Bug Summary

File:gromacs/linearalgebra/mtxio.c
Location:line 238, column 9
Description:Value stored to 'bDum' is never read

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
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#include "mtxio.h"
38
39#ifdef HAVE_CONFIG_H1
40#include <config.h>
41#endif
42
43/* This module provides routines to read/write sparse or full storage
44 * matrices from/to files. It is normally used for the Hessian matrix
45 * in normal mode analysis.
46 */
47
48#include "gromacs/legacyheaders/copyrite.h"
49#include "gromacs/fileio/gmxfio.h"
50#include "gromacs/fileio/xdrf.h"
51#include "gromacs/linearalgebra/sparsematrix.h"
52#include "gromacs/utility/fatalerror.h"
53#include "gromacs/utility/smalloc.h"
54
55/* Just a number to identify our file type */
56#define GMX_MTXIO_MAGIC_NUMBER0x34ce8fd2 0x34ce8fd2
57
58#define GMX_MTXIO_FULL_MATRIX0 0
59#define GMX_MTXIO_SPARSE_MATRIX1 1
60
61
62
63/* Matrix file format definition:
64 *
65 * All entries are stored in XDR format.
66 *
67 * 1. Magic number integer, should be GMX_MTXIO_MAGIC_NUMBER
68 * 2. An XDR string specifying the Gromacs version used to generate the file.
69 * 3. Integer to denote precision. 1 if double, 0 if single precision.
70 * 4. Two integers specifying number of rows and columns.
71 * 5. Integer to denote storage type:
72 * GMX_MTXIO_FULL_MATRIX or GMX_MTXIO_SPARSE_MATRIX
73 *
74 * 6. Matrix data.
75 * a) In case of full matrix, this is nrow*ncol floating-point values.
76 * b) In case of sparse matrix the data is:
77 * - Integer specifying compressed_symmetric format (1=yes, 0=no)
78 * - Integer specifying number of rows (again)
79 * - nrow integers specifying the number of data entries on each row ("ndata")
80 * - All the actual entries for each row, stored contiguous.
81 * Each entry consists of an integer column index and floating-point data value.
82 */
83
84void gmx_mtxio_write(const char * filename,
85 int nrow,
86 int ncol,
87 real * full_matrix,
88 gmx_sparsematrix_t * sparse_matrix)
89{
90 t_fileio *fio;
91 XDR * xd;
92 int i, j, prec;
93 gmx_bool bDum = TRUE1;
94 gmx_bool bRead = FALSE0;
95 size_t sz;
96
97 if (full_matrix != NULL((void*)0) && sparse_matrix != NULL((void*)0))
98 {
99 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 99, "Both full AND sparse matrix specified to gmx_mtxio_write().\n");
100 }
101
102 fio = gmx_fio_open(filename, "w");
103 gmx_fio_checktype(fio);
104 xd = gmx_fio_getxdr(fio);
105
106 /* Write magic number */
107 i = GMX_MTXIO_MAGIC_NUMBER0x34ce8fd2;
108 gmx_fio_do_int(fio, i)gmx_fio_doe_int(fio, &i, ("i"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 108);
109
110 /* Write generating Gromacs version */
111 gmx_fio_write_string(fio, GromacsVersion())gmx_fio_writee_string(fio, GromacsVersion(), ("GromacsVersion()"
), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 111);
112
113 /* Write 1 for double, 0 for single precision */
114 if (sizeof(real) == sizeof(double))
115 {
116 prec = 1;
117 }
118 else
119 {
120 prec = 0;
121 }
122 gmx_fio_do_int(fio, prec)gmx_fio_doe_int(fio, &prec, ("prec"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 122);
123
124 gmx_fio_do_int(fio, nrow)gmx_fio_doe_int(fio, &nrow, ("nrow"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 124);
125 gmx_fio_do_int(fio, ncol)gmx_fio_doe_int(fio, &ncol, ("ncol"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 125);
126
127 if (full_matrix != NULL((void*)0))
128 {
129 /* Full matrix storage format */
130 i = GMX_MTXIO_FULL_MATRIX0;
131 gmx_fio_do_int(fio, i)gmx_fio_doe_int(fio, &i, ("i"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 131);
132 sz = nrow*ncol;
133 bDum = gmx_fio_ndo_real(fio, full_matrix, sz)gmx_fio_ndoe_real(fio, full_matrix, sz, ("full_matrix"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 133);
134 }
135 else
136 {
137 /* Sparse storage */
138 i = GMX_MTXIO_SPARSE_MATRIX1;
139 gmx_fio_do_int(fio, i)gmx_fio_doe_int(fio, &i, ("i"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 139);
140
141 gmx_fio_do_gmx_bool(fio, sparse_matrix->compressed_symmetric)gmx_fio_doe_gmx_bool(fio, &sparse_matrix->compressed_symmetric
, ("sparse_matrix->compressed_symmetric"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 141);
142 gmx_fio_do_int(fio, sparse_matrix->nrow)gmx_fio_doe_int(fio, &sparse_matrix->nrow, ("sparse_matrix->nrow"
), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 142);
143 if (sparse_matrix->nrow != nrow)
144 {
145 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 145, "Internal inconsistency in sparse matrix.\n");
146 }
147 bDum = gmx_fio_ndo_int(fio, sparse_matrix->ndata, sparse_matrix->nrow)gmx_fio_ndoe_int(fio, sparse_matrix->ndata, sparse_matrix->
nrow, ("sparse_matrix->ndata"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 147);
148 for (i = 0; i < sparse_matrix->nrow; i++)
149 {
150 for (j = 0; j < sparse_matrix->ndata[i]; j++)
151 {
152 gmx_fio_do_int(fio, sparse_matrix->data[i][j].col)gmx_fio_doe_int(fio, &sparse_matrix->data[i][j].col, (
"sparse_matrix->data[i][j].col"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 152);
153 gmx_fio_do_real(fio, sparse_matrix->data[i][j].value)gmx_fio_doe_real(fio, &sparse_matrix->data[i][j].value
, ("sparse_matrix->data[i][j].value"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 153);
154 }
155 }
156 }
157 gmx_fio_close(fio);
158}
159
160
161void
162gmx_mtxio_read (const char * filename,
163 int * nrow,
164 int * ncol,
165 real ** full_matrix,
166 gmx_sparsematrix_t ** sparse_matrix)
167{
168 t_fileio *fio;
169 XDR * xd;
170 int i, j, prec;
171 gmx_bool bDum = TRUE1;
172 gmx_bool bRead = TRUE1;
173 char gmxver[256];
174 size_t sz;
175
176 fio = gmx_fio_open(filename, "r");
177 gmx_fio_checktype(fio);
178 xd = gmx_fio_getxdr(fio);
179
180 /* Read and check magic number */
181 i = GMX_MTXIO_MAGIC_NUMBER0x34ce8fd2;
182 gmx_fio_do_int(fio, i)gmx_fio_doe_int(fio, &i, ("i"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 182);
183
184 if (i != GMX_MTXIO_MAGIC_NUMBER0x34ce8fd2)
185 {
186 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 186,
187 "No matrix data found in file. Note that the Hessian matrix format changed\n"
188 "in Gromacs 3.3 to enable portable files and sparse matrix storage.\n");
189 }
190
191 /* Read generating Gromacs version */
192 gmx_fio_do_string(fio, gmxver)gmx_fio_doe_string(fio, gmxver, ("gmxver"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 192);
193
194 /* Write 1 for double, 0 for single precision */
195 if (sizeof(real) == sizeof(double))
196 {
197 prec = 1;
198 }
199 else
200 {
201 prec = 0;
202 }
203 gmx_fio_do_int(fio, prec)gmx_fio_doe_int(fio, &prec, ("prec"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 203);
204
205 fprintf(stderrstderr, "Reading %s precision matrix generated by Gromacs %s\n",
206 (prec == 1) ? "double" : "single", gmxver);
207
208 gmx_fio_do_int(fio, i)gmx_fio_doe_int(fio, &i, ("i"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 208);
209 *nrow = i;
210 gmx_fio_do_int(fio, i)gmx_fio_doe_int(fio, &i, ("i"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 210);
211 *ncol = i;
212
213 gmx_fio_do_int(fio, i)gmx_fio_doe_int(fio, &i, ("i"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 213);
214
215 if (i == GMX_MTXIO_FULL_MATRIX0 && NULL((void*)0) != full_matrix)
216 {
217 printf("Full matrix storage format, nrow=%d, ncols=%d\n", *nrow, *ncol);
218
219 sz = (*nrow) * (*ncol);
220 snew((*full_matrix), sz)((*full_matrix)) = save_calloc("(*full_matrix)", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 220, (sz), sizeof(*((*full_matrix))));
221 bDum = gmx_fio_ndo_real(fio, (*full_matrix), sz)gmx_fio_ndoe_real(fio, (*full_matrix), sz, ("(*full_matrix)")
, "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 221);
222 }
223 else if (NULL((void*)0) != sparse_matrix)
224 {
225 /* Sparse storage */
226 printf("Sparse matrix storage format, nrow=%d, ncols=%d\n", *nrow, *ncol);
227
228 snew((*sparse_matrix), 1)((*sparse_matrix)) = save_calloc("(*sparse_matrix)", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 228, (1), sizeof(*((*sparse_matrix))));
229 gmx_fio_do_gmx_bool(fio, (*sparse_matrix)->compressed_symmetric)gmx_fio_doe_gmx_bool(fio, &(*sparse_matrix)->compressed_symmetric
, ("(*sparse_matrix)->compressed_symmetric"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 229);
230 gmx_fio_do_int(fio, (*sparse_matrix)->nrow)gmx_fio_doe_int(fio, &(*sparse_matrix)->nrow, ("(*sparse_matrix)->nrow"
), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 230);
231 if ((*sparse_matrix)->nrow != *nrow)
232 {
233 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 233, "Internal inconsistency in sparse matrix.\n");
234 }
235 snew((*sparse_matrix)->ndata, (*sparse_matrix)->nrow)((*sparse_matrix)->ndata) = save_calloc("(*sparse_matrix)->ndata"
, "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 235, ((*sparse_matrix)->nrow), sizeof(*((*sparse_matrix)
->ndata)));
236 snew((*sparse_matrix)->nalloc, (*sparse_matrix)->nrow)((*sparse_matrix)->nalloc) = save_calloc("(*sparse_matrix)->nalloc"
, "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 236, ((*sparse_matrix)->nrow), sizeof(*((*sparse_matrix)
->nalloc)));
237 snew((*sparse_matrix)->data, (*sparse_matrix)->nrow)((*sparse_matrix)->data) = save_calloc("(*sparse_matrix)->data"
, "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 237, ((*sparse_matrix)->nrow), sizeof(*((*sparse_matrix)
->data)));
238 bDum = gmx_fio_ndo_int(fio, (*sparse_matrix)->ndata,gmx_fio_ndoe_int(fio, (*sparse_matrix)->ndata, (*sparse_matrix
)->nrow, ("(*sparse_matrix)->ndata"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 239)
Value stored to 'bDum' is never read
239 (*sparse_matrix)->nrow)gmx_fio_ndoe_int(fio, (*sparse_matrix)->ndata, (*sparse_matrix
)->nrow, ("(*sparse_matrix)->ndata"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 239);
240
241 for (i = 0; i < (*sparse_matrix)->nrow; i++)
242 {
243 (*sparse_matrix)->nalloc[i] = (*sparse_matrix)->ndata[i] + 10;
244 snew(((*sparse_matrix)->data[i]), (*sparse_matrix)->nalloc[i])(((*sparse_matrix)->data[i])) = save_calloc("((*sparse_matrix)->data[i])"
, "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 244, ((*sparse_matrix)->nalloc[i]), sizeof(*(((*sparse_matrix
)->data[i]))));
245
246 for (j = 0; j < (*sparse_matrix)->ndata[i]; j++)
247 {
248 gmx_fio_do_int(fio, (*sparse_matrix)->data[i][j].col)gmx_fio_doe_int(fio, &(*sparse_matrix)->data[i][j].col
, ("(*sparse_matrix)->data[i][j].col"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 248);
249 gmx_fio_do_real(fio, (*sparse_matrix)->data[i][j].value)gmx_fio_doe_real(fio, &(*sparse_matrix)->data[i][j].value
, ("(*sparse_matrix)->data[i][j].value"), "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/mtxio.c"
, 249);
250 }
251 }
252 }
253 gmx_fio_close(fio);
254}