Bug Summary

File:gromacs/gmxana/gmx_saltbr.c
Location:line 204, column 5
Description:Value stored to 'natoms' 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) 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 *
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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
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24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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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36 */
37#ifdef HAVE_CONFIG_H1
38#include <config.h>
39#endif
40#include <math.h>
41#include <string.h>
42
43#include "macros.h"
44#include "gromacs/math/vec.h"
45#include "typedefs.h"
46#include "gromacs/fileio/filenm.h"
47#include "gromacs/fileio/trxio.h"
48#include "gromacs/commandline/pargs.h"
49#include "gromacs/utility/futil.h"
50#include "gromacs/utility/fatalerror.h"
51#include "gromacs/utility/smalloc.h"
52#include "pbc.h"
53#include "gromacs/fileio/xvgr.h"
54#include "gmx_ana.h"
55
56#include "gromacs/utility/fatalerror.h"
57
58typedef struct {
59 char *label;
60 int cg;
61 real q;
62} t_charge;
63
64static t_charge *mk_charge(t_atoms *atoms, t_block *cgs, int *nncg)
65{
66 t_charge *cg = NULL((void*)0);
67 char buf[32];
68 int i, j, ncg, resnr, anr;
69 real qq;
70
71 /* Find the charged groups */
72 ncg = 0;
73 for (i = 0; (i < cgs->nr); i++)
74 {
75 qq = 0.0;
76 for (j = cgs->index[i]; (j < cgs->index[i+1]); j++)
77 {
78 qq += atoms->atom[j].q;
79 }
80 if (fabs(qq) > 1.0e-5)
81 {
82 srenew(cg, ncg+1)(cg) = save_realloc("cg", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_saltbr.c"
, 82, (cg), (ncg+1), sizeof(*(cg)));
83 cg[ncg].q = qq;
84 cg[ncg].cg = i;
85 anr = cgs->index[i];
86 resnr = atoms->atom[anr].resind;
87 sprintf(buf, "%s%d-%d",
88 *(atoms->resinfo[resnr].name),
89 atoms->resinfo[resnr].nr,
90 anr+1);
91 cg[ncg].label = 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)));
92 ncg++;
93 }
94 }
95 *nncg = ncg;
96
97 for (i = 0; (i < ncg); i++)
98 {
99 printf("CG: %10s Q: %6g Atoms:",
100 cg[i].label, cg[i].q);
101 for (j = cgs->index[cg[i].cg]; (j < cgs->index[cg[i].cg+1]); j++)
102 {
103 printf(" %4d", j);
104 }
105 printf("\n");
106 }
107
108 return cg;
109}
110
111static real calc_dist(t_pbc *pbc, rvec x[], t_block *cgs, int icg, int jcg)
112{
113 int i, j;
114 rvec dx;
115 real d2, mindist2 = 1000;
116
117 for (i = cgs->index[icg]; (i < cgs->index[icg+1]); i++)
118 {
119 for (j = cgs->index[jcg]; (j < cgs->index[jcg+1]); j++)
120 {
121 pbc_dx(pbc, x[i], x[j], dx);
122 d2 = norm2(dx);
123 if (d2 < mindist2)
124 {
125 mindist2 = d2;
126 }
127 }
128 }
129 return sqrt(mindist2);
130}
131
132int gmx_saltbr(int argc, char *argv[])
133{
134 const char *desc[] = {
135 "[THISMODULE] plots the distance between all combination of charged groups",
136 "as a function of time. The groups are combined in different ways.",
137 "A minimum distance can be given (i.e. a cut-off), such that groups",
138 "that are never closer than that distance will not be plotted.[PAR]",
139 "Output will be in a number of fixed filenames, [TT]min-min.xvg[tt], [TT]plus-min.xvg[tt]",
140 "and [TT]plus-plus.xvg[tt], or files for every individual ion pair if the [TT]-sep[tt]",
141 "option is selected. In this case, files are named as [TT]sb-(Resname)(Resnr)-(Atomnr)[tt].",
142 "There may be [BB]many[bb] such files."
143 };
144 static gmx_bool bSep = FALSE0;
145 static real truncate = 1000.0;
146 t_pargs pa[] = {
147 { "-t", FALSE0, etREAL, {&truncate},
148 "Groups that are never closer than this distance are not plotted" },
149 { "-sep", FALSE0, etBOOL, {&bSep},
150 "Use separate files for each interaction (may be MANY)" }
151 };
152 t_filenm fnm[] = {
153 { efTRX, "-f", NULL((void*)0), ffREAD1<<1 },
154 { efTPX, NULL((void*)0), NULL((void*)0), ffREAD1<<1 },
155 };
156#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
157
158 FILE *out[3], *fp;
159 static const char *title[3] = {
160 "Distance between positively charged groups",
161 "Distance between negatively charged groups",
162 "Distance between oppositely charged groups"
163 };
164 static const char *fn[3] = {
165 "plus-plus.xvg",
166 "min-min.xvg",
167 "plus-min.xvg"
168 };
169 int nset[3] = {0, 0, 0};
170
171 t_topology *top;
172 int ePBC;
173 char *buf;
174 t_trxstatus *status;
175 int i, j, k, m, nnn, teller, ncg, n1, n2, n3, natoms;
176 real t, *time, qi, qj;
177 t_charge *cg;
178 real ***cgdist;
179 int **nWithin;
180
181 double t0, dt;
182 char label[234];
183 t_pbc pbc;
184 rvec *x;
185 matrix box;
186 output_env_t oenv;
187
188 if (!parse_common_args(&argc, argv, PCA_CAN_TIME((1<<6) | (1<<7) | (1<<14)) | PCA_BE_NICE(1<<13),
189 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))
190 {
191 return 0;
192 }
193
194 top = read_top(ftp2fn(efTPX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), &ePBC);
195 cg = mk_charge(&top->atoms, &(top->cgs), &ncg);
196 snew(cgdist, ncg)(cgdist) = save_calloc("cgdist", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_saltbr.c"
, 196, (ncg), sizeof(*(cgdist)));
197 snew(nWithin, ncg)(nWithin) = save_calloc("nWithin", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_saltbr.c"
, 197, (ncg), sizeof(*(nWithin)));
198 for (i = 0; (i < ncg); i++)
199 {
200 snew(cgdist[i], ncg)(cgdist[i]) = save_calloc("cgdist[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_saltbr.c"
, 200, (ncg), sizeof(*(cgdist[i])));
201 snew(nWithin[i], ncg)(nWithin[i]) = save_calloc("nWithin[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_saltbr.c"
, 201, (ncg), sizeof(*(nWithin[i])));
202 }
203
204 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), &t, &x, box);
Value stored to 'natoms' is never read
205
206 teller = 0;
207 time = NULL((void*)0);
208 do
209 {
210 srenew(time, teller+1)(time) = save_realloc("time", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_saltbr.c"
, 210, (time), (teller+1), sizeof(*(time)));
211 time[teller] = t;
212
213 set_pbc(&pbc, ePBC, box);
214
215 for (i = 0; (i < ncg); i++)
216 {
217 for (j = i+1; (j < ncg); j++)
218 {
219 srenew(cgdist[i][j], teller+1)(cgdist[i][j]) = save_realloc("cgdist[i][j]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_saltbr.c"
, 219, (cgdist[i][j]), (teller+1), sizeof(*(cgdist[i][j])));
220 cgdist[i][j][teller] =
221 calc_dist(&pbc, x, &(top->cgs), cg[i].cg, cg[j].cg);
222 if (cgdist[i][j][teller] < truncate)
223 {
224 nWithin[i][j] = 1;
225 }
226 }
227 }
228
229 teller++;
230 }
231 while (read_next_x(oenv, status, &t, x, box));
232 fprintf(stderrstderr, "\n");
233 close_trj(status);
234
235 if (bSep)
236 {
237 snew(buf, 256)(buf) = save_calloc("buf", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_saltbr.c"
, 237, (256), sizeof(*(buf)));
238 for (i = 0; (i < ncg); i++)
239 {
240 for (j = i+1; (j < ncg); j++)
241 {
242 if (nWithin[i][j])
243 {
244 sprintf(buf, "sb-%s:%s.xvg", cg[i].label, cg[j].label);
245 fp = xvgropen(buf, buf, "Time (ps)", "Distance (nm)", oenv);
246 for (k = 0; (k < teller); k++)
247 {
248 fprintf(fp, "%10g %10g\n", time[k], cgdist[i][j][k]);
249 }
250 gmx_ffclose(fp);
251 }
252 }
253 }
254 sfree(buf)save_free("buf", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_saltbr.c"
, 254, (buf));
255 }
256 else
257 {
258
259 for (m = 0; (m < 3); m++)
260 {
261 out[m] = xvgropen(fn[m], title[m], "Time (ps)", "Distance (nm)", oenv);
262 }
263
264 snew(buf, 256)(buf) = save_calloc("buf", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_saltbr.c"
, 264, (256), sizeof(*(buf)));
265 for (i = 0; (i < ncg); i++)
266 {
267 qi = cg[i].q;
268 for (j = i+1; (j < ncg); j++)
269 {
270 qj = cg[j].q;
271 if (nWithin[i][j])
272 {
273 sprintf(buf, "%s:%s", cg[i].label, cg[j].label);
274 if (qi*qj < 0)
275 {
276 nnn = 2;
277 }
278 else if (qi+qj > 0)
279 {
280 nnn = 0;
281 }
282 else
283 {
284 nnn = 1;
285 }
286
287 if (nset[nnn] == 0)
288 {
289 xvgr_legend(out[nnn], 1, (const char**)&buf, oenv);
290 }
291 else
292 {
293 if (output_env_get_xvg_format(oenv) == exvgXMGR)
294 {
295 fprintf(out[nnn], "@ legend string %d \"%s\"\n", nset[nnn], buf);
296 }
297 else if (output_env_get_xvg_format(oenv) == exvgXMGRACE)
298 {
299 fprintf(out[nnn], "@ s%d legend \"%s\"\n", nset[nnn], buf);
300 }
301 }
302 nset[nnn]++;
303 nWithin[i][j] = nnn+1;
304 }
305 }
306 }
307 for (k = 0; (k < teller); k++)
308 {
309 for (m = 0; (m < 3); m++)
310 {
311 fprintf(out[m], "%10g", time[k]);
312 }
313
314 for (i = 0; (i < ncg); i++)
315 {
316 for (j = i+1; (j < ncg); j++)
317 {
318 nnn = nWithin[i][j];
319 if (nnn > 0)
320 {
321 fprintf(out[nnn-1], " %10g", cgdist[i][j][k]);
322 }
323 }
324 }
325 for (m = 0; (m < 3); m++)
326 {
327 fprintf(out[m], "\n");
328 }
329 }
330 for (m = 0; (m < 3); m++)
331 {
332 gmx_ffclose(out[m]);
333 if (nset[m] == 0)
334 {
335 remove(fn[m]);
336 }
337 }
338 }
339
340 return 0;
341}