/*
+ * 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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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
-#include <ctype.h>
+#include <assert.h>
#include <math.h>
+#include <stdlib.h>
+#include <string.h>
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "statutil.h"
-#include "maths.h"
-#include "futil.h"
-#include "index.h"
-#include "copyrite.h"
-#include "typedefs.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "tpxio.h"
-#include "vec.h"
-#include "matio.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/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
int gmx_vanhove(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_vanhove[tt] computes the Van Hove correlation function.",
+ "[THISMODULE] computes the Van Hove correlation function.",
"The Van Hove G(r,t) is the probability that a particle that is at r[SUB]0[sub]",
"at time zero can be found at position r[SUB]0[sub]+r at time t.",
- "[TT]g_vanhove[tt] determines G not for a vector r, but for the length of r.",
+ "[THISMODULE] determines G not for a vector r, but for the length of r.",
"Thus it gives the probability that a particle moves a distance of r",
"in time t.",
"Jumps across the periodic boundaries are removed.",
FILE *fp;
t_rgb rlo = {1, 1, 1}, rhi = {0, 0, 0};
- parse_common_args(&argc, argv, PCA_CAN_VIEW | 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_VIEW | PCA_CAN_TIME,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
matfile = opt2fn_null("-om", NFILE, fnm);
if (opt2parg_bSet("-fr", NPA, pa))
srenew(sbox, nalloc);
srenew(sx, nalloc);
}
+ assert(time != NULL); assert(sbox != NULL);
time[nfr] = t;
copy_mat(box, sbox[nfr]);
nfr++;
}
- while (read_next_x(oenv, status, &t, natom, x, box));
+ while (read_next_x(oenv, status, &t, x, box));
/* clean up */
sfree(x);
for (i = 0; i < isize; i++)
{
d2 = distance2(sx[f][i], sx[ff][i]);
- bin = (int)(sqrt(d2)*invbin);
+ bin = (int)(sqrt(d2)*invbin + 0.5);
if (bin >= nalloc)
{
nallocn = 10*(bin/10) + 11;
{
ticky[i] = i*rbin;
}
- fp = ffopen(matfile, "w");
+ fp = gmx_ffopen(matfile, "w");
write_xpm(fp, MAT_SPATIAL_Y, "Van Hove function", "G (1/nm)",
sbin == 0 ? "time (ps)" : "sqrt(time) (ps^1/2)", "r (nm)",
mat_nx, nbin, tickx, ticky, mat, 0, matmax, rlo, rhi, &nlev);
- ffclose(fp);
+ gmx_ffclose(fp);
}
if (orfile)
{
fp = xvgropen(orfile, "Van Hove function", "r (nm)", "G (nm\\S-1\\N)", oenv);
- fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
+ }
snew(legend, nr);
for (fbin = 0; fbin < nr; fbin++)
{
sprintf(buf, "%g ps", (fbin + 1)*fshift*dt);
- legend[fbin] = strdup(buf);
+ legend[fbin] = gmx_strdup(buf);
}
xvgr_legend(fp, nr, (const char**)legend, oenv);
for (i = 0; i < nalloc; i++)
}
fprintf(fp, "\n");
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
if (otfile)
{
sprintf(buf, "Probability of moving less than %g nm", rint);
fp = xvgropen(otfile, buf, "t (ps)", "", oenv);
- fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
+ }
for (f = 0; f <= ftmax; f++)
{
fprintf(fp, "%g %g\n", f*dt, (real)pt[f]/(tcount[f]*isize));
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
do_view(oenv, matfile, NULL);
do_view(oenv, orfile, NULL);
do_view(oenv, otfile, NULL);
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff