Bug Summary

File:gromacs/gmxpreprocess/h_db.c
Location:line 198, column 5
Description:Null pointer passed as an argument to a 'nonnull' parameter

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/* This file is completely threadsafe - keep it that way! */
38#ifdef HAVE_CONFIG_H1
39#include <config.h>
40#endif
41
42#include <stdlib.h>
43#include <string.h>
44
45#include "gromacs/utility/cstringutil.h"
46#include "gromacs/utility/smalloc.h"
47#include "gromacs/utility/futil.h"
48#include "symtab.h"
49#include "h_db.h"
50#include "gromacs/fileio/gmxfio.h"
51#include "fflibutil.h"
52#include "gromacs/utility/fatalerror.h"
53#include "macros.h"
54
55/* Number of control atoms for each 'add' type.
56 *
57 * There are 11 types of adding hydrogens, numbered from 1 thru
58 * 11. Each of these has a specific number of control atoms, that
59 * determine how the hydrogens are added. Here these number are
60 * given. Because arrays start at 0, an extra dummy for index 0 is
61 * added.
62 */
63const int ncontrol[] = { -1, 3, 3, 3, 3, 4, 3, 1, 3, 3, 1, 1 };
64#define maxcontrol((int)(sizeof(ncontrol)/sizeof((ncontrol)[0]))) asize(ncontrol)((int)(sizeof(ncontrol)/sizeof((ncontrol)[0])))
65
66int compaddh(const void *a, const void *b)
67{
68 t_hackblock *ah, *bh;
69
70 ah = (t_hackblock *)a;
71 bh = (t_hackblock *)b;
72 return gmx_strcasecmp(ah->name, bh->name);
73}
74
75void print_ab(FILE *out, t_hack *hack, char *nname)
76{
77 int i;
78
79 fprintf(out, "%d\t%d\t%s", hack->nr, hack->tp, nname);
80 for (i = 0; (i < hack->nctl); i++)
81 {
82 fprintf(out, "\t%s", hack->a[i]);
83 }
84 fprintf(out, "\n");
85}
86
87
88void read_ab(char *line, const char *fn, t_hack *hack)
89{
90 int i, nh, tp, ns;
91 char a[4][12];
92 char hn[32];
93
94 ns = sscanf(line, "%d%d%s%s%s%s%s", &nh, &tp, hn, a[0], a[1], a[2], a[3]);
95 if (ns < 4)
96 {
97 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/h_db.c"
, 97, "wrong format in input file %s on line\n%s\n", fn, line);
98 }
99
100 hack->nr = nh;
101 hack->tp = tp;
102 if ((tp < 1) || (tp >= maxcontrol((int)(sizeof(ncontrol)/sizeof((ncontrol)[0])))))
103 {
104 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/h_db.c"
, 104, "Error in hdb file %s:\nH-type should be in 1-%d. Offending line:\n%s", fn, maxcontrol((int)(sizeof(ncontrol)/sizeof((ncontrol)[0])))-1, line);
105 }
106
107 hack->nctl = ns - 3;
108 if ((hack->nctl != ncontrol[hack->tp]) && (ncontrol[hack->tp] != -1))
109 {
110 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/h_db.c"
, 110, "Error in hdb file %s:\nWrong number of control atoms (%d iso %d) on line:\n%s\n", fn, hack->nctl, ncontrol[hack->tp], line);
111 }
112 for (i = 0; (i < hack->nctl); i++)
113 {
114 hack->a[i] = strdup(a[i])(__extension__ (__builtin_constant_p (a[i]) && ((size_t
)(const void *)((a[i]) + 1) - (size_t)(const void *)(a[i]) ==
1) ? (((const char *) (a[i]))[0] == '\0' ? (char *) calloc (
(size_t) 1, (size_t) 1) : ({ size_t __len = strlen (a[i]) + 1
; char *__retval = (char *) malloc (__len); if (__retval != (
(void*)0)) __retval = (char *) memcpy (__retval, a[i], __len)
; __retval; })) : __strdup (a[i])));
115 }
116 for (; i < 4; i++)
117 {
118 hack->a[i] = NULL((void*)0);
119 }
120 hack->oname = NULL((void*)0);
121 hack->nname = strdup(hn)(__extension__ (__builtin_constant_p (hn) && ((size_t
)(const void *)((hn) + 1) - (size_t)(const void *)(hn) == 1) ?
(((const char *) (hn))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (hn) + 1; char *__retval
= (char *) malloc (__len); if (__retval != ((void*)0)) __retval
= (char *) memcpy (__retval, hn, __len); __retval; })) : __strdup
(hn)));
122 hack->atom = NULL((void*)0);
123 hack->cgnr = NOTSET-12345;
124 hack->bXSet = FALSE0;
125 for (i = 0; i < DIM3; i++)
126 {
127 hack->newx[i] = NOTSET-12345;
128 }
129}
130
131static void read_h_db_file(const char *hfn, int *nahptr, t_hackblock **ah)
132{
133 FILE *in;
134 char filebase[STRLEN4096], line[STRLEN4096], buf[STRLEN4096];
135 int i, n, nab, nah;
136 t_hackblock *aah;
137
138 if (debug)
4
←
Assuming 'debug' is null
→
5
←
Taking false branch
→
139 {
140 fprintf(debug, "Hydrogen Database (%s):\n", hfn);
141 }
142
143 fflib_filename_base(hfn, filebase, STRLEN4096);
144 /* Currently filebase is read and set, but not used.
145 * hdb entries from any hdb file and be applied to rtp entries
146 * in any rtp file.
147 */
148
149 in = fflib_open(hfn);
150
151 nah = *nahptr;
152 aah = *ah;
6
←
Null pointer value stored to 'aah'
→
153 while (fgets2(line, STRLEN4096-1, in))
7
←
Loop condition is false. Execution continues on line 195
→
154 {
155 if (sscanf(line, "%s%n", buf, &n) != 1)
156 {
157 fprintf(stderrstderr, "Error in hdb file: nah = %d\nline = '%s'\n",
158 nah, line);
159 break;
160 }
161 if (debug)
162 {
163 fprintf(debug, "%s", buf);
164 }
165 srenew(aah, nah+1)(aah) = save_realloc("aah", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/h_db.c"
, 165, (aah), (nah+1), sizeof(*(aah)));
166 clear_t_hackblock(&aah[nah]);
167 aah[nah].name = 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)));
168 aah[nah].filebase = strdup(filebase)(__extension__ (__builtin_constant_p (filebase) && ((
size_t)(const void *)((filebase) + 1) - (size_t)(const void *
)(filebase) == 1) ? (((const char *) (filebase))[0] == '\0' ?
(char *) calloc ((size_t) 1, (size_t) 1) : ({ size_t __len =
strlen (filebase) + 1; char *__retval = (char *) malloc (__len
); if (__retval != ((void*)0)) __retval = (char *) memcpy (__retval
, filebase, __len); __retval; })) : __strdup (filebase)));
169
170 if (sscanf(line+n, "%d", &nab) == 1)
171 {
172 if (debug)
173 {
174 fprintf(debug, " %d\n", nab);
175 }
176 snew(aah[nah].hack, nab)(aah[nah].hack) = save_calloc("aah[nah].hack", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/h_db.c"
, 176, (nab), sizeof(*(aah[nah].hack)));
177 aah[nah].nhack = nab;
178 for (i = 0; (i < nab); i++)
179 {
180 if (feof(in))
181 {
182 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/h_db.c"
, 182, "Expected %d lines of hydrogens, found only %d "
183 "while reading Hydrogen Database %s residue %s",
184 nab, i-1, aah[nah].name, hfn);
185 }
186 if (NULL((void*)0) == fgets(buf, STRLEN4096, in))
187 {
188 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/h_db.c"
, 188, "Error reading from file %s", hfn);
189 }
190 read_ab(buf, hfn, &(aah[nah].hack[i]));
191 }
192 }
193 nah++;
194 }
195 gmx_ffclose(in);
196
197 /* Sort the list (necessary to be able to use bsearch */
198 qsort(aah, nah, (size_t)sizeof(**ah), compaddh);
8
←
Null pointer passed as an argument to a 'nonnull' parameter
199
200 /*
201 if (debug)
202 dump_h_db(hfn,nah,aah);
203 */
204
205 *nahptr = nah;
206 *ah = aah;
207}
208
209int read_h_db(const char *ffdir, t_hackblock **ah)
210{
211 int nhdbf, f;
212 char **hdbf;
213 int nah;
214 FILE *fp;
215
216 /* Read the hydrogen database file(s).
217 * Do not generate an error when no files are found.
218 */
219 nhdbf = fflib_search_file_end(ffdir, ".hdb", FALSE0, &hdbf);
220 nah = 0;
221 *ah = NULL((void*)0);
222 for (f = 0; f < nhdbf; f++)
1
Assuming 'f' is < 'nhdbf'
→
2
←
Loop condition is true. Entering loop body
→
223 {
224 read_h_db_file(hdbf[f], &nah, ah);
3
←
Calling 'read_h_db_file'
→
225 sfree(hdbf[f])save_free("hdbf[f]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/h_db.c"
, 225, (hdbf[f]));
226 }
227 sfree(hdbf)save_free("hdbf", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/h_db.c"
, 227, (hdbf));
228
229 return nah;
230}
231
232t_hackblock *search_h_db(int nh, t_hackblock ah[], char *key)
233{
234 t_hackblock ahkey, *result;
235
236 if (nh <= 0)
237 {
238 return NULL((void*)0);
239 }
240
241 ahkey.name = key;
242
243 result = (t_hackblock *)bsearch(&ahkey, ah, nh, (size_t)sizeof(ah[0]), compaddh);
244
245 return result;
246}