/*
+ * 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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+ * 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
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
#include <string.h>
-#include "macros.h"
-#include "vec.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "filenm.h"
-#include "statutil.h"
-#include "copyrite.h"
-#include "futil.h"
-#include "gmx_fatal.h"
-#include "smalloc.h"
-#include "pbc.h"
-#include "xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/fileio/xvgr.h"
#include "gmx_ana.h"
+#include "gromacs/utility/fatalerror.h"
typedef struct {
char *label;
*(atoms->resinfo[resnr].name),
atoms->resinfo[resnr].nr,
anr+1);
- cg[ncg].label = strdup(buf);
+ cg[ncg].label = gmx_strdup(buf);
ncg++;
}
}
int gmx_saltbr(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_saltbr[tt] plots the distance between all combination of charged groups",
+ "[THISMODULE] plots the distance between all combination of charged groups",
"as a function of time. The groups are combined in different ways.",
"A minimum distance can be given (i.e. a cut-off), such that groups",
"that are never closer than that distance will not be plotted.[PAR]",
matrix box;
output_env_t oenv;
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
cg = mk_charge(&top->atoms, &(top->cgs), &ncg);
teller++;
}
- while (read_next_x(oenv, status, &t, natoms, x, box));
+ while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
close_trj(status);
{
fprintf(fp, "%10g %10g\n", time[k], cgdist[i][j][k]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
}
}
}
for (m = 0; (m < 3); m++)
{
- ffclose(out[m]);
+ gmx_ffclose(out[m]);
if (nset[m] == 0)
{
remove(fn[m]);
}
}
}
- thanx(stderr);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff