/*
+ * 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 <stdio.h>
+#include "gmxpre.h"
#include <math.h>
-#include "confio.h"
-#include "copyrite.h"
-#include "gmx_fatal.h"
-#include "futil.h"
-#include "gstat.h"
-#include "macros.h"
-#include "maths.h"
-#include "physics.h"
-#include "index.h"
-#include "smalloc.h"
-#include "statutil.h"
+#include <stdio.h>
#include <string.h>
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "strdb.h"
-#include "xvgr.h"
-#include "pbc.h"
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/units.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gmx_ana.h"
+#include "gromacs/fileio/trxio.h"
#define NK 24
}
fprintf(fp, "\n");
}
- ffclose(fp);
+ gmx_ffclose(fp);
do_view(oenv, fn_trans, "-nxy");
}
low_do_autocorr(fn_tca, oenv, "Transverse Current Autocorrelation Functions",
nframes, ntc, ncorr, tc, dt, eacNormal,
- 1, FALSE, FALSE, FALSE, 0, 0, 0, 0);
+ 1, FALSE, FALSE, FALSE, 0, 0, 0);
do_view(oenv, fn_tca, "-nxy");
fp = xvgropen(fn_tc, "Transverse Current Autocorrelation Functions",
}
fprintf(fp, "\n");
}
- ffclose(fp);
+ gmx_ffclose(fp);
do_view(oenv, fn_tc, "-nxy");
if (fn_cub)
tcafc[kc][i] /= tcafc[kc][0];
fprintf(fp_cub, "%g %g\n", i*dt, tcafc[kc][i]);
}
- fprintf(fp_cub, "&\n");
+ fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
tcafc[kc][0] = 1.0;
}
}
fp_vk = xvgropen(fn_vk, "Fits", "k (nm\\S-1\\N)",
"\\8h\\4 (10\\S-3\\N kg m\\S-1\\N s\\S-1\\N)", oenv);
- fprintf(fp_vk, "@ s0 symbol 2\n");
- fprintf(fp_vk, "@ s0 symbol color 1\n");
- fprintf(fp_vk, "@ s0 linestyle 0\n");
- if (fn_cub)
+ if (output_env_get_print_xvgr_codes(oenv))
{
- fprintf(fp_vk, "@ s1 symbol 3\n");
- fprintf(fp_vk, "@ s1 symbol color 2\n");
+ fprintf(fp_vk, "@ s0 symbol 2\n");
+ fprintf(fp_vk, "@ s0 symbol color 1\n");
+ fprintf(fp_vk, "@ s0 linestyle 0\n");
+ if (fn_cub)
+ {
+ fprintf(fp_vk, "@ s1 symbol 3\n");
+ fprintf(fp_vk, "@ s1 symbol color 2\n");
+ }
}
fp = xvgropen(fn_tcf, "TCAF Fits", "Time (ps)", "", oenv);
for (k = 0; k < nk; k++)
{
fprintf(fp, "%g %g\n", i*dt, fit_function(effnVAC, fitparms, i*dt));
}
- fprintf(fp, "&\n");
+ fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
- ffclose(fp);
+ gmx_ffclose(fp);
do_view(oenv, fn_tcf, "-nxy");
if (fn_cub)
{
fprintf(stdout, "Averaged over k-vectors:\n");
- fprintf(fp_vk, "&\n");
+ fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
for (k = 0; k < nkc; k++)
{
tcafc[k][0] = 1.0;
{
fprintf(fp_cub, "%g %g\n", i*dt, fit_function(effnVAC, fitparms, i*dt));
}
- fprintf(fp_cub, "&\n");
+ fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
- fprintf(fp_vk, "&\n");
- ffclose(fp_cub);
+ fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
+ gmx_ffclose(fp_cub);
do_view(oenv, fn_cub, "-nxy");
}
- ffclose(fp_vk);
+ gmx_ffclose(fp_vk);
do_view(oenv, fn_vk, "-nxy");
}
int gmx_tcaf(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_tcaf[tt] computes tranverse current autocorrelations.",
+ "[THISMODULE] computes tranverse current autocorrelations.",
"These are used to estimate the shear viscosity, [GRK]eta[grk].",
"For details see: Palmer, Phys. Rev. E 49 (1994) pp 359-366.[PAR]",
"Transverse currents are calculated using the",
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
TRUE);
opt2fn("-of", NFILE, fnm), opt2fn_null("-oc", NFILE, fnm),
opt2fn("-ov", NFILE, fnm), oenv);
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff