Bug Summary

File:gromacs/gmxana/gmx_mk_angndx.c
Location:line 210, column 9
Description:Array access (from variable 'opt') 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) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2012,2013,2014, 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
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14 * of the License, or (at your option) any later version.
15 *
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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
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25 *
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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
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33 *
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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 "typedefs.h"
43#include "gromacs/utility/smalloc.h"
44#include "gromacs/commandline/pargs.h"
45#include "macros.h"
46#include "gromacs/utility/futil.h"
47#include "gromacs/utility/fatalerror.h"
48#include "gromacs/fileio/trxio.h"
49
50static int calc_ntype(int nft, int *ft, t_idef *idef)
51{
52 int i, f, nf = 0;
53
54 for (i = 0; (i < idef->ntypes); i++)
55 {
56 for (f = 0; f < nft; f++)
57 {
58 if (idef->functype[i] == ft[f])
59 {
60 nf++;
61 }
62 }
63 }
64
65 return nf;
66}
67
68static void fill_ft_ind(int nft, int *ft, t_idef *idef,
69 int ft_ind[], char *grpnames[])
70{
71 char buf[125];
72 int i, f, ftype, ind = 0;
73
74 /* Loop over all the function types in the topology */
75 for (i = 0; (i < idef->ntypes); i++)
76 {
77 ft_ind[i] = -1;
78 /* Check all the selected function types */
79 for (f = 0; f < nft; f++)
80 {
81 ftype = ft[f];
82 if (idef->functype[i] == ftype)
83 {
84 ft_ind[i] = ind;
85 switch (ftype)
86 {
87 case F_ANGLES:
88 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
89 idef->iparams[i].harmonic.krA);
90 break;
91 case F_G96ANGLES:
92 sprintf(buf, "Cos_th=%.1f_%.2f", idef->iparams[i].harmonic.rA,
93 idef->iparams[i].harmonic.krA);
94 break;
95 case F_UREY_BRADLEY:
96 sprintf(buf, "UB_th=%.1f_%.2f2f", idef->iparams[i].u_b.thetaA,
97 idef->iparams[i].u_b.kthetaA);
98 break;
99 case F_QUARTIC_ANGLES:
100 sprintf(buf, "Q_th=%.1f_%.2f_%.2f", idef->iparams[i].qangle.theta,
101 idef->iparams[i].qangle.c[0], idef->iparams[i].qangle.c[1]);
102 break;
103 case F_TABANGLES:
104 sprintf(buf, "Table=%d_%.2f", idef->iparams[i].tab.table,
105 idef->iparams[i].tab.kA);
106 break;
107 case F_PDIHS:
108 sprintf(buf, "Phi=%.1f_%d_%.2f", idef->iparams[i].pdihs.phiA,
109 idef->iparams[i].pdihs.mult, idef->iparams[i].pdihs.cpA);
110 break;
111 case F_IDIHS:
112 sprintf(buf, "Xi=%.1f_%.2f", idef->iparams[i].harmonic.rA,
113 idef->iparams[i].harmonic.krA);
114 break;
115 case F_RBDIHS:
116 sprintf(buf, "RB-A1=%.2f", idef->iparams[i].rbdihs.rbcA[1]);
117 break;
118 case F_RESTRANGLES:
119 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
120 idef->iparams[i].harmonic.krA);
121 break;
122 case F_RESTRDIHS:
123 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
124 idef->iparams[i].harmonic.krA);
125 break;
126 case F_CBTDIHS:
127 sprintf(buf, "CBT-A1=%.2f", idef->iparams[i].cbtdihs.cbtcA[1]);
128 break;
129
130 default:
131 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_mk_angndx.c"
, 131, "Unsupported function type '%s' selected",
132 interaction_function[ftype].longname);
133 }
134 grpnames[ind] = 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)));
135 ind++;
136 }
137 }
138 }
139}
140
141static void fill_ang(int nft, int *ft, int fac,
142 int nr[], int *index[], int ft_ind[], t_topology *top,
143 gmx_bool bNoH, real hq)
144{
145 int f, ftype, i, j, indg, nr_fac;
146 gmx_bool bUse;
147 t_idef *idef;
148 t_atom *atom;
149 t_iatom *ia;
150
151
152 idef = &top->idef;
153 atom = top->atoms.atom;
154
155 for (f = 0; f < nft; f++)
156 {
157 ftype = ft[f];
158 ia = idef->il[ftype].iatoms;
159 for (i = 0; (i < idef->il[ftype].nr); )
160 {
161 indg = ft_ind[ia[0]];
162 if (indg == -1)
163 {
164 gmx_incons("Routine fill_ang")_gmx_error("incons", "Routine fill_ang", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_mk_angndx.c"
, 164);
165 }
166 bUse = TRUE1;
167 if (bNoH)
168 {
169 for (j = 0; j < fac; j++)
170 {
171 if (atom[ia[1+j]].m < 1.5)
172 {
173 bUse = FALSE0;
174 }
175 }
176 }
177 if (hq)
178 {
179 for (j = 0; j < fac; j++)
180 {
181 if (atom[ia[1+j]].m < 1.5 && fabs(atom[ia[1+j]].q) < hq)
182 {
183 bUse = FALSE0;
184 }
185 }
186 }
187 if (bUse)
188 {
189 if (nr[indg] % 1000 == 0)
190 {
191 srenew(index[indg], fac*(nr[indg]+1000))(index[indg]) = save_realloc("index[indg]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_mk_angndx.c"
, 191, (index[indg]), (fac*(nr[indg]+1000)), sizeof(*(index[indg
])));
192 }
193 nr_fac = fac*nr[indg];
194 for (j = 0; (j < fac); j++)
195 {
196 index[indg][nr_fac+j] = ia[j+1];
197 }
198 nr[indg]++;
199 }
200 ia += interaction_function[ftype].nratoms+1;
201 i += interaction_function[ftype].nratoms+1;
202 }
203 }
204}
205
206static int *select_ftype(const char *opt, int *nft, int *mult)
207{
208 int *ft = NULL((void*)0), ftype;
209
210 if (opt[0] == 'a')
4
←
Array access (from variable 'opt') results in a null pointer dereference
211 {
212 *mult = 3;
213 for (ftype = 0; ftype < F_NRE; ftype++)
214 {
215 if ((interaction_function[ftype].flags & IF_ATYPE1<<5) ||
216 ftype == F_TABANGLES)
217 {
218 (*nft)++;
219 srenew(ft, *nft)(ft) = save_realloc("ft", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_mk_angndx.c"
, 219, (ft), (*nft), sizeof(*(ft)));
220 ft[*nft-1] = ftype;
221 }
222 }
223 }
224 else
225 {
226 *mult = 4;
227 *nft = 1;
228 snew(ft, *nft)(ft) = save_calloc("ft", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_mk_angndx.c"
, 228, (*nft), sizeof(*(ft)));
229 switch (opt[0])
230 {
231 case 'd':
232 ft[0] = F_PDIHS;
233 break;
234 case 'i':
235 ft[0] = F_IDIHS;
236 break;
237 case 'r':
238 ft[0] = F_RBDIHS;
239 break;
240 default:
241 break;
242 }
243 }
244
245 return ft;
246}
247
248int gmx_mk_angndx(int argc, char *argv[])
249{
250 static const char *desc[] = {
251 "[THISMODULE] makes an index file for calculation of",
252 "angle distributions etc. It uses a run input file ([TT].tpx[tt]) for the",
253 "definitions of the angles, dihedrals etc."
254 };
255 static const char *opt[] = { NULL((void*)0), "angle", "dihedral", "improper", "ryckaert-bellemans", NULL((void*)0) };
256 static gmx_bool bH = TRUE1;
257 static real hq = -1;
258 t_pargs pa[] = {
259 { "-type", FALSE0, etENUM, {opt},
260 "Type of angle" },
261 { "-hyd", FALSE0, etBOOL, {&bH},
262 "Include angles with atoms with mass < 1.5" },
263 { "-hq", FALSE0, etREAL, {&hq},
264 "Ignore angles with atoms with mass < 1.5 and magnitude of their charge less than this value" }
265 };
266
267 output_env_t oenv;
268 FILE *out;
269 t_topology *top;
270 int i, j, ntype;
271 int nft = 0, *ft, mult = 0;
272 int **index;
273 int *ft_ind;
274 int *nr;
275 char **grpnames;
276 t_filenm fnm[] = {
277 { efTPX, NULL((void*)0), NULL((void*)0), ffREAD1<<1 },
278 { efNDX, NULL((void*)0), "angle", ffWRITE1<<2 }
279 };
280#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
281
282 if (!parse_common_args(&argc, argv, 0, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm, asize(pa)((int)(sizeof(pa)/sizeof((pa)[0]))), pa,
1
Taking false branch
→
283 asize(desc)((int)(sizeof(desc)/sizeof((desc)[0]))), desc, 0, NULL((void*)0), &oenv))
284 {
285 return 0;
286 }
287
288
289 ft = select_ftype(opt[0], &nft, &mult);
2
←
Passing null pointer value via 1st parameter 'opt'
→
3
←
Calling 'select_ftype'
→
290
291 top = read_top(ftp2fn(efTPX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), NULL((void*)0));
292
293 ntype = calc_ntype(nft, ft, &(top->idef));
294 snew(grpnames, ntype)(grpnames) = save_calloc("grpnames", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_mk_angndx.c"
, 294, (ntype), sizeof(*(grpnames)));
295 snew(ft_ind, top->idef.ntypes)(ft_ind) = save_calloc("ft_ind", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_mk_angndx.c"
, 295, (top->idef.ntypes), sizeof(*(ft_ind)));
296 fill_ft_ind(nft, ft, &top->idef, ft_ind, grpnames);
297
298 snew(nr, ntype)(nr) = save_calloc("nr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_mk_angndx.c"
, 298, (ntype), sizeof(*(nr)));
299 snew(index, ntype)(index) = save_calloc("index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_mk_angndx.c"
, 299, (ntype), sizeof(*(index)));
300 fill_ang(nft, ft, mult, nr, index, ft_ind, top, !bH, hq);
301
302 out = ftp2FILE(efNDX, NFILE, fnm, "w")gmx_ffopen(ftp2fn(efNDX, ((int)(sizeof(fnm)/sizeof((fnm)[0]))
), fnm), "w");
303 for (i = 0; (i < ntype); i++)
304 {
305 if (nr[i] > 0)
306 {
307 fprintf(out, "[ %s ]\n", grpnames[i]);
308 for (j = 0; (j < nr[i]*mult); j++)
309 {
310 fprintf(out, " %5d", index[i][j]+1);
311 if ((j % 12) == 11)
312 {
313 fprintf(out, "\n");
314 }
315 }
316 fprintf(out, "\n");
317 }
318 }
319 gmx_ffclose(out);
320
321 return 0;
322}