/*
+ * 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,
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+ * 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
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*
- * 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:
- * GROwing Monsters And Cloning Shrimps
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <string.h>
#include <stdlib.h>
-#include "sysstuff.h"
-#include "princ.h"
-#include "gromacs/fileio/futil.h"
-#include "vec.h"
-#include "smalloc.h"
-#include "typedefs.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "index.h"
-#include "symtab.h"
-#include "readinp.h"
+
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
#include "readir.h"
-#include <string.h>
-#include "mdatoms.h"
-#include "pbc.h"
-#include "pull.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
static char pulldim[STRLEN];
}
static void init_pull_group(t_pull_group *pg,
- const char *wbuf)
+ const char *wbuf)
{
double d;
int n, m;
string2dvec(origin_buf, origin);
if (pcrd->group[0] != 0 && dnorm(origin) > 0)
{
- gmx_fatal(FARGS,"The pull origin can only be set with an absolute reference");
+ gmx_fatal(FARGS, "The pull origin can only be set with an absolute reference");
}
if (eGeom == epullgDIST)
RTYPE("pull-r1", pull->cyl_r1, 1.0);
CTYPE("Switch from r1 to r0 in case of dynamic reaction force");
RTYPE("pull-r0", pull->cyl_r0, 1.5);
- RTYPE("pull_constr_tol", pull->constr_tol, 1E-6);
+ RTYPE("pull-constr-tol", pull->constr_tol, 1E-6);
EETYPE("pull-start", *bStart, yesno_names);
EETYPE("pull-print-reference", pull->bPrintRef, yesno_names);
ITYPE("pull-nstxout", pull->nstxout, 10);
return grpbuf;
}
-void make_pull_groups(t_pull *pull,
+void make_pull_groups(t_pull *pull,
char **pgnames,
const t_blocka *grps, char **gnames)
{
{
pgrp = &pull->group[g];
+ if (strcmp(pgnames[g], "") == 0)
+ {
+ gmx_fatal(FARGS, "Group pull_group%d required by grompp was undefined.", g);
+ }
+
ig = search_string(pgnames[g], grps->nr, gnames);
pgrp->nat = grps->index[ig+1] - grps->index[ig];
init_pull(NULL, ir, 0, NULL, mtop, NULL, oenv, lambda, FALSE, 0);
md = init_mdatoms(NULL, mtop, ir->efep);
- atoms2md(mtop, ir, 0, NULL, 0, mtop->natoms, md);
+ atoms2md(mtop, ir, 0, NULL, mtop->natoms, md);
if (ir->efep)
{
update_mdatoms(md, lambda);
{
pcrd = &pull->coord[c];
- pgrp0 = &pull->group[pcrd->group[0]];
- pgrp1 = &pull->group[pcrd->group[1]];
+ pgrp0 = &pull->group[pcrd->group[0]];
+ pgrp1 = &pull->group[pcrd->group[1]];
fprintf(stderr, "%8d %8d %8d\n",
pcrd->group[0], pgrp0->nat, pgrp0->pbcatom+1);
fprintf(stderr, "%8d %8d %8d ",
pcrd->group[1], pgrp1->nat, pgrp1->pbcatom+1);
- init = pcrd->init;
+ init = pcrd->init;
pcrd->init = 0;
if (pcrd->rate == 0)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff