Bug Summary

File:gromacs/gmxana/gmx_rotmat.c
Location:line 259, column 9
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) 2009,2010,2011,2012,2013,2014, 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#ifdef HAVE_CONFIG_H1
36#include <config.h>
37#endif
38
39#include <math.h>
40#include <string.h>
41
42#include "gromacs/commandline/pargs.h"
43#include "typedefs.h"
44#include "gromacs/utility/smalloc.h"
45#include "macros.h"
46#include "gromacs/math/vec.h"
47#include "pbc.h"
48#include "gromacs/utility/futil.h"
49#include "index.h"
50#include "mshift.h"
51#include "gromacs/fileio/xvgr.h"
52#include "viewit.h"
53#include "rmpbc.h"
54#include "gromacs/fileio/tpxio.h"
55#include "gromacs/fileio/trxio.h"
56#include "gmx_ana.h"
57
58#include "gromacs/math/do_fit.h"
59
60static void get_refx(output_env_t oenv, const char *trxfn, int nfitdim, int skip,
61 int gnx, int *index,
62 gmx_bool bMW, t_topology *top, int ePBC, rvec *x_ref)
63{
64 int natoms, nfr_all, nfr, i, j, a, r, c, min_fr;
65 t_trxstatus *status;
66 real *ti, min_t;
67 double tot_mass, msd, *srmsd, min_srmsd, srmsd_tot;
68 rvec *x, **xi;
69 real xf;
70 matrix box, R;
71 real *w_rls;
72 gmx_rmpbc_t gpbc = NULL((void*)0);
73
74
75 nfr_all = 0;
76 nfr = 0;
77 snew(ti, 100)(ti) = save_calloc("ti", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 77, (100), sizeof(*(ti)));
78 snew(xi, 100)(xi) = save_calloc("xi", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 78, (100), sizeof(*(xi)));
79 natoms = read_first_x(oenv, &status, trxfn, &ti[nfr], &x, box);
80
81 snew(w_rls, gnx)(w_rls) = save_calloc("w_rls", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 81, (gnx), sizeof(*(w_rls)));
82 tot_mass = 0;
83 for (a = 0; a < gnx; a++)
84 {
85 if (index[a] >= natoms)
86 {
87 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 87, "Atom index (%d) is larger than the number of atoms in the trajecory (%d)", index[a]+1, natoms);
88 }
89 w_rls[a] = (bMW ? top->atoms.atom[index[a]].m : 1.0);
90 tot_mass += w_rls[a];
91 }
92 gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
93
94 do
95 {
96 if (nfr_all % skip == 0)
97 {
98 gmx_rmpbc(gpbc, natoms, box, x);
99 snew(xi[nfr], gnx)(xi[nfr]) = save_calloc("xi[nfr]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 99, (gnx), sizeof(*(xi[nfr])));
100 for (i = 0; i < gnx; i++)
101 {
102 copy_rvec(x[index[i]], xi[nfr][i]);
103 }
104 reset_x(gnx, NULL((void*)0), gnx, NULL((void*)0), xi[nfr], w_rls);
105 nfr++;
106 if (nfr % 100 == 0)
107 {
108 srenew(ti, nfr+100)(ti) = save_realloc("ti", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 108, (ti), (nfr+100), sizeof(*(ti)));
109 srenew(xi, nfr+100)(xi) = save_realloc("xi", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 109, (xi), (nfr+100), sizeof(*(xi)));
110 }
111 }
112 nfr_all++;
113 }
114 while (read_next_x(oenv, status, &ti[nfr], x, box));
115 close_trj(status);
116 sfree(x)save_free("x", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 116, (x));
117
118 gmx_rmpbc_done(gpbc);
119
120 snew(srmsd, nfr)(srmsd) = save_calloc("srmsd", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 120, (nfr), sizeof(*(srmsd)));
121 for (i = 0; i < nfr; i++)
122 {
123 printf("\rProcessing frame %d of %d", i, nfr);
124 for (j = i+1; j < nfr; j++)
125 {
126 calc_fit_R(nfitdim, gnx, w_rls, xi[i], xi[j], R);
127
128 msd = 0;
129 for (a = 0; a < gnx; a++)
130 {
131 for (r = 0; r < DIM3; r++)
132 {
133 xf = 0;
134 for (c = 0; c < DIM3; c++)
135 {
136 xf += R[r][c]*xi[j][a][c];
137 }
138 msd += w_rls[a]*sqr(xi[i][a][r] - xf);
139 }
140 }
141 msd /= tot_mass;
142 srmsd[i] += sqrt(msd);
143 srmsd[j] += sqrt(msd);
144 }
145 sfree(xi[i])save_free("xi[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 145, (xi[i]));
146 }
147 printf("\n");
148 sfree(w_rls)save_free("w_rls", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 148, (w_rls));
149
150 min_srmsd = GMX_REAL_MAX3.40282346E+38;
151 min_fr = -1;
152 min_t = -1;
153 srmsd_tot = 0;
154 for (i = 0; i < nfr; i++)
155 {
156 srmsd[i] /= (nfr - 1);
157 if (srmsd[i] < min_srmsd)
158 {
159 min_srmsd = srmsd[i];
160 min_fr = i;
161 min_t = ti[i];
162 }
163 srmsd_tot += srmsd[i];
164 }
165 sfree(srmsd)save_free("srmsd", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 165, (srmsd));
166
167 printf("Average RMSD between all structures: %.3f\n", srmsd_tot/nfr);
168 printf("Structure with lowest RMSD to all others: time %g, av. RMSD %.3f\n",
169 min_t, min_srmsd);
170
171 for (a = 0; a < gnx; a++)
172 {
173 copy_rvec(xi[min_fr][a], x_ref[index[a]]);
174 }
175
176 sfree(xi)save_free("xi", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 176, (xi));
177}
178
179int gmx_rotmat(int argc, char *argv[])
180{
181 const char *desc[] = {
182 "[THISMODULE] plots the rotation matrix required for least squares fitting",
183 "a conformation onto the reference conformation provided with",
184 "[TT]-s[tt]. Translation is removed before fitting.",
185 "The output are the three vectors that give the new directions",
186 "of the x, y and z directions of the reference conformation,",
187 "for example: (zx,zy,zz) is the orientation of the reference",
188 "z-axis in the trajectory frame.",
189 "[PAR]",
190 "This tool is useful for, for instance,",
191 "determining the orientation of a molecule",
192 "at an interface, possibly on a trajectory produced with",
193 "[TT]gmx trjconv -fit rotxy+transxy[tt] to remove the rotation",
194 "in the [IT]x-y[it] plane.",
195 "[PAR]",
196 "Option [TT]-ref[tt] determines a reference structure for fitting,",
197 "instead of using the structure from [TT]-s[tt]. The structure with",
198 "the lowest sum of RMSD's to all other structures is used.",
199 "Since the computational cost of this procedure grows with",
200 "the square of the number of frames, the [TT]-skip[tt] option",
201 "can be useful. A full fit or only a fit in the [IT]x-y[it] plane can",
202 "be performed.",
203 "[PAR]",
204 "Option [TT]-fitxy[tt] fits in the [IT]x-y[it] plane before determining",
205 "the rotation matrix."
206 };
207 const char *reffit[] =
208 { NULL((void*)0), "none", "xyz", "xy", NULL((void*)0) };
209 static int skip = 1;
210 static gmx_bool bFitXY = FALSE0, bMW = TRUE1;
211 t_pargs pa[] = {
212 { "-ref", FALSE0, etENUM, {reffit},
213 "Determine the optimal reference structure" },
214 { "-skip", FALSE0, etINT, {&skip},
215 "Use every nr-th frame for [TT]-ref[tt]" },
216 { "-fitxy", FALSE0, etBOOL, {&bFitXY},
217 "Fit the x/y rotation before determining the rotation" },
218 { "-mw", FALSE0, etBOOL, {&bMW},
219 "Use mass weighted fitting" }
220 };
221 FILE *out;
222 t_trxstatus *status;
223 t_topology top;
224 int ePBC;
225 rvec *x_ref, *x;
226 matrix box, R;
227 real t;
228 int natoms, i;
229 char *grpname, title[256];
230 int gnx;
231 gmx_rmpbc_t gpbc = NULL((void*)0);
232 atom_id *index;
233 output_env_t oenv;
234 real *w_rls;
235 const char *leg[] = { "xx", "xy", "xz", "yx", "yy", "yz", "zx", "zy", "zz" };
236#define NLEG((int)(sizeof(leg)/sizeof((leg)[0]))) asize(leg)((int)(sizeof(leg)/sizeof((leg)[0])))
237 t_filenm fnm[] = {
238 { efTRX, "-f", NULL((void*)0), ffREAD1<<1 },
239 { efTPS, NULL((void*)0), NULL((void*)0), ffREAD1<<1 },
240 { efNDX, NULL((void*)0), NULL((void*)0), ffOPTRD(1<<1 | 1<<3) },
241 { efXVG, NULL((void*)0), "rotmat", ffWRITE1<<2 }
242 };
243#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
244
245 if (!parse_common_args(&argc, argv, PCA_CAN_TIME((1<<6) | (1<<7) | (1<<14)) | PCA_CAN_VIEW(1<<5) | PCA_BE_NICE(1<<13),
1
Taking false branch
→
246 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))
247 {
248 return 0;
249 }
250
251 read_tps_conf(ftp2fn(efTPS, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), title, &top, &ePBC, &x_ref, NULL((void*)0), box, bMW);
252
253 gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
254
255 gmx_rmpbc(gpbc, top.atoms.nr, box, x_ref);
256
257 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), 1, &gnx, &index, &grpname);
258
259 if (reffit[0][0] != 'n')
2
←
Array access results in a null pointer dereference
260 {
261 get_refx(oenv, ftp2fn(efTRX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), reffit[0][2] == 'z' ? 3 : 2, skip,
262 gnx, index, bMW, &top, ePBC, x_ref);
263 }
264
265 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), &t, &x, box);
266
267 snew(w_rls, natoms)(w_rls) = save_calloc("w_rls", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 267, (natoms), sizeof(*(w_rls)));
268 for (i = 0; i < gnx; i++)
269 {
270 if (index[i] >= natoms)
271 {
272 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotmat.c"
, 272, "Atom index (%d) is larger than the number of atoms in the trajecory (%d)", index[i]+1, natoms);
273 }
274 w_rls[index[i]] = (bMW ? top.atoms.atom[index[i]].m : 1.0);
275 }
276
277 if (reffit[0][0] == 'n')
278 {
279 reset_x(gnx, index, natoms, NULL((void*)0), x_ref, w_rls);
280 }
281
282 out = xvgropen(ftp2fn(efXVG, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
283 "Fit matrix", "Time (ps)", "", oenv);
284 xvgr_legend(out, NLEG((int)(sizeof(leg)/sizeof((leg)[0]))), leg, oenv);
285
286 do
287 {
288 gmx_rmpbc(gpbc, natoms, box, x);
289
290 reset_x(gnx, index, natoms, NULL((void*)0), x, w_rls);
291
292 if (bFitXY)
293 {
294 do_fit_ndim(2, natoms, w_rls, x_ref, x);
295 }
296
297 calc_fit_R(DIM3, natoms, w_rls, x_ref, x, R);
298
299 fprintf(out,
300 "%7g %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f\n",
301 t,
302 R[XX0][XX0], R[XX0][YY1], R[XX0][ZZ2],
303 R[YY1][XX0], R[YY1][YY1], R[YY1][ZZ2],
304 R[ZZ2][XX0], R[ZZ2][YY1], R[ZZ2][ZZ2]);
305 }
306 while (read_next_x(oenv, status, &t, x, box));
307
308 gmx_rmpbc_done(gpbc);
309
310 close_trj(status);
311
312 gmx_ffclose(out);
313
314 do_view(oenv, ftp2fn(efXVG, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), "-nxy");
315
316 return 0;
317}