-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
+ *
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*
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+ * 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.
*
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- * GROwing Monsters And Cloning Shrimps
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdio.h>
-#include "typedefs.h"
-#include "tpxio.h"
-#include "smalloc.h"
-#include "vec.h"
-#include "main.h"
-#include "mvdata.h"
-#include "gmx_fatal.h"
-#include "symtab.h"
-#include "txtdump.h"
-#include "mdatoms.h"
-#include "mdrun.h"
-#include "statutil.h"
-#include "names.h"
-#include "calcgrid.h"
-#include "gmx_random.h"
-#include "update.h"
-#include "mdebin.h"
-
-#define BUFSIZE 256
-
-#define NOT_FINISHED(l1,l2) \
- printf("not finished yet: lines %d .. %d in %s\n",l1,l2,__FILE__)
-
-static char *int_title(const char *title,int nodeid,char buf[], int size)
-{
- sprintf(buf,"%s (%d)",title,nodeid);
-
- return buf;
-}
-void set_state_entries(t_state *state,const t_inputrec *ir,int nnodes)
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/mvdata.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
+#define BUFSIZE 256
+
+#define NOT_FINISHED(l1, l2) \
+ printf("not finished yet: lines %d .. %d in %s\n", l1, l2, __FILE__)
+
+void set_state_entries(t_state *state, const t_inputrec *ir)
{
- int nnhpres;
+ int nnhpres;
- /* The entries in the state in the tpx file might not correspond
- * with what is needed, so we correct this here.
- */
- state->flags = 0;
- if (ir->efep != efepNO || ir->bExpanded)
- {
- state->flags |= (1<<estLAMBDA);
- state->flags |= (1<<estFEPSTATE);
- }
- state->flags |= (1<<estX);
- if (state->lambda==NULL)
+ /* The entries in the state in the tpx file might not correspond
+ * with what is needed, so we correct this here.
+ */
+ state->flags = 0;
+ if (ir->efep != efepNO || ir->bExpanded)
{
- snew(state->lambda,efptNR);
+ state->flags |= (1<<estLAMBDA);
+ state->flags |= (1<<estFEPSTATE);
}
- if (state->x == NULL)
- snew(state->x,state->nalloc);
- if (EI_DYNAMICS(ir->eI)) {
- state->flags |= (1<<estV);
- if (state->v == NULL)
- snew(state->v,state->nalloc);
- }
- if (ir->eI == eiSD2) {
- state->flags |= (1<<estSDX);
- if (state->sd_X == NULL) {
- /* sd_X is not stored in the tpx file, so we need to allocate it */
- snew(state->sd_X,state->nalloc);
+ state->flags |= (1<<estX);
+ if (state->lambda == NULL)
+ {
+ snew(state->lambda, efptNR);
+ }
+ if (state->x == NULL)
+ {
+ snew(state->x, state->nalloc);
+ }
+ if (EI_DYNAMICS(ir->eI))
+ {
+ state->flags |= (1<<estV);
+ if (state->v == NULL)
+ {
+ snew(state->v, state->nalloc);
+ }
+ }
+ if (ir->eI == eiSD2)
+ {
+ state->flags |= (1<<estSDX);
+ if (state->sd_X == NULL)
+ {
+ /* sd_X is not stored in the tpx file, so we need to allocate it */
+ snew(state->sd_X, state->nalloc);
+ }
}
- }
if (ir->eI == eiCG)
{
state->flags |= (1<<estCGP);
if (state->cg_p == NULL)
{
/* cg_p is not stored in the tpx file, so we need to allocate it */
- snew(state->cg_p,state->nalloc);
+ snew(state->cg_p, state->nalloc);
}
}
- if (EI_SD(ir->eI) || ir->eI == eiBD || ir->etc == etcVRESCALE) {
- state->nrng = gmx_rng_n();
- state->nrngi = 1;
- if (EI_SD(ir->eI) || ir->eI == eiBD) {
- /* This will be correct later with DD */
- state->nrng *= nnodes;
- state->nrngi *= nnodes;
- }
- state->flags |= ((1<<estLD_RNG) | (1<<estLD_RNGI));
- snew(state->ld_rng, state->nrng);
- snew(state->ld_rngi,state->nrngi);
- } else {
- state->nrng = 0;
- }
-
- if (ir->bExpanded)
- {
- state->nmcrng = gmx_rng_n();
- snew(state->mc_rng,state->nmcrng);
- snew(state->mc_rngi,1);
- }
- state->nnhpres = 0;
- if (ir->ePBC != epbcNONE) {
- state->flags |= (1<<estBOX);
- if (PRESERVE_SHAPE(*ir)) {
- state->flags |= (1<<estBOX_REL);
- }
- if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
- {
- state->flags |= (1<<estBOXV);
- }
- if (ir->epc != epcNO)
- {
- if (IR_NPT_TROTTER(ir) || (IR_NPH_TROTTER(ir)))
- {
- state->nnhpres = 1;
- state->flags |= (1<<estNHPRES_XI);
- state->flags |= (1<<estNHPRES_VXI);
- state->flags |= (1<<estSVIR_PREV);
- state->flags |= (1<<estFVIR_PREV);
- state->flags |= (1<<estVETA);
- state->flags |= (1<<estVOL0);
- }
- else
- {
- state->flags |= (1<<estPRES_PREV);
- }
- }
- }
+ state->nnhpres = 0;
+ if (ir->ePBC != epbcNONE)
+ {
+ state->flags |= (1<<estBOX);
+ if (PRESERVE_SHAPE(*ir))
+ {
+ state->flags |= (1<<estBOX_REL);
+ }
+ if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
+ {
+ state->flags |= (1<<estBOXV);
+ }
+ if (ir->epc != epcNO)
+ {
+ if (IR_NPT_TROTTER(ir) || (IR_NPH_TROTTER(ir)))
+ {
+ state->nnhpres = 1;
+ state->flags |= (1<<estNHPRES_XI);
+ state->flags |= (1<<estNHPRES_VXI);
+ state->flags |= (1<<estSVIR_PREV);
+ state->flags |= (1<<estFVIR_PREV);
+ state->flags |= (1<<estVETA);
+ state->flags |= (1<<estVOL0);
+ }
+ else
+ {
+ state->flags |= (1<<estPRES_PREV);
+ }
+ }
+ }
- if (ir->etc == etcNOSEHOOVER) {
- state->flags |= (1<<estNH_XI);
- state->flags |= (1<<estNH_VXI);
- }
+ if (ir->etc == etcNOSEHOOVER)
+ {
+ state->flags |= (1<<estNH_XI);
+ state->flags |= (1<<estNH_VXI);
+ }
- if (ir->etc == etcVRESCALE) {
- state->flags |= (1<<estTC_INT);
- }
+ if (ir->etc == etcVRESCALE)
+ {
+ state->flags |= (1<<estTC_INT);
+ }
- init_gtc_state(state,state->ngtc,state->nnhpres,ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
- init_ekinstate(&state->ekinstate,ir);
+ init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
+ init_ekinstate(&state->ekinstate, ir);
- init_energyhistory(&state->enerhist);
- init_df_history(&state->dfhist,ir->fepvals->n_lambda,ir->expandedvals->init_wl_delta);
+ init_energyhistory(&state->enerhist);
+ init_df_history(&state->dfhist, ir->fepvals->n_lambda);
+ state->swapstate.eSwapCoords = ir->eSwapCoords;
}
-void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
+void init_parallel(t_commrec *cr, t_inputrec *inputrec,
gmx_mtop_t *mtop)
{
- bcast_ir_mtop(cr,inputrec,mtop);
-
- if (inputrec->eI == eiBD || EI_SD(inputrec->eI)) {
- /* Make sure the random seeds are different on each node */
- inputrec->ld_seed += cr->nodeid;
- }
+ bcast_ir_mtop(cr, inputrec, mtop);
}
-
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff