/*
+ * 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
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- * 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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+ * 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 "confio.h"
-#include "statutil.h"
-#include "pbc.h"
-#include "force.h"
-#include "gmx_fatal.h"
-#include "futil.h"
-#include "maths.h"
-#include "macros.h"
-#include "vec.h"
-#include "tpxio.h"
-#include "mdrun.h"
-#include "main.h"
-#include "random.h"
-#include "index.h"
-#include "mtop_util.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 "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 "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;
rvec dx;
- gmx_large_int_t maxrand;
+ gmx_int64_t maxrand;
ei = -1;
nw = *nwater;
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
}
int gmx_genion(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]genion[tt] randomly replaces solvent molecules with monoatomic ions.",
+ "[THISMODULE] randomly replaces solvent molecules with monoatomic ions.",
"The group of solvent molecules should be continuous and all molecules",
"should have the same number of atoms.",
"The user should add the ion molecules to the topology file or use",
"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 [TT]genbox[tt]."
+ "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;
}