From d9c95dcc4cbeb7c31b8b5d5db797ab96f65cb697 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Thu, 14 Dec 2017 17:32:35 +0100
Subject: [PATCH] Backported gmx-2016.4 patch from plumed 2.4
---
.../src/programs/mdrun/md.cpp | 97 ++++++++++++++++++-
.../src/programs/mdrun/mdrun.cpp | 15 +++
.../src/programs/mdrun/repl_ex.cpp | 30 +++++-
.../src/programs/mdrun/repl_ex.h | 87 +++++++++++++++++
.../src/programs/mdrun/repl_ex.h.preplumed | 79 +++++++++++++++
5 files changed, 302 insertions(+), 6 deletions(-)
create mode 100644 patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h
create mode 100644 patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h.preplumed
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 f3b524385..b6e0fd4d4 100644
--- a/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp
+++ b/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp
@@ -127,6 +127,10 @@ extern int plumedswitch;
extern plumed plumedmain;
/* END PLUMED */
+/* PLUMED HREX */
+extern int plumed_hrex;
+/* END PLUMED HREX */
+
#ifdef GMX_FAHCORE
#include "corewrap.h"
#endif
@@ -727,8 +731,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
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;
+ real real_delta_t=ir->delta_t;
plumed_cmd(plumedmain,"setTimestep",&real_delta_t);
plumed_cmd(plumedmain,"init",NULL);
@@ -1087,6 +1090,91 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
}
clear_mat(force_vir);
+ /* PLUMED HREX */
+ gmx_bool bHREX = bDoReplEx && plumed_hrex;
+
+ if (plumedswitch && bHREX) {
+ gmx_enerdata_t *hrex_enerd;
+ 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);
+ }
+
+ if (DOMAINDECOMP(cr)) {
+ dd_collect_state(cr->dd,state,state_global);
+ } 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);
+ }else{
+ if(repl+1<nrepl) exchange_state(cr->ms,repl+1,state_global);
+ }
+ }
+ 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);
+ }
+ }
+ 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 |
+ 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)) {
+ dd_collect_state(cr->dd,state,state_global);
+ } 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);
+ }else{
+ if(repl+1<nrepl) exchange_state(cr->ms,repl+1,state_global);
+ }
+ }
+
+ 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);
+ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
+ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
+ }
+ }
+ }
+ /* END PLUMED HREX */
+
/* We write a checkpoint at this MD step when:
* either at an NS step when we signalled through gs,
* or at the last step (but not when we do not want confout),
@@ -1179,6 +1267,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
if(pversion>3) plumed_cmd(plumedmain,"doCheckPoint",&checkp);
plumed_cmd(plumedmain,"setForces",&f[0][0]);
plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+ if(plumedNeedsEnergy) force_flags |= GMX_FORCE_ENERGY | GMX_FORCE_VIRIAL;
clear_mat(plumed_vir);
plumed_cmd(plumedmain,"setVirial",&plumed_vir[0][0]);
}
@@ -1200,9 +1289,9 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
msmul(plumed_vir,0.5,plumed_vir);
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(bDoReplEx) plumed_cmd(plumedmain,"GREX savePositions",NULL);
if(plumedWantsToStop) ir->nsteps=step_rel+1;
+ if(bHREX) plumed_cmd(plumedmain,"GREX cacheLocalUNow",&enerd->term[F_EPOT]);
}
/* END PLUMED */
}
diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp
index cf0f72cf8..2b131b65d 100644
--- a/patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp
+++ b/patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp
@@ -78,6 +78,10 @@ extern plumed plumedmain;
extern void(*plumedcmd)(plumed,const char*,const void*);
/* END PLUMED */
+/* PLUMED HREX */
+int plumed_hrex;
+/* END PLUMED HREX */
+
/*! \brief Return whether either of the command-line parameters that
* will trigger a multi-simulation is set */
static bool is_multisim_option_set(int argc, const char *const argv[])
@@ -403,6 +407,8 @@ int gmx_mdrun(int argc, char *argv[])
"Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
+ { "-hrex", FALSE, etBOOL, {&plumed_hrex},
+ "Enable hamiltonian replica exchange" },
{ "-imdport", FALSE, etINT, {&imdport},
"HIDDENIMD listening port" },
{ "-imdwait", FALSE, etBOOL, {&bIMDwait},
@@ -571,6 +577,15 @@ int gmx_mdrun(int argc, char *argv[])
plumed_cmd(plumedmain,"setPlumedDat",ftp2fn(efDAT,NFILE,fnm));
plumedswitch=1;
}
+ /* PLUMED HREX*/
+ if(getenv("PLUMED_HREX")) plumed_hrex=1;
+ if(plumed_hrex){
+ if(!plumedswitch) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) requires -plumed");
+ if(repl_ex_nst==0) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) replica exchange");
+ if(repl_ex_nex!=0) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) not compatible with -nex");
+ }
+ /* END PLUMED HREX */
+
/* END PLUMED */
rc = gmx::mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose,
diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp
index 70d9f30b8..a7165fcac 100644
--- a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp
+++ b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp
@@ -67,6 +67,10 @@ extern int plumedswitch;
extern plumed plumedmain;
/* END PLUMED */
+/* PLUMED HREX */
+extern int plumed_hrex;
+/* END PLUMED HREX */
+
#define PROBABILITYCUTOFF 100
/* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
@@ -543,7 +547,9 @@ static void exchange_rvecs(const gmx_multisim_t gmx_unused *ms, int gmx_unused b
}
}
-static void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
+/* PLUMED HREX */
+void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
+/* END PLUMED HREX */
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
@@ -623,7 +629,9 @@ static void copy_ints(const int *s, int *d, int n)
#define scopy_reals(v, n) copy_reals(state->v, state_local->v, n);
#define scopy_ints(v, n) copy_ints(state->v, state_local->v, n);
-static void copy_state_nonatomdata(t_state *state, t_state *state_local)
+/* PLUMED HREX */
+void copy_state_nonatomdata(t_state *state, t_state *state_local)
+/* END PLUMED HREX */
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
@@ -866,6 +874,11 @@ static real calc_delta(FILE *fplog, gmx_bool bPrint, struct gmx_repl_ex *re, int
{
fprintf(fplog, "Repl %d <-> %d dE_term = %10.3e (kT)\n", a, b, delta);
}
+/* PLUMED HREX */
+/* this is necessary because with plumed HREX the energy contribution is
+ already taken into account */
+ if(plumed_hrex) delta=0.0;
+/* END PLUMED HREX */
if (re->bNPT)
{
/* revist the calculation for 5.0. Might be some improvements. */
@@ -980,6 +993,7 @@ test_for_replica_exchange(FILE *fplog,
/* PLUMED */
int plumed_test_exchange_pattern=0;
+ if(plumed_test_exchange_pattern && plumed_hrex) gmx_fatal(FARGS,"hrex not compatible with ad hoc exchange patterns");
/* END PLUMED */
if (bMultiEx)
@@ -1488,3 +1502,15 @@ void print_replica_exchange_statistics(FILE *fplog, struct gmx_repl_ex *re)
/* print the transition matrix */
print_transition_matrix(fplog, re->nrepl, re->nmoves, re->nattempt);
}
+
+/* PLUMED HREX */
+int replica_exchange_get_repl(const gmx_repl_ex_t re){
+ return re->repl;
+};
+
+int replica_exchange_get_nrepl(const gmx_repl_ex_t re){
+ return re->nrepl;
+};
+/* END PLUMED HREX */
+
+
diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h
new file mode 100644
index 000000000..32499012a
--- /dev/null
+++ b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h
@@ -0,0 +1,87 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef _repl_ex_h
+#define _repl_ex_h
+
+#include <cstdio>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_enerdata_t;
+struct gmx_multisim_t;
+struct t_commrec;
+struct t_inputrec;
+struct t_state;
+
+/* Abstract type for replica exchange */
+typedef struct gmx_repl_ex *gmx_repl_ex_t;
+
+gmx_repl_ex_t init_replica_exchange(FILE *fplog,
+ const gmx_multisim_t *ms,
+ const t_state *state,
+ const t_inputrec *ir,
+ int nst, int nmultiex, int init_seed);
+/* Should only be called on the master nodes */
+
+gmx_bool replica_exchange(FILE *fplog,
+ const t_commrec *cr,
+ gmx_repl_ex_t re,
+ t_state *state, gmx_enerdata_t *enerd,
+ t_state *state_local,
+ gmx_int64_t step, real time);
+/* Attempts replica exchange, should be called on all nodes.
+ * Returns TRUE if this state has been exchanged.
+ * When running each replica in parallel,
+ * this routine collects the state on the master node before exchange.
+ * With domain decomposition, the global state after exchange is stored
+ * in state and still needs to be redistributed over the nodes.
+ */
+
+void print_replica_exchange_statistics(FILE *fplog, gmx_repl_ex_t re);
+/* Should only be called on the master nodes */
+
+/* PLUMED HREX */
+extern int replica_exchange_get_repl(const gmx_repl_ex_t re);
+extern int replica_exchange_get_nrepl(const gmx_repl_ex_t re);
+extern void pd_collect_state(const t_commrec *cr, t_state *state);
+extern void exchange_state(const gmx_multisim_t *ms, int b, t_state *state);
+extern void copy_state_nonatomdata(t_state *state, t_state *state_local);
+/* END PLUMED HREX */
+
+#endif /* _repl_ex_h */
diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h.preplumed b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h.preplumed
new file mode 100644
index 000000000..dcb47d1fd
--- /dev/null
+++ b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h.preplumed
@@ -0,0 +1,79 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef _repl_ex_h
+#define _repl_ex_h
+
+#include <cstdio>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_enerdata_t;
+struct gmx_multisim_t;
+struct t_commrec;
+struct t_inputrec;
+struct t_state;
+
+/* Abstract type for replica exchange */
+typedef struct gmx_repl_ex *gmx_repl_ex_t;
+
+gmx_repl_ex_t init_replica_exchange(FILE *fplog,
+ const gmx_multisim_t *ms,
+ const t_state *state,
+ const t_inputrec *ir,
+ int nst, int nmultiex, int init_seed);
+/* Should only be called on the master nodes */
+
+gmx_bool replica_exchange(FILE *fplog,
+ const t_commrec *cr,
+ gmx_repl_ex_t re,
+ t_state *state, gmx_enerdata_t *enerd,
+ t_state *state_local,
+ gmx_int64_t step, real time);
+/* Attempts replica exchange, should be called on all nodes.
+ * Returns TRUE if this state has been exchanged.
+ * When running each replica in parallel,
+ * this routine collects the state on the master node before exchange.
+ * With domain decomposition, the global state after exchange is stored
+ * in state and still needs to be redistributed over the nodes.
+ */
+
+void print_replica_exchange_statistics(FILE *fplog, gmx_repl_ex_t re);
+/* Should only be called on the master nodes */
+
+#endif /* _repl_ex_h */
--
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