-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2011,2012,2013,2014, 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.
*
- * 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
+ * GROMACS is free software; you can redistribute it and/or
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+ * 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.
*
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <stdio.h>
-#include <math.h>
+#include "gmxpre.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 <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "strdb.h"
-#include "xvgr.h"
-#include "correl.h"
-#include "gmx_ana.h"
+
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fft/fft.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
enum {
VACF, MVACF, DOS, DOS_SOLID, DOS_DIFF, DOS_CP, DOS_S, DOS_A, DOS_E, DOS_NR
DD = pow(10.0, 0.125);
fp = xvgropen("fy.xvg", "Fig. 2, Lin2003a", "Delta", "y or fy", oenv);
xvgr_legend(fp, asize(leg), leg, oenv);
- fprintf(fp, "@ world 1e-05, 0, 1000, 1\n");
- fprintf(fp, "@ xaxes scale Logarithmic\n");
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "@ world 1e-05, 0, 1000, 1\n");
+ fprintf(fp, "@ xaxes scale Logarithmic\n");
+ }
for (Delta = 1e-5; (Delta <= 1000); Delta *= DD)
{
f = calc_fluidicity(Delta, toler);
int gmx_dos(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_dos[tt] computes the Density of States from a simulations.",
+ "[THISMODULE] computes the Density of States from a simulations.",
"In order for this to be meaningful the velocities must be saved",
"in the trajecotry with sufficiently high frequency such as to cover",
"all vibrations. For flexible systems that would be around a few fs",
t_filenm fnm[] = {
{ efTRN, "-f", NULL, ffREAD },
- { efTPX, "-s", NULL, ffREAD },
+ { efTPR, "-s", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-vacf", "vacf", ffWRITE },
{ efXVG, "-mvacf", "mvacf", ffWRITE },
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc,
asize(bugs), bugs, &oenv))
{
please_cite(fplog, "Pascal2011a");
please_cite(fplog, "Caleman2011b");
- read_tps_conf(ftp2fn(efTPX, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
+ read_tps_conf(ftp2fn(efTPR, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
TRUE);
V = det(box);
tmass = 0;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff