/*
+ * 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.
+ *
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <stdio.h>
#include <string.h>
-#include "physics.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "txtdump.h"
-#include "bondf.h"
-#include "xvgr.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "gstat.h"
-#include "confio.h"
+
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
void print_one(const output_env_t oenv, const char *base, const char *name,
const char *title, const char *ylabel, int nf, real time[],
{
fprintf(fp, "%10g %10g\n", time[k], data[k]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
-static int calc_RBbin(real phi, int multiplicity, real core_frac)
+static int calc_RBbin(real phi, int gmx_unused multiplicity, real gmx_unused core_frac)
{
/* multiplicity and core_frac NOT used,
* just given to enable use of pt-to-fn in caller low_ana_dih_trans*/
{
fprintf(fp, "%10.3f %10d\n", time[j], tr_f[j]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
/* Compute histogram from # transitions per dihedral */
fprintf(fp, "%10.3f %10d\n", ttime/i, tr_f[i]);
}
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
sfree(tr_f);
}
-void mk_multiplicity_lookup (int *multiplicity, int maxchi, real **dih,
+void mk_multiplicity_lookup (int *multiplicity, int maxchi,
int nlist, t_dlist dlist[], int nangles)
{
/* new by grs - for dihedral j (as in dih[j]) get multiplicity from dlist
}
-void mk_chi_lookup (int **lookup, int maxchi, real **dih,
+void mk_chi_lookup (int **lookup, int maxchi,
int nlist, t_dlist dlist[])
{
int i, j, Dih, Chi;
j = 0;
- for (Dih = 0; (Dih < NONCHI+maxchi); Dih++)
+ /* NONCHI points to chi1, therefore we have to start counting there. */
+ for (Dih = NONCHI; (Dih < NONCHI+maxchi); Dih++)
{
for (i = 0; (i < nlist); i++)
{
}
-void get_chi_product_traj (real **dih, int nframes, int nangles, int nlist,
+void get_chi_product_traj (real **dih, int nframes, int nlist,
int maxchi, t_dlist dlist[], real time[],
int **lookup, int *multiplicity, gmx_bool bRb, gmx_bool bNormalize,
real core_frac, gmx_bool bAll, const char *fnall,
sprintf(histitle, "cumulative rotamer distribution for %s", dlist[i].name);
fprintf(stderr, " and %s ", hisfile);
fp = xvgropen(hisfile, histitle, "number", "", oenv);
- fprintf(fp, "@ xaxis tick on\n");
- fprintf(fp, "@ xaxis tick major 1\n");
- fprintf(fp, "@ type xy\n");
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "@ xaxis tick on\n");
+ fprintf(fp, "@ xaxis tick major 1\n");
+ fprintf(fp, "@ type xy\n");
+ }
for (k = 0; (k < nbin); k++)
{
if (bNormalize)
fprintf(fp, "%5d %10d\n", k, chi_prhist[k]);
}
}
- fprintf(fp, "&\n");
- ffclose(fp);
+ fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
+ gmx_ffclose(fp);
}
/* and finally print out occupancies to a single file */
}
sfree(chi_prtrj);
- ffclose(fpall);
+ gmx_ffclose(fpall);
fprintf(stderr, "\n");
}
*S2 = tdc*tdc+tds*tds;
}
-static void calc_angles(FILE *log, t_pbc *pbc,
+static void calc_angles(struct t_pbc *pbc,
int n3, atom_id index[], real ang[], rvec x_s[])
{
int i, ix, t1, t2;
}
}
-static void calc_dihs(FILE *log, t_pbc *pbc,
+static void calc_dihs(struct t_pbc *pbc,
int n4, atom_id index[], real ang[], rvec x_s[])
{
int i, ix, t1, t2, t3;
real *dih[],
const output_env_t oenv)
{
- t_pbc *pbc;
- t_trxstatus *status;
- int i, angind, natoms, total, teller;
- int nangles, n_alloc;
- real t, fraction, pifac, aa, angle;
- real *angles[2];
- matrix box;
- rvec *x;
- int cur = 0;
+ struct t_pbc *pbc;
+ t_trxstatus *status;
+ int i, angind, natoms, total, teller;
+ int nangles, n_alloc;
+ real t, fraction, pifac, aa, angle;
+ real *angles[2];
+ matrix box;
+ rvec *x;
+ int cur = 0;
#define prev (1-cur)
snew(pbc, 1);
if (bAngles)
{
- calc_angles(stdout, pbc, isize, index, angles[cur], x);
+ calc_angles(pbc, isize, index, angles[cur], x);
}
else
{
- calc_dihs(stdout, pbc, isize, index, angles[cur], x);
+ calc_dihs(pbc, isize, index, angles[cur], x);
/* Trans fraction */
fraction = calc_fraction(angles[cur], nangles);
/* Increment loop counter */
teller++;
}
- while (read_next_x(oenv, status, &t, natoms, x, box));
+ while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
sfree(x);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff