202 -1.0361
+ 14.000000 6 0.0000 0.0000
+ 14.000000 7 0.0000 0.0000
+ 14.000000 8 0.0000 0.0000
+ 14.000000 9 0.0000 0.0000
+ 14.000000 10 0.0000 0.0000
+ 14.000000 11 0.0000 0.0000
+ 14.000000 12 0.0000 0.0000
+ 14.000000 13 0.0000 0.0000
+ 14.000000 14 1.4282 1.4506
+ 15.000000 0 0.0000 0.0000
+ 15.000000 1 0.0000 0.0000
+ 15.000000 2 0.8362 0.8493
+ 15.000000 3 0.0000 0.0000
+ 15.000000 4 0.0000 0.0000
+ 15.000000 5 -0.8362 -0.8493
+ 15.000000 6 0.0000 0.0000
+ 15.000000 7 0.0000 0.0000
+ 15.000000 8 0.0000 0.0000
+ 15.000000 9 0.0000 0.0000
+ 15.000000 10 0.0000 0.0000
+ 15.000000 11 0.0000 0.0000
+ 15.000000 12 0.0000 0.0000
+ 15.000000 13 0.0000 0.0000
+ 15.000000 14 1.2543 1.2739
+ 16.000000 0 0.0000 0.0000
+ 16.000000 1 0.0000 0.0000
+ 16.000000 2 0.6506 0.6608
+ 16.000000 3 0.0000 0.0000
+ 16.000000 4 0.0000 0.0000
+ 16.000000 5 -0.6506 -0.6608
+ 16.000000 6 0.0000 0.0000
+ 16.000000 7 0.0000 0.0000
+ 16.000000 8 0.0000 0.0000
+ 16.000000 9 0.0000 0.0000
+ 16.000000 10 0.0000 0.0000
+ 16.000000 11 0.0000 0.0000
+ 16.000000 12 0.0000 0.0000
+ 16.000000 13 0.0000 0.0000
+ 16.000000 14 1.0410 1.0573
+ 17.000000 0 0.0000 0.0000
+ 17.000000 1 0.0000 0.0000
+ 17.000000 2 0.4901 0.4978
+ 17.000000 3 0.0000 0.0000
+ 17.000000 4 0.0000 0.0000
+ 17.000000 5 -0.4901 -0.4978
+ 17.000000 6 0.0000 0.0000
+ 17.000000 7 0.0000 0.0000
+ 17.000000 8 0.0000 0.0000
+ 17.000000 9 0.0000 0.0000
+ 17.000000 10 0.0000 0.0000
+ 17.000000 11 0.0000 0.0000
+ 17.000000 12 0.0000 0.0000
+ 17.000000 13 0.0000 0.0000
+ 17.000000 14 0.8333 0.8463
+ 18.000000 0 0.0000 0.0000
+ 18.000000 1 0.0000 0.0000
+ 18.000000 2 0.3628 0.3684
+ 18.000000 3 0.0000 0.0000
+ 18.000000 4 0.0000 0.0000
+ 18.000000 5 -0.3628 -0.3684
+ 18.000000 6 0.0000 0.0000
+ 18.000000 7 0.0000 0.0000
+ 18.000000 8 0.0000 0.0000
+ 18.000000 9 0.0000 0.0000
+ 18.000000 10 0.0000 0.0000
+ 18.000000 11 0.0000 0.0000
+ 18.000000 12 0.0000 0.0000
+ 18.000000 13 0.0000 0.0000
+ 18.000000 14 0.6530 0.6632
+ 19.000000 0 0.0000 0.0000
+ 19.000000 1 0.0000 0.0000
+ 19.000000 2 0.2665 0.2707
+ 19.000000 3 0.0000 0.0000
+ 19.000000 4 0.0000 0.0000
+ 19.000000 5 -0.2665 -0.2707
+ 19.000000 6 0.0000 0.0000
+ 19.000000 7 0.0000 0.0000
+ 19.000000 8 0.0000 0.0000
+ 19.000000 9 0.0000 0.0000
+ 19.000000 10 0.0000 0.0000
+ 19.000000 11 0.0000 0.0000
+ 19.000000 12 0.0000 0.0000
+ 19.000000 13 0.0000 0.0000
+ 19.000000 14 0.5064 0.5143
+ 20.000000 0 0.0000 0.0000
+ 20.000000 1 0.0000 0.0000
+ 20.000000 2 0.1956 0.1987
+ 20.000000 3 0.0000 0.0000
+ 20.000000 4 0.0000 0.0000
+ 20.000000 5 -0.1956 -0.1987
+ 20.000000 6 0.0000 0.0000
+ 20.000000 7 0.0000 0.0000
+ 20.000000 8 0.0000 0.0000
+ 20.000000 9 0.0000 0.0000
+ 20.000000 10 0.0000 0.0000
+ 20.000000 11 0.0000 0.0000
+ 20.000000 12 0.0000 0.0000
+ 20.000000 13 0.0000 0.0000
+ 20.000000 14 0.3913 0.3974
+ 21.000000 0 0.0000 0.0000
+ 21.000000 1 0.0000 0.0000
+ 21.000000 2 0.1441 0.1464
+ 21.000000 3 0.0000 0.0000
+ 21.000000 4 0.0000 0.0000
+ 21.000000 5 -0.1441 -0.1464
+ 21.000000 6 0.0000 0.0000
+ 21.000000 7 0.0000 0.0000
+ 21.000000 8 0.0000 0.0000
+ 21.000000 9 0.0000 0.0000
+ 21.000000 10 0.0000 0.0000
+ 21.000000 11 0.0000 0.0000
+ 21.000000 12 0.0000 0.0000
+ 21.000000 13 0.0000 0.0000
+ 21.000000 14 0.3026 0.3074
+ 22.000000 0 0.0000 0.0000
+ 22.000000 1 0.0000 0.0000
+ 22.000000 2 0.1068 0.1085
+ 22.000000 3 0.0000 0.0000
+ 22.000000 4 0.0000 0.0000
+ 22.000000 5 -0.1068 -0.1085
+ 22.000000 6 0.0000 0.0000
+ 22.000000 7 0.0000 0.0000
+ 22.000000 8 0.0000 0.0000
+ 22.000000 9 0.0000 0.0000
+ 22.000000 10 0.0000 0.0000
+ 22.000000 11 0.0000 0.0000
+ 22.000000 12 0.0000 0.0000
+ 22.000000 13 0.0000 0.0000
+ 22.000000 14 0.2350 0.2387
+ 23.000000 0 0.0000 0.0000
+ 23.000000 1 0.0000 0.0000
+ 23.000000 2 0.0798 0.0810
+ 23.000000 3 0.0000 0.0000
+ 23.000000 4 0.0000 0.0000
+ 23.000000 5 -0.0798 -0.0810
+ 23.000000 6 0.0000 0.0000
+ 23.000000 7 0.0000 0.0000
+ 23.000000 8 0.0000 0.0000
+ 23.000000 9 0.0000 0.0000
+ 23.000000 10 0.0000 0.0000
+ 23.000000 11 0.0000 0.0000
+ 23.000000 12 0.0000 0.0000
+ 23.000000 13 0.0000 0.0000
+ 23.000000 14 0.1835 0.1863
+ 24.000000 0 0.0000 0.0000
+ 24.000000 1 0.0000 0.0000
+ 24.000000 2 0.0601 0.0610
+ 24.000000 3 0.0000 0.0000
+ 24.000000 4 0.0000 0.0000
+ 24.000000 5 -0.0601 -0.0610
+ 24.000000 6 0.0000 0.0000
+ 24.000000 7 0.0000 0.0000
+ 24.000000 8 0.0000 0.0000
+ 24.000000 9 0.0000 0.0000
+ 24.000000 10 0.0000 0.0000
+ 24.000000 11 0.0000 0.0000
+ 24.000000 12 0.0000 0.0000
+ 24.000000 13 0.0000 0.0000
+ 24.000000 14 0.1442 0.1464
+ 25.000000 0 0.0000 0.0000
+ 25.000000 1 0.0000 0.0000
+ 25.000000 2 0.0456 0.0463
+ 25.000000 3 0.0000 0.0000
+ 25.000000 4 0.0000 0.0000
+ 25.000000 5 -0.0456 -0.0463
+ 25.000000 6 0.0000 0.0000
+ 25.000000 7 0.0000 0.0000
+ 25.000000 8 0.0000 0.0000
+ 25.000000 9 0.0000 0.0000
+ 25.000000 10 0.0000 0.0000
+ 25.000000 11 0.0000 0.0000
+ 25.000000 12 0.0000 0.0000
+ 25.000000 13 0.0000 0.0000
+ 25.000000 14 0.1141 0.1159
+ 26.000000 0 0.0000 0.0000
+ 26.000000 1 0.0000 0.0000
+ 26.000000 2 0.0000 0.0000
+ 26.000000 3 0.0000 0.0000
+ 26.000000 4 0.0000 0.0000
+ 26.000000 5 0.0000 0.0000
+ 26.000000 6 0.0000 0.0000
+ 26.000000 7 0.0000 0.0000
+ 26.000000 8 0.0000 0.0000
+ 26.000000 9 0.0000 0.0000
+ 26.000000 10 0.0000 0.0000
+ 26.000000 11 0.0000 0.0000
+ 26.000000 12 0.0000 0.0000
+ 26.000000 13 0.0000 0.0000
+ 26.000000 14 0.0000 0.0000
+ 27.000000 0 0.0000 0.0000
+ 27.000000 1 0.0000 0.0000
+ 27.000000 2 0.0000 0.0000
+ 27.000000 3 0.0000 0.0000
+ 27.000000 4 0.0000 0.0000
+ 27.000000 5 0.0000 0.0000
+ 27.000000 6 0.0000 0.0000
+ 27.000000 7 0.0000 0.0000
+ 27.000000 8 0.0000 0.0000
+ 27.000000 9 0.0000 0.0000
+ 27.000000 10 0.0000 0.0000
+ 27.000000 11 0.0000 0.0000
+ 27.000000 12 0.0000 0.0000
+ 27.000000 13 0.0000 0.0000
+ 27.000000 14 0.0000 0.0000
+ 28.000000 0 0.0000 0.0000
+ 28.000000 1 0.0000 0.0000
+ 28.000000 2 0.0000 0.0000
+ 28.000000 3 0.0000 0.0000
+ 28.000000 4 0.0000 0.0000
+ 28.000000 5 0.0000 0.0000
+ 28.000000 6 0.0000 0.0000
+ 28.000000 7 0.0000 0.0000
+ 28.000000 8 0.0000 0.0000
+ 28.000000 9 0.0000 0.0000
+ 28.000000 10 0.0000 0.0000
+ 28.000000 11 0.0000 0.0000
+ 28.000000 12 0.0000 0.0000
+ 28.000000 13 0.0000 0.0000
+ 28.000000 14 0.0000 0.0000
+ 29.000000 0 0.0000 0.0000
+ 29.000000 1 0.0000 0.0000
+ 29.000000 2 0.0000 0.0000
+ 29.000000 3 0.0000 0.0000
+ 29.000000 4 0.0000 0.0000
+ 29.000000 5 0.0000 0.0000
+ 29.000000 6 0.0000 0.0000
+ 29.000000 7 0.0000 0.0000
+ 29.000000 8 0.0000 0.0000
+ 29.000000 9 0.0000 0.0000
+ 29.000000 10 0.0000 0.0000
+ 29.000000 11 0.0000 0.0000
+ 29.000000 12 0.0000 0.0000
+ 29.000000 13 0.0000 0.0000
+ 29.000000 14 0.0000 0.0000
diff --git a/regtest/basic/rt20/plumed.dat b/regtest/basic/rt20/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..4144f43bd73e50961a065b961e1d593fcf709470
--- /dev/null
+++ b/regtest/basic/rt20/plumed.dat
@@ -0,0 +1,17 @@
+c: COORDINATION GROUPA=1 GROUPB=2 SWITCH={RATIONAL R_0=1.3 D_MAX=2.6}
+cs: COORDINATION GROUPA=1 GROUPB=2 SWITCH={RATIONAL R_0=1.3 D_MAX=2.6 STRETCH}
+csn: COORDINATION GROUPA=1 GROUPB=2 SWITCH={RATIONAL R_0=1.3 D_MAX=2.6 STRETCH} NUMERICAL_DERIVATIVES
+
+PRINT ...
+ ARG=c,cs
+ FILE=COLVAR
+... PRINT
+
+DUMPDERIVATIVES ARG=c,cs FILE=deriv FMT=%8.4f
+
+# this has been used to debug derivatives
+# I don't use it in regtest since it fails doe to numerical noise (0.0 vs -0.0)
+# DUMPDERIVATIVES ARG=c,cs,csn FILE=deriv FMT=%8.4f
+
+ENDPLUMED
+
diff --git a/regtest/basic/rt20/trajectory.xyz b/regtest/basic/rt20/trajectory.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..1ffefa2bc6642b08d83ee9c13755698369c8a52f
--- /dev/null
+++ b/regtest/basic/rt20/trajectory.xyz
@@ -0,0 +1,120 @@
+2
+10 10 10
+X 0 0 0.0
+X 0 0 0.0
+2
+10 10 10
+X 0 0 0.0
+X 0 0 0.1
+2
+10 10 10
+X 0 0 0.0
+X 0 0 0.2
+2
+10 10 10
+X 0 0 0.0
+X 0 0 0.3
+2
+10 10 10
+X 0 0 0.0
+X 0 0 0.4
+2
+10 10 10
+X 0 0 0.0
+X 0 0 0.5
+2
+10 10 10
+X 0 0 0.0
+X 0 0 0.6
+2
+10 10 10
+X 0 0 0.0
+X 0 0 0.7
+2
+10 10 10
+X 0 0 0.0
+X 0 0 0.8
+2
+10 10 10
+X 0 0 0.0
+X 0 0 0.9
+2
+10 10 10
+X 0 0 0.0
+X 0 0 1.0
+2
+10 10 10
+X 0 0 0.0
+X 0 0 1.1
+2
+10 10 10
+X 0 0 0.0
+X 0 0 1.2
+2
+10 10 10
+X 0 0 0.0
+X 0 0 1.3
+2
+10 10 10
+X 0 0 0.0
+X 0 0 1.4
+2
+10 10 10
+X 0 0 0.0
+X 0 0 1.5
+2
+10 10 10
+X 0 0 0.0
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+2
+10 10 10
+X 0 0 0.0
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+2
+10 10 10
+X 0 0 0.0
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+2
+10 10 10
+X 0 0 0.0
+X 0 0 1.9
+2
+10 10 10
+X 0 0 0.0
+X 0 0 2.0
+2
+10 10 10
+X 0 0 0.0
+X 0 0 2.1
+2
+10 10 10
+X 0 0 0.0
+X 0 0 2.2
+2
+10 10 10
+X 0 0 0.0
+X 0 0 2.3
+2
+10 10 10
+X 0 0 0.0
+X 0 0 2.4
+2
+10 10 10
+X 0 0 0.0
+X 0 0 2.5
+2
+10 10 10
+X 0 0 0.0
+X 0 0 2.6
+2
+10 10 10
+X 0 0 0.0
+X 0 0 2.7
+2
+10 10 10
+X 0 0 0.0
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+2
+10 10 10
+X 0 0 0.0
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diff --git a/regtest/basic/rt32/Makefile b/regtest/basic/rt32/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt32/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt32/ala12_trajectory.xyz b/regtest/basic/rt32/ala12_trajectory.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..ddf508adda823167b0ab6b2a0e0bdd87cdbf3fa4
--- /dev/null
+++ b/regtest/basic/rt32/ala12_trajectory.xyz
@@ -0,0 +1,1608 @@
+132
+ 100. 100. 100.
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+132
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+O -1.0599 -1.4173 1.5026
+N -1.1411 -1.216 1.543
+H -1.1328 -1.1277 1.5914
+CA -1.2738 -1.2403 1.4902
+HA -1.3137 -1.3313 1.535
+CB -1.3597 -1.1237 1.5385
+HB1 -1.3433 -1.1114 1.6455
+HB2 -1.4618 -1.1565 1.5189
+HB3 -1.348 -1.0373 1.4731
+C -1.2747 -1.2495 1.3383
+O -1.3512 -1.3262 1.2802
+N -1.1922 -1.1707 1.269
+H -1.1237 -1.1077 1.3083
+CA -1.1513 -1.1982 1.1327
+HA -1.2372 -1.176 1.0693
+CB -1.0416 -1.1019 1.0881
+HB1 -1.034 -1.1113 0.9798
+HB2 -0.9443 -1.1358 1.1235
+HB3 -1.0724 -1.0009 1.1152
+C -1.0894 -1.3328 1.098
+O -1.1352 -1.3977 1.0042
+N -0.9896 -1.387 1.1682
+H -0.9408 -1.3202 1.226
+CA -0.9417 -1.5219 1.1456
+HA -0.9183 -1.533 1.0397
+CB -0.8119 -1.5322 1.2252
+HB1 -0.7397 -1.4552 1.1982
+HB2 -0.7645 -1.6289 1.2085
+HB3 -0.8257 -1.5162 1.3322
+C -1.0474 -1.6237 1.1859
+O -1.0773 -1.7205 1.1162
+N -1.0886 -1.6161 1.3126
+H -1.0569 -1.5344 1.3629
+CH3 -1.1572 -1.7212 1.385
+HH31 -1.195 -1.794 1.3133
+HH32 -1.2449 -1.6718 1.4269
+HH33 -1.087 -1.7662 1.4552
+132
+ 100. 100. 100.
+HH31 -0.2903 -0.4936 2.2511
+CH3 -0.3554 -0.4221 2.3013
+HH32 -0.3134 -0.3702 2.3875
+HH33 -0.3845 -0.3471 2.2278
+C -0.4693 -0.5062 2.3572
+O -0.4404 -0.6134 2.4099
+N -0.5902 -0.4497 2.3617
+H -0.606 -0.3656 2.3079
+CA -0.7023 -0.4967 2.4405
+HA -0.6978 -0.6055 2.4363
+CB -0.6758 -0.4641 2.5872
+HB1 -0.5739 -0.4911 2.6149
+HB2 -0.7353 -0.5343 2.6456
+HB3 -0.6909 -0.3588 2.611
+C -0.8361 -0.4435 2.3912
+O -0.8479 -0.4099 2.2736
+N -0.9318 -0.4365 2.484
+H -0.9173 -0.4698 2.5783
+CA -1.0652 -0.3821 2.4689
+HA -1.1217 -0.4317 2.5479
+CB -1.0601 -0.2317 2.494
+HB1 -1.1624 -0.1962 2.4817
+HB2 -0.9933 -0.1823 2.4235
+HB3 -1.0219 -0.2109 2.594
+C -1.1273 -0.4334 2.3397
+O -1.146 -0.5518 2.3125
+N -1.1584 -0.338 2.2517
+H -1.1465 -0.2436 2.2858
+CA -1.2114 -0.361 2.1188
+HA -1.2996 -0.4233 2.1335
+CB -1.2354 -0.2218 2.0611
+HB1 -1.2804 -0.2439 1.9642
+HB2 -1.1446 -0.1632 2.0471
+HB3 -1.2965 -0.1578 2.1247
+C -1.1097 -0.4227 2.0238
+O -1.145 -0.4982 1.9335
+N -0.983 -0.3817 2.0324
+H -0.9502 -0.3307 2.1133
+CA -0.8819 -0.4197 1.9358
+HA -0.9196 -0.3863 1.8391
+CB -0.7542 -0.337 1.9474
+HB1 -0.6826 -0.3634 1.8695
+HB2 -0.7092 -0.3472 2.0461
+HB3 -0.7687 -0.2325 1.92
+C -0.8642 -0.5708 1.9317
+O -0.8759 -0.627 1.8231
+N -0.8504 -0.6334 2.0489
+H -0.8457 -0.5752 2.1313
+CA -0.8501 -0.7758 2.0754
+HA -0.7596 -0.8264 2.0419
+CB -0.8502 -0.8017 2.2258
+HB1 -0.8422 -0.9104 2.2284
+HB2 -0.9411 -0.7669 2.2749
+HB3 -0.7644 -0.7542 2.2734
+C -0.9644 -0.8426 2.0003
+O -0.9443 -0.9298 1.9161
+N -1.088 -0.8017 2.0301
+H -1.0928 -0.7245 2.0951
+CA -1.2132 -0.8486 1.9741
+HA -1.2101 -0.9541 2.0013
+CB -1.3285 -0.7762 2.043
+HB1 -1.3551 -0.817 2.1405
+HB2 -1.4177 -0.7965 1.9837
+HB3 -1.3135 -0.6683 2.0477
+C -1.2179 -0.8401 1.8222
+O -1.2545 -0.938 1.7575
+N -1.1825 -0.7259 1.7628
+H -1.1632 -0.6471 1.823
+CA -1.1576 -0.7141 1.6206
+HA -1.252 -0.7467 1.5768
+CB -1.1186 -0.5684 1.5976
+HB1 -1.1223 -0.5491 1.4903
+HB2 -1.0201 -0.5462 1.6385
+HB3 -1.1878 -0.5004 1.6472
+C -1.0519 -0.8129 1.5735
+O -1.0699 -0.8821 1.4735
+N -0.9422 -0.8269 1.6483
+H -0.9334 -0.7637 1.7266
+CA -0.8342 -0.9176 1.615
+HA -0.797 -0.897 1.5146
+CB -0.7092 -0.9012 1.701
+HB1 -0.6274 -0.946 1.6446
+HB2 -0.7271 -0.9402 1.8012
+HB3 -0.688 -0.7949 1.7123
+C -0.8863 -1.0605 1.6093
+O -0.8634 -1.1312 1.5114
+N -0.9608 -1.1038 1.7113
+H -0.9734 -1.0496 1.7956
+CA -1.0241 -1.2339 1.7036
+HA -0.9468 -1.3089 1.6868
+CB -1.0865 -1.2775 1.8358
+HB1 -1.0134 -1.289 1.9159
+HB2 -1.1333 -1.3758 1.83
+HB3 -1.168 -1.2074 1.8536
+C -1.1252 -1.242 1.5902
+O -1.1313 -1.3381 1.5137
+N -1.2077 -1.1404 1.5641
+H -1.2028 -1.058 1.6224
+CA -1.324 -1.1571 1.4793
+HA -1.3825 -1.244 1.5092
+CB -1.4149 -1.0357 1.4962
+HB1 -1.4666 -1.0421 1.592
+HB2 -1.4958 -1.0505 1.4246
+HB3 -1.3665 -0.9383 1.4903
+C -1.2856 -1.171 1.3327
+O -1.3258 -1.2594 1.2572
+N -1.1988 -1.0808 1.2863
+H -1.1486 -1.0217 1.3509
+CA -1.1525 -1.0652 1.1498
+HA -1.2326 -1.086 1.079
+CB -1.1041 -0.9227 1.1245
+HB1 -1.0469 -0.9211 1.0317
+HB2 -1.0376 -0.8769 1.1977
+HB3 -1.1868 -0.8534 1.1089
+C -1.0402 -1.1612 1.1131
+O -1.0289 -1.1958 0.9957
+N -0.9564 -1.1942 1.2117
+H -0.98 -1.1503 1.2995
+CA -0.8413 -1.2797 1.191
+HA -0.8427 -1.3236 1.0913
+CB -0.7175 -1.1916 1.206
+HB1 -0.6353 -1.2626 1.2153
+HB2 -0.7221 -1.1471 1.3054
+HB3 -0.6859 -1.1207 1.1295
+C -0.8443 -1.4065 1.2751
+O -0.8599 -1.5134 1.2166
+N -0.8294 -1.4 1.4076
+H -0.8321 -1.3054 1.4429
+CH3 -0.8343 -1.5143 1.4966
+HH31 -0.9377 -1.534 1.5249
+HH32 -0.772 -1.496 1.5842
+HH33 -0.8059 -1.6078 1.4483
+132
+ 100. 100. 100.
+HH31 0.0719 -1.0155 1.8871
+CH3 0.0342 -0.9163 1.912
+HH32 0.0467 -0.8869 2.0162
+HH33 0.0759 -0.8309 1.8585
+C -0.1141 -0.9265 1.8792
+O -0.1527 -0.9711 1.7715
+N -0.207 -0.8868 1.9664
+H -0.1739 -0.8481 2.0537
+CA -0.3513 -0.8991 1.9619
+HA -0.3857 -0.9265 1.8622
+CB -0.4042 -0.9983 2.0651
+HB1 -0.5131 -0.9971 2.0713
+HB2 -0.3692 -0.9631 2.1621
+HB3 -0.3827 -1.1024 2.0408
+C -0.4146 -0.7633 1.989
+O -0.426 -0.7207 2.1038
+N -0.4567 -0.6923 1.8841
+H -0.4405 -0.7288 1.7914
+CA -0.5332 -0.5706 1.9021
+HA -0.4997 -0.5101 1.9864
+CB -0.5235 -0.4721 1.7859
+HB1 -0.4193 -0.4505 1.7626
+HB2 -0.5784 -0.3814 1.8111
+HB3 -0.5619 -0.5266 1.6997
+C -0.6786 -0.6104 1.9234
+O -0.7378 -0.6818 1.8428
+N -0.7386 -0.5626 2.0326
+H -0.6891 -0.5213 2.1103
+CA -0.8758 -0.5935 2.0677
+HA -0.869 -0.702 2.0753
+CB -0.9043 -0.5339 2.2052
+HB1 -0.8937 -0.4255 2.2001
+HB2 -0.8464 -0.5754 2.2878
+HB3 -1.0109 -0.5454 2.2246
+C -0.9806 -0.5565 1.9637
+O -0.9717 -0.4487 1.9055
+N -1.0786 -0.6443 1.9409
+H -1.0788 -0.7246 2.0021
+CA -1.1862 -0.6098 1.8502
+HA -1.1906 -0.5019 1.8354
+CB -1.1562 -0.6663 1.7116
+HB1 -1.1367 -0.7735 1.7121
+HB2 -1.0762 -0.6041 1.6713
+HB3 -1.2422 -0.65 1.6465
+C -1.3204 -0.6552 1.9057
+O -1.4251 -0.6002 1.8723
+N -1.3269 -0.7618 1.9858
+H -1.2354 -0.8025 1.9987
+CA -1.4369 -0.8189 2.0609
+HA -1.3936 -0.9179 2.075
+CB -1.4608 -0.7508 2.1953
+HB1 -1.5586 -0.7846 2.2295
+HB2 -1.4787 -0.6446 2.1785
+HB3 -1.38 -0.7852 2.26
+C -1.5681 -0.8331 1.985
+O -1.6073 -0.9436 1.9481
+N -1.6389 -0.722 1.9636
+H -1.5783 -0.6474 1.9949
+CA -1.7493 -0.7011 1.8721
+HA -1.8316 -0.7528 1.9214
+CB -1.7833 -0.5525 1.8657
+HB1 -1.6943 -0.4895 1.8649
+HB2 -1.8483 -0.5227 1.948
+HB3 -1.839 -0.5205 1.7776
+C -1.7285 -0.7617 1.734
+O -1.8055 -0.8434 1.684
+N -1.6168 -0.729 1.6686
+H -1.546 -0.681 1.7222
+CA -1.5961 -0.7596 1.5284
+HA -1.6882 -0.7901 1.4788
+CB -1.5475 -0.6349 1.455
+HB1 -1.6191 -0.5541 1.4704
+HB2 -1.5413 -0.6569 1.3485
+HB3 -1.4476 -0.6202 1.496
+C -1.5095 -0.8841 1.5152
+O -1.4058 -0.8883 1.4494
+N -1.5555 -0.9846 1.5901
+H -1.6492 -0.9732 1.6261
+CA -1.4801 -1.0903 1.6544
+HA -1.5514 -1.1318 1.7257
+CB -1.4528 -1.209 1.5625
+HB1 -1.418 -1.1685 1.4675
+HB2 -1.5439 -1.2671 1.5482
+HB3 -1.3694 -1.2653 1.6043
+C -1.362 -1.0423 1.7375
+O -1.3312 -0.9239 1.7488
+N -1.2996 -1.1343 1.8115
+H -1.3208 -1.2325 1.8012
+CA -1.2245 -1.1122 1.9334
+HA -1.2939 -1.0799 2.011
+CB -1.1615 -1.2439 1.978
+HB1 -1.0949 -1.282 1.9006
+HB2 -1.2379 -1.317 2.0044
+HB3 -1.1021 -1.2275 2.0679
+C -1.1102 -1.0129 1.9183
+O -1.1062 -0.9147 1.9921
+N -1.0125 -1.0363 1.8304
+H -1.0203 -1.1264 1.7855
+CA -0.8932 -0.9547 1.8205
+HA -0.9243 -0.8505 1.8286
+CB -0.7957 -0.9883 1.933
+HB1 -0.8397 -0.9534 2.0264
+HB2 -0.6989 -0.9381 1.9309
+HB3 -0.7885 -1.097 1.9337
+C -0.8255 -0.9767 1.6859
+O -0.8572 -1.0749 1.6193
+N -0.737 -0.8822 1.6536
+H -0.7309 -0.797 1.7076
+CA -0.6678 -0.8823 1.5262
+HA -0.6881 -0.9746 1.4719
+CB -0.7144 -0.77 1.434
+HB1 -0.8199 -0.7781 1.4078
+HB2 -0.6608 -0.7749 1.3392
+HB3 -0.7044 -0.6799 1.4945
+C -0.5176 -0.8814 1.5504
+O -0.467 -0.8196 1.6438
+N -0.4376 -0.9463 1.4654
+H -0.4807 -0.9842 1.3822
+CA -0.2927 -0.945 1.4648
+HA -0.2656 -0.9836 1.5631
+CB -0.2435 -1.0469 1.3624
+HB1 -0.2937 -1.0187 1.2698
+HB2 -0.2697 -1.1494 1.3885
+HB3 -0.135 -1.0426 1.3535
+C -0.2347 -0.8086 1.4304
+O -0.2774 -0.7438 1.3351
+N -0.1407 -0.7645 1.5143
+H -0.1028 -0.8276 1.5834
+CH3 -0.0782 -0.6355 1.4931
+HH31 0.0191 -0.6293 1.5417
+HH32 -0.1488 -0.5672 1.5404
+HH33 -0.0738 -0.6169 1.3857
diff --git a/regtest/basic/rt32/colvar.reference b/regtest/basic/rt32/colvar.reference
new file mode 100644
index 0000000000000000000000000000000000000000..d0a5388f0f275594869eb88a2fefe3890478c70c
--- /dev/null
+++ b/regtest/basic/rt32/colvar.reference
@@ -0,0 +1,17 @@
+#! FIELDS time t1 t2
+#! SET min_t1 -pi
+#! SET max_t1 pi
+#! SET min_t2 -pi
+#! SET max_t2 pi
+ 0.000000 -1.8728 2.3957
+ 0.050000 -2.5165 -1.9143
+ 0.100000 -2.3534 0.0136
+ 0.150000 -0.7575 -0.5192
+ 0.200000 -1.3854 -0.8962
+ 0.250000 -2.7667 2.6100
+ 0.300000 -2.1098 -0.6434
+ 0.350000 0.8568 -0.7541
+ 0.400000 -1.0107 -1.1730
+ 0.450000 -2.9961 2.8152
+ 0.500000 -1.2175 -1.0536
+ 0.550000 -1.0110 -1.3091
diff --git a/regtest/basic/rt32/config b/regtest/basic/rt32/config
new file mode 100644
index 0000000000000000000000000000000000000000..ee7a7413c8137fa91c186a2e3aa5dc8157a1d81b
--- /dev/null
+++ b/regtest/basic/rt32/config
@@ -0,0 +1,2 @@
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
diff --git a/regtest/basic/rt32/helix.pdb b/regtest/basic/rt32/helix.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..179f70a008a07477ef32f240be113712e470e668
--- /dev/null
+++ b/regtest/basic/rt32/helix.pdb
@@ -0,0 +1,133 @@
+ATOM 1 HH31 ACE 1 -9.105 -2.402 21.804 0.00 0.00
+ATOM 2 CH3 ACE 1 -8.930 -3.352 22.308 0.00 0.00
+ATOM 3 HH32 ACE 1 -9.504 -3.501 23.223 0.00 0.00
+ATOM 4 HH33 ACE 1 -9.067 -4.173 21.604 0.00 0.00
+ATOM 5 C ACE 1 -7.450 -3.303 22.659 0.00 0.00
+ATOM 6 O ACE 1 -6.909 -2.213 22.834 0.00 0.00
+ATOM 7 N ALA 2 -6.812 -4.475 22.683 0.00 0.00
+ATOM 8 H ALA 2 -7.324 -5.304 22.418 0.00 0.00
+ATOM 9 CA ALA 2 -5.397 -4.597 22.969 1.00 1.00
+ATOM 10 HA ALA 2 -4.882 -3.860 22.353 0.00 0.00
+ATOM 11 CB ALA 2 -5.075 -4.366 24.443 0.00 0.00
+ATOM 12 HB1 ALA 2 -4.010 -4.351 24.674 0.00 0.00
+ATOM 13 HB2 ALA 2 -5.438 -5.144 25.114 0.00 0.00
+ATOM 14 HB3 ALA 2 -5.561 -3.425 24.701 0.00 0.00
+ATOM 15 C ALA 2 -4.909 -5.948 22.466 0.00 0.00
+ATOM 16 O ALA 2 -4.728 -6.129 21.264 0.00 0.00
+ATOM 17 N ALA 3 -4.848 -6.965 23.328 0.00 0.00
+ATOM 18 H ALA 3 -5.121 -6.790 24.285 0.00 0.00
+ATOM 19 CA ALA 3 -4.722 -8.399 23.159 1.00 1.00
+ATOM 20 HA ALA 3 -3.768 -8.522 22.645 0.00 0.00
+ATOM 21 CB ALA 3 -4.609 -9.090 24.515 0.00 0.00
+ATOM 22 HB1 ALA 3 -3.760 -8.709 25.082 0.00 0.00
+ATOM 23 HB2 ALA 3 -4.510 -10.142 24.246 0.00 0.00
+ATOM 24 HB3 ALA 3 -5.489 -9.125 25.158 0.00 0.00
+ATOM 25 C ALA 3 -5.753 -9.060 22.256 0.00 0.00
+ATOM 26 O ALA 3 -5.359 -9.754 21.321 0.00 0.00
+ATOM 27 N ALA 4 -7.036 -8.865 22.568 0.00 0.00
+ATOM 28 H ALA 4 -7.040 -8.063 23.182 0.00 0.00
+ATOM 29 CA ALA 4 -8.201 -9.234 21.789 1.00 1.00
+ATOM 30 HA ALA 4 -7.869 -9.845 20.949 0.00 0.00
+ATOM 31 CB ALA 4 -9.165 -9.957 22.726 0.00 0.00
+ATOM 32 HB1 ALA 4 -8.633 -10.787 23.190 0.00 0.00
+ATOM 33 HB2 ALA 4 -10.099 -10.329 22.305 0.00 0.00
+ATOM 34 HB3 ALA 4 -9.400 -9.257 23.527 0.00 0.00
+ATOM 35 C ALA 4 -8.724 -7.907 21.258 0.00 0.00
+ATOM 36 O ALA 4 -8.269 -6.846 21.676 0.00 0.00
+ATOM 37 N ALA 5 -9.566 -7.899 20.221 0.00 0.00
+ATOM 38 H ALA 5 -9.630 -8.819 19.810 0.00 0.00
+ATOM 39 CA ALA 5 -9.923 -6.793 19.356 1.00 1.00
+ATOM 40 HA ALA 5 -10.138 -5.948 20.009 0.00 0.00
+ATOM 41 CB ALA 5 -8.791 -6.404 18.409 0.00 0.00
+ATOM 42 HB1 ALA 5 -8.531 -7.143 17.651 0.00 0.00
+ATOM 43 HB2 ALA 5 -7.859 -6.290 18.963 0.00 0.00
+ATOM 44 HB3 ALA 5 -8.983 -5.483 17.859 0.00 0.00
+ATOM 45 C ALA 5 -11.178 -7.047 18.532 0.00 0.00
+ATOM 46 O ALA 5 -11.516 -8.217 18.366 0.00 0.00
+ATOM 47 N ALA 6 -11.927 -6.054 18.049 0.00 0.00
+ATOM 48 H ALA 6 -11.603 -5.097 18.052 0.00 0.00
+ATOM 49 CA ALA 6 -13.240 -6.259 17.469 1.00 1.00
+ATOM 50 HA ALA 6 -13.121 -7.160 16.866 0.00 0.00
+ATOM 51 CB ALA 6 -14.367 -6.396 18.489 0.00 0.00
+ATOM 52 HB1 ALA 6 -15.329 -6.504 17.990 0.00 0.00
+ATOM 53 HB2 ALA 6 -14.356 -5.552 19.178 0.00 0.00
+ATOM 54 HB3 ALA 6 -14.135 -7.227 19.155 0.00 0.00
+ATOM 55 C ALA 6 -13.632 -5.087 16.582 0.00 0.00
+ATOM 56 O ALA 6 -13.364 -3.936 16.918 0.00 0.00
+ATOM 57 N ALA 7 -14.207 -5.433 15.428 0.00 0.00
+ATOM 58 H ALA 7 -14.289 -6.440 15.399 0.00 0.00
+ATOM 59 CA ALA 7 -14.898 -4.580 14.482 1.00 1.00
+ATOM 60 HA ALA 7 -15.364 -3.792 15.074 0.00 0.00
+ATOM 61 CB ALA 7 -13.891 -3.800 13.642 0.00 0.00
+ATOM 62 HB1 ALA 7 -14.478 -3.098 13.049 0.00 0.00
+ATOM 63 HB2 ALA 7 -13.232 -4.434 13.048 0.00 0.00
+ATOM 64 HB3 ALA 7 -13.289 -3.155 14.282 0.00 0.00
+ATOM 65 C ALA 7 -15.946 -5.170 13.549 0.00 0.00
+ATOM 66 O ALA 7 -17.154 -5.054 13.744 0.00 0.00
+ATOM 67 N ALA 8 -15.477 -6.023 12.635 0.00 0.00
+ATOM 68 H ALA 8 -14.472 -6.108 12.571 0.00 0.00
+ATOM 69 CA ALA 8 -16.137 -7.083 11.902 1.00 1.00
+ATOM 70 HA ALA 8 -17.209 -7.030 12.095 0.00 0.00
+ATOM 71 CB ALA 8 -15.913 -6.901 10.403 0.00 0.00
+ATOM 72 HB1 ALA 8 -16.476 -6.072 9.975 0.00 0.00
+ATOM 73 HB2 ALA 8 -16.105 -7.811 9.835 0.00 0.00
+ATOM 74 HB3 ALA 8 -14.837 -6.728 10.420 0.00 0.00
+ATOM 75 C ALA 8 -15.549 -8.405 12.374 0.00 0.00
+ATOM 76 O ALA 8 -14.368 -8.711 12.226 0.00 0.00
+ATOM 77 N ALA 9 -16.457 -9.114 13.049 0.00 0.00
+ATOM 78 H ALA 9 -17.362 -8.674 13.143 0.00 0.00
+ATOM 79 CA ALA 9 -16.134 -10.157 14.001 1.00 1.00
+ATOM 80 HA ALA 9 -17.002 -10.541 14.537 0.00 0.00
+ATOM 81 CB ALA 9 -15.583 -11.305 13.160 0.00 0.00
+ATOM 82 HB1 ALA 9 -14.572 -10.975 12.918 0.00 0.00
+ATOM 83 HB2 ALA 9 -16.217 -11.496 12.294 0.00 0.00
+ATOM 84 HB3 ALA 9 -15.599 -12.271 13.664 0.00 0.00
+ATOM 85 C ALA 9 -15.269 -9.591 15.119 0.00 0.00
+ATOM 86 O ALA 9 -15.214 -8.375 15.293 0.00 0.00
+ATOM 87 N ALA 10 -14.681 -10.478 15.924 0.00 0.00
+ATOM 88 H ALA 10 -14.907 -11.462 15.897 0.00 0.00
+ATOM 89 CA ALA 10 -13.672 -10.148 16.910 1.00 1.00
+ATOM 90 HA ALA 10 -13.288 -9.136 16.780 0.00 0.00
+ATOM 91 CB ALA 10 -14.348 -10.169 18.278 0.00 0.00
+ATOM 92 HB1 ALA 10 -14.897 -9.229 18.335 0.00 0.00
+ATOM 93 HB2 ALA 10 -13.581 -10.251 19.048 0.00 0.00
+ATOM 94 HB3 ALA 10 -14.889 -11.094 18.478 0.00 0.00
+ATOM 95 C ALA 10 -12.514 -11.131 16.810 0.00 0.00
+ATOM 96 O ALA 10 -12.670 -12.212 16.247 0.00 0.00
+ATOM 97 N ALA 11 -11.304 -10.734 17.209 0.00 0.00
+ATOM 98 H ALA 11 -11.300 -9.774 17.523 0.00 0.00
+ATOM 99 CA ALA 11 -10.028 -11.384 16.987 1.00 1.00
+ATOM 100 HA ALA 11 -10.121 -12.468 16.930 0.00 0.00
+ATOM 101 CB ALA 11 -9.496 -11.025 15.603 0.00 0.00
+ATOM 102 HB1 ALA 11 -8.583 -11.593 15.421 0.00 0.00
+ATOM 103 HB2 ALA 11 -9.380 -9.942 15.574 0.00 0.00
+ATOM 104 HB3 ALA 11 -10.131 -11.309 14.763 0.00 0.00
+ATOM 105 C ALA 11 -9.012 -11.121 18.089 0.00 0.00
+ATOM 106 O ALA 11 -9.298 -10.314 18.971 0.00 0.00
+ATOM 107 N ALA 12 -7.836 -11.750 18.022 0.00 0.00
+ATOM 108 H ALA 12 -7.676 -12.430 17.292 0.00 0.00
+ATOM 109 CA ALA 12 -6.626 -11.294 18.676 1.00 1.00
+ATOM 110 HA ALA 12 -6.953 -10.965 19.663 0.00 0.00
+ATOM 111 CB ALA 12 -5.678 -12.473 18.875 0.00 0.00
+ATOM 112 HB1 ALA 12 -5.215 -12.710 17.917 0.00 0.00
+ATOM 113 HB2 ALA 12 -6.285 -13.303 19.237 0.00 0.00
+ATOM 114 HB3 ALA 12 -4.881 -12.167 19.553 0.00 0.00
+ATOM 115 C ALA 12 -6.012 -10.138 17.899 0.00 0.00
+ATOM 116 O ALA 12 -6.378 -9.893 16.752 0.00 0.00
+ATOM 117 N ALA 13 -5.091 -9.417 18.543 0.00 0.00
+ATOM 118 H ALA 13 -5.077 -9.637 19.529 0.00 0.00
+ATOM 119 CA ALA 13 -4.233 -8.407 17.956 1.00 1.00
+ATOM 120 HA ALA 13 -3.980 -8.732 16.947 0.00 0.00
+ATOM 121 CB ALA 13 -4.967 -7.073 17.857 0.00 0.00
+ATOM 122 HB1 ALA 13 -4.295 -6.295 17.497 0.00 0.00
+ATOM 123 HB2 ALA 13 -5.447 -6.756 18.783 0.00 0.00
+ATOM 124 HB3 ALA 13 -5.784 -7.235 17.154 0.00 0.00
+ATOM 125 C ALA 13 -2.955 -8.248 18.767 0.00 0.00
+ATOM 126 O ALA 13 -1.984 -8.964 18.535 0.00 0.00
+ATOM 127 N NME 14 -2.923 -7.389 19.788 0.00 0.00
+ATOM 128 H NME 14 -3.729 -6.821 20.007 0.00 0.00
+ATOM 129 CH3 NME 14 -1.690 -7.089 20.487 0.00 0.00
+ATOM 130 HH31 NME 14 -1.873 -6.629 21.459 0.00 0.00
+ATOM 131 HH32 NME 14 -1.152 -6.284 19.986 0.00 0.00
+ATOM 132 HH33 NME 14 -1.135 -8.020 20.602 0.00 0.00
+END
diff --git a/regtest/basic/rt32/plumed.dat b/regtest/basic/rt32/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..46d2e0a8abad59ba0f0c9b3865949db64bcd6cc9
--- /dev/null
+++ b/regtest/basic/rt32/plumed.dat
@@ -0,0 +1,4 @@
+MOLINFO STRUCTURE=helix.pdb
+TORSION ATOMS=@phi-4 LABEL=t1
+TORSION ATOMS=@psi-6 LABEL=t2
+PRINT ARG=t1,t2 FILE=colvar FMT=%8.4f
diff --git a/regtest/basic/rt47/COLVAR.reference b/regtest/basic/rt47/COLVAR.reference
index f801c819d14a9c75d13b129651f4e0d04da61d6c..1f2b96667ed1b98773314fc04b94c2482c1f5024 100644
--- a/regtest/basic/rt47/COLVAR.reference
+++ b/regtest/basic/rt47/COLVAR.reference
@@ -1,3 +1,3 @@
-#! FIELDS time r1 r1x
- 0.000000 7.58483137 7.58483137
- 0.050000 7.04954250 7.04954250
+#! FIELDS time r1 r1x r2
+ 0.000000 7.58483137 7.58483137 7.42427685
+ 0.050000 7.04954250 7.04954250 6.90115669
diff --git a/regtest/basic/rt47/plumed.dat b/regtest/basic/rt47/plumed.dat
index 5f60001b7c311dcf719a1b95b0d84c0144298bc4..3518775266e23253340ea2473746be8b3b3811e7 100644
--- a/regtest/basic/rt47/plumed.dat
+++ b/regtest/basic/rt47/plumed.dat
@@ -1,7 +1,10 @@
r1: RMSD REFERENCE=ref.pdb TYPE=OPTIMAL-FAST
r1x: RMSD REFERENCE=refx.pdb TYPE=OPTIMAL-FAST
+r2: RMSD REFERENCE=ref2.pdb TYPE=OPTIMAL-FAST
+#num-r2: RMSD REFERENCE=ref2.pdb TYPE=OPTIMAL-FAST NUMERICAL_DERIVATIVES
DUMPDERIVATIVES FILE=deriv ARG=r1,r1x FMT=%12.8f
+#DUMPDERIVATIVES FILE=check ARG=r2,num-r2 FMT=%12.8f
PRINT ...
STRIDE=1
diff --git a/regtest/basic/rt47/ref2.pdb b/regtest/basic/rt47/ref2.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..c47ea1f3e5a79543d0f6f6f07228fe1339777258
--- /dev/null
+++ b/regtest/basic/rt47/ref2.pdb
@@ -0,0 +1,8 @@
+ATOM 1 A XXX 2 0.000 1.000 0.000 1.00 2.00 DIA O
+ATOM 2 A XXX 2 0.000 1.000 0.000 2.00 1.00 DIA O
+ATOM 3 A XXX 2 0.000 1.000 0.000 3.00 2.00 DIA O
+ATOM 4 A XXX 2 0.000 0.000 0.000 1.00 1.00 DIA O
+ATOM 5 A XXX 2 0.000 1.000 0.000 2.00 2.00 DIA O
+ATOM 6 A XXX 2 0.000 2.000 0.000 3.00 1.00 DIA O
+ATOM 7 A XXX 2 0.000 0.000 0.000 1.00 2.00 DIA O
+ATOM 8 A XXX 2 1.000 0.000 0.000 2.00 1.00 DIA O
diff --git a/regtest/basic/rt54/helix-nm.gro.reference b/regtest/basic/rt54/helix-nm.gro.reference
index b08cf48e72c5773f8431b24dbcd3b8983e124263..6143d662aed3720d20513b4e60c45428d7ec0690 100644
--- a/regtest/basic/rt54/helix-nm.gro.reference
+++ b/regtest/basic/rt54/helix-nm.gro.reference
@@ -1,1620 +1,1620 @@
Made with PLUMED t=0.000000
132
- 1ACE HH31 1 -0.911 -0.240 2.180 0.0000 0.0000 0.0000
- 1ACE CH3 2 -0.893 -0.335 2.231 0.0000 0.0000 0.0000
- 1ACE HH32 3 -0.950 -0.350 2.322 0.0000 0.0000 0.0000
- 1ACE HH33 4 -0.907 -0.417 2.160 0.0000 0.0000 0.0000
- 1ACE C 5 -0.745 -0.330 2.266 0.0000 0.0000 0.0000
- 1ACE O 6 -0.691 -0.221 2.283 0.0000 0.0000 0.0000
- 2ALA N 7 -0.681 -0.448 2.268 0.0000 0.0000 0.0000
- 2ALA H 8 -0.732 -0.530 2.242 0.0000 0.0000 0.0000
- 2ALA CA 9 -0.540 -0.460 2.297 0.0000 0.0000 0.0000
- 2ALA HA 10 -0.488 -0.386 2.235 0.0000 0.0000 0.0000
- 2ALA CB 11 -0.507 -0.437 2.444 0.0000 0.0000 0.0000
- 2ALA HB1 12 -0.401 -0.435 2.467 0.0000 0.0000 0.0000
- 2ALA HB2 13 -0.544 -0.514 2.511 0.0000 0.0000 0.0000
- 2ALA HB3 14 -0.556 -0.343 2.470 0.0000 0.0000 0.0000
- 2ALA C 15 -0.491 -0.595 2.247 0.0000 0.0000 0.0000
- 2ALA O 16 -0.473 -0.613 2.126 0.0000 0.0000 0.0000
- 3ALA N 17 -0.485 -0.697 2.333 0.0000 0.0000 0.0000
- 3ALA H 18 -0.512 -0.679 2.429 0.0000 0.0000 0.0000
- 3ALA CA 19 -0.472 -0.840 2.316 0.0000 0.0000 0.0000
- 3ALA HA 20 -0.377 -0.852 2.264 0.0000 0.0000 0.0000
- 3ALA CB 21 -0.461 -0.909 2.451 0.0000 0.0000 0.0000
- 3ALA HB1 22 -0.376 -0.871 2.508 0.0000 0.0000 0.0000
- 3ALA HB2 23 -0.451 -1.014 2.425 0.0000 0.0000 0.0000
- 3ALA HB3 24 -0.549 -0.913 2.516 0.0000 0.0000 0.0000
- 3ALA C 25 -0.575 -0.906 2.226 0.0000 0.0000 0.0000
- 3ALA O 26 -0.536 -0.975 2.132 0.0000 0.0000 0.0000
- 4ALA N 27 -0.704 -0.887 2.257 0.0000 0.0000 0.0000
- 4ALA H 28 -0.704 -0.806 2.318 0.0000 0.0000 0.0000
- 4ALA CA 29 -0.820 -0.923 2.179 0.0000 0.0000 0.0000
- 4ALA HA 30 -0.787 -0.985 2.095 0.0000 0.0000 0.0000
- 4ALA CB 31 -0.916 -0.996 2.273 0.0000 0.0000 0.0000
- 4ALA HB1 32 -0.863 -1.079 2.319 0.0000 0.0000 0.0000
- 4ALA HB2 33 -1.010 -1.033 2.231 0.0000 0.0000 0.0000
- 4ALA HB3 34 -0.940 -0.926 2.353 0.0000 0.0000 0.0000
- 4ALA C 35 -0.872 -0.791 2.126 0.0000 0.0000 0.0000
- 4ALA O 36 -0.827 -0.685 2.168 0.0000 0.0000 0.0000
- 5ALA N 37 -0.957 -0.790 2.022 0.0000 0.0000 0.0000
- 5ALA H 38 -0.963 -0.882 1.981 0.0000 0.0000 0.0000
- 5ALA CA 39 -0.992 -0.679 1.936 0.0000 0.0000 0.0000
- 5ALA HA 40 -1.014 -0.595 2.001 0.0000 0.0000 0.0000
- 5ALA CB 41 -0.879 -0.640 1.841 0.0000 0.0000 0.0000
- 5ALA HB1 42 -0.853 -0.714 1.765 0.0000 0.0000 0.0000
- 5ALA HB2 43 -0.786 -0.629 1.896 0.0000 0.0000 0.0000
- 5ALA HB3 44 -0.898 -0.548 1.786 0.0000 0.0000 0.0000
- 5ALA C 45 -1.118 -0.705 1.853 0.0000 0.0000 0.0000
- 5ALA O 46 -1.152 -0.822 1.837 0.0000 0.0000 0.0000
- 6ALA N 47 -1.193 -0.605 1.805 0.0000 0.0000 0.0000
- 6ALA H 48 -1.160 -0.510 1.805 0.0000 0.0000 0.0000
- 6ALA CA 49 -1.324 -0.626 1.747 0.0000 0.0000 0.0000
- 6ALA HA 50 -1.312 -0.716 1.687 0.0000 0.0000 0.0000
- 6ALA CB 51 -1.437 -0.640 1.849 0.0000 0.0000 0.0000
- 6ALA HB1 52 -1.533 -0.650 1.799 0.0000 0.0000 0.0000
- 6ALA HB2 53 -1.436 -0.555 1.918 0.0000 0.0000 0.0000
- 6ALA HB3 54 -1.413 -0.723 1.916 0.0000 0.0000 0.0000
- 6ALA C 55 -1.363 -0.509 1.658 0.0000 0.0000 0.0000
- 6ALA O 56 -1.336 -0.394 1.692 0.0000 0.0000 0.0000
- 7ALA N 57 -1.421 -0.543 1.543 0.0000 0.0000 0.0000
- 7ALA H 58 -1.429 -0.644 1.540 0.0000 0.0000 0.0000
- 7ALA CA 59 -1.490 -0.458 1.448 0.0000 0.0000 0.0000
- 7ALA HA 60 -1.536 -0.379 1.507 0.0000 0.0000 0.0000
- 7ALA CB 61 -1.389 -0.380 1.364 0.0000 0.0000 0.0000
- 7ALA HB1 62 -1.448 -0.310 1.305 0.0000 0.0000 0.0000
- 7ALA HB2 63 -1.323 -0.443 1.305 0.0000 0.0000 0.0000
- 7ALA HB3 64 -1.329 -0.316 1.428 0.0000 0.0000 0.0000
- 7ALA C 65 -1.595 -0.517 1.355 0.0000 0.0000 0.0000
- 7ALA O 66 -1.715 -0.505 1.374 0.0000 0.0000 0.0000
- 8ALA N 67 -1.548 -0.602 1.264 0.0000 0.0000 0.0000
- 8ALA H 68 -1.447 -0.611 1.257 0.0000 0.0000 0.0000
- 8ALA CA 69 -1.614 -0.708 1.190 0.0000 0.0000 0.0000
- 8ALA HA 70 -1.721 -0.703 1.210 0.0000 0.0000 0.0000
- 8ALA CB 71 -1.591 -0.690 1.040 0.0000 0.0000 0.0000
- 8ALA HB1 72 -1.648 -0.607 0.998 0.0000 0.0000 0.0000
- 8ALA HB2 73 -1.611 -0.781 0.984 0.0000 0.0000 0.0000
- 8ALA HB3 74 -1.484 -0.673 1.042 0.0000 0.0000 0.0000
- 8ALA C 75 -1.555 -0.841 1.237 0.0000 0.0000 0.0000
- 8ALA O 76 -1.437 -0.871 1.223 0.0000 0.0000 0.0000
- 9ALA N 77 -1.646 -0.911 1.305 0.0000 0.0000 0.0000
- 9ALA H 78 -1.736 -0.867 1.314 0.0000 0.0000 0.0000
- 9ALA CA 79 -1.613 -1.016 1.400 0.0000 0.0000 0.0000
- 9ALA HA 80 -1.700 -1.054 1.454 0.0000 0.0000 0.0000
- 9ALA CB 81 -1.558 -1.131 1.316 0.0000 0.0000 0.0000
- 9ALA HB1 82 -1.457 -1.097 1.292 0.0000 0.0000 0.0000
- 9ALA HB2 83 -1.622 -1.150 1.229 0.0000 0.0000 0.0000
- 9ALA HB3 84 -1.560 -1.227 1.366 0.0000 0.0000 0.0000
- 9ALA C 85 -1.527 -0.959 1.512 0.0000 0.0000 0.0000
- 9ALA O 86 -1.521 -0.838 1.529 0.0000 0.0000 0.0000
- 10ALA N 87 -1.468 -1.048 1.592 0.0000 0.0000 0.0000
- 10ALA H 88 -1.491 -1.146 1.590 0.0000 0.0000 0.0000
- 10ALA CA 89 -1.367 -1.015 1.691 0.0000 0.0000 0.0000
- 10ALA HA 90 -1.329 -0.914 1.678 0.0000 0.0000 0.0000
- 10ALA CB 91 -1.435 -1.017 1.828 0.0000 0.0000 0.0000
- 10ALA HB1 92 -1.490 -0.923 1.834 0.0000 0.0000 0.0000
- 10ALA HB2 93 -1.358 -1.025 1.905 0.0000 0.0000 0.0000
- 10ALA HB3 94 -1.489 -1.109 1.848 0.0000 0.0000 0.0000
- 10ALA C 95 -1.251 -1.113 1.681 0.0000 0.0000 0.0000
- 10ALA O 96 -1.267 -1.221 1.625 0.0000 0.0000 0.0000
- 11ALA N 97 -1.130 -1.073 1.721 0.0000 0.0000 0.0000
- 11ALA H 98 -1.130 -0.977 1.752 0.0000 0.0000 0.0000
- 11ALA CA 99 -1.003 -1.138 1.699 0.0000 0.0000 0.0000
- 11ALA HA 100 -1.012 -1.247 1.693 0.0000 0.0000 0.0000
- 11ALA CB 101 -0.950 -1.103 1.560 0.0000 0.0000 0.0000
- 11ALA HB1 102 -0.858 -1.159 1.542 0.0000 0.0000 0.0000
- 11ALA HB2 103 -0.938 -0.994 1.557 0.0000 0.0000 0.0000
- 11ALA HB3 104 -1.013 -1.131 1.476 0.0000 0.0000 0.0000
- 11ALA C 105 -0.901 -1.112 1.809 0.0000 0.0000 0.0000
- 11ALA O 106 -0.930 -1.031 1.897 0.0000 0.0000 0.0000
- 12ALA N 107 -0.784 -1.175 1.802 0.0000 0.0000 0.0000
- 12ALA H 108 -0.768 -1.243 1.729 0.0000 0.0000 0.0000
- 12ALA CA 109 -0.663 -1.129 1.868 0.0000 0.0000 0.0000
- 12ALA HA 110 -0.695 -1.097 1.966 0.0000 0.0000 0.0000
- 12ALA CB 111 -0.568 -1.247 1.888 0.0000 0.0000 0.0000
- 12ALA HB1 112 -0.521 -1.271 1.792 0.0000 0.0000 0.0000
- 12ALA HB2 113 -0.628 -1.330 1.924 0.0000 0.0000 0.0000
- 12ALA HB3 114 -0.488 -1.217 1.955 0.0000 0.0000 0.0000
- 12ALA C 115 -0.601 -1.014 1.790 0.0000 0.0000 0.0000
- 12ALA O 116 -0.638 -0.989 1.675 0.0000 0.0000 0.0000
- 13ALA N 117 -0.509 -0.942 1.854 0.0000 0.0000 0.0000
- 13ALA H 118 -0.508 -0.964 1.953 0.0000 0.0000 0.0000
- 13ALA CA 119 -0.423 -0.841 1.796 0.0000 0.0000 0.0000
- 13ALA HA 120 -0.398 -0.873 1.695 0.0000 0.0000 0.0000
- 13ALA CB 121 -0.497 -0.707 1.786 0.0000 0.0000 0.0000
- 13ALA HB1 122 -0.429 -0.630 1.750 0.0000 0.0000 0.0000
- 13ALA HB2 123 -0.545 -0.676 1.878 0.0000 0.0000 0.0000
- 13ALA HB3 124 -0.578 -0.724 1.715 0.0000 0.0000 0.0000
- 13ALA C 125 -0.296 -0.825 1.877 0.0000 0.0000 0.0000
- 13ALA O 126 -0.198 -0.896 1.854 0.0000 0.0000 0.0000
- 14NME N 127 -0.292 -0.739 1.979 0.0000 0.0000 0.0000
- 14NME H 128 -0.373 -0.682 2.001 0.0000 0.0000 0.0000
- 14NME CH3 129 -0.169 -0.709 2.049 0.0000 0.0000 0.0000
- 14NME HH31 130 -0.187 -0.663 2.146 0.0000 0.0000 0.0000
- 14NME HH32 131 -0.115 -0.628 1.999 0.0000 0.0000 0.0000
- 14NME HH33 132 -0.114 -0.802 2.060 0.0000 0.0000 0.0000
+ 1ACE HH31 1 -0.911 -0.240 2.180
+ 1ACE CH3 2 -0.893 -0.335 2.231
+ 1ACE HH32 3 -0.950 -0.350 2.322
+ 1ACE HH33 4 -0.907 -0.417 2.160
+ 1ACE C 5 -0.745 -0.330 2.266
+ 1ACE O 6 -0.691 -0.221 2.283
+ 2ALA N 7 -0.681 -0.448 2.268
+ 2ALA H 8 -0.732 -0.530 2.242
+ 2ALA CA 9 -0.540 -0.460 2.297
+ 2ALA HA 10 -0.488 -0.386 2.235
+ 2ALA CB 11 -0.507 -0.437 2.444
+ 2ALA HB1 12 -0.401 -0.435 2.467
+ 2ALA HB2 13 -0.544 -0.514 2.511
+ 2ALA HB3 14 -0.556 -0.343 2.470
+ 2ALA C 15 -0.491 -0.595 2.247
+ 2ALA O 16 -0.473 -0.613 2.126
+ 3ALA N 17 -0.485 -0.697 2.333
+ 3ALA H 18 -0.512 -0.679 2.429
+ 3ALA CA 19 -0.472 -0.840 2.316
+ 3ALA HA 20 -0.377 -0.852 2.264
+ 3ALA CB 21 -0.461 -0.909 2.451
+ 3ALA HB1 22 -0.376 -0.871 2.508
+ 3ALA HB2 23 -0.451 -1.014 2.425
+ 3ALA HB3 24 -0.549 -0.913 2.516
+ 3ALA C 25 -0.575 -0.906 2.226
+ 3ALA O 26 -0.536 -0.975 2.132
+ 4ALA N 27 -0.704 -0.887 2.257
+ 4ALA H 28 -0.704 -0.806 2.318
+ 4ALA CA 29 -0.820 -0.923 2.179
+ 4ALA HA 30 -0.787 -0.985 2.095
+ 4ALA CB 31 -0.916 -0.996 2.273
+ 4ALA HB1 32 -0.863 -1.079 2.319
+ 4ALA HB2 33 -1.010 -1.033 2.231
+ 4ALA HB3 34 -0.940 -0.926 2.353
+ 4ALA C 35 -0.872 -0.791 2.126
+ 4ALA O 36 -0.827 -0.685 2.168
+ 5ALA N 37 -0.957 -0.790 2.022
+ 5ALA H 38 -0.963 -0.882 1.981
+ 5ALA CA 39 -0.992 -0.679 1.936
+ 5ALA HA 40 -1.014 -0.595 2.001
+ 5ALA CB 41 -0.879 -0.640 1.841
+ 5ALA HB1 42 -0.853 -0.714 1.765
+ 5ALA HB2 43 -0.786 -0.629 1.896
+ 5ALA HB3 44 -0.898 -0.548 1.786
+ 5ALA C 45 -1.118 -0.705 1.853
+ 5ALA O 46 -1.152 -0.822 1.837
+ 6ALA N 47 -1.193 -0.605 1.805
+ 6ALA H 48 -1.160 -0.510 1.805
+ 6ALA CA 49 -1.324 -0.626 1.747
+ 6ALA HA 50 -1.312 -0.716 1.687
+ 6ALA CB 51 -1.437 -0.640 1.849
+ 6ALA HB1 52 -1.533 -0.650 1.799
+ 6ALA HB2 53 -1.436 -0.555 1.918
+ 6ALA HB3 54 -1.413 -0.723 1.916
+ 6ALA C 55 -1.363 -0.509 1.658
+ 6ALA O 56 -1.336 -0.394 1.692
+ 7ALA N 57 -1.421 -0.543 1.543
+ 7ALA H 58 -1.429 -0.644 1.540
+ 7ALA CA 59 -1.490 -0.458 1.448
+ 7ALA HA 60 -1.536 -0.379 1.507
+ 7ALA CB 61 -1.389 -0.380 1.364
+ 7ALA HB1 62 -1.448 -0.310 1.305
+ 7ALA HB2 63 -1.323 -0.443 1.305
+ 7ALA HB3 64 -1.329 -0.316 1.428
+ 7ALA C 65 -1.595 -0.517 1.355
+ 7ALA O 66 -1.715 -0.505 1.374
+ 8ALA N 67 -1.548 -0.602 1.264
+ 8ALA H 68 -1.447 -0.611 1.257
+ 8ALA CA 69 -1.614 -0.708 1.190
+ 8ALA HA 70 -1.721 -0.703 1.210
+ 8ALA CB 71 -1.591 -0.690 1.040
+ 8ALA HB1 72 -1.648 -0.607 0.998
+ 8ALA HB2 73 -1.611 -0.781 0.984
+ 8ALA HB3 74 -1.484 -0.673 1.042
+ 8ALA C 75 -1.555 -0.841 1.237
+ 8ALA O 76 -1.437 -0.871 1.223
+ 9ALA N 77 -1.646 -0.911 1.305
+ 9ALA H 78 -1.736 -0.867 1.314
+ 9ALA CA 79 -1.613 -1.016 1.400
+ 9ALA HA 80 -1.700 -1.054 1.454
+ 9ALA CB 81 -1.558 -1.131 1.316
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.050000
132
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.100000
132
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+ 14NME HH33 132 -0.351 -0.995 1.683
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.150000
132
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- 9ALA HB1 82 -1.013 -0.637 1.180 0.0000 0.0000 0.0000
- 9ALA HB2 83 -0.966 -0.672 1.348 0.0000 0.0000 0.0000
- 9ALA HB3 84 -1.027 -0.519 1.295 0.0000 0.0000 0.0000
- 9ALA C 85 -1.177 -0.841 1.311 0.0000 0.0000 0.0000
- 9ALA O 86 -1.100 -0.907 1.242 0.0000 0.0000 0.0000
- 10ALA N 87 -1.275 -0.897 1.382 0.0000 0.0000 0.0000
- 10ALA H 88 -1.332 -0.838 1.441 0.0000 0.0000 0.0000
- 10ALA CA 89 -1.312 -1.037 1.391 0.0000 0.0000 0.0000
- 10ALA HA 90 -1.387 -1.032 1.470 0.0000 0.0000 0.0000
- 10ALA CB 91 -1.385 -1.082 1.265 0.0000 0.0000 0.0000
- 10ALA HB1 92 -1.476 -1.140 1.280 0.0000 0.0000 0.0000
- 10ALA HB2 93 -1.322 -1.140 1.198 0.0000 0.0000 0.0000
- 10ALA HB3 94 -1.421 -0.997 1.207 0.0000 0.0000 0.0000
- 10ALA C 95 -1.211 -1.134 1.453 0.0000 0.0000 0.0000
- 10ALA O 96 -1.250 -1.201 1.549 0.0000 0.0000 0.0000
- 11ALA N 97 -1.083 -1.138 1.417 0.0000 0.0000 0.0000
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- 11ALA CA 99 -0.963 -1.202 1.466 0.0000 0.0000 0.0000
- 11ALA HA 100 -0.948 -1.294 1.409 0.0000 0.0000 0.0000
- 11ALA CB 101 -0.847 -1.114 1.421 0.0000 0.0000 0.0000
- 11ALA HB1 102 -0.845 -1.022 1.480 0.0000 0.0000 0.0000
- 11ALA HB2 103 -0.853 -1.086 1.316 0.0000 0.0000 0.0000
- 11ALA HB3 104 -0.747 -1.152 1.444 0.0000 0.0000 0.0000
- 11ALA C 105 -0.969 -1.225 1.616 0.0000 0.0000 0.0000
- 11ALA O 106 -0.934 -1.330 1.670 0.0000 0.0000 0.0000
- 12ALA N 107 -1.014 -1.127 1.695 0.0000 0.0000 0.0000
- 12ALA H 108 -1.035 -1.045 1.640 0.0000 0.0000 0.0000
- 12ALA CA 109 -1.037 -1.122 1.838 0.0000 0.0000 0.0000
- 12ALA HA 110 -1.078 -1.023 1.858 0.0000 0.0000 0.0000
- 12ALA CB 111 -1.133 -1.228 1.889 0.0000 0.0000 0.0000
- 12ALA HB1 112 -1.076 -1.315 1.921 0.0000 0.0000 0.0000
- 12ALA HB2 113 -1.200 -1.251 1.806 0.0000 0.0000 0.0000
- 12ALA HB3 114 -1.198 -1.197 1.971 0.0000 0.0000 0.0000
- 12ALA C 115 -0.909 -1.119 1.920 0.0000 0.0000 0.0000
- 12ALA O 116 -0.897 -1.034 2.008 0.0000 0.0000 0.0000
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- 13ALA H 118 -0.824 -1.254 1.802 0.0000 0.0000 0.0000
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- 13ALA HA 120 -0.713 -1.247 2.075 0.0000 0.0000 0.0000
- 13ALA CB 121 -0.640 -1.362 1.933 0.0000 0.0000 0.0000
- 13ALA HB1 122 -0.561 -1.394 2.001 0.0000 0.0000 0.0000
- 13ALA HB2 123 -0.599 -1.344 1.833 0.0000 0.0000 0.0000
- 13ALA HB3 124 -0.710 -1.445 1.931 0.0000 0.0000 0.0000
- 13ALA C 125 -0.592 -1.111 1.959 0.0000 0.0000 0.0000
- 13ALA O 126 -0.578 -1.059 1.849 0.0000 0.0000 0.0000
- 14NME N 127 -0.524 -1.074 2.068 0.0000 0.0000 0.0000
- 14NME H 128 -0.509 -1.137 2.146 0.0000 0.0000 0.0000
- 14NME CH3 129 -0.439 -0.957 2.073 0.0000 0.0000 0.0000
- 14NME HH31 130 -0.371 -0.964 1.988 0.0000 0.0000 0.0000
- 14NME HH32 131 -0.379 -0.945 2.164 0.0000 0.0000 0.0000
- 14NME HH33 132 -0.505 -0.872 2.065 0.0000 0.0000 0.0000
+ 1ACE HH31 1 -0.559 -1.143 2.590
+ 1ACE CH3 2 -0.542 -1.233 2.531
+ 1ACE HH32 3 -0.439 -1.267 2.525
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+ 1ACE O 6 -0.594 -1.272 2.300
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+ 4ALA HB2 33 -0.976 -0.208 2.127
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+ 11ALA HB1 102 -0.845 -1.022 1.480
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+ 14NME HH32 131 -0.379 -0.945 2.164
+ 14NME HH33 132 -0.505 -0.872 2.065
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.200000
132
- 1ACE HH31 1 -0.645 -0.326 2.596 0.0000 0.0000 0.0000
- 1ACE CH3 2 -0.672 -0.294 2.495 0.0000 0.0000 0.0000
- 1ACE HH32 3 -0.746 -0.215 2.506 0.0000 0.0000 0.0000
- 1ACE HH33 4 -0.579 -0.270 2.443 0.0000 0.0000 0.0000
- 1ACE C 5 -0.739 -0.407 2.419 0.0000 0.0000 0.0000
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- 2ALA N 7 -0.754 -0.521 2.488 0.0000 0.0000 0.0000
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- 2ALA HB3 14 -0.845 -0.838 2.572 0.0000 0.0000 0.0000
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- 2ALA O 16 -0.943 -0.692 2.267 0.0000 0.0000 0.0000
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+ 1ACE HH31 1 -0.645 -0.326 2.596
+ 1ACE CH3 2 -0.672 -0.294 2.495
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.250000
132
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.300000
132
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.350000
132
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- 11ALA HA 100 -1.091 -1.135 1.232 0.0000 0.0000 0.0000
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- 11ALA HB3 104 -1.151 -0.886 1.226 0.0000 0.0000 0.0000
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- 11ALA O 106 -0.847 -1.180 1.269 0.0000 0.0000 0.0000
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- 12ALA HA 110 -0.670 -1.144 1.428 0.0000 0.0000 0.0000
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- 12ALA HB1 112 -0.541 -0.946 1.414 0.0000 0.0000 0.0000
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- 12ALA HB3 114 -0.679 -0.939 1.298 0.0000 0.0000 0.0000
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- 13ALA HA 120 -0.830 -1.130 1.860 0.0000 0.0000 0.0000
- 13ALA CB 121 -0.735 -1.315 1.875 0.0000 0.0000 0.0000
- 13ALA HB1 122 -0.639 -1.364 1.857 0.0000 0.0000 0.0000
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- 13ALA HB3 124 -0.742 -1.320 1.984 0.0000 0.0000 0.0000
- 13ALA C 125 -0.631 -1.095 1.919 0.0000 0.0000 0.0000
- 13ALA O 126 -0.671 -1.037 2.019 0.0000 0.0000 0.0000
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- 14NME CH3 129 -0.388 -1.051 1.961 0.0000 0.0000 0.0000
- 14NME HH31 130 -0.300 -1.105 1.927 0.0000 0.0000 0.0000
- 14NME HH32 131 -0.420 -1.061 2.064 0.0000 0.0000 0.0000
- 14NME HH33 132 -0.367 -0.946 1.937 0.0000 0.0000 0.0000
+ 1ACE HH31 1 -0.326 -0.921 2.604
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+ 14NME HH31 130 -0.300 -1.105 1.927
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+ 14NME HH33 132 -0.367 -0.946 1.937
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.400000
132
- 1ACE HH31 1 -0.264 -1.191 1.743 0.0000 0.0000 0.0000
- 1ACE CH3 2 -0.363 -1.148 1.752 0.0000 0.0000 0.0000
- 1ACE HH32 3 -0.355 -1.057 1.693 0.0000 0.0000 0.0000
- 1ACE HH33 4 -0.426 -1.225 1.706 0.0000 0.0000 0.0000
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.450000
132
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+ 14NME HH33 132 -1.087 -1.766 1.455
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.500000
132
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- 1ACE CH3 2 -0.355 -0.422 2.301 0.0000 0.0000 0.0000
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diff --git a/regtest/basic/rt54/helix-pr.gro.reference b/regtest/basic/rt54/helix-pr.gro.reference
new file mode 100644
index 0000000000000000000000000000000000000000..9202d01137297ee3b3695d5333eeee77c4ff9ada
--- /dev/null
+++ b/regtest/basic/rt54/helix-pr.gro.reference
@@ -0,0 +1,1620 @@
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diff --git a/regtest/basic/rt54/helix-pr.xyz.reference b/regtest/basic/rt54/helix-pr.xyz.reference
new file mode 100644
index 0000000000000000000000000000000000000000..35368e8bb1cbb4a30f83f5c7a5ca01db4781b059
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+HB3 -1.350000000000 -10.430000000000 13.540000000000
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+HH33 -0.740000000000 -6.170000000000 13.860000000000
diff --git a/regtest/basic/rt54/helix-sub.gro.reference b/regtest/basic/rt54/helix-sub.gro.reference
index ace75e242be67fea4582bbac592b103fd72758cc..1600268fb3472e19655aaf6c491dce84a9c2be77 100644
--- a/regtest/basic/rt54/helix-sub.gro.reference
+++ b/regtest/basic/rt54/helix-sub.gro.reference
@@ -1,192 +1,192 @@
Made with PLUMED t=0.000000
13
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- 1ACE CH3 2 -0.893 -0.335 2.231 0.0000 0.0000 0.0000
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- 1ACE O 6 -0.691 -0.221 2.283 0.0000 0.0000 0.0000
- 14NME N 127 -0.292 -0.739 1.979 0.0000 0.0000 0.0000
- 14NME H 128 -0.373 -0.682 2.001 0.0000 0.0000 0.0000
- 14NME CH3 129 -0.169 -0.709 2.049 0.0000 0.0000 0.0000
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- 14NME HH32 131 -0.115 -0.628 1.999 0.0000 0.0000 0.0000
- 14NME HH33 132 -0.114 -0.802 2.060 0.0000 0.0000 0.0000
- 0 X 133 -0.529 -0.510 2.140 0.0000 0.0000 0.0000
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+ 0 X 133 -0.529 -0.510 2.140
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.050000
13
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- 1ACE CH3 2 -0.086 -1.241 1.583 0.0000 0.0000 0.0000
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- 1ACE O 6 -0.296 -1.249 1.476 0.0000 0.0000 0.0000
- 14NME N 127 -0.249 -1.196 1.196 0.0000 0.0000 0.0000
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- 0 X 133 -0.145 -1.245 1.365 0.0000 0.0000 0.0000
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+ 0 X 133 -0.145 -1.245 1.365
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.100000
13
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.150000
13
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.200000
13
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.250000
13
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- 0 X 133 -0.081 -0.844 2.090 0.0000 0.0000 0.0000
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+ 0 X 133 -0.081 -0.844 2.090
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.300000
13
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+ 0 X 133 -0.768 -0.999 1.528
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.350000
13
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+ 0 X 133 -0.409 -0.967 2.234
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.400000
13
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+ 0 X 133 -0.283 -0.909 1.670
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.450000
13
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+ 0 X 133 -0.936 -1.139 1.780
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.500000
13
- 1ACE HH31 1 -0.290 -0.494 2.251 0.0000 0.0000 0.0000
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- 14NME HH32 131 -0.772 -1.496 1.584 0.0000 0.0000 0.0000
- 14NME HH33 132 -0.806 -1.608 1.448 0.0000 0.0000 0.0000
- 0 X 133 -0.605 -0.967 1.903 0.0000 0.0000 0.0000
+ 1ACE HH31 1 -0.290 -0.494 2.251
+ 1ACE CH3 2 -0.355 -0.422 2.301
+ 1ACE HH32 3 -0.313 -0.370 2.388
+ 1ACE HH33 4 -0.385 -0.347 2.228
+ 1ACE C 5 -0.469 -0.506 2.357
+ 1ACE O 6 -0.440 -0.613 2.410
+ 14NME N 127 -0.829 -1.400 1.408
+ 14NME H 128 -0.832 -1.305 1.443
+ 14NME CH3 129 -0.834 -1.514 1.497
+ 14NME HH31 130 -0.938 -1.534 1.525
+ 14NME HH32 131 -0.772 -1.496 1.584
+ 14NME HH33 132 -0.806 -1.608 1.448
+ 0 X 133 -0.605 -0.967 1.903
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.550000
13
- 1ACE HH31 1 0.072 -1.016 1.887 0.0000 0.0000 0.0000
- 1ACE CH3 2 0.034 -0.916 1.912 0.0000 0.0000 0.0000
- 1ACE HH32 3 0.047 -0.887 2.016 0.0000 0.0000 0.0000
- 1ACE HH33 4 0.076 -0.831 1.859 0.0000 0.0000 0.0000
- 1ACE C 5 -0.114 -0.927 1.879 0.0000 0.0000 0.0000
- 1ACE O 6 -0.153 -0.971 1.772 0.0000 0.0000 0.0000
- 14NME N 127 -0.141 -0.764 1.514 0.0000 0.0000 0.0000
- 14NME H 128 -0.103 -0.828 1.583 0.0000 0.0000 0.0000
- 14NME CH3 129 -0.078 -0.635 1.493 0.0000 0.0000 0.0000
- 14NME HH31 130 0.019 -0.629 1.542 0.0000 0.0000 0.0000
- 14NME HH32 131 -0.149 -0.567 1.540 0.0000 0.0000 0.0000
- 14NME HH33 132 -0.074 -0.617 1.386 0.0000 0.0000 0.0000
- 0 X 133 -0.047 -0.799 1.699 0.0000 0.0000 0.0000
+ 1ACE HH31 1 0.072 -1.016 1.887
+ 1ACE CH3 2 0.034 -0.916 1.912
+ 1ACE HH32 3 0.047 -0.887 2.016
+ 1ACE HH33 4 0.076 -0.831 1.859
+ 1ACE C 5 -0.114 -0.927 1.879
+ 1ACE O 6 -0.153 -0.971 1.772
+ 14NME N 127 -0.141 -0.764 1.514
+ 14NME H 128 -0.103 -0.828 1.583
+ 14NME CH3 129 -0.078 -0.635 1.493
+ 14NME HH31 130 0.019 -0.629 1.542
+ 14NME HH32 131 -0.149 -0.567 1.540
+ 14NME HH33 132 -0.074 -0.617 1.386
+ 0 X 133 -0.047 -0.799 1.699
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
diff --git a/regtest/basic/rt54/helix.gro.reference b/regtest/basic/rt54/helix.gro.reference
index b08cf48e72c5773f8431b24dbcd3b8983e124263..6143d662aed3720d20513b4e60c45428d7ec0690 100644
--- a/regtest/basic/rt54/helix.gro.reference
+++ b/regtest/basic/rt54/helix.gro.reference
@@ -1,1620 +1,1620 @@
Made with PLUMED t=0.000000
132
- 1ACE HH31 1 -0.911 -0.240 2.180 0.0000 0.0000 0.0000
- 1ACE CH3 2 -0.893 -0.335 2.231 0.0000 0.0000 0.0000
- 1ACE HH32 3 -0.950 -0.350 2.322 0.0000 0.0000 0.0000
- 1ACE HH33 4 -0.907 -0.417 2.160 0.0000 0.0000 0.0000
- 1ACE C 5 -0.745 -0.330 2.266 0.0000 0.0000 0.0000
- 1ACE O 6 -0.691 -0.221 2.283 0.0000 0.0000 0.0000
- 2ALA N 7 -0.681 -0.448 2.268 0.0000 0.0000 0.0000
- 2ALA H 8 -0.732 -0.530 2.242 0.0000 0.0000 0.0000
- 2ALA CA 9 -0.540 -0.460 2.297 0.0000 0.0000 0.0000
- 2ALA HA 10 -0.488 -0.386 2.235 0.0000 0.0000 0.0000
- 2ALA CB 11 -0.507 -0.437 2.444 0.0000 0.0000 0.0000
- 2ALA HB1 12 -0.401 -0.435 2.467 0.0000 0.0000 0.0000
- 2ALA HB2 13 -0.544 -0.514 2.511 0.0000 0.0000 0.0000
- 2ALA HB3 14 -0.556 -0.343 2.470 0.0000 0.0000 0.0000
- 2ALA C 15 -0.491 -0.595 2.247 0.0000 0.0000 0.0000
- 2ALA O 16 -0.473 -0.613 2.126 0.0000 0.0000 0.0000
- 3ALA N 17 -0.485 -0.697 2.333 0.0000 0.0000 0.0000
- 3ALA H 18 -0.512 -0.679 2.429 0.0000 0.0000 0.0000
- 3ALA CA 19 -0.472 -0.840 2.316 0.0000 0.0000 0.0000
- 3ALA HA 20 -0.377 -0.852 2.264 0.0000 0.0000 0.0000
- 3ALA CB 21 -0.461 -0.909 2.451 0.0000 0.0000 0.0000
- 3ALA HB1 22 -0.376 -0.871 2.508 0.0000 0.0000 0.0000
- 3ALA HB2 23 -0.451 -1.014 2.425 0.0000 0.0000 0.0000
- 3ALA HB3 24 -0.549 -0.913 2.516 0.0000 0.0000 0.0000
- 3ALA C 25 -0.575 -0.906 2.226 0.0000 0.0000 0.0000
- 3ALA O 26 -0.536 -0.975 2.132 0.0000 0.0000 0.0000
- 4ALA N 27 -0.704 -0.887 2.257 0.0000 0.0000 0.0000
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- 4ALA CB 31 -0.916 -0.996 2.273 0.0000 0.0000 0.0000
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- 5ALA C 45 -1.118 -0.705 1.853 0.0000 0.0000 0.0000
- 5ALA O 46 -1.152 -0.822 1.837 0.0000 0.0000 0.0000
- 6ALA N 47 -1.193 -0.605 1.805 0.0000 0.0000 0.0000
- 6ALA H 48 -1.160 -0.510 1.805 0.0000 0.0000 0.0000
- 6ALA CA 49 -1.324 -0.626 1.747 0.0000 0.0000 0.0000
- 6ALA HA 50 -1.312 -0.716 1.687 0.0000 0.0000 0.0000
- 6ALA CB 51 -1.437 -0.640 1.849 0.0000 0.0000 0.0000
- 6ALA HB1 52 -1.533 -0.650 1.799 0.0000 0.0000 0.0000
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- 6ALA C 55 -1.363 -0.509 1.658 0.0000 0.0000 0.0000
- 6ALA O 56 -1.336 -0.394 1.692 0.0000 0.0000 0.0000
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- 12ALA HB1 112 -0.521 -1.271 1.792 0.0000 0.0000 0.0000
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- 13ALA CB 121 -0.497 -0.707 1.786 0.0000 0.0000 0.0000
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+ 14NME CH3 129 -0.169 -0.709 2.049
+ 14NME HH31 130 -0.187 -0.663 2.146
+ 14NME HH32 131 -0.115 -0.628 1.999
+ 14NME HH33 132 -0.114 -0.802 2.060
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.050000
132
- 1ACE HH31 1 -0.022 -1.191 1.511 0.0000 0.0000 0.0000
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- 7ALA HB3 64 -1.871 -0.502 1.793 0.0000 0.0000 0.0000
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- 10ALA HA 90 -1.031 -1.040 1.975 0.0000 0.0000 0.0000
- 10ALA CB 91 -1.127 -1.229 1.941 0.0000 0.0000 0.0000
- 10ALA HB1 92 -1.210 -1.273 1.887 0.0000 0.0000 0.0000
- 10ALA HB2 93 -1.126 -1.256 2.047 0.0000 0.0000 0.0000
- 10ALA HB3 94 -1.043 -1.286 1.901 0.0000 0.0000 0.0000
- 10ALA C 95 -1.100 -1.066 1.767 0.0000 0.0000 0.0000
- 10ALA O 96 -1.203 -1.084 1.703 0.0000 0.0000 0.0000
- 11ALA N 97 -0.980 -1.044 1.712 0.0000 0.0000 0.0000
- 11ALA H 98 -0.897 -1.014 1.760 0.0000 0.0000 0.0000
- 11ALA CA 99 -0.959 -1.027 1.570 0.0000 0.0000 0.0000
- 11ALA HA 100 -1.029 -1.091 1.518 0.0000 0.0000 0.0000
- 11ALA CB 101 -0.985 -0.884 1.522 0.0000 0.0000 0.0000
- 11ALA HB1 102 -0.933 -0.812 1.585 0.0000 0.0000 0.0000
- 11ALA HB2 103 -1.088 -0.847 1.527 0.0000 0.0000 0.0000
- 11ALA HB3 104 -0.955 -0.878 1.418 0.0000 0.0000 0.0000
- 11ALA C 105 -0.818 -1.079 1.542 0.0000 0.0000 0.0000
- 11ALA O 106 -0.720 -1.010 1.567 0.0000 0.0000 0.0000
- 12ALA N 107 -0.810 -1.192 1.471 0.0000 0.0000 0.0000
- 12ALA H 108 -0.899 -1.232 1.447 0.0000 0.0000 0.0000
- 12ALA CA 109 -0.694 -1.250 1.405 0.0000 0.0000 0.0000
- 12ALA HA 110 -0.616 -1.248 1.481 0.0000 0.0000 0.0000
- 12ALA CB 111 -0.729 -1.394 1.371 0.0000 0.0000 0.0000
- 12ALA HB1 112 -0.756 -1.445 1.464 0.0000 0.0000 0.0000
- 12ALA HB2 113 -0.635 -1.447 1.353 0.0000 0.0000 0.0000
- 12ALA HB3 114 -0.810 -1.405 1.299 0.0000 0.0000 0.0000
- 12ALA C 115 -0.643 -1.158 1.295 0.0000 0.0000 0.0000
- 12ALA O 116 -0.717 -1.094 1.220 0.0000 0.0000 0.0000
- 13ALA N 117 -0.510 -1.144 1.290 0.0000 0.0000 0.0000
- 13ALA H 118 -0.454 -1.190 1.361 0.0000 0.0000 0.0000
- 13ALA CA 119 -0.445 -1.053 1.199 0.0000 0.0000 0.0000
- 13ALA HA 120 -0.510 -1.024 1.117 0.0000 0.0000 0.0000
- 13ALA CB 121 -0.388 -0.929 1.268 0.0000 0.0000 0.0000
- 13ALA HB1 122 -0.291 -0.949 1.314 0.0000 0.0000 0.0000
- 13ALA HB2 123 -0.462 -0.882 1.333 0.0000 0.0000 0.0000
- 13ALA HB3 124 -0.372 -0.861 1.185 0.0000 0.0000 0.0000
- 13ALA C 125 -0.332 -1.121 1.123 0.0000 0.0000 0.0000
- 13ALA O 126 -0.322 -1.111 1.001 0.0000 0.0000 0.0000
- 14NME N 127 -0.249 -1.196 1.196 0.0000 0.0000 0.0000
- 14NME H 128 -0.277 -1.213 1.292 0.0000 0.0000 0.0000
- 14NME CH3 129 -0.133 -1.261 1.139 0.0000 0.0000 0.0000
- 14NME HH31 130 -0.121 -1.218 1.040 0.0000 0.0000 0.0000
- 14NME HH32 131 -0.148 -1.369 1.146 0.0000 0.0000 0.0000
- 14NME HH33 132 -0.043 -1.233 1.193 0.0000 0.0000 0.0000
+ 1ACE HH31 1 -0.022 -1.191 1.511
+ 1ACE CH3 2 -0.086 -1.241 1.583
+ 1ACE HH32 3 -0.085 -1.347 1.559
+ 1ACE HH33 4 -0.041 -1.210 1.677
+ 1ACE C 5 -0.234 -1.207 1.574
+ 1ACE O 6 -0.296 -1.249 1.476
+ 2ALA N 7 -0.285 -1.128 1.669
+ 2ALA H 8 -0.219 -1.076 1.724
+ 2ALA CA 9 -0.423 -1.089 1.690
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+ 2ALA HB3 14 -0.614 -1.180 1.738
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+ 2ALA O 16 -0.330 -0.930 1.841
+ 3ALA N 17 -0.553 -0.923 1.818
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+ 3ALA HB1 22 -0.553 -0.687 1.740
+ 3ALA HB2 23 -0.412 -0.690 1.848
+ 3ALA HB3 24 -0.548 -0.603 1.901
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+ 4ALA N 27 -0.780 -0.703 2.006
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+ 4ALA HB2 33 -1.089 -0.713 2.162
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+ 5ALA HB2 43 -1.117 -0.206 1.827
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+ 6ALA N 47 -1.330 -0.348 2.118
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+ 11ALA HB1 102 -0.933 -0.812 1.585
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+ 12ALA HB1 112 -0.756 -1.445 1.464
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+ 13ALA N 117 -0.510 -1.144 1.290
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+ 13ALA HB1 122 -0.291 -0.949 1.314
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+ 14NME N 127 -0.249 -1.196 1.196
+ 14NME H 128 -0.277 -1.213 1.292
+ 14NME CH3 129 -0.133 -1.261 1.139
+ 14NME HH31 130 -0.121 -1.218 1.040
+ 14NME HH32 131 -0.148 -1.369 1.146
+ 14NME HH33 132 -0.043 -1.233 1.193
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.100000
132
- 1ACE HH31 1 -1.697 -0.728 1.714 0.0000 0.0000 0.0000
- 1ACE CH3 2 -1.714 -0.818 1.773 0.0000 0.0000 0.0000
- 1ACE HH32 3 -1.805 -0.789 1.825 0.0000 0.0000 0.0000
- 1ACE HH33 4 -1.737 -0.908 1.716 0.0000 0.0000 0.0000
- 1ACE C 5 -1.589 -0.834 1.859 0.0000 0.0000 0.0000
- 1ACE O 6 -1.546 -0.746 1.933 0.0000 0.0000 0.0000
- 2ALA N 7 -1.531 -0.952 1.836 0.0000 0.0000 0.0000
- 2ALA H 8 -1.561 -1.001 1.753 0.0000 0.0000 0.0000
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- 2ALA HA 10 -1.452 -0.954 2.023 0.0000 0.0000 0.0000
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- 2ALA HB3 14 -1.555 -1.188 1.965 0.0000 0.0000 0.0000
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- 2ALA O 16 -1.280 -0.855 1.817 0.0000 0.0000 0.0000
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- 3ALA HB3 24 -0.879 -1.056 2.038 0.0000 0.0000 0.0000
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- 3ALA O 26 -0.983 -0.990 1.732 0.0000 0.0000 0.0000
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- 12ALA CB 111 -0.979 -1.500 1.633 0.0000 0.0000 0.0000
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- 12ALA HB3 114 -0.969 -1.553 1.538 0.0000 0.0000 0.0000
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- 14NME CH3 129 -0.405 -1.081 1.724 0.0000 0.0000 0.0000
- 14NME HH31 130 -0.330 -1.159 1.742 0.0000 0.0000 0.0000
- 14NME HH32 131 -0.445 -1.056 1.822 0.0000 0.0000 0.0000
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+ 1ACE HH31 1 -1.697 -0.728 1.714
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+ 14NME HH33 132 -0.351 -0.995 1.683
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.150000
132
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- 1ACE CH3 2 -0.542 -1.233 2.531 0.0000 0.0000 0.0000
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+ 14NME HH33 132 -0.505 -0.872 2.065
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.200000
132
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+ 1ACE HH31 1 -0.645 -0.326 2.596
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.250000
132
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.300000
132
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- 12ALA CB 111 -0.825 -0.915 1.250 0.0000 0.0000 0.0000
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- 12ALA HB2 113 -0.895 -0.846 1.201 0.0000 0.0000 0.0000
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- 13ALA HB1 122 -0.690 -1.383 1.469 0.0000 0.0000 0.0000
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+ 14NME HH33 132 -0.327 -1.051 1.598
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.350000
132
- 1ACE HH31 1 -0.326 -0.921 2.604 0.0000 0.0000 0.0000
- 1ACE CH3 2 -0.404 -0.848 2.581 0.0000 0.0000 0.0000
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- 10ALA CB 91 -1.366 -1.258 1.641 0.0000 0.0000 0.0000
- 10ALA HB1 92 -1.454 -1.246 1.578 0.0000 0.0000 0.0000
- 10ALA HB2 93 -1.402 -1.248 1.744 0.0000 0.0000 0.0000
- 10ALA HB3 94 -1.313 -1.352 1.623 0.0000 0.0000 0.0000
- 10ALA C 95 -1.229 -1.154 1.450 0.0000 0.0000 0.0000
- 10ALA O 96 -1.240 -1.254 1.380 0.0000 0.0000 0.0000
- 11ALA N 97 -1.140 -1.059 1.420 0.0000 0.0000 0.0000
- 11ALA H 98 -1.131 -0.991 1.494 0.0000 0.0000 0.0000
- 11ALA CA 99 -1.053 -1.062 1.304 0.0000 0.0000 0.0000
- 11ALA HA 100 -1.091 -1.135 1.232 0.0000 0.0000 0.0000
- 11ALA CB 101 -1.050 -0.921 1.245 0.0000 0.0000 0.0000
- 11ALA HB1 102 -1.008 -0.932 1.145 0.0000 0.0000 0.0000
- 11ALA HB2 103 -0.986 -0.861 1.311 0.0000 0.0000 0.0000
- 11ALA HB3 104 -1.151 -0.886 1.226 0.0000 0.0000 0.0000
- 11ALA C 105 -0.911 -1.102 1.339 0.0000 0.0000 0.0000
- 11ALA O 106 -0.847 -1.180 1.269 0.0000 0.0000 0.0000
- 12ALA N 107 -0.855 -1.044 1.446 0.0000 0.0000 0.0000
- 12ALA H 108 -0.911 -0.977 1.497 0.0000 0.0000 0.0000
- 12ALA CA 109 -0.712 -1.052 1.469 0.0000 0.0000 0.0000
- 12ALA HA 110 -0.670 -1.144 1.428 0.0000 0.0000 0.0000
- 12ALA CB 111 -0.649 -0.931 1.402 0.0000 0.0000 0.0000
- 12ALA HB1 112 -0.541 -0.946 1.414 0.0000 0.0000 0.0000
- 12ALA HB2 113 -0.676 -0.836 1.448 0.0000 0.0000 0.0000
- 12ALA HB3 114 -0.679 -0.939 1.298 0.0000 0.0000 0.0000
- 12ALA C 115 -0.700 -1.049 1.621 0.0000 0.0000 0.0000
- 12ALA O 116 -0.692 -0.943 1.682 0.0000 0.0000 0.0000
- 13ALA N 117 -0.722 -1.163 1.688 0.0000 0.0000 0.0000
- 13ALA H 118 -0.725 -1.253 1.641 0.0000 0.0000 0.0000
- 13ALA CA 119 -0.732 -1.169 1.832 0.0000 0.0000 0.0000
- 13ALA HA 120 -0.830 -1.130 1.860 0.0000 0.0000 0.0000
- 13ALA CB 121 -0.735 -1.315 1.875 0.0000 0.0000 0.0000
- 13ALA HB1 122 -0.639 -1.364 1.857 0.0000 0.0000 0.0000
- 13ALA HB2 123 -0.826 -1.366 1.846 0.0000 0.0000 0.0000
- 13ALA HB3 124 -0.742 -1.320 1.984 0.0000 0.0000 0.0000
- 13ALA C 125 -0.631 -1.095 1.919 0.0000 0.0000 0.0000
- 13ALA O 126 -0.671 -1.037 2.019 0.0000 0.0000 0.0000
- 14NME N 127 -0.501 -1.107 1.889 0.0000 0.0000 0.0000
- 14NME H 128 -0.473 -1.155 1.805 0.0000 0.0000 0.0000
- 14NME CH3 129 -0.388 -1.051 1.961 0.0000 0.0000 0.0000
- 14NME HH31 130 -0.300 -1.105 1.927 0.0000 0.0000 0.0000
- 14NME HH32 131 -0.420 -1.061 2.064 0.0000 0.0000 0.0000
- 14NME HH33 132 -0.367 -0.946 1.937 0.0000 0.0000 0.0000
+ 1ACE HH31 1 -0.326 -0.921 2.604
+ 1ACE CH3 2 -0.404 -0.848 2.581
+ 1ACE HH32 3 -0.482 -0.848 2.657
+ 1ACE HH33 4 -0.367 -0.745 2.579
+ 1ACE C 5 -0.470 -0.880 2.448
+ 1ACE O 6 -0.409 -0.934 2.357
+ 2ALA N 7 -0.603 -0.866 2.443
+ 2ALA H 8 -0.638 -0.830 2.530
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+ 2ALA HA 10 -0.651 -0.951 2.254
+ 2ALA CB 11 -0.827 -0.891 2.347
+ 2ALA HB1 12 -0.881 -0.842 2.267
+ 2ALA HB2 13 -0.862 -0.854 2.444
+ 2ALA HB3 14 -0.851 -0.997 2.340
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+ 3ALA N 17 -0.640 -0.740 2.115
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+ 3ALA HB2 23 -0.458 -0.670 1.922
+ 3ALA HB3 24 -0.572 -0.601 1.813
+ 3ALA C 25 -0.769 -0.559 1.993
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+ 4ALA N 27 -0.824 -0.498 2.098
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+ 5ALA HB3 44 -1.115 -0.214 1.700
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+ 6ALA HB3 54 -0.819 -0.652 1.622
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+ 10ALA HB1 92 -1.454 -1.246 1.578
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+ 10ALA HB3 94 -1.313 -1.352 1.623
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+ 11ALA HB1 102 -1.008 -0.932 1.145
+ 11ALA HB2 103 -0.986 -0.861 1.311
+ 11ALA HB3 104 -1.151 -0.886 1.226
+ 11ALA C 105 -0.911 -1.102 1.339
+ 11ALA O 106 -0.847 -1.180 1.269
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+ 12ALA H 108 -0.911 -0.977 1.497
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+ 12ALA HB1 112 -0.541 -0.946 1.414
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+ 14NME HH31 130 -0.300 -1.105 1.927
+ 14NME HH32 131 -0.420 -1.061 2.064
+ 14NME HH33 132 -0.367 -0.946 1.937
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.400000
132
- 1ACE HH31 1 -0.264 -1.191 1.743 0.0000 0.0000 0.0000
- 1ACE CH3 2 -0.363 -1.148 1.752 0.0000 0.0000 0.0000
- 1ACE HH32 3 -0.355 -1.057 1.693 0.0000 0.0000 0.0000
- 1ACE HH33 4 -0.426 -1.225 1.706 0.0000 0.0000 0.0000
- 1ACE C 5 -0.420 -1.129 1.892 0.0000 0.0000 0.0000
- 1ACE O 6 -0.459 -1.224 1.960 0.0000 0.0000 0.0000
- 2ALA N 7 -0.423 -1.003 1.934 0.0000 0.0000 0.0000
- 2ALA H 8 -0.418 -0.933 1.861 0.0000 0.0000 0.0000
- 2ALA CA 9 -0.438 -0.947 2.067 0.0000 0.0000 0.0000
- 2ALA HA 10 -0.469 -1.016 2.145 0.0000 0.0000 0.0000
- 2ALA CB 11 -0.299 -0.894 2.101 0.0000 0.0000 0.0000
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- 2ALA HB2 13 -0.226 -0.975 2.096 0.0000 0.0000 0.0000
- 2ALA HB3 14 -0.297 -0.838 2.194 0.0000 0.0000 0.0000
- 2ALA C 15 -0.540 -0.834 2.075 0.0000 0.0000 0.0000
- 2ALA O 16 -0.647 -0.851 2.133 0.0000 0.0000 0.0000
- 3ALA N 17 -0.510 -0.720 2.013 0.0000 0.0000 0.0000
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- 3ALA CB 21 -0.526 -0.476 1.972 0.0000 0.0000 0.0000
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- 3ALA HB2 23 -0.489 -0.493 1.871 0.0000 0.0000 0.0000
- 3ALA HB3 24 -0.439 -0.456 2.033 0.0000 0.0000 0.0000
- 3ALA C 25 -0.712 -0.632 1.911 0.0000 0.0000 0.0000
- 3ALA O 26 -0.706 -0.594 1.794 0.0000 0.0000 0.0000
- 4ALA N 27 -0.819 -0.682 1.974 0.0000 0.0000 0.0000
- 4ALA H 28 -0.817 -0.723 2.067 0.0000 0.0000 0.0000
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- 4ALA CB 31 -1.050 -0.735 2.018 0.0000 0.0000 0.0000
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- 14NME H 128 -0.298 -0.673 1.420 0.0000 0.0000 0.0000
- 14NME CH3 129 -0.157 -0.652 1.575 0.0000 0.0000 0.0000
- 14NME HH31 130 -0.121 -0.717 1.655 0.0000 0.0000 0.0000
- 14NME HH32 131 -0.163 -0.554 1.623 0.0000 0.0000 0.0000
- 14NME HH33 132 -0.080 -0.648 1.497 0.0000 0.0000 0.0000
+ 1ACE HH31 1 -0.264 -1.191 1.743
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+ 3ALA HB2 23 -0.489 -0.493 1.871
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.450000
132
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.500000
132
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100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Made with PLUMED t=0.550000
132
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- 5ALA HB3 44 -1.242 -0.650 1.647 0.0000 0.0000 0.0000
- 5ALA C 45 -1.320 -0.655 1.906 0.0000 0.0000 0.0000
- 5ALA O 46 -1.425 -0.600 1.872 0.0000 0.0000 0.0000
- 6ALA N 47 -1.327 -0.762 1.986 0.0000 0.0000 0.0000
- 6ALA H 48 -1.235 -0.803 1.999 0.0000 0.0000 0.0000
- 6ALA CA 49 -1.437 -0.819 2.061 0.0000 0.0000 0.0000
- 6ALA HA 50 -1.394 -0.918 2.075 0.0000 0.0000 0.0000
- 6ALA CB 51 -1.461 -0.751 2.195 0.0000 0.0000 0.0000
- 6ALA HB1 52 -1.559 -0.785 2.229 0.0000 0.0000 0.0000
- 6ALA HB2 53 -1.479 -0.645 2.179 0.0000 0.0000 0.0000
- 6ALA HB3 54 -1.380 -0.785 2.260 0.0000 0.0000 0.0000
- 6ALA C 55 -1.568 -0.833 1.985 0.0000 0.0000 0.0000
- 6ALA O 56 -1.607 -0.944 1.948 0.0000 0.0000 0.0000
- 7ALA N 57 -1.639 -0.722 1.964 0.0000 0.0000 0.0000
- 7ALA H 58 -1.578 -0.647 1.995 0.0000 0.0000 0.0000
- 7ALA CA 59 -1.749 -0.701 1.872 0.0000 0.0000 0.0000
- 7ALA HA 60 -1.832 -0.753 1.921 0.0000 0.0000 0.0000
- 7ALA CB 61 -1.783 -0.553 1.866 0.0000 0.0000 0.0000
- 7ALA HB1 62 -1.694 -0.489 1.865 0.0000 0.0000 0.0000
- 7ALA HB2 63 -1.848 -0.523 1.948 0.0000 0.0000 0.0000
- 7ALA HB3 64 -1.839 -0.521 1.778 0.0000 0.0000 0.0000
- 7ALA C 65 -1.729 -0.762 1.734 0.0000 0.0000 0.0000
- 7ALA O 66 -1.806 -0.843 1.684 0.0000 0.0000 0.0000
- 8ALA N 67 -1.617 -0.729 1.669 0.0000 0.0000 0.0000
- 8ALA H 68 -1.546 -0.681 1.722 0.0000 0.0000 0.0000
- 8ALA CA 69 -1.596 -0.760 1.528 0.0000 0.0000 0.0000
- 8ALA HA 70 -1.688 -0.790 1.479 0.0000 0.0000 0.0000
- 8ALA CB 71 -1.548 -0.635 1.455 0.0000 0.0000 0.0000
- 8ALA HB1 72 -1.619 -0.554 1.470 0.0000 0.0000 0.0000
- 8ALA HB2 73 -1.541 -0.657 1.349 0.0000 0.0000 0.0000
- 8ALA HB3 74 -1.448 -0.620 1.496 0.0000 0.0000 0.0000
- 8ALA C 75 -1.510 -0.884 1.515 0.0000 0.0000 0.0000
- 8ALA O 76 -1.406 -0.888 1.449 0.0000 0.0000 0.0000
- 9ALA N 77 -1.556 -0.985 1.590 0.0000 0.0000 0.0000
- 9ALA H 78 -1.649 -0.973 1.626 0.0000 0.0000 0.0000
- 9ALA CA 79 -1.480 -1.090 1.654 0.0000 0.0000 0.0000
- 9ALA HA 80 -1.551 -1.132 1.726 0.0000 0.0000 0.0000
- 9ALA CB 81 -1.453 -1.209 1.562 0.0000 0.0000 0.0000
- 9ALA HB1 82 -1.418 -1.169 1.468 0.0000 0.0000 0.0000
- 9ALA HB2 83 -1.544 -1.267 1.548 0.0000 0.0000 0.0000
- 9ALA HB3 84 -1.369 -1.265 1.604 0.0000 0.0000 0.0000
- 9ALA C 85 -1.362 -1.042 1.738 0.0000 0.0000 0.0000
- 9ALA O 86 -1.331 -0.924 1.749 0.0000 0.0000 0.0000
- 10ALA N 87 -1.300 -1.134 1.812 0.0000 0.0000 0.0000
- 10ALA H 88 -1.321 -1.232 1.801 0.0000 0.0000 0.0000
- 10ALA CA 89 -1.224 -1.112 1.933 0.0000 0.0000 0.0000
- 10ALA HA 90 -1.294 -1.080 2.011 0.0000 0.0000 0.0000
- 10ALA CB 91 -1.161 -1.244 1.978 0.0000 0.0000 0.0000
- 10ALA HB1 92 -1.095 -1.282 1.901 0.0000 0.0000 0.0000
- 10ALA HB2 93 -1.238 -1.317 2.004 0.0000 0.0000 0.0000
- 10ALA HB3 94 -1.102 -1.228 2.068 0.0000 0.0000 0.0000
- 10ALA C 95 -1.110 -1.013 1.918 0.0000 0.0000 0.0000
- 10ALA O 96 -1.106 -0.915 1.992 0.0000 0.0000 0.0000
- 11ALA N 97 -1.012 -1.036 1.830 0.0000 0.0000 0.0000
- 11ALA H 98 -1.020 -1.126 1.786 0.0000 0.0000 0.0000
- 11ALA CA 99 -0.893 -0.955 1.821 0.0000 0.0000 0.0000
- 11ALA HA 100 -0.924 -0.851 1.829 0.0000 0.0000 0.0000
- 11ALA CB 101 -0.796 -0.988 1.933 0.0000 0.0000 0.0000
- 11ALA HB1 102 -0.840 -0.953 2.026 0.0000 0.0000 0.0000
- 11ALA HB2 103 -0.699 -0.938 1.931 0.0000 0.0000 0.0000
- 11ALA HB3 104 -0.788 -1.097 1.934 0.0000 0.0000 0.0000
- 11ALA C 105 -0.826 -0.977 1.686 0.0000 0.0000 0.0000
- 11ALA O 106 -0.857 -1.075 1.619 0.0000 0.0000 0.0000
- 12ALA N 107 -0.737 -0.882 1.654 0.0000 0.0000 0.0000
- 12ALA H 108 -0.731 -0.797 1.708 0.0000 0.0000 0.0000
- 12ALA CA 109 -0.668 -0.882 1.526 0.0000 0.0000 0.0000
- 12ALA HA 110 -0.688 -0.975 1.472 0.0000 0.0000 0.0000
- 12ALA CB 111 -0.714 -0.770 1.434 0.0000 0.0000 0.0000
- 12ALA HB1 112 -0.820 -0.778 1.408 0.0000 0.0000 0.0000
- 12ALA HB2 113 -0.661 -0.775 1.339 0.0000 0.0000 0.0000
- 12ALA HB3 114 -0.704 -0.680 1.495 0.0000 0.0000 0.0000
- 12ALA C 115 -0.518 -0.881 1.550 0.0000 0.0000 0.0000
- 12ALA O 116 -0.467 -0.820 1.644 0.0000 0.0000 0.0000
- 13ALA N 117 -0.438 -0.946 1.465 0.0000 0.0000 0.0000
- 13ALA H 118 -0.481 -0.984 1.382 0.0000 0.0000 0.0000
- 13ALA CA 119 -0.293 -0.945 1.465 0.0000 0.0000 0.0000
- 13ALA HA 120 -0.266 -0.984 1.563 0.0000 0.0000 0.0000
- 13ALA CB 121 -0.244 -1.047 1.362 0.0000 0.0000 0.0000
- 13ALA HB1 122 -0.294 -1.019 1.270 0.0000 0.0000 0.0000
- 13ALA HB2 123 -0.270 -1.149 1.389 0.0000 0.0000 0.0000
- 13ALA HB3 124 -0.135 -1.043 1.354 0.0000 0.0000 0.0000
- 13ALA C 125 -0.235 -0.809 1.430 0.0000 0.0000 0.0000
- 13ALA O 126 -0.277 -0.744 1.335 0.0000 0.0000 0.0000
- 14NME N 127 -0.141 -0.764 1.514 0.0000 0.0000 0.0000
- 14NME H 128 -0.103 -0.828 1.583 0.0000 0.0000 0.0000
- 14NME CH3 129 -0.078 -0.635 1.493 0.0000 0.0000 0.0000
- 14NME HH31 130 0.019 -0.629 1.542 0.0000 0.0000 0.0000
- 14NME HH32 131 -0.149 -0.567 1.540 0.0000 0.0000 0.0000
- 14NME HH33 132 -0.074 -0.617 1.386 0.0000 0.0000 0.0000
+ 1ACE HH31 1 0.072 -1.016 1.887
+ 1ACE CH3 2 0.034 -0.916 1.912
+ 1ACE HH32 3 0.047 -0.887 2.016
+ 1ACE HH33 4 0.076 -0.831 1.859
+ 1ACE C 5 -0.114 -0.927 1.879
+ 1ACE O 6 -0.153 -0.971 1.772
+ 2ALA N 7 -0.207 -0.887 1.966
+ 2ALA H 8 -0.174 -0.848 2.054
+ 2ALA CA 9 -0.351 -0.899 1.962
+ 2ALA HA 10 -0.386 -0.927 1.862
+ 2ALA CB 11 -0.404 -0.998 2.065
+ 2ALA HB1 12 -0.513 -0.997 2.071
+ 2ALA HB2 13 -0.369 -0.963 2.162
+ 2ALA HB3 14 -0.383 -1.102 2.041
+ 2ALA C 15 -0.415 -0.763 1.989
+ 2ALA O 16 -0.426 -0.721 2.104
+ 3ALA N 17 -0.457 -0.692 1.884
+ 3ALA H 18 -0.441 -0.729 1.791
+ 3ALA CA 19 -0.533 -0.571 1.902
+ 3ALA HA 20 -0.500 -0.510 1.986
+ 3ALA CB 21 -0.523 -0.472 1.786
+ 3ALA HB1 22 -0.419 -0.451 1.763
+ 3ALA HB2 23 -0.578 -0.381 1.811
+ 3ALA HB3 24 -0.562 -0.527 1.700
+ 3ALA C 25 -0.679 -0.610 1.923
+ 3ALA O 26 -0.738 -0.682 1.843
+ 4ALA N 27 -0.739 -0.563 2.033
+ 4ALA H 28 -0.689 -0.521 2.110
+ 4ALA CA 29 -0.876 -0.594 2.068
+ 4ALA HA 30 -0.869 -0.702 2.075
+ 4ALA CB 31 -0.904 -0.534 2.205
+ 4ALA HB1 32 -0.894 -0.425 2.200
+ 4ALA HB2 33 -0.846 -0.575 2.288
+ 4ALA HB3 34 -1.011 -0.545 2.225
+ 4ALA C 35 -0.981 -0.556 1.964
+ 4ALA O 36 -0.972 -0.449 1.905
+ 5ALA N 37 -1.079 -0.644 1.941
+ 5ALA H 38 -1.079 -0.725 2.002
+ 5ALA CA 39 -1.186 -0.610 1.850
+ 5ALA HA 40 -1.191 -0.502 1.835
+ 5ALA CB 41 -1.156 -0.666 1.712
+ 5ALA HB1 42 -1.137 -0.773 1.712
+ 5ALA HB2 43 -1.076 -0.604 1.671
+ 5ALA HB3 44 -1.242 -0.650 1.647
+ 5ALA C 45 -1.320 -0.655 1.906
+ 5ALA O 46 -1.425 -0.600 1.872
+ 6ALA N 47 -1.327 -0.762 1.986
+ 6ALA H 48 -1.235 -0.803 1.999
+ 6ALA CA 49 -1.437 -0.819 2.061
+ 6ALA HA 50 -1.394 -0.918 2.075
+ 6ALA CB 51 -1.461 -0.751 2.195
+ 6ALA HB1 52 -1.559 -0.785 2.229
+ 6ALA HB2 53 -1.479 -0.645 2.179
+ 6ALA HB3 54 -1.380 -0.785 2.260
+ 6ALA C 55 -1.568 -0.833 1.985
+ 6ALA O 56 -1.607 -0.944 1.948
+ 7ALA N 57 -1.639 -0.722 1.964
+ 7ALA H 58 -1.578 -0.647 1.995
+ 7ALA CA 59 -1.749 -0.701 1.872
+ 7ALA HA 60 -1.832 -0.753 1.921
+ 7ALA CB 61 -1.783 -0.553 1.866
+ 7ALA HB1 62 -1.694 -0.489 1.865
+ 7ALA HB2 63 -1.848 -0.523 1.948
+ 7ALA HB3 64 -1.839 -0.521 1.778
+ 7ALA C 65 -1.729 -0.762 1.734
+ 7ALA O 66 -1.806 -0.843 1.684
+ 8ALA N 67 -1.617 -0.729 1.669
+ 8ALA H 68 -1.546 -0.681 1.722
+ 8ALA CA 69 -1.596 -0.760 1.528
+ 8ALA HA 70 -1.688 -0.790 1.479
+ 8ALA CB 71 -1.548 -0.635 1.455
+ 8ALA HB1 72 -1.619 -0.554 1.470
+ 8ALA HB2 73 -1.541 -0.657 1.349
+ 8ALA HB3 74 -1.448 -0.620 1.496
+ 8ALA C 75 -1.510 -0.884 1.515
+ 8ALA O 76 -1.406 -0.888 1.449
+ 9ALA N 77 -1.556 -0.985 1.590
+ 9ALA H 78 -1.649 -0.973 1.626
+ 9ALA CA 79 -1.480 -1.090 1.654
+ 9ALA HA 80 -1.551 -1.132 1.726
+ 9ALA CB 81 -1.453 -1.209 1.562
+ 9ALA HB1 82 -1.418 -1.169 1.468
+ 9ALA HB2 83 -1.544 -1.267 1.548
+ 9ALA HB3 84 -1.369 -1.265 1.604
+ 9ALA C 85 -1.362 -1.042 1.738
+ 9ALA O 86 -1.331 -0.924 1.749
+ 10ALA N 87 -1.300 -1.134 1.812
+ 10ALA H 88 -1.321 -1.232 1.801
+ 10ALA CA 89 -1.224 -1.112 1.933
+ 10ALA HA 90 -1.294 -1.080 2.011
+ 10ALA CB 91 -1.161 -1.244 1.978
+ 10ALA HB1 92 -1.095 -1.282 1.901
+ 10ALA HB2 93 -1.238 -1.317 2.004
+ 10ALA HB3 94 -1.102 -1.228 2.068
+ 10ALA C 95 -1.110 -1.013 1.918
+ 10ALA O 96 -1.106 -0.915 1.992
+ 11ALA N 97 -1.012 -1.036 1.830
+ 11ALA H 98 -1.020 -1.126 1.786
+ 11ALA CA 99 -0.893 -0.955 1.821
+ 11ALA HA 100 -0.924 -0.851 1.829
+ 11ALA CB 101 -0.796 -0.988 1.933
+ 11ALA HB1 102 -0.840 -0.953 2.026
+ 11ALA HB2 103 -0.699 -0.938 1.931
+ 11ALA HB3 104 -0.788 -1.097 1.934
+ 11ALA C 105 -0.826 -0.977 1.686
+ 11ALA O 106 -0.857 -1.075 1.619
+ 12ALA N 107 -0.737 -0.882 1.654
+ 12ALA H 108 -0.731 -0.797 1.708
+ 12ALA CA 109 -0.668 -0.882 1.526
+ 12ALA HA 110 -0.688 -0.975 1.472
+ 12ALA CB 111 -0.714 -0.770 1.434
+ 12ALA HB1 112 -0.820 -0.778 1.408
+ 12ALA HB2 113 -0.661 -0.775 1.339
+ 12ALA HB3 114 -0.704 -0.680 1.495
+ 12ALA C 115 -0.518 -0.881 1.550
+ 12ALA O 116 -0.467 -0.820 1.644
+ 13ALA N 117 -0.438 -0.946 1.465
+ 13ALA H 118 -0.481 -0.984 1.382
+ 13ALA CA 119 -0.293 -0.945 1.465
+ 13ALA HA 120 -0.266 -0.984 1.563
+ 13ALA CB 121 -0.244 -1.047 1.362
+ 13ALA HB1 122 -0.294 -1.019 1.270
+ 13ALA HB2 123 -0.270 -1.149 1.389
+ 13ALA HB3 124 -0.135 -1.043 1.354
+ 13ALA C 125 -0.235 -0.809 1.430
+ 13ALA O 126 -0.277 -0.744 1.335
+ 14NME N 127 -0.141 -0.764 1.514
+ 14NME H 128 -0.103 -0.828 1.583
+ 14NME CH3 129 -0.078 -0.635 1.493
+ 14NME HH31 130 0.019 -0.629 1.542
+ 14NME HH32 131 -0.149 -0.567 1.540
+ 14NME HH33 132 -0.074 -0.617 1.386
100.0000000 100.0000000 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
diff --git a/regtest/basic/rt54/plumed.dat b/regtest/basic/rt54/plumed.dat
index 84814922ce5ed222946c12a772544ec3d5da2ded..9e23de5b281284a29630e3e40e00768915c41ee4 100644
--- a/regtest/basic/rt54/plumed.dat
+++ b/regtest/basic/rt54/plumed.dat
@@ -18,6 +18,10 @@ DUMPATOMS FILE=helix.ttt TYPE=gro
DUMPATOMS FILE=helix-nm.gro ATOMS=1-132 UNITS=nm
DUMPATOMS FILE=helix-nm.xyz ATOMS=1-132 UNITS=nm
+# this is to test precision
+DUMPATOMS FILE=helix-pr.gro ATOMS=1-132 PRECISION=12
+DUMPATOMS FILE=helix-pr.xyz ATOMS=1-132 PRECISION=12
+
# dump only a subset, plus a fictitious atom (without molinfo data)
c: COM ATOMS=1-6,127-132
DUMPATOMS FILE=helix-sub.xyz ATOMS=1-6,127-132,c
diff --git a/regtest/crystallization/.gitignore b/regtest/crystallization/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..1774e730ac0b0f39a477383ecc38e28eec46c933
--- /dev/null
+++ b/regtest/crystallization/.gitignore
@@ -0,0 +1,2 @@
+tmp
+report.txt
diff --git a/regtest/crystallization/Makefile b/regtest/crystallization/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..42480767ae852294cf2d7269ac5a1c16064d1849
--- /dev/null
+++ b/regtest/crystallization/Makefile
@@ -0,0 +1,2 @@
+include ../scripts/module.make
+
diff --git a/regtest/crystallization/rt-average-vec/LJ75C_global-minima.xyz b/regtest/crystallization/rt-average-vec/LJ75C_global-minima.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..7a7838540c0ffca19332460bf2432370d44f17ef
--- /dev/null
+++ b/regtest/crystallization/rt-average-vec/LJ75C_global-minima.xyz
@@ -0,0 +1,77 @@
+75
+20.0 20.0 20.0
+ Ar 2.156314665600000 0.332416216700000 0.513126025200000
+ Ar -2.156300474800000 -0.332412410700000 -0.513124876500000
+ Ar -0.702793674600000 2.171863642800000 -0.858784503500000
+ Ar 0.659045453900000 1.787780916200000 -1.522472201000000
+ Ar 0.798449910200000 -2.248251783800000 0.506226343900000
+ Ar -0.022636417900000 -2.295872820200000 -0.822727880400000
+ Ar -0.756863594600000 -1.513752823700000 1.756176946900000
+ Ar 0.051864419700000 -0.348964899200000 2.413282592900000
+ Ar 0.114224421200000 -1.090981090200000 -2.178339734900000
+ Ar -0.034338688200000 2.145430444700000 1.159468509200000
+ Ar 1.070320378200000 0.145259276700000 -2.186711386800000
+ Ar -1.177239405500000 1.247469885700000 1.733878573200000
+ Ar 0.010844723900000 -0.018042493100000 -2.438845596400000
+ Ar -1.093809429700000 1.982092729600000 0.907363491000000
+ Ar -0.117770227300000 1.410814751600000 1.985981610200000
+ Ar 1.173690836800000 -0.927676514000000 -1.926197168900000
+ Ar -1.007603949500000 -0.512322527600000 2.161176171000000
+ Ar 0.302601633400000 -1.350397093600000 2.008299558700000
+ Ar -0.261011523000000 -2.411582646900000 0.254092900100000
+ Ar 1.036829515600000 -2.132552598000000 -0.570596656300000
+ Ar 0.356676405400000 2.335191057400000 -0.606680557200000
+ Ar -0.400425624500000 1.624470895400000 -1.774581006300000
+ Ar 1.349148818900000 0.926092205800000 -1.454662633700000
+ Ar -0.564466336500000 -1.552560006200000 -1.436945362700000
+ Ar -1.378122819300000 1.696930711100000 -0.122776624400000
+ Ar 1.078388723900000 -1.457641190100000 1.227279110900000
+ Ar 0.575519981700000 0.550681434300000 2.039449397100000
+ Ar -1.545431600800000 0.223683232300000 1.534762826600000
+ Ar -1.042548187100000 -1.784615887600000 0.722556802300000
+ Ar 0.742830086900000 2.023907149300000 0.381913813000000
+ Ar 1.556488992400000 -1.225623767800000 -0.932202708400000
+ Ar -0.771799746600000 0.599152152500000 -1.959385975200000
+ Ar 1.745878547400000 0.627498670300000 -0.470657762200000
+ Ar -1.760343983900000 0.681454293600000 -0.316521837600000
+ Ar -1.354310310500000 -0.940115477200000 -0.972314742200000
+ Ar 1.849356012400000 -0.446260911400000 -0.209937642600000
+ Ar 1.610773063900000 -0.562042410600000 0.867687532800000
+ Ar -1.843837957400000 -0.053731949600000 0.510633022800000
+ Ar 1.359827429100000 0.440160015000000 1.272977638900000
+ Ar 1.443325159700000 1.175334182300000 0.445833172900000
+ Ar -1.592886743700000 -1.055916847200000 0.105328100700000
+ Ar -1.457777920800000 0.133636901400000 -1.233032111000000
+ Ar -1.076487121600000 1.148907502800000 -1.042104966700000
+ Ar 0.828272207800000 -0.453763210700000 1.634879884000000
+ Ar 1.319158943500000 -1.342662121700000 0.147803726500000
+ Ar -0.804802818000000 -1.670085100500000 -0.357641985000000
+ Ar -0.669308472100000 -0.477199145600000 -1.699732539500000
+ Ar 0.660344455700000 1.288464576900000 1.211845922900000
+ Ar 1.047478118400000 1.476333464500000 -0.536671658000000
+ Ar -1.295696717800000 -0.781217521500000 1.129462457400000
+ Ar 1.454651107900000 -0.149798804300000 -1.194276651500000
+ Ar -1.463622086600000 0.961017498400000 0.706433381100000
+ Ar 0.017818765500000 -1.612093134200000 0.969488030600000
+ Ar -0.482253277000000 0.385020251300000 1.777145426100000
+ Ar -0.315878924400000 1.850046605700000 0.128851061600000
+ Ar 0.287065951400000 0.758371962700000 -1.697510602900000
+ Ar 0.493241127600000 -1.381350362800000 -1.177970225000000
+ Ar -0.232532468700000 -0.614374457300000 1.375192981300000
+ Ar 0.255877017100000 -1.498767288700000 -0.104386431400000
+ Ar -0.014431970900000 1.305992147000000 -0.785402010600000
+ Ar -0.399611419500000 1.119060383400000 0.954295218000000
+ Ar 0.390688302700000 -0.311916192400000 -1.439703399700000
+ Ar -1.068344333300000 -0.164686987700000 -0.254226648300000
+ Ar 1.068339195400000 0.164695077000000 0.254225311900000
+ Ar -0.688853047800000 0.838281616600000 -0.062441472700000
+ Ar 0.374609000600000 1.002225786100000 0.190625601700000
+ Ar -0.388945345900000 0.295265142100000 -0.970914657300000
+ Ar -0.771620441500000 0.109542329000000 0.757460793900000
+ Ar 0.291841482800000 0.273493762700000 1.010522496000000
+ Ar 0.674512112800000 0.459200123500000 -0.717840848000000
+ Ar 0.777079029300000 -0.605146646100000 -0.459410991300000
+ Ar -0.286381855900000 -0.769080419800000 -0.712481556500000
+ Ar 0.540589242000000 -0.719920721500000 0.608779082400000
+ Ar -0.522870216900000 -0.883863029800000 0.355710852500000
+ Ar -0.000006107200000 0.000004299100000 -0.000000755700000
diff --git a/regtest/crystallization/rt-average-vec/Makefile b/regtest/crystallization/rt-average-vec/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/crystallization/rt-average-vec/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-average-vec/colvar.reference b/regtest/crystallization/rt-average-vec/colvar.reference
new file mode 100644
index 0000000000000000000000000000000000000000..f8c55b9298ce5358e0455a1b7f3e5ef3c042e77d
--- /dev/null
+++ b/regtest/crystallization/rt-average-vec/colvar.reference
@@ -0,0 +1,2 @@
+#! FIELDS time a6a
+ 0.000000 0.3079
diff --git a/regtest/crystallization/rt-average-vec/config b/regtest/crystallization/rt-average-vec/config
new file mode 100644
index 0000000000000000000000000000000000000000..2048daf60309595eadf1a6dc9d834de4e1e73784
--- /dev/null
+++ b/regtest/crystallization/rt-average-vec/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz LJ75C_global-minima.xyz"
diff --git a/regtest/crystallization/rt-average-vec/derivatives.reference b/regtest/crystallization/rt-average-vec/derivatives.reference
new file mode 100644
index 0000000000000000000000000000000000000000..d20a6882e1e954bf8a9c1fc479eaa109df78afa7
--- /dev/null
+++ b/regtest/crystallization/rt-average-vec/derivatives.reference
@@ -0,0 +1,235 @@
+#! FIELDS time parameter a6a
+ 0.000000 0 -0.0122
+ 0.000000 1 -0.0019
+ 0.000000 2 -0.0029
+ 0.000000 3 0.0122
+ 0.000000 4 0.0019
+ 0.000000 5 0.0029
+ 0.000000 6 -0.0006
+ 0.000000 7 0.0021
+ 0.000000 8 -0.0015
+ 0.000000 9 0.0006
+ 0.000000 10 0.0023
+ 0.000000 11 -0.0012
+ 0.000000 12 0.0011
+ 0.000000 13 -0.0024
+ 0.000000 14 -0.0001
+ 0.000000 15 -0.0002
+ 0.000000 16 -0.0026
+ 0.000000 17 -0.0003
+ 0.000000 18 -0.0010
+ 0.000000 19 -0.0011
+ 0.000000 20 0.0022
+ 0.000000 21 0.0002
+ 0.000000 22 -0.0010
+ 0.000000 23 0.0025
+ 0.000000 24 0.0000
+ 0.000000 25 -0.0006
+ 0.000000 26 -0.0026
+ 0.000000 27 -0.0001
+ 0.000000 28 0.0020
+ 0.000000 29 0.0018
+ 0.000000 30 0.0013
+ 0.000000 31 -0.0005
+ 0.000000 32 -0.0023
+ 0.000000 33 -0.0013
+ 0.000000 34 0.0018
+ 0.000000 35 0.0014
+ 0.000000 36 0.0001
+ 0.000000 37 -0.0007
+ 0.000000 38 -0.0026
+ 0.000000 39 -0.0013
+ 0.000000 40 0.0018
+ 0.000000 41 0.0015
+ 0.000000 42 -0.0001
+ 0.000000 43 0.0020
+ 0.000000 44 0.0017
+ 0.000000 45 0.0013
+ 0.000000 46 -0.0004
+ 0.000000 47 -0.0023
+ 0.000000 48 -0.0010
+ 0.000000 49 -0.0012
+ 0.000000 50 0.0022
+ 0.000000 51 0.0002
+ 0.000000 52 -0.0009
+ 0.000000 53 0.0025
+ 0.000000 54 -0.0002
+ 0.000000 55 -0.0026
+ 0.000000 56 -0.0004
+ 0.000000 57 0.0010
+ 0.000000 58 -0.0025
+ 0.000000 59 0.0000
+ 0.000000 60 0.0006
+ 0.000000 61 0.0023
+ 0.000000 62 -0.0012
+ 0.000000 63 -0.0007
+ 0.000000 64 0.0021
+ 0.000000 65 -0.0014
+ 0.000000 66 -0.0023
+ 0.000000 67 -0.0001
+ 0.000000 68 -0.0011
+ 0.000000 69 0.0026
+ 0.000000 70 -0.0001
+ 0.000000 71 0.0002
+ 0.000000 72 0.0023
+ 0.000000 73 0.0010
+ 0.000000 74 0.0006
+ 0.000000 75 -0.0024
+ 0.000000 76 -0.0009
+ 0.000000 77 -0.0003
+ 0.000000 78 -0.0026
+ 0.000000 79 -0.0002
+ 0.000000 80 -0.0000
+ 0.000000 81 0.0023
+ 0.000000 82 0.0005
+ 0.000000 83 0.0011
+ 0.000000 84 0.0024
+ 0.000000 85 -0.0001
+ 0.000000 86 0.0009
+ 0.000000 87 -0.0025
+ 0.000000 88 0.0002
+ 0.000000 89 -0.0005
+ 0.000000 90 -0.0023
+ 0.000000 91 -0.0008
+ 0.000000 92 -0.0010
+ 0.000000 93 0.0025
+ 0.000000 94 0.0006
+ 0.000000 95 0.0000
+ 0.000000 96 -0.0037
+ 0.000000 97 -0.0005
+ 0.000000 98 -0.0011
+ 0.000000 99 0.0037
+ 0.000000 100 0.0008
+ 0.000000 101 0.0009
+ 0.000000 102 0.0038
+ 0.000000 103 0.0004
+ 0.000000 104 0.0008
+ 0.000000 105 -0.0037
+ 0.000000 106 -0.0007
+ 0.000000 107 -0.0010
+ 0.000000 108 -0.0038
+ 0.000000 109 -0.0008
+ 0.000000 110 -0.0008
+ 0.000000 111 0.0037
+ 0.000000 112 0.0006
+ 0.000000 113 0.0011
+ 0.000000 114 -0.0038
+ 0.000000 115 -0.0005
+ 0.000000 116 -0.0007
+ 0.000000 117 -0.0038
+ 0.000000 118 -0.0004
+ 0.000000 119 -0.0009
+ 0.000000 120 0.0038
+ 0.000000 121 0.0004
+ 0.000000 122 0.0010
+ 0.000000 123 0.0038
+ 0.000000 124 0.0007
+ 0.000000 125 0.0007
+ 0.000000 126 0.0018
+ 0.000000 127 0.0010
+ 0.000000 128 0.0000
+ 0.000000 129 -0.0019
+ 0.000000 130 -0.0006
+ 0.000000 131 0.0003
+ 0.000000 132 -0.0016
+ 0.000000 133 -0.0011
+ 0.000000 134 -0.0005
+ 0.000000 135 0.0019
+ 0.000000 136 -0.0005
+ 0.000000 137 0.0004
+ 0.000000 138 0.0020
+ 0.000000 139 0.0001
+ 0.000000 140 -0.0004
+ 0.000000 141 -0.0020
+ 0.000000 142 0.0003
+ 0.000000 143 0.0001
+ 0.000000 144 -0.0018
+ 0.000000 145 0.0004
+ 0.000000 146 -0.0008
+ 0.000000 147 0.0016
+ 0.000000 148 -0.0001
+ 0.000000 149 0.0012
+ 0.000000 150 -0.0016
+ 0.000000 151 -0.0004
+ 0.000000 152 -0.0012
+ 0.000000 153 0.0016
+ 0.000000 154 0.0009
+ 0.000000 155 0.0009
+ 0.000000 156 0.0000
+ 0.000000 157 -0.0013
+ 0.000000 158 0.0008
+ 0.000000 159 -0.0004
+ 0.000000 160 0.0003
+ 0.000000 161 0.0015
+ 0.000000 162 -0.0003
+ 0.000000 163 0.0015
+ 0.000000 164 0.0001
+ 0.000000 165 0.0002
+ 0.000000 166 0.0006
+ 0.000000 167 -0.0014
+ 0.000000 168 0.0004
+ 0.000000 169 -0.0012
+ 0.000000 170 -0.0010
+ 0.000000 171 -0.0001
+ 0.000000 172 -0.0002
+ 0.000000 173 0.0004
+ 0.000000 174 0.0001
+ 0.000000 175 -0.0005
+ 0.000000 176 -0.0000
+ 0.000000 177 -0.0000
+ 0.000000 178 0.0004
+ 0.000000 179 -0.0002
+ 0.000000 180 -0.0001
+ 0.000000 181 0.0003
+ 0.000000 182 0.0003
+ 0.000000 183 0.0001
+ 0.000000 184 -0.0001
+ 0.000000 185 -0.0004
+ 0.000000 186 -0.0005
+ 0.000000 187 -0.0001
+ 0.000000 188 -0.0001
+ 0.000000 189 0.0005
+ 0.000000 190 0.0001
+ 0.000000 191 0.0001
+ 0.000000 192 -0.0002
+ 0.000000 193 -0.0003
+ 0.000000 194 -0.0001
+ 0.000000 195 0.0003
+ 0.000000 196 -0.0003
+ 0.000000 197 0.0000
+ 0.000000 198 -0.0002
+ 0.000000 199 -0.0002
+ 0.000000 200 0.0002
+ 0.000000 201 -0.0001
+ 0.000000 202 -0.0001
+ 0.000000 203 -0.0003
+ 0.000000 204 0.0003
+ 0.000000 205 -0.0000
+ 0.000000 206 -0.0002
+ 0.000000 207 0.0002
+ 0.000000 208 -0.0001
+ 0.000000 209 0.0003
+ 0.000000 210 0.0001
+ 0.000000 211 0.0003
+ 0.000000 212 0.0002
+ 0.000000 213 -0.0003
+ 0.000000 214 0.0002
+ 0.000000 215 0.0001
+ 0.000000 216 0.0002
+ 0.000000 217 0.0003
+ 0.000000 218 -0.0001
+ 0.000000 219 -0.0002
+ 0.000000 220 0.0002
+ 0.000000 221 -0.0002
+ 0.000000 222 0.0000
+ 0.000000 223 0.0000
+ 0.000000 224 0.0000
+ 0.000000 225 0.1428
+ 0.000000 226 0.0344
+ 0.000000 227 0.0531
+ 0.000000 228 0.0344
+ 0.000000 229 -0.0751
+ 0.000000 230 0.0082
+ 0.000000 231 0.0531
+ 0.000000 232 0.0082
+ 0.000000 233 -0.0678
diff --git a/regtest/crystallization/rt-average-vec/plumed.dat b/regtest/crystallization/rt-average-vec/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..20f3aca06846dfacacb7b5d952e3bd877ae4f80a
--- /dev/null
+++ b/regtest/crystallization/rt-average-vec/plumed.dat
@@ -0,0 +1,5 @@
+Q6 SPECIES=1-75 SWITCH={GAUSSIAN D_0=1.391 R_0=0.01} LABEL=q6
+AVERAGE_VECTOR ARG=q6 LABEL=a6a
+
+PRINT ARG=a6a FILE=colvar FMT=%8.4f
+DUMPDERIVATIVES ARG=a6a FILE=derivatives FMT=%8.4f
diff --git a/regtest/crystallization/rt-averaged-q6-lowmem/64.xyz b/regtest/crystallization/rt-averaged-q6-lowmem/64.xyz
new file mode 100755
index 0000000000000000000000000000000000000000..90b3ae19c7598dd32c498e7105925df054c3e788
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6-lowmem/64.xyz
@@ -0,0 +1,66 @@
+ 64
+12.41642 12.41642 12.41642
+ Ge 1.473000000000 2.211000000000 8.700200000000
+ Ge 4.886500000000 3.830000000000 6.593500000000
+ Ge 3.807000000000 1.978700000000 10.045000000000
+ Ge 5.002000000000 3.883500000000 1.357000000000
+ Ge 9.636000000000 1.604000000000 8.697700000000
+ Ge 6.559800000000 11.084000000000 9.650400000000
+ Ge 0.627000000000 0.390000000000 2.224300000000
+ Ge 3.341900000000 6.765300000000 1.369500000000
+ Ge 5.032000000000 9.650500000000 2.785000000000
+ Ge 1.682700000000 10.392700000000 5.459500000000
+ Ge 3.517300000000 12.039000000000 5.930600000000
+ Ge 1.072000000000 5.374900000000 12.335000000000
+ Ge 0.863390000000 11.308000000000 0.275000000000
+ Ge 5.867800000000 0.672000000000 6.605200000000
+ Ge 3.961000000000 8.414000000000 8.691600000000
+ Ge 11.570960000000 10.444000000000 2.125000000000
+ Ge 1.736000000000 6.845200000000 6.129000000000
+ Ge 7.557300000000 8.842800000000 6.611800000000
+ Ge 2.785800000000 2.591200000000 1.833300000000
+ Ge 11.564000000000 11.555000000000 10.928000000000
+ Ge 3.324000000000 11.334000000000 12.095000000000
+ Ge 10.532000000000 9.377700000000 6.724000000000
+ Ge 7.157000000000 11.468000000000 12.063000000000
+ Ge 0.027000000000 4.622000000000 5.996200000000
+ Ge 4.564000000000 6.513200000000 5.370200000000
+ Ge 12.189770000000 7.981000000000 2.257000000000
+ Ge 8.973100000000 0.437000000000 4.852800000000
+ Ge 9.086200000000 9.857000000000 0.975000000000
+ Ge 6.516500000000 12.170000000000 2.438600000000
+ Ge 8.955900000000 4.612000000000 4.478000000000
+ Ge 7.419000000000 3.301600000000 0.450000000000
+ Ge 10.808000000000 7.170600000000 11.109000000000
+ Te 4.818200000000 9.096200000000 6.189300000000
+ Te 10.663400000000 6.726900000000 5.343000000000
+ Te 7.021700000000 4.814600000000 10.649000000000
+ Te 3.253500000000 5.713300000000 8.267800000000
+ Te 10.322000000000 1.250000000000 2.209500000000
+ Te 0.300000000000 5.033000000000 8.902400000000
+ Te 12.092000000000 0.227000000000 8.527200000000
+ Te 6.329000000000 2.634100000000 8.525500000000
+ Te 8.044800000000 11.712000000000 7.575400000000
+ Te 2.150000000000 8.302000000000 3.591400000000
+ Te 11.581000000000 11.201000000000 4.824700000000
+ Te 3.960900000000 4.755000000000 11.528710000000
+ Te 3.815300000000 12.139000000000 3.263700000000
+ Te 9.419700000000 7.232700000000 1.010000000000
+ Te 1.211700000000 1.726300000000 12.223470000000
+ Te 0.798460000000 8.988100000000 7.517700000000
+ Te 10.078000000000 9.503000000000 9.977500000000
+ Te 9.336700000000 0.894000000000 11.469560000000
+ Te 7.251000000000 5.783400000000 6.399000000000
+ Te 3.740000000000 11.515000000000 9.383700000000
+ Te 10.329000000000 2.726600000000 5.835100000000
+ Te 6.722900000000 8.386100000000 9.226500000000
+ Te 1.247000000000 4.660000000000 2.609100000000
+ Te 5.628500000000 6.170200000000 2.845000000000
+ Te 4.742900000000 9.191800000000 0.212000000000
+ Te 5.134400000000 0.984830000000 12.244000000000
+ Te 8.033800000000 10.061100000000 3.578600000000
+ Te 9.840000000000 4.825000000000 9.743000000000
+ Te 6.760000000000 2.189000000000 4.410700000000
+ Te 2.334000000000 2.201000000000 6.079000000000
+ Te 9.930600000000 3.982900000000 1.562000000000
+ Te 0.806810000000 8.091100000000 12.264000000000
diff --git a/regtest/crystallization/rt-averaged-q6-lowmem/Makefile b/regtest/crystallization/rt-averaged-q6-lowmem/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6-lowmem/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-averaged-q6-lowmem/colv.reference b/regtest/crystallization/rt-averaged-q6-lowmem/colv.reference
new file mode 100644
index 0000000000000000000000000000000000000000..8d69c80ee2192c76108352c9c7255dee723a579b
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6-lowmem/colv.reference
@@ -0,0 +1,2 @@
+#! FIELDS time q6.mean
+ 0.000000 0.245096
diff --git a/regtest/crystallization/rt-averaged-q6-lowmem/colv3.reference b/regtest/crystallization/rt-averaged-q6-lowmem/colv3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..bb98831d129bc94a645980f032244eb7a5b1982e
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6-lowmem/colv3.reference
@@ -0,0 +1,2 @@
+#! FIELDS time w6.mean
+ 0.000000 0.065847
diff --git a/regtest/crystallization/rt-averaged-q6-lowmem/config b/regtest/crystallization/rt-averaged-q6-lowmem/config
new file mode 100644
index 0000000000000000000000000000000000000000..e07432072a91405171ff68d3c3d22a09fde3346c
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6-lowmem/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz 64.xyz"
diff --git a/regtest/crystallization/rt-averaged-q6-lowmem/deriv3.reference b/regtest/crystallization/rt-averaged-q6-lowmem/deriv3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..a4db1306390ea48453f5fd99e61681cce3b7da31
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6-lowmem/deriv3.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter w6.mean
+ 0.000000 0 0.0018
+ 0.000000 1 0.0008
+ 0.000000 2 -0.0002
+ 0.000000 3 -0.0006
+ 0.000000 4 -0.0002
+ 0.000000 5 -0.0068
+ 0.000000 6 0.0016
+ 0.000000 7 0.0024
+ 0.000000 8 -0.0052
+ 0.000000 9 -0.0011
+ 0.000000 10 -0.0004
+ 0.000000 11 0.0032
+ 0.000000 12 0.0009
+ 0.000000 13 0.0012
+ 0.000000 14 -0.0001
+ 0.000000 15 -0.0013
+ 0.000000 16 -0.0039
+ 0.000000 17 -0.0010
+ 0.000000 18 -0.0018
+ 0.000000 19 0.0008
+ 0.000000 20 0.0005
+ 0.000000 21 -0.0016
+ 0.000000 22 -0.0004
+ 0.000000 23 -0.0013
+ 0.000000 24 0.0041
+ 0.000000 25 -0.0011
+ 0.000000 26 -0.0032
+ 0.000000 27 -0.0009
+ 0.000000 28 -0.0018
+ 0.000000 29 0.0040
+ 0.000000 30 -0.0014
+ 0.000000 31 0.0030
+ 0.000000 32 0.0020
+ 0.000000 33 0.0010
+ 0.000000 34 -0.0015
+ 0.000000 35 0.0025
+ 0.000000 36 0.0000
+ 0.000000 37 0.0010
+ 0.000000 38 -0.0022
+ 0.000000 39 -0.0003
+ 0.000000 40 0.0014
+ 0.000000 41 -0.0002
+ 0.000000 42 0.0003
+ 0.000000 43 -0.0000
+ 0.000000 44 0.0001
+ 0.000000 45 -0.0000
+ 0.000000 46 -0.0014
+ 0.000000 47 -0.0006
+ 0.000000 48 -0.0012
+ 0.000000 49 0.0000
+ 0.000000 50 -0.0018
+ 0.000000 51 -0.0005
+ 0.000000 52 0.0005
+ 0.000000 53 0.0001
+ 0.000000 54 -0.0012
+ 0.000000 55 0.0039
+ 0.000000 56 0.0024
+ 0.000000 57 -0.0011
+ 0.000000 58 -0.0029
+ 0.000000 59 -0.0025
+ 0.000000 60 0.0002
+ 0.000000 61 -0.0043
+ 0.000000 62 -0.0021
+ 0.000000 63 -0.0045
+ 0.000000 64 0.0030
+ 0.000000 65 0.0025
+ 0.000000 66 -0.0003
+ 0.000000 67 -0.0016
+ 0.000000 68 0.0003
+ 0.000000 69 0.0008
+ 0.000000 70 -0.0019
+ 0.000000 71 -0.0008
+ 0.000000 72 0.0011
+ 0.000000 73 0.0022
+ 0.000000 74 0.0026
+ 0.000000 75 -0.0006
+ 0.000000 76 -0.0032
+ 0.000000 77 -0.0009
+ 0.000000 78 0.0016
+ 0.000000 79 -0.0015
+ 0.000000 80 0.0008
+ 0.000000 81 -0.0002
+ 0.000000 82 -0.0003
+ 0.000000 83 -0.0006
+ 0.000000 84 0.0038
+ 0.000000 85 0.0018
+ 0.000000 86 -0.0012
+ 0.000000 87 -0.0006
+ 0.000000 88 -0.0017
+ 0.000000 89 0.0053
+ 0.000000 90 0.0004
+ 0.000000 91 0.0027
+ 0.000000 92 0.0013
+ 0.000000 93 0.0044
+ 0.000000 94 0.0031
+ 0.000000 95 -0.0037
+ 0.000000 96 0.0011
+ 0.000000 97 -0.0000
+ 0.000000 98 0.0011
+ 0.000000 99 -0.0003
+ 0.000000 100 0.0007
+ 0.000000 101 -0.0025
+ 0.000000 102 -0.0018
+ 0.000000 103 -0.0017
+ 0.000000 104 -0.0015
+ 0.000000 105 0.0034
+ 0.000000 106 -0.0002
+ 0.000000 107 0.0025
+ 0.000000 108 0.0017
+ 0.000000 109 0.0046
+ 0.000000 110 0.0002
+ 0.000000 111 0.0014
+ 0.000000 112 0.0005
+ 0.000000 113 -0.0020
+ 0.000000 114 0.0051
+ 0.000000 115 0.0000
+ 0.000000 116 -0.0030
+ 0.000000 117 0.0030
+ 0.000000 118 -0.0012
+ 0.000000 119 0.0041
+ 0.000000 120 -0.0030
+ 0.000000 121 -0.0009
+ 0.000000 122 0.0019
+ 0.000000 123 0.0034
+ 0.000000 124 -0.0002
+ 0.000000 125 -0.0045
+ 0.000000 126 0.0011
+ 0.000000 127 -0.0012
+ 0.000000 128 0.0004
+ 0.000000 129 0.0021
+ 0.000000 130 -0.0040
+ 0.000000 131 -0.0011
+ 0.000000 132 -0.0010
+ 0.000000 133 -0.0012
+ 0.000000 134 -0.0025
+ 0.000000 135 -0.0004
+ 0.000000 136 -0.0017
+ 0.000000 137 0.0011
+ 0.000000 138 0.0039
+ 0.000000 139 -0.0019
+ 0.000000 140 -0.0017
+ 0.000000 141 -0.0004
+ 0.000000 142 0.0017
+ 0.000000 143 0.0045
+ 0.000000 144 0.0005
+ 0.000000 145 0.0003
+ 0.000000 146 0.0001
+ 0.000000 147 -0.0043
+ 0.000000 148 0.0001
+ 0.000000 149 -0.0005
+ 0.000000 150 -0.0012
+ 0.000000 151 0.0029
+ 0.000000 152 0.0046
+ 0.000000 153 -0.0024
+ 0.000000 154 0.0018
+ 0.000000 155 -0.0015
+ 0.000000 156 0.0025
+ 0.000000 157 0.0005
+ 0.000000 158 -0.0039
+ 0.000000 159 -0.0007
+ 0.000000 160 -0.0028
+ 0.000000 161 -0.0002
+ 0.000000 162 -0.0054
+ 0.000000 163 -0.0020
+ 0.000000 164 0.0052
+ 0.000000 165 0.0020
+ 0.000000 166 -0.0019
+ 0.000000 167 0.0049
+ 0.000000 168 -0.0006
+ 0.000000 169 0.0044
+ 0.000000 170 0.0033
+ 0.000000 171 0.0004
+ 0.000000 172 0.0019
+ 0.000000 173 -0.0009
+ 0.000000 174 0.0006
+ 0.000000 175 -0.0041
+ 0.000000 176 0.0042
+ 0.000000 177 -0.0045
+ 0.000000 178 0.0009
+ 0.000000 179 0.0022
+ 0.000000 180 -0.0009
+ 0.000000 181 0.0016
+ 0.000000 182 -0.0062
+ 0.000000 183 -0.0018
+ 0.000000 184 -0.0019
+ 0.000000 185 -0.0013
+ 0.000000 186 -0.0031
+ 0.000000 187 0.0001
+ 0.000000 188 0.0002
+ 0.000000 189 -0.0034
+ 0.000000 190 0.0051
+ 0.000000 191 -0.0007
+ 0.000000 192 -0.0552
+ 0.000000 193 -0.0319
+ 0.000000 194 -0.0141
+ 0.000000 195 -0.0319
+ 0.000000 196 -0.0972
+ 0.000000 197 0.0628
+ 0.000000 198 -0.0141
+ 0.000000 199 0.0628
+ 0.000000 200 -0.0608
diff --git a/regtest/crystallization/rt-averaged-q6-lowmem/plumed.dat b/regtest/crystallization/rt-averaged-q6-lowmem/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..d4e57b0e2329aaf37d4f191430822ebd172aa3b1
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6-lowmem/plumed.dat
@@ -0,0 +1,7 @@
+Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN LABEL=q6
+PRINT ARG=q6.* FILE=colv
+
+LOCAL_AVERAGE ARG=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LOWMEM LABEL=w6
+PRINT ARG=w6.* FILE=colv3
+DUMPDERIVATIVES ARG=w6.* FILE=deriv3 FMT=%8.4f
+
diff --git a/regtest/crystallization/rt-averaged-q6/64.xyz b/regtest/crystallization/rt-averaged-q6/64.xyz
new file mode 100755
index 0000000000000000000000000000000000000000..90b3ae19c7598dd32c498e7105925df054c3e788
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6/64.xyz
@@ -0,0 +1,66 @@
+ 64
+12.41642 12.41642 12.41642
+ Ge 1.473000000000 2.211000000000 8.700200000000
+ Ge 4.886500000000 3.830000000000 6.593500000000
+ Ge 3.807000000000 1.978700000000 10.045000000000
+ Ge 5.002000000000 3.883500000000 1.357000000000
+ Ge 9.636000000000 1.604000000000 8.697700000000
+ Ge 6.559800000000 11.084000000000 9.650400000000
+ Ge 0.627000000000 0.390000000000 2.224300000000
+ Ge 3.341900000000 6.765300000000 1.369500000000
+ Ge 5.032000000000 9.650500000000 2.785000000000
+ Ge 1.682700000000 10.392700000000 5.459500000000
+ Ge 3.517300000000 12.039000000000 5.930600000000
+ Ge 1.072000000000 5.374900000000 12.335000000000
+ Ge 0.863390000000 11.308000000000 0.275000000000
+ Ge 5.867800000000 0.672000000000 6.605200000000
+ Ge 3.961000000000 8.414000000000 8.691600000000
+ Ge 11.570960000000 10.444000000000 2.125000000000
+ Ge 1.736000000000 6.845200000000 6.129000000000
+ Ge 7.557300000000 8.842800000000 6.611800000000
+ Ge 2.785800000000 2.591200000000 1.833300000000
+ Ge 11.564000000000 11.555000000000 10.928000000000
+ Ge 3.324000000000 11.334000000000 12.095000000000
+ Ge 10.532000000000 9.377700000000 6.724000000000
+ Ge 7.157000000000 11.468000000000 12.063000000000
+ Ge 0.027000000000 4.622000000000 5.996200000000
+ Ge 4.564000000000 6.513200000000 5.370200000000
+ Ge 12.189770000000 7.981000000000 2.257000000000
+ Ge 8.973100000000 0.437000000000 4.852800000000
+ Ge 9.086200000000 9.857000000000 0.975000000000
+ Ge 6.516500000000 12.170000000000 2.438600000000
+ Ge 8.955900000000 4.612000000000 4.478000000000
+ Ge 7.419000000000 3.301600000000 0.450000000000
+ Ge 10.808000000000 7.170600000000 11.109000000000
+ Te 4.818200000000 9.096200000000 6.189300000000
+ Te 10.663400000000 6.726900000000 5.343000000000
+ Te 7.021700000000 4.814600000000 10.649000000000
+ Te 3.253500000000 5.713300000000 8.267800000000
+ Te 10.322000000000 1.250000000000 2.209500000000
+ Te 0.300000000000 5.033000000000 8.902400000000
+ Te 12.092000000000 0.227000000000 8.527200000000
+ Te 6.329000000000 2.634100000000 8.525500000000
+ Te 8.044800000000 11.712000000000 7.575400000000
+ Te 2.150000000000 8.302000000000 3.591400000000
+ Te 11.581000000000 11.201000000000 4.824700000000
+ Te 3.960900000000 4.755000000000 11.528710000000
+ Te 3.815300000000 12.139000000000 3.263700000000
+ Te 9.419700000000 7.232700000000 1.010000000000
+ Te 1.211700000000 1.726300000000 12.223470000000
+ Te 0.798460000000 8.988100000000 7.517700000000
+ Te 10.078000000000 9.503000000000 9.977500000000
+ Te 9.336700000000 0.894000000000 11.469560000000
+ Te 7.251000000000 5.783400000000 6.399000000000
+ Te 3.740000000000 11.515000000000 9.383700000000
+ Te 10.329000000000 2.726600000000 5.835100000000
+ Te 6.722900000000 8.386100000000 9.226500000000
+ Te 1.247000000000 4.660000000000 2.609100000000
+ Te 5.628500000000 6.170200000000 2.845000000000
+ Te 4.742900000000 9.191800000000 0.212000000000
+ Te 5.134400000000 0.984830000000 12.244000000000
+ Te 8.033800000000 10.061100000000 3.578600000000
+ Te 9.840000000000 4.825000000000 9.743000000000
+ Te 6.760000000000 2.189000000000 4.410700000000
+ Te 2.334000000000 2.201000000000 6.079000000000
+ Te 9.930600000000 3.982900000000 1.562000000000
+ Te 0.806810000000 8.091100000000 12.264000000000
diff --git a/regtest/crystallization/rt-averaged-q6/Makefile b/regtest/crystallization/rt-averaged-q6/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-averaged-q6/colv.reference b/regtest/crystallization/rt-averaged-q6/colv.reference
new file mode 100644
index 0000000000000000000000000000000000000000..8d69c80ee2192c76108352c9c7255dee723a579b
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6/colv.reference
@@ -0,0 +1,2 @@
+#! FIELDS time q6.mean
+ 0.000000 0.245096
diff --git a/regtest/crystallization/rt-averaged-q6/colv3.reference b/regtest/crystallization/rt-averaged-q6/colv3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..bb98831d129bc94a645980f032244eb7a5b1982e
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6/colv3.reference
@@ -0,0 +1,2 @@
+#! FIELDS time w6.mean
+ 0.000000 0.065847
diff --git a/regtest/crystallization/rt-averaged-q6/config b/regtest/crystallization/rt-averaged-q6/config
new file mode 100644
index 0000000000000000000000000000000000000000..e07432072a91405171ff68d3c3d22a09fde3346c
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz 64.xyz"
diff --git a/regtest/crystallization/rt-averaged-q6/deriv.reference b/regtest/crystallization/rt-averaged-q6/deriv.reference
new file mode 100644
index 0000000000000000000000000000000000000000..a7c522e7376756146f4ece8e74bc7b27bf920713
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6/deriv.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter q6.mean
+ 0.000000 0 0.0012
+ 0.000000 1 0.0016
+ 0.000000 2 -0.0017
+ 0.000000 3 -0.0003
+ 0.000000 4 0.0017
+ 0.000000 5 -0.0031
+ 0.000000 6 -0.0013
+ 0.000000 7 -0.0015
+ 0.000000 8 -0.0023
+ 0.000000 9 0.0000
+ 0.000000 10 0.0022
+ 0.000000 11 0.0030
+ 0.000000 12 -0.0009
+ 0.000000 13 -0.0010
+ 0.000000 14 -0.0002
+ 0.000000 15 -0.0018
+ 0.000000 16 -0.0026
+ 0.000000 17 -0.0006
+ 0.000000 18 0.0009
+ 0.000000 19 -0.0008
+ 0.000000 20 0.0013
+ 0.000000 21 -0.0024
+ 0.000000 22 0.0041
+ 0.000000 23 -0.0008
+ 0.000000 24 0.0026
+ 0.000000 25 -0.0023
+ 0.000000 26 -0.0015
+ 0.000000 27 -0.0021
+ 0.000000 28 0.0029
+ 0.000000 29 0.0037
+ 0.000000 30 -0.0017
+ 0.000000 31 -0.0015
+ 0.000000 32 0.0018
+ 0.000000 33 -0.0027
+ 0.000000 34 -0.0000
+ 0.000000 35 0.0003
+ 0.000000 36 0.0006
+ 0.000000 37 -0.0016
+ 0.000000 38 0.0004
+ 0.000000 39 -0.0020
+ 0.000000 40 0.0019
+ 0.000000 41 -0.0005
+ 0.000000 42 0.0016
+ 0.000000 43 -0.0053
+ 0.000000 44 0.0001
+ 0.000000 45 -0.0031
+ 0.000000 46 -0.0020
+ 0.000000 47 -0.0020
+ 0.000000 48 -0.0014
+ 0.000000 49 0.0010
+ 0.000000 50 -0.0059
+ 0.000000 51 0.0021
+ 0.000000 52 -0.0023
+ 0.000000 53 0.0027
+ 0.000000 54 0.0011
+ 0.000000 55 0.0006
+ 0.000000 56 -0.0010
+ 0.000000 57 -0.0005
+ 0.000000 58 -0.0017
+ 0.000000 59 -0.0010
+ 0.000000 60 -0.0001
+ 0.000000 61 0.0010
+ 0.000000 62 0.0016
+ 0.000000 63 0.0017
+ 0.000000 64 0.0000
+ 0.000000 65 -0.0029
+ 0.000000 66 0.0003
+ 0.000000 67 0.0033
+ 0.000000 68 -0.0041
+ 0.000000 69 -0.0007
+ 0.000000 70 0.0014
+ 0.000000 71 -0.0004
+ 0.000000 72 0.0029
+ 0.000000 73 0.0013
+ 0.000000 74 -0.0008
+ 0.000000 75 0.0017
+ 0.000000 76 -0.0046
+ 0.000000 77 -0.0000
+ 0.000000 78 0.0009
+ 0.000000 79 -0.0008
+ 0.000000 80 0.0009
+ 0.000000 81 -0.0001
+ 0.000000 82 -0.0002
+ 0.000000 83 -0.0006
+ 0.000000 84 0.0009
+ 0.000000 85 -0.0012
+ 0.000000 86 0.0001
+ 0.000000 87 0.0015
+ 0.000000 88 0.0018
+ 0.000000 89 -0.0039
+ 0.000000 90 0.0008
+ 0.000000 91 0.0005
+ 0.000000 92 0.0029
+ 0.000000 93 0.0025
+ 0.000000 94 0.0016
+ 0.000000 95 0.0016
+ 0.000000 96 -0.0017
+ 0.000000 97 -0.0001
+ 0.000000 98 0.0022
+ 0.000000 99 -0.0024
+ 0.000000 100 0.0009
+ 0.000000 101 0.0004
+ 0.000000 102 -0.0017
+ 0.000000 103 -0.0014
+ 0.000000 104 0.0004
+ 0.000000 105 0.0002
+ 0.000000 106 -0.0033
+ 0.000000 107 -0.0020
+ 0.000000 108 -0.0001
+ 0.000000 109 0.0039
+ 0.000000 110 0.0014
+ 0.000000 111 -0.0004
+ 0.000000 112 0.0018
+ 0.000000 113 -0.0021
+ 0.000000 114 0.0037
+ 0.000000 115 -0.0004
+ 0.000000 116 0.0011
+ 0.000000 117 0.0042
+ 0.000000 118 -0.0016
+ 0.000000 119 -0.0004
+ 0.000000 120 0.0011
+ 0.000000 121 -0.0003
+ 0.000000 122 0.0016
+ 0.000000 123 0.0018
+ 0.000000 124 0.0034
+ 0.000000 125 0.0002
+ 0.000000 126 0.0009
+ 0.000000 127 0.0013
+ 0.000000 128 0.0007
+ 0.000000 129 0.0010
+ 0.000000 130 -0.0032
+ 0.000000 131 0.0021
+ 0.000000 132 -0.0027
+ 0.000000 133 -0.0000
+ 0.000000 134 0.0009
+ 0.000000 135 -0.0045
+ 0.000000 136 -0.0014
+ 0.000000 137 -0.0014
+ 0.000000 138 0.0004
+ 0.000000 139 -0.0003
+ 0.000000 140 -0.0025
+ 0.000000 141 0.0032
+ 0.000000 142 0.0037
+ 0.000000 143 0.0005
+ 0.000000 144 -0.0003
+ 0.000000 145 0.0047
+ 0.000000 146 -0.0015
+ 0.000000 147 -0.0011
+ 0.000000 148 0.0004
+ 0.000000 149 -0.0015
+ 0.000000 150 -0.0006
+ 0.000000 151 -0.0028
+ 0.000000 152 0.0036
+ 0.000000 153 -0.0040
+ 0.000000 154 -0.0003
+ 0.000000 155 -0.0031
+ 0.000000 156 0.0021
+ 0.000000 157 -0.0002
+ 0.000000 158 0.0002
+ 0.000000 159 0.0016
+ 0.000000 160 0.0010
+ 0.000000 161 0.0036
+ 0.000000 162 -0.0004
+ 0.000000 163 -0.0028
+ 0.000000 164 0.0055
+ 0.000000 165 0.0014
+ 0.000000 166 -0.0034
+ 0.000000 167 0.0023
+ 0.000000 168 -0.0002
+ 0.000000 169 -0.0002
+ 0.000000 170 -0.0006
+ 0.000000 171 -0.0009
+ 0.000000 172 0.0009
+ 0.000000 173 -0.0003
+ 0.000000 174 0.0032
+ 0.000000 175 -0.0053
+ 0.000000 176 0.0037
+ 0.000000 177 -0.0019
+ 0.000000 178 -0.0020
+ 0.000000 179 0.0011
+ 0.000000 180 -0.0000
+ 0.000000 181 0.0060
+ 0.000000 182 -0.0033
+ 0.000000 183 -0.0027
+ 0.000000 184 0.0016
+ 0.000000 185 0.0005
+ 0.000000 186 -0.0009
+ 0.000000 187 -0.0031
+ 0.000000 188 -0.0009
+ 0.000000 189 -0.0005
+ 0.000000 190 0.0049
+ 0.000000 191 0.0003
+ 0.000000 192 -0.1431
+ 0.000000 193 -0.0326
+ 0.000000 194 0.0101
+ 0.000000 195 -0.0326
+ 0.000000 196 -0.1712
+ 0.000000 197 0.0351
+ 0.000000 198 0.0101
+ 0.000000 199 0.0351
+ 0.000000 200 -0.1192
diff --git a/regtest/crystallization/rt-averaged-q6/deriv3.reference b/regtest/crystallization/rt-averaged-q6/deriv3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..a4db1306390ea48453f5fd99e61681cce3b7da31
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6/deriv3.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter w6.mean
+ 0.000000 0 0.0018
+ 0.000000 1 0.0008
+ 0.000000 2 -0.0002
+ 0.000000 3 -0.0006
+ 0.000000 4 -0.0002
+ 0.000000 5 -0.0068
+ 0.000000 6 0.0016
+ 0.000000 7 0.0024
+ 0.000000 8 -0.0052
+ 0.000000 9 -0.0011
+ 0.000000 10 -0.0004
+ 0.000000 11 0.0032
+ 0.000000 12 0.0009
+ 0.000000 13 0.0012
+ 0.000000 14 -0.0001
+ 0.000000 15 -0.0013
+ 0.000000 16 -0.0039
+ 0.000000 17 -0.0010
+ 0.000000 18 -0.0018
+ 0.000000 19 0.0008
+ 0.000000 20 0.0005
+ 0.000000 21 -0.0016
+ 0.000000 22 -0.0004
+ 0.000000 23 -0.0013
+ 0.000000 24 0.0041
+ 0.000000 25 -0.0011
+ 0.000000 26 -0.0032
+ 0.000000 27 -0.0009
+ 0.000000 28 -0.0018
+ 0.000000 29 0.0040
+ 0.000000 30 -0.0014
+ 0.000000 31 0.0030
+ 0.000000 32 0.0020
+ 0.000000 33 0.0010
+ 0.000000 34 -0.0015
+ 0.000000 35 0.0025
+ 0.000000 36 0.0000
+ 0.000000 37 0.0010
+ 0.000000 38 -0.0022
+ 0.000000 39 -0.0003
+ 0.000000 40 0.0014
+ 0.000000 41 -0.0002
+ 0.000000 42 0.0003
+ 0.000000 43 -0.0000
+ 0.000000 44 0.0001
+ 0.000000 45 -0.0000
+ 0.000000 46 -0.0014
+ 0.000000 47 -0.0006
+ 0.000000 48 -0.0012
+ 0.000000 49 0.0000
+ 0.000000 50 -0.0018
+ 0.000000 51 -0.0005
+ 0.000000 52 0.0005
+ 0.000000 53 0.0001
+ 0.000000 54 -0.0012
+ 0.000000 55 0.0039
+ 0.000000 56 0.0024
+ 0.000000 57 -0.0011
+ 0.000000 58 -0.0029
+ 0.000000 59 -0.0025
+ 0.000000 60 0.0002
+ 0.000000 61 -0.0043
+ 0.000000 62 -0.0021
+ 0.000000 63 -0.0045
+ 0.000000 64 0.0030
+ 0.000000 65 0.0025
+ 0.000000 66 -0.0003
+ 0.000000 67 -0.0016
+ 0.000000 68 0.0003
+ 0.000000 69 0.0008
+ 0.000000 70 -0.0019
+ 0.000000 71 -0.0008
+ 0.000000 72 0.0011
+ 0.000000 73 0.0022
+ 0.000000 74 0.0026
+ 0.000000 75 -0.0006
+ 0.000000 76 -0.0032
+ 0.000000 77 -0.0009
+ 0.000000 78 0.0016
+ 0.000000 79 -0.0015
+ 0.000000 80 0.0008
+ 0.000000 81 -0.0002
+ 0.000000 82 -0.0003
+ 0.000000 83 -0.0006
+ 0.000000 84 0.0038
+ 0.000000 85 0.0018
+ 0.000000 86 -0.0012
+ 0.000000 87 -0.0006
+ 0.000000 88 -0.0017
+ 0.000000 89 0.0053
+ 0.000000 90 0.0004
+ 0.000000 91 0.0027
+ 0.000000 92 0.0013
+ 0.000000 93 0.0044
+ 0.000000 94 0.0031
+ 0.000000 95 -0.0037
+ 0.000000 96 0.0011
+ 0.000000 97 -0.0000
+ 0.000000 98 0.0011
+ 0.000000 99 -0.0003
+ 0.000000 100 0.0007
+ 0.000000 101 -0.0025
+ 0.000000 102 -0.0018
+ 0.000000 103 -0.0017
+ 0.000000 104 -0.0015
+ 0.000000 105 0.0034
+ 0.000000 106 -0.0002
+ 0.000000 107 0.0025
+ 0.000000 108 0.0017
+ 0.000000 109 0.0046
+ 0.000000 110 0.0002
+ 0.000000 111 0.0014
+ 0.000000 112 0.0005
+ 0.000000 113 -0.0020
+ 0.000000 114 0.0051
+ 0.000000 115 0.0000
+ 0.000000 116 -0.0030
+ 0.000000 117 0.0030
+ 0.000000 118 -0.0012
+ 0.000000 119 0.0041
+ 0.000000 120 -0.0030
+ 0.000000 121 -0.0009
+ 0.000000 122 0.0019
+ 0.000000 123 0.0034
+ 0.000000 124 -0.0002
+ 0.000000 125 -0.0045
+ 0.000000 126 0.0011
+ 0.000000 127 -0.0012
+ 0.000000 128 0.0004
+ 0.000000 129 0.0021
+ 0.000000 130 -0.0040
+ 0.000000 131 -0.0011
+ 0.000000 132 -0.0010
+ 0.000000 133 -0.0012
+ 0.000000 134 -0.0025
+ 0.000000 135 -0.0004
+ 0.000000 136 -0.0017
+ 0.000000 137 0.0011
+ 0.000000 138 0.0039
+ 0.000000 139 -0.0019
+ 0.000000 140 -0.0017
+ 0.000000 141 -0.0004
+ 0.000000 142 0.0017
+ 0.000000 143 0.0045
+ 0.000000 144 0.0005
+ 0.000000 145 0.0003
+ 0.000000 146 0.0001
+ 0.000000 147 -0.0043
+ 0.000000 148 0.0001
+ 0.000000 149 -0.0005
+ 0.000000 150 -0.0012
+ 0.000000 151 0.0029
+ 0.000000 152 0.0046
+ 0.000000 153 -0.0024
+ 0.000000 154 0.0018
+ 0.000000 155 -0.0015
+ 0.000000 156 0.0025
+ 0.000000 157 0.0005
+ 0.000000 158 -0.0039
+ 0.000000 159 -0.0007
+ 0.000000 160 -0.0028
+ 0.000000 161 -0.0002
+ 0.000000 162 -0.0054
+ 0.000000 163 -0.0020
+ 0.000000 164 0.0052
+ 0.000000 165 0.0020
+ 0.000000 166 -0.0019
+ 0.000000 167 0.0049
+ 0.000000 168 -0.0006
+ 0.000000 169 0.0044
+ 0.000000 170 0.0033
+ 0.000000 171 0.0004
+ 0.000000 172 0.0019
+ 0.000000 173 -0.0009
+ 0.000000 174 0.0006
+ 0.000000 175 -0.0041
+ 0.000000 176 0.0042
+ 0.000000 177 -0.0045
+ 0.000000 178 0.0009
+ 0.000000 179 0.0022
+ 0.000000 180 -0.0009
+ 0.000000 181 0.0016
+ 0.000000 182 -0.0062
+ 0.000000 183 -0.0018
+ 0.000000 184 -0.0019
+ 0.000000 185 -0.0013
+ 0.000000 186 -0.0031
+ 0.000000 187 0.0001
+ 0.000000 188 0.0002
+ 0.000000 189 -0.0034
+ 0.000000 190 0.0051
+ 0.000000 191 -0.0007
+ 0.000000 192 -0.0552
+ 0.000000 193 -0.0319
+ 0.000000 194 -0.0141
+ 0.000000 195 -0.0319
+ 0.000000 196 -0.0972
+ 0.000000 197 0.0628
+ 0.000000 198 -0.0141
+ 0.000000 199 0.0628
+ 0.000000 200 -0.0608
diff --git a/regtest/crystallization/rt-averaged-q6/plumed.dat b/regtest/crystallization/rt-averaged-q6/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..90d5b57759bd3b969b81498f00bd36b1133b6f87
--- /dev/null
+++ b/regtest/crystallization/rt-averaged-q6/plumed.dat
@@ -0,0 +1,10 @@
+Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN LABEL=q6
+# Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN NUMERICAL_DERIVATIVES LABEL=q6n
+PRINT ARG=q6.* FILE=colv
+DUMPDERIVATIVES ARG=q6.* FILE=deriv FMT=%8.4f
+
+LOCAL_AVERAGE ARG=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LABEL=w6
+# LOCAL_AVERAGE ARG=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN NUMERICAL_DERIVATIVES LABEL=w6n
+PRINT ARG=w6.* FILE=colv3
+DUMPDERIVATIVES ARG=w6.* FILE=deriv3 FMT=%8.4f
+
diff --git a/regtest/crystallization/rt-nbonds-q6-lowmem/64.xyz b/regtest/crystallization/rt-nbonds-q6-lowmem/64.xyz
new file mode 100755
index 0000000000000000000000000000000000000000..90b3ae19c7598dd32c498e7105925df054c3e788
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6-lowmem/64.xyz
@@ -0,0 +1,66 @@
+ 64
+12.41642 12.41642 12.41642
+ Ge 1.473000000000 2.211000000000 8.700200000000
+ Ge 4.886500000000 3.830000000000 6.593500000000
+ Ge 3.807000000000 1.978700000000 10.045000000000
+ Ge 5.002000000000 3.883500000000 1.357000000000
+ Ge 9.636000000000 1.604000000000 8.697700000000
+ Ge 6.559800000000 11.084000000000 9.650400000000
+ Ge 0.627000000000 0.390000000000 2.224300000000
+ Ge 3.341900000000 6.765300000000 1.369500000000
+ Ge 5.032000000000 9.650500000000 2.785000000000
+ Ge 1.682700000000 10.392700000000 5.459500000000
+ Ge 3.517300000000 12.039000000000 5.930600000000
+ Ge 1.072000000000 5.374900000000 12.335000000000
+ Ge 0.863390000000 11.308000000000 0.275000000000
+ Ge 5.867800000000 0.672000000000 6.605200000000
+ Ge 3.961000000000 8.414000000000 8.691600000000
+ Ge 11.570960000000 10.444000000000 2.125000000000
+ Ge 1.736000000000 6.845200000000 6.129000000000
+ Ge 7.557300000000 8.842800000000 6.611800000000
+ Ge 2.785800000000 2.591200000000 1.833300000000
+ Ge 11.564000000000 11.555000000000 10.928000000000
+ Ge 3.324000000000 11.334000000000 12.095000000000
+ Ge 10.532000000000 9.377700000000 6.724000000000
+ Ge 7.157000000000 11.468000000000 12.063000000000
+ Ge 0.027000000000 4.622000000000 5.996200000000
+ Ge 4.564000000000 6.513200000000 5.370200000000
+ Ge 12.189770000000 7.981000000000 2.257000000000
+ Ge 8.973100000000 0.437000000000 4.852800000000
+ Ge 9.086200000000 9.857000000000 0.975000000000
+ Ge 6.516500000000 12.170000000000 2.438600000000
+ Ge 8.955900000000 4.612000000000 4.478000000000
+ Ge 7.419000000000 3.301600000000 0.450000000000
+ Ge 10.808000000000 7.170600000000 11.109000000000
+ Te 4.818200000000 9.096200000000 6.189300000000
+ Te 10.663400000000 6.726900000000 5.343000000000
+ Te 7.021700000000 4.814600000000 10.649000000000
+ Te 3.253500000000 5.713300000000 8.267800000000
+ Te 10.322000000000 1.250000000000 2.209500000000
+ Te 0.300000000000 5.033000000000 8.902400000000
+ Te 12.092000000000 0.227000000000 8.527200000000
+ Te 6.329000000000 2.634100000000 8.525500000000
+ Te 8.044800000000 11.712000000000 7.575400000000
+ Te 2.150000000000 8.302000000000 3.591400000000
+ Te 11.581000000000 11.201000000000 4.824700000000
+ Te 3.960900000000 4.755000000000 11.528710000000
+ Te 3.815300000000 12.139000000000 3.263700000000
+ Te 9.419700000000 7.232700000000 1.010000000000
+ Te 1.211700000000 1.726300000000 12.223470000000
+ Te 0.798460000000 8.988100000000 7.517700000000
+ Te 10.078000000000 9.503000000000 9.977500000000
+ Te 9.336700000000 0.894000000000 11.469560000000
+ Te 7.251000000000 5.783400000000 6.399000000000
+ Te 3.740000000000 11.515000000000 9.383700000000
+ Te 10.329000000000 2.726600000000 5.835100000000
+ Te 6.722900000000 8.386100000000 9.226500000000
+ Te 1.247000000000 4.660000000000 2.609100000000
+ Te 5.628500000000 6.170200000000 2.845000000000
+ Te 4.742900000000 9.191800000000 0.212000000000
+ Te 5.134400000000 0.984830000000 12.244000000000
+ Te 8.033800000000 10.061100000000 3.578600000000
+ Te 9.840000000000 4.825000000000 9.743000000000
+ Te 6.760000000000 2.189000000000 4.410700000000
+ Te 2.334000000000 2.201000000000 6.079000000000
+ Te 9.930600000000 3.982900000000 1.562000000000
+ Te 0.806810000000 8.091100000000 12.264000000000
diff --git a/regtest/crystallization/rt-nbonds-q6-lowmem/Makefile b/regtest/crystallization/rt-nbonds-q6-lowmem/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6-lowmem/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-nbonds-q6-lowmem/colv1.reference b/regtest/crystallization/rt-nbonds-q6-lowmem/colv1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..f7e414b390cb145b2d13e7b838d33dd429d5958f
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6-lowmem/colv1.reference
@@ -0,0 +1,2 @@
+#! FIELDS time w6
+ 0.000000 15.644050
diff --git a/regtest/crystallization/rt-nbonds-q6-lowmem/colv2.reference b/regtest/crystallization/rt-nbonds-q6-lowmem/colv2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..451673022fb702691286987acf2d5b277bc7bfe5
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6-lowmem/colv2.reference
@@ -0,0 +1,2 @@
+#! FIELDS time w4
+ 0.000000 33.811763
diff --git a/regtest/crystallization/rt-nbonds-q6-lowmem/config b/regtest/crystallization/rt-nbonds-q6-lowmem/config
new file mode 100644
index 0000000000000000000000000000000000000000..e07432072a91405171ff68d3c3d22a09fde3346c
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6-lowmem/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz 64.xyz"
diff --git a/regtest/crystallization/rt-nbonds-q6-lowmem/deriv1.reference b/regtest/crystallization/rt-nbonds-q6-lowmem/deriv1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..4ae8c2f9ab79270caaf5636b4dfab792b761672d
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6-lowmem/deriv1.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter w6
+ 0.000000 0 0.7514
+ 0.000000 1 0.8829
+ 0.000000 2 2.4315
+ 0.000000 3 -3.5375
+ 0.000000 4 0.4772
+ 0.000000 5 -7.9712
+ 0.000000 6 2.0752
+ 0.000000 7 1.1725
+ 0.000000 8 -8.6674
+ 0.000000 9 -1.9002
+ 0.000000 10 0.5045
+ 0.000000 11 2.9522
+ 0.000000 12 -0.0081
+ 0.000000 13 0.0463
+ 0.000000 14 0.0087
+ 0.000000 15 -0.2558
+ 0.000000 16 -3.3394
+ 0.000000 17 -0.2597
+ 0.000000 18 -3.1012
+ 0.000000 19 -0.1783
+ 0.000000 20 0.0649
+ 0.000000 21 -0.7516
+ 0.000000 22 -0.5258
+ 0.000000 23 -0.8601
+ 0.000000 24 3.2547
+ 0.000000 25 -1.6845
+ 0.000000 26 -2.5631
+ 0.000000 27 0.8457
+ 0.000000 28 -3.3966
+ 0.000000 29 0.5749
+ 0.000000 30 -1.3306
+ 0.000000 31 5.7719
+ 0.000000 32 1.3995
+ 0.000000 33 1.2680
+ 0.000000 34 -0.2292
+ 0.000000 35 3.0950
+ 0.000000 36 0.0658
+ 0.000000 37 -0.1235
+ 0.000000 38 -2.4627
+ 0.000000 39 0.7487
+ 0.000000 40 1.8047
+ 0.000000 41 2.7807
+ 0.000000 42 -0.8925
+ 0.000000 43 2.1895
+ 0.000000 44 0.6505
+ 0.000000 45 5.0409
+ 0.000000 46 0.9839
+ 0.000000 47 1.7225
+ 0.000000 48 -1.6594
+ 0.000000 49 -0.4666
+ 0.000000 50 -1.9308
+ 0.000000 51 -1.1826
+ 0.000000 52 1.9000
+ 0.000000 53 -2.8092
+ 0.000000 54 -0.3462
+ 0.000000 55 3.0319
+ 0.000000 56 3.5796
+ 0.000000 57 -0.2071
+ 0.000000 58 -1.4985
+ 0.000000 59 -2.6203
+ 0.000000 60 -0.4259
+ 0.000000 61 -4.6751
+ 0.000000 62 -1.0700
+ 0.000000 63 -3.6946
+ 0.000000 64 4.2730
+ 0.000000 65 3.1233
+ 0.000000 66 -0.0293
+ 0.000000 67 1.2701
+ 0.000000 68 -3.1647
+ 0.000000 69 1.8323
+ 0.000000 70 -2.1267
+ 0.000000 71 -0.8128
+ 0.000000 72 2.0135
+ 0.000000 73 4.0780
+ 0.000000 74 4.1323
+ 0.000000 75 -1.8653
+ 0.000000 76 -3.2481
+ 0.000000 77 -0.3972
+ 0.000000 78 2.6436
+ 0.000000 79 -4.5409
+ 0.000000 80 -0.4981
+ 0.000000 81 -1.4292
+ 0.000000 82 -1.3215
+ 0.000000 83 0.3626
+ 0.000000 84 1.6686
+ 0.000000 85 0.4591
+ 0.000000 86 -0.4051
+ 0.000000 87 -0.2418
+ 0.000000 88 -3.1329
+ 0.000000 89 8.6219
+ 0.000000 90 0.6028
+ 0.000000 91 1.6546
+ 0.000000 92 2.4560
+ 0.000000 93 3.0714
+ 0.000000 94 1.1745
+ 0.000000 95 -4.8228
+ 0.000000 96 2.9876
+ 0.000000 97 2.7857
+ 0.000000 98 -0.5444
+ 0.000000 99 0.2690
+ 0.000000 100 1.0255
+ 0.000000 101 -1.3537
+ 0.000000 102 -1.9146
+ 0.000000 103 -2.3371
+ 0.000000 104 -0.6904
+ 0.000000 105 6.5071
+ 0.000000 106 0.0346
+ 0.000000 107 3.0002
+ 0.000000 108 0.2787
+ 0.000000 109 5.2995
+ 0.000000 110 -0.4218
+ 0.000000 111 0.5027
+ 0.000000 112 0.8729
+ 0.000000 113 -1.3573
+ 0.000000 114 3.9230
+ 0.000000 115 -1.8850
+ 0.000000 116 -5.0122
+ 0.000000 117 3.8191
+ 0.000000 118 0.4467
+ 0.000000 119 5.0885
+ 0.000000 120 -2.2489
+ 0.000000 121 -2.3297
+ 0.000000 122 1.1179
+ 0.000000 123 1.4748
+ 0.000000 124 -2.1647
+ 0.000000 125 -5.6072
+ 0.000000 126 -1.3841
+ 0.000000 127 -1.6793
+ 0.000000 128 0.6054
+ 0.000000 129 0.0390
+ 0.000000 130 -5.9543
+ 0.000000 131 -1.5910
+ 0.000000 132 -1.6559
+ 0.000000 133 0.2025
+ 0.000000 134 -3.6084
+ 0.000000 135 2.8223
+ 0.000000 136 -0.9791
+ 0.000000 137 3.9020
+ 0.000000 138 4.3932
+ 0.000000 139 -0.1796
+ 0.000000 140 -0.5022
+ 0.000000 141 -0.9469
+ 0.000000 142 1.1155
+ 0.000000 143 5.3109
+ 0.000000 144 1.3264
+ 0.000000 145 0.5365
+ 0.000000 146 0.5109
+ 0.000000 147 -3.5125
+ 0.000000 148 0.3803
+ 0.000000 149 -1.2272
+ 0.000000 150 -2.2695
+ 0.000000 151 3.1281
+ 0.000000 152 4.3139
+ 0.000000 153 -2.2924
+ 0.000000 154 0.0233
+ 0.000000 155 -3.1646
+ 0.000000 156 2.7875
+ 0.000000 157 -0.7124
+ 0.000000 158 -5.9856
+ 0.000000 159 -3.0120
+ 0.000000 160 -2.8344
+ 0.000000 161 -1.8310
+ 0.000000 162 -3.4288
+ 0.000000 163 -3.9051
+ 0.000000 164 5.2396
+ 0.000000 165 2.7985
+ 0.000000 166 -1.7127
+ 0.000000 167 5.7990
+ 0.000000 168 2.6108
+ 0.000000 169 3.8428
+ 0.000000 170 3.0649
+ 0.000000 171 -0.4821
+ 0.000000 172 5.3284
+ 0.000000 173 0.2070
+ 0.000000 174 -0.2515
+ 0.000000 175 -4.1468
+ 0.000000 176 6.4385
+ 0.000000 177 -4.7109
+ 0.000000 178 1.1203
+ 0.000000 179 0.4099
+ 0.000000 180 -0.3328
+ 0.000000 181 0.4363
+ 0.000000 182 -8.0394
+ 0.000000 183 -1.0587
+ 0.000000 184 -4.6100
+ 0.000000 185 1.0052
+ 0.000000 186 -3.3639
+ 0.000000 187 -0.1659
+ 0.000000 188 0.2976
+ 0.000000 189 -6.6979
+ 0.000000 190 7.8299
+ 0.000000 191 -2.0159
+ 0.000000 192 41.4373
+ 0.000000 193 -31.4183
+ 0.000000 194 -11.1354
+ 0.000000 195 -31.4183
+ 0.000000 196 -29.9501
+ 0.000000 197 42.7567
+ 0.000000 198 -11.1354
+ 0.000000 199 42.7567
+ 0.000000 200 0.8950
diff --git a/regtest/crystallization/rt-nbonds-q6-lowmem/deriv2.reference b/regtest/crystallization/rt-nbonds-q6-lowmem/deriv2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..bf0d41c9add811736cc319922cde8e3439a8608e
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6-lowmem/deriv2.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter w4
+ 0.000000 0 -0.2546
+ 0.000000 1 1.7915
+ 0.000000 2 1.4219
+ 0.000000 3 -3.4107
+ 0.000000 4 -3.2102
+ 0.000000 5 -3.8684
+ 0.000000 6 0.5841
+ 0.000000 7 0.5244
+ 0.000000 8 -0.5506
+ 0.000000 9 1.6802
+ 0.000000 10 -2.4090
+ 0.000000 11 4.3098
+ 0.000000 12 0.5170
+ 0.000000 13 3.1692
+ 0.000000 14 -0.7917
+ 0.000000 15 8.7314
+ 0.000000 16 3.2534
+ 0.000000 17 4.5937
+ 0.000000 18 0.1529
+ 0.000000 19 -1.3610
+ 0.000000 20 0.6062
+ 0.000000 21 2.1473
+ 0.000000 22 1.1462
+ 0.000000 23 1.7843
+ 0.000000 24 -2.5136
+ 0.000000 25 2.2836
+ 0.000000 26 -3.1486
+ 0.000000 27 -3.4742
+ 0.000000 28 -0.1403
+ 0.000000 29 0.3266
+ 0.000000 30 6.6218
+ 0.000000 31 -0.2614
+ 0.000000 32 -2.2848
+ 0.000000 33 0.9558
+ 0.000000 34 -3.4443
+ 0.000000 35 -1.7551
+ 0.000000 36 -5.0356
+ 0.000000 37 2.2322
+ 0.000000 38 -5.9115
+ 0.000000 39 -0.3786
+ 0.000000 40 -7.1256
+ 0.000000 41 0.3157
+ 0.000000 42 2.2955
+ 0.000000 43 -1.3930
+ 0.000000 44 0.4939
+ 0.000000 45 1.7099
+ 0.000000 46 -0.1880
+ 0.000000 47 2.4970
+ 0.000000 48 -5.8590
+ 0.000000 49 -4.2949
+ 0.000000 50 -1.0078
+ 0.000000 51 -4.0462
+ 0.000000 52 2.7627
+ 0.000000 53 0.5621
+ 0.000000 54 -0.4197
+ 0.000000 55 0.7168
+ 0.000000 56 1.4767
+ 0.000000 57 0.0492
+ 0.000000 58 -1.3670
+ 0.000000 59 6.6129
+ 0.000000 60 -3.1318
+ 0.000000 61 1.9615
+ 0.000000 62 4.0257
+ 0.000000 63 3.3679
+ 0.000000 64 5.1249
+ 0.000000 65 1.0571
+ 0.000000 66 -2.6718
+ 0.000000 67 1.9511
+ 0.000000 68 -3.0899
+ 0.000000 69 3.3844
+ 0.000000 70 3.5373
+ 0.000000 71 -2.5662
+ 0.000000 72 1.3854
+ 0.000000 73 -0.8866
+ 0.000000 74 3.2630
+ 0.000000 75 -5.8850
+ 0.000000 76 -7.2364
+ 0.000000 77 -2.0470
+ 0.000000 78 1.2118
+ 0.000000 79 2.7032
+ 0.000000 80 -2.0353
+ 0.000000 81 -0.2827
+ 0.000000 82 -1.6227
+ 0.000000 83 0.6232
+ 0.000000 84 1.2917
+ 0.000000 85 3.0123
+ 0.000000 86 7.6244
+ 0.000000 87 -1.9792
+ 0.000000 88 0.8384
+ 0.000000 89 6.2483
+ 0.000000 90 -1.2618
+ 0.000000 91 1.6919
+ 0.000000 92 4.9239
+ 0.000000 93 -0.0553
+ 0.000000 94 6.5349
+ 0.000000 95 -6.0543
+ 0.000000 96 -1.0205
+ 0.000000 97 0.3694
+ 0.000000 98 -7.0517
+ 0.000000 99 -0.9435
+ 0.000000 100 -1.6073
+ 0.000000 101 9.8342
+ 0.000000 102 -4.7203
+ 0.000000 103 2.7525
+ 0.000000 104 -7.9241
+ 0.000000 105 5.5616
+ 0.000000 106 1.2297
+ 0.000000 107 3.8689
+ 0.000000 108 -2.2532
+ 0.000000 109 -0.5728
+ 0.000000 110 -2.1037
+ 0.000000 111 -0.3446
+ 0.000000 112 -1.8839
+ 0.000000 113 1.1764
+ 0.000000 114 -0.9034
+ 0.000000 115 -2.5301
+ 0.000000 116 -3.4934
+ 0.000000 117 3.9375
+ 0.000000 118 0.0475
+ 0.000000 119 1.0507
+ 0.000000 120 -4.9949
+ 0.000000 121 -2.8268
+ 0.000000 122 0.4098
+ 0.000000 123 1.7328
+ 0.000000 124 -3.0211
+ 0.000000 125 -0.2859
+ 0.000000 126 1.8651
+ 0.000000 127 2.0405
+ 0.000000 128 -2.1358
+ 0.000000 129 -2.7030
+ 0.000000 130 2.5471
+ 0.000000 131 -0.2810
+ 0.000000 132 1.5934
+ 0.000000 133 -3.1017
+ 0.000000 134 -1.6080
+ 0.000000 135 0.7564
+ 0.000000 136 3.7250
+ 0.000000 137 0.8031
+ 0.000000 138 0.7069
+ 0.000000 139 -0.2153
+ 0.000000 140 -1.0334
+ 0.000000 141 1.1444
+ 0.000000 142 1.5002
+ 0.000000 143 1.0250
+ 0.000000 144 -0.4688
+ 0.000000 145 -2.3582
+ 0.000000 146 6.2597
+ 0.000000 147 3.1187
+ 0.000000 148 -2.1759
+ 0.000000 149 2.7629
+ 0.000000 150 -2.4924
+ 0.000000 151 -3.7095
+ 0.000000 152 -1.7532
+ 0.000000 153 -4.1347
+ 0.000000 154 -1.7478
+ 0.000000 155 -2.9066
+ 0.000000 156 1.3769
+ 0.000000 157 -1.3631
+ 0.000000 158 -7.2793
+ 0.000000 159 -1.2756
+ 0.000000 160 -0.2989
+ 0.000000 161 0.2878
+ 0.000000 162 1.8778
+ 0.000000 163 -3.2438
+ 0.000000 164 -5.5374
+ 0.000000 165 -3.6191
+ 0.000000 166 6.7136
+ 0.000000 167 2.8478
+ 0.000000 168 5.8495
+ 0.000000 169 -3.5060
+ 0.000000 170 2.3624
+ 0.000000 171 2.2127
+ 0.000000 172 1.3909
+ 0.000000 173 -0.8028
+ 0.000000 174 -3.6181
+ 0.000000 175 -4.5232
+ 0.000000 176 -1.1553
+ 0.000000 177 1.1278
+ 0.000000 178 0.8887
+ 0.000000 179 5.3118
+ 0.000000 180 0.6350
+ 0.000000 181 -0.7556
+ 0.000000 182 -3.5560
+ 0.000000 183 0.0509
+ 0.000000 184 1.2030
+ 0.000000 185 0.0213
+ 0.000000 186 3.0273
+ 0.000000 187 2.3146
+ 0.000000 188 -3.1933
+ 0.000000 189 1.4907
+ 0.000000 190 2.4234
+ 0.000000 191 -3.5761
+ 0.000000 192 -43.8368
+ 0.000000 193 28.3463
+ 0.000000 194 -28.0159
+ 0.000000 195 28.3463
+ 0.000000 196 -48.0443
+ 0.000000 197 -6.5965
+ 0.000000 198 -28.0159
+ 0.000000 199 -6.5965
+ 0.000000 200 -183.6319
diff --git a/regtest/crystallization/rt-nbonds-q6-lowmem/plumed.dat b/regtest/crystallization/rt-nbonds-q6-lowmem/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..eef159413816426636a931c0ba5a0c26d32d0fa8
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6-lowmem/plumed.dat
@@ -0,0 +1,15 @@
+Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN LABEL=q6
+# Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN NUMERICAL_DERIVATIVES LABEL=q6n
+
+NLINKS ARG=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} LOWMEM LABEL=w6
+# NLINKS ARG=q6n SWITCH={RATIONAL D_0=3.0 R_0=1.5} NUMERICAL_DERIVATIVES LABEL=w6n
+PRINT ARG=w6 FILE=colv1
+DUMPDERIVATIVES ARG=w6 FILE=deriv1 FMT=%8.4f
+
+Q4 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN LABEL=q4
+# Q4 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN NUMERICAL_DERIVATIVES LABEL=q4n
+
+NLINKS ARG=q4 SWITCH={RATIONAL D_0=3.0 R_0=1.5} LOWMEM LABEL=w4
+# NLINKS ARG=q4n SWITCH={RATIONAL D_0=3.0 R_0=1.5} NUMERICAL_DERIVATIVES LABEL=w4n
+PRINT ARG=w4 FILE=colv2
+DUMPDERIVATIVES ARG=w4 FILE=deriv2 FMT=%8.4f
diff --git a/regtest/crystallization/rt-nbonds-q6/64.xyz b/regtest/crystallization/rt-nbonds-q6/64.xyz
new file mode 100755
index 0000000000000000000000000000000000000000..90b3ae19c7598dd32c498e7105925df054c3e788
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6/64.xyz
@@ -0,0 +1,66 @@
+ 64
+12.41642 12.41642 12.41642
+ Ge 1.473000000000 2.211000000000 8.700200000000
+ Ge 4.886500000000 3.830000000000 6.593500000000
+ Ge 3.807000000000 1.978700000000 10.045000000000
+ Ge 5.002000000000 3.883500000000 1.357000000000
+ Ge 9.636000000000 1.604000000000 8.697700000000
+ Ge 6.559800000000 11.084000000000 9.650400000000
+ Ge 0.627000000000 0.390000000000 2.224300000000
+ Ge 3.341900000000 6.765300000000 1.369500000000
+ Ge 5.032000000000 9.650500000000 2.785000000000
+ Ge 1.682700000000 10.392700000000 5.459500000000
+ Ge 3.517300000000 12.039000000000 5.930600000000
+ Ge 1.072000000000 5.374900000000 12.335000000000
+ Ge 0.863390000000 11.308000000000 0.275000000000
+ Ge 5.867800000000 0.672000000000 6.605200000000
+ Ge 3.961000000000 8.414000000000 8.691600000000
+ Ge 11.570960000000 10.444000000000 2.125000000000
+ Ge 1.736000000000 6.845200000000 6.129000000000
+ Ge 7.557300000000 8.842800000000 6.611800000000
+ Ge 2.785800000000 2.591200000000 1.833300000000
+ Ge 11.564000000000 11.555000000000 10.928000000000
+ Ge 3.324000000000 11.334000000000 12.095000000000
+ Ge 10.532000000000 9.377700000000 6.724000000000
+ Ge 7.157000000000 11.468000000000 12.063000000000
+ Ge 0.027000000000 4.622000000000 5.996200000000
+ Ge 4.564000000000 6.513200000000 5.370200000000
+ Ge 12.189770000000 7.981000000000 2.257000000000
+ Ge 8.973100000000 0.437000000000 4.852800000000
+ Ge 9.086200000000 9.857000000000 0.975000000000
+ Ge 6.516500000000 12.170000000000 2.438600000000
+ Ge 8.955900000000 4.612000000000 4.478000000000
+ Ge 7.419000000000 3.301600000000 0.450000000000
+ Ge 10.808000000000 7.170600000000 11.109000000000
+ Te 4.818200000000 9.096200000000 6.189300000000
+ Te 10.663400000000 6.726900000000 5.343000000000
+ Te 7.021700000000 4.814600000000 10.649000000000
+ Te 3.253500000000 5.713300000000 8.267800000000
+ Te 10.322000000000 1.250000000000 2.209500000000
+ Te 0.300000000000 5.033000000000 8.902400000000
+ Te 12.092000000000 0.227000000000 8.527200000000
+ Te 6.329000000000 2.634100000000 8.525500000000
+ Te 8.044800000000 11.712000000000 7.575400000000
+ Te 2.150000000000 8.302000000000 3.591400000000
+ Te 11.581000000000 11.201000000000 4.824700000000
+ Te 3.960900000000 4.755000000000 11.528710000000
+ Te 3.815300000000 12.139000000000 3.263700000000
+ Te 9.419700000000 7.232700000000 1.010000000000
+ Te 1.211700000000 1.726300000000 12.223470000000
+ Te 0.798460000000 8.988100000000 7.517700000000
+ Te 10.078000000000 9.503000000000 9.977500000000
+ Te 9.336700000000 0.894000000000 11.469560000000
+ Te 7.251000000000 5.783400000000 6.399000000000
+ Te 3.740000000000 11.515000000000 9.383700000000
+ Te 10.329000000000 2.726600000000 5.835100000000
+ Te 6.722900000000 8.386100000000 9.226500000000
+ Te 1.247000000000 4.660000000000 2.609100000000
+ Te 5.628500000000 6.170200000000 2.845000000000
+ Te 4.742900000000 9.191800000000 0.212000000000
+ Te 5.134400000000 0.984830000000 12.244000000000
+ Te 8.033800000000 10.061100000000 3.578600000000
+ Te 9.840000000000 4.825000000000 9.743000000000
+ Te 6.760000000000 2.189000000000 4.410700000000
+ Te 2.334000000000 2.201000000000 6.079000000000
+ Te 9.930600000000 3.982900000000 1.562000000000
+ Te 0.806810000000 8.091100000000 12.264000000000
diff --git a/regtest/crystallization/rt-nbonds-q6/Makefile b/regtest/crystallization/rt-nbonds-q6/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-nbonds-q6/colv1.reference b/regtest/crystallization/rt-nbonds-q6/colv1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..f7e414b390cb145b2d13e7b838d33dd429d5958f
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6/colv1.reference
@@ -0,0 +1,2 @@
+#! FIELDS time w6
+ 0.000000 15.644050
diff --git a/regtest/crystallization/rt-nbonds-q6/colv2.reference b/regtest/crystallization/rt-nbonds-q6/colv2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..451673022fb702691286987acf2d5b277bc7bfe5
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6/colv2.reference
@@ -0,0 +1,2 @@
+#! FIELDS time w4
+ 0.000000 33.811763
diff --git a/regtest/crystallization/rt-nbonds-q6/config b/regtest/crystallization/rt-nbonds-q6/config
new file mode 100644
index 0000000000000000000000000000000000000000..e07432072a91405171ff68d3c3d22a09fde3346c
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz 64.xyz"
diff --git a/regtest/crystallization/rt-nbonds-q6/deriv1.reference b/regtest/crystallization/rt-nbonds-q6/deriv1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..4ae8c2f9ab79270caaf5636b4dfab792b761672d
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6/deriv1.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter w6
+ 0.000000 0 0.7514
+ 0.000000 1 0.8829
+ 0.000000 2 2.4315
+ 0.000000 3 -3.5375
+ 0.000000 4 0.4772
+ 0.000000 5 -7.9712
+ 0.000000 6 2.0752
+ 0.000000 7 1.1725
+ 0.000000 8 -8.6674
+ 0.000000 9 -1.9002
+ 0.000000 10 0.5045
+ 0.000000 11 2.9522
+ 0.000000 12 -0.0081
+ 0.000000 13 0.0463
+ 0.000000 14 0.0087
+ 0.000000 15 -0.2558
+ 0.000000 16 -3.3394
+ 0.000000 17 -0.2597
+ 0.000000 18 -3.1012
+ 0.000000 19 -0.1783
+ 0.000000 20 0.0649
+ 0.000000 21 -0.7516
+ 0.000000 22 -0.5258
+ 0.000000 23 -0.8601
+ 0.000000 24 3.2547
+ 0.000000 25 -1.6845
+ 0.000000 26 -2.5631
+ 0.000000 27 0.8457
+ 0.000000 28 -3.3966
+ 0.000000 29 0.5749
+ 0.000000 30 -1.3306
+ 0.000000 31 5.7719
+ 0.000000 32 1.3995
+ 0.000000 33 1.2680
+ 0.000000 34 -0.2292
+ 0.000000 35 3.0950
+ 0.000000 36 0.0658
+ 0.000000 37 -0.1235
+ 0.000000 38 -2.4627
+ 0.000000 39 0.7487
+ 0.000000 40 1.8047
+ 0.000000 41 2.7807
+ 0.000000 42 -0.8925
+ 0.000000 43 2.1895
+ 0.000000 44 0.6505
+ 0.000000 45 5.0409
+ 0.000000 46 0.9839
+ 0.000000 47 1.7225
+ 0.000000 48 -1.6594
+ 0.000000 49 -0.4666
+ 0.000000 50 -1.9308
+ 0.000000 51 -1.1826
+ 0.000000 52 1.9000
+ 0.000000 53 -2.8092
+ 0.000000 54 -0.3462
+ 0.000000 55 3.0319
+ 0.000000 56 3.5796
+ 0.000000 57 -0.2071
+ 0.000000 58 -1.4985
+ 0.000000 59 -2.6203
+ 0.000000 60 -0.4259
+ 0.000000 61 -4.6751
+ 0.000000 62 -1.0700
+ 0.000000 63 -3.6946
+ 0.000000 64 4.2730
+ 0.000000 65 3.1233
+ 0.000000 66 -0.0293
+ 0.000000 67 1.2701
+ 0.000000 68 -3.1647
+ 0.000000 69 1.8323
+ 0.000000 70 -2.1267
+ 0.000000 71 -0.8128
+ 0.000000 72 2.0135
+ 0.000000 73 4.0780
+ 0.000000 74 4.1323
+ 0.000000 75 -1.8653
+ 0.000000 76 -3.2481
+ 0.000000 77 -0.3972
+ 0.000000 78 2.6436
+ 0.000000 79 -4.5409
+ 0.000000 80 -0.4981
+ 0.000000 81 -1.4292
+ 0.000000 82 -1.3215
+ 0.000000 83 0.3626
+ 0.000000 84 1.6686
+ 0.000000 85 0.4591
+ 0.000000 86 -0.4051
+ 0.000000 87 -0.2418
+ 0.000000 88 -3.1329
+ 0.000000 89 8.6219
+ 0.000000 90 0.6028
+ 0.000000 91 1.6546
+ 0.000000 92 2.4560
+ 0.000000 93 3.0714
+ 0.000000 94 1.1745
+ 0.000000 95 -4.8228
+ 0.000000 96 2.9876
+ 0.000000 97 2.7857
+ 0.000000 98 -0.5444
+ 0.000000 99 0.2690
+ 0.000000 100 1.0255
+ 0.000000 101 -1.3537
+ 0.000000 102 -1.9146
+ 0.000000 103 -2.3371
+ 0.000000 104 -0.6904
+ 0.000000 105 6.5071
+ 0.000000 106 0.0346
+ 0.000000 107 3.0002
+ 0.000000 108 0.2787
+ 0.000000 109 5.2995
+ 0.000000 110 -0.4218
+ 0.000000 111 0.5027
+ 0.000000 112 0.8729
+ 0.000000 113 -1.3573
+ 0.000000 114 3.9230
+ 0.000000 115 -1.8850
+ 0.000000 116 -5.0122
+ 0.000000 117 3.8191
+ 0.000000 118 0.4467
+ 0.000000 119 5.0885
+ 0.000000 120 -2.2489
+ 0.000000 121 -2.3297
+ 0.000000 122 1.1179
+ 0.000000 123 1.4748
+ 0.000000 124 -2.1647
+ 0.000000 125 -5.6072
+ 0.000000 126 -1.3841
+ 0.000000 127 -1.6793
+ 0.000000 128 0.6054
+ 0.000000 129 0.0390
+ 0.000000 130 -5.9543
+ 0.000000 131 -1.5910
+ 0.000000 132 -1.6559
+ 0.000000 133 0.2025
+ 0.000000 134 -3.6084
+ 0.000000 135 2.8223
+ 0.000000 136 -0.9791
+ 0.000000 137 3.9020
+ 0.000000 138 4.3932
+ 0.000000 139 -0.1796
+ 0.000000 140 -0.5022
+ 0.000000 141 -0.9469
+ 0.000000 142 1.1155
+ 0.000000 143 5.3109
+ 0.000000 144 1.3264
+ 0.000000 145 0.5365
+ 0.000000 146 0.5109
+ 0.000000 147 -3.5125
+ 0.000000 148 0.3803
+ 0.000000 149 -1.2272
+ 0.000000 150 -2.2695
+ 0.000000 151 3.1281
+ 0.000000 152 4.3139
+ 0.000000 153 -2.2924
+ 0.000000 154 0.0233
+ 0.000000 155 -3.1646
+ 0.000000 156 2.7875
+ 0.000000 157 -0.7124
+ 0.000000 158 -5.9856
+ 0.000000 159 -3.0120
+ 0.000000 160 -2.8344
+ 0.000000 161 -1.8310
+ 0.000000 162 -3.4288
+ 0.000000 163 -3.9051
+ 0.000000 164 5.2396
+ 0.000000 165 2.7985
+ 0.000000 166 -1.7127
+ 0.000000 167 5.7990
+ 0.000000 168 2.6108
+ 0.000000 169 3.8428
+ 0.000000 170 3.0649
+ 0.000000 171 -0.4821
+ 0.000000 172 5.3284
+ 0.000000 173 0.2070
+ 0.000000 174 -0.2515
+ 0.000000 175 -4.1468
+ 0.000000 176 6.4385
+ 0.000000 177 -4.7109
+ 0.000000 178 1.1203
+ 0.000000 179 0.4099
+ 0.000000 180 -0.3328
+ 0.000000 181 0.4363
+ 0.000000 182 -8.0394
+ 0.000000 183 -1.0587
+ 0.000000 184 -4.6100
+ 0.000000 185 1.0052
+ 0.000000 186 -3.3639
+ 0.000000 187 -0.1659
+ 0.000000 188 0.2976
+ 0.000000 189 -6.6979
+ 0.000000 190 7.8299
+ 0.000000 191 -2.0159
+ 0.000000 192 41.4373
+ 0.000000 193 -31.4183
+ 0.000000 194 -11.1354
+ 0.000000 195 -31.4183
+ 0.000000 196 -29.9501
+ 0.000000 197 42.7567
+ 0.000000 198 -11.1354
+ 0.000000 199 42.7567
+ 0.000000 200 0.8950
diff --git a/regtest/crystallization/rt-nbonds-q6/deriv2.reference b/regtest/crystallization/rt-nbonds-q6/deriv2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..bf0d41c9add811736cc319922cde8e3439a8608e
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6/deriv2.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter w4
+ 0.000000 0 -0.2546
+ 0.000000 1 1.7915
+ 0.000000 2 1.4219
+ 0.000000 3 -3.4107
+ 0.000000 4 -3.2102
+ 0.000000 5 -3.8684
+ 0.000000 6 0.5841
+ 0.000000 7 0.5244
+ 0.000000 8 -0.5506
+ 0.000000 9 1.6802
+ 0.000000 10 -2.4090
+ 0.000000 11 4.3098
+ 0.000000 12 0.5170
+ 0.000000 13 3.1692
+ 0.000000 14 -0.7917
+ 0.000000 15 8.7314
+ 0.000000 16 3.2534
+ 0.000000 17 4.5937
+ 0.000000 18 0.1529
+ 0.000000 19 -1.3610
+ 0.000000 20 0.6062
+ 0.000000 21 2.1473
+ 0.000000 22 1.1462
+ 0.000000 23 1.7843
+ 0.000000 24 -2.5136
+ 0.000000 25 2.2836
+ 0.000000 26 -3.1486
+ 0.000000 27 -3.4742
+ 0.000000 28 -0.1403
+ 0.000000 29 0.3266
+ 0.000000 30 6.6218
+ 0.000000 31 -0.2614
+ 0.000000 32 -2.2848
+ 0.000000 33 0.9558
+ 0.000000 34 -3.4443
+ 0.000000 35 -1.7551
+ 0.000000 36 -5.0356
+ 0.000000 37 2.2322
+ 0.000000 38 -5.9115
+ 0.000000 39 -0.3786
+ 0.000000 40 -7.1256
+ 0.000000 41 0.3157
+ 0.000000 42 2.2955
+ 0.000000 43 -1.3930
+ 0.000000 44 0.4939
+ 0.000000 45 1.7099
+ 0.000000 46 -0.1880
+ 0.000000 47 2.4970
+ 0.000000 48 -5.8590
+ 0.000000 49 -4.2949
+ 0.000000 50 -1.0078
+ 0.000000 51 -4.0462
+ 0.000000 52 2.7627
+ 0.000000 53 0.5621
+ 0.000000 54 -0.4197
+ 0.000000 55 0.7168
+ 0.000000 56 1.4767
+ 0.000000 57 0.0492
+ 0.000000 58 -1.3670
+ 0.000000 59 6.6129
+ 0.000000 60 -3.1318
+ 0.000000 61 1.9615
+ 0.000000 62 4.0257
+ 0.000000 63 3.3679
+ 0.000000 64 5.1249
+ 0.000000 65 1.0571
+ 0.000000 66 -2.6718
+ 0.000000 67 1.9511
+ 0.000000 68 -3.0899
+ 0.000000 69 3.3844
+ 0.000000 70 3.5373
+ 0.000000 71 -2.5662
+ 0.000000 72 1.3854
+ 0.000000 73 -0.8866
+ 0.000000 74 3.2630
+ 0.000000 75 -5.8850
+ 0.000000 76 -7.2364
+ 0.000000 77 -2.0470
+ 0.000000 78 1.2118
+ 0.000000 79 2.7032
+ 0.000000 80 -2.0353
+ 0.000000 81 -0.2827
+ 0.000000 82 -1.6227
+ 0.000000 83 0.6232
+ 0.000000 84 1.2917
+ 0.000000 85 3.0123
+ 0.000000 86 7.6244
+ 0.000000 87 -1.9792
+ 0.000000 88 0.8384
+ 0.000000 89 6.2483
+ 0.000000 90 -1.2618
+ 0.000000 91 1.6919
+ 0.000000 92 4.9239
+ 0.000000 93 -0.0553
+ 0.000000 94 6.5349
+ 0.000000 95 -6.0543
+ 0.000000 96 -1.0205
+ 0.000000 97 0.3694
+ 0.000000 98 -7.0517
+ 0.000000 99 -0.9435
+ 0.000000 100 -1.6073
+ 0.000000 101 9.8342
+ 0.000000 102 -4.7203
+ 0.000000 103 2.7525
+ 0.000000 104 -7.9241
+ 0.000000 105 5.5616
+ 0.000000 106 1.2297
+ 0.000000 107 3.8689
+ 0.000000 108 -2.2532
+ 0.000000 109 -0.5728
+ 0.000000 110 -2.1037
+ 0.000000 111 -0.3446
+ 0.000000 112 -1.8839
+ 0.000000 113 1.1764
+ 0.000000 114 -0.9034
+ 0.000000 115 -2.5301
+ 0.000000 116 -3.4934
+ 0.000000 117 3.9375
+ 0.000000 118 0.0475
+ 0.000000 119 1.0507
+ 0.000000 120 -4.9949
+ 0.000000 121 -2.8268
+ 0.000000 122 0.4098
+ 0.000000 123 1.7328
+ 0.000000 124 -3.0211
+ 0.000000 125 -0.2859
+ 0.000000 126 1.8651
+ 0.000000 127 2.0405
+ 0.000000 128 -2.1358
+ 0.000000 129 -2.7030
+ 0.000000 130 2.5471
+ 0.000000 131 -0.2810
+ 0.000000 132 1.5934
+ 0.000000 133 -3.1017
+ 0.000000 134 -1.6080
+ 0.000000 135 0.7564
+ 0.000000 136 3.7250
+ 0.000000 137 0.8031
+ 0.000000 138 0.7069
+ 0.000000 139 -0.2153
+ 0.000000 140 -1.0334
+ 0.000000 141 1.1444
+ 0.000000 142 1.5002
+ 0.000000 143 1.0250
+ 0.000000 144 -0.4688
+ 0.000000 145 -2.3582
+ 0.000000 146 6.2597
+ 0.000000 147 3.1187
+ 0.000000 148 -2.1759
+ 0.000000 149 2.7629
+ 0.000000 150 -2.4924
+ 0.000000 151 -3.7095
+ 0.000000 152 -1.7532
+ 0.000000 153 -4.1347
+ 0.000000 154 -1.7478
+ 0.000000 155 -2.9066
+ 0.000000 156 1.3769
+ 0.000000 157 -1.3631
+ 0.000000 158 -7.2793
+ 0.000000 159 -1.2756
+ 0.000000 160 -0.2989
+ 0.000000 161 0.2878
+ 0.000000 162 1.8778
+ 0.000000 163 -3.2438
+ 0.000000 164 -5.5374
+ 0.000000 165 -3.6191
+ 0.000000 166 6.7136
+ 0.000000 167 2.8478
+ 0.000000 168 5.8495
+ 0.000000 169 -3.5060
+ 0.000000 170 2.3624
+ 0.000000 171 2.2127
+ 0.000000 172 1.3909
+ 0.000000 173 -0.8028
+ 0.000000 174 -3.6181
+ 0.000000 175 -4.5232
+ 0.000000 176 -1.1553
+ 0.000000 177 1.1278
+ 0.000000 178 0.8887
+ 0.000000 179 5.3118
+ 0.000000 180 0.6350
+ 0.000000 181 -0.7556
+ 0.000000 182 -3.5560
+ 0.000000 183 0.0509
+ 0.000000 184 1.2030
+ 0.000000 185 0.0213
+ 0.000000 186 3.0273
+ 0.000000 187 2.3146
+ 0.000000 188 -3.1933
+ 0.000000 189 1.4907
+ 0.000000 190 2.4234
+ 0.000000 191 -3.5761
+ 0.000000 192 -43.8368
+ 0.000000 193 28.3463
+ 0.000000 194 -28.0159
+ 0.000000 195 28.3463
+ 0.000000 196 -48.0443
+ 0.000000 197 -6.5965
+ 0.000000 198 -28.0159
+ 0.000000 199 -6.5965
+ 0.000000 200 -183.6319
diff --git a/regtest/crystallization/rt-nbonds-q6/plumed.dat b/regtest/crystallization/rt-nbonds-q6/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..0d6d4a995ef20dbe68d26a802fce12464fd194a5
--- /dev/null
+++ b/regtest/crystallization/rt-nbonds-q6/plumed.dat
@@ -0,0 +1,15 @@
+Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN LABEL=q6
+# Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN NUMERICAL_DERIVATIVES LABEL=q6n
+
+NLINKS ARG=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} LABEL=w6
+# NLINKS ARG=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} NUMERICAL_DERIVATIVES LABEL=w6n
+PRINT ARG=w6 FILE=colv1
+DUMPDERIVATIVES ARG=w6 FILE=deriv1 FMT=%8.4f
+
+Q4 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN LABEL=q4
+# Q4 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN NUMERICAL_DERIVATIVES LABEL=q4n
+
+NLINKS ARG=q4 SWITCH={RATIONAL D_0=3.0 R_0=1.5} LABEL=w4
+# NLINKS ARG=q4 SWITCH={RATIONAL D_0=3.0 R_0=1.5} NUMERICAL_DERIVATIVES LABEL=w4n
+PRINT ARG=w4 FILE=colv2
+DUMPDERIVATIVES ARG=w4 FILE=deriv2 FMT=%8.4f
diff --git a/regtest/crystallization/rt-q6-lowmem/64.xyz b/regtest/crystallization/rt-q6-lowmem/64.xyz
new file mode 100755
index 0000000000000000000000000000000000000000..90b3ae19c7598dd32c498e7105925df054c3e788
--- /dev/null
+++ b/regtest/crystallization/rt-q6-lowmem/64.xyz
@@ -0,0 +1,66 @@
+ 64
+12.41642 12.41642 12.41642
+ Ge 1.473000000000 2.211000000000 8.700200000000
+ Ge 4.886500000000 3.830000000000 6.593500000000
+ Ge 3.807000000000 1.978700000000 10.045000000000
+ Ge 5.002000000000 3.883500000000 1.357000000000
+ Ge 9.636000000000 1.604000000000 8.697700000000
+ Ge 6.559800000000 11.084000000000 9.650400000000
+ Ge 0.627000000000 0.390000000000 2.224300000000
+ Ge 3.341900000000 6.765300000000 1.369500000000
+ Ge 5.032000000000 9.650500000000 2.785000000000
+ Ge 1.682700000000 10.392700000000 5.459500000000
+ Ge 3.517300000000 12.039000000000 5.930600000000
+ Ge 1.072000000000 5.374900000000 12.335000000000
+ Ge 0.863390000000 11.308000000000 0.275000000000
+ Ge 5.867800000000 0.672000000000 6.605200000000
+ Ge 3.961000000000 8.414000000000 8.691600000000
+ Ge 11.570960000000 10.444000000000 2.125000000000
+ Ge 1.736000000000 6.845200000000 6.129000000000
+ Ge 7.557300000000 8.842800000000 6.611800000000
+ Ge 2.785800000000 2.591200000000 1.833300000000
+ Ge 11.564000000000 11.555000000000 10.928000000000
+ Ge 3.324000000000 11.334000000000 12.095000000000
+ Ge 10.532000000000 9.377700000000 6.724000000000
+ Ge 7.157000000000 11.468000000000 12.063000000000
+ Ge 0.027000000000 4.622000000000 5.996200000000
+ Ge 4.564000000000 6.513200000000 5.370200000000
+ Ge 12.189770000000 7.981000000000 2.257000000000
+ Ge 8.973100000000 0.437000000000 4.852800000000
+ Ge 9.086200000000 9.857000000000 0.975000000000
+ Ge 6.516500000000 12.170000000000 2.438600000000
+ Ge 8.955900000000 4.612000000000 4.478000000000
+ Ge 7.419000000000 3.301600000000 0.450000000000
+ Ge 10.808000000000 7.170600000000 11.109000000000
+ Te 4.818200000000 9.096200000000 6.189300000000
+ Te 10.663400000000 6.726900000000 5.343000000000
+ Te 7.021700000000 4.814600000000 10.649000000000
+ Te 3.253500000000 5.713300000000 8.267800000000
+ Te 10.322000000000 1.250000000000 2.209500000000
+ Te 0.300000000000 5.033000000000 8.902400000000
+ Te 12.092000000000 0.227000000000 8.527200000000
+ Te 6.329000000000 2.634100000000 8.525500000000
+ Te 8.044800000000 11.712000000000 7.575400000000
+ Te 2.150000000000 8.302000000000 3.591400000000
+ Te 11.581000000000 11.201000000000 4.824700000000
+ Te 3.960900000000 4.755000000000 11.528710000000
+ Te 3.815300000000 12.139000000000 3.263700000000
+ Te 9.419700000000 7.232700000000 1.010000000000
+ Te 1.211700000000 1.726300000000 12.223470000000
+ Te 0.798460000000 8.988100000000 7.517700000000
+ Te 10.078000000000 9.503000000000 9.977500000000
+ Te 9.336700000000 0.894000000000 11.469560000000
+ Te 7.251000000000 5.783400000000 6.399000000000
+ Te 3.740000000000 11.515000000000 9.383700000000
+ Te 10.329000000000 2.726600000000 5.835100000000
+ Te 6.722900000000 8.386100000000 9.226500000000
+ Te 1.247000000000 4.660000000000 2.609100000000
+ Te 5.628500000000 6.170200000000 2.845000000000
+ Te 4.742900000000 9.191800000000 0.212000000000
+ Te 5.134400000000 0.984830000000 12.244000000000
+ Te 8.033800000000 10.061100000000 3.578600000000
+ Te 9.840000000000 4.825000000000 9.743000000000
+ Te 6.760000000000 2.189000000000 4.410700000000
+ Te 2.334000000000 2.201000000000 6.079000000000
+ Te 9.930600000000 3.982900000000 1.562000000000
+ Te 0.806810000000 8.091100000000 12.264000000000
diff --git a/regtest/crystallization/rt-q6-lowmem/Makefile b/regtest/crystallization/rt-q6-lowmem/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/crystallization/rt-q6-lowmem/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-q6-lowmem/colv.reference b/regtest/crystallization/rt-q6-lowmem/colv.reference
new file mode 100644
index 0000000000000000000000000000000000000000..8d69c80ee2192c76108352c9c7255dee723a579b
--- /dev/null
+++ b/regtest/crystallization/rt-q6-lowmem/colv.reference
@@ -0,0 +1,2 @@
+#! FIELDS time q6.mean
+ 0.000000 0.245096
diff --git a/regtest/crystallization/rt-q6-lowmem/colv3.reference b/regtest/crystallization/rt-q6-lowmem/colv3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..511ac4b2209d7e98efef88f378746a702b6b6fa7
--- /dev/null
+++ b/regtest/crystallization/rt-q6-lowmem/colv3.reference
@@ -0,0 +1,2 @@
+#! FIELDS time w6.mean
+ 0.000000 0.036242
diff --git a/regtest/crystallization/rt-q6-lowmem/config b/regtest/crystallization/rt-q6-lowmem/config
new file mode 100644
index 0000000000000000000000000000000000000000..e07432072a91405171ff68d3c3d22a09fde3346c
--- /dev/null
+++ b/regtest/crystallization/rt-q6-lowmem/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz 64.xyz"
diff --git a/regtest/crystallization/rt-q6-lowmem/deriv.reference b/regtest/crystallization/rt-q6-lowmem/deriv.reference
new file mode 100644
index 0000000000000000000000000000000000000000..a7c522e7376756146f4ece8e74bc7b27bf920713
--- /dev/null
+++ b/regtest/crystallization/rt-q6-lowmem/deriv.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter q6.mean
+ 0.000000 0 0.0012
+ 0.000000 1 0.0016
+ 0.000000 2 -0.0017
+ 0.000000 3 -0.0003
+ 0.000000 4 0.0017
+ 0.000000 5 -0.0031
+ 0.000000 6 -0.0013
+ 0.000000 7 -0.0015
+ 0.000000 8 -0.0023
+ 0.000000 9 0.0000
+ 0.000000 10 0.0022
+ 0.000000 11 0.0030
+ 0.000000 12 -0.0009
+ 0.000000 13 -0.0010
+ 0.000000 14 -0.0002
+ 0.000000 15 -0.0018
+ 0.000000 16 -0.0026
+ 0.000000 17 -0.0006
+ 0.000000 18 0.0009
+ 0.000000 19 -0.0008
+ 0.000000 20 0.0013
+ 0.000000 21 -0.0024
+ 0.000000 22 0.0041
+ 0.000000 23 -0.0008
+ 0.000000 24 0.0026
+ 0.000000 25 -0.0023
+ 0.000000 26 -0.0015
+ 0.000000 27 -0.0021
+ 0.000000 28 0.0029
+ 0.000000 29 0.0037
+ 0.000000 30 -0.0017
+ 0.000000 31 -0.0015
+ 0.000000 32 0.0018
+ 0.000000 33 -0.0027
+ 0.000000 34 -0.0000
+ 0.000000 35 0.0003
+ 0.000000 36 0.0006
+ 0.000000 37 -0.0016
+ 0.000000 38 0.0004
+ 0.000000 39 -0.0020
+ 0.000000 40 0.0019
+ 0.000000 41 -0.0005
+ 0.000000 42 0.0016
+ 0.000000 43 -0.0053
+ 0.000000 44 0.0001
+ 0.000000 45 -0.0031
+ 0.000000 46 -0.0020
+ 0.000000 47 -0.0020
+ 0.000000 48 -0.0014
+ 0.000000 49 0.0010
+ 0.000000 50 -0.0059
+ 0.000000 51 0.0021
+ 0.000000 52 -0.0023
+ 0.000000 53 0.0027
+ 0.000000 54 0.0011
+ 0.000000 55 0.0006
+ 0.000000 56 -0.0010
+ 0.000000 57 -0.0005
+ 0.000000 58 -0.0017
+ 0.000000 59 -0.0010
+ 0.000000 60 -0.0001
+ 0.000000 61 0.0010
+ 0.000000 62 0.0016
+ 0.000000 63 0.0017
+ 0.000000 64 0.0000
+ 0.000000 65 -0.0029
+ 0.000000 66 0.0003
+ 0.000000 67 0.0033
+ 0.000000 68 -0.0041
+ 0.000000 69 -0.0007
+ 0.000000 70 0.0014
+ 0.000000 71 -0.0004
+ 0.000000 72 0.0029
+ 0.000000 73 0.0013
+ 0.000000 74 -0.0008
+ 0.000000 75 0.0017
+ 0.000000 76 -0.0046
+ 0.000000 77 -0.0000
+ 0.000000 78 0.0009
+ 0.000000 79 -0.0008
+ 0.000000 80 0.0009
+ 0.000000 81 -0.0001
+ 0.000000 82 -0.0002
+ 0.000000 83 -0.0006
+ 0.000000 84 0.0009
+ 0.000000 85 -0.0012
+ 0.000000 86 0.0001
+ 0.000000 87 0.0015
+ 0.000000 88 0.0018
+ 0.000000 89 -0.0039
+ 0.000000 90 0.0008
+ 0.000000 91 0.0005
+ 0.000000 92 0.0029
+ 0.000000 93 0.0025
+ 0.000000 94 0.0016
+ 0.000000 95 0.0016
+ 0.000000 96 -0.0017
+ 0.000000 97 -0.0001
+ 0.000000 98 0.0022
+ 0.000000 99 -0.0024
+ 0.000000 100 0.0009
+ 0.000000 101 0.0004
+ 0.000000 102 -0.0017
+ 0.000000 103 -0.0014
+ 0.000000 104 0.0004
+ 0.000000 105 0.0002
+ 0.000000 106 -0.0033
+ 0.000000 107 -0.0020
+ 0.000000 108 -0.0001
+ 0.000000 109 0.0039
+ 0.000000 110 0.0014
+ 0.000000 111 -0.0004
+ 0.000000 112 0.0018
+ 0.000000 113 -0.0021
+ 0.000000 114 0.0037
+ 0.000000 115 -0.0004
+ 0.000000 116 0.0011
+ 0.000000 117 0.0042
+ 0.000000 118 -0.0016
+ 0.000000 119 -0.0004
+ 0.000000 120 0.0011
+ 0.000000 121 -0.0003
+ 0.000000 122 0.0016
+ 0.000000 123 0.0018
+ 0.000000 124 0.0034
+ 0.000000 125 0.0002
+ 0.000000 126 0.0009
+ 0.000000 127 0.0013
+ 0.000000 128 0.0007
+ 0.000000 129 0.0010
+ 0.000000 130 -0.0032
+ 0.000000 131 0.0021
+ 0.000000 132 -0.0027
+ 0.000000 133 -0.0000
+ 0.000000 134 0.0009
+ 0.000000 135 -0.0045
+ 0.000000 136 -0.0014
+ 0.000000 137 -0.0014
+ 0.000000 138 0.0004
+ 0.000000 139 -0.0003
+ 0.000000 140 -0.0025
+ 0.000000 141 0.0032
+ 0.000000 142 0.0037
+ 0.000000 143 0.0005
+ 0.000000 144 -0.0003
+ 0.000000 145 0.0047
+ 0.000000 146 -0.0015
+ 0.000000 147 -0.0011
+ 0.000000 148 0.0004
+ 0.000000 149 -0.0015
+ 0.000000 150 -0.0006
+ 0.000000 151 -0.0028
+ 0.000000 152 0.0036
+ 0.000000 153 -0.0040
+ 0.000000 154 -0.0003
+ 0.000000 155 -0.0031
+ 0.000000 156 0.0021
+ 0.000000 157 -0.0002
+ 0.000000 158 0.0002
+ 0.000000 159 0.0016
+ 0.000000 160 0.0010
+ 0.000000 161 0.0036
+ 0.000000 162 -0.0004
+ 0.000000 163 -0.0028
+ 0.000000 164 0.0055
+ 0.000000 165 0.0014
+ 0.000000 166 -0.0034
+ 0.000000 167 0.0023
+ 0.000000 168 -0.0002
+ 0.000000 169 -0.0002
+ 0.000000 170 -0.0006
+ 0.000000 171 -0.0009
+ 0.000000 172 0.0009
+ 0.000000 173 -0.0003
+ 0.000000 174 0.0032
+ 0.000000 175 -0.0053
+ 0.000000 176 0.0037
+ 0.000000 177 -0.0019
+ 0.000000 178 -0.0020
+ 0.000000 179 0.0011
+ 0.000000 180 -0.0000
+ 0.000000 181 0.0060
+ 0.000000 182 -0.0033
+ 0.000000 183 -0.0027
+ 0.000000 184 0.0016
+ 0.000000 185 0.0005
+ 0.000000 186 -0.0009
+ 0.000000 187 -0.0031
+ 0.000000 188 -0.0009
+ 0.000000 189 -0.0005
+ 0.000000 190 0.0049
+ 0.000000 191 0.0003
+ 0.000000 192 -0.1431
+ 0.000000 193 -0.0326
+ 0.000000 194 0.0101
+ 0.000000 195 -0.0326
+ 0.000000 196 -0.1712
+ 0.000000 197 0.0351
+ 0.000000 198 0.0101
+ 0.000000 199 0.0351
+ 0.000000 200 -0.1192
diff --git a/regtest/crystallization/rt-q6-lowmem/deriv3.reference b/regtest/crystallization/rt-q6-lowmem/deriv3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2692feba41081ea512941549a0bebe17769351ab
--- /dev/null
+++ b/regtest/crystallization/rt-q6-lowmem/deriv3.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter w6.mean
+ 0.000000 0 0.0017
+ 0.000000 1 0.0017
+ 0.000000 2 0.0049
+ 0.000000 3 -0.0079
+ 0.000000 4 0.0010
+ 0.000000 5 -0.0191
+ 0.000000 6 0.0042
+ 0.000000 7 0.0026
+ 0.000000 8 -0.0191
+ 0.000000 9 -0.0045
+ 0.000000 10 0.0010
+ 0.000000 11 0.0068
+ 0.000000 12 -0.0001
+ 0.000000 13 0.0001
+ 0.000000 14 0.0001
+ 0.000000 15 -0.0004
+ 0.000000 16 -0.0072
+ 0.000000 17 -0.0002
+ 0.000000 18 -0.0069
+ 0.000000 19 -0.0003
+ 0.000000 20 -0.0000
+ 0.000000 21 -0.0015
+ 0.000000 22 -0.0003
+ 0.000000 23 -0.0023
+ 0.000000 24 0.0072
+ 0.000000 25 -0.0040
+ 0.000000 26 -0.0057
+ 0.000000 27 0.0023
+ 0.000000 28 -0.0078
+ 0.000000 29 0.0012
+ 0.000000 30 -0.0029
+ 0.000000 31 0.0131
+ 0.000000 32 0.0032
+ 0.000000 33 0.0033
+ 0.000000 34 -0.0012
+ 0.000000 35 0.0079
+ 0.000000 36 0.0002
+ 0.000000 37 -0.0002
+ 0.000000 38 -0.0054
+ 0.000000 39 0.0017
+ 0.000000 40 0.0049
+ 0.000000 41 0.0065
+ 0.000000 42 -0.0022
+ 0.000000 43 0.0053
+ 0.000000 44 0.0015
+ 0.000000 45 0.0113
+ 0.000000 46 0.0021
+ 0.000000 47 0.0040
+ 0.000000 48 -0.0040
+ 0.000000 49 -0.0010
+ 0.000000 50 -0.0038
+ 0.000000 51 -0.0027
+ 0.000000 52 0.0047
+ 0.000000 53 -0.0066
+ 0.000000 54 0.0000
+ 0.000000 55 0.0066
+ 0.000000 56 0.0076
+ 0.000000 57 -0.0008
+ 0.000000 58 -0.0033
+ 0.000000 59 -0.0064
+ 0.000000 60 -0.0007
+ 0.000000 61 -0.0101
+ 0.000000 62 -0.0022
+ 0.000000 63 -0.0087
+ 0.000000 64 0.0100
+ 0.000000 65 0.0074
+ 0.000000 66 -0.0004
+ 0.000000 67 0.0031
+ 0.000000 68 -0.0076
+ 0.000000 69 0.0045
+ 0.000000 70 -0.0045
+ 0.000000 71 -0.0019
+ 0.000000 72 0.0048
+ 0.000000 73 0.0098
+ 0.000000 74 0.0093
+ 0.000000 75 -0.0042
+ 0.000000 76 -0.0076
+ 0.000000 77 -0.0009
+ 0.000000 78 0.0060
+ 0.000000 79 -0.0106
+ 0.000000 80 -0.0006
+ 0.000000 81 -0.0031
+ 0.000000 82 -0.0031
+ 0.000000 83 0.0004
+ 0.000000 84 0.0034
+ 0.000000 85 0.0012
+ 0.000000 86 -0.0012
+ 0.000000 87 -0.0002
+ 0.000000 88 -0.0075
+ 0.000000 89 0.0214
+ 0.000000 90 0.0007
+ 0.000000 91 0.0037
+ 0.000000 92 0.0057
+ 0.000000 93 0.0081
+ 0.000000 94 0.0026
+ 0.000000 95 -0.0120
+ 0.000000 96 0.0061
+ 0.000000 97 0.0051
+ 0.000000 98 -0.0013
+ 0.000000 99 0.0005
+ 0.000000 100 0.0022
+ 0.000000 101 -0.0038
+ 0.000000 102 -0.0045
+ 0.000000 103 -0.0058
+ 0.000000 104 -0.0015
+ 0.000000 105 0.0149
+ 0.000000 106 -0.0006
+ 0.000000 107 0.0064
+ 0.000000 108 0.0011
+ 0.000000 109 0.0127
+ 0.000000 110 -0.0015
+ 0.000000 111 0.0012
+ 0.000000 112 0.0023
+ 0.000000 113 -0.0029
+ 0.000000 114 0.0085
+ 0.000000 115 -0.0047
+ 0.000000 116 -0.0120
+ 0.000000 117 0.0090
+ 0.000000 118 0.0005
+ 0.000000 119 0.0119
+ 0.000000 120 -0.0053
+ 0.000000 121 -0.0054
+ 0.000000 122 0.0036
+ 0.000000 123 0.0026
+ 0.000000 124 -0.0051
+ 0.000000 125 -0.0119
+ 0.000000 126 -0.0028
+ 0.000000 127 -0.0041
+ 0.000000 128 0.0008
+ 0.000000 129 0.0006
+ 0.000000 130 -0.0136
+ 0.000000 131 -0.0040
+ 0.000000 132 -0.0037
+ 0.000000 133 0.0007
+ 0.000000 134 -0.0078
+ 0.000000 135 0.0070
+ 0.000000 136 -0.0022
+ 0.000000 137 0.0096
+ 0.000000 138 0.0094
+ 0.000000 139 -0.0005
+ 0.000000 140 -0.0005
+ 0.000000 141 -0.0022
+ 0.000000 142 0.0025
+ 0.000000 143 0.0113
+ 0.000000 144 0.0033
+ 0.000000 145 0.0013
+ 0.000000 146 0.0012
+ 0.000000 147 -0.0076
+ 0.000000 148 0.0015
+ 0.000000 149 -0.0030
+ 0.000000 150 -0.0055
+ 0.000000 151 0.0080
+ 0.000000 152 0.0098
+ 0.000000 153 -0.0048
+ 0.000000 154 0.0001
+ 0.000000 155 -0.0062
+ 0.000000 156 0.0065
+ 0.000000 157 -0.0024
+ 0.000000 158 -0.0151
+ 0.000000 159 -0.0066
+ 0.000000 160 -0.0061
+ 0.000000 161 -0.0043
+ 0.000000 162 -0.0081
+ 0.000000 163 -0.0085
+ 0.000000 164 0.0119
+ 0.000000 165 0.0063
+ 0.000000 166 -0.0047
+ 0.000000 167 0.0134
+ 0.000000 168 0.0060
+ 0.000000 169 0.0087
+ 0.000000 170 0.0066
+ 0.000000 171 -0.0009
+ 0.000000 172 0.0114
+ 0.000000 173 0.0004
+ 0.000000 174 -0.0004
+ 0.000000 175 -0.0097
+ 0.000000 176 0.0144
+ 0.000000 177 -0.0117
+ 0.000000 178 0.0026
+ 0.000000 179 0.0020
+ 0.000000 180 -0.0007
+ 0.000000 181 0.0015
+ 0.000000 182 -0.0189
+ 0.000000 183 -0.0024
+ 0.000000 184 -0.0105
+ 0.000000 185 0.0025
+ 0.000000 186 -0.0088
+ 0.000000 187 -0.0002
+ 0.000000 188 0.0007
+ 0.000000 189 -0.0152
+ 0.000000 190 0.0183
+ 0.000000 191 -0.0046
+ 0.000000 192 0.0519
+ 0.000000 193 -0.0782
+ 0.000000 194 -0.0255
+ 0.000000 195 -0.0782
+ 0.000000 196 -0.1128
+ 0.000000 197 0.0867
+ 0.000000 198 -0.0255
+ 0.000000 199 0.0867
+ 0.000000 200 -0.0399
diff --git a/regtest/crystallization/rt-q6-lowmem/plumed.dat b/regtest/crystallization/rt-q6-lowmem/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..7c76774d7961b9cc0f05274803f50696b5326f37
--- /dev/null
+++ b/regtest/crystallization/rt-q6-lowmem/plumed.dat
@@ -0,0 +1,9 @@
+Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN LABEL=q6
+# Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN NUMERICAL_DERIVATIVES LABEL=q6n
+PRINT ARG=q6.* FILE=colv
+DUMPDERIVATIVES ARG=q6.* FILE=deriv FMT=%8.4f
+
+LOCAL_Q6 ARG=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LOWMEM LABEL=w6
+PRINT ARG=w6.* FILE=colv3
+DUMPDERIVATIVES ARG=w6.* FILE=deriv3 FMT=%8.4f
+
diff --git a/regtest/crystallization/rt-q6-subset/64.xyz b/regtest/crystallization/rt-q6-subset/64.xyz
new file mode 100755
index 0000000000000000000000000000000000000000..90b3ae19c7598dd32c498e7105925df054c3e788
--- /dev/null
+++ b/regtest/crystallization/rt-q6-subset/64.xyz
@@ -0,0 +1,66 @@
+ 64
+12.41642 12.41642 12.41642
+ Ge 1.473000000000 2.211000000000 8.700200000000
+ Ge 4.886500000000 3.830000000000 6.593500000000
+ Ge 3.807000000000 1.978700000000 10.045000000000
+ Ge 5.002000000000 3.883500000000 1.357000000000
+ Ge 9.636000000000 1.604000000000 8.697700000000
+ Ge 6.559800000000 11.084000000000 9.650400000000
+ Ge 0.627000000000 0.390000000000 2.224300000000
+ Ge 3.341900000000 6.765300000000 1.369500000000
+ Ge 5.032000000000 9.650500000000 2.785000000000
+ Ge 1.682700000000 10.392700000000 5.459500000000
+ Ge 3.517300000000 12.039000000000 5.930600000000
+ Ge 1.072000000000 5.374900000000 12.335000000000
+ Ge 0.863390000000 11.308000000000 0.275000000000
+ Ge 5.867800000000 0.672000000000 6.605200000000
+ Ge 3.961000000000 8.414000000000 8.691600000000
+ Ge 11.570960000000 10.444000000000 2.125000000000
+ Ge 1.736000000000 6.845200000000 6.129000000000
+ Ge 7.557300000000 8.842800000000 6.611800000000
+ Ge 2.785800000000 2.591200000000 1.833300000000
+ Ge 11.564000000000 11.555000000000 10.928000000000
+ Ge 3.324000000000 11.334000000000 12.095000000000
+ Ge 10.532000000000 9.377700000000 6.724000000000
+ Ge 7.157000000000 11.468000000000 12.063000000000
+ Ge 0.027000000000 4.622000000000 5.996200000000
+ Ge 4.564000000000 6.513200000000 5.370200000000
+ Ge 12.189770000000 7.981000000000 2.257000000000
+ Ge 8.973100000000 0.437000000000 4.852800000000
+ Ge 9.086200000000 9.857000000000 0.975000000000
+ Ge 6.516500000000 12.170000000000 2.438600000000
+ Ge 8.955900000000 4.612000000000 4.478000000000
+ Ge 7.419000000000 3.301600000000 0.450000000000
+ Ge 10.808000000000 7.170600000000 11.109000000000
+ Te 4.818200000000 9.096200000000 6.189300000000
+ Te 10.663400000000 6.726900000000 5.343000000000
+ Te 7.021700000000 4.814600000000 10.649000000000
+ Te 3.253500000000 5.713300000000 8.267800000000
+ Te 10.322000000000 1.250000000000 2.209500000000
+ Te 0.300000000000 5.033000000000 8.902400000000
+ Te 12.092000000000 0.227000000000 8.527200000000
+ Te 6.329000000000 2.634100000000 8.525500000000
+ Te 8.044800000000 11.712000000000 7.575400000000
+ Te 2.150000000000 8.302000000000 3.591400000000
+ Te 11.581000000000 11.201000000000 4.824700000000
+ Te 3.960900000000 4.755000000000 11.528710000000
+ Te 3.815300000000 12.139000000000 3.263700000000
+ Te 9.419700000000 7.232700000000 1.010000000000
+ Te 1.211700000000 1.726300000000 12.223470000000
+ Te 0.798460000000 8.988100000000 7.517700000000
+ Te 10.078000000000 9.503000000000 9.977500000000
+ Te 9.336700000000 0.894000000000 11.469560000000
+ Te 7.251000000000 5.783400000000 6.399000000000
+ Te 3.740000000000 11.515000000000 9.383700000000
+ Te 10.329000000000 2.726600000000 5.835100000000
+ Te 6.722900000000 8.386100000000 9.226500000000
+ Te 1.247000000000 4.660000000000 2.609100000000
+ Te 5.628500000000 6.170200000000 2.845000000000
+ Te 4.742900000000 9.191800000000 0.212000000000
+ Te 5.134400000000 0.984830000000 12.244000000000
+ Te 8.033800000000 10.061100000000 3.578600000000
+ Te 9.840000000000 4.825000000000 9.743000000000
+ Te 6.760000000000 2.189000000000 4.410700000000
+ Te 2.334000000000 2.201000000000 6.079000000000
+ Te 9.930600000000 3.982900000000 1.562000000000
+ Te 0.806810000000 8.091100000000 12.264000000000
diff --git a/regtest/crystallization/rt-q6-subset/Makefile b/regtest/crystallization/rt-q6-subset/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/crystallization/rt-q6-subset/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-q6-subset/colv3.reference b/regtest/crystallization/rt-q6-subset/colv3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..17de575c442c0e27b62129b798bed4017a7bba0a
--- /dev/null
+++ b/regtest/crystallization/rt-q6-subset/colv3.reference
@@ -0,0 +1,2 @@
+#! FIELDS time w6.mean
+ 0.000000 -0.005288
diff --git a/regtest/crystallization/rt-q6-subset/config b/regtest/crystallization/rt-q6-subset/config
new file mode 100644
index 0000000000000000000000000000000000000000..e07432072a91405171ff68d3c3d22a09fde3346c
--- /dev/null
+++ b/regtest/crystallization/rt-q6-subset/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz 64.xyz"
diff --git a/regtest/crystallization/rt-q6-subset/deriv3.reference b/regtest/crystallization/rt-q6-subset/deriv3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..4baa519f0d44d453d73b38a5c014931119a14e23
--- /dev/null
+++ b/regtest/crystallization/rt-q6-subset/deriv3.reference
@@ -0,0 +1,586 @@
+#! FIELDS time parameter w6.mean
+ 0.000000 0 -0.0191
+ 0.000000 1 -0.0137
+ 0.000000 2 0.0086
+ 0.000000 3 -0.0108
+ 0.000000 4 0.0103
+ 0.000000 5 -0.0439
+ 0.000000 6 0.0300
+ 0.000000 7 -0.0181
+ 0.000000 8 -0.0697
+ 0.000000 9 -0.0128
+ 0.000000 10 -0.0013
+ 0.000000 11 0.0243
+ 0.000000 12 0.0036
+ 0.000000 13 0.0324
+ 0.000000 14 0.0102
+ 0.000000 15 -0.0072
+ 0.000000 16 0.0092
+ 0.000000 17 0.0004
+ 0.000000 18 -0.0106
+ 0.000000 19 -0.0049
+ 0.000000 20 -0.0031
+ 0.000000 21 0.0087
+ 0.000000 22 -0.0073
+ 0.000000 23 -0.0134
+ 0.000000 24 -0.0027
+ 0.000000 25 0.0038
+ 0.000000 26 -0.0061
+ 0.000000 27 -0.0024
+ 0.000000 28 0.0045
+ 0.000000 29 -0.0032
+ 0.000000 30 -0.0134
+ 0.000000 31 -0.0220
+ 0.000000 32 0.0061
+ 0.000000 33 0.0000
+ 0.000000 34 0.0000
+ 0.000000 35 -0.0000
+ 0.000000 36 0.0091
+ 0.000000 37 0.0053
+ 0.000000 38 -0.0099
+ 0.000000 39 -0.0000
+ 0.000000 40 0.0000
+ 0.000000 41 0.0000
+ 0.000000 42 0.0000
+ 0.000000 43 -0.0001
+ 0.000000 44 -0.0001
+ 0.000000 45 -0.0133
+ 0.000000 46 0.0004
+ 0.000000 47 0.0048
+ 0.000000 48 0.0117
+ 0.000000 49 -0.0055
+ 0.000000 50 0.0012
+ 0.000000 51 -0.0006
+ 0.000000 52 -0.0006
+ 0.000000 53 0.0005
+ 0.000000 54 0.0070
+ 0.000000 55 0.0014
+ 0.000000 56 0.0147
+ 0.000000 57 -0.0000
+ 0.000000 58 0.0002
+ 0.000000 59 0.0002
+ 0.000000 60 0.0000
+ 0.000000 61 0.0000
+ 0.000000 62 0.0000
+ 0.000000 63 0.0096
+ 0.000000 64 -0.0058
+ 0.000000 65 0.0032
+ 0.000000 66 0.0000
+ 0.000000 67 0.0000
+ 0.000000 68 0.0000
+ 0.000000 69 -0.0040
+ 0.000000 70 -0.0035
+ 0.000000 71 0.0148
+ 0.000000 72 -0.0008
+ 0.000000 73 0.0051
+ 0.000000 74 0.0074
+ 0.000000 75 0.0005
+ 0.000000 76 -0.0009
+ 0.000000 77 -0.0009
+ 0.000000 78 0.0003
+ 0.000000 79 -0.0005
+ 0.000000 80 -0.0002
+ 0.000000 81 0.0035
+ 0.000000 82 0.0005
+ 0.000000 83 -0.0010
+ 0.000000 84 0.0037
+ 0.000000 85 0.0027
+ 0.000000 86 -0.0008
+ 0.000000 87 0.0077
+ 0.000000 88 0.0014
+ 0.000000 89 -0.0000
+ 0.000000 90 -0.0000
+ 0.000000 91 0.0000
+ 0.000000 92 0.0000
+ 0.000000 93 0.0074
+ 0.000000 94 -0.0047
+ 0.000000 95 0.0023
+ 0.000000 96 -0.0000
+ 0.000000 97 -0.0000
+ 0.000000 98 0.0000
+ 0.000000 99 -0.0101
+ 0.000000 100 0.0184
+ 0.000000 101 -0.0038
+ 0.000000 102 -0.0063
+ 0.000000 103 -0.0019
+ 0.000000 104 0.0027
+ 0.000000 105 0.0025
+ 0.000000 106 0.0028
+ 0.000000 107 0.0029
+ 0.000000 108 0.0000
+ 0.000000 109 0.0000
+ 0.000000 110 0.0000
+ 0.000000 111 -0.0000
+ 0.000000 112 0.0001
+ 0.000000 113 -0.0001
+ 0.000000 114 0.0000
+ 0.000000 115 0.0000
+ 0.000000 116 -0.0000
+ 0.000000 117 -0.0030
+ 0.000000 118 -0.0143
+ 0.000000 119 -0.0110
+ 0.000000 120 0.0055
+ 0.000000 121 0.0043
+ 0.000000 122 0.0234
+ 0.000000 123 -0.0000
+ 0.000000 124 0.0000
+ 0.000000 125 0.0000
+ 0.000000 126 -0.0040
+ 0.000000 127 0.0007
+ 0.000000 128 -0.0057
+ 0.000000 129 0.0024
+ 0.000000 130 -0.0056
+ 0.000000 131 -0.0244
+ 0.000000 132 0.0020
+ 0.000000 133 -0.0059
+ 0.000000 134 0.0076
+ 0.000000 135 -0.0070
+ 0.000000 136 0.0009
+ 0.000000 137 0.0080
+ 0.000000 138 -0.0000
+ 0.000000 139 0.0000
+ 0.000000 140 0.0000
+ 0.000000 141 0.0000
+ 0.000000 142 -0.0002
+ 0.000000 143 -0.0001
+ 0.000000 144 -0.0003
+ 0.000000 145 -0.0181
+ 0.000000 146 0.0127
+ 0.000000 147 0.0003
+ 0.000000 148 -0.0033
+ 0.000000 149 0.0012
+ 0.000000 150 -0.0001
+ 0.000000 151 -0.0000
+ 0.000000 152 0.0000
+ 0.000000 153 0.0085
+ 0.000000 154 -0.0073
+ 0.000000 155 0.0006
+ 0.000000 156 -0.0000
+ 0.000000 157 0.0000
+ 0.000000 158 0.0000
+ 0.000000 159 -0.0000
+ 0.000000 160 -0.0001
+ 0.000000 161 -0.0004
+ 0.000000 162 -0.0097
+ 0.000000 163 0.0027
+ 0.000000 164 -0.0004
+ 0.000000 165 0.0014
+ 0.000000 166 -0.0010
+ 0.000000 167 0.0075
+ 0.000000 168 0.0057
+ 0.000000 169 -0.0039
+ 0.000000 170 0.0127
+ 0.000000 171 0.0075
+ 0.000000 172 -0.0013
+ 0.000000 173 0.0002
+ 0.000000 174 -0.0000
+ 0.000000 175 -0.0000
+ 0.000000 176 -0.0000
+ 0.000000 177 0.0019
+ 0.000000 178 0.0004
+ 0.000000 179 0.0028
+ 0.000000 180 -0.0020
+ 0.000000 181 -0.0043
+ 0.000000 182 0.0106
+ 0.000000 183 -0.0000
+ 0.000000 184 -0.0001
+ 0.000000 185 0.0000
+ 0.000000 186 0.0051
+ 0.000000 187 0.0206
+ 0.000000 188 -0.0031
+ 0.000000 189 0.0000
+ 0.000000 190 0.0000
+ 0.000000 191 0.0000
+ 0.000000 192 0.0019
+ 0.000000 193 0.0029
+ 0.000000 194 -0.0073
+ 0.000000 195 0.0023
+ 0.000000 196 0.0096
+ 0.000000 197 -0.0043
+ 0.000000 198 0.0013
+ 0.000000 199 0.0055
+ 0.000000 200 0.0042
+ 0.000000 201 0.0019
+ 0.000000 202 -0.0002
+ 0.000000 203 -0.0001
+ 0.000000 204 -0.0000
+ 0.000000 205 0.0000
+ 0.000000 206 -0.0000
+ 0.000000 207 0.0012
+ 0.000000 208 -0.0027
+ 0.000000 209 0.0013
+ 0.000000 210 0.0000
+ 0.000000 211 -0.0003
+ 0.000000 212 -0.0001
+ 0.000000 213 0.0013
+ 0.000000 214 0.0109
+ 0.000000 215 -0.0054
+ 0.000000 216 -0.0001
+ 0.000000 217 0.0002
+ 0.000000 218 0.0004
+ 0.000000 219 -0.0003
+ 0.000000 220 -0.0015
+ 0.000000 221 -0.0009
+ 0.000000 222 -0.0018
+ 0.000000 223 0.0074
+ 0.000000 224 0.0049
+ 0.000000 225 -0.0098
+ 0.000000 226 0.0064
+ 0.000000 227 0.0011
+ 0.000000 228 0.0016
+ 0.000000 229 0.0001
+ 0.000000 230 0.0016
+ 0.000000 231 -0.0085
+ 0.000000 232 0.0037
+ 0.000000 233 -0.0005
+ 0.000000 234 -0.0006
+ 0.000000 235 -0.0015
+ 0.000000 236 0.0006
+ 0.000000 237 -0.0000
+ 0.000000 238 -0.0000
+ 0.000000 239 0.0000
+ 0.000000 240 0.0069
+ 0.000000 241 -0.0061
+ 0.000000 242 0.0014
+ 0.000000 243 -0.0003
+ 0.000000 244 -0.0006
+ 0.000000 245 0.0003
+ 0.000000 246 0.0048
+ 0.000000 247 -0.0115
+ 0.000000 248 0.0025
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+ 0.000000 332 -0.0013
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+ 0.000000 337 0.0040
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+ 0.000000 340 -0.0127
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+ 0.000000 342 0.0030
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+ 0.000000 344 0.0002
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+ 0.000000 346 0.0008
+ 0.000000 347 0.0018
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+ 0.000000 390 0.0020
+ 0.000000 391 -0.0009
+ 0.000000 392 0.0006
+ 0.000000 393 0.0075
+ 0.000000 394 0.0046
+ 0.000000 395 0.0039
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+ 0.000000 398 0.0081
+ 0.000000 399 -0.0021
+ 0.000000 400 -0.0004
+ 0.000000 401 -0.0004
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+ 0.000000 414 0.0010
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+ 0.000000 419 0.0035
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+ 0.000000 422 0.0052
+ 0.000000 423 0.0012
+ 0.000000 424 0.0111
+ 0.000000 425 0.0006
+ 0.000000 426 0.0050
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+ 0.000000 429 -0.0047
+ 0.000000 430 0.0037
+ 0.000000 431 0.0004
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+ 0.000000 433 0.0000
+ 0.000000 434 -0.0060
+ 0.000000 435 -0.0014
+ 0.000000 436 -0.0048
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+ 0.000000 439 -0.0050
+ 0.000000 440 -0.0004
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+ 0.000000 444 -0.0086
+ 0.000000 445 0.0052
+ 0.000000 446 -0.0016
+ 0.000000 447 -0.0002
+ 0.000000 448 0.0058
+ 0.000000 449 -0.0011
+ 0.000000 450 0.0006
+ 0.000000 451 0.0015
+ 0.000000 452 -0.0064
+ 0.000000 453 0.0039
+ 0.000000 454 0.0065
+ 0.000000 455 -0.0128
+ 0.000000 456 0.0001
+ 0.000000 457 0.0023
+ 0.000000 458 -0.0008
+ 0.000000 459 0.0036
+ 0.000000 460 0.0021
+ 0.000000 461 0.0002
+ 0.000000 462 0.0063
+ 0.000000 463 -0.0021
+ 0.000000 464 0.0005
+ 0.000000 465 0.0048
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+ 0.000000 471 0.0046
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+ 0.000000 473 0.0066
+ 0.000000 474 0.0095
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+ 0.000000 478 -0.0016
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+ 0.000000 482 -0.0125
+ 0.000000 483 0.0014
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+ 0.000000 486 -0.0090
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+ 0.000000 488 -0.0069
+ 0.000000 489 -0.0041
+ 0.000000 490 -0.0083
+ 0.000000 491 0.0012
+ 0.000000 492 -0.0025
+ 0.000000 493 0.0085
+ 0.000000 494 0.0036
+ 0.000000 495 0.0052
+ 0.000000 496 -0.0105
+ 0.000000 497 0.0021
+ 0.000000 498 0.0005
+ 0.000000 499 -0.0120
+ 0.000000 500 -0.0061
+ 0.000000 501 0.0051
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+ 0.000000 503 -0.0001
+ 0.000000 504 -0.0041
+ 0.000000 505 0.0107
+ 0.000000 506 0.0041
+ 0.000000 507 -0.0021
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+ 0.000000 509 0.0050
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+ 0.000000 511 0.0032
+ 0.000000 512 -0.0068
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+ 0.000000 514 0.0019
+ 0.000000 515 -0.0068
+ 0.000000 516 0.0017
+ 0.000000 517 0.0071
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+ 0.000000 537 -0.0022
+ 0.000000 538 -0.0096
+ 0.000000 539 -0.0013
+ 0.000000 540 0.0134
+ 0.000000 541 -0.0018
+ 0.000000 542 0.0017
+ 0.000000 543 -0.0111
+ 0.000000 544 0.0019
+ 0.000000 545 -0.0031
+ 0.000000 546 0.0064
+ 0.000000 547 0.0009
+ 0.000000 548 -0.0135
+ 0.000000 549 0.0007
+ 0.000000 550 0.0006
+ 0.000000 551 0.0105
+ 0.000000 552 0.0005
+ 0.000000 553 0.0014
+ 0.000000 554 -0.0022
+ 0.000000 555 -0.0012
+ 0.000000 556 0.0060
+ 0.000000 557 0.0008
+ 0.000000 558 0.0025
+ 0.000000 559 0.0027
+ 0.000000 560 0.0021
+ 0.000000 561 -0.0055
+ 0.000000 562 0.0032
+ 0.000000 563 0.0013
+ 0.000000 564 -0.0069
+ 0.000000 565 -0.0046
+ 0.000000 566 -0.0031
+ 0.000000 567 -0.0114
+ 0.000000 568 0.0003
+ 0.000000 569 0.0010
+ 0.000000 570 -0.0065
+ 0.000000 571 0.0040
+ 0.000000 572 -0.0078
+ 0.000000 573 0.0011
+ 0.000000 574 0.0004
+ 0.000000 575 -0.0037
+ 0.000000 576 -0.0231
+ 0.000000 577 -0.1953
+ 0.000000 578 0.0762
+ 0.000000 579 -0.1953
+ 0.000000 580 0.0424
+ 0.000000 581 -0.1586
+ 0.000000 582 0.0762
+ 0.000000 583 -0.1586
+ 0.000000 584 -0.0484
diff --git a/regtest/crystallization/rt-q6-subset/plumed.dat b/regtest/crystallization/rt-q6-subset/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..6fcffbed047fb4fd35158108e7886cdae02eadd2
--- /dev/null
+++ b/regtest/crystallization/rt-q6-subset/plumed.dat
@@ -0,0 +1,7 @@
+Q6 SPECIESA=1-5 SPECIESB=1-64 D_0=3.0 R_0=1.5 LABEL=q6a
+Q6 SPECIESA=6-64 SPECIESB=1-64 D_0=3.0 R_0=1.5 LABEL=q6b
+
+LOCAL_Q6 ARG=q6a,q6b SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LOWMEM LABEL=w6
+PRINT ARG=w6.* FILE=colv3
+DUMPDERIVATIVES ARG=w6.* FILE=deriv3 FMT=%8.4f
+
diff --git a/regtest/crystallization/rt-q6/64.xyz b/regtest/crystallization/rt-q6/64.xyz
new file mode 100755
index 0000000000000000000000000000000000000000..90b3ae19c7598dd32c498e7105925df054c3e788
--- /dev/null
+++ b/regtest/crystallization/rt-q6/64.xyz
@@ -0,0 +1,66 @@
+ 64
+12.41642 12.41642 12.41642
+ Ge 1.473000000000 2.211000000000 8.700200000000
+ Ge 4.886500000000 3.830000000000 6.593500000000
+ Ge 3.807000000000 1.978700000000 10.045000000000
+ Ge 5.002000000000 3.883500000000 1.357000000000
+ Ge 9.636000000000 1.604000000000 8.697700000000
+ Ge 6.559800000000 11.084000000000 9.650400000000
+ Ge 0.627000000000 0.390000000000 2.224300000000
+ Ge 3.341900000000 6.765300000000 1.369500000000
+ Ge 5.032000000000 9.650500000000 2.785000000000
+ Ge 1.682700000000 10.392700000000 5.459500000000
+ Ge 3.517300000000 12.039000000000 5.930600000000
+ Ge 1.072000000000 5.374900000000 12.335000000000
+ Ge 0.863390000000 11.308000000000 0.275000000000
+ Ge 5.867800000000 0.672000000000 6.605200000000
+ Ge 3.961000000000 8.414000000000 8.691600000000
+ Ge 11.570960000000 10.444000000000 2.125000000000
+ Ge 1.736000000000 6.845200000000 6.129000000000
+ Ge 7.557300000000 8.842800000000 6.611800000000
+ Ge 2.785800000000 2.591200000000 1.833300000000
+ Ge 11.564000000000 11.555000000000 10.928000000000
+ Ge 3.324000000000 11.334000000000 12.095000000000
+ Ge 10.532000000000 9.377700000000 6.724000000000
+ Ge 7.157000000000 11.468000000000 12.063000000000
+ Ge 0.027000000000 4.622000000000 5.996200000000
+ Ge 4.564000000000 6.513200000000 5.370200000000
+ Ge 12.189770000000 7.981000000000 2.257000000000
+ Ge 8.973100000000 0.437000000000 4.852800000000
+ Ge 9.086200000000 9.857000000000 0.975000000000
+ Ge 6.516500000000 12.170000000000 2.438600000000
+ Ge 8.955900000000 4.612000000000 4.478000000000
+ Ge 7.419000000000 3.301600000000 0.450000000000
+ Ge 10.808000000000 7.170600000000 11.109000000000
+ Te 4.818200000000 9.096200000000 6.189300000000
+ Te 10.663400000000 6.726900000000 5.343000000000
+ Te 7.021700000000 4.814600000000 10.649000000000
+ Te 3.253500000000 5.713300000000 8.267800000000
+ Te 10.322000000000 1.250000000000 2.209500000000
+ Te 0.300000000000 5.033000000000 8.902400000000
+ Te 12.092000000000 0.227000000000 8.527200000000
+ Te 6.329000000000 2.634100000000 8.525500000000
+ Te 8.044800000000 11.712000000000 7.575400000000
+ Te 2.150000000000 8.302000000000 3.591400000000
+ Te 11.581000000000 11.201000000000 4.824700000000
+ Te 3.960900000000 4.755000000000 11.528710000000
+ Te 3.815300000000 12.139000000000 3.263700000000
+ Te 9.419700000000 7.232700000000 1.010000000000
+ Te 1.211700000000 1.726300000000 12.223470000000
+ Te 0.798460000000 8.988100000000 7.517700000000
+ Te 10.078000000000 9.503000000000 9.977500000000
+ Te 9.336700000000 0.894000000000 11.469560000000
+ Te 7.251000000000 5.783400000000 6.399000000000
+ Te 3.740000000000 11.515000000000 9.383700000000
+ Te 10.329000000000 2.726600000000 5.835100000000
+ Te 6.722900000000 8.386100000000 9.226500000000
+ Te 1.247000000000 4.660000000000 2.609100000000
+ Te 5.628500000000 6.170200000000 2.845000000000
+ Te 4.742900000000 9.191800000000 0.212000000000
+ Te 5.134400000000 0.984830000000 12.244000000000
+ Te 8.033800000000 10.061100000000 3.578600000000
+ Te 9.840000000000 4.825000000000 9.743000000000
+ Te 6.760000000000 2.189000000000 4.410700000000
+ Te 2.334000000000 2.201000000000 6.079000000000
+ Te 9.930600000000 3.982900000000 1.562000000000
+ Te 0.806810000000 8.091100000000 12.264000000000
diff --git a/regtest/crystallization/rt-q6/Makefile b/regtest/crystallization/rt-q6/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/crystallization/rt-q6/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-q6/colv.reference b/regtest/crystallization/rt-q6/colv.reference
new file mode 100644
index 0000000000000000000000000000000000000000..8d69c80ee2192c76108352c9c7255dee723a579b
--- /dev/null
+++ b/regtest/crystallization/rt-q6/colv.reference
@@ -0,0 +1,2 @@
+#! FIELDS time q6.mean
+ 0.000000 0.245096
diff --git a/regtest/crystallization/rt-q6/colv2.reference b/regtest/crystallization/rt-q6/colv2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..9429375c744b2ffa30efb090c4b3938789f57b75
--- /dev/null
+++ b/regtest/crystallization/rt-q6/colv2.reference
@@ -0,0 +1,2 @@
+#! FIELDS time c.mean
+ 0.000000 13.570253
diff --git a/regtest/crystallization/rt-q6/colv3.reference b/regtest/crystallization/rt-q6/colv3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..511ac4b2209d7e98efef88f378746a702b6b6fa7
--- /dev/null
+++ b/regtest/crystallization/rt-q6/colv3.reference
@@ -0,0 +1,2 @@
+#! FIELDS time w6.mean
+ 0.000000 0.036242
diff --git a/regtest/crystallization/rt-q6/colv4.reference b/regtest/crystallization/rt-q6/colv4.reference
new file mode 100644
index 0000000000000000000000000000000000000000..8bd82ca0535e0cc01c70b169fc340d11c00bb64f
--- /dev/null
+++ b/regtest/crystallization/rt-q6/colv4.reference
@@ -0,0 +1,2 @@
+#! FIELDS time q4.mean
+ 0.000000 0.153825
diff --git a/regtest/crystallization/rt-q6/config b/regtest/crystallization/rt-q6/config
new file mode 100644
index 0000000000000000000000000000000000000000..e07432072a91405171ff68d3c3d22a09fde3346c
--- /dev/null
+++ b/regtest/crystallization/rt-q6/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz 64.xyz"
diff --git a/regtest/crystallization/rt-q6/deriv.reference b/regtest/crystallization/rt-q6/deriv.reference
new file mode 100644
index 0000000000000000000000000000000000000000..a7c522e7376756146f4ece8e74bc7b27bf920713
--- /dev/null
+++ b/regtest/crystallization/rt-q6/deriv.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter q6.mean
+ 0.000000 0 0.0012
+ 0.000000 1 0.0016
+ 0.000000 2 -0.0017
+ 0.000000 3 -0.0003
+ 0.000000 4 0.0017
+ 0.000000 5 -0.0031
+ 0.000000 6 -0.0013
+ 0.000000 7 -0.0015
+ 0.000000 8 -0.0023
+ 0.000000 9 0.0000
+ 0.000000 10 0.0022
+ 0.000000 11 0.0030
+ 0.000000 12 -0.0009
+ 0.000000 13 -0.0010
+ 0.000000 14 -0.0002
+ 0.000000 15 -0.0018
+ 0.000000 16 -0.0026
+ 0.000000 17 -0.0006
+ 0.000000 18 0.0009
+ 0.000000 19 -0.0008
+ 0.000000 20 0.0013
+ 0.000000 21 -0.0024
+ 0.000000 22 0.0041
+ 0.000000 23 -0.0008
+ 0.000000 24 0.0026
+ 0.000000 25 -0.0023
+ 0.000000 26 -0.0015
+ 0.000000 27 -0.0021
+ 0.000000 28 0.0029
+ 0.000000 29 0.0037
+ 0.000000 30 -0.0017
+ 0.000000 31 -0.0015
+ 0.000000 32 0.0018
+ 0.000000 33 -0.0027
+ 0.000000 34 -0.0000
+ 0.000000 35 0.0003
+ 0.000000 36 0.0006
+ 0.000000 37 -0.0016
+ 0.000000 38 0.0004
+ 0.000000 39 -0.0020
+ 0.000000 40 0.0019
+ 0.000000 41 -0.0005
+ 0.000000 42 0.0016
+ 0.000000 43 -0.0053
+ 0.000000 44 0.0001
+ 0.000000 45 -0.0031
+ 0.000000 46 -0.0020
+ 0.000000 47 -0.0020
+ 0.000000 48 -0.0014
+ 0.000000 49 0.0010
+ 0.000000 50 -0.0059
+ 0.000000 51 0.0021
+ 0.000000 52 -0.0023
+ 0.000000 53 0.0027
+ 0.000000 54 0.0011
+ 0.000000 55 0.0006
+ 0.000000 56 -0.0010
+ 0.000000 57 -0.0005
+ 0.000000 58 -0.0017
+ 0.000000 59 -0.0010
+ 0.000000 60 -0.0001
+ 0.000000 61 0.0010
+ 0.000000 62 0.0016
+ 0.000000 63 0.0017
+ 0.000000 64 0.0000
+ 0.000000 65 -0.0029
+ 0.000000 66 0.0003
+ 0.000000 67 0.0033
+ 0.000000 68 -0.0041
+ 0.000000 69 -0.0007
+ 0.000000 70 0.0014
+ 0.000000 71 -0.0004
+ 0.000000 72 0.0029
+ 0.000000 73 0.0013
+ 0.000000 74 -0.0008
+ 0.000000 75 0.0017
+ 0.000000 76 -0.0046
+ 0.000000 77 -0.0000
+ 0.000000 78 0.0009
+ 0.000000 79 -0.0008
+ 0.000000 80 0.0009
+ 0.000000 81 -0.0001
+ 0.000000 82 -0.0002
+ 0.000000 83 -0.0006
+ 0.000000 84 0.0009
+ 0.000000 85 -0.0012
+ 0.000000 86 0.0001
+ 0.000000 87 0.0015
+ 0.000000 88 0.0018
+ 0.000000 89 -0.0039
+ 0.000000 90 0.0008
+ 0.000000 91 0.0005
+ 0.000000 92 0.0029
+ 0.000000 93 0.0025
+ 0.000000 94 0.0016
+ 0.000000 95 0.0016
+ 0.000000 96 -0.0017
+ 0.000000 97 -0.0001
+ 0.000000 98 0.0022
+ 0.000000 99 -0.0024
+ 0.000000 100 0.0009
+ 0.000000 101 0.0004
+ 0.000000 102 -0.0017
+ 0.000000 103 -0.0014
+ 0.000000 104 0.0004
+ 0.000000 105 0.0002
+ 0.000000 106 -0.0033
+ 0.000000 107 -0.0020
+ 0.000000 108 -0.0001
+ 0.000000 109 0.0039
+ 0.000000 110 0.0014
+ 0.000000 111 -0.0004
+ 0.000000 112 0.0018
+ 0.000000 113 -0.0021
+ 0.000000 114 0.0037
+ 0.000000 115 -0.0004
+ 0.000000 116 0.0011
+ 0.000000 117 0.0042
+ 0.000000 118 -0.0016
+ 0.000000 119 -0.0004
+ 0.000000 120 0.0011
+ 0.000000 121 -0.0003
+ 0.000000 122 0.0016
+ 0.000000 123 0.0018
+ 0.000000 124 0.0034
+ 0.000000 125 0.0002
+ 0.000000 126 0.0009
+ 0.000000 127 0.0013
+ 0.000000 128 0.0007
+ 0.000000 129 0.0010
+ 0.000000 130 -0.0032
+ 0.000000 131 0.0021
+ 0.000000 132 -0.0027
+ 0.000000 133 -0.0000
+ 0.000000 134 0.0009
+ 0.000000 135 -0.0045
+ 0.000000 136 -0.0014
+ 0.000000 137 -0.0014
+ 0.000000 138 0.0004
+ 0.000000 139 -0.0003
+ 0.000000 140 -0.0025
+ 0.000000 141 0.0032
+ 0.000000 142 0.0037
+ 0.000000 143 0.0005
+ 0.000000 144 -0.0003
+ 0.000000 145 0.0047
+ 0.000000 146 -0.0015
+ 0.000000 147 -0.0011
+ 0.000000 148 0.0004
+ 0.000000 149 -0.0015
+ 0.000000 150 -0.0006
+ 0.000000 151 -0.0028
+ 0.000000 152 0.0036
+ 0.000000 153 -0.0040
+ 0.000000 154 -0.0003
+ 0.000000 155 -0.0031
+ 0.000000 156 0.0021
+ 0.000000 157 -0.0002
+ 0.000000 158 0.0002
+ 0.000000 159 0.0016
+ 0.000000 160 0.0010
+ 0.000000 161 0.0036
+ 0.000000 162 -0.0004
+ 0.000000 163 -0.0028
+ 0.000000 164 0.0055
+ 0.000000 165 0.0014
+ 0.000000 166 -0.0034
+ 0.000000 167 0.0023
+ 0.000000 168 -0.0002
+ 0.000000 169 -0.0002
+ 0.000000 170 -0.0006
+ 0.000000 171 -0.0009
+ 0.000000 172 0.0009
+ 0.000000 173 -0.0003
+ 0.000000 174 0.0032
+ 0.000000 175 -0.0053
+ 0.000000 176 0.0037
+ 0.000000 177 -0.0019
+ 0.000000 178 -0.0020
+ 0.000000 179 0.0011
+ 0.000000 180 -0.0000
+ 0.000000 181 0.0060
+ 0.000000 182 -0.0033
+ 0.000000 183 -0.0027
+ 0.000000 184 0.0016
+ 0.000000 185 0.0005
+ 0.000000 186 -0.0009
+ 0.000000 187 -0.0031
+ 0.000000 188 -0.0009
+ 0.000000 189 -0.0005
+ 0.000000 190 0.0049
+ 0.000000 191 0.0003
+ 0.000000 192 -0.1431
+ 0.000000 193 -0.0326
+ 0.000000 194 0.0101
+ 0.000000 195 -0.0326
+ 0.000000 196 -0.1712
+ 0.000000 197 0.0351
+ 0.000000 198 0.0101
+ 0.000000 199 0.0351
+ 0.000000 200 -0.1192
diff --git a/regtest/crystallization/rt-q6/deriv2.reference b/regtest/crystallization/rt-q6/deriv2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..33b692b27208a3d39b227b155d95dd4b70f562bd
--- /dev/null
+++ b/regtest/crystallization/rt-q6/deriv2.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter c.mean
+ 0.000000 0 0.0097
+ 0.000000 1 -0.0011
+ 0.000000 2 0.0021
+ 0.000000 3 -0.0394
+ 0.000000 4 0.0102
+ 0.000000 5 0.0040
+ 0.000000 6 0.0262
+ 0.000000 7 0.0234
+ 0.000000 8 -0.0092
+ 0.000000 9 -0.0410
+ 0.000000 10 -0.0517
+ 0.000000 11 0.0031
+ 0.000000 12 -0.0217
+ 0.000000 13 -0.0134
+ 0.000000 14 -0.0057
+ 0.000000 15 -0.0011
+ 0.000000 16 0.0435
+ 0.000000 17 -0.0060
+ 0.000000 18 -0.0021
+ 0.000000 19 -0.0027
+ 0.000000 20 0.0279
+ 0.000000 21 -0.0030
+ 0.000000 22 -0.0048
+ 0.000000 23 0.0250
+ 0.000000 24 0.0056
+ 0.000000 25 0.0392
+ 0.000000 26 0.0204
+ 0.000000 27 0.0104
+ 0.000000 28 0.0120
+ 0.000000 29 -0.0064
+ 0.000000 30 0.0051
+ 0.000000 31 -0.0027
+ 0.000000 32 0.0143
+ 0.000000 33 -0.0089
+ 0.000000 34 -0.0177
+ 0.000000 35 -0.0153
+ 0.000000 36 0.0081
+ 0.000000 37 0.0058
+ 0.000000 38 0.0060
+ 0.000000 39 0.0140
+ 0.000000 40 -0.0551
+ 0.000000 41 -0.0152
+ 0.000000 42 0.0027
+ 0.000000 43 0.0130
+ 0.000000 44 0.0054
+ 0.000000 45 -0.0078
+ 0.000000 46 0.0027
+ 0.000000 47 0.0034
+ 0.000000 48 -0.0020
+ 0.000000 49 -0.0247
+ 0.000000 50 -0.0523
+ 0.000000 51 -0.0227
+ 0.000000 52 0.0411
+ 0.000000 53 -0.0164
+ 0.000000 54 0.0507
+ 0.000000 55 -0.0270
+ 0.000000 56 -0.0041
+ 0.000000 57 0.0178
+ 0.000000 58 -0.0327
+ 0.000000 59 0.0111
+ 0.000000 60 -0.0226
+ 0.000000 61 -0.0163
+ 0.000000 62 0.0183
+ 0.000000 63 0.0010
+ 0.000000 64 0.0038
+ 0.000000 65 -0.0115
+ 0.000000 66 0.0263
+ 0.000000 67 0.0133
+ 0.000000 68 -0.0225
+ 0.000000 69 0.0137
+ 0.000000 70 0.0298
+ 0.000000 71 0.0288
+ 0.000000 72 -0.0176
+ 0.000000 73 0.0002
+ 0.000000 74 -0.0362
+ 0.000000 75 0.0012
+ 0.000000 76 0.0366
+ 0.000000 77 0.0618
+ 0.000000 78 0.0363
+ 0.000000 79 -0.0291
+ 0.000000 80 0.0062
+ 0.000000 81 0.0065
+ 0.000000 82 0.0436
+ 0.000000 83 -0.0052
+ 0.000000 84 -0.0335
+ 0.000000 85 0.0507
+ 0.000000 86 -0.0176
+ 0.000000 87 -0.0421
+ 0.000000 88 -0.0190
+ 0.000000 89 -0.0439
+ 0.000000 90 -0.0161
+ 0.000000 91 -0.0130
+ 0.000000 92 0.0097
+ 0.000000 93 -0.0292
+ 0.000000 94 0.0403
+ 0.000000 95 0.0037
+ 0.000000 96 0.0280
+ 0.000000 97 0.0328
+ 0.000000 98 0.0060
+ 0.000000 99 0.0391
+ 0.000000 100 0.0353
+ 0.000000 101 -0.0400
+ 0.000000 102 0.0064
+ 0.000000 103 -0.0312
+ 0.000000 104 -0.0096
+ 0.000000 105 0.0576
+ 0.000000 106 -0.0213
+ 0.000000 107 0.0062
+ 0.000000 108 -0.0314
+ 0.000000 109 -0.0415
+ 0.000000 110 -0.0242
+ 0.000000 111 0.0201
+ 0.000000 112 -0.0282
+ 0.000000 113 -0.0207
+ 0.000000 114 0.0460
+ 0.000000 115 -0.0120
+ 0.000000 116 -0.0141
+ 0.000000 117 -0.0271
+ 0.000000 118 -0.0292
+ 0.000000 119 0.0454
+ 0.000000 120 0.0001
+ 0.000000 121 0.0197
+ 0.000000 122 -0.0060
+ 0.000000 123 -0.0321
+ 0.000000 124 0.0626
+ 0.000000 125 -0.0135
+ 0.000000 126 0.0164
+ 0.000000 127 -0.0240
+ 0.000000 128 0.0045
+ 0.000000 129 -0.0391
+ 0.000000 130 0.0116
+ 0.000000 131 -0.0139
+ 0.000000 132 0.0054
+ 0.000000 133 -0.0348
+ 0.000000 134 -0.0281
+ 0.000000 135 -0.0199
+ 0.000000 136 -0.0443
+ 0.000000 137 -0.0068
+ 0.000000 138 -0.0165
+ 0.000000 139 0.0111
+ 0.000000 140 -0.0048
+ 0.000000 141 0.0374
+ 0.000000 142 -0.0216
+ 0.000000 143 0.0240
+ 0.000000 144 0.0112
+ 0.000000 145 0.0245
+ 0.000000 146 0.0321
+ 0.000000 147 -0.0017
+ 0.000000 148 -0.0077
+ 0.000000 149 -0.0134
+ 0.000000 150 -0.0074
+ 0.000000 151 -0.0199
+ 0.000000 152 0.0592
+ 0.000000 153 -0.0233
+ 0.000000 154 -0.0017
+ 0.000000 155 -0.0161
+ 0.000000 156 0.0194
+ 0.000000 157 -0.0028
+ 0.000000 158 0.0438
+ 0.000000 159 0.0039
+ 0.000000 160 -0.0017
+ 0.000000 161 0.0189
+ 0.000000 162 0.0178
+ 0.000000 163 -0.0033
+ 0.000000 164 0.0215
+ 0.000000 165 0.0011
+ 0.000000 166 -0.0257
+ 0.000000 167 0.0101
+ 0.000000 168 -0.0109
+ 0.000000 169 0.0328
+ 0.000000 170 0.0256
+ 0.000000 171 0.0062
+ 0.000000 172 -0.0062
+ 0.000000 173 -0.0137
+ 0.000000 174 -0.0162
+ 0.000000 175 0.0071
+ 0.000000 176 0.0204
+ 0.000000 177 -0.0114
+ 0.000000 178 -0.0090
+ 0.000000 179 -0.0025
+ 0.000000 180 -0.0231
+ 0.000000 181 0.0044
+ 0.000000 182 -0.0187
+ 0.000000 183 -0.0119
+ 0.000000 184 0.0134
+ 0.000000 185 -0.0111
+ 0.000000 186 0.0253
+ 0.000000 187 0.0153
+ 0.000000 188 -0.0110
+ 0.000000 189 0.0067
+ 0.000000 190 -0.0028
+ 0.000000 191 -0.0329
+ 0.000000 192 15.4541
+ 0.000000 193 0.4015
+ 0.000000 194 0.1687
+ 0.000000 195 0.4015
+ 0.000000 196 14.7038
+ 0.000000 197 0.3340
+ 0.000000 198 0.1687
+ 0.000000 199 0.3340
+ 0.000000 200 15.4941
diff --git a/regtest/crystallization/rt-q6/deriv3.reference b/regtest/crystallization/rt-q6/deriv3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2692feba41081ea512941549a0bebe17769351ab
--- /dev/null
+++ b/regtest/crystallization/rt-q6/deriv3.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter w6.mean
+ 0.000000 0 0.0017
+ 0.000000 1 0.0017
+ 0.000000 2 0.0049
+ 0.000000 3 -0.0079
+ 0.000000 4 0.0010
+ 0.000000 5 -0.0191
+ 0.000000 6 0.0042
+ 0.000000 7 0.0026
+ 0.000000 8 -0.0191
+ 0.000000 9 -0.0045
+ 0.000000 10 0.0010
+ 0.000000 11 0.0068
+ 0.000000 12 -0.0001
+ 0.000000 13 0.0001
+ 0.000000 14 0.0001
+ 0.000000 15 -0.0004
+ 0.000000 16 -0.0072
+ 0.000000 17 -0.0002
+ 0.000000 18 -0.0069
+ 0.000000 19 -0.0003
+ 0.000000 20 -0.0000
+ 0.000000 21 -0.0015
+ 0.000000 22 -0.0003
+ 0.000000 23 -0.0023
+ 0.000000 24 0.0072
+ 0.000000 25 -0.0040
+ 0.000000 26 -0.0057
+ 0.000000 27 0.0023
+ 0.000000 28 -0.0078
+ 0.000000 29 0.0012
+ 0.000000 30 -0.0029
+ 0.000000 31 0.0131
+ 0.000000 32 0.0032
+ 0.000000 33 0.0033
+ 0.000000 34 -0.0012
+ 0.000000 35 0.0079
+ 0.000000 36 0.0002
+ 0.000000 37 -0.0002
+ 0.000000 38 -0.0054
+ 0.000000 39 0.0017
+ 0.000000 40 0.0049
+ 0.000000 41 0.0065
+ 0.000000 42 -0.0022
+ 0.000000 43 0.0053
+ 0.000000 44 0.0015
+ 0.000000 45 0.0113
+ 0.000000 46 0.0021
+ 0.000000 47 0.0040
+ 0.000000 48 -0.0040
+ 0.000000 49 -0.0010
+ 0.000000 50 -0.0038
+ 0.000000 51 -0.0027
+ 0.000000 52 0.0047
+ 0.000000 53 -0.0066
+ 0.000000 54 0.0000
+ 0.000000 55 0.0066
+ 0.000000 56 0.0076
+ 0.000000 57 -0.0008
+ 0.000000 58 -0.0033
+ 0.000000 59 -0.0064
+ 0.000000 60 -0.0007
+ 0.000000 61 -0.0101
+ 0.000000 62 -0.0022
+ 0.000000 63 -0.0087
+ 0.000000 64 0.0100
+ 0.000000 65 0.0074
+ 0.000000 66 -0.0004
+ 0.000000 67 0.0031
+ 0.000000 68 -0.0076
+ 0.000000 69 0.0045
+ 0.000000 70 -0.0045
+ 0.000000 71 -0.0019
+ 0.000000 72 0.0048
+ 0.000000 73 0.0098
+ 0.000000 74 0.0093
+ 0.000000 75 -0.0042
+ 0.000000 76 -0.0076
+ 0.000000 77 -0.0009
+ 0.000000 78 0.0060
+ 0.000000 79 -0.0106
+ 0.000000 80 -0.0006
+ 0.000000 81 -0.0031
+ 0.000000 82 -0.0031
+ 0.000000 83 0.0004
+ 0.000000 84 0.0034
+ 0.000000 85 0.0012
+ 0.000000 86 -0.0012
+ 0.000000 87 -0.0002
+ 0.000000 88 -0.0075
+ 0.000000 89 0.0214
+ 0.000000 90 0.0007
+ 0.000000 91 0.0037
+ 0.000000 92 0.0057
+ 0.000000 93 0.0081
+ 0.000000 94 0.0026
+ 0.000000 95 -0.0120
+ 0.000000 96 0.0061
+ 0.000000 97 0.0051
+ 0.000000 98 -0.0013
+ 0.000000 99 0.0005
+ 0.000000 100 0.0022
+ 0.000000 101 -0.0038
+ 0.000000 102 -0.0045
+ 0.000000 103 -0.0058
+ 0.000000 104 -0.0015
+ 0.000000 105 0.0149
+ 0.000000 106 -0.0006
+ 0.000000 107 0.0064
+ 0.000000 108 0.0011
+ 0.000000 109 0.0127
+ 0.000000 110 -0.0015
+ 0.000000 111 0.0012
+ 0.000000 112 0.0023
+ 0.000000 113 -0.0029
+ 0.000000 114 0.0085
+ 0.000000 115 -0.0047
+ 0.000000 116 -0.0120
+ 0.000000 117 0.0090
+ 0.000000 118 0.0005
+ 0.000000 119 0.0119
+ 0.000000 120 -0.0053
+ 0.000000 121 -0.0054
+ 0.000000 122 0.0036
+ 0.000000 123 0.0026
+ 0.000000 124 -0.0051
+ 0.000000 125 -0.0119
+ 0.000000 126 -0.0028
+ 0.000000 127 -0.0041
+ 0.000000 128 0.0008
+ 0.000000 129 0.0006
+ 0.000000 130 -0.0136
+ 0.000000 131 -0.0040
+ 0.000000 132 -0.0037
+ 0.000000 133 0.0007
+ 0.000000 134 -0.0078
+ 0.000000 135 0.0070
+ 0.000000 136 -0.0022
+ 0.000000 137 0.0096
+ 0.000000 138 0.0094
+ 0.000000 139 -0.0005
+ 0.000000 140 -0.0005
+ 0.000000 141 -0.0022
+ 0.000000 142 0.0025
+ 0.000000 143 0.0113
+ 0.000000 144 0.0033
+ 0.000000 145 0.0013
+ 0.000000 146 0.0012
+ 0.000000 147 -0.0076
+ 0.000000 148 0.0015
+ 0.000000 149 -0.0030
+ 0.000000 150 -0.0055
+ 0.000000 151 0.0080
+ 0.000000 152 0.0098
+ 0.000000 153 -0.0048
+ 0.000000 154 0.0001
+ 0.000000 155 -0.0062
+ 0.000000 156 0.0065
+ 0.000000 157 -0.0024
+ 0.000000 158 -0.0151
+ 0.000000 159 -0.0066
+ 0.000000 160 -0.0061
+ 0.000000 161 -0.0043
+ 0.000000 162 -0.0081
+ 0.000000 163 -0.0085
+ 0.000000 164 0.0119
+ 0.000000 165 0.0063
+ 0.000000 166 -0.0047
+ 0.000000 167 0.0134
+ 0.000000 168 0.0060
+ 0.000000 169 0.0087
+ 0.000000 170 0.0066
+ 0.000000 171 -0.0009
+ 0.000000 172 0.0114
+ 0.000000 173 0.0004
+ 0.000000 174 -0.0004
+ 0.000000 175 -0.0097
+ 0.000000 176 0.0144
+ 0.000000 177 -0.0117
+ 0.000000 178 0.0026
+ 0.000000 179 0.0020
+ 0.000000 180 -0.0007
+ 0.000000 181 0.0015
+ 0.000000 182 -0.0189
+ 0.000000 183 -0.0024
+ 0.000000 184 -0.0105
+ 0.000000 185 0.0025
+ 0.000000 186 -0.0088
+ 0.000000 187 -0.0002
+ 0.000000 188 0.0007
+ 0.000000 189 -0.0152
+ 0.000000 190 0.0183
+ 0.000000 191 -0.0046
+ 0.000000 192 0.0519
+ 0.000000 193 -0.0782
+ 0.000000 194 -0.0255
+ 0.000000 195 -0.0782
+ 0.000000 196 -0.1128
+ 0.000000 197 0.0867
+ 0.000000 198 -0.0255
+ 0.000000 199 0.0867
+ 0.000000 200 -0.0399
diff --git a/regtest/crystallization/rt-q6/deriv4.reference b/regtest/crystallization/rt-q6/deriv4.reference
new file mode 100644
index 0000000000000000000000000000000000000000..80babbe054de23b000b132bc080cf2d23e041880
--- /dev/null
+++ b/regtest/crystallization/rt-q6/deriv4.reference
@@ -0,0 +1,202 @@
+#! FIELDS time parameter q4.mean
+ 0.000000 0 0.0019
+ 0.000000 1 -0.0025
+ 0.000000 2 -0.0023
+ 0.000000 3 0.0007
+ 0.000000 4 0.0026
+ 0.000000 5 0.0016
+ 0.000000 6 -0.0005
+ 0.000000 7 -0.0020
+ 0.000000 8 0.0010
+ 0.000000 9 0.0047
+ 0.000000 10 0.0019
+ 0.000000 11 0.0002
+ 0.000000 12 0.0009
+ 0.000000 13 0.0002
+ 0.000000 14 -0.0009
+ 0.000000 15 -0.0009
+ 0.000000 16 -0.0022
+ 0.000000 17 0.0005
+ 0.000000 18 -0.0009
+ 0.000000 19 0.0014
+ 0.000000 20 -0.0026
+ 0.000000 21 0.0003
+ 0.000000 22 0.0002
+ 0.000000 23 0.0001
+ 0.000000 24 -0.0026
+ 0.000000 25 -0.0005
+ 0.000000 26 0.0016
+ 0.000000 27 -0.0007
+ 0.000000 28 0.0001
+ 0.000000 29 -0.0004
+ 0.000000 30 0.0004
+ 0.000000 31 0.0001
+ 0.000000 32 -0.0029
+ 0.000000 33 0.0007
+ 0.000000 34 -0.0014
+ 0.000000 35 0.0006
+ 0.000000 36 0.0029
+ 0.000000 37 -0.0010
+ 0.000000 38 -0.0015
+ 0.000000 39 -0.0003
+ 0.000000 40 0.0023
+ 0.000000 41 0.0012
+ 0.000000 42 0.0000
+ 0.000000 43 0.0003
+ 0.000000 44 -0.0003
+ 0.000000 45 0.0012
+ 0.000000 46 0.0005
+ 0.000000 47 0.0016
+ 0.000000 48 -0.0002
+ 0.000000 49 0.0020
+ 0.000000 50 0.0010
+ 0.000000 51 -0.0018
+ 0.000000 52 -0.0004
+ 0.000000 53 0.0011
+ 0.000000 54 -0.0028
+ 0.000000 55 0.0024
+ 0.000000 56 0.0022
+ 0.000000 57 0.0006
+ 0.000000 58 0.0006
+ 0.000000 59 -0.0019
+ 0.000000 60 0.0033
+ 0.000000 61 -0.0023
+ 0.000000 62 -0.0018
+ 0.000000 63 0.0036
+ 0.000000 64 -0.0012
+ 0.000000 65 0.0005
+ 0.000000 66 -0.0031
+ 0.000000 67 -0.0018
+ 0.000000 68 -0.0007
+ 0.000000 69 -0.0014
+ 0.000000 70 -0.0007
+ 0.000000 71 0.0000
+ 0.000000 72 0.0007
+ 0.000000 73 -0.0003
+ 0.000000 74 0.0007
+ 0.000000 75 0.0029
+ 0.000000 76 0.0044
+ 0.000000 77 -0.0035
+ 0.000000 78 -0.0030
+ 0.000000 79 0.0040
+ 0.000000 80 -0.0001
+ 0.000000 81 -0.0037
+ 0.000000 82 -0.0005
+ 0.000000 83 0.0010
+ 0.000000 84 0.0017
+ 0.000000 85 -0.0008
+ 0.000000 86 0.0016
+ 0.000000 87 0.0023
+ 0.000000 88 0.0012
+ 0.000000 89 0.0048
+ 0.000000 90 -0.0021
+ 0.000000 91 0.0005
+ 0.000000 92 -0.0011
+ 0.000000 93 -0.0017
+ 0.000000 94 -0.0020
+ 0.000000 95 -0.0001
+ 0.000000 96 0.0026
+ 0.000000 97 -0.0016
+ 0.000000 98 -0.0003
+ 0.000000 99 -0.0027
+ 0.000000 100 -0.0015
+ 0.000000 101 0.0047
+ 0.000000 102 0.0028
+ 0.000000 103 0.0039
+ 0.000000 104 0.0004
+ 0.000000 105 -0.0030
+ 0.000000 106 0.0014
+ 0.000000 107 0.0001
+ 0.000000 108 0.0028
+ 0.000000 109 0.0031
+ 0.000000 110 -0.0004
+ 0.000000 111 -0.0002
+ 0.000000 112 0.0024
+ 0.000000 113 0.0005
+ 0.000000 114 -0.0003
+ 0.000000 115 0.0005
+ 0.000000 116 0.0032
+ 0.000000 117 -0.0031
+ 0.000000 118 0.0006
+ 0.000000 119 -0.0039
+ 0.000000 120 -0.0045
+ 0.000000 121 0.0007
+ 0.000000 122 0.0013
+ 0.000000 123 -0.0003
+ 0.000000 124 -0.0036
+ 0.000000 125 0.0021
+ 0.000000 126 0.0043
+ 0.000000 127 -0.0007
+ 0.000000 128 -0.0023
+ 0.000000 129 0.0044
+ 0.000000 130 0.0018
+ 0.000000 131 0.0012
+ 0.000000 132 -0.0005
+ 0.000000 133 -0.0017
+ 0.000000 134 -0.0003
+ 0.000000 135 -0.0025
+ 0.000000 136 0.0026
+ 0.000000 137 0.0005
+ 0.000000 138 -0.0021
+ 0.000000 139 -0.0000
+ 0.000000 140 0.0016
+ 0.000000 141 -0.0032
+ 0.000000 142 -0.0006
+ 0.000000 143 -0.0024
+ 0.000000 144 0.0021
+ 0.000000 145 -0.0033
+ 0.000000 146 0.0005
+ 0.000000 147 0.0008
+ 0.000000 148 -0.0003
+ 0.000000 149 -0.0002
+ 0.000000 150 0.0018
+ 0.000000 151 -0.0005
+ 0.000000 152 -0.0012
+ 0.000000 153 -0.0005
+ 0.000000 154 -0.0004
+ 0.000000 155 0.0007
+ 0.000000 156 -0.0012
+ 0.000000 157 -0.0007
+ 0.000000 158 -0.0054
+ 0.000000 159 -0.0003
+ 0.000000 160 0.0004
+ 0.000000 161 0.0002
+ 0.000000 162 0.0009
+ 0.000000 163 -0.0023
+ 0.000000 164 -0.0023
+ 0.000000 165 -0.0008
+ 0.000000 166 0.0012
+ 0.000000 167 -0.0020
+ 0.000000 168 0.0003
+ 0.000000 169 0.0014
+ 0.000000 170 0.0002
+ 0.000000 171 -0.0010
+ 0.000000 172 -0.0017
+ 0.000000 173 -0.0004
+ 0.000000 174 -0.0005
+ 0.000000 175 -0.0011
+ 0.000000 176 -0.0000
+ 0.000000 177 0.0002
+ 0.000000 178 -0.0005
+ 0.000000 179 -0.0023
+ 0.000000 180 0.0014
+ 0.000000 181 -0.0042
+ 0.000000 182 0.0017
+ 0.000000 183 -0.0024
+ 0.000000 184 -0.0000
+ 0.000000 185 0.0009
+ 0.000000 186 0.0005
+ 0.000000 187 -0.0017
+ 0.000000 188 0.0010
+ 0.000000 189 0.0013
+ 0.000000 190 0.0014
+ 0.000000 191 0.0011
+ 0.000000 192 -0.2881
+ 0.000000 193 -0.0055
+ 0.000000 194 -0.0166
+ 0.000000 195 -0.0055
+ 0.000000 196 -0.2648
+ 0.000000 197 -0.0367
+ 0.000000 198 -0.0166
+ 0.000000 199 -0.0367
+ 0.000000 200 -0.2513
diff --git a/regtest/crystallization/rt-q6/plumed.dat b/regtest/crystallization/rt-q6/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..f027c26db923a0735219637fdca0a0ba145946a2
--- /dev/null
+++ b/regtest/crystallization/rt-q6/plumed.dat
@@ -0,0 +1,19 @@
+COORDINATIONNUMBER SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LABEL=c
+# COORDINATIONNUMBER SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN NUMERICAL_DERIVATIVES LABEL=cn
+PRINT ARG=c.* FILE=colv2
+DUMPDERIVATIVES ARG=c.* FILE=deriv2 FMT=%8.4f
+
+Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN LABEL=q6
+# Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN NUMERICAL_DERIVATIVES LABEL=q6n
+PRINT ARG=q6.* FILE=colv
+DUMPDERIVATIVES ARG=q6.* FILE=deriv FMT=%8.4f
+
+Q4 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN LABEL=q4
+# Q4 SPECIES=1-64 D_0=3.0 R_0=1.5 MEAN NUMERICAL_DERIVATIVES LABEL=q4n
+PRINT ARG=q4.* FILE=colv4
+DUMPDERIVATIVES ARG=q4.* FILE=deriv4 FMT=%8.4f
+
+LOCAL_Q6 ARG=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LABEL=w6
+# LOCAL_Q6 ARG=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN NUMERICAL_DERIVATIVES LABEL=w6n
+PRINT ARG=w6.* FILE=colv3
+DUMPDERIVATIVES ARG=w6.* FILE=deriv3 FMT=%8.4f
diff --git a/regtest/has-almost/Makefile b/regtest/has-almost/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..42480767ae852294cf2d7269ac5a1c16064d1849
--- /dev/null
+++ b/regtest/has-almost/Makefile
@@ -0,0 +1,2 @@
+include ../scripts/module.make
+
diff --git a/regtest/manyrestraints/Makefile b/regtest/manyrestraints/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..42480767ae852294cf2d7269ac5a1c16064d1849
--- /dev/null
+++ b/regtest/manyrestraints/Makefile
@@ -0,0 +1,2 @@
+include ../scripts/module.make
+
diff --git a/regtest/multicolvar/Makefile b/regtest/multicolvar/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..42480767ae852294cf2d7269ac5a1c16064d1849
--- /dev/null
+++ b/regtest/multicolvar/Makefile
@@ -0,0 +1,2 @@
+include ../scripts/module.make
+
diff --git a/regtest/multicolvar/rt-ang-neigh/Makefile b/regtest/multicolvar/rt-ang-neigh/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/multicolvar/rt-ang-neigh/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/multicolvar/rt-ang-neigh/colvar.reference b/regtest/multicolvar/rt-ang-neigh/colvar.reference
new file mode 100644
index 0000000000000000000000000000000000000000..825cad18589c8d2df0915fb4e35bf84de37c0f47
--- /dev/null
+++ b/regtest/multicolvar/rt-ang-neigh/colvar.reference
@@ -0,0 +1,12 @@
+#! FIELDS time a1.between-1 a1.between-2 a1.between-3 a2.between-1 a2.between-2 a2.between-3
+ 0.000000 0.0605 18.5048 5.6674 0.0605 18.5048 5.6674
+ 1.000000 0.1125 16.6779 5.1212 0.0855 16.6073 5.1203
+ 2.000000 0.2972 17.8013 5.7915 0.2965 17.7994 5.7912
+ 3.000000 0.1657 16.7803 7.0126 0.1655 16.7797 7.0125
+ 4.000000 0.0758 19.0966 5.0760 0.0758 19.0964 5.0759
+ 5.000000 0.0518 17.0844 4.8058 0.0518 17.0843 4.8058
+ 6.000000 0.0466 17.6176 5.5832 0.0465 17.6175 5.5832
+ 7.000000 0.0583 18.0687 4.8021 0.0583 18.0687 4.8021
+ 8.000000 0.0541 15.8351 4.9973 0.0541 15.8350 4.9973
+ 9.000000 0.2105 16.5103 5.6424 0.2102 16.5092 5.6423
+ 10.000000 0.0693 18.5251 5.3055 0.0693 18.5251 5.3055
diff --git a/regtest/multicolvar/rt-ang-neigh/config b/regtest/multicolvar/rt-ang-neigh/config
new file mode 100644
index 0000000000000000000000000000000000000000..de5d8ff6b6c40bfea3da8a7fffb7921d209e86de
--- /dev/null
+++ b/regtest/multicolvar/rt-ang-neigh/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --igro trajout.gro"
diff --git a/regtest/multicolvar/rt-ang-neigh/plumed.dat b/regtest/multicolvar/rt-ang-neigh/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..8b1a28b5de96638f36ae871020ac6c5018130adc
--- /dev/null
+++ b/regtest/multicolvar/rt-ang-neigh/plumed.dat
@@ -0,0 +1,3 @@
+ANGLES GROUPA=1-20:4 GROUPB=1-500:4 SWITCH={EXP D_0=0.3 R_0=0.02} HISTOGRAM={GAUSSIAN LOWER=0 UPPER=pi NBINS=3 SMEAR=0.2} TOL=1E-6 LABEL=a1
+ANGLES GROUPA=1-20:4 GROUPB=1-500:4 SWITCH={EXP D_0=0.3 R_0=0.02} HISTOGRAM={GAUSSIAN LOWER=0 UPPER=pi NBINS=3 SMEAR=0.2} TOL=1E-6 NL_TOL=1E-15 NL_STRIDE=10 LABEL=a2
+PRINT ARG=a1.*,a2.* FILE=colvar FMT=%8.4f
diff --git a/regtest/multicolvar/rt-ang-neigh/trajout.gro b/regtest/multicolvar/rt-ang-neigh/trajout.gro
new file mode 100644
index 0000000000000000000000000000000000000000..a8149f407a3ec07d0cb5c9ba9f32e11fed52ed94
--- /dev/null
+++ b/regtest/multicolvar/rt-ang-neigh/trajout.gro
@@ -0,0 +1,19041 @@
+Generated by trjconv : water tip4p/2005 t= 0.00000
+ 1728
+ 1water OW 1 1.783 2.094 1.523
+ 1water MW 2 1.772 2.088 1.514
+ 1water HW 3 1.775 2.004 1.492
+ 1water HW 4 1.708 2.140 1.486
+ 2water OW 5 1.815 1.785 1.889
+ 2water MW 6 1.805 1.790 1.878
+ 2water HW 7 1.808 1.873 1.851
+ 2water HW 8 1.746 1.735 1.846
+ 3water OW 9 2.001 1.689 1.496
+ 3water MW 10 2.013 1.684 1.488
+ 3water HW 11 2.011 1.602 1.456
+ 3water HW 12 2.083 1.734 1.476
+ 4water OW 13 1.964 2.194 1.920
+ 4water MW 14 1.975 2.192 1.930
+ 4water HW 15 2.045 2.144 1.909
+ 4water HW 16 1.968 2.227 2.010
+ 5water OW 17 2.008 2.208 1.419
+ 5water MW 18 1.999 2.204 1.407
+ 5water HW 19 2.021 2.226 1.326
+ 5water HW 20 1.926 2.159 1.423
+ 6water OW 21 2.033 1.684 1.756
+ 6water MW 22 2.021 1.690 1.748
+ 6water HW 23 2.021 1.686 1.661
+ 6water HW 24 1.954 1.724 1.792
+ 7water OW 25 1.775 1.830 1.400
+ 7water MW 26 1.785 1.824 1.390
+ 7water HW 27 1.850 1.773 1.417
+ 7water HW 28 1.774 1.841 1.305
+ 8water OW 29 1.782 2.041 1.782
+ 8water MW 30 1.793 2.051 1.777
+ 8water HW 31 1.801 2.065 1.691
+ 8water HW 32 1.846 2.090 1.833
+ 9water OW 33 2.226 2.092 1.531
+ 9water MW 34 2.213 2.096 1.539
+ 9water HW 35 2.142 2.121 1.496
+ 9water HW 36 2.214 2.090 1.626
+ 10water OW 37 2.233 1.816 1.879
+ 10water MW 38 2.235 1.804 1.870
+ 10water HW 39 2.164 1.759 1.844
+ 10water HW 40 2.314 1.780 1.843
+ 11water OW 41 2.480 1.722 1.505
+ 11water MW 42 2.478 1.734 1.496
+ 11water HW 43 2.398 1.762 1.475
+ 11water HW 44 2.549 1.777 1.468
+ 12water OW 45 2.414 2.218 1.873
+ 12water MW 46 2.425 2.225 1.865
+ 12water HW 47 2.413 2.306 1.836
+ 12water HW 48 2.499 2.182 1.847
+ 13water OW 49 2.446 2.244 1.429
+ 13water MW 50 2.435 2.251 1.437
+ 13water HW 51 2.443 2.335 1.458
+ 13water HW 52 2.363 2.206 1.458
+ 14water OW 53 2.463 1.693 1.779
+ 14water MW 54 2.465 1.682 1.768
+ 14water HW 55 2.464 1.706 1.684
+ 14water HW 56 2.476 1.599 1.791
+ 15water OW 57 2.239 1.835 1.427
+ 15water MW 58 2.240 1.848 1.419
+ 15water HW 59 2.245 1.924 1.461
+ 15water HW 60 2.238 1.846 1.332
+ 16water OW 61 2.185 2.071 1.804
+ 16water MW 62 2.197 2.064 1.811
+ 16water HW 63 2.194 1.980 1.832
+ 16water HW 64 2.267 2.112 1.831
+ 17water OW 65 1.764 2.111 0.006
+ 17water MW 66 1.765 2.098 0.014
+ 17water HW 67 1.763 2.104 0.101
+ 17water HW 68 1.775 2.021 -0.025
+ 18water OW 69 1.739 1.829 0.379
+ 18water MW 70 1.739 1.817 0.369
+ 18water HW 71 1.815 1.796 0.331
+ 18water HW 72 1.666 1.774 0.351
+ 19water OW 73 1.993 1.698 0.031
+ 19water MW 74 2.004 1.696 0.021
+ 19water HW 75 2.007 1.624 -0.027
+ 19water HW 76 2.065 1.758 0.012
+ 20water OW 77 2.029 2.186 0.382
+ 20water MW 78 2.042 2.193 0.376
+ 20water HW 79 2.113 2.147 0.358
+ 20water HW 80 2.040 2.279 0.364
+ 21water OW 81 1.999 2.275 2.186
+ 21water MW 82 2.001 2.261 2.193
+ 21water HW 83 2.080 2.236 2.219
+ 21water HW 84 1.931 2.212 2.210
+ 22water OW 85 1.970 1.685 0.305
+ 22water MW 86 1.980 1.693 0.296
+ 22water HW 87 1.969 1.690 0.209
+ 22water HW 88 2.045 1.738 0.331
+ 23water OW 89 1.764 1.842 2.151
+ 23water MW 90 1.777 1.835 2.145
+ 23water HW 91 1.785 1.825 2.059
+ 23water HW 92 1.839 1.808 2.199
+ 24water OW 93 1.802 2.087 0.282
+ 24water MW 94 1.810 2.083 0.295
+ 24water HW 95 1.884 2.123 0.315
+ 24water HW 96 1.777 2.021 0.347
+ 25water OW 97 2.206 2.130 0.049
+ 25water MW 98 2.215 2.127 0.037
+ 25water HW 99 2.275 2.186 0.012
+ 25water HW 100 2.206 2.052 -0.007
+ 26water OW 101 2.212 1.817 0.383
+ 26water MW 102 2.223 1.810 0.391
+ 26water HW 103 2.221 1.814 0.478
+ 26water HW 104 2.285 1.764 0.351
+ 27water OW 105 2.456 1.733 0.013
+ 27water MW 106 2.452 1.719 0.018
+ 27water HW 107 2.446 1.652 -0.038
+ 27water HW 108 2.436 1.707 0.103
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+ 28water HW 111 2.561 2.191 0.383
+ 28water HW 112 2.410 2.193 0.378
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+ 29water MW 114 2.433 2.229 2.136
+ 29water HW 115 2.503 2.184 2.163
+ 29water HW 116 2.418 2.242 2.052
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+ 30water MW 118 2.453 1.697 0.300
+ 30water HW 119 2.455 1.610 0.313
+ 30water HW 120 2.520 1.747 0.323
+ 31water OW 121 2.208 1.858 2.149
+ 31water MW 122 2.221 1.855 2.141
+ 31water HW 123 2.218 1.870 2.055
+ 31water HW 124 2.293 1.826 2.179
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+ 32water MW 126 2.282 2.060 0.308
+ 32water HW 127 2.261 1.981 0.339
+ 32water HW 128 2.261 2.082 0.226
+ 33water OW 129 1.787 2.113 0.717
+ 33water MW 130 1.797 2.122 0.725
+ 33water HW 131 1.778 2.139 0.809
+ 33water HW 132 1.870 2.152 0.689
+ 34water OW 133 1.793 1.861 1.134
+ 34water MW 134 1.801 1.864 1.121
+ 34water HW 135 1.780 1.934 1.073
+ 34water HW 136 1.866 1.812 1.097
+ 35water OW 137 2.027 1.719 0.772
+ 35water MW 138 2.016 1.712 0.763
+ 35water HW 139 1.953 1.760 0.728
+ 35water HW 140 2.020 1.626 0.749
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+ 36water MW 142 2.004 2.220 1.129
+ 36water HW 143 2.065 2.161 1.107
+ 36water HW 144 2.013 2.303 1.104
+ 37water OW 145 2.037 2.210 0.675
+ 37water MW 146 2.050 2.203 0.670
+ 37water HW 147 2.065 2.199 0.584
+ 37water HW 148 2.106 2.169 0.727
+ 38water OW 149 2.037 1.723 1.050
+ 38water MW 150 2.033 1.714 1.038
+ 38water HW 151 2.015 1.630 1.048
+ 38water HW 152 2.029 1.751 0.959
+ 39water OW 153 1.809 1.828 0.661
+ 39water MW 154 1.809 1.841 0.652
+ 39water HW 155 1.799 1.833 0.566
+ 39water HW 156 1.817 1.919 0.689
+ 40water OW 157 1.778 2.113 0.994
+ 40water MW 158 1.776 2.121 1.007
+ 40water HW 159 1.696 2.148 1.030
+ 40water HW 160 1.845 2.142 1.055
+ 41water OW 161 2.263 2.069 0.780
+ 41water MW 162 2.274 2.076 0.788
+ 41water HW 163 2.270 2.076 0.875
+ 41water HW 164 2.339 2.117 0.746
+ 42water OW 165 2.253 1.857 1.139
+ 42water MW 166 2.252 1.844 1.131
+ 42water HW 167 2.325 1.806 1.101
+ 42water HW 168 2.174 1.808 1.115
+ 43water OW 169 2.495 1.673 0.757
+ 43water MW 170 2.495 1.685 0.747
+ 43water HW 171 2.420 1.719 0.720
+ 43water HW 172 2.571 1.717 0.718
+ 44water OW 173 2.497 2.200 1.148
+ 44water MW 174 2.496 2.214 1.154
+ 44water HW 175 2.486 2.223 1.240
+ 44water HW 176 2.497 2.284 1.102
+ 45water OW 177 2.487 2.219 0.679
+ 45water MW 178 2.484 2.231 0.669
+ 45water HW 179 2.482 2.215 0.584
+ 45water HW 180 2.468 2.310 0.700
+ 46water OW 181 2.448 1.683 1.042
+ 46water MW 182 2.449 1.669 1.036
+ 46water HW 183 2.460 1.660 0.950
+ 46water HW 184 2.443 1.599 1.087
+ 47water OW 185 2.256 1.819 0.656
+ 47water MW 186 2.246 1.826 0.666
+ 47water HW 187 2.259 1.908 0.690
+ 47water HW 188 2.179 1.780 0.697
+ 48water OW 189 2.249 2.103 1.064
+ 48water MW 190 2.260 2.094 1.071
+ 48water HW 191 2.336 2.129 1.095
+ 48water HW 192 2.242 2.010 1.087
+ 49water OW 193 1.792 0.524 1.492
+ 49water MW 194 1.781 0.518 1.483
+ 49water HW 195 1.717 0.571 1.457
+ 49water HW 196 1.782 0.435 1.458
+ 50water OW 197 1.789 0.270 1.862
+ 50water MW 198 1.778 0.264 1.871
+ 50water HW 199 1.779 0.275 1.957
+ 50water HW 200 1.714 0.218 1.833
+ 51water OW 201 2.025 0.132 1.520
+ 51water MW 202 2.023 0.121 1.531
+ 51water HW 203 2.027 0.145 1.615
+ 51water HW 204 2.010 0.038 1.509
+ 52water OW 205 2.034 0.672 1.856
+ 52water MW 206 2.035 0.660 1.846
+ 52water HW 207 1.963 0.617 1.823
+ 52water HW 208 2.113 0.639 1.812
+ 53water OW 209 2.014 0.652 1.404
+ 53water MW 210 2.004 0.659 1.414
+ 53water HW 211 1.937 0.615 1.448
+ 53water HW 212 2.018 0.743 1.434
+ 54water OW 213 1.986 0.097 1.791
+ 54water MW 214 1.974 0.093 1.800
+ 54water HW 215 1.907 0.146 1.813
+ 54water HW 216 1.977 0.014 1.838
+ 55water OW 217 1.809 0.270 1.391
+ 55water MW 218 1.823 0.269 1.384
+ 55water HW 219 1.894 0.250 1.430
+ 55water HW 220 1.827 0.280 1.297
+ 56water OW 221 1.823 0.521 1.779
+ 56water MW 222 1.821 0.509 1.770
+ 56water HW 223 1.811 0.430 1.805
+ 56water HW 224 1.821 0.520 1.683
+ 57water OW 225 2.244 0.525 1.478
+ 57water MW 226 2.243 0.538 1.469
+ 57water HW 227 2.313 0.570 1.429
+ 57water HW 228 2.165 0.576 1.460
+ 58water OW 229 2.192 0.276 1.858
+ 58water MW 230 2.186 0.268 1.870
+ 58water HW 231 2.217 0.277 1.950
+ 58water HW 232 2.118 0.215 1.854
+ 59water OW 233 2.466 0.190 1.487
+ 59water MW 234 2.453 0.187 1.495
+ 59water HW 235 2.376 0.179 1.455
+ 59water HW 236 2.460 0.178 1.582
+ 60water OW 237 2.464 0.687 1.843
+ 60water MW 238 2.456 0.692 1.831
+ 60water HW 239 2.396 0.640 1.794
+ 60water HW 240 2.470 0.772 1.800
+ 61water OW 241 2.471 0.637 1.367
+ 61water MW 242 2.480 0.643 1.378
+ 61water HW 243 2.472 0.725 1.404
+ 61water HW 244 2.541 0.591 1.413
+ 62water OW 245 2.428 0.132 1.773
+ 62water MW 246 2.429 0.145 1.781
+ 62water HW 247 2.509 0.173 1.804
+ 62water HW 248 2.358 0.190 1.804
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+ 63water MW 250 2.237 0.243 1.374
+ 63water HW 251 2.184 0.193 1.422
+ 63water HW 252 2.256 0.324 1.401
+ 64water OW 253 2.248 0.534 1.746
+ 64water MW 254 2.245 0.523 1.735
+ 64water HW 255 2.260 0.540 1.651
+ 64water HW 256 2.216 0.445 1.761
+ 65water OW 257 1.740 0.544 2.171
+ 65water MW 258 1.750 0.533 2.166
+ 65water HW 259 1.831 0.556 2.144
+ 65water HW 260 1.723 0.451 2.157
+ 66water OW 261 1.785 0.252 0.355
+ 66water MW 262 1.784 0.264 0.364
+ 66water HW 263 1.776 0.251 0.450
+ 66water HW 264 1.783 0.345 0.331
+ 67water OW 265 2.005 0.202 0.028
+ 67water MW 266 2.007 0.189 0.036
+ 67water HW 267 2.010 0.190 0.123
+ 67water HW 268 2.018 0.114 -0.008
+ 68water OW 269 2.014 0.642 0.383
+ 68water MW 270 2.014 0.632 0.371
+ 68water HW 271 1.938 0.599 0.343
+ 68water HW 272 2.089 0.607 0.335
+ 69water OW 273 1.997 0.599 2.126
+ 69water MW 274 2.009 0.599 2.117
+ 69water HW 275 1.999 0.612 2.031
+ 69water HW 276 2.089 0.587 2.150
+ 70water OW 277 2.024 0.094 0.283
+ 70water MW 278 2.023 0.108 0.290
+ 70water HW 279 2.096 0.147 0.317
+ 70water HW 280 1.945 0.145 0.301
+ 71water OW 281 1.755 0.268 2.136
+ 71water MW 282 1.757 0.257 2.146
+ 71water HW 283 1.838 0.244 2.177
+ 71water HW 284 1.690 0.209 2.174
+ 72water OW 285 1.777 0.512 0.271
+ 72water MW 286 1.763 0.517 0.266
+ 72water HW 287 1.739 0.503 0.184
+ 72water HW 288 1.711 0.560 0.321
+ 73water OW 289 2.253 0.538 0.011
+ 73water MW 290 2.255 0.525 0.018
+ 73water HW 291 2.268 0.452 -0.028
+ 73water HW 292 2.254 0.522 0.105
+ 74water OW 293 2.256 0.259 0.375
+ 74water MW 294 2.267 0.255 0.385
+ 74water HW 295 2.343 0.223 0.357
+ 74water HW 296 2.252 0.266 0.470
+ 75water OW 297 2.491 0.163 2.219
+ 75water MW 298 2.503 0.154 2.215
+ 75water HW 299 2.581 0.191 2.203
+ 75water HW 300 2.493 0.068 2.206
+ 76water OW 301 2.503 0.610 0.393
+ 76water MW 302 2.502 0.623 0.401
+ 76water HW 303 2.511 0.620 0.488
+ 76water HW 304 2.491 0.699 0.360
+ 77water OW 305 2.480 0.687 2.138
+ 77water MW 306 2.468 0.681 2.130
+ 77water HW 307 2.403 0.643 2.173
+ 77water HW 308 2.469 0.682 2.043
+ 78water OW 309 2.494 0.142 0.293
+ 78water MW 310 2.490 0.129 0.286
+ 78water HW 311 2.474 0.128 0.200
+ 78water HW 312 2.486 0.055 0.333
+ 79water OW 313 2.263 0.289 2.128
+ 79water MW 314 2.260 0.280 2.140
+ 79water HW 315 2.179 0.269 2.168
+ 79water HW 316 2.327 0.241 2.181
+ 80water OW 317 2.262 0.514 0.283
+ 80water MW 318 2.271 0.504 0.291
+ 80water HW 319 2.349 0.531 0.318
+ 80water HW 320 2.242 0.424 0.310
+ 81water OW 321 1.826 0.540 0.736
+ 81water MW 322 1.814 0.534 0.729
+ 81water HW 323 1.750 0.587 0.701
+ 81water HW 324 1.809 0.448 0.716
+ 82water OW 325 1.816 0.270 1.127
+ 82water MW 326 1.805 0.278 1.120
+ 82water HW 327 1.813 0.363 1.106
+ 82water HW 328 1.733 0.236 1.093
+ 83water OW 329 1.978 0.123 0.740
+ 83water MW 330 1.989 0.115 0.732
+ 83water HW 331 1.984 0.028 0.728
+ 83water HW 332 2.054 0.158 0.694
+ 84water OW 333 2.041 0.633 1.123
+ 84water MW 334 2.051 0.625 1.132
+ 84water HW 335 2.043 0.626 1.218
+ 84water HW 336 2.115 0.580 1.093
+ 85water OW 337 2.063 0.652 0.671
+ 85water MW 338 2.051 0.648 0.662
+ 85water HW 339 1.978 0.618 0.700
+ 85water HW 340 2.055 0.659 0.576
+ 86water OW 341 2.012 0.115 1.009
+ 86water MW 342 2.000 0.121 1.002
+ 86water HW 343 1.940 0.165 1.047
+ 86water HW 344 1.994 0.113 0.915
+ 87water OW 345 1.769 0.270 0.660
+ 87water MW 346 1.768 0.257 0.668
+ 87water HW 347 1.840 0.211 0.686
+ 87water HW 348 1.690 0.231 0.697
+ 88water OW 349 1.799 0.523 1.013
+ 88water MW 350 1.810 0.531 1.005
+ 88water HW 351 1.877 0.567 1.046
+ 88water HW 352 1.802 0.536 0.918
+ 89water OW 353 2.278 0.523 0.754
+ 89water MW 354 2.268 0.528 0.765
+ 89water HW 355 2.201 0.578 0.741
+ 89water HW 356 2.282 0.509 0.849
+ 90water OW 357 2.261 0.216 1.098
+ 90water MW 358 2.248 0.212 1.105
+ 90water HW 359 2.241 0.218 1.192
+ 90water HW 360 2.180 0.186 1.057
+ 91water OW 361 2.444 0.132 0.744
+ 91water MW 362 2.458 0.133 0.751
+ 91water HW 363 2.462 0.121 0.837
+ 91water HW 364 2.530 0.149 0.705
+ 92water OW 365 2.471 0.645 1.091
+ 92water MW 366 2.484 0.643 1.100
+ 92water HW 367 2.480 0.658 1.185
+ 92water HW 368 2.557 0.614 1.063
+ 93water OW 369 2.520 0.622 0.664
+ 93water MW 370 2.509 0.628 0.673
+ 93water HW 371 2.515 0.709 0.703
+ 93water HW 372 2.440 0.578 0.692
+ 94water OW 373 2.484 0.089 1.004
+ 94water MW 374 2.482 0.102 1.012
+ 94water HW 375 2.549 0.155 1.028
+ 94water HW 376 2.401 0.124 1.037
+ 95water OW 377 2.213 0.236 0.656
+ 95water MW 378 2.223 0.243 0.666
+ 95water HW 379 2.204 0.322 0.697
+ 95water HW 380 2.295 0.201 0.690
+ 96water OW 381 2.258 0.496 1.047
+ 96water MW 382 2.271 0.489 1.052
+ 96water HW 383 2.342 0.538 1.064
+ 96water HW 384 2.273 0.404 1.067
+ 97water OW 385 1.798 1.273 1.482
+ 97water MW 386 1.787 1.266 1.473
+ 97water HW 387 1.800 1.184 1.447
+ 97water HW 388 1.715 1.309 1.451
+ 98water OW 389 1.813 1.047 1.875
+ 98water MW 390 1.824 1.042 1.885
+ 98water HW 391 1.812 1.050 1.971
+ 98water HW 392 1.898 1.008 1.853
+ 99water OW 393 2.037 0.905 1.489
+ 99water MW 394 2.036 0.918 1.480
+ 99water HW 395 2.110 0.954 1.452
+ 99water HW 396 1.959 0.951 1.459
+ 100water OW 397 2.036 1.411 1.849
+ 100water MW 398 2.024 1.416 1.842
+ 100water HW 399 1.963 1.360 1.814
+ 100water HW 400 2.015 1.502 1.828
+ 101water OW 401 2.030 1.426 1.397
+ 101water MW 402 2.018 1.420 1.389
+ 101water HW 403 1.957 1.375 1.432
+ 101water HW 404 2.012 1.432 1.303
+ 102water OW 405 2.030 0.927 1.747
+ 102water MW 406 2.030 0.913 1.740
+ 102water HW 407 2.038 0.910 1.653
+ 102water HW 408 2.023 0.840 1.787
+ 103water OW 409 1.795 1.028 1.380
+ 103water MW 410 1.788 1.023 1.367
+ 103water HW 411 1.821 1.041 1.289
+ 103water HW 412 1.713 0.979 1.374
+ 104water OW 413 1.809 1.312 1.753
+ 104water MW 414 1.813 1.298 1.747
+ 104water HW 415 1.839 1.234 1.800
+ 104water HW 416 1.810 1.286 1.661
+ 105water OW 417 2.282 1.294 1.430
+ 105water MW 418 2.283 1.309 1.427
+ 105water HW 419 2.360 1.350 1.428
+ 105water HW 420 2.210 1.354 1.411
+ 106water OW 421 2.260 1.018 1.862
+ 106water MW 422 2.249 1.024 1.853
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 10.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 20.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 30.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 40.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 50.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 60.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 70.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 80.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 90.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 100.00000
+ 1728
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+ 352water MW 1406 1.292 0.527 1.821
+ 352water HW 1407 1.363 0.565 1.854
+ 352water HW 1408 1.215 0.569 1.822
+ 353water OW 1409 0.899 0.477 2.222
+ 353water MW 1410 0.899 0.491 2.215
+ 353water HW 1411 0.972 0.532 2.193
+ 353water HW 1412 0.821 0.528 2.200
+ 354water OW 1413 0.866 0.238 0.384
+ 354water MW 1414 0.878 0.242 0.375
+ 354water HW 1415 0.881 0.322 0.340
+ 354water HW 1416 0.942 0.185 0.359
+ 355water OW 1417 1.055 0.151 2.228
+ 355water MW 1418 1.048 0.143 2.217
+ 355water HW 1419 1.053 0.056 2.217
+ 355water HW 1420 0.999 0.184 2.158
+ 356water OW 1421 1.125 0.676 0.429
+ 356water MW 1422 1.116 0.681 0.418
+ 356water HW 1423 1.060 0.627 0.378
+ 356water HW 1424 1.123 0.764 0.392
+ 357water OW 1425 1.101 0.665 2.163
+ 357water MW 1426 1.113 0.672 2.171
+ 357water HW 1427 1.104 0.755 2.196
+ 357water HW 1428 1.186 0.628 2.188
+ 358water OW 1429 1.102 0.126 0.306
+ 358water MW 1430 1.111 0.134 0.297
+ 358water HW 1431 1.095 0.144 0.212
+ 358water HW 1432 1.182 0.171 0.334
+ 359water OW 1433 0.845 0.262 2.072
+ 359water MW 1434 0.836 0.267 2.083
+ 359water HW 1435 0.762 0.227 2.105
+ 359water HW 1436 0.863 0.339 2.126
+ 360water OW 1437 0.927 0.531 0.285
+ 360water MW 1438 0.914 0.532 0.277
+ 360water HW 1439 0.843 0.565 0.314
+ 360water HW 1440 0.912 0.504 0.194
+ 361water OW 1441 1.336 0.527 0.074
+ 361water MW 1442 1.338 0.514 0.082
+ 361water HW 1443 1.327 0.511 0.168
+ 361water HW 1444 1.358 0.442 0.037
+ 362water OW 1445 1.289 0.280 0.423
+ 362water MW 1446 1.302 0.283 0.415
+ 362water HW 1447 1.358 0.218 0.400
+ 362water HW 1448 1.318 0.363 0.384
+ 363water OW 1449 1.519 0.100 0.069
+ 363water MW 1450 1.508 0.109 0.076
+ 363water HW 1451 1.454 0.156 0.027
+ 363water HW 1452 1.499 0.108 0.163
+ 364water OW 1453 1.535 0.702 0.350
+ 364water MW 1454 1.537 0.712 0.361
+ 364water HW 1455 1.551 0.689 0.444
+ 364water HW 1456 1.532 0.797 0.339
+ 365water OW 1457 1.493 0.716 2.184
+ 365water MW 1458 1.493 0.702 2.190
+ 365water HW 1459 1.566 0.654 2.186
+ 365water HW 1460 1.420 0.669 2.225
+ 366water OW 1461 1.499 0.114 0.343
+ 366water MW 1462 1.512 0.112 0.352
+ 366water HW 1463 1.523 0.038 0.395
+ 366water HW 1464 1.574 0.174 0.353
+ 367water OW 1465 1.315 0.267 2.172
+ 367water MW 1466 1.304 0.262 2.162
+ 367water HW 1467 1.222 0.247 2.188
+ 367water HW 1468 1.326 0.255 2.078
+ 368water OW 1469 1.335 0.530 0.343
+ 368water MW 1470 1.335 0.545 0.345
+ 368water HW 1471 1.259 0.585 0.360
+ 368water HW 1472 1.408 0.592 0.338
+ 369water OW 1473 0.900 0.477 0.751
+ 369water MW 1474 0.891 0.469 0.741
+ 369water HW 1475 0.919 0.390 0.715
+ 369water HW 1476 0.817 0.502 0.710
+ 370water OW 1477 0.868 0.201 1.111
+ 370water MW 1478 0.880 0.201 1.121
+ 370water HW 1479 0.957 0.173 1.093
+ 370water HW 1480 0.870 0.228 1.203
+ 371water OW 1481 1.090 0.050 0.768
+ 371water MW 1482 1.080 0.046 0.757
+ 371water HW 1483 1.010 0.095 0.740
+ 371water HW 1484 1.094 -0.028 0.714
+ 372water OW 1485 1.068 0.656 1.159
+ 372water MW 1486 1.071 0.646 1.149
+ 372water HW 1487 1.154 0.632 1.125
+ 372water HW 1488 1.007 0.598 1.114
+ 373water OW 1489 1.105 0.662 0.701
+ 373water MW 1490 1.095 0.655 0.692
+ 373water HW 1491 1.103 0.661 0.605
+ 373water HW 1492 1.029 0.610 0.728
+ 374water OW 1493 1.137 0.113 1.035
+ 374water MW 1494 1.143 0.122 1.024
+ 374water HW 1495 1.204 0.181 1.045
+ 374water HW 1496 1.115 0.114 0.942
+ 375water OW 1497 0.877 0.186 0.649
+ 375water MW 1498 0.864 0.187 0.641
+ 375water HW 1499 0.790 0.159 0.677
+ 375water HW 1500 0.865 0.217 0.559
+ 376water OW 1501 0.881 0.466 1.034
+ 376water MW 1502 0.881 0.453 1.026
+ 376water HW 1503 0.889 0.460 0.939
+ 376water HW 1504 0.869 0.375 1.063
+ 377water OW 1505 1.337 0.486 0.794
+ 377water MW 1506 1.324 0.480 0.786
+ 377water HW 1507 1.320 0.395 0.769
+ 377water HW 1508 1.259 0.534 0.764
+ 378water OW 1509 1.339 0.295 1.106
+ 378water MW 1510 1.351 0.302 1.102
+ 378water HW 1511 1.353 0.389 1.106
+ 378water HW 1512 1.420 0.258 1.072
+ 379water OW 1513 1.543 0.129 0.764
+ 379water MW 1514 1.532 0.120 0.758
+ 379water HW 1515 1.542 0.035 0.743
+ 379water HW 1516 1.455 0.159 0.742
+ 380water OW 1517 1.574 0.707 1.164
+ 380water MW 1518 1.580 0.696 1.173
+ 380water HW 1519 1.640 0.641 1.142
+ 380water HW 1520 1.554 0.691 1.256
+ 381water OW 1521 1.587 0.642 0.624
+ 381water MW 1522 1.577 0.649 0.633
+ 381water HW 1523 1.586 0.732 0.655
+ 381water HW 1524 1.507 0.604 0.658
+ 382water OW 1525 1.551 0.153 1.033
+ 382water MW 1526 1.550 0.140 1.024
+ 382water HW 1527 1.557 0.145 0.938
+ 382water HW 1528 1.537 0.063 1.064
+ 383water OW 1529 1.293 0.247 0.697
+ 383water MW 1530 1.285 0.239 0.687
+ 383water HW 1531 1.232 0.177 0.719
+ 383water HW 1532 1.291 0.252 0.601
+ 384water OW 1533 1.323 0.583 1.074
+ 384water MW 1534 1.333 0.589 1.064
+ 384water HW 1535 1.333 0.560 0.982
+ 384water HW 1536 1.387 0.653 1.089
+ 385water OW 1537 0.872 1.288 1.491
+ 385water MW 1538 0.865 1.276 1.498
+ 385water HW 1539 0.831 1.289 1.578
+ 385water HW 1540 0.861 1.198 1.460
+ 386water OW 1541 0.830 1.048 1.884
+ 386water MW 1542 0.832 1.062 1.892
+ 386water HW 1543 0.845 1.058 1.978
+ 386water HW 1544 0.830 1.138 1.850
+ 387water OW 1545 1.065 0.924 1.490
+ 387water MW 1546 1.062 0.913 1.500
+ 387water HW 1547 1.051 0.933 1.584
+ 387water HW 1548 1.057 0.830 1.473
+ 388water OW 1549 1.048 1.451 1.827
+ 388water MW 1550 1.048 1.464 1.835
+ 388water HW 1551 1.056 1.465 1.922
+ 388water HW 1552 1.035 1.539 1.792
+ 389water OW 1553 1.114 1.396 1.393
+ 389water MW 1554 1.115 1.388 1.407
+ 389water HW 1555 1.193 1.366 1.439
+ 389water HW 1556 1.042 1.367 1.449
+ 390water OW 1557 1.042 0.915 1.772
+ 390water MW 1558 1.043 0.925 1.783
+ 390water HW 1559 1.117 0.941 1.826
+ 390water HW 1560 0.970 0.970 1.802
+ 391water OW 1561 0.845 1.043 1.373
+ 391water MW 1562 0.849 1.035 1.385
+ 391water HW 1563 0.787 0.992 1.429
+ 391water HW 1564 0.932 1.033 1.412
+ 392water OW 1565 0.829 1.281 1.776
+ 392water MW 1566 0.830 1.292 1.787
+ 392water HW 1567 0.757 1.328 1.820
+ 392water HW 1568 0.908 1.320 1.812
+ 393water OW 1569 1.311 1.255 1.528
+ 393water MW 1570 1.318 1.266 1.536
+ 393water HW 1571 1.374 1.319 1.497
+ 393water HW 1572 1.298 1.276 1.620
+ 394water OW 1573 1.264 1.037 1.881
+ 394water MW 1574 1.275 1.044 1.873
+ 394water HW 1575 1.348 1.002 1.849
+ 394water HW 1576 1.262 1.127 1.849
+ 395water OW 1577 1.560 0.948 1.502
+ 395water MW 1578 1.545 0.950 1.507
+ 395water HW 1579 1.479 0.945 1.451
+ 395water HW 1580 1.531 0.968 1.591
+ 396water OW 1581 1.500 1.466 1.847
+ 396water MW 1582 1.511 1.461 1.857
+ 396water HW 1583 1.583 1.424 1.826
+ 396water HW 1584 1.499 1.472 1.942
+ 397water OW 1585 1.498 1.456 1.473
+ 397water MW 1586 1.498 1.468 1.463
+ 397water HW 1587 1.506 1.549 1.494
+ 397water HW 1588 1.492 1.454 1.378
+ 398water OW 1589 1.511 0.964 1.784
+ 398water MW 1590 1.522 0.960 1.794
+ 398water HW 1591 1.585 1.019 1.812
+ 398water HW 1592 1.519 0.884 1.837
+ 399water OW 1593 1.318 1.005 1.375
+ 399water MW 1594 1.308 1.013 1.383
+ 399water HW 1595 1.231 0.980 1.406
+ 399water HW 1596 1.330 1.094 1.407
+ 400water OW 1597 1.264 1.308 1.811
+ 400water MW 1598 1.263 1.323 1.811
+ 400water HW 1599 1.336 1.371 1.804
+ 400water HW 1600 1.185 1.362 1.818
+ 401water OW 1601 0.887 1.349 0.062
+ 401water MW 1602 0.884 1.360 0.051
+ 401water HW 1603 0.802 1.376 0.025
+ 401water HW 1604 0.951 1.402 0.015
+ 402water OW 1605 0.851 1.016 0.417
+ 402water MW 1606 0.850 1.031 0.422
+ 402water HW 1607 0.853 1.042 0.509
+ 402water HW 1608 0.846 1.099 0.368
+ 403water OW 1609 1.065 0.921 0.050
+ 403water MW 1610 1.076 0.929 0.057
+ 403water HW 1611 1.136 0.973 0.012
+ 403water HW 1612 1.074 0.934 0.144
+ 404water OW 1613 1.087 1.466 0.445
+ 404water MW 1614 1.075 1.463 0.454
+ 404water HW 1615 1.085 1.476 0.540
+ 404water HW 1616 1.000 1.433 0.422
+ 405water OW 1617 1.070 1.475 2.118
+ 405water MW 1618 1.079 1.482 2.129
+ 405water HW 1619 1.072 1.567 2.145
+ 405water HW 1620 1.134 1.432 2.174
+ 406water OW 1621 1.089 0.911 0.336
+ 406water MW 1622 1.087 0.926 0.341
+ 406water HW 1623 1.155 0.980 0.345
+ 406water HW 1624 1.007 0.953 0.364
+ 407water OW 1625 0.858 1.070 2.185
+ 407water MW 1626 0.868 1.076 2.196
+ 407water HW 1627 0.936 1.028 2.221
+ 407water HW 1628 0.853 1.154 2.231
+ 408water OW 1629 0.865 1.280 0.348
+ 408water MW 1630 0.858 1.288 0.337
+ 408water HW 1631 0.898 1.304 0.262
+ 408water HW 1632 0.777 1.318 0.351
+ 409water OW 1633 1.270 1.345 0.024
+ 409water MW 1634 1.266 1.333 0.033
+ 409water HW 1635 1.246 1.258 -0.007
+ 409water HW 1636 1.259 1.341 0.119
+ 410water OW 1637 1.279 1.088 0.395
+ 410water MW 1638 1.289 1.097 0.387
+ 410water HW 1639 1.370 1.070 0.371
+ 410water HW 1640 1.263 1.176 0.362
+ 411water OW 1641 1.529 0.992 0.065
+ 411water MW 1642 1.534 0.982 0.055
+ 411water HW 1643 1.597 1.004 -0.001
+ 411water HW 1644 1.498 0.903 0.052
+ 412water OW 1645 1.513 1.466 0.347
+ 412water MW 1646 1.524 1.462 0.356
+ 412water HW 1647 1.600 1.434 0.322
+ 412water HW 1648 1.515 1.470 0.442
+ 413water OW 1649 1.514 1.467 2.155
+ 413water MW 1650 1.504 1.477 2.160
+ 413water HW 1651 1.420 1.454 2.168
+ 413water HW 1652 1.529 1.559 2.178
+ 414water OW 1653 1.542 0.986 0.338
+ 414water MW 1654 1.554 0.993 0.330
+ 414water HW 1655 1.623 1.020 0.376
+ 414water HW 1656 1.549 1.008 0.245
+ 415water OW 1657 1.258 1.072 2.163
+ 415water MW 1658 1.270 1.069 2.154
+ 415water HW 1659 1.348 1.066 2.193
+ 415water HW 1660 1.262 1.052 2.069
+ 416water OW 1661 1.268 1.346 0.300
+ 416water MW 1662 1.273 1.356 0.311
+ 416water HW 1663 1.219 1.383 0.374
+ 416water HW 1664 1.355 1.384 0.308
+ 417water OW 1665 0.840 1.318 0.767
+ 417water MW 1666 0.843 1.305 0.774
+ 417water HW 1667 0.844 1.231 0.727
+ 417water HW 1668 0.857 1.303 0.860
+ 418water OW 1669 0.791 1.013 1.098
+ 418water MW 1670 0.795 1.026 1.105
+ 418water HW 1671 0.816 1.095 1.056
+ 418water HW 1672 0.797 1.031 1.192
+ 419water OW 1673 1.056 0.930 0.771
+ 419water MW 1674 1.057 0.917 0.779
+ 419water HW 1675 1.053 0.917 0.866
+ 419water HW 1676 1.068 0.843 0.735
+ 420water OW 1677 1.109 1.431 1.126
+ 420water MW 1678 1.120 1.422 1.132
+ 420water HW 1679 1.119 1.406 1.218
+ 420water HW 1680 1.183 1.388 1.082
+ 421water OW 1681 1.084 1.459 0.715
+ 421water MW 1682 1.072 1.464 0.723
+ 421water HW 1683 1.003 1.412 0.734
+ 421water HW 1684 1.070 1.546 0.754
+ 422water OW 1685 1.065 0.903 1.053
+ 422water MW 1686 1.055 0.896 1.063
+ 422water HW 1687 0.980 0.937 1.081
+ 422water HW 1688 1.072 0.818 1.096
+ 423water OW 1689 0.835 1.061 0.701
+ 423water MW 1690 0.838 1.046 0.704
+ 423water HW 1691 0.772 0.989 0.714
+ 423water HW 1692 0.921 1.020 0.712
+ 424water OW 1693 0.867 1.275 1.030
+ 424water MW 1694 0.871 1.289 1.037
+ 424water HW 1695 0.953 1.316 1.041
+ 424water HW 1696 0.807 1.335 1.073
+ 425water OW 1697 1.346 1.278 0.735
+ 425water MW 1698 1.332 1.275 0.730
+ 425water HW 1699 1.274 1.338 0.715
+ 425water HW 1700 1.311 1.191 0.718
+ 426water OW 1701 1.328 1.008 1.108
+ 426water MW 1702 1.316 1.002 1.116
+ 426water HW 1703 1.321 1.003 1.203
+ 426water HW 1704 1.246 0.969 1.076
+ 427water OW 1705 1.533 0.902 0.708
+ 427water MW 1706 1.520 0.903 0.717
+ 427water HW 1707 1.442 0.916 0.682
+ 427water HW 1708 1.530 0.895 0.803
+ 428water OW 1709 1.525 1.418 1.209
+ 428water MW 1710 1.514 1.423 1.198
+ 428water HW 1711 1.531 1.498 1.156
+ 428water HW 1712 1.440 1.379 1.184
+ 429water OW 1713 1.543 1.470 0.630
+ 429water MW 1714 1.533 1.471 0.642
+ 429water HW 1715 1.521 1.545 0.685
+ 429water HW 1716 1.492 1.398 0.667
+ 430water OW 1717 1.544 0.933 0.987
+ 430water MW 1718 1.537 0.928 0.999
+ 430water HW 1719 1.466 0.968 1.029
+ 430water HW 1720 1.570 0.859 1.041
+ 431water OW 1721 1.289 1.007 0.673
+ 431water MW 1722 1.275 1.008 0.667
+ 431water HW 1723 1.203 0.994 0.713
+ 431water HW 1724 1.269 1.034 0.583
+ 432water OW 1725 1.321 1.287 1.032
+ 432water MW 1726 1.322 1.275 1.022
+ 432water HW 1727 1.349 1.285 0.940
+ 432water HW 1728 1.301 1.196 1.053
+ 2.71084 2.34766 2.21339
diff --git a/regtest/multicolvar/rt-dihcor/Makefile b/regtest/multicolvar/rt-dihcor/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/multicolvar/rt-dihcor/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/multicolvar/rt-dihcor/config b/regtest/multicolvar/rt-dihcor/config
new file mode 100644
index 0000000000000000000000000000000000000000..ba8b778571e71d71dd136e9098170c96b46493fe
--- /dev/null
+++ b/regtest/multicolvar/rt-dihcor/config
@@ -0,0 +1,4 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+extra_files="../../trajectories/trajectory.xyz"
diff --git a/regtest/multicolvar/rt-dihcor/derivatives.reference b/regtest/multicolvar/rt-dihcor/derivatives.reference
new file mode 100644
index 0000000000000000000000000000000000000000..61df93168dbab4ddbadd4d58f546052a1bf3ab25
--- /dev/null
+++ b/regtest/multicolvar/rt-dihcor/derivatives.reference
@@ -0,0 +1,286 @@
+#! FIELDS time parameter c1 c1num
+ 0.000000 0 -0.1041 -0.1041
+ 0.000000 1 0.1044 0.1044
+ 0.000000 2 0.0357 0.0357
+ 0.000000 3 -0.1213 -0.1213
+ 0.000000 4 -0.1363 -0.1363
+ 0.000000 5 -0.0436 -0.0436
+ 0.000000 6 0.5638 0.5638
+ 0.000000 7 0.0959 0.0959
+ 0.000000 8 0.0251 0.0251
+ 0.000000 9 -0.3384 -0.3384
+ 0.000000 10 -0.0641 -0.0641
+ 0.000000 11 -0.0172 -0.0172
+ 0.000000 12 0.1046 0.1046
+ 0.000000 13 0.0958 0.0958
+ 0.000000 14 -0.0924 -0.0924
+ 0.000000 15 -0.0580 -0.0580
+ 0.000000 16 0.0011 0.0011
+ 0.000000 17 0.0545 0.0545
+ 0.000000 18 -0.0229 -0.0229
+ 0.000000 19 -0.1796 -0.1796
+ 0.000000 20 0.0106 0.0106
+ 0.000000 21 -0.0238 -0.0238
+ 0.000000 22 0.0828 0.0828
+ 0.000000 23 0.0273 0.0273
+ 0.000000 24 0.2318 0.2318
+ 0.000000 25 0.2122 0.2122
+ 0.000000 26 -0.2047 -0.2047
+ 0.000000 27 -0.1284 -0.1284
+ 0.000000 28 0.0023 0.0023
+ 0.000000 29 0.1207 0.1207
+ 0.000000 30 -0.0508 -0.0508
+ 0.000000 31 -0.3979 -0.3979
+ 0.000000 32 0.0235 0.0235
+ 0.000000 33 -0.0526 -0.0526
+ 0.000000 34 0.1833 0.1833
+ 0.000000 35 0.0606 0.0606
+ 0.000000 36 -0.1939 -0.1939
+ 0.000000 37 -0.2698 -0.2698
+ 0.000000 38 0.2272 0.2272
+ 0.000000 39 0.2757 0.2757
+ 0.000000 40 0.3202 0.3202
+ 0.000000 41 -0.3184 -0.3184
+ 0.000000 42 -0.0357 -0.0357
+ 0.000000 43 0.1389 0.1389
+ 0.000000 44 0.0283 0.0283
+ 0.000000 45 -0.0461 -0.0461
+ 0.000000 46 -0.1893 -0.1893
+ 0.000000 47 0.0630 0.0630
+ 0.000000 48 -0.3333 -0.3333
+ 0.000000 49 0.2108 0.2108
+ 0.000000 50 0.2426 0.2426
+ 0.000000 51 0.2108 0.2108
+ 0.000000 52 0.5382 0.5382
+ 0.000000 53 -0.0342 -0.0342
+ 0.000000 54 0.2426 0.2426
+ 0.000000 55 -0.0342 -0.0342
+ 0.000000 56 -0.2049 -0.2049
+ 0.005000 0 -0.0551 -0.0551
+ 0.005000 1 0.0557 0.0557
+ 0.005000 2 0.0186 0.0186
+ 0.005000 3 -0.0765 -0.0765
+ 0.005000 4 -0.0907 -0.0907
+ 0.005000 5 -0.0288 -0.0288
+ 0.005000 6 0.3224 0.3224
+ 0.005000 7 0.0940 0.0940
+ 0.005000 8 0.0278 0.0278
+ 0.005000 9 -0.1908 -0.1908
+ 0.005000 10 -0.0590 -0.0590
+ 0.005000 11 -0.0175 -0.0175
+ 0.005000 12 0.0568 0.0568
+ 0.005000 13 0.0532 0.0532
+ 0.005000 14 -0.0489 -0.0489
+ 0.005000 15 -0.0268 -0.0268
+ 0.005000 16 0.0007 0.0007
+ 0.005000 17 0.0254 0.0254
+ 0.005000 18 -0.0193 -0.0193
+ 0.005000 19 -0.0982 -0.0982
+ 0.005000 20 0.0092 0.0092
+ 0.005000 21 -0.0107 -0.0107
+ 0.005000 22 0.0443 0.0443
+ 0.005000 23 0.0142 0.0142
+ 0.005000 24 0.2388 0.2388
+ 0.005000 25 0.2235 0.2235
+ 0.005000 26 -0.2053 -0.2053
+ 0.005000 27 -0.1125 -0.1125
+ 0.005000 28 0.0030 0.0030
+ 0.005000 29 0.1067 0.1067
+ 0.005000 30 -0.0813 -0.0813
+ 0.005000 31 -0.4125 -0.4125
+ 0.005000 32 0.0388 0.0388
+ 0.005000 33 -0.0450 -0.0450
+ 0.005000 34 0.1860 0.1860
+ 0.005000 35 0.0598 0.0598
+ 0.005000 36 -0.1526 -0.1526
+ 0.005000 37 -0.3296 -0.3296
+ 0.005000 38 0.2329 0.2329
+ 0.005000 39 0.2213 0.2213
+ 0.005000 40 0.4168 0.4168
+ 0.005000 41 -0.3274 -0.3274
+ 0.005000 42 -0.0374 -0.0374
+ 0.005000 43 0.1117 0.1117
+ 0.005000 44 0.0248 0.0248
+ 0.005000 45 -0.0313 -0.0313
+ 0.005000 46 -0.1988 -0.1988
+ 0.005000 47 0.0697 0.0697
+ 0.005000 48 -0.2387 -0.2387
+ 0.005000 49 0.1850 0.1850
+ 0.005000 50 0.1887 0.1887
+ 0.005000 51 0.1850 0.1850
+ 0.005000 52 0.4202 0.4202
+ 0.005000 53 -0.0472 -0.0472
+ 0.005000 54 0.1887 0.1887
+ 0.005000 55 -0.0472 -0.0472
+ 0.005000 56 -0.1814 -0.1814
+ 0.010000 0 0.0162 0.0162
+ 0.010000 1 -0.0173 -0.0173
+ 0.010000 2 -0.0054 -0.0054
+ 0.010000 3 0.0257 0.0257
+ 0.010000 4 0.0370 0.0370
+ 0.010000 5 0.0114 0.0114
+ 0.010000 6 -0.1021 -0.1021
+ 0.010000 7 -0.0506 -0.0506
+ 0.010000 8 -0.0155 -0.0155
+ 0.010000 9 0.0603 0.0603
+ 0.010000 10 0.0309 0.0309
+ 0.010000 11 0.0094 0.0094
+ 0.010000 12 -0.0165 -0.0165
+ 0.010000 13 -0.0176 -0.0176
+ 0.010000 14 0.0154 0.0154
+ 0.010000 15 0.0063 0.0063
+ 0.010000 16 0.0009 0.0009
+ 0.010000 17 -0.0064 -0.0064
+ 0.010000 18 0.0072 0.0072
+ 0.010000 19 0.0296 0.0296
+ 0.010000 20 -0.0050 -0.0050
+ 0.010000 21 0.0030 0.0030
+ 0.010000 22 -0.0129 -0.0129
+ 0.010000 23 -0.0041 -0.0041
+ 0.010000 24 0.2365 0.2365
+ 0.010000 25 0.2535 0.2535
+ 0.010000 26 -0.2220 -0.2220
+ 0.010000 27 -0.0907 -0.0907
+ 0.010000 28 -0.0127 -0.0127
+ 0.010000 29 0.0917 0.0917
+ 0.010000 30 -0.1030 -0.1030
+ 0.010000 31 -0.4260 -0.4260
+ 0.010000 32 0.0720 0.0720
+ 0.010000 33 -0.0429 -0.0429
+ 0.010000 34 0.1852 0.1852
+ 0.010000 35 0.0583 0.0583
+ 0.010000 36 -0.1190 -0.1190
+ 0.010000 37 -0.3806 -0.3806
+ 0.010000 38 0.2273 0.2273
+ 0.010000 39 0.1639 0.1639
+ 0.010000 40 0.4814 0.4814
+ 0.010000 41 -0.3042 -0.3042
+ 0.010000 42 -0.0163 -0.0163
+ 0.010000 43 0.1072 0.1072
+ 0.010000 44 -0.0020 -0.0020
+ 0.010000 45 -0.0287 -0.0287
+ 0.010000 46 -0.2080 -0.2080
+ 0.010000 47 0.0789 0.0789
+ 0.010000 48 -0.0929 -0.0929
+ 0.010000 49 0.1000 0.1000
+ 0.010000 50 0.1338 0.1338
+ 0.010000 51 0.1000 0.1000
+ 0.010000 52 0.2519 0.2519
+ 0.010000 53 -0.0733 -0.0733
+ 0.010000 54 0.1338 0.1338
+ 0.010000 55 -0.0733 -0.0733
+ 0.010000 56 -0.1589 -0.1589
+ 0.015000 0 0.1023 0.1023
+ 0.015000 1 -0.1201 -0.1201
+ 0.015000 2 -0.0333 -0.0333
+ 0.015000 3 0.1587 0.1587
+ 0.015000 4 0.3507 0.3507
+ 0.015000 5 0.1013 0.1013
+ 0.015000 6 -0.6418 -0.6418
+ 0.015000 7 -0.5893 -0.5893
+ 0.015000 8 -0.1736 -0.1736
+ 0.015000 9 0.3809 0.3809
+ 0.015000 10 0.3588 0.3588
+ 0.015000 11 0.1056 0.1056
+ 0.015000 12 -0.1076 -0.1076
+ 0.015000 13 -0.1292 -0.1292
+ 0.015000 14 0.1119 0.1119
+ 0.015000 15 0.0303 0.0303
+ 0.015000 16 0.0107 0.0107
+ 0.015000 17 -0.0331 -0.0331
+ 0.015000 18 0.0590 0.0590
+ 0.015000 19 0.2015 0.2015
+ 0.015000 20 -0.0529 -0.0529
+ 0.015000 21 0.0184 0.0184
+ 0.015000 22 -0.0830 -0.0830
+ 0.015000 23 -0.0259 -0.0259
+ 0.015000 24 0.2365 0.2365
+ 0.015000 25 0.2839 0.2839
+ 0.015000 26 -0.2460 -0.2460
+ 0.015000 27 -0.0665 -0.0665
+ 0.015000 28 -0.0235 -0.0235
+ 0.015000 29 0.0728 0.0728
+ 0.015000 30 -0.1295 -0.1295
+ 0.015000 31 -0.4427 -0.4427
+ 0.015000 32 0.1163 0.1163
+ 0.015000 33 -0.0404 -0.0404
+ 0.015000 34 0.1823 0.1823
+ 0.015000 35 0.0568 0.0568
+ 0.015000 36 -0.1110 -0.1110
+ 0.015000 37 -0.4001 -0.4001
+ 0.015000 38 0.2118 0.2118
+ 0.015000 39 0.1419 0.1419
+ 0.015000 40 0.4957 0.4957
+ 0.015000 41 -0.2685 -0.2685
+ 0.015000 42 0.0076 0.0076
+ 0.015000 43 0.1124 0.1124
+ 0.015000 44 -0.0269 -0.0269
+ 0.015000 45 -0.0385 -0.0385
+ 0.015000 46 -0.2080 -0.2080
+ 0.015000 47 0.0836 0.0836
+ 0.015000 48 0.1324 0.1324
+ 0.015000 49 0.0366 0.0366
+ 0.015000 50 0.0786 0.0786
+ 0.015000 51 0.0366 0.0366
+ 0.015000 52 -0.0185 -0.0185
+ 0.015000 53 -0.0943 -0.0943
+ 0.015000 54 0.0786 0.0786
+ 0.015000 55 -0.0943 -0.0943
+ 0.015000 56 -0.1139 -0.1139
+ 0.020000 0 0.1634 0.1634
+ 0.020000 1 -0.2067 -0.2067
+ 0.020000 2 -0.0509 -0.0509
+ 0.020000 3 0.1311 0.1311
+ 0.020000 4 0.7385 0.7385
+ 0.020000 5 0.1960 0.1960
+ 0.020000 6 -0.7194 -0.7194
+ 0.020000 7 -1.3637 -1.3637
+ 0.020000 8 -0.3712 -0.3712
+ 0.020000 9 0.4249 0.4249
+ 0.020000 10 0.8318 0.8318
+ 0.020000 11 0.2261 0.2261
+ 0.020000 12 -0.1790 -0.1790
+ 0.020000 13 -0.2167 -0.2167
+ 0.020000 14 0.1980 0.1980
+ 0.020000 15 0.0402 0.0402
+ 0.020000 16 0.0169 0.0169
+ 0.020000 17 -0.0463 -0.0463
+ 0.020000 18 0.1079 0.1079
+ 0.020000 19 0.3350 0.3350
+ 0.020000 20 -0.1075 -0.1075
+ 0.020000 21 0.0309 0.0309
+ 0.020000 22 -0.1351 -0.1351
+ 0.020000 23 -0.0443 -0.0443
+ 0.020000 24 0.2359 0.2359
+ 0.020000 25 0.2856 0.2856
+ 0.020000 26 -0.2610 -0.2610
+ 0.020000 27 -0.0529 -0.0529
+ 0.020000 28 -0.0223 -0.0223
+ 0.020000 29 0.0610 0.0610
+ 0.020000 30 -0.1422 -0.1422
+ 0.020000 31 -0.4415 -0.4415
+ 0.020000 32 0.1417 0.1417
+ 0.020000 33 -0.0408 -0.0408
+ 0.020000 34 0.1781 0.1781
+ 0.020000 35 0.0583 0.0583
+ 0.020000 36 -0.1347 -0.1347
+ 0.020000 37 -0.3875 -0.3875
+ 0.020000 38 0.2094 0.2094
+ 0.020000 39 0.1662 0.1662
+ 0.020000 40 0.4698 0.4698
+ 0.020000 41 -0.2581 -0.2581
+ 0.020000 42 0.0211 0.0211
+ 0.020000 43 0.1232 0.1232
+ 0.020000 44 -0.0349 -0.0349
+ 0.020000 45 -0.0526 -0.0526
+ 0.020000 46 -0.2054 -0.2054
+ 0.020000 47 0.0836 0.0836
+ 0.020000 48 0.2775 0.2775
+ 0.020000 49 0.0663 0.0663
+ 0.020000 50 0.0517 0.0517
+ 0.020000 51 0.0663 0.0663
+ 0.020000 52 -0.2228 -0.2228
+ 0.020000 53 -0.0706 -0.0706
+ 0.020000 54 0.0517 0.0517
+ 0.020000 55 -0.0706 -0.0706
+ 0.020000 56 -0.0547 -0.0547
diff --git a/regtest/multicolvar/rt-dihcor/plumed.dat b/regtest/multicolvar/rt-dihcor/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..f87fb4a77a7dbfec79c7ee022246b9b3e3cb1cb2
--- /dev/null
+++ b/regtest/multicolvar/rt-dihcor/plumed.dat
@@ -0,0 +1,3 @@
+DIHCOR ATOMS1=1,3,6,10,2,4,7,9 ATOMS2=2,4,7,9,5,8,11,13 LABEL=c1
+DIHCOR ATOMS1=1,3,6,10,2,4,7,9 ATOMS2=2,4,7,9,5,8,11,13 NUMERICAL_DERIVATIVES LABEL=c1num
+DUMPDERIVATIVES ARG=c1.*,c1num.* STRIDE=1 FILE=derivatives FMT=%8.4f
diff --git a/regtest/multicolvar/rt-dist-neigh/Makefile b/regtest/multicolvar/rt-dist-neigh/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/multicolvar/rt-dist-neigh/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/multicolvar/rt-dist-neigh/colvar.reference b/regtest/multicolvar/rt-dist-neigh/colvar.reference
new file mode 100644
index 0000000000000000000000000000000000000000..89dbeae911c3a66a81bf2358cd4294f2dd97b297
--- /dev/null
+++ b/regtest/multicolvar/rt-dist-neigh/colvar.reference
@@ -0,0 +1,52 @@
+#! FIELDS time d2.less_than
+ 0.000000 854.7727
+ 1.000000 837.5221
+ 2.000000 840.2001
+ 3.000000 846.4986
+ 4.000000 843.2889
+ 5.000000 839.8029
+ 6.000000 840.1277
+ 7.000000 841.9655
+ 8.000000 843.1134
+ 9.000000 842.5805
+ 10.000000 839.4631
+ 11.000000 840.3086
+ 12.000000 842.0280
+ 13.000000 841.5898
+ 14.000000 844.8086
+ 15.000000 843.1613
+ 16.000000 841.1931
+ 17.000000 848.3286
+ 18.000000 842.6680
+ 19.000000 839.0177
+ 20.000000 843.7235
+ 21.000000 839.1062
+ 22.000000 840.9770
+ 23.000000 841.3274
+ 24.000000 836.8310
+ 25.000000 844.1026
+ 26.000000 842.4590
+ 27.000000 840.1475
+ 28.000000 840.2638
+ 29.000000 841.9837
+ 30.000000 844.6061
+ 31.000000 842.1193
+ 32.000000 843.7406
+ 33.000000 846.2886
+ 34.000000 843.1589
+ 35.000000 843.8051
+ 36.000000 843.4368
+ 37.000000 839.2747
+ 38.000000 834.3683
+ 39.000000 841.7771
+ 40.000000 840.5095
+ 41.000000 837.1599
+ 42.000000 842.3846
+ 43.000000 837.3686
+ 44.000000 839.7449
+ 45.000000 841.1080
+ 46.000000 835.9918
+ 47.000000 839.5425
+ 48.000000 841.0311
+ 49.000000 842.8998
+ 50.000000 841.8295
diff --git a/regtest/multicolvar/rt-dist-neigh/config b/regtest/multicolvar/rt-dist-neigh/config
new file mode 100644
index 0000000000000000000000000000000000000000..de5d8ff6b6c40bfea3da8a7fffb7921d209e86de
--- /dev/null
+++ b/regtest/multicolvar/rt-dist-neigh/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --igro trajout.gro"
diff --git a/regtest/multicolvar/rt-dist-neigh/plumed.dat b/regtest/multicolvar/rt-dist-neigh/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..3de2e831501999804c71a127141974d174122255
--- /dev/null
+++ b/regtest/multicolvar/rt-dist-neigh/plumed.dat
@@ -0,0 +1,3 @@
+#DISTANCES GROUP=1-1725:4 LESS_THAN={EXP D_0=0.3 R_0=0.02} TOL=1E-3 LABEL=d1
+DISTANCES GROUP=1-1725:4 LESS_THAN={EXP D_0=0.3 R_0=0.02} TOL=1E-3 NL_TOL=1E-9 NL_STRIDE=10 LABEL=d2
+PRINT ARG=d2.* FILE=colvar FMT=%8.4f
diff --git a/regtest/multicolvar/rt-dist-neigh/trajout.gro b/regtest/multicolvar/rt-dist-neigh/trajout.gro
new file mode 100644
index 0000000000000000000000000000000000000000..06b307c8d51b4e868caec971ef436e5c737e2b2f
--- /dev/null
+++ b/regtest/multicolvar/rt-dist-neigh/trajout.gro
@@ -0,0 +1,88281 @@
+Generated by trjconv : water tip4p/2005 t= 0.00000
+ 1728
+ 1water OW 1 1.783 2.094 1.523
+ 1water MW 2 1.772 2.088 1.514
+ 1water HW 3 1.775 2.004 1.492
+ 1water HW 4 1.708 2.140 1.486
+ 2water OW 5 1.815 1.785 1.889
+ 2water MW 6 1.805 1.790 1.878
+ 2water HW 7 1.808 1.873 1.851
+ 2water HW 8 1.746 1.735 1.846
+ 3water OW 9 2.001 1.689 1.496
+ 3water MW 10 2.013 1.684 1.488
+ 3water HW 11 2.011 1.602 1.456
+ 3water HW 12 2.083 1.734 1.476
+ 4water OW 13 1.964 2.194 1.920
+ 4water MW 14 1.975 2.192 1.930
+ 4water HW 15 2.045 2.144 1.909
+ 4water HW 16 1.968 2.227 2.010
+ 5water OW 17 2.008 2.208 1.419
+ 5water MW 18 1.999 2.204 1.407
+ 5water HW 19 2.021 2.226 1.326
+ 5water HW 20 1.926 2.159 1.423
+ 6water OW 21 2.033 1.684 1.756
+ 6water MW 22 2.021 1.690 1.748
+ 6water HW 23 2.021 1.686 1.661
+ 6water HW 24 1.954 1.724 1.792
+ 7water OW 25 1.775 1.830 1.400
+ 7water MW 26 1.785 1.824 1.390
+ 7water HW 27 1.850 1.773 1.417
+ 7water HW 28 1.774 1.841 1.305
+ 8water OW 29 1.782 2.041 1.782
+ 8water MW 30 1.793 2.051 1.777
+ 8water HW 31 1.801 2.065 1.691
+ 8water HW 32 1.846 2.090 1.833
+ 9water OW 33 2.226 2.092 1.531
+ 9water MW 34 2.213 2.096 1.539
+ 9water HW 35 2.142 2.121 1.496
+ 9water HW 36 2.214 2.090 1.626
+ 10water OW 37 2.233 1.816 1.879
+ 10water MW 38 2.235 1.804 1.870
+ 10water HW 39 2.164 1.759 1.844
+ 10water HW 40 2.314 1.780 1.843
+ 11water OW 41 2.480 1.722 1.505
+ 11water MW 42 2.478 1.734 1.496
+ 11water HW 43 2.398 1.762 1.475
+ 11water HW 44 2.549 1.777 1.468
+ 12water OW 45 2.414 2.218 1.873
+ 12water MW 46 2.425 2.225 1.865
+ 12water HW 47 2.413 2.306 1.836
+ 12water HW 48 2.499 2.182 1.847
+ 13water OW 49 2.446 2.244 1.429
+ 13water MW 50 2.435 2.251 1.437
+ 13water HW 51 2.443 2.335 1.458
+ 13water HW 52 2.363 2.206 1.458
+ 14water OW 53 2.463 1.693 1.779
+ 14water MW 54 2.465 1.682 1.768
+ 14water HW 55 2.464 1.706 1.684
+ 14water HW 56 2.476 1.599 1.791
+ 15water OW 57 2.239 1.835 1.427
+ 15water MW 58 2.240 1.848 1.419
+ 15water HW 59 2.245 1.924 1.461
+ 15water HW 60 2.238 1.846 1.332
+ 16water OW 61 2.185 2.071 1.804
+ 16water MW 62 2.197 2.064 1.811
+ 16water HW 63 2.194 1.980 1.832
+ 16water HW 64 2.267 2.112 1.831
+ 17water OW 65 1.764 2.111 0.006
+ 17water MW 66 1.765 2.098 0.014
+ 17water HW 67 1.763 2.104 0.101
+ 17water HW 68 1.775 2.021 -0.025
+ 18water OW 69 1.739 1.829 0.379
+ 18water MW 70 1.739 1.817 0.369
+ 18water HW 71 1.815 1.796 0.331
+ 18water HW 72 1.666 1.774 0.351
+ 19water OW 73 1.993 1.698 0.031
+ 19water MW 74 2.004 1.696 0.021
+ 19water HW 75 2.007 1.624 -0.027
+ 19water HW 76 2.065 1.758 0.012
+ 20water OW 77 2.029 2.186 0.382
+ 20water MW 78 2.042 2.193 0.376
+ 20water HW 79 2.113 2.147 0.358
+ 20water HW 80 2.040 2.279 0.364
+ 21water OW 81 1.999 2.275 2.186
+ 21water MW 82 2.001 2.261 2.193
+ 21water HW 83 2.080 2.236 2.219
+ 21water HW 84 1.931 2.212 2.210
+ 22water OW 85 1.970 1.685 0.305
+ 22water MW 86 1.980 1.693 0.296
+ 22water HW 87 1.969 1.690 0.209
+ 22water HW 88 2.045 1.738 0.331
+ 23water OW 89 1.764 1.842 2.151
+ 23water MW 90 1.777 1.835 2.145
+ 23water HW 91 1.785 1.825 2.059
+ 23water HW 92 1.839 1.808 2.199
+ 24water OW 93 1.802 2.087 0.282
+ 24water MW 94 1.810 2.083 0.295
+ 24water HW 95 1.884 2.123 0.315
+ 24water HW 96 1.777 2.021 0.347
+ 25water OW 97 2.206 2.130 0.049
+ 25water MW 98 2.215 2.127 0.037
+ 25water HW 99 2.275 2.186 0.012
+ 25water HW 100 2.206 2.052 -0.007
+ 26water OW 101 2.212 1.817 0.383
+ 26water MW 102 2.223 1.810 0.391
+ 26water HW 103 2.221 1.814 0.478
+ 26water HW 104 2.285 1.764 0.351
+ 27water OW 105 2.456 1.733 0.013
+ 27water MW 106 2.452 1.719 0.018
+ 27water HW 107 2.446 1.652 -0.038
+ 27water HW 108 2.436 1.707 0.103
+ 28water OW 109 2.485 2.237 0.418
+ 28water MW 110 2.485 2.225 0.408
+ 28water HW 111 2.561 2.191 0.383
+ 28water HW 112 2.410 2.193 0.378
+ 29water OW 113 2.423 2.235 2.147
+ 29water MW 114 2.433 2.229 2.136
+ 29water HW 115 2.503 2.184 2.163
+ 29water HW 116 2.418 2.242 2.052
+ 30water OW 117 2.440 1.703 0.294
+ 30water MW 118 2.453 1.697 0.300
+ 30water HW 119 2.455 1.610 0.313
+ 30water HW 120 2.520 1.747 0.323
+ 31water OW 121 2.208 1.858 2.149
+ 31water MW 122 2.221 1.855 2.141
+ 31water HW 123 2.218 1.870 2.055
+ 31water HW 124 2.293 1.826 2.179
+ 32water OW 125 2.289 2.070 0.317
+ 32water MW 126 2.282 2.060 0.308
+ 32water HW 127 2.261 1.981 0.339
+ 32water HW 128 2.261 2.082 0.226
+ 33water OW 129 1.787 2.113 0.717
+ 33water MW 130 1.797 2.122 0.725
+ 33water HW 131 1.778 2.139 0.809
+ 33water HW 132 1.870 2.152 0.689
+ 34water OW 133 1.793 1.861 1.134
+ 34water MW 134 1.801 1.864 1.121
+ 34water HW 135 1.780 1.934 1.073
+ 34water HW 136 1.866 1.812 1.097
+ 35water OW 137 2.027 1.719 0.772
+ 35water MW 138 2.016 1.712 0.763
+ 35water HW 139 1.953 1.760 0.728
+ 35water HW 140 2.020 1.626 0.749
+ 36water OW 141 1.992 2.216 1.137
+ 36water MW 142 2.004 2.220 1.129
+ 36water HW 143 2.065 2.161 1.107
+ 36water HW 144 2.013 2.303 1.104
+ 37water OW 145 2.037 2.210 0.675
+ 37water MW 146 2.050 2.203 0.670
+ 37water HW 147 2.065 2.199 0.584
+ 37water HW 148 2.106 2.169 0.727
+ 38water OW 149 2.037 1.723 1.050
+ 38water MW 150 2.033 1.714 1.038
+ 38water HW 151 2.015 1.630 1.048
+ 38water HW 152 2.029 1.751 0.959
+ 39water OW 153 1.809 1.828 0.661
+ 39water MW 154 1.809 1.841 0.652
+ 39water HW 155 1.799 1.833 0.566
+ 39water HW 156 1.817 1.919 0.689
+ 40water OW 157 1.778 2.113 0.994
+ 40water MW 158 1.776 2.121 1.007
+ 40water HW 159 1.696 2.148 1.030
+ 40water HW 160 1.845 2.142 1.055
+ 41water OW 161 2.263 2.069 0.780
+ 41water MW 162 2.274 2.076 0.788
+ 41water HW 163 2.270 2.076 0.875
+ 41water HW 164 2.339 2.117 0.746
+ 42water OW 165 2.253 1.857 1.139
+ 42water MW 166 2.252 1.844 1.131
+ 42water HW 167 2.325 1.806 1.101
+ 42water HW 168 2.174 1.808 1.115
+ 43water OW 169 2.495 1.673 0.757
+ 43water MW 170 2.495 1.685 0.747
+ 43water HW 171 2.420 1.719 0.720
+ 43water HW 172 2.571 1.717 0.718
+ 44water OW 173 2.497 2.200 1.148
+ 44water MW 174 2.496 2.214 1.154
+ 44water HW 175 2.486 2.223 1.240
+ 44water HW 176 2.497 2.284 1.102
+ 45water OW 177 2.487 2.219 0.679
+ 45water MW 178 2.484 2.231 0.669
+ 45water HW 179 2.482 2.215 0.584
+ 45water HW 180 2.468 2.310 0.700
+ 46water OW 181 2.448 1.683 1.042
+ 46water MW 182 2.449 1.669 1.036
+ 46water HW 183 2.460 1.660 0.950
+ 46water HW 184 2.443 1.599 1.087
+ 47water OW 185 2.256 1.819 0.656
+ 47water MW 186 2.246 1.826 0.666
+ 47water HW 187 2.259 1.908 0.690
+ 47water HW 188 2.179 1.780 0.697
+ 48water OW 189 2.249 2.103 1.064
+ 48water MW 190 2.260 2.094 1.071
+ 48water HW 191 2.336 2.129 1.095
+ 48water HW 192 2.242 2.010 1.087
+ 49water OW 193 1.792 0.524 1.492
+ 49water MW 194 1.781 0.518 1.483
+ 49water HW 195 1.717 0.571 1.457
+ 49water HW 196 1.782 0.435 1.458
+ 50water OW 197 1.789 0.270 1.862
+ 50water MW 198 1.778 0.264 1.871
+ 50water HW 199 1.779 0.275 1.957
+ 50water HW 200 1.714 0.218 1.833
+ 51water OW 201 2.025 0.132 1.520
+ 51water MW 202 2.023 0.121 1.531
+ 51water HW 203 2.027 0.145 1.615
+ 51water HW 204 2.010 0.038 1.509
+ 52water OW 205 2.034 0.672 1.856
+ 52water MW 206 2.035 0.660 1.846
+ 52water HW 207 1.963 0.617 1.823
+ 52water HW 208 2.113 0.639 1.812
+ 53water OW 209 2.014 0.652 1.404
+ 53water MW 210 2.004 0.659 1.414
+ 53water HW 211 1.937 0.615 1.448
+ 53water HW 212 2.018 0.743 1.434
+ 54water OW 213 1.986 0.097 1.791
+ 54water MW 214 1.974 0.093 1.800
+ 54water HW 215 1.907 0.146 1.813
+ 54water HW 216 1.977 0.014 1.838
+ 55water OW 217 1.809 0.270 1.391
+ 55water MW 218 1.823 0.269 1.384
+ 55water HW 219 1.894 0.250 1.430
+ 55water HW 220 1.827 0.280 1.297
+ 56water OW 221 1.823 0.521 1.779
+ 56water MW 222 1.821 0.509 1.770
+ 56water HW 223 1.811 0.430 1.805
+ 56water HW 224 1.821 0.520 1.683
+ 57water OW 225 2.244 0.525 1.478
+ 57water MW 226 2.243 0.538 1.469
+ 57water HW 227 2.313 0.570 1.429
+ 57water HW 228 2.165 0.576 1.460
+ 58water OW 229 2.192 0.276 1.858
+ 58water MW 230 2.186 0.268 1.870
+ 58water HW 231 2.217 0.277 1.950
+ 58water HW 232 2.118 0.215 1.854
+ 59water OW 233 2.466 0.190 1.487
+ 59water MW 234 2.453 0.187 1.495
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 10.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 20.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 30.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 40.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 50.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 60.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 70.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 80.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 90.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 100.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 110.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 120.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 130.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 140.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 150.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 160.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 170.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 180.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 190.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 200.00000
+ 1728
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+ 432water HW 1728 1.317 1.257 1.140
+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 210.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 220.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 230.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 240.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 250.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 260.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 270.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 280.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 290.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 300.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 310.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 320.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 330.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 340.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 350.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 360.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 370.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 380.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 390.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 400.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 410.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 420.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 430.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 440.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 450.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 460.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 470.00000
+ 1728
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+ 432water HW 1728 1.285 1.211 1.089
+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 480.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 490.00000
+ 1728
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+ 2.71084 2.34766 2.21339
+Generated by trjconv : water tip4p/2005 t= 500.00000
+ 1728
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+ 328water OW 1309 0.856 2.127 1.054
+ 328water MW 1310 0.858 2.114 1.045
+ 328water HW 1311 0.869 2.124 0.959
+ 328water HW 1312 0.858 2.035 1.081
+ 329water OW 1313 1.282 2.131 0.733
+ 329water MW 1314 1.273 2.141 0.741
+ 329water HW 1315 1.224 2.198 0.697
+ 329water HW 1316 1.273 2.140 0.828
+ 330water OW 1317 1.228 1.868 1.103
+ 330water MW 1318 1.232 1.853 1.102
+ 330water HW 1319 1.313 1.827 1.087
+ 330water HW 1320 1.167 1.795 1.112
+ 331water OW 1321 1.518 1.667 0.780
+ 331water MW 1322 1.517 1.682 0.775
+ 331water HW 1323 1.589 1.732 0.778
+ 331water HW 1324 1.443 1.713 0.743
+ 332water OW 1325 1.488 2.237 1.135
+ 332water MW 1326 1.478 2.229 1.142
+ 332water HW 1327 1.410 2.197 1.097
+ 332water HW 1328 1.485 2.214 1.228
+ 333water OW 1329 1.531 2.222 0.663
+ 333water MW 1330 1.531 2.208 0.670
+ 333water HW 1331 1.606 2.172 0.696
+ 333water HW 1332 1.455 2.166 0.682
+ 334water OW 1333 1.468 1.748 1.067
+ 334water MW 1334 1.481 1.749 1.059
+ 334water HW 1335 1.481 1.724 0.975
+ 334water HW 1336 1.553 1.780 1.096
+ 335water OW 1337 1.347 1.869 0.697
+ 335water MW 1338 1.342 1.882 0.690
+ 335water HW 1339 1.318 1.877 0.606
+ 335water HW 1340 1.338 1.957 0.733
+ 336water OW 1341 1.251 2.135 0.985
+ 336water MW 1342 1.241 2.128 0.995
+ 336water HW 1343 1.246 2.042 1.009
+ 336water HW 1344 1.179 2.176 1.033
+ 337water OW 1345 0.830 0.529 1.549
+ 337water MW 1346 0.843 0.535 1.555
+ 337water HW 1347 0.898 0.584 1.509
+ 337water HW 1348 0.859 0.517 1.639
+ 338water OW 1349 0.841 0.256 1.864
+ 338water MW 1350 0.845 0.265 1.877
+ 338water HW 1351 0.857 0.350 1.867
+ 338water HW 1352 0.851 0.227 1.955
+ 339water OW 1353 1.045 0.212 1.533
+ 339water MW 1354 1.057 0.212 1.542
+ 339water HW 1355 1.052 0.183 1.624
+ 339water HW 1356 1.133 0.239 1.509
+ 340water OW 1357 1.135 0.645 1.909
+ 340water MW 1358 1.131 0.656 1.919
+ 340water HW 1359 1.127 0.738 1.890
+ 340water HW 1360 1.111 0.637 2.001
+ 341water OW 1361 1.047 0.625 1.425
+ 341water MW 1362 1.059 0.625 1.415
+ 341water HW 1363 1.047 0.659 1.336
+ 341water HW 1364 1.137 0.597 1.441
+ 342water OW 1365 1.078 0.166 1.794
+ 342water MW 1366 1.065 0.160 1.801
+ 342water HW 1367 1.006 0.215 1.833
+ 342water HW 1368 1.055 0.074 1.809
+ 343water OW 1369 0.816 0.301 1.330
+ 343water MW 1370 0.825 0.303 1.343
+ 343water HW 1371 0.897 0.256 1.355
+ 343water HW 1372 0.800 0.363 1.402
+ 344water OW 1373 0.914 0.521 1.829
+ 344water MW 1374 0.915 0.536 1.834
+ 344water HW 1375 0.993 0.567 1.856
+ 344water HW 1376 0.844 0.586 1.840
+ 345water OW 1377 1.321 0.571 1.468
+ 345water MW 1378 1.321 0.561 1.479
+ 345water HW 1379 1.299 0.478 1.462
+ 345water HW 1380 1.340 0.585 1.561
+ 346water OW 1381 1.305 0.305 1.879
+ 346water MW 1382 1.298 0.313 1.867
+ 346water HW 1383 1.331 0.390 1.843
+ 346water HW 1384 1.230 0.278 1.825
+ 347water OW 1385 1.491 0.137 1.521
+ 347water MW 1386 1.502 0.145 1.528
+ 347water HW 1387 1.501 0.150 1.615
+ 347water HW 1388 1.563 0.185 1.482
+ 348water OW 1389 1.543 0.735 1.889
+ 348water MW 1390 1.552 0.726 1.897
+ 348water HW 1391 1.619 0.689 1.854
+ 348water HW 1392 1.538 0.708 1.981
+ 349water OW 1393 1.525 0.708 1.357
+ 349water MW 1394 1.514 0.714 1.366
+ 349water HW 1395 1.522 0.795 1.397
+ 349water HW 1396 1.442 0.667 1.382
+ 350water OW 1397 1.515 0.156 1.781
+ 350water MW 1398 1.505 0.151 1.792
+ 350water HW 1399 1.501 0.067 1.815
+ 350water HW 1400 1.455 0.211 1.831
+ 351water OW 1401 1.280 0.276 1.439
+ 351water MW 1402 1.290 0.269 1.430
+ 351water HW 1403 1.272 0.259 1.345
+ 351water HW 1404 1.363 0.236 1.464
+ 352water OW 1405 1.360 0.568 1.760
+ 352water MW 1406 1.358 0.578 1.771
+ 352water HW 1407 1.424 0.626 1.802
+ 352water HW 1408 1.278 0.586 1.805
+ 353water OW 1409 0.823 0.496 2.188
+ 353water MW 1410 0.826 0.510 2.181
+ 353water HW 1411 0.907 0.537 2.164
+ 353water HW 1412 0.757 0.560 2.163
+ 354water OW 1413 0.870 0.273 0.382
+ 354water MW 1414 0.880 0.279 0.372
+ 354water HW 1415 0.871 0.362 0.347
+ 354water HW 1416 0.944 0.229 0.340
+ 355water OW 1417 1.102 0.105 0.038
+ 355water MW 1418 1.092 0.098 0.028
+ 355water HW 1419 1.098 0.012 0.017
+ 355water HW 1420 1.033 0.144 -0.015
+ 356water OW 1421 1.101 0.654 0.364
+ 356water MW 1422 1.088 0.658 0.357
+ 356water HW 1423 1.025 0.598 0.348
+ 356water HW 1424 1.077 0.739 0.328
+ 357water OW 1425 1.066 0.626 2.164
+ 357water MW 1426 1.077 0.633 2.173
+ 357water HW 1427 1.065 0.714 2.203
+ 357water HW 1428 1.148 0.588 2.195
+ 358water OW 1429 1.100 0.148 0.309
+ 358water MW 1430 1.113 0.148 0.301
+ 358water HW 1431 1.111 0.119 0.219
+ 358water HW 1432 1.188 0.174 0.337
+ 359water OW 1433 0.842 0.226 2.134
+ 359water MW 1434 0.830 0.232 2.141
+ 359water HW 1435 0.765 0.180 2.166
+ 359water HW 1436 0.829 0.317 2.160
+ 360water OW 1437 0.858 0.525 0.272
+ 360water MW 1438 0.849 0.533 0.262
+ 360water HW 1439 0.787 0.586 0.292
+ 360water HW 1440 0.863 0.524 0.176
+ 361water OW 1441 1.297 0.524 0.052
+ 361water MW 1442 1.303 0.512 0.061
+ 361water HW 1443 1.316 0.525 0.146
+ 361water HW 1444 1.317 0.435 0.024
+ 362water OW 1445 1.342 0.248 0.414
+ 362water MW 1446 1.355 0.254 0.407
+ 362water HW 1447 1.424 0.204 0.392
+ 362water HW 1448 1.356 0.338 0.383
+ 363water OW 1449 1.563 0.106 0.030
+ 363water MW 1450 1.553 0.115 0.038
+ 363water HW 1451 1.476 0.136 0.002
+ 363water HW 1452 1.574 0.141 0.118
+ 364water OW 1453 1.549 0.684 0.416
+ 364water MW 1454 1.548 0.698 0.423
+ 364water HW 1455 1.547 0.704 0.510
+ 364water HW 1456 1.543 0.769 0.373
+ 365water OW 1457 1.507 0.663 2.172
+ 365water MW 1458 1.505 0.648 2.176
+ 365water HW 1459 1.573 0.594 2.174
+ 365water HW 1460 1.425 0.620 2.196
+ 366water OW 1461 1.566 0.156 0.310
+ 366water MW 1462 1.577 0.148 0.318
+ 366water HW 1463 1.563 0.065 0.340
+ 366water HW 1464 1.652 0.187 0.338
+ 367water OW 1465 1.307 0.264 2.178
+ 367water MW 1466 1.294 0.259 2.170
+ 367water HW 1467 1.233 0.213 2.212
+ 367water HW 1468 1.286 0.277 2.086
+ 368water OW 1469 1.361 0.527 0.322
+ 368water MW 1470 1.360 0.541 0.328
+ 368water HW 1471 1.281 0.576 0.341
+ 368water HW 1472 1.432 0.584 0.352
+ 369water OW 1473 0.866 0.591 0.747
+ 369water MW 1474 0.857 0.583 0.737
+ 369water HW 1475 0.873 0.499 0.719
+ 369water HW 1476 0.790 0.625 0.700
+ 370water OW 1477 0.849 0.286 1.053
+ 370water MW 1478 0.859 0.282 1.064
+ 370water HW 1479 0.935 0.244 1.042
+ 370water HW 1480 0.841 0.298 1.147
+ 371water OW 1481 1.062 0.170 0.787
+ 371water MW 1482 1.055 0.169 0.773
+ 371water HW 1483 1.011 0.238 0.743
+ 371water HW 1484 1.060 0.095 0.727
+ 372water OW 1485 1.088 0.712 1.167
+ 372water MW 1486 1.088 0.700 1.158
+ 372water HW 1487 1.160 0.650 1.156
+ 372water HW 1488 1.020 0.682 1.107
+ 373water OW 1489 1.104 0.658 0.642
+ 373water MW 1490 1.091 0.657 0.634
+ 373water HW 1491 1.092 0.637 0.550
+ 373water HW 1492 1.015 0.668 0.677
+ 374water OW 1493 1.101 0.162 1.048
+ 374water MW 1494 1.109 0.168 1.037
+ 374water HW 1495 1.178 0.217 1.059
+ 374water HW 1496 1.089 0.154 0.954
+ 375water OW 1497 0.885 0.344 0.669
+ 375water MW 1498 0.873 0.339 0.660
+ 375water HW 1499 0.805 0.302 0.701
+ 375water HW 1500 0.873 0.348 0.574
+ 376water OW 1501 0.899 0.552 1.020
+ 376water MW 1502 0.896 0.541 1.008
+ 376water HW 1503 0.888 0.570 0.926
+ 376water HW 1504 0.886 0.457 1.027
+ 377water OW 1505 1.334 0.569 0.794
+ 377water MW 1506 1.324 0.561 0.787
+ 377water HW 1507 1.338 0.475 0.778
+ 377water HW 1508 1.253 0.598 0.753
+ 378water OW 1509 1.333 0.260 1.155
+ 378water MW 1510 1.344 0.265 1.146
+ 378water HW 1511 1.337 0.346 1.113
+ 378water HW 1512 1.412 0.215 1.125
+ 379water OW 1513 1.552 0.134 0.768
+ 379water MW 1514 1.539 0.129 0.761
+ 379water HW 1515 1.535 0.047 0.732
+ 379water HW 1516 1.471 0.182 0.752
+ 380water OW 1517 1.538 0.651 1.106
+ 380water MW 1518 1.550 0.645 1.114
+ 380water HW 1519 1.607 0.593 1.074
+ 380water HW 1520 1.560 0.664 1.198
+ 381water OW 1521 1.554 0.684 0.687
+ 381water MW 1522 1.543 0.693 0.694
+ 381water HW 1523 1.564 0.775 0.713
+ 381water HW 1524 1.466 0.660 0.717
+ 382water OW 1525 1.554 0.145 1.040
+ 382water MW 1526 1.548 0.133 1.032
+ 382water HW 1527 1.536 0.141 0.946
+ 382water HW 1528 1.524 0.060 1.073
+ 383water OW 1529 1.334 0.287 0.694
+ 383water MW 1530 1.322 0.283 0.685
+ 383water HW 1531 1.246 0.260 0.720
+ 383water HW 1532 1.334 0.281 0.599
+ 384water OW 1533 1.300 0.508 1.069
+ 384water MW 1534 1.309 0.519 1.060
+ 384water HW 1535 1.282 0.540 0.980
+ 384water HW 1536 1.381 0.554 1.094
+ 385water OW 1537 0.837 1.312 1.499
+ 385water MW 1538 0.841 1.300 1.507
+ 385water HW 1539 0.825 1.296 1.593
+ 385water HW 1540 0.883 1.235 1.467
+ 386water OW 1541 0.906 1.017 1.880
+ 386water MW 1542 0.904 1.030 1.888
+ 386water HW 1543 0.882 1.024 1.972
+ 386water HW 1544 0.913 1.107 1.850
+ 387water OW 1545 1.109 0.878 1.520
+ 387water MW 1546 1.108 0.866 1.530
+ 387water HW 1547 1.125 0.883 1.614
+ 387water HW 1548 1.088 0.786 1.504
+ 388water OW 1549 1.019 1.452 1.863
+ 388water MW 1550 1.017 1.466 1.870
+ 388water HW 1551 1.016 1.468 1.957
+ 388water HW 1552 1.010 1.539 1.823
+ 389water OW 1553 1.038 1.499 1.434
+ 389water MW 1554 1.036 1.486 1.442
+ 389water HW 1555 1.101 1.454 1.489
+ 389water HW 1556 0.958 1.446 1.440
+ 390water OW 1557 1.129 0.905 1.795
+ 390water MW 1558 1.125 0.917 1.804
+ 390water HW 1559 1.189 0.970 1.832
+ 390water HW 1560 1.042 0.931 1.827
+ 391water OW 1561 0.917 1.074 1.399
+ 391water MW 1562 0.912 1.064 1.410
+ 391water HW 1563 0.827 1.059 1.428
+ 391water HW 1564 0.969 1.012 1.451
+ 392water OW 1565 0.844 1.283 1.771
+ 392water MW 1566 0.846 1.295 1.781
+ 392water HW 1567 0.775 1.330 1.817
+ 392water HW 1568 0.925 1.330 1.794
+ 393water OW 1569 1.257 1.379 1.518
+ 393water MW 1570 1.269 1.375 1.527
+ 393water HW 1571 1.349 1.372 1.495
+ 393water HW 1572 1.253 1.356 1.611
+ 394water OW 1573 1.324 1.087 1.869
+ 394water MW 1574 1.334 1.096 1.861
+ 394water HW 1575 1.403 1.061 1.821
+ 394water HW 1576 1.321 1.182 1.859
+ 395water OW 1577 1.508 0.946 1.497
+ 395water MW 1578 1.499 0.952 1.508
+ 395water HW 1579 1.423 0.986 1.480
+ 395water HW 1580 1.519 0.953 1.592
+ 396water OW 1581 1.535 1.475 1.864
+ 396water MW 1582 1.545 1.466 1.871
+ 396water HW 1583 1.605 1.423 1.824
+ 396water HW 1584 1.544 1.459 1.958
+ 397water OW 1585 1.523 1.449 1.443
+ 397water MW 1586 1.520 1.461 1.435
+ 397water HW 1587 1.494 1.534 1.474
+ 397water HW 1588 1.526 1.457 1.348
+ 398water OW 1589 1.540 0.966 1.764
+ 398water MW 1590 1.551 0.962 1.774
+ 398water HW 1591 1.619 1.012 1.791
+ 398water HW 1592 1.542 0.883 1.811
+ 399water OW 1593 1.271 1.066 1.400
+ 399water MW 1594 1.259 1.071 1.409
+ 399water HW 1595 1.200 1.011 1.433
+ 399water HW 1596 1.249 1.155 1.431
+ 400water OW 1597 1.267 1.371 1.805
+ 400water MW 1598 1.266 1.385 1.812
+ 400water HW 1599 1.340 1.430 1.824
+ 400water HW 1600 1.190 1.416 1.839
+ 401water OW 1601 0.834 1.274 0.018
+ 401water MW 1602 0.835 1.289 0.016
+ 401water HW 1603 0.763 1.338 0.022
+ 401water HW 1604 0.912 1.326 0.001
+ 402water OW 1605 0.885 1.068 0.371
+ 402water MW 1606 0.885 1.081 0.379
+ 402water HW 1607 0.887 1.080 0.466
+ 402water HW 1608 0.881 1.157 0.336
+ 403water OW 1609 1.059 0.911 0.003
+ 403water MW 1610 1.070 0.919 0.010
+ 403water HW 1611 1.128 0.965 -0.035
+ 403water HW 1612 1.075 0.915 0.097
+ 404water OW 1613 1.092 1.452 0.404
+ 404water MW 1614 1.080 1.447 0.413
+ 404water HW 1615 1.085 1.455 0.500
+ 404water HW 1616 1.008 1.417 0.375
+ 405water OW 1617 1.047 1.433 2.144
+ 405water MW 1618 1.059 1.438 2.153
+ 405water HW 1619 1.064 1.521 2.179
+ 405water HW 1620 1.121 1.380 2.175
+ 406water OW 1621 1.092 0.907 0.262
+ 406water MW 1622 1.093 0.920 0.271
+ 406water HW 1623 1.170 0.949 0.300
+ 406water HW 1624 1.019 0.962 0.292
+ 407water OW 1625 0.817 1.005 2.169
+ 407water MW 1626 0.829 1.015 2.171
+ 407water HW 1627 0.908 0.980 2.181
+ 407water HW 1628 0.818 1.101 2.170
+ 408water OW 1629 0.843 1.328 0.299
+ 408water MW 1630 0.831 1.334 0.292
+ 408water HW 1631 0.824 1.329 0.206
+ 408water HW 1632 0.768 1.370 0.340
+ 409water OW 1633 1.268 1.250 0.005
+ 409water MW 1634 1.268 1.238 0.015
+ 409water HW 1635 1.272 1.157 -0.015
+ 409water HW 1636 1.264 1.254 0.101
+ 410water OW 1637 1.308 1.046 0.392
+ 410water MW 1638 1.318 1.051 0.382
+ 410water HW 1639 1.380 1.000 0.350
+ 410water HW 1640 1.312 1.135 0.357
+ 411water OW 1641 1.551 0.977 0.023
+ 411water MW 1642 1.564 0.974 0.014
+ 411water HW 1643 1.618 1.038 -0.010
+ 411water HW 1644 1.577 0.892 -0.012
+ 412water OW 1645 1.550 1.426 0.436
+ 412water MW 1646 1.560 1.419 0.445
+ 412water HW 1647 1.629 1.379 0.409
+ 412water HW 1648 1.548 1.417 0.531
+ 413water OW 1649 1.483 1.415 2.150
+ 413water MW 1650 1.473 1.419 2.161
+ 413water HW 1651 1.410 1.361 2.180
+ 413water HW 1652 1.481 1.493 2.206
+ 414water OW 1653 1.539 0.928 0.312
+ 414water MW 1654 1.549 0.937 0.303
+ 414water HW 1655 1.601 0.995 0.341
+ 414water HW 1656 1.548 0.927 0.216
+ 415water OW 1657 1.307 0.989 2.136
+ 415water MW 1658 1.321 0.990 2.129
+ 415water HW 1659 1.395 0.980 2.175
+ 415water HW 1660 1.324 1.005 2.043
+ 416water OW 1661 1.327 1.311 0.270
+ 416water MW 1662 1.329 1.322 0.281
+ 416water HW 1663 1.262 1.365 0.316
+ 416water HW 1664 1.411 1.339 0.307
+ 417water OW 1665 0.856 1.359 0.796
+ 417water MW 1666 0.856 1.345 0.802
+ 417water HW 1667 0.851 1.275 0.750
+ 417water HW 1668 0.859 1.335 0.888
+ 418water OW 1669 0.888 1.040 1.122
+ 418water MW 1670 0.889 1.052 1.132
+ 418water HW 1671 0.904 1.132 1.102
+ 418water HW 1672 0.879 1.038 1.218
+ 419water OW 1673 1.083 0.930 0.709
+ 419water MW 1674 1.087 0.918 0.717
+ 419water HW 1675 1.090 0.923 0.804
+ 419water HW 1676 1.112 0.845 0.676
+ 420water OW 1677 1.085 1.401 1.172
+ 420water MW 1678 1.098 1.400 1.181
+ 420water HW 1679 1.103 1.443 1.256
+ 420water HW 1680 1.164 1.350 1.154
+ 421water OW 1681 1.080 1.485 0.673
+ 421water MW 1682 1.071 1.493 0.683
+ 421water HW 1683 0.995 1.457 0.707
+ 421water HW 1684 1.095 1.570 0.713
+ 422water OW 1685 1.118 0.923 0.978
+ 422water MW 1686 1.111 0.919 0.991
+ 422water HW 1687 1.063 0.979 1.033
+ 422water HW 1688 1.119 0.838 1.023
+ 423water OW 1689 0.858 1.110 0.642
+ 423water MW 1690 0.858 1.098 0.651
+ 423water HW 1691 0.783 1.054 0.663
+ 423water HW 1692 0.931 1.072 0.690
+ 424water OW 1693 0.839 1.302 1.083
+ 424water MW 1694 0.837 1.316 1.090
+ 424water HW 1695 0.904 1.360 1.123
+ 424water HW 1696 0.755 1.346 1.097
+ 425water OW 1697 1.292 1.320 0.775
+ 425water MW 1698 1.282 1.317 0.763
+ 425water HW 1699 1.229 1.380 0.736
+ 425water HW 1700 1.283 1.239 0.723
+ 426water OW 1701 1.317 1.044 1.126
+ 426water MW 1702 1.310 1.034 1.135
+ 426water HW 1703 1.321 1.039 1.221
+ 426water HW 1704 1.255 0.975 1.101
+ 427water OW 1705 1.562 0.984 0.722
+ 427water MW 1706 1.548 0.984 0.729
+ 427water HW 1707 1.477 1.004 0.683
+ 427water HW 1708 1.543 0.965 0.814
+ 428water OW 1709 1.544 1.487 1.154
+ 428water MW 1710 1.532 1.494 1.147
+ 428water HW 1711 1.533 1.580 1.134
+ 428water HW 1712 1.464 1.446 1.120
+ 429water OW 1713 1.555 1.403 0.707
+ 429water MW 1714 1.544 1.410 0.714
+ 429water HW 1715 1.553 1.494 0.738
+ 429water HW 1716 1.470 1.367 0.731
+ 430water OW 1717 1.533 0.908 0.980
+ 430water MW 1718 1.524 0.905 0.992
+ 430water HW 1719 1.469 0.964 1.024
+ 430water HW 1720 1.528 0.825 1.026
+ 431water OW 1721 1.315 1.064 0.654
+ 431water MW 1722 1.305 1.055 0.646
+ 431water HW 1723 1.243 1.013 0.691
+ 431water HW 1724 1.309 1.049 0.560
+ 432water OW 1725 1.326 1.310 1.059
+ 432water MW 1726 1.324 1.297 1.051
+ 432water HW 1727 1.316 1.300 0.964
+ 432water HW 1728 1.323 1.220 1.093
+ 2.71084 2.34766 2.21339
diff --git a/regtest/multicolvar/rt-sprint/Makefile b/regtest/multicolvar/rt-sprint/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/multicolvar/rt-sprint/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/multicolvar/rt-sprint/colvar.reference b/regtest/multicolvar/rt-sprint/colvar.reference
new file mode 100644
index 0000000000000000000000000000000000000000..04c9397dd6fbc644025982f59082b4cb00b8fbfd
--- /dev/null
+++ b/regtest/multicolvar/rt-sprint/colvar.reference
@@ -0,0 +1,18 @@
+#! FIELDS time ss.aa0 ss.aa1 ss.aa2 ss.aa3 ss.aa4 ss.aa5 ss.aa6 ss.aa7 ss.aa8 ss.aa9 ss.aa10 ss.aa11 ss.aa12 ss.aa13
+ 0.000000 4.6419 6.0632 6.1581 6.1588 6.4828 6.4895 6.8567 2.7487 2.7496 3.2158 3.2972 3.3002 3.5708 3.5727
+ 1.000000 5.8879 5.9824 6.0344 6.0796 6.4405 6.9432 7.1897 3.0307 3.0555 3.1203 3.3415 3.5160 3.6172 4.0368
+ 2.000000 5.5023 5.8045 5.9213 5.9916 6.1783 6.3161 6.4699 2.8745 3.1502 3.3023 3.4359 3.5402 3.7582 4.0200
+ 3.000000 5.4075 5.5786 5.8003 6.0605 6.1389 6.6391 6.7378 2.8069 3.1223 3.1291 3.3933 3.6409 4.0698 4.2879
+ 4.000000 5.4487 5.4653 5.6167 5.9594 6.4644 6.6199 6.9774 2.7674 2.9206 3.1827 3.4475 3.5723 4.2203 4.5450
+ 5.000000 5.8821 5.8821 5.8845 5.8845 5.8861 5.8963 5.8963 3.3549 3.3584 3.3584 3.3784 3.3784 3.4041 3.4041
+ 6.000000 5.7865 5.9230 6.0762 6.3384 6.4910 7.4292 7.8610 2.7869 2.8071 2.8072 3.0500 3.6363 3.7908 4.4693
+ 7.000000 5.6959 5.7783 6.4257 6.5346 6.6417 7.3627 7.5493 2.6189 2.6695 3.1743 3.1848 3.7441 3.8198 3.8911
+ 8.000000 3.9801 6.1602 6.5242 6.5244 6.6727 7.3000 7.3007 2.2038 2.2054 3.0656 3.1561 3.1562 3.8773 3.8775
+ 9.000000 3.1441 5.1850 6.1753 6.1753 6.7558 6.7559 7.3867 1.7190 1.9932 3.1433 3.1433 3.4588 3.4589 4.5090
+ 10.000000 2.6856 4.5889 6.2007 6.3569 6.6190 6.9819 7.0862 1.5286 1.5286 3.2115 3.2167 3.4300 4.2474 4.2476
+ 11.000000 1.9044 2.7928 4.1486 4.9250 5.5725 6.1807 6.4234 1.1614 1.1658 3.1261 3.3631 3.6928 4.0992 4.1208
+ 12.000000 3.8279 5.3013 6.0450 6.0450 6.3891 6.3892 7.1793 2.1907 2.3741 2.9944 3.0827 3.0827 3.3256 3.3257
+ 13.000000 3.1948 4.8342 6.1370 6.4611 6.5331 7.1671 7.3430 1.4230 2.8196 3.1100 3.3468 3.3518 4.2910 4.2920
+ 14.000000 3.5386 5.4587 6.1050 6.1173 6.7973 6.8382 7.6329 1.5730 3.0701 3.0761 3.1049 3.5010 3.5059 4.5673
+ 15.000000 5.2389 5.5466 5.8188 5.9540 6.1001 6.5796 6.9787 2.8276 3.0649 3.2850 3.3500 3.3500 3.6339 3.7524
+ 16.000000 6.5160 6.5164 6.8251 6.8254 7.5418 7.6267 8.0331 2.8615 2.8621 3.0705 3.0707 4.0205 4.2613 4.2614
diff --git a/regtest/multicolvar/rt-sprint/config b/regtest/multicolvar/rt-sprint/config
new file mode 100644
index 0000000000000000000000000000000000000000..3edebcebb8e3f5e9a6a8b24e9fdff24c518c5d40
--- /dev/null
+++ b/regtest/multicolvar/rt-sprint/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz isomers.xyz"
diff --git a/regtest/multicolvar/rt-sprint/deriv.reference b/regtest/multicolvar/rt-sprint/deriv.reference
new file mode 100644
index 0000000000000000000000000000000000000000..fa3b68064933c576e7890d9f9e4e924922b45e3d
--- /dev/null
+++ b/regtest/multicolvar/rt-sprint/deriv.reference
@@ -0,0 +1,868 @@
+#! FIELDS time parameter ss.aa0 ss.aa1 ss.aa2 ss.aa3 ss.aa4 ss.aa5 ss.aa6 ss.aa7 ss.aa8 ss.aa9 ss.aa10 ss.aa11 ss.aa12 ss.aa13
+ 0.000000 0 -0.5072 0.7923 0.4947 1.0592 -0.0299 0.3764 0.9470 -1.2449 -0.8196 0.2491 0.0699 0.3840 -0.5192 0.6137
+ 0.000000 1 0.0017 -0.0009 0.0006 -0.0010 0.0106 0.0003 0.0100 0.0009 0.0005 -0.0014 -0.0000 -0.0015 0.0019 -0.0003
+ 0.000000 2 -0.2927 0.4574 0.9378 -0.0405 0.4534 -0.2519 0.5475 -0.2275 -0.9643 0.1438 0.4032 -0.1413 1.0089 -0.9541
+ 0.000000 3 -0.6983 0.9890 0.4689 0.6677 1.4817 0.3335 -0.1173 -0.7103 -0.4442 0.3405 0.6983 0.1549 0.0100 -0.0643
+ 0.000000 4 -0.0335 -0.0298 -0.0269 -0.0122 -0.1599 -0.0243 -0.0210 -0.0187 -0.0008 0.0009 -0.0501 0.0099 -0.0307 0.0066
+ 0.000000 5 -0.9096 0.1836 0.2226 -0.2360 -1.2355 -0.7277 -0.4324 -0.4824 -0.3360 0.2595 0.8630 0.0309 -0.0487 -0.2313
+ 0.000000 6 -0.3347 0.3825 -0.1067 0.5537 -0.3268 0.0432 -0.5082 -0.2371 -0.1533 1.0176 0.0033 0.3191 -0.9965 0.0313
+ 0.000000 7 -0.0007 0.0009 0.0095 -0.0004 0.0089 -0.0008 0.0002 -0.0007 -0.0011 0.0003 0.0020 -0.0010 0.0017 -0.0013
+ 0.000000 8 0.0598 -0.3157 -2.2116 -0.6800 -0.2317 -0.5637 -0.5443 0.1577 0.1632 -0.1863 -0.1584 -0.1045 -0.1061 -0.0098
+ 0.000000 9 0.0988 -1.9445 -0.4311 -0.0925 -0.7779 -0.2764 -0.3971 0.1415 0.1728 -0.1621 -0.6465 0.3352 -0.1746 0.1066
+ 0.000000 10 -0.0035 0.0312 0.0061 0.0017 0.0279 -0.0009 -0.0009 -0.0032 -0.0043 0.0040 0.0042 0.0000 0.0023 -0.0038
+ 0.000000 11 0.0572 -1.1239 0.1419 -0.4444 0.1303 -0.7393 -0.2291 0.1179 0.0638 -0.0938 0.7601 -0.9401 0.2239 -0.2629
+ 0.000000 12 -0.1157 -0.0818 -0.3121 -1.9657 -0.4658 -0.3627 -0.7255 0.0644 0.0179 0.3477 0.0688 -0.1349 0.0069 -0.5898
+ 0.000000 13 -0.0019 0.0025 0.0021 0.0217 0.0198 0.0015 0.0005 -0.0021 -0.0026 0.0007 0.0004 0.0021 0.0011 -0.0002
+ 0.000000 14 -0.3198 0.4890 0.8197 1.0126 0.3187 -0.1667 -0.1679 -0.2143 -0.2841 0.9745 0.3287 0.0819 0.0321 -0.8100
+ 0.000000 15 -1.1392 0.6546 0.1296 0.4272 -0.4641 -0.3282 -0.4329 -0.5145 -0.7757 0.3958 0.1043 1.0992 -0.2331 -0.0371
+ 0.000000 16 0.0017 -0.0004 0.0008 0.0008 0.0291 0.0290 0.0038 -0.0010 -0.0010 -0.0031 -0.0005 -0.0006 0.0023 0.0023
+ 0.000000 17 -0.1504 0.7663 0.6988 0.2944 0.6536 1.9012 0.1140 -0.2172 -0.3752 0.1659 0.1194 0.1737 0.0606 0.0341
+ 0.000000 18 2.0485 -0.2030 -0.1361 -0.0111 0.2875 0.6216 0.3939 0.3281 0.4108 -0.2230 -0.1827 -0.0935 0.0494 0.4299
+ 0.000000 19 0.0339 -0.0043 -0.0013 -0.0045 0.0219 0.0003 0.0057 0.0071 0.0063 -0.0042 -0.0011 -0.0043 0.0036 -0.0010
+ 0.000000 20 1.1816 -0.1171 0.0659 -0.1506 0.5511 -0.0264 0.2273 0.2846 0.1415 -0.1286 -0.0024 -0.1569 0.4679 -0.1912
+ 0.000000 21 -0.1106 0.0696 0.6569 -0.1044 0.3610 -0.1094 0.1998 -0.1803 -0.1299 0.0045 0.5178 -0.1360 1.8310 -0.1455
+ 0.000000 22 0.0003 -0.0006 0.0010 -0.0011 0.0063 -0.0008 0.0007 0.0005 -0.0003 -0.0007 0.0008 -0.0011 0.0104 -0.0009
+ 0.000000 23 -0.4864 0.2013 0.0552 0.1739 -0.2515 0.0012 -0.5715 -0.5354 -0.2022 0.1788 0.2059 0.1608 -1.5500 0.0254
+ 0.000000 24 -0.0845 0.3268 0.0007 0.1248 -0.3115 0.0188 -0.0982 -0.0714 -0.0385 0.3852 -0.0764 0.0970 -0.3879 0.0126
+ 0.000000 25 -0.0028 0.0030 0.0087 -0.0030 0.0228 -0.0038 -0.0016 -0.0022 -0.0034 0.0015 0.0448 -0.0032 0.0051 -0.0043
+ 0.000000 26 0.2289 -0.5658 -0.5098 0.0078 -0.5137 0.1722 0.1106 0.1597 0.2101 -0.3559 -2.4064 0.0676 -0.3133 0.2071
+ 0.000000 27 0.2795 -0.4613 -0.6355 -0.3294 -0.0189 0.0848 0.1902 0.2064 0.2146 -2.0684 -0.4874 -0.1177 0.0447 0.1282
+ 0.000000 28 -0.0004 0.0007 0.0005 0.0002 0.0018 -0.0003 -0.0003 -0.0003 -0.0004 0.0043 0.0004 0.0001 0.0001 -0.0003
+ 0.000000 29 0.1615 -0.2664 -0.0134 -0.5437 0.1091 -0.0711 0.1099 0.1287 0.1145 -1.1948 0.1454 -0.4948 0.1221 -0.0222
+ 0.000000 30 0.1561 -0.3268 0.0694 -0.4416 0.1589 -0.6022 0.0469 0.1630 0.1027 -0.1156 0.1072 -2.1248 0.1860 -0.4657
+ 0.000000 31 -0.0001 0.0001 0.0000 0.0002 0.0006 0.0001 -0.0001 -0.0001 -0.0001 0.0001 -0.0000 0.0016 0.0000 0.0000
+ 0.000000 32 -0.1877 0.5663 0.1043 0.2555 -0.0698 -0.0129 -0.1404 -0.1385 -0.1418 0.5119 0.0503 1.1366 -0.0926 -0.1795
+ 0.000000 33 -0.4767 0.2092 0.0983 0.3765 -0.0537 -0.0372 -0.3953 -0.2402 -0.5541 0.1571 0.0712 0.4374 -0.0508 -0.4263
+ 0.000000 34 0.0001 -0.0002 -0.0002 0.0001 0.0018 0.0005 0.0003 -0.0000 0.0001 -0.0003 -0.0001 0.0000 0.0001 0.0040
+ 0.000000 35 0.1474 -0.0402 -0.1772 0.5411 -0.0954 0.4371 0.4587 -0.0114 0.1114 -0.0854 -0.1979 0.3453 -0.1385 2.3585
+ 0.000000 36 0.2935 -0.1443 -0.1411 -0.0452 -0.0374 0.2404 0.3255 0.0666 1.3964 -0.1201 -0.1206 -0.0393 -0.0400 0.3901
+ 0.000000 37 0.0009 -0.0004 -0.0002 -0.0004 0.0014 -0.0000 0.0004 0.0007 0.0040 -0.0003 -0.0001 -0.0003 0.0002 0.0001
+ 0.000000 38 0.5128 -0.2197 -0.1719 -0.1541 0.0183 0.0894 0.4718 0.6549 1.7690 -0.1713 -0.1391 -0.1243 0.0418 0.0915
+ 0.000000 39 0.5905 -0.2623 -0.1559 -0.2193 0.1970 -0.0027 0.5711 2.2288 0.6002 -0.2083 -0.1272 -0.1806 0.2741 0.0162
+ 0.000000 40 0.0042 -0.0019 -0.0007 -0.0021 0.0071 -0.0008 0.0020 0.0190 0.0031 -0.0016 -0.0005 -0.0017 0.0019 -0.0007
+ 0.000000 41 -0.0026 -0.0149 0.0380 -0.0361 0.1630 -0.0415 0.0459 0.3230 -0.2700 -0.0182 0.0282 -0.0348 0.2919 -0.0555
+ 0.000000 42 5.1774 4.7280 3.4935 5.1533 5.0276 4.6456 6.0495 4.7491 3.7941 3.6549 2.3790 3.9891 3.9624 3.7719
+ 0.000000 43 0.0698 -0.0989 -0.0469 -0.0668 -0.1482 -0.0334 0.0117 0.0710 0.0444 -0.0340 -0.0698 -0.0155 -0.0010 0.0064
+ 0.000000 44 2.0411 0.4572 0.0435 -0.9146 -0.1480 0.0780 1.3557 1.5544 2.1101 0.4792 -0.0221 -0.9478 -0.2566 -0.1445
+ 0.000000 45 0.0698 -0.0989 -0.0469 -0.0668 -0.1482 -0.0334 0.0117 0.0710 0.0444 -0.0340 -0.0698 -0.0155 -0.0010 0.0064
+ 0.000000 46 0.0033 0.0030 0.0027 0.0012 0.0160 0.0024 0.0021 0.0019 0.0001 -0.0001 0.0050 -0.0010 0.0031 -0.0007
+ 0.000000 47 0.0910 -0.0184 -0.0223 0.0236 0.1235 0.0728 0.0432 0.0482 0.0336 -0.0259 -0.0863 -0.0031 0.0049 0.0231
+ 0.000000 48 2.0411 0.4572 0.0435 -0.9146 -0.1480 0.0780 1.3557 1.5544 2.1101 0.4792 -0.0221 -0.9478 -0.2566 -0.1445
+ 0.000000 49 0.0910 -0.0184 -0.0223 0.0236 0.1235 0.0728 0.0432 0.0482 0.0336 -0.0259 -0.0863 -0.0031 0.0049 0.0231
+ 0.000000 50 2.8143 4.2056 5.6647 3.9967 4.6842 5.0710 4.4840 1.6724 2.6309 3.1059 4.5477 2.9392 4.0044 4.1900
+ 1.000000 0 -0.2241 -0.4899 -0.3942 -2.3598 -0.4640 -0.2804 -0.6080 0.0503 -0.1770 -0.0141 0.0073 0.0286 -0.0961 -0.0414
+ 1.000000 1 0.2781 0.4291 -0.0600 0.8577 0.1289 -0.0339 -0.1074 0.5665 0.1226 0.1520 -0.0107 -0.1289 0.0309 -0.1525
+ 1.000000 2 0.3365 0.5368 -0.7124 -0.0451 0.1414 -0.2236 -0.3035 0.8199 0.0451 0.2938 0.0823 -0.3272 -0.4506 -0.1620
+ 1.000000 3 0.4694 -0.0171 -0.3697 0.3359 -0.5679 -0.9773 -0.4664 0.3552 1.0177 0.0944 -0.1843 -0.6061 -0.3208 -1.0522
+ 1.000000 4 0.4155 0.3377 0.2207 0.1821 0.3290 1.5156 0.1028 0.0494 0.1525 -0.0004 -0.0238 0.1195 0.7223 -0.1701
+ 1.000000 5 0.8894 0.7221 -0.4601 0.3389 0.4964 0.7075 -0.0772 0.3438 0.4415 0.2541 0.1214 -1.0727 -0.8213 -0.1340
+ 1.000000 6 0.4611 0.1551 0.2780 0.8105 -0.0902 0.3509 1.3708 0.0619 0.2045 -0.1124 -0.6229 0.2400 0.4451 -0.0085
+ 1.000000 7 0.1438 0.4735 0.0890 -0.0282 0.2669 -0.0324 1.0320 -0.0319 -0.1110 0.1294 0.5784 -0.0729 0.4717 0.0201
+ 1.000000 8 0.6236 0.9209 -0.5914 0.2963 0.4019 -0.1717 0.3796 0.2425 0.0673 0.3942 0.7232 -1.2193 -0.9143 -0.1098
+ 1.000000 9 0.8316 0.3939 0.0809 0.5735 2.0688 0.4144 0.0613 0.2149 0.0815 0.4925 0.1273 -0.1883 -0.0382 -0.2350
+ 1.000000 10 0.1037 0.1034 -0.2343 -0.0989 -0.8814 -0.3999 -0.2797 0.1512 0.0411 0.4913 -0.0642 -0.0857 0.0082 -0.7430
+ 1.000000 11 0.3994 0.2580 -0.7898 0.0247 -0.9738 -0.4788 -0.3778 0.3102 0.1095 0.7926 -0.0406 -0.3063 -0.4185 -0.6640
+ 1.000000 12 0.4246 0.4301 -0.1049 0.6462 -0.2164 0.1426 -0.3292 0.9448 0.2968 0.0464 -0.8547 -0.1102 -0.0712 -0.2451
+ 1.000000 13 -0.2136 -1.4412 0.0325 -0.3758 -0.1716 -0.2796 -0.3253 -0.1245 -0.0545 -0.1354 -0.1380 0.1169 0.1087 -0.0239
+ 1.000000 14 -0.1645 -1.9054 -0.1459 -0.3414 -0.2700 -0.3559 -0.5052 0.1080 0.0071 -0.1645 -0.3306 0.0844 -0.0104 -0.0445
+ 1.000000 15 -1.7076 -0.4739 0.0934 -0.0290 -0.7532 -0.0793 -0.2930 -0.1728 0.4752 -0.7681 -0.2218 0.1845 0.1399 0.0377
+ 1.000000 16 -0.6672 0.0693 -0.0452 -0.2243 0.0602 -0.3886 -0.1314 -0.0585 -0.4856 0.4158 0.1044 0.0147 0.0245 0.0064
+ 1.000000 17 -1.6033 -0.0412 -0.1792 -0.3482 -0.1023 -0.5732 -0.2333 -0.1569 -0.6071 0.3417 0.1151 0.0455 -0.0496 0.0558
+ 1.000000 18 0.2458 0.0361 -0.1519 0.5164 -0.2880 0.0774 -0.2103 0.1393 0.2716 0.0094 -0.1605 -0.1063 -0.0196 -0.6293
+ 1.000000 19 0.1058 0.1517 -0.1685 -0.0266 0.1426 -0.1007 -0.0937 0.0531 -0.0123 0.0795 0.0554 -0.1083 0.0339 -0.4093
+ 1.000000 20 0.0684 0.0809 2.2265 0.4197 0.4780 0.3138 0.3820 -0.1322 0.0105 -0.1283 0.0261 0.2391 0.2684 0.5108
+ 1.000000 21 0.0367 0.6237 -0.1349 -0.1229 0.4285 -0.1226 0.2892 -0.0156 -0.1342 0.4668 2.2402 -0.1351 -0.1144 0.1167
+ 1.000000 22 0.0801 0.0269 -0.0250 0.0672 -0.1282 -0.0073 -0.2846 0.0730 0.0617 0.1149 -0.7859 -0.0142 0.0095 -0.3143
+ 1.000000 23 0.1100 0.1475 -0.0937 0.0596 -0.0828 -0.0358 -0.3128 0.0912 0.0528 0.2350 -0.5939 -0.0581 -0.0550 -0.2701
+ 1.000000 24 0.3997 0.1001 -0.0760 0.1134 -0.1670 -0.0184 -0.0986 0.4082 0.0776 0.3973 -0.2758 -0.0610 -0.0507 -0.0894
+ 1.000000 25 -0.3357 -0.3176 0.1677 -0.0117 -0.3246 0.1058 0.0573 -0.2151 0.0165 -1.4367 -0.2229 0.1440 0.1282 0.0739
+ 1.000000 26 -0.3319 -0.3858 0.1904 0.0120 -0.4643 0.1300 0.0492 -0.1687 0.0406 -1.7669 -0.3410 0.1674 0.1411 0.0770
+ 1.000000 27 -0.3645 -0.5683 0.1997 -0.1898 -0.0681 0.0961 0.1312 -1.5942 -0.0149 -0.4704 -0.0221 0.1696 0.1454 0.1390
+ 1.000000 28 -0.1591 -0.0211 0.0582 -0.3028 0.0471 -0.0267 0.0591 -0.6924 -0.2705 0.0684 0.0509 0.0578 0.0477 0.0616
+ 1.000000 29 -0.3349 -0.1976 0.1374 -0.4851 0.0504 -0.0080 0.1257 -1.4706 -0.4018 -0.0471 0.0681 0.1306 0.1006 0.1317
+ 1.000000 30 -0.2298 -0.1980 0.5938 -0.0728 0.1218 0.5794 0.3714 -0.2131 -0.1016 -0.1922 -0.0759 0.4596 0.2248 2.2126
+ 1.000000 31 -0.2054 -0.0535 0.3779 -0.1683 0.4829 0.1313 0.3335 -0.1859 -0.1586 -0.0692 0.4020 0.2386 0.1471 1.9445
+ 1.000000 32 0.0970 0.1906 -0.3960 0.0234 0.3848 -0.0848 -0.0132 0.0512 0.0033 0.1221 0.3293 -0.5076 -0.2137 0.0197
+ 1.000000 33 -0.4473 -0.0030 0.0299 -0.4203 0.1159 -0.4413 0.0841 -0.2478 -2.1411 0.0448 0.1345 0.0768 0.0325 0.1146
+ 1.000000 34 0.2945 0.0524 -0.0625 0.1461 -0.0350 -0.0217 -0.0720 0.2739 0.6783 0.0266 -0.0398 -0.0631 -0.0309 -0.0708
+ 1.000000 35 0.3261 0.0861 -0.1319 0.1035 -0.0124 -0.1319 -0.0815 0.3416 0.3741 0.0580 -0.0167 -0.0936 -0.0987 -0.0697
+ 1.000000 36 0.1118 0.0497 -0.1306 0.1522 -0.0630 0.0474 -0.2291 0.0806 0.1107 0.0386 -0.0365 -0.2403 -0.4737 -0.1299
+ 1.000000 37 0.2298 0.2571 -0.5148 0.0199 0.1134 -0.4831 -0.3642 0.1936 0.0523 0.2154 0.1220 -0.7415 -2.1499 -0.1733
+ 1.000000 38 -0.0862 -0.0907 0.3316 0.0799 0.0560 0.3671 0.3521 -0.1117 -0.0129 -0.1181 -0.0365 0.1383 1.9332 0.0961
+ 1.000000 39 -0.0074 -0.0387 0.0866 0.0466 -0.0572 0.2111 -0.0733 -0.0117 0.0333 -0.0330 -0.0547 0.2883 0.1970 -0.1899
+ 1.000000 40 -0.0704 -0.0676 0.1642 -0.0364 -0.0300 0.0213 0.0735 -0.0524 -0.0324 -0.0516 -0.0279 0.5231 0.4481 -0.0494
+ 1.000000 41 -0.3296 -0.3223 0.6144 -0.1381 -0.1033 0.5452 0.6161 -0.2683 -0.1301 -0.2666 -0.1063 2.7796 0.5888 0.5630
+ 1.000000 42 5.3492 4.1950 1.2554 6.1920 5.0920 3.6257 3.5024 3.9480 4.6561 3.0298 4.1554 0.1103 0.3912 3.4361
+ 1.000000 43 -0.4345 -0.9190 0.6590 -1.3012 -0.8887 -0.4185 0.9119 -0.3319 -1.1183 -0.7374 -0.8447 0.7930 0.8246 2.0439
+ 1.000000 44 1.8803 0.1672 -0.0845 1.3818 -0.9712 0.3263 0.1818 1.4274 0.5114 0.0963 -0.8109 0.0459 -0.4341 -0.9074
+ 1.000000 45 -0.4345 -0.9190 0.6590 -1.3012 -0.8887 -0.4185 0.9119 -0.3319 -1.1183 -0.7374 -0.8447 0.7930 0.8246 2.0439
+ 1.000000 46 1.2357 2.0608 0.9876 0.9686 2.0033 2.2730 1.8059 0.8699 0.6621 1.6311 1.5745 0.9560 2.8614 2.6440
+ 1.000000 47 2.7142 3.6171 -0.7726 1.1677 2.5353 0.9786 0.9030 2.0596 1.0064 2.8228 1.9875 -0.6379 -2.8766 0.4413
+ 1.000000 48 1.8803 0.1672 -0.0845 1.3818 -0.9712 0.3263 0.1818 1.4274 0.5114 0.0963 -0.8109 0.0459 -0.4341 -0.9074
+ 1.000000 49 2.7142 3.6171 -0.7726 1.1677 2.5353 0.9786 0.9030 2.0596 1.0064 2.8228 1.9875 -0.6379 -2.8766 0.4413
+ 1.000000 50 3.2829 3.8264 5.9338 2.7309 3.6194 4.4478 4.3990 2.0500 1.2963 2.4128 1.8270 5.9561 4.7948 2.7327
+ 2.000000 0 -2.1522 -0.2755 -0.2672 -0.4729 -0.3056 -0.4198 -0.2767 -0.2201 -0.0522 -0.0189 0.0529 0.0695 0.0139 -0.1020
+ 2.000000 1 1.0993 0.3618 0.0462 0.4303 0.0331 -0.0569 -0.1297 0.1742 0.6754 0.1449 -0.0638 -0.1564 -0.1534 -0.0038
+ 2.000000 2 0.0001 0.3076 -0.1946 0.4474 0.0979 -0.6090 -0.2292 0.0820 0.7021 0.2594 0.0664 -0.1182 -0.3151 -0.3915
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diff --git a/regtest/multicolvar/rt-sprint/isomers.xyz b/regtest/multicolvar/rt-sprint/isomers.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..b2e13cfc8b20cf42ffb8fe5f46fc7c60e944722e
--- /dev/null
+++ b/regtest/multicolvar/rt-sprint/isomers.xyz
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+C 1.6497486847 0.1111914945 -0.6008610691
+C 2.6822985931 -0.0428705181 0.2351190345
+H -2.7246380605 1.2456585787 0.7403753487
+H 3.7065573872 0.0228505815 -0.1198801266
+H -2.7233995381 -1.4294218812 0.249561475
+H -0.2502976774 -2.1377635139 -0.4963987013
+H -0.2523062432 2.17488206 0.2948588833
+H 2.5347681503 -0.2382579738 1.2938751157
+H 1.8474040421 0.306304919 -1.6579046083
+ 14
+20. 20. 20.
+C -0.3268880184 -1.1225661863 0.0057476319
+C 0.3224838419 0.242571611 -0.0010674721
+C -0.6632342477 1.1848620258 -0.0069904025
+C -1.9706138845 0.5322354429 -0.0033053962
+C -1.8004313627 -0.8107973874 0.0037759054
+C 1.7548530798 0.4879550824 -0.001726157
+C 2.7192039842 -0.4218518742 0.0032576903
+H -2.918956917 1.0583116676 -0.0064631009
+H 3.8004584961 -0.4296852223 0.0036570135
+H -2.5795907991 -1.5637037397 0.0076834224
+H -0.0279837518 -1.7164204069 -0.8694035705
+H -0.5086053484 2.2590307272 -0.0130727359
+H -0.0279589721 -1.7080329459 0.8865910344
+H 2.0503969375 1.5460476349 -0.0071428619
+ 14
+20. 20. 20.
+C -0.3433050762 -1.1218935585 0.3391480836
+C 0.2884433054 0.2173684997 0.6356520881
+C -0.7379376276 1.1980654355 0.103397679
+C -1.7973035056 0.512994475 -0.3779214644
+C -1.5530373169 -0.9290191374 -0.2288240656
+C 1.6869346258 0.4349181759 0.0842788728
+C 2.3887656224 -0.4340982608 -0.6085946274
+H -2.6947529952 0.9434528502 -0.8091353179
+H 3.3628791843 -0.4790354827 -1.0772011906
+H -2.2464613522 -1.7041658354 -0.5365247865
+H 0.1274394883 -2.0686348236 0.5735610537
+H -0.6112733462 2.2739934949 0.1312204813
+H 0.3439470531 0.34546056 1.7325976079
+H 2.1228618035 1.4189154606 0.3026627558
+ 14
+20. 20. 20.
+C -1.1546248859 1.1846559302 -0.0238240514
+C 0.2447829453 1.153365704 -0.0186792624
+C 0.9505605821 -0.0660700814 0.0135292595
+C 0.1494829221 -1.195175863 0.0387881023
+C -1.2261065286 -1.2363931886 0.035518762
+C -1.8958604454 0.0006792201 0.0030038874
+C 2.4602605077 -0.126184807 0.0196096687
+H -1.7776989405 -2.1721576307 0.0568196702
+H -2.9822663385 0.0291213058 -0.0010804376
+H -1.6671451057 2.1419505783 -0.0489696091
+H 2.8305896355 -0.6373750533 0.9148559052
+H 0.8059862014 2.0855707768 -0.0398588374
+H 2.8360254686 -0.6783830426 -0.8486434031
+H 2.8924429819 0.8781911514 -0.0024496542
+ 14
+20. 20. 20.
+ C 0.181753 0.891929 -0.918639
+ C -0.330615 -0.508508 -1.211079
+ C -1.723079 -0.703888 -0.635420
+ C -1.549978 -0.682084 0.697045
+ C -0.039010 -0.471135 0.960794
+ C 0.362766 0.920235 0.412610
+ C 0.513072 -1.342484 -0.236363
+ H -2.308220 -0.731926 1.471414
+ H 0.310820 -0.709777 1.967858
+ H 0.666255 1.759532 1.029471
+ H -2.649282 -0.757330 -1.194547
+ H 0.285482 1.701126 -1.631330
+ H 1.592393 -1.241132 -0.376285
+ H 0.217728 -2.392904 -0.172103
diff --git a/regtest/multicolvar/rt-sprint/plumed.dat b/regtest/multicolvar/rt-sprint/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..1abbe6f31994942f925202540bee8045fb69e8b9
--- /dev/null
+++ b/regtest/multicolvar/rt-sprint/plumed.dat
@@ -0,0 +1,21 @@
+DENSITY SPECIES=1-7 LABEL=c
+DENSITY SPECIES=8-14 LABEL=h
+
+SPRINT ...
+ ARG=c,h
+ SWITCH11={RATIONAL R_0=2.6 NN=6 MM=12}
+ SWITCH12={RATIONAL R_0=2.2 NN=6 MM=12}
+ SWITCH22={RATIONAL R_0=2.2 NN=6 MM=12}
+ LABEL=ss
+... SPRINT
+
+# SPRINT ...
+# ARG=c,h
+# SWITCH11={RATIONAL R_0=2.6 NN=6 MM=12}
+# SWITCH12={RATIONAL R_0=2.2 NN=6 MM=12}
+# SWITCH22={RATIONAL R_0=2.2 NN=6 MM=12}
+# NUMERICAL_DERIVATIVES LABEL=ssnum
+# ... SPRINT
+
+PRINT ARG=ss.* FILE=colvar FMT=%8.4f
+DUMPDERIVATIVES ARG=ss.* FILE=deriv FMT=%8.4f
diff --git a/regtest/multicolvar/rt24-lowmem/Makefile b/regtest/multicolvar/rt24-lowmem/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/multicolvar/rt24-lowmem/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/multicolvar/rt24-lowmem/config b/regtest/multicolvar/rt24-lowmem/config
new file mode 100644
index 0000000000000000000000000000000000000000..ba8b778571e71d71dd136e9098170c96b46493fe
--- /dev/null
+++ b/regtest/multicolvar/rt24-lowmem/config
@@ -0,0 +1,4 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+extra_files="../../trajectories/trajectory.xyz"
diff --git a/regtest/multicolvar/rt24-lowmem/derivatives.reference b/regtest/multicolvar/rt24-lowmem/derivatives.reference
new file mode 100644
index 0000000000000000000000000000000000000000..3327b172bb32f0b4e86939e0e8b99c9ac1e45af0
--- /dev/null
+++ b/regtest/multicolvar/rt24-lowmem/derivatives.reference
@@ -0,0 +1,196 @@
+#! FIELDS time parameter c1.moment-3 c1num.moment-3
+ 0.000000 0 -0.0208 -0.0208
+ 0.000000 1 -0.0169 -0.0169
+ 0.000000 2 -0.0194 -0.0194
+ 0.000000 3 0.0178 0.0178
+ 0.000000 4 -0.0196 -0.0196
+ 0.000000 5 0.0124 0.0124
+ 0.000000 6 0.0186 0.0186
+ 0.000000 7 0.0253 0.0253
+ 0.000000 8 -0.0227 -0.0227
+ 0.000000 9 -0.0033 -0.0033
+ 0.000000 10 0.0016 0.0016
+ 0.000000 11 0.0184 0.0184
+ 0.000000 12 -0.0025 -0.0025
+ 0.000000 13 0.0048 0.0048
+ 0.000000 14 -0.0068 -0.0068
+ 0.000000 15 0.0133 0.0133
+ 0.000000 16 -0.0193 -0.0193
+ 0.000000 17 0.0190 0.0190
+ 0.000000 18 -0.0078 -0.0078
+ 0.000000 19 0.0012 0.0012
+ 0.000000 20 -0.0102 -0.0102
+ 0.000000 21 -0.0222 -0.0222
+ 0.000000 22 0.0094 0.0094
+ 0.000000 23 0.0236 0.0236
+ 0.000000 24 0.0339 0.0339
+ 0.000000 25 0.0116 0.0116
+ 0.000000 26 0.0040 0.0040
+ 0.000000 27 -0.0271 -0.0271
+ 0.000000 28 0.0018 0.0018
+ 0.000000 29 -0.0183 -0.0183
+ 0.000000 30 -0.0133 -0.0133
+ 0.000000 31 0.0114 0.0114
+ 0.000000 32 0.0134 0.0134
+ 0.000000 33 0.0114 0.0114
+ 0.000000 34 -0.0316 -0.0316
+ 0.000000 35 -0.0081 -0.0081
+ 0.000000 36 0.0134 0.0134
+ 0.000000 37 -0.0081 -0.0081
+ 0.000000 38 0.0045 0.0045
+ 0.005000 0 -0.0223 -0.0223
+ 0.005000 1 -0.0156 -0.0156
+ 0.005000 2 -0.0191 -0.0191
+ 0.005000 3 0.0235 0.0235
+ 0.005000 4 -0.0283 -0.0283
+ 0.005000 5 0.0110 0.0110
+ 0.005000 6 0.0160 0.0160
+ 0.005000 7 0.0301 0.0301
+ 0.005000 8 -0.0240 -0.0240
+ 0.005000 9 -0.0026 -0.0026
+ 0.005000 10 -0.0013 -0.0013
+ 0.005000 11 0.0192 0.0192
+ 0.005000 12 -0.0034 -0.0034
+ 0.005000 13 0.0074 0.0074
+ 0.005000 14 -0.0086 -0.0086
+ 0.005000 15 0.0173 0.0173
+ 0.005000 16 -0.0223 -0.0223
+ 0.005000 17 0.0204 0.0204
+ 0.005000 18 -0.0093 -0.0093
+ 0.005000 19 0.0057 0.0057
+ 0.005000 20 -0.0093 -0.0093
+ 0.005000 21 -0.0291 -0.0291
+ 0.005000 22 0.0074 0.0074
+ 0.005000 23 0.0310 0.0310
+ 0.005000 24 0.0379 0.0379
+ 0.005000 25 0.0152 0.0152
+ 0.005000 26 0.0011 0.0011
+ 0.005000 27 -0.0279 -0.0279
+ 0.005000 28 0.0018 0.0018
+ 0.005000 29 -0.0218 -0.0218
+ 0.005000 30 -0.0187 -0.0187
+ 0.005000 31 0.0171 0.0171
+ 0.005000 32 0.0153 0.0153
+ 0.005000 33 0.0171 0.0171
+ 0.005000 34 -0.0349 -0.0349
+ 0.005000 35 -0.0139 -0.0139
+ 0.005000 36 0.0153 0.0153
+ 0.005000 37 -0.0139 -0.0139
+ 0.005000 38 0.0026 0.0026
+ 0.010000 0 -0.0435 -0.0435
+ 0.010000 1 -0.0277 -0.0277
+ 0.010000 2 -0.0118 -0.0118
+ 0.010000 3 0.0220 0.0220
+ 0.010000 4 -0.0400 -0.0400
+ 0.010000 5 0.0242 0.0242
+ 0.010000 6 0.0282 0.0282
+ 0.010000 7 0.0505 0.0505
+ 0.010000 8 -0.0292 -0.0292
+ 0.010000 9 -0.0115 -0.0115
+ 0.010000 10 -0.0095 -0.0095
+ 0.010000 11 0.0488 0.0488
+ 0.010000 12 0.0366 0.0366
+ 0.010000 13 0.0482 0.0482
+ 0.010000 14 -0.0129 -0.0129
+ 0.010000 15 0.0158 0.0158
+ 0.010000 16 -0.0262 -0.0262
+ 0.010000 17 0.0139 0.0139
+ 0.010000 18 -0.0322 -0.0322
+ 0.010000 19 -0.0070 -0.0070
+ 0.010000 20 -0.0079 -0.0079
+ 0.010000 21 -0.0388 -0.0388
+ 0.010000 22 -0.0015 -0.0015
+ 0.010000 23 0.0227 0.0227
+ 0.010000 24 0.0459 0.0459
+ 0.010000 25 0.0197 0.0197
+ 0.010000 26 -0.0007 -0.0007
+ 0.010000 27 -0.0226 -0.0226
+ 0.010000 28 -0.0065 -0.0065
+ 0.010000 29 -0.0471 -0.0471
+ 0.010000 30 -0.0125 -0.0125
+ 0.010000 31 0.0338 0.0338
+ 0.010000 32 0.0275 0.0275
+ 0.010000 33 0.0338 0.0338
+ 0.010000 34 -0.0320 -0.0320
+ 0.010000 35 -0.0288 -0.0288
+ 0.010000 36 0.0275 0.0275
+ 0.010000 37 -0.0288 -0.0288
+ 0.010000 38 0.0157 0.0157
+ 0.015000 0 -0.0593 -0.0593
+ 0.015000 1 -0.0403 -0.0403
+ 0.015000 2 -0.0024 -0.0024
+ 0.015000 3 0.0190 0.0190
+ 0.015000 4 -0.0411 -0.0411
+ 0.015000 5 0.0342 0.0342
+ 0.015000 6 0.0349 0.0349
+ 0.015000 7 0.0563 0.0563
+ 0.015000 8 -0.0296 -0.0296
+ 0.015000 9 -0.0165 -0.0165
+ 0.015000 10 -0.0069 -0.0069
+ 0.015000 11 0.0843 0.0843
+ 0.015000 12 0.0871 0.0871
+ 0.015000 13 0.0900 0.0900
+ 0.015000 14 -0.0129 -0.0129
+ 0.015000 15 0.0129 0.0129
+ 0.015000 16 -0.0218 -0.0218
+ 0.015000 17 -0.0020 -0.0020
+ 0.015000 18 -0.0720 -0.0720
+ 0.015000 19 -0.0321 -0.0321
+ 0.015000 20 -0.0027 -0.0027
+ 0.015000 21 -0.0397 -0.0397
+ 0.015000 22 -0.0092 -0.0092
+ 0.015000 23 -0.0037 -0.0037
+ 0.015000 24 0.0446 0.0446
+ 0.015000 25 0.0185 0.0185
+ 0.015000 26 0.0006 0.0006
+ 0.015000 27 -0.0109 -0.0109
+ 0.015000 28 -0.0134 -0.0134
+ 0.015000 29 -0.0658 -0.0658
+ 0.015000 30 0.0126 0.0126
+ 0.015000 31 0.0524 0.0524
+ 0.015000 32 0.0364 0.0364
+ 0.015000 33 0.0524 0.0524
+ 0.015000 34 -0.0236 -0.0236
+ 0.015000 35 -0.0430 -0.0430
+ 0.015000 36 0.0364 0.0364
+ 0.015000 37 -0.0430 -0.0430
+ 0.015000 38 0.0374 0.0374
+ 0.020000 0 -0.0469 -0.0469
+ 0.020000 1 -0.0370 -0.0370
+ 0.020000 2 -0.0003 -0.0003
+ 0.020000 3 0.0176 0.0176
+ 0.020000 4 -0.0284 -0.0284
+ 0.020000 5 0.0285 0.0285
+ 0.020000 6 0.0255 0.0255
+ 0.020000 7 0.0391 0.0391
+ 0.020000 8 -0.0207 -0.0207
+ 0.020000 9 -0.0134 -0.0134
+ 0.020000 10 0.0111 0.0111
+ 0.020000 11 0.0654 0.0654
+ 0.020000 12 0.0737 0.0737
+ 0.020000 13 0.0687 0.0687
+ 0.020000 14 -0.0063 -0.0063
+ 0.020000 15 0.0108 0.0108
+ 0.020000 16 -0.0136 -0.0136
+ 0.020000 17 -0.0079 -0.0079
+ 0.020000 18 -0.0657 -0.0657
+ 0.020000 19 -0.0359 -0.0359
+ 0.020000 20 0.0030 0.0030
+ 0.020000 21 -0.0307 -0.0307
+ 0.020000 22 -0.0080 -0.0080
+ 0.020000 23 -0.0050 -0.0050
+ 0.020000 24 0.0378 0.0378
+ 0.020000 25 0.0165 0.0165
+ 0.020000 26 0.0030 0.0030
+ 0.020000 27 -0.0086 -0.0086
+ 0.020000 28 -0.0124 -0.0124
+ 0.020000 29 -0.0598 -0.0598
+ 0.020000 30 0.0167 0.0167
+ 0.020000 31 0.0506 0.0506
+ 0.020000 32 0.0295 0.0295
+ 0.020000 33 0.0506 0.0506
+ 0.020000 34 -0.0183 -0.0183
+ 0.020000 35 -0.0397 -0.0397
+ 0.020000 36 0.0295 0.0295
+ 0.020000 37 -0.0397 -0.0397
+ 0.020000 38 0.0287 0.0287
diff --git a/regtest/multicolvar/rt24-lowmem/plumed.dat b/regtest/multicolvar/rt24-lowmem/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..46271444605d42ceb7d4051546d8f193dceeb5a6
--- /dev/null
+++ b/regtest/multicolvar/rt24-lowmem/plumed.dat
@@ -0,0 +1,3 @@
+COORDINATIONNUMBER SPECIES=1-10 SWITCH={RATIONAL R_0=1.0} MOMENTS=3 LABEL=c1
+COORDINATIONNUMBER SPECIES=1-10 SWITCH={RATIONAL R_0=1.0} MOMENTS=3 NUMERICAL_DERIVATIVES LABEL=c1num
+DUMPDERIVATIVES ARG=c1.*,c1num.* STRIDE=1 FILE=derivatives FMT=%8.4f
diff --git a/regtest/multicolvar/rt45/plumed.dat b/regtest/multicolvar/rt45/plumed.dat
index 2492a77c73f3023dd19ddacfebe539196677cf73..e2c2550b4cfdbfcc6e10a67370fc63090ddd6b26 100644
--- a/regtest/multicolvar/rt45/plumed.dat
+++ b/regtest/multicolvar/rt45/plumed.dat
@@ -11,7 +11,7 @@ ANGLES ...
MORE_THAN={GAUSSIAN R_0=0.5pi}
BETWEEN1={GAUSSIAN LOWER=0.25pi UPPER=0.75pi NORM}
BETWEEN2={GAUSSIAN LOWER=0.25pi UPPER=0.75pi}
- NL_STRIDE=20 TOL=0.001
+ TOL=0.001
LABEL=a2
... ANGLES
diff --git a/regtest/scripts/exe.make b/regtest/scripts/exe.make
new file mode 100644
index 0000000000000000000000000000000000000000..5d23649262c8aeb43b5cc0c60a94f7d750409f76
--- /dev/null
+++ b/regtest/scripts/exe.make
@@ -0,0 +1,4 @@
+
+exe:
+ $(CXX) -c $(CPPFLAGS) $(ADDCPPFLAGS) $(CXXFLAGS) *.cpp
+ $(LD) *.o -o $@ $(PLUMED_LOAD)
diff --git a/regtest/scripts/module.make b/regtest/scripts/module.make
new file mode 100644
index 0000000000000000000000000000000000000000..ff878d02af0a9755fa59f26dfb8028a2a9685828
--- /dev/null
+++ b/regtest/scripts/module.make
@@ -0,0 +1,20 @@
+SUBDIRS := $(subst /Makefile,,$(wildcard rt*/Makefile))
+SUBDIRSCLEAN := $(addsuffix .clean,$(SUBDIRS))
+SUBDIRSVALGRIND := $(addsuffix .valgrind,$(SUBDIRS))
+
+.PHONY: all clean valgrind $(SUBDIRS) $(SUBDIRSCLEAN) $(SUBDIRSVALGRIND)
+
+all: $(SUBDIRS)
+
+clean: $(SUBDIRSCLEAN)
+
+valgrind: $(SUBDIRSVALGRIND)
+
+$(SUBDIRS):
+ $(MAKE) -C $@
+
+$(SUBDIRSCLEAN): %.clean:
+ $(MAKE) -C $* clean
+
+$(SUBDIRSVALGRIND): %.valgrind:
+ $(MAKE) -C $* valgrind
diff --git a/regtest/scripts/run b/regtest/scripts/run
index 9c489174d1c60892bd0b3bf4690efb8849422f74..63e51509ae0997ae3b08a47f141bba9322fced42 100755
--- a/regtest/scripts/run
+++ b/regtest/scripts/run
@@ -84,8 +84,6 @@ case "$type" in
}
echo "Run simplemd"
$mpi $valgrind $plumed simplemd < in > out 2> err
- echo "Done. Here is the error file:"
- cat err
;;
(driver)
echo "Run driver"
@@ -94,9 +92,7 @@ if ((mpiprocs==0)) ; then
else
$mpi $valgrind plumed driver $arg > out 2> err
fi
- echo "Done. Here is the error file:"
- cat err
- ;;
+ ;;
(sum_hills)
echo "Run driver"
if ((mpiprocs==0)) ; then
@@ -104,12 +100,21 @@ if ((mpiprocs==0)) ; then
else
$mpi $valgrind plumed sum_hills $arg > out 2> err
fi
- echo "Done. Here is the error file:"
- cat err
+ ;;
+(make)
+ echo "Run Make"
+ plumed info --configuration > Makefile.conf
+ plumed --is-installed || ln -s $(plumed info --root)/src plumed
+ cat <(plumed info --configuration) $(plumed info --root)/src/lib/Plumed.inc.static ../../../scripts/exe.make > Makefile
+ make exe 1>out 2> err
+ $mpi $valgrind ./exe $arg >> out 2>> err
;;
(*) echo "unknown test type" ; exit 1 ;;
esac
+echo "Done. Here is the error file:"
+cat err
+
if ls *.reference > /dev/null
then
diff --git a/regtest/secondarystructure/Makefile b/regtest/secondarystructure/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..42480767ae852294cf2d7269ac5a1c16064d1849
--- /dev/null
+++ b/regtest/secondarystructure/Makefile
@@ -0,0 +1,2 @@
+include ../scripts/module.make
+
diff --git a/regtest/trajectories/molfile_plugin/diala.pdb b/regtest/trajectories/molfile_plugin/diala.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..f75ac626cde690577bc6595b523ea833dc23d231
--- /dev/null
+++ b/regtest/trajectories/molfile_plugin/diala.pdb
@@ -0,0 +1,22 @@
+ATOM 1 CL ALA 1 14.180 11.030 15.600 1.00 1.00
+ATOM 2 HL1 ALA 1 14.500 10.270 14.860 1.00 1.00
+ATOM 3 HL2 ALA 1 15.070 11.370 16.170 1.00 1.00
+ATOM 4 HL3 ALA 1 13.450 10.570 16.310 1.00 1.00
+ATOM 5 CLP ALA 1 13.570 12.180 14.890 1.00 1.00
+ATOM 6 OL ALA 1 13.850 12.430 13.730 1.00 1.00
+ATOM 7 NL ALA 1 12.700 12.930 15.590 1.00 1.00
+ATOM 8 HL ALA 1 12.500 12.710 16.540 1.00 1.00
+ATOM 9 CA ALA 1 11.990 14.060 15.020 1.00 1.00
+ATOM 10 HA ALA 1 11.740 13.840 13.990 1.00 1.00
+ATOM 11 CB ALA 1 10.690 14.290 15.810 1.00 1.00
+ATOM 12 HB1 ALA 1 10.060 13.370 15.780 1.00 1.00
+ATOM 13 HB2 ALA 1 10.900 14.540 16.870 1.00 1.00
+ATOM 14 HB3 ALA 1 10.100 15.120 15.370 1.00 1.00
+ATOM 15 CRP ALA 1 12.840 15.330 15.010 1.00 1.00
+ATOM 16 OR ALA 1 12.550 16.310 15.690 1.00 1.00
+ATOM 17 NR ALA 1 13.930 15.330 14.220 1.00 1.00
+ATOM 18 HR ALA 1 14.140 14.490 13.710 1.00 1.00
+ATOM 19 CR ALA 1 14.810 16.470 14.090 1.00 1.00
+ATOM 20 HR1 ALA 1 14.360 17.230 13.420 1.00 1.00
+ATOM 21 HR2 ALA 1 15.000 16.940 15.080 1.00 1.00
+ATOM 22 HR3 ALA 1 15.790 16.150 13.670 1.00 1.00
diff --git a/regtest/trajectories/molfile_plugin/test0.pdb b/regtest/trajectories/molfile_plugin/test0.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..f8a042d2808aaa6163c6e757f07238515a01f191
--- /dev/null
+++ b/regtest/trajectories/molfile_plugin/test0.pdb
@@ -0,0 +1,23 @@
+ATOM 1 CL ALA 1 -3.220 0.160 1.920 1.00 1.00
+ATOM 2 HL1 ALA 1 -3.170 1.240 2.190 1.00 1.00
+ATOM 3 HL2 ALA 1 -3.960 0.030 1.100 1.00 1.00
+ATOM 4 HL3 ALA 1 -3.520 -0.440 2.810 1.00 1.00
+ATOM 5 CLP ALA 1 -1.800 -0.210 1.630 1.00 1.00
+ATOM 6 OL ALA 1 -1.100 -0.890 2.410 1.00 1.00
+ATOM 7 NL ALA 1 -1.400 0.350 0.520 1.00 1.00
+ATOM 8 HL ALA 1 -1.940 0.980 -0.030 1.00 1.00
+ATOM 9 CA ALA 1 -0.060 0.000 0.060 1.00 1.00
+ATOM 10 HA ALA 1 0.060 -1.060 0.230 1.00 1.00
+ATOM 11 CB ALA 1 -0.020 0.050 -1.500 1.00 1.00
+ATOM 12 HB1 ALA 1 0.880 -0.430 -1.930 1.00 1.00
+ATOM 13 HB2 ALA 1 -0.910 -0.400 -1.990 1.00 1.00
+ATOM 14 HB3 ALA 1 -0.080 1.110 -1.820 1.00 1.00
+ATOM 15 CRP ALA 1 1.160 0.770 0.730 1.00 1.00
+ATOM 16 OR ALA 1 1.790 1.670 0.150 1.00 1.00
+ATOM 17 NR ALA 1 1.470 0.480 1.990 1.00 1.00
+ATOM 18 HR ALA 1 0.910 -0.190 2.480 1.00 1.00
+ATOM 19 CR ALA 1 2.650 1.120 2.570 1.00 1.00
+ATOM 20 HR1 ALA 1 3.480 1.140 1.830 1.00 1.00
+ATOM 21 HR2 ALA 1 2.460 2.210 2.710 1.00 1.00
+ATOM 22 HR3 ALA 1 3.040 0.570 3.460 1.00 1.00
+END
diff --git a/regtest/trajectories/molfile_plugin/test1.pdb b/regtest/trajectories/molfile_plugin/test1.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..de1f2ef6e1fa23272346634f2f2309f944274282
--- /dev/null
+++ b/regtest/trajectories/molfile_plugin/test1.pdb
@@ -0,0 +1,23 @@
+ATOM 1 CL ALA 1 -3.180 1.480 1.220 1.00 1.00
+ATOM 2 HL1 ALA 1 -3.850 2.230 0.740 1.00 1.00
+ATOM 3 HL2 ALA 1 -3.750 0.530 1.320 1.00 1.00
+ATOM 4 HL3 ALA 1 -2.840 1.900 2.180 1.00 1.00
+ATOM 5 CLP ALA 1 -1.940 1.420 0.400 1.00 1.00
+ATOM 6 OL ALA 1 -1.490 2.320 -0.280 1.00 1.00
+ATOM 7 NL ALA 1 -1.370 0.320 0.600 1.00 1.00
+ATOM 8 HL ALA 1 -1.800 -0.350 1.210 1.00 1.00
+ATOM 9 CA ALA 1 -0.050 -0.010 0.100 1.00 1.00
+ATOM 10 HA ALA 1 0.020 -1.070 0.330 1.00 1.00
+ATOM 11 CB ALA 1 0.030 -0.060 -1.430 1.00 1.00
+ATOM 12 HB1 ALA 1 -0.350 0.890 -1.860 1.00 1.00
+ATOM 13 HB2 ALA 1 1.020 -0.250 -1.900 1.00 1.00
+ATOM 14 HB3 ALA 1 -0.840 -0.660 -1.760 1.00 1.00
+ATOM 15 CRP ALA 1 1.200 0.720 0.740 1.00 1.00
+ATOM 16 OR ALA 1 1.910 0.150 1.520 1.00 1.00
+ATOM 17 NR ALA 1 1.370 2.030 0.430 1.00 1.00
+ATOM 18 HR ALA 1 0.620 2.450 -0.080 1.00 1.00
+ATOM 19 CR ALA 1 2.550 2.840 0.680 1.00 1.00
+ATOM 20 HR1 ALA 1 2.910 3.140 -0.330 1.00 1.00
+ATOM 21 HR2 ALA 1 2.270 3.850 1.050 1.00 1.00
+ATOM 22 HR3 ALA 1 3.340 2.290 1.240 1.00 1.00
+END
diff --git a/regtest/trajectories/molfile_plugin/traj.dcd b/regtest/trajectories/molfile_plugin/traj.dcd
new file mode 100644
index 0000000000000000000000000000000000000000..f0e8afcd82aa43fb4cca9cb367a973183e280479
Binary files /dev/null and b/regtest/trajectories/molfile_plugin/traj.dcd differ
diff --git a/regtest/trajectories/molfile_plugin/traj.xtc b/regtest/trajectories/molfile_plugin/traj.xtc
new file mode 100644
index 0000000000000000000000000000000000000000..eadbea87298af1a37b88f75c1b300410c6be05db
Binary files /dev/null and b/regtest/trajectories/molfile_plugin/traj.xtc differ
diff --git a/src/.gitignore b/src/.gitignore
index 7e53ca2ce072504c1d7e0095f8466f61f4e4d363..cabbf00ca882721f335f43a8cf7a265b341cc97d 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -10,6 +10,7 @@
!/colvar
!/config
!/core
+!/crystallization
!/function
!/generic
!/header.sh
diff --git a/src/Makefile b/src/Makefile
index ef179b10dff7f839e196b1fa860b9ad1fec1be84..17d33b58534a7afbd6c2cc524dd39970ad6137d3 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -14,8 +14,8 @@ uninstall:
$(MAKE) -C lib uninstall
# list of all the contained directories which can be cleaned
-SUBDIRS =$(subst /Makefile,,$(wildcard */Makefile))
-SUBDIRSCLEAN=$(addsuffix .clean,$(SUBDIRS))
+SUBDIRS :=$(subst /Makefile,,$(wildcard */Makefile))
+SUBDIRSCLEAN :=$(addsuffix .clean,$(SUBDIRS))
.PHONY: $(SUBDIRS)
# this is cleaning all subdirectories
@@ -28,11 +28,23 @@ $(SUBDIRSCLEAN): %.clean:
cppcheck:
cppcheck --std=c++03 --std=posix -j 4 --platform=unix64 -q --enable=all */*.{h,cpp}
+.PHONY: mod-light mod-heavy mod-reset
+mod-light:
+ maketools/mod.sh light
+mod-heavy:
+ maketools/mod.sh heavy
+mod-reset:
+ maketools/mod.sh reset
+
+
.PHONY: help
help:
@echo "Available targets are"
@echo " all: compile everything (default)"
@echo " clean: clean everything"
@echo " cppcheck: check source (requires cppcheck installed)"
+ @echo " mod-light: disable all optional modules"
+ @echo " mod-heavy: enable all optional modules"
+ @echo " mod-reset: reset optional modules to their default"
diff --git a/src/README b/src/README
index faac06e2dab0a4e995c7bab0a5424b38f709852e..b015c7386d0b05b461616adbf61ebb682bdd6c10 100644
--- a/src/README
+++ b/src/README
@@ -15,4 +15,15 @@ All the other directories are "modules". Modules are of three type:
Notice that these .on and .off files are not to be distributed/included in git,
as they reflect local wishes!
+As a quick trick to enable all modules, including those which are off by default
+make mod-heavy
+
+On the other hand, to disable all modules which are not compulsory:
+make mod-light
+Notice that this will result in a library which cannot do anything, but can be useful
+to quickly compile tool library
+
+To reset modules, removing all .on and .off files:
+make mod-reset
+
The type of the module can be set by adding a file module.type (see e.g. core/module.type)
diff --git a/src/analysis/Analysis.cpp b/src/analysis/Analysis.cpp
index 45483eadc847512ec597ca1e07b5e86c59d26fd9..d78a42337e5af3aeb763070849742d665a6604ed 100644
--- a/src/analysis/Analysis.cpp
+++ b/src/analysis/Analysis.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/analysis/Analysis.h b/src/analysis/Analysis.h
index 9431ca3b5085a75f9d37d999ee734f7aec8ed4a4..09d0891b4111f4e192e54dcc86607289eabb594d 100644
--- a/src/analysis/Analysis.h
+++ b/src/analysis/Analysis.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/analysis/Commit.cpp b/src/analysis/Commit.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..80ee81eca12bffd28bc8b39305fc5c9c5292d85a
--- /dev/null
+++ b/src/analysis/Commit.cpp
@@ -0,0 +1,151 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+
+#include "core/ActionPilot.h"
+#include "core/ActionWithArguments.h"
+#include "core/ActionRegister.h"
+#include "core/PlumedMain.h"
+
+namespace PLMD {
+namespace analysis {
+
+//+PLUMEDOC ANALYSIS COMMITTOR
+/*
+Does a committor analysis.
+
+\par Examples
+The following input monitors two torsional angles during a simulation
+and outputs a histogram as a function of them at the end of the simulation.
+\verbatim
+TORSION ATOMS=1,2,3,4 LABEL=r1
+TORSION ATOMS=2,3,4,5 LABEL=r2
+COMMITTOR ...
+ ARG=r1,r2
+ STRIDE=10
+ BASIN_A_LOWER=0.15,0.20
+ BASIN_A_UPPER=0.25,0.40
+ BASIN_B_LOWER=-0.15,-0.20
+ BASIN_B_UPPER=-0.25,-0.40
+... COMMITTOR
+\endverbatim
+
+*/
+//+ENDPLUMEDOC
+
+class Committor :
+public ActionPilot,
+public ActionWithArguments
+{
+private:
+ std::string file;
+ OFile ofile;
+ std::string fmt;
+ std::vector<double> amin, amax;
+ std::vector<double> bmin, bmax;
+public:
+ static void registerKeywords( Keywords& keys );
+ Committor(const ActionOptions&ao);
+ void calculate();
+ void apply(){}
+ ~Committor();
+};
+
+PLUMED_REGISTER_ACTION(Committor,"COMMITTOR")
+
+void Committor::registerKeywords( Keywords& keys ){
+ Action::registerKeywords(keys);
+ ActionPilot::registerKeywords(keys);
+ ActionWithArguments::registerKeywords(keys);
+ keys.use("ARG");
+ keys.add("compulsory","STRIDE","1","the frequency with which the CVs are analysed");
+ keys.add("compulsory","BASIN_A_LOWER","the lower bounds of Basin A");
+ keys.add("compulsory","BASIN_A_UPPER","the upper bounds of Basin A");
+ keys.add("compulsory","BASIN_B_LOWER","the lower bounds of Basin B");
+ keys.add("compulsory","BASIN_B_UPPER","the upper bounds of Basin B");
+ keys.add("optional","FILE","the name of the file on which to output these quantities");
+ keys.add("optional","FMT","the format that should be used to output real numbers");
+}
+
+Committor::Committor(const ActionOptions&ao):
+Action(ao),
+ActionPilot(ao),
+ActionWithArguments(ao),
+fmt("%f"),
+amin(getNumberOfArguments()),
+amax(getNumberOfArguments()),
+bmin(getNumberOfArguments()),
+bmax(getNumberOfArguments())
+{
+ ofile.link(*this);
+ parse("FILE",file);
+ if(file.length()>0){
+ ofile.open(file);
+ log.printf(" on file %s\n",file.c_str());
+ } else {
+ log.printf(" on plumed log file\n");
+ ofile.link(log);
+ }
+ parse("FMT",fmt);
+ fmt=" "+fmt;
+ log.printf(" with format %s\n",fmt.c_str());
+ for(unsigned i=0;i<getNumberOfArguments();++i) ofile.setupPrintValue( getPntrToArgument(i) );
+ parseVector("BASIN_A_LOWER",amin);
+ parseVector("BASIN_A_UPPER",amax);
+ parseVector("BASIN_B_LOWER",bmin);
+ parseVector("BASIN_B_UPPER",bmax);
+ checkRead();
+ if(bmin>bmax||amin>amax) plumed_merror("COMMITTOR: UPPER bounds must always be greater than LOWER bounds");
+
+ log.printf(" BASIN A definition\n");
+ for(unsigned i=0;i<amin.size();++i) log.printf(" %lf - %lf\n", amin[i], amax[i]);
+ log.printf(" BASIN B definition\n");
+ for(unsigned i=0;i<bmin.size();++i) log.printf(" %lf - %lf\n", bmin[i], bmax[i]);
+}
+
+void Committor::calculate(){
+ unsigned ba=1,bb=1;
+
+ for(unsigned i=0;i<getNumberOfArguments();++i){
+ if(getArgument(i)>amin[i]&&getArgument(i)<amax[i]) ba*=1; else ba*=0;
+ if(getArgument(i)>bmin[i]&&getArgument(i)<bmax[i]) bb*=1; else bb*=0;
+ }
+ if(ba||bb) {
+ ofile.fmtField(" %f");
+ ofile.printField("time",getTime());
+ for(unsigned i=0;i<getNumberOfArguments();i++){
+ ofile.fmtField(fmt);
+ ofile.printField( getPntrToArgument(i), getArgument(i) );
+ }
+ ofile.printField();
+ if(ba) ofile.addConstantField("COMMITTED TO BASIN A");
+ if(bb) ofile.addConstantField("COMMITTED TO BASIN B");
+ ofile.printField();
+ ofile.flush();
+ plumed.stop();
+ }
+}
+
+Committor::~Committor(){
+}
+
+}
+}
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index 6aa301884b69c41ca8665869cec6bc1322af0c67..260a941b0c8ccd9d8092d5e4c1bbcc62a078094b 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/bias/ABMD.cpp b/src/bias/ABMD.cpp
index 1d955ccbb73c0b65e52e07dafd7b989fa1f4e845..a9d37926d1b093cf13ddd1ca92b0b29a76dbac96 100644
--- a/src/bias/ABMD.cpp
+++ b/src/bias/ABMD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/bias/ActionRegister.h b/src/bias/ActionRegister.h
index 9b8cf2b186071aca60769999b5b5b38fb4b4bb6e..02a444c68ecc956ef5acff1edd94a4c28433aa27 100644
--- a/src/bias/ActionRegister.h
+++ b/src/bias/ActionRegister.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/bias/Bias.cpp b/src/bias/Bias.cpp
index 1eda1f53895eaf4ce7c6ebbb545103753270bbf3..510b8bc4b4c2c1282817d30ce373112c9df75c34 100644
--- a/src/bias/Bias.cpp
+++ b/src/bias/Bias.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/bias/Bias.h b/src/bias/Bias.h
index cb8f20dd5530d2fca08ddc755aec704efa953282..dc573e616b1aeacab1ef8fe7a3afcc9c0eab854b 100644
--- a/src/bias/Bias.h
+++ b/src/bias/Bias.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index 076597501748911a91b1c235fbdda034a5cec73c..294d79adfb90e26eb8e43e3c8bc01848ba44a978 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/bias/LWalls.cpp b/src/bias/LWalls.cpp
index 7109d4913a0fc3c584945e68652d0a6959bf3fd6..1f2854644b9f3d76336f1e54271e64346f52418a 100644
--- a/src/bias/LWalls.cpp
+++ b/src/bias/LWalls.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index 0fcc257f8a821a428d6fa87af66db59de6f654ce..4a1c334f6828c4fa243b7f836dfd223966243eb6 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -163,7 +163,6 @@ METAD ...
PRINT ARG=d1,d2,restraint.bias STRIDE=100 FILE=COLVAR
\endverbatim
-
\par
Multiple walkers can be also use as in \cite multiplewalkers
These are enabled by setting the number of walker used, the id of the
@@ -185,6 +184,12 @@ id of the present walker (starting from 0 ) and the WALKERS_DIR is the directory
where all the walkers are located. WALKERS_RSTRIDE is the number of step between
one update and the other.
+\par
+The kinetics of the transitions between basins can also be analysed on the fly as
+in \cite PRL230602. The flag ACCELERATION turn on accumulation of the acceleration
+factor that can then be used to determine the rate. This method can be used together
+with \ref COMMITTOR analysis to stop the simulation when the system get to the target basin.
+It must be used together with Well-Tempered Metadynamics.
*/
//+ENDPLUMEDOC
@@ -227,6 +232,9 @@ private:
string mw_dir_;
int mw_id_;
int mw_rstride_;
+ bool walkers_mpi;
+ bool acceleration;
+ double acc;
vector<IFile*> ifiles;
vector<string> ifilesnames;
double uppI_;
@@ -284,6 +292,8 @@ void MetaD::registerKeywords(Keywords& keys){
keys.add("optional","GRID_RFILE","a grid file from which the bias should be read at the initial step of the simulation");
keys.add("optional","SIGMA_MAX","the upper bounds for the sigmas (in CV units) when using adaptive hills. Negative number means no bounds ");
keys.add("optional","SIGMA_MIN","the lower bounds for the sigmas (in CV units) when using adaptive hills. Negative number means no bounds ");
+ keys.addFlag("WALKERS_MPI",false,"Switch on MPI version of multiple walkers - not compatible with other WALKERS_* options");
+ keys.addFlag("ACCELERATION",false,"Set to TRUE if you want to compute the metadynamics acceleration factor.");
}
MetaD::~MetaD(){
@@ -311,6 +321,8 @@ dp_(NULL), adaptive_(FlexibleBin::none),
flexbin(NULL),
// Multiple walkers initialization
mw_n_(1), mw_dir_("./"), mw_id_(0), mw_rstride_(1),
+walkers_mpi(false),
+acceleration(false), acc(0.0),
// Interval initialization
uppI_(-1), lowI_(-1), doInt_(false),
isFirstStep(true)
@@ -412,6 +424,9 @@ isFirstStep(true)
parse("WALKERS_DIR",mw_dir_);
parse("WALKERS_RSTRIDE",mw_rstride_);
+ // MPI version
+ parseFlag("WALKERS_MPI",walkers_mpi);
+
// Inteval keyword
vector<double> tmpI(2);
parseVector("INTERVAL",tmpI);
@@ -425,6 +440,9 @@ isFirstStep(true)
spline=false;
}
+ acceleration=false;
+ parseFlag("ACCELERATION",acceleration);
+
checkRead();
log.printf(" Gaussian width ");
@@ -464,6 +482,12 @@ isFirstStep(true)
addComponent("bias"); componentIsNotPeriodic("bias");
+ if(acceleration) {
+ if(!welltemp_) error("The calculation of the acceleration works only if Well-Tempered Metadynamics is on");
+ log.printf(" calculation on the fly of the acceleration factor");
+ addComponent("acc"); componentIsNotPeriodic("acc");
+ }
+
// for performance
dp_ = new double[getNumberOfArguments()];
@@ -499,6 +523,8 @@ isFirstStep(true)
}
}
+ if(walkers_mpi && mw_n_>1) error("MPI version of multiple walkers is not compatible with filesystem version of multiple walkers");
+
// creating vector of ifile* for hills reading
// open all files at the beginning and read Gaussians if restarting
for(int i=0;i<mw_n_;++i){
@@ -543,6 +569,8 @@ isFirstStep(true)
"Branduardi, Bussi, and Parrinello, J. Chem. Theory Comput. 8, 2247 (2012)");
if(doInt_) log<<plumed.cite(
"Baftizadeh, Cossio, Pietrucci, and Laio, Curr. Phys. Chem. 2, 79 (2012)");
+ if(acceleration) log<<plumed.cite(
+ "Pratyush and Parrinello, Phys. Rev. Lett. 111, 230602 (2013)");
log<<"\n";
}
@@ -665,8 +693,8 @@ void MetaD::addGaussian(const Gaussian& hill)
BiasGrid_->getPoint(ineigh,xx);
allbias[i]=evaluateGaussian(xx,hill,&allder[ncv*i]);
}
- comm.Sum(&allbias[0],allbias.size());
- comm.Sum(&allder[0],allder.size());
+ comm.Sum(allbias);
+ comm.Sum(allder);
for(unsigned i=0;i<neighbors.size();++i){
unsigned ineigh=neighbors[i];
for(unsigned j=0;j<ncv;++j){der[j]=allder[ncv*i+j];}
@@ -733,8 +761,8 @@ double MetaD::getBiasAndDerivatives(const vector<double>& cv, double* der)
//finite difference test
//finiteDifferenceGaussian(cv,hills_[i]);
}
- comm.Sum(&bias,1);
- if(der) comm.Sum(&der[0],getNumberOfArguments());
+ comm.Sum(bias);
+ if(der) comm.Sum(der,getNumberOfArguments());
}else{
if(der){
vector<double> vder(getNumberOfArguments());
@@ -849,7 +877,12 @@ void MetaD::calculate()
for(unsigned i=0;i<ncv;++i){der[i]=0.0;}
double ene=getBiasAndDerivatives(cv,der);
getPntrToComponent("bias")->set(ene);
-
+// calculate the acceleration factor
+ if(acceleration&&!isFirstStep) {
+ acc += exp(ene/(plumed.getAtoms().getKBoltzmann()*temp_));
+ double mean_acc = acc/((double) getStep());
+ getPntrToComponent("acc")->set(mean_acc);
+ }
// set Forces
for(unsigned i=0;i<ncv;++i){
const double f=-der[i];
@@ -888,10 +921,52 @@ void MetaD::update(){
}else{
thissigma=sigma0_; // returns normal sigma
}
- Gaussian newhill=Gaussian(cv,thissigma,height,multivariate);
- addGaussian(newhill);
+// In case we use walkers_mpi, it is now necessary to communicate with other replicas.
+ if(walkers_mpi){
+ int nw=0;
+ int mw=0;
+ if(comm.Get_rank()==0){
+// Only root of group can communicate with other walkers
+ nw=multi_sim_comm.Get_size();
+ mw=multi_sim_comm.Get_rank();
+ }
+// Communicate to the other members of the same group
+// info abount number of walkers and walker index
+ comm.Bcast(nw,0);
+ comm.Bcast(mw,0);
+// Allocate arrays to store all walkers hills
+ std::vector<double> all_cv(nw*cv.size(),0.0);
+ std::vector<double> all_sigma(nw*thissigma.size(),0.0);
+ std::vector<double> all_height(nw,0.0);
+ std::vector<int> all_multivariate(nw,0);
+ if(comm.Get_rank()==0){
+// Communicate (only root)
+ multi_sim_comm.Allgather(cv,all_cv);
+ multi_sim_comm.Allgather(thissigma,all_sigma);
+ multi_sim_comm.Allgather(height,all_height);
+ multi_sim_comm.Allgather(int(multivariate),all_multivariate);
+ }
+// Share info with group members
+ comm.Bcast(all_cv,0);
+ comm.Bcast(all_sigma,0);
+ comm.Bcast(all_height,0);
+ comm.Bcast(all_multivariate,0);
+ for(int i=0;i<nw;i++){
+// actually add hills one by one
+ std::vector<double> cv_now(cv.size());
+ std::vector<double> sigma_now(thissigma.size());
+ for(unsigned j=0;j<cv.size();j++) cv_now[j]=all_cv[i*cv.size()+j];
+ for(unsigned j=0;j<thissigma.size();j++) sigma_now[j]=all_sigma[i*thissigma.size()+j];
+ Gaussian newhill=Gaussian(cv_now,sigma_now,all_height[i],all_multivariate[i]);
+ addGaussian(newhill);
+ writeGaussian(newhill,hillsOfile_);
+ }
+ } else {
+ Gaussian newhill=Gaussian(cv,thissigma,height,multivariate);
+ addGaussian(newhill);
// print on HILLS file
- writeGaussian(newhill,hillsOfile_);
+ writeGaussian(newhill,hillsOfile_);
+ }
}
// dump grid on file
if(wgridstride_>0&&getStep()%wgridstride_==0){
diff --git a/src/bias/MovingRestraint.cpp b/src/bias/MovingRestraint.cpp
index 2ab5d3fde62617f7526663d0d4265b7cc242b9d7..e72998c24ee894db359376f872da72892c63411a 100644
--- a/src/bias/MovingRestraint.cpp
+++ b/src/bias/MovingRestraint.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -166,7 +166,7 @@ verse(getNumberOfArguments())
// add the centers of the restraint as additional components that can be retrieved (useful for debug)
std::string comp;
- for(int i=0;i< getNumberOfArguments() ;i++){
+ for(unsigned i=0;i< getNumberOfArguments() ;i++){
comp=getPntrToArgument(i)->getName()+"_cntr"; // each spring has its own center
addComponent(comp); componentIsNotPeriodic(comp);
comp=getPntrToArgument(i)->getName()+"_work"; // each spring has its own work
diff --git a/src/bias/Restraint.cpp b/src/bias/Restraint.cpp
index 3abe6bf439d0a89a5d7bd08a3231a237556c4c8e..c120b5abfb5f5e90c403512b055a2d2abbc9a3f7 100644
--- a/src/bias/Restraint.cpp
+++ b/src/bias/Restraint.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/bias/UWalls.cpp b/src/bias/UWalls.cpp
index c1a6faf13c2479160350096a86d5d9fd6305eb07..7ff5e8afe95593bfce58c7b83c344d6436941929 100644
--- a/src/bias/UWalls.cpp
+++ b/src/bias/UWalls.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/bias/Value.cpp b/src/bias/Value.cpp
index 1258892b43ad4fd4c09c35a6292c9f01d40592cf..6baa0ace4e91d8d93c0f2ff3bcbdb9e6b7f64611 100644
--- a/src/bias/Value.cpp
+++ b/src/bias/Value.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/cltools/CLTool.h b/src/cltools/CLTool.h
index 95768bc2c3e8ddc980183331c78fdf4d70a4e5b3..31cefe194db5ccea5bfebfac98c00b2551366e56 100644
--- a/src/cltools/CLTool.h
+++ b/src/cltools/CLTool.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/cltools/CLToolRegister.h b/src/cltools/CLToolRegister.h
index 15be6d72a9f415f300c47840c6bdbdf4994d479d..99e1bb16e5b5a4f428645c81d9d1f3487e5882fa 100644
--- a/src/cltools/CLToolRegister.h
+++ b/src/cltools/CLToolRegister.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
index 966f8da6543887c93aefb64e8ea9ca66a28e8d12..9c64240d9e9fbe355870dd4f8017bc085a996659 100644
--- a/src/cltools/Driver.cpp
+++ b/src/cltools/Driver.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -28,9 +28,16 @@
#include <cstdio>
#include <cstring>
#include <vector>
+#include <map>
#include "tools/Units.h"
#include "tools/PDB.h"
+// when using molfile plugin
+#ifdef __PLUMED_HAS_MOLFILE
+#include "libmolfile_plugin.h"
+#include "molfile_plugin.h"
+#endif
+
using namespace std;
namespace PLMD {
@@ -66,8 +73,47 @@ had we run the calculation we are running with driver when the MD simulation was
plumed driver --plumed plumed.dat --ixyz trajectory.xyz --trajectory-stride 100 --timestep 0.001
\endverbatim
+Additionally, when you recompile with the -D__PLUMED_HAS_MOLFILE you have access to all the types of file read
+by vmd. In order to do so, you should add
+\verbatim
+DYNAMIC_LIBS= [all the usual libs] \\
+ -lmolfile_plugin -ltcl8.5 -L/mypathtomolfilelibrary/ -L/mypathtotcl
+CPPFLAGS= [all the usual flags] \\
+ -D__PLUMED_HAS_MOLFILE -I/mypathtolibmolfile_plugin.h/ -I/mypathtomolfile_plugin.h/
+\endverbatim
+
+The easy way to get this is to download the SOURCE of VMD and you find a plugins directory. Just adapt build.sh and
+compile it. At the end, you should get the molfile plugin compiled. Just locate libmolfile_plugin.a ibmolfile_plugin.h
+and molfile_plugin.h.
+When you succeed you can use the following
+
+\verbatim
+plumed driver --plumed plumed.dat --pdb diala.pdb --mf_xtc traj.xtc --trajectory-stride 100 --timestep 0.001
+\endverbatim
+
+where the prefix --mf_ stands for the molfile plugin format accepted. There are many available. Check them in VMD.
+Limitations therein applies.
+
*/
//+ENDPLUMEDOC
+//
+
+#ifdef __PLUMED_HAS_MOLFILE
+static vector<molfile_plugin_t *> plugins;
+static map <string, unsigned> pluginmap;
+static int register_cb(void *v, vmdplugin_t *p){
+ //const char *key = p->name;
+ std::pair<std::map<string,unsigned>::iterator,bool> ret;
+ ret = pluginmap.insert ( std::pair<string,unsigned>(string(p->name),plugins.size()) );
+ if (ret.second==false) {
+ //cerr<<"MOLFILE: found duplicate plugin for "<<key<<" : not inserted "<<endl;
+ }else{
+ //cerr<<"MOLFILE: loading plugin "<<key<<" number "<<plugins.size()-1<<endl;
+ plugins.push_back((molfile_plugin_t *)p);
+ }
+ return VMDPLUGIN_SUCCESS;
+}
+#endif
template<typename real>
class Driver : public CLTool {
@@ -99,15 +145,23 @@ void Driver<real>::registerKeywords( Keywords& keys ){
keys.add("hidden","--debug-pd","use a fake particle decomposition");
keys.add("hidden","--debug-grex","use a fake gromacs-like replica exchange, specify exchange stride");
keys.add("hidden","--debug-grex-log","log file for debug=grex");
+#ifdef __PLUMED_HAS_MOLFILE
+ MOLFILE_INIT_ALL
+ MOLFILE_REGISTER_ALL(NULL, register_cb)
+ for(int i=0;i<plugins.size();i++){
+ string kk="--mf_"+string(plugins[i]->name);
+ string mm=" molfile: the trajectory in "+string(plugins[i]->name)+" format " ;
+ //cerr<<"REGISTERING "<<kk<<mm<<endl;
+ keys.add("atoms",kk,mm);
+ }
+#endif
}
-
template<typename real>
Driver<real>::Driver(const CLToolOptions& co ):
CLTool(co)
{
inputdata=commandline;
}
-
template<typename real>
string Driver<real>::description()const{ return "analyze trajectories with plumed"; }
@@ -197,12 +251,33 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
string trajectory_fmt;
+ bool use_molfile=false;
+#ifdef __PLUMED_HAS_MOLFILE
+ molfile_plugin_t *api=NULL;
+ void *h_in=NULL;
+ molfile_timestep_t ts_in; // this is the structure that has the timestep
+#endif
+
// Read in an xyz file
string trajectoryFile(""), pdbfile("");
bool pbc_cli_given=false; vector<double> pbc_cli_box(9,0.0);
if(!noatoms){
std::string traj_xyz; parse("--ixyz",traj_xyz);
std::string traj_gro; parse("--igro",traj_gro);
+#ifdef __PLUMED_HAS_MOLFILE
+ for(int i=0;i<plugins.size();i++){
+ string molfile_key="--mf_"+string(plugins[i]->name);
+ string traj_molfile;
+ parse(molfile_key,traj_molfile);
+ if(traj_molfile.length()>0){
+ fprintf(out,"\nDRIVER: Found molfile format trajectory %s with name %s\n",plugins[i]->name,traj_molfile.c_str());
+ trajectoryFile=traj_molfile;
+ trajectory_fmt=string(plugins[i]->name);
+ use_molfile=true;
+ api = plugins[i];
+ }
+ }
+#endif
if(traj_xyz.length()>0 && traj_gro.length()>0){
fprintf(stderr,"ERROR: cannot provide more than one trajectory file\n");
if(grex_log)fclose(grex_log);
@@ -277,19 +352,28 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
trajectoryFile+="."+n;
}
+
+ int natoms;
+
FILE* fp=NULL; FILE* fp_forces=NULL;
if(!noatoms){
if (trajectoryFile=="-")
fp=in;
else {
- fp=fopen(trajectoryFile.c_str(),"r");
- if(!fp){
- string msg="ERROR: Error opening XYZ file "+trajectoryFile;
- fprintf(stderr,"%s\n",msg.c_str());
- return 1;
+ if(use_molfile==true){
+#ifdef __PLUMED_HAS_MOLFILE
+ h_in = api->open_file_read(trajectoryFile.c_str(), trajectory_fmt.c_str(), &natoms);
+ ts_in.coords = (float *)malloc(3*natoms * sizeof(float));
+#endif
+ }else{
+ fp=fopen(trajectoryFile.c_str(),"r");
+ if(!fp){
+ string msg="ERROR: Error opening trajectory file "+trajectoryFile;
+ fprintf(stderr,"%s\n",msg.c_str());
+ return 1;
+ }
}
}
-
if(dumpforces.length()>0){
if(Communicator::initialized() && pc.Get_size()>1){
string n;
@@ -324,14 +408,29 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
while(true){
if(!noatoms){
- if(!Tools::getline(fp,line)) break;
+ if(use_molfile==true){
+#ifdef __PLUMED_HAS_MOLFILE
+ int rc;
+ rc = api->read_next_timestep(h_in, natoms, &ts_in);
+ //if(rc==MOLFILE_SUCCESS){
+ // printf(" read this one :success \n");
+ //}
+ if(rc==MOLFILE_EOF){
+ printf(" read this one :eof or error \n");
+ break;
+ }
+#endif
+ }else{
+ if(!Tools::getline(fp,line)) break;
+ }
}
- int natoms;
bool first_step=false;
if(!noatoms){
- if(trajectory_fmt=="gro") if(!Tools::getline(fp,line)) error("premature end of trajectory file");
- sscanf(line.c_str(),"%100d",&natoms);
+ if(use_molfile==false){
+ if(trajectory_fmt=="gro") if(!Tools::getline(fp,line)) error("premature end of trajectory file");
+ sscanf(line.c_str(),"%100d",&natoms);
+ }
}
if(checknatoms<0 && !noatoms){
pd_nlocal=natoms;
@@ -339,6 +438,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
first_step=true;
masses.assign(natoms,real(1.0));
charges.assign(natoms,real(0.0));
+//case pdb: structure
if(pdbfile.length()>0){
for(unsigned i=0;i<pdb.size();++i){
AtomNumber an=pdb.getAtomNumbers()[i];
@@ -378,8 +478,8 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
start[i+1]=start[i]+loc[i];
}
loc[npe-1]=natoms-start[npe-1];
- intracomm.Bcast(&loc[0],npe,0);
- intracomm.Bcast(&start[0],npe,0);
+ intracomm.Bcast(loc,0);
+ intracomm.Bcast(start,0);
pd_nlocal=loc[intracomm.Get_rank()];
pd_start=start[intracomm.Get_rank()];
if(intracomm.Get_rank()==0){
@@ -423,6 +523,36 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
p.cmd("setStep",&step);
p.cmd("setStopFlag",&plumedStopCondition);
if(!noatoms){
+ if(use_molfile){
+#ifdef __PLUMED_HAS_MOLFILE
+ if(pbc_cli_given==false) {
+ // info on the cell: convert using pbcset.tcl from pbctools in vmd distribution
+ real cosBC=cos(ts_in.alpha*pi/180.);
+ //double sinBC=sin(ts_in.alpha*pi/180.);
+ real cosAC=cos(ts_in.beta*pi/180.);
+ real cosAB=cos(ts_in.gamma*pi/180.);
+ real sinAB=sin(ts_in.gamma*pi/180.);
+ real Ax=ts_in.A;
+ real Bx=ts_in.B*cosAB;
+ real By=ts_in.B*sinAB;
+ real Cx=ts_in.C*cosAC;
+ real Cy=(ts_in.C*ts_in.B*cosBC-Cx*Bx)/By;
+ real Cz=sqrt(ts_in.C*ts_in.C-Cx*Cx-Cy*Cy);
+ cell[0]=Ax/10.;cell[1]=0.;cell[2]=0.;
+ cell[3]=Bx/10.;cell[4]=By/10.;cell[5]=0.;
+ cell[6]=Cx/10.;cell[7]=Cy/10.;cell[8]=Cz/10.;
+ //cerr<<"CELL "<<cell[0]<<" "<<cell[1]<<" "<<cell[2]<<" "<<cell[3]<<" "<<cell[4]<<" "<<cell[5]<<" "<<cell[6]<<" "<<cell[7]<<" "<<cell[8]<<endl;
+ }else{
+ for(unsigned i=0;i<9;i++)cell[i]=pbc_cli_box[i];
+ }
+ // info on coords
+ // the order is xyzxyz...
+ for(unsigned i=0;i<3*natoms;i++){
+ coordinates[i]=real(ts_in.coords[i]/10.); //convert to nm
+ //cerr<<"COOR "<<coordinates[i]<<endl;
+ }
+#endif
+ }else{
if(trajectory_fmt=="xyz"){
if(!Tools::getline(fp,line)) error("premature end of trajectory file");
@@ -493,6 +623,8 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
if(words.size()>8) Tools::convert(words[8],cell[7]);
}
+ }
+
if(debug_dd){
for(int i=0;i<dd_nlocal;++i){
int kk=dd_gatindex[i];
@@ -516,8 +648,8 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
p.cmd("calc");
// this is necessary as only processor zero is adding to the virial:
- intracomm.Bcast(&virial[0],9,0);
- if(debug_pd) intracomm.Sum(&forces[0],natoms*3);
+ intracomm.Bcast(virial,0);
+ if(debug_pd) intracomm.Sum(forces);
if(debug_dd){
for(int i=0;i<dd_nlocal;i++){
forces[3*dd_gatindex[i]+0]=dd_forces[3*i+0];
@@ -525,7 +657,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
forces[3*dd_gatindex[i]+2]=dd_forces[3*i+2];
}
dd_forces.assign(3*natoms,0.0);
- intracomm.Sum(&forces[0],natoms*3);
+ intracomm.Sum(forces);
}
if(debug_grex &&step%grex_stride==0){
p.cmd("GREX savePositions");
@@ -567,6 +699,9 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
if(fp_forces) fclose(fp_forces);
if(fp && fp!=in)fclose(fp);
+#ifdef __PLUMED_HAS_MOLFILE
+ if(h_in) api->close_file_read(h_in);
+#endif
if(grex_log) fclose(grex_log);
return 0;
diff --git a/src/cltools/GenTemplate.cpp b/src/cltools/GenTemplate.cpp
index 5a91936b6c3fb90e3f13f289538ab9e49fce18e1..d04972bebf7e7260741d34b5016658712b502dcc 100644
--- a/src/cltools/GenTemplate.cpp
+++ b/src/cltools/GenTemplate.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/cltools/Info.cpp b/src/cltools/Info.cpp
index ea987817b0c5bbeb44c7e8dcc6a3d7ea75b2d493..b157c8b7d427427a9c9b97b42f4ed30150f92936 100644
--- a/src/cltools/Info.cpp
+++ b/src/cltools/Info.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/cltools/Manual.cpp b/src/cltools/Manual.cpp
index d39579207139a76a8f6cd1f19dfac9576aaa369a..5d773dd65afa446f489f3996ddfaa5e8c9c8e026 100644
--- a/src/cltools/Manual.cpp
+++ b/src/cltools/Manual.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/cltools/SimpleMD.cpp b/src/cltools/SimpleMD.cpp
index 22413465654f563cd324131401e8fa10f90ea2f6..fa94f46f795899c8ff2dad4223e40baff7b978ef 100644
--- a/src/cltools/SimpleMD.cpp
+++ b/src/cltools/SimpleMD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -429,6 +429,7 @@ int main(FILE* in,FILE*out,PLMD::Communicator& pc){
int maxneighbour; // maximum average number of neighbours per atom
int ndim; // dimensionality of the system (1, 2, or 3)
int idum; // seed
+ int plumedWantsToStop; // stop flag
bool wrapatoms; // if true, atomic coordinates are written wrapped in minimal cell
string inputfile; // name of file with starting configuration (xyz)
string outputfile; // name of file with final configuration (xyz)
@@ -498,7 +499,7 @@ int main(FILE* in,FILE*out,PLMD::Communicator& pc){
list.resize(listsize);
// masses are hard-coded to 1
- for(unsigned i=0;i<natoms;++i) masses[i]=1.0;
+ for(int i=0;i<natoms;++i) masses[i]=1.0;
// energy integral initialized to 0
engint=0.0;
@@ -564,6 +565,7 @@ int main(FILE* in,FILE*out,PLMD::Communicator& pc){
if(plumed){
int istepplusone=istep+1;
+ plumedWantsToStop=0;
for(int i=0;i<3;i++)for(int k=0;k<3;k++) cell9[i][k]=0.0;
for(int i=0;i<3;i++) cell9[i][i]=cell[i];
plumed->cmd("setStep",&istepplusone);
@@ -572,7 +574,9 @@ int main(FILE* in,FILE*out,PLMD::Communicator& pc){
plumed->cmd("setEnergy",&engconf);
plumed->cmd("setPositions",&positions[0]);
plumed->cmd("setBox",cell9);
+ plumed->cmd("setStopFlag",&plumedWantsToStop);
plumed->cmd("calc");
+ if(plumedWantsToStop) nstep=istep;
}
// remove forces if ndim<3
if(ndim<3)
diff --git a/src/cltools/SumHills.cpp b/src/cltools/SumHills.cpp
index 11d141ae6c2110dfda1d69f60d808851f4833ebe..43c1a0ee4410de5631d0fdd438ccc3c6fddf0146 100644
--- a/src/cltools/SumHills.cpp
+++ b/src/cltools/SumHills.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -315,7 +315,7 @@ int CLToolSumHills::main(FILE* in,FILE*out,Communicator& pc){
if(Communicator::initialized()) plumed.cmd("setMPIComm",&pc.Get_comm());
plumed.cmd("init",&nn);
vector <bool> isdone(cvs.size(),false);
- for(int i=0;i<cvs.size();i++){
+ for(unsigned i=0;i<cvs.size();i++){
if(!isdone[i]){
isdone[i]=true;
std::vector<std::string> actioninput;
@@ -516,7 +516,7 @@ bool CLToolSumHills::findCvsAndPeriodic(std::string filename, std::vector< std::
ifile.scanFieldList(fields);
size_t founds,foundm,foundp;
bool before_sigma=true;
- for(int i=0;i<fields.size();i++){
+ for(unsigned i=0;i<fields.size();i++){
size_t pos = 0;
//found=(fields[i].find("sigma_", pos) || fields[i].find("min_", pos) || fields[i].find("max_", pos) ) ;
founds=fields[i].find("sigma_", pos) ;
diff --git a/src/colvar/ActionRegister.h b/src/colvar/ActionRegister.h
index 916d9be78345eaf940d9061302ab0078d8f3a363..96e9c2cbac82b6acdba79e30ad1e0acfdba2121e 100644
--- a/src/colvar/ActionRegister.h
+++ b/src/colvar/ActionRegister.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/Angle.cpp b/src/colvar/Angle.cpp
index 3be01a3e251640efb63d6d3f53109ab7a293917d..89eddcd97df73707bf779d56de317ea3030ecb20 100644
--- a/src/colvar/Angle.cpp
+++ b/src/colvar/Angle.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -37,8 +37,29 @@ Calculate an angle.
This command can be used to compute the angle between three atoms. Alternatively
if four atoms appear in the atom
-specification it calculates the angle between the vector joining atoms 1 and 2 and that joining
-atoms 3 and 4.
+specification it calculates the angle between
+two vectors identified by two pairs of atoms.
+
+If _three_ atoms are given, the angle is defined as:
+\f[
+\theta=\arccos\left(\frac{ {\bf r}_{21}\cdot {\bf r}_{23}}{
+|{\bf r}_{21}| |{\bf r}_{23}|}\right)
+\f]
+Here \f$ {\bf r}_{ij}\f$ is the distance vector among the
+i-th and the j-th listed atom.
+
+If _four_ atoms are given, the angle is defined as:
+\f[
+\theta=\arccos\left(\frac{ {\bf r}_{21}\cdot {\bf r}_{34}}{
+|{\bf r}_{21}| |{\bf r}_{34}|}\right)
+\f]
+
+Notice that angles defined in this way are non-periodic variables and
+their value is limited by definition between 0 and \f$\pi\f$.
+
+The vectors \f$ {\bf r}_{ij}\f$ are by default evaluated taking
+periodic boundary conditions into account.
+This behavior can be changed with the NOPBC flag.
\par Examples
@@ -59,6 +80,7 @@ PRINT ARG=b FILE=COLVAR2
\endverbatim
(see also \ref PRINT)
+
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/CH3Shifts.cpp b/src/colvar/CH3Shifts.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..0af0f4f737b9a9e71eaebcc818262d1f612d1f8f
--- /dev/null
+++ b/src/colvar/CH3Shifts.cpp
@@ -0,0 +1,411 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifdef __PLUMED_HAS_ALMOST
+
+#include "Colvar.h"
+#include "ActionRegister.h"
+#include "core/PlumedMain.h"
+#include "core/Atoms.h"
+#include "tools/Communicator.h"
+
+#include <string>
+#include <cmath>
+#include <cassert>
+
+#include <almost/mdb.h>
+#include <almost/pdb.h>
+#include <almost/camshift3/meth/methcs.h>
+#include <almost/io/formostream.h>
+
+using namespace std;
+using namespace Almost;
+
+namespace PLMD{
+
+//+PLUMEDOC COLVAR CH3SHIFTS
+/*
+This collective variable calculates a scoring function based on the comparison of backcalculated and
+experimental methyl groups chemical shifts for a protein (ALA:HB; ILE:HD,HG2; LEU:HD1,HD2; THR:HG2;
+VAL:HG1,HG2).
+
+CH3Shift \cite Sahakyan:2011bn is employed to back calculate the chemical shifts that are then compared
+with a set of experimental values to generate a score \cite Robustelli:2010dn \cite Granata:2013dk.
+
+It is also possible to backcalculate the chemical shifts from multiple replicas and then average them
+to perform Replica-Averaged Restrained MD simulations \cite Camilloni:2012je \cite Camilloni:2013hs.
+
+HOW TO COMPILE IT
+
+In general the system for which chemical shifts are to be calculated must be completly included in
+ATOMS. It should also be made WHOLE before the the backcalculation. CH3Shift is included in the
+free package ALMOST v.2.1 that can be dowload via SVN (svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code).
+ALMOST 2.1 can be found in branches/almost-2.1/ and it can be compiled:
+
+\verbatim
+./configure
+make
+\endverbatim
+
+Once the code is compiled you should see the ALMOST library libAlm.a in src/lib/
+
+PLUMED 2 must then be compiled by linking ALMOST:
+
+\verbatim
+in DYNAMIC_LIBS the following paths should be added:
+
+-L/ALMOST_BASE_PATH/branches/almost-2.1/src/lib -lAlm \
+-L/ALMOST_BASE_PATH/branches/almost-2.1/lib/sqlite-3.6.23.1 -lsqlite3 -lz -lbz2 \
+-L/ALMOST_BASE_PATH/branches/almost-2.1/src/forcefield -lnbimpl \
+-L/ALMOST_BASE_PATH/branches/almost-2.1/src/lib/modules -lshx
+
+and in CPPFLAGS
+
+-I/ALMOST_BASE_PATH/almost/branches/almost-2.1/include \
+-I/ALMOST_BASE_PATH/almost/branches/almost-2.1/include/almost \
+-I/ALMOST_BASE_PATH/almost/branches/almost-2.1/lib/sqlite-3.6.23.1 -D__PLUMED_HAS_ALMOST
+
+with ALMOST_BASE_PATH the full path to the ALMOST folder
+\endverbatim
+
+HOW TO USE IT
+
+To use CH3Shift takes from a text file the experimental chemical shifts:
+
+\verbatim
+CH3shifts.dat:
+
+\endverbatim
+
+A template.pdb file is needed to the generate a topology of the protein within ALMOST. For histidines in protonation
+states different from D the HIE/HIP name should be used in the template.pdb. GLH and ASH can be used for the alternative
+protonation of GLU and ASP. Non-standard amino acids and other molecules are not yet supported! If multiple chains are
+present the chain identifier must be in the standard PDB format, together with the TER keyword at the end of each chain.
+Residues numbering should always go from 1 to N in both the chemical shifts files as well as in the template.pdb file.
+Two more keywords can be used to setup the topology: CYS-DISU to tell ALMOST to look for disulphide bridges and TERMINI
+to define the protonation state of the the chain's termini (currently only DEFAULT (NH3+, CO2-) and NONE (NH, CO)).
+
+One more standard file is also needed, that is an ALMOST force-field file, corresponding to the force-field family used in
+the MD code, (a03_cs2_gromacs.mdb for the amber family or all22_gromacs.mdb for the charmm family).
+
+All the above files must be in a single folder that must be specified with the keyword DATA (multiple definition of the
+CV can point to different folders).
+
+\par Examples
+
+case 1:
+
+\verbatim
+WHOLEMOLECULES ENTITY0=1-174
+cs: CH3SHIFTS ATOMS=1-174 DATA=data/ FF=a03_gromacs.mdb FLAT=0.0 NRES=13 ENSEMBLE
+cse: RESTRAINT ARG=cs SLOPE=24 KAPPA=0 AT=0.
+PRINT ARG=cs,cse.bias
+\endverbatim
+
+case 2:
+
+\verbatim
+WHOLEMOLECULES ENTITY0=1-174
+cs: CH3SHIFTS ATOMS=1-174 DATA=data/ FF=a03_gromacs.mdb FLAT=1.0 NRES=13 TERMINI=DEFAULT,NONE CYS-DISU WRITE_CS=1000
+PRINT ARG=cs
+\endverbatim
+
+(See also \ref WHOLEMOLECULES, \ref RESTRAINT and \ref PRINT)
+
+*/
+//+ENDPLUMEDOC
+
+class CH3Shifts : public Colvar {
+ vector<MethCS*> meth_list;
+ Molecules molecules;
+ int numResidues;
+ int pperiod;
+ int ens_dim;
+ bool ensemble;
+ bool serial;
+ double **sh;
+ double ene_pl2alm;
+ double len_pl2alm;
+ double for_pl2alm;
+public:
+ CH3Shifts(const ActionOptions&);
+ ~CH3Shifts();
+ static void registerKeywords( Keywords& keys );
+ virtual void calculate();
+};
+
+PLUMED_REGISTER_ACTION(CH3Shifts,"CH3SHIFTS")
+
+void CH3Shifts::registerKeywords( Keywords& keys ){
+ Colvar::registerKeywords( keys );
+ //keys.addFlag("SERIAL",false,"Perform the calculation in serial - for debug purpose.");
+ keys.add("atoms","ATOMS","The atoms to be included in the calculation, e.g. the whole protein.");
+ keys.add("compulsory","DATA","data/","The folder with the experimental chemical shifts.");
+ keys.add("compulsory","FF","a03_gromacs.mdb","The ALMOST force-field to map the atoms' names.");
+ keys.add("compulsory","FLAT","1.0","Flat region in the scoring function.");
+ keys.add("compulsory","NEIGH_FREQ","10","Period in step for neighbour list update.");
+ keys.add("compulsory","WRITE_CS","0","Write chemical shifts period.");
+ keys.add("compulsory","NRES","Number of residues, corresponding to the number of chemical shifts.");
+ keys.add("optional","TERMINI","Defines the protonation states of the chain-termini.");
+ keys.addFlag("CYS-DISU",false,"Set to TRUE if your system has disulphide bridges.");
+ keys.addFlag("ENSEMBLE",false,"Set to TRUE if you want to average over multiple replicas.");
+ keys.remove("NOPBC");
+}
+
+CH3Shifts::CH3Shifts(const ActionOptions&ao):
+PLUMED_COLVAR_INIT(ao)
+{
+ string stringadb;
+ string stringamdb;
+ string stringapdb;
+
+ serial=false;
+ //parseFlag("SERIAL",serial);
+
+ string stringa_data;
+ parse("DATA",stringa_data);
+
+ string stringa_forcefield;
+ parse("FF",stringa_forcefield);
+
+ bool disu=false;
+ parseFlag("CYS-DISU",disu);
+
+ double grains=1.0;
+ parse("FLAT", grains);
+
+ int neigh_f=10;
+ parse("NEIGH_FREQ", neigh_f);
+
+ int w_period=0;
+ parse("WRITE_CS", w_period);
+ pperiod=w_period;
+
+ parse("NRES", numResidues);
+
+ ensemble=false;
+ parseFlag("ENSEMBLE",ensemble);
+ if(ensemble&&comm.Get_rank()==0) {
+ if(multi_sim_comm.Get_size()<2) plumed_merror("You CANNOT run Replica-Averaged simulations without running multiple replicas!\n");
+ else ens_dim=multi_sim_comm.Get_size();
+ } else ens_dim=0;
+ if(ensemble) comm.Sum(&ens_dim, 1);
+
+ stringadb = stringa_data + string("/CH3shifts.dat");
+ stringamdb = stringa_data + string("/") + stringa_forcefield;
+ stringapdb = stringa_data + string("/template.pdb");
+
+ log.printf(" loading force-field %s\n", stringamdb.c_str()); log.flush();
+ Almost::MDB mdb((char*)stringamdb.c_str());
+ log.printf(" loading template %s\n", stringapdb.c_str()); log.flush();
+ Almost::PDB pdb((char*)stringapdb.c_str());
+
+ vector<string> termini;
+ string stringa_mol;
+ parse("TERMINI",stringa_mol);
+ if(stringa_mol.length()>0) {
+ unsigned num_chains = pdb[0].size();
+ vector<string> data=Tools::getWords(stringa_mol,",");
+ if(data.size()!=2*num_chains) plumed_merror("You have to define both the NTerm and the CTerm for each chain of your system!\n");
+ for(unsigned i=0;i<data.size();i++) termini.push_back(data[i]);
+ } else {
+ unsigned num_chains = pdb[0].size();
+ for(unsigned i=0;i<(2*num_chains);i++) termini.push_back("DEFAULT");
+ }
+
+ log.printf(" building molecule ..."); log.flush();
+ for(unsigned i=0;i<pdb[0].size();i++){
+ unsigned j=2*i;
+ string str;
+ str +='A'+i;
+ Protein p(str);
+ p.build_missing(pdb[0][i],mdb,termini[j],termini[j+1]);
+ if(disu) p.auto_disu_bonds(2.9,mdb);
+ molecules.add_protein(p);
+ }
+ log.printf(" done!\n"); log.flush();
+ log.printf(" Writing converted template.pdb ...\n"); log.flush();
+ mol2pdb(molecules,"converted-template.pdb");
+
+ log.printf(" Initialization of the predictor ...\n"); log.flush();
+ MethCS* a = new MethCS(molecules);
+
+ log.printf(" Reading experimental data ...\n"); log.flush();
+ a->read_cs(stringadb);
+ log.printf(" Setting parameters ...\n"); log.flush();
+ /*unsigned stride=comm.Get_size();
+ unsigned rank=comm.Get_rank();
+ if(serial) {stride=1; rank=0;}
+ if(stride>1) log.printf(" Parallelized over %d processors\n", stride);
+ a.set_mpi(stride, rank);*/
+
+ if(ensemble) { log.printf(" ENSEMBLE averaging over %i replicas\n", ens_dim); }
+ a->set_w_cs(1);
+ a->set_flat_bottom_const(grains);
+ a->set_box_nupdate(neigh_f);
+ a->set_box_cutnb(11.); // cut-off for neigh-list
+ meth_list.push_back(a);
+
+ sh = new double*[numResidues];
+ sh[0] = new double[numResidues*8];
+ for (int i=1; i<numResidues; i++) sh[i]=sh[i-1]+8;
+
+ /* Energy and Lenght conversion */
+ ene_pl2alm = 4.186/plumed.getAtoms().getUnits().getEnergy();
+ len_pl2alm = 10.00*plumed.getAtoms().getUnits().getLength();
+ for_pl2alm = ene_pl2alm*len_pl2alm;
+ log.printf(" Conversion table from plumed to Almost:\n");
+ log.printf(" Energy %lf\n", ene_pl2alm);
+ log.printf(" Length %lf\n", len_pl2alm);
+
+ vector<AtomNumber> atoms;
+ parseAtomList("ATOMS",atoms);
+ checkRead();
+
+ log<<" Bibliography "
+ <<plumed.cite("Sahakyan AB, Vranken WF, Cavalli A, Vendruscolo M, J. Biomol. NMR 50, 331 (2011)")
+ <<plumed.cite("Camilloni C, Robustelli P, De Simone A, Cavalli A, Vendruscolo M, J. Am. Chem. Soc. 134, 3968 (2012)") <<"\n";
+
+ addValueWithDerivatives();
+ setNotPeriodic();
+ requestAtoms(atoms);
+ log.printf(" DONE!\n"); log.flush();
+}
+
+CH3Shifts::~CH3Shifts()
+{
+ delete[] sh[0];
+ delete[] sh;
+}
+
+void CH3Shifts::calculate()
+{
+ double energy=0.;
+ Tensor virial;
+ virial.zero();
+ vector<Vector> deriv(getNumberOfAtoms());
+ int N = getNumberOfAtoms();
+ Coor<double> coor(N);
+ Coor<double> forces(N);
+
+ forces.clear();
+ for(int i=0; i<numResidues; i++) for(unsigned j=0; j<6; j++) sh[i][j]=0.;
+
+ for (int i = 0; i < N; i++) {
+ int ipos = 4 * i;
+ Vector Pos = getPosition(i);
+ coor.coor[ipos] = len_pl2alm*Pos[0];
+ coor.coor[ipos+1] = len_pl2alm*Pos[1];
+ coor.coor[ipos+2] = len_pl2alm*Pos[2];
+ }
+
+ double fact=1.0;
+ if(!ensemble) {
+ energy = meth_list[0]->calc_cs_force(coor, forces);
+ bool printout=false;
+ if(pperiod>0&&comm.Get_rank()==0) printout = (!(getStep()%pperiod));
+ if(printout) {
+ string csfile;
+ char tmps1[21];
+ // add to the name the label of the cv in such a way to have different files
+ // when there is more than one defined variable
+ sprintf(tmps1, "%li", getStep());
+ csfile = string("cs")+tmps1+string(".dat");
+ meth_list[0]->write_cs(csfile.c_str());
+ }
+ } else {
+ meth_list[0]->calc_cs(coor);
+ bool printout=false;
+ if(pperiod>0&&comm.Get_rank()==0) printout = (!(getStep()%pperiod));
+ if(printout) {
+ string csfile;
+ char tmps1[21], tmps2[21];
+ // add to the name the label of the cv in such a way to have different files
+ // when there is more than one defined variable
+ sprintf(tmps1, "%li", getStep());
+ sprintf(tmps2, "%i", multi_sim_comm.Get_rank());
+ csfile = string("cs")+tmps2+"-"+tmps1+string(".dat");
+ meth_list[0]->write_cs(csfile.c_str());
+ }
+ unsigned size = meth_list[0]->ala_calc_hb.size();
+ for(unsigned j=0;j<size;j++) sh[0][j] = meth_list[0]->ala_calc_hb[j];
+ size = meth_list[0]->ile_calc_hd.size();
+ for(unsigned j=0;j<size;j++) sh[1][j] = meth_list[0]->ile_calc_hd[j];
+ size = meth_list[0]->ile_calc_hg2.size();
+ for(unsigned j=0;j<size;j++) sh[2][j] = meth_list[0]->ile_calc_hg2[j];
+ size = meth_list[0]->leu_calc_hd1.size();
+ for(unsigned j=0;j<size;j++) sh[3][j] = meth_list[0]->leu_calc_hd1[j];
+ size = meth_list[0]->leu_calc_hd2.size();
+ for(unsigned j=0;j<size;j++) sh[4][j] = meth_list[0]->leu_calc_hd2[j];
+ size = meth_list[0]->thr_calc_hg2.size();
+ for(unsigned j=0;j<size;j++) sh[5][j] = meth_list[0]->thr_calc_hg2[j];
+ size = meth_list[0]->val_calc_hg1.size();
+ for(unsigned j=0;j<size;j++) sh[6][j] = meth_list[0]->val_calc_hg1[j];
+ size = meth_list[0]->val_calc_hg2.size();
+ for(unsigned j=0;j<size;j++) sh[7][j] = meth_list[0]->val_calc_hg2[j];
+ fact = 1./((double) ens_dim);
+ if(comm.Get_rank()==0) { // I am the master of my replica
+ // among replicas
+ multi_sim_comm.Sum(&sh[0][0], numResidues*8);
+ multi_sim_comm.Barrier();
+ for(unsigned i=0;i<8;i++) for(int j=0;j<numResidues;j++) sh[j][i] *= fact;
+ } else for(unsigned i=0;i<8;i++) for(int j=0;j<numResidues;j++) sh[j][i] = 0.;
+ // inside each replica
+ comm.Sum(&sh[0][0], numResidues*8);
+ // now send the averaged shifts back to almost
+ size = meth_list[0]->ala_calc_hb.size();
+ for(unsigned j=0;j<size;j++) meth_list[0]->ala_calc_hb[j] = sh[0][j];
+ size = meth_list[0]->ile_calc_hd.size();
+ for(unsigned j=0;j<size;j++) meth_list[0]->ile_calc_hd[j] = sh[1][j];
+ size = meth_list[0]->ile_calc_hg2.size();
+ for(unsigned j=0;j<size;j++) meth_list[0]->ile_calc_hg2[j] = sh[2][j];
+ size = meth_list[0]->leu_calc_hd1.size();
+ for(unsigned j=0;j<size;j++) meth_list[0]->leu_calc_hd1[j] = sh[3][j];
+ size = meth_list[0]->leu_calc_hd2.size();
+ for(unsigned j=0;j<size;j++) meth_list[0]->leu_calc_hd2[j] = sh[4][j];
+ size = meth_list[0]->thr_calc_hg2.size();
+ for(unsigned j=0;j<size;j++) meth_list[0]->thr_calc_hg2[j] = sh[5][j];
+ size = meth_list[0]->val_calc_hg1.size();
+ for(unsigned j=0;j<size;j++) meth_list[0]->val_calc_hg1[j] = sh[6][j];
+ size = meth_list[0]->val_calc_hg2.size();
+ for(unsigned j=0;j<size;j++) meth_list[0]->val_calc_hg2[j] = sh[7][j];
+ // calculate all the forces now
+ energy = meth_list[0]->ens_calc_cs_force(coor, forces);
+ }
+
+ for (int i = 0; i < N; i++)
+ {
+ Vector For;
+ int ipos = 4 * i;
+ For[0] = forces.coor[ipos];
+ For[1] = forces.coor[ipos+1];
+ For[2] = forces.coor[ipos+2];
+ deriv[i] = fact*for_pl2alm*For;
+ virial=virial+(-1.*Tensor(getPosition(i),deriv[i]));
+ }
+
+ for(unsigned i=0;i<getNumberOfAtoms();++i) setAtomsDerivatives(i,deriv[i]);
+ setValue (ene_pl2alm*energy);
+ setBoxDerivatives (virial);
+}
+
+}
+#endif
diff --git a/src/colvar/CS2Backbone.cpp b/src/colvar/CS2Backbone.cpp
index 37b9b18a4d6d990205f51983c192c8ddfab8e8bc..c5994ef4af774af23654b77fa2b132be72bfab24 100644
--- a/src/colvar/CS2Backbone.cpp
+++ b/src/colvar/CS2Backbone.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -87,8 +87,7 @@ with ALMOST_BASE_PATH the full path to the ALMOST folder
HOW TO USE IT
-To use CamShift as a restraint or as collective variable or as a replica-averaged restraint
-first of all the experimental data are needed. CamShift uses backbone and Cb chemical shifts
+To use CamShift a set of experimental data is needed. CamShift uses backbone and Cb chemical shifts
that must be provided as text files:
\verbatim
@@ -174,7 +173,7 @@ PLUMED_REGISTER_ACTION(CS2Backbone,"CS2BACKBONE")
void CS2Backbone::registerKeywords( Keywords& keys ){
Colvar::registerKeywords( keys );
keys.addFlag("SERIAL",false,"Perform the calculation in serial - for debug purpose.");
- keys.add("atoms","ATOMS","The atoms to be included in the calculatios, e.g. the whole protein.");
+ keys.add("atoms","ATOMS","The atoms to be included in the calculation, e.g. the whole protein.");
keys.add("compulsory","DATA","data/","The folder with the experimental chemical shifts.");
keys.add("compulsory","FF","a03_gromacs.mdb","The ALMOST force-field to map the atoms' names.");
keys.add("compulsory","FLAT","1.0","Flat region in the scoring function.");
@@ -239,12 +238,12 @@ PLUMED_COLVAR_INIT(ao)
string stringa_mol;
parse("TERMINI",stringa_mol);
if(stringa_mol.length()>0) {
- int num_chains = pdb[0].size();
+ unsigned num_chains = pdb[0].size();
vector<string> data=Tools::getWords(stringa_mol,",");
if(data.size()!=2*num_chains) plumed_merror("You have to define both the NTerm and the CTerm for each chain of your system!\n");
for(unsigned i=0;i<data.size();i++) termini.push_back(data[i]);
} else {
- int num_chains = pdb[0].size();
+ unsigned num_chains = pdb[0].size();
for(unsigned i=0;i<(2*num_chains);i++) termini.push_back("DEFAULT");
}
@@ -285,8 +284,10 @@ PLUMED_COLVAR_INIT(ao)
log.printf(" Initializing N shifts %s\n", stringadb.c_str()); log.flush();
a.read_cs(stringadb, "N");
/* this is a workaround for those chemical shifts that can result in too large forces */
- a.remove_problematic("GLN","CB");
- a.remove_problematic("ILE","CB");
+ a.remove_problematic("GLN", "CB");
+ a.remove_problematic("ILE", "CB");
+ a.remove_problematic("PRO", "N"); a.remove_problematic("PRO", "H");
+ a.remove_problematic("GLY", "HA"); a.remove_problematic("GLY", "CB");
/* this is a workaround for those chemical shifts that are not parameterized */
a.remove_problematic("HIE", "HA"); a.remove_problematic("HIP", "HA"); a.remove_problematic("HSP", "HA");
a.remove_problematic("HIE", "H"); a.remove_problematic("HIP", "H"); a.remove_problematic("HSP", "H");
diff --git a/src/colvar/Cell.cpp b/src/colvar/Cell.cpp
index f0de733aea66eb110c1ed09f3f0882707f9cf876..981ad9e14c629fc1897ca55ed6cb6fd8368a712d 100644
--- a/src/colvar/Cell.cpp
+++ b/src/colvar/Cell.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/Colvar.h b/src/colvar/Colvar.h
index ee3f2ee447b217e5ca2dd1e0143b0448fe63209f..24cb14b3fcdd1e5ac6c2a1a646134ed32dab2d04 100644
--- a/src/colvar/Colvar.h
+++ b/src/colvar/Colvar.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/Constant.cpp b/src/colvar/Constant.cpp
index d0231dac110986236d0db89d8676fded1b5152eb..a783f09c174d261625efa78b9763dc823de0ff83 100644
--- a/src/colvar/Constant.cpp
+++ b/src/colvar/Constant.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/ContactMap.cpp b/src/colvar/ContactMap.cpp
index 914df1d907b65b4f6a74da55bb731110b0ef43bb..679ecc06e90d89b7cc36e6b34fd8a8cdab8d86df 100644
--- a/src/colvar/ContactMap.cpp
+++ b/src/colvar/ContactMap.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -166,7 +166,7 @@ void ContactMap::calculate(){
}
double dfunc=0.;
- coord = sfs[i].calculate(distance.modulo(), dfunc);
+ coord = sfs[i].calculateSqr(distance.modulo2(), dfunc);
if( !dosum ) {
Value* val=getPntrToComponent( i );
setAtomsDerivatives( val, i0, (-dfunc)*distance );
diff --git a/src/colvar/Coordination.cpp b/src/colvar/Coordination.cpp
index 7f3d0d0f62a116c9c0d5daa159f202c70de484f4..8de701f19ff4e64a3fa9a8ee842fa23804a40541 100644
--- a/src/colvar/Coordination.cpp
+++ b/src/colvar/Coordination.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -106,7 +106,7 @@ CoordinationBase(ao)
double Coordination::pairing(double distance,double&dfunc,unsigned i,unsigned j)const{
(void) i; // avoid warnings
(void) j; // avoid warnings
- return switchingFunction.calculate(distance,dfunc);
+ return switchingFunction.calculateSqr(distance,dfunc);
}
}
diff --git a/src/colvar/CoordinationBase.cpp b/src/colvar/CoordinationBase.cpp
index f29ab31008a06148750aa066faeecec8ef5c338a..0b9b6546b552af8dc6e84013f41f961fc9e56a11 100644
--- a/src/colvar/CoordinationBase.cpp
+++ b/src/colvar/CoordinationBase.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -108,7 +108,6 @@ CoordinationBase::~CoordinationBase(){
void CoordinationBase::prepare(){
if(nl->getStride()>0){
- if(getExchangeStep()) error("Neighbor lists for this collective variable are not compatible with replica exchange, sorry for that!");
if(firsttime || (getStep()%nl->getStride()==0)){
requestAtoms(nl->getFullAtomList());
invalidateList=true;
@@ -118,6 +117,7 @@ void CoordinationBase::prepare(){
invalidateList=false;
if(getExchangeStep()) error("Neighbor lists should be updated on exchange steps - choose a NL_STRIDE which divides the exchange stride!");
}
+ if(getExchangeStep()) firsttime=true;
}
}
@@ -156,7 +156,7 @@ void CoordinationBase::calculate()
}
double dfunc=0.;
- ncoord += pairing(distance.modulo(), dfunc,i0,i1);
+ ncoord += pairing(distance.modulo2(), dfunc,i0,i1);
deriv[i0] = deriv[i0] + (-dfunc)*distance ;
deriv[i1] = deriv[i1] + dfunc*distance ;
@@ -164,9 +164,9 @@ void CoordinationBase::calculate()
}
if(!serial){
- comm.Sum(&ncoord,1);
+ comm.Sum(ncoord);
if(!deriv.empty()) comm.Sum(&deriv[0][0],3*deriv.size());
- comm.Sum(&virial[0][0],9);
+ comm.Sum(virial);
}
for(unsigned i=0;i<deriv.size();++i) setAtomsDerivatives(i,deriv[i]);
diff --git a/src/colvar/CoordinationBase.h b/src/colvar/CoordinationBase.h
index bc32f934a9b1b793cb3d62980cd71315d2ac167b..16eaca49bd00f4d851ed034001d7a2184cdb9ba4 100644
--- a/src/colvar/CoordinationBase.h
+++ b/src/colvar/CoordinationBase.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/DHEnergy.cpp b/src/colvar/DHEnergy.cpp
index 024c1c5cf0a72c3d7f96e032b676c536b6c2e908..204540566034914a44a90f32fcf674b5d8188319 100644
--- a/src/colvar/DHEnergy.cpp
+++ b/src/colvar/DHEnergy.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -118,7 +118,8 @@ constant(0.0)
log<<" Bibliography "<<plumed.cite("Do, Carloni, Varani and Bussi, J. Chem. Theory Comput. 9, 1720 (2013)")<<" \n";
}
-double DHEnergy::pairing(double distance,double&dfunc,unsigned i,unsigned j)const{
+double DHEnergy::pairing(double distance2,double&dfunc,unsigned i,unsigned j)const{
+ double distance=std::sqrt(distance2);
if(getAbsoluteIndex(i)==getAbsoluteIndex(j)){
dfunc=0.0;
return 0.0;
diff --git a/src/colvar/DRMSD.cpp b/src/colvar/DRMSD.cpp
index ba487342589358281fe56a2ac78c38aa76a2ac8d..4ef02e72c49df888406bad7ce90c5cba9001c07a 100644
--- a/src/colvar/DRMSD.cpp
+++ b/src/colvar/DRMSD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/Dipole.cpp b/src/colvar/Dipole.cpp
index 8363783f2a4218d4c78b350ca4f5fbd36fb429ef..687688be0b17cfa3f90beec6de45df8ef52c721f 100644
--- a/src/colvar/Dipole.cpp
+++ b/src/colvar/Dipole.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/Distance.cpp b/src/colvar/Distance.cpp
index 992ad73bfa1c81ba505515792224acd7a9573d2d..9cef1fc25abaacb3f528f47783b00a326b6f6be2 100644
--- a/src/colvar/Distance.cpp
+++ b/src/colvar/Distance.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -33,6 +33,12 @@ namespace colvar{
//+PLUMEDOC COLVAR DISTANCE
/*
Calculate the distance between a pair of atoms.
+By default the distance is computed taking into account periodic
+boundary conditions. This behavior can be changed with the NOPBC flag.
+Moreover, single components (x,y, and z) can be also computed.
+
+Notice that single components will not have the proper periodicity!
+A possible hack is shown in one of the examples below.
\par Examples
@@ -46,6 +52,54 @@ PRINT ARG=d1,d2,d2c.x
\endverbatim
(See also \ref PRINT).
+The following input computes the end-to-end distance for a polymer
+of 100 atoms and keeps it at a value around 5.
+\verbatim
+WHOLEMOLECULES ENTITY0=1-100
+e2e: DISTANCE ATOMS=1,100 NOPBC
+RESTRAINT ARG=e2e KAPPA=1 AT=5
+\endverbatim
+(See also \ref WHOLEMOLECULES and \ref RESTRAINT).
+
+Notice that NOPBC is used
+to be sure that if the end-to-end distance is larger than half the simulation
+box the distance is compute properly. Also notice that, since many MD
+codes break molecules across cell boundary, it might be necessary to
+use the \ref WHOLEMOLECULES keyword (also notice that it should be
+_before_ distance). The list of atoms provided to WHOLEMOLECULES
+here contains all the atoms between 1 and 100. Strictly speaking, this
+is not necessary. If you know for sure that atoms with difference in
+the index say equal to 10 are _not_ going to be farther than half cell
+you can e.g. use
+\verbatim
+WHOLEMOLECULES ENTITY0=1,10,20,30,40,50,60,70,80,90,100
+e2e: DISTANCE ATOMS=1,100 NOPBC
+RESTRAINT ARG=e2e KAPPA=1 AT=5
+\endverbatim
+Just be sure that the ordered list provide to WHOLEMOLECULES has the following
+properties:
+- Consecutive atoms should be closer than half-cell throughout the entire simulation.
+- Atoms required later for the distance (e.g. 1 and 100) should be included in the list
+
+The following example shows how to take into account periodicity e.g.
+in z-component of a distance
+\verbatim
+# this is a center of mass of a large group
+c: COM ATOMS=1-100
+# this is the distance between atom 101 and the group
+d: DISTANCE ATOMS=c,101 COMPONENTS
+# this makes a new variable, dd, equal to d and periodic, with domain -10,10
+# this is the right choise if e.g. the cell is orthorombic and its size in
+# z direction is 20.
+dz: COMBINE ARG=d.z PERIODIC=-10,10
+# metadynamics on dd
+METAD ARG=dz SIGMA=0.1 HEIGHT=0.1 PACE=200
+\endverbatim
+(see also \ref COM, \ref COMBINE, and \ref METAD)
+
+
+
+
*/
//+ENDPLUMEDOC
@@ -96,6 +150,7 @@ pbc(true)
addComponentWithDerivatives("x"); componentIsNotPeriodic("x");
addComponentWithDerivatives("y"); componentIsNotPeriodic("y");
addComponentWithDerivatives("z"); componentIsNotPeriodic("z");
+ log<<" WARNING: components will not have the proper periodicity - see manual\n";
}
requestAtoms(atoms);
diff --git a/src/colvar/Energy.cpp b/src/colvar/Energy.cpp
index 4afc5b3887b82176b76c5ead2816372e46fa8993..00e819d82ae2a2666eea46d5a1d1212a432b34cf 100644
--- a/src/colvar/Energy.cpp
+++ b/src/colvar/Energy.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/Fake.cpp b/src/colvar/Fake.cpp
index 59085b3fa442042ad405a42ad425b2e67a6c548f..9753bfb9ce62225a89c7052b9395cff0d662cb0e 100644
--- a/src/colvar/Fake.cpp
+++ b/src/colvar/Fake.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -89,7 +89,7 @@ PLUMED_COLVAR_INIT(ao)
if(period.size()!=0){
plumed_massert(getNumberOfComponents()*2==period.size(),"the periodicty should coincide with the number of components");
if(comps.size()!=0){
- for(unsigned i=0;i<getNumberOfComponents();i++){
+ for(int i=0;i<getNumberOfComponents();i++){
string pp=comps[i];
if(period[i*2]!="none" && period[i*2+1]!="none" ){
componentIsPeriodic(pp,period[i*2],period[i*2+1]);
@@ -106,7 +106,7 @@ PLUMED_COLVAR_INIT(ao)
}
}else{
if(comps.size()!=0){
- for(unsigned i=0;i<getNumberOfComponents();i++){
+ for(int i=0;i<getNumberOfComponents();i++){
componentIsNotPeriodic(getPntrToComponent(i)->getName());
}
} else {
diff --git a/src/colvar/Gyration.cpp b/src/colvar/Gyration.cpp
index 1650637c26a3569b91d9795ff3a3dbb042e112a4..cd3c3c1974d1f68e11619c0cc1d602bfdb7a500e 100644
--- a/src/colvar/Gyration.cpp
+++ b/src/colvar/Gyration.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/PathMSD.cpp b/src/colvar/PathMSD.cpp
index 5b8d2463952f03bedb1a9fc083ffea199cdbd786..0341086fd3dd2aa9c7163c6789b4d7c0fc8c199d 100644
--- a/src/colvar/PathMSD.cpp
+++ b/src/colvar/PathMSD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/PathMSDBase.cpp b/src/colvar/PathMSDBase.cpp
index e741bc58280e98f25bff9f212527ea6c3d5ccda6..7537ee824f0c4c8b70b38e9d3415801ad310342c 100644
--- a/src/colvar/PathMSDBase.cpp
+++ b/src/colvar/PathMSDBase.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -137,8 +137,8 @@ void PathMSDBase::calculate(){
for(unsigned j=0;j<nat;j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
}
// reduce over all processors
- comm.Sum(&tmp_distances[0],imgVec.size());
- comm.Sum(&tmp_derivs2[0][0],3*imgVec.size()*nat);
+ comm.Sum(tmp_distances);
+ comm.Sum(tmp_derivs2);
// assign imgVec[i].distance and imgVec[i].distder
for(unsigned i=0;i<imgVec.size();i++){
imgVec[i].distance=tmp_distances[i];
diff --git a/src/colvar/PathMSDBase.h b/src/colvar/PathMSDBase.h
index f43b668be2a3e4ef3412940b45e81c2437275b20..9bebb826ee675e3ddd7933700a2a96c89ca76fcb 100644
--- a/src/colvar/PathMSDBase.h
+++ b/src/colvar/PathMSDBase.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/PropertyMap.cpp b/src/colvar/PropertyMap.cpp
index f80d4b97df49214ecd4357bf1140800d8f3685c1..92c34b375217690c5b40af62b13bcb17daaa3fb2 100644
--- a/src/colvar/PropertyMap.cpp
+++ b/src/colvar/PropertyMap.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/RMSD.cpp b/src/colvar/RMSD.cpp
index f0650658e2739a6532b1c08927b29a11fd6b5709..d0d3a4241d8759e83ced31f3f61aec4eccc4c519 100644
--- a/src/colvar/RMSD.cpp
+++ b/src/colvar/RMSD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/Template.cpp b/src/colvar/Template.cpp
index b4fb010937aec024360dc1a28bf267b627cf9dab..ec34f9b02a4ad099fa73ca3c0f670b398a124ae8 100644
--- a/src/colvar/Template.cpp
+++ b/src/colvar/Template.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/colvar/Torsion.cpp b/src/colvar/Torsion.cpp
index 6e2a3bfa2247be3ed9ec701610955ebe304d1a41..66d94fcec18a977fd63fd7f997654d5917b65528 100644
--- a/src/colvar/Torsion.cpp
+++ b/src/colvar/Torsion.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -50,6 +50,19 @@ t: TORSION ATOMS=1,2,3,4
PRINT ARG=t FILE=COLVAR
\endverbatim
+If you are working with a protein you can specify the special named torsion angles \f$\phi\f$ and \f$\psi\f$
+by using TORSION in combination with the \ref MOLINFO command. This can be done by using the following
+syntax.
+
+\verbatim
+MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
+t1: TORSION ATOMS=@phi-3
+t2: TORSION ATOMS=@psi-4
+PRINT ARG=t1,t2 FILE=colvar STRIDE=10
+\endverbatim
+
+Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
+Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Volume.cpp b/src/colvar/Volume.cpp
index abfdfe1c7a818a64400a965ccdf6cdb8d948025d..ecad4320b5667569b764aa84a2a78f86affb6f2f 100644
--- a/src/colvar/Volume.cpp
+++ b/src/colvar/Volume.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/config/Config.cpp.in b/src/config/Config.cpp.in
index 968122359164e5c631d87d20214f2197ba9bf9c0..4c326f2773518b93e59e2864a61201c1ba4d621a 100644
--- a/src/config/Config.cpp.in
+++ b/src/config/Config.cpp.in
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -30,6 +30,10 @@ std::string getSoExt(){
return "@SOEXT@";
}
+bool isInstalled(){
+ return @ISINSTALLED@;
+}
+
std::string getPlumedRoot(){
return "@PLUMED_ROOT@";
}
@@ -74,6 +78,14 @@ bool hasCregex(){
#endif
}
+bool hasMolfile(){
+#if __PLUMED_HAS_MOLFILE
+ return true;
+#else
+ return false;
+#endif
+}
+
}
diff --git a/src/config/Config.h b/src/config/Config.h
index 884e275d2e5e7eec6197e624977bf4b595692e27..81d7fc78b6fae1886dbfb6461390d49b6d3932d0 100644
--- a/src/config/Config.h
+++ b/src/config/Config.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -39,8 +39,12 @@ bool hasDlopen();
bool hasAlmost();
+bool isInstalled();
+
bool hasCregex();
+bool hasMolfile();
+
}
}
diff --git a/src/config/Makefile b/src/config/Makefile
index 77ea8d01af1e89ee5a055d297d9286e7662f3c5a..c6af230bd383952854afa6f43a1ee27c6e231606 100644
--- a/src/config/Makefile
+++ b/src/config/Makefile
@@ -7,6 +7,7 @@
all:
@echo "Updating ConfigInstall.cpp"
@sed "s/@SOEXT@/$(SOEXT)/g" Config.cpp.in | \
+ sed "s/@ISINSTALLED@/true/g" | \
../maketools/update-plumedroot.sh ConfigInstall.cpp
$(MAKE) do-all
@@ -16,12 +17,14 @@ do-all: Config.o ConfigInstall.o compile_options.sh
ConfigInstall.cpp:
@echo "Updating ConfigInstall.cpp"
@sed "s/@SOEXT@/$(SOEXT)/g" Config.cpp.in | \
- ../maketools/update-plumedroot.sh ConfigInstall.cpp
+ sed "s/@ISINSTALLED@/true/g" | \
+ ../maketools/update-plumedroot.sh ConfigInstall.cpp
# file to import compilation options inside c++
Config.cpp: Config.cpp.in Config.h
@echo Building Config.cpp, a object containing configuration infos
@sed "s/@SOEXT@/$(SOEXT)/g" $< | \
+ sed "s/@ISINSTALLED@/false/g" | \
sed "s|@PLUMED_ROOT@|$(CURDIR:src/config=)|g" > $@
links:
diff --git a/src/core/Action.cpp b/src/core/Action.cpp
index b0e8d4a41cf3c4eb3ed9b655cfc5a38cd0e909ce..6837840e38d546d9f0b71798da7f4934dd0f2abc 100644
--- a/src/core/Action.cpp
+++ b/src/core/Action.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -106,7 +106,7 @@ void Action::parseFlag(const std::string&key,bool & t){
plumed_massert(keywords.exists(key), "keyword " + key + " has not been registered");
// Check keyword is a flag
if(!keywords.style(key,"nohtml")){
- plumed_massert(keywords.style(key,"flag"), "keyword " + key + " is not a flag");
+ plumed_massert(keywords.style(key,"flag") || keywords.style(key,"hidden"), "keyword " + key + " is not a flag");
}
// Read in the flag otherwise get the default value from the keywords object
@@ -121,7 +121,7 @@ void Action::parseFlag(const std::string&key,bool & t){
}
void Action::addDependency(Action*action){
- after.insert(action);
+ after.push_back(action);
}
void Action::activate(){
diff --git a/src/core/Action.h b/src/core/Action.h
index 471a15de3571b231784d02f3cc0053803f8af38c..69b49eeb8caae8027cd95da8ba0b8c30bac71bad 100644
--- a/src/core/Action.h
+++ b/src/core/Action.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -72,7 +72,7 @@ class Action
std::vector<std::string> line;
public:
- typedef std::set<Action*> Dependencies;
+ typedef std::vector<Action*> Dependencies;
private:
/// Actions on which this Action depends.
diff --git a/src/core/ActionAtomistic.cpp b/src/core/ActionAtomistic.cpp
index 821156f5fa744fe133522595ca6dbdcf04a1d664..7faa3da03e53b345e809077de076ece628c59f16 100644
--- a/src/core/ActionAtomistic.cpp
+++ b/src/core/ActionAtomistic.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -22,6 +22,7 @@
#include "ActionAtomistic.h"
#include "PlumedMain.h"
#include "ActionSet.h"
+#include "SetupMolInfo.h"
#include <vector>
#include <string>
#include "ActionWithValue.h"
@@ -45,6 +46,8 @@ ActionAtomistic::ActionAtomistic(const ActionOptions&ao):
Action(ao),
pbc(*new(Pbc)),
lockRequestAtoms(false),
+donotretrieve(false),
+donotforce(false),
atoms(plumed.getAtoms())
{
atoms.add(this);
@@ -84,6 +87,10 @@ void ActionAtomistic::calculateNumericalDerivatives( ActionWithValue* a ){
calculateAtomicNumericalDerivatives( a, 0 );
}
+void ActionAtomistic::changeBox( const Tensor& newbox ){
+ pbc.setBox( newbox );
+}
+
void ActionAtomistic::calculateAtomicNumericalDerivatives( ActionWithValue* a, const unsigned& startnum ){
if(!a){
a=dynamic_cast<ActionWithValue*>(this);
@@ -102,7 +109,7 @@ void ActionAtomistic::calculateAtomicNumericalDerivatives( ActionWithValue* a, c
positions[i][k]=positions[i][k]+delta;
a->calculate();
positions[i][k]=savedPositions[i][k];
- for(unsigned j=0;j<nval;j++){
+ for(int j=0;j<nval;j++){
value[j*natoms+i][k]=a->getOutputQuantity(j);
}
}
@@ -116,12 +123,12 @@ void ActionAtomistic::calculateAtomicNumericalDerivatives( ActionWithValue* a, c
box(i,k)=arg0;
pbc.setBox(box);
for(int j=0;j<natoms;j++) positions[j]=savedPositions[j];
- for(unsigned j=0;j<nval;j++) valuebox[j](i,k)=a->getOutputQuantity(j);
+ for(int j=0;j<nval;j++) valuebox[j](i,k)=a->getOutputQuantity(j);
}
a->calculate();
a->clearDerivatives();
- for(unsigned j=0;j<nval;j++){
+ for(int j=0;j<nval;j++){
Value* v=a->copyOutput(j);
double ref=v->get();
if(v->hasDerivatives()){
@@ -158,6 +165,18 @@ void ActionAtomistic::parseAtomList(const std::string&key,const int num, std::ve
AtomNumber atom;
ok=Tools::convert(strings[i],atom); // this is converting strings to AtomNumbers
if(ok) t.push_back(atom);
+// here we check if this is a special symbol for MOLINFO
+ if( !ok && strings[i].compare(0,1,"@")==0 ){
+ std::size_t dot=strings[i].find_first_of("@"); std::string symbol=strings[i].substr(dot+1);
+ vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
+ if( moldat.size()>0 ){
+ vector<AtomNumber> atom_list; moldat[0]->interpretSymbol( symbol, atom_list );
+ if( atom_list.size()>0 ){ ok=true; t.insert(t.end(),atom_list.begin(),atom_list.end()); }
+ else { error(strings[i] + " is not a label plumed knows"); }
+ } else {
+ error("atoms specified using @ symbol but no MOLINFO was available");
+ }
+ }
// here we check if the atom name is the name of a group
if(!ok){
if(atoms.groups.count(strings[i])){
@@ -178,7 +197,8 @@ void ActionAtomistic::parseAtomList(const std::string&key,const int num, std::ve
}
}
}
- plumed_massert(ok,"it was not possible to interpret atom name " + strings[i]);
+ if(!ok) error("it was not possible to interpret atom name " + strings[i]);
+ // plumed_massert(ok,"it was not possible to interpret atom name " + strings[i]);
}
}
@@ -186,6 +206,9 @@ void ActionAtomistic::parseAtomList(const std::string&key,const int num, std::ve
void ActionAtomistic::retrieveAtoms(){
box=atoms.box;
pbc=atoms.pbc;
+ Colvar*cc=dynamic_cast<Colvar*>(this);
+ if(cc && cc->checkIsEnergy()) energy=atoms.getEnergy();
+ if(donotretrieve) return;
chargesWereSet=atoms.chargesWereSet();
const vector<Vector> & p(atoms.positions);
const vector<double> & c(atoms.charges);
@@ -193,11 +216,10 @@ void ActionAtomistic::retrieveAtoms(){
for(unsigned j=0;j<indexes.size();j++) positions[j]=p[indexes[j].index()];
for(unsigned j=0;j<indexes.size();j++) charges[j]=c[indexes[j].index()];
for(unsigned j=0;j<indexes.size();j++) masses[j]=m[indexes[j].index()];
- Colvar*cc=dynamic_cast<Colvar*>(this);
- if(cc && cc->checkIsEnergy()) energy=atoms.getEnergy();
}
void ActionAtomistic::setForcesOnAtoms( const std::vector<double>& forcesToApply, unsigned ind ){
+ if(donotforce) return;
for(unsigned i=0;i<indexes.size();++i){
forces[i][0]=forcesToApply[ind]; ind++;
forces[i][1]=forcesToApply[ind]; ind++;
@@ -216,6 +238,7 @@ void ActionAtomistic::setForcesOnAtoms( const std::vector<double>& forcesToApply
}
void ActionAtomistic::applyForces(){
+ if(donotforce) return;
vector<Vector> & f(atoms.forces);
Tensor & v(atoms.virial);
for(unsigned j=0;j<indexes.size();j++) f[indexes[j].index()]+=forces[j];
@@ -223,6 +246,13 @@ void ActionAtomistic::applyForces(){
atoms.forceOnEnergy+=forceOnEnergy;
}
+void ActionAtomistic::clearOutputForces(){
+ if(donotforce) return;
+ for(unsigned i=0;i<forces.size();++i)forces[i].zero();
+ forceOnEnergy=0.0;
+}
+
+
void ActionAtomistic::readAtomsFromPDB( const PDB& pdb ){
Colvar*cc=dynamic_cast<Colvar*>(this);
if(cc && cc->checkIsEnergy()) error("can't read energies from pdb files");
diff --git a/src/core/ActionAtomistic.h b/src/core/ActionAtomistic.h
index 70a5e0be902dc301b62d6a3534d8f547ef569ada..53d9320f2eb6b91ed3fe9741a8c068ee73bcc5e7 100644
--- a/src/core/ActionAtomistic.h
+++ b/src/core/ActionAtomistic.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -24,12 +24,12 @@
#include "Action.h"
#include "tools/Tensor.h"
+#include "Atoms.h"
#include <vector>
#include <set>
namespace PLMD {
-class Atoms;
class Pbc;
class PDB;
@@ -55,6 +55,9 @@ class ActionAtomistic :
bool lockRequestAtoms; // forbid changes to request atoms
+ bool donotretrieve;
+ bool donotforce;
+
protected:
Atoms& atoms;
@@ -66,9 +69,15 @@ public:
/// MAYBE WE HAVE TO FIND SOMETHING MORE CLEAR FOR DYNAMIC
/// LISTS OF ATOMS
void requestAtoms(const std::vector<AtomNumber> & a);
-/// Get position of i-th atom
+/// Get position of i-th atom (access by relative index)
const Vector & getPosition(int)const;
-/// Get position of i-th atom
+/// Get position of i-th atom (access by absolute AtomNumber).
+/// With direct access to the global atom array
+ const Vector & getPosition(AtomNumber)const;
+/// Get modifiable position of i-th atom (access by absolute AtomNumber).
+/// Should be used by action that need to modify the stored atomic coordinates
+ Vector & modifyPosition(AtomNumber);
+/// Get box shape
const Tensor & getBox()const;
/// Get the array of all positions
const std::vector<Vector> & getPositions()const;
@@ -96,10 +105,22 @@ public:
void parseAtomList(const std::string&key,std::vector<AtomNumber> &t);
/// Parse an list of atom with a numbred keyword
void parseAtomList(const std::string&key,const int num, std::vector<AtomNumber> &t);
+/// Change the box shape
+ void changeBox( const Tensor& newbox );
/// Get reference to Pbc
const Pbc & getPbc() const;
/// Add the forces to the atoms
void setForcesOnAtoms( const std::vector<double>& forcesToApply, unsigned ind=0 );
+/// Skip atom retrieval - use with care.
+/// If this function is called during initialization, then atoms are
+/// not going to be retrieved. Can be used for optimization. Notice that
+/// calling getPosition(int) in an Action where DoNotRetrieve() was called might
+/// lead to undefined behavior.
+ void doNotRetrieve(){donotretrieve=true;}
+/// Skip atom forces - use with care.
+/// If this function is called during initialization, then forces are
+/// not going to be propagated. Can be used for optimization.
+ void doNotForce(){donotforce=true;}
public:
// virtual functions:
@@ -133,6 +154,16 @@ const Vector & ActionAtomistic::getPosition(int i)const{
return positions[i];
}
+inline
+const Vector & ActionAtomistic::getPosition(AtomNumber i)const{
+ return atoms.positions[i.index()];
+}
+
+inline
+Vector & ActionAtomistic::modifyPosition(AtomNumber i){
+ return atoms.positions[i.index()];
+}
+
inline
double ActionAtomistic::getMass(int i)const{
return masses[i];
@@ -179,13 +210,6 @@ Tensor & ActionAtomistic::modifyVirial(){
return virial;
}
-inline
-void ActionAtomistic::clearOutputForces(){
- for(unsigned i=0;i<forces.size();++i)forces[i].zero();
- forceOnEnergy=0.0;
-}
-
-
inline
double & ActionAtomistic::modifyForceOnEnergy(){
return forceOnEnergy;
diff --git a/src/core/ActionPilot.cpp b/src/core/ActionPilot.cpp
index 7644656a8d0283c772145faa7c649f8fa8b72f22..6a2900e24b4a5e01aab34404eb40e9835d83f434 100644
--- a/src/core/ActionPilot.cpp
+++ b/src/core/ActionPilot.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionPilot.h b/src/core/ActionPilot.h
index 747658a028c3590818953774fe2a8a7865e25a52..e760a31893ffc821141238d73f8f06c4b958a8eb 100644
--- a/src/core/ActionPilot.h
+++ b/src/core/ActionPilot.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionRegister.cpp b/src/core/ActionRegister.cpp
index 4adbc3a6d3e596fb85eb378eca18cc491f3d7aa0..f459fac3373e8a79e7406f21309d94e6e86374dc 100644
--- a/src/core/ActionRegister.cpp
+++ b/src/core/ActionRegister.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionRegister.h b/src/core/ActionRegister.h
index 5bc7ca69eb5a79dd63bf00111c4187487b19be8a..25514bb4d590038db3b78b64abb4255a8d9a1a30 100644
--- a/src/core/ActionRegister.h
+++ b/src/core/ActionRegister.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionSet.cpp b/src/core/ActionSet.cpp
index a212ca2db8fb73038ff18eb4c1d2d8946adb5d94..6958d062e1aee99b5aba95991e358776bf221d38 100644
--- a/src/core/ActionSet.cpp
+++ b/src/core/ActionSet.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionSet.h b/src/core/ActionSet.h
index 48a16cd9158057dae8b3a833d0ab5e28baf814e2..335952498c634fc62f717c8b7ee1247b9aca6fe1 100644
--- a/src/core/ActionSet.h
+++ b/src/core/ActionSet.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionSetup.cpp b/src/core/ActionSetup.cpp
index b7297f1cc0053fe52a2facb7b42a12be7ea27e2c..504386a4818b88799a782fc39e2a8de7fac55ba4 100644
--- a/src/core/ActionSetup.cpp
+++ b/src/core/ActionSetup.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionSetup.h b/src/core/ActionSetup.h
index 074d2a48abe1cd40ed2f60ffcaa53c96598f167c..08a599e7f4e04822023477c442873b1b910b29f5 100644
--- a/src/core/ActionSetup.h
+++ b/src/core/ActionSetup.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionWithArguments.cpp b/src/core/ActionWithArguments.cpp
index bc601ccee9841b869fb4a12e3e2cdb4672f4ca86..0238bfa4b2ea4cd76eb554a16964ae6e1fb54dc6 100644
--- a/src/core/ActionWithArguments.cpp
+++ b/src/core/ActionWithArguments.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -249,13 +249,13 @@ void ActionWithArguments::calculateNumericalDerivatives( ActionWithValue* a ){
arguments[i]->set(arg0+sqrt(epsilon));
a->calculate();
arguments[i]->set(arg0);
- for(unsigned j=0;j<nval;j++){
+ for(int j=0;j<nval;j++){
value[i*nval+j]=a->getOutputQuantity(j);
}
}
a->calculate();
a->clearDerivatives();
- for(unsigned j=0;j<nval;j++){
+ for(int j=0;j<nval;j++){
Value* v=a->copyOutput(j);
if( v->hasDerivatives() ) for(int i=0;i<npar;i++) v->addDerivative(i,(value[i*nval+j]-a->getOutputQuantity(j))/sqrt(epsilon));
}
diff --git a/src/core/ActionWithArguments.h b/src/core/ActionWithArguments.h
index 36dfd94f6b76094956985390611223812c79633b..c9d1315002b5f9a452ffda848b2a5fdd51768e10 100644
--- a/src/core/ActionWithArguments.h
+++ b/src/core/ActionWithArguments.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionWithValue.cpp b/src/core/ActionWithValue.cpp
index a9c65b659b4bffcb982480b4e8d160b92c2c672e..e7d0d4eee1af954ed5ce9f265d06503f0a95e686 100644
--- a/src/core/ActionWithValue.cpp
+++ b/src/core/ActionWithValue.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionWithValue.h b/src/core/ActionWithValue.h
index 707a5ab587392be71c028105f9a2ae0622dfe447..6ff1199fbbe259323396558f0e86baa5ebd5fd11 100644
--- a/src/core/ActionWithValue.h
+++ b/src/core/ActionWithValue.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionWithVirtualAtom.cpp b/src/core/ActionWithVirtualAtom.cpp
index bc1a8089f390485cca4ec40ef521119a1f56f263..9c446d7010d2a1ec1044cc420ef08c208b235fae 100644
--- a/src/core/ActionWithVirtualAtom.cpp
+++ b/src/core/ActionWithVirtualAtom.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ActionWithVirtualAtom.h b/src/core/ActionWithVirtualAtom.h
index 568640b5d1374dfac2f13fdfdc1edcdf22795aa0..f9b391af8702d7a493226031672f34f79ab94c0c 100644
--- a/src/core/ActionWithVirtualAtom.h
+++ b/src/core/ActionWithVirtualAtom.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/Atoms.cpp b/src/core/Atoms.cpp
index f53a705e1fdbc58c6c9066878e798b470d135b8e..2ce582a1e1b119f887eb14b57a9a7d278671aaaa 100644
--- a/src/core/Atoms.cpp
+++ b/src/core/Atoms.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -32,6 +32,10 @@ using namespace std;
namespace PLMD {
+/// We assume that charges and masses are constant along the simulation
+/// Set this to false if you want to revert to the original (expensive) behavior
+static const bool shareMassAndChargeOnlyAtFirstStep=true;
+
class PlumedMain;
Atoms::Atoms(PlumedMain&plumed):
@@ -47,6 +51,7 @@ Atoms::Atoms(PlumedMain&plumed):
boxHasBeenSet(false),
forcesHaveBeenSet(0),
virialHasBeenSet(false),
+ massAndChargeOK(false),
plumed(plumed),
naturalUnits(false),
timestep(0.0),
@@ -127,6 +132,13 @@ void Atoms::setForces(void*p,int i){
void Atoms::share(){
std::set<AtomNumber> unique;
+// At first step I scatter all the atoms so as to store their mass and charge
+// Notice that this works with the assumption that charges and masses are
+// not changing during the simulation!
+ if(!massAndChargeOK && shareMassAndChargeOnlyAtFirstStep){
+ shareAll();
+ return;
+ }
if(dd && int(gatindex.size())<natoms){
for(unsigned i=0;i<actions.size();i++) if(actions[i]->isActive()) {
unique.insert(actions[i]->getUnique().begin(),actions[i]->getUnique().end());
@@ -145,9 +157,14 @@ void Atoms::shareAll(){
void Atoms::share(const std::set<AtomNumber>& unique){
plumed_assert( positionsHaveBeenSet==3 && massesHaveBeenSet );
mdatoms->getBox(box);
- mdatoms->getMasses(gatindex,masses);
- mdatoms->getCharges(gatindex,charges);
mdatoms->getPositions(gatindex,positions);
+// how many double per atom should be scattered:
+ int ndata=3;
+ if(!massAndChargeOK){
+ ndata=5;
+ mdatoms->getCharges(gatindex,charges);
+ mdatoms->getMasses(gatindex,masses);
+ }
if(dd && int(gatindex.size())<natoms){
if(dd.async){
for(unsigned i=0;i<dd.mpi_request_positions.size();i++) dd.mpi_request_positions[i].wait();
@@ -157,11 +174,13 @@ void Atoms::share(const std::set<AtomNumber>& unique){
for(std::set<AtomNumber>::const_iterator p=unique.begin();p!=unique.end();++p){
if(dd.g2l[p->index()]>=0){
dd.indexToBeSent[count]=p->index();
- dd.positionsToBeSent[5*count+0]=positions[p->index()][0];
- dd.positionsToBeSent[5*count+1]=positions[p->index()][1];
- dd.positionsToBeSent[5*count+2]=positions[p->index()][2];
- dd.positionsToBeSent[5*count+3]=masses[p->index()];
- dd.positionsToBeSent[5*count+4]=charges[p->index()];
+ dd.positionsToBeSent[ndata*count+0]=positions[p->index()][0];
+ dd.positionsToBeSent[ndata*count+1]=positions[p->index()][1];
+ dd.positionsToBeSent[ndata*count+2]=positions[p->index()][2];
+ if(!massAndChargeOK){
+ dd.positionsToBeSent[ndata*count+3]=masses[p->index()];
+ dd.positionsToBeSent[ndata*count+4]=charges[p->index()];
+ }
count++;
}
}
@@ -170,7 +189,7 @@ void Atoms::share(const std::set<AtomNumber>& unique){
dd.mpi_request_index.resize(dd.Get_size());
for(int i=0;i<dd.Get_size();i++){
dd.mpi_request_index[i]=dd.Isend(&dd.indexToBeSent[0],count,i,666);
- dd.mpi_request_positions[i]=dd.Isend(&dd.positionsToBeSent[0],5*count,i,667);
+ dd.mpi_request_positions[i]=dd.Isend(&dd.positionsToBeSent[0],ndata*count,i,667);
}
}else{
const int n=(dd.Get_size());
@@ -178,20 +197,22 @@ void Atoms::share(const std::set<AtomNumber>& unique){
vector<int> displ(n);
vector<int> counts5(n);
vector<int> displ5(n);
- dd.Allgather(&count,1,&counts[0],1);
+ dd.Allgather(count,counts);
displ[0]=0;
for(int i=1;i<n;++i) displ[i]=displ[i-1]+counts[i-1];
- for(int i=0;i<n;++i) counts5[i]=counts[i]*5;
- for(int i=0;i<n;++i) displ5[i]=displ[i]*5;
+ for(int i=0;i<n;++i) counts5[i]=counts[i]*ndata;
+ for(int i=0;i<n;++i) displ5[i]=displ[i]*ndata;
dd.Allgatherv(&dd.indexToBeSent[0],count,&dd.indexToBeReceived[0],&counts[0],&displ[0]);
- dd.Allgatherv(&dd.positionsToBeSent[0],5*count,&dd.positionsToBeReceived[0],&counts5[0],&displ5[0]);
+ dd.Allgatherv(&dd.positionsToBeSent[0],ndata*count,&dd.positionsToBeReceived[0],&counts5[0],&displ5[0]);
int tot=displ[n-1]+counts[n-1];
for(int i=0;i<tot;i++){
- positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[5*i+0];
- positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[5*i+1];
- positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[5*i+2];
- masses[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[5*i+3];
- charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[5*i+4];
+ positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[ndata*i+0];
+ positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[ndata*i+1];
+ positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[ndata*i+2];
+ if(!massAndChargeOK){
+ masses[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+3];
+ charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+4];
+ }
}
}
}
@@ -203,9 +224,12 @@ void Atoms::share(const std::set<AtomNumber>& unique){
void Atoms::wait(){
dataCanBeSet=false; // Everything should be set by this stage
+// How many double per atom should be scattered
+ int ndata=3;
+ if(!massAndChargeOK)ndata=5;
if(dd){
- dd.Bcast(&box[0][0],9,0);
+ dd.Bcast(box,0);
}
pbc.setBox(box);
@@ -219,19 +243,24 @@ void Atoms::wait(){
for(int i=0;i<dd.Get_size();i++){
dd.Recv(&dd.indexToBeReceived[count],dd.indexToBeReceived.size()-count,i,666,status);
int c=status.Get_count<int>();
- dd.Recv(&dd.positionsToBeReceived[5*count],dd.positionsToBeReceived.size()-5*count,i,667);
+ dd.Recv(&dd.positionsToBeReceived[ndata*count],dd.positionsToBeReceived.size()-ndata*count,i,667);
count+=c;
}
for(int i=0;i<count;i++){
- positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[5*i+0];
- positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[5*i+1];
- positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[5*i+2];
- masses[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[5*i+3];
- charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[5*i+4];
+ positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[ndata*i+0];
+ positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[ndata*i+1];
+ positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[ndata*i+2];
+ if(!massAndChargeOK){
+ masses[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+3];
+ charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+4];
+ }
}
}
- if(collectEnergy) dd.Sum(&energy,1);
+ if(collectEnergy) dd.Sum(energy);
}
+// I take note that masses and charges have been set once for all
+// at the beginning of the simulation.
+ if(shareMassAndChargeOnlyAtFirstStep) massAndChargeOK=true;
}
void Atoms::updateForces(){
@@ -334,7 +363,7 @@ void Atoms::createFullList(int*n){
std::sort(fullListTmp.begin(),fullListTmp.end());
int nn=std::unique(fullListTmp.begin(),fullListTmp.end())-fullListTmp.begin();
fullList.resize(nn);
- for(unsigned i=0;i<nn;++i) fullList[i]=fullListTmp[i].index();
+ for(int i=0;i<nn;++i) fullList[i]=fullListTmp[i].index();
*n=nn;
}
diff --git a/src/core/Atoms.h b/src/core/Atoms.h
index b6e36ce0e8fce9242ec62830d58dd201c94d9167..ee3daeae2ec2d3a28bc7638fb18686c51847c05c 100644
--- a/src/core/Atoms.h
+++ b/src/core/Atoms.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -69,6 +69,7 @@ class Atoms
bool boxHasBeenSet;
unsigned forcesHaveBeenSet;
bool virialHasBeenSet;
+ bool massAndChargeOK;
std::map<std::string,std::vector<AtomNumber> > groups;
@@ -194,7 +195,6 @@ public:
bool usingNaturalUnits()const;
void setNaturalUnits(bool n){naturalUnits=n;}
void setMDNaturalUnits(bool n){MDnaturalUnits=n;}
- Vector & modifyPosition(AtomNumber i){ return positions[i.index()];}
};
inline
@@ -204,7 +204,7 @@ const int & Atoms::getNatoms()const{
inline
bool Atoms::isVirtualAtom(AtomNumber i)const{
- return i.index()>=getNatoms();
+ return i.index()>=(unsigned) getNatoms();
}
inline
diff --git a/src/core/CLTool.cpp b/src/core/CLTool.cpp
index 598d56d1d20711e0e1be0a69f33ab3d570091ed1..ca9d55261f7be147a347bea056d87068bd888df5 100644
--- a/src/core/CLTool.cpp
+++ b/src/core/CLTool.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -72,7 +72,7 @@ bool CLTool::readCommandLineArgs( int argc, char**argv, FILE*out ){
std::string prefix(""), a(""), thiskey;
// Set all flags to default false
- for(int k=0;k<keywords.size();++k){
+ for(unsigned k=0;k<keywords.size();++k){
thiskey=keywords.get(k);
if( keywords.style(thiskey,"flag") ) inputData.insert(std::pair<std::string,std::string>(thiskey,"false"));
}
@@ -86,7 +86,7 @@ bool CLTool::readCommandLineArgs( int argc, char**argv, FILE*out ){
printhelp=true;
} else {
bool found=false;
- for(int k=0;k<keywords.size();++k){
+ for(unsigned k=0;k<keywords.size();++k){
thiskey=keywords.get(k);
if( keywords.style(thiskey,"flag") ){
if( a==thiskey ){ found=true; inputData[thiskey]="true"; }
@@ -127,7 +127,7 @@ bool CLTool::readCommandLineArgs( int argc, char**argv, FILE*out ){
void CLTool::setRemainingToDefault(FILE* out){
std::string def, thiskey;
- for(int k=0;k<keywords.size();++k){
+ for(unsigned k=0;k<keywords.size();++k){
thiskey=keywords.get(k);
if( keywords.style(thiskey,"compulsory") ){
if( inputData.count(thiskey)==0 ){
@@ -174,7 +174,7 @@ bool CLTool::readInputFile( int argc, char**argv, FILE* in, FILE*out ){
char buffer[256]; std::string line; line.resize(256);
while(fgets(buffer,256,mystdin)){
line=buffer;
- for(int i=0;i<line.length();++i) if(line[i]=='#' || line[i]=='\n') line.erase(i);
+ for(unsigned i=0;i<line.length();++i) if(line[i]=='#' || line[i]=='\n') line.erase(i);
Tools::stripLeadingAndTrailingBlanks( line );
if(line.length()==0) continue;
sscanf(line.c_str(),"%255s",buffer);
diff --git a/src/core/CLTool.h b/src/core/CLTool.h
index 3a1f5291e953a931fc52df4a92775353fc43b266..59f440dce570ada74fbcb0c2c2cfbbe6ca6976d4 100644
--- a/src/core/CLTool.h
+++ b/src/core/CLTool.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/CLToolMain.cpp b/src/core/CLToolMain.cpp
index 9d13933d593148b90e934647d961c0a31b1e5186..1d2fa942c2f096b0c42e3b6fae7db5a364aa8008 100644
--- a/src/core/CLToolMain.cpp
+++ b/src/core/CLToolMain.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -126,6 +126,10 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,Communicator& pc){
return (config::hasCregex()?0:1);
} else if(a=="--has-dlopen"){
return (config::hasDlopen()?0:1);
+ } else if(a=="--has-molfile"){
+ return (config::hasMolfile()?0:1);
+ } else if(a=="--is-installed"){
+ return (config::isInstalled()?0:1);
} else if(a=="--no-mpi"){
// this is ignored, as it is parsed in main
if(i>1){
@@ -184,6 +188,7 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,Communicator& pc){
" plumed [command] -h|--help: to print help for a specific command\n"
"Options:\n"
" [help|-h|--help] : to print this help\n"
+ " [--is-installed] : fails if plumed is not installed\n"
" [--has-mpi] : fails if plumed is running without MPI\n"
" [--has-matheval] : fails if plumed is compiled without matheval\n"
" [--has-almost] : fails if plumed is compiled without almost\n"
diff --git a/src/core/CLToolMain.h b/src/core/CLToolMain.h
index 6b8a41eeb2a6f026a44de477c474fb346d3277a6..05298a17fa949507c09654235b341ccc65c09d40 100644
--- a/src/core/CLToolMain.h
+++ b/src/core/CLToolMain.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/CLToolRegister.cpp b/src/core/CLToolRegister.cpp
index 62b88eed6835a3442248542fb04edeeaf46fe0ab..eed2a216afeb30dc2e325af258c366691a5dc735 100644
--- a/src/core/CLToolRegister.cpp
+++ b/src/core/CLToolRegister.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/CLToolRegister.h b/src/core/CLToolRegister.h
index fcd138695af0406f0e71f300075baacbf02a1a76..40ba1c7c012a740d66ad492404111990eb5adfed 100644
--- a/src/core/CLToolRegister.h
+++ b/src/core/CLToolRegister.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/Colvar.cpp b/src/core/Colvar.cpp
index fcbfe1d52ff9040ccb6e38bb25c99c452b8abcf7..116d8ab70cc7d31fb1643cbbd79ab0e79b918c3d 100644
--- a/src/core/Colvar.cpp
+++ b/src/core/Colvar.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/Colvar.h b/src/core/Colvar.h
index d0ec27ddebb2f4dcc8c7b02936778c12870410c2..15e3a3dd9765be6dc2e55db3fad1f1542b21b511 100644
--- a/src/core/Colvar.h
+++ b/src/core/Colvar.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ExchangePatterns.cpp b/src/core/ExchangePatterns.cpp
index 897fa15869f7fb65c8ffee229f292b2adbadfc07..c59afebaaa391ef96a24bfe75fc5d80d354ec8f5 100644
--- a/src/core/ExchangePatterns.cpp
+++ b/src/core/ExchangePatterns.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/ExchangePatterns.h b/src/core/ExchangePatterns.h
index 5276c97b2e9cf8f514b54762a00c1daf0f2b40cb..c338893c9a0b39b28aef6d7c457f4b6c17261fd5 100644
--- a/src/core/ExchangePatterns.h
+++ b/src/core/ExchangePatterns.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/FlexibleBin.cpp b/src/core/FlexibleBin.cpp
index 7e2ad6e0a970334063d77b904437df064343b9b5..d90620338f53bee50fbd2d2d163d7d9e1c39133b 100644
--- a/src/core/FlexibleBin.cpp
+++ b/src/core/FlexibleBin.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -195,7 +195,7 @@ vector<double> FlexibleBin::getInverseMatrix() const{
for (i=0;i<ncv;i++){//loop on the dimension
// find the largest one: if it is smaller than min then rescale
if( limitmin[i] ){
- unsigned imax;
+ unsigned imax=0;
double fmax=-1.e10;
for (j=0;j<ncv;j++){//loop on components
double fact=pow(eigenvals[j]*eigenvecs[j][i],2);
diff --git a/src/core/FlexibleBin.h b/src/core/FlexibleBin.h
index 472264981a2548a4b173dc5596b76e11d020c1f4..b17228d20d7e99f16828fa24e37f9e787785d34e 100644
--- a/src/core/FlexibleBin.h
+++ b/src/core/FlexibleBin.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/GREX.cpp b/src/core/GREX.cpp
index f2cd77e606b7885708870d212d3ae7fdacf6e3e5..b9097ede74514b01a9e93d422ba7aa8ee159d601 100644
--- a/src/core/GREX.cpp
+++ b/src/core/GREX.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -79,13 +79,13 @@ void GREX::cmd(const string&key,void*val){
std::string s;
// note that for PEs!=root this is automatically 0 (comm defaults to MPI_COMM_SELF)
myreplica=intercomm.Get_rank();
- intracomm.Sum(&myreplica,1);
+ intracomm.Sum(myreplica);
Tools::convert(myreplica,s);
plumedMain.setSuffix("."+s);
}else if(key=="prepare"){
CHECK_INIT(initialized,key);
if(intracomm.Get_rank()==0) return;
- intracomm.Bcast(&partner,1,0);
+ intracomm.Bcast(partner,0);
calculate();
}else if(key=="setPartner"){
CHECK_INIT(initialized,key);
@@ -96,7 +96,7 @@ void GREX::cmd(const string&key,void*val){
}else if(key=="calculate"){
CHECK_INIT(initialized,key);
if(intracomm.Get_rank()!=0) return;
- intracomm.Bcast(&partner,1,0);
+ intracomm.Bcast(partner,0);
calculate();
}else if(key=="getLocalDeltaBias"){
CHECK_INIT(initialized,key);
@@ -109,14 +109,14 @@ void GREX::cmd(const string&key,void*val){
double x;
atoms.MD2double(val,x);
localUNow=x*(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy());
- intracomm.Sum(&localUNow,1);
+ intracomm.Sum(localUNow);
}else if(key=="cacheLocalUSwap"){
CHECK_INIT(initialized,key);
CHECK_NULL(val,key);
double x;
atoms.MD2double(val,x);
localUSwap=x*(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy());
- intracomm.Sum(&localUSwap,1);
+ intracomm.Sum(localUSwap);
}else if(key=="getForeignDeltaBias"){
CHECK_INIT(initialized,key);
CHECK_NULL(val,key);
@@ -127,7 +127,7 @@ void GREX::cmd(const string&key,void*val){
if(intracomm.Get_rank()!=0) return;
allDeltaBias.assign(intercomm.Get_size(),0.0);
allDeltaBias[intercomm.Get_rank()]=localDeltaBias;
- intercomm.Sum(&allDeltaBias[0],intercomm.Get_size());
+ intercomm.Sum(allDeltaBias);
}else{
// multi word commands
std::vector<std::string> words=Tools::getWords(key);
@@ -165,11 +165,11 @@ void GREX::calculate(){
vector<char> rbuf(nn);
localDeltaBias=-plumedMain.getBias();
if(intracomm.Get_rank()==0){
- Communicator::Request req=intercomm.Isend(&buffer.c_str()[0],nn,partner,1066);
- intercomm.Recv(&rbuf[0],rbuf.size(),partner,1066);
+ Communicator::Request req=intercomm.Isend(buffer,partner,1066);
+ intercomm.Recv(rbuf,partner,1066);
req.wait();
}
- intracomm.Bcast(&rbuf[0],nn,0);
+ intracomm.Bcast(rbuf,0);
istringstream i(string(&rbuf[0],rbuf.size()));
atoms.readBinary(i);
plumedMain.setExchangeStep(true);
@@ -179,12 +179,12 @@ void GREX::calculate(){
localDeltaBias+=plumedMain.getBias();
localDeltaBias+=localUSwap-localUNow;
if(intracomm.Get_rank()==0){
- Communicator::Request req=intercomm.Isend(&localDeltaBias,1,partner,1067);
- intercomm.Recv(&foreignDeltaBias,1,partner,1067);
+ Communicator::Request req=intercomm.Isend(localDeltaBias,partner,1067);
+ intercomm.Recv(foreignDeltaBias,partner,1067);
req.wait();
//fprintf(stderr,">>> %d %d %20.12f %20.12f %20.12f %20.12f\n",intercomm.Get_rank(),partner,localDeltaBias,foreignDeltaBias,localUSwap,localUNow);
}
- intracomm.Bcast(&foreignDeltaBias,1,0);
+ intracomm.Bcast(foreignDeltaBias,0);
}
}
diff --git a/src/core/GREX.h b/src/core/GREX.h
index 18a779e4ed19fb020c7a6436707dee519c2772bb..5dcdd8241dea266f6c755c2e15a0fa1e3f137a9a 100644
--- a/src/core/GREX.h
+++ b/src/core/GREX.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/MDAtoms.cpp b/src/core/MDAtoms.cpp
index a55e0a0c0a06113ff3f3b33fa433727578e0956c..890e4a0243341b75ed6c2d4a0bf92e47efbd14ea 100644
--- a/src/core/MDAtoms.cpp
+++ b/src/core/MDAtoms.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/MDAtoms.h b/src/core/MDAtoms.h
index e68cd28d5bd5646227dd8953f08dcd6b23b73ba3..7bf8c9ca95f6d75d9022eefeec3a2874cb472a15 100644
--- a/src/core/MDAtoms.h
+++ b/src/core/MDAtoms.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index 9d87ab894cb3b8da96fa4261e9f481d6add53b60..4ff03880c75e4aa9f1d27746723f1554e87d3e36 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -353,7 +353,7 @@ void PlumedMain::init(){
log<<"PLUMED is starting\n";
log<<"PLUMED compiled on " __DATE__ " at " __TIME__ "\n";
log<<"Please cite this paper when using PLUMED ";
- log<<cite("Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. DOI:10.1016/j.cpc.2013.09.018 (2013)");
+ log<<cite("Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)");
log<<"\n";
log<<"For further information see the PLUMED web page at http://www.plumed-code.org\n";
log.printf("Molecular dynamics engine: %s\n",MDEngine.c_str());
diff --git a/src/core/PlumedMain.h b/src/core/PlumedMain.h
index 3d035399cec118d3bd7cb72e6a937cd3cba19f2e..3ecb3a9d6cfe3cd30329590a4d875ece62f3c6d4 100644
--- a/src/core/PlumedMain.h
+++ b/src/core/PlumedMain.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/PlumedMainInitializer.cpp b/src/core/PlumedMainInitializer.cpp
index 23399a826807635fa241a9ff59601f40fd6b629f..db1d67a3cd435d4531f4178c4f0c63acd3a0cffb 100644
--- a/src/core/PlumedMainInitializer.cpp
+++ b/src/core/PlumedMainInitializer.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/SetupMolInfo.cpp b/src/core/SetupMolInfo.cpp
index ea6be1c7c068896e57eff204084be021dbed5ac2..d0cb3159b961948183d8d01c664f5aceeeda03bf 100644
--- a/src/core/SetupMolInfo.cpp
+++ b/src/core/SetupMolInfo.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -24,6 +24,7 @@
#include "ActionRegister.h"
#include "ActionSet.h"
#include "PlumedMain.h"
+#include "tools/MolDataClass.h"
#include "tools/PDB.h"
@@ -42,6 +43,7 @@ void SetupMolInfo::registerKeywords( Keywords& keys ){
keys.add("compulsory","STRUCTURE","a file in pdb format containing a reference structure. "
"This is used to defines the atoms in the various residues, chains, etc . "
"For more details on the PDB file format visit http://www.wwpdb.org/docs.html");
+ keys.add("compulsory","MOLTYPE","protein","what kind of molecule is contained in the pdb file");
keys.add("atoms","CHAIN","(for masochists ( mostly Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure.");
}
@@ -55,6 +57,9 @@ ActionSetup(ao),
ActionAtomistic(ao),
pdb(*new(PDB))
{
+ // Read what is contained in the pdb file
+ parse("MOLTYPE",mytype);
+
std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
if( moldat.size()!=0 ) error("cannot use more than one MOLINFO action in input");
@@ -73,8 +78,8 @@ pdb(*new(PDB))
if( read_backbone.size()==0 ){
std::string reference; parse("STRUCTURE",reference);
-
if( ! pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/plumed.getAtoms().getUnits().getLength()))plumed_merror("missing input file " + reference );
+
std::vector<std::string> chains; pdb.getChainNames( chains );
log.printf(" pdb file named %s contains %d chains \n",reference.c_str(), chains.size() );
for(unsigned i=0;i<chains.size();++i){
@@ -87,10 +92,13 @@ pdb(*new(PDB))
log.printf(" chain named %s contains residues %u to %u and atoms %d to %d \n",chains[i].c_str(),start,end,astart.serial(),aend.serial());
}
}
- pdb.renameAtoms("HA1","CB"); // This is a hack to make this work with GLY residues
}
-void SetupMolInfo::getBackbone( std::vector<std::string>& restrings, const std::vector<std::string>& atnames, std::vector< std::vector<AtomNumber> >& backbone ){
+void SetupMolInfo::getBackbone( std::vector<std::string>& restrings, const std::string& fortype, std::vector< std::vector<AtomNumber> >& backbone ){
+ if( fortype!=mytype ) error("cannot calculate a variable designed for " + fortype + " molecules for molecule type " + mytype );
+ if( MolDataClass::numberOfAtomsPerResidueInBackbone( mytype )==0 ) error("backbone is not defined for molecule type " + mytype );
+ bool useter=false; // This is used to deal with terminal groups in WHOLEMOLECULES
+
if( read_backbone.size()!=0 ){
if( restrings.size()!=1 ) error("cannot interpret anything other than all for residues when using CHAIN keywords");
if( restrings[0]!="all" ) error("cannot interpret anything other than all for residues when using CHAIN keywords");
@@ -101,11 +109,18 @@ void SetupMolInfo::getBackbone( std::vector<std::string>& restrings, const std::
}
} else {
if( restrings.size()==1 ){
- if( restrings[0]=="all" ){
+ useter=( restrings[0].find("ter")!=std::string::npos );
+ if( restrings[0].find("all")!=std::string::npos ){
std::vector<std::string> chains; pdb.getChainNames( chains );
for(unsigned i=0;i<chains.size();++i){
unsigned r_start, r_end; std::string errmsg, mm, nn;
pdb.getResidueRange( chains[i], r_start, r_end, errmsg );
+ if( !useter ){
+ std::string resname = pdb.getResidueName( r_start );
+ if( MolDataClass::isTerminalGroup( mytype, resname ) ) r_start++;
+ resname = pdb.getResidueName( r_end );
+ if( MolDataClass::isTerminalGroup( mytype, resname ) ) r_end--;
+ }
Tools::convert(r_start,mm); Tools::convert(r_end,nn);
if(i==0) restrings[0] = mm + "-" + nn;
else restrings.push_back( mm + "-" + nn );
@@ -131,28 +146,35 @@ void SetupMolInfo::getBackbone( std::vector<std::string>& restrings, const std::
// And now get the backbone atoms from each segment
backbone.resize( segments.size() );
- std::vector<AtomNumber> atomnumbers( atnames.size() );
+ std::vector<std::string> atnames; std::vector<AtomNumber> atomnumbers;
for(unsigned i=0;i<segments.size();++i){
for(unsigned j=0;j<segments[i].size();++j){
- bool terminus=( j==0 || j==segments[i].size()-1 );
- bool foundatoms=pdb.getBackbone( segments[i][j], atnames, atomnumbers );
- if( terminus && !foundatoms ){
+ std::string resname=pdb.getResidueName( segments[i][j] );
+ if( !MolDataClass::allowedResidue(mytype, resname) ){
std::string num; Tools::convert( segments[i][j], num );
- warning("Assuming residue " + num + " is a terminal group");
- } else if( !foundatoms ){
+ error("residue " + num + " is not recognized for moltype " + mytype );
+ }
+ if( !useter && MolDataClass::isTerminalGroup( mytype, resname ) ){
+ std::string num; Tools::convert( segments[i][j], num );
+ error("residue " + num + " appears to be a terminal group");
+ }
+ if( resname=="GLY" ) warning("GLY residues are achiral - assuming HA1 atom is in CB position");
+ MolDataClass::getBackboneForResidue( mytype, segments[i][j], pdb, atomnumbers );
+ if( atomnumbers.size()==0 ){
std::string num; Tools::convert( segments[i][j], num );
error("Could not find required backbone atom in residue number " + num );
- } else if( foundatoms ){
+ } else {
for(unsigned k=0;k<atomnumbers.size();++k) backbone[i].push_back( atomnumbers[k] );
}
+ atomnumbers.resize(0);
}
}
}
- for(unsigned i=0;i<backbone.size();++i){
- if( backbone[i].size()%atnames.size()!=0 ) error("number of atoms in one of the segments of backbone is not a multiple of the number of atoms in each residue");
- }
}
+void SetupMolInfo::interpretSymbol( const std::string& symbol, std::vector<AtomNumber>& atoms )const{
+ MolDataClass::specialSymbol( mytype, symbol, pdb, atoms );
+}
std::string SetupMolInfo::getAtomName(AtomNumber a)const{
return pdb.getAtomName(a);
diff --git a/src/core/SetupMolInfo.h b/src/core/SetupMolInfo.h
index b3b0253c1396d92c766583bb8d674826cc867f67..fb94da89825a959581ab10c646b8da26b801dea5 100644
--- a/src/core/SetupMolInfo.h
+++ b/src/core/SetupMolInfo.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -34,16 +34,21 @@ class SetupMolInfo :
public ActionSetup,
public ActionAtomistic {
private:
+/// A pdb file containing the topology
PDB& pdb;
+/// The type of molecule in the pdb
+ std::string mytype;
+/// The backbone that was read in from the pdb file
std::vector< std::vector<AtomNumber> > read_backbone;
public:
~SetupMolInfo();
static void registerKeywords( Keywords& keys );
SetupMolInfo(const ActionOptions&ao);
- void getBackbone( std::vector<std::string>& resstrings, const std::vector<std::string>& atnames, std::vector< std::vector<AtomNumber> >& backbone );
+ void getBackbone( std::vector<std::string>& resstrings, const std::string& fortype, std::vector< std::vector<AtomNumber> >& backbone );
std::string getAtomName(AtomNumber a)const;
unsigned getResidueNumber(AtomNumber a)const;
std::string getResidueName(AtomNumber a)const;
+ void interpretSymbol( const std::string& symbol, std::vector<AtomNumber>& atoms )const;
};
}
diff --git a/src/core/TargetDist.cpp b/src/core/TargetDist.cpp
index 54121ad4cf11bc4c7e8156405def1b09d8587ba0..bcca57595165d0ddbad57d08cd2cef650fbccefa 100644
--- a/src/core/TargetDist.cpp
+++ b/src/core/TargetDist.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/TargetDist.h b/src/core/TargetDist.h
index 0a9674e5293137f75a4688da4df6d1619088a733..6c46bcaaebe6dd6b95954b39d97b00faca308041 100644
--- a/src/core/TargetDist.h
+++ b/src/core/TargetDist.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/Value.cpp b/src/core/Value.cpp
index ce57b3371f715edd55efd123032a458034085dd8..63c0f0d7786963d0b5f33a13d31d5b2eab9508bb 100644
--- a/src/core/Value.cpp
+++ b/src/core/Value.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/Value.h b/src/core/Value.h
index dbf1fd85bf77a865c6b8fadb015834e06b3a40c0..76159e911cbb58722d05d226e135bb27c0d2ee7a 100644
--- a/src/core/Value.h
+++ b/src/core/Value.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/core/WithCmd.h b/src/core/WithCmd.h
index bf84fb7116bfcfd80d04377320b195f49069d3ea..17fcdfd0c5a0474e6f7cf04e9444a49730062f7c 100644
--- a/src/core/WithCmd.h
+++ b/src/core/WithCmd.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/crystallization/.gitignore b/src/crystallization/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..4888552338441b5d99a97ec7a2cb2ce448e9e4e6
--- /dev/null
+++ b/src/crystallization/.gitignore
@@ -0,0 +1,9 @@
+/*
+# in this directory, only accept source, Makefile and README
+!/.gitignore
+!/*.c
+!/*.cpp
+!/*.h
+!/Makefile
+!/README
+!/module.type
diff --git a/src/crystallization/LocalSteinhardt.h b/src/crystallization/LocalSteinhardt.h
new file mode 100644
index 0000000000000000000000000000000000000000..ffd5becad80f9aeae3e7d6b5f8849d1132140c4f
--- /dev/null
+++ b/src/crystallization/LocalSteinhardt.h
@@ -0,0 +1,44 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_crystallization_LocalSteinhardt_h
+#define __PLUMED_crystallization_LocalSteinhardt_h
+#include "OrientationSphere.h"
+
+namespace PLMD {
+namespace crystallization {
+
+template<class T>
+class LocalSteinhardt : public OrientationSphere {
+public:
+ static void registerKeywords( Keywords& keys ){
+ OrientationSphere::registerKeywords(keys);
+ }
+ LocalSteinhardt(const ActionOptions& ao): Action(ao), OrientationSphere(ao)
+ {
+ T* mc=dynamic_cast<T*>( getBaseMultiColvar(0) );
+ if(!mc) error("input action is not calculating the correct vectors");
+ }
+};
+
+}
+}
+#endif
diff --git a/src/crystallization/Makefile b/src/crystallization/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..f68246671ed0ea23ad4d282dde1568ae2024d9e4
--- /dev/null
+++ b/src/crystallization/Makefile
@@ -0,0 +1,4 @@
+USE=core tools vesselbase multicolvar
+
+# generic makefile
+include ../maketools/make.module
diff --git a/src/crystallization/MoleculeOrientation.cpp b/src/crystallization/MoleculeOrientation.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..72e07c081b89bf9a166160f08fafa020ff4e5ab2
--- /dev/null
+++ b/src/crystallization/MoleculeOrientation.cpp
@@ -0,0 +1,115 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "core/ActionRegister.h"
+#include "VectorMultiColvar.h"
+
+namespace PLMD {
+namespace crystallization {
+
+//+PLUMEDOC MCOLVAR MOLECULES
+/*
+Calculate the vectors connecting a pair of atoms in order to represent the orientation of a molecule.
+
+At its simplest this command can be used to calculate the average length of an internal vector in a
+collection of different molecules. When used in conjunction with MutiColvarFunctions in can be used
+to do a variety of more complex tasks.
+
+\par Examples
+
+The following input tells plumed to calculate the distances between two of the atoms in a molecule.
+This is done for the same set of atoms four different molecules and the average separation is then
+calculated.
+
+\verbatim
+MOLECULES MOL1=1,2 MOL2=3,4 MOL3=5,6 MOL4=7,8 MEAN LABEL=mm
+PRINT ARG=mm.mean FILE=colvar
+\endverbatim
+
+
+*/
+//+ENDPLUMEDOC
+
+
+class MoleculeOrientation : public VectorMultiColvar {
+private:
+public:
+ static void registerKeywords( Keywords& keys );
+ MoleculeOrientation( const ActionOptions& ao );
+ void calculateVector();
+ Vector getCentralAtom();
+};
+
+PLUMED_REGISTER_ACTION(MoleculeOrientation,"MOLECULES")
+
+void MoleculeOrientation::registerKeywords( Keywords& keys ){
+ VectorMultiColvar::registerKeywords( keys ); keys.use("MEAN");
+ keys.add("numbered","MOL","The numerical indices of the atoms in the molecule. The orientation of the molecule is equal to "
+ "the vector connecting the first two atoms specified. If a third atom is specified its position "
+ "is used to specify where the molecule is. If a third atom is not present the molecule is assumed "
+ "to be at the center of the vector connecting the first two atoms.");
+ keys.reset_style("MOL","atoms");
+}
+
+MoleculeOrientation::MoleculeOrientation( const ActionOptions& ao ):
+Action(ao),
+VectorMultiColvar(ao)
+{
+ int natoms=-1;
+ readAtomsLikeKeyword("MOL",natoms);
+ if( natoms!=2 && natoms!=3 ) error("number of atoms in molecule specification is wrong. Should be two or three.");
+ setVectorDimensionality( 3, false, natoms );
+}
+
+void MoleculeOrientation::calculateVector(){
+ Vector distance; distance=getSeparation( getPosition(0), getPosition(1) );
+
+ addAtomsDerivative( 0, 0, Vector(-1.0,0,0) );
+ addAtomsDerivative( 0, 1, Vector(+1.0,0,0) );
+ addBoxDerivatives( 0, Tensor(distance,Vector(-1.0,0,0)) );
+ addComponent( 0, distance[0] );
+
+ addAtomsDerivative( 1, 0, Vector(0,-1.0,0) );
+ addAtomsDerivative( 1, 1, Vector(0,+1.0,0) );
+ addBoxDerivatives( 1, Tensor(distance,Vector(0,-1.0,0)) );
+ addComponent( 1, distance[1] );
+
+ addAtomsDerivative( 2, 0, Vector(0,0,-1.0) );
+ addAtomsDerivative( 2, 1, Vector(0,0,+1.0) );
+ addBoxDerivatives( 2, Tensor(distance,Vector(0,0,-1.0)) );
+ addComponent( 2, distance[2] );
+}
+
+Vector MoleculeOrientation::getCentralAtom(){
+ if( getNAtoms()==2 ){
+ Vector com; com.zero();
+ com+=0.5*getPosition(0);
+ com+=0.5*getPosition(1);
+ addCentralAtomDerivatives( 0, 0.5*Tensor::identity() );
+ addCentralAtomDerivatives( 1, 0.5*Tensor::identity() );
+ return com;
+ }
+ addCentralAtomDerivatives( 2, Tensor::identity() );
+ return getPosition(2);
+}
+
+}
+}
diff --git a/src/crystallization/OrientationSphere.cpp b/src/crystallization/OrientationSphere.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..85dd895160a36184347a496541d0201ae78e01d9
--- /dev/null
+++ b/src/crystallization/OrientationSphere.cpp
@@ -0,0 +1,138 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "VectorMultiColvar.h"
+#include "OrientationSphere.h"
+
+using namespace std;
+
+namespace PLMD{
+namespace crystallization {
+
+void OrientationSphere::registerKeywords( Keywords& keys ){
+ multicolvar::MultiColvarFunction::registerKeywords( keys );
+ keys.add("compulsory","NN","6","The n parameter of the switching function ");
+ keys.add("compulsory","MM","12","The m parameter of the switching function ");
+ keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
+ keys.add("compulsory","R_0","The r_0 parameter of the switching function");
+ keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. "
+ "The following provides information on the \\ref switchingfunction that are available. "
+ "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
+ // Use actionWithDistributionKeywords
+ keys.use("MEAN"); keys.use("MORE_THAN"); keys.use("LESS_THAN");
+ keys.use("MIN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
+}
+
+OrientationSphere::OrientationSphere(const ActionOptions&ao):
+Action(ao),
+MultiColvarFunction(ao)
+{
+ // Resize everything that stores a vector now that we know the
+ // number of components
+ unsigned ncomponents=getBaseMultiColvar(0)->getNumberOfQuantities() - 5;
+ catom_orient.resize( ncomponents );
+ catom_der.resize( ncomponents );
+ this_orient.resize( ncomponents );
+
+ // Weight of this does not have derivatives
+ weightHasDerivatives=false;
+ // Read in the switching function
+ std::string sw, errors; parse("SWITCH",sw);
+ if(sw.length()>0){
+ switchingFunction.set(sw,errors);
+ } else {
+ double r_0=-1.0, d_0; int nn, mm;
+ parse("NN",nn); parse("MM",mm);
+ parse("R_0",r_0); parse("D_0",d_0);
+ if( r_0<0.0 ) error("you must set a value for R_0");
+ switchingFunction.set(nn,mm,r_0,d_0);
+ }
+ log.printf(" degree of overlap in orientation between central molecule and those within %s\n",( switchingFunction.description() ).c_str() );
+
+ // Finish the setup of the object
+ buildSymmetryFunctionLists( true );
+
+ // And check everything has been read in correctly
+ checkRead();
+}
+
+void OrientationSphere::calculateWeight(){
+ weightHasDerivatives=true; // The weight has no derivatives really
+ setElementValue(1,1.0);
+}
+
+double OrientationSphere::compute(){
+ // Make sure derivatives for central atom are only calculated once
+ VectorMultiColvar* vv = dynamic_cast<VectorMultiColvar*>( getBaseMultiColvar(0) );
+ vv->firstcall=true;
+
+ weightHasDerivatives=true; // The weight has no derivatives really
+ double sw, value=0, denom=0, dot, f_dot, dot_df, dfunc; Vector distance;
+
+ getValueForBaseTask(0, catom_orient );
+ for(unsigned i=1;i<getNAtoms();++i){
+ distance=getSeparation( getPositionOfCentralAtom(0), getPositionOfCentralAtom(i) );
+ sw = switchingFunction.calculateSqr( distance.modulo2(), dfunc );
+ if( sw>=getTolerance() ){
+ getValueForBaseTask( i, this_orient );
+ // Calculate the dot product wrt to this position
+ dot=0; for(unsigned k=0;k<catom_orient.size();++k) dot+=catom_orient[k]*this_orient[k];
+ f_dot = transformDotProduct( dot, dot_df );
+ // N.B. We are assuming here that the imaginary part of the dot product is zero
+ for(unsigned k=0;k<catom_orient.size();++k){
+ this_orient[k]*=sw*dot_df; catom_der[k]=sw*dot_df*catom_orient[k];
+ }
+
+ // Set the derivatives wrt of the numerator
+ addOrientationDerivatives( 0, this_orient );
+ addOrientationDerivatives( i, catom_der );
+ addCentralAtomsDerivatives( 0, 0, f_dot*(-dfunc)*distance );
+ addCentralAtomsDerivatives( i, 0, f_dot*(dfunc)*distance );
+ addBoxDerivatives( f_dot*(-dfunc)*Tensor(distance,distance) );
+ value += sw*f_dot;
+ // Set the derivatives wrt to the numerator
+ addCentralAtomsDerivatives( 0, 1, (-dfunc)*distance );
+ addCentralAtomsDerivatives( i, 1, (dfunc)*distance );
+ addBoxDerivativesOfWeight( (-dfunc)*Tensor(distance,distance) );
+ denom += sw;
+ } else {
+ removeAtomRequest( i, sw );
+ }
+ }
+
+ // Now divide everything
+ unsigned nder = getNumberOfDerivatives();
+ for(unsigned i=0;i<nder;++i){
+ setElementDerivative( i, getElementDerivative(i)/denom - (value*getElementDerivative(nder+i))/(denom*denom) );
+ setElementDerivative( nder + i, 0.0 );
+ }
+ weightHasDerivatives=false; // Weight has no derivatives we just use the holder for weight to store some stuff
+ return value / denom;
+}
+
+Vector OrientationSphere::getCentralAtom(){
+ addDerivativeOfCentralAtomPos( 0, Tensor::identity() );
+ return getPositionOfCentralAtom(0);
+}
+
+}
+}
+
diff --git a/src/crystallization/OrientationSphere.h b/src/crystallization/OrientationSphere.h
new file mode 100644
index 0000000000000000000000000000000000000000..e11548a027d36b9fb2c9be4d376252a045bf6c1e
--- /dev/null
+++ b/src/crystallization/OrientationSphere.h
@@ -0,0 +1,56 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_crystallization_OrientationSphere_h
+#define __PLUMED_crystallization_OrientationSphere_h
+
+#include "multicolvar/MultiColvarFunction.h"
+#include "tools/SwitchingFunction.h"
+
+#include <string>
+#include <cmath>
+
+namespace PLMD {
+namespace crystallization {
+
+class OrientationSphere : public multicolvar::MultiColvarFunction {
+private:
+ std::vector<double> catom_orient, catom_der, this_orient;
+ std::vector<double> catom_iorient, catom_ider, this_iorient;
+ SwitchingFunction switchingFunction;
+public:
+ static void registerKeywords( Keywords& keys );
+ OrientationSphere(const ActionOptions&);
+ double compute();
+ void calculateWeight();
+ virtual double transformDotProduct( const double& dot, double& df );
+ Vector getCentralAtom();
+ bool isPeriodic(){ return false; }
+};
+
+inline
+double OrientationSphere::transformDotProduct( const double& dot, double& df ){
+ df=1.0; return dot;
+}
+
+}
+}
+#endif
diff --git a/src/crystallization/Q4.cpp b/src/crystallization/Q4.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..cdc7b8222dc3f8f3d9d269345711318dbc6b7b47
--- /dev/null
+++ b/src/crystallization/Q4.cpp
@@ -0,0 +1,82 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "Steinhardt.h"
+#include "LocalSteinhardt.h"
+#include "core/ActionRegister.h"
+
+//+PLUMEDOC MCOLVAR Q4
+/*
+Calculate 4th order Steinhardt parameters.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+//+PLUMEDOC MCOLVARF LOCAL_Q4
+/*
+Calculate 4th order Steinhardt parameters.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+namespace PLMD {
+namespace crystallization {
+
+class Q4 : public Steinhardt {
+public:
+ static void registerKeywords( Keywords& keys );
+ Q4( const ActionOptions& ao );
+};
+
+PLUMED_REGISTER_ACTION(Q4,"Q4")
+typedef LocalSteinhardt<Q4> LOCAL_Q4;
+PLUMED_REGISTER_ACTION(LOCAL_Q4,"LOCAL_Q4")
+
+void Q4::registerKeywords( Keywords& keys ){
+ Steinhardt::registerKeywords( keys );
+}
+
+Q4::Q4(const ActionOptions& ao ):
+Action(ao),
+Steinhardt(ao)
+{
+ setAngularMomentum(4);
+
+ normaliz.resize( 5 );
+ normaliz[0] = sqrt( ( 9.0*24.0 ) / (4.0*pi*24.0) );
+ normaliz[1] = -sqrt( ( 9.0*6.0 ) / (4.0*pi*120.0) );
+ normaliz[2] = sqrt( ( 9.0*2.0) / (4.0*pi*720.0) );
+ normaliz[3] = -sqrt( ( 9.0*1) / (4.0*pi*5040.0) );
+ normaliz[4] = sqrt( (9.0*1) / (4.0*pi*40320.0) );
+
+ coeff_poly.resize( 5 );
+ coeff_poly[0]=0.375; coeff_poly[1]=0.0;
+ coeff_poly[2]=-3.75; coeff_poly[3]=0.0;
+ coeff_poly[4]=4.375;
+}
+
+}
+}
+
diff --git a/src/crystallization/Q6.cpp b/src/crystallization/Q6.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..90b5f7001b909bf28b8b19a0fd5988c0bbf4bd66
--- /dev/null
+++ b/src/crystallization/Q6.cpp
@@ -0,0 +1,85 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "Steinhardt.h"
+#include "LocalSteinhardt.h"
+#include "core/ActionRegister.h"
+
+//+PLUMEDOC MCOLVAR Q6
+/*
+Calculate 6th order Steinhardt parameters.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+//+PLUMEDOC MCOLVARF LOCAL_Q6
+/*
+Calculate 4th order Steinhardt parameters.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+namespace PLMD {
+namespace crystallization {
+
+class Q6 : public Steinhardt {
+public:
+ static void registerKeywords( Keywords& keys );
+ Q6( const ActionOptions& ao );
+};
+
+PLUMED_REGISTER_ACTION(Q6,"Q6")
+typedef LocalSteinhardt<Q6> LOCAL_Q6;
+PLUMED_REGISTER_ACTION(LOCAL_Q6,"LOCAL_Q6")
+
+void Q6::registerKeywords( Keywords& keys ){
+ Steinhardt::registerKeywords( keys );
+}
+
+Q6::Q6(const ActionOptions& ao ):
+Action(ao),
+Steinhardt(ao)
+{
+ setAngularMomentum(6);
+
+ normaliz.resize( 7 );
+ normaliz[0] = sqrt( ( 13.0*720.0 ) / (4.0*pi*720.0) );
+ normaliz[1] = -sqrt( ( 13.0*120.0 ) / (4.0*pi*5040) );
+ normaliz[2] = sqrt( ( 13.0*24) / (4.0*pi*40320) );
+ normaliz[3] = -sqrt( ( 13.0*6) / (4.0*pi*362880) );
+ normaliz[4] = sqrt( (13.0*2) / (4.0*pi*3628800) );
+ normaliz[5] = -sqrt( (13.0*1) / (4.0*pi*39916800) );
+ normaliz[6] = sqrt( (13.0*1) / (4.0*pi*479001600) );
+
+ coeff_poly.resize( 7 );
+ coeff_poly[0]=-0.3125; coeff_poly[1]=0.0;
+ coeff_poly[2]=6.5625; coeff_poly[3]=0.0;
+ coeff_poly[4]=-19.6875; coeff_poly[5]=0.0;
+ coeff_poly[6]=14.4375;
+}
+
+}
+}
+
diff --git a/src/crystallization/Steinhardt.cpp b/src/crystallization/Steinhardt.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..1b0f1d49652b3248dc9231e7a4f9a5ad16039445
--- /dev/null
+++ b/src/crystallization/Steinhardt.cpp
@@ -0,0 +1,186 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include <complex>
+#include "Steinhardt.h"
+
+namespace PLMD {
+namespace crystallization {
+
+void Steinhardt::registerKeywords( Keywords& keys ){
+ VectorMultiColvar::registerKeywords( keys );
+ keys.add("compulsory","NN","12","The n parameter of the switching function ");
+ keys.add("compulsory","MM","24","The m parameter of the switching function ");
+ keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
+ keys.add("compulsory","R_0","The r_0 parameter of the switching function");
+ keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. "
+ "The following provides information on the \\ref switchingfunction that are available. "
+ "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
+ keys.use("SPECIES"); keys.use("SPECIESA"); keys.use("SPECIESB");
+ keys.use("MEAN"); keys.use("LESS_THAN"); keys.use("MORE_THAN");
+ keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS"); keys.use("MIN");
+}
+
+Steinhardt::Steinhardt( const ActionOptions& ao ):
+Action(ao),
+VectorMultiColvar(ao)
+{
+ // Read in the switching function
+ std::string sw, errors; parse("SWITCH",sw);
+ if(sw.length()>0){
+ switchingFunction.set(sw,errors);
+ } else {
+ double r_0=-1.0, d_0; int nn, mm;
+ parse("NN",nn); parse("MM",mm);
+ parse("R_0",r_0); parse("D_0",d_0);
+ if( r_0<0.0 ) error("you must set a value for R_0");
+ switchingFunction.set(nn,mm,r_0,d_0);
+ }
+ log.printf(" Steinhardt parameter of central atom and those within %s\n",( switchingFunction.description() ).c_str() );
+}
+
+void Steinhardt::setAngularMomentum( const unsigned& ang ){
+ tmom=ang; setVectorDimensionality( 2*ang + 1, true, 2 );
+}
+
+void Steinhardt::calculateVector(){
+ double dfunc, dpoly_ass, md, tq6, itq6, real_z, imag_z;
+ Vector distance, dz, myrealvec, myimagvec, real_dz, imag_dz;
+ // The square root of -1
+ std::complex<double> ii( 0.0, 1.0 ), dp_x, dp_y, dp_z;
+
+ double sw, poly_ass, dlen, nbond=0.0; std::complex<double> powered;
+ for(unsigned i=1;i<getNAtoms();++i){
+ distance=getSeparation( getPosition(0), getPosition(i) );
+ dlen=distance.modulo(); sw = switchingFunction.calculate( dlen, dfunc );
+ if( sw>=getTolerance() ){
+ nbond += sw; // Accumulate total number of bonds
+ double dlen3 = dlen*dlen*dlen;
+
+ // Store derivatives of weight
+ MultiColvarBase::addAtomsDerivatives( 0, getAtomIndex(0), (-dfunc)*distance );
+ MultiColvarBase::addAtomsDerivatives( 0, getAtomIndex(i), (+dfunc)*distance );
+ MultiColvarBase::addBoxDerivatives( 0, (-dfunc)*Tensor( distance,distance ) );
+
+ // Do stuff for m=0
+ poly_ass=deriv_poly( 0, distance[2]/dlen, dpoly_ass );
+ // Derivatives of z/r wrt x, y, z
+ dz = -( distance[2] / dlen3 )*distance; dz[2] += (1.0 / dlen);
+ // Derivative wrt to the vector connecting the two atoms
+ myrealvec = (+sw)*dpoly_ass*dz + poly_ass*(+dfunc)*distance;
+ // Accumulate the derivatives
+ addAtomsDerivative( tmom, 0, -myrealvec );
+ addAtomsDerivative( tmom, i, myrealvec );
+ addBoxDerivatives( tmom, Tensor( -myrealvec,distance ) );
+ // And store the vector function
+ addComponent( tmom, sw*poly_ass );
+
+ // The complex number of which we have to take powers
+ std::complex<double> com1( distance[0]/dlen ,distance[1]/dlen );
+
+ // Do stuff for all other m values
+ for(unsigned m=1;m<=tmom;++m){
+ // Calculate Legendre Polynomial
+ poly_ass=deriv_poly( m, distance[2]/dlen, dpoly_ass );
+ // Calculate powe of complex number
+ powered=pow(com1,m-1); md=static_cast<double>(m);
+ // Real and imaginary parts of z
+ real_z = real(com1*powered); imag_z = imag(com1*powered );
+
+ // Calculate steinhardt parameter
+ tq6=poly_ass*real_z; // Real part of steinhardt parameter
+ itq6=poly_ass*imag_z; // Imaginary part of steinhardt parameter
+
+ // Derivatives wrt ( x/r + iy )^m
+ dp_x = md*powered*( (1.0/dlen)-(distance[0]*distance[0])/dlen3-ii*(distance[0]*distance[1])/dlen3 );
+ dp_y = md*powered*( ii*(1.0/dlen)-(distance[0]*distance[1])/dlen3-ii*(distance[1]*distance[1])/dlen3 );
+ dp_z = md*powered*( -(distance[0]*distance[2])/dlen3-ii*(distance[1]*distance[2])/dlen3 );
+
+ // Derivatives of real and imaginary parts of above
+ real_dz[0] = real( dp_x ); real_dz[1] = real( dp_y ); real_dz[2] = real( dp_z );
+ imag_dz[0] = imag( dp_x ); imag_dz[1] = imag( dp_y ); imag_dz[2] = imag( dp_z );
+
+ // Complete derivative of steinhardt parameter
+ myrealvec = (+sw)*dpoly_ass*real_z*dz + (+dfunc)*distance*tq6 + (+sw)*poly_ass*real_dz;
+ myimagvec = (+sw)*dpoly_ass*imag_z*dz + (+dfunc)*distance*itq6 + (+sw)*poly_ass*imag_dz;
+
+ // Real part
+ addComponent( tmom+m, sw*tq6 );
+ addAtomsDerivative( tmom+m, 0, -myrealvec );
+ addAtomsDerivative( tmom+m, i, myrealvec );
+ addBoxDerivatives( tmom+m, Tensor( -myrealvec,distance ) );
+ // Imaginary part
+ addImaginaryComponent( tmom+m, sw*itq6 );
+ addImaginaryAtomsDerivative( tmom+m, 0, -myimagvec );
+ addImaginaryAtomsDerivative( tmom+m, i, myimagvec );
+ addImaginaryBoxDerivatives( tmom+m, Tensor( -myimagvec,distance ) );
+ // Store -m part of vector
+ double pref=pow(-1.0,m);
+ // -m part of vector is just +m part multiplied by (-1.0)**m and multiplied by complex
+ // conjugate of Legendre polynomial
+ // Real part
+ addComponent( tmom-m, pref*sw*tq6 );
+ addAtomsDerivative( tmom-m, 0, -pref*myrealvec );
+ addAtomsDerivative( tmom-m, i, pref*myrealvec );
+ addBoxDerivatives( tmom-m, pref*Tensor( -myrealvec,distance ) );
+ // Imaginary part
+ addImaginaryComponent( tmom-m, -pref*sw*itq6 );
+ addImaginaryAtomsDerivative( tmom-m, 0, pref*myimagvec );
+ addImaginaryAtomsDerivative( tmom-m, i, -pref*myimagvec );
+ addImaginaryBoxDerivatives( tmom-m, pref*Tensor( myimagvec,distance ) );
+ }
+ } else {
+ removeAtomRequest( i, sw );
+ }
+ }
+
+ // Normalize
+ setElementValue(0, nbond ); updateActiveAtoms();
+ for(unsigned i=0;i<2*getNumberOfComponentsInVector();++i) quotientRule( 5+i, 0, 5+i );
+ // Clear tempory stuff
+ clearDerivativesAfterTask(0);
+}
+
+double Steinhardt::deriv_poly( const unsigned& m, const double& val, double& df ){
+ double fact=1.0;
+ for(unsigned j=1;j<=m;++j) fact=fact*j;
+ double res=coeff_poly[m]*fact;
+
+ double pow=1.0, xi=val, dxi=1.0; df=0.0;
+ for(int i=m+1;i<=tmom;++i){
+ double fact=1.0;
+ for(unsigned j=i-m+1;j<=i;++j) fact=fact*j;
+ res=res+coeff_poly[i]*fact*xi;
+ df = df + pow*coeff_poly[i]*fact*dxi;
+ xi=xi*val; dxi=dxi*val; pow+=1.0;
+ }
+ df = df*normaliz[m];
+ return normaliz[m]*res;
+}
+
+Vector Steinhardt::getCentralAtom(){
+ addCentralAtomDerivatives( 0, Tensor::identity() );
+ return getPosition(0);
+
+}
+
+}
+}
diff --git a/src/crystallization/Steinhardt.h b/src/crystallization/Steinhardt.h
new file mode 100644
index 0000000000000000000000000000000000000000..2f12d92de369ec332c8b33b2039da5ba8d16c51d
--- /dev/null
+++ b/src/crystallization/Steinhardt.h
@@ -0,0 +1,50 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_crystallization_Steinhardt_h
+#define __PLUMED_crystallization_Steinhardt_h
+
+#include <complex>
+#include "tools/SwitchingFunction.h"
+#include "VectorMultiColvar.h"
+
+namespace PLMD {
+namespace crystallization {
+
+class Steinhardt : public VectorMultiColvar {
+private:
+ unsigned tmom;
+ SwitchingFunction switchingFunction;
+protected:
+ std::vector<double> coeff_poly;
+ std::vector<double> normaliz;
+ void setAngularMomentum( const unsigned& ang );
+public:
+ static void registerKeywords( Keywords& keys );
+ Steinhardt( const ActionOptions& ao );
+ void calculateVector();
+ Vector getCentralAtom();
+ double deriv_poly( const unsigned&, const double&, double& );
+};
+
+}
+}
+#endif
diff --git a/src/crystallization/StoreVectorsVessel.cpp b/src/crystallization/StoreVectorsVessel.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..65f9cef76077201eae2bf7525e5128df1fce1af1
--- /dev/null
+++ b/src/crystallization/StoreVectorsVessel.cpp
@@ -0,0 +1,149 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "vesselbase/VesselRegister.h"
+#include "vesselbase/ActionWithVessel.h"
+#include "multicolvar/MultiColvarFunction.h"
+#include "StoreVectorsVessel.h"
+#include "VectorMultiColvar.h"
+
+namespace PLMD {
+namespace crystallization{
+
+void StoreVectorsVessel::registerKeywords( Keywords& keys ){
+ vesselbase::StoreDataVessel::registerKeywords(keys);
+}
+
+StoreVectorsVessel::StoreVectorsVessel( const vesselbase::VesselOptions& da ):
+StoreDataVessel(da),
+store_director(false)
+{
+ vecs=dynamic_cast<VectorMultiColvar*>( getAction() );
+ plumed_assert( vecs );
+ if( vecs->complexvec ) ncomponents=2*vecs->ncomponents;
+ else ncomponents = vecs->ncomponents;
+
+ completeSetup( 5, ncomponents ); myfvec.resize( ncomponents );
+}
+
+void StoreVectorsVessel::usedInFunction( const bool& store ){
+ store_director=store; resize();
+}
+
+void StoreVectorsVessel::recompute( const unsigned& ivec, const unsigned& jstore ){
+ plumed_dbg_assert( usingLowMem() );
+ // Set the task we want to reperform
+ setTaskToRecompute( ivec );
+ // Reperform the task
+ vecs->performTask();
+ // Store the derivatives
+ storeDerivativesLowMem( jstore );
+ // Normalize the vector if it is required
+ if( store_director ) normalizeVector( jstore );
+ // Clear up afterwards
+ vecs->clearAfterTask();
+
+}
+
+bool StoreVectorsVessel::calculate(){
+ storeValues( vecs->getCurrentPositionInTaskList() ); // Store the values of the components of the vector
+
+ if(!store_director) return true;
+ if( !usingLowMem() ) normalizeVector( vecs->getCurrentPositionInTaskList() );
+ else normalizeVector( -1 ); // Ensures vector components are normalized
+ return true;
+}
+
+void StoreVectorsVessel::normalizeVector( const int& jstore ){
+ unsigned myelem = vecs->getCurrentPositionInTaskList();
+ bool lowmemory = usingLowMem(); double norm2=0.0, norm;
+
+ if( (lowmemory && jstore<0) || !lowmemory ){
+ for(unsigned icomp=0;icomp<ncomponents;++icomp) norm2 += getComponent( myelem, icomp ) * getComponent( myelem, icomp );
+ norm=sqrt( norm2 );
+ for(unsigned icomp=0;icomp<ncomponents;++icomp){
+ myfvec[icomp]=getComponent( myelem, icomp );
+ setComponent( myelem, icomp, getComponent( myelem, icomp ) / norm );
+ }
+ } else {
+ for(unsigned icomp=0;icomp<ncomponents;++icomp){
+ myfvec[icomp] = vecs->getElementValue( 5+icomp ); norm2 += myfvec[icomp] * myfvec[icomp];
+ }
+ norm=sqrt( norm2 );
+ }
+ double norm3=norm2*norm, weight = 1.0 / norm, wdf = -1.0 / norm3;
+
+ if( !lowmemory ) {
+ plumed_dbg_assert( jstore<getAction()->getFullNumberOfTasks() );
+ for(unsigned ider=0;ider<getNumberOfDerivatives(myelem);++ider){
+ double comp2=0.0; unsigned ibuf = myelem * ncomponents * getNumberOfDerivativeSpacesPerComponent() + 1 + ider;
+ for(unsigned jcomp=0;jcomp<ncomponents;++jcomp){
+ comp2 += myfvec[jcomp]*getBufferElement(ibuf);
+ ibuf += getNumberOfDerivativeSpacesPerComponent();
+ }
+ ibuf = myelem * ncomponents * getNumberOfDerivativeSpacesPerComponent() + 1 + ider;
+ for(unsigned jcomp=0;jcomp<ncomponents;++jcomp){
+ setBufferElement( ibuf, weight*getBufferElement(ibuf) + wdf*comp2*myfvec[jcomp] );
+ ibuf += getNumberOfDerivativeSpacesPerComponent();
+ }
+ }
+ } else if( jstore>0 ) {
+ unsigned maxder = vecs->getNumberOfDerivatives();
+ for(unsigned ider=0;ider<getNumberOfDerivatives(jstore);++ider){
+ double comp2=0.0; unsigned ibuf = jstore * ncomponents * maxder + ider;
+ for(unsigned jcomp=0;jcomp<ncomponents;++jcomp){
+ comp2 += myfvec[jcomp]*getLocalDerivative( ibuf );
+ ibuf += maxder;
+ }
+ ibuf = jstore * ncomponents * maxder + ider;
+ for(unsigned jcomp=0;jcomp<ncomponents;++jcomp){
+ setLocalDerivative( ibuf, weight*getLocalDerivative( ibuf ) + wdf*comp2*myfvec[jcomp] );
+ ibuf += maxder;
+ }
+ }
+ }
+}
+
+void StoreVectorsVessel::chainRuleForComponent( const unsigned& icolv, const unsigned& jin, const unsigned& jout, const unsigned& base_cv_no,
+ const double& weight, multicolvar::MultiColvarFunction* funcout ){
+ if( usingLowMem() ){
+ unsigned ibuf = ( icolv*ncomponents + jin ) * getAction()->getNumberOfDerivatives();
+ for(unsigned ider=0;ider<getNumberOfDerivatives(icolv);++ider){
+ funcout->addStoredDerivative( jout, base_cv_no, getStoredIndex( icolv, ider ), weight*getLocalDerivative(ibuf+ider) );
+ }
+ } else {
+ unsigned ibuf = (icolv*ncomponents + jin ) * getNumberOfDerivativeSpacesPerComponent() + 1;
+ for(unsigned ider=0;ider<getNumberOfDerivatives(icolv);++ider){
+ funcout->addStoredDerivative( jout, base_cv_no, getStoredIndex( icolv, ider ), weight*getBufferElement(ibuf+ider) );
+ }
+ }
+}
+
+void StoreVectorsVessel::chainRuleForVector( const unsigned& icolv, const unsigned& jout, const unsigned& base_cv_no,
+ const std::vector<double>& df, multicolvar::MultiColvarFunction* funcout ){
+ chainRule( icolv, df );
+ for(unsigned ider=0;ider<getNumberOfDerivatives(icolv);++ider){
+ funcout->addStoredDerivative( jout, base_cv_no, getStoredIndex( icolv, ider ), getFinalDerivative(ider) );
+ }
+}
+
+}
+}
diff --git a/src/crystallization/StoreVectorsVessel.h b/src/crystallization/StoreVectorsVessel.h
new file mode 100644
index 0000000000000000000000000000000000000000..537f548598e895541a603ce6d9201ae5ecdb4396
--- /dev/null
+++ b/src/crystallization/StoreVectorsVessel.h
@@ -0,0 +1,76 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_crystallization_StoreVectorsVessel_h
+#define __PLUMED_crystallization_StoreVectorsVessel_h
+
+#include "tools/DynamicList.h"
+#include "vesselbase/StoreDataVessel.h"
+
+namespace PLMD {
+
+class multicolvar::MultiColvarFunction;
+
+namespace crystallization {
+
+class VectorMultiColvar;
+
+class StoreVectorsVessel : public vesselbase::StoreDataVessel {
+friend class VectorMultiColvar;
+private:
+/// We want to store the director rather than the value
+ bool store_director;
+ unsigned ncomponents;
+ std::vector<double> myfvec;
+ VectorMultiColvar* vecs;
+ void normalizeVector( const int& );
+public:
+ static void registerKeywords( Keywords& keys );
+/// Constructor
+ StoreVectorsVessel( const vesselbase::VesselOptions& );
+/// This turns on the full use of this action for storage
+ void usedInFunction( const bool& );
+/// This makes sure vectors are normalized (they are already stored)
+ bool calculate();
+/// This reperforms a calculation
+ void recompute( const unsigned& , const unsigned& );
+/// This does nothing
+ std::string description(){ return ""; }
+/// Get the orientation of the ith vector
+ void getVector( const unsigned& , std::vector<double>& );
+/// Chain rule for component
+ void chainRuleForComponent( const unsigned& , const unsigned& , const unsigned& jout, const unsigned& , const double& , multicolvar::MultiColvarFunction* );
+/// Chain rule for whole vector
+ void chainRuleForVector( const unsigned& , const unsigned& , const unsigned& , const std::vector<double>& , multicolvar::MultiColvarFunction* );
+};
+
+inline
+void StoreVectorsVessel::getVector( const unsigned& imol, std::vector<double>& vec ){
+ plumed_dbg_assert( vec.size()==getNumberOfComponents() );
+ for(unsigned i=0;i<getNumberOfComponents();++i) vec[i]=getComponent( imol, i );
+}
+
+
+
+}
+}
+#endif
+
diff --git a/src/crystallization/VectorAverage.cpp b/src/crystallization/VectorAverage.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..27d515c1d75017c7608789ce5c8bc33666474f0e
--- /dev/null
+++ b/src/crystallization/VectorAverage.cpp
@@ -0,0 +1,162 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "core/ActionWithValue.h"
+#include "core/ActionRegister.h"
+#include "core/PlumedMain.h"
+#include "core/ActionSet.h"
+#include "vesselbase/BridgeVessel.h"
+#include "vesselbase/ActionWithVessel.h"
+#include "VectorMultiColvar.h"
+
+//+PLUMEDOC MCOLVARF AVERAGE_VECTOR
+/*
+Calculate an average vector
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+namespace PLMD {
+namespace crystallization {
+
+class VectorAverage :
+ public PLMD::ActionWithValue,
+ public vesselbase::ActionWithVessel
+{
+private:
+ vesselbase::BridgeVessel* myBridgeVessel;
+ VectorMultiColvar* mycolv;
+ std::vector<double> values, derivatives;
+public:
+ static void registerKeywords( Keywords& keys );
+ VectorAverage(const ActionOptions&ao);
+/// Don't actually clear the derivatives when this is called from plumed main.
+/// They are calculated inside another action and clearing them would be bad
+ void clearDerivatives(){}
+ void doJobsRequiredBeforeTaskList();
+ unsigned getNumberOfDerivatives();
+ void performTask();
+ void finishComputations();
+ void calculate(){}
+ void apply();
+ void calculateNumericalDerivatives( ActionWithValue* a=NULL );
+ bool isPeriodic();
+ void deactivate_task();
+};
+
+PLUMED_REGISTER_ACTION(VectorAverage,"AVERAGE_VECTOR")
+
+void VectorAverage::registerKeywords( Keywords& keys ){
+ Action::registerKeywords( keys );
+ ActionWithValue::registerKeywords( keys );
+ ActionWithVessel::registerKeywords( keys );
+ keys.add("compulsory","ARG","the label of the action that calculates the vectors we are interested in averaging");
+}
+
+VectorAverage::VectorAverage(const ActionOptions&ao):
+Action(ao),
+ActionWithValue(ao),
+ActionWithVessel(ao)
+{
+ std::string mlab; parse("ARG",mlab);
+ mycolv = plumed.getActionSet().selectWithLabel<crystallization::VectorMultiColvar*>(mlab);
+ if(!mycolv) error("action labeled " + mlab + " does not exist or is not a multicolvar");
+ std::string functype=mycolv->getName();
+ log.printf(" calculating average %s vector\n",functype.c_str() );
+
+ if( checkNumericalDerivatives() ){
+ // If we use numerical derivatives we have to force the base
+ // multicolvar to also use numerical derivatives
+ ActionWithValue* vv=dynamic_cast<ActionWithValue*>( mycolv );
+ plumed_assert( vv ); vv->useNumericalDerivatives();
+ }
+
+ // Now set up the bridging vessel (has to be done this way for internal arrays to be resized properly)
+ addDependency(mycolv); myBridgeVessel = mycolv->addBridgingVessel( this );
+ // And create value
+ addValueWithDerivatives(); setNotPeriodic();
+ // Resize everything
+ unsigned nder = mycolv->getNumberOfDerivatives();
+ unsigned ncomp = mycolv->getNumberOfQuantities() - 5;
+ values.resize( ncomp ); derivatives.resize( ncomp*nder );
+ getPntrToComponent(0)->resizeDerivatives( nder );
+}
+
+void VectorAverage::doJobsRequiredBeforeTaskList(){
+ ActionWithValue::clearDerivatives();
+ values.assign( values.size(), 0.0 );
+ derivatives.assign( derivatives.size(), 0.0 );
+}
+
+unsigned VectorAverage::getNumberOfDerivatives(){
+ return mycolv->getNumberOfDerivatives();
+}
+
+void VectorAverage::performTask(){
+ unsigned nder=mycolv->getNumberOfDerivatives();
+ for(unsigned i=5;i<mycolv->getNumberOfQuantities();++i){
+ values[i-5] += mycolv->getElementValue( i );
+ unsigned nl=(i-5)*nder, nj=i*nder;
+ for(unsigned j=0;j<mycolv->getNumberOfDerivatives();++j){
+ derivatives[nl+j] += mycolv->getElementDerivative( nj + j );
+ }
+ }
+}
+
+void VectorAverage::finishComputations(){
+ comm.Sum( values ); comm.Sum( derivatives );
+ double norm = static_cast<double>( mycolv->getFullNumberOfTasks() );
+ double sum=0; unsigned nder = mycolv->getNumberOfDerivatives();
+ for(unsigned i=0;i<values.size();++i){ values[i]/=norm; sum+=values[i]*values[i]; }
+
+ double inorm = 1.0 / ( norm*sqrt(sum) );
+ Value* val=getPntrToComponent(0); val->set( sqrt(sum) );
+ for(unsigned icomp=0;icomp<values.size();++icomp){
+ for(unsigned jder=0;jder<mycolv->getNumberOfDerivatives();++jder){
+ val->addDerivative( jder, inorm*values[icomp]*derivatives[nder*icomp+jder] );
+ }
+ }
+}
+
+void VectorAverage::apply(){
+ Value* val=getPntrToComponent(0);
+ std::vector<double> tforces( mycolv->getNumberOfDerivatives(), 0 );
+ if( val->applyForce( tforces ) ) mycolv->addForcesOnAtoms( tforces );
+}
+
+void VectorAverage::calculateNumericalDerivatives( ActionWithValue* a ){
+ myBridgeVessel->completeNumericalDerivatives();
+}
+
+bool VectorAverage::isPeriodic(){
+ plumed_merror("This should never be called");
+ return mycolv->isPeriodic();
+}
+
+void VectorAverage::deactivate_task(){
+ plumed_merror("This should never be called");
+}
+
+
+}
+}
diff --git a/src/crystallization/VectorMultiColvar.cpp b/src/crystallization/VectorMultiColvar.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..b7a9d7c11b795fb4be53aa19b07db65d20319fe4
--- /dev/null
+++ b/src/crystallization/VectorMultiColvar.cpp
@@ -0,0 +1,193 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "multicolvar/MultiColvarFunction.h"
+#include "VectorMultiColvar.h"
+
+namespace PLMD {
+namespace crystallization {
+
+void VectorMultiColvar::registerKeywords( Keywords& keys ){
+ MultiColvar::registerKeywords( keys );
+}
+
+VectorMultiColvar::VectorMultiColvar(const ActionOptions& ao):
+PLUMED_MULTICOLVAR_INIT(ao),
+firstcall(false),
+vecs(NULL)
+{
+ setLowMemOption(true);
+}
+
+void VectorMultiColvar::setVectorDimensionality( const unsigned& ncomp, const bool& comp, const int& nat ){
+ // Store number of derivatives and if vectors are complex
+ ncomponents = ncomp; complexvec=comp;
+ if(complexvec) dervec.resize( 2*ncomponents );
+ else dervec.resize( ncomponents );
+ // Read in the atoms if we are using multicolvar reading
+ int natoms=nat; readAtoms( natoms );
+ // Create the store vector object
+ std::string param; vesselbase::VesselOptions da("","",0,param,this);
+ Keywords keys; StoreVectorsVessel::registerKeywords( keys );
+ vesselbase::VesselOptions da2(da,keys);
+ vecs = new StoreVectorsVessel(da2);
+ // Add the vessel to the base
+ addVessel(vecs);
+ // Read in any vessels
+ readVesselKeywords();
+ // Resize a holder for the derivatives of the norm of the vector
+}
+
+double VectorMultiColvar::doCalculation(){
+ // Now calculate the vector
+ calculateVector();
+ // Sort out the active derivatives
+ updateActiveAtoms();
+
+ // Now calculate the norm of the vector (this is what we return here)
+ double norm=0, inorm;
+ if(complexvec){
+ for(unsigned i=0;i<ncomponents;++i) norm += getComponent(i)*getComponent(i) + getImaginaryComponent(i)*getImaginaryComponent(i);
+ norm=sqrt(norm); inorm = 1.0 / norm;
+ for(unsigned i=0;i<ncomponents;++i){ dervec[i] = inorm*getComponent(i); dervec[ncomponents+i] = inorm*getImaginaryComponent(i); }
+ } else {
+ for(unsigned i=0;i<ncomponents;++i) norm += getComponent(i)*getComponent(i);
+ norm=sqrt(norm); inorm = 1.0 / norm;
+ for(unsigned i=0;i<ncomponents;++i) dervec[i] = inorm*getComponent(i);
+ }
+
+ if( usingLowMem() ){
+ vecs->storeDerivativesLowMem( 0 );
+ vecs->chainRule( 0, dervec );
+ } else {
+ vecs->storeDerivativesHighMem( getCurrentPositionInTaskList() );
+ vecs->chainRule( getCurrentPositionInTaskList(), dervec );
+ }
+
+ // Add derivatives to base multicolvars
+ Vector tmpd;
+ for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
+ unsigned k=atoms_with_derivatives[i];
+ tmpd[0]=vecs->getFinalDerivative(3*i+0);
+ tmpd[1]=vecs->getFinalDerivative(3*i+1);
+ tmpd[2]=vecs->getFinalDerivative(3*i+2);
+ MultiColvarBase::addAtomsDerivatives( 0, k, tmpd );
+ }
+ unsigned vvbase=3*atoms_with_derivatives.getNumberActive(); Tensor tmpv;
+ for(unsigned i=0;i<3;++i){
+ for(unsigned j=0;j<3;++j){
+ tmpv(i,j) = vecs->getFinalDerivative( vvbase+3*i+j );
+ }
+ }
+ MultiColvarBase::addBoxDerivatives( 0, tmpv );
+
+
+ return norm;
+}
+
+void VectorMultiColvar::useInMultiColvarFunction( const bool store_director ){
+ if( setupCentralAtomVessel() ) return;
+ vecs->usedInFunction( store_director );
+}
+
+void VectorMultiColvar::getValueForTask( const unsigned& iatom, std::vector<double>& vals ) const {
+ vecs->getVector( iatom, vals );
+}
+
+void VectorMultiColvar::addWeightedValueDerivatives( const unsigned& iatom, const unsigned& base_cv_no, const double& weight, multicolvar::MultiColvarFunction* func ){
+ if( usingLowMem() ){
+ vecs->recompute( iatom, 1 );
+ for(unsigned j=0;j<getNumberOfQuantities()-5;++j) vecs->chainRuleForComponent( 1, j, 5+j, base_cv_no, weight, func );
+ } else {
+ for(unsigned j=0;j<getNumberOfQuantities()-5;++j) vecs->chainRuleForComponent( iatom, j, 5+j, base_cv_no, weight, func );
+ }
+}
+
+void VectorMultiColvar::finishWeightedAverageCalculation( multicolvar::MultiColvarFunction* func ){
+ // And calculate the norm of the vector
+ double norm=0, inorm; std::vector<unsigned> tmpindices( 1 + func->getNumberOfDerivatives() );
+ if(complexvec){
+ for(unsigned i=0;i<ncomponents;++i){
+ // Calculate average vector
+ func->quotientRule(5+i, 1, 5+i); func->quotientRule(5+ncomponents+i, 1, 5+ncomponents+i);
+ // Calculate length of vector
+ norm += func->getElementValue(5+i)*func->getElementValue(5+i) + func->getElementValue(5+ncomponents+i)*func->getElementValue(5+ncomponents+i);
+ }
+ norm=sqrt(norm); inorm = 1.0 / norm;
+ for(unsigned i=0;i<ncomponents;++i){
+ dervec[i] = inorm*func->getElementValue(5+i); dervec[ncomponents+i] = inorm*func->getElementValue(5+ncomponents+i);
+ }
+ func->getIndexList( 1, 0, func->getNumberOfDerivatives(), tmpindices );
+ unsigned nder = func->getNumberOfDerivatives();
+ for(unsigned i=0;i<tmpindices[0];++i){
+ unsigned ind = tmpindices[1+i];
+ for(unsigned j=0;j<ncomponents;++j){
+ func->addElementDerivative( ind, dervec[j]*func->getElementDerivative(nder*(5+j) + ind) );
+ func->addElementDerivative( ind, dervec[ncomponents+j]*func->getElementDerivative(nder*(5+ncomponents+j) + ind) );
+ }
+ }
+ } else {
+ for(unsigned i=0;i<ncomponents;++i){
+ // Calculate average vector
+ func->quotientRule(5+i, 1, 5+i);
+ // Calculate length of vector
+ norm += func->getElementValue(5+i)*func->getElementValue(5+i);
+ }
+ norm=sqrt(norm); inorm = 1.0 / norm;
+ for(unsigned i=0;i<ncomponents;++i) dervec[i] = inorm*func->getElementValue(5+i);
+ func->getIndexList( 1, 0, func->getNumberOfDerivatives(), tmpindices );
+ // And set derivatives given magnitude of the vector
+ unsigned nder = func->getNumberOfDerivatives();
+ for(unsigned i=0;i<tmpindices[0];++i){
+ unsigned ind = tmpindices[1+i];
+ for(unsigned j=0;j<ncomponents;++j){
+ func->addElementDerivative( ind, dervec[j]*func->getElementDerivative(nder*(5+j) + ind) );
+ }
+ }
+ }
+ func->setElementValue( 0, norm );
+}
+
+void VectorMultiColvar::addOrientationDerivativesToBase( const unsigned& iatom, const unsigned& jstore, const unsigned& base_cv_no,
+ const std::vector<double>& der, multicolvar::MultiColvarFunction* func ){
+ if( usingLowMem() ){
+ if(jstore==1){
+ if(firstcall){ vecs->recompute( iatom, jstore ); firstcall=false; }
+ vecs->chainRuleForVector( jstore, 0, base_cv_no, der, func );
+ } else {
+ vecs->recompute( iatom, jstore );
+ vecs->chainRuleForVector( jstore, 0, base_cv_no, der, func );
+ }
+ } else {
+ vecs->chainRuleForVector( iatom, 0, base_cv_no, der, func );
+ }
+}
+
+void VectorMultiColvar::addForcesOnAtoms( const std::vector<double>& inforces ){
+ plumed_dbg_assert( inforces.size()==getNumberOfDerivatives() );
+ std::vector<double> oldforces( getNumberOfDerivatives() );
+ getForcesFromVessels( oldforces );
+ for(unsigned i=0;i<getNumberOfDerivatives();++i) oldforces[i]+=inforces[i];
+ setForcesOnAtoms( oldforces );
+}
+
+}
+}
diff --git a/src/crystallization/VectorMultiColvar.h b/src/crystallization/VectorMultiColvar.h
new file mode 100644
index 0000000000000000000000000000000000000000..9f04b8e4b2be540c1e2012ebf2eca1e3535cfbbe
--- /dev/null
+++ b/src/crystallization/VectorMultiColvar.h
@@ -0,0 +1,189 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_crystallization_VectorMultiColvar_h
+#define __PLUMED_crystallization_VectorMultiColvar_h
+
+#include "tools/Matrix.h"
+#include "multicolvar/MultiColvar.h"
+#include "StoreVectorsVessel.h"
+
+namespace PLMD {
+namespace crystallization {
+
+class VectorMultiColvar : public multicolvar::MultiColvar {
+friend class StoreVectorsVessel;
+friend class OrientationSphere;
+friend class VectorAverage;
+private:
+/// Are the vectors complex
+ bool complexvec;
+/// Used to make sure central atom position is only calculated
+/// once when using orientation sphere
+ bool firstcall;
+/// How many components does the vector have
+ unsigned ncomponents;
+/// This object stores the vectors
+ StoreVectorsVessel* vecs;
+/// This is a tempory vector that is used to store derivatives
+ std::vector<double> dervec;
+protected:
+/// Set the dimensionality of the vector
+ void setVectorDimensionality( const unsigned&, const bool&, const int& );
+/// Add some value to the ith component of the vector
+ void addComponent( const unsigned&, const double& );
+/// Get the ith component
+ double getComponent( const unsigned& ) const ;
+/// Set the ith component
+ void setComponent( const unsigned&, const double& );
+/// Add derivatives of ith component of vector with repect to jth atom
+ void addAtomsDerivative( const unsigned&, const unsigned&, const Vector& );
+/// Add atomic derivatives to all components of matrix (note iatom is treated literally here - cf above)
+ void addAtomDerivativeToAllRealComponents( const unsigned& iatom, const std::vector<double>& vec, const Vector& avec );
+/// Add derivatives of ith component of vector with respect to the box
+ void addBoxDerivatives( const unsigned&, const Tensor& );
+/// Add box derivatives to all components of matrix
+ void addBoxDerivativesToAllRealComponents( const std::vector<double>& vec, const Tensor& avec );
+/// Add some value to the imaginary part of the ith component of the vector
+ void addImaginaryComponent( const unsigned&, const double& );
+/// Get the ith component
+ double getImaginaryComponent( const unsigned& ) const ;
+/// Set the ith component
+ void setImaginaryComponent( const unsigned&, const double& );
+/// Add derivatives of the imaginary part of the ith component of vector with repect to jth atom
+ void addImaginaryAtomsDerivative( const unsigned&, const unsigned&, const Vector& );
+/// Add atomic derivatives to all components of matrix (note iatom is treated literally here - cf above)
+ void addAtomDerivativeToAllImagComponents( const unsigned& iatom, const std::vector<double>& vec, const Vector& avec );
+/// Add derivatives of the imaginary part of the ith component of vector with respect to the box
+ void addImaginaryBoxDerivatives( const unsigned&, const Tensor& );
+/// Add box derivatives to all components of matrix
+ void addBoxDerivativesToAllImagComponents( const std::vector<double>& vec, const Tensor& avec );
+/// This can be used to accumulate derivative from a store of vectors
+ void accumulateDerivativesFromVector( const unsigned& ivec, const unsigned& base_cv_no, const double& weight, StoreVectorsVessel* vectors );
+/// Used in vector average to add forces from vector the the forces from here
+ void addForcesOnAtoms( const std::vector<double>& inforces );
+public:
+ static void registerKeywords( Keywords& keys );
+ VectorMultiColvar(const ActionOptions&);
+ ~VectorMultiColvar(){}
+/// The norm of a vector is not periodic
+ virtual bool isPeriodic(){ return false; }
+/// Calculate the multicolvar
+ double doCalculation();
+/// This shouldn't do anything
+ double compute(){ plumed_error(); }
+/// Calculate the vector
+ virtual void calculateVector()=0;
+/// Get the number of components in the vector
+ unsigned getNumberOfComponentsInVector() const ;
+/// Get the number of quantities we are calculating per step
+ unsigned getNumberOfQuantities();
+/// Store bits and bobs so they can be used in a function
+ void useInMultiColvarFunction( const bool store_director );
+/// Get the vector
+ void getValueForTask( const unsigned& iatom, std::vector<double>& vals ) const ;
+/// Used to accumulate values
+ void addWeightedValueDerivatives( const unsigned& iatom, const unsigned& base_cv_no, const double& weight, multicolvar::MultiColvarFunction* func );
+/// Used for calculating weighted averages
+ void finishWeightedAverageCalculation( multicolvar::MultiColvarFunction* func );
+/// Used in functions to add derivatives to the orientation vector
+ void addOrientationDerivativesToBase( const unsigned& iatom, const unsigned& jstore, const unsigned& base_cv_no,
+ const std::vector<double>& der, multicolvar::MultiColvarFunction* func );
+/// Can we differentiate the orientation - yes we can the multicolvar is a vector
+ bool hasDifferentiableOrientation() const { return true; }
+};
+
+inline
+unsigned VectorMultiColvar::getNumberOfComponentsInVector() const {
+ return ncomponents;
+}
+
+inline
+void VectorMultiColvar::addComponent( const unsigned& icomp, const double& val ){
+ plumed_dbg_assert( icomp<ncomponents );
+ addElementValue( 5 + icomp, val );
+}
+
+inline
+void VectorMultiColvar::setComponent( const unsigned& icomp, const double& val ){
+ plumed_dbg_assert( icomp<ncomponents );
+ setElementValue( 5 + icomp, val );
+}
+
+inline
+double VectorMultiColvar::getComponent( const unsigned& icomp ) const {
+ plumed_dbg_assert( icomp<ncomponents );
+ return getElementValue( 5 + icomp );
+}
+
+
+inline
+void VectorMultiColvar::addAtomsDerivative( const unsigned& icomp, const unsigned& jatom, const Vector& der ){
+ plumed_dbg_assert( icomp<ncomponents && jatom<getNAtoms() );
+ MultiColvarBase::addAtomsDerivatives( 5 + icomp, getAtomIndex(jatom), der );
+}
+
+inline
+void VectorMultiColvar::addBoxDerivatives( const unsigned& icomp, const Tensor& vir ){
+ plumed_dbg_assert( icomp<ncomponents );
+ MultiColvarBase::addBoxDerivatives( 5 + icomp, vir );
+}
+
+inline
+void VectorMultiColvar::addImaginaryComponent( const unsigned& icomp, const double& val ){
+ plumed_dbg_assert( icomp<ncomponents && complexvec );
+ addElementValue( 5 + ncomponents + icomp, val );
+}
+
+inline
+void VectorMultiColvar::setImaginaryComponent( const unsigned& icomp, const double& val ){
+ plumed_dbg_assert( icomp<ncomponents && complexvec );
+ setElementValue( 5 + ncomponents + icomp, val );
+}
+
+inline
+double VectorMultiColvar::getImaginaryComponent( const unsigned& icomp ) const {
+ plumed_dbg_assert( icomp<ncomponents && complexvec );
+ return getElementValue( 5 + ncomponents + icomp );
+}
+
+inline
+void VectorMultiColvar::addImaginaryAtomsDerivative( const unsigned& icomp, const unsigned& jatom, const Vector& der){
+ plumed_dbg_assert( icomp<ncomponents && complexvec && jatom<getNAtoms() );
+ MultiColvarBase::addAtomsDerivatives( 5 + ncomponents + icomp, getAtomIndex(jatom), der );
+}
+
+inline
+void VectorMultiColvar::addImaginaryBoxDerivatives( const unsigned& icomp, const Tensor& vir ){
+ plumed_dbg_assert( icomp<ncomponents && complexvec );
+ MultiColvarBase::addBoxDerivatives( 5 + ncomponents + icomp, vir );
+}
+
+inline
+unsigned VectorMultiColvar::getNumberOfQuantities(){
+ if( complexvec ) return 5 + 2*ncomponents;
+ return 5 + ncomponents;
+}
+
+}
+}
+#endif
+
diff --git a/src/crystallization/module.type b/src/crystallization/module.type
new file mode 100644
index 0000000000000000000000000000000000000000..de832730330473a1870bd368868640da677460ae
--- /dev/null
+++ b/src/crystallization/module.type
@@ -0,0 +1 @@
+default-off
diff --git a/src/function/ActionRegister.h b/src/function/ActionRegister.h
index 4ab846ed5a3dbbea33dd58e7b6a2820bf27f5fa6..7ea989156b006d49467ffca2ca51d77760d279c9 100644
--- a/src/function/ActionRegister.h
+++ b/src/function/ActionRegister.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/function/Combine.cpp b/src/function/Combine.cpp
index 3182af24660faa64624839af9792aa8e7da1b298..7391469dbb96520342473f57ae4661685165cd35 100644
--- a/src/function/Combine.cpp
+++ b/src/function/Combine.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/function/FuncPathMSD.cpp b/src/function/FuncPathMSD.cpp
index ee8b1e8070ab28da4267a52d8cb4ea1b607a9a5f..9eb0d11119561905d161c720933465ae071f7756 100644
--- a/src/function/FuncPathMSD.cpp
+++ b/src/function/FuncPathMSD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -217,7 +217,7 @@ void FuncPathMSD::prepare(){
// resize the effective list
neighpair.resize(neigh_size);
log.printf(" NEIGH LIST NOW INCLUDE INDEXES: ");
- for(unsigned i=0;i<neigh_size;++i)log.printf(" %f ",indexmap[neighpair[i].first]);log.printf(" \n");
+ for(int i=0;i<neigh_size;++i)log.printf(" %f ",indexmap[neighpair[i].first]);log.printf(" \n");
}else{
if( int(getStep())%int(neigh_stride/getTimeStep())==0 ){
log.printf(" Time %f : recalculating full neighlist \n",getStep()*getTimeStep());
@@ -249,7 +249,7 @@ void FuncPathMSD::prepare(){
requestArguments(argstocall);
//now resize the derivatives as well
//for each value in this action
- for(unsigned i=0;i< getNumberOfComponents();i++){
+ for(int i=0;i< getNumberOfComponents();i++){
//resize the derivative to the number the
getPntrToComponent(i)->clearDerivatives();
getPntrToComponent(i)->resizeDerivatives(getNumberOfArguments());
diff --git a/src/function/FuncSumHills.cpp b/src/function/FuncSumHills.cpp
index 56681747d13d15f6531de9291617caa6cf941324..e57eab05bee2509d58192466db843cc0feaaf224 100644
--- a/src/function/FuncSumHills.cpp
+++ b/src/function/FuncSumHills.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/function/Function.cpp b/src/function/Function.cpp
index 1cf3fad01a83ecb5605810299b4666e442aacf26..af63afab95af5f3af6f2c7677ed1c35bea46872c 100644
--- a/src/function/Function.cpp
+++ b/src/function/Function.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/function/Function.h b/src/function/Function.h
index 918a33b384583a913528123e83fe9191f9d6d7dc..f73892b0517a29ed37831bec81a54ce07be74aa9 100644
--- a/src/function/Function.h
+++ b/src/function/Function.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/function/Matheval.cpp b/src/function/Matheval.cpp
index 201d4672fd20d811df1becfe0964e13962473581..cd84551fc8f2347bf86164c80a4d3eae29b08440 100644
--- a/src/function/Matheval.cpp
+++ b/src/function/Matheval.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/function/Piecewise.cpp b/src/function/Piecewise.cpp
index 1299ed103fb2d55b4bdf102affc2b568d42f3260..0c7b9ff3a7b63adc824d52771b573761e1692db3 100644
--- a/src/function/Piecewise.cpp
+++ b/src/function/Piecewise.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -101,7 +101,7 @@ Function(ao)
if(i>0 && points[i].first<=points[i-1].first) error("points abscissas should be monotonously increasing");
}
- for(int i=0;i<getNumberOfArguments();i++)
+ for(unsigned i=0;i<getNumberOfArguments();i++)
if(getPntrToArgument(i)->isPeriodic())
error("Cannot use PIECEWISE on periodic arguments");
@@ -109,7 +109,7 @@ Function(ao)
addValueWithDerivatives();
setNotPeriodic();
}else{
- for(int i=0;i<getNumberOfArguments();i++){
+ for(unsigned i=0;i<getNumberOfArguments();i++){
string s; Tools::convert(i+1,s);
addComponentWithDerivatives(s);
getPntrToComponent(i)->setNotPeriodic();
@@ -123,9 +123,9 @@ Function(ao)
}
void Piecewise::calculate(){
- for(int i=0;i<getNumberOfArguments();i++){
+ for(unsigned i=0;i<getNumberOfArguments();i++){
double val=getArgument(i);
- int p=0;
+ unsigned p=0;
for(;p<points.size();p++){
if(val<points[p].first) break;
}
diff --git a/src/function/Sort.cpp b/src/function/Sort.cpp
index 5a83ed75b145f0aaf248bc8c904ded076282669d..6a0e7597e2f4e79d004ea3613fab89d88fe8b757 100644
--- a/src/function/Sort.cpp
+++ b/src/function/Sort.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -94,7 +94,7 @@ void Sort::calculate(){
}
// STL sort sorts based on first element (value) then second (index)
sort(vals.begin(),vals.end());
- for(unsigned i=0;i<getNumberOfComponents();++i){
+ for(int i=0;i<getNumberOfComponents();++i){
Value* v=getPntrToComponent(i);
v->set(vals[i].first);
setDerivative(v,vals[i].second,1.0);
diff --git a/src/function/Target.cpp b/src/function/Target.cpp
index d01642a82195c2f0d7e69c5c41eee4dc4af21bea..8d40a1f42512d00da8567286433b0206e07cd735 100644
--- a/src/function/Target.cpp
+++ b/src/function/Target.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/generic/Debug.cpp b/src/generic/Debug.cpp
index c1e2b0f1ef6b205f2d86a98587f96bb7743a6809..79c7ac55ea11930e3c0098509df2ce9eb901a7da 100644
--- a/src/generic/Debug.cpp
+++ b/src/generic/Debug.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/generic/DumpAtoms.cpp b/src/generic/DumpAtoms.cpp
index 48bb7a0b2866006ff103e6bcdd4abf1ac5689a42..b5ce9c83a208bf8c5a3b87adbbfdfaa24b13f841 100644
--- a/src/generic/DumpAtoms.cpp
+++ b/src/generic/DumpAtoms.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -94,6 +94,9 @@ class DumpAtoms:
std::vector<unsigned> residueNumbers;
std::vector<std::string> residueNames;
std::string type;
+ std::string fmt_gro_pos;
+ std::string fmt_gro_box;
+ std::string fmt_xyz;
public:
DumpAtoms(const ActionOptions&);
~DumpAtoms();
@@ -113,6 +116,7 @@ void DumpAtoms::registerKeywords( Keywords& keys ){
keys.add("atoms", "ATOMS", "the atom indices whose positions you would like to print out");
keys.add("compulsory", "FILE", "file on which to output coordinates. .gro extension is automatically detected");
keys.add("compulsory", "UNITS","PLUMED","the units in which to print out the coordinates. PLUMED means internal PLUMED units");
+ keys.add("optional", "PRECISION","The number of digits in trajectory file");
keys.add("optional", "TYPE","file type, either xyz or gro, can override an automatically detected file extension");
}
@@ -141,6 +145,24 @@ DumpAtoms::DumpAtoms(const ActionOptions&ao):
type=ntype;
}
+ fmt_gro_pos="%8.3f";
+ fmt_gro_box="%12.7f";
+ fmt_xyz="%f";
+
+ string precision;
+ parse("PRECISION",precision);
+ if(precision.length()>0){
+ int p;
+ Tools::convert(precision,p);
+ log<<" with precision "<<p<<"\n";
+ string a,b;
+ Tools::convert(p+5,a);
+ Tools::convert(p,b);
+ fmt_gro_pos="%"+a+"."+b+"f";
+ fmt_gro_box=fmt_gro_pos;
+ fmt_xyz=fmt_gro_box;
+ }
+
parseAtomList("ATOMS",atoms);
std::string unitname; parse("UNITS",unitname);
@@ -175,9 +197,9 @@ void DumpAtoms::update(){
of.printf("%d\n",getNumberOfAtoms());
const Tensor & t(getPbc().getBox());
if(getPbc().isOrthorombic()){
- of.printf(" %f %f %f\n",lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2));
+ of.printf((" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+"\n").c_str(),lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2));
}else{
- of.printf(" %f %f %f %f %f %f %f %f %f\n",
+ of.printf((" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+"\n").c_str(),
lenunit*t(0,0),lenunit*t(0,1),lenunit*t(0,2),
lenunit*t(1,0),lenunit*t(1,1),lenunit*t(1,2),
lenunit*t(2,0),lenunit*t(2,1),lenunit*t(2,2)
@@ -187,7 +209,7 @@ void DumpAtoms::update(){
const char* defname="X";
const char* name=defname;
if(names.size()>0) if(names[i].length()>0) name=names[i].c_str();
- of.printf("%s %f %f %f\n",name,lenunit*getPosition(i)(0),lenunit*getPosition(i)(1),lenunit*getPosition(i)(2));
+ of.printf(("%s "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+"\n").c_str(),name,lenunit*getPosition(i)(0),lenunit*getPosition(i)(1),lenunit*getPosition(i)(2));
}
} else if(type=="gro"){
const Tensor & t(getPbc().getBox());
@@ -201,10 +223,11 @@ void DumpAtoms::update(){
if(residueNumbers.size()>0) residueNumber=residueNumbers[i];
std::string resname="";
if(residueNames.size()>0) resname=residueNames[i];
- of.printf("%5u%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f\n",residueNumber,resname.c_str(),name,getAbsoluteIndex(i).serial(),
- lenunit*getPosition(i)(0),lenunit*getPosition(i)(1),lenunit*getPosition(i)(2),0.0,0.0,0.0);
+ of.printf(("%5u%-5s%5s%5d"+fmt_gro_pos+fmt_gro_pos+fmt_gro_pos+"\n").c_str(),
+ residueNumber,resname.c_str(),name,getAbsoluteIndex(i).serial(),
+ lenunit*getPosition(i)(0),lenunit*getPosition(i)(1),lenunit*getPosition(i)(2));
}
- of.printf("%12.7f %12.7f %12.7f %12.7f %12.7f %12.7f %12.7f %12.7f %12.7f\n",
+ of.printf((fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+"\n").c_str(),
lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2),
lenunit*t(0,1),lenunit*t(0,2),lenunit*t(1,0),
lenunit*t(1,2),lenunit*t(2,0),lenunit*t(2,1));
diff --git a/src/generic/DumpDerivatives.cpp b/src/generic/DumpDerivatives.cpp
index b4a0f52a217edb586305ab76f0b0b8e2d7e6e3fb..cdbd0b1ca8331b8d3b894762b8d0f08a912c079b 100644
--- a/src/generic/DumpDerivatives.cpp
+++ b/src/generic/DumpDerivatives.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/generic/DumpForces.cpp b/src/generic/DumpForces.cpp
index 4dfdfd56656198a3633e223da4f14da86d6e21e4..e1554f2f782475f74051ed1715b10cc1ed4d3ed1 100644
--- a/src/generic/DumpForces.cpp
+++ b/src/generic/DumpForces.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/generic/DumpProjections.cpp b/src/generic/DumpProjections.cpp
index 6f622e1f754b9be20a72a6e7506ff085cbb53f7e..3d74b1ba25fcd459fe0fd86936ee7a19e387f34f 100644
--- a/src/generic/DumpProjections.cpp
+++ b/src/generic/DumpProjections.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/generic/Flush.cpp b/src/generic/Flush.cpp
index 7a17d4addc19522ee7be2512bd748fe4f91d4138..ca29a23befba1b5aad2c1674fb49c388526368ff 100644
--- a/src/generic/Flush.cpp
+++ b/src/generic/Flush.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/generic/Group.cpp b/src/generic/Group.cpp
index b7e17d88b0a76dfe3351597bc25fc85d3c83448f..e99b23ac64570c0ada05ea5eee9bebd2e86a6ce6 100644
--- a/src/generic/Group.cpp
+++ b/src/generic/Group.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -23,6 +23,10 @@
#include "core/ActionRegister.h"
#include "core/ActionAtomistic.h"
#include "core/Atoms.h"
+#include "tools/IFile.h"
+#include "tools/Tools.h"
+#include <string>
+#include <vector>
using namespace std;
@@ -38,6 +42,9 @@ Notice that this command just creates a shortcut, and does not imply any real ca
It is just convenient to better organize input files. Might be used in combination with
the \ref INCLUDE command so as to store long group definitions in a separate files.
+Finally, lists can be imported from ndx files (GROMACS format). Use NDX_FILE to set the name of
+the index file and NDX_GROUP to set the name of the group to be imported (default is first one).
+
\par Examples
This command create a group of atoms containing atoms 1,4,7,11 and 14 (labeled 'o'), and another containing
@@ -61,6 +68,15 @@ c: COORDINATION GROUPA=o GROUPB=h R_0=0.3
(see also \ref INCLUDE and \ref COORDINATION).
The groups.dat file could be very long and include lists of thousand atoms without cluttering the main plumed.dat file.
+A GROMACS index file can also be imported
+\verbatim
+# import group named 'protein' from file index.ndx
+pro: GROUP NDX_FILE=index.ndx NDX_GROUP=protein
+# dump all the atoms of the protein on a trajectory file
+DUMPATOMS ATOMS=pro FILE=traj.gro
+\endverbatim
+(see also \ref DUMPATOMS)
+
*/
//+ENDPLUMEDOC
@@ -84,6 +100,39 @@ Group::Group(const ActionOptions&ao):
{
vector<AtomNumber> atoms;
parseAtomList("ATOMS",atoms);
+ std::string ndxfile,ndxgroup;
+ parse("NDX_FILE",ndxfile);
+ parse("NDX_GROUP",ndxgroup);
+ if(ndxfile.length()>0 && atoms.size()>0) error("either use explicit atom list or import from index file");
+ if(ndxfile.length()==0 && ndxgroup.size()>0) error("NDX_GROUP can be only used is NDX_FILE is also used");
+
+ if(ndxfile.length()>0){
+ if(ndxgroup.size()>0) log<<" importing group '"+ndxgroup+"'";
+ else log<<" importing first group";
+ log<<" from index file "<<ndxfile<<"\n";
+
+ IFile ifile;
+ ifile.open(ndxfile);
+ std::string line;
+ std::string groupname;
+ bool firstgroup=true;
+ bool groupfound=false;
+ while(ifile.getline(line)){
+ std::vector<std::string> words=Tools::getWords(line);
+ if(words.size()>=3 && words[0]=="[" && words[2]=="]"){
+ if(groupname.length()>0) firstgroup=false;
+ groupname=words[1];
+ if(groupname==ndxgroup || ndxgroup.length()==0) groupfound=true;
+ } else if(groupname==ndxgroup || (firstgroup && ndxgroup.length()==0)){
+ for(unsigned i=0;i<words.size();i++){
+ AtomNumber at; Tools::convert(words[i],at);
+ atoms.push_back(at);
+ }
+ }
+ }
+ if(!groupfound) error("group has not been found in index file");
+ }
+
this->atoms.insertGroup(getLabel(),atoms);
log.printf(" of atoms ");
for(unsigned i=0;i<atoms.size();i++) log.printf(" %d",atoms[i].serial());
@@ -94,6 +143,8 @@ void Group::registerKeywords( Keywords& keys ){
Action::registerKeywords( keys );
ActionAtomistic::registerKeywords( keys );
keys.add("atoms", "ATOMS", "the numerical indexes for the set of atoms in the group");
+ keys.add("optional", "NDX_FILE", "the name of index file (gromacs syntax)");
+ keys.add("optional", "NDX_GROUP", "the name of the group to be imported (gromacs syntax) - first group found is used by default");
}
Group::~Group(){
diff --git a/src/generic/Include.cpp b/src/generic/Include.cpp
index 401168d001a414a3237aa09c8b9ba40b2318e590..36109314b49dc82341637574f644c7bd2c3496ed 100644
--- a/src/generic/Include.cpp
+++ b/src/generic/Include.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/generic/Print.cpp b/src/generic/Print.cpp
index 9fec9e43eb7347754280343945d6dc3a99257111..8b2da75f0805884a950af34505cd01c91e3772bb 100644
--- a/src/generic/Print.cpp
+++ b/src/generic/Print.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/generic/RandomExchanges.cpp b/src/generic/RandomExchanges.cpp
index 0a5467d84735c0c89e9a82e55afdcaca22dbe24d..29d86823d1a26ea7d16f37b3a4737b725568be40 100644
--- a/src/generic/RandomExchanges.cpp
+++ b/src/generic/RandomExchanges.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/generic/Read.cpp b/src/generic/Read.cpp
index 3f0243c8bc9802ee02efc97ab58e9055579e4280..4dc957f02b301f5a8ddf501f2f204acbc40e0622 100644
--- a/src/generic/Read.cpp
+++ b/src/generic/Read.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -34,8 +34,21 @@ namespace generic{
/*
Read quantities from a colvar file.
+This Action can be used with driver to read in a colvar file that was generated during
+an MD simulation
+
\par Examples
+This input reads in data from a file called input_colvar.data that was generated
+in a calculation that involved PLUMED. The first command reads in the data from the
+column headed phi1 while the second reads in the data from the column headed phi2.
+
+\verbatim
+rphi1: READ FILE=input_colvar.data VALUES=phi1
+rphi2: READ FILE=input_colvar.data VALUES=phi2
+PRINT ARG=rphi1,rphi2 STRIDE=500 FILE=output_colvar.data
+\endverbatim
+
*/
//+ENDPLUMEDOC
@@ -114,23 +127,27 @@ nlinesPerStep(1)
ifile->scanFieldList( fieldnames );
for(unsigned i=0;i<fieldnames.size();++i){
if( fieldnames[i].substr(0,dot)==label ){
- readvals.push_back(new Value(this, fieldnames[i], false) );
- addComponent( fieldnames[i].substr(dot+1) ); componentIsNotPeriodic( fieldnames[i].substr(dot+1) );
+ readvals.push_back(new Value(this, fieldnames[i], false) ); addComponent( fieldnames[i].substr(dot+1) );
+ if( ifile->FieldExist("min_" + fieldnames[i]) ) componentIsPeriodic( fieldnames[i].substr(dot+1), "-pi","pi" );
+ else componentIsNotPeriodic( fieldnames[i].substr(dot+1) );
}
}
} else {
- readvals.push_back(new Value(this, valread[0], false) );
- addComponent( name ); componentIsNotPeriodic( valread[0].substr(dot+1) );
+ readvals.push_back(new Value(this, valread[0], false) ); addComponent( name );
+ if( ifile->FieldExist("min_" + valread[0]) ) componentIsPeriodic( valread[0].substr(dot+1), "-pi", "pi" );
+ else componentIsNotPeriodic( valread[0].substr(dot+1) );
for(unsigned i=1;i<valread.size();++i) {
if( valread[i].substr(0,dot)!=label ) error("all values must be from the same Action when using READ");;
- readvals.push_back(new Value(this, valread[i], false) );
- addComponent( valread[i].substr(dot+1) ); componentIsNotPeriodic( valread[i].substr(dot+1) );
+ readvals.push_back(new Value(this, valread[i], false) ); addComponent( valread[i].substr(dot+1) );
+ if( ifile->FieldExist("min_" + valread[i]) ) componentIsPeriodic( valread[i].substr(dot+1), "-pi", "pi" );
+ else componentIsNotPeriodic( valread[i].substr(dot+1) );
}
}
} else {
if( valread.size()!=1 ) error("all values must be from the same Action when using READ");
- readvals.push_back(new Value(this, valread[0], false) );
- addValue(); setNotPeriodic();
+ readvals.push_back(new Value(this, valread[0], false) ); addValue();
+ if( ifile->FieldExist("min_" + valread[0]) ) setPeriodic( "-pi", "pi" );
+ else setNotPeriodic();
log.printf(" reading value %s and storing as %s\n",valread[0].c_str() ,getLabel().c_str() );
}
checkRead();
@@ -164,12 +181,12 @@ void Read::prepare(){
void Read::calculate(){
std::string smin, smax;
for(unsigned i=0;i<readvals.size();++i){
- ifile->scanField( readvals[i] );
- getPntrToComponent(i)->set( readvals[i]->get() );
- if( readvals[i]->isPeriodic() ){
- readvals[i]->getDomain( smin, smax );
- getPntrToComponent(i)->setDomain( smin, smax );
- }
+ ifile->scanField( readvals[i] );
+ getPntrToComponent(i)->set( readvals[i]->get() );
+ if( readvals[i]->isPeriodic() ){
+ readvals[i]->getDomain( smin, smax );
+ getPntrToComponent(i)->setDomain( smin, smax );
+ }
}
}
diff --git a/src/generic/Time.cpp b/src/generic/Time.cpp
index 88fd3bed4e8b44589be3e84a72c54237bff2aa82..52bf6cfa1e867b322ddefa3ed09290a35f722d4c 100644
--- a/src/generic/Time.cpp
+++ b/src/generic/Time.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/generic/WholeMolecules.cpp b/src/generic/WholeMolecules.cpp
index ff3f38dedf0b3388b5a8fcc9e6f84efcd53e886e..79cd57a79cdf1b757ff7e525515f3e1159d2c310 100644
--- a/src/generic/WholeMolecules.cpp
+++ b/src/generic/WholeMolecules.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -85,7 +85,7 @@ protein
\verbatim
MOLINFO REFERENCE=helix.pdb
-WHOLEMOLECULES STRIDE=1 RESIDUES=ALL RES_ATOMS=N,CA,CB,C,O
+WHOLEMOLECULES STRIDE=1 RESIDUES=all MOLTYPE=protein
\endverbatim
(See also \ref MOLINFO)
@@ -112,11 +112,11 @@ void WholeMolecules::registerKeywords( Keywords& keys ){
keys.add("compulsory","STRIDE","1","the frequency with which molecules are reassembled. Unless you are completely certain about what you are doing leave this set equal to 1!");
keys.add("numbered","ENTITY","the atoms that make up a molecule that you wish to align. To specify multiple molecules use a list of ENTITY keywords: ENTITY1, ENTITY2,...");
keys.reset_style("ENTITY","atoms");
- keys.add("residues","RESIDUES","this command specifies a set of residues which all must be aligned. It must be used in tandem with the \\ref MOLINFO "
- "action and the RES_ATOMS keyword. If you wish to use all the residues from all the chains in your system you can do so by "
+ keys.add("residues","RESIDUES","this command specifies that the backbone atoms in a set of residues all must be aligned. It must be used in tandem with the \\ref MOLINFO "
+ "action and the MOLTYPE keyword. If you wish to use all the residues from all the chains in your system you can do so by "
"specifying all. Alternatively, if you wish to use a subset of the residues you can specify the particular residues "
"you are interested in as a list of numbers");
- keys.add("optional","RES_ATOMS","this command tells plumed what atoms should be aligned in each of the residues that are being aligned");
+ keys.add("optional","MOLTYPE","the type of molecule that is under study. This is used to define the backbone atoms");
}
WholeMolecules::WholeMolecules(const ActionOptions&ao):
@@ -139,12 +139,15 @@ ActionAtomistic(ao)
// Read residues to align from MOLINFO
vector<string> resstrings; parseVector("RESIDUES",resstrings);
if( resstrings.size()>0 ){
- vector<string> backnames; parseVector("RES_ATOMS",backnames);
- if(backnames.size()==0) error("Found RESIDUES keyword without any specification of the atoms that should be in a residue - use RES_ATOMS");
+ if( resstrings.size()==1 ){
+ if( resstrings[0]=="all" ) resstrings[0]="all-ter"; // Include terminal groups in alignment
+ }
+ string moltype; parse("MOLTYPE",moltype);
+ if(moltype.length()==0) error("Found RESIDUES keyword without specification of the moleclue - use MOLTYPE");
std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
if( moldat.size()==0 ) error("Unable to find MOLINFO in input");
std::vector< std::vector<AtomNumber> > backatoms;
- moldat[0]->getBackbone( resstrings, backnames, backatoms );
+ moldat[0]->getBackbone( resstrings, moltype, backatoms );
for(unsigned i=0;i<backatoms.size();++i){
log.printf(" atoms in entity %d : ", groups.size()+1 );
for(unsigned j=0;j<backatoms[i].size();++j) log.printf("%d ",backatoms[i][j].serial() );
@@ -159,13 +162,15 @@ ActionAtomistic(ao)
checkRead();
Tools::removeDuplicates(merge);
requestAtoms(merge);
+ doNotRetrieve();
+ doNotForce();
}
void WholeMolecules::calculate(){
for(unsigned i=0;i<groups.size();++i){
for(unsigned j=0;j<groups[i].size()-1;++j){
- Vector & first (atoms.modifyPosition(groups[i][j]));
- Vector & second (atoms.modifyPosition(groups[i][j+1]));
+ const Vector & first (getPosition(groups[i][j]));
+ Vector & second (modifyPosition(groups[i][j+1]));
second=first+pbcDistance(first,second);
}
}
diff --git a/src/header.sh b/src/header.sh
index bbcf2865cd5d94c955be10ca66311b944e7ae610..6bd234c665e253ba7f779bdef806a0492731a520 100755
--- a/src/header.sh
+++ b/src/header.sh
@@ -13,7 +13,7 @@ COPYRIGHT="\
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/imd/ActionIMD.cpp b/src/imd/ActionIMD.cpp
index 9a9760b43dc72afd0ada279c9d5e44a4955a9ffa..e33835f1658a1f3bf43a8dc5daeebedf7a562f78 100644
--- a/src/imd/ActionIMD.cpp
+++ b/src/imd/ActionIMD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/lib/Makefile b/src/lib/Makefile
index 83a37538794ca7daeb19f2b888c92946886bf7ae..94ed7ce95d3bd1a732e1eb7847a8f807c90ac12d 100644
--- a/src/lib/Makefile
+++ b/src/lib/Makefile
@@ -1,8 +1,8 @@
# here we build the list of modules to be linked in plumedKernel
-KERNEL_MODULES=$(addprefix ../,$(shell ../maketools/find_modules.sh))
+KERNEL_MODULES := $(addprefix ../,$(shell ../maketools/find_modules.sh))
# This adds modules which are built anyway and linked with some ad hoc procedure
-DIRS=$(sort ../config ../wrapper ../main $(KERNEL_MODULES))
+DIRS := $(sort ../config ../wrapper ../main $(KERNEL_MODULES))
# include the machine dependent configuration
@@ -26,31 +26,31 @@ SRC_MAIN=../main/main.cpp
# source for plumed kernel
# everything else
-SRC_KERNEL=$(shell for dir in $(KERNEL_MODULES) ; do ls $$dir/*.cpp 2>/dev/null ; ls $$dir/*.c 2>/dev/null ; done) ../config/Config$(PLUMED_INSTALL).o
+SRC_KERNEL := $(shell for dir in $(KERNEL_MODULES) ; do ls $$dir/*.cpp 2>/dev/null ; ls $$dir/*.c 2>/dev/null ; done) ../config/Config$(PLUMED_INSTALL).o
# corresponding objects:
-OBJ_WRAPPER=../wrapper/PlumedStatic.o
-OBJ_DYNAMIC_WRAPPER=../wrapper/Plumed.o
-OBJ_MAIN=$(SRC_MAIN:.cpp=.o)
-XXX=$(SRC_KERNEL:.cpp=.o)
-OBJ_KERNEL=$(XXX:.c=.o)
-ALL_OBJ=$(OBJ_KERNEL) $(OBJ_WRAPPER) $(OBJ_DYNAMIC_WRAPPER) $(OBJ_MAIN)
+OBJ_WRAPPER := ../wrapper/PlumedStatic.o
+OBJ_DYNAMIC_WRAPPER := ../wrapper/Plumed.o
+OBJ_MAIN := $(SRC_MAIN:.cpp=.o)
+XXX := $(SRC_KERNEL:.cpp=.o)
+OBJ_KERNEL := $(XXX:.c=.o)
+ALL_OBJ := $(OBJ_KERNEL) $(OBJ_WRAPPER) $(OBJ_DYNAMIC_WRAPPER) $(OBJ_MAIN)
# plumed kernel
-PLUMED_KERNEL=$(PLUMED_LIBDIR)libplumedKernel.$(SOEXT)
+PLUMED_KERNEL := $(PLUMED_LIBDIR)libplumedKernel.$(SOEXT)
# plumed library (kernel + wrapper)
-PLUMED_SHARED_OBJ=$(PLUMED_LIBDIR)libplumed.$(SOEXT)
+PLUMED_SHARED_OBJ := $(PLUMED_LIBDIR)libplumed.$(SOEXT)
# plumed scripts
-PLUMED_SCRIPTS_SH=$(shell cd ../../scripts/ ; ls *.sh 2>/dev/null)
-PLUMED_SCRIPTS=$(PLUMED_SCRIPTS_SH:.sh=)
-PLUMED_SCRIPTS_EXE=$(addprefix $(PLUMED_LIBDIR)plumed-,$(PLUMED_SCRIPTS))
+PLUMED_SCRIPTS_SH := $(shell cd ../../scripts/ ; ls *.sh 2>/dev/null)
+PLUMED_SCRIPTS := $(PLUMED_SCRIPTS_SH:.sh=)
+PLUMED_SCRIPTS_EXE := $(addprefix $(PLUMED_LIBDIR)plumed-,$(PLUMED_SCRIPTS))
# plumed main exec
-PLUMED_MAIN_STATIC=$(PLUMED_LIBDIR)plumed
-PLUMED_MAIN_SHARED=$(PLUMED_LIBDIR)plumed-shared
-PLUMED_MAIN_RUNTIME=$(PLUMED_LIBDIR)plumed-runtime
+PLUMED_MAIN_STATIC := $(PLUMED_LIBDIR)plumed
+PLUMED_MAIN_SHARED := $(PLUMED_LIBDIR)plumed-shared
+PLUMED_MAIN_RUNTIME := $(PLUMED_LIBDIR)plumed-runtime
.PHONY: all dirs $(DIRS) all-static Plumed.cmake Plumed.inc
ifdef SOEXT
diff --git a/src/main/main.cpp b/src/main/main.cpp
index f75f6535e44c5468c20db540389670d4e7ccfc0a..53dc39943e7cc01b1df4547c404bf40e7a32325b 100644
--- a/src/main/main.cpp
+++ b/src/main/main.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/maketools/make.module b/src/maketools/make.module
index 8957c52f57ea07baa26d8fbcb2bb76eee661122b..1a0090d0cf4fcacef6bc9e8eab84aea3908a7fd2 100644
--- a/src/maketools/make.module
+++ b/src/maketools/make.module
@@ -47,6 +47,10 @@ obj: $(OBJ)
lib:
cd ../lib ; make
+.PHONY: install
+install:
+ cd ../lib ; make install
+
-include $(DEP)
# if machine dependent configuration has not been found:
diff --git a/src/maketools/mod.sh b/src/maketools/mod.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5dccd7f83c93a8e65e8860ed99ae311a4cdc8db0
--- /dev/null
+++ b/src/maketools/mod.sh
@@ -0,0 +1,16 @@
+#! /bin/bash
+
+case "$1" in
+(light)
+ rm -fr *.on *.off
+ touch $(grep default */module.type | awk 'BEGIN{FS="/"}{printf($1".off ")}') ;;
+(heavy)
+ rm -fr *.on *.off
+ touch $(grep default */module.type | awk 'BEGIN{FS="/"}{printf($1".on ")}') ;;
+(reset)
+ rm -fr *.on *.off;;
+(*)
+ echo "ERROR"
+ exit ;;
+esac
+
diff --git a/src/manyrestraints/ManyRestraintsBase.cpp b/src/manyrestraints/ManyRestraintsBase.cpp
index c47fdc9fbb64580a10b596d15ce239079f02b6b5..7646e88dd12bbadad8756127f37f987c4381567a 100644
--- a/src/manyrestraints/ManyRestraintsBase.cpp
+++ b/src/manyrestraints/ManyRestraintsBase.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -46,8 +46,7 @@ ActionWithVessel(ao)
void ManyRestraintsBase::createRestraints( const unsigned& nrestraints ){
std::string fake_input;
- for(unsigned i=0;i<nrestraints;++i) taskList.addIndexToList(i);
- taskList.activateAll();
+ for(unsigned i=0;i<nrestraints;++i) addTaskToList(i);
addVessel( "SUM", fake_input, 0, "bias" );
readVesselKeywords();
forcesToApply.resize( getNumberOfDerivatives() );
diff --git a/src/manyrestraints/ManyRestraintsBase.h b/src/manyrestraints/ManyRestraintsBase.h
index 6b66ad790480e9b09231f884a27b63f1078b5a43..c3aea2fad9ebcb95fa6adcb66ba26dce8140da94 100644
--- a/src/manyrestraints/ManyRestraintsBase.h
+++ b/src/manyrestraints/ManyRestraintsBase.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/manyrestraints/Sphere.cpp b/src/manyrestraints/Sphere.cpp
index 1d7333455d70c9c5b91ad208b22f04f021b31f5a..a97ab3a8c85debbcb960e56a391de77bdc4a6c2d 100644
--- a/src/manyrestraints/Sphere.cpp
+++ b/src/manyrestraints/Sphere.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -39,7 +39,7 @@ public:
static void registerKeywords( Keywords& keys );
Sphere( const ActionOptions& );
bool isPeriodic(){ return false; }
- void performTask( const unsigned& j );
+ void performTask();
void calculate();
};
@@ -90,13 +90,13 @@ void Sphere::calculate(){
runAllTasks();
}
-void Sphere::performTask( const unsigned& j ){
+void Sphere::performTask(){
Vector distance;
if(!nopbc){
- distance=pbcDistance(com,getPosition(current));
+ distance=pbcDistance(com,getPosition( getCurrentTask() ));
} else {
- distance=delta(com,getPosition(current));
+ distance=delta(com,getPosition( getCurrentTask() ));
}
double value=distance.modulo();
@@ -111,7 +111,7 @@ void Sphere::performTask( const unsigned& j ){
for(unsigned i=0;i<getNumberOfAtoms();++i) addAtomsDerivatives( i, -com_deriv[i]*f*distance );
// Add derivatives for other atom
- addAtomsDerivatives( current, f*distance );
+ addAtomsDerivatives( getCurrentTask(), f*distance );
// Add derivatives for virial
addBoxDerivatives( -f*Tensor(distance,distance) );
diff --git a/src/multicolvar/ActionVolume.cpp b/src/multicolvar/ActionVolume.cpp
index e50a9c69d611a32e85053a6e7a28e809e67ddc0d..4da86d37da720d69145fa11e63e9774253edb347 100644
--- a/src/multicolvar/ActionVolume.cpp
+++ b/src/multicolvar/ActionVolume.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -47,8 +47,7 @@ Action(ao),
ActionAtomistic(ao),
ActionWithValue(ao),
ActionWithVessel(ao),
-updateFreq(0),
-lastUpdate(0)
+updateFreq(0)
{
std::string mlab; parse("ARG",mlab);
mycolv = plumed.getActionSet().selectWithLabel<multicolvar::MultiColvarBase*>(mlab);
@@ -70,8 +69,10 @@ lastUpdate(0)
if( !mycolv->isDensity() && updateFreq%mycolv->updateFreq!=0 ){
error("update frequency must be a multiple of update frequency for base multicolvar");
}
+ firsttime=true;
log.printf(" Updating contributors every %d steps.\n",updateFreq);
} else {
+ firsttime=false; contributorsAreUnlocked=true; // This will lock during first prepare step
log.printf(" Updating contributors every step.\n");
}
@@ -84,15 +85,14 @@ lastUpdate(0)
if( mycolv->isDensity() ){
std::string input;
addVessel( "SUM", input, -1 ); // -1 here means that this value will be named getLabel()
- resizeFunctions();
} else {
readVesselKeywords();
}
// Now set up the bridging vessel (has to be done this way for internal arrays to be resized properly)
addDependency(mycolv); myBridgeVessel = mycolv->addBridgingVessel( this );
- // Setup a dynamic list
- resizeLocalArrays();
+ // And resize atoms
+ finishTaskListUpdate();
}
void ActionVolume::requestAtoms( const std::vector<AtomNumber>& atoms ){
@@ -110,28 +110,26 @@ void ActionVolume::doJobsRequiredBeforeTaskList(){
void ActionVolume::prepare(){
bool updatetime=false;
if( contributorsAreUnlocked ){ updatetime=true; lockContributors(); }
- if( updateFreq>0 && (getStep()-lastUpdate)>=updateFreq ){
- if( !mycolv->isDensity() ){
- mycolv->taskList.activateAll();
- for(unsigned i=0;i<mycolv->taskList.getNumberActive();++i) mycolv->colvar_atoms[i].activateAll();
- mycolv->unlockContributors(); mycolv->resizeDynamicArrays();
- plumed_dbg_assert( mycolv->getNumberOfVessels()==0 );
- } else {
- plumed_massert( mycolv->contributorsAreUnlocked, "contributors are not unlocked in base multicolvar" );
+ if( updateFreq>0 ){
+ if( firsttime || getStep()%updateFreq==0 ){
+ if( !mycolv->isDensity() ){
+ mycolv->unlockContributors();
+ } else {
+ plumed_massert( mycolv->contributorsAreUnlocked, "contributors are not unlocked in base multicolvar" );
+ }
+ unlockContributors();
+ firsttime=false;
}
- unlockContributors();
- updatetime=true;
}
- if( updatetime ) resizeLocalArrays();
}
-void ActionVolume::resizeLocalArrays(){
+void ActionVolume::finishTaskListUpdate(){
activeAtoms.clear();
for(unsigned i=0;i<mycolv->getNumberOfAtoms();++i) activeAtoms.addIndexToList(i);
activeAtoms.deactivateAll();
}
-void ActionVolume::performTask( const unsigned& j ){
+void ActionVolume::performTask(){
activeAtoms.deactivateAll(); // Currently no atoms are active so deactivate them all
Vector catom_pos=mycolv->retrieveCentralAtomPos();
@@ -239,6 +237,8 @@ void ActionVolume::clearDerivativesAfterTask( const unsigned& ider ){
setElementDerivative( nvir, 0.0 ); nvir++;
}
plumed_dbg_assert( (nvir-vstart)==getNumberOfDerivatives() );
+ // Clear values
+ thisval_wasset[ider]=false; setElementValue( ider, 0.0 ); thisval_wasset[ider]=false;
}
void ActionVolume::calculateNumericalDerivatives( ActionWithValue* a ){
diff --git a/src/multicolvar/ActionVolume.h b/src/multicolvar/ActionVolume.h
index d1a8ee86ca66e9d1b487f2fd01853d12fe8e3fc8..ac19cf381412f67e86261f4a3c03b525d0f00afb 100644
--- a/src/multicolvar/ActionVolume.h
+++ b/src/multicolvar/ActionVolume.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -60,14 +60,12 @@ private:
/// The vessel that bridges
vesselbase::BridgeVessel* myBridgeVessel;
/// Everything for controlling the updating of neighbor lists
+ bool firsttime;
int updateFreq;
- unsigned lastUpdate;
/// Fast merging of derivatives (automatic skips of zero contributions)
DynamicList<unsigned> activeAtoms;
/// This is used to store forces temporarily in apply
std::vector<double> tmpforces;
-/// This sets up array above
- void resizeLocalArrays();
protected:
double getSigma() const ;
/// Get the cell box
@@ -91,6 +89,8 @@ public:
/// Don't actually clear the derivatives when this is called from plumed main.
/// They are calculated inside another action and clearing them would be bad
void clearDerivatives(){}
+// This is used during neighbor list update step
+ void finishTaskListUpdate();
/// Get the number of derivatives for this action
unsigned getNumberOfDerivatives(); // N.B. This is replacing the virtual function in ActionWithValue
/// Is the output quantity periodic
@@ -100,7 +100,7 @@ public:
/// Do jobs required before tasks are undertaken
void doJobsRequiredBeforeTaskList();
/// This calculates all the vessels and is called from within a bridge vessel
- void performTask(const unsigned& i );
+ void performTask();
/// Routines that have to be defined so as not to have problems with virtual methods
void deactivate_task();
void calculate(){}
diff --git a/src/multicolvar/AdjacencyMatrixAction.cpp b/src/multicolvar/AdjacencyMatrixAction.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..45eb5855ab0969b20c80c71fc9727f4b71404491
--- /dev/null
+++ b/src/multicolvar/AdjacencyMatrixAction.cpp
@@ -0,0 +1,183 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "AdjacencyMatrixAction.h"
+
+namespace PLMD {
+namespace multicolvar {
+
+void AdjacencyMatrixAction::registerKeywords( Keywords& keys ){
+ MultiColvarFunction::registerKeywords( keys );
+ keys.add("numbered","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. "
+ "The following provides information on the \\ref switchingfunction that are available. "
+ "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
+}
+
+AdjacencyMatrixAction::AdjacencyMatrixAction(const ActionOptions& ao):
+Action(ao),
+MultiColvarFunction(ao),
+tmpdf(1)
+{
+ // Weight of this does have derivatives
+ weightHasDerivatives=true;
+ // Read in the switching function
+ if( getNumberOfBaseMultiColvars()==1 ){
+ switchingFunction.resize(1,1);
+ std::string sw, errors; parse("SWITCH",sw);
+ if(sw.length()==0) error("missing SWITCH keyword");
+ switchingFunction(0,0).set(sw,errors);
+ log.printf(" constructing adjacency matrix between atoms that are within %s\n", ( switchingFunction(0,0).description() ).c_str() );
+ } else {
+ unsigned nfunc=getNumberOfBaseMultiColvars();
+ switchingFunction.resize( nfunc,nfunc );
+ for(unsigned i=0;i<nfunc;++i){
+ // Retrieve the base number
+ unsigned ibase;
+ if( nfunc<10 ){
+ ibase=(i+1)*10;
+ } else if ( nfunc<100 ){
+ ibase=(i+1)*100;
+ } else {
+ error("wow this is an error I never would have expected");
+ }
+
+ for(unsigned j=i;j<nfunc;++j){
+ plumed_assert( j*(i+1)<0.5*(nfunc*nfunc+nfunc) );
+ std::string sw, errors; parseNumbered("SWITCH",ibase+j+1,sw);
+ if(sw.length()==0){
+ std::string num; Tools::convert(ibase+j+1,num);
+ error("could not find SWITCH" + num + " keyword. Need one SWITCH keyword for each distinct base-multicolvar-pair type");
+ }
+ switchingFunction(j,i).set(sw,errors);
+ if( j!=i) switchingFunction(i,j).set(sw,errors);
+ log.printf(" %d th and %d th multicolvar groups must be within %s\n",i+1,j+1,(switchingFunction(i,j).description()).c_str() );
+ }
+ }
+ }
+
+ // Build atom lists
+ buildAtomListWithPairs( true );
+ // Build active elements array
+ for(unsigned i=0;i<getFullNumberOfTasks();++i) active_elements.addIndexToList( i );
+
+ if( getNumberOfVessels()!=0 ) error("there should be no vessel keywords");
+ // Create the storeAdjacencyMatrixVessel
+ std::string param; vesselbase::VesselOptions da("","",0,param,this);
+ Keywords keys; AdjacencyMatrixVessel::registerKeywords( keys );
+ vesselbase::VesselOptions da2(da,keys);
+ mat = new AdjacencyMatrixVessel(da2);
+ // Add the vessel to the base
+ addVessel( mat );
+ // And resize everything
+ resizeFunctions();
+
+ // One component for regular multicolvar and nelements for vectormulticolvar
+ unsigned ncomp;
+ if( getBaseMultiColvar(0)->getNumberOfQuantities()==5 ){ ncomp = 1; }
+ else { ncomp = getBaseMultiColvar(0)->getNumberOfQuantities() - 5; }
+ orient0.resize( ncomp ); orient1.resize( ncomp );
+
+ // And check everything has been read in correctly
+ checkRead();
+}
+
+void AdjacencyMatrixAction::doJobsRequiredBeforeTaskList(){
+ // Do jobs required by ActionWithVessel
+ ActionWithVessel::doJobsRequiredBeforeTaskList();
+ // Make it possible only to go through loop once
+ gathered=false; active_elements.deactivateAll();
+ // Dont calculate derivatives on first loop
+ if( usingLowMem() ) dertime=false;
+ else dertime=true;
+}
+
+void AdjacencyMatrixAction::calculateWeight(){
+ Vector distance = getSeparation( getPositionOfCentralAtom(0), getPositionOfCentralAtom(1) );
+ double dfunc, sw = switchingFunction( getBaseColvarNumber(0),getBaseColvarNumber(1) ).calculate( distance.modulo(), dfunc );
+ setElementValue(1,sw);
+}
+
+double AdjacencyMatrixAction::compute(){
+ active_elements.activate( getCurrentPositionInTaskList() );
+
+ getValueForBaseTask( 0, orient0 );
+ getValueForBaseTask( 1, orient1 );
+
+ double f_dot, dot_df, dot; dot=0;
+ for(unsigned k=0;k<orient0.size();++k) dot+=orient0[k]*orient1[k];
+ f_dot=dot; dot_df=1.0;
+ // Add smac stuff here if required
+
+ // Retrieve the weight of the connection
+ double weight = getElementValue(1);
+
+ if( dertime ){
+ // Add contribution due to separation between atoms
+ Vector distance = getSeparation( getPositionOfCentralAtom(0), getPositionOfCentralAtom(1) );
+ double dfunc, sw = switchingFunction( getBaseColvarNumber(0), getBaseColvarNumber(1) ).calculate( distance.modulo(), dfunc );
+ addCentralAtomsDerivatives( 0, 0, (-dfunc)*f_dot*distance );
+ addCentralAtomsDerivatives( 1, 0, (dfunc)*f_dot*distance );
+ MultiColvarBase::addBoxDerivatives( 0, (-dfunc)*f_dot*Tensor(distance,distance) );
+
+ // And derivatives of orientation
+ for(unsigned k=0;k<orient0.size();++k){
+ orient0[k]*=sw*dot_df; orient1[k]*=sw*dot_df;
+ }
+ addOrientationDerivatives( 0, orient1 );
+ addOrientationDerivatives( 1, orient0 );
+ }
+ return weight*f_dot;
+}
+
+void AdjacencyMatrixAction::setMatrixIndexesForTask( const unsigned& ii ){
+ unsigned icolv = active_elements[ii];
+ unsigned tcode = getActiveTask( icolv );
+ bool check = MultiColvarBase::setupCurrentAtomList( tcode );
+ plumed_assert( check );
+}
+
+void AdjacencyMatrixAction::retrieveMatrix( Matrix<double>& mymatrix ){
+ // Gather active elements in matrix
+ if(!gathered) active_elements.mpi_gatherActiveMembers( comm );
+ gathered=true;
+
+ for(unsigned i=0;i<active_elements.getNumberActive();++i){
+ setMatrixIndexesForTask( i );
+ unsigned j = current_atoms[1], k = current_atoms[0];
+ mymatrix(k,j)=mymatrix(j,k)=getMatrixElement( i );
+ }
+}
+
+void AdjacencyMatrixAction::addDerivativesOnMatrixElement( const unsigned& ielem, const unsigned& jrow, const double& df, Matrix<double>& der ){
+ plumed_dbg_assert( ielem<active_elements.getNumberActive() );
+ tmpdf[0]=df; unsigned jelem=active_elements[ielem];
+
+ if( usingLowMem() ){
+ mat->recompute( jelem, 0 ); mat->chainRule( 0, tmpdf );
+ for(unsigned i=0;i<mat->getNumberOfDerivatives(0);++i) der( jrow, mat->getStoredIndex(0,i) ) += mat->getFinalDerivative(i);
+ } else {
+ mat->chainRule( jelem, tmpdf );
+ for(unsigned i=0;i<mat->getNumberOfDerivatives(jelem);++i) der( jrow, mat->getStoredIndex(jelem,i) ) += mat->getFinalDerivative(i);
+ }
+}
+
+}
+}
diff --git a/src/multicolvar/AdjacencyMatrixAction.h b/src/multicolvar/AdjacencyMatrixAction.h
new file mode 100644
index 0000000000000000000000000000000000000000..058a46f6d009df1bc8f52b52dc85163a0ab54033
--- /dev/null
+++ b/src/multicolvar/AdjacencyMatrixAction.h
@@ -0,0 +1,85 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_multicolvar_AdjacencyMatrixAction_h
+#define __PLUMED_multicolvar_AdjacencyMatrixAction_h
+
+#include "MultiColvarFunction.h"
+#include "tools/SwitchingFunction.h"
+#include "tools/Matrix.h"
+#include "AdjacencyMatrixVessel.h"
+
+namespace PLMD {
+namespace multicolvar {
+
+class AdjacencyMatrixAction : public MultiColvarFunction {
+friend class AdjacencyMatrixVessel;
+private:
+/// Flag to make sure derivatives are calculated infrequently
+ bool dertime;
+/// This is the vessel that stores the adjacency matrix
+ AdjacencyMatrixVessel* mat;
+/// Tempory vectors for storing vectors
+ std::vector<double> tmpdf, orient0, orient1;
+/// switching function
+ Matrix<SwitchingFunction> switchingFunction;
+/// Which matrix elements have value
+ bool gathered;
+ DynamicList<unsigned> active_elements;
+protected:
+/// Get the adjacency matrix
+ void retrieveMatrix( Matrix<double>& mymatrix );
+/// Get number of active matrix elements
+ unsigned getNumberOfActiveMatrixElements();
+/// Put the indices of the matrix elements in current atoms
+ void setMatrixIndexesForTask( const unsigned& ii );
+/// Get an element of the adjacency matrix
+ double getMatrixElement( const unsigned& ielem ) const ;
+/// Add derivatives to a matrix element
+ void addDerivativesOnMatrixElement( const unsigned& ielem, const unsigned& jrow, const double& df, Matrix<double>& der );
+public:
+ static void registerKeywords( Keywords& keys );
+ AdjacencyMatrixAction(const ActionOptions&);
+ double compute();
+ void calculateWeight();
+ void doJobsRequiredBeforeTaskList();
+/// Finish the calculation
+ virtual void completeCalculation()=0;
+/// None of these things are allowed
+ bool isPeriodic(){ return false; }
+ Vector getCentralAtom(){ plumed_merror("cannot find central atoms for adjacency matrix actions"); Vector dum; return dum; }
+};
+
+inline
+unsigned AdjacencyMatrixAction::getNumberOfActiveMatrixElements(){
+ if(!gathered) active_elements.mpi_gatherActiveMembers( comm );
+ gathered=true; return active_elements.getNumberActive();
+}
+
+inline
+double AdjacencyMatrixAction::getMatrixElement( const unsigned& ielem ) const {
+ return mat->getComponent( active_elements[ielem], 0 );
+}
+
+}
+}
+
+#endif
diff --git a/src/multicolvar/AdjacencyMatrixVessel.cpp b/src/multicolvar/AdjacencyMatrixVessel.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..00da76c24ce91802a89e51465c5b471f7a283e06
--- /dev/null
+++ b/src/multicolvar/AdjacencyMatrixVessel.cpp
@@ -0,0 +1,63 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "vesselbase/ActionWithVessel.h"
+#include "AdjacencyMatrixVessel.h"
+#include "AdjacencyMatrixAction.h"
+
+namespace PLMD {
+namespace multicolvar {
+
+void AdjacencyMatrixVessel::registerKeywords( Keywords& keys ){
+ StoreDataVessel::registerKeywords(keys);
+}
+
+AdjacencyMatrixVessel::AdjacencyMatrixVessel( const vesselbase::VesselOptions& da ):
+StoreDataVessel(da),
+tmpdf(1)
+{
+ function=dynamic_cast<AdjacencyMatrixAction*>( getAction() );
+ plumed_assert( function );
+ completeSetup( 0, 1 ); nrows = function->getFullNumberOfTasks();
+}
+
+void AdjacencyMatrixVessel::recompute( const unsigned& ivec, const unsigned& jstore ){
+ plumed_dbg_assert( function->usingLowMem() && function->dertime );
+
+ // Set the task we want to reperform
+ setTaskToRecompute( ivec );
+ // Reperform the task
+ if( function->dertime ){
+ function->performTask();
+ storeDerivativesLowMem( jstore );
+ function->clearAfterTask();
+ }
+}
+
+void AdjacencyMatrixVessel::finish(){
+ StoreDataVessel::finish();
+ function->dertime=true;
+ function->completeCalculation();
+}
+
+}
+}
+
diff --git a/src/multicolvar/AdjacencyMatrixVessel.h b/src/multicolvar/AdjacencyMatrixVessel.h
new file mode 100644
index 0000000000000000000000000000000000000000..4650a81f4e9a9f7f11943524b16f2daecdae528a
--- /dev/null
+++ b/src/multicolvar/AdjacencyMatrixVessel.h
@@ -0,0 +1,62 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_multicolvar_AdjacencyMatrixVessel_h
+#define __PLUMED_multicolvar_AdjacencyMatrixVessel_h
+
+#include "vesselbase/StoreDataVessel.h"
+
+namespace PLMD {
+namespace multicolvar {
+
+class AdjacencyMatrixAction;
+
+class AdjacencyMatrixVessel : public vesselbase::StoreDataVessel {
+friend class VectorMultiColvar;
+private:
+ unsigned nrows;
+/// Pointer to underlying action
+ AdjacencyMatrixAction* function;
+/// Tempory vector for chain rule
+ std::vector<double> tmpdf;
+public:
+ static void registerKeywords( Keywords& keys );
+/// Constructor
+ AdjacencyMatrixVessel( const vesselbase::VesselOptions& );
+/// This does nothing
+ std::string description(){ return ""; }
+/// This recomputes the colvar
+ void recompute( const unsigned& ivec, const unsigned& jstore );
+/// Get the i,j th element of the matrix
+ double getElement( const unsigned& ivec );
+/// Finish the calculation
+ void finish();
+};
+
+inline
+double AdjacencyMatrixVessel::getElement( const unsigned& ivec ){
+ return getComponent( ivec, 0 );
+}
+
+}
+}
+#endif
+
diff --git a/src/multicolvar/AlphaBeta.cpp b/src/multicolvar/AlphaBeta.cpp
index dc28588958f76f632f0569f529c64f0e218e67b9..e8ec6501b276a1a838e3f9aee81be17062d19d38 100644
--- a/src/multicolvar/AlphaBeta.cpp
+++ b/src/multicolvar/AlphaBeta.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -70,6 +70,25 @@ LABEL=ab
PRINT ARG=ab FILE=colvar STRIDE=10
\endverbatim
+Writing out the atoms involved in all the torsions in this way can be rather tedious. Thankfully if you are working with protein you
+can avoid this by using the \ref MOLINFO command. PLUMED uses the pdb file that you provide to this command to learn
+about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:
+
+\verbatim
+MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
+ALPHABETA ...
+ATOMS1=@phi-3 REFERENCE=3.14
+ATOMS2=@psi-3
+ATOMS4=@phi-4
+LABEL=ab
+... ALPHABETA
+PRINT ARG=ab FILE=colvar STRIDE=10
+\endverbatim
+
+Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
+Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
+
+
*/
//+ENDPLUMEDOC
@@ -79,7 +98,7 @@ private:
public:
static void registerKeywords( Keywords& keys );
AlphaBeta(const ActionOptions&);
- virtual double compute( const unsigned& j );
+ virtual double compute();
bool isPeriodic(){ return false; }
Vector getCentralAtom();
};
@@ -100,7 +119,7 @@ PLUMED_MULTICOLVAR_INIT(ao)
// Read in the atoms
int natoms=4; readAtoms( natoms );
// Resize target
- target.resize( taskList.fullSize() );
+ target.resize( getFullNumberOfTasks() );
// Read in reference values
unsigned ntarget=0;
@@ -116,7 +135,6 @@ PLUMED_MULTICOLVAR_INIT(ao)
}
// And setup the ActionWithVessel
- readVesselKeywords();
if( getNumberOfVessels()==0 ){
std::string fake_input;
addVessel( "SUM", fake_input, -1 ); // -1 here means that this value will be named getLabel()
@@ -127,7 +145,7 @@ PLUMED_MULTICOLVAR_INIT(ao)
checkRead();
}
-double AlphaBeta::compute( const unsigned& j ){
+double AlphaBeta::compute(){
Vector d0,d1,d2;
d0=getSeparation(getPosition(1),getPosition(0));
d1=getSeparation(getPosition(2),getPosition(1));
@@ -136,8 +154,9 @@ double AlphaBeta::compute( const unsigned& j ){
Vector dd0,dd1,dd2;
PLMD::Torsion t;
double value = t.compute(d0,d1,d2,dd0,dd1,dd2);
- double svalue = -0.5*sin(value-target[current]);
- double cvalue = 1.+cos(value-target[current]);
+ unsigned tindex = getCurrentPositionInTaskList();
+ double svalue = -0.5*sin(value-target[tindex]);
+ double cvalue = 1.+cos(value-target[tindex]);
dd0 *= svalue;
dd1 *= svalue;
diff --git a/src/multicolvar/Angles.cpp b/src/multicolvar/Angles.cpp
index e01469986c13a76a2b71a81d694ef7f058fc5eb8..558f09369f0f110f6319956aa17cfce63e1de300 100644
--- a/src/multicolvar/Angles.cpp
+++ b/src/multicolvar/Angles.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -92,8 +92,9 @@ private:
public:
static void registerKeywords( Keywords& keys );
Angles(const ActionOptions&);
-// active methods:
- virtual double compute( const unsigned& j );
+/// Updates neighbor list
+ virtual void doJobsRequiredBeforeTaskList();
+ virtual double compute();
/// Returns the number of coordinates of the field
void calculateWeight();
bool isPeriodic(){ return false; }
@@ -129,8 +130,6 @@ Angles::Angles(const ActionOptions&ao):
PLUMED_MULTICOLVAR_INIT(ao),
use_sf(false)
{
- // Read in the atoms
- int natoms=3; readAtoms( natoms );
std::string sfinput,errors; parse("SWITCH",sfinput);
if( sfinput.length()>0 ){
use_sf=true;
@@ -155,38 +154,46 @@ use_sf(false)
log.printf(" only calculating angles when the distance between GROUPA and GROUPC atoms is less than %s\n", sf2.description().c_str() );
}
}
-
- // And setup the ActionWithVessel
- readVesselKeywords();
+ // Read in the atoms
+ int natoms=3; readAtoms( natoms );
// And check everything has been read in correctly
checkRead();
}
+// This should give big speed ups during neighbor list update steps
+void Angles::doJobsRequiredBeforeTaskList(){
+ // Do jobs required by action with vessel
+ ActionWithVessel::doJobsRequiredBeforeTaskList();
+ if( !use_sf || getCurrentNumberOfActiveTasks()==ablocks[0].size() ) return ;
+ // First step of update of three body neighbor list
+ threeBodyNeighborList( sf1 );
+}
+
void Angles::calculateWeight(){
- dij=getSeparation( getPosition(1), getPosition(2) );
- dik=getSeparation( getPosition(1), getPosition(0) );
+ dij=getSeparation( getPosition(0), getPosition(2) );
+ dik=getSeparation( getPosition(0), getPosition(1) );
if(!use_sf){ setWeight(1.0); return; }
double w1, w2, dw1, dw2, wtot;
- w1=sf1.calculate( dij.modulo(), dw1 );
- w2=sf2.calculate( dik.modulo(), dw2 );
+ w1=sf1.calculateSqr( dij.modulo2(), dw1 );
+ w2=sf2.calculateSqr( dik.modulo2(), dw2 );
wtot=w1*w2; dw1*=w2; dw2*=w1;
setWeight( wtot );
if( wtot<getTolerance() ) return;
- addAtomsDerivativeOfWeight( 0, dw2*dik );
- addAtomsDerivativeOfWeight( 1, -dw1*dij - dw2*dik );
+ addAtomsDerivativeOfWeight( 1, dw2*dik );
+ addAtomsDerivativeOfWeight( 0, -dw1*dij - dw2*dik );
addAtomsDerivativeOfWeight( 2, dw1*dij );
addBoxDerivativesOfWeight( (-dw1)*Tensor(dij,dij) + (-dw2)*Tensor(dik,dik) );
}
-double Angles::compute( const unsigned& j ){
+double Angles::compute(){
Vector ddij,ddik; PLMD::Angle a;
double angle=a.compute(dij,dik,ddij,ddik);
// And finish the calculation
- addAtomsDerivatives( 0, ddik );
- addAtomsDerivatives( 1, - ddik - ddij );
+ addAtomsDerivatives( 1, ddik );
+ addAtomsDerivatives( 0, - ddik - ddij );
addAtomsDerivatives( 2, ddij );
addBoxDerivatives( -(Tensor(dij,ddij)+Tensor(dik,ddik)) );
@@ -194,8 +201,8 @@ double Angles::compute( const unsigned& j ){
}
Vector Angles::getCentralAtom(){
- addCentralAtomDerivatives( 1, Tensor::identity() );
- return getPosition(1);
+ addCentralAtomDerivatives( 0, Tensor::identity() );
+ return getPosition(0);
}
}
diff --git a/src/multicolvar/Bridge.cpp b/src/multicolvar/Bridge.cpp
index 8efacd4094b6ba1d9bfd98981c8511908b52bf6c..6bc63479948fd9f9ec70e4f911b78680abb57d0f 100644
--- a/src/multicolvar/Bridge.cpp
+++ b/src/multicolvar/Bridge.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -67,8 +67,8 @@ public:
static void registerKeywords( Keywords& keys );
Bridge(const ActionOptions&);
// active methods:
- virtual double compute( const unsigned& j );
-/// Returns the number of coordinates of the field
+ virtual double compute();
+ void doJobsRequiredBeforeTaskList();
void calculateWeight();
bool isPeriodic(){ return false; }
Vector getCentralAtom();
@@ -121,7 +121,6 @@ PLUMED_MULTICOLVAR_INIT(ao)
log.printf(" distance between bridging atoms and atoms in GROUPB must be less than %s\n",sf2.description().c_str());
// And setup the ActionWithVessel
- readVesselKeywords();
if( getNumberOfVessels()!=0 ) error("should not have vessels for this action");
std::string fake_input;
addVessel( "SUM", fake_input, -1 ); // -1 here means that this value will be named getLabel()
@@ -130,31 +129,38 @@ PLUMED_MULTICOLVAR_INIT(ao)
checkRead();
}
+void Bridge::doJobsRequiredBeforeTaskList(){
+ // Do jobs required by action with vessel
+ ActionWithVessel::doJobsRequiredBeforeTaskList();
+ // First step of update of three body neighbor list
+ threeBodyNeighborList( sf1 );
+}
+
void Bridge::calculateWeight(){
- Vector dij=getSeparation( getPosition(1), getPosition(0) );
- double dw, w=sf1.calculate( dij.modulo(), dw );
+ Vector dij=getSeparation( getPosition(0), getPosition(1) );
+ double dw, w=sf1.calculateSqr( dij.modulo2(), dw );
setWeight( w );
if( w<getTolerance() ) return;
- addAtomsDerivativeOfWeight( 1, -dw*dij );
- addAtomsDerivativeOfWeight( 0, dw*dij );
+ addAtomsDerivativeOfWeight( 0, -dw*dij );
+ addAtomsDerivativeOfWeight( 1, dw*dij );
addBoxDerivativesOfWeight( (-dw)*Tensor(dij,dij) );
}
-double Bridge::compute( const unsigned& j ){
- Vector dik=getSeparation( getPosition(1), getPosition(2) );
- double dw, w=sf2.calculate( dik.modulo(), dw );
+double Bridge::compute(){
+ Vector dik=getSeparation( getPosition(0), getPosition(2) );
+ double dw, w=sf2.calculateSqr( dik.modulo2(), dw );
// And finish the calculation
- addAtomsDerivatives( 1, -dw*dik );
+ addAtomsDerivatives( 0, -dw*dik );
addAtomsDerivatives( 2, dw*dik );
addBoxDerivatives( (-dw)*Tensor(dik,dik) );
return w;
}
Vector Bridge::getCentralAtom(){
- addCentralAtomDerivatives( 1, Tensor::identity() );
- return getPosition(1);
+ addCentralAtomDerivatives( 0, Tensor::identity() );
+ return getPosition(0);
}
}
diff --git a/src/multicolvar/CoordinationNumbers.cpp b/src/multicolvar/CoordinationNumbers.cpp
index d8d1a64015a4060438b09f01e632192233e503ca..5eba870fa488aa2475d21d3ad967d98217620499 100644
--- a/src/multicolvar/CoordinationNumbers.cpp
+++ b/src/multicolvar/CoordinationNumbers.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -70,7 +70,7 @@ public:
static void registerKeywords( Keywords& keys );
CoordinationNumbers(const ActionOptions&);
// active methods:
- virtual double compute( const unsigned& j );
+ virtual double compute();
Vector getCentralAtom();
/// Returns the number of coordinates of the field
bool isPeriodic(){ return false; }
@@ -89,7 +89,7 @@ void CoordinationNumbers::registerKeywords( Keywords& keys ){
"The following provides information on the \\ref switchingfunction that are available. "
"When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
// Use actionWithDistributionKeywords
- keys.use("MEAN"); keys.use("MORE_THAN"); keys.use("LESS_THAN");
+ keys.use("MEAN"); keys.use("MORE_THAN"); keys.use("LESS_THAN"); keys.use("MAX");
keys.use("MIN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
}
@@ -111,28 +111,21 @@ PLUMED_MULTICOLVAR_INIT(ao)
log.printf(" coordination of central atom and those within %s\n",( switchingFunction.description() ).c_str() );
// Read in the atoms
- int natoms; readAtoms( natoms );
+ int natoms=2; readAtoms( natoms );
// And setup the ActionWithVessel
- readVesselKeywords();
-
- // Create the groups for the neighbor list
- std::vector<AtomNumber> ga_lista, gb_lista; AtomNumber aa;
- aa.setIndex(0); ga_lista.push_back(aa);
- for(unsigned i=1;i<natoms;++i){ aa.setIndex(i); gb_lista.push_back(aa); }
- // And check everything has been read in correctly
checkRead();
}
-double CoordinationNumbers::compute( const unsigned& j ){
+double CoordinationNumbers::compute(){
double value=0, dfunc; Vector distance;
// Calculate the coordination number
double sw;
for(unsigned i=1;i<getNAtoms();++i){
distance=getSeparation( getPosition(0), getPosition(i) );
- sw = switchingFunction.calculate( distance.modulo(), dfunc );
- if( sw>=getTolerance() ){ // nl_cut<0 ){
- value += sw; // switchingFunction.calculate( distance.modulo(), dfunc );
+ sw = switchingFunction.calculateSqr( distance.modulo2(), dfunc );
+ if( sw>=getTolerance() ){
+ value += sw;
addAtomsDerivatives( 0, (-dfunc)*distance );
addAtomsDerivatives( i, (dfunc)*distance );
addBoxDerivatives( (-dfunc)*Tensor(distance,distance) );
diff --git a/src/multicolvar/DHEnergy.cpp b/src/multicolvar/DHEnergy.cpp
index 7a27f8d890de972358388fe5d0e3009cfb9799c3..0b9094a4c3c97b3a2cbe9aefa8298d745f916d80 100644
--- a/src/multicolvar/DHEnergy.cpp
+++ b/src/multicolvar/DHEnergy.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/multicolvar/Density.cpp b/src/multicolvar/Density.cpp
index 0794f598cd816993b206dbaaccb414afccc92891..a1b0cdf86822ef4adafa649ccb3fa3cb9726daa5 100644
--- a/src/multicolvar/Density.cpp
+++ b/src/multicolvar/Density.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -54,11 +54,15 @@ public:
static void registerKeywords( Keywords& keys );
Density(const ActionOptions&);
// active methods:
- virtual double compute( const unsigned& j );
+ virtual double compute();
Vector getCentralAtom();
/// Returns the number of coordinates of the field
bool isPeriodic(){ return false; }
bool isDensity(){ return true; }
+ bool hasDifferentiableOrientation() const { return true; }
+ void addOrientationDerivativesToBase( const unsigned& iatom, const unsigned& jstore, const unsigned& base_cv_no,
+ const std::vector<double>& weight, MultiColvarFunction* func ){}
+ void getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices );
};
PLUMED_REGISTER_ACTION(Density,"DENSITY")
@@ -71,13 +75,12 @@ void Density::registerKeywords( Keywords& keys ){
Density::Density(const ActionOptions&ao):
PLUMED_MULTICOLVAR_INIT(ao)
{
- int nat; readAtoms( nat );
- readVesselKeywords();
+ int nat=1; readAtoms( nat );
// And check everything has been read in correctly
checkRead();
}
-double Density::compute( const unsigned& j ){
+double Density::compute(){
return 1.0;
}
@@ -86,6 +89,10 @@ Vector Density::getCentralAtom(){
return getPosition(0);
}
+void Density::getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices ){
+ indices[jstore]=0;
+}
+
}
}
diff --git a/src/multicolvar/DihedralCorrelation.cpp b/src/multicolvar/DihedralCorrelation.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..fdd01aa7a904c6528e6a241205e3b10714dc9938
--- /dev/null
+++ b/src/multicolvar/DihedralCorrelation.cpp
@@ -0,0 +1,169 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "MultiColvar.h"
+#include "tools/Torsion.h"
+#include "core/ActionRegister.h"
+
+#include <string>
+#include <cmath>
+
+using namespace std;
+
+namespace PLMD{
+namespace multicolvar{
+
+//+PLUMEDOC COLVAR DIHCOR
+/*
+Measures the degree of similarity between dihedral angles.
+
+This colvar calculates the following quantity.
+
+\f[
+s = \frac{1}{2} \sum_i \left[ 1 + \cos( \phi_i - \psi_i ) \right]
+\f]
+
+where the \f$\phi_i\f$ and \f$\psi\f$ values and the instantaneous values for the \ref TORSION angles of interest.
+
+\par Examples
+
+The following provides an example input for the dihcor action
+
+\verbatim
+DIHCOR ...
+ ATOMS1=1,2,3,4,5,6,7,8
+ ATOMS2=5,6,7,8,9,10,11,12
+ LABEL=dih
+... DIHCOR
+PRINT ARG=dih FILE=colvar STRIDE=10
+\endverbatim
+
+In the above input we are calculating the correation between the torsion angle involving atoms 1, 2, 3 and 4 and the torsion angle
+involving atoms 5, 6, 7 and 8. This is then added to the correlation betwene the torsion angle involving atoms 5, 6, 7 and 8 and the
+correlation angle involving atoms 9, 10, 11 and 12.
+
+Writing out the atoms involved in all the torsions in this way can be rather tedious. Thankfully if you are working with protein you
+can avoid this by using the \ref MOLINFO command. PLUMED uses the pdb file that you provide to this command to learn
+about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:
+
+\verbatim
+MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
+DIHCOR ...
+ATOMS1=@phi-3,@psi-3
+ATOMS2=@psi-3,@phi-4
+ATOMS4=@phi-4,@psi-4
+... DIHCOR
+PRINT ARG=dih FILE=colvar STRIDE=10
+\endverbatim
+
+Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
+Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
+
+*/
+//+ENDPLUMEDOC
+
+class DihedralCorrelation : public MultiColvar {
+private:
+public:
+ static void registerKeywords( Keywords& keys );
+ DihedralCorrelation(const ActionOptions&);
+ virtual double compute();
+ bool isPeriodic(){ return false; }
+ Vector getCentralAtom();
+};
+
+PLUMED_REGISTER_ACTION(DihedralCorrelation,"DIHCOR")
+
+void DihedralCorrelation::registerKeywords( Keywords& keys ){
+ MultiColvar::registerKeywords( keys );
+ keys.use("ATOMS");
+}
+
+DihedralCorrelation::DihedralCorrelation(const ActionOptions&ao):
+PLUMED_MULTICOLVAR_INIT(ao)
+{
+ // Read in the atoms
+ int natoms=8; readAtoms( natoms );
+
+ // And setup the ActionWithVessel
+ if( getNumberOfVessels()==0 ){
+ std::string fake_input;
+ addVessel( "SUM", fake_input, -1 ); // -1 here means that this value will be named getLabel()
+ readVesselKeywords(); // This makes sure resizing is done
+ }
+
+ // And check everything has been read in correctly
+ checkRead();
+}
+
+double DihedralCorrelation::compute(){
+ Vector d10,d11,d12;
+ d10=getSeparation(getPosition(1),getPosition(0));
+ d11=getSeparation(getPosition(2),getPosition(1));
+ d12=getSeparation(getPosition(3),getPosition(2));
+
+ Vector dd10,dd11,dd12; PLMD::Torsion t1;
+ double phi1 = t1.compute(d10,d11,d12,dd10,dd11,dd12);
+
+ Vector d20,d21,d22;
+ d20=getSeparation(getPosition(5),getPosition(4));
+ d21=getSeparation(getPosition(6),getPosition(5));
+ d22=getSeparation(getPosition(7),getPosition(6));
+
+ Vector dd20,dd21,dd22; PLMD::Torsion t2;
+ double phi2 = t2.compute( d20, d21, d22, dd20, dd21, dd22 );
+
+ // Calculate value
+ double value = 0.5 * ( 1 + cos( phi2 - phi1 ) );
+ // Derivatives wrt phi1
+ dd10 *= 0.5*sin( phi2 - phi1 );
+ dd11 *= 0.5*sin( phi2 - phi1 );
+ dd12 *= 0.5*sin( phi2 - phi1 );
+ // And add
+ addAtomsDerivatives(0,dd10);
+ addAtomsDerivatives(1,dd11-dd10);
+ addAtomsDerivatives(2,dd12-dd11);
+ addAtomsDerivatives(3,-dd12);
+ addBoxDerivatives (-(extProduct(d10,dd10)+extProduct(d11,dd11)+extProduct(d12,dd12)));
+ // Derivative wrt phi2
+ dd20 *= -0.5*sin( phi2 - phi1 );
+ dd21 *= -0.5*sin( phi2 - phi1 );
+ dd22 *= -0.5*sin( phi2 - phi1 );
+ // And add
+ addAtomsDerivatives(4,dd20);
+ addAtomsDerivatives(5,dd21-dd20);
+ addAtomsDerivatives(6,dd22-dd21);
+ addAtomsDerivatives(7,-dd22);
+ addBoxDerivatives (-(extProduct(d20,dd20)+extProduct(d21,dd21)+extProduct(d22,dd22)));
+
+ return value;
+}
+
+Vector DihedralCorrelation::getCentralAtom(){
+ addCentralAtomDerivatives( 1, 0.25*Tensor::identity() );
+ addCentralAtomDerivatives( 2, 0.25*Tensor::identity() );
+ addCentralAtomDerivatives( 5, 0.25*Tensor::identity() );
+ addCentralAtomDerivatives( 6, 0.25*Tensor::identity() );
+ return 0.25*( getPosition(1) + getPosition(2) + getPosition(5) + getPosition(6) );
+}
+
+}
+}
diff --git a/src/multicolvar/Distances.cpp b/src/multicolvar/Distances.cpp
index bbe066e2b0c0ab02d1eebe80330a15ea725aca38..1bf16e36debf7689005ae3fe9d1b84ab743fdda6 100644
--- a/src/multicolvar/Distances.cpp
+++ b/src/multicolvar/Distances.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -80,7 +80,7 @@ public:
static void registerKeywords( Keywords& keys );
Distances(const ActionOptions&);
// active methods:
- virtual double compute( const unsigned& j );
+ virtual double compute();
/// Returns the number of coordinates of the field
bool isPeriodic(){ return false; }
Vector getCentralAtom();
@@ -91,7 +91,7 @@ PLUMED_REGISTER_ACTION(Distances,"DISTANCES")
void Distances::registerKeywords( Keywords& keys ){
MultiColvar::registerKeywords( keys );
keys.use("ATOMS");
- keys.use("MEAN"); keys.use("MIN"); keys.use("LESS_THAN"); keys.use("DHENERGY");
+ keys.use("MEAN"); keys.use("MIN"); keys.use("MAX"); keys.use("LESS_THAN"); keys.use("DHENERGY");
keys.use("MORE_THAN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
keys.add("atoms-1","GROUP","Calculate the distance between each distinct pair of atoms in the group");
keys.add("atoms-2","GROUPA","Calculate the distances between all the atoms in GROUPA and all "
@@ -105,13 +105,11 @@ PLUMED_MULTICOLVAR_INIT(ao)
{
// Read in the atoms
int natoms=2; readAtoms( natoms );
- // And setup the ActionWithVessel
- readVesselKeywords();
// And check everything has been read in correctly
checkRead();
}
-double Distances::compute( const unsigned& j ){
+double Distances::compute(){
Vector distance;
distance=getSeparation( getPosition(0), getPosition(1) );
const double value=distance.modulo();
diff --git a/src/multicolvar/LocalAverage.cpp b/src/multicolvar/LocalAverage.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..9da67a5a8497b879864eaf3347d65e86140cbea1
--- /dev/null
+++ b/src/multicolvar/LocalAverage.cpp
@@ -0,0 +1,155 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "MultiColvarFunction.h"
+#include "core/ActionRegister.h"
+#include "tools/SwitchingFunction.h"
+
+//+PLUMEDOC MCOLVARF LOCAL_AVERAGE
+/*
+Calculate averages over spherical regions centered on atoms
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+namespace PLMD {
+namespace multicolvar {
+
+class LocalAverage : public MultiColvarFunction {
+private:
+/// Ensures we deal with vectors properly
+ unsigned jstart;
+/// The values of the quantities we need to differentiate
+ std::vector<double> values;
+/// The switching function that tells us if atoms are close enough together
+ SwitchingFunction switchingFunction;
+public:
+ static void registerKeywords( Keywords& keys );
+ LocalAverage(const ActionOptions&);
+/// We have to overwrite this here
+ unsigned getNumberOfQuantities();
+/// Actually do the calculation
+ double compute();
+/// This returns the position of the central atom
+ Vector getCentralAtom();
+/// Is the variable periodic
+ bool isPeriodic(){ return false; }
+};
+
+PLUMED_REGISTER_ACTION(LocalAverage,"LOCAL_AVERAGE")
+
+void LocalAverage::registerKeywords( Keywords& keys ){
+ MultiColvarFunction::registerKeywords( keys );
+ keys.add("compulsory","NN","6","The n parameter of the switching function ");
+ keys.add("compulsory","MM","12","The m parameter of the switching function ");
+ keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
+ keys.add("compulsory","R_0","The r_0 parameter of the switching function");
+ keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. "
+ "The following provides information on the \\ref switchingfunction that are available. "
+ "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
+ // Use actionWithDistributionKeywords
+ keys.remove("LOWMEM"); keys.use("MEAN"); keys.use("MORE_THAN"); keys.use("LESS_THAN");
+ keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
+ keys.addFlag("LOWMEM",false,"lower the memory requirements");
+}
+
+LocalAverage::LocalAverage(const ActionOptions& ao):
+Action(ao),
+MultiColvarFunction(ao)
+{
+ // Read in the switching function
+ std::string sw, errors; parse("SWITCH",sw);
+ if(sw.length()>0){
+ switchingFunction.set(sw,errors);
+ } else {
+ double r_0=-1.0, d_0; int nn, mm;
+ parse("NN",nn); parse("MM",mm);
+ parse("R_0",r_0); parse("D_0",d_0);
+ if( r_0<0.0 ) error("you must set a value for R_0");
+ switchingFunction.set(nn,mm,r_0,d_0);
+ }
+ log.printf(" averaging over central molecule and those within %s\n",( switchingFunction.description() ).c_str() );
+ buildSymmetryFunctionLists( false );
+
+ // One component for regular multicolvar and nelements for vectormulticolvar
+ if( getBaseMultiColvar(0)->getNumberOfQuantities()==5 ){ values.resize( 1 ); jstart=0; }
+ else { values.resize( getBaseMultiColvar(0)->getNumberOfQuantities() - 5 ); jstart=5; }
+}
+
+unsigned LocalAverage::getNumberOfQuantities(){
+ return jstart + values.size();
+}
+
+double LocalAverage::compute(){
+ weightHasDerivatives=true;
+
+ Vector distance; double sw, dfunc, nbond=1;
+
+ getValueForBaseTask( 0, values );
+ for(unsigned j=0;j<values.size();++j) addElementValue( jstart + j, values[j] );
+
+ accumulateWeightedAverageAndDerivatives( 0, 1.0 );
+ for(unsigned i=1;i<getNAtoms();++i){
+ distance=getSeparation( getPositionOfCentralAtom(0), getPositionOfCentralAtom(i) );
+ sw = switchingFunction.calculateSqr( distance.modulo2(), dfunc );
+ if( sw>=getTolerance() ){
+ Tensor vir(distance,distance);
+ getValueForBaseTask( i, values );
+ accumulateWeightedAverageAndDerivatives( i, sw );
+ for(unsigned j=0;j<values.size();++j){
+ addElementValue( jstart + j, sw*values[j] );
+ addCentralAtomsDerivatives( 0, jstart+j, (-dfunc)*values[j]*distance );
+ addCentralAtomsDerivatives( i, jstart+j, (+dfunc)*values[j]*distance );
+ MultiColvarBase::addBoxDerivatives( jstart+j, (-dfunc)*values[j]*vir ); // This is a complex number?
+ }
+ nbond += sw;
+ addCentralAtomsDerivatives( 0, 1, (-dfunc)*distance );
+ addCentralAtomsDerivatives( i, 1, (+dfunc)*distance );
+ MultiColvarBase::addBoxDerivatives( 1, (-dfunc)*vir );
+ } else {
+ removeAtomRequest( i, sw );
+ }
+ }
+
+ // Set the tempory weight
+ setElementValue( 1, nbond );
+ // Update all dynamic lists
+ updateActiveAtoms();
+ // Finish the calculation
+ getBaseMultiColvar(0)->finishWeightedAverageCalculation( this );
+
+ // Clear working derivatives
+ clearDerivativesAfterTask(1);
+ // Weight doesn't really have derivatives (just use the holder for convenience)
+ weightHasDerivatives=false; setElementValue( 1, 1.0 );
+
+ return getElementValue(0);
+}
+
+Vector LocalAverage::getCentralAtom(){
+ addDerivativeOfCentralAtomPos( 0, Tensor::identity() );
+ return getPositionOfCentralAtom(0);
+}
+
+}
+}
diff --git a/src/multicolvar/MultiColvar.cpp b/src/multicolvar/MultiColvar.cpp
index f96b610ba547bda16cebb2b98e607f27adff4768..7449a90b046864ad08146a54348ed91ccb48a263 100644
--- a/src/multicolvar/MultiColvar.cpp
+++ b/src/multicolvar/MultiColvar.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -59,15 +59,6 @@ verbose_output(false)
parseFlag("VERBOSE",verbose_output);
}
-void MultiColvar::addColvar( const std::vector<unsigned>& newatoms ){
- if( verbose_output ){
- log.printf(" Colvar %d is calculated from atoms : ", colvar_atoms.size()+1);
- for(unsigned i=0;i<newatoms.size();++i) log.printf("%d ",all_atoms(newatoms[i]).serial() );
- log.printf("\n");
- }
- MultiColvarBase::addColvar( newatoms );
-}
-
void MultiColvar::readAtoms( int& natoms ){
if( keywords.exists("ATOMS") ) readAtomsLikeKeyword( "ATOMS", natoms );
if( keywords.exists("GROUP") ) readGroupsKeyword( natoms );
@@ -79,9 +70,10 @@ void MultiColvar::readAtoms( int& natoms ){
}
void MultiColvar::readAtomsLikeKeyword( const std::string & key, int& natoms ){
+ plumed_assert( !usespecies );
if( all_atoms.fullSize()>0 ) return;
- std::vector<AtomNumber> t; std::vector<unsigned> newlist;
+ std::vector<AtomNumber> t;
for(int i=1;;++i ){
parseAtomList(key, i, t );
if( t.empty() ) break;
@@ -92,21 +84,33 @@ void MultiColvar::readAtomsLikeKeyword( const std::string & key, int& natoms ){
log.printf("\n");
}
- if( i==1 && natoms<0 ) natoms=t.size();
+ if( i==1 && natoms<0 ){ natoms=t.size(); ablocks.resize(natoms); }
+ else if( i==1 ) ablocks.resize(natoms);
if( t.size()!=natoms ){
- std::string ss; Tools::convert(i,ss);
- error(key + ss + " keyword has the wrong number of atoms");
+ std::string ss; Tools::convert(i,ss);
+ error(key + ss + " keyword has the wrong number of atoms");
}
for(unsigned j=0;j<natoms;++j){
- newlist.push_back( natoms*(i-1)+j );
- all_atoms.addIndexToList( t[j] );
+ ablocks[j].push_back( natoms*(i-1)+j ); all_atoms.addIndexToList( t[j] );
+ }
+ t.resize(0);
+ }
+ if( all_atoms.fullSize()>0 ){
+ current_atoms.resize( natoms ); nblock=ablocks[0].size();
+ for(unsigned i=0;i<nblock;++i){
+ if( natoms<4 ){
+ unsigned cvcode=0, tmpc=1;
+ for(unsigned j=0;j<natoms;++j){ cvcode += i*tmpc; tmpc *= nblock; }
+ addTaskToList( cvcode );
+ } else {
+ addTaskToList( i );
+ }
}
- t.resize(0); addColvar( newlist );
- newlist.clear();
}
}
void MultiColvar::readGroupsKeyword( int& natoms ){
+ plumed_assert( !usespecies );
if( all_atoms.fullSize()>0 ) return;
if( natoms==2 ){
@@ -123,22 +127,20 @@ void MultiColvar::readGroupsKeyword( int& natoms ){
std::vector<AtomNumber> t;
parseAtomList("GROUP",t);
if( !t.empty() ){
+ ablocks.resize( natoms ); current_atoms.resize( natoms );
for(unsigned i=0;i<t.size();++i) all_atoms.addIndexToList( t[i] );
- std::vector<unsigned> newlist;
if(natoms==2){
+ nblock=t.size(); for(unsigned i=0;i<2;++i) ablocks[i].resize(nblock);
+ for(unsigned i=0;i<t.size();++i){ ablocks[0][i]=i; ablocks[1][i]=i; }
for(unsigned i=1;i<t.size();++i){
- for(unsigned j=0;j<i;++j){
- newlist.push_back(i); newlist.push_back(j); addColvar( newlist ); newlist.clear();
- }
+ for(unsigned j=0;j<i;++j) addTaskToList( i*nblock + j );
}
} else if(natoms==3){
+ nblock=t.size(); for(unsigned i=0;i<3;++i) ablocks[i].resize(nblock);
+ for(unsigned i=0;i<t.size();++i){ ablocks[0][i]=i; ablocks[1][i]=i; ablocks[2][i]=i; }
for(unsigned i=2;i<t.size();++i){
for(unsigned j=1;j<i;++j){
- for(unsigned k=0;k<j;++k){
- newlist.push_back(i); newlist.push_back(j);
- newlist.push_back(k); addColvar( newlist );
- newlist.clear();
- }
+ for(unsigned k=0;k<j;++k) addTaskToList( i*nblock*nblock + j*nblock + k );
}
}
}
@@ -160,16 +162,27 @@ void MultiColvar::readGroupsKeyword( int& natoms ){
void MultiColvar::readTwoGroups( const std::string& key1, const std::string& key2 ){
plumed_assert( all_atoms.fullSize()==0 );
+ ablocks.resize( 2 ); current_atoms.resize( 2 );
std::vector<AtomNumber> t1, t2; std::vector<unsigned> newlist;
parseAtomList(key1,t1); parseAtomList(key2,t2);
if( t1.empty() ) error("missing atom specification " + key1);
if ( t2.empty() ) error("missing atom specification " + key2);
- for(unsigned i=0;i<t1.size();++i) all_atoms.addIndexToList( t1[i] );
- for(unsigned i=0;i<t2.size();++i) all_atoms.addIndexToList( t2[i] );
+
+ if( t1.size()>t2.size() ) nblock = t1.size();
+ else nblock=t2.size();
+
+ ablocks[0].resize( t1.size() );
+ for(unsigned i=0;i<t1.size();++i){
+ all_atoms.addIndexToList( t1[i] ); ablocks[0][i]=i;
+ }
+ ablocks[1].resize( t2.size() );
+ for(unsigned i=0;i<t2.size();++i){
+ all_atoms.addIndexToList( t2[i] ); ablocks[1][i]=t1.size() + i;
+ }
for(unsigned i=0;i<t1.size();++i){
for(unsigned j=0;j<t2.size();++j){
- newlist.push_back(i); newlist.push_back( t1.size() + j ); addColvar( newlist ); newlist.clear();
+ if( all_atoms(ablocks[0][i])!=all_atoms(ablocks[1][j]) ) addTaskToList( i*nblock + j );
}
}
if( !verbose_output ){
@@ -185,24 +198,35 @@ void MultiColvar::readTwoGroups( const std::string& key1, const std::string& key
void MultiColvar::readThreeGroups( const std::string& key1, const std::string& key2, const std::string& key3, const bool& allow2 ){
plumed_assert( all_atoms.fullSize()==0 );
+ ablocks.resize( 3 ); current_atoms.resize( 3 );
std::vector<AtomNumber> t1, t2, t3; std::vector<unsigned> newlist;
parseAtomList(key1,t1); parseAtomList(key2,t2);
if( t1.empty() ) error("missing atom specification " + key1);
if( t2.empty() ) error("missing atom specification " + key2);
- for(unsigned i=0;i<t1.size();++i) all_atoms.addIndexToList( t1[i] );
- for(unsigned i=0;i<t2.size();++i) all_atoms.addIndexToList( t2[i] );
+ ablocks[0].resize( t1.size() );
+ for(unsigned i=0;i<t1.size();++i){
+ all_atoms.addIndexToList( t1[i] ); ablocks[0][i]=i;
+ }
+ ablocks[1].resize( t2.size() );
+ for(unsigned i=0;i<t2.size();++i){
+ all_atoms.addIndexToList( t2[i] ); ablocks[1][i] = t1.size() + i;
+ }
parseAtomList(key3,t3);
if( t3.empty() && !allow2 ){
error("missing atom specification " + key3);
} else if( t3.empty() ){
+ if( t2.size()>t1.size() ) nblock=t2.size();
+ else nblock=t1.size();
+
+ ablocks[2].resize( t2.size() );
+ for(unsigned i=0;i<t2.size();++i) ablocks[2][i]=t1.size() + i;
for(unsigned i=0;i<t1.size();++i){
for(unsigned j=1;j<t2.size();++j){
for(unsigned k=0;k<j;++k){
- newlist.push_back( t1.size() + j );
- newlist.push_back(i);
- newlist.push_back( t1.size() + k );
- addColvar( newlist ); newlist.clear();
+ if( all_atoms(ablocks[0][i])!=all_atoms(ablocks[1][j]) &&
+ all_atoms(ablocks[0][i])!=all_atoms(ablocks[2][k]) &&
+ all_atoms(ablocks[1][j])!=all_atoms(ablocks[2][k]) ) addTaskToList( nblock*nblock*i + nblock*j + k );
}
}
}
@@ -216,14 +240,20 @@ void MultiColvar::readThreeGroups( const std::string& key1, const std::string& k
log.printf("\n");
}
} else {
- for(unsigned i=0;i<t3.size();++i) all_atoms.addIndexToList( t3[i] );
+ if( t2.size()>t1.size() ) nblock=t2.size();
+ else nblock=t1.size();
+ if( t3.size()>nblock ) nblock=t3.size();
+
+ ablocks[2].resize( t3.size() );
+ for(unsigned i=0;i<t3.size();++i){
+ all_atoms.addIndexToList( t3[i] ); ablocks[2][i] = t1.size() + t2.size() + i;
+ }
for(unsigned i=0;i<t1.size();++i){
for(unsigned j=0;j<t2.size();++j){
for(unsigned k=0;k<t3.size();++k){
- newlist.push_back( t1.size() + j );
- newlist.push_back(i);
- newlist.push_back( t1.size() + t2.size() + k );
- addColvar( newlist ); newlist.clear();
+ if( all_atoms(ablocks[0][i])!=all_atoms(ablocks[1][j]) &&
+ all_atoms(ablocks[0][i])!=all_atoms(ablocks[2][k]) &&
+ all_atoms(ablocks[1][j])!=all_atoms(ablocks[2][k]) ) addTaskToList( nblock*nblock*i + nblock*j + k );
}
}
}
@@ -243,22 +273,18 @@ void MultiColvar::readThreeGroups( const std::string& key1, const std::string& k
}
void MultiColvar::readSpeciesKeyword( int& natoms ){
+ plumed_assert( usespecies );
if( all_atoms.fullSize()>0 ) return ;
+ ablocks.resize( natoms-1 );
std::vector<AtomNumber> t;
parseAtomList("SPECIES",t);
if( !t.empty() ){
- natoms=t.size();
for(unsigned i=0;i<t.size();++i) all_atoms.addIndexToList( t[i] );
- std::vector<unsigned> newlist;
if( keywords.exists("SPECIESA") && keywords.exists("SPECIESB") ){
- for(unsigned i=0;i<t.size();++i){
- newlist.push_back(i);
- for(unsigned j=0;j<t.size();++j){
- if(i!=j) newlist.push_back(j);
- }
- addColvar( newlist ); newlist.clear();
- }
+ plumed_assert( natoms==2 ); current_atoms.resize( t.size() );
+ for(unsigned i=0;i<t.size();++i) addTaskToList(i);
+ ablocks[0].resize( t.size() ); for(unsigned i=0;i<t.size();++i) ablocks[0][i]=i;
if( !verbose_output ){
log.printf(" generating colvars from %d atoms of a particular type\n",t.size() );
log.printf(" atoms involved : ");
@@ -266,13 +292,13 @@ void MultiColvar::readSpeciesKeyword( int& natoms ){
log.printf("\n");
}
} else if( !( keywords.exists("SPECIESA") && keywords.exists("SPECIESB") ) ){
- std::vector<unsigned> newlist; verbose_output=false; // Make sure we don't do verbose output
+ std::vector<unsigned> newlist; usespecies=false; verbose_output=false; // Make sure we don't do verbose output
log.printf(" involving atoms : ");
+ current_atoms.resize(1); ablocks.resize(1); ablocks[0].resize( t.size() );
for(unsigned i=0;i<t.size();++i){
- newlist.push_back(i); addColvar( newlist ); newlist.clear();
- log.printf(" %d",t[i].serial() );
+ addTaskToList(i); ablocks[0][i]=i; log.printf(" %d",t[i].serial() );
}
- log.printf("\n");
+ log.printf("\n");
} else {
plumed_merror("SPECIES keyword is not for density or coordination like CV");
}
@@ -282,17 +308,9 @@ void MultiColvar::readSpeciesKeyword( int& natoms ){
if( !t1.empty() ){
parseAtomList("SPECIESB",t2);
if ( t2.empty() ) error("SPECIESB keyword defines no atoms or is missing. Use either SPECIESA and SPECIESB or just SPECIES");
- natoms=1+t2.size();
- for(unsigned i=0;i<t1.size();++i) all_atoms.addIndexToList( t1[i] );
- for(unsigned i=0;i<t2.size();++i) all_atoms.addIndexToList( t2[i] );
- std::vector<unsigned> newlist;
- for(unsigned i=0;i<t1.size();++i){
- newlist.push_back(i);
- for(unsigned j=0;j<t2.size();++j){
- if( t1[i]!=t2[j] ) newlist.push_back( t1.size() + j );
- }
- addColvar( newlist ); newlist.clear();
- }
+ current_atoms.resize( 1+ t2.size() );
+ for(unsigned i=0;i<t1.size();++i){ all_atoms.addIndexToList( t1[i] ); addTaskToList(i); }
+ ablocks[0].resize( t2.size() ); for(unsigned i=0;i<t2.size();++i){ all_atoms.addIndexToList( t2[i] ); ablocks[0][i]=t1.size() + i; }
if( !verbose_output ){
log.printf(" generating colvars from a group of %d central atoms and %d other atoms\n",t1.size(), t2.size() );
log.printf(" central atoms are : ");
@@ -306,28 +324,70 @@ void MultiColvar::readSpeciesKeyword( int& natoms ){
}
}
-void MultiColvar::resizeDynamicArrays(){
- for(unsigned i=0;i<taskList.getNumberActive();++i){
- unsigned n=taskList[i];
- for(unsigned j=0;j<colvar_atoms[n].getNumberActive();++j){
- all_atoms.activate( colvar_atoms[n][j] );
+void MultiColvar::threeBodyNeighborList( const SwitchingFunction& sf ){
+ plumed_dbg_assert( !usespecies && ablocks.size()==3 );
+ if( !contributorsAreUnlocked ) return;
+
+ unsigned stride=comm.Get_size();
+ unsigned rank=comm.Get_rank();
+ if( serialCalculation() ){ stride=1; rank=0; }
+
+ unsigned ik=0; double w, dw; Vector dij;
+ std::vector<unsigned> inactive_tasks( getCurrentNumberOfActiveTasks(), 0 );
+ for(unsigned i=0;i<ablocks[0].size();++i){
+ for(unsigned j=0;j<ablocks[1].size();++j){
+
+ if( (ik++)%stride!=rank ) continue;
+
+ dij=getSeparation( ActionAtomistic::getPosition(ablocks[0][i]), ActionAtomistic::getPosition(ablocks[1][j]) );
+ w = sf.calculateSqr( dij.modulo2(), dw );
+ if( w<getNLTolerance() ){
+ // Deactivate all tasks involving i and j
+ for(unsigned k=0;k<getCurrentNumberOfActiveTasks();++k){
+ unsigned ind=std::floor( getActiveTask(k) / decoder[0] );
+ if( ind!=i ) continue;
+ unsigned ind2=std::floor( (getActiveTask(k) - ind*decoder[0]) / decoder[1] );
+ if( ind2!=j ) continue;
+ inactive_tasks[k] = 1;
+ }
+ }
}
}
+ if( !serialCalculation() ) comm.Sum( inactive_tasks );
+ std::vector<bool> activeTasks( getCurrentNumberOfActiveTasks(), false );
+ deactivateAllTasks();
+ for(unsigned i=0;i<activeTasks.size();++i){
+ if( inactive_tasks[i]==0 ) activeTasks[i]=true;
+ }
+ activateTheseTasks( activeTasks );
+}
+
+void MultiColvar::finishTaskListUpdate(){
+ updateCSphereArrays(); // Stuff for atom centered symmetry function nlist
+ // Get the atoms we need
+ all_atoms.deactivateAll();
+ for(unsigned i=0;i<getCurrentNumberOfActiveTasks();++i){
+ bool check=setupCurrentAtomList( getActiveTask(i) );
+ plumed_assert( check );
+ for(unsigned j=0;j<natomsper;++j) all_atoms.activate( current_atoms[j] );
+ }
all_atoms.updateActiveMembers();
// Request the atoms
ActionAtomistic::requestAtoms( all_atoms.retrieveActiveList() );
+ // Resize arrays in MultiColvarBase
+ resizeLocalArrays();
}
void MultiColvar::calculate(){
+ if( checkNumericalDerivatives() ) calculationsRequiredBeforeNumericalDerivatives();
runAllTasks();
}
-double MultiColvar::doCalculation( const unsigned& j ){
- double val=compute(j);
+void MultiColvar::updateActiveAtoms(){
+ if( atoms_with_derivatives.updateComplete() ) return;
atoms_with_derivatives.emptyActiveMembers();
for(unsigned i=0;i<getNAtoms();++i) atoms_with_derivatives.updateIndex( getAtomIndex(i) );
atoms_with_derivatives.sortActiveList();
- return val;
}
Vector MultiColvar::calculateCentralAtomPosition(){
diff --git a/src/multicolvar/MultiColvar.h b/src/multicolvar/MultiColvar.h
index edc87b2efdfc6a2805da6052e5cc0fb7a7fd8b66..36e49ac11a00c7a689ae5afd74ca1a00c20ecbdc 100644
--- a/src/multicolvar/MultiColvar.h
+++ b/src/multicolvar/MultiColvar.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -23,6 +23,7 @@
#define __PLUMED_multicolvar_MultiColvar_h
#include "MultiColvarBase.h"
+#include "tools/SwitchingFunction.h"
#include <vector>
#define PLUMED_MULTICOLVAR_INIT(ao) Action(ao),MultiColvar(ao)
@@ -38,14 +39,12 @@ thereof, whtin it there is \ref AddingAMultiColvar "information" as to how to go
class MultiColvar : public MultiColvarBase {
private:
-/// Have atoms been read in
+/// Do we want lots of details in the output
bool verbose_output;
/// Read in the various GROUP keywords
void readGroupsKeyword( int& natoms );
/// Read in the various SPECIES keywords
void readSpeciesKeyword( int& natoms );
-/// Update the atoms request
- void requestAtoms();
protected:
/// Read in all the keywords that can be used to define atoms
void readAtoms( int& natoms );
@@ -55,6 +54,8 @@ protected:
void readTwoGroups( const std::string& key1, const std::string& key2 );
/// Read three groups
void readThreeGroups( const std::string& key1, const std::string& key2, const std::string& key3, const bool& allow2 );
+/// This is used to make neighbor list update fast when three atoms are involved in the colvar (e.g. ANGLES, WATERBRIDGE)
+ void threeBodyNeighborList( const SwitchingFunction& sf );
/// Add a collective variable
void addColvar( const std::vector<unsigned>& newatoms );
/// Add some derivatives for an atom
@@ -63,20 +64,25 @@ protected:
void addAtomsDerivativeOfWeight( const unsigned& i, const Vector& wder );
/// Add derivatives to the central atom position
void addCentralAtomDerivatives( const unsigned& iatom, const Tensor& der );
+/// Get the index of an atom
+ unsigned getAtomIndex( const unsigned& iatom ) const ;
public:
MultiColvar(const ActionOptions&);
~MultiColvar(){}
static void registerKeywords( Keywords& keys );
/// Resize all the dynamic arrays (used at neighbor list update time and during setup)
- void resizeDynamicArrays();
+// virtual void resizeDynamicArrays();
/// Get the position of atom iatom
const Vector & getPosition(unsigned) const;
+/// This is used in VectorMultiColvar. In there we use a MultiColvar as if it is
+/// a MultiColvarFunction so we can calculate functions of vectors that output functions
+ virtual void calculationsRequiredBeforeNumericalDerivatives(){}
+/// Finish the update of the task list
+ void finishTaskListUpdate();
/// Calculate the multicolvar
virtual void calculate();
-/// Do the calculation
- double doCalculation( const unsigned& j );
-/// Actually compute the colvar
- virtual double compute( const unsigned& j )=0;
+/// Update the atoms that have derivatives
+ void updateActiveAtoms();
/// Calculate the position of the central atom
Vector calculateCentralAtomPosition();
/// Get the position of the central atom
@@ -87,8 +93,29 @@ public:
double getCharge(unsigned) const ;
/// Get the absolute index of atom iatom
AtomNumber getAbsoluteIndex(unsigned) const ;
+/// Get base quantity index
+ unsigned getBaseQuantityIndex( const unsigned& code );
+/// Return true if two indexes are the same
+ bool same_index( const unsigned&, const unsigned& );
};
+inline
+unsigned MultiColvar::getBaseQuantityIndex( const unsigned& code ){
+ return all_atoms.linkIndex( code );
+}
+
+inline
+bool MultiColvar::same_index( const unsigned& code1, const unsigned& code2 ){
+ return ( all_atoms(code1)==all_atoms(code2) );
+}
+
+inline
+unsigned MultiColvar::getAtomIndex( const unsigned& iatom ) const {
+ plumed_dbg_assert( iatom<natomsper );
+ return current_atoms[iatom];
+// return all_atoms.linkIndex( colvar_atoms[current][iatom] );
+}
+
inline
const Vector & MultiColvar::getPosition( unsigned iatom ) const {
return ActionAtomistic::getPosition( getAtomIndex(iatom) );
@@ -111,12 +138,12 @@ AtomNumber MultiColvar::getAbsoluteIndex(unsigned iatom) const {
inline
void MultiColvar::addAtomsDerivatives(const int& iatom, const Vector& der){
- MultiColvarBase::addAtomsDerivatives( getAtomIndex(iatom), der );
+ MultiColvarBase::addAtomsDerivatives( 0, getAtomIndex(iatom), der );
}
inline
void MultiColvar::addAtomsDerivativeOfWeight( const unsigned& iatom, const Vector& wder ){
- MultiColvarBase::addAtomsDerivativeOfWeight( getAtomIndex(iatom), wder );
+ MultiColvarBase::addAtomsDerivatives( 1, getAtomIndex(iatom), wder );
}
inline
diff --git a/src/multicolvar/MultiColvarBase.cpp b/src/multicolvar/MultiColvarBase.cpp
index 4078b86c7c247d864403f228e74778025989f1c6..d609ed73263eb5b7fd5f9b36ff7dd8a4e939811a 100644
--- a/src/multicolvar/MultiColvarBase.cpp
+++ b/src/multicolvar/MultiColvarBase.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -20,6 +20,7 @@
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "MultiColvarBase.h"
+#include "MultiColvarFunction.h"
#include "vesselbase/Vessel.h"
#include "tools/Pbc.h"
#include <vector>
@@ -48,58 +49,88 @@ ActionWithValue(ao),
ActionWithVessel(ao),
usepbc(false),
updateFreq(0),
-lastUpdate(0)
+mycatoms(NULL), // This will be destroyed by ActionWithVesel
+myvalues(NULL), // This will be destroyed by ActionWithVesel
+usespecies(false)
{
if( keywords.exists("NOPBC") ){
bool nopbc=!usepbc; parseFlag("NOPBC",nopbc);
usepbc=!nopbc;
}
+ if( keywords.exists("SPECIES") ) usespecies=true;
if( keywords.exists("NL_STRIDE") ) parse("NL_STRIDE",updateFreq);
- if(updateFreq>0) log.printf(" Updating contributors every %d steps.\n",updateFreq);
- else log.printf(" Updating contributors every step.\n");
+ if(updateFreq>0){
+ firsttime=true;
+ log.printf(" Updating contributors every %d steps.\n",updateFreq);
+ } else {
+ firsttime=false; contributorsAreUnlocked=true; // This will lock during first prepare step methinks
+ log.printf(" Updating contributors every step.\n");
+ }
}
-void MultiColvarBase::addColvar( const std::vector<unsigned>& newatoms ){
- DynamicList<unsigned> newlist; newlist.setupMPICommunication( comm );
- for(unsigned i=0;i<newatoms.size();++i) newlist.addIndexToList( newatoms[i] );
- taskList.addIndexToList( colvar_atoms.size() );
- colvar_atoms.push_back( newlist );
+void MultiColvarBase::copyAtomListToFunction( MultiColvarBase* myfunction ){
+ for(unsigned i=0;i<all_atoms.fullSize();++i) myfunction->all_atoms.addIndexToList( all_atoms(i) );
+}
+
+void MultiColvarBase::copyActiveAtomsToFunction( MultiColvarBase* myfunction, const unsigned& start ){
+ for(unsigned i=0;i<all_atoms.getNumberActive();++i){
+ unsigned iatom=all_atoms.linkIndex( i );
+ myfunction->all_atoms.activate( start + iatom );
+ }
}
void MultiColvarBase::setupMultiColvarBase(){
- // Activate everything
- taskList.activateAll();
- for(unsigned i=0;i<colvar_atoms.size();++i) colvar_atoms[i].activateAll();
- // Resize stuff in derived classes
- resizeDynamicArrays();
- // Resize local arrays
- resizeLocalArrays();
- // And resize the local vessels
- resizeFunctions();
-}
+ // Setup decoder array
+ if( !usespecies && ablocks.size()<4 ){
+ decoder.resize( ablocks.size() ); unsigned code=1;
+ for(unsigned i=0;i<ablocks.size();++i){ decoder[ablocks.size()-1-i]=code; code *= nblock; }
+ } else if( ablocks.size()==1 ) {
+ // Setup coordination sphere
+ csphere_atoms.resize( getFullNumberOfTasks() ); unsigned nflags=0;
+ for(unsigned i=0;i<getFullNumberOfTasks();++i){
+ for(unsigned j=0;j<ablocks[0].size();++j){
+ if( !same_index( getActiveTask(i), ablocks[0][j] ) ){
+ csphere_atoms[i].addIndexToList( ablocks[0][j] ); nflags++;
+ }
+ }
+ csphere_atoms[i].activateAll();
+ }
+ csphere_flags.resize( nflags, 0 );
+ }
+ // Do an initial task list update
+ finishTaskListUpdate();
+ // Setup underlying ActionWithVessel
+ readVesselKeywords();
+}
+
void MultiColvarBase::prepare(){
- bool updatetime=false;
- if( contributorsAreUnlocked ){
- taskList.mpi_gatherActiveMembers( comm );
- mpi_gatherActiveMembers( comm, colvar_atoms );
- lockContributors(); updatetime=true;
- }
- if( updateFreq>0 && (getStep()-lastUpdate)>=updateFreq ){
- taskList.activateAll();
- for(unsigned i=0;i<taskList.getNumberActive();++i) colvar_atoms[i].activateAll();
- unlockContributors(); updatetime=true; lastUpdate=getStep();
- }
- if(updatetime){
- // Resize stuff in derived classes
- resizeDynamicArrays();
- // Resize local arrays
- resizeLocalArrays();
- // Resize vessels
- resizeFunctions();
+ if( contributorsAreUnlocked ) lockContributors();
+ if( updateFreq>0 ){
+ if( firsttime || getStep()%updateFreq==0 ){ firsttime=false; unlockContributors(); }
}
}
+void MultiColvarBase::updateCSphereArrays(){
+ if( !usespecies || isDensity() ) return ;
+
+ if( contributorsAreUnlocked ){
+ if( !serialCalculation() ) comm.Sum( csphere_flags );
+ unsigned istart=0;
+ for(unsigned i=0;i<getCurrentNumberOfActiveTasks();++i){
+ csphere_atoms[i].deactivateAll();
+ for(unsigned j=0;j<csphere_atoms[i].fullSize();++j){
+ if( csphere_flags[istart+j]==0 ) csphere_atoms[i].activate(j);
+ }
+ csphere_atoms[i].updateActiveMembers();
+ istart += csphere_atoms[i].fullSize();
+ }
+ plumed_assert( istart==csphere_flags.size() );
+ } else {
+ for(unsigned i=0;i<csphere_flags.size();++i) csphere_flags[i]=0;
+ }
+}
+
void MultiColvarBase::resizeLocalArrays(){
atoms_with_derivatives.clear();
for(unsigned i=0;i<getNumberOfAtoms();++i) atoms_with_derivatives.addIndexToList( i );
@@ -108,54 +139,102 @@ void MultiColvarBase::resizeLocalArrays(){
atomsWithCatomDer.clear();
for(unsigned i=0;i<getNumberOfAtoms();++i) atomsWithCatomDer.addIndexToList( i );
atomsWithCatomDer.deactivateAll();
- central_derivs.resize( getNumberOfAtoms() );
- for(unsigned i=0;i<central_derivs.size();++i) central_derivs[i].zero();
// Resize tempory forces array
forcesToApply.resize( getNumberOfDerivatives() );
}
-void MultiColvarBase::performTask( const unsigned& j ){
+bool MultiColvarBase::setupCurrentAtomList( const unsigned& taskCode ){
+ if( usespecies ){
+ natomsper=1;
+ current_atoms[0]=getBaseQuantityIndex( taskCode );
+ if( contributorsAreUnlocked ){
+ csphere_start=0; for(unsigned i=0;i<taskCode;++i) csphere_start+=csphere_atoms[i].fullSize();
+ }
+ for(unsigned j=0;j<ablocks.size();++j){
+ for(unsigned i=0;i<csphere_atoms[taskCode].getNumberActive();++i){
+ current_atoms[natomsper]=getBaseQuantityIndex( csphere_atoms[taskCode][i] );
+ natomsper++;
+ }
+ }
+ if( natomsper==1 ) return isDensity();
+ } else if( current_atoms.size()<4 ){
+ natomsper=current_atoms.size();
+ unsigned scode = taskCode;
+ for(unsigned i=0;i<ablocks.size();++i){
+ unsigned ind=std::floor( scode / decoder[i] );
+ current_atoms[i]=getBaseQuantityIndex( ablocks[i][ind] );
+ scode -= ind*decoder[i];
+ }
+ } else {
+ natomsper=current_atoms.size();
+ for(unsigned i=0;i<ablocks.size();++i) current_atoms[i]=getBaseQuantityIndex( ablocks[i][taskCode] );
+ }
+ return true;
+}
+
+void MultiColvarBase::performTask(){
// Currently no atoms have derivatives so deactivate those that are active
atoms_with_derivatives.deactivateAll();
+ // Currently no central atoms have derivatives so deactive them all
+ atomsWithCatomDer.deactivateAll();
+ // Retrieve the atom list
+ if( !setupCurrentAtomList( getCurrentTask() ) ) return;
// Do nothing if there are no active atoms in the colvar
- if( colvar_atoms[current].getNumberActive()==0 ){
- setElementValue(1,0.0);
- return;
- }
+// if( colvar_atoms[current].getNumberActive()==0 ){
+// setElementValue(1,0.0);
+// return;
+// } Add retrieve atoms here
+
// Do a quick check on the size of this contribution
calculateWeight();
- if( getElementValue(1)<getTolerance() ) return;
+ if( getElementValue(1)<getTolerance() ){
+ updateActiveAtoms();
+ return;
+ }
// Compute everything
- double vv=doCalculation( j );
+ double vv=doCalculation();
// Set the value of this element in ActionWithVessel
setElementValue( 0, vv );
return;
}
+double MultiColvarBase::doCalculation(){
+ double val=compute(); updateActiveAtoms();
+ return val;
+}
+
Vector MultiColvarBase::retrieveCentralAtomPos(){
ibox=getPbc().getInvBox().transpose();
- // Prepare to retrieve central atom
- for(unsigned i=0;i<atomsWithCatomDer.getNumberActive();++i){
- central_derivs[ atomsWithCatomDer[i] ].zero();
+ if( atomsWithCatomDer.getNumberActive()==0 ){
+ Vector cvec = calculateCentralAtomPosition();
+ for(unsigned i=0;i<3;++i) setElementValue( 2+i, cvec[i] );
+ return cvec;
}
- atomsWithCatomDer.deactivateAll();
-
- // Retrieve the central atom position
- return calculateCentralAtomPosition();
+ Vector cvec;
+ for(unsigned i=0;i<3;++i) cvec[i]=getElementValue( 2+i );
+ return cvec;
}
void MultiColvarBase::addCentralAtomDerivatives( const unsigned& iatom, const Tensor& der ){
plumed_dbg_assert( iatom<getNumberOfAtoms() );
atomsWithCatomDer.activate(iatom);
- central_derivs[iatom] += der;
+ unsigned nder = 3*getNumberOfAtoms() + 9;
+ for(unsigned i=0;i<3;++i){
+ for(unsigned j=0;j<3;++j){
+ addElementDerivative( (2+j)*nder + 3*iatom + i, der(j,i) );
+ }
+ }
}
-double MultiColvarBase::getCentralAtomDerivative( const unsigned& iatom, const unsigned jcomp, const Vector& df ) const {
+double MultiColvarBase::getCentralAtomDerivative( const unsigned& iatom, const unsigned& jcomp, const Vector& df ){
plumed_dbg_assert( atomsWithCatomDer.isActive(iatom) && jcomp<3 );
- return df[0]*central_derivs[iatom](0,jcomp) + df[1]*central_derivs[iatom](1,jcomp) + df[2]*central_derivs[iatom](2,jcomp);
+ unsigned nder = 3*getNumberOfAtoms() + 9;
+ return df[0]*getElementDerivative( 2*nder + 3*iatom + jcomp ) +
+ df[1]*getElementDerivative( 3*nder + 3*iatom + jcomp ) +
+ df[2]*getElementDerivative( 4*nder + 3*iatom + jcomp );
}
Vector MultiColvarBase::getSeparation( const Vector& vec1, const Vector& vec2 ) const {
@@ -163,6 +242,68 @@ Vector MultiColvarBase::getSeparation( const Vector& vec1, const Vector& vec2 )
else{ return delta( vec1, vec2 ); }
}
+unsigned MultiColvarBase::getInternalIndex( const AtomNumber& iatom ) const {
+ plumed_massert( usespecies && ablocks.size()==1, "This should only be used to interogate atom centered multicolvars");
+ unsigned katom=0; bool found=false;
+ for(unsigned i=0;i<ablocks[0].size();++i){
+ if( all_atoms[ all_atoms.linkIndex(ablocks[0][i]) ]==iatom ){
+ katom=i; found=true;
+ }
+ }
+ if(!true) error("could not find required atom in any of the quantities calculated by the base multicolvar");
+ return katom;
+}
+
+void MultiColvarBase::getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices ){
+ indices[jstore]=3*atoms_with_derivatives.getNumberActive() + 9;
+ if( indices[jstore]>maxder ) error("too many derivatives to store. Run with LOWMEM");
+
+ unsigned kder = ntotal + jstore*maxder;
+ for(unsigned jder=0;jder<atoms_with_derivatives.getNumberActive();++jder){
+ unsigned iatom = 3*atoms_with_derivatives[jder];
+ for(unsigned icomp=0;icomp<3;++icomp){ indices[ kder ] = iatom+icomp; kder++; }
+ }
+ unsigned nbase = 3*getNumberOfAtoms();
+ for(unsigned icomp=0;icomp<9;++icomp){ indices[ kder ] = nbase + icomp; kder++; }
+}
+
+void MultiColvarBase::getCentralAtomIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices ) const {
+ indices[jstore]=3*atomsWithCatomDer.getNumberActive();
+ if( indices[jstore]>maxder ) error("too many derivatives to store. Run with LOWMEM");
+
+ unsigned kder = ntotal + jstore*maxder;
+ for(unsigned jder=0;jder<atomsWithCatomDer.getNumberActive();++jder){
+ unsigned iatom = 3*atomsWithCatomDer[jder];
+ for(unsigned icomp=0;icomp<3;++icomp){ indices[ kder ] = iatom+icomp; kder++; }
+ }
+}
+
+void MultiColvarBase::activateIndexes( const unsigned& istart, const unsigned& number, const std::vector<unsigned>& indexes ){
+ plumed_assert( number>0 );
+ for(unsigned i=0;i<number-9;i+=3){
+ plumed_dbg_assert( indexes[istart+i]%3==0 ); unsigned iatom=indexes[istart+i]/3;
+ atoms_with_derivatives.activate( iatom );
+ }
+}
+
+void MultiColvarBase::quotientRule( const unsigned& uder, const unsigned& vder, const unsigned& iout ){
+ unsigned ustart=uder*getNumberOfDerivatives();
+ unsigned vstart=vder*getNumberOfDerivatives();
+ unsigned istart=iout*getNumberOfDerivatives();
+ double weight = getElementValue( vder ), pref = getElementValue( uder ) / (weight*weight);
+ for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
+ unsigned n=3*atoms_with_derivatives[i], nx=n, ny=n+1, nz=n+2;
+ setElementDerivative( istart + nx, getElementDerivative(ustart+nx) / weight - pref*getElementDerivative(vstart+nx) );
+ setElementDerivative( istart + ny, getElementDerivative(ustart+ny) / weight - pref*getElementDerivative(vstart+ny) );
+ setElementDerivative( istart + nz, getElementDerivative(ustart+nz) / weight - pref*getElementDerivative(vstart+nz) );
+ }
+ unsigned vbase=3*getNumberOfAtoms();
+ for(unsigned i=0;i<9;++i){
+ setElementDerivative( istart + vbase + i, getElementDerivative(ustart+vbase+i) / weight - pref*getElementDerivative(vstart+vbase+i) );
+ }
+ thisval_wasset[iout]=false; setElementValue( iout, getElementValue(uder) / weight );
+}
+
void MultiColvarBase::mergeDerivatives( const unsigned& ider, const double& df ){
unsigned vstart=getNumberOfDerivatives()*ider;
for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
@@ -179,15 +320,26 @@ void MultiColvarBase::mergeDerivatives( const unsigned& ider, const double& df )
void MultiColvarBase::clearDerivativesAfterTask( const unsigned& ider ){
unsigned vstart=getNumberOfDerivatives()*ider;
- for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
- unsigned iatom=vstart+3*atoms_with_derivatives[i];
- setElementDerivative( iatom, 0.0 ); iatom++;
- setElementDerivative( iatom, 0.0 ); iatom++;
- setElementDerivative( iatom, 0.0 );
- }
- unsigned nvir=vstart+3*getNumberOfAtoms();
- for(unsigned j=0;j<9;++j){
- setElementDerivative( nvir, 0.0 ); nvir++;
+ thisval_wasset[ider]=false; setElementValue( ider, 0.0 );
+ thisval_wasset[ider]=false;
+ if( ider>1 && ider<5 ){
+ for(unsigned i=0;i<atomsWithCatomDer.getNumberActive();++i){
+ unsigned iatom=vstart+3*atomsWithCatomDer[i];
+ setElementDerivative( iatom, 0.0 ); iatom++;
+ setElementDerivative( iatom, 0.0 ); iatom++;
+ setElementDerivative( iatom, 0.0 );
+ }
+ } else {
+ for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
+ unsigned iatom=vstart+3*atoms_with_derivatives[i];
+ setElementDerivative( iatom, 0.0 ); iatom++;
+ setElementDerivative( iatom, 0.0 ); iatom++;
+ setElementDerivative( iatom, 0.0 );
+ }
+ unsigned nvir=vstart+3*getNumberOfAtoms();
+ for(unsigned j=0;j<9;++j){
+ setElementDerivative( nvir, 0.0 ); nvir++;
+ }
}
}
@@ -195,20 +347,66 @@ void MultiColvarBase::apply(){
if( getForcesFromVessels( forcesToApply ) ) setForcesOnAtoms( forcesToApply );
}
-StoreCentralAtomsVessel* MultiColvarBase::getCentralAtoms(){
- // Look to see if vectors have already been created
- StoreCentralAtomsVessel* mycatoms;
- for(unsigned i=0;i<getNumberOfVessels();++i){
- mycatoms=dynamic_cast<StoreCentralAtomsVessel*>( getPntrToVessel(i) );
- if( mycatoms ) return mycatoms;
+bool MultiColvarBase::setupCentralAtomVessel(){
+ if( mycatoms ) return true;
+ vesselbase::VesselOptions da("","",0,"",this);
+ mycatoms=new StoreCentralAtomsVessel(da);
+ addVessel(mycatoms);
+ return false;
+}
+
+void MultiColvarBase::useInMultiColvarFunction( const bool store_director ){
+ // Create the store central atoms vessel
+ if( setupCentralAtomVessel() ) return;
+
+ // Create the store values vessel
+ vesselbase::VesselOptions ta("","",0,"",this);
+ myvalues=new StoreColvarVessel(ta); // Currently ignoring weights - good thing?
+ addVessel(myvalues);
+
+ // Make sure resizing of vessels is done
+ resizeFunctions();
+ return;
+}
+
+Vector MultiColvarBase::getCentralAtomPosition( const unsigned& iatom ) const {
+ plumed_dbg_assert( mycatoms );
+ return mycatoms->getPosition( iatom );
+}
+
+void MultiColvarBase::addCentralAtomDerivativeToFunction( const unsigned& iatom, const unsigned& jout, const unsigned& base_cv_no, const Vector& der, MultiColvarFunction* func ){
+ plumed_dbg_assert( mycatoms );
+ if( usingLowMem() ){
+ mycatoms->recompute( iatom, 0 ); ;
+ mycatoms->addAtomsDerivatives( 0, jout, base_cv_no, der, func );
+ } else{
+ mycatoms->addAtomsDerivatives( iatom, jout, base_cv_no, der, func );
}
+}
+
+void MultiColvarBase::getValueForTask( const unsigned& iatom, std::vector<double>& vals ) const {
+ plumed_dbg_assert( myvalues && vals.size() );
+ vals[0]=myvalues->getValue( iatom );
+}
+
+void MultiColvarBase::addWeightedValueDerivatives( const unsigned& iatom, const unsigned& base_cv_no, const double& weight, MultiColvarFunction* func ){
+ plumed_dbg_assert( myvalues );
+ if( usingLowMem() ){
+ myvalues->recompute( iatom, 0 );
+ myvalues->chainRuleForComponent( 0, 0, base_cv_no, weight, func );
+ } else {
+ myvalues->chainRuleForComponent( iatom, 0, base_cv_no, weight, func );
+ }
+}
- // Create the vessel
- vesselbase::VesselOptions da("","",0,"",this);
- StoreCentralAtomsVessel* sv=new StoreCentralAtomsVessel(da);
- addVessel(sv); resizeFunctions(); // This makes sure resizing of vessels is done
- return sv;
+void MultiColvarBase::finishWeightedAverageCalculation( MultiColvarFunction* func ){
+ func->quotientRule( 0, 1, 0 );
}
+
+void MultiColvarBase::addOrientationDerivativesToBase( const unsigned& iatom, const unsigned& jstore, const unsigned& base_cv_no,
+ const std::vector<double>& weight, MultiColvarFunction* func ) {
+ plumed_merror("This should not be called - invalid use of multicolvar in function");
+}
}
}
diff --git a/src/multicolvar/MultiColvarBase.h b/src/multicolvar/MultiColvarBase.h
index be756e02f2c82bd6f1434b26b939b27d502328f1..faa8e095149d3da21bed18e81e80af4a4c54bc78 100644
--- a/src/multicolvar/MultiColvarBase.h
+++ b/src/multicolvar/MultiColvarBase.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -26,6 +26,7 @@
#include "core/ActionWithValue.h"
#include "tools/DynamicList.h"
#include "vesselbase/ActionWithVessel.h"
+#include "StoreColvarVessel.h"
#include "StoreCentralAtomsVessel.h"
#include <vector>
@@ -39,7 +40,6 @@ class MultiColvarBase :
{
friend class ActionVolume;
friend class VolumeSubcell;
-friend class StoreColvarVessel;
friend class StoreCentralAtomsVessel;
friend class MultiColvarFunction;
friend class MultiColvar;
@@ -48,43 +48,58 @@ private:
bool usepbc;
/// Everything for controlling the updating of neighbor lists
int updateFreq;
- unsigned lastUpdate;
+ bool firsttime;
/// The list of all the atoms involved in the colvar
DynamicList<AtomNumber> all_atoms;
-/// A dynamic list containing those atoms with derivatives
- DynamicList<unsigned> atoms_with_derivatives;
-/// The lists of the atoms involved in each of the individual colvars
-/// note these refer to the atoms in all_atoms
- std::vector< DynamicList<unsigned> > colvar_atoms;
/// Variables used for central atoms
Tensor ibox;
DynamicList<unsigned> atomsWithCatomDer;
- std::vector<Tensor> central_derivs;
/// The forces we are going to apply to things
std::vector<double> forcesToApply;
+/// Neighbor lists for coordination numbers
+ unsigned csphere_start;
+ std::vector<unsigned> csphere_flags;
+ std::vector<DynamicList<unsigned> > csphere_atoms;
+/// A copy of the vessel containing the catoms
+ StoreCentralAtomsVessel* mycatoms;
+/// A copy of the vessel containg the values of each colvar
+ StoreColvarVessel* myvalues;
+/// This does neighbor list update for atom centered symmetry functions
+ void updateCSphereArrays();
/// This resizes the local arrays after neighbor list updates and during initialization
void resizeLocalArrays();
protected:
-/// Add a colvar to the set of colvars we are calculating (in practise just a list of atoms)
- void addColvar( const std::vector<unsigned>& newatoms );
+/// A dynamic list containing those atoms with derivatives
+ DynamicList<unsigned> atoms_with_derivatives;
+/// Using the species keyword to read in atoms
+ bool usespecies;
+/// Number of atoms in each block
+ unsigned nblock;
+/// This is used when turning cvcodes into atom numbers
+ std::vector<unsigned> decoder;
+/// Blocks of atom numbers
+ std::vector< std::vector<unsigned> > ablocks;
+/// Number of atoms in the cv - set at start of calculation
+ unsigned natomsper;
+/// Vector containing the indices of the current atoms
+ std::vector<unsigned> current_atoms;
/// Finish setting up the multicolvar base
void setupMultiColvarBase();
/// Get the separation between a pair of vectors
Vector getSeparation( const Vector& vec1, const Vector& vec2 ) const ;
/// Do we use pbc to calculate this quantity
bool usesPbc() const ;
-/// Return the index of an atom
- unsigned getAtomIndex( const unsigned& ) const ;
-/// Add some derivatives for an atom
- void addAtomsDerivatives(const int&,const Vector&);
-/// Add some derivatives to the virial
+/// Add some derivatives for an atom
+ void addAtomsDerivatives(const unsigned&, const unsigned&, const Vector& );
+/// Add some derivatives for a box
+ void addBoxDerivatives(const unsigned&, const Tensor& );
+/// Add some derivatives of the value to the virial
void addBoxDerivatives(const Tensor&);
/// Retrieve derivative of central atom position wrt jcomp'th component of position of iatom'th atom
- double getCentralAtomDerivative( const unsigned& iatom, const unsigned jcomp, const Vector& df ) const ;
+ double getCentralAtomDerivative( const unsigned& iatom, const unsigned& jcomp, const Vector& df );
/// Set a weight for this colvar (used in MEAN and HISTOGRAM)
void setWeight( const double& weight );
/// Set the derivative of the weight (used in MEAN and HISTOGRAM)
- void addAtomsDerivativeOfWeight( const unsigned& i, const Vector& wder );
void addBoxDerivativesOfWeight( const Tensor& vir );
/// Get the number of atoms in this particular colvar
unsigned getNAtoms() const;
@@ -92,39 +107,78 @@ protected:
void removeAtomRequest( const unsigned& aa, const double& weight );
/// Add derivative of central atom position wrt to position of iatom'th atom
void addCentralAtomDerivatives( const unsigned& iatom, const Tensor& der );
+/// Get the indices for the central atom
+ void getCentralAtomIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices ) const ;
+/// This sets up the list of atoms that are involved in this colvar
+ bool setupCurrentAtomList( const unsigned& taskCode );
+/// This is used internally to setup central atom stuff
+ bool setupCentralAtomVessel();
public:
MultiColvarBase(const ActionOptions&);
~MultiColvarBase(){}
static void registerKeywords( Keywords& keys );
+/// Used in setupCurrentAtomList to get atom numbers
+/// Base quantities are different in MultiColvar and MultiColvarFunction
+ virtual unsigned getBaseQuantityIndex( const unsigned& code )=0;
+/// Are two indexes corresponding to the same thing
+ virtual bool same_index( const unsigned&, const unsigned& )=0;
/// Prepare for the calculation
void prepare();
- virtual void resizeDynamicArrays()=0;
-/// Return the size of the colvar_atoms array
- unsigned getNumberOfColvars() const ;
+// virtual void resizeDynamicArrays()=0;
/// Perform one of the tasks
- void performTask( const unsigned& j );
+ void performTask();
/// And a virtual function which actually computes the colvar
- virtual double doCalculation( const unsigned& j )=0;
+ virtual double doCalculation();
+/// Update the atoms that have derivatives
+ virtual void updateActiveAtoms()=0;
+/// This is replaced once we have a function to calculate the cv
+ virtual double compute()=0;
/// These replace the functions in ActionWithVessel to make the code faster
void mergeDerivatives( const unsigned& ider, const double& df );
void clearDerivativesAfterTask( const unsigned& ider );
/// Apply the forces from this action
void apply();
-/// Deactivate one of the tasks
- void deactivate_task();
/// Get the number of derivatives for this action
unsigned getNumberOfDerivatives(); // N.B. This is replacing the virtual function in ActionWithValue
+/// Get the number of quantities that are calculated each time
+ virtual unsigned getNumberOfQuantities();
/// Retrieve the position of the central atom
Vector retrieveCentralAtomPos();
/// You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations
virtual void calculateWeight();
/// A virtual routine to get the position of the central atom - used for things like cv gradient
virtual Vector calculateCentralAtomPosition()=0;
+/// Get the list of indices that have derivatives
+ void getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices );
/// Is this a density?
virtual bool isDensity(){ return false; }
-/// Return a pointer to the vessel that stores the positions of
-/// all the central atoms
- StoreCentralAtomsVessel* getCentralAtoms();
+/// Store central atoms so that this can be used in a function
+ virtual void useInMultiColvarFunction( const bool store_director );
+/// Copy the list of atoms involved to a second MultiColvarBase (used by functions)
+ void copyAtomListToFunction( MultiColvarBase* myfunction );
+/// Calculate and store getElementValue(uder)/getElementValue(vder) and its derivatives in getElementValue(iout)
+ void quotientRule( const unsigned& uder, const unsigned& vder, const unsigned& iout );
+/// Return the number of the colvar in which iatom is the first atom
+ unsigned getInternalIndex( const AtomNumber& iatom ) const ;
+/// Make sure the same list of atoms is active in a function
+ void copyActiveAtomsToFunction( MultiColvarBase* myfunction, const unsigned& start );
+/// Activate the atoms that have derivatives from a storeDataVessel
+ void activateIndexes( const unsigned& istart, const unsigned& number, const std::vector<unsigned>& indexes );
+/// Get the position of the iatom th central atom (used in multicolvarfunction)
+ Vector getCentralAtomPosition( const unsigned& iatom ) const ;
+/// Add central atom derivatives to a multicolvar function
+ void addCentralAtomDerivativeToFunction( const unsigned& iatom, const unsigned& jout, const unsigned& base_cv_no, const Vector& der, MultiColvarFunction* func );
+/// Get the value for this task
+ virtual void getValueForTask( const unsigned& iatom, std::vector<double>& vals ) const ;
+/// Used to accumulate values
+ virtual void addWeightedValueDerivatives( const unsigned& iatom, const unsigned& base_cv_no, const double& weight, MultiColvarFunction* func );
+/// Used for calculating weighted averages
+ virtual void finishWeightedAverageCalculation( MultiColvarFunction* func );
+/// Add derivatives to the orientations
+ virtual void addOrientationDerivativesToBase( const unsigned& iatom, const unsigned& jstore, const unsigned& base_cv_no,
+ const std::vector<double>& weight, MultiColvarFunction* func );
+/// This is true if multicolvar is calculating a vector or if the multicolvar is the density
+ virtual bool hasDifferentiableOrientation() const { return false; }
};
inline
@@ -132,24 +186,12 @@ unsigned MultiColvarBase::getNumberOfDerivatives(){
return 3*getNumberOfAtoms()+9;
}
-inline
-unsigned MultiColvarBase::getAtomIndex( const unsigned& iatom ) const {
- plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() );
- return all_atoms.linkIndex( colvar_atoms[current][iatom] );
-}
-
inline
void MultiColvarBase::removeAtomRequest( const unsigned& i, const double& weight ){
+ plumed_dbg_assert( usespecies );
if( !contributorsAreUnlocked ) return;
plumed_dbg_assert( weight<getTolerance() );
- if( weight<getNLTolerance() ) colvar_atoms[current].deactivate( i );
-}
-
-inline
-void MultiColvarBase::deactivate_task(){
- if( !contributorsAreUnlocked ) return; // Deactivating tasks only possible during neighbor list update
- colvar_atoms[current].deactivateAll(); // Deactivate all atom requests for this colvar
- ActionWithVessel::deactivate_task(); // Deactivate the colvar from the list
+ if( weight<getNLTolerance() ) csphere_flags[ csphere_start + i ] = 1;
}
inline
@@ -158,35 +200,31 @@ bool MultiColvarBase::usesPbc() const {
}
inline
-unsigned MultiColvarBase::getNumberOfColvars() const {
- return colvar_atoms.size();
+unsigned MultiColvarBase::getNumberOfQuantities(){
+ return 5;
}
inline
unsigned MultiColvarBase::getNAtoms() const {
- return colvar_atoms[current].getNumberActive();
+ return natomsper; // colvar_atoms[current].getNumberActive();
}
inline
-void MultiColvarBase::addAtomsDerivatives(const int& iatom, const Vector& der){
+void MultiColvarBase::addAtomsDerivatives(const unsigned& ielem, const unsigned& iatom, const Vector& der ){
atoms_with_derivatives.activate(iatom);
- addElementDerivative( 3*iatom+0, der[0] );
- addElementDerivative( 3*iatom+1, der[1] );
- addElementDerivative( 3*iatom+2, der[2] );
-}
+ unsigned ibase=ielem*getNumberOfDerivatives() + 3*iatom;
+ for(unsigned i=0;i<3;++i) addElementDerivative( ibase + i, der[i] );
+}
+
+inline
+void MultiColvarBase::addBoxDerivatives(const unsigned& ielem, const Tensor& vir ){
+ unsigned ibase=ielem*getNumberOfDerivatives() + 3*getNumberOfAtoms();
+ for(unsigned i=0;i<3;++i) for(unsigned j=0;j<3;++j) addElementDerivative( ibase+3*i+j, vir(i,j) );
+}
inline
void MultiColvarBase::addBoxDerivatives(const Tensor& vir){
- unsigned nstart=3*getNumberOfAtoms();
- addElementDerivative( nstart+0, vir(0,0) );
- addElementDerivative( nstart+1, vir(0,1) );
- addElementDerivative( nstart+2, vir(0,2) );
- addElementDerivative( nstart+3, vir(1,0) );
- addElementDerivative( nstart+4, vir(1,1) );
- addElementDerivative( nstart+5, vir(1,2) );
- addElementDerivative( nstart+6, vir(2,0) );
- addElementDerivative( nstart+7, vir(2,1) );
- addElementDerivative( nstart+8, vir(2,2) );
+ addBoxDerivatives( 0, vir );
}
inline
@@ -199,27 +237,9 @@ void MultiColvarBase::setWeight( const double& weight ){
setElementValue( 1, weight );
}
-inline
-void MultiColvarBase::addAtomsDerivativeOfWeight( const unsigned& iatom, const Vector& wder ){
- unsigned nstart = 3*getNumberOfAtoms() + 9 + 3*iatom;
- atoms_with_derivatives.activate(iatom);
- addElementDerivative( nstart + 0, wder[0] );
- addElementDerivative( nstart + 1, wder[1] );
- addElementDerivative( nstart + 2, wder[2] );
-}
-
inline
void MultiColvarBase::addBoxDerivativesOfWeight( const Tensor& vir ){
- int nstart = 6*getNumberOfAtoms() + 9;
- addElementDerivative( nstart+0, vir(0,0) );
- addElementDerivative( nstart+1, vir(0,1) );
- addElementDerivative( nstart+2, vir(0,2) );
- addElementDerivative( nstart+3, vir(1,0) );
- addElementDerivative( nstart+4, vir(1,1) );
- addElementDerivative( nstart+5, vir(1,2) );
- addElementDerivative( nstart+6, vir(2,0) );
- addElementDerivative( nstart+7, vir(2,1) );
- addElementDerivative( nstart+8, vir(2,2) );
+ addBoxDerivatives( 1, vir );
}
}
diff --git a/src/multicolvar/MultiColvarFunction.cpp b/src/multicolvar/MultiColvarFunction.cpp
index 85f0a32f3968ff2dc033f7180bbd5dda7f14f511..99e58c4fc38399db6ffb60a4cd19475414b986fa 100644
--- a/src/multicolvar/MultiColvarFunction.cpp
+++ b/src/multicolvar/MultiColvarFunction.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -22,6 +22,7 @@
#include "MultiColvarFunction.h"
#include "core/PlumedMain.h"
#include "core/ActionSet.h"
+#include "tools/Pbc.h"
#include "MultiColvarBase.h"
namespace PLMD {
@@ -29,107 +30,213 @@ namespace multicolvar {
void MultiColvarFunction::registerKeywords( Keywords& keys ){
MultiColvarBase::registerKeywords( keys );
- keys.add("compulsory","ARG","the label of the action that calculates the vectors we are interested in");
+ keys.add("compulsory","ARG","the labels of the action that calculates the multicolvars we are interested in");
+ keys.reset_style("NUMERICAL_DERIVATIVES","hidden");
}
MultiColvarFunction::MultiColvarFunction(const ActionOptions& ao):
Action(ao),
MultiColvarBase(ao)
{
- std::string mlab; parse("ARG",mlab);
- log.printf(" using vectors calculated by action %s\n",mlab.c_str() );
- mycolv = plumed.getActionSet().selectWithLabel<multicolvar::MultiColvarBase*>(mlab);
- if(!mycolv) error("action labeled " + mlab + " does not exist or is not a multicolvar");
- addDependency(mycolv);
-
- // Checks for neighbor list
- if( mycolv->updateFreq>0 && updateFreq>0 ){
- if( updateFreq%mycolv->updateFreq!=0 ) error("update frequency must be a multiple of the update frequency in the base colvar");
+ // Read in the arguments
+ std::string mname; std::vector<std::string> mlabs; parseVector("ARG",mlabs);
+ log.printf(" using colvars calculated by actions ");
+ for(unsigned i=0;i<mlabs.size();++i){
+ log.printf("%s ",mlabs[i].c_str() );
+ MultiColvarBase* mycolv = plumed.getActionSet().selectWithLabel<MultiColvarBase*>(mlabs[i]);
+ if(!mycolv) error("action labeled " + mlabs[i] + " does not exist or is not a multicolvar");
+ // Check all base multicolvars are of same type
+ if( i==0 ){
+ mname = mycolv->getName();
+ if( mycolv->isPeriodic() ) error("multicolvar functions don't work with this multicolvar");
+ } else {
+ if( mname!=mycolv->getName() ) error("All input multicolvars must be of same type");
+ }
+ // Make sure we use low memory option in base colvar
+ mycolv->setLowMemOption( usingLowMem() );
+ // Checks for neighbor list
+ if( mycolv->updateFreq>0 && updateFreq>0 ){
+ if( updateFreq%mycolv->updateFreq!=0 ) error("update frequency must be a multiple of the update frequency in the base colvar");
+ }
+ // Add the dependency
+ addDependency(mycolv);
+ // And store the multicolvar base
+ mybasemulticolvars.push_back( mycolv );
+ // And track which variable stores each colvar
+ for(unsigned j=0;j<mycolv->getFullNumberOfTasks();++j) colvar_label.push_back( i );
}
-
- // Retrieve the central atoms
- catoms = mycolv->getCentralAtoms();
+ log.printf("\n");
}
-void MultiColvarFunction::completeSetup(){
- // Copy list of atoms involved from base multicolvar
- for(unsigned i=0;i<mycolv->all_atoms.fullSize();++i){
- all_atoms.addIndexToList( mycolv->all_atoms(i) );
+void MultiColvarFunction::buildSymmetryFunctionLists( const bool store_director ){
+ if( mybasemulticolvars.size()>2 ) error("Found too many multicolvars in ARG specification. You can use either 1 or 2");
+
+ // Make sure information is stored in the required multicolvars
+ for(unsigned i=0;i<mybasemulticolvars.size();++i) mybasemulticolvars[i]->useInMultiColvarFunction( store_director );
+
+ usespecies=true; ablocks.resize( 1 );
+ for(unsigned i=0;i<mybasemulticolvars[0]->getFullNumberOfTasks();++i) addTaskToList( i );
+
+ unsigned ntotal=0;
+ for(unsigned i=0;i<mybasemulticolvars.size();++i){
+ ntotal += mybasemulticolvars[i]->getFullNumberOfTasks();
}
+ unsigned k=0, start=0;
+ current_atoms.resize( 1 + ntotal ); ablocks[0].resize( ntotal );
+ for(unsigned i=0;i<mybasemulticolvars.size();++i){
+ for(unsigned j=0;j<mybasemulticolvars[i]->getFullNumberOfTasks();++j){
+ ablocks[0][k]=start + j; k++;
+ }
+ start += mybasemulticolvars[i]->getFullNumberOfTasks();
+ }
+ // Copy lists of atoms involved from base multicolvars
+ for(unsigned i=0;i<mybasemulticolvars.size();++i) mybasemulticolvars[i]->copyAtomListToFunction( this );
+ // Do all setup stuff in MultiColvarBase
setupMultiColvarBase();
}
-Vector MultiColvarFunction::getSeparation( const Vector& vec1, const Vector& vec2 ) const {
- return mycolv->getSeparation( vec1, vec2 );
+void MultiColvarFunction::buildAtomListWithPairs( const bool& allow_intra_group ){
+ if( !allow_intra_group && mybasemulticolvars.size()>2 ) error("only two input multicolvars allowed with this function");
+
+ // Make sure information is stored in the required multicolvars
+ for(unsigned i=0;i<mybasemulticolvars.size();++i) mybasemulticolvars[i]->useInMultiColvarFunction( true );
+
+ usespecies=false; ablocks.resize(2); current_atoms.resize( 2 );
+ if( !allow_intra_group && mybasemulticolvars.size()==2 ){
+ nblock = mybasemulticolvars[0]->getFullNumberOfTasks();
+ if( mybasemulticolvars[1]->getFullNumberOfTasks()>nblock ) nblock = mybasemulticolvars[1]->getFullNumberOfTasks();
+
+ ablocks[0].resize( mybasemulticolvars[0]->getFullNumberOfTasks() );
+ for(unsigned i=0;i<mybasemulticolvars[0]->getFullNumberOfTasks();++i) ablocks[0][i] = i;
+ ablocks[1].resize( mybasemulticolvars[1]->getFullNumberOfTasks() ); unsigned istart = ablocks[0].size();
+ for(unsigned i=0;i<mybasemulticolvars[1]->getFullNumberOfTasks();++i) ablocks[1][i] = istart + i;
+ for(unsigned i=0;i<ablocks[0].size();++i){
+ for(unsigned j=0;j<ablocks[1].size();++j) addTaskToList( i*nblock + j );
+ }
+ } else {
+ nblock = 0; for(unsigned i=0;i<mybasemulticolvars.size();++i) nblock += mybasemulticolvars[i]->getFullNumberOfTasks();
+ ablocks[0].resize( nblock ); ablocks[1].resize( nblock );
+ for(unsigned i=0;i<nblock;++i){ ablocks[0][i] = i; ablocks[1][i] = i; }
+ for(unsigned i=1;i<nblock;++i){
+ for(unsigned j=0;j<i;++j) addTaskToList( i*nblock + j );
+ }
+ }
+ // Copy lists of atoms involved from base multicolvars
+ for(unsigned i=0;i<mybasemulticolvars.size();++i) mybasemulticolvars[i]->copyAtomListToFunction( this );
+ // Do all setup stuff in MultiColvarBase
+ setupMultiColvarBase();
}
-void MultiColvarFunction::unlockContributors(){
- plumed_massert( mycolv->contributorsAreUnlocked,"contributors in base colvar are not unlocked");
- ActionWithVessel::unlockContributors();
-}
+void MultiColvarFunction::finishTaskListUpdate(){
+ updateCSphereArrays(); // Stuff for atom centered symmetry function nlist
+ // Make a list of the tasks required
+ std::vector< std::vector<bool> > additionalTasks( mybasemulticolvars.size() );
+ for(unsigned i=0;i<mybasemulticolvars.size();++i){
+ additionalTasks[i].resize(mybasemulticolvars[i]->getFullNumberOfTasks(), false );
+ }
-void MultiColvarFunction::lockContributors(){
- mycolv->unlockContributors();
- mpi_gatherActiveMembers( comm, colvar_atoms );
-
- // Store tasks that are currently active in base colvar
- unsigned nactive=mycolv->taskList.getNumberActive();
- std::vector<unsigned> active_tasks( nactive );
- for(unsigned i=0;i<nactive;++i) active_tasks[i]=mycolv->taskList[i];
-
- // Now get the tasks that are active from here
- mycolv->taskList.deactivateAll();
- for(unsigned i=0;i<taskList.getNumberActive();++i){
- unsigned n=taskList[i];
- for(unsigned j=0;j<colvar_atoms[n].getNumberActive();++j){
- mycolv->taskList.activate( colvar_atoms[n][j] );
+ // Find what we are required to calculate from base multcolvar
+ for(unsigned i=0;i<getCurrentNumberOfActiveTasks();++i){
+ bool check=setupCurrentAtomList( getActiveTask(i) );
+ plumed_assert( check );
+ for(unsigned j=0;j<natomsper;++j){
+ unsigned mmc = colvar_label[current_atoms[j]];
+ unsigned tl = convertToLocalIndex( current_atoms[j], mmc );
+ additionalTasks[mmc][tl] = true;
}
}
- // Add in tasks that are active in base
- for(unsigned i=0;i<nactive;++i) mycolv->taskList.activate( active_tasks[i] );
-
- // Redo preparation step
- mycolv->prepare();
-
- // And lock
- ActionWithVessel::lockContributors();
-}
-
-void MultiColvarFunction::resizeDynamicArrays(){
- // Copy what is active in the base MultiColvar here
- plumed_dbg_assert( all_atoms.fullSize()==mycolv->all_atoms.fullSize() );
- all_atoms.deactivateAll();
- for(unsigned i=0;i<mycolv->all_atoms.getNumberActive();++i){
- unsigned iatom=mycolv->all_atoms.linkIndex( i );
- all_atoms.activate( iatom );
+ // Deactivate all atoms
+ all_atoms.deactivateAll(); unsigned start=0;
+ for(unsigned i=0;i<mybasemulticolvars.size();++i){
+ // Add these requirements in the base colvar
+ mybasemulticolvars[i]->activateTheseTasks( additionalTasks[i] );
+ // Redo preparation step for base colvar
+ mybasemulticolvars[i]->prepare();
+ // Copy the active atoms here
+ mybasemulticolvars[i]->copyActiveAtomsToFunction( this, start );
+ // Make sure we are updating the correct atoms
+ start += mybasemulticolvars[i]->all_atoms.fullSize();
}
+ // Update all atoms array
all_atoms.updateActiveMembers();
// Request the atoms
ActionAtomistic::requestAtoms( all_atoms.retrieveActiveList() );
- // Rerequest the dependency
- addDependency(mycolv);
+ // Re-add all the dependencies
+ for(unsigned i=0;i<mybasemulticolvars.size();++i) addDependency(mybasemulticolvars[i]);
+ // Resize arrays in MultiColvarBase
+ resizeLocalArrays();
+ // Make numerical derivatives work
+ if( checkNumericalDerivatives() ) numder_store.resize( getNumberOfComponents(), getNumberOfDerivatives() );
}
void MultiColvarFunction::calculate(){
if( checkNumericalDerivatives() ){
// Clear any derivatives in base colvar that were
// accumulated from previous calculations
- mycolv->clearDerivatives();
+ for(unsigned i=0;i<mybasemulticolvars.size();++i) mybasemulticolvars[i]->clearDerivatives();
// And recalculate
- mycolv->calculate();
+ for(unsigned i=0;i<mybasemulticolvars.size();++i) mybasemulticolvars[i]->calculate();
+ // Copy the box from the base multicolvar here
+ unsigned maxb=mybasemulticolvars.size() - 1;
+ changeBox( mybasemulticolvars[maxb]->getBox() );
}
runAllTasks();
}
-double MultiColvarFunction::doCalculation( const unsigned& j ){
- double val=compute(j);
- atoms_with_derivatives.updateActiveMembers();
- return val;
+void MultiColvarFunction::calculateNumericalDerivatives( ActionWithValue* a ){
+ unsigned pstart=0;
+ for(unsigned i=0;i<mybasemulticolvars.size();++i){
+ mybasemulticolvars[i]->calculateAtomicNumericalDerivatives( this, pstart );
+ for(unsigned k=0;k<getNumberOfComponents();++k){
+ Value* val=getPntrToComponent(k);
+ for(unsigned j=0;j<3*mybasemulticolvars[i]->getNumberOfAtoms();++j){
+ numder_store(k,pstart+j) = val->getDerivative(pstart + j);
+ }
+ }
+ pstart += 3*mybasemulticolvars[i]->getNumberOfAtoms();
+ }
+
+ // Note numerical derivatives only work for virial if mybasemulticolvars.size()==1
+ if( mybasemulticolvars.size()==1 ){
+ for(unsigned k=0;k<getNumberOfComponents();++k){
+ Value* val=getPntrToComponent(k);
+ for(unsigned j=0;j<9;++j) numder_store(k,pstart+j) = val->getDerivative(pstart + j);
+ }
+ }
+
+ // Now transfer to multicolvar
+ clearDerivatives();
+ for(unsigned j=0;j<getNumberOfComponents();++j){
+ Value* val=getPntrToComponent(j);
+ for(unsigned i=0;i<getNumberOfDerivatives();++i) val->addDerivative( i, numder_store(j,i) );
+ }
}
-void MultiColvarFunction::calculateNumericalDerivatives( ActionWithValue* a ){
- mycolv->calculateNumericalDerivatives( this );
+void MultiColvarFunction::addStoredDerivative( const unsigned& jout, const unsigned& base_cv_no, const unsigned& base_index, const double& der ){
+ plumed_dbg_assert( jout<getNumberOfQuantities() && base_cv_no<mybasemulticolvars.size() && base_index<mybasemulticolvars[base_cv_no]->getNumberOfDerivatives() );
+
+ unsigned mbase = 3*mybasemulticolvars[base_cv_no]->getNumberOfAtoms(), tbase = 3*getNumberOfAtoms();
+ if( base_index>=mbase ){
+ // Add virial element
+ unsigned jindex = base_index - mbase + tbase;
+ addElementDerivative( jout*getNumberOfDerivatives() + jindex, der );
+ } else {
+ // Add atomic element
+ unsigned offset=0; for(unsigned i=0;i<base_cv_no;++i) offset += 3*mybasemulticolvars[i]->getNumberOfAtoms();
+ unsigned jindex = offset + base_index;
+ plumed_dbg_assert( jindex<3*getNumberOfAtoms() );
+ addElementDerivative( jout*getNumberOfDerivatives() + jindex, der );
+ unsigned iatom = std::floor( jindex / 3 );
+ atoms_with_derivatives.activate( iatom );
+ }
+}
+
+void MultiColvarFunction::updateActiveAtoms(){
+ if( atoms_with_derivatives.updateComplete() ) return;
+ atoms_with_derivatives.emptyActiveMembers();
+ for(unsigned i=0;i<getNumberOfAtoms();++i) atoms_with_derivatives.updateIndex(i);
+ atoms_with_derivatives.sortActiveList();
}
Vector MultiColvarFunction::calculateCentralAtomPosition(){
diff --git a/src/multicolvar/MultiColvarFunction.h b/src/multicolvar/MultiColvarFunction.h
index 8b1f59fe9fdfe102813267105f31deb465b7274d..e2cd2991d5aa69cf23d13d8e2c88f6554d446e5d 100644
--- a/src/multicolvar/MultiColvarFunction.h
+++ b/src/multicolvar/MultiColvarFunction.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -22,6 +22,7 @@
#ifndef __PLUMED_multicolvar_MultiColvarFunction_h
#define __PLUMED_multicolvar_MultiColvarFunction_h
+#include "tools/Matrix.h"
#include "MultiColvarBase.h"
#include "StoreCentralAtomsVessel.h"
@@ -31,26 +32,40 @@ namespace multicolvar {
class MultiColvarFunction : public MultiColvarBase {
private:
/// The multicolvar from which we construct these quantities
- multicolvar::MultiColvarBase* mycolv;
-/// The central atom positions
- multicolvar::StoreCentralAtomsVessel* catoms;
+ std::vector<multicolvar::MultiColvarBase*> mybasemulticolvars;
+/// This is used to keep track of what is calculated where
+ std::vector<unsigned> colvar_label;
+/// Used for numerical derivatives
+ Matrix<double> numder_store;
protected:
-/// Get the number of functions in the multicolvar we are operating on
- unsigned getNumberOfBaseFunctions() const;
-/// Return a pointer to the multicolvar we are using as a base function
- MultiColvarBase* getPntrToMultiColvar();
-/// Finish off the setup of the VectorFunction
- void completeSetup();
+/// Get the total number of tasks that this calculation is based on
+ unsigned getFullNumberOfBaseTasks() const ;
+/// Get the index of the ith colvar we are using
+ unsigned getColvarIndex( const unsigned& ) const;
/// Get the position of one of the central atoms
Vector getPositionOfCentralAtom(const unsigned&) const;
/// Add derivatives of value wrt to an atomic position
- void addCentralAtomsDerivatives( const unsigned& , const Vector& );
-/// Add derivatives of weight wrt to an atomic position
- void addCentralAtomsDerivativesOfWeight( const unsigned& , const Vector& );
-/// We use the distance from mycolv as otherwise numerical derivatives dont work
- Vector getSeparation( const Vector& vec1, const Vector& vec2 ) const ;
+ void addCentralAtomsDerivatives( const unsigned& , const unsigned& , const Vector& );
+/// Retrieve the value calculated by the iatom th base task
+ void getValueForBaseTask( const unsigned& iatom, std::vector<double>& vals );
+/// Add the value and derivatives of this quantity
+ void accumulateWeightedAverageAndDerivatives( const unsigned& iatom, const double& weight );
/// Add derivative wrt to the position of the central atom
void addDerivativeOfCentralAtomPos( const unsigned& iatom, const Tensor& der );
+/// Convert an index in the global array to an index in the individual base colvars
+ unsigned convertToLocalIndex( const unsigned& index, const unsigned& mcv_code ) const ;
+/// Add derivatives to the orientation
+ void addOrientationDerivatives( const unsigned& iatom, const std::vector<double>& der );
+/// Build colvars for atoms as if they were symmetry functions
+ void buildSymmetryFunctionLists( const bool store_director );
+/// Build a colvar for each pair of atoms
+ void buildAtomListWithPairs( const bool& allow_intra_group );
+/// Get the number of base multicolvars
+ unsigned getNumberOfBaseMultiColvars() const ;
+/// Get an example of the underlying multicolvar
+ MultiColvarBase* getBaseMultiColvar( const unsigned& icolv );
+/// Return the base multicolvar index that this colvar is a part of
+ unsigned getBaseColvarNumber( const unsigned& iatom ) const ;
public:
MultiColvarFunction(const ActionOptions&);
static void registerKeywords( Keywords& keys );
@@ -59,48 +74,77 @@ public:
void lockContributors();
/// Active element in atoms_with_derivatives
void atomHasDerivative( const unsigned& iatom );
+/// Used to get atom numbers
+ unsigned getBaseQuantityIndex( const unsigned& code );
+/// Are two indexes the same
+ bool same_index( const unsigned& code1, const unsigned& code2 );
+/// Finish task list update
+ void finishTaskListUpdate();
/// Resize the dynamic arrays
void resizeDynamicArrays();
+/// Update the atoms that are active
+ void updateActiveAtoms();
/// Regular calculate
void calculate();
/// Calculate the numerical derivatives for this action
void calculateNumericalDerivatives( ActionWithValue* a=NULL );
-/// Do the calculation
- double doCalculation( const unsigned& j );
-/// Actually compute the colvar
- virtual double compute( const unsigned& j )=0;
/// Calculate the position of the central atom
Vector calculateCentralAtomPosition();
/// Get the position of the central atom
virtual Vector getCentralAtom()=0;
+/// Add derivatives from storage vessels in MultiColvarBase
+ void addStoredDerivative( const unsigned&, const unsigned&, const unsigned&, const double& );
};
inline
-unsigned MultiColvarFunction::getNumberOfBaseFunctions() const {
- return mycolv->colvar_atoms.size();
+unsigned MultiColvarFunction::getBaseQuantityIndex( const unsigned& code ){
+ return code;
+}
+
+inline
+bool MultiColvarFunction::same_index( const unsigned& code1, const unsigned& code2 ){
+ return ( code1==code2 );
+}
+
+inline
+unsigned MultiColvarFunction::getFullNumberOfBaseTasks() const {
+ return colvar_label.size();
+}
+
+
+inline
+unsigned MultiColvarFunction::getNumberOfBaseMultiColvars() const {
+ return mybasemulticolvars.size();
+}
+
+inline
+MultiColvarBase* MultiColvarFunction::getBaseMultiColvar( const unsigned& icolv ){
+ plumed_dbg_assert( icolv<mybasemulticolvars.size() );
+ return mybasemulticolvars[icolv];
}
inline
-MultiColvarBase* MultiColvarFunction::getPntrToMultiColvar(){
- return mycolv;
+unsigned MultiColvarFunction::convertToLocalIndex( const unsigned& index, const unsigned& mcv_code ) const {
+ unsigned t1 = index;
+ for(unsigned k=0;k<mcv_code;++k) t1 -= mybasemulticolvars[k]->getFullNumberOfTasks();
+ return t1;
}
inline
-Vector MultiColvarFunction::getPositionOfCentralAtom( const unsigned& iatom ) const {
- plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() );
- return catoms->getPosition( colvar_atoms[current][iatom] );
+unsigned MultiColvarFunction::getBaseColvarNumber( const unsigned& iatom ) const {
+ return colvar_label[ current_atoms[iatom] ];
}
inline
-void MultiColvarFunction::addCentralAtomsDerivatives( const unsigned& iatom, const Vector& der ){
- plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() );
- catoms->addAtomsDerivatives( colvar_atoms[current][iatom], der, this );
+Vector MultiColvarFunction::getPositionOfCentralAtom( const unsigned& iatom ) const {
+ plumed_dbg_assert( iatom<natomsper ); unsigned mmc = colvar_label[ current_atoms[iatom] ];
+ return mybasemulticolvars[mmc]->getCentralAtomPosition( convertToLocalIndex(current_atoms[iatom],mmc) );
}
inline
-void MultiColvarFunction::addCentralAtomsDerivativesOfWeight( const unsigned& iatom, const Vector& der ){
- plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() );
- catoms->addAtomsDerivativeOfWeight( colvar_atoms[current][iatom], der, this );
+void MultiColvarFunction::addCentralAtomsDerivatives( const unsigned& iatom, const unsigned& jout, const Vector& der ){
+ plumed_dbg_assert( iatom<natomsper ); unsigned mmc = colvar_label[ current_atoms[iatom] ];
+ mybasemulticolvars[mmc]->addCentralAtomDerivativeToFunction( convertToLocalIndex(current_atoms[iatom],mmc), jout, mmc, der, this );
}
inline
@@ -110,9 +154,31 @@ void MultiColvarFunction::atomHasDerivative( const unsigned& iatom ){
inline
void MultiColvarFunction::addDerivativeOfCentralAtomPos( const unsigned& iatom, const Tensor& der ){
- catoms->addDerivativeOfCentralAtomPos( colvar_atoms[current][iatom], der, this );
+ plumed_dbg_assert( iatom<natomsper ); unsigned mmc = colvar_label[ current_atoms[iatom] ]; Vector tmpder;
+ for(unsigned i=0;i<3;++i){
+ for(unsigned j=0;j<3;++j) tmpder[j]=der(i,j);
+ mybasemulticolvars[mmc]->addCentralAtomDerivativeToFunction( convertToLocalIndex(current_atoms[iatom],mmc), (2+i), mmc, tmpder, this );
+ }
+}
+
+inline
+void MultiColvarFunction::getValueForBaseTask( const unsigned& iatom, std::vector<double>& vals ){
+ plumed_dbg_assert( iatom<natomsper ); unsigned mmc = colvar_label[ current_atoms[iatom] ];
+ mybasemulticolvars[mmc]->getValueForTask( convertToLocalIndex(current_atoms[iatom],mmc), vals );
}
+inline
+void MultiColvarFunction::accumulateWeightedAverageAndDerivatives( const unsigned& iatom, const double& weight ){
+ plumed_dbg_assert( iatom<natomsper ); unsigned mmc = colvar_label[ current_atoms[iatom] ];
+ mybasemulticolvars[mmc]->addWeightedValueDerivatives( convertToLocalIndex(current_atoms[iatom],mmc), mmc, weight, this );
+}
+
+inline
+void MultiColvarFunction::addOrientationDerivatives( const unsigned& iatom , const std::vector<double>& der ){
+ plumed_dbg_assert( iatom<natomsper ); unsigned mmc = colvar_label[ current_atoms[iatom] ];
+ unsigned jout=2; if( usespecies && iatom==0 ) jout=1;
+ mybasemulticolvars[mmc]->addOrientationDerivativesToBase( convertToLocalIndex(current_atoms[iatom],mmc), jout, mmc, der, this );
+}
}
}
diff --git a/src/multicolvar/NumberOfLinks.cpp b/src/multicolvar/NumberOfLinks.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..7e174227295485e7bb94204e211b53668b21dc11
--- /dev/null
+++ b/src/multicolvar/NumberOfLinks.cpp
@@ -0,0 +1,155 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "MultiColvarFunction.h"
+#include "core/ActionRegister.h"
+#include "tools/SwitchingFunction.h"
+
+#include <string>
+#include <cmath>
+
+//+PLUMEDOC MCOLVARF NLINKS
+/*
+Calculate number of pairs of atoms/molecules that are "linked"
+
+In its simplest guise this coordinate calculates a coordination number. Each pair
+of atoms is assumed "linked" if they are within some cutoff of each other. In more
+complex applications each entity is a vector and this quantity measures whether
+pairs of vectors are (a) within a certain cutoff and (b) if the two vectors have
+similar orientations
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+namespace PLMD {
+namespace multicolvar {
+
+class NumberOfLinks : public MultiColvarFunction {
+private:
+/// The values of the quantities in the dot products
+ std::vector<double> orient0, orient1;
+/// The switching function that tells us if atoms are close enough together
+ SwitchingFunction switchingFunction;
+public:
+ static void registerKeywords( Keywords& keys );
+ NumberOfLinks(const ActionOptions&);
+/// Do the stuff with the switching functions
+ void calculateWeight();
+/// Actually do the calculation
+ double compute();
+/// This returns the position of the central atom
+ Vector getCentralAtom();
+/// Is the variable periodic
+ bool isPeriodic(){ return false; }
+};
+
+PLUMED_REGISTER_ACTION(NumberOfLinks,"NLINKS")
+
+void NumberOfLinks::registerKeywords( Keywords& keys ){
+ MultiColvarFunction::registerKeywords( keys );
+ keys.add("compulsory","NN","6","The n parameter of the switching function ");
+ keys.add("compulsory","MM","12","The m parameter of the switching function ");
+ keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
+ keys.add("compulsory","R_0","The r_0 parameter of the switching function");
+ keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. "
+ "The following provides information on the \\ref switchingfunction that are available. "
+ "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
+ // Use actionWithDistributionKeywords
+ keys.remove("LOWMEM");
+ keys.addFlag("LOWMEM",false,"lower the memory requirements");
+}
+
+NumberOfLinks::NumberOfLinks(const ActionOptions& ao):
+Action(ao),
+MultiColvarFunction(ao)
+{
+ // The weight of this does have derivatives
+ weightHasDerivatives=true;
+
+ // Read in the switching function
+ std::string sw, errors; parse("SWITCH",sw);
+ if(sw.length()>0){
+ switchingFunction.set(sw,errors);
+ } else {
+ double r_0=-1.0, d_0; int nn, mm;
+ parse("NN",nn); parse("MM",mm);
+ parse("R_0",r_0); parse("D_0",d_0);
+ if( r_0<0.0 ) error("you must set a value for R_0");
+ switchingFunction.set(nn,mm,r_0,d_0);
+ }
+ log.printf(" calculating number of links with atoms separation of %s\n",( switchingFunction.description() ).c_str() );
+ buildAtomListWithPairs( false );
+
+ for(unsigned i=0;i<getNumberOfBaseMultiColvars();++i){
+ if( !getBaseMultiColvar(i)->hasDifferentiableOrientation() ) error("cannot use multicolvar of type " + getBaseMultiColvar(i)->getName() );
+ }
+
+ // Resize these ready for business
+ if( getBaseMultiColvar(0)->getNumberOfQuantities()==5 ){
+ orient0.resize( 1 ); orient1.resize( 1 );
+ } else {
+ orient0.resize( getBaseMultiColvar(0)->getNumberOfQuantities() - 5 );
+ orient1.resize( getBaseMultiColvar(0)->getNumberOfQuantities() - 5 );
+ }
+
+ // Create holders for the collective variable
+ readVesselKeywords();
+ plumed_assert( getNumberOfVessels()==0 );
+ std::string input; addVessel( "SUM", input, -1 );
+ readVesselKeywords();
+}
+
+void NumberOfLinks::calculateWeight(){
+ Vector distance = getSeparation( getPositionOfCentralAtom(0), getPositionOfCentralAtom(1) );
+ double dfunc, sw = switchingFunction.calculateSqr( distance.modulo2(), dfunc );
+ addCentralAtomsDerivatives( 0, 1, (-dfunc)*distance );
+ addCentralAtomsDerivatives( 1, 1, (dfunc)*distance );
+ MultiColvarBase::addBoxDerivatives( 1, (-dfunc)*Tensor(distance,distance) );
+ setElementValue(1,sw);
+}
+
+double NumberOfLinks::compute(){
+ getValueForBaseTask( 0, orient0 );
+ getValueForBaseTask( 1, orient1 );
+
+ double dot=0;
+ for(unsigned k=0;k<orient0.size();++k){
+ dot+=orient0[k]*orient1[k];
+ }
+// for(unsigned k=0;k<orient0.size();++k){
+// orient0[k]*=dot_df; orient1[k]*=dot_df;
+// }
+ addOrientationDerivatives( 0, orient1 );
+ addOrientationDerivatives( 1, orient0 );
+
+ return dot;
+}
+
+Vector NumberOfLinks::getCentralAtom(){
+ addDerivativeOfCentralAtomPos( 0, 0.5*Tensor::identity() );
+ addDerivativeOfCentralAtomPos( 1, 0.5*Tensor::identity() );
+ return 0.5*( getPositionOfCentralAtom(0) + getPositionOfCentralAtom(1) );
+}
+
+}
+}
diff --git a/src/multicolvar/Sprint.cpp b/src/multicolvar/Sprint.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..a2629488eb8777d18246b42cdf63391371951e02
--- /dev/null
+++ b/src/multicolvar/Sprint.cpp
@@ -0,0 +1,188 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "AdjacencyMatrixAction.h"
+#include "core/ActionRegister.h"
+
+//+PLUMEDOC MCOLVARF SPRINT
+/*
+Calculate SPRINT topological variables.
+
+The SPRINT topological variables are calculated from the largest eigenvalue, \f$\lambda\f$ of
+an \f$n\times n\f$ adjacency matrix and its corresponding eigenvector, \f$\mathbf{V}\f$, using:
+
+\f[
+s_i = \sqrt{n} \lambda v_i
+\f]
+
+You can use different quantities to measure whether or not two given atoms/molecules are
+adjacent or not in the adjacency matrix. The simplest measure of adjacency is is whether
+two atoms/molecules are within some cutoff of each other. Further complexity can be added by
+insisting that two molecules are adjacent if they are within a certain distance of each
+other and if they have similar orientations.
+
+\par Examples
+
+This example input calculates the 7 SPRINT coordinates for a 7 atom cluster of Lennard-Jones
+atoms and prints their values to a file. In this input the SPRINT coordinates are calculated
+in the manner described in ?? so two atoms are adjacent if they are within a cutoff:
+
+\verbatim
+DENSITY SPECIES=1-7 LABEL=d1
+SPRINT ARG=d1 SWITCH={RATIONAL R_0=0.1} LABEL=ss
+PRINT ARG=ss.* FILE=colvar
+\endverbatim
+
+This example input calculates the 14 SPRINT coordinates foa a molecule composed of 7 hydrogen and
+7 carbon atoms. Once again two atoms are adjacent if they are within a cutoff:
+
+\verbatim
+DENSITY SPECIES=1-7 LABEL=c
+DENSITY SPECIES=8-14 LABEL=h
+
+SPRINT ...
+ ARG=c,h
+ SWITCH11={RATIONAL R_0=2.6 NN=6 MM=12}
+ SWITCH12={RATIONAL R_0=2.2 NN=6 MM=12}
+ SWITCH22={RATIONAL R_0=2.2 NN=6 MM=12}
+ LABEL=ss
+... SPRINT
+
+PRINT ARG=ss.* FILE=colvar
+\endverbatim
+
+*/
+//+ENDPLUMEDOC
+
+
+namespace PLMD {
+namespace multicolvar {
+
+class Sprint : public AdjacencyMatrixAction {
+private:
+/// Square root of number of atoms
+ double sqrtn;
+/// Largest eigenvalue
+ double lambda;
+/// Vector that stores eigenvalues
+ std::vector<double> eigvals;
+/// Vector that stores max eigenvector
+ std::vector< std::pair<double,int> > maxeig;
+/// Adjacency matrix
+ Matrix<double> mymatrix;
+/// Matrix that stores eigenvectors
+ Matrix<double> eigenvecs;
+public:
+/// Create manual
+ static void registerKeywords( Keywords& keys );
+/// Constructor
+ Sprint(const ActionOptions&);
+/// Do the matrix calculation
+ void completeCalculation();
+};
+
+PLUMED_REGISTER_ACTION(Sprint,"SPRINT")
+
+void Sprint::registerKeywords( Keywords& keys ){
+ AdjacencyMatrixAction::registerKeywords( keys );
+}
+
+Sprint::Sprint(const ActionOptions&ao):
+Action(ao),
+AdjacencyMatrixAction(ao),
+eigvals( getFullNumberOfBaseTasks() ),
+maxeig( getFullNumberOfBaseTasks() ),
+mymatrix( getFullNumberOfBaseTasks(), getFullNumberOfBaseTasks() ),
+eigenvecs( getFullNumberOfBaseTasks(), getFullNumberOfBaseTasks() )
+{
+ // Check for bad colvar input
+ for(unsigned i=0;i<getNumberOfBaseMultiColvars();++i){
+ if( !getBaseMultiColvar(i)->hasDifferentiableOrientation() ) error("cannot use multicolvar of type " + getBaseMultiColvar(i)->getName() );
+ }
+
+ // Create all the values
+ sqrtn = sqrt( static_cast<double>( getFullNumberOfBaseTasks() ) );
+ for(unsigned i=0;i<getFullNumberOfBaseTasks();++i){
+ std::string num; Tools::convert(i,num);
+ addComponentWithDerivatives("aa"+num);
+ componentIsNotPeriodic("aa"+num);
+ getPntrToComponent(i)->resizeDerivatives( getNumberOfDerivatives() );
+ }
+}
+
+void Sprint::completeCalculation(){
+ // Get the adjacency matrix
+ retrieveMatrix( mymatrix );
+ // Diagonalize it
+ diagMat( mymatrix, eigvals, eigenvecs );
+ // Get the maximum eigevalue
+ double lambda = eigvals[ getFullNumberOfBaseTasks()-1 ];
+ // Get the corresponding eigenvector
+ for(unsigned j=0;j<maxeig.size();++j){
+ maxeig[j].first = fabs( eigenvecs( getFullNumberOfBaseTasks()-1, j ) );
+ maxeig[j].second = j;
+ // Must make all components of principle eigenvector +ve
+ eigenvecs( getFullNumberOfBaseTasks()-1, j ) = maxeig[j].first;
+ }
+
+ // Reorder each block of eigevectors
+ unsigned startnum=0;
+ for(unsigned j=0;j<getNumberOfBaseMultiColvars();++j){
+ unsigned nthis = getBaseMultiColvar(j)->getFullNumberOfTasks();
+ // Sort into ascending order
+ std::sort( maxeig.begin() + startnum, maxeig.begin() + startnum + nthis );
+ // Used so we can do sorting in blocks
+ startnum += nthis;
+ }
+ // Set the sprint coordinates
+ for(unsigned icomp=0;icomp<getNumberOfComponents();++icomp){
+ getPntrToComponent(icomp)->set( sqrtn*lambda*maxeig[icomp].first );
+ }
+
+ // Parallelism
+ unsigned rank, stride;
+ if( serialCalculation() ){ stride=1; rank=0; }
+ else { rank=comm.Get_rank(); stride=comm.Get_size(); }
+
+ // Derivatives
+ Matrix<double> mymat_ders( getNumberOfComponents(), getNumberOfDerivatives() );
+ unsigned nval = getFullNumberOfBaseTasks(); mymat_ders=0;
+ for(unsigned i=rank;i<getNumberOfActiveMatrixElements();i+=stride){
+ setMatrixIndexesForTask( i ); unsigned j=current_atoms[0], k=current_atoms[1];
+ double tmp1 = 2 * eigenvecs(nval-1,j)*eigenvecs(nval-1,k);
+ for(unsigned icomp=0;icomp<getNumberOfComponents();++icomp){
+ double tmp2 = 0.;
+ for(unsigned n=0;n<nval-1;++n){ // Need care on following line
+ tmp2 += eigenvecs(n,maxeig[icomp].second) * ( eigenvecs(n,j)*eigenvecs(nval-1,k) + eigenvecs(n,k)*eigenvecs(nval-1,j) ) / ( lambda - eigvals[n] );
+ }
+ addDerivativesOnMatrixElement( i, icomp, sqrtn*( tmp1*maxeig[icomp].first + tmp2*lambda ), mymat_ders );
+ }
+ }
+ if( !serialCalculation() ) comm.Sum( mymat_ders );
+
+ for(unsigned j=0;j<getNumberOfComponents();++j){
+ Value* val=getPntrToComponent(j);
+ for(unsigned i=0;i<getNumberOfDerivatives();++i) val->addDerivative( i, mymat_ders(j,i) );
+ }
+}
+
+}
+}
diff --git a/src/multicolvar/StoreCentralAtomsVessel.cpp b/src/multicolvar/StoreCentralAtomsVessel.cpp
index 7020937fd9db6b3f270cd1dcfb60df039c2b633c..360ea2d12fa60d8024041f563840284f3920bc45 100644
--- a/src/multicolvar/StoreCentralAtomsVessel.cpp
+++ b/src/multicolvar/StoreCentralAtomsVessel.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -21,135 +21,60 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "vesselbase/VesselRegister.h"
#include "vesselbase/ActionWithVessel.h"
+#include "tools/DynamicList.h"
#include "MultiColvar.h"
#include "MultiColvarFunction.h"
#include "StoreCentralAtomsVessel.h"
-#define CATOMS_MAXATOMS 2
-
namespace PLMD {
namespace multicolvar {
StoreCentralAtomsVessel::StoreCentralAtomsVessel( const vesselbase::VesselOptions& da ):
-Vessel(da),
-nspace(1 + 3*CATOMS_MAXATOMS)
+StoreDataVessel(da),
+tmpdf(3)
{
- mycolv=dynamic_cast<MultiColvar*>( getAction() );
- plumed_assert( mycolv );
- // Resize the active derivative lists
- active_atoms.resize( mycolv->colvar_atoms.size() );
+ mycolv=dynamic_cast<MultiColvarBase*>( getAction() );
+ plumed_assert( mycolv ); completeSetup( 2, 3 );
}
-void StoreCentralAtomsVessel::resize(){
- unsigned nfunc=mycolv->colvar_atoms.size();
- unsigned bsize=0; start.resize( nfunc +1 );
- for(unsigned i=0;i<nfunc;++i){
- start[i] = bsize;
- bsize += 3*( 1 + 3*CATOMS_MAXATOMS );
- }
- start[nfunc]=bsize;
- resizeBuffer( bsize );
- // Update the active_derivative lists
- for(unsigned i=0;i<active_atoms.size();++i){
- active_atoms[i].clear(); active_atoms[i].setupMPICommunication( comm );
- for(unsigned j=0;j<mycolv->getNumberOfAtoms();++j){
- active_atoms[i].addIndexToList(j);
- }
+void StoreCentralAtomsVessel::getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& aindexes ){
+ aindexes[jstore]=3*mycolv->atomsWithCatomDer.getNumberActive();
+ if( aindexes[jstore]>maxder ) error("too many derivatives to store. Run with LOWMEM");
+ unsigned kder = ntotal + jstore*maxder;
+ for(unsigned jder=0;jder<mycolv->atomsWithCatomDer.getNumberActive();++jder){
+ unsigned iatom = 3*mycolv->atomsWithCatomDer[jder];
+ for(unsigned icomp=0;icomp<3;++icomp){ aindexes[ kder ] = iatom+icomp; kder++; }
}
}
-bool StoreCentralAtomsVessel::calculate(){
- Vector catom_pos=mycolv->retrieveCentralAtomPos();
-
- // Store the value
- unsigned ibuf=start[mycolv->current];
- for(unsigned i=0;i<3;++i){ addToBufferElement( ibuf, catom_pos[i] ); ibuf+=nspace; }
- plumed_dbg_assert( ibuf==start[mycolv->current+1] );
-
- // Chect there is sufficent space for the derivatives
- plumed_massert( 3*mycolv->atomsWithCatomDer.getNumberActive()<=3*CATOMS_MAXATOMS,
- "increase CATOMS_MAXATOMS in StoreCentralAtomsVessel");
-
- // Store the derivatives
- active_atoms[mycolv->current].deactivateAll();
- for(unsigned j=0;j<mycolv->atomsWithCatomDer.getNumberActive();++j){
- unsigned n=mycolv->atomsWithCatomDer[j];
- active_atoms[mycolv->current].activate(n);
- ibuf = start[mycolv->current] + 1 + 3*j;
- for(unsigned i=0;i<3;++i){
- for(unsigned k=0;k<3;++k) addToBufferElement( ibuf+k, mycolv->central_derivs[n](i,k) );
- ibuf += nspace;
- }
- }
-
- return true;
+Vector StoreCentralAtomsVessel::getPosition( const unsigned& iatom ){
+ Vector pos; for(unsigned i=0;i<3;++i) pos[i]=getComponent( iatom, i );
+ return pos;
}
-void StoreCentralAtomsVessel::finish(){
- mpi_gatherActiveMembers( comm, active_atoms );
+void StoreCentralAtomsVessel::performTask( const unsigned& itask ){
+ mycolv->atomsWithCatomDer.deactivateAll();
+ bool check=mycolv->setupCurrentAtomList( mycolv->getCurrentTask() );
+ plumed_dbg_assert( check );
+ Vector ignore = mycolv->retrieveCentralAtomPos();
}
-Vector StoreCentralAtomsVessel::getPosition( const unsigned& ivec ) const {
- plumed_dbg_assert( ivec<mycolv->colvar_atoms.size() );
- unsigned pos=start[ivec]; Vector mypos;
- for(unsigned i=0;i<3;++i){
- mypos[i] = getBufferElement( pos );
- pos+=nspace;
- }
- plumed_dbg_assert( pos==start[ivec+1] );
- return mypos;
+void StoreCentralAtomsVessel::finishTask( const unsigned& itask ){
+ mycolv->atomsWithCatomDer.deactivateAll();
+ Vector ignore = mycolv->retrieveCentralAtomPos();
}
-void StoreCentralAtomsVessel::addAtomsDerivatives( const unsigned& iatom, const Vector& df, MultiColvarFunction* funcout ) const {
- plumed_dbg_assert( iatom<mycolv->colvar_atoms.size() );
-
- Vector thisder;
- for(unsigned ider=0;ider<active_atoms[iatom].getNumberActive();++ider){
- unsigned ibuf=start[iatom] + 1 + 3*ider; thisder.zero();
- for(unsigned jcomp=0;jcomp<3;++jcomp){
- thisder[0]+=df[jcomp]*getBufferElement(ibuf);
- thisder[1]+=df[jcomp]*getBufferElement(ibuf+1);
- thisder[2]+=df[jcomp]*getBufferElement(ibuf+2);
- ibuf+=nspace;
- }
- unsigned jatom = active_atoms[iatom][ider];
- funcout->addAtomsDerivatives( jatom, thisder );
+void StoreCentralAtomsVessel::addAtomsDerivatives( const unsigned& iatom, const unsigned& jout, const unsigned& base_cv_no,
+ const Vector& df, MultiColvarFunction* funcout ){
+ for(unsigned ider=0;ider<getNumberOfDerivatives(iatom);ider+=3){
+ for(unsigned i=0;i<3;++i) tmpdf[i]=df[0];
+ funcout->addStoredDerivative( jout, base_cv_no, getStoredIndex( iatom, ider+0 ), chainRule(iatom, ider+0, tmpdf) );
+ for(unsigned i=0;i<3;++i) tmpdf[i]=df[1];
+ funcout->addStoredDerivative( jout, base_cv_no, getStoredIndex( iatom, ider+1 ), chainRule(iatom, ider+1, tmpdf) );
+ for(unsigned i=0;i<3;++i) tmpdf[i]=df[2];
+ funcout->addStoredDerivative( jout, base_cv_no, getStoredIndex( iatom, ider+2 ), chainRule(iatom, ider+2, tmpdf) );
}
}
-void StoreCentralAtomsVessel::addAtomsDerivativeOfWeight( const unsigned& iatom, const Vector& df, MultiColvarFunction* funcout ) const {
- plumed_dbg_assert( iatom<mycolv->colvar_atoms.size() );
-
- Vector thisder;
- for(unsigned ider=0;ider<active_atoms[iatom].getNumberActive();++ider){
- unsigned ibuf=start[iatom] + 1 + 3*ider; thisder.zero();
- for(unsigned jcomp=0;jcomp<3;++jcomp){
- thisder[0]+=df[jcomp]*getBufferElement(ibuf);
- thisder[1]+=df[jcomp]*getBufferElement(ibuf+1);
- thisder[2]+=df[jcomp]*getBufferElement(ibuf+2);
- ibuf+=nspace;
- }
- unsigned jatom = active_atoms[iatom][ider];
- funcout->addAtomsDerivativeOfWeight( jatom, thisder );
- }
-}
-
-void StoreCentralAtomsVessel::addDerivativeOfCentralAtomPos( const unsigned& iatom, const Tensor& df, MultiColvarFunction* funcout ) const {
- plumed_dbg_assert( iatom<mycolv->colvar_atoms.size() );
-
- Tensor thisder;
- for(unsigned ider=0;ider<active_atoms[iatom].getNumberActive();++ider){
- unsigned ibuf=start[iatom] + 1 + 3*ider; thisder.zero();
- for(unsigned jcomp=0;jcomp<3;++jcomp){
- for(unsigned kcomp=0;kcomp<3;++kcomp){
- for(unsigned k=0;k<3;++k) thisder(jcomp,kcomp)+=df(jcomp,k)*getBufferElement(ibuf+k*nspace+kcomp);
- }
- }
- unsigned jatom = active_atoms[iatom][ider];
- funcout->addCentralAtomDerivatives( jatom, thisder );
- }
-}
-
-
}
}
diff --git a/src/multicolvar/StoreCentralAtomsVessel.h b/src/multicolvar/StoreCentralAtomsVessel.h
index c6045eb19d284cb64887ee95a069953cb292e7d5..338e1ce96ff16ffe1b77d3e85337acebc91f9cad 100644
--- a/src/multicolvar/StoreCentralAtomsVessel.h
+++ b/src/multicolvar/StoreCentralAtomsVessel.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -22,8 +22,7 @@
#ifndef __PLUMED_multicolvar_StoreCentralAtomsVessel_h
#define __PLUMED_multicolvar_StoreCentralAtomsVessel_h
-#include "tools/DynamicList.h"
-#include "vesselbase/Vessel.h"
+#include "vesselbase/StoreDataVessel.h"
namespace PLMD {
namespace multicolvar {
@@ -31,35 +30,26 @@ namespace multicolvar {
class MultiColvarBase;
class MultiColvarFunction;
-class StoreCentralAtomsVessel : public vesselbase::Vessel {
+class StoreCentralAtomsVessel : public vesselbase::StoreDataVessel {
private:
+/// The base multicolvar
MultiColvarBase* mycolv;
- std::vector<unsigned> start;
- unsigned nspace;
- std::vector< DynamicList<unsigned> > active_atoms;
+/// A vector that is used to store derivatives
+ std::vector<double> tmpdf;
public:
/// Constructor
StoreCentralAtomsVessel( const vesselbase::VesselOptions& );
-/// Return the number of terms
- unsigned getNumberOfTerms(){ return 2; }
-/// This does the resizing of the buffer
- void resize();
/// This does nothing
std::string description(){ return ""; }
-/// This should mpi gather the active atoms
- void finish();
-/// This does nothing
- bool applyForce(std::vector<double>&){ return false; }
-/// This makes sure all vectors are stored
- bool calculate();
/// Get the orientation of the ith vector
- Vector getPosition( const unsigned& ) const ;
+ Vector getPosition( const unsigned& );
+/// Recalculate the central atom position
+ void performTask( const unsigned& );
+ void finishTask( const unsigned& );
+/// Get the indices
+ void getIndexList( const unsigned& , const unsigned& , const unsigned& , std::vector<unsigned>& );
/// Add derivatives to central atom position
- void addAtomsDerivatives( const unsigned& iatom, const Vector& df, MultiColvarFunction* funcout ) const ;
-/// Add derivatives of the weight wrt to the central atom position
- void addAtomsDerivativeOfWeight( const unsigned& iatom, const Vector& df, MultiColvarFunction* funcout ) const ;
-/// Add derivative to the central atom position
- void addDerivativeOfCentralAtomPos( const unsigned& iatom, const Tensor& df, MultiColvarFunction* funcout ) const ;
+ void addAtomsDerivatives( const unsigned& iatom, const unsigned& jout, const unsigned& base_cv_no, const Vector& df, MultiColvarFunction* funcout );
};
}
diff --git a/src/multicolvar/StoreColvarVessel.cpp b/src/multicolvar/StoreColvarVessel.cpp
index f4af283e9bfbbcc4f3ccec2938e9cd58f719dc6a..d7072d818f5ed60dbf4ca2cb989dc30049dd5dc5 100644
--- a/src/multicolvar/StoreColvarVessel.cpp
+++ b/src/multicolvar/StoreColvarVessel.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -19,118 +19,37 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "vesselbase/ActionWithVessel.h"
#include "StoreColvarVessel.h"
-#include "MultiColvarBase.h"
-
-#define MAXDERIVATIVES 300
+#include "MultiColvarFunction.h"
namespace PLMD {
-namespace multicolvar{
+namespace multicolvar {
void StoreColvarVessel::registerKeywords( Keywords& keys ){
- Vessel::registerKeywords( keys );
- plumed_assert( keys.size()==0 );
+ StoreDataVessel::registerKeywords( keys );
}
-StoreColvarVessel::StoreColvarVessel( const vesselbase::VesselOptions& da ):
-Vessel(da)
+StoreColvarVessel::StoreColvarVessel( const vesselbase::VesselOptions& da):
+StoreDataVessel(da)
{
- mycolv=dynamic_cast<MultiColvarBase*>( getAction() );
- plumed_assert( mycolv );
- diffweight=mycolv->weightHasDerivatives;
- // Resize the active derivative lists
- active_atoms.resize( mycolv->colvar_atoms.size() );
-}
-
-void StoreColvarVessel::resize(){
- unsigned nfunc=mycolv->colvar_atoms.size();
- bufsize=0; start.resize( nfunc +1 );
- for(unsigned i=0;i<nfunc;++i){
- start[i] = bufsize;
- bufsize += 1 + MAXDERIVATIVES;
- }
- start[nfunc]=bufsize;
- resizeBuffer( 2*bufsize ); local_resizing();
- // Build the arrays of indexes
- for(unsigned i=0;i<active_atoms.size();++i){
- active_atoms[i].clear(); active_atoms[i].setupMPICommunication( comm );
- for(unsigned j=0;j<mycolv->getNumberOfAtoms();++j) active_atoms[i].addIndexToList(j);
- }
-}
-
-bool StoreColvarVessel::calculate(){
- plumed_massert( 3*mycolv->atoms_with_derivatives.getNumberActive()+9<=MAXDERIVATIVES,
- "Error increase MAXDERIVATIVES in StoreColvarVessel");
-
- unsigned ibuf=start[mycolv->current];
- setBufferElement( ibuf, mycolv->getElementValue(0) ); ibuf++;
- for(unsigned j=0;j<mycolv->atoms_with_derivatives.getNumberActive();++j){
- unsigned iatom=mycolv->atoms_with_derivatives[j];
- active_atoms[mycolv->current].activate(iatom);
- unsigned ider=3*iatom;
- setBufferElement( ibuf, mycolv->getElementDerivative(ider) ); ider++; ibuf++;
- setBufferElement( ibuf, mycolv->getElementDerivative(ider) ); ider++; ibuf++;
- setBufferElement( ibuf, mycolv->getElementDerivative(ider) ); ibuf++;
- }
- unsigned ivir=3*mycolv->getNumberOfAtoms();
- for(unsigned j=0;j<9;++j){
- setBufferElement( ibuf, mycolv->getElementDerivative(ivir) ); ivir++; ibuf++;
- }
- ibuf=bufsize+start[mycolv->current];
- setBufferElement( ibuf, mycolv->getElementValue(1) ); ibuf++;
- if(diffweight){
- unsigned nder=mycolv->getNumberOfDerivatives();
- for(unsigned j=0;j<mycolv->atoms_with_derivatives.getNumberActive();++j){
- unsigned ider=nder+3*mycolv->atoms_with_derivatives[j];
- setBufferElement( ibuf, mycolv->getElementDerivative(ider) ); ider++; ibuf++;
- setBufferElement( ibuf, mycolv->getElementDerivative(ider) ); ider++; ibuf++;
- setBufferElement( ibuf, mycolv->getElementDerivative(ider) ); ibuf++;
- }
- unsigned ivir=nder + 3*mycolv->getNumberOfAtoms();
- for(unsigned j=0;j<9;++j){
- setBufferElement( ibuf, mycolv->getElementDerivative(ivir) ); ivir++; ibuf++;
- }
- }
- return true;
+ if( weightHasDerivatives() ) error("this quantity cannot be calculated if weights have derivatives");
+ completeSetup( 0, 1 );
}
-void StoreColvarVessel::finish(){
- mpi_gatherActiveMembers( comm, active_atoms );
- performCalculationUsingAllValues();
-}
-
-void StoreColvarVessel::addDerivatives( const unsigned& ival, double& pref, Value* value_out ){
- for(unsigned i=0;i<active_atoms[ival].getNumberActive();++i){
- unsigned jbuf=start[ival] + 1 + 3*i;
- value_out->addDerivative( 3*active_atoms[ival][i] + 0, pref*getBufferElement(jbuf) ); jbuf++;
- value_out->addDerivative( 3*active_atoms[ival][i] + 1, pref*getBufferElement(jbuf) ); jbuf++;
- value_out->addDerivative( 3*active_atoms[ival][i] + 2, pref*getBufferElement(jbuf) );
- }
- unsigned jbuf=start[ival] + 1 + 3*active_atoms[ival].getNumberActive();
- unsigned nder=3*mycolv->getNumberOfAtoms();
- for(unsigned i=0;i<9;++i){
- value_out->addDerivative( nder, pref*getBufferElement(jbuf) ); nder++; jbuf++;
- }
-}
-
-void StoreColvarVessel::addWeightDerivatives( const unsigned& ival, double& pref, Value* value_out ){
- if(!diffweight) return;
-
- unsigned jbuf=bufsize+start[ival]+1;
- for(unsigned i=0;i<active_atoms[ival].getNumberActive();++i){
- value_out->addDerivative( 3*active_atoms[ival][i] + 0, pref*getBufferElement(jbuf) ); jbuf++;
- value_out->addDerivative( 3*active_atoms[ival][i] + 1, pref*getBufferElement(jbuf) ); jbuf++;
- value_out->addDerivative( 3*active_atoms[ival][i] + 2, pref*getBufferElement(jbuf) ); jbuf++;
- }
- jbuf=bufsize+start[ival] + 1 + 3*active_atoms[ival].getNumberActive();
- unsigned nder=3*mycolv->getNumberOfAtoms();
- for(unsigned i=0;i<9;++i){
- value_out->addDerivative( nder, pref*getBufferElement(jbuf) ); nder++; jbuf++;
+void StoreColvarVessel::chainRuleForComponent( const unsigned& icolv, const unsigned& jout, const unsigned& base_cv_no,
+ const double& weight, MultiColvarFunction* funcout ){
+ if( usingLowMem() ){
+ unsigned ibuf = icolv*getAction()->getNumberOfDerivatives();
+ for(unsigned ider=0;ider<getNumberOfDerivatives(icolv);++ider){
+ funcout->addStoredDerivative( jout, base_cv_no, getStoredIndex( icolv, ider ), weight*getLocalDerivative(ibuf+ider) );
+ }
+ } else {
+ unsigned ibuf = icolv*getNumberOfDerivativeSpacesPerComponent() + 1;
+ for(unsigned ider=0;ider<getNumberOfDerivatives(icolv);++ider){
+ funcout->addStoredDerivative( jout, base_cv_no, getStoredIndex( icolv, ider ), weight*getBufferElement(ibuf+ider) );
+ }
}
}
-
}
}
-
diff --git a/src/multicolvar/StoreColvarVessel.h b/src/multicolvar/StoreColvarVessel.h
index 8a8edfc5ad8aac9799c75d703e0ebc5dba6644e4..3bfd6d22746206a8fe054b32459ee7e166af25c3 100644
--- a/src/multicolvar/StoreColvarVessel.h
+++ b/src/multicolvar/StoreColvarVessel.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -25,66 +25,25 @@
#include <string>
#include <cstring>
#include <vector>
-#include "vesselbase/Vessel.h"
-#include "tools/DynamicList.h"
+#include "vesselbase/StoreDataVessel.h"
namespace PLMD {
-namespace multicolvar{
+namespace multicolvar {
-class MultiColvarBase;
+class MultiColvarFunction;
-class StoreColvarVessel : public vesselbase::Vessel {
-private:
- unsigned bufsize;
- std::vector<unsigned> start;
- MultiColvarBase* mycolv;
- std::vector< DynamicList<unsigned> > active_atoms;
-protected:
-/// Are the weights differentiable
- bool diffweight;
-/// Get the number of stored colvar values
- unsigned getNumberOfStoredColvars() const ;
-/// Get the ith value in the vessel
- double getValue( const unsigned& ) const ;
-/// Get the weight of the ith quantity in the vessel
- double getWeight( const unsigned& ) const ;
-/// Add the derivatives from the value
- void addDerivatives( const unsigned& ival, double& pref, Value* value_out );
-/// Add the derivatives from the weight of the value
- void addWeightDerivatives( const unsigned& ival, double& pref, Value* value_out );
+class StoreColvarVessel : public vesselbase::StoreDataVessel {
public:
static void registerKeywords( Keywords& keys );
-/// Constructor
StoreColvarVessel( const vesselbase::VesselOptions& );
-/// Return the number of terms
- unsigned getNumberOfTerms(){ return 2; }
-/// This does the resizing of the buffer
- void resize();
-/// This makes sure things further down the chain are resized
- virtual void local_resizing()=0;
-/// This makes sure all values are stored
- bool calculate();
-/// Makes sure the dynamic lists are gathered
- void finish();
-/// Do the calculation
- virtual void performCalculationUsingAllValues()=0;
+ double getValue( const unsigned& );
+ virtual std::string description(){ return ""; }
+ void chainRuleForComponent( const unsigned& , const unsigned& , const unsigned& , const double& , MultiColvarFunction* );
};
inline
-double StoreColvarVessel::getValue( const unsigned& ival ) const {
- plumed_dbg_assert( ival<start.size()-1 );
- return getBufferElement( start[ival] );
-}
-
-inline
-double StoreColvarVessel::getWeight( const unsigned& ival ) const {
- plumed_dbg_assert( ival<start.size()-1 );
- return getBufferElement( bufsize + start[ival] );
-}
-
-inline
-unsigned StoreColvarVessel::getNumberOfStoredColvars() const {
- return start.size()-1;
+double StoreColvarVessel::getValue( const unsigned& ival ){
+ return getComponent( ival, 0 );
}
}
diff --git a/src/multicolvar/VolumeAround.cpp b/src/multicolvar/VolumeAround.cpp
index 88219736508ee9139f5e7fd5c1b59917f8828ce9..91f50ed82b2985495e74b820c39b6e9bac75cbd7 100644
--- a/src/multicolvar/VolumeAround.cpp
+++ b/src/multicolvar/VolumeAround.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/secondarystructure/AlphaRMSD.cpp b/src/secondarystructure/AlphaRMSD.cpp
index dad9fbf91b040954ec951327cb520935a58ea830..d7431f6835baa53b72ac0ca41ec09451e34c1c63 100644
--- a/src/secondarystructure/AlphaRMSD.cpp
+++ b/src/secondarystructure/AlphaRMSD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -94,9 +94,7 @@ Action(ao),
SecondaryStructureRMSD(ao)
{
// read in the backbone atoms
- std::vector<std::string> backnames(5); std::vector<unsigned> chains;
- backnames[0]="N"; backnames[1]="CA"; backnames[2]="CB"; backnames[3]="C"; backnames[4]="O";
- readBackboneAtoms( backnames, chains);
+ std::vector<unsigned> chains; readBackboneAtoms( "protein", chains);
// This constructs all conceivable sections of alpha helix in the backbone of the chains
unsigned nres, nprevious=0; std::vector<unsigned> nlist(30);
diff --git a/src/secondarystructure/AntibetaRMSD.cpp b/src/secondarystructure/AntibetaRMSD.cpp
index 728bf8b276116b9fc877e385c3f2f6d8b3ba5972..d4d8778495f623fcabea3aa576baf823c6782cbb 100644
--- a/src/secondarystructure/AntibetaRMSD.cpp
+++ b/src/secondarystructure/AntibetaRMSD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -101,9 +101,7 @@ Action(ao),
SecondaryStructureRMSD(ao)
{
// read in the backbone atoms
- std::vector<std::string> backnames(5); std::vector<unsigned> chains;
- backnames[0]="N"; backnames[1]="CA"; backnames[2]="CB"; backnames[3]="C"; backnames[4]="O";
- readBackboneAtoms( backnames, chains );
+ std::vector<unsigned> chains; readBackboneAtoms( "protein", chains );
bool intra_chain(false), inter_chain(false);
std::string style; parse("STYLE",style);
diff --git a/src/secondarystructure/ParabetaRMSD.cpp b/src/secondarystructure/ParabetaRMSD.cpp
index d8feb878c1a0dba712bf2f3dc03f358d77c5aabe..95d936ee2917622f9d5cf3634cc6cb0d284dadde 100644
--- a/src/secondarystructure/ParabetaRMSD.cpp
+++ b/src/secondarystructure/ParabetaRMSD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -101,9 +101,7 @@ Action(ao),
SecondaryStructureRMSD(ao)
{
// read in the backbone atoms
- std::vector<std::string> backnames(5); std::vector<unsigned> chains;
- backnames[0]="N"; backnames[1]="CA"; backnames[2]="CB"; backnames[3]="C"; backnames[4]="O";
- readBackboneAtoms( backnames, chains );
+ std::vector<unsigned> chains; readBackboneAtoms( "protein", chains );
bool intra_chain(false), inter_chain(false);
std::string style; parse("STYLE",style);
diff --git a/src/secondarystructure/SecondaryStructureRMSD.cpp b/src/secondarystructure/SecondaryStructureRMSD.cpp
index d8a330170a04a88b43f96a022a3f63f51728221c..973ef985bb20af6d768c07eadc4f0cb619eb715a 100644
--- a/src/secondarystructure/SecondaryStructureRMSD.cpp
+++ b/src/secondarystructure/SecondaryStructureRMSD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -58,7 +58,7 @@ void SecondaryStructureRMSD::registerKeywords( Keywords& keys ){
keys.add("hidden","NL_STRIDE","the frequency with which the neighbor list should be updated. Between neighbour list update steps all quantities "
"that contributed less than TOL at the previous neighbor list update step are ignored.");
ActionWithVessel::registerKeywords( keys );
- keys.use("LESS_THAN"); keys.use("MIN");
+ keys.use("LESS_THAN"); keys.use("MIN"); keys.use("NL_TOL");
}
SecondaryStructureRMSD::SecondaryStructureRMSD(const ActionOptions&ao):
@@ -67,8 +67,6 @@ ActionAtomistic(ao),
ActionWithValue(ao),
ActionWithVessel(ao),
updateFreq(0),
-lastUpdate(0),
-reduceAtNextStep(false),
align_strands(false),
s_cutoff(0),
align_atom_1(0),
@@ -82,8 +80,13 @@ align_atom_2(0)
parseFlag("VERBOSE",verbose_output);
if( keywords.exists("NL_STRIDE") ) parse("NL_STRIDE",updateFreq);
- if(updateFreq>0) log.printf(" Updating contributors every %d steps.\n",updateFreq);
- else log.printf(" Updating contributors every step.\n");
+ if(updateFreq>0){
+ firsttime=true;
+ log.printf(" Updating contributors every %d steps.\n",updateFreq);
+ } else {
+ firsttime=false; contributorsAreUnlocked=true; // This will lock during first prepare step methinks
+ log.printf(" Updating contributors every step.\n");
+ }
if( keywords.exists("STRANDS_CUTOFF") ){
parse("STRANDS_CUTOFF",s_cutoff); align_strands=true;
@@ -100,7 +103,7 @@ void SecondaryStructureRMSD::setAtomsFromStrands( const unsigned& atom1, const u
align_atom_1=atom1; align_atom_2=atom2;
}
-void SecondaryStructureRMSD::readBackboneAtoms( const std::vector<std::string>& backnames, std::vector<unsigned>& chain_lengths ){
+void SecondaryStructureRMSD::readBackboneAtoms( const std::string& moltype, std::vector<unsigned>& chain_lengths ){
std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
if( moldat.size()==0 ) error("Unable to find MOLINFO in input");
@@ -115,7 +118,7 @@ void SecondaryStructureRMSD::readBackboneAtoms( const std::vector<std::string>&
}
}
std::vector< std::vector<AtomNumber> > backatoms;
- moldat[0]->getBackbone( resstrings, backnames, backatoms );
+ moldat[0]->getBackbone( resstrings, moltype, backatoms );
chain_lengths.resize( backatoms.size() );
for(unsigned i=0;i<backatoms.size();++i){
@@ -131,7 +134,7 @@ void SecondaryStructureRMSD::addColvar( const std::vector<unsigned>& newatoms ){
for(unsigned i=0;i<newatoms.size();++i) log.printf("%d ",all_atoms(newatoms[i]).serial() );
log.printf("\n");
}
- taskList.addIndexToList( colvar_atoms.size() );
+ addTaskToList( colvar_atoms.size() );
colvar_atoms.push_back( newatoms );
}
@@ -148,13 +151,8 @@ void SecondaryStructureRMSD::setSecondaryStructure( std::vector<Vector>& structu
}
if( secondary_rmsd.size()==0 && secondary_drmsd.size()==0 ){
- pos.resize( structure.size() ); taskList.activateAll();
- for(unsigned i=0;i<taskList.getNumberActive();++i){
- for(unsigned j=0;j<colvar_atoms[i].size();++j) all_atoms.activate( colvar_atoms[i][j] );
- }
- all_atoms.updateActiveMembers();
- ActionAtomistic::requestAtoms( all_atoms.retrieveActiveList() );
- forcesToApply.resize( getNumberOfDerivatives() );
+ pos.resize( structure.size() );
+ finishTaskListUpdate();
readVesselKeywords();
if( getNumberOfVessels()==0 ){
@@ -190,32 +188,27 @@ void SecondaryStructureRMSD::setSecondaryStructure( std::vector<Vector>& structu
}
void SecondaryStructureRMSD::prepare(){
- bool updatetime=false;
- if( reduceAtNextStep ){
- taskList.mpi_gatherActiveMembers( comm );
- reduceAtNextStep=false; updatetime=true;
+ if( contributorsAreUnlocked ) lockContributors();
+ if( updateFreq>0 ){
+ if( firsttime || getStep()%updateFreq==0 ){ firsttime=false; unlockContributors(); }
}
- if( updateFreq>0 && (getStep()-lastUpdate)>=updateFreq ){
- taskList.activateAll();
- reduceAtNextStep=true; updatetime=true;
- lastUpdate=getStep();
- }
- if(updatetime){
- for(unsigned i=0;i<taskList.getNumberActive();++i){
- for(unsigned j=0;j<colvar_atoms[i].size();++j) all_atoms.activate( colvar_atoms[i][j] );
- }
- all_atoms.updateActiveMembers();
- ActionAtomistic::requestAtoms( all_atoms.retrieveActiveList() );
- forcesToApply.resize( getNumberOfDerivatives() );
- resizeFunctions();
+}
+
+void SecondaryStructureRMSD::finishTaskListUpdate(){
+ all_atoms.deactivateAll();
+ for(unsigned i=0;i<getCurrentNumberOfActiveTasks();++i){
+ for(unsigned j=0;j<colvar_atoms[getActiveTask(i)].size();++j) all_atoms.activate( colvar_atoms[getActiveTask(i)][j] );
}
+ all_atoms.updateActiveMembers();
+ ActionAtomistic::requestAtoms( all_atoms.retrieveActiveList() );
+ forcesToApply.resize( getNumberOfDerivatives() );
}
void SecondaryStructureRMSD::calculate(){
runAllTasks();
}
-void SecondaryStructureRMSD::performTask( const unsigned& j ){
+void SecondaryStructureRMSD::performTask(){
// Retrieve the positions
for(unsigned i=0;i<pos.size();++i) pos[i]=ActionAtomistic::getPosition( getAtomIndex(i) );
@@ -254,13 +247,14 @@ void SecondaryStructureRMSD::performTask( const unsigned& j ){
if( nr<r ){ closest=i; r=nr; }
}
}
- setElementValue(1,1.0); setElementValue(0,r);
+ setElementValue(1,1.0);
+ setElementValue(0,r);
return;
}
void SecondaryStructureRMSD::mergeDerivatives( const unsigned& ider, const double& df ){
plumed_dbg_assert( ider==0 );
- for(unsigned i=0;i<colvar_atoms[current].size();++i){
+ for(unsigned i=0;i<colvar_atoms[getCurrentTask()].size();++i){
unsigned thisatom=getAtomIndex(i), thispos=3*thisatom;
Vector ader=der[closest][i];
accumulateDerivative( thispos, df*ader[0] ); thispos++;
@@ -269,7 +263,7 @@ void SecondaryStructureRMSD::mergeDerivatives( const unsigned& ider, const doubl
}
if( alignType!="DRMSD" ){
vir[closest].zero();
- for(unsigned i=0;i<colvar_atoms[current].size();++i){
+ for(unsigned i=0;i<colvar_atoms[getCurrentTask()].size();++i){
vir[closest]+=(-1.0*Tensor( pos[i], der[closest][i] ));
}
}
@@ -291,5 +285,9 @@ void SecondaryStructureRMSD::apply(){
if( getForcesFromVessels( forcesToApply ) ) setForcesOnAtoms( forcesToApply );
}
+void SecondaryStructureRMSD::clearDerivativesAfterTask( const unsigned& ival ){
+ thisval_wasset[ival]=false; setElementValue( ival, 0.0 ); thisval_wasset[ival]=false;
+}
+
}
}
diff --git a/src/secondarystructure/SecondaryStructureRMSD.h b/src/secondarystructure/SecondaryStructureRMSD.h
index f048c8a44cbbb3c67df2ae260005f9cc1af23b2b..4523c2c34e972e6aa35f07d7ca20379a39eaf7eb 100644
--- a/src/secondarystructure/SecondaryStructureRMSD.h
+++ b/src/secondarystructure/SecondaryStructureRMSD.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -61,8 +61,7 @@ private:
std::vector<Tensor> vir;
/// Everything for controlling the updating of neighbor lists
int updateFreq;
- unsigned lastUpdate;
- bool reduceAtNextStep;
+ bool firsttime;
/// Variables for strands cutoff
bool align_strands;
double s_cutoff;
@@ -75,7 +74,7 @@ private:
unsigned getAtomIndex( const unsigned& iatom );
protected:
/// Get the atoms in the backbone
- void readBackboneAtoms( const std::vector<std::string>& backnames, std::vector<unsigned>& chain_lengths );
+ void readBackboneAtoms( const std::string& backnames, std::vector<unsigned>& chain_lengths );
/// Add a set of atoms to calculat ethe rmsd from
void addColvar( const std::vector<unsigned>& newatoms );
/// Set a reference configuration
@@ -89,9 +88,10 @@ public:
unsigned getNumberOfFunctionsInAction();
unsigned getNumberOfDerivatives();
void prepare();
+ void finishTaskListUpdate();
void calculate();
- void performTask( const unsigned& j );
- void clearDerivativesAfterTask( const unsigned& ){}
+ void performTask();
+ void clearDerivativesAfterTask( const unsigned& );
void apply();
void mergeDerivatives( const unsigned& , const double& );
bool isPeriodic(){ return false; }
@@ -109,7 +109,7 @@ unsigned SecondaryStructureRMSD::getNumberOfDerivatives(){
inline
unsigned SecondaryStructureRMSD::getAtomIndex( const unsigned& iatom ){
- return all_atoms.linkIndex( colvar_atoms[current][iatom] );
+ return all_atoms.linkIndex( colvar_atoms[getCurrentTask()][iatom] );
}
}
diff --git a/src/setup/ActionSetup.h b/src/setup/ActionSetup.h
index fce3e5fc50203dd2e87b2f69344a515d9a0e7e6a..591a3ec6436308ce74959dc3c157cdfd26b75ed8 100644
--- a/src/setup/ActionSetup.h
+++ b/src/setup/ActionSetup.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/setup/Load.cpp b/src/setup/Load.cpp
index f34bec59be056f590a582a2184b9232ec0592a03..c6895ea2441cb37a442e2a2631a1d171a0678f70 100644
--- a/src/setup/Load.cpp
+++ b/src/setup/Load.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/setup/MolInfo.cpp b/src/setup/MolInfo.cpp
index b9035d96297ad3003767723a0fabd465576a950c..e854919a7eee35ed55a37f2b3049b3485c531076 100644
--- a/src/setup/MolInfo.cpp
+++ b/src/setup/MolInfo.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -39,8 +39,12 @@ using this command you can find the backbone atoms in your structure automatical
Please be aware that the pdb parser in plumed is far from perfect. You should thus check the log file
and examine what plumed is actually doing whenenver you use the MOLINFO action.
-\bug At the moment all atoms named HA1 are treated as if they are CB atoms. This makes it possible to deal
-with GLY residues in colvars like \ref ALPHARMSD.
+\bug At the moment the HA1 atoms in a GLY residues are treated as if they are the CB atoms. This may or
+may not be true - GLY is problematic for secondary structure residues as it is achiral.
+
+\bug If you use WHOLEMOLECULES RESIDUES=1-10 for a 18 amino acid protein
+( 18 amino acids + 2 terminal groups = 20 residues ) the code will fail as it will not be able to
+interpret termnal residue 1.
\par Examples
diff --git a/src/setup/Restart.cpp b/src/setup/Restart.cpp
index 04f0ba87a4e09879dfc61a036c2cfddde2c1a4e2..c8daa6653200d75b95e49e03ff6916b9a147b8be 100644
--- a/src/setup/Restart.cpp
+++ b/src/setup/Restart.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/setup/Units.cpp b/src/setup/Units.cpp
index c5402f50a62930f683efd35dc2c20c1e2a97e8fb..650973be7ea9caa37f7f6ce8a4c475baa0333825 100644
--- a/src/setup/Units.cpp
+++ b/src/setup/Units.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Angle.cpp b/src/tools/Angle.cpp
index 361988e864d3be895c5438228ea2b8e5b5480b46..2579cba0648327bc3c967a3e5b3f70aff7913698 100644
--- a/src/tools/Angle.cpp
+++ b/src/tools/Angle.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Angle.h b/src/tools/Angle.h
index 3207a3e9532eecfddb038250c120c9196dce8f9b..e6a7fbebdd3ef8fa9a324a15b8c68e4855db6f58 100644
--- a/src/tools/Angle.h
+++ b/src/tools/Angle.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/AtomNumber.h b/src/tools/AtomNumber.h
index 5be81e9f711ebb8ce68a5ab8178e5a057582d3d8..b724f7e68783e94f8275abec49892a176746a687 100644
--- a/src/tools/AtomNumber.h
+++ b/src/tools/AtomNumber.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/BiasRepresentation.cpp b/src/tools/BiasRepresentation.cpp
index 66c3033cbe4537d84481571c963f7b5ea2c44951..ea6697cb0e43e5a4f061354cd87ef677fd2c4623 100644
--- a/src/tools/BiasRepresentation.cpp
+++ b/src/tools/BiasRepresentation.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -137,7 +137,7 @@ void BiasRepresentation::pushKernel( IFile *ifile ){
biasf.push_back(dummyd);
// the domain does not pertain to the kernel but to the values here defined
string mins,maxs,minv,maxv,mini,maxi;mins="min_";maxs="max_";
- for(unsigned i=0 ; i<ndim; i++){
+ for(int i=0 ; i<ndim; i++){
if(values[i]->isPeriodic()){
ifile->scanField(mins+names[i],minv);
ifile->scanField(maxs+names[i],maxv);
@@ -155,7 +155,7 @@ void BiasRepresentation::pushKernel( IFile *ifile ){
vector<double> der(ndim);
vector<double> xx(ndim);
if(mycomm.Get_size()==1){
- for(int i=0;i<neighbors.size();++i){
+ for(unsigned i=0;i<neighbors.size();++i){
unsigned ineigh=neighbors[i];
for(int j=0;j<ndim;++j){der[j]=0.0;}
BiasGrid_->getPoint(ineigh,xx);
@@ -189,11 +189,11 @@ void BiasRepresentation::pushKernel( IFile *ifile ){
// a pointer of double as it was in old gaussian
for(int j=0;j<ndim;++j){ allder[ndim*i+j]=tmpder[j];tmpder[j]=0.;}
}
- mycomm.Sum(&allbias[0],allbias.size());
- mycomm.Sum(&allder[0],allder.size());
+ mycomm.Sum(allbias);
+ mycomm.Sum(allder);
for(unsigned i=0;i<neighbors.size();++i){
unsigned ineigh=neighbors[i];
- for(unsigned j=0;j<ndim;++j){der[j]=allder[ndim*i+j];}
+ for(int j=0;j<ndim;++j){der[j]=allder[ndim*i+j];}
BiasGrid_->addValueAndDerivatives(ineigh,allbias[i],der);
}
}
@@ -220,7 +220,7 @@ void BiasRepresentation::getMinMaxBin(vector<double> &vmin, vector<double> &vmax
ss=hills[i]->getContinuousSupport();
}
cc=hills[i]->getCenter();
- for(unsigned j=0;j<ndim;j++){
+ for(int j=0;j<ndim;j++){
double dmin=cc[j]-ss[j];
double dmax=cc[j]+ss[j];
double ddiv=ss[j]/double(ndiv);
@@ -229,7 +229,7 @@ void BiasRepresentation::getMinMaxBin(vector<double> &vmin, vector<double> &vmax
if(ddiv<binsize[j])binsize[j]=ddiv;
}
}
- for(unsigned j=0;j<ndim;j++){
+ for(int j=0;j<ndim;j++){
// reset to periodicity
if(values[j]->isPeriodic()){
double minv,maxv;
diff --git a/src/tools/BiasRepresentation.h b/src/tools/BiasRepresentation.h
index cfa4d011c4b444bd7c7ff3833e0eb7f65ac4540f..b5e8db08625408cf7f0ef659e6390b958a51e16c 100644
--- a/src/tools/BiasRepresentation.h
+++ b/src/tools/BiasRepresentation.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Citations.cpp b/src/tools/Citations.cpp
index 82ec01633b458e35e0736874aa63ee2c5e31067b..e76df9561d63c0af6b064017fb2006fad3600ad6 100644
--- a/src/tools/Citations.cpp
+++ b/src/tools/Citations.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Citations.h b/src/tools/Citations.h
index eaaf1fbcbfdbe88ee1ed999006a0382a5d366031..c13ed8688b1a11823396a044d571a7a2ecdbb793 100644
--- a/src/tools/Citations.h
+++ b/src/tools/Citations.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Communicator.cpp b/src/tools/Communicator.cpp
index a94f567fb5797a934d3604c20639f06a6456e1b7..d4765cdd39f79ce4cf464579ec309719acb42ff5 100644
--- a/src/tools/Communicator.cpp
+++ b/src/tools/Communicator.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -38,6 +38,8 @@ Communicator::Communicator(const Communicator&pc){
Set_comm(pc.communicator);
}
+Communicator::Status Communicator::StatusIgnore;
+
Communicator& Communicator::operator=(const Communicator&pc){
if (this != &pc){
Set_comm(pc.communicator);
@@ -121,6 +123,88 @@ void Communicator::Abort(int errorcode){
#endif
}
+void Communicator::Bcast(Data data,int root){
+#if defined(__PLUMED_MPI)
+ if(initialized()) MPI_Bcast(data.pointer,data.size,data.type,root,communicator);
+#else
+ (void) data;
+ (void) root;
+#endif
+}
+
+void Communicator::Sum(Data data){
+#if defined(__PLUMED_MPI)
+ if(initialized()) MPI_Allreduce(MPI_IN_PLACE,data.pointer,data.size,data.type,MPI_SUM,communicator);
+#else
+ (void) data;
+#endif
+}
+
+Communicator::Request Communicator::Isend(ConstData data,int source,int tag){
+ Request req;
+#ifdef __PLUMED_MPI
+ plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
+ void*s=const_cast<void*>((const void*)data.pointer);
+ MPI_Isend(s,data.size,data.type,source,tag,communicator,&req.r);
+#else
+ (void) data;
+ (void) source;
+ (void) tag;
+ plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
+#endif
+ return req;
+}
+
+void Communicator::Allgatherv(ConstData in,Data out,const int*recvcounts,const int*displs){
+#if defined(__PLUMED_MPI)
+ plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
+ void*s=const_cast<void*>((const void*)in.pointer);
+ void*r=const_cast<void*>((const void*)out.pointer);
+ int*rc=const_cast<int*>(recvcounts);
+ int*di=const_cast<int*>(displs);
+ if(s==NULL)s=MPI_IN_PLACE;
+ MPI_Allgatherv(s,in.size,in.type,r,rc,di,out.type,communicator);
+#else
+ (void) in;
+ (void) out;
+ (void) recvcounts;
+ (void) displs;
+ plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
+#endif
+}
+
+void Communicator::Allgather(ConstData in,Data out){
+#if defined(__PLUMED_MPI)
+ plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
+ void*s=const_cast<void*>((const void*)in.pointer);
+ void*r=const_cast<void*>((const void*)out.pointer);
+ if(s==NULL)s=MPI_IN_PLACE;
+ MPI_Allgather(s,in.size,in.type,r,out.size/Get_size(),out.type,communicator);
+#else
+ (void) in;
+ (void) out;
+ plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
+#endif
+}
+
+void Communicator::Recv(Data data,int source,int tag,Status&status){
+#ifdef __PLUMED_MPI
+ plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
+ if(&status==&StatusIgnore) MPI_Recv(data.pointer,data.size,data.type,source,tag,communicator,MPI_STATUS_IGNORE);
+ else MPI_Recv(data.pointer,data.size,data.type,source,tag,communicator,&status.s);
+#else
+ (void) data;
+ (void) source;
+ (void) tag;
+ (void) status;
+ plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
+#endif
+}
+
+
+
+
+
void Communicator::Barrier()const{
#ifdef __PLUMED_MPI
if(initialized()) MPI_Barrier(communicator);
@@ -140,19 +224,11 @@ bool Communicator::initialized(){
else return false;
}
-void Communicator::Request::wait(){
-#ifdef __PLUMED_MPI
- plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
- MPI_Wait(&r,MPI_STATUS_IGNORE);
-#else
- plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
-#endif
-}
-
void Communicator::Request::wait(Status&s){
#ifdef __PLUMED_MPI
plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
- MPI_Wait(&r,&s.s);
+ if(&s==&StatusIgnore) MPI_Wait(&r,MPI_STATUS_IGNORE);
+ else MPI_Wait(&r,&s.s);
#else
(void) s;
plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
@@ -166,6 +242,13 @@ template<> MPI_Datatype Communicator::getMPIType<int>() { return MPI_INT;}
template<> MPI_Datatype Communicator::getMPIType<char>() { return MPI_CHAR;}
template<> MPI_Datatype Communicator::getMPIType<unsigned>() { return MPI_UNSIGNED;}
template<> MPI_Datatype Communicator::getMPIType<long unsigned>() { return MPI_UNSIGNED_LONG;}
+#else
+template<> MPI_Datatype Communicator::getMPIType<float>(){ return MPI_Datatype();}
+template<> MPI_Datatype Communicator::getMPIType<double>(){ return MPI_Datatype();}
+template<> MPI_Datatype Communicator::getMPIType<int>(){ return MPI_Datatype();}
+template<> MPI_Datatype Communicator::getMPIType<char>(){ return MPI_Datatype();}
+template<> MPI_Datatype Communicator::getMPIType<unsigned>(){ return MPI_Datatype();}
+template<> MPI_Datatype Communicator::getMPIType<long unsigned>(){ return MPI_Datatype();}
#endif
@@ -173,8 +256,23 @@ void Communicator::Split(int color,int key,Communicator&pc)const{
#ifdef __PLUMED_MPI
MPI_Comm_split(communicator,color,key,&pc.communicator);
#else
+ (void) color;
+ (void) key;
+ (void) pc;
+ plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
+#endif
+}
+
+int Communicator::Status::Get_count(MPI_Datatype type)const{
+ int i;
+#ifdef __PLUMED_MPI
+ plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
+ MPI_Get_count(const_cast<MPI_Status*>(&s),type,&i);
+#else
+ i=0;
plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
#endif
+ return i;
}
}
diff --git a/src/tools/Communicator.h b/src/tools/Communicator.h
index e53a68eab617df5ecfe50dcbe22d515864b1a44a..d703c3a24cefa3664ddcfa7b3bbf8f0e9ca0c53f 100644
--- a/src/tools/Communicator.h
+++ b/src/tools/Communicator.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -26,16 +26,23 @@
#endif
#include <cstdlib>
#include "Exception.h"
+#include <vector>
+#include <string>
+#include "Vector.h"
+#include "Tensor.h"
+#include "Matrix.h"
namespace PLMD{
#ifndef __PLUMED_MPI
-/// Surrogate of MPI types when MPI library is not available
- class MPI_Comm {
- int dummy;
- public:
- MPI_Comm():dummy(0){};
- };
+/// Surrogate of MPI_Comm when MPI library is not available
+ class MPI_Comm {};
+/// Surrogate of MPI_Datatype when MPI library is not available
+ class MPI_Datatype {};
+/// Surrogate of MPI_Status when MPI library is not available
+ class MPI_Status {};
+/// Surrogate of MPI_Request when MPI library is not available
+ class MPI_Request {};
#endif
/// \ingroup TOOLBOX
@@ -44,26 +51,93 @@ namespace PLMD{
class Communicator{
/// Communicator
MPI_Comm communicator;
-#ifdef __PLUMED_MPI
+/// Function returning the MPI type.
+/// You can use it to access to the MPI type of a C++ type, e.g.
+/// `MPI_Datatype type=getMPIType<double>();`
template <class T>
static MPI_Datatype getMPIType();
-#endif
+/// Structure defining a buffer for MPI.
+/// It contains info on the pointed data and its type and size. It is useful to
+/// allow wrapper of MPI functions where the triplet (buffer,type,size)
+/// is grouped into a single object. It can be built starting from
+/// different kinds of data. To implement compatibility of MPI wrappers
+/// with e.g. vectors, add constructors here.
+ struct Data{
+ void*pointer;
+ int size;
+ MPI_Datatype type;
+/// Init from pointer and size
+ template <typename T> Data(T*p,int s): pointer(p), size(s), type(getMPIType<T>()) {}
+/// Init from reference
+ template <typename T> Data(T&p): pointer(&p), size(1), type(getMPIType<T>()) {}
+/// Init from pointer to VectorGeneric
+ template <unsigned n> Data(VectorGeneric<n> *p,int s): pointer(p), size(n*s), type(getMPIType<double>()) {}
+/// Init from reference to VectorGeneric
+ template <unsigned n> Data(VectorGeneric<n> &p): pointer(&p), size(n), type(getMPIType<double>()) {}
+/// Init from pointer to TensorGeneric
+ template <unsigned n,unsigned m> Data(TensorGeneric<n,m> *p,int s): pointer(p), size(n*m*s), type(getMPIType<double>()) {}
+/// Init from reference to TensorGeneric
+ template <unsigned n,unsigned m> Data(TensorGeneric<n,m> &p): pointer(&p), size(n*m), type(getMPIType<double>()) {}
+/// Init from reference to std::vector
+ template <typename T> Data(std::vector<T>&v){
+ if(v.size()>0){ Data d(&v[0],v.size()); pointer=d.pointer; size=d.size; type=d.type; }
+ else { pointer=NULL; size=0; }
+ }
+/// Init from reference to PLMD::Matrix
+ template <typename T> Data(Matrix<T>&m ){
+ if(m.nrows()*m.ncols()>0){ Data d(&m(0,0),m.nrows()*m.ncols()); pointer=d.pointer; size=d.size; type=d.type; }
+ else{ pointer=NULL; size=0; }
+ }
+/// Init from reference to std::string
+ Data(std::string&s){
+ if(s.size()>0){ Data d(&s[0],s.size()); pointer=d.pointer; size=d.size; type=d.type; }
+ else { pointer=NULL; size=0; }
+ }
+ };
+/// Const version of Communicator::Data
+/// See Communicator::Data documentation
+ struct ConstData{
+ const void*pointer;
+ int size;
+ MPI_Datatype type;
+ template <typename T> ConstData(const T*p,int s): pointer(p), size(s), type(getMPIType<T>()) {}
+ template <typename T> ConstData(const T&p): pointer(&p), size(1), type(getMPIType<T>()) {}
+ template <unsigned n> ConstData(const VectorGeneric<n> *p,int s): pointer(p), size(n*s), type(getMPIType<double>()) {}
+ template <unsigned n> ConstData(const VectorGeneric<n> &p): pointer(&p), size(n), type(getMPIType<double>()) {}
+ template <unsigned n,unsigned m> ConstData(const TensorGeneric<n,m> *p,int s): pointer(p), size(n*m*s), type(getMPIType<double>()) {}
+ template <unsigned n,unsigned m> ConstData(const TensorGeneric<n,m> &p): pointer(&p), size(n*m), type(getMPIType<double>()) {}
+ template <typename T> ConstData(const std::vector<T>&v){
+ if(v.size()>0){ ConstData d(&v[0],v.size()); pointer=d.pointer; size=d.size; type=d.type; }
+ else { pointer=NULL; size=0; }
+ }
+ template <typename T> ConstData(const Matrix<T>&m ){
+ if(m.nrows()*m.ncols()>0){ ConstData d(&m(0,0),m.nrows()*m.ncols()); pointer=d.pointer; size=d.size; type=d.type; }
+ else{ pointer=NULL; size=0; }
+ }
+ ConstData(const std::string&s){
+ if(s.size()>0){ ConstData d(&s[0],s.size()); pointer=d.pointer; size=d.size; type=d.type; }
+ else { pointer=NULL; size=0; }
+ }
+ };
public:
+/// Wrapper class for MPI_Status
class Status{
+ int Get_count(MPI_Datatype)const;
public:
-#ifdef __PLUMED_MPI
MPI_Status s;
-#endif
template <class T>
- int Get_count()const;
+ int Get_count()const{return Get_count(getMPIType<T>());}
};
+/// Special status used when status should be ignored.
+/// E.g. `Recv(a,0,1,Communicator::StatusIgnore);`
+/// Notice that this is the default for Recv, so this is equivalent to
+/// `Recv(a,0,1);`
+ static Status StatusIgnore;
+/// Wrapper class for MPI_Request
class Request{
public:
-#ifdef __PLUMED_MPI
MPI_Request r;
-#endif
- void wait();
- void wait(Status&);
+ void wait(Status&s=StatusIgnore);
};
/// Default constructor
Communicator();
@@ -79,18 +153,20 @@ public:
int Get_rank()const;
/// Obtain the number of processes
int Get_size()const;
-/// Set from a real MPI communicator
- void Set_comm(MPI_Comm);
+/// Set from a real MPI communicator.
+/// \param comm MPI communicator
+ void Set_comm(MPI_Comm comm);
/// Reference to MPI communicator
MPI_Comm & Get_comm();
-/// Set from a pointer to a real MPI communicator (C)
+/// Set from a pointer to a real MPI communicator (C).
/// \param comm Pointer to a C MPI communicator
void Set_comm(void*comm);
-/// Set from a pointer to a real MPI communicator (FORTRAN)
+/// Set from a pointer to a real MPI communicator (FORTRAN).
/// \param comm Pointer to a FORTRAN MPI communicator (INTEGER)
void Set_fcomm(void*comm);
-/// Wrapper to MPI_Abort
- void Abort(int);
+/// Wrapper to MPI_Abort.
+/// \param code Error code
+ void Abort(int code);
/// Wrapper to MPI_Barrier
void Barrier()const;
/// Tests if MPI library is initialized
@@ -99,147 +175,58 @@ public:
/// Returns MPI_COMM_WORLD if MPI is initialized, otherwise the default communicator
static Communicator & Get_world();
-/// Wrapper for MPI_Allreduce with MPI_SUM
- template <class T>
- void Sum(T*,int);
-/// Wrapper for MPI_Allgatherv
- template <class T>
- void Allgatherv(const T*,int,T*,const int*,const int*);
- template <class T>
- void Allgather(const T*,int,T*,int);
- template <class T>
- Request Isend(const T*,int,int,int);
- template <class T>
- void Recv(T*,int,int,int,Status&);
- template <class T>
- void Recv(T*,int,int,int);
- template <class T>
- void Bcast(T*,int,int);
+/// Wrapper for MPI_Allreduce with MPI_SUM (data struct)
+ void Sum(Data);
+/// Wrapper for MPI_Allreduce with MPI_SUM (pointer)
+ template <class T> void Sum(T*buf,int count){Sum(Data(buf,count));}
+/// Wrapper for MPI_Allreduce with MPI_SUM (reference)
+ template <class T> void Sum(T&buf){Sum(Data(buf));}
+
+/// Wrapper for MPI_Bcast (data struct)
+ void Bcast(Data,int);
+/// Wrapper for MPI_Bcast (pointer)
+ template <class T> void Bcast(T*buf,int count,int root){Bcast(Data(buf,count),root);}
+/// Wrapper for MPI_Bcast (reference)
+ template <class T> void Bcast(T&buf,int root){Bcast(Data(buf),root);}
+
+/// Wrapper for MPI_Isend (data struct)
+ Request Isend(ConstData,int,int);
+/// Wrapper for MPI_Isend (pointer)
+ template <class T> Request Isend(const T*buf,int count,int source,int tag){return Isend(ConstData(buf,count),source,tag);}
+/// Wrapper for MPI_Isend (reference)
+ template <class T> Request Isend(const T&buf,int source,int tag){return Isend(ConstData(buf),source,tag);}
+
+/// Wrapper for MPI_Allgatherv (data struct)
+ void Allgatherv(ConstData in,Data out,const int*,const int*);
+/// Wrapper for MPI_Allgatherv (pointer)
+ template <class T> void Allgatherv(const T*sendbuf,int sendcount,T*recvbuf,const int*recvcounts,const int*displs){
+ Allgatherv(ConstData(sendbuf,sendcount),Data(recvbuf,0),recvcounts,displs);}
+/// Wrapper for MPI_Allgatherv (reference)
+ template <class T> void Allgatherv(const T&sendbuf,T&recvbuf,const int*recvcounts,const int*displs){
+ Allgatherv(ConstData(sendbuf),Data(recvbuf),recvcounts,displs);}
+
+/// Wrapper for MPI_Allgather (data struct)
+ void Allgather(ConstData in,Data out);
+/// Wrapper for MPI_Allgatherv (pointer)
+ template <class T> void Allgather(const T*sendbuf,int sendcount,T*recvbuf,int recvcount){
+ Allgather(ConstData(sendbuf,sendcount),Data(recvbuf,recvcount*Get_size()));
+ }
+/// Wrapper for MPI_Allgatherv (reference)
+ template <class T> void Allgather(const T&sendbuf,T&recvbuf){
+ Allgather(ConstData(sendbuf),Data(recvbuf));
+ }
+
+/// Wrapper for MPI_Recv (data struct)
+ void Recv(Data,int,int,Status&s=StatusIgnore);
+/// Wrapper for MPI_Recv (pointer)
+ template <class T> void Recv(T*buf,int count,int source,int tag,Status&s=StatusIgnore){Recv(Data(buf,count),source,tag,s);}
+/// Wrapper for MPI_Recv (reference)
+ template <class T> void Recv(T&buf,int source,int tag,Status&s=StatusIgnore){Recv(Data(buf),source,tag,s);}
/// Wrapper to MPI_Comm_split
void Split(int,int,Communicator&)const;
};
-template<class T>
-void Communicator::Sum(T*b,int count){
-#if defined(__PLUMED_MPI)
- if(initialized()) MPI_Allreduce(MPI_IN_PLACE,b,count,getMPIType<T>(),MPI_SUM,communicator);
-#else
- (void) b;
- (void) count;
-#endif
-}
-
-template<class T>
-void Communicator::Bcast(T*b,int count,int root){
-#if defined(__PLUMED_MPI)
- if(initialized()) MPI_Bcast(b,count,getMPIType<T>(),root,communicator);
-#else
- (void) b;
- (void) count;
- (void) root;
-#endif
-}
-
-
-template<class T>
-void Communicator::Allgatherv(const T*sendbuf,int sendcount,T*recvbuf,const int*recvcounts,const int*displs){
-#if defined(__PLUMED_MPI)
- plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
- void*s=const_cast<void*>((const void*)sendbuf);
- void*r=const_cast<void*>((const void*)recvbuf);
- int*rc=const_cast<int*>(recvcounts);
- int*di=const_cast<int*>(displs);
- if(s==NULL)s=MPI_IN_PLACE;
- MPI_Allgatherv(s,sendcount,getMPIType<T>(),r,rc,di,getMPIType<T>(),communicator);
-#else
- (void) sendbuf;
- (void) sendcount;
- (void) recvbuf;
- (void) recvcounts;
- (void) displs;
- plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
-#endif
-}
-
-template<class T>
-void Communicator::Allgather(const T*sendbuf,int sendcount,T*recvbuf,int recvcount){
-#if defined(__PLUMED_MPI)
- plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
- void*s=const_cast<void*>((const void*)sendbuf);
- void*r=const_cast<void*>((const void*)recvbuf);
- if(s==NULL)s=MPI_IN_PLACE;
- MPI_Allgather(s,sendcount,getMPIType<T>(),r,recvcount,getMPIType<T>(),communicator);
-#else
- (void) sendbuf;
- (void) sendcount;
- (void) recvbuf;
- (void) recvcount;
- plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
-#endif
-}
-
-template <class T>
-Communicator::Request Communicator::Isend(const T*buf,int count,int source,int tag){
- Request req;
-#ifdef __PLUMED_MPI
- plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
- void*s=const_cast<void*>((const void*)buf);
- MPI_Isend(s,count,getMPIType<T>(),source,tag,communicator,&req.r);
-#else
- (void) buf;
- (void) count;
- (void) source;
- (void) tag;
- plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
-#endif
- return req;
-}
-
-template <class T>
-void Communicator::Recv(T*buf,int count,int source,int tag,Status&status){
-#ifdef __PLUMED_MPI
- plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
- MPI_Recv(buf,count,getMPIType<T>(),source,tag,communicator,&status.s);
-#else
- (void) buf;
- (void) count;
- (void) source;
- (void) tag;
- (void) status;
- plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
-#endif
-}
-
-template <class T>
-void Communicator::Recv(T*buf,int count,int source,int tag){
-#ifdef __PLUMED_MPI
- plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
- MPI_Recv(buf,count,getMPIType<T>(),source,tag,communicator,MPI_STATUS_IGNORE);
-#else
- (void) buf;
- (void) count;
- (void) source;
- (void) tag;
- plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
-#endif
-}
-
-template<class T>
-int Communicator::Status::Get_count()const{
- int i;
-#ifdef __PLUMED_MPI
- plumed_massert(initialized(),"you are trying to use an MPI function, but MPI is not initialized");
- MPI_Get_count(const_cast<MPI_Status*>(&s),getMPIType<T>(),&i);
-#else
- i=0;
- plumed_merror("you are trying to use an MPI function, but PLUMED has been compiled without MPI support");
-#endif
- return i;
-}
-
-
-
}
#endif
diff --git a/src/tools/CubicInterpolation.cpp b/src/tools/CubicInterpolation.cpp
index cec8c00624eec9f331d2dc9ecd057d8d0d67b682..3ee83ba1c9e462113c67a820b977454f96f97508 100644
--- a/src/tools/CubicInterpolation.cpp
+++ b/src/tools/CubicInterpolation.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/CubicInterpolation.h b/src/tools/CubicInterpolation.h
index 70f405fc6043641b26b074d739b090c4ceb57fe8..b99e22e30a4bd39570f850e5c6451a23a8e1d996 100644
--- a/src/tools/CubicInterpolation.h
+++ b/src/tools/CubicInterpolation.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/DLLoader.cpp b/src/tools/DLLoader.cpp
index ae3488a18d82d4621bcb829ef37cbf1704206666..edb1ec01816d35d9b8ba7d99861ed8fb1724a024 100644
--- a/src/tools/DLLoader.cpp
+++ b/src/tools/DLLoader.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/DLLoader.h b/src/tools/DLLoader.h
index 674d7e05a151da04f4b886c2e218244e41d5c7ae..8fb525da26795ca700297dff48b667f09deed93b 100644
--- a/src/tools/DLLoader.h
+++ b/src/tools/DLLoader.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/DRMSD.cpp b/src/tools/DRMSD.cpp
index 4afe3951d78eb0579bd69428c81605aa3114d6b8..e076f8a62d7799ad3e6aa41841f4959a1d8c4f9e 100644
--- a/src/tools/DRMSD.cpp
+++ b/src/tools/DRMSD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/DRMSD.h b/src/tools/DRMSD.h
index 2b0b52fbf845e7986a1ecf22248c743068ea9e9e..4a7f16046c3455711f1114bf6316d491bebc850b 100644
--- a/src/tools/DRMSD.h
+++ b/src/tools/DRMSD.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/DynamicList.h b/src/tools/DynamicList.h
index 5ba1d6f108960257ca067e77e52264faa69d9457..d1a3e4c5d160ebde1ae39569f9800b058d7c7c78 100644
--- a/src/tools/DynamicList.h
+++ b/src/tools/DynamicList.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -151,8 +151,8 @@ private:
unsigned nprocessors;
/// The rank of the node we are on
unsigned rank;
-/// This is a flag that is used internally to ensure that dynamic lists are being used properly
- bool allWereActivated;
+/// These are flags that are used internally to ensure that dynamic lists are being used properly
+ bool allWereActivated, allWereDeactivated;
public:
/// Constructor
DynamicList():nactive(0),nprocessors(1),rank(0),allWereActivated(false) {}
@@ -178,8 +178,10 @@ public:
void setupMPICommunication( Communicator& comm );
/// Add something to the active list
void addIndexToList( const T & ii );
+/// Find the index of in the list which has value t
+ int getIndexOfElement( const T& t ) const ;
/// Make a particular element inactive
- void deactivate( const unsigned ii );
+ void deactivate( const T& t );
/// Make everything in the list inactive
void deactivateAll();
/// Make something active
@@ -195,6 +197,8 @@ public:
/// This can be used for a fast version of updateActiveMembers in which only a subset of the
/// indexes are checked
void updateIndex( const unsigned& ii );
+/// This tells one if an update has been completed
+ bool updateComplete() const ;
/// This sorts the elements in the active list
void sortActiveList();
/// Retriee the list of active objects
@@ -243,17 +247,32 @@ void DynamicList<T>::setupMPICommunication( Communicator& comm ){
}
template <typename T>
-void DynamicList<T>::deactivate( const unsigned ii ){
- plumed_dbg_massert(ii<all.size(),"ii is out of bounds");
+int DynamicList<T>::getIndexOfElement( const T& t ) const {
+ bool found=false;
+ for(unsigned i=0;i<all.size();++i){
+ if( t==all[i] ){ found=true; return i; }
+ }
+ plumed_merror("Could not find an element in the dynamic list");
+ return 0;
+}
+
+template <typename T>
+void DynamicList<T>::deactivate( const T& t ){
plumed_dbg_assert( allWereActivated );
- if( onoff[ii]==0 || onoff[ii]%nprocessors!=0 ) return ;
+ unsigned ii=getIndexOfElement( t );
+ if( onoff[ii]==0 || onoff[ii]%nprocessors!=0 ) return;
+ // Deactivates the component
if( rank==0 ) onoff[ii]=nprocessors-1;
else onoff[ii]=nprocessors-rank;
}
template <typename T>
void DynamicList<T>::deactivateAll(){
+ allWereDeactivated=true; allWereActivated=false;
for(unsigned i=0;i<nactive;++i) onoff[ active[i] ]= 0;
+ nactive=0;
+ // Reset translator
+ for(unsigned i=0;i<all.size();++i) translator[i]=i;
#ifndef NDEBUG
for(unsigned i=0;i<onoff.size();++i) plumed_dbg_assert( onoff[i]==0 );
#endif
@@ -269,7 +288,8 @@ void DynamicList<T>::activate( const unsigned ii ){
template <typename T>
void DynamicList<T>::activateAll(){
for(unsigned i=0;i<onoff.size();++i) onoff[i]=nprocessors;
- updateActiveMembers(); allWereActivated=true;
+ allWereActivated=true; updateActiveMembers(); allWereActivated=true;
+
}
template <typename T>
@@ -283,20 +303,23 @@ void DynamicList<T>::mpi_gatherActiveMembers(Communicator& comm){
template <typename T>
void DynamicList<T>::updateActiveMembers(){
- unsigned kk=0;
+ plumed_dbg_assert( allWereActivated || allWereDeactivated );
+ unsigned kk=0; allWereActivated=allWereDeactivated=false;
for(unsigned i=0;i<all.size();++i){
if( onoff[i]>0 && onoff[i]%nprocessors==0 ){ translator[i]=kk; active[kk]=i; kk++; }
}
- nactive=kk; allWereActivated=false;
+ nactive=kk;
}
template <typename T>
void DynamicList<T>::emptyActiveMembers(){
+ plumed_dbg_assert( allWereActivated || allWereDeactivated );
nactive=0;
}
template <typename T>
void DynamicList<T>::updateIndex( const unsigned& ii ){
+ plumed_dbg_assert( allWereActivated || allWereDeactivated );
if( onoff[ii]>0 && onoff[ii]%nprocessors==0 ){
translator[nactive]=nactive; active[nactive]=ii; nactive++;
}
@@ -304,16 +327,23 @@ void DynamicList<T>::updateIndex( const unsigned& ii ){
template <typename T>
void DynamicList<T>::sortActiveList(){
+ plumed_dbg_assert( allWereActivated || allWereDeactivated );
+ allWereActivated=allWereDeactivated=false;
std::sort( active.begin(), active.begin()+nactive );
for(unsigned i=0;i<nactive;++i) translator[ active[i] ]=i;
}
template <typename T>
unsigned DynamicList<T>::linkIndex( const unsigned& ii ) const {
- plumed_dbg_assert( onoff[ii]>0 && onoff[ii]%nprocessors==0 );
return translator[ii];
}
+template <typename T>
+bool DynamicList<T>::updateComplete() const {
+ if( !allWereActivated && !allWereDeactivated ) return true;
+ return false;
+}
+
template <typename U>
void mpi_gatherActiveMembers(Communicator& comm, std::vector< DynamicList<U> >& ll ){
// Setup an array to hold all data
diff --git a/src/tools/Exception.cpp b/src/tools/Exception.cpp
index d718f0f2436a16fc2d52fddbd7a26eb4f17c7757..1696ccd06de186669d792847069bbc12c1d6824b 100644
--- a/src/tools/Exception.cpp
+++ b/src/tools/Exception.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Exception.h b/src/tools/Exception.h
index 4194c345c32005431c9e3a90cdbde379e69e2821..0515ccb25bba4d1786d65143a9294abd16743295 100644
--- a/src/tools/Exception.h
+++ b/src/tools/Exception.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/File.h b/src/tools/File.h
index 79acb724350ec89f07f11349543a130b469f5f68..a332a7fdf9cf749542e6e4dc1014e699e26482b3 100644
--- a/src/tools/File.h
+++ b/src/tools/File.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/FileBase.cpp b/src/tools/FileBase.cpp
index 3aa88dd3bdd2b38baa53b8bd927bb29a42b3f08a..b85621accb3997b9bd32315889cd5de1bed04769 100644
--- a/src/tools/FileBase.cpp
+++ b/src/tools/FileBase.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/FileBase.h b/src/tools/FileBase.h
index 9988d127d745d76c5c1aa8ba634d2e06378e28be..0ab890fe17733b36d1af62d04b60e45cf8edca63 100644
--- a/src/tools/FileBase.h
+++ b/src/tools/FileBase.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Grid.cpp b/src/tools/Grid.cpp
index 5194f54c6dab5e230c374cebcc3595e2be5df0b3..02557db57f9c97a9d162f5294551e6e9fe059a23 100644
--- a/src/tools/Grid.cpp
+++ b/src/tools/Grid.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -376,8 +376,6 @@ double Grid::getMaxValue() const {
}
-
-
double Grid::getValue(const vector<unsigned> & indices) const {
return getValue(getIndex(indices));
}
diff --git a/src/tools/Grid.h b/src/tools/Grid.h
index ed23fab8f88f78a3d17c7217a1ae72416f70b8ce..bb179b307903b8b11aa26982c859407a322caf4b 100644
--- a/src/tools/Grid.h
+++ b/src/tools/Grid.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/HistogramBead.cpp b/src/tools/HistogramBead.cpp
index a1a2e4fa6ea0464dec093274d850ed4ad8992ef0..640a8f5789d67180c3e431cfe51a35c8a4a63d1f 100644
--- a/src/tools/HistogramBead.cpp
+++ b/src/tools/HistogramBead.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/HistogramBead.h b/src/tools/HistogramBead.h
index 92b8dac253cda0818b0af433e7cf93c1f0ef621a..81e784e9ab1c2019cf66f4fcf6e4bbb365a2c7c4 100644
--- a/src/tools/HistogramBead.h
+++ b/src/tools/HistogramBead.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/IFile.cpp b/src/tools/IFile.cpp
index 3b2c2eb10764da51eb8ab7c631a625ab117e233b..00e9ca30b51bfe467a155d46d77710dfda71bd9a 100644
--- a/src/tools/IFile.cpp
+++ b/src/tools/IFile.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/IFile.h b/src/tools/IFile.h
index 0927784444e899834e66d2c6719282588d6f9039..253edb2fee565ecd6be13b2015efa723f177f026 100644
--- a/src/tools/IFile.h
+++ b/src/tools/IFile.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Kearsley.cpp b/src/tools/Kearsley.cpp
index 41477826b81606137be929d9d1f589ac57c04455..0517e44f9312471997b485b0629efac76ed24bca 100644
--- a/src/tools/Kearsley.cpp
+++ b/src/tools/Kearsley.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Kearsley.h b/src/tools/Kearsley.h
index dfa83ed1b2281e971f5ae0df7f4b730b899d5c20..8d53dca0ba4e1125f456130306c289bec0417e6b 100644
--- a/src/tools/Kearsley.h
+++ b/src/tools/Kearsley.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/KernelFunctions.cpp b/src/tools/KernelFunctions.cpp
index d7049166fed566ee33cead017836fcc090a668b6..2046a4374ff0c393ed78a202a5182c96ecc7b8c6 100644
--- a/src/tools/KernelFunctions.cpp
+++ b/src/tools/KernelFunctions.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/KernelFunctions.h b/src/tools/KernelFunctions.h
index 8ce991584f458d7f72982b814edaa73886d2fded..4f1271f90462f9fd75a7689c43b012c1c60f86be 100644
--- a/src/tools/KernelFunctions.h
+++ b/src/tools/KernelFunctions.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Keywords.cpp b/src/tools/Keywords.cpp
index 0281f5f839de6a8ae1553ae9b21c6f97bbc772ad..fddc1fd66d059507f17ca633fd6f1a0fdd8cd339 100644
--- a/src/tools/Keywords.cpp
+++ b/src/tools/Keywords.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Keywords.h b/src/tools/Keywords.h
index 5d3af797b12698cda360add85a419f8014d957d7..ef85ca9833e40bda52e9558a3e7be05d84e92208 100644
--- a/src/tools/Keywords.h
+++ b/src/tools/Keywords.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/LatticeReduction.cpp b/src/tools/LatticeReduction.cpp
index aaecefde9ea349b89942486bf58bffc1401c78f9..1e89c29ada9572042211f155ff03ccf18d487dc5 100644
--- a/src/tools/LatticeReduction.cpp
+++ b/src/tools/LatticeReduction.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/LatticeReduction.h b/src/tools/LatticeReduction.h
index fc8f9f6c9ad2601469c947bb0c942911a36999e2..5f5537bbaa0fb547f9cbf46fbb9613f85e58aab1 100644
--- a/src/tools/LatticeReduction.h
+++ b/src/tools/LatticeReduction.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Log.cpp b/src/tools/Log.cpp
index e3e98e900bf094e87b6a4f614fe12cfd1d49dfa2..8977c57f6208f75ff391cbb3a5ba28d80c188300 100644
--- a/src/tools/Log.cpp
+++ b/src/tools/Log.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Log.h b/src/tools/Log.h
index f37f0613451ebac27b0102f6e2e18359d7f39fc9..da4876d1201e910b0dda15bc4edbf9396c765ce5 100644
--- a/src/tools/Log.h
+++ b/src/tools/Log.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Matrix.h b/src/tools/Matrix.h
index 90b45b96f65ab7cface5194c910ecab2c64f205e..c94df931b515dcc9b699870a44924cf0fb0dd31f 100644
--- a/src/tools/Matrix.h
+++ b/src/tools/Matrix.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/MatrixSquareBracketsAccess.h b/src/tools/MatrixSquareBracketsAccess.h
index a81c458916092422583a80037571bf9e0a2f7438..5cd79428cb9265f9c11a036fcdaa23bf652b85cd 100644
--- a/src/tools/MatrixSquareBracketsAccess.h
+++ b/src/tools/MatrixSquareBracketsAccess.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/MolDataClass.cpp b/src/tools/MolDataClass.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..a080268d56094264be07e7cce632e266030f68b0
--- /dev/null
+++ b/src/tools/MolDataClass.cpp
@@ -0,0 +1,133 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "MolDataClass.h"
+#include "Exception.h"
+#include "Tools.h"
+#include "PDB.h"
+
+namespace PLMD {
+
+unsigned MolDataClass::numberOfAtomsPerResidueInBackbone( const std::string& type ){
+ if( type=="protein" ) return 5;
+ else return 0;
+}
+
+bool MolDataClass::allowedResidue( const std::string& type, const std::string& residuename ){
+ if( type=="protein" ){
+ if(residuename=="ALA") return true;
+ else if(residuename=="ARG") return true;
+ else if(residuename=="ASN") return true;
+ else if(residuename=="ASP") return true;
+ else if(residuename=="CYS") return true;
+ else if(residuename=="GLN") return true;
+ else if(residuename=="GLU") return true;
+ else if(residuename=="GLY") return true;
+ else if(residuename=="HIS") return true;
+ else if(residuename=="ILE") return true;
+ else if(residuename=="LEU") return true;
+ else if(residuename=="LYS") return true;
+ else if(residuename=="MET") return true;
+ else if(residuename=="PHE") return true;
+ else if(residuename=="PRO") return true;
+ else if(residuename=="SER") return true;
+ else if(residuename=="THR") return true;
+ else if(residuename=="TRP") return true;
+ else if(residuename=="TYR") return true;
+ else if(residuename=="VAL") return true;
+// Terminal groups
+ else if(residuename=="ACE") return true;
+ else if(residuename=="NME") return true;
+ else return false;
+ }
+ return false;
+}
+
+void MolDataClass::getBackboneForResidue( const std::string& type, const unsigned& residuenum, const PDB& mypdb, std::vector<AtomNumber>& atoms ){
+ std::string residuename=mypdb.getResidueName( residuenum );
+ plumed_massert( MolDataClass::allowedResidue( type, residuename ), "residue " + residuename + " unrecognized for molecule type " + type );
+ if( type=="protein" ){
+ if( residuename=="GLY"){
+ atoms.resize(5);
+ atoms[0]=mypdb.getNamedAtomFromResidue("N",residuenum);
+ atoms[1]=mypdb.getNamedAtomFromResidue("CA",residuenum);
+ atoms[2]=mypdb.getNamedAtomFromResidue("HA1",residuenum);
+ atoms[3]=mypdb.getNamedAtomFromResidue("C",residuenum);
+ atoms[4]=mypdb.getNamedAtomFromResidue("O",residuenum);
+ } else if( residuename=="ACE"){
+ atoms.resize(1);
+ atoms[0]=mypdb.getNamedAtomFromResidue("C",residuenum);
+ } else if( residuename=="NME"){
+ atoms.resize(1);
+ atoms[0]=mypdb.getNamedAtomFromResidue("N",residuenum);
+ } else {
+ atoms.resize(5);
+ atoms[0]=mypdb.getNamedAtomFromResidue("N",residuenum);
+ atoms[1]=mypdb.getNamedAtomFromResidue("CA",residuenum);
+ atoms[2]=mypdb.getNamedAtomFromResidue("CB",residuenum);
+ atoms[3]=mypdb.getNamedAtomFromResidue("C",residuenum);
+ atoms[4]=mypdb.getNamedAtomFromResidue("O",residuenum);
+ }
+ } else {
+ plumed_merror(type + " is not a valid molecule type");
+ }
+}
+
+bool MolDataClass::isTerminalGroup( const std::string& type, const std::string& residuename ){
+ if( type=="protein" ){
+ if( residuename=="ACE" ) return true;
+ else if( residuename=="NME" ) return true;
+ else return false;
+ } else {
+ plumed_merror(type + " is not a valid molecule type");
+ }
+ return false;
+}
+
+void MolDataClass::specialSymbol( const std::string& type, const std::string& symbol, const PDB& mypdb, std::vector<AtomNumber>& numbers ){
+ if( type=="protein" ){
+ if( symbol.find("phi")!=std::string::npos ){
+ std::size_t dash=symbol.find_first_of('-');
+ unsigned resnum; Tools::convert( symbol.substr(dash+1), resnum );
+ std::string resname = mypdb.getResidueName(resnum);
+ if( !allowedResidue( type, resname ) || isTerminalGroup( type, resname ) ) return ;
+ numbers.resize(4);
+ numbers[0]=mypdb.getNamedAtomFromResidue("C",resnum-1);
+ numbers[1]=mypdb.getNamedAtomFromResidue("N",resnum);
+ numbers[2]=mypdb.getNamedAtomFromResidue("CA",resnum);
+ numbers[3]=mypdb.getNamedAtomFromResidue("C",resnum);
+ } else if( symbol.find("psi")!=std::string::npos ){
+ std::size_t dash=symbol.find_first_of('-');
+ unsigned resnum; Tools::convert( symbol.substr(dash+1), resnum );
+ std::string resname = mypdb.getResidueName(resnum);
+ if( !allowedResidue( type, resname ) || isTerminalGroup( type, resname ) ) return ;
+ numbers.resize(4);
+ numbers[0]=mypdb.getNamedAtomFromResidue("N",resnum);
+ numbers[1]=mypdb.getNamedAtomFromResidue("CA",resnum);
+ numbers[2]=mypdb.getNamedAtomFromResidue("C",resnum);
+ numbers[3]=mypdb.getNamedAtomFromResidue("N",resnum+1);
+ }
+ } else {
+ plumed_merror(type + " is not a valid molecule type");
+ }
+}
+
+}
diff --git a/src/tools/MolDataClass.h b/src/tools/MolDataClass.h
new file mode 100644
index 0000000000000000000000000000000000000000..6247795da56a5cf8df72eb8104b7ce4dd464de70
--- /dev/null
+++ b/src/tools/MolDataClass.h
@@ -0,0 +1,51 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_tools_MolDataClass_h
+#define __PLUMED_tools_MolDataClass_h
+
+#include <vector>
+#include <string>
+#include "AtomNumber.h"
+
+namespace PLMD{
+
+class PDB;
+
+/// This class provides information on various kinds of molecules
+/// for instance the kinds of residues that are in a protein
+/// the atoms involved in the backbone of a particular residue etc
+class MolDataClass {
+public:
+/// Return true if the residue name is one of the allowed reisude names e.g. one of the 20 amino acids for proteins
+ static bool allowedResidue( const std::string& type, const std::string& residuename );
+/// Return the number of atoms in the backbone per residue e.g. 5 for proteins
+ static unsigned numberOfAtomsPerResidueInBackbone( const std::string& type );
+/// Return the names of the atoms in the backbone e.g. N, CA, CB, C, O for most protein residues
+ static void getBackboneForResidue( const std::string& type, const unsigned& residuenum, const PDB& mypdb, std::vector<AtomNumber>& atoms );
+/// Return true if the residue is a terminal group e.g. ACE, NME for proteins
+ static bool isTerminalGroup( const std::string& type, const std::string& residuename );
+/// Used to interpret special symbols - currently phi and psi
+ static void specialSymbol( const std::string& type, const std::string& symbol, const PDB& mypdb, std::vector<AtomNumber>& numbers );
+};
+
+}
+#endif
diff --git a/src/tools/NeighborList.cpp b/src/tools/NeighborList.cpp
index d34681a6782146b3d23e18221659183b74bc0998..6b6f36d6532614b27d59bdbed527cdff83c9455b 100644
--- a/src/tools/NeighborList.cpp
+++ b/src/tools/NeighborList.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/NeighborList.h b/src/tools/NeighborList.h
index 9bcfab5d93bb514165186eae56f25af28ad9506c..fb6412302ede455d0f7dea9bcd7b4b01ccd24537 100644
--- a/src/tools/NeighborList.h
+++ b/src/tools/NeighborList.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/OFile.cpp b/src/tools/OFile.cpp
index effc8fa18e54ff5b0f46ea052789161f48f3ed27..55f6ac6a950f768ba09df404522a3a5db2ee8d75 100644
--- a/src/tools/OFile.cpp
+++ b/src/tools/OFile.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -32,6 +32,7 @@
#include <iostream>
#include <string>
#include <cstdlib>
+#include <cerrno>
namespace PLMD{
@@ -42,7 +43,7 @@ size_t OFile::llwrite(const char*ptr,size_t s){
if(!fp) plumed_merror("writing on uninitilized File");
r=fwrite(ptr,1,s,fp);
}
- if(comm) comm->Bcast(&r,1,0);
+ if(comm) comm->Bcast(r,0);
return r;
}
@@ -240,6 +241,7 @@ void OFile::backupFile( const std::string& bstring, const std::string& fname ){
FILE* ff=std::fopen(const_cast<char*>(fname.c_str()),"r");
FILE* fff=NULL;
if(ff){
+ std::fclose(ff);
std::string backup;
size_t found=fname.find_last_of("/\\");
std::string directory=fname.substr(0,found+1);
@@ -251,12 +253,11 @@ void OFile::backupFile( const std::string& bstring, const std::string& fname ){
backup=directory+bstring +"."+num+"."+file;
fff=std::fopen(backup.c_str(),"r");
if(!fff) break;
+ else std::fclose(fff);
}
int check=rename(fname.c_str(),backup.c_str());
- plumed_massert(check==0,"renaming "+fname+" into "+backup+" failed for some reason");
+ plumed_massert(check==0,"renaming "+fname+" into "+backup+" failed for reason: "+strerror(errno));
}
- if(ff) std::fclose(ff);
- if(fff) std::fclose(fff);
}
}
diff --git a/src/tools/OFile.h b/src/tools/OFile.h
index 3c6b76cc03a8bcc754e83a7bbfc56198ebe4caea..cad69614bf63bed24b207414ab024f0bb1240733 100644
--- a/src/tools/OFile.h
+++ b/src/tools/OFile.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/OptimalAlignment.cpp b/src/tools/OptimalAlignment.cpp
index 00e88ac7b7ca87ab7619ff550737380ad7bd8959..a0a6355f7d64176417d044730855aa9773fb4cf5 100644
--- a/src/tools/OptimalAlignment.cpp
+++ b/src/tools/OptimalAlignment.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/OptimalAlignment.h b/src/tools/OptimalAlignment.h
index 7f6f6e49e91f3961e7ffa765e8cd563697ac362e..da011b23fb798f19ea43d0f6e18ca10dd6378479 100644
--- a/src/tools/OptimalAlignment.h
+++ b/src/tools/OptimalAlignment.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/PDB.cpp b/src/tools/PDB.cpp
index b43c4673f64dea528016abfaad424579778d4737..c89edff60f9ddffb5b87c51126df7a995b58158f 100644
--- a/src/tools/PDB.cpp
+++ b/src/tools/PDB.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -191,22 +191,20 @@ void PDB::getAtomRange( const std::string& chainname, AtomNumber& a_start, AtomN
if(inres) a_end=numbers[size()-1];
}
-bool PDB::getBackbone( const unsigned& resnumber, const std::vector<std::string>& backnames, std::vector<AtomNumber>& backnumbers ) const {
- if( backnames.size()!=backnumbers.size() ) plumed_merror("mismatch between number of backbone names and number of backbone numbers");
- bool foundresidue=false; std::vector<bool> found( backnames.size(), false );
+std::string PDB::getResidueName( const unsigned& resnum ) const {
for(unsigned i=0;i<size();++i){
- if( residue[i]==resnumber ){
- foundresidue=true;
- for(unsigned bno=0;bno<backnames.size();++bno){
- if( backnames[bno]==atomsymb[i] ){ backnumbers[bno]=numbers[i]; found[bno]=true; }
- }
- }
+ if( residue[i]==resnum ) return residuenames[i];
}
- if(!foundresidue){ return false; }
- for(unsigned i=0;i<found.size();++i){
- if( !found[i] ) return false;
+ return "";
+}
+
+AtomNumber PDB::getNamedAtomFromResidue( const std::string& aname, const unsigned& resnum ) const {
+ for(unsigned i=0;i<size();++i){
+ if( residue[i]==resnum && atomsymb[i]==aname ) return numbers[i];
}
- return true;
+ std::string num; Tools::convert( resnum, num );
+ plumed_merror("residue " + num + " does not contain an atom named " + aname );
+ return numbers[0]; // This is to stop compiler errors
}
std::string PDB::getChainID(const unsigned& resnumber) const {
@@ -216,10 +214,18 @@ std::string PDB::getChainID(const unsigned& resnumber) const {
plumed_merror("Not enough residues in pdb input file");
}
-void PDB::renameAtoms( const std::string& old_name, const std::string& new_name ){
+bool PDB::checkForResidue( const std::string& name ) const {
for(unsigned i=0;i<size();++i){
- if( atomsymb[i]==old_name ) atomsymb[i]=new_name;
- }
+ if( residuenames[i]==name ) return true;
+ }
+ return false;
+}
+
+bool PDB::checkForAtom( const std::string& name ) const {
+ for(unsigned i=0;i<size();++i){
+ if( atomsymb[i]==name ) return true;
+ }
+ return false;
}
Log& operator<<(Log& ostr, const PDB& pdb){
diff --git a/src/tools/PDB.h b/src/tools/PDB.h
index d05279150a5b4fa694ff6885948a15b87174916f..74e847e06fc325cec0343e9b8a2f875c55d22ca2 100644
--- a/src/tools/PDB.h
+++ b/src/tools/PDB.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -71,12 +71,8 @@ public:
void getResidueRange( const std::string& chainname, unsigned& res_start, unsigned& res_end, std::string& errmsg ) const;
/// Get the atoms in each of the chains
void getAtomRange( const std::string& chainname, AtomNumber& a_start, AtomNumber& a_end, std::string& errmsg ) const;
-/// Get the atoms in the backbone of a particular residue
- bool getBackbone( const unsigned& resnumber, const std::vector<std::string>& backnames, std::vector<AtomNumber>& backnumbers ) const ;
/// Get the chain ID that a particular residue is a part of
std::string getChainID(const unsigned& resnumber) const;
-/// This allows you to give atoms a new name - this is used to rename the HB1 atoms in GLY residues CB so that alpharmsd works
- void renameAtoms( const std::string& old_name, const std::string& new_name );
///use the log to dump information
friend Log& operator<<(Log& ostr, const PDB& pdb);
/// return the name of a specific atom
@@ -85,6 +81,14 @@ public:
unsigned getResidueNumber(AtomNumber a) const;
/// return the residue name for a specific atom
std::string getResidueName(AtomNumber a) const;
+/// get the name of the resnum'th residue
+ std::string getResidueName(const unsigned& resnum ) const;
+/// Check if any of the residues are named name
+ bool checkForResidue( const std::string& name ) const ;
+/// Check if any of the atoms are named atom
+ bool checkForAtom( const std::string& name ) const ;
+/// Return the atom named aname from residue number resnum
+ AtomNumber getNamedAtomFromResidue( const std::string& aname, const unsigned& resnum ) const;
};
}
diff --git a/src/tools/Pbc.cpp b/src/tools/Pbc.cpp
index 15e1ba401f072aed1f623f3a28a1c3876852a2d1..6477155ea3174bb6bbc16297b51cdc8c9f5bffff 100644
--- a/src/tools/Pbc.cpp
+++ b/src/tools/Pbc.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -184,7 +184,7 @@ Vector Pbc::distance(const Vector&v1,const Vector&v2,int*nshifts)const{
double lbest(modulo2(best));
// loop over possible shifts:
if(nshifts) *nshifts+=myshifts.size();
- for(int i=0;i<myshifts.size();i++){
+ for(unsigned i=0;i<myshifts.size();i++){
Vector trial=d+myshifts[i];
double ltrial=modulo2(trial);
if(ltrial<lbest){
diff --git a/src/tools/Pbc.h b/src/tools/Pbc.h
index 804feae5bd64455a12fd30a0da7a6fb5b02cf585..afd30c472bc0d123c18c90cc2650a410f7d5e63a 100644
--- a/src/tools/Pbc.h
+++ b/src/tools/Pbc.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -62,11 +62,6 @@ class Pbc{
/// depending on the sign of the scaled coordinates representing
/// a distance vector.
void buildShifts(std::vector<Vector> shifts[2][2][2])const;
-/// Full search (for testing)
- void fullSearch(Vector&)const;
-/// internal version of distance, also returns the number
-/// of attempted shifts (used in Pbc::test()).
- Vector distance(const Vector&,const Vector&,int*nshifts)const;
public:
/// Perform some check. Useful for debugging.
static void test();
@@ -76,6 +71,9 @@ public:
double distance( const bool pbc, const Vector& v1, const Vector& v2 ) const;
/// Computes v2-v1, using minimal image convention
Vector distance(const Vector& v1,const Vector& v2)const;
+/// version of distance which also returns the number
+/// of attempted shifts
+ Vector distance(const Vector&,const Vector&,int*nshifts)const;
/// Set the lattice vectors.
/// b[i][j] is the j-th component of the i-th vector
void setBox(const Tensor&b);
@@ -92,6 +90,9 @@ public:
Vector scaledToReal(const Vector&)const;
/// Returns true if the box vectors are orthogonal
bool isOrthorombic()const;
+/// Full search (for testing).
+/// Perform a full search on vector
+ void fullSearch(Vector&)const;
};
inline
diff --git a/src/tools/RMSD.cpp b/src/tools/RMSD.cpp
index 63878a1bdd4ea715dc0c6b98c10b6fc5edcfdf5d..8772dd45ccccbc13a6a0d00282a4ee7f7a3d9c8e 100644
--- a/src/tools/RMSD.cpp
+++ b/src/tools/RMSD.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -22,46 +22,20 @@
#include "RMSD.h"
#include "PDB.h"
#include "Log.h"
-#include "OptimalAlignment.h"
#include "Exception.h"
#include <cmath>
#include <iostream>
#include "Matrix.h"
#include "Tools.h"
+#include "Tensor.h"
using namespace std;
namespace PLMD{
RMSD::RMSD(Log & log ):
alignmentMethod(SIMPLE),
- myoptimalalignment(NULL),
log(&log){}
-RMSD& RMSD::operator=(const RMSD& v){
- alignmentMethod=v.alignmentMethod;
- reference=v.reference;
- align=v.align;
- displace=v.displace;
-// in this manner the new RMSD is built empty and will just allocate its own
-// myoptimalalignment when used (in calculate())
- myoptimalalignment=NULL;
-
- log=v.log;
- return *this ;
-}
-
-
-RMSD::RMSD(const RMSD & oldrmsd):
- alignmentMethod(oldrmsd.alignmentMethod),
- reference(oldrmsd.reference),
- align(oldrmsd.align),
- displace(oldrmsd.align),
-// in this manner the new RMSD is built empty and will just allocate its own
-// myoptimalalignment when used (in calculate())
- myoptimalalignment(NULL),
- log( oldrmsd.log )
- { }
-
void RMSD::set(const PDB&pdb, string mytype ){
setReference(pdb.getPositions());
@@ -71,7 +45,6 @@ void RMSD::set(const PDB&pdb, string mytype ){
}
void RMSD::setType(string mytype){
- myoptimalalignment=NULL;
alignmentMethod=SIMPLE; // initialize with the simplest case: no rotation
if (mytype=="SIMPLE"){
@@ -95,9 +68,6 @@ void RMSD::clear(){
align.clear();
displace.clear();
}
-RMSD::~RMSD(){
- if(myoptimalalignment!=NULL) delete myoptimalalignment;
-}
string RMSD::getMethod(){
string mystring;
@@ -114,18 +84,34 @@ void RMSD::setReference(const vector<Vector> & reference){
this->reference=reference;
plumed_massert(align.empty(),"you should first clear() an RMSD object, then set a new referece");
plumed_massert(displace.empty(),"you should first clear() an RMSD object, then set a new referece");
- align.resize(n,1.0);
- displace.resize(n,1.0);
+ align.resize(n,1.0/n);
+ displace.resize(n,1.0/n);
+ Vector center;
+ for(unsigned i=0;i<n;i++) center+=this->reference[i]*align[i];
+ for(unsigned i=0;i<n;i++) this->reference[i]-=center;
}
void RMSD::setAlign(const vector<double> & align){
+ unsigned n=reference.size();
plumed_massert(this->align.size()==align.size(),"mismatch in dimension of align/displace arrays");
this->align=align;
+ double w=0.0;
+ for(unsigned i=0;i<n;i++) w+=this->align[i];
+ double inv=1.0/w;
+ for(unsigned i=0;i<n;i++) this->align[i]*=inv;
+ Vector center;
+ for(unsigned i=0;i<n;i++) center+=reference[i]*this->align[i];
+ for(unsigned i=0;i<n;i++) reference[i]-=center;
}
void RMSD::setDisplace(const vector<double> & displace){
+ unsigned n=reference.size();
plumed_massert(this->displace.size()==displace.size(),"mismatch in dimension of align/displace arrays");
this->displace=displace;
+ double w=0.0;
+ for(unsigned i=0;i<n;i++) w+=this->displace[i];
+ double inv=1.0/w;
+ for(unsigned i=0;i<n;i++) this->displace[i]*=inv;
}
double RMSD::calculate(const std::vector<Vector> & positions,std::vector<Vector> &derivatives, bool squared){
@@ -139,29 +125,13 @@ double RMSD::calculate(const std::vector<Vector> & positions,std::vector<Vector>
break;
case OPTIMAL_FAST:
// this is calling the fastest option:
- ret=optimalAlignment<false>(align,displace,positions,reference,derivatives,squared);
+ if(align==displace) ret=optimalAlignment<false,true>(align,displace,positions,reference,derivatives,squared);
+ else ret=optimalAlignment<false,false>(align,displace,positions,reference,derivatives,squared);
break;
case OPTIMAL:
- bool fastversion=true;
- // this is because fast version only works with align==displace
- if (align!=displace) fastversion=false;
- if (fastversion){
// this is the fast routine but in the "safe" mode, which gives less numerical error:
- ret=optimalAlignment<true>(align,displace,positions,reference,derivatives,squared);
- } else {
- if (myoptimalalignment==NULL){ // do full initialization
- //
- // I create the object only here
- // since the alignment object require to know both position and reference
- // and it is possible only at calculate time
- //
- myoptimalalignment=new OptimalAlignment(align,displace,positions,reference,log);
- }
- // this changes the P0 according the running frame
- (*myoptimalalignment).assignP0(positions);
- ret=(*myoptimalalignment).calculate(squared, derivatives);
- //(*myoptimalalignment).weightedFindiffTest(false);
- }
+ if(align==displace) ret=optimalAlignment<true,true>(align,displace,positions,reference,derivatives,squared);
+ else ret=optimalAlignment<true,false>(align,displace,positions,reference,derivatives,squared);
break;
}
@@ -176,8 +146,6 @@ double RMSD::simpleAlignment(const std::vector<double> & align,
Log* &log,
std::vector<Vector> & derivatives, bool squared) {
double dist(0);
- double anorm(0);
- double dnorm(0);
unsigned n=reference.size();
Vector apositions;
@@ -188,88 +156,67 @@ double RMSD::simpleAlignment(const std::vector<double> & align,
for(unsigned i=0;i<n;i++){
double aw=align[i];
double dw=displace[i];
- anorm+=aw;
- dnorm+=dw;
apositions+=positions[i]*aw;
areference+=reference[i]*aw;
dpositions+=positions[i]*dw;
dreference+=reference[i]*dw;
}
- double invdnorm=1.0/dnorm;
- double invanorm=1.0/anorm;
-
- apositions*=invanorm;
- areference*=invanorm;
- dpositions*=invdnorm;
- dreference*=invdnorm;
-
Vector shift=((apositions-areference)-(dpositions-dreference));
for(unsigned i=0;i<n;i++){
Vector d=(positions[i]-apositions)-(reference[i]-areference);
dist+=displace[i]*d.modulo2();
- derivatives[i]=2*(invdnorm*displace[i]*d+invanorm*align[i]*shift);
+ derivatives[i]=2*(displace[i]*d+align[i]*shift);
}
- dist*=invdnorm;
if(!squared){
- // sqrt and normalization
+ // sqrt
dist=sqrt(dist);
- ///// sqrt and normalization on derivatives
+ ///// sqrt on derivatives
for(unsigned i=0;i<n;i++){derivatives[i]*=(0.5/dist);}
}
return dist;
}
-template <bool safe>
+// notice that in the current implementation the safe argument only makes sense for
+// align==displace
+template <bool safe,bool alEqDis>
double RMSD::optimalAlignment(const std::vector<double> & align,
const std::vector<double> & displace,
const std::vector<Vector> & positions,
const std::vector<Vector> & reference ,
std::vector<Vector> & derivatives, bool squared) {
- plumed_massert(displace==align,"OPTIMAL_FAST version of RMSD can only be used when displace weights are same as align weights");
-
double dist(0);
- double norm(0);
const unsigned n=reference.size();
// This is the trace of positions*positions + reference*reference
- double sum00w(0);
+ double rr00(0);
+ double rr11(0);
// This is positions*reference
- Tensor sum01w;
+ Tensor rr01;
derivatives.resize(n);
Vector cpositions;
- Vector creference;
// first expensive loop: compute centers
for(unsigned iat=0;iat<n;iat++){
double w=align[iat];
- norm+=w;
cpositions+=positions[iat]*w;
- creference+=reference[iat]*w;
}
- double invnorm=1.0/norm;
- cpositions*=invnorm;
- creference*=invnorm;
-
// second expensive loop: compute second moments wrt centers
for(unsigned iat=0;iat<n;iat++){
double w=align[iat];
- sum00w+=(dotProduct(positions[iat]-cpositions,positions[iat]-cpositions)
- +dotProduct(reference[iat]-creference,reference[iat]-creference))*w;
- sum01w+=Tensor(positions[iat]-cpositions,reference[iat]-creference)*w;
+ rr00+=dotProduct(positions[iat]-cpositions,positions[iat]-cpositions)*w;
+ rr11+=dotProduct(reference[iat],reference[iat])*w;
+ rr01+=Tensor(positions[iat]-cpositions,reference[iat])*w;
}
- double rr00=sum00w*invnorm;
- Tensor rr01=sum01w*invnorm;
-
Matrix<double> m=Matrix<double>(4,4);
- m[0][0]=rr00+2.0*(-rr01[0][0]-rr01[1][1]-rr01[2][2]);
- m[1][1]=rr00+2.0*(-rr01[0][0]+rr01[1][1]+rr01[2][2]);
- m[2][2]=rr00+2.0*(+rr01[0][0]-rr01[1][1]+rr01[2][2]);
- m[3][3]=rr00+2.0*(+rr01[0][0]+rr01[1][1]-rr01[2][2]);
+ m[0][0]=2.0*(-rr01[0][0]-rr01[1][1]-rr01[2][2]);
+ m[1][1]=2.0*(-rr01[0][0]+rr01[1][1]+rr01[2][2]);
+ m[2][2]=2.0*(+rr01[0][0]-rr01[1][1]+rr01[2][2]);
+ m[3][3]=2.0*(+rr01[0][0]+rr01[1][1]-rr01[2][2]);
m[0][1]=2.0*(-rr01[1][2]+rr01[2][1]);
m[0][2]=2.0*(+rr01[0][2]-rr01[2][0]);
m[0][3]=2.0*(-rr01[0][1]+rr01[1][0]);
@@ -283,6 +230,26 @@ double RMSD::optimalAlignment(const std::vector<double> & align,
m[3][1] = m[1][3];
m[3][2] = m[2][3];
+ Tensor dm_drr01[4][4];
+ if(!alEqDis){
+ dm_drr01[0][0] = 2.0*Tensor(-1.0, 0.0, 0.0, 0.0,-1.0, 0.0, 0.0, 0.0,-1.0);
+ dm_drr01[1][1] = 2.0*Tensor(-1.0, 0.0, 0.0, 0.0,+1.0, 0.0, 0.0, 0.0,+1.0);
+ dm_drr01[2][2] = 2.0*Tensor(+1.0, 0.0, 0.0, 0.0,-1.0, 0.0, 0.0, 0.0,+1.0);
+ dm_drr01[3][3] = 2.0*Tensor(+1.0, 0.0, 0.0, 0.0,+1.0, 0.0, 0.0, 0.0,-1.0);
+ dm_drr01[0][1] = 2.0*Tensor( 0.0, 0.0, 0.0, 0.0, 0.0,-1.0, 0.0,+1.0, 0.0);
+ dm_drr01[0][2] = 2.0*Tensor( 0.0, 0.0,+1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0);
+ dm_drr01[0][3] = 2.0*Tensor( 0.0,-1.0, 0.0, +1.0, 0.0, 0.0, 0.0, 0.0, 0.0);
+ dm_drr01[1][2] = 2.0*Tensor( 0.0,-1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0);
+ dm_drr01[1][3] = 2.0*Tensor( 0.0, 0.0,-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0);
+ dm_drr01[2][3] = 2.0*Tensor( 0.0, 0.0, 0.0, 0.0, 0.0,-1.0, 0.0,-1.0, 0.0);
+ dm_drr01[1][0] = dm_drr01[0][1];
+ dm_drr01[2][0] = dm_drr01[0][2];
+ dm_drr01[2][1] = dm_drr01[1][2];
+ dm_drr01[3][0] = dm_drr01[0][3];
+ dm_drr01[3][1] = dm_drr01[1][3];
+ dm_drr01[3][2] = dm_drr01[2][3];
+ }
+
vector<double> eigenvals;
Matrix<double> eigenvecs;
int diagerror=diagMat(m, eigenvals, eigenvecs );
@@ -294,12 +261,31 @@ double RMSD::optimalAlignment(const std::vector<double> & align,
plumed_merror(msg);
}
- dist=eigenvals[0];
+ dist=eigenvals[0]+rr00+rr11;
Matrix<double> ddist_dm(4,4);
Vector4d q(eigenvecs[0][0],eigenvecs[0][1],eigenvecs[0][2],eigenvecs[0][3]);
+ Tensor dq_drr01[4];
+ if(!alEqDis){
+ double dq_dm[4][4][4];
+ for(unsigned i=0;i<4;i++) for(unsigned j=0;j<4;j++) for(unsigned k=0;k<4;k++){
+ double tmp=0.0;
+// perturbation theory for matrix m
+ for(unsigned l=1;l<4;l++) tmp+=eigenvecs[l][j]*eigenvecs[l][i]/(eigenvals[0]-eigenvals[l])*eigenvecs[0][k];
+ dq_dm[i][j][k]=tmp;
+ }
+// propagation to _drr01
+ for(unsigned i=0;i<4;i++){
+ Tensor tmp;
+ for(unsigned j=0;j<4;j++) for(unsigned k=0;k<4;k++) {
+ tmp+=dq_dm[i][j][k]*dm_drr01[j][k];
+ }
+ dq_drr01[i]=tmp;
+ }
+ }
+
// This is the rotation matrix that brings reference to positions
// i.e. matmul(rotation,reference[iat])+shift is fitted to positions[iat]
@@ -314,28 +300,71 @@ double RMSD::optimalAlignment(const std::vector<double> & align,
rotation[2][0]=2*(+q[0]*q[2]+q[1]*q[3]);
rotation[2][1]=2*(-q[0]*q[1]+q[2]*q[3]);
- double prefactor=2.0*invnorm;
- Vector shift=cpositions-matmul(rotation,creference);
+
+ Tensor drotation_drr01[3][3];
+ if(!alEqDis){
+ drotation_drr01[0][0]=2*q[0]*dq_drr01[0]+2*q[1]*dq_drr01[1]-2*q[2]*dq_drr01[2]-2*q[3]*dq_drr01[3];
+ drotation_drr01[1][1]=2*q[0]*dq_drr01[0]-2*q[1]*dq_drr01[1]+2*q[2]*dq_drr01[2]-2*q[3]*dq_drr01[3];
+ drotation_drr01[2][2]=2*q[0]*dq_drr01[0]-2*q[1]*dq_drr01[1]-2*q[2]*dq_drr01[2]+2*q[3]*dq_drr01[3];
+ drotation_drr01[0][1]=2*(+(q[0]*dq_drr01[3]+dq_drr01[0]*q[3])+(q[1]*dq_drr01[2]+dq_drr01[1]*q[2]));
+ drotation_drr01[0][2]=2*(-(q[0]*dq_drr01[2]+dq_drr01[0]*q[2])+(q[1]*dq_drr01[3]+dq_drr01[1]*q[3]));
+ drotation_drr01[1][2]=2*(+(q[0]*dq_drr01[1]+dq_drr01[0]*q[1])+(q[2]*dq_drr01[3]+dq_drr01[2]*q[3]));
+ drotation_drr01[1][0]=2*(-(q[0]*dq_drr01[3]+dq_drr01[0]*q[3])+(q[1]*dq_drr01[2]+dq_drr01[1]*q[2]));
+ drotation_drr01[2][0]=2*(+(q[0]*dq_drr01[2]+dq_drr01[0]*q[2])+(q[1]*dq_drr01[3]+dq_drr01[1]*q[3]));
+ drotation_drr01[2][1]=2*(-(q[0]*dq_drr01[1]+dq_drr01[0]*q[1])+(q[2]*dq_drr01[3]+dq_drr01[2]*q[3]));
+ }
+
+ double prefactor=2.0;
- if(!squared) prefactor*=0.5/sqrt(dist);
+ if(!squared && alEqDis) prefactor*=0.5/sqrt(dist);
// if "safe", recompute dist here to a better accuracy
- if(safe) dist=0.0;
+ if(safe || !alEqDis) dist=0.0;
// If safe is set to "false", MSD is taken from the eigenvalue of the M matrix
// If safe is set to "true", MSD is recomputed from the rotational matrix
// For some reason, this last approach leads to less numerical noise but adds an overhead
+ Tensor ddist_drotation;
+ Vector ddist_dcpositions;
+
// third expensive loop: derivatives
for(unsigned iat=0;iat<n;iat++){
+ Vector d(positions[iat]-cpositions - matmul(rotation,reference[iat]));
+ if(alEqDis){
// there is no need for derivatives of rotation and shift here as it is by construction zero
// (similar to Hellman-Feynman forces)
- Vector d(positions[iat]-shift - matmul(rotation,reference[iat]));
- derivatives[iat]= prefactor*align[iat]*d;
- if(safe) dist+=align[iat]*invnorm*modulo2(d);
+ derivatives[iat]= prefactor*align[iat]*d;
+ if(safe) dist+=align[iat]*modulo2(d);
+ } else {
+// the case for align != displace is different, sob:
+ dist+=displace[iat]*modulo2(d);
+// these are the derivatives assuming the roto-translation as frozen
+ derivatives[iat]=2*displace[iat]*d;
+// here I accumulate derivatives wrt rotation matrix ..
+ ddist_drotation+=-2*displace[iat]*extProduct(d,reference[iat]);
+// .. and cpositions
+ ddist_dcpositions+=-2*displace[iat]*d;
+ }
}
- if(!squared) dist=sqrt(dist);
+ if(!alEqDis){
+ Tensor ddist_drr01;
+ for(unsigned i=0;i<3;i++) for(unsigned j=0;j<3;j++) ddist_drr01+=ddist_drotation[i][j]*drotation_drr01[i][j];
+ for(unsigned iat=0;iat<n;iat++){
+// this is propagating to positions.
+// I am implicitly using the derivative of rr01 wrt positions here
+ derivatives[iat]+=matmul(ddist_drr01,reference[iat])*align[iat];
+ derivatives[iat]+=ddist_dcpositions*align[iat];
+ }
+ }
+ if(!squared){
+ dist=sqrt(dist);
+ if(!alEqDis){
+ double xx=0.5/dist;
+ for(unsigned iat=0;iat<n;iat++) derivatives[iat]*=xx;
+ }
+ }
return dist;
}
diff --git a/src/tools/RMSD.h b/src/tools/RMSD.h
index 1d82bab708425951fd0c7cc07cb8e24a3faf60b2..531471e4966dd7c2cdbe680460fc92d641c55ead 100644
--- a/src/tools/RMSD.h
+++ b/src/tools/RMSD.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -30,7 +30,6 @@ namespace PLMD{
class Log;
class PDB;
-class OptimalAlignment;
/** \ingroup TOOLBOX
A class that implements RMSD calculations
@@ -63,20 +62,17 @@ class RMSD
{
enum AlignmentMethod {SIMPLE, OPTIMAL, OPTIMAL_FAST};
AlignmentMethod alignmentMethod;
+// Reference coordinates
std::vector<Vector> reference;
+// Weights for alignment
std::vector<double> align;
+// Weights for deviation
std::vector<double> displace;
- OptimalAlignment *myoptimalalignment;
+// Logfile
Log *log;
public:
/// Constructor
RMSD(Log & log );
-/// a copy constructor
- RMSD(const RMSD &);
-/// assignment
- RMSD& operator=(const RMSD& );
-/// the destructor needs to delete the myalignment object eventually
- ~RMSD();
/// clear the structure
void clear();
/// set reference, align and displace from input pdb structure
@@ -98,7 +94,7 @@ public:
const std::vector<Vector> & reference ,
Log* &log,
std::vector<Vector> & derivatives, bool squared=false);
-template <bool safe>
+template <bool safe,bool alEqDis>
double optimalAlignment(const std::vector<double> & align,
const std::vector<double> & displace,
const std::vector<Vector> & positions,
diff --git a/src/tools/Random.cpp b/src/tools/Random.cpp
index 7b3f9cd01da381726d4a16e081c5d89a4a87c070..6f8ff30238fbd0969ab178b29eba9365d44e6819 100644
--- a/src/tools/Random.cpp
+++ b/src/tools/Random.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -120,7 +120,7 @@ void Random::toString(std::string & str)const{
void Random::fromString(const std::string & str){
std::string s=str;
- for(int i=0;i<s.length();i++) if(s[i]=='|') s[i]=' ';
+ for(unsigned i=0;i<s.length();i++) if(s[i]=='|') s[i]=' ';
std::istringstream istr(s.c_str());
istr>>idum>>iy;
for (int i = 0; i < NTAB; i++) istr>>iv[i];
diff --git a/src/tools/Random.h b/src/tools/Random.h
index 7000b19e152f3d94f98f57f86e7b2754b673dc27..302adca3e451636dd406c3f75f9a654dbd4b6859 100644
--- a/src/tools/Random.h
+++ b/src/tools/Random.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Stopwatch.cpp b/src/tools/Stopwatch.cpp
index 68d2a0d2c1d01ada8a298dad580d1e54687f1a67..a08e24b44f5a163c42cc2d087abf47e84bab1f58 100644
--- a/src/tools/Stopwatch.cpp
+++ b/src/tools/Stopwatch.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Stopwatch.h b/src/tools/Stopwatch.h
index 217889c549695c22a8f66f33838415f13d98b391..9f6a1f5d6e743ff82e8f57fa8a069416010aa8bc 100644
--- a/src/tools/Stopwatch.h
+++ b/src/tools/Stopwatch.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/SwitchingFunction.cpp b/src/tools/SwitchingFunction.cpp
index c5122e6f7e13870821753d36f30873a0803d7e68..4bcc41ffcdc387674c9e967f23402edbb114417f 100644
--- a/src/tools/SwitchingFunction.cpp
+++ b/src/tools/SwitchingFunction.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -87,6 +87,19 @@ s(r) = \left[ 1 + ( 2^{a/b} -1 )\left( \frac{r-d_0}{r_0} \right)\right]^{-b/a}
For all the switching functions in the above table one can also specify a further (optional) parameter using the parameter
keyword D_MAX to assert that for \f$r>d_{\textrm{max}}\f$ the switching function can be assumed equal to zero.
+In this case it is suggested to also use the STRETCH flag, which will bring the swtiching function
+smoothly to zero by stretching and shifting it. To be more clear, using
+\verbatim
+KEYWORD={RATIONAL R_0=1 D_MAX=3 STRETCH}
+\endverbatim
+the resulting switching function will be
+\f$
+s(r) = \frac{s'(r)-s'(d_{max})}{s'(0)-s'(d_{max})}
+\f$
+where
+\f$
+s'(r)=\frac{1-r^6}{1-r^{12}}
+\f$
*/
//+ENDPLUMEDOC
@@ -106,19 +119,27 @@ void SwitchingFunction::set(const std::string & definition,std::string& errormsg
string name=data[0];
data.erase(data.begin());
invr0=0.0;
+ invr0_2=0.0;
d0=0.0;
dmax=std::numeric_limits<double>::max();
+ dmax_2=std::numeric_limits<double>::max();
+ stretch=1.0;
+ shift=0.0;
init=true;
double r0;
bool found_r0=Tools::parse(data,"R_0",r0);
if(!found_r0) errormsg="R_0 is required";
invr0=1.0/r0;
+ invr0_2=invr0*invr0;
Tools::parse(data,"D_0",d0);
Tools::parse(data,"D_MAX",dmax);
+ dmax_2=dmax*dmax;
+ bool dostretch=false;
+ Tools::parseFlag(data,"STRETCH",dostretch);
if(name=="RATIONAL"){
- type=spline;
+ type=rational;
nn=6;
mm=12;
Tools::parse(data,"NN",nn);
@@ -136,12 +157,20 @@ void SwitchingFunction::set(const std::string & definition,std::string& errormsg
errormsg="found the following rogue keywords in switching function input : ";
for(unsigned i=0;i<data.size();++i) errormsg = errormsg + data[i] + " ";
}
+
+ if(dostretch){
+ double dummy;
+ double s0=calculate(0.0,dummy);
+ double sd=calculate(dmax,dummy);
+ stretch=1.0/(s0-sd);
+ shift=-sd*stretch;
+ }
}
std::string SwitchingFunction::description() const {
std::ostringstream ostr;
ostr<<1./invr0<<". Using ";
- if(type==spline){
+ if(type==rational){
ostr<<"rational";
} else if(type==exponential){
ostr<<"exponential";
@@ -153,7 +182,7 @@ std::string SwitchingFunction::description() const {
plumed_merror("Unknown switching function type");
}
ostr<<" swiching function with parameters d0="<<d0;
- if(type==spline){
+ if(type==rational){
ostr<<" nn="<<nn<<" mm="<<mm;
} else if(type==smap){
ostr<<" a="<<a<<" b="<<b;
@@ -161,23 +190,8 @@ std::string SwitchingFunction::description() const {
return ostr.str();
}
-double SwitchingFunction::calculate(double distance,double&dfunc)const{
- plumed_massert(init,"you are trying to use an unset SwitchingFunction");
- if(distance>dmax){
- dfunc=0.0;
- return 0.0;
- }
- const double rdist = (distance-d0)*invr0;
- double result;
- if(rdist<=0.){
- result=1.;
- dfunc=0.0;
- }else{
- if(type==smap){
- double sx=c*pow( rdist, a );
- result=pow( 1.0 + sx, d );
- dfunc=-b*sx/rdist*result/(1.0+sx);
- } else if(type==spline){
+double SwitchingFunction::do_rational(double rdist,double&dfunc,int nn,int mm)const{
+ double result;
if(2*nn==mm){
// if 2*N==M, then (1.0-rdist^N)/(1.0-rdist^M) = 1.0/(1.0+rdist^N)
double rNdist=Tools::fastpow(rdist,nn-1);
@@ -198,6 +212,47 @@ double SwitchingFunction::calculate(double distance,double&dfunc)const{
dfunc = ((-nn*rNdist*iden)+(func*(iden*mm)*rMdist));
}
}
+ return result;
+}
+
+double SwitchingFunction::calculateSqr(double distance2,double&dfunc)const{
+ if(type==rational && nn%2==0 && mm%2==0 && d0==0.0){
+ if(distance2>dmax_2){
+ dfunc=0.0;
+ return 0.0;
+ }
+ const double rdist_2 = distance2*invr0_2;
+ double result=do_rational(rdist_2,dfunc,nn/2,mm/2);
+// chain rule:
+ dfunc*=2*invr0_2;
+// stretch:
+ result=result*stretch+shift;
+ dfunc*=stretch;
+ return result;
+ } else {
+ double distance=std::sqrt(distance2);
+ return calculate(distance,dfunc);
+ }
+}
+
+double SwitchingFunction::calculate(double distance,double&dfunc)const{
+ plumed_massert(init,"you are trying to use an unset SwitchingFunction");
+ if(distance>dmax){
+ dfunc=0.0;
+ return 0.0;
+ }
+ const double rdist = (distance-d0)*invr0;
+ double result;
+ if(rdist<=0.){
+ result=1.;
+ dfunc=0.0;
+ }else{
+ if(type==smap){
+ double sx=c*pow( rdist, a );
+ result=pow( 1.0 + sx, d );
+ dfunc=-b*sx/rdist*result/(1.0+sx);
+ } else if(type==rational){
+ result=do_rational(rdist,dfunc,nn,mm);
}else if(type==exponential){
result=exp(-rdist);
dfunc=-result;
@@ -211,28 +266,38 @@ double SwitchingFunction::calculate(double distance,double&dfunc)const{
// (I think this is misleading and I would like to modify it - GB)
dfunc/=distance;
}
+
+ result=result*stretch+shift;
+ dfunc*=stretch;
+
return result;
}
SwitchingFunction::SwitchingFunction():
init(false),
- type(spline),
+ type(rational),
nn(6),
mm(12),
invr0(0.0),
d0(0.0),
- dmax(0.0)
+ dmax(0.0),
+ invr0_2(0.0),
+ dmax_2(0.0),
+ stretch(1.0),
+ shift(0.0)
{
}
void SwitchingFunction::set(int nn,int mm,double r0,double d0){
init=true;
- type=spline;
+ type=rational;
this->nn=nn;
this->mm=mm;
this->invr0=1.0/r0;
+ this->invr0_2=this->invr0*this->invr0;
this->d0=d0;
this->dmax=d0+r0*pow(0.00001,1./(nn-mm));
+ this->dmax_2=this->dmax*this->dmax;
}
double SwitchingFunction::get_r0() const {
diff --git a/src/tools/SwitchingFunction.h b/src/tools/SwitchingFunction.h
index 9723a36f58b1d0fe787cc87758dfffa1475303d7..285ede543124fe67d3b27000559a43970e48b609 100644
--- a/src/tools/SwitchingFunction.h
+++ b/src/tools/SwitchingFunction.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -30,25 +30,67 @@ class Log;
class Keywords;
/// \ingroup TOOLBOX
-/// Small class to compure switching functions in the form
-/// In the future we might extend it so as to be set using
-/// a string:
-/// void set(std::string);
-/// which can then be parsed for more complex stuff, e.g. exponentials
-/// tabulated functions from file, matheval, etc...
+/// Small class to compure switching functions.
+/// Switching functions are created using set() and
+/// then can be used with function calculate() or calculateSqr().
+/// Since this is typically computed on a distance vector,
+/// the second all (calculateSqr()) allows to skip the calculation
+/// of a square root in some case, thus potentially increasing
+/// performances.
class SwitchingFunction{
+/// This is to check that switching function has been initialized
bool init;
- enum {spline,exponential,gaussian,smap} type;
- int nn,mm,a,b;
- double invr0,d0,dmax,c,d;
+/// Type of function
+ enum {rational,exponential,gaussian,smap} type;
+/// Inverse of scaling length.
+/// We store the inverse to avoid a division
+ double invr0;
+/// Minimum distance (before this, function is one)
+ double d0;
+/// Maximum distance (after this, function is zero)
+ double dmax;
+/// Exponents for rational function
+ int nn,mm;
+/// Parameters for smap function
+ int a,b;
+ double c,d;
+/// Square of invr0, useful in calculateSqr()
+ double invr0_2;
+/// Square of dmax, useful in calculateSqr()
+ double dmax_2;
+/// Parameters for stretching the function to zero at d_max
+ double stretch,shift;
+/// Low-level tool to compute rational functions.
+/// It is separated since it is called both by calculate() and calculateSqr()
+ double do_rational(double rdist,double&dfunc,int nn,int mm)const;
public:
static void registerKeywords( Keywords& keys );
+/// Constructor
SwitchingFunction();
+/// Set a "rational" switching function.
+/// Notice that a d_max is set automatically to a value such that
+/// f(d_max)=0.00001.
void set(int nn,int mm,double r_0,double d_0);
+/// Set an arbitrary switching function.
+/// Parse the string in definition and possibly returns errors
+/// in the errormsg string
void set(const std::string& definition, std::string& errormsg);
+/// Returns a string with a description of the switching function
std::string description() const ;
+/// Compute the switching function.
+/// Returns s(x). df will be set to the value of the derivative
+/// of the switching function _divided_by_x
double calculate(double x,double&df)const;
+/// Compute the switching function.
+/// Returns \f$ s(\sqrt{x})\f$ .
+/// df will be set to the \f$ \frac{1}{\sqrt{x}}\frac{ds}{d\sqrt{x}}= 2 \frac{ds}{dx}\f$
+/// (same as calculate()).
+/// The advantage is that in some case the expensive square root can be avoided
+/// (namely for rational functions, if nn and mm are even and d0 is zero)
+ double calculateSqr(double distance2,double&dfunc)const;
+/// Returns d0
double get_d0() const;
+/// Returns r0
double get_r0() const;
};
diff --git a/src/tools/Tensor.cpp b/src/tools/Tensor.cpp
index 522c616edd2f39ffb63d875c1b4cf6c85c539b46..29a324518623539db8eb924f7df810c4d306351a 100644
--- a/src/tools/Tensor.cpp
+++ b/src/tools/Tensor.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Tensor.h b/src/tools/Tensor.h
index e15c9154d76fc876842316951fb9b6cd2db8df11..1355fa06b4188a6d1db153870bc4201045982f59 100644
--- a/src/tools/Tensor.h
+++ b/src/tools/Tensor.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Tools.cpp b/src/tools/Tools.cpp
index a60723572e6013251cd2f21d29898a232a39b6f7..e54e3580fe13952514a7dc8e3186ca96da61459f 100644
--- a/src/tools/Tools.cpp
+++ b/src/tools/Tools.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -231,29 +231,36 @@ bool Tools::getKey(vector<string>& line,const string & key,string & s){
void Tools::interpretRanges(std::vector<std::string>&s){
vector<string> news;
for(vector<string>::iterator p=s.begin();p!=s.end();++p){
- vector<string> words;
- words=getWords(*p,"-");
- int a;
- bool found=false;
- if(words.size()==2 && convert(words[0],a)){
- int b,c=1;
- vector<string> bwords=getWords(words[1],":");
- if(bwords.size()==2 && convert(bwords[0],b) && convert(bwords[1],c)) found=true;
- else if(convert(words[1],b)){
- c=1;
- found=true;
+ news.push_back(*p);
+ size_t dash=p->find("-");
+ if(dash==string::npos) continue;
+ int first;
+ if(!Tools::convert(p->substr(0,dash),first)) continue;
+ int stride=1;
+ int second;
+ size_t colon=p->substr(dash+1).find(":");
+ if(colon!=string::npos){
+ if(!Tools::convert(p->substr(dash+1).substr(0,colon),second) ||
+ !Tools::convert(p->substr(dash+1).substr(colon+1),stride)) continue;
+ } else {
+ if(!Tools::convert(p->substr(dash+1),second)) continue;
+ }
+ news.resize(news.size()-1);
+ if(first<=second){
+ plumed_massert(stride>0,"interpreting ranges "+ *p + ", stride should be positive");
+ for(int i=first;i<=second;i+=stride){
+ string ss;
+ convert(i,ss);
+ news.push_back(ss);
}
- if(found){
- plumed_massert(b>=a,"interpreting ranges "+ *p + ", second number should be larger than first number");
- plumed_massert(c>0,"interpreting ranges "+ *p + ", stride should be positive");
- for(int i=a;i<=b;i+=c){
- string ss;
- convert(i,ss);
- news.push_back(ss);
- }
+ } else {
+ plumed_massert(stride<0,"interpreting ranges "+ *p + ", stride should be positive");
+ for(int i=first;i>=second;i+=stride){
+ string ss;
+ convert(i,ss);
+ news.push_back(ss);
}
}
- if(!found) news.push_back(*p);
}
s=news;
}
diff --git a/src/tools/Tools.h b/src/tools/Tools.h
index 57dc2b5b9542ad726328a8aafc53adb77997c9a6..a1e1950ce4fd18c91e7f494ff028466ae1544012 100644
--- a/src/tools/Tools.h
+++ b/src/tools/Tools.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Torsion.cpp b/src/tools/Torsion.cpp
index 1d6fad1a5e5ca936583b35a642f3781faa12517c..793434cebd9e80104f75fa3fe23234af87c8a8e4 100644
--- a/src/tools/Torsion.cpp
+++ b/src/tools/Torsion.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Torsion.h b/src/tools/Torsion.h
index aea0d68e105f2e314920185a35caacfbf89bced4..b6cae8f41598a447053463bc68ff68a4a24a6d02 100644
--- a/src/tools/Torsion.h
+++ b/src/tools/Torsion.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Units.cpp b/src/tools/Units.cpp
index c0b6ccd4c892039ba44a5b8dcd01050c70487f35..0fa7aa79794002731225430a326662abd3ab77e9 100644
--- a/src/tools/Units.cpp
+++ b/src/tools/Units.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Units.h b/src/tools/Units.h
index 732a1dab5558c381412e3c952314a2653782ccc5..ab42e78c24d081e9c6142ed7e35b0f6d4b9963b8 100644
--- a/src/tools/Units.h
+++ b/src/tools/Units.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Vector.cpp b/src/tools/Vector.cpp
index 6af4d27bac6315cb3dc9e1f594776753b3700871..d5c1d2e58e26c04b64eb3997d1bbca9701712c07 100644
--- a/src/tools/Vector.cpp
+++ b/src/tools/Vector.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/tools/Vector.h b/src/tools/Vector.h
index 8de6451715fa058cf1ec1d78a8b65f104cefa40b..8e07ba49343efb577a32d9585334eaa50a902e40 100644
--- a/src/tools/Vector.h
+++ b/src/tools/Vector.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vatom/ActionRegister.h b/src/vatom/ActionRegister.h
index 7e7f911617e593acb965d91975cfb28753fbbd50..42df9e9ea2a16274399485fdcdaa1d1516134462 100644
--- a/src/vatom/ActionRegister.h
+++ b/src/vatom/ActionRegister.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vatom/ActionWithVirtualAtom.h b/src/vatom/ActionWithVirtualAtom.h
index 867202fa7111182ed7f0f620c47cfc6e639099dc..2a47f1686df519653f66439d5b3af9e15356f622 100644
--- a/src/vatom/ActionWithVirtualAtom.h
+++ b/src/vatom/ActionWithVirtualAtom.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vatom/COM.cpp b/src/vatom/COM.cpp
index 50c960a9f90b59ac0fc89fc78fe2b991a2dd092f..e60c39e932788d64c9cf5583af2271b561823e2c 100644
--- a/src/vatom/COM.cpp
+++ b/src/vatom/COM.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vatom/Center.cpp b/src/vatom/Center.cpp
index 6fd0558c84e39a431591225b4e4ad28e8e6e21f7..dda8e9050371fd58d495a1dbad7bafb43bd4ba55 100644
--- a/src/vatom/Center.cpp
+++ b/src/vatom/Center.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vatom/Ghost.cpp b/src/vatom/Ghost.cpp
index 8d6ecaf446e21c94d74705683302e5f0159525c6..9122a2441451574373fdaf6ba4d614f3318af227 100644
--- a/src/vatom/Ghost.cpp
+++ b/src/vatom/Ghost.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vesselbase/ActionWithVessel.cpp b/src/vesselbase/ActionWithVessel.cpp
index 49232fa170d0e9cd9ad1c408b38148ffec4e8b5b..d2c39608dd16c5a48f5ca958e158513b1e944281 100644
--- a/src/vesselbase/ActionWithVessel.cpp
+++ b/src/vesselbase/ActionWithVessel.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -39,20 +39,28 @@ void ActionWithVessel::registerKeywords(Keywords& keys){
"keyword and the value for NL_TOL must be set less than the value for TOL. This keyword ensures that "
"quantities, which are much less than TOL and which will thus not added to the sums being accumulated "
"are not calculated at every step. They are only calculated when the neighbor list is updated.");
+ keys.add("hidden","MAXDERIVATIVES","The maximum number of derivatives that can be used when storing data. This controls when "
+ "we have to start using lowmem");
keys.addFlag("SERIAL",false,"do the calculation in serial. Do not parallelize");
+ keys.addFlag("LOWMEM",false,"lower the memory requirements");
keys.add( vesselRegister().getKeywords() );
}
ActionWithVessel::ActionWithVessel(const ActionOptions&ao):
Action(ao),
- read(false),
serial(false),
+ lowmem(false),
contributorsAreUnlocked(false),
weightHasDerivatives(false)
{
+ maxderivatives=309; parse("MAXDERIVATIVES",maxderivatives);
if( keywords.exists("SERIAL") ) parseFlag("SERIAL",serial);
else serial=true;
if(serial)log.printf(" doing calculation in serial\n");
+ if( keywords.exists("LOWMEM") ){
+ parseFlag("LOWMEM",lowmem);
+ if(lowmem)log.printf(" lowering memory requirements\n");
+ }
tolerance=nl_tolerance=epsilon;
if( keywords.exists("TOL") ) parse("TOL",tolerance);
if( tolerance>epsilon){
@@ -62,8 +70,6 @@ ActionWithVessel::ActionWithVessel(const ActionOptions&ao):
if( nl_tolerance>epsilon ) log.printf(" and ignoring quantities less than %lf inbetween neighbor list update steps\n",nl_tolerance);
else log.printf("\n");
}
- // Setup stuff for communicating what tasks have been deactivated across all nodes
- taskList.setupMPICommunication( comm );
}
ActionWithVessel::~ActionWithVessel(){
@@ -71,18 +77,18 @@ ActionWithVessel::~ActionWithVessel(){
}
void ActionWithVessel::addVessel( const std::string& name, const std::string& input, const int numlab, const std::string thislab ){
- read=true; VesselOptions da(name,thislab,numlab,input,this);
+ VesselOptions da(name,thislab,numlab,input,this);
Vessel* vv=vesselRegister().create(name,da); vv->checkRead();
addVessel(vv);
}
void ActionWithVessel::addVessel( Vessel* vv ){
ShortcutVessel* sv=dynamic_cast<ShortcutVessel*>(vv);
- if(!sv) functions.push_back(vv);
+ if(!sv){ functions.push_back(vv); }
}
BridgeVessel* ActionWithVessel::addBridgingVessel( ActionWithVessel* tome ){
- read=true; VesselOptions da("","",0,"",this);
+ VesselOptions da("","",0,"",this);
BridgeVessel* bv=new BridgeVessel(da);
bv->setOutputAction( tome );
functions.push_back( dynamic_cast<Vessel*>(bv) );
@@ -90,7 +96,18 @@ BridgeVessel* ActionWithVessel::addBridgingVessel( ActionWithVessel* tome ){
return bv;
}
+void ActionWithVessel::addTaskToList( const unsigned& taskCode ){
+ plumed_assert( functions.size()==0 ); // We cannot add more tasks after vessels added
+ indexOfTaskInFullList.push_back( fullTaskList.size() );
+ fullTaskList.push_back( taskCode ); partialTaskList.push_back( taskCode );
+ taskFlags.push_back(0); nactive_tasks = fullTaskList.size();
+ plumed_assert( partialTaskList.size()==nactive_tasks && indexOfTaskInFullList.size()==nactive_tasks && taskFlags.size()==nactive_tasks );
+}
+
void ActionWithVessel::readVesselKeywords(){
+ // Set maxderivatives if it is too big
+ if( maxderivatives>getNumberOfDerivatives() ) maxderivatives=getNumberOfDerivatives();
+
// Loop over all keywords find the vessels and create appropriate functions
for(unsigned i=0;i<keywords.size();++i){
std::string thiskey,input; thiskey=keywords.getKeyword(i);
@@ -127,39 +144,72 @@ void ActionWithVessel::readVesselKeywords(){
}
void ActionWithVessel::resizeFunctions(){
- unsigned tmpnval,nvals=2, bufsize=0;
+ unsigned bufsize=0;
for(unsigned i=0;i<functions.size();++i){
functions[i]->bufstart=bufsize;
functions[i]->resize();
bufsize+=functions[i]->bufsize;
- tmpnval=functions[i]->getNumberOfTerms();
- plumed_massert( tmpnval>1 , "There should always be at least two terms - one for the value and one for the weight");
- if(tmpnval>nvals) nvals=tmpnval;
}
- unsigned nder=getNumberOfDerivatives();
- thisval.resize( nvals ); thisval_wasset.resize( nvals, false );
- derivatives.resize( nvals*nder, 0.0 );
+ thisval.resize( getNumberOfQuantities() ); thisval_wasset.resize( getNumberOfQuantities(), false );
+ derivatives.resize( getNumberOfQuantities()*getNumberOfDerivatives(), 0.0 );
buffer.resize( bufsize );
tmpforces.resize( getNumberOfDerivatives() );
}
-void ActionWithVessel::deactivate_task(){
- plumed_dbg_assert( contributorsAreUnlocked );
- for(unsigned i=0;i<taskList.fullSize();++i){
- if( taskList(i)==current ) taskList.deactivate(i);
+void ActionWithVessel::unlockContributors(){
+ if( contributorsAreUnlocked ) return;
+ nactive_tasks = fullTaskList.size();
+ for(unsigned i=0;i<fullTaskList.size();++i){
+ partialTaskList[i] = fullTaskList[i]; taskFlags[i]=0;
+ indexOfTaskInFullList[i]=i;
}
+ finishTaskListUpdate();
+ contributorsAreUnlocked=true;
+ resizeFunctions();
+}
+
+void ActionWithVessel::lockContributors(){
+ nactive_tasks = 0;
+ for(unsigned i=0;i<fullTaskList.size();++i){
+ // Deactivate sets inactive tasks to number not equal to zero
+ if( taskFlags[i]==0 ){
+ partialTaskList[nactive_tasks] = fullTaskList[i];
+ indexOfTaskInFullList[nactive_tasks]=i;
+ nactive_tasks++;
+ }
+ }
+ finishTaskListUpdate();
+ contributorsAreUnlocked=false;
+ resizeFunctions();
}
-//Vessel* ActionWithVessel::getVessel( const std::string& name ){
-// std::string myname;
-// for(unsigned i=0;i<functions.size();++i){
-// if( functions[i]->getLabel(myname) ){
-// if( myname==name ) return functions[i];
-// }
-// }
-// error("there is no vessel with name " + name);
-// return NULL;
-//}
+void ActionWithVessel::deactivateAllTasks(){
+ plumed_assert( contributorsAreUnlocked );
+ nactive_tasks = 0;
+}
+
+void ActionWithVessel::activateTheseTasks( std::vector<bool>& additionalTasks ){
+ plumed_dbg_assert( additionalTasks.size()==fullTaskList.size() );
+ // Activate tasks that are already active locally
+ for(unsigned i=0;i<nactive_tasks;++i) additionalTasks[ indexOfTaskInFullList[i] ] = true;
+
+ nactive_tasks = 0;
+ for(unsigned i=0;i<fullTaskList.size();++i){
+ // Deactivate sets inactive tasks to number not equal to zero
+ if( additionalTasks[i] ){
+ partialTaskList[nactive_tasks] = fullTaskList[i];
+ indexOfTaskInFullList[nactive_tasks]=i;
+ nactive_tasks++;
+ } else {
+ taskFlags[i]=1;
+ }
+ }
+}
+
+void ActionWithVessel::deactivate_task(){
+ plumed_dbg_assert( contributorsAreUnlocked );
+ taskFlags[task_index]=1;
+}
void ActionWithVessel::doJobsRequiredBeforeTaskList(){
// Clear all data from previous calculations
@@ -169,7 +219,8 @@ void ActionWithVessel::doJobsRequiredBeforeTaskList(){
}
void ActionWithVessel::runAllTasks(){
- plumed_massert( read, "you must have a call to readVesselKeywords somewhere" );
+ if( getExchangeStep() && nactive_tasks!=fullTaskList.size() ) error("contributors must be unlocked during exchange steps");
+ plumed_massert( functions.size()>0, "you must have a call to readVesselKeywords somewhere" );
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if(serial){ stride=1; rank=0; }
@@ -177,11 +228,13 @@ void ActionWithVessel::runAllTasks(){
// Make sure jobs are done
doJobsRequiredBeforeTaskList();
- for(unsigned i=rank;i<taskList.getNumberActive();i+=stride){
+ for(unsigned i=rank;i<nactive_tasks;i+=stride){
+ // The index of the task in the full list
+ task_index=indexOfTaskInFullList[i];
// Store the task we are currently working on
- current=taskList[i];
+ current=partialTaskList[i];
// Calculate the stuff in the loop for this action
- performTask(i);
+ performTask();
// Weight should be between zero and one
plumed_dbg_assert( thisval[1]>=0 && thisval[1]<=1.0 );
@@ -204,16 +257,24 @@ void ActionWithVessel::runAllTasks(){
finishComputations();
}
+void ActionWithVessel::getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices ){
+ indices[jstore]=getNumberOfDerivatives();
+ if( indices[jstore]>maxder ) error("too many derivatives to store. Run with LOWMEM");
+
+ unsigned kder = ntotal + jstore*getNumberOfDerivatives();
+ for(unsigned jder=0;jder<getNumberOfDerivatives();++jder){ indices[ kder ] = jder; kder++; }
+}
+
void ActionWithVessel::clearAfterTask(){
// Clear the derivatives from this step
for(unsigned k=0;k<thisval.size();++k){
- thisval_wasset[k]=false;
clearDerivativesAfterTask(k);
}
}
void ActionWithVessel::clearDerivativesAfterTask( const unsigned& ider ){
unsigned kstart=ider*getNumberOfDerivatives();
+ thisval[ider]=0.0; thisval_wasset[ider]=false;
for(unsigned j=0;j<getNumberOfDerivatives();++j) derivatives[ kstart+j ]=0.0;
}
@@ -230,7 +291,10 @@ bool ActionWithVessel::calculateAllVessels(){
void ActionWithVessel::finishComputations(){
// MPI Gather everything
- if(!serial && buffer.size()>0) comm.Sum( &buffer[0],buffer.size() );
+ if( !serial && buffer.size()>0 ) comm.Sum( buffer );
+ // Update the elements that are makign contributions to the sum here
+ // this causes problems if we do it in prepare
+ if( !serial && contributorsAreUnlocked ) comm.Sum( taskFlags );
// Set the final value of the function
for(unsigned j=0;j<functions.size();++j) functions[j]->finish();
@@ -261,7 +325,7 @@ bool ActionWithVessel::getForcesFromVessels( std::vector<double>& forcesToApply
plumed_dbg_assert( forcesToApply.size()==getNumberOfDerivatives() );
forcesToApply.assign( forcesToApply.size(),0.0 );
bool wasforced=false;
- for(int i=0;i<getNumberOfVessels();++i){
+ for(unsigned i=0;i<getNumberOfVessels();++i){
if( (functions[i]->applyForce( tmpforces )) ){
wasforced=true;
for(unsigned j=0;j<forcesToApply.size();++j) forcesToApply[j]+=tmpforces[j];
diff --git a/src/vesselbase/ActionWithVessel.h b/src/vesselbase/ActionWithVessel.h
index bdf39e5f9f72afa78a8af1044f210c9c18b8e4ac..f6e4ef7b756fa7b31f0e67b2a010d6299c05b329 100644
--- a/src/vesselbase/ActionWithVessel.h
+++ b/src/vesselbase/ActionWithVessel.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -46,20 +46,21 @@ class ActionWithVessel : public virtual Action {
friend class Vessel;
friend class ShortcutVessel;
friend class FunctionVessel;
+friend class StoreDataVessel;
friend class BridgeVessel;
private:
-/// This is used to ensure that we have properly read the action
- bool read;
/// Do all calculations in serial
bool serial;
+/// Lower memory requirements
+ bool lowmem;
+/// The maximum number of derivatives we can use before we need to invoke lowmem
+ unsigned maxderivatives;
/// The tolerance on the accumulators
double tolerance;
/// Tolerance for quantities being put in neighbor lists
double nl_tolerance;
/// The value of the current element in the sum
std::vector<double> thisval;
-/// A boolean that makes sure we don't accumulate very wrong derivatives
- std::vector<bool> thisval_wasset;
/// Vector of derivatives for the object
std::vector<double> derivatives;
/// The buffers we use for mpi summing DistributionFunction objects
@@ -70,17 +71,27 @@ private:
std::vector<Vessel*> functions;
/// Tempory storage for forces
std::vector<double> tmpforces;
+/// Ths full list of tasks we have to perform
+ std::vector<unsigned> fullTaskList;
+/// The current number of active tasks
+ unsigned nactive_tasks, task_index, current;
+/// The indices of the tasks in the full list of tasks
+ std::vector<unsigned> indexOfTaskInFullList;
+/// The list of currently active tasks
+ std::vector<unsigned> partialTaskList;
+/// This list is used to update the neighbor list
+ std::vector<unsigned> taskFlags;
protected:
+/// A boolean that makes sure we don't accumulate very wrong derivatives
+ std::vector<bool> thisval_wasset;
/// The terms in the series are locked
bool contributorsAreUnlocked;
/// Does the weight have derivatives
bool weightHasDerivatives;
-/// The numerical index of the task we are curently performing
- unsigned current;
/// This is used for numerical derivatives of bridge variables
unsigned bridgeVariable;
-/// The list of tasks we have to perform
- DynamicList<unsigned> taskList;
+/// Set the maximum number of derivatives
+ void setMaximumNumberOfDerivatives( const unsigned& );
/// Add a vessel to the list of vessels
void addVessel( const std::string& name, const std::string& input, const int numlab=0, const std::string thislab="" );
void addVessel( Vessel* vv );
@@ -98,12 +109,8 @@ protected:
Vessel* getPntrToVessel( const unsigned& i );
/// Calculate the values of all the vessels
void runAllTasks();
-/// Finish running all the calculations
- void finishComputations();
/// Resize all the functions when the number of derivatives change
void resizeFunctions();
-/// Set the derivative of the jth element wrt to a numbered element
- void setElementDerivative( const unsigned&, const double& );
/// This loops over all the vessels calculating them and also
/// sets all the element derivatives equal to zero
bool calculateAllVessels();
@@ -113,13 +120,33 @@ protected:
void accumulateDerivative( const unsigned& ider, const double& df );
/// Clear tempory data that is calculated for each task
void clearAfterTask();
+/// Is the calculation being done in serial
+ bool serialCalculation() const;
+/// Are we using low memory
+ bool usingLowMem() const ;
+/// Set that we are using low memory
+ void setLowMemOption(const bool& );
+/// Get the number of tasks that are currently active
+ unsigned getCurrentNumberOfActiveTasks() const ;
+/// Get the ith of the currently active tasks
+ unsigned getActiveTask( const unsigned& ii ) const ;
+/// Get the position of the ith active task in the full list
+ unsigned getPositionInFullTaskList( const unsigned& ii ) const ;
+/// Get the current task's position in the task list
+ unsigned getCurrentPositionInTaskList() const ;
+/// Return the number that provides instructions for the current task
+ unsigned getCurrentTask() const ;
+/// Deactivate all the tasks in the task list
+ void deactivateAllTasks();
+/// Add a task to the full list
+ void addTaskToList( const unsigned& taskCode );
public:
static void registerKeywords(Keywords& keys);
ActionWithVessel(const ActionOptions&ao);
~ActionWithVessel();
-/// Used to make sure we are calculating everything during neighbor list update step
- virtual void unlockContributors();
- virtual void lockContributors();
+ void unlockContributors();
+ void lockContributors();
+ virtual void finishTaskListUpdate(){};
/// Activate the jth colvar
/// Deactivate the current task in future loops
virtual void deactivate_task();
@@ -128,28 +155,46 @@ public:
void chainRuleForElementDerivatives( const unsigned&, const unsigned& , const unsigned& , const unsigned& , const double& , Vessel* );
virtual void mergeDerivatives( const unsigned& ider, const double& df );
virtual void clearDerivativesAfterTask( const unsigned& );
+/// Finish running all the calculations
+ virtual void finishComputations();
/// Are the base quantities periodic
virtual bool isPeriodic()=0;
/// What are the domains of the base quantities
virtual void retrieveDomain( std::string& min, std::string& max);
/// Get the number of derivatives for final calculated quantity
virtual unsigned getNumberOfDerivatives()=0;
+/// Get the number of quantities that are calculated during each task
+ virtual unsigned getNumberOfQuantities();
+/// Get the list of indices that have derivatives
+ virtual void getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices );
+/// Switch on additional tasks
+ void activateTheseTasks( std::vector<bool>& addtionalTasks );
/// Do any jobs that are required before the task list is undertaken
virtual void doJobsRequiredBeforeTaskList();
+/// Get the full size of the taskList dynamic list
+ unsigned getFullNumberOfTasks() const ;
+/// Get the index for a particular numbered task
+// unsigned getIndexForTask( const unsigned& itask ) const ;
/// Calculate one of the functions in the distribution
- virtual void performTask( const unsigned& j )=0;
+ virtual void performTask()=0;
/// Return a pointer to the field
Vessel* getVessel( const std::string& name );
+/// Set the derivative of the jth element wrt to a numbered element
+ void setElementDerivative( const unsigned&, const double& );
/// Add some derivative of the quantity in the sum wrt to a numbered element
void addElementDerivative( const unsigned&, const double& );
/// Set the value of the element
void setElementValue( const unsigned& , const double& );
+/// Add to an element value
+ void addElementValue( const unsigned&, const double& );
/// Get the value of this element
double getElementValue( const unsigned& ival ) const ;
/// Retrieve the derivative of the quantity in the sum wrt to a numbered element
double getElementDerivative( const unsigned& ) const ;
/// Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume
virtual void applyBridgeForces( const std::vector<double>& bb ){ plumed_error(); }
+/// These are overwritten in MultiColvarFunction
+ virtual void activateIndexes( const unsigned&, const unsigned&, const std::vector<unsigned>& ){}
};
inline
@@ -167,6 +212,11 @@ unsigned ActionWithVessel::getNumberOfVessels() const {
return functions.size();
}
+inline
+unsigned ActionWithVessel::getNumberOfQuantities(){
+ return 2;
+}
+
inline
Vessel* ActionWithVessel::getPntrToVessel( const unsigned& i ){
plumed_dbg_assert( i<functions.size() );
@@ -182,11 +232,17 @@ inline
void ActionWithVessel::setElementValue( const unsigned& ival, const double& val ){
// Element 0 is reserved for the value we are accumulating
// Element 1 is reserved for the normalization constant for calculating AVERAGES, normalized HISTOGRAMS
- plumed_dbg_massert( !thisval_wasset[ival], "In action named " + getName() + " with label " + getLabel() );
+ // plumed_dbg_massert( !thisval_wasset[ival], "In action named " + getName() + " with label " + getLabel() );
thisval[ival]=val;
thisval_wasset[ival]=true;
}
+inline
+void ActionWithVessel::addElementValue( const unsigned& ival, const double& val ){
+ thisval[ival]+=val;
+ thisval_wasset[ival]=true;
+}
+
inline
double ActionWithVessel::getElementDerivative( const unsigned& ider ) const {
plumed_dbg_assert( ider<derivatives.size() );
@@ -216,14 +272,55 @@ void ActionWithVessel::accumulateDerivative( const unsigned& ider, const double&
}
inline
-void ActionWithVessel::unlockContributors(){
- plumed_dbg_assert( taskList.getNumberActive()==taskList.fullSize() );
- contributorsAreUnlocked=true;
+unsigned ActionWithVessel::getFullNumberOfTasks() const {
+ return fullTaskList.size();
+}
+
+inline
+unsigned ActionWithVessel::getCurrentNumberOfActiveTasks() const {
+ return nactive_tasks;
+}
+
+inline
+unsigned ActionWithVessel::getActiveTask( const unsigned& ii ) const {
+ plumed_dbg_assert( ii<nactive_tasks );
+ return partialTaskList[ii];
+}
+
+inline
+unsigned ActionWithVessel::getPositionInFullTaskList( const unsigned& ii ) const {
+ plumed_dbg_assert( ii<nactive_tasks );
+ return indexOfTaskInFullList[ii];
+}
+
+// inline
+// unsigned ActionWithVessel::getIndexForTask( const unsigned& itask ) const {
+// return taskList.linkIndex( itask );
+// }
+
+inline
+bool ActionWithVessel::serialCalculation() const {
+ return serial;
+}
+
+inline
+bool ActionWithVessel::usingLowMem() const {
+ return lowmem;
+}
+
+inline
+void ActionWithVessel::setLowMemOption(const bool& l){
+ lowmem=l;
+}
+
+inline
+unsigned ActionWithVessel::getCurrentTask() const {
+ return current;
}
inline
-void ActionWithVessel::lockContributors(){
- contributorsAreUnlocked=false;
+unsigned ActionWithVessel::getCurrentPositionInTaskList() const {
+ return task_index;
}
}
diff --git a/src/vesselbase/Between.cpp b/src/vesselbase/Between.cpp
index f8c60c2dda65784823496f219842cc1d9ce834bc..af32667898421dfd16ea18475e19b50587d4c034 100644
--- a/src/vesselbase/Between.cpp
+++ b/src/vesselbase/Between.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -86,7 +86,9 @@ bool Between::calculate(){
double val=getAction()->getElementValue(0);
double dval, f = hist.calculate(val, dval);
- addValueIgnoringTolerance(1,weight);
+ bool bigw=addValueUsingTolerance(1,weight);
+ if( !bigw ) return false;
+
double contr=weight*f;
bool addval=addValueUsingTolerance(0,contr);
if( addval ){
diff --git a/src/vesselbase/BridgeVessel.cpp b/src/vesselbase/BridgeVessel.cpp
index c206c15dcd385d61f31e72a63242e3e1c4654419..200d70c6a799a07ec3fecb72fe99208e1efe7f9b 100644
--- a/src/vesselbase/BridgeVessel.cpp
+++ b/src/vesselbase/BridgeVessel.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -57,7 +57,7 @@ void BridgeVessel::prepare(){
}
bool BridgeVessel::calculate(){
- myOutputAction->performTask( getAction()->current );
+ myOutputAction->performTask();
if( myOutputAction->thisval[1]<myOutputAction->getTolerance() ){
myOutputAction->clearAfterTask();
return ( !myOutputAction->contributorsAreUnlocked || myOutputAction->thisval[1]>=myOutputAction->getNLTolerance() );
@@ -70,7 +70,7 @@ void BridgeVessel::finish(){
myOutputAction->finishComputations();
if( myOutputAction->checkNumericalDerivatives() ){
if ( inum<mynumerical_values.size() ){
- for(unsigned i=0;i<myOutputValues->getNumberOfComponents();++i){
+ for(int i=0;i<myOutputValues->getNumberOfComponents();++i){
mynumerical_values[inum]=myOutputValues->getOutputQuantity(i);
inum++;
}
@@ -87,12 +87,12 @@ void BridgeVessel::completeNumericalDerivatives(){
ActionWithVessel* vval=dynamic_cast<ActionWithVessel*>( myOutputAction );
for(unsigned i=0;i<nextra;++i){
vval->bridgeVariable=i; getAction()->calculate();
- for(unsigned j=0;j<myOutputValues->getNumberOfComponents();++j) tmpder(j,i) = myOutputValues->getOutputQuantity(j);
+ for(int j=0;j<myOutputValues->getNumberOfComponents();++j) tmpder(j,i) = myOutputValues->getOutputQuantity(j);
}
vval->bridgeVariable=nextra; getAction()->calculate();
inum=0; // Reset inum now that we have finished calling calculate
std::vector<double> base( myOutputValues->getNumberOfComponents() );
- for(unsigned j=0;j<myOutputValues->getNumberOfComponents();++j) base[j] = myOutputValues->getOutputQuantity(j);
+ for(int j=0;j<myOutputValues->getNumberOfComponents();++j) base[j] = myOutputValues->getOutputQuantity(j);
const double delta=sqrt(epsilon);
ActionAtomistic* aa=dynamic_cast<ActionAtomistic*>( getAction() );
diff --git a/src/vesselbase/BridgeVessel.h b/src/vesselbase/BridgeVessel.h
index cf158c2a18247234c1f8e455c85dba256bbe29a2..6e66bf8c16746ebc0f476ac8ceff6aee0eba045a 100644
--- a/src/vesselbase/BridgeVessel.h
+++ b/src/vesselbase/BridgeVessel.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -54,8 +54,6 @@ public:
bool applyForce( std::vector<double>& forces );
/// Should not be called
std::string description();
-/// Want to get rid of this function
- unsigned getNumberOfTerms(){ return 2; }
/// Jobs to do before the task list starts
void prepare();
/// Actually do the calculation
diff --git a/src/vesselbase/FunctionVessel.cpp b/src/vesselbase/FunctionVessel.cpp
index e24e2d749a0215680ad6d23708678c6ac0496157..cc83ab8b7a314ec9d0bba6fa7abbbe64766a6f77 100644
--- a/src/vesselbase/FunctionVessel.cpp
+++ b/src/vesselbase/FunctionVessel.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -53,13 +53,13 @@ std::string FunctionVessel::description(){
void FunctionVessel::resize(){
nderivatives=getAction()->getNumberOfDerivatives();
- resizeBuffer( (1+nderivatives)*getNumberOfTerms() );
+ resizeBuffer( (1+nderivatives)*2 );
final_value->resizeDerivatives( nderivatives );
}
void FunctionVessel::mergeFinalDerivatives( const std::vector<double>& df ){
- plumed_dbg_assert( df.size()==getNumberOfTerms() );
- for(unsigned i=0;i<getNumberOfTerms();++i){
+ plumed_dbg_assert( df.size()==2 );
+ for(unsigned i=0;i<2;++i){
unsigned ider=i*( nderivatives + 1 ) + 1;
for(unsigned k=0;k<nderivatives;++k){
final_value->addDerivative( k, df[i]*getBufferElement( ider ) ); ider++;
diff --git a/src/vesselbase/FunctionVessel.h b/src/vesselbase/FunctionVessel.h
index 5d4a0cd0b34dd279c9588c6a7d0178da2a477b1b..937003fd4d4592b8980f4401b6d7b93b5ad4a565 100644
--- a/src/vesselbase/FunctionVessel.h
+++ b/src/vesselbase/FunctionVessel.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -33,7 +33,7 @@ namespace vesselbase{
/**
\ingroup TOOLBOX
-Objects that inherit from FunctionVessel can be used (in tandem with PLMD::ActionWithVessel) to calculate
+Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to calculate
functions of the form \f$\prod_k H_k[ \sum_j \prod_i g_i(x) ]\f$. They should take in a series of values
and return one single value.
*/
@@ -68,8 +68,6 @@ public:
std::string description();
/// The rest of the description of what we are calculating
virtual std::string function_description()=0;
-/// Return number of terms
- virtual unsigned getNumberOfTerms(){ return 2; }
};
inline
@@ -86,7 +84,7 @@ void FunctionVessel::addValueIgnoringTolerance( const unsigned& jval, const doub
inline
double FunctionVessel::getFinalValue(const unsigned& j){
- plumed_dbg_assert( j<getNumberOfTerms() );
+ plumed_dbg_assert( j<2 );
return getBufferElement( (nderivatives+1)*j );
}
diff --git a/src/vesselbase/Histogram.cpp b/src/vesselbase/Histogram.cpp
index a5fb083c8b69a3fba966ae7d0608a6216fc859b9..4cfad44eac8dd4db9c26e42538cd1e5a03b8826d 100644
--- a/src/vesselbase/Histogram.cpp
+++ b/src/vesselbase/Histogram.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vesselbase/LessThan.cpp b/src/vesselbase/LessThan.cpp
index 5b80a6d67c372757f92eabbb7e41827ea250fc17..083de4050a0f895da4152e34fd0836e3f33c616a 100644
--- a/src/vesselbase/LessThan.cpp
+++ b/src/vesselbase/LessThan.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vesselbase/Max.cpp b/src/vesselbase/Max.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..4c50428c4889fa442e711e94b0051926357fead9
--- /dev/null
+++ b/src/vesselbase/Max.cpp
@@ -0,0 +1,86 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "VesselRegister.h"
+#include "FunctionVessel.h"
+#include "ActionWithVessel.h"
+
+namespace PLMD {
+namespace vesselbase{
+
+class Max : public FunctionVessel {
+private:
+ std::vector<double> df;
+ double beta;
+public:
+ static void registerKeywords( Keywords& keys );
+ static void reserveKeyword( Keywords& keys );
+ Max( const VesselOptions& da );
+ std::string function_description();
+ bool calculate();
+ void finish();
+};
+
+PLUMED_REGISTER_VESSEL(Max,"MAX")
+
+void Max::registerKeywords( Keywords& keys ){
+ FunctionVessel::registerKeywords( keys );
+ keys.add("compulsory","BETA","the value of beta for the equation in the manual");
+}
+
+void Max::reserveKeyword( Keywords& keys ){
+ keys.reserve("optional","MAX","calculate the maximum value. "
+ "To make this quantity continuous the maximum is calculated using "
+ "\\f$ \\textrm{max} = \\beta \\log \\sum_i \\exp\\left( \\frac{s_i}{\\beta}\\right) } \\f$ "
+ "The value of \\f$\\beta\\f$ in this function is specified using (BETA=\\f$\\beta\\f$)",true);
+}
+
+Max::Max( const VesselOptions& da ) :
+FunctionVessel(da),
+df(2)
+{
+ if( getAction()->isPeriodic() ) error("max is not a meaningful option for periodic variables");
+ parse("BETA",beta);
+
+ if( diffweight ) error("can't calculate max if weight is differentiable");
+}
+
+std::string Max::function_description(){
+ std::string str_beta; Tools::convert( beta, str_beta );
+ return "the maximum value. Beta is equal to " + str_beta;
+}
+
+bool Max::calculate(){
+ double val=getAction()->getElementValue(0);
+ double dval, f = exp(val/beta); dval=f/beta;
+ addValueIgnoringTolerance(0,f);
+ getAction()->chainRuleForElementDerivatives( 0, 0, dval, this );
+ return true;
+}
+
+void Max::finish(){
+ double valin=getFinalValue(0); double dist=beta*std::log( valin );
+ setOutputValue( dist ); df[0]=beta/valin; df[1]=0.0;
+ mergeFinalDerivatives( df );
+}
+
+}
+}
diff --git a/src/vesselbase/Mean.cpp b/src/vesselbase/Mean.cpp
index 4a7ccf36f42a05ba85384da5ac87642204b00d8f..ba2cf28e3f103d15df1d66a5e39b9c80462e4ddc 100644
--- a/src/vesselbase/Mean.cpp
+++ b/src/vesselbase/Mean.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vesselbase/Min.cpp b/src/vesselbase/Min.cpp
index 405bb21cea8e9944d23f7f7a0367a2fe17468306..c3200753c5c94b9e50a0e919af0d646bd54dfa7d 100644
--- a/src/vesselbase/Min.cpp
+++ b/src/vesselbase/Min.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/multicolvar/Moments.cpp b/src/vesselbase/Moments.cpp
similarity index 87%
rename from src/multicolvar/Moments.cpp
rename to src/vesselbase/Moments.cpp
index 929ac618038448349bed63202be2499c86073bb8..bf971532c0e51cb718699661a3b4d826196fef86 100644
--- a/src/multicolvar/Moments.cpp
+++ b/src/vesselbase/Moments.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -19,18 +19,18 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "vesselbase/VesselRegister.h"
-#include "StoreColvarVessel.h"
-#include "vesselbase/ActionWithVessel.h"
+#include "VesselRegister.h"
+#include "StoreValueVessel.h"
+#include "ActionWithVessel.h"
namespace PLMD {
-namespace multicolvar{
+namespace vesselbase{
// This is the most efficient implementation
// The calculation of all the colvars is parallelized
// but the loops for calculating moments are not
// Feel free to reimplement this if you know how
-class Moments : public StoreColvarVessel {
+class Moments : public StoreValueVessel {
private:
std::vector<unsigned> powers;
std::vector<Value*> value_out;
@@ -39,15 +39,15 @@ public:
static void reserveKeyword( Keywords& keys );
Moments( const vesselbase::VesselOptions& da );
std::string description();
- void performCalculationUsingAllValues();
- void local_resizing();
+ void resize();
+ void finish();
bool applyForce( std::vector<double>& forces );
};
PLUMED_REGISTER_VESSEL(Moments,"MOMENTS")
void Moments::registerKeywords( Keywords& keys ){
- StoreColvarVessel::registerKeywords( keys );
+ StoreValueVessel::registerKeywords( keys );
}
void Moments::reserveKeyword( Keywords& keys ){
@@ -58,11 +58,10 @@ void Moments::reserveKeyword( Keywords& keys ){
}
Moments::Moments( const vesselbase::VesselOptions& da) :
-StoreColvarVessel(da)
+StoreValueVessel(da)
{
ActionWithValue* a=dynamic_cast<ActionWithValue*>( getAction() );
plumed_massert(a,"cannot create passable values as base action does not inherit from ActionWithValue");
- plumed_massert(!diffweight,"cannot do weighted moments properly");
std::vector<std::string> moments=Tools::getWords(getAllInput(),"\t\n ,");
Tools::interpretRanges(moments); unsigned nn;
@@ -76,7 +75,8 @@ StoreColvarVessel(da)
}
}
-void Moments::local_resizing(){
+void Moments::resize(){
+ StoreDataVessel::resize();
unsigned nder=getAction()->getNumberOfDerivatives();
for(unsigned i=0;i<value_out.size();++i) value_out[i]->resizeDerivatives( nder );
}
@@ -92,9 +92,11 @@ std::string Moments::description(){
return descri;
}
-void Moments::performCalculationUsingAllValues(){
+void Moments::finish(){
+ StoreDataVessel::finish();
+
const double pi=3.141592653589793238462643383279502884197169399375105820974944592307;
- unsigned nvals=getNumberOfStoredColvars();
+ unsigned nvals=getAction()->getFullNumberOfTasks();
double mean=0; Value myvalue;
if( getAction()->isPeriodic() ){
@@ -115,12 +117,17 @@ void Moments::performCalculationUsingAllValues(){
for(unsigned i=0;i<nvals;++i) dev1+=pow( myvalue.difference( mean, getValue(i) ), powers[npow] - 1 );
dev1/=static_cast<double>( nvals );
- double pref, tmp, moment=0;
+ std::vector<double> pref(1); double tmp, moment=0;
for(unsigned i=0;i<nvals;++i){
tmp=myvalue.difference( mean, getValue(i) );
- pref=pow( tmp, powers[npow] - 1 ) - dev1;
+ pref[0]=pow( tmp, powers[npow] - 1 ) - dev1;
moment+=pow( tmp, powers[npow] );
- addDerivatives( i, pref, value_out[npow] );
+ if( usingLowMem() ){
+ recompute( i, 0 ); // Not very efficient
+ chainRule( 0, pref, value_out[npow] );
+ } else {
+ chainRule( i, pref, value_out[npow] );
+ }
}
value_out[npow]->chainRule( powers[npow] / static_cast<double>( nvals ) );
value_out[npow]->set( moment / static_cast<double>( nvals ) );
diff --git a/src/vesselbase/MoreThan.cpp b/src/vesselbase/MoreThan.cpp
index eb5f715ec9ed65ef47b66bebd842d2c10990736f..228557fda84652b1a836b7a0974ad13375ecf860 100644
--- a/src/vesselbase/MoreThan.cpp
+++ b/src/vesselbase/MoreThan.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vesselbase/ShortcutVessel.cpp b/src/vesselbase/ShortcutVessel.cpp
index 8e59925732ad0867554448718ea58653cb9fabd2..dbe470d6e37d0e5278dafad03c2adacbd85dce05 100644
--- a/src/vesselbase/ShortcutVessel.cpp
+++ b/src/vesselbase/ShortcutVessel.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vesselbase/ShortcutVessel.h b/src/vesselbase/ShortcutVessel.h
index e34ac3d8a1dc54a666d964eb35da5b817bc41b75..fc5151caeae67760373322664688cf3d358c8476 100644
--- a/src/vesselbase/ShortcutVessel.h
+++ b/src/vesselbase/ShortcutVessel.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -38,7 +38,6 @@ public:
static void registerKeywords( Keywords& keys );
ShortcutVessel( const VesselOptions& );
std::string description(){ return ""; }
- unsigned getNumberOfTerms(){ plumed_error(); return 0; }
void resize(){ plumed_error(); }
bool calculate(){ plumed_error(); }
void finish(){ plumed_error(); }
diff --git a/src/vesselbase/StoreDataVessel.cpp b/src/vesselbase/StoreDataVessel.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..d32d07743f691e457dd0ebc285b98ab0beefa0c2
--- /dev/null
+++ b/src/vesselbase/StoreDataVessel.cpp
@@ -0,0 +1,210 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "StoreDataVessel.h"
+
+namespace PLMD {
+namespace vesselbase {
+
+void StoreDataVessel::registerKeywords( Keywords& keys ){
+ Vessel::registerKeywords(keys);
+}
+
+StoreDataVessel::StoreDataVessel( const VesselOptions& da ):
+Vessel(da),
+max_lowmem_stash(3),
+vecsize(0)
+{
+}
+
+void StoreDataVessel::completeSetup( const unsigned& dstart, const unsigned& nvec ){
+ if( (dstart+nvec)>getAction()->getNumberOfQuantities() ) error("this vessel can not be used with this action");
+ data_start=dstart; vecsize = nvec; fvec.resize( vecsize );
+}
+
+void StoreDataVessel::resize(){
+ plumed_dbg_assert( vecsize>0 );
+ final_derivatives.resize( getAction()->getNumberOfDerivatives() );
+ if( getAction()->lowmem ){
+ nspace = 1;
+ active_der.resize( max_lowmem_stash * ( 1 + getAction()->getNumberOfDerivatives() ) );
+ local_derivatives.resize( max_lowmem_stash * vecsize * getAction()->getNumberOfDerivatives() );
+ } else {
+ nspace = 1 + getAction()->maxderivatives;
+ active_der.resize( getAction()->getFullNumberOfTasks() * ( 1 + getAction()->maxderivatives ) );
+ }
+ resizeBuffer( getAction()->getFullNumberOfTasks()*vecsize*nspace );
+}
+
+void StoreDataVessel::prepare(){
+// Clear bookeeping arrays
+ active_der.assign(active_der.size(),0);
+}
+
+void StoreDataVessel::getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices ){
+ getAction()->getIndexList( ntotal, jstore, maxder, indices );
+}
+
+void StoreDataVessel::setTaskToRecompute( const unsigned& ivec ){
+ getAction()->current = getAction()->fullTaskList[ivec];
+ getAction()->task_index = ivec;
+}
+
+void StoreDataVessel::recompute( const unsigned& ivec, const unsigned& jstore ){
+ plumed_dbg_assert( getAction()->lowmem && jstore<max_lowmem_stash );
+ // Set the task we want to reperform
+ setTaskToRecompute( ivec );
+ // Reperform the task
+ performTask( jstore );
+ // Store the derivatives
+ storeDerivativesLowMem( jstore );
+
+ // Clear up afterwards
+ getAction()->clearAfterTask();
+}
+
+void StoreDataVessel::storeValues( const unsigned& myelem ){
+ ActionWithVessel* act = getAction();
+ unsigned ibuf = myelem * vecsize * nspace;
+ for(unsigned icomp=data_start;icomp<data_start + vecsize;++icomp){
+ setBufferElement( ibuf, act->getElementValue( icomp ) ); ibuf+=nspace;
+ }
+}
+
+void StoreDataVessel::storeDerivativesHighMem( const unsigned& myelem ){
+ plumed_dbg_assert( myelem<getAction()->getFullNumberOfTasks() );
+ ActionWithVessel* act=getAction();
+ getIndexList( act->getFullNumberOfTasks(), myelem, nspace-1, active_der );
+
+ // Store the values of the components and the derivatives if
+ unsigned nder = act->getNumberOfDerivatives();
+ for(unsigned icomp=data_start;icomp<data_start + vecsize;++icomp){
+ unsigned ibuf = myelem * ( vecsize*nspace ) + (icomp-data_start)*nspace + 1;
+ unsigned kder = act->getFullNumberOfTasks() + myelem * ( nspace - 1 );
+ for(unsigned jder=0;jder<active_der[myelem];++jder){
+ addToBufferElement( ibuf, act->getElementDerivative(nder*icomp + active_der[ kder ]) );
+ kder++; ibuf++;
+ }
+ }
+}
+
+void StoreDataVessel::storeDerivativesLowMem( const unsigned& jstore ){
+ // Store the indexes that have derivatives
+ ActionWithVessel* act=getAction();
+ unsigned nder = act->getNumberOfDerivatives();
+ getIndexList( max_lowmem_stash, jstore, nder, active_der );
+
+ // Stash the derivatives
+ for(unsigned icomp=data_start;icomp<data_start + vecsize;++icomp){
+ unsigned ibuf = jstore * vecsize * nder + (icomp-data_start)*nder;
+ unsigned kder = max_lowmem_stash + jstore*nder;
+ for(unsigned jder=0;jder<active_der[jstore];++jder){
+ local_derivatives[ibuf] = act->getElementDerivative( nder*icomp + active_der[ kder ] );
+ ibuf++; kder++;
+ }
+ }
+}
+
+bool StoreDataVessel::calculate(){
+ unsigned myelem = getAction()->getCurrentPositionInTaskList();
+ // Normalize vector if it is required
+ finishTask( myelem );
+
+ // Store the values
+ storeValues( myelem );
+
+ // Store the derivatives if we are not using low memory
+ if( !(getAction()->lowmem) ) storeDerivativesHighMem( myelem );
+
+ return true;
+}
+
+void StoreDataVessel::finish(){
+ if(!getAction()->lowmem) comm.Sum( &active_der[0], active_der.size() );
+}
+
+double StoreDataVessel::chainRule( const unsigned& ival, const unsigned& ider, const std::vector<double>& df ){
+ plumed_dbg_assert( df.size()==vecsize );
+ // Clear final derivatives array
+ final_derivatives.assign( final_derivatives.size(), 0.0 );
+
+ double dfout = 0.0;
+ if(getAction()->lowmem){
+ plumed_dbg_assert( ival<max_lowmem_stash );
+ unsigned maxder = getAction()->getNumberOfDerivatives();
+ unsigned ibuf=ival*(vecsize*maxder) + ider;
+ for(unsigned icomp=0;icomp<vecsize;++icomp){
+ dfout+=df[icomp]*local_derivatives[ibuf];
+ ibuf+=maxder;
+ }
+ } else {
+ plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() );
+ unsigned ibuf=ival*(vecsize*nspace) + 1 + ider;
+ for(unsigned icomp=0;icomp<vecsize;++icomp){
+ dfout+=df[icomp]*getBufferElement(ibuf);
+ ibuf+=nspace;
+ }
+ }
+ return dfout;
+}
+
+void StoreDataVessel::chainRule( const unsigned& ival, const std::vector<double>& df ){
+ plumed_dbg_assert( df.size()==vecsize );
+ // Clear final derivatives array
+ final_derivatives.assign( final_derivatives.size(), 0.0 );
+
+ if(getAction()->lowmem){
+ plumed_dbg_assert( ival<max_lowmem_stash );
+ unsigned maxder = getAction()->getNumberOfDerivatives();
+ for(unsigned ider=0;ider<active_der[ival];++ider){
+ final_derivatives[ider]=0.0;
+ unsigned ibuf=ival*(vecsize*maxder) + ider;
+ for(unsigned jcomp=0;jcomp<vecsize;++jcomp){
+ final_derivatives[ider]+=df[jcomp]*local_derivatives[ibuf];
+ ibuf+=maxder;
+ }
+ }
+ } else {
+ plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() );
+ for(unsigned ider=0;ider<active_der[ival];++ider){
+ final_derivatives[ider]=0.0;
+ unsigned ibuf=ival*(vecsize*nspace) + 1 + ider;
+ for(unsigned jcomp=0;jcomp<vecsize;++jcomp){
+ final_derivatives[ider]+=df[jcomp]*getBufferElement(ibuf);
+ ibuf+=nspace;
+ }
+ }
+ }
+}
+
+void StoreDataVessel::chainRule( const unsigned& ival, const std::vector<double>& df, Value* val ){
+ plumed_dbg_assert( val->getNumberOfDerivatives()==final_derivatives.size() );
+ chainRule( ival, df );
+
+ unsigned kder;
+ if( getAction()->lowmem ) kder = max_lowmem_stash + ival*getAction()->getNumberOfDerivatives();
+ else kder = getAction()->getFullNumberOfTasks() + ival*(nspace-1);
+
+ for(unsigned i=0;i<active_der[ival];++i) val->addDerivative( active_der[kder+i] , final_derivatives[i] );
+}
+
+}
+}
diff --git a/src/vesselbase/StoreDataVessel.h b/src/vesselbase/StoreDataVessel.h
new file mode 100644
index 0000000000000000000000000000000000000000..7e21e7e01606a1f378a3b3777a827be92182e28c
--- /dev/null
+++ b/src/vesselbase/StoreDataVessel.h
@@ -0,0 +1,197 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_vesselbase_StoreDataVessel_h
+#define __PLUMED_vesselbase_StoreDataVessel_h
+
+#include <string>
+#include <cstring>
+#include <vector>
+#include "Vessel.h"
+
+namespace PLMD {
+namespace vesselbase {
+
+/**
+\ingroup TOOLBOX
+Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel)
+to store values and derivatives for a set of scalars or vectors that are calculated by a
+PLMD::vesselbase::ActionWithVessel. Functions of these stored quantities can then be calculated in a
+second step.
+*/
+
+class StoreDataVessel : public Vessel {
+private:
+/// What is the maximum number of vectors we are going to
+/// have to store when using lowmem option
+ unsigned max_lowmem_stash;
+/// The start point for the data we are storing in this particular object
+ unsigned data_start;
+/// The size of the vector we are computing
+ unsigned vecsize;
+/// The amount of data per vector element
+ unsigned nspace;
+/// The active derivative elements
+ std::vector<unsigned> active_der;
+/// This is a tempory vector that is used to store data
+ std::vector<double> fvec;
+/// The local derivatives
+ std::vector<double> local_derivatives;
+/// The final derivatives
+ std::vector<double> final_derivatives;
+protected:
+/// Is the weight differentiable
+ bool weightHasDerivatives();
+/// Are we using low mem option
+ bool usingLowMem();
+/// Finish the setup of the storage object by setting how much
+/// data has to be stored
+ void completeSetup( const unsigned& , const unsigned& );
+/// Return value of nspace
+ unsigned getNumberOfDerivativeSpacesPerComponent() const ;
+/// Retrieve the values from the underlying ActionWithVessel
+ void storeValues( const unsigned& );
+/// Set the Task that needs redoing
+ void setTaskToRecompute( const unsigned& ivec );
+/// Set a component of one of the vectors
+ void setComponent( const unsigned& , const unsigned& , const double& );
+/// This is the proper chain rule for vectors
+ double chainRule( const unsigned&, const unsigned&, const std::vector<double>& );
+/// Chain rule the vector and output derivatives to a value
+ void chainRule( const unsigned& , const std::vector<double>&, Value* );
+/// Get the ibuf'th local derivative value
+ double getLocalDerivative( const unsigned& ibuf );
+/// Set the ibuf'th local derivative value
+ void setLocalDerivative( const unsigned& ibuf, const double& val );
+public:
+ static void registerKeywords( Keywords& keys );
+ StoreDataVessel( const VesselOptions& );
+/// Return the number of components in the vector
+ unsigned getNumberOfComponents() const { return vecsize; }
+/// Do all resizing of data
+ virtual void resize();
+/// Clear certain data before start of main loop
+ void prepare();
+/// Get the number of derivatives for the ith value
+ unsigned getNumberOfDerivatives( const unsigned& );
+/// Get one of the stored indexes
+ unsigned getStoredIndex( const unsigned& , const unsigned& );
+/// Get a component of the stored vector
+ double getComponent( const unsigned& , const unsigned& );
+/// Recalculate a vector - used in lowmem mode
+ virtual void recompute( const unsigned& , const unsigned& );
+/// This reperforms the task in the underlying action
+ virtual void performTask( const unsigned& );
+/// This reperforms the task
+ virtual void finishTask( const unsigned& ){};
+/// Chain rule and store output in local array called final_derivatives
+/// with vectors this does chain rule for dot products
+ void chainRule( const unsigned& , const std::vector<double>& );
+/// Get the ider'th final derivative value
+ double getFinalDerivative( const unsigned& ider ) const ;
+/// This stores the data when not using lowmem
+ bool calculate();
+/// This stores the data we get from the calculation
+ void storeDerivativesLowMem( const unsigned& );
+/// This stores the data we get from the calculation
+ void storeDerivativesHighMem( const unsigned& );
+/// Final step in gathering data
+ virtual void finish();
+/// Activate indexes (this is used at end of chain rule)
+ virtual void activateIndices( ActionWithVessel* ){}
+/// Get the list of indices that we are storing data for
+ virtual void getIndexList( const unsigned& , const unsigned& , const unsigned& , std::vector<unsigned>& );
+/// Forces on vectors should always be applied elsewhere
+ virtual bool applyForce(std::vector<double>&){ return false; }
+};
+
+inline
+bool StoreDataVessel::weightHasDerivatives(){
+ return getAction()->weightHasDerivatives;
+}
+
+inline
+bool StoreDataVessel::usingLowMem(){
+ return getAction()->lowmem;
+}
+
+inline
+void StoreDataVessel::performTask( const unsigned& ivec ){
+ if( usingLowMem() ) getAction()->performTask();
+}
+
+inline
+double StoreDataVessel::getComponent( const unsigned& ival, const unsigned& jcomp ){
+ plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() && jcomp<vecsize );
+ return getBufferElement( ival*(vecsize*nspace) + jcomp*nspace );
+}
+
+inline
+void StoreDataVessel::setComponent( const unsigned& ival, const unsigned& jcomp, const double& val ){
+ plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() && jcomp<vecsize );
+ setBufferElement( ival*(vecsize*nspace) + jcomp*nspace, val );
+}
+
+inline
+unsigned StoreDataVessel::getNumberOfDerivativeSpacesPerComponent() const {
+ return nspace;
+}
+
+inline
+unsigned StoreDataVessel::getNumberOfDerivatives( const unsigned& ival ){
+ plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() );
+ return active_der[ival];
+}
+
+inline
+unsigned StoreDataVessel::getStoredIndex( const unsigned& ival, const unsigned& jindex ){
+ plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() && jindex<active_der[ival] );
+
+ unsigned kder;
+ if( getAction()->lowmem ) kder = max_lowmem_stash + ival*getAction()->getNumberOfDerivatives();
+ else kder = getAction()->getFullNumberOfTasks() + ival*(nspace-1);
+
+ return active_der[kder + jindex];
+}
+
+inline
+double StoreDataVessel::getLocalDerivative( const unsigned& ibuf ){
+ plumed_dbg_assert( getAction()->lowmem && ibuf<local_derivatives.size() );
+ return local_derivatives[ibuf];
+}
+
+inline
+double StoreDataVessel::getFinalDerivative( const unsigned& ider ) const {
+ plumed_dbg_assert( ider<final_derivatives.size() );
+ return final_derivatives[ider];
+}
+
+inline
+void StoreDataVessel::setLocalDerivative( const unsigned& ibuf, const double& val ){
+ plumed_dbg_assert( getAction()->lowmem && ibuf<local_derivatives.size() );
+ local_derivatives[ibuf]=val;
+}
+
+}
+}
+#endif
+
+
diff --git a/src/vesselbase/StoreValueAndWeightVessel.cpp b/src/vesselbase/StoreValueAndWeightVessel.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..aa401d71bba4b4255f08e2a2fb858d7a68707320
--- /dev/null
+++ b/src/vesselbase/StoreValueAndWeightVessel.cpp
@@ -0,0 +1,38 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "StoreValueAndWeightVessel.h"
+
+namespace PLMD {
+namespace vesselbase {
+
+void StoreValueAndWeightVessel::registerKeywords( Keywords& keys ){
+ StoreDataVessel::registerKeywords( keys );
+}
+
+StoreValueAndWeightVessel::StoreValueAndWeightVessel( const VesselOptions& da):
+StoreDataVessel(da)
+{
+ completeSetup( 0, 2 );
+}
+
+}
+}
diff --git a/src/vesselbase/StoreValueAndWeightVessel.h b/src/vesselbase/StoreValueAndWeightVessel.h
new file mode 100644
index 0000000000000000000000000000000000000000..9ec34a35d9536422c58a8020b422c20e63e34ce2
--- /dev/null
+++ b/src/vesselbase/StoreValueAndWeightVessel.h
@@ -0,0 +1,54 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_vesselbase_StoreValueAndWeightVessel_h
+#define __PLUMED_vesselbase_StoreValueAndWeightVessel_h
+
+#include <string>
+#include <cstring>
+#include <vector>
+#include "StoreDataVessel.h"
+
+namespace PLMD {
+namespace vesselbase {
+
+class StoreValueAndWeightVessel : public StoreDataVessel {
+public:
+ static void registerKeywords( Keywords& keys );
+ StoreValueAndWeightVessel( const VesselOptions& );
+ double getValue( const unsigned& );
+ double getWeight( const unsigned& );
+};
+
+inline
+double StoreValueAndWeightVessel::getValue( const unsigned& ival ){
+ return getComponent( ival, 0 );
+}
+
+inline
+double StoreValueAndWeightVessel::getWeight( const unsigned& ival ){
+ return getComponent( ival, 1 );
+}
+
+
+}
+}
+#endif
diff --git a/src/vesselbase/StoreValueVessel.cpp b/src/vesselbase/StoreValueVessel.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..66b58467ba9b1c47d8b0304c9aaccba5ae2d7040
--- /dev/null
+++ b/src/vesselbase/StoreValueVessel.cpp
@@ -0,0 +1,39 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "StoreValueVessel.h"
+
+namespace PLMD {
+namespace vesselbase {
+
+void StoreValueVessel::registerKeywords( Keywords& keys ){
+ StoreDataVessel::registerKeywords( keys );
+}
+
+StoreValueVessel::StoreValueVessel( const VesselOptions& da):
+StoreDataVessel(da)
+{
+ if( weightHasDerivatives() ) error("this quantity cannot be calculated if weights have derivatives");
+ completeSetup( 0, 1 );
+}
+
+}
+}
diff --git a/src/vesselbase/StoreValueVessel.h b/src/vesselbase/StoreValueVessel.h
new file mode 100644
index 0000000000000000000000000000000000000000..fec3d69e12b9d50e0da4d8d348c68fbb5cfe9837
--- /dev/null
+++ b/src/vesselbase/StoreValueVessel.h
@@ -0,0 +1,48 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_vesselbase_StoreValueVessel_h
+#define __PLUMED_vesselbase_StoreValueVessel_h
+
+#include <string>
+#include <cstring>
+#include <vector>
+#include "StoreDataVessel.h"
+
+namespace PLMD {
+namespace vesselbase {
+
+class StoreValueVessel : public StoreDataVessel {
+public:
+ static void registerKeywords( Keywords& keys );
+ StoreValueVessel( const VesselOptions& );
+ double getValue( const unsigned& );
+ virtual std::string description(){ return ""; }
+};
+
+inline
+double StoreValueVessel::getValue( const unsigned& ival ){
+ return getComponent( ival, 0 );
+}
+
+}
+}
+#endif
diff --git a/src/vesselbase/Sum.cpp b/src/vesselbase/Sum.cpp
index 30b6da604200aa39e22bc53654a2f574ee86db65..0a37a44b0f61018e972f0d9c2f8cef28f94623b2 100644
--- a/src/vesselbase/Sum.cpp
+++ b/src/vesselbase/Sum.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vesselbase/Vessel.cpp b/src/vesselbase/Vessel.cpp
index 40217d3db03017dea1cfe57b03949993a28fed3f..27f6705b518137620569a9afb39fc868284f5b80 100644
--- a/src/vesselbase/Vessel.cpp
+++ b/src/vesselbase/Vessel.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vesselbase/Vessel.h b/src/vesselbase/Vessel.h
index 98323b311036633f903fca0799b7cabf33368c7d..7f9d8d4ba605412fbe9c91645ce6462b33abb13c 100644
--- a/src/vesselbase/Vessel.h
+++ b/src/vesselbase/Vessel.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
@@ -161,8 +161,6 @@ public:
virtual void resize()=0;
/// Retrieve the forces on the quantities in the vessel
virtual bool applyForce( std::vector<double>& forces )=0;
-/// Retrieve the number of terms we need to accumulate
- virtual unsigned getNumberOfTerms()=0;
};
template<class T>
diff --git a/src/vesselbase/VesselRegister.cpp b/src/vesselbase/VesselRegister.cpp
index a8d1aaf87cfdcb36c9ee0d4fb62e4dedaba71171..a51d3bf3120a5e9750649feedeb3148ea31b8fc5 100644
--- a/src/vesselbase/VesselRegister.cpp
+++ b/src/vesselbase/VesselRegister.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/vesselbase/VesselRegister.h b/src/vesselbase/VesselRegister.h
index abccc4ca523243420355da96a72f11c8889a1c1e..f3fc8d187b982bdb18b431823f73001955ed27e1 100644
--- a/src/vesselbase/VesselRegister.h
+++ b/src/vesselbase/VesselRegister.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/wrapper/Plumed.c b/src/wrapper/Plumed.c
index 18580dfc257b889490ef146d1d658d33be02cd9d..3aa3e6920e2cddeae2d934112fabf1fdb675017c 100644
--- a/src/wrapper/Plumed.c
+++ b/src/wrapper/Plumed.c
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/wrapper/Plumed.h b/src/wrapper/Plumed.h
index f41cb74bb86658d7fd2baecc86569ec79e9be0e6..39e312b2be2324583c577e15a933f16d9701c89b 100644
--- a/src/wrapper/Plumed.h
+++ b/src/wrapper/Plumed.h
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/src/wrapper/PlumedStatic.cpp b/src/wrapper/PlumedStatic.cpp
index e90af4695f5c30f2b25f1ce7ff26563f94808b18..8c3f52890993a71bfaafab6a3f879e0e6b7adb27 100644
--- a/src/wrapper/PlumedStatic.cpp
+++ b/src/wrapper/PlumedStatic.cpp
@@ -4,7 +4,7 @@
See http://www.plumed-code.org for more information.
- This file is part of plumed, version 2.0.
+ This file is part of plumed, version 2.
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
diff --git a/user-doc/Colvar.txt b/user-doc/Colvar.txt
index b6711a649b3133035b88e55fae3e5c976e7f2da4..2e1b1320d2d34cf7841e050a21131d084b9a3103 100644
--- a/user-doc/Colvar.txt
+++ b/user-doc/Colvar.txt
@@ -39,6 +39,20 @@ could also be specified using:
COM ATOMS=1-51:10
\endverbatim
+One can also obtain a list of decreasing indexes e.g. with
+
+\verbatim
+GROUP ATOMS=51-1:-10
+# same as GROUP ATOMS=51,41,31,21,11,1
+\endverbatim
+
+Notice that most expressions are invariant with respect to a change in the order of the atoms,
+but some of them depend on that order. E.g., with \ref WHOLEMOLECULES it could be useful to
+specify atom lists in a reversed order.
+
+
+
+
In addition, for certain colvars, pdb files can be read in using the following keywords:
@TOPOLOGY@
diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index 6b7ab2cd677ab04557f2bb30e20e0053b265c47c..a6adad9f2b50d469324fc980830a3ba916da9063 100644
--- a/user-doc/Doxyfile
+++ b/user-doc/Doxyfile
@@ -465,7 +465,6 @@ INPUT = IntroPP.txt \
ColvarPP.txt \
FunctionsPP.txt \
InstallationPP.txt \
- WhatsNew.txt \
GlossaryPP.txt \
TutorialsPP.txt \
ModulesPP.txt \
diff --git a/user-doc/Installation.txt b/user-doc/Installation.txt
index da5a75ccda03b5575ee9efadc37d4c191013fa73..f0564329c28beeb9464bdbbea69e4aa9f4ff5b49 100644
--- a/user-doc/Installation.txt
+++ b/user-doc/Installation.txt
@@ -160,7 +160,7 @@ An alternative is to also define the environment variable PLUMED_LIBSUFFIX. E.g.
\endverbatim
will install plumed executable with name "plumed-v2.0". All the other files will be renamed accordingly,
e.g. the PLUMED library will be loaded with "-lplumed-v2.0" and the PLUMED header files
-will be included with "#include <plumed-v2.0/tools/Vector.h>. This trick is useful if you
+will be included with "\#include <plumed-v2.0/tools/Vector.h>". This trick is useful if you
do not want to set up modules, but we think using modules (see above) is more flexible.
\section Patching Patching your MD code
diff --git a/user-doc/Intro.txt b/user-doc/Intro.txt
index cb1709434c5b0b8d3130d33825c5a9d371929d6a..c78bdb1984cff46be97113ed643e6bffb7695543 100644
--- a/user-doc/Intro.txt
+++ b/user-doc/Intro.txt
@@ -1,19 +1,24 @@
/**
\mainpage Introduction
+\warning This is the manual for the development version of PLUMED. It might
+contain buggy code. See this page: \ref CHANGES-UNRELEASED
+
PLUMED is a plugin that works with a large number of molecular dynamics codes. It can be used
to analyse features of the dynamics on-the-fly or to perform a wide variety of free energy methods.
The original PLUMED 1 was highly successful and had over 1000 users. PLUMED 2 \cite plumed2 constitues an
extensive rewrite of the original in a way that makes it more modular and thus easier to implement
new methods, more straightforward to add it to MD codes and hopefully simpler to use.
This is the user manual - if you want to modify PLUMED or to understand how it works internally, have a look at the
-<a href="../../developer-doc/html/index.html"> developer manual </a>. Alternatively, to look at a list of the new
-features available in PLUMED 2 and to work out how to install PLUMED 2 in your MD code check out:
+<a href="../../developer-doc/html/index.html"> developer manual </a>.
+
+To know the difference between PLUMED 1 and PLUMED 2, and to
+follow the development of PLUMED 2, you can checkout the detailed changelog:
+- Changes for \ref CHANGES-2-0
-- \subpage WhatsNew
-- \subpage Installation
+A short tutorial explaining how to move from PLUMED 1 to PLUMED 2 is also available (see \ref moving)
-See also \ref CHANGES-2-0
+To install PLUMED 2, see this page: \subpage Installation
\section qintro A quick introduction
@@ -70,7 +75,10 @@ PRINT ARG=d1 FILE=colvar STRIDE=10
(see \ref PRINT)
then PLUMED will print out the value of the distance between atoms 1 and 2 every 10 steps to the file colvar as you have told
-PLUMED to take the value calculated by the action d1 and to print it.
+PLUMED to take the value calculated by the action d1 and to print it. You can use any character string to label your actions
+as long as it does not begin with the symbol @. Strings beginning with @ are used by within PLUMED to reference special,
+code-generated groups of atoms and to give labels to any Actions for which the user does not provide a label in the input.
+
Notice that if a word followed by a column is added at the beginning of the line (e.g. pippo:), PLUMED automatically
removes it and adds an equivalent label (LABEL=pippo).
Thus, a completely equivalent result can be obtained with the following shortcut:
diff --git a/user-doc/Modules.txt b/user-doc/Modules.txt
index 0b6d9c5604a1e772babd27a07b29b4f82e2e4228..f4996b6cb2abaff1d5d21614bfa80172ccea5afd 100644
--- a/user-doc/Modules.txt
+++ b/user-doc/Modules.txt
@@ -1,47 +1,23 @@
/**
-@page mymodules Modules
+@page mymodules module
-PLUMED 2 is written and maintained by five core developers none of whom work full
-time on the maintanence and upkeep of the code. From our point of view it is thus
-desirable to keep the core of the code small. In addition, we are very keen that
-users who contribute functionality to PLUMED get the plaudits that they deserve.
-For these reasons many of PLUMED's more advanced functionalities are provided in
-modules that users can download. To download a module you simply change to the
-<c> plumed2/mymodules </c> directory and issue the following command:
+The functionality in PLUMED 2 is divided into a small number of modules. Some
+users may only wish to use a subset of the functionality available within the
+code while others may wish to use some of PLUMED's more complicated features.
+For this reason the plumed source code is divided into modules, which users can
+activate or deactivate to their hearts content.
-\verbatim
-./plumed-get-module.sh <name of module>
-\endverbatim
+- To activate a module add a file called modulename.on to the plumed2/src directory
+- To deactivate a module add a file called modulename.off to the plumed2/src directory
-The following optional modules can be added to PLUMED 2:
+Obviously, in the above instructions modulename should be replaced by the name of the
+module that you would like to activate or deactivate.
-@MODULES@
-
-\section addmodule Adding a module
-
-If you have a PLUMED module that you would like us to advertise on the website
-you should copy the directory structure from <c> plumed2/template-module </c>
-as well as all the files inside that directory and place your source and regtest
-files in appropriate directories. You are responsible for finding a suitable
-web repository to host the code that you have developed (we use http://www.assembla.com
-for PLUMED). You do not need to give us write access to your repository as ensuring that
-your code keeps working with any new release of PLUMED is YOUR responsibility.
-
-Once you are ready to release your code simply send any email to one of the developers
-with a txt file that contains the following information in the following format:
-
-\verbatim
-NAME: <the name of your module>
+Some modules are active by default in the version of PLUMED 2 that you download from
+the website while others are inactive. The following lists all of the modules that
+are available in plumed and tells you whether or not they are active by default.
-AUTHOR: <the list of people involved in the development of the module>
-
-REPOSITORY: <the command that retreives the code e.g. git clone git@git.assembla.com:plumed2.git>
-
-DESCRIPTION:
-
-<a short description of what it is your module calculates>
-<citations and equations can be included using the usual doxygen commands>
-\endverbatim
+@MODULES@
*/
diff --git a/user-doc/WhatsNew.txt b/user-doc/WhatsNew.txt
deleted file mode 100644
index 9836803f383e996313bacb48bd0389e5b9d8c3f4..0000000000000000000000000000000000000000
--- a/user-doc/WhatsNew.txt
+++ /dev/null
@@ -1,44 +0,0 @@
-/**
-\page WhatsNew What's new
-
-\section NewFeatures List of new features
-
-- Input file (plumed.dat) syntax is much more flexible and has more
- error checking. Units are treated
- consistently, so that the plumed.dat file can be ported from on
- MD code to another.
-- PLUMED is now compiled as a library, independently of the MD code.
- This simplifies the patching procedure. Moreover, on systems where
- this is possible, PLUMED library will be loaded runtime. This will
- allow updating PLUMED without recompiling or relinking the MD code.
-- Interfacing with MD codes is simpler. Hopefully, in the future, these
- interface will be maitained by the developers of the MD codes
- independently from PLUMED developers. This will allow more MD codes
- to be compatible with PLUMED.
-- It is now possible to develop and release collective variables,
- free energy methods and other addons independently from PLUMED
- developers. This will allow more collective variables and
- free energy methods to be available.
-- Correction to the virial is computed so that constant pressure simulations
- are possible.
-- Centers of mass can be used as if they were extra virtual atoms. Thus,
- they can be used in any CV (e.g. also in RMSD, coordination, etc.).
-- Different collective variables can be printed on different output files
- and with a different stride. Moreover, variables are not computed on the
- steps on which they are not necessary. This allows for more flexible
- analysis (e.g. rarely computed heavy variables combined with often computed
- light variables).
-- And many others...
-
-Caveats:
-- PLUMED 2 input file (plumed.dat) has a syntax which is not
- compatible with PLUMED 1.
- Transition should be easy, but cannot
- be done just using the new version with the old input file.
-- PLUMED 2 is written in C++, thus requires a C++ compiler
-- PLUMED 2 may not include all the features that were available
- in PLUMED 1.
-
-A tutorial explaining how to move from PLUMED 1 to PLUMED 2 is available (see \ref moving).
-
-*/
diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib
index 84be6870badde5df087a62aed50b15f9a1b78f0e..b2c70a405db01cdfc04556eb13ff39f8a57a04ff 100644
--- a/user-doc/bibliography.bib
+++ b/user-doc/bibliography.bib
@@ -20,8 +20,10 @@
author={Gareth A. Tribello and Massimiliano Bonomi and Davide Branduardi and Carlo Camilloni and Giovanni Bussi},
title={PLUMED 2: New feathers for an old bird},
journal={Comput.~Phys.~Commun.},
- note={DOI:10.1016/j.cpc.2013.09.018}
- year=2013
+ volume=185,
+ number=2,
+ pages={604--613},
+ year=2014
}
@@ -1964,3 +1966,28 @@ pages = {1838--1843},
pages={79--91},
year={2012}
}
+
+@article{Sahakyan:2011bn,
+author = {Sahakyan, Aleksandr B and Vranken, Wim F and Cavalli, Andrea and Vendruscolo, Michele},
+title = {{Structure-based prediction of methyl chemical shifts in proteins}},
+journal = {J. Biomol. NMR},
+year = {2011},
+volume = {50},
+number = {4},
+pages = {331--346},
+}
+
+@article{PRL230602,
+ title = {From Metadynamics to Dynamics},
+ author = {Tiwary, Pratyush and Parrinello, Michele},
+ journal = {Phys. Rev. Lett.},
+ volume = {111},
+ issue = {23},
+ pages = {230602},
+ numpages = {5},
+ year = {2013},
+ month = {Dec},
+ doi = {10.1103/PhysRevLett.111.230602},
+ url = {http://link.aps.org/doi/10.1103/PhysRevLett.111.230602},
+ publisher = {American Physical Society}
+}
diff --git a/user-doc/extract b/user-doc/extract
index 6443e5d4d2bece46f110c1f24342f08c5086079d..d361a36779f675d14d53204cdbd247ffd939b5d9 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -18,7 +18,13 @@ done
# Create the list of codes that plumed works with from the set of available patches
for file in ../patches/*.diff
do
- echo "- $file" | sed -e 's/.diff//' | sed -e 's/..\/patches\///' >> automatic/codes.list
+ myengine=`echo "$file" | sed -e 's/.diff//' | sed -e 's/..\/patches\///'`
+ mytag=`echo "$myengine" | sed -e 's/\./\_/g'`
+ echo "- \subpage $mytag" >> automatic/codes.list
+ echo "/**" >> automatic/$myengine.txt
+ echo "\page $mytag $myengine" >> automatic/$myengine.txt
+ plumed patch -e $myengine -i -q >> automatic/$myengine.txt
+ echo "*/" >> automatic/$myengine.txt
done
## Check for utilities that register actions with no documentation
@@ -105,53 +111,62 @@ done
# Find what modules the user has installed
# Find the list of modules
-if [ -d ../mymodules ] ; then
- sed -i '' -e 's/type="user" visible="no" url="mymodules.html"/type="user" visible="yes" url="mymodules.html"/' PlumedLayout.xml
- for file in `ls ../mymodules/available-modules/`
- do
- #Â Check if module has been installed
- if [ -d "../mymodules/$file" ] ; then
- # Generate documentation and accreditation on modules page
- echo "\section $file" >> automatic/mymodules.list
- echo >> automatic/mymodules.list
- echo "<table align=center frame=void width=95%% celpadding=5%%>" >> automatic/mymodules.list
- echo "<tr> <td width=70%%> </td> </tr> <td>" >> automatic/mymodules.list
- author=`grep AUTHOR: ../mymodules/available-modules/"$file" | sed -e 's/AUTHOR://'`
- echo "<b> author: $author </b>" >> automatic/mymodules.list
- echo "</td> </tr>" >> automatic/mymodules.list
- echo "<tr> <td colspan="2">" >> automatic/mymodules.list
- dline=`grep -n DESCRIPTION: ../mymodules/available-modules/"$file" | sed -n 's/^\([0-9]*\)[:].*/\1/p'` >> automatic/mymodules.list
- tail -n +$(($dline+1)) ../mymodules/available-modules/"$file" >> automatic/mymodules.list
- echo "</td> </tr> </table>" >> automatic/mymodules.list
- echo >> automatic/mymodules.list
- echo >> automatic/mymodules.list
-
- # Find src files in module and add a link to the module description
- for srcfile in `ls ../mymodules/"$file"/src/*cpp` ; do
- ndocs=`grep PLUMEDOC "$srcfile" | wc -l | awk '{print $1}'`
- for ((line=1;line<$ndocs;++line)) ; do
- docfile=`grep PLUMEDOC "$srcfile" | grep -v END | head -n $line | tail -n 1 | awk '{print $3}'`
- cat automatic/"$docfile".tmp |
- {
- while read -r LINE ; do
- if `echo $LINE | grep "\section $docfile" 1>/dev/null 2>&1`
- then
- echo $LINE
- echo "<table align=center frame=void width=95%% celpadding=5%%>"
- echo "<tr> <td width=70%%> </td> <td>"
- echo "<b> This is part of the \ref $file module </b>"
- echo "</td> </tr> </table>"
- else
- echo "$LINE"
- fi
- done
- } > automatic/"$docfile"1.tmp
- mv automatic/"$docfile"1.tmp automatic/"$docfile".tmp
- done
- done
- fi
- done
-fi
+# if [ -d ../mymodules ] ; then
+# sed -i '' -e 's/type="user" visible="no" url="mymodules.html"/type="user" visible="yes" url="mymodules.html"/' PlumedLayout.xml
+echo "<table align=center frame=void width=65%% cellpadding=5%%>" > automatic/modules.list
+echo "<tr> <td> <b> Module name </b> </td> <td> <b> Default behavior </b> </td> </tr>" >> automatic/modules.list
+for file in `ls ../src/*/module.type | sed -e 's/..\/src\///' | sed -e 's/\/module.type//'`
+do
+ dstr=`head ../src/$file/module.type`
+ if [ "$dstr" != "always" ] ; then
+ echo "<tr> <td> $file </td>" >> automatic/modules.list
+ if [ "$dstr" == "default-on" ] ; then
+ echo "<td> on </td> </tr>" >> automatic/modules.list
+ else
+ echo "<td> off </td> </tr>" >> automatic/modules.list
+ fi
+# # Generate documentation and accreditation on modules page
+# echo "\section $file" >> automatic/mymodules.list
+# echo >> automatic/mymodules.list
+# echo "<table align=center frame=void width=95%% celpadding=5%%>" >> automatic/mymodules.list
+# echo "<tr> <td width=70%%> </td> </tr> <td>" >> automatic/mymodules.list
+# author=`grep AUTHOR: ../mymodules/available-modules/"$file" | sed -e 's/AUTHOR://'`
+# echo "<b> author: $author </b>" >> automatic/mymodules.list
+# echo "</td> </tr>" >> automatic/mymodules.list
+# echo "<tr> <td colspan="2">" >> automatic/mymodules.list
+# dline=`grep -n DESCRIPTION: ../mymodules/available-modules/"$file" | sed -n 's/^\([0-9]*\)[:].*/\1/p'` >> automatic/mymodules.list
+# tail -n +$(($dline+1)) ../mymodules/available-modules/"$file" >> automatic/mymodules.list
+# echo "</td> </tr> </table>" >> automatic/mymodules.list
+# echo >> automatic/mymodules.list
+# echo >> automatic/mymodules.list
+
+ # Find src files in module and add a link to the module description
+ for srcfile in `ls ../src/"$file"/*cpp` ; do
+ ndocs=`grep PLUMEDOC "$srcfile" | grep -v END | wc -l | awk '{print $1}'`
+ for ((line=1;line<=$ndocs;++line)) ; do
+ docfile=`grep PLUMEDOC "$srcfile" | grep -v END | head -n $line | tail -n 1 | awk '{print $3}'`
+ cat automatic/"$docfile".tmp |
+ {
+ while read -r LINE ; do
+ if `echo $LINE | grep "section $docfile" 1>/dev/null 2>&1`
+ then
+ echo $LINE
+ echo "<table align=center frame=void width=95%% celpadding=5%%>"
+ echo "<tr> <td width=70%%> </td> <td>"
+ echo "<b> This is part of the $file \\ref mymodules </b>"
+ echo "</td> </tr> </table>"
+ else
+ echo "$LINE"
+ fi
+ done
+ } > automatic/"$docfile"1.tmp
+ mv automatic/"$docfile"1.tmp automatic/"$docfile".tmp
+ done
+ done
+ fi
+done
+echo "</table>" >> automatic/modules.list
+# fi
# Generate all the documentation from keywords
source ../sourceme.sh
@@ -237,7 +252,7 @@ cat $file.txt |
echo "</table>"
elif [ "$LINE" = "@MODULES@" ]
then
- cat automatic/mymodules.list
+ cat automatic/modules.list
elif [ "$LINE" = "@FUNCTION@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
diff --git a/user-doc/tutorials/moving.txt b/user-doc/tutorials/moving.txt
index bb80f85ce5d45910a76f647f9b60270ee23a769d..7331d00fb243f6bce02a2dd737868ee5e0260da7 100644
--- a/user-doc/tutorials/moving.txt
+++ b/user-doc/tutorials/moving.txt
@@ -93,7 +93,7 @@ equivalent. You should read the documentation for the Plumed 2 Action.
</TR>
<TR>
<TD> COMMITMENT </TD>
- <TD> <b> currently missing</b> </TD>
+ <TD> \ref COMMITTOR </TD>
</TR>
<TR>
<TD> PROJ_GRAD </TD>
@@ -145,7 +145,7 @@ equivalent. You should read the documentation for the Plumed 2 Action.
</TR>
<TR>
<TD> DIHCOR </TD>
- <TD> <b> currently missing </b>, can be emulated with multiple \ref TORSION combined with \ref MATHEVAL</TD>
+ <TD> \ref DIHCOR </TD>
</TR>
<TR>
<TD> ALPHABETA </TD>
@@ -197,7 +197,7 @@ equivalent. You should read the documentation for the Plumed 2 Action.
</TR>
<TR>
<TD> SPRINT </TD>
- <TD> <b> currently missing </b> </TD>
+ <TD> <b> \ref SPRINT </b> </TD>
</TR>
<TR>
<TD> RDF </TD>