-/* -*- 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.
-
- * 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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+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
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+ * in the README & COPYING files - if they are missing, get the
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "topio.h"
+
+#include <assert.h>
+#include <ctype.h>
+#include <errno.h>
#include <math.h>
-#include <sys/types.h>
#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
-#include <errno.h>
-#include <ctype.h>
-#include <assert.h>
-
-#include "futil.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "gmxfio.h"
-#include "txtdump.h"
-#include "physics.h"
-#include "macros.h"
-#include "names.h"
-#include "string2.h"
-#include "symtab.h"
-#include "gmx_fatal.h"
-#include "warninp.h"
-#include "vsite_parm.h"
-
-#include "grompp.h"
-#include "toputil.h"
-#include "toppush.h"
-#include "topdirs.h"
-#include "gpp_nextnb.h"
-#include "topio.h"
-#include "topshake.h"
-#include "gmxcpp.h"
-#include "gpp_bond_atomtype.h"
-#include "genborn.h"
-#include "maths.h"
-#define CPPMARK '#' /* mark from cpp */
-#define OPENDIR '[' /* starting sign for directive */
-#define CLOSEDIR ']' /* ending sign for directive */
+#include <sys/types.h>
-#define PM() \
- printf("line: %d, maxavail: %d\n", __LINE__, maxavail()); \
- fflush(stdout)
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxpreprocess/gmxcpp.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/gmxpreprocess/topshake.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/vsite_parm.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+
+#define OPENDIR '[' /* starting sign for directive */
+#define CLOSEDIR ']' /* ending sign for directive */
static void free_nbparam(t_nbparam **param, int nr)
{
char buf[256];
int i, mb, nmol, ri, pt;
double q;
- real m;
+ real m, mB;
t_atoms *atoms;
/* Check mass and charge */
{
q += nmol*atoms->atom[i].q;
m = atoms->atom[i].m;
+ mB = atoms->atom[i].mB;
pt = atoms->atom[i].ptype;
/* If the particle is an atom or a nucleus it must have a mass,
* else, if it is a shell, a vsite or a bondshell it can have mass zero
*/
- if ((m <= 0.0) && ((pt == eptAtom) || (pt == eptNucleus)))
+ if (((m <= 0.0) || (mB <= 0.0)) && ((pt == eptAtom) || (pt == eptNucleus)))
{
ri = atoms->atom[i].resind;
- sprintf(buf, "atom %s (Res %s-%d) has mass %g\n",
+ sprintf(buf, "atom %s (Res %s-%d) has mass %g (state A) / %g (state B)\n",
*(atoms->atomname[i]),
*(atoms->resinfo[ri].name),
atoms->resinfo[ri].nr,
- m);
+ m, mB);
warning_error(wi, buf);
}
else
- if ((m != 0) && (pt == eptVSite))
+ if (((m != 0) || (mB != 0)) && (pt == eptVSite))
{
ri = atoms->atom[i].resind;
- sprintf(buf, "virtual site %s (Res %s-%d) has non-zero mass %g\n"
+ sprintf(buf, "virtual site %s (Res %s-%d) has non-zero mass %g (state A) / %g (state B)\n"
" Check your topology.\n",
*(atoms->atomname[i]),
*(atoms->resinfo[ri].name),
atoms->resinfo[ri].nr,
- m);
+ m, mB);
warning_error(wi, buf);
/* The following statements make LINCS break! */
/* atoms->atom[i].m=0; */
else
{
srenew(cppopts, ++ncppopts);
- cppopts[ncppopts-1] = strdup(buf);
+ cppopts[ncppopts-1] = gmx_strdup(buf);
}
sfree(buf);
ptr = rptr;
comb = 0;
/* Init the number of CMAP torsion angles and grid spacing */
- plist->grid_spacing = 0;
- plist->nc = 0;
+ plist[F_CMAP].grid_spacing = 0;
+ plist[F_CMAP].nc = 0;
bWarn_copy_A_B = bFEP;
set_warning_line(wi, cpp_cur_file(&handle), cpp_cur_linenr(&handle));
- pline = strdup(line);
+ pline = gmx_strdup(line);
/* Strip trailing '\' from pline, if it exists */
sl = strlen(pline);
/* Since we depend on the '\' being present to continue to read, we copy line
* to a tmp string, strip the '\' from that string, and cat it to pline
*/
- tmp_line = strdup(line);
+ tmp_line = gmx_strdup(line);
sl = strlen(tmp_line);
if ((sl > 0) && (tmp_line[sl-1] == CONTINUE))
* without the brackets into dirstr, then
* skip spaces and tabs on either side of directive
*/
- dirstr = strdup((pline+1));
+ dirstr = gmx_strdup((pline+1));
if ((dummy2 = strchr (dirstr, CLOSEDIR)) != NULL)
{
(*dummy2) = 0;
bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
break;
case d_cmap:
- push_cmap(d, plist, mi0->plist, &(mi0->atoms), atype, pline,wi);
+ push_cmap(d, plist, mi0->plist, &(mi0->atoms), atype, pline, wi);
break;
case d_vsitesn:
- push_vsitesn(d, plist, &(mi0->atoms), pline, wi);
+ push_vsitesn(d, mi0->plist, &(mi0->atoms), pline, wi);
break;
case d_exclusions:
assert(block2);
}
default:
fprintf (stderr, "case: %d\n", d);
- invalid_case();
+ gmx_incons("unknown directive");
}
}
}
{
gmx_fatal(FARGS, cpp_error(&handle, status));
}
+ cpp_done();
if (out)
{
gmx_fio_fclose(out);
j = 0;
while (j < molt->ilist[i].nr)
{
- bexcl = FALSE;
a1 = molt->ilist[i].iatoms[j+1];
a2 = molt->ilist[i].iatoms[j+2];
bexcl = ((bQMMM[a1] && bQMMM[a2]) ||
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff