From 9191f051096d02a6dcac8fceba17dcace789792a Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Tue, 7 Jul 2015 12:24:23 +0200
Subject: [PATCH] gromacs 5.1 patch fix
---
.../src/gromacs/mdlib/minimize.cpp | 2 +-
.../gromacs-5.1.0.diff/src/programs/mdrun/md.cpp | 14 +++++++-------
.../src/programs/mdrun/mdrun.cpp | 1 -
3 files changed, 8 insertions(+), 9 deletions(-)
diff --git a/patches/gromacs-5.1.0.diff/src/gromacs/mdlib/minimize.cpp b/patches/gromacs-5.1.0.diff/src/gromacs/mdlib/minimize.cpp
index 8f754b36c..9a90c5dba 100644
--- a/patches/gromacs-5.1.0.diff/src/gromacs/mdlib/minimize.cpp
+++ b/patches/gromacs-5.1.0.diff/src/gromacs/mdlib/minimize.cpp
@@ -791,7 +791,7 @@ static void evaluate_energy(FILE *fplog, t_commrec *cr,
int plumedNeedsEnergy=0;
matrix plumed_vir;
if(plumedswitch){
- long int lstep=count; (*plumedcmd)(plumedmain,"setStepLong",&count);
+ long int lstep=count; (*plumedcmd)(plumedmain,"setStepLong",&lstep);
(*plumedcmd) (plumedmain,"setPositions",&ems->s.x[0][0]);
(*plumedcmd) (plumedmain,"setMasses",&mdatoms->massT[0]);
(*plumedcmd) (plumedmain,"setCharges",&mdatoms->chargeA[0]);
diff --git a/patches/gromacs-5.1.0.diff/src/programs/mdrun/md.cpp b/patches/gromacs-5.1.0.diff/src/programs/mdrun/md.cpp
index dcef103cd..a914b2d7f 100644
--- a/patches/gromacs-5.1.0.diff/src/programs/mdrun/md.cpp
+++ b/patches/gromacs-5.1.0.diff/src/programs/mdrun/md.cpp
@@ -1000,13 +1000,6 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
}
if (DOMAINDECOMP(cr))
-
- /* PLUMED */
- if(plumedswitch){
- plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
- plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
- }
- /* END PLUMED */
{
/* Repartition the domain decomposition */
dd_partition_system(fplog, step, cr,
@@ -1016,6 +1009,13 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
vsite, shellfc, constr,
nrnb, wcycle,
do_verbose && !bPMETunePrinting);
+
+ /* PLUMED */
+ if(plumedswitch){
+ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
+ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
+ }
+ /* END PLUMED */
}
}
diff --git a/patches/gromacs-5.1.0.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-5.1.0.diff/src/programs/mdrun/mdrun.cpp
index ac0ec96e0..626a3c002 100644
--- a/patches/gromacs-5.1.0.diff/src/programs/mdrun/mdrun.cpp
+++ b/patches/gromacs-5.1.0.diff/src/programs/mdrun/mdrun.cpp
@@ -547,7 +547,6 @@ int gmx_mdrun(int argc, char *argv[])
if (opt2bSet("-plumed",NFILE,fnm)) plumedswitch=1;
if(plumedswitch){
plumedcmd=plumed_cmd;
- int plumed_is_there=0;
int real_precision=sizeof(real);
real energyUnits=1.0;
real lengthUnits=1.0;
--
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