-/* -*- 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.
+ *
+ * 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.
*
- * If you want to redistribute modifications, 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 www.gromacs.org.
+ * 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.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * 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.
*
- * For more info, check our website at http://www.gromacs.org
+ * 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.
*
- * And Hey:
- * GROningen Mixture of Alchemy and Childrens' Stories
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/disre.h"
+
+#include "config.h"
#include <math.h>
-#include "typedefs.h"
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "xvgr.h"
-#include "gmx_fatal.h"
-#include "bondf.h"
-#include "copyrite.h"
-#include "disre.h"
-#include "main.h"
-#include "mtop_util.h"
+#include <stdlib.h>
+
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
void init_disres(FILE *fplog, const gmx_mtop_t *mtop,
- t_inputrec *ir, const t_commrec *cr, gmx_bool bPartDecomp,
+ t_inputrec *ir, const t_commrec *cr,
t_fcdata *fcd, t_state *state, gmx_bool bIsREMD)
{
int fa, nmol, i, npair, np;
}
}
- if (cr && PAR(cr) && !bPartDecomp)
+ if (cr && PAR(cr))
{
/* Temporary check, will be removed when disre is implemented with DD */
- const char *notestr = "NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd)";
+ const char *notestr = "NOTE: atoms involved in distance restraints should be within the same domain. If this is not the case mdrun generates a fatal error. If you encounter this, use a single MPI rank (Verlet+OpenMP+GPUs work fine).";
if (MASTER(cr))
{
if (dd->dr_tau != 0 || ir->eDisre == edrEnsemble || cr->ms != NULL ||
dd->nres != dd->npair)
{
- gmx_fatal(FARGS, "Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd)");
+ gmx_fatal(FARGS, "Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use a single MPI rank%s", cr->ms ? " per simulation" : "");
}
if (ir->nstdisreout != 0)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff