-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
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*
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- * This source code is part of
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-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "statutil.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "copyrite.h"
-#include "futil.h"
-#include "readinp.h"
-#include "statutil.h"
-#include "txtdump.h"
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
#include "gstat.h"
-#include "gmx_statistics.h"
-#include "xvgr.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gmx_ana.h"
#include "geminate.h"
}
fprintf(stdout, "\n");
- ffclose(fp);
+ gmx_ffclose(fp);
}
static void regression_analysis(int n, gmx_bool bXYdy,
int i, s;
double min, max;
int nbin;
-#if (defined SIZEOF_LONG_LONG_INT) && (SIZEOF_LONG_LONG_INT >= 8)
- long long int *histo;
-#else
- double *histo;
-#endif
+ gmx_int64_t *histo;
min = val[0][0];
max = val[0][0];
}
if (s < nset-1)
{
- fprintf(fp, "&\n");
+ fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
static int real_comp(const void *a, const void *b)
double av, var, err;
real *tmp = NULL;
- fp = ffopen(avfile, "w");
+ fp = gmx_ffopen(avfile, "w");
if ((avbar_opt == avbarERROR) && (nset == 1))
{
avbar_opt = avbarNONE;
}
fprintf(fp, "\n");
}
- ffclose(fp);
+ gmx_ffclose(fp);
if (avbar_opt == avbar90)
{
}
fprintf(stdout, "Set %3d: err.est. %g a %g tau1 %g tau2 %g\n",
s+1, ee, a, tau1, tau2);
- fprintf(fp, "@ legend string %d \"av %f\"\n", 2*s, av[s]);
- fprintf(fp, "@ legend string %d \"ee %6g\"\n",
- 2*s+1, sig[s]*anal_ee_inf(fitparm, n*dt));
+ if (output_env_get_xvg_format(oenv) == exvgXMGR)
+ {
+ fprintf(fp, "@ legend string %d \"av %f\"\n", 2*s, av[s]);
+ fprintf(fp, "@ legend string %d \"ee %6g\"\n", 2*s+1, sig[s]*anal_ee_inf(fitparm, n*dt));
+ }
+ else if (output_env_get_xvg_format(oenv) == exvgXMGRACE)
+ {
+ fprintf(fp, "@ s%d legend \"av %f\"\n", 2*s, av[s]);
+ fprintf(fp, "@ s%d legend \"ee %6g\"\n", 2*s+1, sig[s]*anal_ee_inf(fitparm, n*dt));
+ }
for (i = 0; i < nbs; i++)
{
fprintf(fp, "%g %g %g\n", tbs[i], sig[s]*sqrt(ybs[i]/(n*dt)),
s+1, sig[s]*anal_ee_inf(ac_fit, n*dt),
ac_fit[1], ac_fit[0], ac_fit[2]);
- fprintf(fp, "&\n");
+ fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
for (i = 0; i < nbs; i++)
{
fprintf(fp, "%g %g\n", tbs[i],
}
if (s < nset-1)
{
- fprintf(fp, "&\n");
+ fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
}
sfree(fitsig);
sfree(ybs);
sfree(tbs);
- ffclose(fp);
+ gmx_ffclose(fp);
}
static void luzar_correl(int nn, real *time, int nset, real **val, real temp,
int gmx_analyze(int argc, char *argv[])
{
static const char *desc[] = {
- "[TT]g_analyze[tt] reads an ASCII file and analyzes data sets.",
+ "[THISMODULE] reads an ASCII file and analyzes data sets.",
"A line in the input file may start with a time",
"(see option [TT]-time[tt]) and any number of [IT]y[it]-values may follow.",
"Multiple sets can also be",
"All options, except for [TT]-av[tt] and [TT]-power[tt], assume that the",
"points are equidistant in time.[PAR]",
- "[TT]g_analyze[tt] always shows the average and standard deviation of each",
+ "[THISMODULE] always shows the average and standard deviation of each",
"set, as well as the relative deviation of the third",
"and fourth cumulant from those of a Gaussian distribution with the same",
"standard deviation.[PAR]",
"zero or with a negative value are ignored.[PAR]"
"Option [TT]-luzar[tt] performs a Luzar & Chandler kinetics analysis",
- "on output from [TT]g_hbond[tt]. The input file can be taken directly",
- "from [TT]g_hbond -ac[tt], and then the same result should be produced."
+ "on output from [gmx-hbond]. The input file can be taken directly",
+ "from [TT]gmx hbond -ac[tt], and then the same result should be produced."
};
static real tb = -1, te = -1, frac = 0.5, filtlen = 0, binwidth = 0.1, aver_start = 0;
static gmx_bool bHaveT = TRUE, bDer = FALSE, bSubAv = TRUE, bAverCorr = FALSE, bXYdy = FALSE;
{ "-regression", FALSE, etBOOL, {&bRegression},
"Perform a linear regression analysis on the data. If [TT]-xydy[tt] is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize [MATH][GRK]chi[grk]^2 = (y - A[SUB]0[sub] x[SUB]0[sub] - A[SUB]1[sub] x[SUB]1[sub] - ... - A[SUB]N[sub] x[SUB]N[sub])^2[math] where now Y is the first data set in the input file and x[SUB]i[sub] the others. Do read the information at the option [TT]-time[tt]." },
{ "-luzar", FALSE, etBOOL, {&bLuzar},
- "Do a Luzar and Chandler analysis on a correlation function and related as produced by [TT]g_hbond[tt]. When in addition the [TT]-xydy[tt] flag is given the second and fourth column will be interpreted as errors in c(t) and n(t)." },
+ "Do a Luzar and Chandler analysis on a correlation function and "
+ "related as produced by [gmx-hbond]. When in addition the "
+ "[TT]-xydy[tt] flag is given the second and fourth column will be "
+ "interpreted as errors in c(t) and n(t)." },
{ "-temp", FALSE, etREAL, {&temp},
"Temperature for the Luzar hydrogen bonding kinetics analysis (K)" },
{ "-fitstart", FALSE, etREAL, {&fit_start},
if (fitfile != NULL)
{
- out_fit = ffopen(fitfile, "w");
+ out_fit = gmx_ffopen(fitfile, "w");
if (bXYdy && nset >= 2)
{
do_fit(out_fit, 0, TRUE, n, t, val, npargs, ppa, oenv);
do_fit(out_fit, s, FALSE, n, t, val, npargs, ppa, oenv);
}
}
- ffclose(out_fit);
+ gmx_ffclose(out_fit);
}
printf(" std. dev. relative deviation of\n");
}
if (s < nset-1)
{
- fprintf(out, "&\n");
+ fprintf(out, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
}
- ffclose(out);
+ gmx_ffclose(out);
fprintf(stderr, "\r%d, time=%g\n", j-1, (j-1)*dt);
}
if (ccfile)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff