Bug Summary

File:gromacs/gmxpreprocess/toputil.c
Location:line 489, column 21
Description:Dereference of null pointer (loaded from field 'rtp')

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) 2012,2014, 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 <math.h>
42#include <string.h>
43
44#include "gromacs/utility/smalloc.h"
45#include "macros.h"
46#include "topdirs.h"
47#include "toputil.h"
48#include "symtab.h"
49#include "gromacs/utility/fatalerror.h"
50#include "gpp_atomtype.h"
51
52/* UTILITIES */
53
54void set_p_string(t_param *p, const char *s)
55{
56 if (s)
57 {
58 if (strlen(s) < sizeof(p->s)-1)
59 {
60 strncpy(p->s, s, sizeof(p->s))__builtin_strncpy (p->s, s, sizeof(p->s));
61 }
62 else
63 {
64 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/toputil.c"
, 64, "Increase MAXSLEN in include/grompp-impl.h to at least %d,"
65 " or shorten your definition of bonds like %s to at most %d",
66 strlen(s)+1, s, MAXSLEN32-1);
67 }
68 }
69 else
70 {
71 strcpy(p->s, "");
72 }
73}
74
75void pr_alloc (int extra, t_params *pr)
76{
77 int i, j;
78
79 /* get new space for arrays */
80 if (extra < 0)
81 {
82 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/toputil.c"
, 82, "Trying to make array smaller.\n");
83 }
84 if (extra == 0)
85 {
86 return;
87 }
88 if ((pr->nr == 0) && (pr->param != NULL((void*)0)))
89 {
90 fprintf(stderrstderr, "Warning: dangling pointer at %lx\n",
91 (unsigned long)pr->param);
92 pr->param = NULL((void*)0);
93 }
94 if (pr->nr+extra > pr->maxnr)
95 {
96 pr->maxnr = max(1.2*pr->maxnr, pr->maxnr + extra)(((1.2*pr->maxnr) > (pr->maxnr + extra)) ? (1.2*pr->
maxnr) : (pr->maxnr + extra) );
97 srenew(pr->param, pr->maxnr)(pr->param) = save_realloc("pr->param", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/toputil.c"
, 97, (pr->param), (pr->maxnr), sizeof(*(pr->param))
);
98 for (i = pr->nr; (i < pr->maxnr); i++)
99 {
100 for (j = 0; (j < MAXATOMLIST6); j++)
101 {
102 pr->param[i].a[j] = 0;
103 }
104 for (j = 0; (j < MAXFORCEPARAM12); j++)
105 {
106 pr->param[i].c[j] = 0;
107 }
108 set_p_string(&(pr->param[i]), "");
109 }
110 }
111}
112
113void init_plist(t_params plist[])
114{
115 int i;
116
117 for (i = 0; (i < F_NRE); i++)
118 {
119 plist[i].nr = 0;
120 plist[i].maxnr = 0;
121 plist[i].param = NULL((void*)0);
122
123 /* CMAP */
124 plist[i].ncmap = 0;
125 plist[i].cmap = NULL((void*)0);
126 plist[i].grid_spacing = 0;
127 plist[i].nc = 0;
128 plist[i].nct = 0;
129 plist[i].cmap_types = NULL((void*)0);
130 }
131}
132
133void cp_param(t_param *dest, t_param *src)
134{
135 int j;
136
137 for (j = 0; (j < MAXATOMLIST6); j++)
138 {
139 dest->a[j] = src->a[j];
140 }
141 for (j = 0; (j < MAXFORCEPARAM12); j++)
142 {
143 dest->c[j] = src->c[j];
144 }
145 strncpy(dest->s, src->s, sizeof(dest->s))__builtin_strncpy (dest->s, src->s, sizeof(dest->s));
146}
147
148void add_param_to_list(t_params *list, t_param *b)
149{
150 int j;
151
152 /* allocate one position extra */
153 pr_alloc (1, list);
154
155 /* fill the arrays */
156 for (j = 0; (j < MAXFORCEPARAM12); j++)
157 {
158 list->param[list->nr].c[j] = b->c[j];
159 }
160 for (j = 0; (j < MAXATOMLIST6); j++)
161 {
162 list->param[list->nr].a[j] = b->a[j];
163 }
164 memset(list->param[list->nr].s, 0, sizeof(list->param[list->nr].s));
165
166 list->nr++;
167}
168
169
170void init_molinfo(t_molinfo *mol)
171{
172 mol->nrexcl = 0;
173 mol->excl_set = FALSE0;
174 mol->bProcessed = FALSE0;
175 init_plist(mol->plist);
176 init_block(&mol->cgs);
177 init_block(&mol->mols);
178 init_blocka(&mol->excls);
179 init_atom(&mol->atoms);
180}
181
182/* FREEING MEMORY */
183
184void done_bt (t_params *pl)
185{
186 sfree(pl->param)save_free("pl->param", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/toputil.c"
, 186, (pl->param));
187}
188
189void done_mi(t_molinfo *mi)
190{
191 int i;
192
193 done_atom (&(mi->atoms));
194 done_block(&(mi->cgs));
195 done_block(&(mi->mols));
196 for (i = 0; (i < F_NRE); i++)
197 {
198 done_bt(&(mi->plist[i]));
199 }
200}
201
202/* PRINTING STRUCTURES */
203
204void print_bt(FILE *out, directive d, gpp_atomtype_t at,
205 int ftype, int fsubtype, t_params plist[],
206 gmx_bool bFullDih)
207{
208 /* This dihp is a DIRTY patch because the dih-types do not use
209 * all four atoms to determine the type.
210 */
211 const int dihp[2][2] = { { 1, 2 }, { 0, 3 } };
212 t_params *bt;
213 int i, j, f, nral, nrfp;
214 gmx_bool bDih = FALSE0, bSwapParity;
215
216 bt = &(plist[ftype]);
217
218 if (!bt->nr)
219 {
220 return;
221 }
222
223 f = 0;
224 switch (ftype)
225 {
226 case F_G96ANGLES:
227 f = 1;
228 break;
229 case F_G96BONDS:
230 f = 1;
231 break;
232 case F_MORSE:
233 f = 2;
234 break;
235 case F_CUBICBONDS:
236 f = 3;
237 break;
238 case F_CONNBONDS:
239 f = 4;
240 break;
241 case F_HARMONIC:
242 f = 5;
243 break;
244 case F_CROSS_BOND_ANGLES:
245 f = 2;
246 break;
247 case F_CROSS_BOND_BONDS:
248 f = 3;
249 break;
250 case F_UREY_BRADLEY:
251 f = 4;
252 break;
253 case F_PDIHS:
254 case F_RBDIHS:
255 case F_FOURDIHS:
256 bDih = TRUE1;
257 break;
258 case F_IDIHS:
259 f = 1;
260 bDih = TRUE1;
261 break;
262 case F_CONSTRNC:
263 f = 1;
264 break;
265 case F_VSITE3FD:
266 f = 1;
267 break;
268 case F_VSITE3FAD:
269 f = 2;
270 break;
271 case F_VSITE3OUT:
272 f = 3;
273 break;
274 case F_VSITE4FDN:
275 f = 1;
276 break;
277 case F_CMAP:
278 f = 1;
279 break;
280
281 default:
282 bDih = FALSE0;
283 }
284 if (bFullDih)
285 {
286 bDih = FALSE0;
287 }
288 if (fsubtype)
289 {
290 f = fsubtype-1;
291 }
292
293 nral = NRAL(ftype)(interaction_function[(ftype)].nratoms);
294 nrfp = NRFP(ftype)((interaction_function[(ftype)].nrfpA)+(interaction_function[
(ftype)].nrfpB));
295
296 /* header */
297 fprintf(out, "[ %s ]\n", dir2str(d));
298 fprintf(out, "; ");
299 if (!bDih)
300 {
301 fprintf (out, "%3s %4s", "ai", "aj");
302 for (j = 2; (j < nral); j++)
303 {
304 fprintf (out, " %3c%c", 'a', 'i'+j);
305 }
306 }
307 else
308 {
309 for (j = 0; (j < 2); j++)
310 {
311 fprintf (out, "%3c%c", 'a', 'i'+dihp[f][j]);
312 }
313 }
314
315 fprintf (out, " funct");
316 for (j = 0; (j < nrfp); j++)
317 {
318 fprintf (out, " %12c%1d", 'c', j);
319 }
320 fprintf (out, "\n");
321
322 /* print bondtypes */
323 for (i = 0; (i < bt->nr); i++)
324 {
325 bSwapParity = (bt->param[i].C0c[0] == NOTSET-12345) && (bt->param[i].C1c[1] == -1);
326 if (!bDih)
327 {
328 for (j = 0; (j < nral); j++)
329 {
330 fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[j], at));
331 }
332 }
333 else
334 {
335 for (j = 0; (j < 2); j++)
336 {
337 fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[dihp[f][j]], at));
338 }
339 }
340 fprintf (out, "%5d ", bSwapParity ? -f-1 : f+1);
341
342 if (bt->param[i].s[0])
343 {
344 fprintf(out, " %s", bt->param[i].s);
345 }
346 else
347 {
348 for (j = 0; (j < nrfp && (bt->param[i].c[j] != NOTSET-12345)); j++)
349 {
350 fprintf (out, "%13.6e ", bt->param[i].c[j]);
351 }
352 }
353
354 fprintf (out, "\n");
355 }
356 fprintf (out, "\n");
357 fflush (out);
358}
359
360void print_blocka(FILE *out, const char *szName,
361 const char *szIndex, const char *szA,
362 t_blocka *block)
363{
364 int i, j;
365
366 fprintf (out, "; %s\n", szName);
367 fprintf (out, "; %4s %s\n", szIndex, szA);
368 for (i = 0; (i < block->nr); i++)
369 {
370 for (i = 0; (i < block->nr); i++)
371 {
372 fprintf (out, "%6d", i+1);
373 for (j = block->index[i]; (j < ((int)block->index[i+1])); j++)
374 {
375 fprintf (out, "%5d", block->a[j]+1);
376 }
377 fprintf (out, "\n");
378 }
379 fprintf (out, "\n");
380 }
381}
382
383void print_excl(FILE *out, int natoms, t_excls excls[])
384{
385 atom_id i;
386 gmx_bool have_excl;
387 int j;
388
389 have_excl = FALSE0;
390 for (i = 0; i < natoms && !have_excl; i++)
391 {
392 have_excl = (excls[i].nr > 0);
393 }
394
395 if (have_excl)
396 {
397 fprintf (out, "[ %s ]\n", dir2str(d_exclusions));
398 fprintf (out, "; %4s %s\n", "i", "excluded from i");
399 for (i = 0; i < natoms; i++)
400 {
401 if (excls[i].nr > 0)
402 {
403 fprintf (out, "%6d ", i+1);
404 for (j = 0; j < excls[i].nr; j++)
405 {
406 fprintf (out, " %5d", excls[i].e[j]+1);
407 }
408 fprintf (out, "\n");
409 }
410 }
411 fprintf (out, "\n");
412 fflush(out);
413 }
414}
415
416static double get_residue_charge(const t_atoms *atoms, int at)
417{
418 int ri;
419 double q;
420
421 ri = atoms->atom[at].resind;
422 q = 0;
423 while (at < atoms->nr && atoms->atom[at].resind == ri)
424 {
425 q += atoms->atom[at].q;
426 at++;
427 }
428
429 return q;
430}
431
432void print_atoms(FILE *out, gpp_atomtype_t atype, t_atoms *at, int *cgnr,
433 gmx_bool bRTPresname)
434{
435 int i, ri;
436 int tpA, tpB;
437 const char *as;
438 char *tpnmA, *tpnmB;
439 double qres, qtot;
440
441 as = dir2str(d_atoms);
442 fprintf(out, "[ %s ]\n", as);
443 fprintf(out, "; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n",
444 "nr", "type", "resnr", "residue", "atom", "cgnr", "charge", "mass", "typeB", "chargeB", "massB");
445
446 qtot = 0;
447
448 if (debug)
1
Assuming 'debug' is null
→
2
←
Taking false branch
→
449 {
450 fprintf(debug, "This molecule has %d atoms and %d residues\n",
451 at->nr, at->nres);
452 }
453
454 if (at->nres)
3
←
Taking true branch
→
455 {
456 /* if the information is present... */
457 for (i = 0; (i < at->nr); i++)
4
←
Loop condition is true. Entering loop body
→
458 {
459 ri = at->atom[i].resind;
460 if ((i == 0 || ri != at->atom[i-1].resind) &&
6
←
Taking false branch
→
461 at->resinfo[ri].rtp != NULL((void*)0))
5
←
Assuming pointer value is null
→
462 {
463 qres = get_residue_charge(at, i);
464 fprintf(out, "; residue %3d %-3s rtp %-4s q ",
465 at->resinfo[ri].nr,
466 *at->resinfo[ri].name,
467 *at->resinfo[ri].rtp);
468 if (fabs(qres) < 0.001)
469 {
470 fprintf(out, " %s", "0.0");
471 }
472 else
473 {
474 fprintf(out, "%+3.1f", qres);
475 }
476 fprintf(out, "\n");
477 }
478 tpA = at->atom[i].type;
479 if ((tpnmA = get_atomtype_name(tpA, atype)) == NULL((void*)0))
7
←
Taking false branch
→
480 {
481 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/toputil.c"
, 481, "tpA = %d, i= %d in print_atoms", tpA, i);
482 }
483
484 fprintf(out, "%6d %10s %6d%c %5s %6s %6d %10g %10g",
485 i+1, tpnmA,
486 at->resinfo[ri].nr,
487 at->resinfo[ri].ic,
488 bRTPresname ?
8
←
Assuming 'bRTPresname' is not equal to 0
→
9
←
'?' condition is true
→
489 *(at->resinfo[at->atom[i].resind].rtp) :
10
←
Dereference of null pointer (loaded from field 'rtp')
490 *(at->resinfo[at->atom[i].resind].name),
491 *(at->atomname[i]), cgnr[i],
492 at->atom[i].q, at->atom[i].m);
493 if (PERTURBED(at->atom[i])(((at->atom[i]).mB != (at->atom[i]).m) || ((at->atom
[i]).qB != (at->atom[i]).q) || ((at->atom[i]).typeB != (
at->atom[i]).type)))
494 {
495 tpB = at->atom[i].typeB;
496 if ((tpnmB = get_atomtype_name(tpB, atype)) == NULL((void*)0))
497 {
498 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/toputil.c"
, 498, "tpB = %d, i= %d in print_atoms", tpB, i);
499 }
500 fprintf(out, " %6s %10g %10g",
501 tpnmB, at->atom[i].qB, at->atom[i].mB);
502 }
503 qtot += (double)at->atom[i].q;
504 if (fabs(qtot) < 4*GMX_REAL_EPS5.96046448E-08)
505 {
506 qtot = 0;
507 }
508 fprintf(out, " ; qtot %.4g\n", qtot);
509 }
510 }
511 fprintf(out, "\n");
512 fflush(out);
513}
514
515void print_bondeds(FILE *out, int natoms, directive d,
516 int ftype, int fsubtype, t_params plist[])
517{
518 t_symtab stab;
519 gpp_atomtype_t atype;
520 t_param *param;
521 t_atom *a;
522 int i;
523
524 atype = init_atomtype();
525 snew(a, 1)(a) = save_calloc("a", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/toputil.c"
, 525, (1), sizeof(*(a)));
526 snew(param, 1)(param) = save_calloc("param", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/toputil.c"
, 526, (1), sizeof(*(param)));
527 open_symtab(&stab);
528 for (i = 0; (i < natoms); i++)
529 {
530 char buf[12];
531 sprintf(buf, "%4d", (i+1));
532 add_atomtype(atype, &stab, a, buf, param, 0, 0, 0, 0, 0, 0, 0);
533 }
534 print_bt(out, d, atype, ftype, fsubtype, plist, TRUE1);
535
536 done_symtab(&stab);
537 sfree(a)save_free("a", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/toputil.c"
, 537, (a));
538 sfree(param)save_free("param", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/toputil.c"
, 538, (param));
539 done_atomtype(atype);
540}