Bug Summary

File:gromacs/gmxana/gmx_genion.c
Location:line 75, column 5
Description:Value stored to 'ei' is never read

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
10 *
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
15 *
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
20 *
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25 *
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
33 *
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
36 */
37#ifdef HAVE_CONFIG_H1
38#include <config.h>
39#endif
40
41#include <ctype.h>
42#include <stdlib.h>
43#include <string.h>
44
45#include "gromacs/utility/cstringutil.h"
46#include "gromacs/utility/smalloc.h"
47#include "gromacs/fileio/confio.h"
48#include "gromacs/commandline/pargs.h"
49#include "pbc.h"
50#include "force.h"
51#include "gromacs/utility/fatalerror.h"
52#include "gromacs/utility/futil.h"
53#include "gromacs/math/utilities.h"
54#include "macros.h"
55#include "gromacs/math/vec.h"
56#include "gromacs/fileio/tpxio.h"
57#include "mdrun.h"
58#include "gromacs/random/random.h"
59#include "index.h"
60#include "mtop_util.h"
61#include "gmx_ana.h"
62
63static void insert_ion(int nsa, int *nwater,
64 gmx_bool bSet[], int repl[], atom_id index[],
65 rvec x[], t_pbc *pbc,
66 int sign, int q, const char *ionname,
67 t_atoms *atoms,
68 real rmin, gmx_rng_t rng)
69{
70 int i, ei, nw;
71 real rmin2;
72 rvec dx;
73 gmx_int64_t maxrand;
74
75 ei = -1;
Value stored to 'ei' is never read
76 nw = *nwater;
77 maxrand = nw;
78 maxrand *= 1000;
79
80 do
81 {
82 ei = nw*gmx_rng_uniform_real(rng);
83 maxrand--;
84 }
85 while (bSet[ei] && (maxrand > 0));
86 if (bSet[ei])
87 {
88 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 88, "No more replaceable solvent!");
89 }
90
91 fprintf(stderrstderr, "Replacing solvent molecule %d (atom %d) with %s\n",
92 ei, index[nsa*ei], ionname);
93
94 /* Replace solvent molecule charges with ion charge */
95 bSet[ei] = TRUE1;
96 repl[ei] = sign;
97
98 atoms->atom[index[nsa*ei]].q = q;
99 for (i = 1; i < nsa; i++)
100 {
101 atoms->atom[index[nsa*ei+i]].q = 0;
102 }
103
104 /* Mark all solvent molecules within rmin as unavailable for substitution */
105 if (rmin > 0)
106 {
107 rmin2 = rmin*rmin;
108 for (i = 0; (i < nw); i++)
109 {
110 if (!bSet[i])
111 {
112 pbc_dx(pbc, x[index[nsa*ei]], x[index[nsa*i]], dx);
113 if (iprod(dx, dx) < rmin2)
114 {
115 bSet[i] = TRUE1;
116 }
117 }
118 }
119 }
120}
121
122
123static char *aname(const char *mname)
124{
125 char *str;
126 int i;
127
128 str = strdup(mname)(__extension__ (__builtin_constant_p (mname) && ((size_t
)(const void *)((mname) + 1) - (size_t)(const void *)(mname) ==
1) ? (((const char *) (mname))[0] == '\0' ? (char *) calloc (
(size_t) 1, (size_t) 1) : ({ size_t __len = strlen (mname) + 1
; char *__retval = (char *) malloc (__len); if (__retval != (
(void*)0)) __retval = (char *) memcpy (__retval, mname, __len
); __retval; })) : __strdup (mname)));
129 i = strlen(str)-1;
130 while (i > 1 && (isdigit(str[i])((*__ctype_b_loc ())[(int) ((str[i]))] & (unsigned short int
) _ISdigit) || (str[i] == '+') || (str[i] == '-')))
131 {
132 str[i] = '\0';
133 i--;
134 }
135
136 return str;
137}
138
139void sort_ions(int nsa, int nw, int repl[], atom_id index[],
140 t_atoms *atoms, rvec x[],
141 const char *p_name, const char *n_name)
142{
143 int i, j, k, r, np, nn, starta, startr, npi, nni;
144 rvec *xt;
145 char **pptr = NULL((void*)0), **nptr = NULL((void*)0), **paptr = NULL((void*)0), **naptr = NULL((void*)0);
146
147 snew(xt, atoms->nr)(xt) = save_calloc("xt", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 147, (atoms->nr), sizeof(*(xt)));
148
149 /* Put all the solvent in front and count the added ions */
150 np = 0;
151 nn = 0;
152 j = index[0];
153 for (i = 0; i < nw; i++)
154 {
155 r = repl[i];
156 if (r == 0)
157 {
158 for (k = 0; k < nsa; k++)
159 {
160 copy_rvec(x[index[nsa*i+k]], xt[j++]);
161 }
162 }
163 else if (r > 0)
164 {
165 np++;
166 }
167 else if (r < 0)
168 {
169 nn++;
170 }
171 }
172
173 if (np+nn > 0)
174 {
175 /* Put the positive and negative ions at the end */
176 starta = index[nsa*(nw - np - nn)];
177 startr = atoms->atom[starta].resind;
178
179 if (np)
180 {
181 snew(pptr, 1)(pptr) = save_calloc("pptr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 181, (1), sizeof(*(pptr)));
182 pptr[0] = strdup(p_name)(__extension__ (__builtin_constant_p (p_name) && ((size_t
)(const void *)((p_name) + 1) - (size_t)(const void *)(p_name
) == 1) ? (((const char *) (p_name))[0] == '\0' ? (char *) calloc
((size_t) 1, (size_t) 1) : ({ size_t __len = strlen (p_name)
+ 1; char *__retval = (char *) malloc (__len); if (__retval !=
((void*)0)) __retval = (char *) memcpy (__retval, p_name, __len
); __retval; })) : __strdup (p_name)));
183 snew(paptr, 1)(paptr) = save_calloc("paptr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 183, (1), sizeof(*(paptr)));
184 paptr[0] = aname(p_name);
185 }
186 if (nn)
187 {
188 snew(nptr, 1)(nptr) = save_calloc("nptr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 188, (1), sizeof(*(nptr)));
189 nptr[0] = strdup(n_name)(__extension__ (__builtin_constant_p (n_name) && ((size_t
)(const void *)((n_name) + 1) - (size_t)(const void *)(n_name
) == 1) ? (((const char *) (n_name))[0] == '\0' ? (char *) calloc
((size_t) 1, (size_t) 1) : ({ size_t __len = strlen (n_name)
+ 1; char *__retval = (char *) malloc (__len); if (__retval !=
((void*)0)) __retval = (char *) memcpy (__retval, n_name, __len
); __retval; })) : __strdup (n_name)));
190 snew(naptr, 1)(naptr) = save_calloc("naptr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 190, (1), sizeof(*(naptr)));
191 naptr[0] = aname(n_name);
192 }
193 npi = 0;
194 nni = 0;
195 for (i = 0; i < nw; i++)
196 {
197 r = repl[i];
198 if (r > 0)
199 {
200 j = starta+npi;
201 k = startr+npi;
202 copy_rvec(x[index[nsa*i]], xt[j]);
203 atoms->atomname[j] = paptr;
204 atoms->atom[j].resind = k;
205 atoms->resinfo[k].name = pptr;
206 npi++;
207 }
208 else if (r < 0)
209 {
210 j = starta+np+nni;
211 k = startr+np+nni;
212 copy_rvec(x[index[nsa*i]], xt[j]);
213 atoms->atomname[j] = naptr;
214 atoms->atom[j].resind = k;
215 atoms->resinfo[k].name = nptr;
216 nni++;
217 }
218 }
219 for (i = index[nsa*nw-1]+1; i < atoms->nr; i++)
220 {
221 j = i-(nsa-1)*(np+nn);
222 atoms->atomname[j] = atoms->atomname[i];
223 atoms->atom[j] = atoms->atom[i];
224 copy_rvec(x[i], xt[j]);
225 }
226 atoms->nr -= (nsa-1)*(np+nn);
227
228 /* Copy the new positions back */
229 for (i = index[0]; i < atoms->nr; i++)
230 {
231 copy_rvec(xt[i], x[i]);
232 }
233 sfree(xt)save_free("xt", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 233, (xt));
234 }
235}
236
237static void update_topol(const char *topinout, int p_num, int n_num,
238 const char *p_name, const char *n_name, char *grpname)
239{
240#define TEMP_FILENM "temp.top"
241 FILE *fpin, *fpout;
242 char buf[STRLEN4096], buf2[STRLEN4096], *temp, **mol_line = NULL((void*)0);
243 int line, i, nsol, nmol_line, sol_line, nsol_last;
244 gmx_bool bMolecules;
245
246 printf("\nProcessing topology\n");
247 fpin = gmx_ffopen(topinout, "r");
248 fpout = gmx_ffopen(TEMP_FILENM, "w");
249
250 line = 0;
251 bMolecules = FALSE0;
252 nmol_line = 0;
253 sol_line = -1;
254 nsol_last = -1;
255 while (fgets(buf, STRLEN4096, fpin))
256 {
257 line++;
258 strcpy(buf2, buf);
259 if ((temp = strchr(buf2, '\n')(__extension__ (__builtin_constant_p ('\n') && !__builtin_constant_p
(buf2) && ('\n') == '\0' ? (char *) __rawmemchr (buf2
, '\n') : __builtin_strchr (buf2, '\n')))) != NULL((void*)0))
260 {
261 temp[0] = '\0';
262 }
263 ltrim(buf2);
264 if (buf2[0] == '[')
265 {
266 buf2[0] = ' ';
267 if ((temp = strchr(buf2, '\n')(__extension__ (__builtin_constant_p ('\n') && !__builtin_constant_p
(buf2) && ('\n') == '\0' ? (char *) __rawmemchr (buf2
, '\n') : __builtin_strchr (buf2, '\n')))) != NULL((void*)0))
268 {
269 temp[0] = '\0';
270 }
271 rtrim(buf2);
272 if (buf2[strlen(buf2)-1] == ']')
273 {
274 buf2[strlen(buf2)-1] = '\0';
275 ltrim(buf2);
276 rtrim(buf2);
277 bMolecules = (gmx_strcasecmp(buf2, "molecules") == 0);
278 }
279 fprintf(fpout, "%s", buf);
280 }
281 else if (!bMolecules)
282 {
283 fprintf(fpout, "%s", buf);
284 }
285 else
286 {
287 /* Check if this is a line with solvent molecules */
288 sscanf(buf, "%s", buf2);
289 if (gmx_strcasecmp(buf2, grpname) == 0)
290 {
291 sol_line = nmol_line;
292 sscanf(buf, "%*s %d", &nsol_last);
293 }
294 /* Store this molecules section line */
295 srenew(mol_line, nmol_line+1)(mol_line) = save_realloc("mol_line", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 295, (mol_line), (nmol_line+1), sizeof(*(mol_line)));
296 mol_line[nmol_line] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
297 nmol_line++;
298 }
299 }
300 gmx_ffclose(fpin);
301
302 if (sol_line == -1)
303 {
304 gmx_ffclose(fpout);
305 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 305, "No line with moleculetype '%s' found the [ molecules ] section of file '%s'", grpname, topinout);
306 }
307 if (nsol_last < p_num+n_num)
308 {
309 gmx_ffclose(fpout);
310 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 310, "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);
311 }
312
313 /* Print all the molecule entries */
314 for (i = 0; i < nmol_line; i++)
315 {
316 if (i != sol_line)
317 {
318 fprintf(fpout, "%s", mol_line[i]);
319 }
320 else
321 {
322 printf("Replacing %d solute molecules in topology file (%s) "
323 " by %d %s and %d %s ions.\n",
324 p_num+n_num, topinout, p_num, p_name, n_num, n_name);
325 nsol_last -= p_num + n_num;
326 if (nsol_last > 0)
327 {
328 fprintf(fpout, "%-10s %d\n", grpname, nsol_last);
329 }
330 if (p_num > 0)
331 {
332 fprintf(fpout, "%-15s %d\n", p_name, p_num);
333 }
334 if (n_num > 0)
335 {
336 fprintf(fpout, "%-15s %d\n", n_name, n_num);
337 }
338 }
339 }
340 gmx_ffclose(fpout);
341 /* use gmx_ffopen to generate backup of topinout */
342 fpout = gmx_ffopen(topinout, "w");
343 gmx_ffclose(fpout);
344 rename(TEMP_FILENM, topinout);
345#undef TEMP_FILENM
346}
347
348int gmx_genion(int argc, char *argv[])
349{
350 const char *desc[] = {
351 "[THISMODULE] randomly replaces solvent molecules with monoatomic ions.",
352 "The group of solvent molecules should be continuous and all molecules",
353 "should have the same number of atoms.",
354 "The user should add the ion molecules to the topology file or use",
355 "the [TT]-p[tt] option to automatically modify the topology.[PAR]",
356 "The ion molecule type, residue and atom names in all force fields",
357 "are the capitalized element names without sign. This molecule name",
358 "should be given with [TT]-pname[tt] or [TT]-nname[tt], and the",
359 "[TT][molecules][tt] section of your topology updated accordingly,",
360 "either by hand or with [TT]-p[tt]. Do not use an atom name instead!",
361 "[PAR]Ions which can have multiple charge states get the multiplicity",
362 "added, without sign, for the uncommon states only.[PAR]",
363 "For larger ions, e.g. sulfate we recommended using [gmx-insert-molecules]."
364 };
365 const char *bugs[] = {
366 "If you specify a salt concentration existing ions are not taken into "
367 "account. In effect you therefore specify the amount of salt to be added.",
368 };
369 static int p_num = 0, n_num = 0, p_q = 1, n_q = -1;
370 static const char *p_name = "NA", *n_name = "CL";
371 static real rmin = 0.6, conc = 0;
372 static int seed = 1993;
373 static gmx_bool bNeutral = FALSE0;
374 static t_pargs pa[] = {
375 { "-np", FALSE0, etINT, {&p_num}, "Number of positive ions" },
376 { "-pname", FALSE0, etSTR, {&p_name}, "Name of the positive ion" },
377 { "-pq", FALSE0, etINT, {&p_q}, "Charge of the positive ion" },
378 { "-nn", FALSE0, etINT, {&n_num}, "Number of negative ions" },
379 { "-nname", FALSE0, etSTR, {&n_name}, "Name of the negative ion" },
380 { "-nq", FALSE0, etINT, {&n_q}, "Charge of the negative ion" },
381 { "-rmin", FALSE0, etREAL, {&rmin}, "Minimum distance between ions" },
382 { "-seed", FALSE0, etINT, {&seed}, "Seed for random number generator" },
383 { "-conc", FALSE0, etREAL, {&conc},
384 "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." },
385 { "-neutral", FALSE0, 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]. "}
386 };
387 t_topology top;
388 rvec *x, *v;
389 real vol, qtot;
390 matrix box;
391 t_atoms atoms;
392 t_pbc pbc;
393 int *repl, ePBC;
394 atom_id *index;
395 char *grpname, title[STRLEN4096];
396 gmx_bool *bSet;
397 int i, nw, nwa, nsa, nsalt, iqtot;
398 output_env_t oenv;
399 gmx_rng_t rng;
400 t_filenm fnm[] = {
401 { efTPX, NULL((void*)0), NULL((void*)0), ffREAD1<<1 },
402 { efNDX, NULL((void*)0), NULL((void*)0), ffOPTRD(1<<1 | 1<<3) },
403 { efSTO, "-o", NULL((void*)0), ffWRITE1<<2 },
404 { efTOP, "-p", "topol", ffOPTRW((1<<1 | 1<<2) | 1<<3) }
405 };
406#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
407
408 if (!parse_common_args(&argc, argv, PCA_BE_NICE(1<<13), NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm, asize(pa)((int)(sizeof(pa)/sizeof((pa)[0]))), pa,
409 asize(desc)((int)(sizeof(desc)/sizeof((desc)[0]))), desc, asize(bugs)((int)(sizeof(bugs)/sizeof((bugs)[0]))), bugs, &oenv))
410 {
411 return 0;
412 }
413
414 /* Check input for something sensible */
415 if ((p_num < 0) || (n_num < 0))
416 {
417 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 417, "Negative number of ions to add?");
418 }
419
420 if (conc > 0 && (p_num > 0 || n_num > 0))
421 {
422 fprintf(stderrstderr, "WARNING: -conc specified, overriding -nn and -np.\n");
423 }
424
425 /* Read atom positions and charges */
426 read_tps_conf(ftp2fn(efTPX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), title, &top, &ePBC, &x, &v, box, FALSE0);
427 atoms = top.atoms;
428
429 /* Compute total charge */
430 qtot = 0;
431 for (i = 0; (i < atoms.nr); i++)
432 {
433 qtot += atoms.atom[i].q;
434 }
435 iqtot = gmx_nint(qtot);
436
437
438 if (conc > 0)
439 {
440 /* Compute number of ions to be added */
441 vol = det(box);
442 nsalt = gmx_nint(conc*vol*AVOGADRO(6.0221367e23)/1e24);
443 p_num = abs(nsalt*n_q);
444 n_num = abs(nsalt*p_q);
445 }
446 if (bNeutral)
447 {
448 int qdelta = p_num*p_q + n_num*n_q + iqtot;
449
450 /* Check if the system is neutralizable
451 * is (qdelta == p_q*p_num + n_q*n_num) solvable for p_num and n_num? */
452 int gcd = gmx_greatest_common_divisor(n_q, p_q);
453 if ((qdelta % gcd) != 0)
454 {
455 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 455, "Can't neutralize this system using -nq %d and"
456 " -pq %d.\n", n_q, p_q);
457 }
458
459 while (qdelta != 0)
460 {
461 while (qdelta < 0)
462 {
463 p_num++;
464 qdelta += p_q;
465 }
466 while (qdelta > 0)
467 {
468 n_num++;
469 qdelta += n_q;
470 }
471 }
472 }
473
474 if ((p_num == 0) && (n_num == 0))
475 {
476 fprintf(stderrstderr, "No ions to add.\n");
477 exit(0);
478 }
479 else
480 {
481 printf("Will try to add %d %s ions and %d %s ions.\n",
482 p_num, p_name, n_num, n_name);
483 printf("Select a continuous group of solvent molecules\n");
484 get_index(&atoms, ftp2fn_null(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), 1, &nwa, &index, &grpname);
485 for (i = 1; i < nwa; i++)
486 {
487 if (index[i] != index[i-1]+1)
488 {
489 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 489, "The solvent group %s is not continuous: "
490 "index[%d]=%d, index[%d]=%d",
491 grpname, i, index[i-1]+1, i+1, index[i]+1);
492 }
493 }
494 nsa = 1;
495 while ((nsa < nwa) &&
496 (atoms.atom[index[nsa]].resind ==
497 atoms.atom[index[nsa-1]].resind))
498 {
499 nsa++;
500 }
501 if (nwa % nsa)
502 {
503 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 503, "Your solvent group size (%d) is not a multiple of %d",
504 nwa, nsa);
505 }
506 nw = nwa/nsa;
507 fprintf(stderrstderr, "Number of (%d-atomic) solvent molecules: %d\n", nsa, nw);
508 if (p_num+n_num > nw)
509 {
510 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 510, "Not enough solvent for adding ions");
511 }
512 }
513
514 if (opt2bSet("-p", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm))
515 {
516 update_topol(opt2fn("-p", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), p_num, n_num, p_name, n_name, grpname);
517 }
518
519 snew(bSet, nw)(bSet) = save_calloc("bSet", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 519, (nw), sizeof(*(bSet)));
520 snew(repl, nw)(repl) = save_calloc("repl", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 520, (nw), sizeof(*(repl)));
521
522 snew(v, atoms.nr)(v) = save_calloc("v", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 522, (atoms.nr), sizeof(*(v)));
523 snew(atoms.pdbinfo, atoms.nr)(atoms.pdbinfo) = save_calloc("atoms.pdbinfo", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 523, (atoms.nr), sizeof(*(atoms.pdbinfo)));
524
525 set_pbc(&pbc, ePBC, box);
526
527 if (seed == 0)
528 {
529 rng = gmx_rng_init(gmx_rng_make_seed());
530 }
531 else
532 {
533 rng = gmx_rng_init(seed);
534 }
535 /* Now loop over the ions that have to be placed */
536 while (p_num-- > 0)
537 {
538 insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
539 1, p_q, p_name, &atoms, rmin, rng);
540 }
541 while (n_num-- > 0)
542 {
543 insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
544 -1, n_q, n_name, &atoms, rmin, rng);
545 }
546 gmx_rng_destroy(rng);
547 fprintf(stderrstderr, "\n");
548
549 if (nw)
550 {
551 sort_ions(nsa, nw, repl, index, &atoms, x, p_name, n_name);
552 }
553
554 sfree(atoms.pdbinfo)save_free("atoms.pdbinfo", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_genion.c"
, 554, (atoms.pdbinfo));
555 atoms.pdbinfo = NULL((void*)0);
556 write_sto_conf(ftp2fn(efSTO, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), *top.name, &atoms, x, NULL((void*)0), ePBC,
557 box);
558
559 return 0;
560}