-/* -*- 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
- *
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- *
- * 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.
+ * 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.
*
- * This program is free software; you can redistribute it and/or
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*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "main.h"
-#include "constr.h"
-#include "copyrite.h"
-#include "physics.h"
-#include "vec.h"
-#include "pbc.h"
-#include "smalloc.h"
-#include "mdrun.h"
-#include "nrnb.h"
-#include "domdec.h"
-#include "partdec.h"
-#include "mtop_util.h"
-#include "gmxfio.h"
-#include "gmx_omp_nthreads.h"
-#include "gmx_omp.h"
+#include <stdlib.h>
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
int b0; /* first constraint for this thread */
{
nlocat = dd_constraints_nlocalatoms(cr->dd);
}
- else if (PARTDECOMP(cr))
- {
- nlocat = pd_constraints_nlocalatoms(cr->pd);
- }
else
{
nlocat = NULL;
for (iter = 0; iter < lincsd->nIter; iter++)
{
- if ((lincsd->bCommIter && DOMAINDECOMP(cr) && cr->dd->constraints) ||
- PARTDECOMP(cr))
+ if ((lincsd->bCommIter && DOMAINDECOMP(cr) && cr->dd->constraints))
{
#pragma omp barrier
#pragma omp master
/* Communicate the corrected non-local coordinates */
if (DOMAINDECOMP(cr))
{
- dd_move_x_constraints(cr->dd, box, xp, NULL);
- }
- else
- {
- pd_move_x_constraints(cr, xp, NULL);
+ dd_move_x_constraints(cr->dd, box, xp, NULL, FALSE);
}
}
}
dlen2 = 2*len2 - norm2(dx);
if (dlen2 < wfac*len2 && (nlocat == NULL || nlocat[b]))
{
+ /* not race free - see detailed comment in caller */
*warn = b;
}
if (dlen2 > 0)
}
start = 0;
}
- else if (PARTDECOMP(cr))
- {
- pd_get_constraint_range(cr->pd, &start, &natoms);
- }
else
{
- start = md->start;
+ start = 0;
natoms = md->homenr;
}
at2con = make_at2con(start, natoms, idef->il, idef->iparams, bDynamics,
*imax = im;
}
-static void dump_conf(gmx_domdec_t *dd, struct gmx_lincsdata *li,
- t_blocka *at2con,
- char *name, gmx_bool bAll, rvec *x, matrix box)
-{
- char str[STRLEN];
- FILE *fp;
- int ac0, ac1, i;
-
- dd_get_constraint_range(dd, &ac0, &ac1);
-
- sprintf(str, "%s_%d_%d_%d.pdb", name, dd->ci[XX], dd->ci[YY], dd->ci[ZZ]);
- fp = gmx_fio_fopen(str, "w");
- fprintf(fp, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1 1\n",
- 10*norm(box[XX]), 10*norm(box[YY]), 10*norm(box[ZZ]),
- 90.0, 90.0, 90.0);
- for (i = 0; i < ac1; i++)
- {
- if (i < dd->nat_home || (bAll && i >= ac0 && i < ac1))
- {
- fprintf(fp, "%-6s%5u %-4.4s%3.3s %c%4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
- "ATOM", ddglatnr(dd, i), "C", "ALA", ' ', i+1,
- 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ],
- 1.0, i < dd->nat_tot ? 0.0 : 1.0);
- }
- }
- if (bAll)
- {
- for (i = 0; i < li->nc; i++)
- {
- fprintf(fp, "CONECT%5d%5d\n",
- ddglatnr(dd, li->bla[2*i]),
- ddglatnr(dd, li->bla[2*i+1]));
- }
- }
- gmx_fio_fclose(fp);
-}
-
gmx_bool constrain_lincs(FILE *fplog, gmx_bool bLog, gmx_bool bEner,
t_inputrec *ir,
- gmx_large_int_t step,
+ gmx_int64_t step,
struct gmx_lincsdata *lincsd, t_mdatoms *md,
t_commrec *cr,
rvec *x, rvec *xprime, rvec *min_proj,
{
real dt_2, dvdl = 0;
+ /* TODO This should probably use invdt, so that sd integrator scaling works properly */
dt_2 = 1.0/(ir->delta_t*ir->delta_t);
for (i = 0; (i < lincsd->nc); i++)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff