From 4d74b6a5c43cc391d1b18a7703ffd26ceee612e6 Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Thu, 9 Nov 2017 22:37:44 +0100
Subject: [PATCH] hrex: gromacs-2016.4
---
CHANGES/v2.4.md | 1 +
.../src/programs/mdrun/md.cpp | 86 ++++++++++++++++++
.../src/programs/mdrun/mdrun.cpp | 15 ++++
.../src/programs/mdrun/repl_ex.cpp | 29 ++++++-
.../src/programs/mdrun/repl_ex.h | 87 +++++++++++++++++++
.../src/programs/mdrun/repl_ex.h.preplumed | 79 +++++++++++++++++
6 files changed, 295 insertions(+), 2 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/CHANGES/v2.4.md b/CHANGES/v2.4.md
index 3d2673bee..d64b99fc5 100644
--- a/CHANGES/v2.4.md
+++ b/CHANGES/v2.4.md
@@ -154,6 +154,7 @@ Fixes after beta release:
- Fixed a bug in EDS module for restarts, where accumulated rate was not stored to restart file, leading to convergence problems.
- (developers) `plumed config makefile_conf` can be used to retrieve `Makefile.conf` file a posteriori.
- Added patch for Quantum ESPRESSO 6.2 (thanks to Ralf Meyer).
+ - Implemented HREX for gromacs-2016.4.
- (developers) Store `MPIEXEC` variable at configure time and use it later for running regtests. Notice that in case
`MPIEXEC` is not specified regtests will be run using the command stored in env var `PLUMED_MPIRUN` or, if this is
also not defined, using `mpirun`.
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..8e808e163 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
@@ -1087,6 +1091,86 @@ 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;
+
+ if(plumedswitch) if(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 |
+ ((inputrecDynamicBox(ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
+ 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);
+ if(plumedswitch){
+ 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),
@@ -1203,6 +1287,8 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
do_per_step(step,repl_ex_nst)) 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..2f35484ec 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. */
@@ -1488,3 +1501,15 @@ 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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