Bug Summary

File:gromacs/linearalgebra/sparsematrix.c
Location:line 110, column 13
Description:Value stored to 'j' 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) 2012,2014, 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 "sparsematrix.h"
38
39#include <assert.h>
40#include <stdlib.h>
41#include <stdio.h>
42
43#include "gromacs/utility/smalloc.h"
44
45gmx_sparsematrix_t *
46gmx_sparsematrix_init(int nrow)
47{
48 int i;
49 gmx_sparsematrix_t *A;
50
51 snew(A, 1)(A) = save_calloc("A", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/sparsematrix.c"
, 51, (1), sizeof(*(A)));
52
53 A->nrow = nrow;
54 snew(A->ndata, nrow)(A->ndata) = save_calloc("A->ndata", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/sparsematrix.c"
, 54, (nrow), sizeof(*(A->ndata)));
55 snew(A->nalloc, nrow)(A->nalloc) = save_calloc("A->nalloc", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/sparsematrix.c"
, 55, (nrow), sizeof(*(A->nalloc)));
56 snew(A->data, nrow)(A->data) = save_calloc("A->data", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/sparsematrix.c"
, 56, (nrow), sizeof(*(A->data)));
57
58 for (i = 0; i < nrow; i++)
59 {
60 A->ndata[i] = 0;
61 A->nalloc[i] = 0;
62 A->data[i] = NULL((void*)0);
63 }
64 return A;
65}
66
67
68
69void
70gmx_sparsematrix_destroy(gmx_sparsematrix_t * A)
71{
72 int i;
73
74 /* Release each row */
75 for (i = 0; i < A->nrow; i++)
76 {
77 if (A->data[i] != NULL((void*)0))
78 {
79 sfree(A->data[i])save_free("A->data[i]", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/sparsematrix.c"
, 79, (A->data[i]));
80 }
81 }
82 /* Release the rowdata arrays */
83 sfree(A->ndata)save_free("A->ndata", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/sparsematrix.c"
, 83, (A->ndata));
84 sfree(A->nalloc)save_free("A->nalloc", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/sparsematrix.c"
, 84, (A->nalloc));
85 sfree(A->data)save_free("A->data", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/sparsematrix.c"
, 85, (A->data));
86 /* Release matrix structure itself */
87 sfree(A)save_free("A", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/sparsematrix.c"
, 87, (A));
88}
89
90
91
92void
93gmx_sparsematrix_print(FILE * stream,
94 gmx_sparsematrix_t * A)
95{
96 int i, j, k;
97
98 for (i = 0; i < A->nrow; i++)
99 {
100 if (A->ndata[i] == 0)
101 {
102 for (j = 0; j < A->nrow; j++)
103 {
104 fprintf(stream, " %6.3f", 0.0);
105 }
106 }
107 else
108 {
109 k = 0;
110 j = 0;
Value stored to 'j' is never read
111 for (j = 0; j < A->ndata[i]; j++)
112 {
113 while (k++ < A->data[i][j].col)
114 {
115 fprintf(stream, " %6.3f", 0.0);
116 }
117 fprintf(stream, " %6.3f", A->data[i][j].value);
118 }
119 while (k++ < A->nrow)
120 {
121 fprintf(stream, " %6.3f", 0.0);
122 }
123 }
124 fprintf(stream, "\n");
125 }
126
127}
128
129
130real
131gmx_sparsematrix_value(gmx_sparsematrix_t * A,
132 int row,
133 int col)
134{
135 gmx_bool found = FALSE0;
136 int i;
137 real value;
138
139 assert(row < A->nrow)((void) (0));
140
141 value = 0;
142
143 /* Find previous value */
144 for (i = 0; i < A->ndata[row] && (found == FALSE0); i++)
145 {
146 if (A->data[row][i].col == col)
147 {
148 found = TRUE1;
149 value = A->data[row][i].value;
150 }
151 }
152
153 /* value=0 if we didn't find any match */
154 return value;
155}
156
157
158
159void
160gmx_sparsematrix_increment_value(gmx_sparsematrix_t * A,
161 int row,
162 int col,
163 real difference)
164{
165 gmx_bool found = FALSE0;
166 int i;
167
168 assert(row < A->nrow)((void) (0));
169
170 /* Try to find a previous entry with this row/col */
171 for (i = 0; i < A->ndata[row] && !found; i++)
172 {
173 if (A->data[row][i].col == col)
174 {
175 found = TRUE1;
176 A->data[row][i].value += difference;
177 }
178 }
179
180 /* Add a new entry if nothing was found */
181 if (!found)
182 {
183 /* add the value at the end of the row */
184 if (A->ndata[row] == A->nalloc[row])
185 {
186 A->nalloc[row] += 100;
187 if (A->data[row] == NULL((void*)0))
188 {
189 snew(A->data[row], A->nalloc[row])(A->data[row]) = save_calloc("A->data[row]", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/sparsematrix.c"
, 189, (A->nalloc[row]), sizeof(*(A->data[row])));
190 }
191 else
192 {
193 srenew(A->data[row], A->nalloc[row])(A->data[row]) = save_realloc("A->data[row]", "/home/alexxy/Develop/gromacs/src/gromacs/linearalgebra/sparsematrix.c"
, 193, (A->data[row]), (A->nalloc[row]), sizeof(*(A->
data[row])));
194 }
195 }
196 A->data[row][A->ndata[row]].col = col;
197 /* Previous value was 0.0 */
198 A->data[row][A->ndata[row]].value = difference;
199 A->ndata[row]++;
200 }
201}
202
203
204/* Routine to compare column values of two entries, used for quicksort of each row.
205 *
206 * The data entries to compare are of the type gmx_sparsematrix_entry_t, but quicksort
207 * uses void pointers as arguments, so we cast them back internally.
208 */
209static int
210compare_columns(const void *v1, const void *v2)
211{
212 int c1 = ((gmx_sparsematrix_entry_t *)v1)->col;
213 int c2 = ((gmx_sparsematrix_entry_t *)v2)->col;
214
215 if (c1 < c2)
216 {
217 return -1;
218 }
219 else if (c1 > c2)
220 {
221 return 1;
222 }
223 else
224 {
225 return 0;
226 }
227}
228
229
230void
231gmx_sparsematrix_compress(gmx_sparsematrix_t * A)
232{
233 int i, j;
234
235 for (i = 0; i < A->nrow; i++)
236 {
237 /* Remove last value on this row while it is zero */
238 while (A->ndata[i] > 0 && A->data[i][A->ndata[i]-1].value == 0)
239 {
240 A->ndata[i]--;
241 }
242
243 /* Go through values on this row and look for more zero elements */
244 for (j = 0; j < A->ndata[i]; j++)
245 {
246 /* If this element was zero, exchange it with the last non-zero
247 * element on the row (yes, this will invalidate the sort order)
248 */
249 if (A->data[i][j].value == 0)
250 {
251 A->data[i][j].value = A->data[i][A->ndata[i]-1].value;
252 A->data[i][j].col = A->data[i][A->ndata[i]-1].col;
253 A->ndata[i]--;
254 }
255 }
256 /* Only non-zero elements remaining on this row. Sort them after column index */
257 qsort((void *)(A->data[i]),
258 A->ndata[i],
259 sizeof(gmx_sparsematrix_entry_t),
260 compare_columns);
261 }
262}
263
264
265void
266gmx_sparsematrix_vector_multiply(gmx_sparsematrix_t * A,
267 real * x,
268 real * y)
269{
270 real s, v, xi;
271 int i, j, k;
272 gmx_sparsematrix_entry_t * data; /* pointer to simplify data access */
273
274 for (i = 0; i < A->nrow; i++)
275 {
276 y[i] = 0;
277 }
278
279 if (A->compressed_symmetric)
280 {
281 for (i = 0; i < A->nrow; i++)
282 {
283 xi = x[i];
284 s = 0.0;
285 data = A->data[i];
286
287 for (k = 0; k < A->ndata[i]; k++)
288 {
289 j = data[k].col;
290 v = data[k].value;
291 s += v * x[j];
292 if (i != j)
293 {
294 y[j] += v * xi;
295 }
296 }
297 y[i] += s;
298 }
299 }
300 else
301 {
302 /* not compressed symmetric storage */
303 for (i = 0; i < A->nrow; i++)
304 {
305 xi = x[i];
306 s = 0.0;
307 data = A->data[i];
308
309 for (k = 0; k < A->ndata[i]; k++)
310 {
311 j = data[k].col;
312 v = data[k].value;
313 s += v * x[j];
314 }
315 y[i] += s;
316 }
317 }
318}