From 2e3d3c5231e8681dba7c7efec8b8f5680383c3c1 Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Wed, 15 Nov 2017 22:16:32 +0100
Subject: [PATCH] hrex: fix for hrex with pressure and some cleaning
---
.../src/programs/mdrun/md.cpp | 85 ++++++++++---------
1 file changed, 45 insertions(+), 40 deletions(-)
diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp b/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp
index 8e808e163..47ad1849e 100644
--- a/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp
+++ b/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp
@@ -1091,24 +1091,26 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
}
clear_mat(force_vir);
-/* PLUMED HREX */
- gmx_bool bHREX;
- bHREX= repl_ex_nst > 0 && (step>0) && !bLastStep && do_per_step(step,repl_ex_nst) && plumed_hrex;
+ /* PLUMED HREX */
+ gmx_bool bHREX = bDoReplEx && plumed_hrex;
- if(plumedswitch) if(bHREX){
+ if (plumedswitch && bHREX) {
gmx_enerdata_t *hrex_enerd;
- snew(hrex_enerd,1);
+ snew(hrex_enerd, 1);
init_enerdata(top_global->groups.grps[egcENER].nr,ir->fepvals->n_lambda,hrex_enerd);
- int repl=-1;
- int nrepl=-1;
- if(MASTER(cr)){
- repl=replica_exchange_get_repl(repl_ex);
- nrepl=replica_exchange_get_nrepl(repl_ex);
+ int repl = -1;
+ int nrepl = -1;
+ if (MASTER(cr)){
+ repl = replica_exchange_get_repl(repl_ex);
+ nrepl = replica_exchange_get_nrepl(repl_ex);
}
- if (DOMAINDECOMP(cr))
+
+ if (DOMAINDECOMP(cr)) {
dd_collect_state(cr->dd,state,state_global);
- else
+ } else {
copy_state_nonatomdata(state, state_global);
+ }
+
if(MASTER(cr)){
if(repl%2==step/repl_ex_nst%2){
if(repl-1>=0) exchange_state(cr->ms,repl-1,state_global);
@@ -1116,36 +1118,40 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
if(repl+1<nrepl) exchange_state(cr->ms,repl+1,state_global);
}
}
- if (!DOMAINDECOMP(cr))
+ if (!DOMAINDECOMP(cr)) {
copy_state_nonatomdata(state_global, state);
+ }
if(PAR(cr)){
if (DOMAINDECOMP(cr)) {
dd_partition_system(fplog,step,cr,TRUE,1,
- state_global,top_global,ir,
- state,&f,mdatoms,top,fr,vsite,constr,
- nrnb,wcycle,FALSE);
+ state_global,top_global,ir,
+ state,&f,mdatoms,top,fr,vsite,constr,
+ nrnb,wcycle,FALSE);
}
}
do_force(fplog, cr, ir, step, nrnb, wcycle, top, groups,
- state->box, state->x, &state->hist,
- f, force_vir, mdatoms, hrex_enerd, fcd,
- state->lambda, graph,
- fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
- GMX_FORCE_STATECHANGED |
- ((inputrecDynamicBox(ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
- GMX_FORCE_ALLFORCES |
- GMX_FORCE_VIRIAL |
- GMX_FORCE_ENERGY |
- GMX_FORCE_DHDL |
- GMX_FORCE_NS);
+ state->box, state->x, &state->hist,
+ f, force_vir, mdatoms, hrex_enerd, fcd,
+ state->lambda, graph,
+ fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
+ GMX_FORCE_STATECHANGED |
+ GMX_FORCE_DYNAMICBOX |
+ GMX_FORCE_ALLFORCES |
+ GMX_FORCE_VIRIAL |
+ GMX_FORCE_ENERGY |
+ GMX_FORCE_DHDL |
+ GMX_FORCE_NS);
+
plumed_cmd(plumedmain,"GREX cacheLocalUSwap",&hrex_enerd->term[F_EPOT]);
sfree(hrex_enerd);
-/* exchange back */
- if (DOMAINDECOMP(cr))
+ /* exchange back */
+ if (DOMAINDECOMP(cr)) {
dd_collect_state(cr->dd,state,state_global);
- else
+ } else {
copy_state_nonatomdata(state, state_global);
+ }
+
if(MASTER(cr)){
if(repl%2==step/repl_ex_nst%2){
if(repl-1>=0) exchange_state(cr->ms,repl-1,state_global);
@@ -1153,23 +1159,22 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
if(repl+1<nrepl) exchange_state(cr->ms,repl+1,state_global);
}
}
- if (!DOMAINDECOMP(cr))
+
+ if (!DOMAINDECOMP(cr)) {
copy_state_nonatomdata(state_global, state);
+ }
if(PAR(cr)){
if (DOMAINDECOMP(cr)) {
dd_partition_system(fplog,step,cr,TRUE,1,
- state_global,top_global,ir,
- state,&f,mdatoms,top,fr,vsite,constr,
- nrnb,wcycle,FALSE);
- if(plumedswitch){
- plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
- plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
- }
+ state_global,top_global,ir,
+ state,&f,mdatoms,top,fr,vsite,constr,
+ nrnb,wcycle,FALSE);
+ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
+ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
}
}
-
}
-/* END PLUMED HREX */
+ /* END PLUMED HREX */
/* We write a checkpoint at this MD step when:
* either at an NS step when we signalled through gs,
--
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