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More const correctness
[gromacs.git] / src / gromacs / mdlib / ns.cpp
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1 /*
2 * This file is part of the GROMACS molecular simulation package.
3 *
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6 * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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36 */
37 #include "gmxpre.h"
38
39 #include "ns.h"
40
41 #include <stdlib.h>
42 #include <string.h>
43
44 #include <cmath>
45
46 #include <algorithm>
47
48 #include "gromacs/domdec/domdec.h"
49 #include "gromacs/domdec/domdec_struct.h"
50 #include "gromacs/gmxlib/network.h"
51 #include "gromacs/gmxlib/nrnb.h"
52 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
53 #include "gromacs/math/functions.h"
54 #include "gromacs/math/utilities.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/math/vecdump.h"
57 #include "gromacs/mdlib/force.h"
58 #include "gromacs/mdlib/nsgrid.h"
59 #include "gromacs/mdlib/qmmm.h"
60 #include "gromacs/mdtypes/commrec.h"
61 #include "gromacs/mdtypes/group.h"
62 #include "gromacs/mdtypes/inputrec.h"
63 #include "gromacs/mdtypes/md_enums.h"
64 #include "gromacs/pbcutil/ishift.h"
65 #include "gromacs/pbcutil/pbc.h"
66 #include "gromacs/topology/mtop_util.h"
67 #include "gromacs/utility/fatalerror.h"
68 #include "gromacs/utility/smalloc.h"
69
70 /*
71 * E X C L U S I O N H A N D L I N G
72 */
73
74 #ifdef DEBUG
75 static void SETEXCL_(t_excl e[], int i, int j)
76 {
77 e[j] = e[j] | (1<<i);
78 }
79 static void RMEXCL_(t_excl e[], int i, int j)
80 {
81 e[j] = e[j] & ~(1<<i);
82 }
83 static gmx_bool ISEXCL_(t_excl e[], int i, int j)
84 {
85 return (gmx_bool)(e[j] & (1<<i));
86 }
87 static gmx_bool NOTEXCL_(t_excl e[], int i, int j)
88 {
89 return !(ISEXCL(e, i, j));
90 }
91 #else
92 #define SETEXCL(e, i, j) (e)[((int) (j))] |= (1<<((int) (i)))
93 #define RMEXCL(e, i, j) (e)[((int) (j))] &= (~(1<<((int) (i))))
94 #define ISEXCL(e, i, j) (gmx_bool) ((e)[((int) (j))] & (1<<((int) (i))))
95 #define NOTEXCL(e, i, j) !(ISEXCL(e, i, j))
96 #endif
97
98 static int
99 round_up_to_simd_width(int length, int simd_width)
100 {
101 int offset;
102
103 offset = (simd_width > 0) ? length % simd_width : 0;
104
105 return (offset == 0) ? length : length-offset+simd_width;
106 }
107 /************************************************
108 *
109 * U T I L I T I E S F O R N S
110 *
111 ************************************************/
112
113 void reallocate_nblist(t_nblist *nl)
114 {
115 if (gmx_debug_at)
116 {
117 fprintf(debug, "reallocating neigborlist (ielec=%d, ivdw=%d, igeometry=%d, type=%d), maxnri=%d\n",
118 nl->ielec, nl->ivdw, nl->igeometry, nl->type, nl->maxnri);
119 }
120 srenew(nl->iinr, nl->maxnri);
121 if (nl->igeometry == GMX_NBLIST_GEOMETRY_CG_CG)
122 {
123 srenew(nl->iinr_end, nl->maxnri);
124 }
125 srenew(nl->gid, nl->maxnri);
126 srenew(nl->shift, nl->maxnri);
127 srenew(nl->jindex, nl->maxnri+1);
128 }
129
130
131 static void init_nblist(FILE *log, t_nblist *nl_sr,
132 int maxsr,
133 int ivdw, int ivdwmod,
134 int ielec, int ielecmod,
135 int igeometry, int type,
136 gmx_bool bElecAndVdwSwitchDiffers)
137 {
138 t_nblist *nl;
139 int homenr;
140
141 {
142 nl = nl_sr;
143 homenr = maxsr;
144
145 if (nl == nullptr)
146 {
147 return;
148 }
149
150
151 /* Set coul/vdw in neighborlist, and for the normal loops we determine
152 * an index of which one to call.
153 */
154 nl->ivdw = ivdw;
155 nl->ivdwmod = ivdwmod;
156 nl->ielec = ielec;
157 nl->ielecmod = ielecmod;
158 nl->type = type;
159 nl->igeometry = igeometry;
160
161 if (nl->type == GMX_NBLIST_INTERACTION_FREE_ENERGY)
162 {
163 nl->igeometry = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
164 }
165
166 /* This will also set the simd_padding_width field */
167 gmx_nonbonded_set_kernel_pointers(log, nl, bElecAndVdwSwitchDiffers);
168
169 /* maxnri is influenced by the number of shifts (maximum is 8)
170 * and the number of energy groups.
171 * If it is not enough, nl memory will be reallocated during the run.
172 * 4 seems to be a reasonable factor, which only causes reallocation
173 * during runs with tiny and many energygroups.
174 */
175 nl->maxnri = homenr*4;
176 nl->maxnrj = 0;
177 nl->nri = -1;
178 nl->nrj = 0;
179 nl->iinr = nullptr;
180 nl->gid = nullptr;
181 nl->shift = nullptr;
182 nl->jindex = nullptr;
183 nl->jjnr = nullptr;
184 nl->excl_fep = nullptr;
185 reallocate_nblist(nl);
186 nl->jindex[0] = 0;
187
188 if (debug)
189 {
190 fprintf(debug, "Initiating neighbourlist (ielec=%d, ivdw=%d, type=%d) for %s interactions,\nwith %d SR atoms.\n",
191 nl->ielec, nl->ivdw, nl->type, gmx_nblist_geometry_names[nl->igeometry], maxsr);
192 }
193 }
194 }
195
196 void init_neighbor_list(FILE *log, t_forcerec *fr, int homenr)
197 {
198 int maxsr, maxsr_wat;
199 int ielec, ivdw, ielecmod, ivdwmod, type;
200 int igeometry_def, igeometry_w, igeometry_ww;
201 int i;
202 gmx_bool bElecAndVdwSwitchDiffers;
203 t_nblists *nbl;
204
205 /* maxsr = homenr-fr->nWatMol*3; */
206 maxsr = homenr;
207
208 if (maxsr < 0)
209 {
210 gmx_fatal(FARGS, "%s, %d: Negative number of short range atoms.\n"
211 "Call your GROMACS dealer for assistance.", __FILE__, __LINE__);
212 }
213 /* This is just for initial allocation, so we do not reallocate
214 * all the nlist arrays many times in a row.
215 * The numbers seem very accurate, but they are uncritical.
216 */
217 maxsr_wat = std::min(fr->nWatMol, (homenr+2)/3);
218
219 /* Determine the values for ielec/ivdw. */
220 ielec = fr->nbkernel_elec_interaction;
221 ivdw = fr->nbkernel_vdw_interaction;
222 ielecmod = fr->nbkernel_elec_modifier;
223 ivdwmod = fr->nbkernel_vdw_modifier;
224 type = GMX_NBLIST_INTERACTION_STANDARD;
225 bElecAndVdwSwitchDiffers = ( (fr->ic->rcoulomb_switch != fr->ic->rvdw_switch) || (fr->ic->rcoulomb != fr->ic->rvdw));
226
227 fr->ns->bCGlist = (getenv("GMX_NBLISTCG") != nullptr);
228 if (!fr->ns->bCGlist)
229 {
230 igeometry_def = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
231 }
232 else
233 {
234 igeometry_def = GMX_NBLIST_GEOMETRY_CG_CG;
235 if (log != nullptr)
236 {
237 fprintf(log, "\nUsing charge-group - charge-group neighbor lists and kernels\n\n");
238 }
239 }
240
241 if (fr->solvent_opt == esolTIP4P)
242 {
243 igeometry_w = GMX_NBLIST_GEOMETRY_WATER4_PARTICLE;
244 igeometry_ww = GMX_NBLIST_GEOMETRY_WATER4_WATER4;
245 }
246 else
247 {
248 igeometry_w = GMX_NBLIST_GEOMETRY_WATER3_PARTICLE;
249 igeometry_ww = GMX_NBLIST_GEOMETRY_WATER3_WATER3;
250 }
251
252 for (i = 0; i < fr->nnblists; i++)
253 {
254 nbl = &(fr->nblists[i]);
255
256 init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ],
257 maxsr, ivdw, ivdwmod, ielec, ielecmod, igeometry_def, type, bElecAndVdwSwitchDiffers);
258 init_nblist(log, &nbl->nlist_sr[eNL_VDW],
259 maxsr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, igeometry_def, type, bElecAndVdwSwitchDiffers);
260 init_nblist(log, &nbl->nlist_sr[eNL_QQ],
261 maxsr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_def, type, bElecAndVdwSwitchDiffers);
262 init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_WATER],
263 maxsr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_w, type, bElecAndVdwSwitchDiffers);
264 init_nblist(log, &nbl->nlist_sr[eNL_QQ_WATER],
265 maxsr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_w, type, bElecAndVdwSwitchDiffers);
266 init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_WATERWATER],
267 maxsr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_ww, type, bElecAndVdwSwitchDiffers);
268 init_nblist(log, &nbl->nlist_sr[eNL_QQ_WATERWATER],
269 maxsr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_ww, type, bElecAndVdwSwitchDiffers);
270
271 /* Did we get the solvent loops so we can use optimized water kernels? */
272 if (nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf == nullptr
273 || nbl->nlist_sr[eNL_QQ_WATER].kernelptr_vf == nullptr
274 || nbl->nlist_sr[eNL_VDWQQ_WATERWATER].kernelptr_vf == nullptr
275 || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == nullptr)
276 {
277 fr->solvent_opt = esolNO;
278 if (log != nullptr)
279 {
280 fprintf(log, "Note: The available nonbonded kernels do not support water optimization - disabling.\n");
281 }
282 }
283
284 if (fr->efep != efepNO)
285 {
286 init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_FREE],
287 maxsr, ivdw, ivdwmod, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
288 init_nblist(log, &nbl->nlist_sr[eNL_VDW_FREE],
289 maxsr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
290 init_nblist(log, &nbl->nlist_sr[eNL_QQ_FREE],
291 maxsr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
292 }
293 }
294 /* QMMM MM list */
295 if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
296 {
297 if (nullptr == fr->QMMMlist)
298 {
299 snew(fr->QMMMlist, 1);
300 }
301 init_nblist(log, fr->QMMMlist,
302 maxsr, 0, 0, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_STANDARD, bElecAndVdwSwitchDiffers);
303 }
304
305 if (log != nullptr)
306 {
307 fprintf(log, "\n");
308 }
309
310 fr->ns->nblist_initialized = TRUE;
311 }
312
313 static void reset_nblist(t_nblist *nl)
314 {
315 nl->nri = -1;
316 nl->nrj = 0;
317 if (nl->jindex)
318 {
319 nl->jindex[0] = 0;
320 }
321 }
322
323 static void reset_neighbor_lists(t_forcerec *fr)
324 {
325 int n, i;
326
327 if (fr->bQMMM)
328 {
329 /* only reset the short-range nblist */
330 reset_nblist(fr->QMMMlist);
331 }
332
333 for (n = 0; n < fr->nnblists; n++)
334 {
335 for (i = 0; i < eNL_NR; i++)
336 {
337 reset_nblist( &(fr->nblists[n].nlist_sr[i]) );
338 }
339 }
340 }
341
342
343
344
345 static inline void new_i_nblist(t_nblist *nlist, int i_atom, int shift, int gid)
346 {
347 int nri = nlist->nri;
348
349 /* Check whether we have to increase the i counter */
350 if ((nri == -1) ||
351 (nlist->iinr[nri] != i_atom) ||
352 (nlist->shift[nri] != shift) ||
353 (nlist->gid[nri] != gid))
354 {
355 /* This is something else. Now see if any entries have
356 * been added in the list of the previous atom.
357 */
358 if ((nri == -1) ||
359 ((nlist->jindex[nri+1] > nlist->jindex[nri]) &&
360 (nlist->gid[nri] != -1)))
361 {
362 /* If so increase the counter */
363 nlist->nri++;
364 nri++;
365 if (nlist->nri >= nlist->maxnri)
366 {
367 nlist->maxnri += over_alloc_large(nlist->nri);
368 reallocate_nblist(nlist);
369 }
370 }
371 /* Set the number of neighbours and the atom number */
372 nlist->jindex[nri+1] = nlist->jindex[nri];
373 nlist->iinr[nri] = i_atom;
374 nlist->gid[nri] = gid;
375 nlist->shift[nri] = shift;
376 }
377 else
378 {
379 /* Adding to previous list. First remove possible previous padding */
380 if (nlist->simd_padding_width > 1)
381 {
382 while (nlist->nrj > 0 && nlist->jjnr[nlist->nrj-1] < 0)
383 {
384 nlist->nrj--;
385 }
386 }
387 }
388 }
389
390 static inline void close_i_nblist(t_nblist *nlist)
391 {
392 int nri = nlist->nri;
393 int len;
394
395 if (nri >= 0)
396 {
397 /* Add elements up to padding. Since we allocate memory in units
398 * of the simd_padding width, we do not have to check for possible
399 * list reallocation here.
400 */
401 while ((nlist->nrj % nlist->simd_padding_width) != 0)
402 {
403 /* Use -4 here, so we can write forces for 4 atoms before real data */
404 nlist->jjnr[nlist->nrj++] = -4;
405 }
406 nlist->jindex[nri+1] = nlist->nrj;
407
408 len = nlist->nrj - nlist->jindex[nri];
409 /* If there are no j-particles we have to reduce the
410 * number of i-particles again, to prevent errors in the
411 * kernel functions.
412 */
413 if ((len == 0) && (nlist->nri > 0))
414 {
415 nlist->nri--;
416 }
417 }
418 }
419
420 static inline void close_nblist(t_nblist *nlist)
421 {
422 /* Only close this nblist when it has been initialized.
423 * Avoid the creation of i-lists with no j-particles.
424 */
425 if (nlist->nrj == 0)
426 {
427 /* Some assembly kernels do not support empty lists,
428 * make sure here that we don't generate any empty lists.
429 * With the current ns code this branch is taken in two cases:
430 * No i-particles at all: nri=-1 here
431 * There are i-particles, but no j-particles; nri=0 here
432 */
433 nlist->nri = 0;
434 }
435 else
436 {
437 /* Close list number nri by incrementing the count */
438 nlist->nri++;
439 }
440 }
441
442 static inline void close_neighbor_lists(t_forcerec *fr, gmx_bool bMakeQMMMnblist)
443 {
444 int n, i;
445
446 if (bMakeQMMMnblist)
447 {
448 close_nblist(fr->QMMMlist);
449 }
450
451 for (n = 0; n < fr->nnblists; n++)
452 {
453 for (i = 0; (i < eNL_NR); i++)
454 {
455 close_nblist(&(fr->nblists[n].nlist_sr[i]));
456 }
457 }
458 }
459
460
461 static inline void add_j_to_nblist(t_nblist *nlist, int j_atom)
462 {
463 int nrj = nlist->nrj;
464
465 if (nlist->nrj >= nlist->maxnrj)
466 {
467 nlist->maxnrj = round_up_to_simd_width(over_alloc_small(nlist->nrj + 1), nlist->simd_padding_width);
468
469 if (gmx_debug_at)
470 {
471 fprintf(debug, "Increasing SR nblist (ielec=%d,ivdw=%d,type=%d,igeometry=%d) j size to %d\n",
472 nlist->ielec, nlist->ivdw, nlist->type, nlist->igeometry, nlist->maxnrj);
473 }
474
475 srenew(nlist->jjnr, nlist->maxnrj);
476 }
477
478 nlist->jjnr[nrj] = j_atom;
479 nlist->nrj++;
480 }
481
482 static inline void add_j_to_nblist_cg(t_nblist *nlist,
483 int j_start, int j_end,
484 t_excl *bexcl, gmx_bool i_is_j)
485 {
486 int nrj = nlist->nrj;
487 int j;
488
489 if (nlist->nrj >= nlist->maxnrj)
490 {
491 nlist->maxnrj = over_alloc_small(nlist->nrj + 1);
492 if (gmx_debug_at)
493 {
494 fprintf(debug, "Increasing SR nblist (ielec=%d,ivdw=%d,type=%d,igeometry=%d) j size to %d\n",
495 nlist->ielec, nlist->ivdw, nlist->type, nlist->igeometry, nlist->maxnrj);
496 }
497
498 srenew(nlist->jjnr, nlist->maxnrj);
499 srenew(nlist->jjnr_end, nlist->maxnrj);
500 srenew(nlist->excl, nlist->maxnrj*MAX_CGCGSIZE);
501 }
502
503 nlist->jjnr[nrj] = j_start;
504 nlist->jjnr_end[nrj] = j_end;
505
506 if (j_end - j_start > MAX_CGCGSIZE)
507 {
508 gmx_fatal(FARGS, "The charge-group - charge-group neighborlist do not support charge groups larger than %d, found a charge group of size %d", MAX_CGCGSIZE, j_end-j_start);
509 }
510
511 /* Set the exclusions */
512 for (j = j_start; j < j_end; j++)
513 {
514 nlist->excl[nrj*MAX_CGCGSIZE + j - j_start] = bexcl[j];
515 }
516 if (i_is_j)
517 {
518 /* Avoid double counting of intra-cg interactions */
519 for (j = 1; j < j_end-j_start; j++)
520 {
521 nlist->excl[nrj*MAX_CGCGSIZE + j] |= (1<<j) - 1;
522 }
523 }
524
525 nlist->nrj++;
526 }
527
528 typedef void
529 put_in_list_t (gmx_bool bHaveVdW[],
530 int ngid,
531 const t_mdatoms *md,
532 int icg,
533 int jgid,
534 int nj,
535 int jjcg[],
536 int index[],
537 t_excl bExcl[],
538 int shift,
539 t_forcerec * fr,
540 gmx_bool bDoVdW,
541 gmx_bool bDoCoul,
542 int solvent_opt);
543
544 static void
545 put_in_list_at(gmx_bool bHaveVdW[],
546 int ngid,
547 const t_mdatoms *md,
548 int icg,
549 int jgid,
550 int nj,
551 int jjcg[],
552 int index[],
553 t_excl bExcl[],
554 int shift,
555 t_forcerec * fr,
556 gmx_bool bDoVdW,
557 gmx_bool bDoCoul,
558 int solvent_opt)
559 {
560 /* The a[] index has been removed,
561 * to put it back in i_atom should be a[i0] and jj should be a[jj].
562 */
563 t_nblist * vdwc;
564 t_nblist * vdw;
565 t_nblist * coul;
566 t_nblist * vdwc_free = nullptr;
567 t_nblist * vdw_free = nullptr;
568 t_nblist * coul_free = nullptr;
569 t_nblist * vdwc_ww = nullptr;
570 t_nblist * coul_ww = nullptr;
571
572 int i, j, jcg, igid, gid, nbl_ind;
573 int jj, jj0, jj1, i_atom;
574 int i0, nicg;
575
576 int *cginfo;
577 int *type, *typeB;
578 real *charge, *chargeB;
579 real qi, qiB;
580 gmx_bool bFreeEnergy, bFree, bFreeJ, bNotEx, *bPert;
581 gmx_bool bDoVdW_i, bDoCoul_i, bDoCoul_i_sol;
582 int iwater, jwater;
583 t_nblist *nlist;
584
585 /* Copy some pointers */
586 cginfo = fr->cginfo;
587 charge = md->chargeA;
588 chargeB = md->chargeB;
589 type = md->typeA;
590 typeB = md->typeB;
591 bPert = md->bPerturbed;
592
593 /* Get atom range */
594 i0 = index[icg];
595 nicg = index[icg+1]-i0;
596
597 /* Get the i charge group info */
598 igid = GET_CGINFO_GID(cginfo[icg]);
599
600 iwater = (solvent_opt != esolNO) ? GET_CGINFO_SOLOPT(cginfo[icg]) : esolNO;
601
602 bFreeEnergy = FALSE;
603 if (md->nPerturbed)
604 {
605 /* Check if any of the particles involved are perturbed.
606 * If not we can do the cheaper normal put_in_list
607 * and use more solvent optimization.
608 */
609 for (i = 0; i < nicg; i++)
610 {
611 bFreeEnergy |= bPert[i0+i];
612 }
613 /* Loop over the j charge groups */
614 for (j = 0; (j < nj && !bFreeEnergy); j++)
615 {
616 jcg = jjcg[j];
617 jj0 = index[jcg];
618 jj1 = index[jcg+1];
619 /* Finally loop over the atoms in the j-charge group */
620 for (jj = jj0; jj < jj1; jj++)
621 {
622 bFreeEnergy |= bPert[jj];
623 }
624 }
625 }
626
627 /* Unpack pointers to neighbourlist structs */
628 if (fr->nnblists == 1)
629 {
630 nbl_ind = 0;
631 }
632 else
633 {
634 nbl_ind = fr->gid2nblists[GID(igid, jgid, ngid)];
635 }
636 nlist = fr->nblists[nbl_ind].nlist_sr;
637
638 if (iwater != esolNO)
639 {
640 vdwc = &nlist[eNL_VDWQQ_WATER];
641 vdw = &nlist[eNL_VDW];
642 coul = &nlist[eNL_QQ_WATER];
643 vdwc_ww = &nlist[eNL_VDWQQ_WATERWATER];
644 coul_ww = &nlist[eNL_QQ_WATERWATER];
645 }
646 else
647 {
648 vdwc = &nlist[eNL_VDWQQ];
649 vdw = &nlist[eNL_VDW];
650 coul = &nlist[eNL_QQ];
651 }
652
653 if (!bFreeEnergy)
654 {
655 if (iwater != esolNO)
656 {
657 /* Loop over the atoms in the i charge group */
658 i_atom = i0;
659 gid = GID(igid, jgid, ngid);
660 /* Create new i_atom for each energy group */
661 if (bDoCoul && bDoVdW)
662 {
663 new_i_nblist(vdwc, i_atom, shift, gid);
664 new_i_nblist(vdwc_ww, i_atom, shift, gid);
665 }
666 if (bDoVdW)
667 {
668 new_i_nblist(vdw, i_atom, shift, gid);
669 }
670 if (bDoCoul)
671 {
672 new_i_nblist(coul, i_atom, shift, gid);
673 new_i_nblist(coul_ww, i_atom, shift, gid);
674 }
675 /* Loop over the j charge groups */
676 for (j = 0; (j < nj); j++)
677 {
678 jcg = jjcg[j];
679
680 if (jcg == icg)
681 {
682 continue;
683 }
684
685 jj0 = index[jcg];
686 jwater = GET_CGINFO_SOLOPT(cginfo[jcg]);
687
688 if (iwater == esolSPC && jwater == esolSPC)
689 {
690 /* Interaction between two SPC molecules */
691 if (!bDoCoul)
692 {
693 /* VdW only - only first atoms in each water interact */
694 add_j_to_nblist(vdw, jj0);
695 }
696 else
697 {
698 /* One entry for the entire water-water interaction */
699 if (!bDoVdW)
700 {
701 add_j_to_nblist(coul_ww, jj0);
702 }
703 else
704 {
705 add_j_to_nblist(vdwc_ww, jj0);
706 }
707 }
708 }
709 else if (iwater == esolTIP4P && jwater == esolTIP4P)
710 {
711 /* Interaction between two TIP4p molecules */
712 if (!bDoCoul)
713 {
714 /* VdW only - only first atoms in each water interact */
715 add_j_to_nblist(vdw, jj0);
716 }
717 else
718 {
719 /* One entry for the entire water-water interaction */
720 if (!bDoVdW)
721 {
722 add_j_to_nblist(coul_ww, jj0);
723 }
724 else
725 {
726 add_j_to_nblist(vdwc_ww, jj0);
727 }
728 }
729 }
730 else
731 {
732 /* j charge group is not water, but i is.
733 * Add entries to the water-other_atom lists; the geometry of the water
734 * molecule doesn't matter - that is taken care of in the nonbonded kernel,
735 * so we don't care if it is SPC or TIP4P...
736 */
737
738 jj1 = index[jcg+1];
739
740 if (!bDoVdW)
741 {
742 for (jj = jj0; (jj < jj1); jj++)
743 {
744 if (charge[jj] != 0)
745 {
746 add_j_to_nblist(coul, jj);
747 }
748 }
749 }
750 else if (!bDoCoul)
751 {
752 for (jj = jj0; (jj < jj1); jj++)
753 {
754 if (bHaveVdW[type[jj]])
755 {
756 add_j_to_nblist(vdw, jj);
757 }
758 }
759 }
760 else
761 {
762 /* _charge_ _groups_ interact with both coulomb and LJ */
763 /* Check which atoms we should add to the lists! */
764 for (jj = jj0; (jj < jj1); jj++)
765 {
766 if (bHaveVdW[type[jj]])
767 {
768 if (charge[jj] != 0)
769 {
770 add_j_to_nblist(vdwc, jj);
771 }
772 else
773 {
774 add_j_to_nblist(vdw, jj);
775 }
776 }
777 else if (charge[jj] != 0)
778 {
779 add_j_to_nblist(coul, jj);
780 }
781 }
782 }
783 }
784 }
785 close_i_nblist(vdw);
786 close_i_nblist(coul);
787 close_i_nblist(vdwc);
788 close_i_nblist(coul_ww);
789 close_i_nblist(vdwc_ww);
790 }
791 else
792 {
793 /* no solvent as i charge group */
794 /* Loop over the atoms in the i charge group */
795 for (i = 0; i < nicg; i++)
796 {
797 i_atom = i0+i;
798 gid = GID(igid, jgid, ngid);
799 qi = charge[i_atom];
800
801 /* Create new i_atom for each energy group */
802 if (bDoVdW && bDoCoul)
803 {
804 new_i_nblist(vdwc, i_atom, shift, gid);
805 }
806 if (bDoVdW)
807 {
808 new_i_nblist(vdw, i_atom, shift, gid);
809 }
810 if (bDoCoul)
811 {
812 new_i_nblist(coul, i_atom, shift, gid);
813 }
814 bDoVdW_i = (bDoVdW && bHaveVdW[type[i_atom]]);
815 bDoCoul_i = (bDoCoul && qi != 0);
816
817 if (bDoVdW_i || bDoCoul_i)
818 {
819 /* Loop over the j charge groups */
820 for (j = 0; (j < nj); j++)
821 {
822 jcg = jjcg[j];
823
824 /* Check for large charge groups */
825 if (jcg == icg)
826 {
827 jj0 = i0 + i + 1;
828 }
829 else
830 {
831 jj0 = index[jcg];
832 }
833
834 jj1 = index[jcg+1];
835 /* Finally loop over the atoms in the j-charge group */
836 for (jj = jj0; jj < jj1; jj++)
837 {
838 bNotEx = NOTEXCL(bExcl, i, jj);
839
840 if (bNotEx)
841 {
842 if (!bDoVdW_i)
843 {
844 if (charge[jj] != 0)
845 {
846 add_j_to_nblist(coul, jj);
847 }
848 }
849 else if (!bDoCoul_i)
850 {
851 if (bHaveVdW[type[jj]])
852 {
853 add_j_to_nblist(vdw, jj);
854 }
855 }
856 else
857 {
858 if (bHaveVdW[type[jj]])
859 {
860 if (charge[jj] != 0)
861 {
862 add_j_to_nblist(vdwc, jj);
863 }
864 else
865 {
866 add_j_to_nblist(vdw, jj);
867 }
868 }
869 else if (charge[jj] != 0)
870 {
871 add_j_to_nblist(coul, jj);
872 }
873 }
874 }
875 }
876 }
877 }
878 close_i_nblist(vdw);
879 close_i_nblist(coul);
880 close_i_nblist(vdwc);
881 }
882 }
883 }
884 else
885 {
886 /* we are doing free energy */
887 vdwc_free = &nlist[eNL_VDWQQ_FREE];
888 vdw_free = &nlist[eNL_VDW_FREE];
889 coul_free = &nlist[eNL_QQ_FREE];
890 /* Loop over the atoms in the i charge group */
891 for (i = 0; i < nicg; i++)
892 {
893 i_atom = i0+i;
894 gid = GID(igid, jgid, ngid);
895 qi = charge[i_atom];
896 qiB = chargeB[i_atom];
897
898 /* Create new i_atom for each energy group */
899 if (bDoVdW && bDoCoul)
900 {
901 new_i_nblist(vdwc, i_atom, shift, gid);
902 }
903 if (bDoVdW)
904 {
905 new_i_nblist(vdw, i_atom, shift, gid);
906 }
907 if (bDoCoul)
908 {
909 new_i_nblist(coul, i_atom, shift, gid);
910 }
911
912 new_i_nblist(vdw_free, i_atom, shift, gid);
913 new_i_nblist(coul_free, i_atom, shift, gid);
914 new_i_nblist(vdwc_free, i_atom, shift, gid);
915
916 bDoVdW_i = (bDoVdW &&
917 (bHaveVdW[type[i_atom]] || bHaveVdW[typeB[i_atom]]));
918 bDoCoul_i = (bDoCoul && (qi != 0 || qiB != 0));
919 /* For TIP4P the first atom does not have a charge,
920 * but the last three do. So we should still put an atom
921 * without LJ but with charge in the water-atom neighborlist
922 * for a TIP4p i charge group.
923 * For SPC type water the first atom has LJ and charge,
924 * so there is no such problem.
925 */
926 if (iwater == esolNO)
927 {
928 bDoCoul_i_sol = bDoCoul_i;
929 }
930 else
931 {
932 bDoCoul_i_sol = bDoCoul;
933 }
934
935 if (bDoVdW_i || bDoCoul_i_sol)
936 {
937 /* Loop over the j charge groups */
938 for (j = 0; (j < nj); j++)
939 {
940 jcg = jjcg[j];
941
942 /* Check for large charge groups */
943 if (jcg == icg)
944 {
945 jj0 = i0 + i + 1;
946 }
947 else
948 {
949 jj0 = index[jcg];
950 }
951
952 jj1 = index[jcg+1];
953 /* Finally loop over the atoms in the j-charge group */
954 bFree = bPert[i_atom];
955 for (jj = jj0; (jj < jj1); jj++)
956 {
957 bFreeJ = bFree || bPert[jj];
958 /* Complicated if, because the water H's should also
959 * see perturbed j-particles
960 */
961 if (iwater == esolNO || i == 0 || bFreeJ)
962 {
963 bNotEx = NOTEXCL(bExcl, i, jj);
964
965 if (bNotEx)
966 {
967 if (bFreeJ)
968 {
969 if (!bDoVdW_i)
970 {
971 if (charge[jj] != 0 || chargeB[jj] != 0)
972 {
973 add_j_to_nblist(coul_free, jj);
974 }
975 }
976 else if (!bDoCoul_i)
977 {
978 if (bHaveVdW[type[jj]] || bHaveVdW[typeB[jj]])
979 {
980 add_j_to_nblist(vdw_free, jj);
981 }
982 }
983 else
984 {
985 if (bHaveVdW[type[jj]] || bHaveVdW[typeB[jj]])
986 {
987 if (charge[jj] != 0 || chargeB[jj] != 0)
988 {
989 add_j_to_nblist(vdwc_free, jj);
990 }
991 else
992 {
993 add_j_to_nblist(vdw_free, jj);
994 }
995 }
996 else if (charge[jj] != 0 || chargeB[jj] != 0)
997 {
998 add_j_to_nblist(coul_free, jj);
999 }
1000 }
1001 }
1002 else if (!bDoVdW_i)
1003 {
1004 /* This is done whether or not bWater is set */
1005 if (charge[jj] != 0)
1006 {
1007 add_j_to_nblist(coul, jj);
1008 }
1009 }
1010 else if (!bDoCoul_i_sol)
1011 {
1012 if (bHaveVdW[type[jj]])
1013 {
1014 add_j_to_nblist(vdw, jj);
1015 }
1016 }
1017 else
1018 {
1019 if (bHaveVdW[type[jj]])
1020 {
1021 if (charge[jj] != 0)
1022 {
1023 add_j_to_nblist(vdwc, jj);
1024 }
1025 else
1026 {
1027 add_j_to_nblist(vdw, jj);
1028 }
1029 }
1030 else if (charge[jj] != 0)
1031 {
1032 add_j_to_nblist(coul, jj);
1033 }
1034 }
1035 }
1036 }
1037 }
1038 }
1039 }
1040 close_i_nblist(vdw);
1041 close_i_nblist(coul);
1042 close_i_nblist(vdwc);
1043 close_i_nblist(vdw_free);
1044 close_i_nblist(coul_free);
1045 close_i_nblist(vdwc_free);
1046 }
1047 }
1048 }
1049
1050 static void
1051 put_in_list_qmmm(gmx_bool gmx_unused bHaveVdW[],
1052 int ngid,
1053 const t_mdatoms * /* md */,
1054 int icg,
1055 int jgid,
1056 int nj,
1057 int jjcg[],
1058 int index[],
1059 t_excl bExcl[],
1060 int shift,
1061 t_forcerec * fr,
1062 gmx_bool gmx_unused bDoVdW,
1063 gmx_bool gmx_unused bDoCoul,
1064 int gmx_unused solvent_opt)
1065 {
1066 t_nblist * coul;
1067 int i, j, jcg, igid, gid;
1068 int jj, jj0, jj1, i_atom;
1069 int i0, nicg;
1070 gmx_bool bNotEx;
1071
1072 /* Get atom range */
1073 i0 = index[icg];
1074 nicg = index[icg+1]-i0;
1075
1076 /* Get the i charge group info */
1077 igid = GET_CGINFO_GID(fr->cginfo[icg]);
1078
1079 coul = fr->QMMMlist;
1080
1081 /* Loop over atoms in the ith charge group */
1082 for (i = 0; i < nicg; i++)
1083 {
1084 i_atom = i0+i;
1085 gid = GID(igid, jgid, ngid);
1086 /* Create new i_atom for each energy group */
1087 new_i_nblist(coul, i_atom, shift, gid);
1088
1089 /* Loop over the j charge groups */
1090 for (j = 0; j < nj; j++)
1091 {
1092 jcg = jjcg[j];
1093
1094 /* Charge groups cannot have QM and MM atoms simultaneously */
1095 if (jcg != icg)
1096 {
1097 jj0 = index[jcg];
1098 jj1 = index[jcg+1];
1099 /* Finally loop over the atoms in the j-charge group */
1100 for (jj = jj0; jj < jj1; jj++)
1101 {
1102 bNotEx = NOTEXCL(bExcl, i, jj);
1103 if (bNotEx)
1104 {
1105 add_j_to_nblist(coul, jj);
1106 }
1107 }
1108 }
1109 }
1110 close_i_nblist(coul);
1111 }
1112 }
1113
1114 static void
1115 put_in_list_cg(gmx_bool gmx_unused bHaveVdW[],
1116 int ngid,
1117 const t_mdatoms * /* md */,
1118 int icg,
1119 int jgid,
1120 int nj,
1121 int jjcg[],
1122 int index[],
1123 t_excl bExcl[],
1124 int shift,
1125 t_forcerec * fr,
1126 gmx_bool gmx_unused bDoVdW,
1127 gmx_bool gmx_unused bDoCoul,
1128 int gmx_unused solvent_opt)
1129 {
1130 int cginfo;
1131 int igid, gid, nbl_ind;
1132 t_nblist * vdwc;
1133 int j, jcg;
1134
1135 cginfo = fr->cginfo[icg];
1136
1137 igid = GET_CGINFO_GID(cginfo);
1138 gid = GID(igid, jgid, ngid);
1139
1140 /* Unpack pointers to neighbourlist structs */
1141 if (fr->nnblists == 1)
1142 {
1143 nbl_ind = 0;
1144 }
1145 else
1146 {
1147 nbl_ind = fr->gid2nblists[gid];
1148 }
1149 vdwc = &fr->nblists[nbl_ind].nlist_sr[eNL_VDWQQ];
1150
1151 /* Make a new neighbor list for charge group icg.
1152 * Currently simply one neighbor list is made with LJ and Coulomb.
1153 * If required, zero interactions could be removed here
1154 * or in the force loop.
1155 */
1156 new_i_nblist(vdwc, index[icg], shift, gid);
1157 vdwc->iinr_end[vdwc->nri] = index[icg+1];
1158
1159 for (j = 0; (j < nj); j++)
1160 {
1161 jcg = jjcg[j];
1162 /* Skip the icg-icg pairs if all self interactions are excluded */
1163 if (!(jcg == icg && GET_CGINFO_EXCL_INTRA(cginfo)))
1164 {
1165 /* Here we add the j charge group jcg to the list,
1166 * exclusions are also added to the list.
1167 */
1168 add_j_to_nblist_cg(vdwc, index[jcg], index[jcg+1], bExcl, icg == jcg);
1169 }
1170 }
1171
1172 close_i_nblist(vdwc);
1173 }
1174
1175 static void setexcl(int start, int end, t_blocka *excl, gmx_bool b,
1176 t_excl bexcl[])
1177 {
1178 int i, k;
1179
1180 if (b)
1181 {
1182 for (i = start; i < end; i++)
1183 {
1184 for (k = excl->index[i]; k < excl->index[i+1]; k++)
1185 {
1186 SETEXCL(bexcl, i-start, excl->a[k]);
1187 }
1188 }
1189 }
1190 else
1191 {
1192 for (i = start; i < end; i++)
1193 {
1194 for (k = excl->index[i]; k < excl->index[i+1]; k++)
1195 {
1196 RMEXCL(bexcl, i-start, excl->a[k]);
1197 }
1198 }
1199 }
1200 }
1201
1202 int calc_naaj(int icg, int cgtot)
1203 {
1204 int naaj;
1205
1206 if ((cgtot % 2) == 1)
1207 {
1208 /* Odd number of charge groups, easy */
1209 naaj = 1 + (cgtot/2);
1210 }
1211 else if ((cgtot % 4) == 0)
1212 {
1213 /* Multiple of four is hard */
1214 if (icg < cgtot/2)
1215 {
1216 if ((icg % 2) == 0)
1217 {
1218 naaj = 1+(cgtot/2);
1219 }
1220 else
1221 {
1222 naaj = cgtot/2;
1223 }
1224 }
1225 else
1226 {
1227 if ((icg % 2) == 1)
1228 {
1229 naaj = 1+(cgtot/2);
1230 }
1231 else
1232 {
1233 naaj = cgtot/2;
1234 }
1235 }
1236 }
1237 else
1238 {
1239 /* cgtot/2 = odd */
1240 if ((icg % 2) == 0)
1241 {
1242 naaj = 1+(cgtot/2);
1243 }
1244 else
1245 {
1246 naaj = cgtot/2;
1247 }
1248 }
1249 #ifdef DEBUG
1250 fprintf(log, "naaj=%d\n", naaj);
1251 #endif
1252
1253 return naaj;
1254 }
1255
1256 /************************************************
1257 *
1258 * S I M P L E C O R E S T U F F
1259 *
1260 ************************************************/
1261
1262 static real calc_image_tric(rvec xi, rvec xj, matrix box,
1263 rvec b_inv, int *shift)
1264 {
1265 /* This code assumes that the cut-off is smaller than
1266 * a half times the smallest diagonal element of the box.
1267 */
1268 const real h25 = 2.5;
1269 real dx, dy, dz;
1270 real r2;
1271 int tx, ty, tz;
1272
1273 /* Compute diff vector */
1274 dz = xj[ZZ] - xi[ZZ];
1275 dy = xj[YY] - xi[YY];
1276 dx = xj[XX] - xi[XX];
1277
1278 /* Perform NINT operation, using trunc operation, therefore
1279 * we first add 2.5 then subtract 2 again
1280 */
1281 tz = static_cast<int>(dz*b_inv[ZZ] + h25);
1282 tz -= 2;
1283 dz -= tz*box[ZZ][ZZ];
1284 dy -= tz*box[ZZ][YY];
1285 dx -= tz*box[ZZ][XX];
1286
1287 ty = static_cast<int>(dy*b_inv[YY] + h25);
1288 ty -= 2;
1289 dy -= ty*box[YY][YY];
1290 dx -= ty*box[YY][XX];
1291
1292 tx = static_cast<int>(dx*b_inv[XX]+h25);
1293 tx -= 2;
1294 dx -= tx*box[XX][XX];
1295
1296 /* Distance squared */
1297 r2 = (dx*dx) + (dy*dy) + (dz*dz);
1298
1299 *shift = XYZ2IS(tx, ty, tz);
1300
1301 return r2;
1302 }
1303
1304 static real calc_image_rect(rvec xi, rvec xj, rvec box_size,
1305 rvec b_inv, int *shift)
1306 {
1307 const real h15 = 1.5;
1308 real ddx, ddy, ddz;
1309 real dx, dy, dz;
1310 real r2;
1311 int tx, ty, tz;
1312
1313 /* Compute diff vector */
1314 dx = xj[XX] - xi[XX];
1315 dy = xj[YY] - xi[YY];
1316 dz = xj[ZZ] - xi[ZZ];
1317
1318 /* Perform NINT operation, using trunc operation, therefore
1319 * we first add 1.5 then subtract 1 again
1320 */
1321 tx = static_cast<int>(dx*b_inv[XX] + h15);
1322 ty = static_cast<int>(dy*b_inv[YY] + h15);
1323 tz = static_cast<int>(dz*b_inv[ZZ] + h15);
1324 tx--;
1325 ty--;
1326 tz--;
1327
1328 /* Correct diff vector for translation */
1329 ddx = tx*box_size[XX] - dx;
1330 ddy = ty*box_size[YY] - dy;
1331 ddz = tz*box_size[ZZ] - dz;
1332
1333 /* Distance squared */
1334 r2 = (ddx*ddx) + (ddy*ddy) + (ddz*ddz);
1335
1336 *shift = XYZ2IS(tx, ty, tz);
1337
1338 return r2;
1339 }
1340
1341 static void add_simple(t_ns_buf * nsbuf,
1342 int nrj,
1343 int cg_j,
1344 gmx_bool bHaveVdW[],
1345 int ngid,
1346 const t_mdatoms *md,
1347 int icg,
1348 int jgid,
1349 t_block *cgs,
1350 t_excl bexcl[],
1351 int shift,
1352 t_forcerec *fr,
1353 put_in_list_t *put_in_list)
1354 {
1355 if (nsbuf->nj + nrj > MAX_CG)
1356 {
1357 put_in_list(bHaveVdW, ngid, md, icg, jgid, nsbuf->ncg, nsbuf->jcg,
1358 cgs->index, bexcl, shift, fr, TRUE, TRUE, fr->solvent_opt);
1359 /* Reset buffer contents */
1360 nsbuf->ncg = nsbuf->nj = 0;
1361 }
1362 nsbuf->jcg[nsbuf->ncg++] = cg_j;
1363 nsbuf->nj += nrj;
1364 }
1365
1366 static void ns_inner_tric(rvec x[],
1367 int icg,
1368 int *i_egp_flags,
1369 int njcg,
1370 int jcg[],
1371 matrix box,
1372 rvec b_inv,
1373 real rcut2,
1374 t_block *cgs,
1375 t_ns_buf **ns_buf,
1376 gmx_bool bHaveVdW[],
1377 int ngid,
1378 const t_mdatoms *md,
1379 t_excl bexcl[],
1380 t_forcerec *fr,
1381 put_in_list_t *put_in_list)
1382 {
1383 int shift;
1384 int j, nrj, jgid;
1385 int *cginfo = fr->cginfo;
1386 int cg_j, *cgindex;
1387
1388 cgindex = cgs->index;
1389 shift = CENTRAL;
1390 for (j = 0; (j < njcg); j++)
1391 {
1392 cg_j = jcg[j];
1393 nrj = cgindex[cg_j+1]-cgindex[cg_j];
1394 if (calc_image_tric(x[icg], x[cg_j], box, b_inv, &shift) < rcut2)
1395 {
1396 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1397 if (!(i_egp_flags[jgid] & EGP_EXCL))
1398 {
1399 add_simple(&ns_buf[jgid][shift], nrj, cg_j,
1400 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, shift, fr,
1401 put_in_list);
1402 }
1403 }
1404 }
1405 }
1406
1407 static void ns_inner_rect(rvec x[],
1408 int icg,
1409 int *i_egp_flags,
1410 int njcg,
1411 int jcg[],
1412 gmx_bool bBox,
1413 rvec box_size,
1414 rvec b_inv,
1415 real rcut2,
1416 t_block *cgs,
1417 t_ns_buf **ns_buf,
1418 gmx_bool bHaveVdW[],
1419 int ngid,
1420 const t_mdatoms *md,
1421 t_excl bexcl[],
1422 t_forcerec *fr,
1423 put_in_list_t *put_in_list)
1424 {
1425 int shift;
1426 int j, nrj, jgid;
1427 int *cginfo = fr->cginfo;
1428 int cg_j, *cgindex;
1429
1430 cgindex = cgs->index;
1431 if (bBox)
1432 {
1433 shift = CENTRAL;
1434 for (j = 0; (j < njcg); j++)
1435 {
1436 cg_j = jcg[j];
1437 nrj = cgindex[cg_j+1]-cgindex[cg_j];
1438 if (calc_image_rect(x[icg], x[cg_j], box_size, b_inv, &shift) < rcut2)
1439 {
1440 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1441 if (!(i_egp_flags[jgid] & EGP_EXCL))
1442 {
1443 add_simple(&ns_buf[jgid][shift], nrj, cg_j,
1444 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, shift, fr,
1445 put_in_list);
1446 }
1447 }
1448 }
1449 }
1450 else
1451 {
1452 for (j = 0; (j < njcg); j++)
1453 {
1454 cg_j = jcg[j];
1455 nrj = cgindex[cg_j+1]-cgindex[cg_j];
1456 if ((rcut2 == 0) || (distance2(x[icg], x[cg_j]) < rcut2))
1457 {
1458 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1459 if (!(i_egp_flags[jgid] & EGP_EXCL))
1460 {
1461 add_simple(&ns_buf[jgid][CENTRAL], nrj, cg_j,
1462 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, CENTRAL, fr,
1463 put_in_list);
1464 }
1465 }
1466 }
1467 }
1468 }
1469
1470 /* ns_simple_core needs to be adapted for QMMM still 2005 */
1471
1472 static int ns_simple_core(t_forcerec *fr,
1473 gmx_localtop_t *top,
1474 const t_mdatoms *md,
1475 matrix box,
1476 rvec box_size,
1477 t_excl bexcl[],
1478 int *aaj,
1479 int ngid,
1480 t_ns_buf **ns_buf,
1481 put_in_list_t *put_in_list,
1482 gmx_bool bHaveVdW[])
1483 {
1484 int naaj, k;
1485 real rlist2;
1486 int nsearch, icg, igid, nn;
1487 int *cginfo;
1488 t_ns_buf *nsbuf;
1489 /* int *i_atoms; */
1490 t_block *cgs = &(top->cgs);
1491 t_blocka *excl = &(top->excls);
1492 rvec b_inv;
1493 int m;
1494 gmx_bool bBox, bTriclinic;
1495 int *i_egp_flags;
1496
1497 rlist2 = gmx::square(fr->rlist);
1498
1499 bBox = (fr->ePBC != epbcNONE);
1500 if (bBox)
1501 {
1502 for (m = 0; (m < DIM); m++)
1503 {
1504 if (gmx_numzero(box_size[m]))
1505 {
1506 gmx_fatal(FARGS, "Dividing by zero box size!");
1507 }
1508 b_inv[m] = 1.0/box_size[m];
1509 }
1510 bTriclinic = TRICLINIC(box);
1511 }
1512 else
1513 {
1514 bTriclinic = FALSE;
1515 }
1516
1517 cginfo = fr->cginfo;
1518
1519 nsearch = 0;
1520 for (icg = fr->cg0; (icg < fr->hcg); icg++)
1521 {
1522 /*
1523 i0 = cgs->index[icg];
1524 nri = cgs->index[icg+1]-i0;
1525 i_atoms = &(cgs->a[i0]);
1526 i_eg_excl = fr->eg_excl + ngid*md->cENER[*i_atoms];
1527 setexcl(nri,i_atoms,excl,TRUE,bexcl);
1528 */
1529 igid = GET_CGINFO_GID(cginfo[icg]);
1530 i_egp_flags = fr->egp_flags + ngid*igid;
1531 setexcl(cgs->index[icg], cgs->index[icg+1], excl, TRUE, bexcl);
1532
1533 naaj = calc_naaj(icg, cgs->nr);
1534 if (bTriclinic)
1535 {
1536 ns_inner_tric(fr->cg_cm, icg, i_egp_flags, naaj, &(aaj[icg]),
1537 box, b_inv, rlist2, cgs, ns_buf,
1538 bHaveVdW, ngid, md, bexcl, fr, put_in_list);
1539 }
1540 else
1541 {
1542 ns_inner_rect(fr->cg_cm, icg, i_egp_flags, naaj, &(aaj[icg]),
1543 bBox, box_size, b_inv, rlist2, cgs, ns_buf,
1544 bHaveVdW, ngid, md, bexcl, fr, put_in_list);
1545 }
1546 nsearch += naaj;
1547
1548 for (nn = 0; (nn < ngid); nn++)
1549 {
1550 for (k = 0; (k < SHIFTS); k++)
1551 {
1552 nsbuf = &(ns_buf[nn][k]);
1553 if (nsbuf->ncg > 0)
1554 {
1555 put_in_list(bHaveVdW, ngid, md, icg, nn, nsbuf->ncg, nsbuf->jcg,
1556 cgs->index, bexcl, k, fr, TRUE, TRUE, fr->solvent_opt);
1557 nsbuf->ncg = nsbuf->nj = 0;
1558 }
1559 }
1560 }
1561 /* setexcl(nri,i_atoms,excl,FALSE,bexcl); */
1562 setexcl(cgs->index[icg], cgs->index[icg+1], excl, FALSE, bexcl);
1563 }
1564 close_neighbor_lists(fr, FALSE);
1565
1566 return nsearch;
1567 }
1568
1569 /************************************************
1570 *
1571 * N S 5 G R I D S T U F F
1572 *
1573 ************************************************/
1574
1575 static inline void get_dx_dd(int Nx, real gridx, real rc2, int xgi, real x,
1576 int ncpddc, int shift_min, int shift_max,
1577 int *g0, int *g1, real *dcx2)
1578 {
1579 real dcx, tmp;
1580 int g_min, g_max, shift_home;
1581
1582 if (xgi < 0)
1583 {
1584 g_min = 0;
1585 g_max = Nx - 1;
1586 *g0 = 0;
1587 *g1 = -1;
1588 }
1589 else if (xgi >= Nx)
1590 {
1591 g_min = 0;
1592 g_max = Nx - 1;
1593 *g0 = Nx;
1594 *g1 = Nx - 1;
1595 }
1596 else
1597 {
1598 if (ncpddc == 0)
1599 {
1600 g_min = 0;
1601 g_max = Nx - 1;
1602 }
1603 else
1604 {
1605 if (xgi < ncpddc)
1606 {
1607 shift_home = 0;
1608 }
1609 else
1610 {
1611 shift_home = -1;
1612 }
1613 g_min = (shift_min == shift_home ? 0 : ncpddc);
1614 g_max = (shift_max == shift_home ? ncpddc - 1 : Nx - 1);
1615 }
1616 if (shift_min > 0)
1617 {
1618 *g0 = g_min;
1619 *g1 = g_min - 1;
1620 }
1621 else if (shift_max < 0)
1622 {
1623 *g0 = g_max + 1;
1624 *g1 = g_max;
1625 }
1626 else
1627 {
1628 *g0 = xgi;
1629 *g1 = xgi;
1630 dcx2[xgi] = 0;
1631 }
1632 }
1633
1634 while (*g0 > g_min)
1635 {
1636 /* Check one grid cell down */
1637 dcx = ((*g0 - 1) + 1)*gridx - x;
1638 tmp = dcx*dcx;
1639 if (tmp >= rc2)
1640 {
1641 break;
1642 }
1643 (*g0)--;
1644 dcx2[*g0] = tmp;
1645 }
1646
1647 while (*g1 < g_max)
1648 {
1649 /* Check one grid cell up */
1650 dcx = (*g1 + 1)*gridx - x;
1651 tmp = dcx*dcx;
1652 if (tmp >= rc2)
1653 {
1654 break;
1655 }
1656 (*g1)++;
1657 dcx2[*g1] = tmp;
1658 }
1659 }
1660
1661
1662 #define calc_dx2(XI, YI, ZI, y) (gmx::square(XI-y[XX]) + gmx::square(YI-y[YY]) + gmx::square(ZI-y[ZZ]))
1663 #define calc_cyl_dx2(XI, YI, y) (gmx::square(XI-y[XX]) + gmx::square(YI-y[YY]))
1664 /****************************************************
1665 *
1666 * F A S T N E I G H B O R S E A R C H I N G
1667 *
1668 * Optimized neighboursearching routine using grid
1669 * at least 1x1x1, see GROMACS manual
1670 *
1671 ****************************************************/
1672
1673
1674 static void get_cutoff2(t_forcerec *fr, real *rs2)
1675 {
1676 *rs2 = gmx::square(fr->rlist);
1677 }
1678
1679 static void init_nsgrid_lists(t_forcerec *fr, int ngid, gmx_ns_t *ns)
1680 {
1681 real rs2;
1682 int j;
1683
1684 get_cutoff2(fr, &rs2);
1685
1686 /* Short range buffers */
1687 snew(ns->nl_sr, ngid);
1688 /* Counters */
1689 snew(ns->nsr, ngid);
1690
1691 for (j = 0; (j < ngid); j++)
1692 {
1693 snew(ns->nl_sr[j], MAX_CG);
1694 }
1695 if (debug)
1696 {
1697 fprintf(debug,
1698 "ns5_core: rs2 = %g (nm^2)\n",
1699 rs2);
1700 }
1701 }
1702
1703 static int nsgrid_core(const t_commrec *cr,
1704 t_forcerec *fr,
1705 matrix box,
1706 int ngid,
1707 gmx_localtop_t *top,
1708 t_grid *grid,
1709 t_excl bexcl[],
1710 gmx_bool *bExcludeAlleg,
1711 const t_mdatoms *md,
1712 put_in_list_t *put_in_list,
1713 gmx_bool bHaveVdW[],
1714 gmx_bool bMakeQMMMnblist)
1715 {
1716 gmx_ns_t *ns;
1717 int **nl_sr;
1718 int *nsr;
1719 gmx_domdec_t *dd;
1720 const t_block *cgs = &(top->cgs);
1721 int *cginfo = fr->cginfo;
1722 /* int *i_atoms,*cgsindex=cgs->index; */
1723 ivec sh0, sh1, shp;
1724 int cell_x, cell_y, cell_z;
1725 int d, tx, ty, tz, dx, dy, dz, cj;
1726 #ifdef ALLOW_OFFDIAG_LT_HALFDIAG
1727 int zsh_ty, zsh_tx, ysh_tx;
1728 #endif
1729 int dx0, dx1, dy0, dy1, dz0, dz1;
1730 int Nx, Ny, Nz, shift = -1, j, nrj, nns, nn = -1;
1731 real gridx, gridy, gridz, grid_x, grid_y;
1732 real *dcx2, *dcy2, *dcz2;
1733 int zgi, ygi, xgi;
1734 int cg0, cg1, icg = -1, cgsnr, i0, igid, naaj, max_jcg;
1735 int jcg0, jcg1, jjcg, cgj0, jgid;
1736 int *grida, *gridnra, *gridind;
1737 rvec *cgcm, grid_offset;
1738 real r2, rs2, XI, YI, ZI, tmp1, tmp2;
1739 int *i_egp_flags;
1740 gmx_bool bDomDec, bTriclinicX, bTriclinicY;
1741 ivec ncpddc;
1742
1743 ns = fr->ns;
1744
1745 bDomDec = DOMAINDECOMP(cr);
1746 dd = cr->dd;
1747
1748 bTriclinicX = ((YY < grid->npbcdim &&
1749 (!bDomDec || dd->nc[YY] == 1) && box[YY][XX] != 0) ||
1750 (ZZ < grid->npbcdim &&
1751 (!bDomDec || dd->nc[ZZ] == 1) && box[ZZ][XX] != 0));
1752 bTriclinicY = (ZZ < grid->npbcdim &&
1753 (!bDomDec || dd->nc[ZZ] == 1) && box[ZZ][YY] != 0);
1754
1755 cgsnr = cgs->nr;
1756
1757 get_cutoff2(fr, &rs2);
1758
1759 nl_sr = ns->nl_sr;
1760 nsr = ns->nsr;
1761
1762 /* Unpack arrays */
1763 cgcm = fr->cg_cm;
1764 Nx = grid->n[XX];
1765 Ny = grid->n[YY];
1766 Nz = grid->n[ZZ];
1767 grida = grid->a;
1768 gridind = grid->index;
1769 gridnra = grid->nra;
1770 nns = 0;
1771
1772 gridx = grid->cell_size[XX];
1773 gridy = grid->cell_size[YY];
1774 gridz = grid->cell_size[ZZ];
1775 grid_x = 1/gridx;
1776 grid_y = 1/gridy;
1777 copy_rvec(grid->cell_offset, grid_offset);
1778 copy_ivec(grid->ncpddc, ncpddc);
1779 dcx2 = grid->dcx2;
1780 dcy2 = grid->dcy2;
1781 dcz2 = grid->dcz2;
1782
1783 #ifdef ALLOW_OFFDIAG_LT_HALFDIAG
1784 zsh_ty = floor(-box[ZZ][YY]/box[YY][YY]+0.5);
1785 zsh_tx = floor(-box[ZZ][XX]/box[XX][XX]+0.5);
1786 ysh_tx = floor(-box[YY][XX]/box[XX][XX]+0.5);
1787 if (zsh_tx != 0 && ysh_tx != 0)
1788 {
1789 /* This could happen due to rounding, when both ratios are 0.5 */
1790 ysh_tx = 0;
1791 }
1792 #endif
1793
1794 if (fr->n_tpi)
1795 {
1796 /* We only want a list for the test particle */
1797 cg0 = cgsnr - 1;
1798 }
1799 else
1800 {
1801 cg0 = grid->icg0;
1802 }
1803 cg1 = grid->icg1;
1804
1805 /* Set the shift range */
1806 for (d = 0; d < DIM; d++)
1807 {
1808 sh0[d] = -1;
1809 sh1[d] = 1;
1810 /* Check if we need periodicity shifts.
1811 * Without PBC or with domain decomposition we don't need them.
1812 */
1813 if (d >= ePBC2npbcdim(fr->ePBC) || (bDomDec && dd->nc[d] > 1))
1814 {
1815 shp[d] = 0;
1816 }
1817 else
1818 {
1819 if (d == XX &&
1820 box[XX][XX] - std::abs(box[YY][XX]) - std::abs(box[ZZ][XX]) < std::sqrt(rs2))
1821 {
1822 shp[d] = 2;
1823 }
1824 else
1825 {
1826 shp[d] = 1;
1827 }
1828 }
1829 }
1830
1831 /* Loop over charge groups */
1832 for (icg = cg0; (icg < cg1); icg++)
1833 {
1834 igid = GET_CGINFO_GID(cginfo[icg]);
1835 /* Skip this charge group if all energy groups are excluded! */
1836 if (bExcludeAlleg[igid])
1837 {
1838 continue;
1839 }
1840
1841 i0 = cgs->index[icg];
1842
1843 if (bMakeQMMMnblist)
1844 {
1845 /* Skip this charge group if it is not a QM atom while making a
1846 * QM/MM neighbourlist
1847 */
1848 if (md->bQM[i0] == FALSE)
1849 {
1850 continue; /* MM particle, go to next particle */
1851 }
1852
1853 /* Compute the number of charge groups that fall within the control
1854 * of this one (icg)
1855 */
1856 naaj = calc_naaj(icg, cgsnr);
1857 jcg0 = icg;
1858 jcg1 = icg + naaj;
1859 max_jcg = cgsnr;
1860 }
1861 else
1862 {
1863 /* make a normal neighbourlist */
1864
1865 if (bDomDec)
1866 {
1867 /* Get the j charge-group and dd cell shift ranges */
1868 dd_get_ns_ranges(cr->dd, icg, &jcg0, &jcg1, sh0, sh1);
1869 max_jcg = 0;
1870 }
1871 else
1872 {
1873 /* Compute the number of charge groups that fall within the control
1874 * of this one (icg)
1875 */
1876 naaj = calc_naaj(icg, cgsnr);
1877 jcg0 = icg;
1878 jcg1 = icg + naaj;
1879
1880 if (fr->n_tpi)
1881 {
1882 /* The i-particle is awlways the test particle,
1883 * so we want all j-particles
1884 */
1885 max_jcg = cgsnr - 1;
1886 }
1887 else
1888 {
1889 max_jcg = jcg1 - cgsnr;
1890 }
1891 }
1892 }
1893
1894 i_egp_flags = fr->egp_flags + igid*ngid;
1895
1896 /* Set the exclusions for the atoms in charge group icg using a bitmask */
1897 setexcl(i0, cgs->index[icg+1], &top->excls, TRUE, bexcl);
1898
1899 ci2xyz(grid, icg, &cell_x, &cell_y, &cell_z);
1900
1901 /* Changed iicg to icg, DvdS 990115
1902 * (but see consistency check above, DvdS 990330)
1903 */
1904 #ifdef NS5DB
1905 fprintf(log, "icg=%5d, naaj=%5d, cell %d %d %d\n",
1906 icg, naaj, cell_x, cell_y, cell_z);
1907 #endif
1908 /* Loop over shift vectors in three dimensions */
1909 for (tz = -shp[ZZ]; tz <= shp[ZZ]; tz++)
1910 {
1911 ZI = cgcm[icg][ZZ]+tz*box[ZZ][ZZ];
1912 /* Calculate range of cells in Z direction that have the shift tz */
1913 zgi = cell_z + tz*Nz;
1914 get_dx_dd(Nz, gridz, rs2, zgi, ZI-grid_offset[ZZ],
1915 ncpddc[ZZ], sh0[ZZ], sh1[ZZ], &dz0, &dz1, dcz2);
1916 if (dz0 > dz1)
1917 {
1918 continue;
1919 }
1920 for (ty = -shp[YY]; ty <= shp[YY]; ty++)
1921 {
1922 YI = cgcm[icg][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
1923 /* Calculate range of cells in Y direction that have the shift ty */
1924 if (bTriclinicY)
1925 {
1926 ygi = (int)(Ny + (YI - grid_offset[YY])*grid_y) - Ny;
1927 }
1928 else
1929 {
1930 ygi = cell_y + ty*Ny;
1931 }
1932 get_dx_dd(Ny, gridy, rs2, ygi, YI-grid_offset[YY],
1933 ncpddc[YY], sh0[YY], sh1[YY], &dy0, &dy1, dcy2);
1934 if (dy0 > dy1)
1935 {
1936 continue;
1937 }
1938 for (tx = -shp[XX]; tx <= shp[XX]; tx++)
1939 {
1940 XI = cgcm[icg][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
1941 /* Calculate range of cells in X direction that have the shift tx */
1942 if (bTriclinicX)
1943 {
1944 xgi = (int)(Nx + (XI - grid_offset[XX])*grid_x) - Nx;
1945 }
1946 else
1947 {
1948 xgi = cell_x + tx*Nx;
1949 }
1950 get_dx_dd(Nx, gridx, rs2, xgi, XI-grid_offset[XX],
1951 ncpddc[XX], sh0[XX], sh1[XX], &dx0, &dx1, dcx2);
1952 if (dx0 > dx1)
1953 {
1954 continue;
1955 }
1956 /* Get shift vector */
1957 shift = XYZ2IS(tx, ty, tz);
1958 #ifdef NS5DB
1959 range_check(shift, 0, SHIFTS);
1960 #endif
1961 for (nn = 0; (nn < ngid); nn++)
1962 {
1963 nsr[nn] = 0;
1964 }
1965 #ifdef NS5DB
1966 fprintf(log, "shift: %2d, dx0,1: %2d,%2d, dy0,1: %2d,%2d, dz0,1: %2d,%2d\n",
1967 shift, dx0, dx1, dy0, dy1, dz0, dz1);
1968 fprintf(log, "cgcm: %8.3f %8.3f %8.3f\n", cgcm[icg][XX],
1969 cgcm[icg][YY], cgcm[icg][ZZ]);
1970 fprintf(log, "xi: %8.3f %8.3f %8.3f\n", XI, YI, ZI);
1971 #endif
1972 for (dx = dx0; (dx <= dx1); dx++)
1973 {
1974 tmp1 = rs2 - dcx2[dx];
1975 for (dy = dy0; (dy <= dy1); dy++)
1976 {
1977 tmp2 = tmp1 - dcy2[dy];
1978 if (tmp2 > 0)
1979 {
1980 for (dz = dz0; (dz <= dz1); dz++)
1981 {
1982 if (tmp2 > dcz2[dz])
1983 {
1984 /* Find grid-cell cj in which possible neighbours are */
1985 cj = xyz2ci(Ny, Nz, dx, dy, dz);
1986
1987 /* Check out how many cgs (nrj) there in this cell */
1988 nrj = gridnra[cj];
1989
1990 /* Find the offset in the cg list */
1991 cgj0 = gridind[cj];
1992
1993 /* Check if all j's are out of range so we
1994 * can skip the whole cell.
1995 * Should save some time, especially with DD.
1996 */
1997 if (nrj == 0 ||
1998 (grida[cgj0] >= max_jcg &&
1999 (grida[cgj0] >= jcg1 || grida[cgj0+nrj-1] < jcg0)))
2000 {
2001 continue;
2002 }
2003
2004 /* Loop over cgs */
2005 for (j = 0; (j < nrj); j++)
2006 {
2007 jjcg = grida[cgj0+j];
2008
2009 /* check whether this guy is in range! */
2010 if ((jjcg >= jcg0 && jjcg < jcg1) ||
2011 (jjcg < max_jcg))
2012 {
2013 r2 = calc_dx2(XI, YI, ZI, cgcm[jjcg]);
2014 if (r2 < rs2)
2015 {
2016 /* jgid = gid[cgsatoms[cgsindex[jjcg]]]; */
2017 jgid = GET_CGINFO_GID(cginfo[jjcg]);
2018 /* check energy group exclusions */
2019 if (!(i_egp_flags[jgid] & EGP_EXCL))
2020 {
2021 if (nsr[jgid] >= MAX_CG)
2022 {
2023 /* Add to short-range list */
2024 put_in_list(bHaveVdW, ngid, md, icg, jgid,
2025 nsr[jgid], nl_sr[jgid],
2026 cgs->index, /* cgsatoms, */ bexcl,
2027 shift, fr, TRUE, TRUE, fr->solvent_opt);
2028 nsr[jgid] = 0;
2029 }
2030 nl_sr[jgid][nsr[jgid]++] = jjcg;
2031 }
2032 }
2033 nns++;
2034 }
2035 }
2036 }
2037 }
2038 }
2039 }
2040 }
2041 /* CHECK whether there is anything left in the buffers */
2042 for (nn = 0; (nn < ngid); nn++)
2043 {
2044 if (nsr[nn] > 0)
2045 {
2046 put_in_list(bHaveVdW, ngid, md, icg, nn, nsr[nn], nl_sr[nn],
2047 cgs->index, /* cgsatoms, */ bexcl,
2048 shift, fr, TRUE, TRUE, fr->solvent_opt);
2049 }
2050 }
2051 }
2052 }
2053 }
2054 setexcl(cgs->index[icg], cgs->index[icg+1], &top->excls, FALSE, bexcl);
2055 }
2056 /* No need to perform any left-over force calculations anymore (as we used to do here)
2057 * since we now save the proper long-range lists for later evaluation.
2058 */
2059
2060 /* Close neighbourlists */
2061 close_neighbor_lists(fr, bMakeQMMMnblist);
2062
2063 return nns;
2064 }
2065
2066 static void ns_realloc_natoms(gmx_ns_t *ns, int natoms)
2067 {
2068 int i;
2069
2070 if (natoms > ns->nra_alloc)
2071 {
2072 ns->nra_alloc = over_alloc_dd(natoms);
2073 srenew(ns->bexcl, ns->nra_alloc);
2074 for (i = 0; i < ns->nra_alloc; i++)
2075 {
2076 ns->bexcl[i] = 0;
2077 }
2078 }
2079 }
2080
2081 void init_ns(FILE *fplog, const t_commrec *cr,
2082 gmx_ns_t *ns, t_forcerec *fr,
2083 const gmx_mtop_t *mtop)
2084 {
2085 int icg, nr_in_cg, maxcg, i, j, jcg, ngid, ncg;
2086
2087 /* Compute largest charge groups size (# atoms) */
2088 nr_in_cg = 1;
2089 for (const gmx_moltype_t &molt : mtop->moltype)
2090 {
2091 const t_block *cgs = &molt.cgs;
2092 for (icg = 0; (icg < cgs->nr); icg++)
2093 {
2094 nr_in_cg = std::max(nr_in_cg, (int)(cgs->index[icg+1]-cgs->index[icg]));
2095 }
2096 }
2097
2098 /* Verify whether largest charge group is <= max cg.
2099 * This is determined by the type of the local exclusion type
2100 * Exclusions are stored in bits. (If the type is not large
2101 * enough, enlarge it, unsigned char -> unsigned short -> unsigned long)
2102 */
2103 maxcg = sizeof(t_excl)*8;
2104 if (nr_in_cg > maxcg)
2105 {
2106 gmx_fatal(FARGS, "Max #atoms in a charge group: %d > %d\n",
2107 nr_in_cg, maxcg);
2108 }
2109
2110 ngid = mtop->groups.grps[egcENER].nr;
2111 snew(ns->bExcludeAlleg, ngid);
2112 for (i = 0; i < ngid; i++)
2113 {
2114 ns->bExcludeAlleg[i] = TRUE;
2115 for (j = 0; j < ngid; j++)
2116 {
2117 if (!(fr->egp_flags[i*ngid+j] & EGP_EXCL))
2118 {
2119 ns->bExcludeAlleg[i] = FALSE;
2120 }
2121 }
2122 }
2123
2124 if (fr->bGrid)
2125 {
2126 /* Grid search */
2127 ns->grid = init_grid(fplog, fr);
2128 init_nsgrid_lists(fr, ngid, ns);
2129 }
2130 else
2131 {
2132 /* Simple search */
2133 snew(ns->ns_buf, ngid);
2134 for (i = 0; (i < ngid); i++)
2135 {
2136 snew(ns->ns_buf[i], SHIFTS);
2137 }
2138 ncg = ncg_mtop(mtop);
2139 snew(ns->simple_aaj, 2*ncg);
2140 for (jcg = 0; (jcg < ncg); jcg++)
2141 {
2142 ns->simple_aaj[jcg] = jcg;
2143 ns->simple_aaj[jcg+ncg] = jcg;
2144 }
2145 }
2146
2147 /* Create array that determines whether or not atoms have VdW */
2148 snew(ns->bHaveVdW, fr->ntype);
2149 for (i = 0; (i < fr->ntype); i++)
2150 {
2151 for (j = 0; (j < fr->ntype); j++)
2152 {
2153 ns->bHaveVdW[i] = (ns->bHaveVdW[i] ||
2154 (fr->bBHAM ?
2155 ((BHAMA(fr->nbfp, fr->ntype, i, j) != 0) ||
2156 (BHAMB(fr->nbfp, fr->ntype, i, j) != 0) ||
2157 (BHAMC(fr->nbfp, fr->ntype, i, j) != 0)) :
2158 ((C6(fr->nbfp, fr->ntype, i, j) != 0) ||
2159 (C12(fr->nbfp, fr->ntype, i, j) != 0))));
2160 }
2161 }
2162 if (debug)
2163 {
2164 pr_bvec(debug, 0, "bHaveVdW", ns->bHaveVdW, fr->ntype, TRUE);
2165 }
2166
2167 ns->nra_alloc = 0;
2168 ns->bexcl = nullptr;
2169 if (!DOMAINDECOMP(cr))
2170 {
2171 ns_realloc_natoms(ns, mtop->natoms);
2172 }
2173
2174 ns->nblist_initialized = FALSE;
2175
2176 /* nbr list debug dump */
2177 {
2178 char *ptr = getenv("GMX_DUMP_NL");
2179 if (ptr)
2180 {
2181 ns->dump_nl = strtol(ptr, nullptr, 10);
2182 if (fplog)
2183 {
2184 fprintf(fplog, "GMX_DUMP_NL = %d", ns->dump_nl);
2185 }
2186 }
2187 else
2188 {
2189 ns->dump_nl = 0;
2190 }
2191 }
2192 }
2193
2194 void done_ns(gmx_ns_t *ns, int numEnergyGroups)
2195 {
2196 sfree(ns->bExcludeAlleg);
2197 if (ns->ns_buf)
2198 {
2199 for (int i = 0; i < numEnergyGroups; i++)
2200 {
2201 sfree(ns->ns_buf[i]);
2202 }
2203 sfree(ns->ns_buf);
2204 }
2205 sfree(ns->simple_aaj);
2206 sfree(ns->bHaveVdW);
2207 done_grid(ns->grid);
2208 sfree(ns);
2209 }
2210
2211 int search_neighbours(FILE *log,
2212 t_forcerec *fr,
2213 matrix box,
2214 gmx_localtop_t *top,
2215 const gmx_groups_t *groups,
2216 const t_commrec *cr,
2217 t_nrnb *nrnb,
2218 const t_mdatoms *md,
2219 gmx_bool bFillGrid)
2220 {
2221 const t_block *cgs = &(top->cgs);
2222 rvec box_size, grid_x0, grid_x1;
2223 int m, ngid;
2224 real min_size, grid_dens;
2225 int nsearch;
2226 gmx_bool bGrid;
2227 int start, end;
2228 gmx_ns_t *ns;
2229 t_grid *grid;
2230 gmx_domdec_zones_t *dd_zones;
2231 put_in_list_t *put_in_list;
2232
2233 ns = fr->ns;
2234
2235 /* Set some local variables */
2236 bGrid = fr->bGrid;
2237 ngid = groups->grps[egcENER].nr;
2238
2239 for (m = 0; (m < DIM); m++)
2240 {
2241 box_size[m] = box[m][m];
2242 }
2243
2244 if (fr->ePBC != epbcNONE)
2245 {
2246 if (gmx::square(fr->rlist) >= max_cutoff2(fr->ePBC, box))
2247 {
2248 gmx_fatal(FARGS, "One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.");
2249 }
2250 if (!bGrid)
2251 {
2252 min_size = std::min(box_size[XX], std::min(box_size[YY], box_size[ZZ]));
2253 if (2*fr->rlist >= min_size)
2254 {
2255 gmx_fatal(FARGS, "One of the box diagonal elements has become smaller than twice the cut-off length.");
2256 }
2257 }
2258 }
2259
2260 if (DOMAINDECOMP(cr))
2261 {
2262 ns_realloc_natoms(ns, cgs->index[cgs->nr]);
2263 }
2264
2265 /* Reset the neighbourlists */
2266 reset_neighbor_lists(fr);
2267
2268 if (bGrid && bFillGrid)
2269 {
2270
2271 grid = ns->grid;
2272 if (DOMAINDECOMP(cr))
2273 {
2274 dd_zones = domdec_zones(cr->dd);
2275 }
2276 else
2277 {
2278 dd_zones = nullptr;
2279
2280 get_nsgrid_boundaries(grid->nboundeddim, box, nullptr, nullptr, nullptr, nullptr,
2281 cgs->nr, fr->cg_cm, grid_x0, grid_x1, &grid_dens);
2282
2283 grid_first(log, grid, nullptr, nullptr, box, grid_x0, grid_x1,
2284 fr->rlist, grid_dens);
2285 }
2286
2287 start = 0;
2288 end = cgs->nr;
2289
2290 if (DOMAINDECOMP(cr))
2291 {
2292 end = cgs->nr;
2293 fill_grid(dd_zones, grid, end, -1, end, fr->cg_cm);
2294 grid->icg0 = 0;
2295 grid->icg1 = dd_zones->izone[dd_zones->nizone-1].cg1;
2296 }
2297 else
2298 {
2299 fill_grid(nullptr, grid, cgs->nr, fr->cg0, fr->hcg, fr->cg_cm);
2300 grid->icg0 = fr->cg0;
2301 grid->icg1 = fr->hcg;
2302 }
2303
2304 calc_elemnr(grid, start, end, cgs->nr);
2305 calc_ptrs(grid);
2306 grid_last(grid, start, end, cgs->nr);
2307
2308 if (gmx_debug_at)
2309 {
2310 check_grid(grid);
2311 print_grid(debug, grid);
2312 }
2313 }
2314 else if (fr->n_tpi)
2315 {
2316 /* Set the grid cell index for the test particle only.
2317 * The cell to cg index is not corrected, but that does not matter.
2318 */
2319 fill_grid(nullptr, ns->grid, fr->hcg, fr->hcg-1, fr->hcg, fr->cg_cm);
2320 }
2321
2322 if (!fr->ns->bCGlist)
2323 {
2324 put_in_list = put_in_list_at;
2325 }
2326 else
2327 {
2328 put_in_list = put_in_list_cg;
2329 }
2330
2331 /* Do the core! */
2332 if (bGrid)
2333 {
2334 grid = ns->grid;
2335 nsearch = nsgrid_core(cr, fr, box, ngid, top,
2336 grid, ns->bexcl, ns->bExcludeAlleg,
2337 md, put_in_list, ns->bHaveVdW,
2338 FALSE);
2339
2340 /* neighbour searching withouth QMMM! QM atoms have zero charge in
2341 * the classical calculation. The charge-charge interaction
2342 * between QM and MM atoms is handled in the QMMM core calculation
2343 * (see QMMM.c). The VDW however, we'd like to compute classically
2344 * and the QM MM atom pairs have just been put in the
2345 * corresponding neighbourlists. in case of QMMM we still need to
2346 * fill a special QMMM neighbourlist that contains all neighbours
2347 * of the QM atoms. If bQMMM is true, this list will now be made:
2348 */
2349 if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
2350 {
2351 nsearch += nsgrid_core(cr, fr, box, ngid, top,
2352 grid, ns->bexcl, ns->bExcludeAlleg,
2353 md, put_in_list_qmmm, ns->bHaveVdW,
2354 TRUE);
2355 }
2356 }
2357 else
2358 {
2359 nsearch = ns_simple_core(fr, top, md, box, box_size,
2360 ns->bexcl, ns->simple_aaj,
2361 ngid, ns->ns_buf, put_in_list, ns->bHaveVdW);
2362 }
2363
2364 inc_nrnb(nrnb, eNR_NS, nsearch);
2365
2366 return nsearch;
2367 }
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