/*
+ * 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) 2012,2013,2014, 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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+ * 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.
*
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "copyrite.h"
-#include "statutil.h"
-#include "macros.h"
-#include "string2.h"
-#include "futil.h"
-#include "gmx_fatal.h"
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static int calc_ntype(int nft, int *ft, t_idef *idef)
{
case F_RBDIHS:
sprintf(buf, "RB-A1=%.2f", idef->iparams[i].rbdihs.rbcA[1]);
break;
+ case F_RESTRANGLES:
+ sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
+ idef->iparams[i].harmonic.krA);
+ break;
+ case F_RESTRDIHS:
+ sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
+ idef->iparams[i].harmonic.krA);
+ break;
+ case F_CBTDIHS:
+ sprintf(buf, "CBT-A1=%.2f", idef->iparams[i].cbtdihs.cbtcA[1]);
+ break;
+
default:
gmx_fatal(FARGS, "Unsupported function type '%s' selected",
interaction_function[ftype].longname);
}
- grpnames[ind] = strdup(buf);
+ grpnames[ind] = gmx_strdup(buf);
ind++;
}
}
int gmx_mk_angndx(int argc, char *argv[])
{
static const char *desc[] = {
- "[TT]mk_angndx[tt] makes an index file for calculation of",
+ "[THISMODULE] makes an index file for calculation of",
"angle distributions etc. It uses a run input file ([TT].tpx[tt]) for the",
"definitions of the angles, dihedrals etc."
};
int *nr;
char **grpnames;
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, "angle", ffWRITE }
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
ft = select_ftype(opt[0], &nft, &mult);
- top = read_top(ftp2fn(efTPX, NFILE, fnm), NULL);
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), NULL);
ntype = calc_ntype(nft, ft, &(top->idef));
snew(grpnames, ntype);
fprintf(out, "\n");
}
}
- ffclose(out);
-
- thanx(stderr);
+ gmx_ffclose(out);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff