#include <sstream>
#include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/fileio/tpxio.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 "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/xvgr.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;
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"
gmx_ffclose(fp);
/* write average and stddev */
- fp = xvgropen(fnres, "Average and stddev from bootstrapping", "z", ylabel, opt->oenv);
+ 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");
}
/* plot IACT along reaction coordinate */
- fp = xvgropen(fn, "Integrated autocorrelation times", "z", "IACT [ps]", opt->oenv);
+ fp = xvgropen(fn, "Integrated autocorrelation times", xlabel, "IACT [ps]", opt->oenv);
if (output_env_get_print_xvgr_codes(opt->oenv))
{
fprintf(fp, "@ s0 symbol 1\n@ s0 symbol size 0.5\n@ s0 line linestyle 0\n");
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]);
/* 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]);