/*
+ * 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:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * 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 <stdlib.h>
#include <string.h>
-#include "string2.h"
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "futil.h"
-#include "symtab.h"
+
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/futil.h"
#include "h_db.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
#include "fflibutil.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-
-/* There are 11 types of adding hydrogens, numbered from
- * 1 thru 11. Each of these has a specific number of
- * control atoms, that determine how the hydrogens are added.
- * Here these number are given. Because arrays start at 0 an
- * extra dummy for index 0 is added
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/legacyheaders/macros.h"
+
+/* Number of control atoms for each 'add' type.
+ *
+ * There are 11 types of adding hydrogens, numbered from 1 thru
+ * 11. Each of these has a specific number of control atoms, that
+ * determine how the hydrogens are added. Here these number are
+ * given. Because arrays start at 0, an extra dummy for index 0 is
+ * added.
*/
const int ncontrol[] = { -1, 3, 3, 3, 3, 4, 3, 1, 3, 3, 1, 1 };
#define maxcontrol asize(ncontrol)
}
for (i = 0; (i < hack->nctl); i++)
{
- hack->a[i] = strdup(a[i]);
+ hack->a[i] = gmx_strdup(a[i]);
}
for (; i < 4; i++)
{
hack->a[i] = NULL;
}
hack->oname = NULL;
- hack->nname = strdup(hn);
+ hack->nname = gmx_strdup(hn);
hack->atom = NULL;
hack->cgnr = NOTSET;
hack->bXSet = FALSE;
}
srenew(aah, nah+1);
clear_t_hackblock(&aah[nah]);
- aah[nah].name = strdup(buf);
- aah[nah].filebase = strdup(filebase);
+ aah[nah].name = gmx_strdup(buf);
+ aah[nah].filebase = gmx_strdup(filebase);
if (sscanf(line+n, "%d", &nab) == 1)
{
}
nah++;
}
- ffclose(in);
+ gmx_ffclose(in);
/* Sort the list (necessary to be able to use bsearch */
qsort(aah, nah, (size_t)sizeof(**ah), compaddh);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff