/*
+ * 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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+ * 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 <ctype.h>
-#include "copyrite.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 "physics.h"
-#include "vec.h"
-#include "tpxio.h"
-#include "mdrun.h"
-#include "calcpot.h"
-#include "main.h"
-#include "random.h"
-#include "index.h"
-#include "mtop_util.h"
-#include "gmx_ana.h"
+#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void insert_ion(int nsa, int *nwater,
gmx_bool bSet[], int repl[], atom_id index[],
- real pot[], rvec x[], t_pbc *pbc,
+ rvec x[], t_pbc *pbc,
int sign, int q, const char *ionname,
- t_mdatoms *mdatoms,
- real rmin, gmx_bool bRandom, int *seed)
+ t_atoms *atoms,
+ real rmin, gmx_rng_t rng)
{
- int i, ii, ei, owater, wlast, m, nw;
- real extr_e, poti, rmin2;
- rvec xei, dx;
- gmx_bool bSub = FALSE;
- gmx_large_int_t maxrand;
+ int i, ei, nw;
+ real rmin2;
+ rvec dx;
+ gmx_int64_t maxrand;
ei = -1;
nw = *nwater;
maxrand = nw;
maxrand *= 1000;
- if (bRandom)
+
+ do
{
- do
- {
- ei = nw*rando(seed);
- maxrand--;
- }
- while (bSet[ei] && (maxrand > 0));
- if (bSet[ei])
- {
- gmx_fatal(FARGS, "No more replaceable solvent!");
- }
+ ei = nw*gmx_rng_uniform_real(rng);
+ maxrand--;
}
- else
+ while (bSet[ei] && (maxrand > 0));
+ if (bSet[ei])
{
- extr_e = 0;
- for (i = 0; (i < nw); i++)
- {
- if (!bSet[i])
- {
- ii = index[nsa*i];
- poti = pot[ii];
- if (q > 0)
- {
- if ((poti <= extr_e) || !bSub)
- {
- extr_e = poti;
- ei = i;
- bSub = TRUE;
- }
- }
- else
- {
- if ((poti >= extr_e) || !bSub)
- {
- extr_e = poti;
- ei = i;
- bSub = TRUE;
- }
- }
- }
- }
- if (ei == -1)
- {
- gmx_fatal(FARGS, "No more replaceable solvent!");
- }
+ gmx_fatal(FARGS, "No more replaceable solvent!");
}
+
fprintf(stderr, "Replacing solvent molecule %d (atom %d) with %s\n",
ei, index[nsa*ei], ionname);
/* Replace solvent molecule charges with ion charge */
bSet[ei] = TRUE;
repl[ei] = sign;
- mdatoms->chargeA[index[nsa*ei]] = q;
+
+ atoms->atom[index[nsa*ei]].q = q;
for (i = 1; i < nsa; i++)
{
- mdatoms->chargeA[index[nsa*ei+i]] = 0;
+ atoms->atom[index[nsa*ei+i]].q = 0;
}
/* Mark all solvent molecules within rmin as unavailable for substitution */
}
}
+
static char *aname(const char *mname)
{
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] replaces solvent molecules by monoatomic ions at",
- "the position of the first atoms with the most favorable electrostatic",
- "potential or at random. The potential is calculated on all atoms, using",
- "normal GROMACS particle-based methods (in contrast to other methods",
- "based on solving the Poisson-Boltzmann equation).",
- "The potential is recalculated after every ion insertion.",
- "If specified in the run input file, a reaction field, shift function",
- "or user function can be used. For the user function a table file",
- "can be specified with the option [TT]-table[tt].",
+ "[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]",
- "With the option [TT]-pot[tt] the potential can be written as B-factors",
- "in a [TT].pdb[tt] file (for visualisation using e.g. Rasmol).",
- "The unit of the potential is 1000 kJ/(mol e), the scaling be changed",
- "with the [TT]-scale[tt] option.[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[] = {
- "Calculation of the potential is not reliable, therefore the [TT]-random[tt] option is now turned on by default.",
- "If you specify a salt concentration existing ions are not taken into account. In effect you therefore specify the amount of salt to be added."
+ "If you specify a salt concentration existing ions are not taken into "
+ "account. In effect you therefore specify the amount of salt to be added.",
};
- static int p_num = 0, n_num = 0, p_q = 1, n_q = -1;
- static const char *p_name = "NA", *n_name = "CL";
- static real rmin = 0.6, scale = 0.001, conc = 0;
- static int seed = 1993;
- static gmx_bool bRandom = TRUE, bNeutral = FALSE;
- static t_pargs pa[] = {
+ static int p_num = 0, n_num = 0, p_q = 1, n_q = -1;
+ static const char *p_name = "NA", *n_name = "CL";
+ static real rmin = 0.6, conc = 0;
+ static int seed = 1993;
+ static gmx_bool bNeutral = FALSE;
+ static t_pargs pa[] = {
{ "-np", FALSE, etINT, {&p_num}, "Number of positive ions" },
{ "-pname", FALSE, etSTR, {&p_name}, "Name of the positive ion" },
{ "-pq", FALSE, etINT, {&p_q}, "Charge of the positive ion" },
{ "-nname", FALSE, etSTR, {&n_name}, "Name of the negative ion" },
{ "-nq", FALSE, etINT, {&n_q}, "Charge of the negative ion" },
{ "-rmin", FALSE, etREAL, {&rmin}, "Minimum distance between ions" },
- { "-random", FALSE, etBOOL, {&bRandom}, "Use random placement of ions instead of based on potential. The rmin option should still work" },
{ "-seed", FALSE, etINT, {&seed}, "Seed for random number generator" },
- { "-scale", FALSE, etREAL, {&scale}, "Scaling factor for the potential for [TT]-pot[tt]" },
{ "-conc", FALSE, etREAL, {&conc},
"Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input [TT].tpr[tt] file. Overrides the [TT]-np[tt] and [TT]-nn[tt] options." },
- { "-neutral", FALSE, etBOOL, {&bNeutral},
- "This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated." }
+ { "-neutral", FALSE, etBOOL, {&bNeutral}, "This option will add enough ions to neutralize the system. These ions are added on top of those specified with [TT]-np[tt]/[TT]-nn[tt] or [TT]-conc[tt]. "}
};
- gmx_mtop_t *mtop;
- gmx_localtop_t *top;
- t_inputrec inputrec;
- t_commrec *cr;
- t_mdatoms *mdatoms;
- gmx_enerdata_t enerd;
- t_graph *graph;
- t_forcerec *fr;
+ t_topology top;
rvec *x, *v;
- real *pot, vol, qtot;
+ real vol, qtot;
matrix box;
t_atoms atoms;
t_pbc pbc;
- int *repl;
+ int *repl, ePBC;
atom_id *index;
- char *grpname;
- gmx_bool *bSet, bPDB;
+ char *grpname, title[STRLEN];
+ gmx_bool *bSet;
int i, nw, nwa, nsa, nsalt, iqtot;
- FILE *fplog;
output_env_t oenv;
+ gmx_rng_t rng;
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
- { efXVG, "-table", "table", ffOPTRD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTO, "-o", NULL, ffWRITE },
- { efLOG, "-g", "genion", ffWRITE },
- { efPDB, "-pot", "pot", ffOPTWR },
{ efTOP, "-p", "topol", ffOPTRW }
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv);
- bPDB = ftp2bSet(efPDB, NFILE, fnm);
- if (bRandom && bPDB)
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, asize(bugs), bugs, &oenv))
{
- fprintf(stderr, "Not computing potential with random option!\n");
- bPDB = FALSE;
+ return 0;
}
/* Check input for something sensible */
gmx_fatal(FARGS, "Negative number of ions to add?");
}
- snew(mtop, 1);
- snew(top, 1);
- fplog = init_calcpot(ftp2fn(efLOG, NFILE, fnm), ftp2fn(efTPX, NFILE, fnm),
- opt2fn("-table", NFILE, fnm), mtop, top, &inputrec, &cr,
- &graph, &mdatoms, &fr, &enerd, &pot, box, &x, oenv);
+ if (conc > 0 && (p_num > 0 || n_num > 0))
+ {
+ fprintf(stderr, "WARNING: -conc specified, overriding -nn and -np.\n");
+ }
- atoms = gmx_mtop_global_atoms(mtop);
+ /* Read atom positions and charges */
+ read_tps_conf(ftp2fn(efTPR, NFILE, fnm), title, &top, &ePBC, &x, &v, box, FALSE);
+ atoms = top.atoms;
+ /* Compute total charge */
qtot = 0;
for (i = 0; (i < atoms.nr); i++)
{
}
iqtot = gmx_nint(qtot);
- if ((conc > 0) || bNeutral)
+
+ if (conc > 0)
{
/* Compute number of ions to be added */
- vol = det(box);
- if (conc > 0)
+ vol = det(box);
+ nsalt = gmx_nint(conc*vol*AVOGADRO/1e24);
+ p_num = abs(nsalt*n_q);
+ n_num = abs(nsalt*p_q);
+ }
+ if (bNeutral)
+ {
+ int qdelta = p_num*p_q + n_num*n_q + iqtot;
+
+ /* Check if the system is neutralizable
+ * is (qdelta == p_q*p_num + n_q*n_num) solvable for p_num and n_num? */
+ int gcd = gmx_greatest_common_divisor(n_q, p_q);
+ if ((qdelta % gcd) != 0)
{
- nsalt = gmx_nint(conc*vol*AVOGADRO/1e24);
- p_num = abs(nsalt*n_q);
- n_num = abs(nsalt*p_q);
- if (bNeutral)
+ gmx_fatal(FARGS, "Can't neutralize this system using -nq %d and"
+ " -pq %d.\n", n_q, p_q);
+ }
+
+ while (qdelta != 0)
+ {
+ while (qdelta < 0)
{
- int qdelta = 0;
- do
- {
- qdelta = (p_num*p_q + n_num*n_q + iqtot);
- if (qdelta < 0)
- {
- p_num += abs(qdelta/p_q);
- qdelta = (p_num*p_q + n_num*n_q + iqtot);
- }
- if (qdelta > 0)
- {
- n_num += abs(qdelta/n_q);
- qdelta = (p_num*p_q + n_num*n_q + iqtot);
- }
- }
- while (qdelta != 0);
+ p_num++;
+ qdelta += p_q;
+ }
+ while (qdelta > 0)
+ {
+ n_num++;
+ qdelta += n_q;
}
}
}
if ((p_num == 0) && (n_num == 0))
{
- if (!bPDB)
- {
- fprintf(stderr, "No ions to add and no potential to calculate.\n");
- exit(0);
- }
- nw = 0;
- nsa = 0; /* to keep gcc happy */
+ 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, inputrec.ePBC, box);
+ set_pbc(&pbc, ePBC, box);
- /* Now loop over the ions that have to be placed */
- do
- {
- if (!bRandom)
+ if (seed == 0)
{
- calc_pot(fplog, cr, mtop, &inputrec, top, x, fr, &enerd, mdatoms, pot, box, graph);
- if (bPDB || debug)
- {
- char buf[STRLEN];
-
- if (debug)
- {
- sprintf(buf, "%d_%s", p_num+n_num, ftp2fn(efPDB, NFILE, fnm));
- }
- else
- {
- strcpy(buf, ftp2fn(efPDB, NFILE, fnm));
- }
- for (i = 0; (i < atoms.nr); i++)
- {
- atoms.pdbinfo[i].bfac = pot[i]*scale;
- }
- write_sto_conf(buf, "Potential calculated by genion",
- &atoms, x, v, inputrec.ePBC, box);
- bPDB = FALSE;
- }
+ rng = gmx_rng_init(gmx_rng_make_seed());
}
- if ((p_num > 0) && (p_num >= n_num))
+ else
{
- insert_ion(nsa, &nw, bSet, repl, index, pot, x, &pbc,
- 1, p_q, p_name, mdatoms, rmin, bRandom, &seed);
- p_num--;
+ rng = gmx_rng_init(seed);
}
- else if (n_num > 0)
+ /* Now loop over the ions that have to be placed */
+ while (p_num-- > 0)
{
- insert_ion(nsa, &nw, bSet, repl, index, pot, x, &pbc,
- -1, n_q, n_name, mdatoms, rmin, bRandom, &seed);
- n_num--;
+ insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
+ 1, p_q, p_name, &atoms, rmin, rng);
}
- }
- while (p_num+n_num > 0);
- fprintf(stderr, "\n");
-
- 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), *mtop->name, &atoms, x, NULL,
- inputrec.ePBC, box);
+ 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");
- thanx(stderr);
+ if (nw)
+ {
+ sort_ions(nsa, nw, repl, index, &atoms, x, p_name, n_name);
+ }
- gmx_log_close(fplog);
+ 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