From dc74333c2ae68ab777f21c509d7f272b5835db55 Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Sat, 13 Apr 2019 21:44:26 +0200
Subject: [PATCH] gmx2019.1 patch cleaned the new organisatoion of the gromacs
source code allows simplifying our patch. Multi-sim is now tested at least
for multiple walkers metad
---
.../src/gromacs/mdlib/force.cpp | 5 +-
.../src/gromacs/mdrun/legacymdrunoptions.cpp | 1 -
.../src/gromacs/mdrun/legacymdrunoptions.h | 1 -
.../src/gromacs/mdrun/minimize.cpp | 49 +++++++++----------
4 files changed, 26 insertions(+), 30 deletions(-)
diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp
index babdf19af..781a63d71 100644
--- a/patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp
+++ b/patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp
@@ -81,7 +81,6 @@
#include "../../../Plumed.h"
int plumedswitch=0;
plumed plumedmain;
-void(*plumedcmd)(plumed,const char*,const void*)=NULL;
/* END PLUMED */
void ns(FILE *fp,
@@ -603,8 +602,8 @@ void do_force_lowlevel(t_forcerec *fr,
/* PLUMED */
if(plumedswitch){
int plumedNeedsEnergy;
- (*plumedcmd)(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
- if(!plumedNeedsEnergy) (*plumedcmd)(plumedmain,"performCalc",NULL);
+ plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+ if(!plumedNeedsEnergy) plumed_cmd(plumedmain,"performCalc",NULL);
}
/* END PLUMED */
}
diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
index 614fd9d6c..370262486 100644
--- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
+++ b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
@@ -211,7 +211,6 @@ int LegacyMdrunOptions::updateFromCommandLine(int argc, char **argv, ArrayRef<co
plumedswitch=0;
if (opt2bSet("-plumed", static_cast<int>(filenames.size()), filenames.data())) plumedswitch=1;
if(plumedswitch){
- plumedcmd=plumed_cmd;
int real_precision=sizeof(real);
real energyUnits=1.0;
real lengthUnits=1.0;
diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h
index 5205b7729..01454f926 100644
--- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h
+++ b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h
@@ -62,7 +62,6 @@
#include "../../../Plumed.h"
extern int plumedswitch;
extern plumed plumedmain;
-extern void(*plumedcmd)(plumed,const char*,const void*);
/* END PLUMED */
/* PLUMED HREX */
diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/minimize.cpp b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/minimize.cpp
index 62a5a07a0..e677e23f3 100644
--- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/minimize.cpp
+++ b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/minimize.cpp
@@ -106,7 +106,6 @@
#include "../../../Plumed.h"
extern int plumedswitch;
extern plumed plumedmain;
-extern void(*plumedcmd)(plumed,const char*,const void*);
/* END PLUMED */
//! Utility structure for manipulating states during EM
@@ -504,36 +503,36 @@ static void init_em(FILE *fplog,
/* PLUMED */
if(plumedswitch){
if(ms && ms->nsim>1) {
- if(MASTER(cr)) (*plumedcmd) (plumedmain,"GREX setMPIIntercomm",&ms->mpi_comm_masters);
+ if(MASTER(cr)) plumed_cmd(plumedmain,"GREX setMPIIntercomm",&ms->mpi_comm_masters);
if(PAR(cr)){
if(DOMAINDECOMP(cr)) {
- (*plumedcmd) (plumedmain,"GREX setMPIIntracomm",&cr->dd->mpi_comm_all);
+ plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->dd->mpi_comm_all);
}else{
- (*plumedcmd) (plumedmain,"GREX setMPIIntracomm",&cr->mpi_comm_mysim);
+ plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->mpi_comm_mysim);
}
}
- (*plumedcmd) (plumedmain,"GREX init",NULL);
+ plumed_cmd(plumedmain,"GREX init",NULL);
}
if(PAR(cr)){
if(DOMAINDECOMP(cr)) {
- (*plumedcmd) (plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
+ plumed_cmd(plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
}else{
- (*plumedcmd) (plumedmain,"setMPIComm",&cr->mpi_comm_mysim);
+ plumed_cmd(plumedmain,"setMPIComm",&cr->mpi_comm_mysim);
}
}
- (*plumedcmd) (plumedmain,"setNatoms",&top_global->natoms);
- (*plumedcmd) (plumedmain,"setMDEngine","gromacs");
- (*plumedcmd) (plumedmain,"setLog",fplog);
+ 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;
- (*plumedcmd) (plumedmain,"setTimestep",&real_delta_t);
- (*plumedcmd) (plumedmain,"init",NULL);
+ plumed_cmd(plumedmain,"setTimestep",&real_delta_t);
+ plumed_cmd(plumedmain,"init",NULL);
if(PAR(cr)){
if(DOMAINDECOMP(cr)) {
int nat_home = dd_numHomeAtoms(*cr->dd);
- (*plumedcmd) (plumedmain,"setAtomsNlocal",&nat_home);
- (*plumedcmd) (plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data());
+ plumed_cmd(plumedmain,"setAtomsNlocal",&nat_home);
+ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data());
}
}
@@ -916,16 +915,16 @@ EnergyEvaluator::run(em_state_t *ems, rvec mu_tot,
int plumedNeedsEnergy=0;
matrix plumed_vir;
if(plumedswitch){
- long int lstep=count; (*plumedcmd)(plumedmain,"setStepLong",&lstep);
- (*plumedcmd) (plumedmain,"setPositions",&ems->s.x[0][0]);
- (*plumedcmd) (plumedmain,"setMasses",&mdAtoms->mdatoms()->massT[0]);
- (*plumedcmd) (plumedmain,"setCharges",&mdAtoms->mdatoms()->chargeA[0]);
- (*plumedcmd) (plumedmain,"setBox",&ems->s.box[0][0]);
- (*plumedcmd) (plumedmain,"prepareCalc",NULL);
- (*plumedcmd) (plumedmain,"setForces",&ems->f[0][0]);
- (*plumedcmd) (plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+ long int lstep=count; plumed_cmd(plumedmain,"setStepLong",&lstep);
+ plumed_cmd(plumedmain,"setPositions",&ems->s.x[0][0]);
+ plumed_cmd(plumedmain,"setMasses",&mdAtoms->mdatoms()->massT[0]);
+ plumed_cmd(plumedmain,"setCharges",&mdAtoms->mdatoms()->chargeA[0]);
+ plumed_cmd(plumedmain,"setBox",&ems->s.box[0][0]);
+ plumed_cmd(plumedmain,"prepareCalc",NULL);
+ plumed_cmd(plumedmain,"setForces",&ems->f[0][0]);
+ plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
clear_mat(plumed_vir);
- (*plumedcmd) (plumedmain,"setVirial",&plumed_vir[0][0]);
+ plumed_cmd(plumedmain,"setVirial",&plumed_vir[0][0]);
}
/* END PLUMED */
@@ -947,8 +946,8 @@ EnergyEvaluator::run(em_state_t *ems, rvec mu_tot,
if(plumedswitch){
if(plumedNeedsEnergy) {
msmul(force_vir,2.0,plumed_vir);
- (*plumedcmd) (plumedmain,"setEnergy",&enerd->term[F_EPOT]);
- (*plumedcmd) (plumedmain,"performCalc",NULL);
+ 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);
--
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