Bug Summary

File:gromacs/gmxana/gmx_sans.c
Location:line 176, column 13
Description:Array access results in a null pointer dereference

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
8 *
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
13 *
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
18 *
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
23 *
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
31 *
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
34 */
35
36#ifdef HAVE_CONFIG_H1
37#include <config.h>
38#endif
39
40#include "gromacs/utility/smalloc.h"
41#include "typedefs.h"
42#include "macros.h"
43#include "gromacs/math/vec.h"
44#include "pbc.h"
45#include "gromacs/fileio/xvgr.h"
46#include "copyrite.h"
47#include "gromacs/commandline/pargs.h"
48#include "index.h"
49#include "gstat.h"
50#include "gmx_ana.h"
51#include "nsfactor.h"
52
53#include "gromacs/utility/futil.h"
54#include "gromacs/fileio/matio.h"
55#include "gromacs/fileio/tpxio.h"
56#include "gromacs/fileio/trxio.h"
57#include "gromacs/utility/fatalerror.h"
58#include "gromacs/utility/gmxomp.h"
59
60int gmx_sans(int argc, char *argv[])
61{
62 const char *desc[] = {
63 "[THISMODULE] computes SANS spectra using Debye formula.",
64 "It currently uses topology file (since it need to assigne element for each atom).",
65 "[PAR]",
66 "Parameters:[PAR]"
67 "[TT]-pr[tt] Computes normalized g(r) function averaged over trajectory[PAR]",
68 "[TT]-prframe[tt] Computes normalized g(r) function for each frame[PAR]",
69 "[TT]-sq[tt] Computes SANS intensity curve averaged over trajectory[PAR]",
70 "[TT]-sqframe[tt] Computes SANS intensity curve for each frame[PAR]",
71 "[TT]-startq[tt] Starting q value in nm[PAR]",
72 "[TT]-endq[tt] Ending q value in nm[PAR]",
73 "[TT]-qstep[tt] Stepping in q space[PAR]",
74 "Note: When using Debye direct method computational cost increases as",
75 "1/2 * N * (N - 1) where N is atom number in group of interest.",
76 "[PAR]",
77 "WARNING: If sq or pr specified this tool can produce large number of files! Up to two times larger than number of frames!"
78 };
79 static gmx_bool bPBC = TRUE1;
80 static gmx_bool bNORM = FALSE0;
81 static real binwidth = 0.2, grid = 0.05; /* bins shouldnt be smaller then smallest bond (~0.1nm) length */
82 static real start_q = 0.0, end_q = 2.0, q_step = 0.01;
83 static real mcover = -1;
84 static unsigned int seed = 0;
85 static int nthreads = -1;
86
87 static const char *emode[] = { NULL((void*)0), "direct", "mc", NULL((void*)0) };
88 static const char *emethod[] = { NULL((void*)0), "debye", "fft", NULL((void*)0) };
89
90 gmx_neutron_atomic_structurefactors_t *gnsf;
91 gmx_sans_t *gsans;
92
93#define NPA((int)(sizeof(pa)/sizeof((pa)[0]))) asize(pa)((int)(sizeof(pa)/sizeof((pa)[0])))
94
95 t_pargs pa[] = {
96 { "-bin", FALSE0, etREAL, {&binwidth},
97 "[HIDDEN]Binwidth (nm)" },
98 { "-mode", FALSE0, etENUM, {emode},
99 "Mode for sans spectra calculation" },
100 { "-mcover", FALSE0, etREAL, {&mcover},
101 "Monte-Carlo coverage should be -1(default) or (0,1]"},
102 { "-method", FALSE0, etENUM, {emethod},
103 "[HIDDEN]Method for sans spectra calculation" },
104 { "-pbc", FALSE0, etBOOL, {&bPBC},
105 "Use periodic boundary conditions for computing distances" },
106 { "-grid", FALSE0, etREAL, {&grid},
107 "[HIDDEN]Grid spacing (in nm) for FFTs" },
108 {"-startq", FALSE0, etREAL, {&start_q},
109 "Starting q (1/nm) "},
110 {"-endq", FALSE0, etREAL, {&end_q},
111 "Ending q (1/nm)"},
112 { "-qstep", FALSE0, etREAL, {&q_step},
113 "Stepping in q (1/nm)"},
114 { "-seed", FALSE0, etINT, {&seed},
115 "Random seed for Monte-Carlo"},
116#ifdef GMX_OPENMP
117 { "-nt", FALSE0, etINT, {&nthreads},
118 "Number of threads to start"},
119#endif
120 };
121 FILE *fp;
122 const char *fnTPX, *fnNDX, *fnTRX, *fnDAT = NULL((void*)0);
123 t_trxstatus *status;
124 t_topology *top = NULL((void*)0);
125 t_atom *atom = NULL((void*)0);
126 gmx_rmpbc_t gpbc = NULL((void*)0);
127 gmx_bool bTPX;
128 gmx_bool bFFT = FALSE0, bDEBYE = FALSE0;
129 gmx_bool bMC = FALSE0;
130 int ePBC = -1;
131 matrix box;
132 char title[STRLEN4096];
133 rvec *x;
134 int natoms;
135 real t;
136 char **grpname = NULL((void*)0);
137 atom_id *index = NULL((void*)0);
138 int isize;
139 int i, j;
140 char *hdr = NULL((void*)0);
141 char *suffix = NULL((void*)0);
142 t_filenm *fnmdup = NULL((void*)0);
143 gmx_radial_distribution_histogram_t *prframecurrent = NULL((void*)0), *pr = NULL((void*)0);
144 gmx_static_structurefactor_t *sqframecurrent = NULL((void*)0), *sq = NULL((void*)0);
145 output_env_t oenv;
146
147#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
148
149 t_filenm fnm[] = {
150 { efTPX, "-s", NULL((void*)0), ffREAD1<<1 },
151 { efTRX, "-f", NULL((void*)0), ffREAD1<<1 },
152 { efNDX, NULL((void*)0), NULL((void*)0), ffOPTRD(1<<1 | 1<<3) },
153 { efDAT, "-d", "nsfactor", ffOPTRD(1<<1 | 1<<3) },
154 { efXVG, "-pr", "pr", ffWRITE1<<2 },
155 { efXVG, "-sq", "sq", ffWRITE1<<2 },
156 { efXVG, "-prframe", "prframe", ffOPTWR(1<<2| 1<<3) },
157 { efXVG, "-sqframe", "sqframe", ffOPTWR(1<<2| 1<<3) }
158 };
159
160 nthreads = gmx_omp_get_max_threads();
161
162 if (!parse_common_args(&argc, argv, PCA_CAN_TIME((1<<6) | (1<<7) | (1<<14)) | PCA_TIME_UNIT(1<<15) | PCA_BE_NICE(1<<13),
1
Taking false branch
→
163 NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm, asize(pa)((int)(sizeof(pa)/sizeof((pa)[0]))), pa, asize(desc)((int)(sizeof(desc)/sizeof((desc)[0]))), desc, 0, NULL((void*)0), &oenv))
164 {
165 return 0;
166 }
167
168 /* check that binwidth not smaller than smallers distance */
169 check_binwidth(binwidth);
170 check_mcover(mcover);
171
172 /* setting number of omp threads globaly */
173 gmx_omp_set_num_threads(nthreads);
174
175 /* Now try to parse opts for modes */
176 switch (emethod[0][0])
2
←
Array access results in a null pointer dereference
177 {
178 case 'd':
179 bDEBYE = TRUE1;
180 switch (emode[0][0])
181 {
182 case 'd':
183 bMC = FALSE0;
184 break;
185 case 'm':
186 bMC = TRUE1;
187 break;
188 default:
189 break;
190 }
191 break;
192 case 'f':
193 bFFT = TRUE1;
194 break;
195 default:
196 break;
197 }
198
199 if (bDEBYE)
200 {
201 if (bMC)
202 {
203 fprintf(stderrstderr, "Using Monte Carlo Debye method to calculate spectrum\n");
204 }
205 else
206 {
207 fprintf(stderrstderr, "Using direct Debye method to calculate spectrum\n");
208 }
209 }
210 else if (bFFT)
211 {
212 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 212, "FFT method not implemented!");
213 }
214 else
215 {
216 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 216, "Unknown combination for mode and method!");
217 }
218
219 /* Try to read files */
220 fnDAT = ftp2fn(efDAT, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
221 fnTPX = ftp2fn(efTPX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
222 fnTRX = ftp2fn(efTRX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
223
224 gnsf = gmx_neutronstructurefactors_init(fnDAT);
225 fprintf(stderrstderr, "Read %d atom names from %s with neutron scattering parameters\n\n", gnsf->nratoms, fnDAT);
226
227 snew(top, 1)(top) = save_calloc("top", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 227, (1), sizeof(*(top)));
228 snew(grpname, 1)(grpname) = save_calloc("grpname", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 228, (1), sizeof(*(grpname)));
229 snew(index, 1)(index) = save_calloc("index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 229, (1), sizeof(*(index)));
230
231 bTPX = read_tps_conf(fnTPX, title, top, &ePBC, &x, NULL((void*)0), box, TRUE1);
232
233 printf("\nPlease select group for SANS spectra calculation:\n");
234 get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), 1, &isize, &index, grpname);
235
236 gsans = gmx_sans_init(top, gnsf);
237
238 /* Prepare reference frame */
239 if (bPBC)
240 {
241 gpbc = gmx_rmpbc_init(&top->idef, ePBC, top->atoms.nr);
242 gmx_rmpbc(gpbc, top->atoms.nr, box, x);
243 }
244
245 natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
246 if (natoms != top->atoms.nr)
247 {
248 fprintf(stderrstderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n", natoms, top->atoms.nr);
249 }
250
251 do
252 {
253 if (bPBC)
254 {
255 gmx_rmpbc(gpbc, top->atoms.nr, box, x);
256 }
257 /* allocate memory for pr */
258 if (pr == NULL((void*)0))
259 {
260 /* in case its first frame to read */
261 snew(pr, 1)(pr) = save_calloc("pr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 261, (1), sizeof(*(pr)));
262 }
263 /* realy calc p(r) */
264 prframecurrent = calc_radial_distribution_histogram(gsans, x, box, index, isize, binwidth, bMC, bNORM, mcover, seed);
265 /* copy prframecurrent -> pr and summ up pr->gr[i] */
266 /* allocate and/or resize memory for pr->gr[i] and pr->r[i] */
267 if (pr->gr == NULL((void*)0))
268 {
269 /* check if we use pr->gr first time */
270 snew(pr->gr, prframecurrent->grn)(pr->gr) = save_calloc("pr->gr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 270, (prframecurrent->grn), sizeof(*(pr->gr)));
271 snew(pr->r, prframecurrent->grn)(pr->r) = save_calloc("pr->r", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 271, (prframecurrent->grn), sizeof(*(pr->r)));
272 }
273 else
274 {
275 /* resize pr->gr and pr->r if needed to preven overruns */
276 if (prframecurrent->grn > pr->grn)
277 {
278 srenew(pr->gr, prframecurrent->grn)(pr->gr) = save_realloc("pr->gr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 278, (pr->gr), (prframecurrent->grn), sizeof(*(pr->
gr)));
279 srenew(pr->r, prframecurrent->grn)(pr->r) = save_realloc("pr->r", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 279, (pr->r), (prframecurrent->grn), sizeof(*(pr->
r)));
280 }
281 }
282 pr->grn = prframecurrent->grn;
283 pr->binwidth = prframecurrent->binwidth;
284 /* summ up gr and fill r */
285 for (i = 0; i < prframecurrent->grn; i++)
286 {
287 pr->gr[i] += prframecurrent->gr[i];
288 pr->r[i] = prframecurrent->r[i];
289 }
290 /* normalize histo */
291 normalize_probability(prframecurrent->grn, prframecurrent->gr);
292 /* convert p(r) to sq */
293 sqframecurrent = convert_histogram_to_intensity_curve(prframecurrent, start_q, end_q, q_step);
294 /* print frame data if needed */
295 if (opt2fn_null("-prframe", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm))
296 {
297 snew(hdr, 25)(hdr) = save_calloc("hdr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 297, (25), sizeof(*(hdr)));
298 snew(suffix, GMX_PATH_MAX)(suffix) = save_calloc("suffix", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 298, (4096), sizeof(*(suffix)));
299 /* prepare header */
300 sprintf(hdr, "g(r), t = %f", t);
301 /* prepare output filename */
302 fnmdup = dup_tfn(NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
303 sprintf(suffix, "-t%.2f", t);
304 add_suffix_to_output_names(fnmdup, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), suffix);
305 fp = xvgropen(opt2fn_null("-prframe", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnmdup), hdr, "Distance (nm)", "Probability", oenv);
306 for (i = 0; i < prframecurrent->grn; i++)
307 {
308 fprintf(fp, "%10.6f%10.6f\n", prframecurrent->r[i], prframecurrent->gr[i]);
309 }
310 done_filenms(NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnmdup);
311 fclose(fp);
312 sfree(hdr)save_free("hdr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 312, (hdr));
313 sfree(suffix)save_free("suffix", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 313, (suffix));
314 sfree(fnmdup)save_free("fnmdup", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 314, (fnmdup));
315 }
316 if (opt2fn_null("-sqframe", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm))
317 {
318 snew(hdr, 25)(hdr) = save_calloc("hdr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 318, (25), sizeof(*(hdr)));
319 snew(suffix, GMX_PATH_MAX)(suffix) = save_calloc("suffix", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 319, (4096), sizeof(*(suffix)));
320 /* prepare header */
321 sprintf(hdr, "I(q), t = %f", t);
322 /* prepare output filename */
323 fnmdup = dup_tfn(NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
324 sprintf(suffix, "-t%.2f", t);
325 add_suffix_to_output_names(fnmdup, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), suffix);
326 fp = xvgropen(opt2fn_null("-sqframe", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnmdup), hdr, "q (nm^-1)", "s(q)/s(0)", oenv);
327 for (i = 0; i < sqframecurrent->qn; i++)
328 {
329 fprintf(fp, "%10.6f%10.6f\n", sqframecurrent->q[i], sqframecurrent->s[i]);
330 }
331 done_filenms(NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnmdup);
332 fclose(fp);
333 sfree(hdr)save_free("hdr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 333, (hdr));
334 sfree(suffix)save_free("suffix", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 334, (suffix));
335 sfree(fnmdup)save_free("fnmdup", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 335, (fnmdup));
336 }
337 /* free pr structure */
338 sfree(prframecurrent->gr)save_free("prframecurrent->gr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 338, (prframecurrent->gr));
339 sfree(prframecurrent->r)save_free("prframecurrent->r", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 339, (prframecurrent->r));
340 sfree(prframecurrent)save_free("prframecurrent", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 340, (prframecurrent));
341 /* free sq structure */
342 sfree(sqframecurrent->q)save_free("sqframecurrent->q", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 342, (sqframecurrent->q));
343 sfree(sqframecurrent->s)save_free("sqframecurrent->s", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 343, (sqframecurrent->s));
344 sfree(sqframecurrent)save_free("sqframecurrent", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 344, (sqframecurrent));
345 }
346 while (read_next_x(oenv, status, &t, x, box));
347 close_trj(status);
348
349 /* normalize histo */
350 normalize_probability(pr->grn, pr->gr);
351 sq = convert_histogram_to_intensity_curve(pr, start_q, end_q, q_step);
352 /* prepare pr.xvg */
353 fp = xvgropen(opt2fn_null("-pr", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), "G(r)", "Distance (nm)", "Probability", oenv);
354 for (i = 0; i < pr->grn; i++)
355 {
356 fprintf(fp, "%10.6f%10.6f\n", pr->r[i], pr->gr[i]);
357 }
358 xvgrclose(fp);
359
360 /* prepare sq.xvg */
361 fp = xvgropen(opt2fn_null("-sq", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), "I(q)", "q (nm^-1)", "s(q)/s(0)", oenv);
362 for (i = 0; i < sq->qn; i++)
363 {
364 fprintf(fp, "%10.6f%10.6f\n", sq->q[i], sq->s[i]);
365 }
366 xvgrclose(fp);
367 /*
368 * Clean up memory
369 */
370 sfree(pr->gr)save_free("pr->gr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 370, (pr->gr));
371 sfree(pr->r)save_free("pr->r", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 371, (pr->r));
372 sfree(pr)save_free("pr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 372, (pr));
373 sfree(sq->q)save_free("sq->q", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 373, (sq->q));
374 sfree(sq->s)save_free("sq->s", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 374, (sq->s));
375 sfree(sq)save_free("sq", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sans.c"
, 375, (sq));
376
377 please_cite(stdoutstdout, "Garmay2012");
378
379 return 0;
380}