/*
+ * 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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*
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+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
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- * Green Red Orange Magenta Azure Cyan Skyblue
+ * To help us fund GROMACS development, we humbly ask that you cite
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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 "gromacs/fileio/futil.h"
-#include "readinp.h"
-#include "statutil.h"
-#include "txtdump.h"
-#include "gstat.h"
-#include "xvgr.h"
-#include "physics.h"
-#include "gromacs/fileio/pdbio.h"
+
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static int index2(int *ibox, int x, int y)
return (ibox[2]*(ibox[1]*x+y)+z);
}
-static gmx_large_int_t indexn(int ndim, const int *ibox, const int *nxyz)
+static gmx_int64_t indexn(int ndim, const int *ibox, const int *nxyz)
{
- gmx_large_int_t d, dd;
+ gmx_int64_t d, dd;
int k, kk;
/* Compute index in 1-D array */
FILE * fp;
int z, i, j, n;
- fp = ffopen(file, "w");
+ fp = gmx_ffopen(file, "w");
/* The REMARKS part is the worst part of the XPLOR format
* and may cause problems with some programs
*/
}
}
fprintf(fp, " -9999\n");
- ffclose(fp);
+ gmx_ffclose(fp);
}
static void write_xplor(const char *file, real *data, int *ibox, real dmin[], real dmax[])
}
typedef struct {
- gmx_large_int_t index;
+ gmx_int64_t index;
real ener;
} t_minimum;
}
}
-static inline
+static gmx_inline
void print_minimum(FILE *fp, int num, const t_minimum *min)
{
fprintf(fp,
- "Minimum %d at index " gmx_large_int_pfmt " energy %10.3f\n",
+ "Minimum %d at index " "%"GMX_PRId64 " energy %10.3f\n",
num, min->index, min->ener);
}
-static inline
+static gmx_inline
void add_minimum(FILE *fp, int num, const t_minimum *min, t_minimum *mm)
{
print_minimum(fp, num, min);
mm[num].ener = min->ener;
}
-static inline
+static gmx_inline
gmx_bool is_local_minimum_from_below(const t_minimum *this_min,
int dimension_index,
int dimension_min,
/* Note over/underflow within W cannot occur. */
}
-static inline
+static gmx_inline
gmx_bool is_local_minimum_from_above(const t_minimum *this_min,
int dimension_index,
int dimension_max,
snew(mm, len);
nmin = 0;
- fp = ffopen(logfile, "w");
+ fp = gmx_ffopen(logfile, "w");
/* Loop over each element in the array of dimenion ndim seeking
* minima with respect to every dimension. Specialized loops for
* speed with ndim == 2 and ndim == 3. */
{
print_minimum(fp, i, &mm[i]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
sfree(mm);
}
static void do_sham(const char *fn, const char *ndx,
const char *xpmP, const char *xpm, const char *xpm2,
- const char *xpm3, const char *xpm4, const char *pdb,
+ const char *xpm3, const char *pdb,
const char *logf,
int n, int neig, real **eig,
gmx_bool bGE, int nenerT, real **enerT,
- int nmap, real *mapindex, real **map,
real Tref,
real pmax, real gmax,
real *emin, real *emax, int nlevels, real pmin,
- const char *mname, int *idim, int *ibox,
+ int *idim, int *ibox,
gmx_bool bXmin, real *xmin, gmx_bool bXmax, real *xmax)
{
FILE *fp;
real *min_eig, *max_eig;
real *axis_x, *axis_y, *axis_z, *axis = NULL;
double *P;
- real **PP, *W, *E, **WW, **EE, *S, **SS, *M, **MM, *bE;
+ real **PP, *W, *E, **WW, **EE, *S, **SS, *M, *bE;
rvec xxx;
char *buf;
- double *bfac, efac, bref, Pmax, Wmin, Wmax, Winf, Emin, Emax, Einf, Smin, Smax, Sinf, Mmin, Mmax, Minf;
+ double *bfac, efac, bref, Pmax, Wmin, Wmax, Winf, Emin, Emax, Einf, Smin, Smax, Sinf, Mmin, Mmax;
real *delta;
int i, j, k, imin, len, index, d, *nbin, *bindex, bi;
int *nxyz, maxbox;
Smax = Emax-Smin;
Sinf = Smax+1;
/* Write out the free energy as a function of bin index */
- fp = ffopen(fn, "w");
+ fp = gmx_ffopen(fn, "w");
for (i = 0; (i < len); i++)
{
if (P[i] != 0)
S[i] = Sinf;
}
}
- ffclose(fp);
+ gmx_ffclose(fp);
/* Organize the structures in the bins */
snew(b, 1);
snew(b->index, len+1);
}
*/
/* Write the index file */
- fp = ffopen(ndx, "w");
+ fp = gmx_ffopen(ndx, "w");
for (i = 0; (i < len); i++)
{
if (nbin[i] > 0)
}
}
}
- ffclose(fp);
+ gmx_ffclose(fp);
snew(axis_x, ibox[0]+1);
snew(axis_y, ibox[1]+1);
snew(axis_z, ibox[2]+1);
axis[j] = min_eig[i] + j/bfac[i];
}
}
- if (map)
- {
- snew(M, len);
- snew(MM, maxbox*maxbox);
- for (i = 0; (i < ibox[0]); i++)
- {
- MM[i] = &(M[i*ibox[1]]);
- }
- Mmin = 1e8;
- Mmax = -1e8;
- for (i = 0; (i < nmap); i++)
- {
- Mmin = min(Mmin, map[0][i]);
- Mmax = max(Mmax, map[0][i]);
- }
- Minf = Mmax*1.05;
- for (i = 0; (i < len); i++)
- {
- M[i] = Minf;
- }
- for (i = 0; (i < nmap); i++)
- {
- index = gmx_nint(mapindex[i]);
- if (index >= len)
- {
- gmx_fatal(FARGS, "Number of bins in file from -mdata option does not correspond to current analysis");
- }
- if (P[index] != 0)
- {
- M[index] = map[0][i];
- }
- }
- }
- else
- {
- MM = NULL;
- Minf = NOTSET;
- }
pick_minima(logf, ibox, neig, len, W);
if (gmax <= 0)
{
EE[i] = &(E[i*ibox[1]]);
SS[i] = &(S[i*ibox[1]]);
}
- fp = ffopen(xpmP, "w");
+ fp = gmx_ffopen(xpmP, "w");
write_xpm(fp, flags, "Probability Distribution", "", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, PP, 0, Pmax, rlo, rhi, &nlevels);
- ffclose(fp);
- fp = ffopen(xpm, "w");
+ gmx_ffclose(fp);
+ fp = gmx_ffopen(xpm, "w");
write_xpm(fp, flags, "Gibbs Energy Landscape", "G (kJ/mol)", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, WW, 0, gmax, rlo, rhi, &nlevels);
- ffclose(fp);
- fp = ffopen(xpm2, "w");
+ gmx_ffclose(fp);
+ fp = gmx_ffopen(xpm2, "w");
write_xpm(fp, flags, "Enthalpy Landscape", "H (kJ/mol)", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, EE,
emin ? *emin : Emin, emax ? *emax : Einf, rlo, rhi, &nlevels);
- ffclose(fp);
- fp = ffopen(xpm3, "w");
+ gmx_ffclose(fp);
+ fp = gmx_ffopen(xpm3, "w");
write_xpm(fp, flags, "Entropy Landscape", "TDS (kJ/mol)", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, SS, 0, Sinf, rlo, rhi, &nlevels);
- ffclose(fp);
- if (map)
- {
- fp = ffopen(xpm4, "w");
- write_xpm(fp, flags, "Custom Landscape", mname, "PC1", "PC2",
- ibox[0], ibox[1], axis_x, axis_y, MM, 0, Minf, rlo, rhi, &nlevels);
- ffclose(fp);
- }
+ gmx_ffclose(fp);
}
else if (neig == 3)
{
/* Dump to PDB file */
- fp = ffopen(pdb, "w");
+ fp = gmx_ffopen(pdb, "w");
for (i = 0; (i < ibox[0]); i++)
{
xxx[XX] = 3*(i+0.5-ibox[0]/2);
}
}
}
- ffclose(fp);
+ gmx_ffclose(fp);
write_xplor("out.xplor", W, ibox, min_eig, max_eig);
- if (map)
- {
- write_xplor("user.xplor", M, ibox, min_eig, max_eig);
- }
nxyz[XX] = imin/(ibox[1]*ibox[2]);
nxyz[YY] = (imin-nxyz[XX]*ibox[1]*ibox[2])/ibox[2];
nxyz[ZZ] = imin % ibox[2];
snew(buf, strlen(xpm)+4);
sprintf(buf, "%s", xpm);
sprintf(&buf[strlen(xpm)-4], "12.xpm");
- fp = ffopen(buf, "w");
+ fp = gmx_ffopen(buf, "w");
write_xpm(fp, flags, "Gibbs Energy Landscape", "W (kJ/mol)", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, WW, 0, gmax, rlo, rhi, &nlevels);
- ffclose(fp);
+ gmx_ffclose(fp);
for (i = 0; (i < ibox[0]); i++)
{
for (j = 0; (j < ibox[2]); j++)
}
}
sprintf(&buf[strlen(xpm)-4], "13.xpm");
- fp = ffopen(buf, "w");
+ fp = gmx_ffopen(buf, "w");
write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC1", "PC3",
ibox[0], ibox[2], axis_x, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
- ffclose(fp);
+ gmx_ffclose(fp);
for (i = 0; (i < ibox[1]); i++)
{
for (j = 0; (j < ibox[2]); j++)
}
}
sprintf(&buf[strlen(xpm)-4], "23.xpm");
- fp = ffopen(buf, "w");
+ fp = gmx_ffopen(buf, "w");
write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC2", "PC3",
ibox[1], ibox[2], axis_y, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
- ffclose(fp);
+ gmx_ffclose(fp);
sfree(buf);
}
- if (map)
- {
- sfree(MM);
- sfree(M);
- }
}
static void ehisto(const char *fh, int n, real **enerT, const output_env_t oenv)
}
fprintf(fp, "\n");
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
int gmx_sham(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_sham[tt] makes multi-dimensional free-energy, enthalpy and entropy plots.",
- "[TT]g_sham[tt] reads one or more [TT].xvg[tt] files and analyzes data sets.",
- "The basic purpose of [TT]g_sham[tt] is to plot Gibbs free energy landscapes",
+ "[THISMODULE] makes multi-dimensional free-energy, enthalpy and entropy plots.",
+ "[THISMODULE] reads one or more [TT].xvg[tt] files and analyzes data sets.",
+ "The basic purpose of [THISMODULE] is to plot Gibbs free energy landscapes",
"(option [TT]-ls[tt])",
"by Bolzmann inverting multi-dimensional histograms (option [TT]-lp[tt]),",
"but it can also",
static rvec nrbox = {32, 32, 32};
static rvec xmin = {0, 0, 0}, xmax = {1, 1, 1};
static int nsets_in = 1, nb_min = 4, resol = 10, nlevels = 25;
- static const char *mname = "";
t_pargs pa[] = {
{ "-time", FALSE, etBOOL, {&bHaveT},
"Expect a time in the input" },
"Maximum enthalpy in output, default is calculate" },
{ "-nlevels", FALSE, etINT, {&nlevels},
"Number of levels for energy landscape" },
- { "-mname", FALSE, etSTR, {&mname},
- "Legend label for the custom landscape" },
};
#define NPA asize(pa)
FILE *out;
- int n, e_n, d_n, nlast, s, nset, e_nset, d_nset, i, j = 0, *idim, *ibox;
- real **val, **et_val, **dt_val, *t, *e_t, e_dt, d_dt, *d_t, dt, tot, error;
+ int n, e_n, nlast, s, nset, e_nset, d_nset, i, j = 0, *idim, *ibox;
+ real **val, **et_val, *t, *e_t, e_dt, d_dt, dt, tot, error;
real *rmin, *rmax;
double *av, *sig, cum1, cum2, cum3, cum4, db;
const char *fn_ge, *fn_ene;
output_env_t oenv;
- gmx_large_int_t num_grid_points;
+ gmx_int64_t num_grid_points;
t_filenm fnm[] = {
{ efXVG, "-f", "graph", ffREAD },
{ efXPM, "-ls", "gibbs", ffOPTWR },
{ efXPM, "-lsh", "enthalpy", ffOPTWR },
{ efXPM, "-lss", "entropy", ffOPTWR },
- { efXPM, "-map", "map", ffOPTWR },
{ efPDB, "-ls3", "gibbs3", ffOPTWR },
- { efXVG, "-mdata", "mapdata", ffOPTRD },
{ efLOG, "-g", "shamlog", ffOPTWR }
};
#define NFILE asize(fnm)
int npargs;
npargs = asize(pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
et_val = NULL;
}
- if (opt2fn_null("-mdata", NFILE, fnm) != NULL)
- {
- dt_val = read_xvg_time(opt2fn("-mdata", NFILE, fnm), bHaveT,
- FALSE, tb, FALSE, te,
- nsets_in, &d_nset, &d_n, &d_dt, &d_t);
- if (d_nset != 1)
- {
- gmx_fatal(FARGS, "Can only handle one mapping data column in %s",
- opt2fn("-mdata", NFILE, fnm));
- }
- }
- else
- {
- dt_val = NULL;
- }
-
if (fn_ene && et_val)
{
ehisto(opt2fn("-histo", NFILE, fnm), e_n, et_val, oenv);
num_grid_points = ibox[0];
for (i = 1; i < nset; i++)
{
- gmx_large_int_t result;
+ gmx_int64_t result;
if (!check_int_multiply_for_overflow(num_grid_points, ibox[i], &result))
{
gmx_fatal(FARGS,
- "The number of dimensions and grid points is too large for this tool\n"
- "to handle with what it knows about the architecture upon which it\n"
- "is running. Use a different machine or consult the GROMACS mailing list.");
+ "The number of dimensions and grid points is too large for this tool.\n");
}
num_grid_points = result;
}
- /* The number of grid points fits in a gmx_large_int_t. */
+ /* The number of grid points fits in a gmx_int64_t. */
do_sham(opt2fn("-dist", NFILE, fnm), opt2fn("-bin", NFILE, fnm),
opt2fn("-lp", NFILE, fnm),
opt2fn("-ls", NFILE, fnm), opt2fn("-lsh", NFILE, fnm),
- opt2fn("-lss", NFILE, fnm), opt2fn("-map", NFILE, fnm),
+ opt2fn("-lss", NFILE, fnm),
opt2fn("-ls3", NFILE, fnm), opt2fn("-g", NFILE, fnm),
- n, nset, val, fn_ge != NULL, e_nset, et_val, d_n, d_t, dt_val, Tref,
+ n, nset, val, fn_ge != NULL, e_nset, et_val, Tref,
pmax, gmax,
opt2parg_bSet("-emin", NPA, pa) ? &emin : NULL,
opt2parg_bSet("-emax", NPA, pa) ? &emax : NULL,
nlevels, pmin,
- mname, idim, ibox,
+ idim, ibox,
opt2parg_bSet("-xmin", NPA, pa), rmin,
opt2parg_bSet("-xmax", NPA, pa), rmax);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff