*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014 by the GROMACS development team, led by
+ * 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.
* 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 "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
}
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)