From 8af4258a4da8d7c0946d13886ce408257c40d29b Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Fri, 24 Apr 2015 15:20:57 +0200
Subject: [PATCH] gromacs 4.5
- updated patch to include api version
- updated patch to inclide virial fix
- updated patch to gromacs 4.5.7
---
...macs-4.5.5.config => gromacs-4.5.7.config} | 0
...{gromacs-4.5.5.diff => gromacs-4.5.7.diff} | 172 ++++++++++--------
2 files changed, 101 insertions(+), 71 deletions(-)
rename patches/{gromacs-4.5.5.config => gromacs-4.5.7.config} (100%)
rename patches/{gromacs-4.5.5.diff => gromacs-4.5.7.diff} (70%)
diff --git a/patches/gromacs-4.5.5.config b/patches/gromacs-4.5.7.config
similarity index 100%
rename from patches/gromacs-4.5.5.config
rename to patches/gromacs-4.5.7.config
diff --git a/patches/gromacs-4.5.5.diff b/patches/gromacs-4.5.7.diff
similarity index 70%
rename from patches/gromacs-4.5.5.diff
rename to patches/gromacs-4.5.7.diff
index d4d422de4..8eeb506ac 100644
--- a/patches/gromacs-4.5.5.diff
+++ b/patches/gromacs-4.5.7.diff
@@ -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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