-/* -*- 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
- *
- * 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
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/*! \internal \file
* \author Jochen Hub <jhub@gwdg.de>
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
+#include <string.h>
+
#include <sstream>
#include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "vec.h"
-#include "copyrite.h"
#include "gromacs/fileio/tpxio.h"
-#include "names.h"
-#include "gmx_random.h"
-#include "gmx_ana.h"
-#include "macros.h"
-
-#include "string2.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
//! longest file names allowed in input files
#define WHAM_MAXFILELEN 2048
+/*! \brief
+ * x-axis legend for output files
+ */
+static const char *xlabel = "\\xx\\f{} (nm)";
+
/*! \brief
* enum for energy units
*/
* \name Using umbrella pull code since gromacs 4.x
*/
/*!\{*/
- int npullcrds; //!< nr of pull coordinates in tpr file
- int pull_geometry; //!< such as distance, direction
- ivec pull_dim; //!< pull dimension with geometry distance
- int pull_ndim; //!< nr of pull_dim != 0
- gmx_bool bPrintRef; //!< Coordinates of reference groups written to pullx.xvg ?
- real *k; //!< force constants in tpr file
- real *init_dist; //!< reference displacements
- real *umbInitDist; //!< reference displacement in umbrella direction
+ int npullcrds; //!< nr of pull coordinates in tpr file
+ int pull_geometry; //!< such as distance, direction
+ ivec pull_dim; //!< pull dimension with geometry distance
+ int pull_ndim; //!< nr of pull_dim != 0
+ gmx_bool bPrintRef; //!< Coordinates of reference groups written to pullx.xvg ?
+ real *k; //!< force constants in tpr file
+ real *init_dist; //!< reference displacements
+ real *umbInitDist; //!< reference displacement in umbrella direction
/*!\}*/
/*!
* \name Using PDO files common until gromacs 3.x
snew(fn, strlen(fnhist)+10);
snew(buf, strlen(fnhist)+10);
sprintf(fn, "%s_cumul.xvg", strncpy(buf, fnhist, strlen(fnhist)-4));
- fp = xvgropen(fn, "CDFs of umbrella windows", "z", "CDF", opt->oenv);
+ fp = xvgropen(fn, "CDFs of umbrella windows", xlabel, "CDF", opt->oenv);
}
nbin = opt->bins;
fprintf(fp, "\n");
}
printf("Wrote cumulative distribution functions to %s\n", fn);
- ffclose(fp);
+ gmx_ffclose(fp);
sfree(fn);
sfree(buf);
}
}
else
{
- fn = strdup(fnhist);
+ fn = gmx_strdup(fnhist);
strcpy(title, "Umbrella histograms");
}
- fp = xvgropen(fn, title, "z", "count", opt->oenv);
+ fp = xvgropen(fn, title, xlabel, "count", opt->oenv);
bins = opt->bins;
/* Write histograms */
fprintf(fp, "\n");
}
- ffclose(fp);
+ gmx_ffclose(fp);
printf("Wrote %s\n", fn);
if (bs_index >= 0)
{
}
/* do bootstrapping */
- fp = xvgropen(fnprof, "Boot strap profiles", "z", ylabel, opt->oenv);
+ fp = xvgropen(fnprof, "Boot strap profiles", xlabel, ylabel, opt->oenv);
for (ib = 0; ib < opt->nBootStrap; ib++)
{
printf(" *******************************************\n"
bsProfiles_av2[i] += tmp*tmp;
fprintf(fp, "%e\t%e\n", (i+0.5)*opt->dz+opt->min, tmp);
}
- fprintf(fp, "&\n");
+ fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(opt->oenv) ? "&" : "");
}
- ffclose(fp);
+ gmx_ffclose(fp);
/* write average and stddev */
- fp = xvgropen(fnres, "Average and stddev from bootstrapping", "z", ylabel, opt->oenv);
- fprintf(fp, "@TYPE xydy\n");
+ fp = xvgropen(fnres, "Average and stddev from bootstrapping", xlabel, ylabel, opt->oenv);
+ if (output_env_get_print_xvgr_codes(opt->oenv))
+ {
+ fprintf(fp, "@TYPE xydy\n");
+ }
for (i = 0; i < opt->bins; i++)
{
bsProfiles_av [i] /= opt->nBootStrap;
stddev = (tmp >= 0.) ? sqrt(tmp) : 0.; /* Catch rouding errors */
fprintf(fp, "%e\t%e\t%e\n", (i+0.5)*opt->dz+opt->min, bsProfiles_av [i], stddev);
}
- ffclose(fp);
+ gmx_ffclose(fp);
printf("Wrote boot strap result to %s\n", fnres);
}
int nread, sizenow, i, block = 1;
FILE *fp;
- fp = ffopen(fn, "r");
+ fp = gmx_ffopen(fn, "r");
nread = 0;
sizenow = 0;
while (fgets(tmp, sizeof(tmp), fp) != NULL)
}
else
{
- pipe = ffopen(fn, "r");
+ pipe = gmx_ffopen(fn, "r");
*bPipeOpen = FALSE;
}
#ifdef HAVE_PIPES
pclose(fp);
#else
- ffclose(fp);
+ gmx_ffclose(fp);
#endif
}
}
else
{
- ffclose(file);
+ gmx_ffclose(file);
}
}
printf("\n");
}
else
{
- ffclose(file);
+ gmx_ffclose(file);
}
}
printf("\n");
{
fprintf(fpcorr, "%g %g\n", k*dt, corr[k]);
}
- fprintf(fpcorr, "&\n");
+ fprintf(fpcorr, "%s\n", output_env_get_print_xvgr_codes(opt->oenv) ? "&" : "");
}
/* esimate integrated correlation time, fitting is too unstable */
printf(" done\n");
if (fpcorr)
{
- ffclose(fpcorr);
+ gmx_ffclose(fpcorr);
}
/* plot IACT along reaction coordinate */
- fp = xvgropen(fn, "Integrated autocorrelation times", "z", "IACT [ps]", opt->oenv);
- fprintf(fp, "@ s0 symbol 1\n@ s0 symbol size 0.5\n@ s0 line linestyle 0\n");
- fprintf(fp, "# WIN tau(gr1) tau(gr2) ...\n");
- for (i = 0; i < nwins; i++)
+ fp = xvgropen(fn, "Integrated autocorrelation times", xlabel, "IACT [ps]", opt->oenv);
+ if (output_env_get_print_xvgr_codes(opt->oenv))
{
- fprintf(fp, "# %3d ", i);
- for (ig = 0; ig < window[i].nPull; ig++)
+ fprintf(fp, "@ s0 symbol 1\n@ s0 symbol size 0.5\n@ s0 line linestyle 0\n");
+ fprintf(fp, "# WIN tau(gr1) tau(gr2) ...\n");
+ for (i = 0; i < nwins; i++)
{
- fprintf(fp, " %11g", window[i].tau[ig]);
+ fprintf(fp, "# %3d ", i);
+ for (ig = 0; ig < window[i].nPull; ig++)
+ {
+ fprintf(fp, " %11g", window[i].tau[ig]);
+ }
+ fprintf(fp, "\n");
}
- fprintf(fp, "\n");
}
for (i = 0; i < nwins; i++)
{
opt->sigSmoothIact);
/* smooth IACT along reaction coordinate and overwrite g=1+2tau */
smoothIact(window, nwins, opt);
- fprintf(fp, "&\n@ s1 symbol 1\n@ s1 symbol size 0.5\n@ s1 line linestyle 0\n");
- fprintf(fp, "@ s1 symbol color 2\n");
+ fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(opt->oenv) ? "&" : "");
+ if (output_env_get_print_xvgr_codes(opt->oenv))
+ {
+ fprintf(fp, "@ s1 symbol 1\n@ s1 symbol size 0.5\n@ s1 line linestyle 0\n");
+ fprintf(fp, "@ s1 symbol color 2\n");
+ }
for (i = 0; i < nwins; i++)
{
for (ig = 0; ig < window[i].nPull; ig++)
}
}
}
- ffclose(fp);
+ gmx_ffclose(fp);
printf("Wrote %s\n", fn);
}
nHist++;
fAv += window[i].forceAv[ig];
}
- /* at the same time, rememer closest histogram */
+ /* at the same time, remember closest histogram */
if (dist < distmin)
{
winmin = i;
}
if (opt->verbose)
{
- fp = xvgropen("pmfintegrated.xvg", "PMF from force integration", "z", "PMF [kJ/mol]", opt->oenv);
+ fp = xvgropen("pmfintegrated.xvg", "PMF from force integration", xlabel, "PMF (kJ/mol)", opt->oenv);
for (j = 0; j < opt->bins; ++j)
{
fprintf(fp, "%g %g\n", (j+0.5)*dz+opt->min, pot[j]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
printf("verbose mode: wrote %s with PMF from interated forces\n", "pmfintegrated.xvg");
}
char fmt[1024], fmtign[1024];
int block = 1, sizenow;
- fp = ffopen(opt->fnGroupsel, "r");
+ fp = gmx_ffopen(opt->fnGroupsel, "r");
opt->groupsel = NULL;
snew(tmpbuf, len);
//! Boolean XOR
#define WHAMBOOLXOR(a, b) ( ((!(a)) && (b)) || ((a) && (!(b))))
-/*! Number of elements in fnm (used for command line parsing) */
+//! Number of elements in fnm (used for command line parsing)
#define NFILE asize(fnm)
//! The main g_wham routine
opt.stepchange = 100;
opt.stepUpdateContrib = 100;
- if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, 0,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &opt.oenv))
{
return 0;
/* write histograms */
histout = xvgropen(opt2fn("-hist", NFILE, fnm), "Umbrella histograms",
- "z", "count", opt.oenv);
+ xlabel, "count", opt.oenv);
for (l = 0; l < opt.bins; ++l)
{
fprintf(histout, "%e\t", (double)(l+0.5)/opt.bins*(opt.max-opt.min)+opt.min);
}
fprintf(histout, "\n");
}
- ffclose(histout);
+ gmx_ffclose(histout);
printf("Wrote %s\n", opt2fn("-hist", NFILE, fnm));
if (opt.bHistOnly)
{
}
/* write profile or density of states */
- profout = xvgropen(opt2fn("-o", NFILE, fnm), title, "z", ylabel, opt.oenv);
+ profout = xvgropen(opt2fn("-o", NFILE, fnm), title, xlabel, ylabel, opt.oenv);
for (i = 0; i < opt.bins; ++i)
{
fprintf(profout, "%e\t%e\n", (double)(i+0.5)/opt.bins*(opt.max-opt.min)+opt.min, profile[i]);
}
- ffclose(profout);
+ gmx_ffclose(profout);
printf("Wrote %s\n", opt2fn("-o", NFILE, fnm));
/* Bootstrap Method */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff