Bug Summary

File:gromacs/mdlib/mdatom.c
Location:line 130, column 5
Description:Value stored to 'molblock' 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#ifdef HAVE_CONFIG_H1
38#include <config.h>
39#endif
40
41#include <math.h>
42
43#include "typedefs.h"
44#include "mdatoms.h"
45#include "gromacs/utility/smalloc.h"
46#include "qmmm.h"
47#include "mtop_util.h"
48#include "gmx_omp_nthreads.h"
49
50#define ALMOST_ZERO1e-30 1e-30
51
52t_mdatoms *init_mdatoms(FILE *fp, gmx_mtop_t *mtop, gmx_bool bFreeEnergy)
53{
54 int mb, a, g, nmol;
55 double tmA, tmB;
56 t_atom *atom;
57 t_mdatoms *md;
58 gmx_mtop_atomloop_all_t aloop;
59 t_ilist *ilist;
60
61 snew(md, 1)(md) = save_calloc("md", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 61, (1), sizeof(*(md)));
62
63 md->nenergrp = mtop->groups.grps[egcENER].nr;
64 md->bVCMgrps = FALSE0;
65 tmA = 0.0;
66 tmB = 0.0;
67
68 aloop = gmx_mtop_atomloop_all_init(mtop);
69 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
70 {
71 if (ggrpnr(&mtop->groups, egcVCM, a)((&mtop->groups)->grpnr[egcVCM] ? (&mtop->groups
)->grpnr[egcVCM][a] : 0) > 0)
72 {
73 md->bVCMgrps = TRUE1;
74 }
75
76 if (bFreeEnergy && PERTURBED(*atom)(((*atom).mB != (*atom).m) || ((*atom).qB != (*atom).q) || ((
*atom).typeB != (*atom).type)))
77 {
78 md->nPerturbed++;
79 if (atom->mB != atom->m)
80 {
81 md->nMassPerturbed++;
82 }
83 if (atom->qB != atom->q)
84 {
85 md->nChargePerturbed++;
86 }
87 if (atom->typeB != atom->type)
88 {
89 md->nTypePerturbed++;
90 }
91 }
92
93 tmA += atom->m;
94 tmB += atom->mB;
95 }
96
97 md->tmassA = tmA;
98 md->tmassB = tmB;
99
100 if (bFreeEnergy && fp)
101 {
102 fprintf(fp,
103 "There are %d atoms and %d charges for free energy perturbation\n",
104 md->nPerturbed, md->nChargePerturbed);
105 }
106
107 md->bOrires = gmx_mtop_ftype_count(mtop, F_ORIRES);
108
109 return md;
110}
111
112void atoms2md(gmx_mtop_t *mtop, t_inputrec *ir,
113 int nindex, int *index,
114 int homenr,
115 t_mdatoms *md)
116{
117 gmx_bool bLJPME;
118 gmx_mtop_atomlookup_t alook;
119 int i;
120 t_grpopts *opts;
121 gmx_groups_t *groups;
122 gmx_molblock_t *molblock;
123
124 bLJPME = EVDW_PME(ir->vdwtype)((ir->vdwtype) == evdwPME);
125
126 opts = &ir->opts;
127
128 groups = &mtop->groups;
129
130 molblock = mtop->molblock;
Value stored to 'molblock' is never read
131
132 /* Index==NULL indicates no DD (unless we have a DD node with no
133 * atoms), so also check for homenr. This should be
134 * signaled properly with an extra parameter or nindex==-1.
135 */
136 if (index == NULL((void*)0) && (homenr > 0))
137 {
138 md->nr = mtop->natoms;
139 }
140 else
141 {
142 md->nr = nindex;
143 }
144
145 if (md->nr > md->nalloc)
146 {
147 md->nalloc = over_alloc_dd(md->nr);
148
149 if (md->nMassPerturbed)
150 {
151 srenew(md->massA, md->nalloc)(md->massA) = save_realloc("md->massA", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 151, (md->massA), (md->nalloc), sizeof(*(md->massA
)));
152 srenew(md->massB, md->nalloc)(md->massB) = save_realloc("md->massB", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 152, (md->massB), (md->nalloc), sizeof(*(md->massB
)));
153 }
154 srenew(md->massT, md->nalloc)(md->massT) = save_realloc("md->massT", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 154, (md->massT), (md->nalloc), sizeof(*(md->massT
)));
155 srenew(md->invmass, md->nalloc)(md->invmass) = save_realloc("md->invmass", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 155, (md->invmass), (md->nalloc), sizeof(*(md->invmass
)));
156 srenew(md->chargeA, md->nalloc)(md->chargeA) = save_realloc("md->chargeA", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 156, (md->chargeA), (md->nalloc), sizeof(*(md->chargeA
)));
157 if (bLJPME)
158 {
159 srenew(md->sqrt_c6A, md->nalloc)(md->sqrt_c6A) = save_realloc("md->sqrt_c6A", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 159, (md->sqrt_c6A), (md->nalloc), sizeof(*(md->sqrt_c6A
)));
160 srenew(md->sigmaA, md->nalloc)(md->sigmaA) = save_realloc("md->sigmaA", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 160, (md->sigmaA), (md->nalloc), sizeof(*(md->sigmaA
)));
161 srenew(md->sigma3A, md->nalloc)(md->sigma3A) = save_realloc("md->sigma3A", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 161, (md->sigma3A), (md->nalloc), sizeof(*(md->sigma3A
)));
162 }
163 if (md->nPerturbed)
164 {
165 srenew(md->chargeB, md->nalloc)(md->chargeB) = save_realloc("md->chargeB", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 165, (md->chargeB), (md->nalloc), sizeof(*(md->chargeB
)));
166 if (bLJPME)
167 {
168 srenew(md->sqrt_c6B, md->nalloc)(md->sqrt_c6B) = save_realloc("md->sqrt_c6B", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 168, (md->sqrt_c6B), (md->nalloc), sizeof(*(md->sqrt_c6B
)));
169 srenew(md->sigmaB, md->nalloc)(md->sigmaB) = save_realloc("md->sigmaB", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 169, (md->sigmaB), (md->nalloc), sizeof(*(md->sigmaB
)));
170 srenew(md->sigma3B, md->nalloc)(md->sigma3B) = save_realloc("md->sigma3B", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 170, (md->sigma3B), (md->nalloc), sizeof(*(md->sigma3B
)));
171 }
172 }
173 srenew(md->typeA, md->nalloc)(md->typeA) = save_realloc("md->typeA", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 173, (md->typeA), (md->nalloc), sizeof(*(md->typeA
)));
174 if (md->nPerturbed)
175 {
176 srenew(md->typeB, md->nalloc)(md->typeB) = save_realloc("md->typeB", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 176, (md->typeB), (md->nalloc), sizeof(*(md->typeB
)));
177 }
178 srenew(md->ptype, md->nalloc)(md->ptype) = save_realloc("md->ptype", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 178, (md->ptype), (md->nalloc), sizeof(*(md->ptype
)));
179 if (opts->ngtc > 1)
180 {
181 srenew(md->cTC, md->nalloc)(md->cTC) = save_realloc("md->cTC", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 181, (md->cTC), (md->nalloc), sizeof(*(md->cTC)));
182 /* We always copy cTC with domain decomposition */
183 }
184 srenew(md->cENER, md->nalloc)(md->cENER) = save_realloc("md->cENER", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 184, (md->cENER), (md->nalloc), sizeof(*(md->cENER
)));
185 if (opts->ngacc > 1)
186 {
187 srenew(md->cACC, md->nalloc)(md->cACC) = save_realloc("md->cACC", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 187, (md->cACC), (md->nalloc), sizeof(*(md->cACC))
);
188 }
189 if (opts->nFreeze &&
190 (opts->ngfrz > 1 ||
191 opts->nFreeze[0][XX0] || opts->nFreeze[0][YY1] || opts->nFreeze[0][ZZ2]))
192 {
193 srenew(md->cFREEZE, md->nalloc)(md->cFREEZE) = save_realloc("md->cFREEZE", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 193, (md->cFREEZE), (md->nalloc), sizeof(*(md->cFREEZE
)));
194 }
195 if (md->bVCMgrps)
196 {
197 srenew(md->cVCM, md->nalloc)(md->cVCM) = save_realloc("md->cVCM", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 197, (md->cVCM), (md->nalloc), sizeof(*(md->cVCM))
);
198 }
199 if (md->bOrires)
200 {
201 srenew(md->cORF, md->nalloc)(md->cORF) = save_realloc("md->cORF", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 201, (md->cORF), (md->nalloc), sizeof(*(md->cORF))
);
202 }
203 if (md->nPerturbed)
204 {
205 srenew(md->bPerturbed, md->nalloc)(md->bPerturbed) = save_realloc("md->bPerturbed", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 205, (md->bPerturbed), (md->nalloc), sizeof(*(md->
bPerturbed)));
206 }
207
208 /* Note that these user t_mdatoms array pointers are NULL
209 * when there is only one group present.
210 * Therefore, when adding code, the user should use something like:
211 * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
212 */
213 if (mtop->groups.grpnr[egcUser1] != NULL((void*)0))
214 {
215 srenew(md->cU1, md->nalloc)(md->cU1) = save_realloc("md->cU1", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 215, (md->cU1), (md->nalloc), sizeof(*(md->cU1)));
216 }
217 if (mtop->groups.grpnr[egcUser2] != NULL((void*)0))
218 {
219 srenew(md->cU2, md->nalloc)(md->cU2) = save_realloc("md->cU2", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 219, (md->cU2), (md->nalloc), sizeof(*(md->cU2)));
220 }
221
222 if (ir->bQMMM)
223 {
224 srenew(md->bQM, md->nalloc)(md->bQM) = save_realloc("md->bQM", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 224, (md->bQM), (md->nalloc), sizeof(*(md->bQM)));
225 }
226 if (ir->bAdress)
227 {
228 srenew(md->wf, md->nalloc)(md->wf) = save_realloc("md->wf", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c"
, 228, (md->wf), (md->nalloc), sizeof(*(md->wf)));
229 srenew(md->tf_table_index, md->nalloc)(md->tf_table_index) = save_realloc("md->tf_table_index"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdatom.c", 229
, (md->tf_table_index), (md->nalloc), sizeof(*(md->tf_table_index
)));
230 }
231 }
232
233 alook = gmx_mtop_atomlookup_init(mtop);
234
235#pragma omp parallel for num_threads(gmx_omp_nthreads_get(emntDefault)) schedule(static)
236 for (i = 0; i < md->nr; i++)
237 {
238 int g, ag, molb;
239 real mA, mB, fac;
240 real c6, c12;
241 t_atom *atom;
242
243 if (index == NULL((void*)0))
244 {
245 ag = i;
246 }
247 else
248 {
249 ag = index[i];
250 }
251 gmx_mtop_atomnr_to_atom(alook, ag, &atom);
252
253 if (md->cFREEZE)
254 {
255 md->cFREEZE[i] = ggrpnr(groups, egcFREEZE, ag)((groups)->grpnr[egcFREEZE] ? (groups)->grpnr[egcFREEZE
][ag] : 0);
256 }
257 if (EI_ENERGY_MINIMIZATION(ir->eI)((ir->eI) == eiSteep || (ir->eI) == eiCG || (ir->eI)
== eiLBFGS))
258 {
259 /* Displacement is proportional to F, masses used for constraints */
260 mA = 1.0;
261 mB = 1.0;
262 }
263 else if (ir->eI == eiBD)
264 {
265 /* With BD the physical masses are irrelevant.
266 * To keep the code simple we use most of the normal MD code path
267 * for BD. Thus for constraining the masses should be proportional
268 * to the friction coefficient. We set the absolute value such that
269 * m/2<(dx/dt)^2> = m/2*2kT/fric*dt = kT/2 => m=fric*dt/2
270 * Then if we set the (meaningless) velocity to v=dx/dt, we get the
271 * correct kinetic energy and temperature using the usual code path.
272 * Thus with BD v*dt will give the displacement and the reported
273 * temperature can signal bad integration (too large time step).
274 */
275 if (ir->bd_fric > 0)
276 {
277 mA = 0.5*ir->bd_fric*ir->delta_t;
278 mB = 0.5*ir->bd_fric*ir->delta_t;
279 }
280 else
281 {
282 /* The friction coefficient is mass/tau_t */
283 fac = ir->delta_t/opts->tau_t[md->cTC ? groups->grpnr[egcTC][ag] : 0];
284 mA = 0.5*atom->m*fac;
285 mB = 0.5*atom->mB*fac;
286 }
287 }
288 else
289 {
290 mA = atom->m;
291 mB = atom->mB;
292 }
293 if (md->nMassPerturbed)
294 {
295 md->massA[i] = mA;
296 md->massB[i] = mB;
297 }
298 md->massT[i] = mA;
299 if (mA == 0.0)
300 {
301 md->invmass[i] = 0;
302 }
303 else if (md->cFREEZE)
304 {
305 g = md->cFREEZE[i];
306 if (opts->nFreeze[g][XX0] && opts->nFreeze[g][YY1] && opts->nFreeze[g][ZZ2])
307 {
308 /* Set the mass of completely frozen particles to ALMOST_ZERO iso 0
309 * to avoid div by zero in lincs or shake.
310 * Note that constraints can still move a partially frozen particle.
311 */
312 md->invmass[i] = ALMOST_ZERO1e-30;
313 }
314 else
315 {
316 md->invmass[i] = 1.0/mA;
317 }
318 }
319 else
320 {
321 md->invmass[i] = 1.0/mA;
322 }
323 md->chargeA[i] = atom->q;
324 md->typeA[i] = atom->type;
325 if (bLJPME)
326 {
327 c6 = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c6;
328 c12 = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c12;
329 md->sqrt_c6A[i] = sqrt(c6);
330 if (c6 == 0.0 || c12 == 0)
331 {
332 md->sigmaA[i] = 1.0;
333 }
334 else
335 {
336 md->sigmaA[i] = pow(c12/c6, 1.0/6.0);
337 }
338 md->sigma3A[i] = 1/(md->sigmaA[i]*md->sigmaA[i]*md->sigmaA[i]);
339 }
340 if (md->nPerturbed)
341 {
342 md->bPerturbed[i] = PERTURBED(*atom)(((*atom).mB != (*atom).m) || ((*atom).qB != (*atom).q) || ((
*atom).typeB != (*atom).type));
343 md->chargeB[i] = atom->qB;
344 md->typeB[i] = atom->typeB;
345 if (bLJPME)
346 {
347 c6 = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c6;
348 c12 = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c12;
349 md->sqrt_c6B[i] = sqrt(c6);
350 if (c6 == 0.0 || c12 == 0)
351 {
352 md->sigmaB[i] = 1.0;
353 }
354 else
355 {
356 md->sigmaB[i] = pow(c12/c6, 1.0/6.0);
357 }
358 md->sigma3B[i] = 1/(md->sigmaB[i]*md->sigmaB[i]*md->sigmaB[i]);
359 }
360 }
361 md->ptype[i] = atom->ptype;
362 if (md->cTC)
363 {
364 md->cTC[i] = groups->grpnr[egcTC][ag];
365 }
366 md->cENER[i] =
367 (groups->grpnr[egcENER] ? groups->grpnr[egcENER][ag] : 0);
368 if (md->cACC)
369 {
370 md->cACC[i] = groups->grpnr[egcACC][ag];
371 }
372 if (md->cVCM)
373 {
374 md->cVCM[i] = groups->grpnr[egcVCM][ag];
375 }
376 if (md->cORF)
377 {
378 md->cORF[i] = groups->grpnr[egcORFIT][ag];
379 }
380
381 if (md->cU1)
382 {
383 md->cU1[i] = groups->grpnr[egcUser1][ag];
384 }
385 if (md->cU2)
386 {
387 md->cU2[i] = groups->grpnr[egcUser2][ag];
388 }
389
390 if (ir->bQMMM)
391 {
392 if (groups->grpnr[egcQMMM] == 0 ||
393 groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1)
394 {
395 md->bQM[i] = TRUE1;
396 }
397 else
398 {
399 md->bQM[i] = FALSE0;
400 }
401 }
402 /* Initialize AdResS weighting functions to adressw */
403 if (ir->bAdress)
404 {
405 md->wf[i] = 1.0;
406 /* if no tf table groups specified, use default table */
407 md->tf_table_index[i] = DEFAULT_TF_TABLE0;
408 if (ir->adress->n_tf_grps > 0)
409 {
410 /* if tf table groups specified, tf is only applied to thoose energy groups*/
411 md->tf_table_index[i] = NO_TF_TABLE255;
412 /* check wether atom is in one of the relevant energy groups and assign a table index */
413 for (g = 0; g < ir->adress->n_tf_grps; g++)
414 {
415 if (md->cENER[i] == ir->adress->tf_table_index[g])
416 {
417 md->tf_table_index[i] = g;
418 }
419 }
420 }
421 }
422 }
423
424 gmx_mtop_atomlookup_destroy(alook);
425
426 md->homenr = homenr;
427 md->lambda = 0;
428}
429
430void update_mdatoms(t_mdatoms *md, real lambda)
431{
432 int al, end;
433 real L1 = 1.0-lambda;
434
435 end = md->nr;
436
437 if (md->nMassPerturbed)
438 {
439 for (al = 0; (al < end); al++)
440 {
441 if (md->bPerturbed[al])
442 {
443 md->massT[al] = L1*md->massA[al]+ lambda*md->massB[al];
444 if (md->invmass[al] > 1.1*ALMOST_ZERO1e-30)
445 {
446 md->invmass[al] = 1.0/md->massT[al];
447 }
448 }
449 }
450 md->tmass = L1*md->tmassA + lambda*md->tmassB;
451 }
452 else
453 {
454 md->tmass = md->tmassA;
455 }
456 md->lambda = lambda;
457}