From bcf3f9d04aba82e5892fd6db9c7cb3ec5e45cdae Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Tue, 28 Apr 2015 10:52:26 +0100
Subject: [PATCH] patches: gmx457 - restart
---
patches/gromacs-4.5.7.diff | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/patches/gromacs-4.5.7.diff b/patches/gromacs-4.5.7.diff
index 8eeb506ac..5fd6d4665 100644
--- a/patches/gromacs-4.5.7.diff
+++ b/patches/gromacs-4.5.7.diff
@@ -51,7 +51,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF
{
if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
{
-@@ -588,10 +601,57 @@
+@@ -588,10 +601,60 @@
}
}
fprintf(fplog,"\n");
@@ -65,7 +65,10 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF
+ /* 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(pversion>2){
++ int res=1;
++ if( (Flags & MD_STARTFROMCPT) ) plumed_cmd(plumedmain,"setRestart",&res);
++ }
+ if(cr->ms && cr->ms->nsim>1) {
+ if(MASTER(cr)) plumed_cmd(plumedmain,"GREX setMPIIntercomm",&cr->ms->mpi_comm_masters);
+ if(PAR(cr)){
@@ -109,7 +112,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF
print_date_and_time(fplog,cr->nodeid,"Started mdrun",runtime);
wallcycle_start(wcycle,ewcRUN);
if (fplog)
-@@ -898,10 +958,17 @@
+@@ -898,10 +961,17 @@
state,&f,mdatoms,top,fr,
vsite,shellfc,constr,
nrnb,wcycle,do_verbose);
@@ -127,7 +130,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF
if (MASTER(cr) && do_log && !bFFscan)
{
-@@ -1038,16 +1105,50 @@
+@@ -1038,16 +1108,50 @@
* in do_force.
* This is parallellized as well, and does communication too.
* Check comments in sim_util.c
--
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