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Commit 7490aa41 authored by Carlo Camilloni's avatar Carlo Camilloni
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Merge branch 'v2.1'

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CHANGES/v2.1.txt
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......@@ -182,10 +182,11 @@ See <a href="http://github.com/plumed/plumed2/commits/v2.1">branch v2.1 on git r
For users:
- Updated gromacs patch 5.0 to 5.0.4
- Updated gromacs patch 4.5.5 to 4.5.7
- Fixed bug in \ref ENSEMBLE derivatives when more than 1 argument was provided
- Fixed bug in \ref GHOST : virial is now computed correctly.
- Fixed a serious bug in virial communicated from plumed to gromacs, for both gromacs versions 4.6 and 5.0.
Patch for gromacs 4.5 is not fixed. See notes <a href="http://github.com/plumed/plumed2/issues/132"> here </a>
See notes <a href="http://github.com/plumed/plumed2/issues/132"> here </a>
This fix requires gromacs to be repatched and could be very important if you run biased simulations in the NPT ensemble.
- Fixed a bug in the virial computed with \ref FIT_TO_TEMPLATE when the reference pdb had center non located at the origin.
- Updated internal molfile plugins to VMD 1.9.2.
......
patches/gromacs-4.5.5.config → patches/gromacs-4.5.7.config
+ 0
− 0
View file @ 7490aa41
File moved
patches/gromacs-4.5.5.diff → patches/gromacs-4.5.7.diff
+ 101
− 71
View file @ 7490aa41
......@@ -18,7 +18,24 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF
#endif
#ifdef GMX_THREADS
#include "tmpi.h"
@@ -427,13 +433,14 @@
@@ -193,10 +199,16 @@
#ifdef GMX_FAHCORE
/* Temporary addition for FAHCORE checkpointing */
int chkpt_ret;
#endif
+ /* PLUMED */
+ int plumedNeedsEnergy=0;
+ int plumedWantsToStop=0;
+ matrix plumed_vir;
+ /* END PLUMED */
+
/* Check for special mdrun options */
bRerunMD = (Flags & MD_RERUN);
bIonize = (Flags & MD_IONIZE);
bFFscan = (Flags & MD_FFSCAN);
bAppend = (Flags & MD_APPENDFILES);
@@ -440,13 +452,14 @@
check_nst_param(fplog,cr,"nstcalcenergy",ir->nstcalcenergy,
"repl_ex_nst",&repl_ex_nst);
/* This check needs to happen before inter-simulation
......@@ -34,116 +51,129 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF
{
if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
{
@@ -574,10 +581,55 @@
@@ -588,10 +601,57 @@
}
}
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);
+ /* PLUMED */
+ if(plumedswitch){
+ /* detect plumed API version */
+ int pversion=0;
+ plumed_cmd(plumedmain,"getApiVersion",&pversion);
+ /* setting kbT is only implemented with api>1) */
+ real kbT=ir->opts.ref_t[0]*BOLTZ;
+ if(pversion>1) plumed_cmd(plumedmain,"setKbT",&kbT);
+
+ 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,"GREX setMPIIntracomm",&cr->dd->mpi_comm_all);
+ plumed_cmd(plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
+ }else{
+ plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->mpi_comm_mysim);
+ plumed_cmd(plumedmain,"setMPIComm",&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);
+
+ 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);
+ 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 */
+
+ /* 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)
@@ -884,10 +936,17 @@
@@ -898,10 +958,17 @@
state,&f,mdatoms,top,fr,
vsite,shellfc,constr,
nrnb,wcycle,do_verbose);
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 */
+
+ /* 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)
{
@@ -1010,16 +1069,40 @@
@@ -1038,16 +1105,50 @@
* in do_force.
* This is parallellized as well, and does communication too.
* Check comments in sim_util.c
*/
+
+ /* PLUMED */
+ 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);
+ }
+ /* END PLUMED */
+
+ /* 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,"setStopFlag",&plumedWantsToStop);
+ plumed_cmd(plumedmain,"setForces",&f[mdatoms->start][0]);
+ plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+ clear_mat(plumed_vir);
+ plumed_cmd(plumedmain,"setVirial",&plumed_vir[0][0]);
+ }
+ /* 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 */
+
- (bNS ? GMX_FORCE_NS : 0) | force_flags);
+ (plumedNeedsEnergy? GMX_FORCE_ENERGY : 0) |(bNS ? GMX_FORCE_NS : 0) | force_flags);
+ /* PLUMED */
+ if(plumedswitch){
+ if(plumedNeedsEnergy){
+ msmul(force_vir,2.0,plumed_vir);
+ plumed_cmd(plumedmain,"setEnergy",&enerd->term[F_EPOT]);
+ plumed_cmd(plumedmain,"performCalc",NULL);
+ msmul(plumed_vir,0.5,force_vir);
+ } else {
+ msmul(plumed_vir,0.5,plumed_vir);
+ plumed_cmd(plumedmain,"performCalc",NULL);
+ m_add(force_vir,plumed_vir,force_vir);
+ }
+ 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);
......@@ -182,7 +212,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/mdrun.c" << \EOF_EOF
#define NFILE asize(fnm)
/* Command line options ! */
@@ -662,16 +669,52 @@
@@ -663,16 +670,52 @@
ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
......
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