* \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 "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 "gmx_ana.h"
-#include "macros.h"
-
-#include "string2.h"
-#include "xvgr.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
*/
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;
}
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 */
}
/* 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) ? "&" : "");
}
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;
{
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 */
}
/* 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++)
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]);
//! 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);
}
/* 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]);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff