/*
+ * 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 3.3.2
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2007, 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) 2001-2007, 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
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- * 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,
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*
- * 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
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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:
- * Groningen Machine for Chemical Simulation
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include <ctype.h>
-
-#include "string2.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "rmpbc.h"
-#include "statutil.h"
-#include "xvgr.h"
-#include "futil.h"
-#include "statutil.h"
-#include "tpxio.h"
-#include "index.h"
-#include "smalloc.h"
-#include "calcgrid.h"
-#include "nrnb.h"
-#include "physics.h"
-#include "coulomb.h"
-#include "pme.h"
-#include "gstat.h"
-#include "matio.h"
-#include "mtop_util.h"
-#include "gmx_ana.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void clust_size(const char *ndx, const char *trx, const char *xpm,
const char *xpmw, const char *ncl, const char *acl,
read_tpxheader(tpr, &tpxh, TRUE, &version, &generation);
if (tpxh.natoms != natoms)
{
- gmx_fatal(FARGS, "tpr (%d atoms) and xtc (%d atoms) do not match!",
+ gmx_fatal(FARGS, "tpr (%d atoms) and trajectory (%d atoms) do not match!",
tpxh.natoms, natoms);
}
ePBC = read_tpx(tpr, NULL, NULL, &natoms, NULL, NULL, NULL, mtop);
{
index[i] = i;
}
- gname = strdup("mols");
+ gname = gmx_strdup("mols");
}
else
{
}
while (read_next_frame(oenv, status, &fr));
close_trx(status);
- ffclose(fp);
- ffclose(gp);
- ffclose(hp);
- ffclose(tp);
+ gmx_ffclose(fp);
+ gmx_ffclose(gp);
+ gmx_ffclose(hp);
+ gmx_ffclose(tp);
gmx_mtop_atomlookup_destroy(alook);
if (max_clust_ind >= 0)
{
- fp = ffopen(mcn, "w");
+ fp = gmx_ffopen(mcn, "w");
fprintf(fp, "[ max_clust ]\n");
for (i = 0; (i < nindex); i++)
{
}
}
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
/* Print the real distribution cluster-size/numer, averaged over the trajectory. */
nhisto += (int)((j+1)*nelem/n_x);
}
fprintf(fp, "%5d %8.3f\n", j+1, 0.0);
- ffclose(fp);
+ gmx_ffclose(fp);
fprintf(stderr, "Total number of atoms in clusters = %d\n", nhisto);
}
fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
cmid = 1;
- fp = ffopen(xpm, "w");
+ fp = gmx_ffopen(xpm, "w");
write_xpm3(fp, 0, "Cluster size distribution", "# clusters", timebuf, "Size",
n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
rlo, rmid, rhi, &nlevels);
- ffclose(fp);
+ gmx_ffclose(fp);
cmid = 100.0;
cmax = 0.0;
for (i = 0; (i < n_x); i++)
}
}
fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
- fp = ffopen(xpmw, "w");
+ fp = gmx_ffopen(xpmw, "w");
write_xpm3(fp, 0, "Weighted cluster size distribution", "Fraction", timebuf,
"Size", n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
rlo, rmid, rhi, &nlevels);
- ffclose(fp);
+ gmx_ffclose(fp);
sfree(clust_index);
sfree(clust_size);
int gmx_clustsize(int argc, char *argv[])
{
const char *desc[] = {
- "This program computes the size distributions of molecular/atomic clusters in",
+ "[THISMODULE] computes the size distributions of molecular/atomic clusters in",
"the gas phase. The output is given in the form of an [TT].xpm[tt] file.",
"The total number of clusters is written to an [TT].xvg[tt] file.[PAR]",
"When the [TT]-mol[tt] option is given clusters will be made out of",
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
rgblo.r = rlo[XX], rgblo.g = rlo[YY], rgblo.b = rlo[ZZ];
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff