/*
+ * 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.
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-
- * This program is free software; you can redistribute it and/or
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- * 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 <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 "statutil.h"
-#include "index.h"
-#include "pdbio.h"
-#include "tpxio.h"
-#include "txtdump.h"
-#include "physics.h"
-#include "random.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/utility/futil.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/units.h"
+#include "gromacs/random/random.h"
#include "eigio.h"
#include "gmx_ana.h"
int gmx_nmens(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_nmens[tt] generates an ensemble around an average structure",
+ "[THISMODULE] generates an ensemble around an average structure",
"in a subspace that is defined by a set of normal modes (eigenvectors).",
"The eigenvectors are assumed to be mass-weighted.",
"The position along each eigenvector is randomly taken from a Gaussian",
real rfac, invfr, rhalf, jr;
int * eigvalnr;
output_env_t oenv;
-
+ gmx_rng_t rng;
unsigned long jran;
const unsigned long im = 0xffff;
const unsigned long ia = 1093;
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
indexfile = ftp2fn_null(efNDX, NFILE, fnm);
if (seed == -1)
{
- seed = make_seed();
+ seed = (int)gmx_rng_make_seed();
+ rng = gmx_rng_init(seed);
+ }
+ else
+ {
+ rng = gmx_rng_init(seed);
}
fprintf(stderr, "Using seed %d and a temperature of %g K\n", seed, temp);
snew(xout1, natoms);
snew(xout2, atoms->nr);
out = open_trx(ftp2fn(efTRO, NFILE, fnm), "w");
- jran = (unsigned long)((real)im*rando(&seed));
+ jran = (unsigned long)((real)im*gmx_rng_uniform_real(rng));
+ gmx_rng_destroy(rng);
for (s = 0; s < nstruct; s++)
{
for (i = 0; i < natoms; i++)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff