diff --git a/patches/gromacs-4.6.0.config b/patches/gromacs-4.6.0.config
new file mode 100644
index 0000000000000000000000000000000000000000..a5d00fcea22295d52544fcd345e60947ff7553ef
--- /dev/null
+++ b/patches/gromacs-4.6.0.config
@@ -0,0 +1,6 @@
+
+
+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
+}
diff --git a/patches/gromacs-4.6.0.diff b/patches/gromacs-4.6.0.diff
new file mode 100644
index 0000000000000000000000000000000000000000..8ce2a443311966a44532a2f004bdfa567441dc46
--- /dev/null
+++ b/patches/gromacs-4.6.0.diff
@@ -0,0 +1,396 @@
+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(${CMAKE_SOURCE_DIR}/Plumed.cmake)
++
+ set(GMXPREPROCESS_SOURCES
+ add_par.c
+ calc_verletbuf.c
+ compute_io.c
+ convparm.c
+@@ -126,11 +128,11 @@
+ set_target_properties(${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 ${GMX_EXTRA_LIBRARIES} ${GMX_OPENMM_LIBRARIES})
++target_link_libraries(mdrun ${GMX_EXTRA_LIBRARIES} ${GMX_OPENMM_LIBRARIES} ${PLUMED_LOAD})
+ set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}" COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+ # this is to circumvent the following MSVC error:
+ # warning LNK4098: defaultlib 'LIBCMT' conflicts with use of other libs
+ # fatal error LNK1169: one or more multiply defined symbols found
+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"
+@@ -688,10 +694,50 @@
+ }
+ }
+ 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)
+@@ -998,10 +1044,17 @@
+ 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)
+ {
+@@ -1137,16 +1190,39 @@
+ /* 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 */
++ if(plumedswitch){
++ plumed_cmd(plumedmain,"setStep",&step);
++ 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);
++ }
++ /* 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);
++
++ /* PLUMED */
++ if(plumedswitch){
++ 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[] = {
+ #ifdef GMX_OPENMM
+ "This is an experimental release of GROMACS for accelerated",
+@@ -463,10 +469,11 @@
+ { efLOG, "-ra", "rotangles",ffOPTWR },
+ { efLOG, "-rs", "rotslabs", ffOPTWR },
+ { efLOG, "-rt", "rottorque",ffOPTWR },
+ { efMTX, "-mtx", "nm", ffOPTWR },
+ { efNDX, "-dn", "dipole", ffOPTWR },
++ { efDAT, "-plumed", "plumed", ffOPTRD }, /* PLUMED */
+ { efRND, "-multidir",NULL, ffOPTRDMULT},
+ { efDAT, "-membed", "membed", ffOPTRD },
+ { efTOP, "-mp", "membed", ffOPTRD },
+ { efNDX, "-mn", "membed", ffOPTRD }
+ };
+@@ -782,18 +789,50 @@
+
+ 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 };
+ const char *erename[ereNR] = { "temperature", "lambda", "end_single_marker", "temperature and lambda"};
+@@ -109,18 +115,20 @@
+
+ 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;
+@@ -251,10 +259,14 @@
+ 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++)
+ {
+ for(j=i+1; j<re->nrepl; j++)
+@@ -270,10 +282,12 @@
+ 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++)
+ {
+@@ -1008,19 +1022,59 @@
+ }
+ else
+ {
+ /* standard nearest neighbor replica exchange */
+ m = (step / re->nst) % 2;
++
++ /* PLUMED */
++ if(plumedswitch){
++ int partner=re->repl;
++ int test=0;
++ plumed_cmd(plumedmain,"getExchangesFlag",&test);
++ if(test>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 d = %10.3e",dplumed,delta);
++ }
++ /* END PLUMED */
+ if (delta <= 0) {
+ /* accepted */
+ prob[i] = 1;
+ bEx[i] = TRUE;
+ }
+@@ -1263,10 +1317,14 @@
+ * 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,
+EOF_EOF
diff --git a/patches/patch.sh b/patches/patch.sh
index 23872ca0938f4d19ff88d9a703f0e2b67d7ba716..31d685abc64c71c47b928b549592149f46fdb31c 100755
--- a/patches/patch.sh
+++ b/patches/patch.sh
@@ -210,6 +210,7 @@ case "$action" in
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 "$diff"
if type -t plumed_after_patch 1>/dev/null ; then
echo "Executing plumed_after_patch function"
@@ -273,7 +274,7 @@ EOF
echo "WARNING: I cannot find Plumed.h and Plumed.inc files. You have likely not patched yet."
else
echo "Removing Plumed.h and Plumed.inc"
- rm Plumed.h Plumed.inc
+ rm Plumed.h Plumed.inc Plumed.cmake
fi
PREPLUMED=$(find . -name "*.preplumed")
if ! test "$PREPLUMED" ; then
diff --git a/src/lib/Makefile b/src/lib/Makefile
index 9b2f6dd3226b4cc35560a97165153e04bb2389c0..d0529d448ce7ca896304702f69b841d325309d68 100644
--- a/src/lib/Makefile
+++ b/src/lib/Makefile
@@ -61,6 +61,7 @@ $(DIRS):
lib: $(PLUMED_KERNEL) $(PLUMED_SHARED_OBJ) $(OBJ_WRAPPER) \
$(PLUMED_MAIN_STATIC) $(PLUMED_MAIN_SHARED) $(PLUMED_MAIN_RUNTIME) \
Plumed.inc Plumed.inc.runtime Plumed.inc.shared Plumed.inc.static \
+ Plumed.cmake Plumed.cmake.runtime Plumed.cmake.shared Plumed.cmake.static \
plumed-patch
plumed-patch:
@@ -116,6 +117,38 @@ Plumed.inc.shared: Plumed.inc
@echo PLUMED_LOAD= '$$(PLUMED_SHARED_LOAD)' >> $@
@echo PLUMED_DEPENDENCIES= '$$(PLUMED_SHARED_DEPENDENCIES)' >> $@
+Plumed.cmake: $(OBJ_KERNEL) $(OBJ_WRAPPER) $(PLUMED_SHARED_OBJ) $(OBJ_DYNAMIC_WRAPPER)
+ @echo Building Plumed.cmake
+ @echo "set(PLUMED_INCLUDE "-I$(realpath ../../include)")" > $@
+ @echo "set(PLUMED_RUNTIME_LOAD " $(realpath $(OBJ_DYNAMIC_WRAPPER)) $(LIBS) $(LDFLAGS)")" >> $@
+ @echo "set(PLUMED_STATIC_LOAD " $(realpath $(OBJ_KERNEL)) $(realpath $(OBJ_WRAPPER)) $(LIBS) $(DYNAMIC_LIBS) $(LDFLAGS)")" >> $@
+ @echo "set(PLUMED_SHARED_LOAD " $(realpath $(PLUMED_SHARED_OBJ)) $(LIBS) $(LDFLAGS)")" >> $@
+ @echo "set(PLUMED_RUNTIME_DEPENDENCIES) " >> $@
+ @echo "set(PLUMED_STATIC_DEPENDENCIES " $(realpath $(OBJ_KERNEL)) $(realpath $(OBJ_WRAPPER))")" >> $@
+ @echo "set(PLUMED_SHARED_DEPENDENCIES " $(realpath $(PLUMED_SHARED_OBJ))")" >> $@
+
+Plumed.cmake.runtime: Plumed.cmake
+ @echo Building Plumed.cmake, runtime-linking version
+ @echo "# PLUMED: runtime installation" > $@
+ @cat $< >> $@
+ @echo "set("PLUMED_LOAD '$${PLUMED_RUNTIME_LOAD}'")" >> $@
+ @echo "set("PLUMED_DEPENDENCIES '$${PLUMED_RUNTIME_DEPENDENCIES}'")" >> $@
+
+Plumed.cmake.static: Plumed.cmake
+ @echo Building Plumed.cmake, static version
+ @echo "# PLUMED: static installation" > $@
+ @cat $< >> $@
+ @echo "set("PLUMED_LOAD '$${PLUMED_STATIC_LOAD}'")" >> $@
+ @echo "set("PLUMED_DEPENDENCIES '$${PLUMED_STATIC_DEPENDENCIES}'")" >> $@
+
+Plumed.cmake.shared: Plumed.cmake
+ @echo Building Plumed.cmake, shared version
+ @echo "# PLUMED: shared installation" > $@
+ @cat $< >> $@
+ @echo "set("PLUMED_LOAD '$${PLUMED_SHARED_LOAD}'")" >> $@
+ @echo "set("PLUMED_DEPENDENCIES '$${PLUMED_SHARED_DEPENDENCIES}'")" >> $@
+
+
# Individual dependencies
-include $(ALL_DEP)