/*
+ * 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.
+ *
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*
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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:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "vsite_parm.h"
-#include <stdio.h>
-#include <math.h>
#include <assert.h>
+#include <math.h>
+#include <stdio.h>
#include <string.h>
-#include "vsite_parm.h"
-#include "smalloc.h"
-#include "resall.h"
-#include "add_par.h"
-#include "vec.h"
-#include "toputil.h"
-#include "physics.h"
-#include "index.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "string2.h"
-#include "physics.h"
-#include "macros.h"
+
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
t_iatom a[4];
fprintf(fp, "bonds:");
for (i = 0; i < nrbond; i++)
{
- fprintf(fp, " %u-%u (%g)",
+ fprintf(fp, " %d-%d (%g)",
bonds[i].AI+1, bonds[i].AJ+1, bonds[i].c);
}
fprintf(fp, "\n");
fprintf(fp, "angles:");
for (i = 0; i < nrang; i++)
{
- fprintf(fp, " %u-%u-%u (%g)",
+ fprintf(fp, " %d-%d-%d (%g)",
angles[i].AI+1, angles[i].AJ+1,
angles[i].AK+1, angles[i].c);
}
fprintf(fp, "idihs:");
for (i = 0; i < nridih; i++)
{
- fprintf(fp, " %u-%u-%u-%u (%g)",
+ fprintf(fp, " %d-%d-%d-%d (%g)",
idihs[i].AI+1, idihs[i].AJ+1,
idihs[i].AK+1, idihs[i].AL+1, idihs[i].c);
}
int i;
for (i = 0; i < 4; i++)
{
- fprintf(debug, "atom %u type %s ",
+ fprintf(debug, "atom %d type %s ",
param->a[i]+1,
get_atomtype_name_AB(&at->atom[param->a[i]], atype));
}
if (debug)
{
- fprintf(debug, "params for vsite3 %u: %g %g\n",
+ fprintf(debug, "params for vsite3 %d: %g %g\n",
param->AI+1, param->C0, param->C1);
}
if (debug)
{
- fprintf(debug, "params for vsite3fd %u: %g %g\n",
+ fprintf(debug, "params for vsite3fd %d: %g %g\n",
param->AI+1, param->C0, param->C1);
}
return bError;
if (debug)
{
- fprintf(debug, "params for vsite3fad %u: %g %g\n",
+ fprintf(debug, "params for vsite3fad %d: %g %g\n",
param->AI+1, param->C0, param->C1);
}
return bError;
int i;
for (i = 0; i < 4; i++)
{
- fprintf(debug, "atom %u type %s ",
+ fprintf(debug, "atom %d type %s ",
param->a[i]+1, get_atomtype_name_AB(&at->atom[param->a[i]], atype));
}
fprintf(debug, "\n");
}
if (debug)
{
- fprintf(debug, "params for vsite3out %u: %g %g %g\n",
+ fprintf(debug, "params for vsite3out %d: %g %g %g\n",
param->AI+1, param->C0, param->C1, param->C2);
}
return bError;
param->C2 = -bij;
if (debug)
{
- fprintf(debug, "params for vsite4fd %u: %g %g %g\n",
+ fprintf(debug, "params for vsite4fd %d: %g %g %g\n",
param->AI+1, param->C0, param->C1, param->C2);
}
}
if (debug)
{
- fprintf(debug, "params for vsite4fdn %u: %g %g %g\n",
+ fprintf(debug, "params for vsite4fdn %d: %g %g %g\n",
param->AI+1, param->C0, param->C1, param->C2);
}
}
if (debug)
{
fprintf(debug, "Found %d bonds, %d angles and %d idihs "
- "for virtual site %u (%s)\n", nrbond, nrang, nridih,
+ "for virtual site %d (%s)\n", nrbond, nrang, nridih,
plist[ftype].param[i].AI+1,
interaction_function[ftype].longname);
print_bad(debug, nrbond, bonds, nrang, angles, nridih, idihs);
atom = ps->param[i].a[k];
if (vsite_type[atom] != NOTSET)
{
- fprintf(stderr, "ERROR: Cannot have constraint (%u-%u) with virtual site (%u)\n",
+ fprintf(stderr, "ERROR: Cannot have constraint (%d-%d) with virtual site (%d)\n",
ps->param[i].AI+1, ps->param[i].AJ+1, atom+1);
n++;
}
nvsite = 0;
if (debug)
{
- fprintf(debug, "constr %u %u:", ps->param[i].AI+1, ps->param[i].AJ+1);
+ fprintf(debug, "constr %d %d:", ps->param[i].AI+1, ps->param[i].AJ+1);
}
for (k = 0; (k < 2) && !bKeep && !bRemove; k++)
{
static void clean_vsite_dihs(t_params *plist, t_pindex pindex[],
int cftype, int vsite_type[])
{
- int ftype, i, parnr, k, l, m, n, nvsite, kept_i, vsnral;
- atom_id atom, constr;
- atom_id vsiteatoms[4];
- gmx_bool bKeep, bUsed, bPresent;
- t_params *ps;
+ int i, kept_i;
+ t_params *ps;
ps = &(plist[cftype]);
- vsnral = 0;
kept_i = 0;
for (i = 0; (i < ps->nr); i++) /* for all dihedrals in the plist */
{
+ int ftype, parnr, k, l, m, n, nvsite;
+ int vsnral = 0; /* keep the compiler happy */
+ atom_id atom, constr;
+ atom_id vsiteatoms[4] = { 0 }; /* init to zero to make gcc4.8 happy */
+ gmx_bool bKeep, bUsed, bPresent;
+
+
bKeep = FALSE;
/* check if all virtual sites are constructed from the same atoms */
nvsite = 0;
atom = ps->param[i].a[k];
if (vsite_type[atom] != NOTSET)
{
- nvsite++;
- if (nvsite == 1)
+ if (nvsite == 0)
{
/* store construction atoms of first vsite */
vsnral = NRAL(pindex[atom].ftype)-1;
}
if (debug)
{
- fprintf(debug, "dih w. vsite: %u %u %u %u\n",
+ fprintf(debug, "dih w. vsite: %d %d %d %d\n",
ps->param[i].AI+1, ps->param[i].AJ+1,
ps->param[i].AK+1, ps->param[i].AL+1);
- fprintf(debug, "vsite %u from: %u %u %u\n",
+ fprintf(debug, "vsite %d from: %d %d %d\n",
atom+1, vsiteatoms[0]+1, vsiteatoms[1]+1, vsiteatoms[2]+1);
}
}
else
- /* check if this vsite is constructed from the same atoms */
- if (vsnral == NRAL(pindex[atom].ftype)-1)
{
- for (m = 0; (m < vsnral) && !bKeep; m++)
+ /* check if this vsite is constructed from the same atoms */
+ if (vsnral == NRAL(pindex[atom].ftype)-1)
{
- bPresent = FALSE;
- constr =
- plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
- for (n = 0; (n < vsnral) && !bPresent; n++)
+ for (m = 0; (m < vsnral) && !bKeep; m++)
{
- if (constr == vsiteatoms[n])
+ bPresent = FALSE;
+ constr =
+ plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
+ for (n = 0; (n < vsnral) && !bPresent; n++)
{
- bPresent = TRUE;
+ if (constr == vsiteatoms[n])
+ {
+ bPresent = TRUE;
+ }
+ }
+ if (!bPresent)
+ {
+ bKeep = TRUE;
}
- }
- if (!bPresent)
- {
- bKeep = TRUE;
}
}
}
+ nvsite++;
}
}
atom = ps->param[i].a[k];
if (vsite_type[atom] == NOTSET)
{
+ /* vsnral will be set here, we don't get here with nvsite==0 */
bUsed = FALSE;
for (m = 0; (m < vsnral) && !bUsed; m++)
{
bKeep = TRUE;
if (debug)
{
- fprintf(debug, "unused atom in dih: %u\n", atom+1);
+ fprintf(debug, "unused atom in dih: %d\n", atom+1);
}
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff