File: | gromacs/mdlib/domdec_top.c |
Location: | line 1976, column 13 |
Description: | Array access (via field 'a') results in a null pointer dereference |
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 | |||
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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); | |||
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 | } |