File: | gromacs/mdlib/domdec_top.c |
Location: | line 355, column 17 |
Description: | Value stored to 'nral' is never read |
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 | |
66 | typedef struct { |
67 | int *index; /* Index for each atom into il */ |
68 | int *il; /* ftype|type|a0|...|an|ftype|... */ |
69 | } gmx_reverse_ilist_t; |
70 | |
71 | typedef struct { |
72 | int a_start; |
73 | int a_end; |
74 | int natoms_mol; |
75 | int type; |
76 | } gmx_molblock_ind_t; |
77 | |
78 | typedef 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 | |
104 | static 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 */ |
122 | static 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 | |
132 | static 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 | |
144 | static 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 | |
281 | static 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 | |
307 | void 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); |
Value stored to 'nral' is never read | |
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 | |
401 | static 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 | |
438 | static 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 | |
468 | static 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 | |
571 | static 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 | |
610 | static 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 | |
616 | static 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 | |
707 | void 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 | |
791 | static 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 | |
809 | static 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 | |
854 | static 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 | |
891 | static 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 | |
1005 | static 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 | |
1028 | static 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 */ |
1045 | static 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 | */ |
1083 | static 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 | */ |
1177 | static 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 | |
1400 | static 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 | |
1414 | static 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 | |
1553 | static 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 | |
1562 | static 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 | |
1578 | static 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 | |
1603 | static 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 | |
1614 | static 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 | |
1791 | void 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 | |
1797 | void 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, <op->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 | <op->idef, vsite, |
1891 | <op->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 | |
1912 | void 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(<op->idef, mdatoms->chargeA, mdatoms->chargeB); |
1922 | } |
1923 | } |
1924 | |
1925 | gmx_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 | |
1949 | void 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 | |
1968 | static 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++) |
1975 | { |
1976 | if (link->a[k] == cg_gl_j) |
1977 | { |
1978 | bFound = TRUE1; |
1979 | } |
1980 | } |
1981 | if (!bFound) |
1982 | { |
1983 | /* Add this charge group link */ |
1984 | if (link->index[cg_gl+1]+1 > link->nalloc_a) |
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; |
1990 | link->index[cg_gl+1]++; |
1991 | } |
1992 | } |
1993 | |
1994 | static 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 | |
2010 | t_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); |
2035 | |
2036 | link->index[0] = 0; |
2037 | cg_offset = 0; |
2038 | ncgi = 0; |
2039 | for (mb = 0; mb < mtop->nmolblock; mb++) |
2040 | { |
2041 | molb = &mtop->molblock[mb]; |
2042 | if (molb->nmol == 0) |
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++) |
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++) |
2063 | { |
2064 | i = ril.index[a]; |
2065 | while (i < ril.index[a+1]) |
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++) |
2072 | { |
2073 | aj = ril.il[i+j]; |
2074 | if (a2c[aj] != cg) |
2075 | { |
2076 | check_link(link, cg_gl, cg_offset+a2c[aj]); |
2077 | } |
2078 | } |
2079 | i += nral_rt(ftype); |
2080 | } |
2081 | if (rt->bExclRequired) |
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) |
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) |
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 | |
2148 | static 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 | |
2225 | static 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 | |
2267 | static 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 | |
2285 | void 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 | } |