Bug Summary

File:gromacs/gmxana/gmx_vanhove.c
Location:line 192, column 5
Description:Value stored to 'natom' 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
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14 * of the License, or (at your option) any later version.
15 *
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20 *
21 * You should have received a copy of the GNU Lesser General Public
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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
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36 */
37#ifdef HAVE_CONFIG_H1
38#include <config.h>
39#endif
40
41#include <math.h>
42#include <stdlib.h>
43#include <string.h>
44
45#include "gromacs/utility/smalloc.h"
46#include "macros.h"
47#include "gromacs/commandline/pargs.h"
48#include "gromacs/math/utilities.h"
49#include "gromacs/utility/futil.h"
50#include "index.h"
51#include "typedefs.h"
52#include "gromacs/fileio/xvgr.h"
53#include "viewit.h"
54#include "gstat.h"
55#include "gromacs/fileio/tpxio.h"
56#include "gromacs/fileio/trxio.h"
57#include "gromacs/math/vec.h"
58#include "gromacs/fileio/matio.h"
59#include "gmx_ana.h"
60
61
62int gmx_vanhove(int argc, char *argv[])
63{
64 const char *desc[] = {
65 "[THISMODULE] computes the Van Hove correlation function.",
66 "The Van Hove G(r,t) is the probability that a particle that is at r[SUB]0[sub]",
67 "at time zero can be found at position r[SUB]0[sub]+r at time t.",
68 "[THISMODULE] determines G not for a vector r, but for the length of r.",
69 "Thus it gives the probability that a particle moves a distance of r",
70 "in time t.",
71 "Jumps across the periodic boundaries are removed.",
72 "Corrections are made for scaling due to isotropic",
73 "or anisotropic pressure coupling.",
74 "[PAR]",
75 "With option [TT]-om[tt] the whole matrix can be written as a function",
76 "of t and r or as a function of [SQRT]t[sqrt] and r (option [TT]-sqrt[tt]).",
77 "[PAR]",
78 "With option [TT]-or[tt] the Van Hove function is plotted for one",
79 "or more values of t. Option [TT]-nr[tt] sets the number of times,",
80 "option [TT]-fr[tt] the number spacing between the times.",
81 "The binwidth is set with option [TT]-rbin[tt]. The number of bins",
82 "is determined automatically.",
83 "[PAR]",
84 "With option [TT]-ot[tt] the integral up to a certain distance",
85 "(option [TT]-rt[tt]) is plotted as a function of time.",
86 "[PAR]",
87 "For all frames that are read the coordinates of the selected particles",
88 "are stored in memory. Therefore the program may use a lot of memory.",
89 "For options [TT]-om[tt] and [TT]-ot[tt] the program may be slow.",
90 "This is because the calculation scales as the number of frames times",
91 "[TT]-fm[tt] or [TT]-ft[tt].",
92 "Note that with the [TT]-dt[tt] option the memory usage and calculation",
93 "time can be reduced."
94 };
95 static int fmmax = 0, ftmax = 0, nlev = 81, nr = 1, fshift = 0;
96 static real sbin = 0, rmax = 2, rbin = 0.01, mmax = 0, rint = 0;
97 t_pargs pa[] = {
98 { "-sqrt", FALSE0, etREAL, {&sbin},
99 "Use [SQRT]t[sqrt] on the matrix axis which binspacing # in [SQRT]ps[sqrt]" },
100 { "-fm", FALSE0, etINT, {&fmmax},
101 "Number of frames in the matrix, 0 is plot all" },
102 { "-rmax", FALSE0, etREAL, {&rmax},
103 "Maximum r in the matrix (nm)" },
104 { "-rbin", FALSE0, etREAL, {&rbin},
105 "Binwidth in the matrix and for [TT]-or[tt] (nm)" },
106 { "-mmax", FALSE0, etREAL, {&mmax},
107 "Maximum density in the matrix, 0 is calculate (1/nm)" },
108 { "-nlevels", FALSE0, etINT, {&nlev},
109 "Number of levels in the matrix" },
110 { "-nr", FALSE0, etINT, {&nr},
111 "Number of curves for the [TT]-or[tt] output" },
112 { "-fr", FALSE0, etINT, {&fshift},
113 "Frame spacing for the [TT]-or[tt] output" },
114 { "-rt", FALSE0, etREAL, {&rint},
115 "Integration limit for the [TT]-ot[tt] output (nm)" },
116 { "-ft", FALSE0, etINT, {&ftmax},
117 "Number of frames in the [TT]-ot[tt] output, 0 is plot all" }
118 };
119#define NPA((int)(sizeof(pa)/sizeof((pa)[0]))) asize(pa)((int)(sizeof(pa)/sizeof((pa)[0])))
120
121 t_filenm fnm[] = {
122 { efTRX, NULL((void*)0), NULL((void*)0), ffREAD1<<1 },
123 { efTPS, NULL((void*)0), NULL((void*)0), ffREAD1<<1 },
124 { efNDX, NULL((void*)0), NULL((void*)0), ffOPTRD(1<<1 | 1<<3) },
125 { efXPM, "-om", "vanhove", ffOPTWR(1<<2| 1<<3) },
126 { efXVG, "-or", "vanhove_r", ffOPTWR(1<<2| 1<<3) },
127 { efXVG, "-ot", "vanhove_t", ffOPTWR(1<<2| 1<<3) }
128 };
129#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
130
131 output_env_t oenv;
132 const char *matfile, *otfile, *orfile;
133 char title[256];
134 t_topology top;
135 int ePBC;
136 matrix boxtop, box, *sbox, avbox, corr;
137 rvec *xtop, *x, **sx;
138 int isize, nalloc, nallocn, natom;
139 t_trxstatus *status;
140 atom_id *index;
141 char *grpname;
142 int nfr, f, ff, i, m, mat_nx = 0, nbin = 0, bin, mbin, fbin;
143 real *time, t, invbin = 0, rmax2 = 0, rint2 = 0, d2;
144 real invsbin = 0, matmax, normfac, dt, *tickx, *ticky;
145 char buf[STRLEN4096], **legend;
146 real **mat = NULL((void*)0);
147 int *pt = NULL((void*)0), **pr = NULL((void*)0), *mcount = NULL((void*)0), *tcount = NULL((void*)0), *rcount = NULL((void*)0);
148 FILE *fp;
149 t_rgb rlo = {1, 1, 1}, rhi = {0, 0, 0};
150
151 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW(1<<5) | PCA_CAN_TIME((1<<6) | (1<<7) | (1<<14)) | PCA_BE_NICE(1<<13),
152 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))
153 {
154 return 0;
155 }
156
157 matfile = opt2fn_null("-om", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
158 if (opt2parg_bSet("-fr", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa))
159 {
160 orfile = opt2fn("-or", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
161 }
162 else
163 {
164 orfile = opt2fn_null("-or", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
165 }
166 if (opt2parg_bSet("-rt", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa))
167 {
168 otfile = opt2fn("-ot", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
169 }
170 else
171 {
172 otfile = opt2fn_null("-ot", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
173 }
174
175 if (!matfile && !otfile && !orfile)
176 {
177 fprintf(stderrstderr,
178 "For output set one (or more) of the output file options\n");
179 exit(0);
180 }
181
182 read_tps_conf(ftp2fn(efTPS, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), title, &top, &ePBC, &xtop, NULL((void*)0), boxtop,
183 FALSE0);
184 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), 1, &isize, &index, &grpname);
185
186 nalloc = 0;
187 time = NULL((void*)0);
188 sbox = NULL((void*)0);
189 sx = NULL((void*)0);
190 clear_mat(avbox);
191
192 natom = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), &t, &x, box);
Value stored to 'natom' is never read
193 nfr = 0;
194 do
195 {
196 if (nfr >= nalloc)
197 {
198 nalloc += 100;
199 srenew(time, nalloc)(time) = save_realloc("time", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 199, (time), (nalloc), sizeof(*(time)));
200 srenew(sbox, nalloc)(sbox) = save_realloc("sbox", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 200, (sbox), (nalloc), sizeof(*(sbox)));
201 srenew(sx, nalloc)(sx) = save_realloc("sx", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 201, (sx), (nalloc), sizeof(*(sx)));
202 }
203
204 time[nfr] = t;
205 copy_mat(box, sbox[nfr]);
206 /* This assumes that the off-diagonal box elements
207 * are not affected by jumps across the periodic boundaries.
208 */
209 m_add(avbox, box, avbox);
210 snew(sx[nfr], isize)(sx[nfr]) = save_calloc("sx[nfr]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 210, (isize), sizeof(*(sx[nfr])));
211 for (i = 0; i < isize; i++)
212 {
213 copy_rvec(x[index[i]], sx[nfr][i]);
214 }
215
216 nfr++;
217 }
218 while (read_next_x(oenv, status, &t, x, box));
219
220 /* clean up */
221 sfree(x)save_free("x", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 221, (x));
222 close_trj(status);
223
224 fprintf(stderrstderr, "Read %d frames\n", nfr);
225
226 dt = (time[nfr-1] - time[0])/(nfr - 1);
227 /* Some ugly rounding to get nice nice times in the output */
228 dt = (int)(10000.0*dt + 0.5)/10000.0;
229
230 invbin = 1.0/rbin;
231
232 if (matfile)
233 {
234 if (fmmax <= 0 || fmmax >= nfr)
235 {
236 fmmax = nfr - 1;
237 }
238 snew(mcount, fmmax)(mcount) = save_calloc("mcount", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 238, (fmmax), sizeof(*(mcount)));
239 nbin = (int)(rmax*invbin + 0.5);
240 if (sbin == 0)
241 {
242 mat_nx = fmmax + 1;
243 }
244 else
245 {
246 invsbin = 1.0/sbin;
247 mat_nx = sqrt(fmmax*dt)*invsbin + 1;
248 }
249 snew(mat, mat_nx)(mat) = save_calloc("mat", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 249, (mat_nx), sizeof(*(mat)));
250 for (f = 0; f < mat_nx; f++)
251 {
252 snew(mat[f], nbin)(mat[f]) = save_calloc("mat[f]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 252, (nbin), sizeof(*(mat[f])));
253 }
254 rmax2 = sqr(nbin*rbin);
255 /* Initialize time zero */
256 mat[0][0] = nfr*isize;
257 mcount[0] += nfr;
258 }
259 else
260 {
261 fmmax = 0;
262 }
263
264 if (orfile)
265 {
266 snew(pr, nr)(pr) = save_calloc("pr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 266, (nr), sizeof(*(pr)));
267 nalloc = 0;
268 snew(rcount, nr)(rcount) = save_calloc("rcount", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 268, (nr), sizeof(*(rcount)));
269 }
270
271 if (otfile)
272 {
273 if (ftmax <= 0)
274 {
275 ftmax = nfr - 1;
276 }
277 snew(tcount, ftmax)(tcount) = save_calloc("tcount", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 277, (ftmax), sizeof(*(tcount)));
278 snew(pt, nfr)(pt) = save_calloc("pt", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 278, (nfr), sizeof(*(pt)));
279 rint2 = rint*rint;
280 /* Initialize time zero */
281 pt[0] = nfr*isize;
282 tcount[0] += nfr;
283 }
284 else
285 {
286 ftmax = 0;
287 }
288
289 msmul(avbox, 1.0/nfr, avbox);
290 for (f = 0; f < nfr; f++)
291 {
292 if (f % 100 == 0)
293 {
294 fprintf(stderrstderr, "\rProcessing frame %d", f);
295 }
296 /* Scale all the configuration to the average box */
297 m_inv_ur0(sbox[f], corr);
298 mmul_ur0(avbox, corr, corr);
299 for (i = 0; i < isize; i++)
300 {
301 mvmul_ur0(corr, sx[f][i], sx[f][i]);
302 if (f > 0)
303 {
304 /* Correct for periodic jumps */
305 for (m = DIM3-1; m >= 0; m--)
306 {
307 while (sx[f][i][m] - sx[f-1][i][m] > 0.5*avbox[m][m])
308 {
309 rvec_dec(sx[f][i], avbox[m]);
310 }
311 while (sx[f][i][m] - sx[f-1][i][m] <= -0.5*avbox[m][m])
312 {
313 rvec_inc(sx[f][i], avbox[m]);
314 }
315 }
316 }
317 }
318 for (ff = 0; ff < f; ff++)
319 {
320 fbin = f - ff;
321 if (fbin <= fmmax || fbin <= ftmax)
322 {
323 if (sbin == 0)
324 {
325 mbin = fbin;
326 }
327 else
328 {
329 mbin = (int)(sqrt(fbin*dt)*invsbin + 0.5);
330 }
331 for (i = 0; i < isize; i++)
332 {
333 d2 = distance2(sx[f][i], sx[ff][i]);
334 if (mbin < mat_nx && d2 < rmax2)
335 {
336 bin = (int)(sqrt(d2)*invbin + 0.5);
337 if (bin < nbin)
338 {
339 mat[mbin][bin] += 1;
340 }
341 }
342 if (fbin <= ftmax && d2 <= rint2)
343 {
344 pt[fbin]++;
345 }
346 }
347 if (matfile)
348 {
349 mcount[mbin]++;
350 }
351 if (otfile)
352 {
353 tcount[fbin]++;
354 }
355 }
356 }
357 if (orfile)
358 {
359 for (fbin = 0; fbin < nr; fbin++)
360 {
361 ff = f - (fbin + 1)*fshift;
362 if (ff >= 0)
363 {
364 for (i = 0; i < isize; i++)
365 {
366 d2 = distance2(sx[f][i], sx[ff][i]);
367 bin = (int)(sqrt(d2)*invbin + 0.5);
368 if (bin >= nalloc)
369 {
370 nallocn = 10*(bin/10) + 11;
371 for (m = 0; m < nr; m++)
372 {
373 srenew(pr[m], nallocn)(pr[m]) = save_realloc("pr[m]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 373, (pr[m]), (nallocn), sizeof(*(pr[m])));
374 for (i = nalloc; i < nallocn; i++)
375 {
376 pr[m][i] = 0;
377 }
378 }
379 nalloc = nallocn;
380 }
381 pr[fbin][bin]++;
382 }
383 rcount[fbin]++;
384 }
385 }
386 }
387 }
388 fprintf(stderrstderr, "\n");
389
390 if (matfile)
391 {
392 matmax = 0;
393 for (f = 0; f < mat_nx; f++)
394 {
395 normfac = 1.0/(mcount[f]*isize*rbin);
396 for (i = 0; i < nbin; i++)
397 {
398 mat[f][i] *= normfac;
399 if (mat[f][i] > matmax && (f != 0 || i != 0))
400 {
401 matmax = mat[f][i];
402 }
403 }
404 }
405 fprintf(stdoutstdout, "Value at (0,0): %.3f, maximum of the rest %.3f\n",
406 mat[0][0], matmax);
407 if (mmax > 0)
408 {
409 matmax = mmax;
410 }
411 snew(tickx, mat_nx)(tickx) = save_calloc("tickx", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 411, (mat_nx), sizeof(*(tickx)));
412 for (f = 0; f < mat_nx; f++)
413 {
414 if (sbin == 0)
415 {
416 tickx[f] = f*dt;
417 }
418 else
419 {
420 tickx[f] = f*sbin;
421 }
422 }
423 snew(ticky, nbin+1)(ticky) = save_calloc("ticky", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 423, (nbin+1), sizeof(*(ticky)));
424 for (i = 0; i <= nbin; i++)
425 {
426 ticky[i] = i*rbin;
427 }
428 fp = gmx_ffopen(matfile, "w");
429 write_xpm(fp, MAT_SPATIAL_Y(1<<1), "Van Hove function", "G (1/nm)",
430 sbin == 0 ? "time (ps)" : "sqrt(time) (ps^1/2)", "r (nm)",
431 mat_nx, nbin, tickx, ticky, mat, 0, matmax, rlo, rhi, &nlev);
432 gmx_ffclose(fp);
433 }
434
435 if (orfile)
436 {
437 fp = xvgropen(orfile, "Van Hove function", "r (nm)", "G (nm\\S-1\\N)", oenv);
438 fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
439 snew(legend, nr)(legend) = save_calloc("legend", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_vanhove.c"
, 439, (nr), sizeof(*(legend)));
440 for (fbin = 0; fbin < nr; fbin++)
441 {
442 sprintf(buf, "%g ps", (fbin + 1)*fshift*dt);
443 legend[fbin] = 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)));
444 }
445 xvgr_legend(fp, nr, (const char**)legend, oenv);
446 for (i = 0; i < nalloc; i++)
447 {
448 fprintf(fp, "%g", i*rbin);
449 for (fbin = 0; fbin < nr; fbin++)
450 {
451 fprintf(fp, " %g",
452 (real)pr[fbin][i]/(rcount[fbin]*isize*rbin*(i == 0 ? 0.5 : 1)));
453 }
454 fprintf(fp, "\n");
455 }
456 gmx_ffclose(fp);
457 }
458
459 if (otfile)
460 {
461 sprintf(buf, "Probability of moving less than %g nm", rint);
462 fp = xvgropen(otfile, buf, "t (ps)", "", oenv);
463 fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
464 for (f = 0; f <= ftmax; f++)
465 {
466 fprintf(fp, "%g %g\n", f*dt, (real)pt[f]/(tcount[f]*isize));
467 }
468 gmx_ffclose(fp);
469 }
470
471 do_view(oenv, matfile, NULL((void*)0));
472 do_view(oenv, orfile, NULL((void*)0));
473 do_view(oenv, otfile, NULL((void*)0));
474
475 return 0;
476}