Bug Summary

File:gromacs/mdlib/domdec_top.c
Location:line 1989, column 39
Description:Array access (via field 'a') results in a null pointer dereference

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 2006,2007,2008,2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
8 *
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
13 *
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
18 *
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
23 *
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
31 *
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
34 */
35
36#ifdef HAVE_CONFIG_H1
37#include <config.h>
38#endif
39
40#include <string.h>
41
42#include "typedefs.h"
43#include "types/commrec.h"
44#include "domdec.h"
45#include "domdec_network.h"
46#include "names.h"
47#include "network.h"
48#include "gromacs/math/vec.h"
49#include "pbc.h"
50#include "chargegroup.h"
51#include "gromacs/gmxlib/topsort.h"
52#include "mtop_util.h"
53#include "mshift.h"
54#include "vsite.h"
55#include "gmx_ga2la.h"
56#include "force.h"
57#include "gmx_omp_nthreads.h"
58
59#include "gromacs/utility/cstringutil.h"
60#include "gromacs/utility/fatalerror.h"
61#include "gromacs/utility/smalloc.h"
62
63/* for dd_init_local_state */
64#define NITEM_DD_INIT_LOCAL_STATE5 5
65
66typedef struct {
67 int *index; /* Index for each atom into il */
68 int *il; /* ftype|type|a0|...|an|ftype|... */
69} gmx_reverse_ilist_t;
70
71typedef struct {
72 int a_start;
73 int a_end;
74 int natoms_mol;
75 int type;
76} gmx_molblock_ind_t;
77
78typedef struct gmx_reverse_top {
79 gmx_bool bExclRequired; /* Do we require all exclusions to be assigned? */
80 gmx_bool bConstr; /* Are there constraints in this revserse top? */
81 gmx_bool bSettle; /* Are there settles in this revserse top? */
82 gmx_bool bBCheck; /* All bonded interactions have to be assigned? */
83 gmx_bool bMultiCGmols; /* Are the multi charge-group molecules? */
84 gmx_reverse_ilist_t *ril_mt; /* Reverse ilist for all moltypes */
85 int ril_mt_tot_size;
86 int ilsort; /* The sorting state of bondeds for free energy */
87 gmx_molblock_ind_t *mbi;
88 int nmolblock;
89
90 /* Work data structures for multi-threading */
91 int nthread;
92 t_idef *idef_thread;
93 int ***vsite_pbc;
94 int **vsite_pbc_nalloc;
95 int *nbonded_thread;
96 t_blocka *excl_thread;
97 int *excl_count_thread;
98
99 /* Pointers only used for an error message */
100 gmx_mtop_t *err_top_global;
101 gmx_localtop_t *err_top_local;
102} gmx_reverse_top_t;
103
104static int nral_rt(int ftype)
105{
106 /* Returns the number of atom entries for il in gmx_reverse_top_t */
107 int nral;
108
109 nral = NRAL(ftype)(interaction_function[(ftype)].nratoms);
110 if (interaction_function[ftype].flags & IF_VSITE1<<1)
111 {
112 /* With vsites the reverse topology contains
113 * two extra entries for PBC.
114 */
115 nral += 2;
116 }
117
118 return nral;
119}
120
121/* This function tells which interactions need to be assigned exactly once */
122static gmx_bool dd_check_ftype(int ftype, gmx_bool bBCheck,
123 gmx_bool bConstr, gmx_bool bSettle)
124{
125 return (((interaction_function[ftype].flags & IF_BOND1) &&
126 !(interaction_function[ftype].flags & IF_VSITE1<<1) &&
127 (bBCheck || !(interaction_function[ftype].flags & IF_LIMZERO1<<7))) ||
128 (bConstr && (ftype == F_CONSTR || ftype == F_CONSTRNC)) ||
129 (bSettle && ftype == F_SETTLE));
130}
131
132static void print_error_header(FILE *fplog, char *moltypename, int nprint)
133{
134 fprintf(fplog, "\nMolecule type '%s'\n", moltypename);
135 fprintf(stderrstderr, "\nMolecule type '%s'\n", moltypename);
136 fprintf(fplog,
137 "the first %d missing interactions, except for exclusions:\n",
138 nprint);
139 fprintf(stderrstderr,
140 "the first %d missing interactions, except for exclusions:\n",
141 nprint);
142}
143
144static void print_missing_interactions_mb(FILE *fplog, t_commrec *cr,
145 gmx_reverse_top_t *rt,
146 char *moltypename,
147 gmx_reverse_ilist_t *ril,
148 int a_start, int a_end,
149 int nat_mol, int nmol,
150 t_idef *idef)
151{
152 int nril_mol, *assigned, *gatindex;
153 int ftype, ftype_j, nral, i, j_mol, j, k, a0, a0_mol, mol, a, a_gl;
154 int nprint;
155 t_ilist *il;
156 t_iatom *ia;
157 gmx_bool bFound;
158
159 nril_mol = ril->index[nat_mol];
160 snew(assigned, nmol*nril_mol)(assigned) = save_calloc("assigned", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 160, (nmol*nril_mol), sizeof(*(assigned)));
161
162 gatindex = cr->dd->gatindex;
163 for (ftype = 0; ftype < F_NRE; ftype++)
164 {
165 if (dd_check_ftype(ftype, rt->bBCheck, rt->bConstr, rt->bSettle))
166 {
167 nral = NRAL(ftype)(interaction_function[(ftype)].nratoms);
168 il = &idef->il[ftype];
169 ia = il->iatoms;
170 for (i = 0; i < il->nr; i += 1+nral)
171 {
172 a0 = gatindex[ia[1]];
173 /* Check if this interaction is in
174 * the currently checked molblock.
175 */
176 if (a0 >= a_start && a0 < a_end)
177 {
178 mol = (a0 - a_start)/nat_mol;
179 a0_mol = (a0 - a_start) - mol*nat_mol;
180 j_mol = ril->index[a0_mol];
181 bFound = FALSE0;
182 while (j_mol < ril->index[a0_mol+1] && !bFound)
183 {
184 j = mol*nril_mol + j_mol;
185 ftype_j = ril->il[j_mol];
186 /* Here we need to check if this interaction has
187 * not already been assigned, since we could have
188 * multiply defined interactions.
189 */
190 if (ftype == ftype_j && ia[0] == ril->il[j_mol+1] &&
191 assigned[j] == 0)
192 {
193 /* Check the atoms */
194 bFound = TRUE1;
195 for (a = 0; a < nral; a++)
196 {
197 if (gatindex[ia[1+a]] !=
198 a_start + mol*nat_mol + ril->il[j_mol+2+a])
199 {
200 bFound = FALSE0;
201 }
202 }
203 if (bFound)
204 {
205 assigned[j] = 1;
206 }
207 }
208 j_mol += 2 + nral_rt(ftype_j);
209 }
210 if (!bFound)
211 {
212 gmx_incons("Some interactions seem to be assigned multiple times")_gmx_error("incons", "Some interactions seem to be assigned multiple times"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 212);
213 }
214 }
215 ia += 1 + nral;
216 }
217 }
218 }
219
220 gmx_sumi(nmol*nril_mol, assigned, cr);
221
222 nprint = 10;
223 i = 0;
224 for (mol = 0; mol < nmol; mol++)
225 {
226 j_mol = 0;
227 while (j_mol < nril_mol)
228 {
229 ftype = ril->il[j_mol];
230 nral = NRAL(ftype)(interaction_function[(ftype)].nratoms);
231 j = mol*nril_mol + j_mol;
232 if (assigned[j] == 0 &&
233 !(interaction_function[ftype].flags & IF_VSITE1<<1))
234 {
235 if (DDMASTER(cr->dd)((cr->dd)->rank == (cr->dd)->masterrank))
236 {
237 if (i == 0)
238 {
239 print_error_header(fplog, moltypename, nprint);
240 }
241 fprintf(fplog, "%20s atoms",
242 interaction_function[ftype].longname);
243 fprintf(stderrstderr, "%20s atoms",
244 interaction_function[ftype].longname);
245 for (a = 0; a < nral; a++)
246 {
247 fprintf(fplog, "%5d", ril->il[j_mol+2+a]+1);
248 fprintf(stderrstderr, "%5d", ril->il[j_mol+2+a]+1);
249 }
250 while (a < 4)
251 {
252 fprintf(fplog, " ");
253 fprintf(stderrstderr, " ");
254 a++;
255 }
256 fprintf(fplog, " global");
257 fprintf(stderrstderr, " global");
258 for (a = 0; a < nral; a++)
259 {
260 fprintf(fplog, "%6d",
261 a_start+mol*nat_mol+ril->il[j_mol+2+a]+1);
262 fprintf(stderrstderr, "%6d",
263 a_start+mol*nat_mol+ril->il[j_mol+2+a]+1);
264 }
265 fprintf(fplog, "\n");
266 fprintf(stderrstderr, "\n");
267 }
268 i++;
269 if (i >= nprint)
270 {
271 break;
272 }
273 }
274 j_mol += 2 + nral_rt(ftype);
275 }
276 }
277
278 sfree(assigned)save_free("assigned", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 278, (assigned));
279}
280
281static void print_missing_interactions_atoms(FILE *fplog, t_commrec *cr,
282 gmx_mtop_t *mtop, t_idef *idef)
283{
284 int mb, a_start, a_end;
285 gmx_molblock_t *molb;
286 gmx_reverse_top_t *rt;
287
288 rt = cr->dd->reverse_top;
289
290 /* Print the atoms in the missing interactions per molblock */
291 a_end = 0;
292 for (mb = 0; mb < mtop->nmolblock; mb++)
293 {
294 molb = &mtop->molblock[mb];
295 a_start = a_end;
296 a_end = a_start + molb->nmol*molb->natoms_mol;
297
298 print_missing_interactions_mb(fplog, cr, rt,
299 *(mtop->moltype[molb->type].name),
300 &rt->ril_mt[molb->type],
301 a_start, a_end, molb->natoms_mol,
302 molb->nmol,
303 idef);
304 }
305}
306
307void dd_print_missing_interactions(FILE *fplog, t_commrec *cr, int local_count, gmx_mtop_t *top_global, t_state *state_local)
308{
309 int ndiff_tot, cl[F_NRE], n, ndiff, rest_global, rest_local;
310 int ftype, nral;
311 char buf[STRLEN4096];
312 gmx_domdec_t *dd;
313 gmx_mtop_t *err_top_global;
314 gmx_localtop_t *err_top_local;
315
316 dd = cr->dd;
317
318 err_top_global = dd->reverse_top->err_top_global;
319 err_top_local = dd->reverse_top->err_top_local;
320
321 if (fplog)
322 {
323 fprintf(fplog, "\nNot all bonded interactions have been properly assigned to the domain decomposition cells\n");
324 fflush(fplog);
325 }
326
327 ndiff_tot = local_count - dd->nbonded_global;
328
329 for (ftype = 0; ftype < F_NRE; ftype++)
330 {
331 nral = NRAL(ftype)(interaction_function[(ftype)].nratoms);
332 cl[ftype] = err_top_local->idef.il[ftype].nr/(1+nral);
333 }
334
335 gmx_sumi(F_NRE, cl, cr);
336
337 if (DDMASTER(dd)((dd)->rank == (dd)->masterrank))
338 {
339 fprintf(fplog, "\nA list of missing interactions:\n");
340 fprintf(stderrstderr, "\nA list of missing interactions:\n");
341 rest_global = dd->nbonded_global;
342 rest_local = local_count;
343 for (ftype = 0; ftype < F_NRE; ftype++)
344 {
345 /* In the reverse and local top all constraints are merged
346 * into F_CONSTR. So in the if statement we skip F_CONSTRNC
347 * and add these constraints when doing F_CONSTR.
348 */
349 if (((interaction_function[ftype].flags & IF_BOND1) &&
350 (dd->reverse_top->bBCheck
351 || !(interaction_function[ftype].flags & IF_LIMZERO1<<7)))
352 || (dd->reverse_top->bConstr && ftype == F_CONSTR)
353 || (dd->reverse_top->bSettle && ftype == F_SETTLE))
354 {
355 nral = NRAL(ftype)(interaction_function[(ftype)].nratoms);
356 n = gmx_mtop_ftype_count(err_top_global, ftype);
357 if (ftype == F_CONSTR)
358 {
359 n += gmx_mtop_ftype_count(err_top_global, F_CONSTRNC);
360 }
361 ndiff = cl[ftype] - n;
362 if (ndiff != 0)
363 {
364 sprintf(buf, "%20s of %6d missing %6d",
365 interaction_function[ftype].longname, n, -ndiff);
366 fprintf(fplog, "%s\n", buf);
367 fprintf(stderrstderr, "%s\n", buf);
368 }
369 rest_global -= n;
370 rest_local -= cl[ftype];
371 }
372 }
373
374 ndiff = rest_local - rest_global;
375 if (ndiff != 0)
376 {
377 sprintf(buf, "%20s of %6d missing %6d", "exclusions",
378 rest_global, -ndiff);
379 fprintf(fplog, "%s\n", buf);
380 fprintf(stderrstderr, "%s\n", buf);
381 }
382 }
383
384 print_missing_interactions_atoms(fplog, cr, err_top_global,
385 &err_top_local->idef);
386 write_dd_pdb("dd_dump_err", 0, "dump", top_global, cr,
387 -1, state_local->x, state_local->box);
388 if (DDMASTER(dd)((dd)->rank == (dd)->masterrank))
389 {
390 if (ndiff_tot > 0)
391 {
392 gmx_incons("One or more interactions were multiple assigned in the domain decompostion")_gmx_error("incons", "One or more interactions were multiple assigned in the domain decompostion"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 392);
393 }
394 else
395 {
396 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 396, "%d of the %d bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (%g nm) or the two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck", -ndiff_tot, cr->dd->nbonded_global, dd_cutoff_mbody(cr->dd), dd_cutoff_twobody(cr->dd));
397 }
398 }
399}
400
401static void global_atomnr_to_moltype_ind(gmx_reverse_top_t *rt, int i_gl,
402 int *mb, int *mt, int *mol, int *i_mol)
403{
404 int molb;
405
406
407 gmx_molblock_ind_t *mbi = rt->mbi;
408 int start = 0;
409 int end = rt->nmolblock; /* exclusive */
410 int mid;
411
412 /* binary search for molblock_ind */
413 while (TRUE1)
414 {
415 mid = (start+end)/2;
416 if (i_gl >= mbi[mid].a_end)
417 {
418 start = mid+1;
419 }
420 else if (i_gl < mbi[mid].a_start)
421 {
422 end = mid;
423 }
424 else
425 {
426 break;
427 }
428 }
429
430 *mb = mid;
431 mbi += mid;
432
433 *mt = mbi->type;
434 *mol = (i_gl - mbi->a_start) / mbi->natoms_mol;
435 *i_mol = (i_gl - mbi->a_start) - (*mol)*mbi->natoms_mol;
436}
437
438static int count_excls(t_block *cgs, t_blocka *excls, int *n_intercg_excl)
439{
440 int n, n_inter, cg, at0, at1, at, excl, atj;
441
442 n = 0;
443 *n_intercg_excl = 0;
444 for (cg = 0; cg < cgs->nr; cg++)
445 {
446 at0 = cgs->index[cg];
447 at1 = cgs->index[cg+1];
448 for (at = at0; at < at1; at++)
449 {
450 for (excl = excls->index[at]; excl < excls->index[at+1]; excl++)
451 {
452 atj = excls->a[excl];
453 if (atj > at)
454 {
455 n++;
456 if (atj < at0 || atj >= at1)
457 {
458 (*n_intercg_excl)++;
459 }
460 }
461 }
462 }
463 }
464
465 return n;
466}
467
468static int low_make_reverse_ilist(t_ilist *il_mt, t_atom *atom,
469 int **vsite_pbc,
470 int *count,
471 gmx_bool bConstr, gmx_bool bSettle,
472 gmx_bool bBCheck,
473 int *r_index, int *r_il,
474 gmx_bool bLinkToAllAtoms,
475 gmx_bool bAssign)
476{
477 int ftype, nral, i, j, nlink, link;
478 t_ilist *il;
479 t_iatom *ia;
480 atom_id a;
481 int nint;
482 gmx_bool bVSite;
483
484 nint = 0;
485 for (ftype = 0; ftype < F_NRE; ftype++)
486 {
487 if ((interaction_function[ftype].flags & (IF_BOND1 | IF_VSITE1<<1)) ||
488 (bConstr && (ftype == F_CONSTR || ftype == F_CONSTRNC)) ||
489 (bSettle && ftype == F_SETTLE))
490 {
491 bVSite = (interaction_function[ftype].flags & IF_VSITE1<<1);
492 nral = NRAL(ftype)(interaction_function[(ftype)].nratoms);
493 il = &il_mt[ftype];
494 ia = il->iatoms;
495 for (i = 0; i < il->nr; i += 1+nral)
496 {
497 ia = il->iatoms + i;
498 if (bLinkToAllAtoms)
499 {
500 if (bVSite)
501 {
502 /* We don't need the virtual sites for the cg-links */
503 nlink = 0;
504 }
505 else
506 {
507 nlink = nral;
508 }
509 }
510 else
511 {
512 /* Couple to the first atom in the interaction */
513 nlink = 1;
514 }
515 for (link = 0; link < nlink; link++)
516 {
517 a = ia[1+link];
518 if (bAssign)
519 {
520 r_il[r_index[a]+count[a]] =
521 (ftype == F_CONSTRNC ? F_CONSTR : ftype);
522 r_il[r_index[a]+count[a]+1] = ia[0];
523 for (j = 1; j < 1+nral; j++)
524 {
525 /* Store the molecular atom number */
526 r_il[r_index[a]+count[a]+1+j] = ia[j];
527 }
528 }
529 if (interaction_function[ftype].flags & IF_VSITE1<<1)
530 {
531 if (bAssign)
532 {
533 /* Add an entry to iatoms for storing
534 * which of the constructing atoms are
535 * vsites again.
536 */
537 r_il[r_index[a]+count[a]+2+nral] = 0;
538 for (j = 2; j < 1+nral; j++)
539 {
540 if (atom[ia[j]].ptype == eptVSite)
541 {
542 r_il[r_index[a]+count[a]+2+nral] |= (2<<j);
543 }
544 }
545 /* Store vsite pbc atom in a second extra entry */
546 r_il[r_index[a]+count[a]+2+nral+1] =
547 (vsite_pbc ? vsite_pbc[ftype-F_VSITE2][i/(1+nral)] : -2);
548 }
549 }
550 else
551 {
552 /* We do not count vsites since they are always
553 * uniquely assigned and can be assigned
554 * to multiple nodes with recursive vsites.
555 */
556 if (bBCheck ||
557 !(interaction_function[ftype].flags & IF_LIMZERO1<<7))
558 {
559 nint++;
560 }
561 }
562 count[a] += 2 + nral_rt(ftype);
563 }
564 }
565 }
566 }
567
568 return nint;
569}
570
571static int make_reverse_ilist(gmx_moltype_t *molt,
572 int **vsite_pbc,
573 gmx_bool bConstr, gmx_bool bSettle,
574 gmx_bool bBCheck,
575 gmx_bool bLinkToAllAtoms,
576 gmx_reverse_ilist_t *ril_mt)
577{
578 int nat_mt, *count, i, nint_mt;
579
580 /* Count the interactions */
581 nat_mt = molt->atoms.nr;
582 snew(count, nat_mt)(count) = save_calloc("count", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 582, (nat_mt), sizeof(*(count)));
583 low_make_reverse_ilist(molt->ilist, molt->atoms.atom, vsite_pbc,
584 count,
585 bConstr, bSettle, bBCheck, NULL((void*)0), NULL((void*)0),
586 bLinkToAllAtoms, FALSE0);
587
588 snew(ril_mt->index, nat_mt+1)(ril_mt->index) = save_calloc("ril_mt->index", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 588, (nat_mt+1), sizeof(*(ril_mt->index)));
589 ril_mt->index[0] = 0;
590 for (i = 0; i < nat_mt; i++)
591 {
592 ril_mt->index[i+1] = ril_mt->index[i] + count[i];
593 count[i] = 0;
594 }
595 snew(ril_mt->il, ril_mt->index[nat_mt])(ril_mt->il) = save_calloc("ril_mt->il", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 595, (ril_mt->index[nat_mt]), sizeof(*(ril_mt->il)));
596
597 /* Store the interactions */
598 nint_mt =
599 low_make_reverse_ilist(molt->ilist, molt->atoms.atom, vsite_pbc,
600 count,
601 bConstr, bSettle, bBCheck,
602 ril_mt->index, ril_mt->il,
603 bLinkToAllAtoms, TRUE1);
604
605 sfree(count)save_free("count", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 605, (count));
606
607 return nint_mt;
608}
609
610static void destroy_reverse_ilist(gmx_reverse_ilist_t *ril)
611{
612 sfree(ril->index)save_free("ril->index", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 612, (ril->index));
613 sfree(ril->il)save_free("ril->il", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 613, (ril->il));
614}
615
616static gmx_reverse_top_t *make_reverse_top(gmx_mtop_t *mtop, gmx_bool bFE,
617 int ***vsite_pbc_molt,
618 gmx_bool bConstr, gmx_bool bSettle,
619 gmx_bool bBCheck, int *nint)
620{
621 int mt, i, mb;
622 gmx_reverse_top_t *rt;
623 int *nint_mt;
624 gmx_moltype_t *molt;
625 int thread;
626
627 snew(rt, 1)(rt) = save_calloc("rt", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 627, (1), sizeof(*(rt)));
628
629 /* Should we include constraints (for SHAKE) in rt? */
630 rt->bConstr = bConstr;
631 rt->bSettle = bSettle;
632 rt->bBCheck = bBCheck;
633
634 rt->bMultiCGmols = FALSE0;
635 snew(nint_mt, mtop->nmoltype)(nint_mt) = save_calloc("nint_mt", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 635, (mtop->nmoltype), sizeof(*(nint_mt)));
636 snew(rt->ril_mt, mtop->nmoltype)(rt->ril_mt) = save_calloc("rt->ril_mt", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 636, (mtop->nmoltype), sizeof(*(rt->ril_mt)));
637 rt->ril_mt_tot_size = 0;
638 for (mt = 0; mt < mtop->nmoltype; mt++)
639 {
640 molt = &mtop->moltype[mt];
641 if (molt->cgs.nr > 1)
642 {
643 rt->bMultiCGmols = TRUE1;
644 }
645
646 /* Make the atom to interaction list for this molecule type */
647 nint_mt[mt] =
648 make_reverse_ilist(molt, vsite_pbc_molt ? vsite_pbc_molt[mt] : NULL((void*)0),
649 rt->bConstr, rt->bSettle, rt->bBCheck, FALSE0,
650 &rt->ril_mt[mt]);
651
652 rt->ril_mt_tot_size += rt->ril_mt[mt].index[molt->atoms.nr];
653 }
654 if (debug)
655 {
656 fprintf(debug, "The total size of the atom to interaction index is %d integers\n", rt->ril_mt_tot_size);
657 }
658
659 *nint = 0;
660 for (mb = 0; mb < mtop->nmolblock; mb++)
661 {
662 *nint += mtop->molblock[mb].nmol*nint_mt[mtop->molblock[mb].type];
663 }
664 sfree(nint_mt)save_free("nint_mt", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 664, (nint_mt));
665
666 if (bFE && gmx_mtop_bondeds_free_energy(mtop))
667 {
668 rt->ilsort = ilsortFE_UNSORTED;
669 }
670 else
671 {
672 rt->ilsort = ilsortNO_FE;
673 }
674
675 /* Make a molblock index for fast searching */
676 snew(rt->mbi, mtop->nmolblock)(rt->mbi) = save_calloc("rt->mbi", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 676, (mtop->nmolblock), sizeof(*(rt->mbi)));
677 rt->nmolblock = mtop->nmolblock;
678 i = 0;
679 for (mb = 0; mb < mtop->nmolblock; mb++)
680 {
681 rt->mbi[mb].a_start = i;
682 i += mtop->molblock[mb].nmol*mtop->molblock[mb].natoms_mol;
683 rt->mbi[mb].a_end = i;
684 rt->mbi[mb].natoms_mol = mtop->molblock[mb].natoms_mol;
685 rt->mbi[mb].type = mtop->molblock[mb].type;
686 }
687
688 rt->nthread = gmx_omp_nthreads_get(emntDomdec);
689 snew(rt->idef_thread, rt->nthread)(rt->idef_thread) = save_calloc("rt->idef_thread", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 689, (rt->nthread), sizeof(*(rt->idef_thread)));
690 if (vsite_pbc_molt != NULL((void*)0))
691 {
692 snew(rt->vsite_pbc, rt->nthread)(rt->vsite_pbc) = save_calloc("rt->vsite_pbc", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 692, (rt->nthread), sizeof(*(rt->vsite_pbc)));
693 snew(rt->vsite_pbc_nalloc, rt->nthread)(rt->vsite_pbc_nalloc) = save_calloc("rt->vsite_pbc_nalloc"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 693, (rt->nthread), sizeof(*(rt->vsite_pbc_nalloc)));
694 for (thread = 0; thread < rt->nthread; thread++)
695 {
696 snew(rt->vsite_pbc[thread], F_VSITEN-F_VSITE2+1)(rt->vsite_pbc[thread]) = save_calloc("rt->vsite_pbc[thread]"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 696, (F_VSITEN-F_VSITE2+1), sizeof(*(rt->vsite_pbc[thread
])));
697 snew(rt->vsite_pbc_nalloc[thread], F_VSITEN-F_VSITE2+1)(rt->vsite_pbc_nalloc[thread]) = save_calloc("rt->vsite_pbc_nalloc[thread]"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 697, (F_VSITEN-F_VSITE2+1), sizeof(*(rt->vsite_pbc_nalloc
[thread])));
698 }
699 }
700 snew(rt->nbonded_thread, rt->nthread)(rt->nbonded_thread) = save_calloc("rt->nbonded_thread"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 700, (rt->nthread), sizeof(*(rt->nbonded_thread)));
701 snew(rt->excl_thread, rt->nthread)(rt->excl_thread) = save_calloc("rt->excl_thread", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 701, (rt->nthread), sizeof(*(rt->excl_thread)));
702 snew(rt->excl_count_thread, rt->nthread)(rt->excl_count_thread) = save_calloc("rt->excl_count_thread"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 702, (rt->nthread), sizeof(*(rt->excl_count_thread)));
703
704 return rt;
705}
706
707void dd_make_reverse_top(FILE *fplog,
708 gmx_domdec_t *dd, gmx_mtop_t *mtop,
709 gmx_vsite_t *vsite,
710 t_inputrec *ir, gmx_bool bBCheck)
711{
712 int mb, n_recursive_vsite, nexcl, nexcl_icg, a;
713 gmx_molblock_t *molb;
714 gmx_moltype_t *molt;
715
716 if (fplog)
717 {
718 fprintf(fplog, "\nLinking all bonded interactions to atoms\n");
719 }
720
721 /* If normal and/or settle constraints act only within charge groups,
722 * we can store them in the reverse top and simply assign them to domains.
723 * Otherwise we need to assign them to multiple domains and set up
724 * the parallel version constraint algoirthm(s).
725 */
726
727 dd->reverse_top = make_reverse_top(mtop, ir->efep != efepNO,
728 vsite ? vsite->vsite_pbc_molt : NULL((void*)0),
729 !dd->bInterCGcons, !dd->bInterCGsettles,
730 bBCheck, &dd->nbonded_global);
731
732 if (dd->reverse_top->ril_mt_tot_size >= 200000 &&
733 mtop->mols.nr > 1 &&
734 mtop->nmolblock == 1 && mtop->molblock[0].nmol == 1)
735 {
736 /* mtop comes from a pre Gromacs 4 tpr file */
737 const char *note = "NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance create a new tpr file with an up to date version of grompp";
738 if (fplog)
739 {
740 fprintf(fplog, "\n%s\n\n", note);
741 }
742 if (DDMASTER(dd)((dd)->rank == (dd)->masterrank))
743 {
744 fprintf(stderrstderr, "\n%s\n\n", note);
745 }
746 }
747
748 dd->reverse_top->bExclRequired = IR_EXCL_FORCES(*ir)((((((*ir).coulombtype) == eelPME || ((*ir).coulombtype) == eelPMESWITCH
|| ((*ir).coulombtype) == eelPMEUSER || ((*ir).coulombtype) ==
eelPMEUSERSWITCH || ((*ir).coulombtype) == eelP3M_AD) || ((*
ir).coulombtype) == eelEWALD) || ((*ir).coulombtype) == eelPOISSON
) || ((((*ir).coulombtype) == eelRF || ((*ir).coulombtype) ==
eelGRF || ((*ir).coulombtype) == eelRF_NEC || ((*ir).coulombtype
) == eelRF_ZERO ) && (*ir).coulombtype != eelRF_NEC) ||
(*ir).implicit_solvent != eisNO);
749
750 nexcl = 0;
751 dd->n_intercg_excl = 0;
752 for (mb = 0; mb < mtop->nmolblock; mb++)
753 {
754 molb = &mtop->molblock[mb];
755 molt = &mtop->moltype[molb->type];
756 nexcl += molb->nmol*count_excls(&molt->cgs, &molt->excls, &nexcl_icg);
757 dd->n_intercg_excl += molb->nmol*nexcl_icg;
758 }
759 if (dd->reverse_top->bExclRequired)
760 {
761 dd->nbonded_global += nexcl;
762 if (EEL_FULL(ir->coulombtype)((((ir->coulombtype) == eelPME || (ir->coulombtype) == eelPMESWITCH
|| (ir->coulombtype) == eelPMEUSER || (ir->coulombtype
) == eelPMEUSERSWITCH || (ir->coulombtype) == eelP3M_AD) ||
(ir->coulombtype) == eelEWALD) || (ir->coulombtype) ==
eelPOISSON) && dd->n_intercg_excl > 0 && fplog)
763 {
764 fprintf(fplog, "There are %d inter charge-group exclusions,\n"
765 "will use an extra communication step for exclusion forces for %s\n",
766 dd->n_intercg_excl, eel_names[ir->coulombtype]);
767 }
768 }
769
770 if (vsite && vsite->n_intercg_vsite > 0)
771 {
772 if (fplog)
773 {
774 fprintf(fplog, "There are %d inter charge-group virtual sites,\n"
775 "will an extra communication step for selected coordinates and forces\n",
776 vsite->n_intercg_vsite);
777 }
778 init_domdec_vsites(dd, vsite->n_intercg_vsite);
779 }
780
781 if (dd->bInterCGcons || dd->bInterCGsettles)
782 {
783 init_domdec_constraints(dd, mtop);
784 }
785 if (fplog)
786 {
787 fprintf(fplog, "\n");
788 }
789}
790
791static gmx_inlineinline void add_ifunc(int nral, t_iatom *tiatoms, t_ilist *il)
792{
793 t_iatom *liatoms;
794 int k;
795
796 if (il->nr+1+nral > il->nalloc)
797 {
798 il->nalloc = over_alloc_large(il->nr+1+nral)(int)(1.19*(il->nr+1+nral) + 1000);
799 srenew(il->iatoms, il->nalloc)(il->iatoms) = save_realloc("il->iatoms", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 799, (il->iatoms), (il->nalloc), sizeof(*(il->iatoms
)));
800 }
801 liatoms = il->iatoms + il->nr;
802 for (k = 0; k <= nral; k++)
803 {
804 liatoms[k] = tiatoms[k];
805 }
806 il->nr += 1 + nral;
807}
808
809static void add_posres(int mol, int a_mol, const gmx_molblock_t *molb,
810 t_iatom *iatoms, const t_iparams *ip_in,
811 t_idef *idef)
812{
813 int n, a_molb;
814 t_iparams *ip;
815
816 /* This position restraint has not been added yet,
817 * so it's index is the current number of position restraints.
818 */
819 n = idef->il[F_POSRES].nr/2;
820 if (n+1 > idef->iparams_posres_nalloc)
821 {
822 idef->iparams_posres_nalloc = over_alloc_dd(n+1);
823 srenew(idef->iparams_posres, idef->iparams_posres_nalloc)(idef->iparams_posres) = save_realloc("idef->iparams_posres"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 823, (idef->iparams_posres), (idef->iparams_posres_nalloc
), sizeof(*(idef->iparams_posres)));
824 }
825 ip = &idef->iparams_posres[n];
826 /* Copy the force constants */
827 *ip = ip_in[iatoms[0]];
828
829 /* Get the position restraint coordinates from the molblock */
830 a_molb = mol*molb->natoms_mol + a_mol;
831 if (a_molb >= molb->nposres_xA)
832 {
833 gmx_incons("Not enough position restraint coordinates")_gmx_error("incons", "Not enough position restraint coordinates"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 833);
834 }
835 ip->posres.pos0A[XX0] = molb->posres_xA[a_molb][XX0];
836 ip->posres.pos0A[YY1] = molb->posres_xA[a_molb][YY1];
837 ip->posres.pos0A[ZZ2] = molb->posres_xA[a_molb][ZZ2];
838 if (molb->nposres_xB > 0)
839 {
840 ip->posres.pos0B[XX0] = molb->posres_xB[a_molb][XX0];
841 ip->posres.pos0B[YY1] = molb->posres_xB[a_molb][YY1];
842 ip->posres.pos0B[ZZ2] = molb->posres_xB[a_molb][ZZ2];
843 }
844 else
845 {
846 ip->posres.pos0B[XX0] = ip->posres.pos0A[XX0];
847 ip->posres.pos0B[YY1] = ip->posres.pos0A[YY1];
848 ip->posres.pos0B[ZZ2] = ip->posres.pos0A[ZZ2];
849 }
850 /* Set the parameter index for idef->iparams_posre */
851 iatoms[0] = n;
852}
853
854static void add_fbposres(int mol, int a_mol, const gmx_molblock_t *molb,
855 t_iatom *iatoms, const t_iparams *ip_in,
856 t_idef *idef)
857{
858 int n, a_molb;
859 t_iparams *ip;
860
861 /* This flat-bottom position restraint has not been added yet,
862 * so it's index is the current number of position restraints.
863 */
864 n = idef->il[F_FBPOSRES].nr/2;
865 if (n+1 > idef->iparams_fbposres_nalloc)
866 {
867 idef->iparams_fbposres_nalloc = over_alloc_dd(n+1);
868 srenew(idef->iparams_fbposres, idef->iparams_fbposres_nalloc)(idef->iparams_fbposres) = save_realloc("idef->iparams_fbposres"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 868, (idef->iparams_fbposres), (idef->iparams_fbposres_nalloc
), sizeof(*(idef->iparams_fbposres)));
869 }
870 ip = &idef->iparams_fbposres[n];
871 /* Copy the force constants */
872 *ip = ip_in[iatoms[0]];
873
874 /* Get the position restriant coordinats from the molblock */
875 a_molb = mol*molb->natoms_mol + a_mol;
876 if (a_molb >= molb->nposres_xA)
877 {
878 gmx_incons("Not enough position restraint coordinates")_gmx_error("incons", "Not enough position restraint coordinates"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 878);
879 }
880 /* Take reference positions from A position of normal posres */
881 ip->fbposres.pos0[XX0] = molb->posres_xA[a_molb][XX0];
882 ip->fbposres.pos0[YY1] = molb->posres_xA[a_molb][YY1];
883 ip->fbposres.pos0[ZZ2] = molb->posres_xA[a_molb][ZZ2];
884
885 /* Note: no B-type for flat-bottom posres */
886
887 /* Set the parameter index for idef->iparams_posre */
888 iatoms[0] = n;
889}
890
891static void add_vsite(gmx_ga2la_t ga2la, int *index, int *rtil,
892 int ftype, int nral,
893 gmx_bool bHomeA, int a, int a_gl, int a_mol,
894 t_iatom *iatoms,
895 t_idef *idef, int **vsite_pbc, int *vsite_pbc_nalloc)
896{
897 int k, ak_gl, vsi, pbc_a_mol;
898 t_iatom tiatoms[1+MAXATOMLIST6], *iatoms_r;
899 int j, ftype_r, nral_r;
900
901 /* Copy the type */
902 tiatoms[0] = iatoms[0];
903
904 if (bHomeA)
905 {
906 /* We know the local index of the first atom */
907 tiatoms[1] = a;
908 }
909 else
910 {
911 /* Convert later in make_local_vsites */
912 tiatoms[1] = -a_gl - 1;
913 }
914
915 for (k = 2; k < 1+nral; k++)
916 {
917 ak_gl = a_gl + iatoms[k] - a_mol;
918 if (!ga2la_get_home(ga2la, ak_gl, &tiatoms[k]))
919 {
920 /* Copy the global index, convert later in make_local_vsites */
921 tiatoms[k] = -(ak_gl + 1);
922 }
923 }
924
925 /* Add this interaction to the local topology */
926 add_ifunc(nral, tiatoms, &idef->il[ftype]);
927 if (vsite_pbc)
928 {
929 vsi = idef->il[ftype].nr/(1+nral) - 1;
930 if (vsi >= vsite_pbc_nalloc[ftype-F_VSITE2])
931 {
932 vsite_pbc_nalloc[ftype-F_VSITE2] = over_alloc_large(vsi+1)(int)(1.19*(vsi+1) + 1000);
933 srenew(vsite_pbc[ftype-F_VSITE2], vsite_pbc_nalloc[ftype-F_VSITE2])(vsite_pbc[ftype-F_VSITE2]) = save_realloc("vsite_pbc[ftype-F_VSITE2]"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 933, (vsite_pbc[ftype-F_VSITE2]), (vsite_pbc_nalloc[ftype-F_VSITE2
]), sizeof(*(vsite_pbc[ftype-F_VSITE2])));
934 }
935 if (bHomeA)
936 {
937 pbc_a_mol = iatoms[1+nral+1];
938 if (pbc_a_mol < 0)
939 {
940 /* The pbc flag is one of the following two options:
941 * -2: vsite and all constructing atoms are within the same cg, no pbc
942 * -1: vsite and its first constructing atom are in the same cg, do pbc
943 */
944 vsite_pbc[ftype-F_VSITE2][vsi] = pbc_a_mol;
945 }
946 else
947 {
948 /* Set the pbc atom for this vsite so we can make its pbc
949 * identical to the rest of the atoms in its charge group.
950 * Since the order of the atoms does not change within a charge
951 * group, we do not need the global to local atom index.
952 */
953 vsite_pbc[ftype-F_VSITE2][vsi] = a + pbc_a_mol - iatoms[1];
954 }
955 }
956 else
957 {
958 /* This vsite is non-home (required for recursion),
959 * and therefore there is no charge group to match pbc with.
960 * But we always turn on full_pbc to assure that higher order
961 * recursion works correctly.
962 */
963 vsite_pbc[ftype-F_VSITE2][vsi] = -1;
964 }
965 }
966
967 if (iatoms[1+nral])
968 {
969 /* Check for recursion */
970 for (k = 2; k < 1+nral; k++)
971 {
972 if ((iatoms[1+nral] & (2<<k)) && (tiatoms[k] < 0))
973 {
974 /* This construction atoms is a vsite and not a home atom */
975 if (gmx_debug_at)
976 {
977 fprintf(debug, "Constructing atom %d of vsite atom %d is a vsite and non-home\n", iatoms[k]+1, a_mol+1);
978 }
979 /* Find the vsite construction */
980
981 /* Check all interactions assigned to this atom */
982 j = index[iatoms[k]];
983 while (j < index[iatoms[k]+1])
984 {
985 ftype_r = rtil[j++];
986 nral_r = NRAL(ftype_r)(interaction_function[(ftype_r)].nratoms);
987 if (interaction_function[ftype_r].flags & IF_VSITE1<<1)
988 {
989 /* Add this vsite (recursion) */
990 add_vsite(ga2la, index, rtil, ftype_r, nral_r,
991 FALSE0, -1, a_gl+iatoms[k]-iatoms[1], iatoms[k],
992 rtil+j, idef, vsite_pbc, vsite_pbc_nalloc);
993 j += 1 + nral_r + 2;
994 }
995 else
996 {
997 j += 1 + nral_r;
998 }
999 }
1000 }
1001 }
1002 }
1003}
1004
1005static void make_la2lc(gmx_domdec_t *dd)
1006{
1007 int *cgindex, *la2lc, cg, a;
1008
1009 cgindex = dd->cgindex;
1010
1011 if (dd->nat_tot > dd->la2lc_nalloc)
1012 {
1013 dd->la2lc_nalloc = over_alloc_dd(dd->nat_tot);
1014 snew(dd->la2lc, dd->la2lc_nalloc)(dd->la2lc) = save_calloc("dd->la2lc", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1014, (dd->la2lc_nalloc), sizeof(*(dd->la2lc)));
1015 }
1016 la2lc = dd->la2lc;
1017
1018 /* Make the local atom to local cg index */
1019 for (cg = 0; cg < dd->ncg_tot; cg++)
1020 {
1021 for (a = cgindex[cg]; a < cgindex[cg+1]; a++)
1022 {
1023 la2lc[a] = cg;
1024 }
1025 }
1026}
1027
1028static real dd_dist2(t_pbc *pbc_null, rvec *cg_cm, const int *la2lc, int i, int j)
1029{
1030 rvec dx;
1031
1032 if (pbc_null)
1033 {
1034 pbc_dx_aiuc(pbc_null, cg_cm[la2lc[i]], cg_cm[la2lc[j]], dx);
1035 }
1036 else
1037 {
1038 rvec_sub(cg_cm[la2lc[i]], cg_cm[la2lc[j]], dx);
1039 }
1040
1041 return norm2(dx);
1042}
1043
1044/* Append the nsrc t_blocka block structures in src to *dest */
1045static void combine_blocka(t_blocka *dest, const t_blocka *src, int nsrc)
1046{
1047 int ni, na, s, i;
1048
1049 ni = src[nsrc-1].nr;
1050 na = 0;
1051 for (s = 0; s < nsrc; s++)
1052 {
1053 na += src[s].nra;
1054 }
1055 if (ni + 1 > dest->nalloc_index)
1056 {
1057 dest->nalloc_index = over_alloc_large(ni+1)(int)(1.19*(ni+1) + 1000);
1058 srenew(dest->index, dest->nalloc_index)(dest->index) = save_realloc("dest->index", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1058, (dest->index), (dest->nalloc_index), sizeof(*(dest
->index)));
1059 }
1060 if (dest->nra + na > dest->nalloc_a)
1061 {
1062 dest->nalloc_a = over_alloc_large(dest->nra+na)(int)(1.19*(dest->nra+na) + 1000);
1063 srenew(dest->a, dest->nalloc_a)(dest->a) = save_realloc("dest->a", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1063, (dest->a), (dest->nalloc_a), sizeof(*(dest->
a)));
1064 }
1065 for (s = 0; s < nsrc; s++)
1066 {
1067 for (i = dest->nr+1; i < src[s].nr+1; i++)
1068 {
1069 dest->index[i] = dest->nra + src[s].index[i];
1070 }
1071 for (i = 0; i < src[s].nra; i++)
1072 {
1073 dest->a[dest->nra+i] = src[s].a[i];
1074 }
1075 dest->nr = src[s].nr;
1076 dest->nra += src[s].nra;
1077 }
1078}
1079
1080/* Append the nsrc t_idef structures in src to *dest,
1081 * virtual sites need special attention, as pbc info differs per vsite.
1082 */
1083static void combine_idef(t_idef *dest, const t_idef *src, int nsrc,
1084 gmx_vsite_t *vsite, int ***vsite_pbc_t)
1085{
1086 int ftype, n, s, i;
1087 t_ilist *ild;
1088 const t_ilist *ils;
1089 gmx_bool vpbc;
1090 int nral1 = 0, ftv = 0;
1091
1092 for (ftype = 0; ftype < F_NRE; ftype++)
1093 {
1094 n = 0;
1095 for (s = 0; s < nsrc; s++)
1096 {
1097 n += src[s].il[ftype].nr;
1098 }
1099 if (n > 0)
1100 {
1101 ild = &dest->il[ftype];
1102
1103 if (ild->nr + n > ild->nalloc)
1104 {
1105 ild->nalloc = over_alloc_large(ild->nr+n)(int)(1.19*(ild->nr+n) + 1000);
1106 srenew(ild->iatoms, ild->nalloc)(ild->iatoms) = save_realloc("ild->iatoms", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1106, (ild->iatoms), (ild->nalloc), sizeof(*(ild->
iatoms)));
1107 }
1108
1109 vpbc = ((interaction_function[ftype].flags & IF_VSITE1<<1) &&
1110 vsite->vsite_pbc_loc != NULL((void*)0));
1111 if (vpbc)
1112 {
1113 nral1 = 1 + NRAL(ftype)(interaction_function[(ftype)].nratoms);
1114 ftv = ftype - F_VSITE2;
1115 if ((ild->nr + n)/nral1 > vsite->vsite_pbc_loc_nalloc[ftv])
1116 {
1117 vsite->vsite_pbc_loc_nalloc[ftv] =
1118 over_alloc_large((ild->nr + n)/nral1)(int)(1.19*((ild->nr + n)/nral1) + 1000);
1119 srenew(vsite->vsite_pbc_loc[ftv],(vsite->vsite_pbc_loc[ftv]) = save_realloc("vsite->vsite_pbc_loc[ftv]"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1120, (vsite->vsite_pbc_loc[ftv]), (vsite->vsite_pbc_loc_nalloc
[ftv]), sizeof(*(vsite->vsite_pbc_loc[ftv])))
1120 vsite->vsite_pbc_loc_nalloc[ftv])(vsite->vsite_pbc_loc[ftv]) = save_realloc("vsite->vsite_pbc_loc[ftv]"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1120, (vsite->vsite_pbc_loc[ftv]), (vsite->vsite_pbc_loc_nalloc
[ftv]), sizeof(*(vsite->vsite_pbc_loc[ftv])));
1121 }
1122 }
1123
1124 for (s = 0; s < nsrc; s++)
1125 {
1126 ils = &src[s].il[ftype];
1127 for (i = 0; i < ils->nr; i++)
1128 {
1129 ild->iatoms[ild->nr+i] = ils->iatoms[i];
1130 }
1131 if (vpbc)
1132 {
1133 for (i = 0; i < ils->nr; i += nral1)
1134 {
1135 vsite->vsite_pbc_loc[ftv][(ild->nr+i)/nral1] =
1136 vsite_pbc_t[s][ftv][i/nral1];
1137 }
1138 }
1139
1140 ild->nr += ils->nr;
1141 }
1142 }
1143 }
1144
1145 /* Position restraints need an additional treatment */
1146 if (dest->il[F_POSRES].nr > 0)
1147 {
1148 n = dest->il[F_POSRES].nr/2;
1149 if (n > dest->iparams_posres_nalloc)
1150 {
1151 dest->iparams_posres_nalloc = over_alloc_large(n)(int)(1.19*(n) + 1000);
1152 srenew(dest->iparams_posres, dest->iparams_posres_nalloc)(dest->iparams_posres) = save_realloc("dest->iparams_posres"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1152, (dest->iparams_posres), (dest->iparams_posres_nalloc
), sizeof(*(dest->iparams_posres)));
1153 }
1154 /* Set n to the number of original position restraints in dest */
1155 for (s = 0; s < nsrc; s++)
1156 {
1157 n -= src[s].il[F_POSRES].nr/2;
1158 }
1159 for (s = 0; s < nsrc; s++)
1160 {
1161 for (i = 0; i < src[s].il[F_POSRES].nr/2; i++)
1162 {
1163 /* Correct the index into iparams_posres */
1164 dest->il[F_POSRES].iatoms[n*2] = n;
1165 /* Copy the position restraint force parameters */
1166 dest->iparams_posres[n] = src[s].iparams_posres[i];
1167 n++;
1168 }
1169 }
1170 }
1171}
1172
1173/* This function looks up and assigns bonded interactions for zone iz.
1174 * With thread parallelizing each thread acts on a different atom range:
1175 * at_start to at_end.
1176 */
1177static int make_bondeds_zone(gmx_domdec_t *dd,
1178 const gmx_domdec_zones_t *zones,
1179 const gmx_molblock_t *molb,
1180 gmx_bool bRCheckMB, ivec rcheck, gmx_bool bRCheck2B,
1181 real rc2,
1182 int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
1183 const t_iparams *ip_in,
1184 t_idef *idef,
1185 int **vsite_pbc,
1186 int *vsite_pbc_nalloc,
1187 int iz, int nzone,
1188 int at_start, int at_end)
1189{
1190 int i, i_gl, mb, mt, mol, i_mol, j, ftype, nral, d, k;
1191 int *index, *rtil;
1192 t_iatom *iatoms, tiatoms[1+MAXATOMLIST6];
1193 gmx_bool bBCheck, bUse, bLocal;
1194 ivec k_zero, k_plus;
1195 gmx_ga2la_t ga2la;
1196 int a_loc;
1197 int kz;
1198 int nizone;
1199 const gmx_domdec_ns_ranges_t *izone;
1200 gmx_reverse_top_t *rt;
1201 int nbonded_local;
1202
1203 nizone = zones->nizone;
1204 izone = zones->izone;
1205
1206 rt = dd->reverse_top;
1207
1208 bBCheck = rt->bBCheck;
1209
1210 nbonded_local = 0;
1211
1212 ga2la = dd->ga2la;
1213
1214 for (i = at_start; i < at_end; i++)
1215 {
1216 /* Get the global atom number */
1217 i_gl = dd->gatindex[i];
1218 global_atomnr_to_moltype_ind(rt, i_gl, &mb, &mt, &mol, &i_mol);
1219 /* Check all interactions assigned to this atom */
1220 index = rt->ril_mt[mt].index;
1221 rtil = rt->ril_mt[mt].il;
1222 j = index[i_mol];
1223 while (j < index[i_mol+1])
1224 {
1225 ftype = rtil[j++];
1226 iatoms = rtil + j;
1227 nral = NRAL(ftype)(interaction_function[(ftype)].nratoms);
1228 if (ftype == F_SETTLE)
1229 {
1230 /* Settles are only in the reverse top when they
1231 * operate within a charge group. So we can assign
1232 * them without checks. We do this only for performance
1233 * reasons; it could be handled by the code below.
1234 */
1235 if (iz == 0)
1236 {
1237 /* Home zone: add this settle to the local topology */
1238 tiatoms[0] = iatoms[0];
1239 tiatoms[1] = i;
1240 tiatoms[2] = i + iatoms[2] - iatoms[1];
1241 tiatoms[3] = i + iatoms[3] - iatoms[1];
1242 add_ifunc(nral, tiatoms, &idef->il[ftype]);
1243 nbonded_local++;
1244 }
1245 j += 1 + nral;
1246 }
1247 else if (interaction_function[ftype].flags & IF_VSITE1<<1)
1248 {
1249 /* The vsite construction goes where the vsite itself is */
1250 if (iz == 0)
1251 {
1252 add_vsite(dd->ga2la, index, rtil, ftype, nral,
1253 TRUE1, i, i_gl, i_mol,
1254 iatoms, idef, vsite_pbc, vsite_pbc_nalloc);
1255 }
1256 j += 1 + nral + 2;
1257 }
1258 else
1259 {
1260 /* Copy the type */
1261 tiatoms[0] = iatoms[0];
1262
1263 if (nral == 1)
1264 {
1265 /* Assign single-body interactions to the home zone */
1266 if (iz == 0)
1267 {
1268 bUse = TRUE1;
1269 tiatoms[1] = i;
1270 if (ftype == F_POSRES)
1271 {
1272 add_posres(mol, i_mol, &molb[mb], tiatoms, ip_in,
1273 idef);
1274 }
1275 else if (ftype == F_FBPOSRES)
1276 {
1277 add_fbposres(mol, i_mol, &molb[mb], tiatoms, ip_in,
1278 idef);
1279 }
1280 }
1281 else
1282 {
1283 bUse = FALSE0;
1284 }
1285 }
1286 else if (nral == 2)
1287 {
1288 /* This is a two-body interaction, we can assign
1289 * analogous to the non-bonded assignments.
1290 */
1291 if (!ga2la_get(ga2la, i_gl+iatoms[2]-i_mol, &a_loc, &kz))
1292 {
1293 bUse = FALSE0;
1294 }
1295 else
1296 {
1297 if (kz >= nzone)
1298 {
1299 kz -= nzone;
1300 }
1301 /* Check zone interaction assignments */
1302 bUse = ((iz < nizone && iz <= kz &&
1303 izone[iz].j0 <= kz && kz < izone[iz].j1) ||
1304 (kz < nizone &&iz > kz &&
1305 izone[kz].j0 <= iz && iz < izone[kz].j1));
1306 if (bUse)
1307 {
1308 tiatoms[1] = i;
1309 tiatoms[2] = a_loc;
1310 /* If necessary check the cgcm distance */
1311 if (bRCheck2B &&
1312 dd_dist2(pbc_null, cg_cm, la2lc,
1313 tiatoms[1], tiatoms[2]) >= rc2)
1314 {
1315 bUse = FALSE0;
1316 }
1317 }
1318 }
1319 }
1320 else
1321 {
1322 /* Assign this multi-body bonded interaction to
1323 * the local node if we have all the atoms involved
1324 * (local or communicated) and the minimum zone shift
1325 * in each dimension is zero, for dimensions
1326 * with 2 DD cells an extra check may be necessary.
1327 */
1328 bUse = TRUE1;
1329 clear_ivec(k_zero);
1330 clear_ivec(k_plus);
1331 for (k = 1; k <= nral && bUse; k++)
1332 {
1333 bLocal = ga2la_get(ga2la, i_gl+iatoms[k]-i_mol,
1334 &a_loc, &kz);
1335 if (!bLocal || kz >= zones->n)
1336 {
1337 /* We do not have this atom of this interaction
1338 * locally, or it comes from more than one cell
1339 * away.
1340 */
1341 bUse = FALSE0;
1342 }
1343 else
1344 {
1345 tiatoms[k] = a_loc;
1346 for (d = 0; d < DIM3; d++)
1347 {
1348 if (zones->shift[kz][d] == 0)
1349 {
1350 k_zero[d] = k;
1351 }
1352 else
1353 {
1354 k_plus[d] = k;
1355 }
1356 }
1357 }
1358 }
1359 bUse = (bUse &&
1360 k_zero[XX0] && k_zero[YY1] && k_zero[ZZ2]);
1361 if (bRCheckMB)
1362 {
1363 for (d = 0; (d < DIM3 && bUse); d++)
1364 {
1365 /* Check if the cg_cm distance falls within
1366 * the cut-off to avoid possible multiple
1367 * assignments of bonded interactions.
1368 */
1369 if (rcheck[d] &&
1370 k_plus[d] &&
1371 dd_dist2(pbc_null, cg_cm, la2lc,
1372 tiatoms[k_zero[d]], tiatoms[k_plus[d]]) >= rc2)
1373 {
1374 bUse = FALSE0;
1375 }
1376 }
1377 }
1378 }
1379 if (bUse)
1380 {
1381 /* Add this interaction to the local topology */
1382 add_ifunc(nral, tiatoms, &idef->il[ftype]);
1383 /* Sum so we can check in global_stat
1384 * if we have everything.
1385 */
1386 if (bBCheck ||
1387 !(interaction_function[ftype].flags & IF_LIMZERO1<<7))
1388 {
1389 nbonded_local++;
1390 }
1391 }
1392 j += 1 + nral;
1393 }
1394 }
1395 }
1396
1397 return nbonded_local;
1398}
1399
1400static void set_no_exclusions_zone(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
1401 int iz, t_blocka *lexcls)
1402{
1403 int a0, a1, a;
1404
1405 a0 = dd->cgindex[zones->cg_range[iz]];
1406 a1 = dd->cgindex[zones->cg_range[iz+1]];
1407
1408 for (a = a0+1; a < a1+1; a++)
1409 {
1410 lexcls->index[a] = lexcls->nra;
1411 }
1412}
1413
1414static int make_exclusions_zone(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
1415 const gmx_moltype_t *moltype,
1416 gmx_bool bRCheck, real rc2,
1417 int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
1418 const int *cginfo,
1419 t_blocka *lexcls,
1420 int iz,
1421 int cg_start, int cg_end)
1422{
1423 int nizone, n, count, jla0, jla1, jla;
1424 int cg, la0, la1, la, a_gl, mb, mt, mol, a_mol, j, aj_mol;
1425 const t_blocka *excls;
1426 gmx_ga2la_t ga2la;
1427 int a_loc;
1428 int cell;
1429
1430 ga2la = dd->ga2la;
1431
1432 jla0 = dd->cgindex[zones->izone[iz].jcg0];
1433 jla1 = dd->cgindex[zones->izone[iz].jcg1];
1434
1435 /* We set the end index, but note that we might not start at zero here */
1436 lexcls->nr = dd->cgindex[cg_end];
1437
1438 n = lexcls->nra;
1439 count = 0;
1440 for (cg = cg_start; cg < cg_end; cg++)
1441 {
1442 /* Here we assume the number of exclusions in one charge group
1443 * is never larger than 1000.
1444 */
1445 if (n+1000 > lexcls->nalloc_a)
1446 {
1447 lexcls->nalloc_a = over_alloc_large(n+1000)(int)(1.19*(n+1000) + 1000);
1448 srenew(lexcls->a, lexcls->nalloc_a)(lexcls->a) = save_realloc("lexcls->a", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1448, (lexcls->a), (lexcls->nalloc_a), sizeof(*(lexcls
->a)));
1449 }
1450 la0 = dd->cgindex[cg];
1451 la1 = dd->cgindex[cg+1];
1452 if (GET_CGINFO_EXCL_INTER(cginfo[cg])( (cginfo[cg]) & (1<<17)) ||
1453 !GET_CGINFO_EXCL_INTRA(cginfo[cg])( (cginfo[cg]) & (1<<16)))
1454 {
1455 /* Copy the exclusions from the global top */
1456 for (la = la0; la < la1; la++)
1457 {
1458 lexcls->index[la] = n;
1459 a_gl = dd->gatindex[la];
1460 global_atomnr_to_moltype_ind(dd->reverse_top, a_gl, &mb, &mt, &mol, &a_mol);
1461 excls = &moltype[mt].excls;
1462 for (j = excls->index[a_mol]; j < excls->index[a_mol+1]; j++)
1463 {
1464 aj_mol = excls->a[j];
1465 /* This computation of jla is only correct intra-cg */
1466 jla = la + aj_mol - a_mol;
1467 if (jla >= la0 && jla < la1)
1468 {
1469 /* This is an intra-cg exclusion. We can skip
1470 * the global indexing and distance checking.
1471 */
1472 /* Intra-cg exclusions are only required
1473 * for the home zone.
1474 */
1475 if (iz == 0)
1476 {
1477 lexcls->a[n++] = jla;
1478 /* Check to avoid double counts */
1479 if (jla > la)
1480 {
1481 count++;
1482 }
1483 }
1484 }
1485 else
1486 {
1487 /* This is a inter-cg exclusion */
1488 /* Since exclusions are pair interactions,
1489 * just like non-bonded interactions,
1490 * they can be assigned properly up
1491 * to the DD cutoff (not cutoff_min as
1492 * for the other bonded interactions).
1493 */
1494 if (ga2la_get(ga2la, a_gl+aj_mol-a_mol, &jla, &cell))
1495 {
1496 if (iz == 0 && cell == 0)
1497 {
1498 lexcls->a[n++] = jla;
1499 /* Check to avoid double counts */
1500 if (jla > la)
1501 {
1502 count++;
1503 }
1504 }
1505 else if (jla >= jla0 && jla < jla1 &&
1506 (!bRCheck ||
1507 dd_dist2(pbc_null, cg_cm, la2lc, la, jla) < rc2))
1508 {
1509 /* jla > la, since jla0 > la */
1510 lexcls->a[n++] = jla;
1511 count++;
1512 }
1513 }
1514 }
1515 }
1516 }
1517 }
1518 else
1519 {
1520 /* There are no inter-cg excls and this cg is self-excluded.
1521 * These exclusions are only required for zone 0,
1522 * since other zones do not see themselves.
1523 */
1524 if (iz == 0)
1525 {
1526 for (la = la0; la < la1; la++)
1527 {
1528 lexcls->index[la] = n;
1529 for (j = la0; j < la1; j++)
1530 {
1531 lexcls->a[n++] = j;
1532 }
1533 }
1534 count += ((la1 - la0)*(la1 - la0 - 1))/2;
1535 }
1536 else
1537 {
1538 /* We don't need exclusions for this cg */
1539 for (la = la0; la < la1; la++)
1540 {
1541 lexcls->index[la] = n;
1542 }
1543 }
1544 }
1545 }
1546
1547 lexcls->index[lexcls->nr] = n;
1548 lexcls->nra = n;
1549
1550 return count;
1551}
1552
1553static void check_alloc_index(t_blocka *ba, int nindex_max)
1554{
1555 if (nindex_max+1 > ba->nalloc_index)
1556 {
1557 ba->nalloc_index = over_alloc_dd(nindex_max+1);
1558 srenew(ba->index, ba->nalloc_index)(ba->index) = save_realloc("ba->index", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1558, (ba->index), (ba->nalloc_index), sizeof(*(ba->
index)));
1559 }
1560}
1561
1562static void check_exclusions_alloc(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
1563 t_blocka *lexcls)
1564{
1565 int nr;
1566 int thread;
1567
1568 nr = dd->cgindex[zones->izone[zones->nizone-1].cg1];
1569
1570 check_alloc_index(lexcls, nr);
1571
1572 for (thread = 1; thread < dd->reverse_top->nthread; thread++)
1573 {
1574 check_alloc_index(&dd->reverse_top->excl_thread[thread], nr);
1575 }
1576}
1577
1578static void finish_local_exclusions(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
1579 t_blocka *lexcls)
1580{
1581 int la0, la;
1582
1583 lexcls->nr = dd->cgindex[zones->izone[zones->nizone-1].cg1];
1584
1585 if (dd->n_intercg_excl == 0)
1586 {
1587 /* There are no exclusions involving non-home charge groups,
1588 * but we need to set the indices for neighborsearching.
1589 */
1590 la0 = dd->cgindex[zones->izone[0].cg1];
1591 for (la = la0; la < lexcls->nr; la++)
1592 {
1593 lexcls->index[la] = lexcls->nra;
1594 }
1595
1596 /* nr is only used to loop over the exclusions for Ewald and RF,
1597 * so we can set it to the number of home atoms for efficiency.
1598 */
1599 lexcls->nr = dd->cgindex[zones->izone[0].cg1];
1600 }
1601}
1602
1603static void clear_idef(t_idef *idef)
1604{
1605 int ftype;
1606
1607 /* Clear the counts */
1608 for (ftype = 0; ftype < F_NRE; ftype++)
1609 {
1610 idef->il[ftype].nr = 0;
1611 }
1612}
1613
1614static int make_local_bondeds_excls(gmx_domdec_t *dd,
1615 gmx_domdec_zones_t *zones,
1616 const gmx_mtop_t *mtop,
1617 const int *cginfo,
1618 gmx_bool bRCheckMB, ivec rcheck, gmx_bool bRCheck2B,
1619 real rc,
1620 int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
1621 t_idef *idef, gmx_vsite_t *vsite,
1622 t_blocka *lexcls, int *excl_count)
1623{
1624 int nzone_bondeds, nzone_excl;
1625 int iz, cg0, cg1;
1626 real rc2;
1627 int nbonded_local;
1628 int thread;
1629 gmx_reverse_top_t *rt;
1630
1631 if (dd->reverse_top->bMultiCGmols)
1632 {
1633 nzone_bondeds = zones->n;
1634 }
1635 else
1636 {
1637 /* Only single charge group molecules, so interactions don't
1638 * cross zone boundaries and we only need to assign in the home zone.
1639 */
1640 nzone_bondeds = 1;
1641 }
1642
1643 if (dd->n_intercg_excl > 0)
1644 {
1645 /* We only use exclusions from i-zones to i- and j-zones */
1646 nzone_excl = zones->nizone;
1647 }
1648 else
1649 {
1650 /* There are no inter-cg exclusions and only zone 0 sees itself */
1651 nzone_excl = 1;
1652 }
1653
1654 check_exclusions_alloc(dd, zones, lexcls);
1655
1656 rt = dd->reverse_top;
1657
1658 rc2 = rc*rc;
1659
1660 /* Clear the counts */
1661 clear_idef(idef);
1662 nbonded_local = 0;
1663
1664 lexcls->nr = 0;
1665 lexcls->nra = 0;
1666 *excl_count = 0;
1667
1668 for (iz = 0; iz < nzone_bondeds; iz++)
1669 {
1670 cg0 = zones->cg_range[iz];
1671 cg1 = zones->cg_range[iz+1];
1672
1673#pragma omp parallel for num_threads(rt->nthread) schedule(static)
1674 for (thread = 0; thread < rt->nthread; thread++)
1675 {
1676 int cg0t, cg1t;
1677 t_idef *idef_t;
1678 int ftype;
1679 int **vsite_pbc;
1680 int *vsite_pbc_nalloc;
1681 t_blocka *excl_t;
1682
1683 cg0t = cg0 + ((cg1 - cg0)* thread )/rt->nthread;
1684 cg1t = cg0 + ((cg1 - cg0)*(thread+1))/rt->nthread;
1685
1686 if (thread == 0)
1687 {
1688 idef_t = idef;
1689 }
1690 else
1691 {
1692 idef_t = &rt->idef_thread[thread];
1693 clear_idef(idef_t);
1694 }
1695
1696 if (vsite && vsite->bHaveChargeGroups && vsite->n_intercg_vsite > 0)
1697 {
1698 if (thread == 0)
1699 {
1700 vsite_pbc = vsite->vsite_pbc_loc;
1701 vsite_pbc_nalloc = vsite->vsite_pbc_loc_nalloc;
1702 }
1703 else
1704 {
1705 vsite_pbc = rt->vsite_pbc[thread];
1706 vsite_pbc_nalloc = rt->vsite_pbc_nalloc[thread];
1707 }
1708 }
1709 else
1710 {
1711 vsite_pbc = NULL((void*)0);
1712 vsite_pbc_nalloc = NULL((void*)0);
1713 }
1714
1715 rt->nbonded_thread[thread] =
1716 make_bondeds_zone(dd, zones,
1717 mtop->molblock,
1718 bRCheckMB, rcheck, bRCheck2B, rc2,
1719 la2lc, pbc_null, cg_cm, idef->iparams,
1720 idef_t,
1721 vsite_pbc, vsite_pbc_nalloc,
1722 iz, zones->n,
1723 dd->cgindex[cg0t], dd->cgindex[cg1t]);
1724
1725 if (iz < nzone_excl)
1726 {
1727 if (thread == 0)
1728 {
1729 excl_t = lexcls;
1730 }
1731 else
1732 {
1733 excl_t = &rt->excl_thread[thread];
1734 excl_t->nr = 0;
1735 excl_t->nra = 0;
1736 }
1737
1738 rt->excl_count_thread[thread] =
1739 make_exclusions_zone(dd, zones,
1740 mtop->moltype, bRCheck2B, rc2,
1741 la2lc, pbc_null, cg_cm, cginfo,
1742 excl_t,
1743 iz,
1744 cg0t, cg1t);
1745 }
1746 }
1747
1748 if (rt->nthread > 1)
1749 {
1750 combine_idef(idef, rt->idef_thread+1, rt->nthread-1,
1751 vsite, rt->vsite_pbc+1);
1752 }
1753
1754 for (thread = 0; thread < rt->nthread; thread++)
1755 {
1756 nbonded_local += rt->nbonded_thread[thread];
1757 }
1758
1759 if (iz < nzone_excl)
1760 {
1761 if (rt->nthread > 1)
1762 {
1763 combine_blocka(lexcls, rt->excl_thread+1, rt->nthread-1);
1764 }
1765
1766 for (thread = 0; thread < rt->nthread; thread++)
1767 {
1768 *excl_count += rt->excl_count_thread[thread];
1769 }
1770 }
1771 }
1772
1773 /* Some zones might not have exclusions, but some code still needs to
1774 * loop over the index, so we set the indices here.
1775 */
1776 for (iz = nzone_excl; iz < zones->nizone; iz++)
1777 {
1778 set_no_exclusions_zone(dd, zones, iz, lexcls);
1779 }
1780
1781 finish_local_exclusions(dd, zones, lexcls);
1782 if (debug)
1783 {
1784 fprintf(debug, "We have %d exclusions, check count %d\n",
1785 lexcls->nra, *excl_count);
1786 }
1787
1788 return nbonded_local;
1789}
1790
1791void dd_make_local_cgs(gmx_domdec_t *dd, t_block *lcgs)
1792{
1793 lcgs->nr = dd->ncg_tot;
1794 lcgs->index = dd->cgindex;
1795}
1796
1797void dd_make_local_top(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
1798 int npbcdim, matrix box,
1799 rvec cellsize_min, ivec npulse,
1800 t_forcerec *fr,
1801 rvec *cgcm_or_x,
1802 gmx_vsite_t *vsite,
1803 gmx_mtop_t *mtop, gmx_localtop_t *ltop)
1804{
1805 gmx_bool bUniqueExcl, bRCheckMB, bRCheck2B, bRCheckExcl;
1806 real rc = -1;
1807 ivec rcheck;
1808 int d, nexcl;
1809 t_pbc pbc, *pbc_null = NULL((void*)0);
1810
1811 if (debug)
1812 {
1813 fprintf(debug, "Making local topology\n");
1814 }
1815
1816 dd_make_local_cgs(dd, &ltop->cgs);
1817
1818 bRCheckMB = FALSE0;
1819 bRCheck2B = FALSE0;
1820 bRCheckExcl = FALSE0;
1821
1822 if (dd->reverse_top->bMultiCGmols)
1823 {
1824 /* We need to check to which cell bondeds should be assigned */
1825 rc = dd_cutoff_twobody(dd);
1826 if (debug)
1827 {
1828 fprintf(debug, "Two-body bonded cut-off distance is %g\n", rc);
1829 }
1830
1831 /* Should we check cg_cm distances when assigning bonded interactions? */
1832 for (d = 0; d < DIM3; d++)
1833 {
1834 rcheck[d] = FALSE0;
1835 /* Only need to check for dimensions where the part of the box
1836 * that is not communicated is smaller than the cut-off.
1837 */
1838 if (d < npbcdim && dd->nc[d] > 1 &&
1839 (dd->nc[d] - npulse[d])*cellsize_min[d] < 2*rc)
1840 {
1841 if (dd->nc[d] == 2)
1842 {
1843 rcheck[d] = TRUE1;
1844 bRCheckMB = TRUE1;
1845 }
1846 /* Check for interactions between two atoms,
1847 * where we can allow interactions up to the cut-off,
1848 * instead of up to the smallest cell dimension.
1849 */
1850 bRCheck2B = TRUE1;
1851 }
1852 if (debug)
1853 {
1854 fprintf(debug,
1855 "dim %d cellmin %f bonded rcheck[%d] = %d, bRCheck2B = %d\n",
1856 d, cellsize_min[d], d, rcheck[d], bRCheck2B);
1857 }
1858 }
1859 if (dd->reverse_top->bExclRequired)
1860 {
1861 bRCheckExcl = bRCheck2B;
1862 }
1863 else
1864 {
1865 /* If we don't have forces on exclusions,
1866 * we don't care about exclusions being assigned mulitple times.
1867 */
1868 bRCheckExcl = FALSE0;
1869 }
1870 if (bRCheckMB || bRCheck2B)
1871 {
1872 make_la2lc(dd);
1873 if (fr->bMolPBC)
1874 {
1875 set_pbc_dd(&pbc, fr->ePBC, dd, TRUE1, box);
1876 pbc_null = &pbc;
1877 }
1878 else
1879 {
1880 pbc_null = NULL((void*)0);
1881 }
1882 }
1883 }
1884
1885 dd->nbonded_local =
1886 make_local_bondeds_excls(dd, zones, mtop, fr->cginfo,
1887 bRCheckMB, rcheck, bRCheck2B, rc,
1888 dd->la2lc,
1889 pbc_null, cgcm_or_x,
1890 &ltop->idef, vsite,
1891 &ltop->excls, &nexcl);
1892
1893 /* The ilist is not sorted yet,
1894 * we can only do this when we have the charge arrays.
1895 */
1896 ltop->idef.ilsort = ilsortUNKNOWN;
1897
1898 if (dd->reverse_top->bExclRequired)
1899 {
1900 dd->nbonded_local += nexcl;
1901
1902 forcerec_set_excl_load(fr, ltop);
1903 }
1904
1905 ltop->atomtypes = mtop->atomtypes;
1906
1907 /* For an error message only */
1908 dd->reverse_top->err_top_global = mtop;
1909 dd->reverse_top->err_top_local = ltop;
1910}
1911
1912void dd_sort_local_top(gmx_domdec_t *dd, t_mdatoms *mdatoms,
1913 gmx_localtop_t *ltop)
1914{
1915 if (dd->reverse_top->ilsort == ilsortNO_FE)
1916 {
1917 ltop->idef.ilsort = ilsortNO_FE;
1918 }
1919 else
1920 {
1921 gmx_sort_ilist_fe(&ltop->idef, mdatoms->chargeA, mdatoms->chargeB);
1922 }
1923}
1924
1925gmx_localtop_t *dd_init_local_top(gmx_mtop_t *top_global)
1926{
1927 gmx_localtop_t *top;
1928 int i;
1929
1930 snew(top, 1)(top) = save_calloc("top", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1930, (1), sizeof(*(top)));
1931
1932 top->idef.ntypes = top_global->ffparams.ntypes;
1933 top->idef.atnr = top_global->ffparams.atnr;
1934 top->idef.functype = top_global->ffparams.functype;
1935 top->idef.iparams = top_global->ffparams.iparams;
1936 top->idef.fudgeQQ = top_global->ffparams.fudgeQQ;
1937 top->idef.cmap_grid = top_global->ffparams.cmap_grid;
1938
1939 for (i = 0; i < F_NRE; i++)
1940 {
1941 top->idef.il[i].iatoms = NULL((void*)0);
1942 top->idef.il[i].nalloc = 0;
1943 }
1944 top->idef.ilsort = ilsortUNKNOWN;
1945
1946 return top;
1947}
1948
1949void dd_init_local_state(gmx_domdec_t *dd,
1950 t_state *state_global, t_state *state_local)
1951{
1952 int buf[NITEM_DD_INIT_LOCAL_STATE5];
1953
1954 if (DDMASTER(dd)((dd)->rank == (dd)->masterrank))
1955 {
1956 buf[0] = state_global->flags;
1957 buf[1] = state_global->ngtc;
1958 buf[2] = state_global->nnhpres;
1959 buf[3] = state_global->nhchainlength;
1960 buf[4] = state_global->dfhist.nlambda;
1961 }
1962 dd_bcast(dd, NITEM_DD_INIT_LOCAL_STATE5*sizeof(int), buf);
1963
1964 init_state(state_local, 0, buf[1], buf[2], buf[3], buf[4]);
1965 state_local->flags = buf[0];
1966}
1967
1968static void check_link(t_blocka *link, int cg_gl, int cg_gl_j)
1969{
1970 int k, aj;
1971 gmx_bool bFound;
1972
1973 bFound = FALSE0;
1974 for (k = link->index[cg_gl]; k < link->index[cg_gl+1]; k++)
44
←
Loop condition is false. Execution continues on line 1981
→
1975 {
1976 if (link->a[k] == cg_gl_j)
1977 {
1978 bFound = TRUE1;
1979 }
1980 }
1981 if (!bFound)
45
←
Taking true branch
→
1982 {
1983 /* Add this charge group link */
1984 if (link->index[cg_gl+1]+1 > link->nalloc_a)
46
←
Taking false branch
→
1985 {
1986 link->nalloc_a = over_alloc_large(link->index[cg_gl+1]+1)(int)(1.19*(link->index[cg_gl+1]+1) + 1000);
1987 srenew(link->a, link->nalloc_a)(link->a) = save_realloc("link->a", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1987, (link->a), (link->nalloc_a), sizeof(*(link->
a)));
1988 }
1989 link->a[link->index[cg_gl+1]] = cg_gl_j;
47
←
Array access (via field 'a') results in a null pointer dereference
1990 link->index[cg_gl+1]++;
1991 }
1992}
1993
1994static int *make_at2cg(t_block *cgs)
1995{
1996 int *at2cg, cg, a;
1997
1998 snew(at2cg, cgs->index[cgs->nr])(at2cg) = save_calloc("at2cg", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 1998, (cgs->index[cgs->nr]), sizeof(*(at2cg)));
1999 for (cg = 0; cg < cgs->nr; cg++)
2000 {
2001 for (a = cgs->index[cg]; a < cgs->index[cg+1]; a++)
2002 {
2003 at2cg[a] = cg;
2004 }
2005 }
2006
2007 return at2cg;
2008}
2009
2010t_blocka *make_charge_group_links(gmx_mtop_t *mtop, gmx_domdec_t *dd,
2011 cginfo_mb_t *cginfo_mb)
2012{
2013 gmx_reverse_top_t *rt;
2014 int mb, cg_offset, cg, cg_gl, a, aj, i, j, ftype, nral, nlink_mol, mol, ncgi;
2015 gmx_molblock_t *molb;
2016 gmx_moltype_t *molt;
2017 t_block *cgs;
2018 t_blocka *excls;
2019 int *a2c;
2020 gmx_reverse_ilist_t ril;
2021 t_blocka *link;
2022 cginfo_mb_t *cgi_mb;
2023
2024 /* For each charge group make a list of other charge groups
2025 * in the system that a linked to it via bonded interactions
2026 * which are also stored in reverse_top.
2027 */
2028
2029 rt = dd->reverse_top;
2030
2031 snew(link, 1)(link) = save_calloc("link", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 2031, (1), sizeof(*(link)));
2032 snew(link->index, ncg_mtop(mtop)+1)(link->index) = save_calloc("link->index", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 2032, (ncg_mtop(mtop)+1), sizeof(*(link->index)));
2033 link->nalloc_a = 0;
2034 link->a = NULL((void*)0);
1
Null pointer value stored to field 'a'
→
2035
2036 link->index[0] = 0;
2037 cg_offset = 0;
2038 ncgi = 0;
2039 for (mb = 0; mb < mtop->nmolblock; mb++)
2
←
Loop condition is true. Entering loop body
→
8
←
Loop condition is true. Entering loop body
→
14
←
Loop condition is true. Entering loop body
→
20
←
Loop condition is true. Entering loop body
→
2040 {
2041 molb = &mtop->molblock[mb];
2042 if (molb->nmol == 0)
3
←
Taking false branch
→
9
←
Taking false branch
→
15
←
Taking false branch
→
21
←
Taking false branch
→
2043 {
2044 continue;
2045 }
2046 molt = &mtop->moltype[molb->type];
2047 cgs = &molt->cgs;
2048 excls = &molt->excls;
2049 a2c = make_at2cg(cgs);
2050 /* Make a reverse ilist in which the interactions are linked
2051 * to all atoms, not only the first atom as in gmx_reverse_top.
2052 * The constraints are discarded here.
2053 */
2054 make_reverse_ilist(molt, NULL((void*)0), FALSE0, FALSE0, FALSE0, TRUE1, &ril);
2055
2056 cgi_mb = &cginfo_mb[mb];
2057
2058 for (cg = 0; cg < cgs->nr; cg++)
4
←
Loop condition is false. Execution continues on line 2100
→
10
←
Loop condition is false. Execution continues on line 2100
→
16
←
Loop condition is false. Execution continues on line 2100
→
22
←
Loop condition is true. Entering loop body
→
2059 {
2060 cg_gl = cg_offset + cg;
2061 link->index[cg_gl+1] = link->index[cg_gl];
2062 for (a = cgs->index[cg]; a < cgs->index[cg+1]; a++)
23
←
Loop condition is true. Entering loop body
→
26
←
Loop condition is true. Entering loop body
→
29
←
Loop condition is true. Entering loop body
→
32
←
Loop condition is true. Entering loop body
→
2063 {
2064 i = ril.index[a];
2065 while (i < ril.index[a+1])
24
←
Loop condition is false. Execution continues on line 2081
→
27
←
Loop condition is false. Execution continues on line 2081
→
30
←
Loop condition is false. Execution continues on line 2081
→
33
←
Loop condition is true. Entering loop body
→
2066 {
2067 ftype = ril.il[i++];
2068 nral = NRAL(ftype)(interaction_function[(ftype)].nratoms);
2069 /* Skip the ifunc index */
2070 i++;
2071 for (j = 0; j < nral; j++)
34
←
Assuming 'j' is < 'nral'
→
35
←
Loop condition is true. Entering loop body
→
37
←
Assuming 'j' is < 'nral'
→
38
←
Loop condition is true. Entering loop body
→
40
←
Assuming 'j' is < 'nral'
→
41
←
Loop condition is true. Entering loop body
→
2072 {
2073 aj = ril.il[i+j];
2074 if (a2c[aj] != cg)
36
←
Taking false branch
→
39
←
Taking false branch
→
42
←
Taking true branch
→
2075 {
2076 check_link(link, cg_gl, cg_offset+a2c[aj]);
43
←
Calling 'check_link'
→
2077 }
2078 }
2079 i += nral_rt(ftype);
2080 }
2081 if (rt->bExclRequired)
25
←
Taking false branch
→
28
←
Taking false branch
→
31
←
Taking false branch
→
2082 {
2083 /* Exclusions always go both ways */
2084 for (j = excls->index[a]; j < excls->index[a+1]; j++)
2085 {
2086 aj = excls->a[j];
2087 if (a2c[aj] != cg)
2088 {
2089 check_link(link, cg_gl, cg_offset+a2c[aj]);
2090 }
2091 }
2092 }
2093 }
2094 if (link->index[cg_gl+1] - link->index[cg_gl] > 0)
2095 {
2096 SET_CGINFO_BOND_INTER(cgi_mb->cginfo[cg])(cgi_mb->cginfo[cg]) = ((cgi_mb->cginfo[cg]) | (1<<
22));
2097 ncgi++;
2098 }
2099 }
2100 nlink_mol = link->index[cg_offset+cgs->nr] - link->index[cg_offset];
2101
2102 cg_offset += cgs->nr;
2103
2104 destroy_reverse_ilist(&ril);
2105 sfree(a2c)save_free("a2c", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 2105, (a2c));
2106
2107 if (debug)
5
←
Assuming 'debug' is null
→
6
←
Taking false branch
→
11
←
Assuming 'debug' is null
→
12
←
Taking false branch
→
17
←
Assuming 'debug' is null
→
18
←
Taking false branch
→
2108 {
2109 fprintf(debug, "molecule type '%s' %d cgs has %d cg links through bonded interac.\n", *molt->name, cgs->nr, nlink_mol);
2110 }
2111
2112 if (molb->nmol > 1)
7
←
Taking false branch
→
13
←
Taking false branch
→
19
←
Taking false branch
→
2113 {
2114 /* Copy the data for the rest of the molecules in this block */
2115 link->nalloc_a += (molb->nmol - 1)*nlink_mol;
2116 srenew(link->a, link->nalloc_a)(link->a) = save_realloc("link->a", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 2116, (link->a), (link->nalloc_a), sizeof(*(link->
a)));
2117 for (mol = 1; mol < molb->nmol; mol++)
2118 {
2119 for (cg = 0; cg < cgs->nr; cg++)
2120 {
2121 cg_gl = cg_offset + cg;
2122 link->index[cg_gl+1] =
2123 link->index[cg_gl+1-cgs->nr] + nlink_mol;
2124 for (j = link->index[cg_gl]; j < link->index[cg_gl+1]; j++)
2125 {
2126 link->a[j] = link->a[j-nlink_mol] + cgs->nr;
2127 }
2128 if (link->index[cg_gl+1] - link->index[cg_gl] > 0 &&
2129 cg_gl - cgi_mb->cg_start < cgi_mb->cg_mod)
2130 {
2131 SET_CGINFO_BOND_INTER(cgi_mb->cginfo[cg_gl - cgi_mb->cg_start])(cgi_mb->cginfo[cg_gl - cgi_mb->cg_start]) = ((cgi_mb->
cginfo[cg_gl - cgi_mb->cg_start]) | (1<<22));
2132 ncgi++;
2133 }
2134 }
2135 cg_offset += cgs->nr;
2136 }
2137 }
2138 }
2139
2140 if (debug)
2141 {
2142 fprintf(debug, "Of the %d charge groups %d are linked via bonded interactions\n", ncg_mtop(mtop), ncgi);
2143 }
2144
2145 return link;
2146}
2147
2148static void bonded_cg_distance_mol(gmx_moltype_t *molt, int *at2cg,
2149 gmx_bool bBCheck, gmx_bool bExcl, rvec *cg_cm,
2150 real *r_2b, int *ft2b, int *a2_1, int *a2_2,
2151 real *r_mb, int *ftmb, int *am_1, int *am_2)
2152{
2153 int ftype, nral, i, j, ai, aj, cgi, cgj;
2154 t_ilist *il;
2155 t_blocka *excls;
2156 real r2_2b, r2_mb, rij2;
2157
2158 r2_2b = 0;
2159 r2_mb = 0;
2160 for (ftype = 0; ftype < F_NRE; ftype++)
2161 {
2162 if (dd_check_ftype(ftype, bBCheck, FALSE0, FALSE0))
2163 {
2164 il = &molt->ilist[ftype];
2165 nral = NRAL(ftype)(interaction_function[(ftype)].nratoms);
2166 if (nral > 1)
2167 {
2168 for (i = 0; i < il->nr; i += 1+nral)
2169 {
2170 for (ai = 0; ai < nral; ai++)
2171 {
2172 cgi = at2cg[il->iatoms[i+1+ai]];
2173 for (aj = 0; aj < nral; aj++)
2174 {
2175 cgj = at2cg[il->iatoms[i+1+aj]];
2176 if (cgi != cgj)
2177 {
2178 rij2 = distance2(cg_cm[cgi], cg_cm[cgj]);
2179 if (nral == 2 && rij2 > r2_2b)
2180 {
2181 r2_2b = rij2;
2182 *ft2b = ftype;
2183 *a2_1 = il->iatoms[i+1+ai];
2184 *a2_2 = il->iatoms[i+1+aj];
2185 }
2186 if (nral > 2 && rij2 > r2_mb)
2187 {
2188 r2_mb = rij2;
2189 *ftmb = ftype;
2190 *am_1 = il->iatoms[i+1+ai];
2191 *am_2 = il->iatoms[i+1+aj];
2192 }
2193 }
2194 }
2195 }
2196 }
2197 }
2198 }
2199 }
2200 if (bExcl)
2201 {
2202 excls = &molt->excls;
2203 for (ai = 0; ai < excls->nr; ai++)
2204 {
2205 cgi = at2cg[ai];
2206 for (j = excls->index[ai]; j < excls->index[ai+1]; j++)
2207 {
2208 cgj = at2cg[excls->a[j]];
2209 if (cgi != cgj)
2210 {
2211 rij2 = distance2(cg_cm[cgi], cg_cm[cgj]);
2212 if (rij2 > r2_2b)
2213 {
2214 r2_2b = rij2;
2215 }
2216 }
2217 }
2218 }
2219 }
2220
2221 *r_2b = sqrt(r2_2b);
2222 *r_mb = sqrt(r2_mb);
2223}
2224
2225static void get_cgcm_mol(gmx_moltype_t *molt, gmx_ffparams_t *ffparams,
2226 int ePBC, t_graph *graph, matrix box,
2227 gmx_vsite_t *vsite,
2228 rvec *x, rvec *xs, rvec *cg_cm)
2229{
2230 int n, i;
2231
2232 if (ePBC != epbcNONE)
2233 {
2234 mk_mshift(NULL((void*)0), graph, ePBC, box, x);
2235
2236 shift_x(graph, box, x, xs);
2237 /* By doing an extra mk_mshift the molecules that are broken
2238 * because they were e.g. imported from another software
2239 * will be made whole again. Such are the healing powers
2240 * of GROMACS.
2241 */
2242 mk_mshift(NULL((void*)0), graph, ePBC, box, xs);
2243 }
2244 else
2245 {
2246 /* We copy the coordinates so the original coordinates remain
2247 * unchanged, just to be 100% sure that we do not affect
2248 * binary reproducibility of simulations.
2249 */
2250 n = molt->cgs.index[molt->cgs.nr];
2251 for (i = 0; i < n; i++)
2252 {
2253 copy_rvec(x[i], xs[i]);
2254 }
2255 }
2256
2257 if (vsite)
2258 {
2259 construct_vsites(vsite, xs, 0.0, NULL((void*)0),
2260 ffparams->iparams, molt->ilist,
2261 epbcNONE, TRUE1, NULL((void*)0), NULL((void*)0));
2262 }
2263
2264 calc_cgcm(NULL((void*)0), 0, molt->cgs.nr, &molt->cgs, xs, cg_cm);
2265}
2266
2267static int have_vsite_molt(gmx_moltype_t *molt)
2268{
2269 int i;
2270 gmx_bool bVSite;
2271
2272 bVSite = FALSE0;
2273 for (i = 0; i < F_NRE; i++)
2274 {
2275 if ((interaction_function[i].flags & IF_VSITE1<<1) &&
2276 molt->ilist[i].nr > 0)
2277 {
2278 bVSite = TRUE1;
2279 }
2280 }
2281
2282 return bVSite;
2283}
2284
2285void dd_bonded_cg_distance(FILE *fplog,
2286 gmx_mtop_t *mtop,
2287 t_inputrec *ir, rvec *x, matrix box,
2288 gmx_bool bBCheck,
2289 real *r_2b, real *r_mb)
2290{
2291 gmx_bool bExclRequired;
2292 int mb, cg_offset, at_offset, *at2cg, mol;
2293 t_graph graph;
2294 gmx_vsite_t *vsite;
2295 gmx_molblock_t *molb;
2296 gmx_moltype_t *molt;
2297 rvec *xs, *cg_cm;
2298 real rmol_2b, rmol_mb;
2299 int ft2b = -1, a_2b_1 = -1, a_2b_2 = -1, ftmb = -1, a_mb_1 = -1, a_mb_2 = -1;
2300 int ftm2b = -1, amol_2b_1 = -1, amol_2b_2 = -1, ftmmb = -1, amol_mb_1 = -1, amol_mb_2 = -1;
2301
2302 bExclRequired = IR_EXCL_FORCES(*ir)((((((*ir).coulombtype) == eelPME || ((*ir).coulombtype) == eelPMESWITCH
|| ((*ir).coulombtype) == eelPMEUSER || ((*ir).coulombtype) ==
eelPMEUSERSWITCH || ((*ir).coulombtype) == eelP3M_AD) || ((*
ir).coulombtype) == eelEWALD) || ((*ir).coulombtype) == eelPOISSON
) || ((((*ir).coulombtype) == eelRF || ((*ir).coulombtype) ==
eelGRF || ((*ir).coulombtype) == eelRF_NEC || ((*ir).coulombtype
) == eelRF_ZERO ) && (*ir).coulombtype != eelRF_NEC) ||
(*ir).implicit_solvent != eisNO);
2303
2304 vsite = init_vsite(mtop, NULL((void*)0), TRUE1);
2305
2306 *r_2b = 0;
2307 *r_mb = 0;
2308 cg_offset = 0;
2309 at_offset = 0;
2310 for (mb = 0; mb < mtop->nmolblock; mb++)
2311 {
2312 molb = &mtop->molblock[mb];
2313 molt = &mtop->moltype[molb->type];
2314 if (molt->cgs.nr == 1 || molb->nmol == 0)
2315 {
2316 cg_offset += molb->nmol*molt->cgs.nr;
2317 at_offset += molb->nmol*molt->atoms.nr;
2318 }
2319 else
2320 {
2321 if (ir->ePBC != epbcNONE)
2322 {
2323 mk_graph_ilist(NULL((void*)0), molt->ilist, 0, molt->atoms.nr, FALSE0, FALSE0,
2324 &graph);
2325 }
2326
2327 at2cg = make_at2cg(&molt->cgs);
2328 snew(xs, molt->atoms.nr)(xs) = save_calloc("xs", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 2328, (molt->atoms.nr), sizeof(*(xs)));
2329 snew(cg_cm, molt->cgs.nr)(cg_cm) = save_calloc("cg_cm", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 2329, (molt->cgs.nr), sizeof(*(cg_cm)));
2330 for (mol = 0; mol < molb->nmol; mol++)
2331 {
2332 get_cgcm_mol(molt, &mtop->ffparams, ir->ePBC, &graph, box,
2333 have_vsite_molt(molt) ? vsite : NULL((void*)0),
2334 x+at_offset, xs, cg_cm);
2335
2336 bonded_cg_distance_mol(molt, at2cg, bBCheck, bExclRequired, cg_cm,
2337 &rmol_2b, &ftm2b, &amol_2b_1, &amol_2b_2,
2338 &rmol_mb, &ftmmb, &amol_mb_1, &amol_mb_2);
2339 if (rmol_2b > *r_2b)
2340 {
2341 *r_2b = rmol_2b;
2342 ft2b = ftm2b;
2343 a_2b_1 = at_offset + amol_2b_1;
2344 a_2b_2 = at_offset + amol_2b_2;
2345 }
2346 if (rmol_mb > *r_mb)
2347 {
2348 *r_mb = rmol_mb;
2349 ftmb = ftmmb;
2350 a_mb_1 = at_offset + amol_mb_1;
2351 a_mb_2 = at_offset + amol_mb_2;
2352 }
2353
2354 cg_offset += molt->cgs.nr;
2355 at_offset += molt->atoms.nr;
2356 }
2357 sfree(cg_cm)save_free("cg_cm", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 2357, (cg_cm));
2358 sfree(xs)save_free("xs", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 2358, (xs));
2359 sfree(at2cg)save_free("at2cg", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 2359, (at2cg));
2360 if (ir->ePBC != epbcNONE)
2361 {
2362 done_graph(&graph);
2363 }
2364 }
2365 }
2366
2367 /* We should have a vsite free routine, but here we can simply free */
2368 sfree(vsite)save_free("vsite", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/domdec_top.c"
, 2368, (vsite));
2369
2370 if (fplog && (ft2b >= 0 || ftmb >= 0))
2371 {
2372 fprintf(fplog,
2373 "Initial maximum inter charge-group distances:\n");
2374 if (ft2b >= 0)
2375 {
2376 fprintf(fplog,
2377 " two-body bonded interactions: %5.3f nm, %s, atoms %d %d\n",
2378 *r_2b, interaction_function[ft2b].longname,
2379 a_2b_1+1, a_2b_2+1);
2380 }
2381 if (ftmb >= 0)
2382 {
2383 fprintf(fplog,
2384 " multi-body bonded interactions: %5.3f nm, %s, atoms %d %d\n",
2385 *r_mb, interaction_function[ftmb].longname,
2386 a_mb_1+1, a_mb_2+1);
2387 }
2388 }
2389}