/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
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- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
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* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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-
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+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <ctype.h>
-#include "string2.h"
-#include "smalloc.h"
-#include "sysstuff.h"
+#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/commandline/pargs.h"
-#include "pbc.h"
-#include "force.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "maths.h"
-#include "macros.h"
-#include "vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
#include "gromacs/fileio/tpxio.h"
-#include "mdrun.h"
-#include "main.h"
-#include "random.h"
-#include "index.h"
-#include "mtop_util.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/random/random.h"
+#include "gromacs/topology/index.h"
#include "gmx_ana.h"
static void insert_ion(int nsa, int *nwater,
rvec x[], t_pbc *pbc,
int sign, int q, const char *ionname,
t_atoms *atoms,
- real rmin, int *seed)
+ real rmin, gmx_rng_t rng)
{
int i, ei, nw;
real rmin2;
do
{
- ei = nw*rando(seed);
+ ei = nw*gmx_rng_uniform_real(rng);
maxrand--;
}
while (bSet[ei] && (maxrand > 0));
char *str;
int i;
- str = strdup(mname);
+ str = gmx_strdup(mname);
i = strlen(str)-1;
while (i > 1 && (isdigit(str[i]) || (str[i] == '+') || (str[i] == '-')))
{
if (np)
{
snew(pptr, 1);
- pptr[0] = strdup(p_name);
+ pptr[0] = gmx_strdup(p_name);
snew(paptr, 1);
paptr[0] = aname(p_name);
}
if (nn)
{
snew(nptr, 1);
- nptr[0] = strdup(n_name);
+ nptr[0] = gmx_strdup(n_name);
snew(naptr, 1);
naptr[0] = aname(n_name);
}
gmx_bool bMolecules;
printf("\nProcessing topology\n");
- fpin = ffopen(topinout, "r");
- fpout = ffopen(TEMP_FILENM, "w");
+ fpin = gmx_ffopen(topinout, "r");
+ fpout = gmx_ffopen(TEMP_FILENM, "w");
line = 0;
bMolecules = FALSE;
}
/* Store this molecules section line */
srenew(mol_line, nmol_line+1);
- mol_line[nmol_line] = strdup(buf);
+ mol_line[nmol_line] = gmx_strdup(buf);
nmol_line++;
}
}
- ffclose(fpin);
+ gmx_ffclose(fpin);
if (sol_line == -1)
{
- ffclose(fpout);
+ gmx_ffclose(fpout);
gmx_fatal(FARGS, "No line with moleculetype '%s' found the [ molecules ] section of file '%s'", grpname, topinout);
}
if (nsol_last < p_num+n_num)
{
- ffclose(fpout);
+ gmx_ffclose(fpout);
gmx_fatal(FARGS, "The last entry for moleculetype '%s' in the [ molecules ] section of file '%s' has less solvent molecules (%d) than were replaced (%d)", grpname, topinout, nsol_last, p_num+n_num);
}
}
}
}
- ffclose(fpout);
- /* use ffopen to generate backup of topinout */
- fpout = ffopen(topinout, "w");
- ffclose(fpout);
+ gmx_ffclose(fpout);
+ /* use gmx_ffopen to generate backup of topinout */
+ fpout = gmx_ffopen(topinout, "w");
+ gmx_ffclose(fpout);
rename(TEMP_FILENM, topinout);
#undef TEMP_FILENM
}
"either by hand or with [TT]-p[tt]. Do not use an atom name instead!",
"[PAR]Ions which can have multiple charge states get the multiplicity",
"added, without sign, for the uncommon states only.[PAR]",
- "For larger ions, e.g. sulfate we recommended using [gmx-genbox]."
+ "For larger ions, e.g. sulfate we recommended using [gmx-insert-molecules]."
};
const char *bugs[] = {
"If you specify a salt concentration existing ions are not taken into "
gmx_bool *bSet;
int i, nw, nwa, nsa, nsalt, iqtot;
output_env_t oenv;
+ gmx_rng_t rng;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
if ((p_num == 0) && (n_num == 0))
{
- fprintf(stderr, "No ions to add.\n");
- exit(0);
+ fprintf(stderr, "No ions to add, will just copy input configuration.\n");
}
else
{
{
gmx_fatal(FARGS, "Not enough solvent for adding ions");
}
- }
- if (opt2bSet("-p", NFILE, fnm))
- {
- update_topol(opt2fn("-p", NFILE, fnm), p_num, n_num, p_name, n_name, grpname);
- }
+ if (opt2bSet("-p", NFILE, fnm))
+ {
+ update_topol(opt2fn("-p", NFILE, fnm), p_num, n_num, p_name, n_name, grpname);
+ }
- snew(bSet, nw);
- snew(repl, nw);
+ snew(bSet, nw);
+ snew(repl, nw);
- snew(v, atoms.nr);
- snew(atoms.pdbinfo, atoms.nr);
+ snew(v, atoms.nr);
+ snew(atoms.pdbinfo, atoms.nr);
- set_pbc(&pbc, ePBC, box);
+ set_pbc(&pbc, ePBC, box);
- /* Now loop over the ions that have to be placed */
- while (p_num-- > 0)
- {
- insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
- 1, p_q, p_name, &atoms, rmin, &seed);
- }
- while (n_num-- > 0)
- {
- insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
- -1, n_q, n_name, &atoms, rmin, &seed);
- }
- fprintf(stderr, "\n");
+ if (seed == 0)
+ {
+ rng = gmx_rng_init(gmx_rng_make_seed());
+ }
+ else
+ {
+ rng = gmx_rng_init(seed);
+ }
+ /* Now loop over the ions that have to be placed */
+ while (p_num-- > 0)
+ {
+ insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
+ 1, p_q, p_name, &atoms, rmin, rng);
+ }
+ while (n_num-- > 0)
+ {
+ insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
+ -1, n_q, n_name, &atoms, rmin, rng);
+ }
+ gmx_rng_destroy(rng);
+ fprintf(stderr, "\n");
- if (nw)
- {
- sort_ions(nsa, nw, repl, index, &atoms, x, p_name, n_name);
- }
+ if (nw)
+ {
+ sort_ions(nsa, nw, repl, index, &atoms, x, p_name, n_name);
+ }
- sfree(atoms.pdbinfo);
- atoms.pdbinfo = NULL;
- write_sto_conf(ftp2fn(efSTO, NFILE, fnm), *top.name, &atoms, x, NULL, ePBC,
- box);
+ sfree(atoms.pdbinfo);
+ atoms.pdbinfo = NULL;
+ }
+ write_sto_conf(ftp2fn(efSTO, NFILE, fnm), *top.name, &atoms, x, NULL, ePBC, box);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff