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Convert gmx_mtop_t to C++
[gromacs.git] / src / gromacs / mdlib / ns.cpp
blobe3e792f43bcb9f0a1534c6016f50bff8790de205
1 /*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
10 *
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
15 *
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30 * derived work must not be called official GROMACS. Details are found
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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 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 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 t_mdatoms gmx_unused * 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 t_mdatoms gmx_unused * 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, int nrj, int cg_j,
1342 gmx_bool bHaveVdW[], int ngid, t_mdatoms *md,
1343 int icg, int jgid, t_block *cgs, t_excl bexcl[],
1344 int shift, t_forcerec *fr, put_in_list_t *put_in_list)
1345 {
1346 if (nsbuf->nj + nrj > MAX_CG)
1347 {
1348 put_in_list(bHaveVdW, ngid, md, icg, jgid, nsbuf->ncg, nsbuf->jcg,
1349 cgs->index, bexcl, shift, fr, TRUE, TRUE, fr->solvent_opt);
1350 /* Reset buffer contents */
1351 nsbuf->ncg = nsbuf->nj = 0;
1352 }
1353 nsbuf->jcg[nsbuf->ncg++] = cg_j;
1354 nsbuf->nj += nrj;
1355 }
1356
1357 static void ns_inner_tric(rvec x[], int icg, int *i_egp_flags,
1358 int njcg, int jcg[],
1359 matrix box, rvec b_inv, real rcut2,
1360 t_block *cgs, t_ns_buf **ns_buf,
1361 gmx_bool bHaveVdW[], int ngid, t_mdatoms *md,
1362 t_excl bexcl[], t_forcerec *fr,
1363 put_in_list_t *put_in_list)
1364 {
1365 int shift;
1366 int j, nrj, jgid;
1367 int *cginfo = fr->cginfo;
1368 int cg_j, *cgindex;
1369
1370 cgindex = cgs->index;
1371 shift = CENTRAL;
1372 for (j = 0; (j < njcg); j++)
1373 {
1374 cg_j = jcg[j];
1375 nrj = cgindex[cg_j+1]-cgindex[cg_j];
1376 if (calc_image_tric(x[icg], x[cg_j], box, b_inv, &shift) < rcut2)
1377 {
1378 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1379 if (!(i_egp_flags[jgid] & EGP_EXCL))
1380 {
1381 add_simple(&ns_buf[jgid][shift], nrj, cg_j,
1382 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, shift, fr,
1383 put_in_list);
1384 }
1385 }
1386 }
1387 }
1388
1389 static void ns_inner_rect(rvec x[], int icg, int *i_egp_flags,
1390 int njcg, int jcg[],
1391 gmx_bool bBox, rvec box_size, rvec b_inv, real rcut2,
1392 t_block *cgs, t_ns_buf **ns_buf,
1393 gmx_bool bHaveVdW[], int ngid, t_mdatoms *md,
1394 t_excl bexcl[], t_forcerec *fr,
1395 put_in_list_t *put_in_list)
1396 {
1397 int shift;
1398 int j, nrj, jgid;
1399 int *cginfo = fr->cginfo;
1400 int cg_j, *cgindex;
1401
1402 cgindex = cgs->index;
1403 if (bBox)
1404 {
1405 shift = CENTRAL;
1406 for (j = 0; (j < njcg); j++)
1407 {
1408 cg_j = jcg[j];
1409 nrj = cgindex[cg_j+1]-cgindex[cg_j];
1410 if (calc_image_rect(x[icg], x[cg_j], box_size, b_inv, &shift) < rcut2)
1411 {
1412 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1413 if (!(i_egp_flags[jgid] & EGP_EXCL))
1414 {
1415 add_simple(&ns_buf[jgid][shift], nrj, cg_j,
1416 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, shift, fr,
1417 put_in_list);
1418 }
1419 }
1420 }
1421 }
1422 else
1423 {
1424 for (j = 0; (j < njcg); j++)
1425 {
1426 cg_j = jcg[j];
1427 nrj = cgindex[cg_j+1]-cgindex[cg_j];
1428 if ((rcut2 == 0) || (distance2(x[icg], x[cg_j]) < rcut2))
1429 {
1430 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1431 if (!(i_egp_flags[jgid] & EGP_EXCL))
1432 {
1433 add_simple(&ns_buf[jgid][CENTRAL], nrj, cg_j,
1434 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, CENTRAL, fr,
1435 put_in_list);
1436 }
1437 }
1438 }
1439 }
1440 }
1441
1442 /* ns_simple_core needs to be adapted for QMMM still 2005 */
1443
1444 static int ns_simple_core(t_forcerec *fr,
1445 gmx_localtop_t *top,
1446 t_mdatoms *md,
1447 matrix box, rvec box_size,
1448 t_excl bexcl[], int *aaj,
1449 int ngid, t_ns_buf **ns_buf,
1450 put_in_list_t *put_in_list, gmx_bool bHaveVdW[])
1451 {
1452 int naaj, k;
1453 real rlist2;
1454 int nsearch, icg, igid, nn;
1455 int *cginfo;
1456 t_ns_buf *nsbuf;
1457 /* int *i_atoms; */
1458 t_block *cgs = &(top->cgs);
1459 t_blocka *excl = &(top->excls);
1460 rvec b_inv;
1461 int m;
1462 gmx_bool bBox, bTriclinic;
1463 int *i_egp_flags;
1464
1465 rlist2 = gmx::square(fr->rlist);
1466
1467 bBox = (fr->ePBC != epbcNONE);
1468 if (bBox)
1469 {
1470 for (m = 0; (m < DIM); m++)
1471 {
1472 if (gmx_numzero(box_size[m]))
1473 {
1474 gmx_fatal(FARGS, "Dividing by zero box size!");
1475 }
1476 b_inv[m] = 1.0/box_size[m];
1477 }
1478 bTriclinic = TRICLINIC(box);
1479 }
1480 else
1481 {
1482 bTriclinic = FALSE;
1483 }
1484
1485 cginfo = fr->cginfo;
1486
1487 nsearch = 0;
1488 for (icg = fr->cg0; (icg < fr->hcg); icg++)
1489 {
1490 /*
1491 i0 = cgs->index[icg];
1492 nri = cgs->index[icg+1]-i0;
1493 i_atoms = &(cgs->a[i0]);
1494 i_eg_excl = fr->eg_excl + ngid*md->cENER[*i_atoms];
1495 setexcl(nri,i_atoms,excl,TRUE,bexcl);
1496 */
1497 igid = GET_CGINFO_GID(cginfo[icg]);
1498 i_egp_flags = fr->egp_flags + ngid*igid;
1499 setexcl(cgs->index[icg], cgs->index[icg+1], excl, TRUE, bexcl);
1500
1501 naaj = calc_naaj(icg, cgs->nr);
1502 if (bTriclinic)
1503 {
1504 ns_inner_tric(fr->cg_cm, icg, i_egp_flags, naaj, &(aaj[icg]),
1505 box, b_inv, rlist2, cgs, ns_buf,
1506 bHaveVdW, ngid, md, bexcl, fr, put_in_list);
1507 }
1508 else
1509 {
1510 ns_inner_rect(fr->cg_cm, icg, i_egp_flags, naaj, &(aaj[icg]),
1511 bBox, box_size, b_inv, rlist2, cgs, ns_buf,
1512 bHaveVdW, ngid, md, bexcl, fr, put_in_list);
1513 }
1514 nsearch += naaj;
1515
1516 for (nn = 0; (nn < ngid); nn++)
1517 {
1518 for (k = 0; (k < SHIFTS); k++)
1519 {
1520 nsbuf = &(ns_buf[nn][k]);
1521 if (nsbuf->ncg > 0)
1522 {
1523 put_in_list(bHaveVdW, ngid, md, icg, nn, nsbuf->ncg, nsbuf->jcg,
1524 cgs->index, bexcl, k, fr, TRUE, TRUE, fr->solvent_opt);
1525 nsbuf->ncg = nsbuf->nj = 0;
1526 }
1527 }
1528 }
1529 /* setexcl(nri,i_atoms,excl,FALSE,bexcl); */
1530 setexcl(cgs->index[icg], cgs->index[icg+1], excl, FALSE, bexcl);
1531 }
1532 close_neighbor_lists(fr, FALSE);
1533
1534 return nsearch;
1535 }
1536
1537 /************************************************
1538 *
1539 * N S 5 G R I D S T U F F
1540 *
1541 ************************************************/
1542
1543 static inline void get_dx_dd(int Nx, real gridx, real rc2, int xgi, real x,
1544 int ncpddc, int shift_min, int shift_max,
1545 int *g0, int *g1, real *dcx2)
1546 {
1547 real dcx, tmp;
1548 int g_min, g_max, shift_home;
1549
1550 if (xgi < 0)
1551 {
1552 g_min = 0;
1553 g_max = Nx - 1;
1554 *g0 = 0;
1555 *g1 = -1;
1556 }
1557 else if (xgi >= Nx)
1558 {
1559 g_min = 0;
1560 g_max = Nx - 1;
1561 *g0 = Nx;
1562 *g1 = Nx - 1;
1563 }
1564 else
1565 {
1566 if (ncpddc == 0)
1567 {
1568 g_min = 0;
1569 g_max = Nx - 1;
1570 }
1571 else
1572 {
1573 if (xgi < ncpddc)
1574 {
1575 shift_home = 0;
1576 }
1577 else
1578 {
1579 shift_home = -1;
1580 }
1581 g_min = (shift_min == shift_home ? 0 : ncpddc);
1582 g_max = (shift_max == shift_home ? ncpddc - 1 : Nx - 1);
1583 }
1584 if (shift_min > 0)
1585 {
1586 *g0 = g_min;
1587 *g1 = g_min - 1;
1588 }
1589 else if (shift_max < 0)
1590 {
1591 *g0 = g_max + 1;
1592 *g1 = g_max;
1593 }
1594 else
1595 {
1596 *g0 = xgi;
1597 *g1 = xgi;
1598 dcx2[xgi] = 0;
1599 }
1600 }
1601
1602 while (*g0 > g_min)
1603 {
1604 /* Check one grid cell down */
1605 dcx = ((*g0 - 1) + 1)*gridx - x;
1606 tmp = dcx*dcx;
1607 if (tmp >= rc2)
1608 {
1609 break;
1610 }
1611 (*g0)--;
1612 dcx2[*g0] = tmp;
1613 }
1614
1615 while (*g1 < g_max)
1616 {
1617 /* Check one grid cell up */
1618 dcx = (*g1 + 1)*gridx - x;
1619 tmp = dcx*dcx;
1620 if (tmp >= rc2)
1621 {
1622 break;
1623 }
1624 (*g1)++;
1625 dcx2[*g1] = tmp;
1626 }
1627 }
1628
1629
1630 #define calc_dx2(XI, YI, ZI, y) (gmx::square(XI-y[XX]) + gmx::square(YI-y[YY]) + gmx::square(ZI-y[ZZ]))
1631 #define calc_cyl_dx2(XI, YI, y) (gmx::square(XI-y[XX]) + gmx::square(YI-y[YY]))
1632 /****************************************************
1633 *
1634 * F A S T N E I G H B O R S E A R C H I N G
1635 *
1636 * Optimized neighboursearching routine using grid
1637 * at least 1x1x1, see GROMACS manual
1638 *
1639 ****************************************************/
1640
1641
1642 static void get_cutoff2(t_forcerec *fr, real *rs2)
1643 {
1644 *rs2 = gmx::square(fr->rlist);
1645 }
1646
1647 static void init_nsgrid_lists(t_forcerec *fr, int ngid, gmx_ns_t *ns)
1648 {
1649 real rs2;
1650 int j;
1651
1652 get_cutoff2(fr, &rs2);
1653
1654 /* Short range buffers */
1655 snew(ns->nl_sr, ngid);
1656 /* Counters */
1657 snew(ns->nsr, ngid);
1658
1659 for (j = 0; (j < ngid); j++)
1660 {
1661 snew(ns->nl_sr[j], MAX_CG);
1662 }
1663 if (debug)
1664 {
1665 fprintf(debug,
1666 "ns5_core: rs2 = %g (nm^2)\n",
1667 rs2);
1668 }
1669 }
1670
1671 static int nsgrid_core(const t_commrec *cr, t_forcerec *fr,
1672 matrix box, int ngid,
1673 gmx_localtop_t *top,
1674 t_grid *grid,
1675 t_excl bexcl[], gmx_bool *bExcludeAlleg,
1676 t_mdatoms *md,
1677 put_in_list_t *put_in_list,
1678 gmx_bool bHaveVdW[],
1679 gmx_bool bMakeQMMMnblist)
1680 {
1681 gmx_ns_t *ns;
1682 int **nl_sr;
1683 int *nsr;
1684 gmx_domdec_t *dd;
1685 t_block *cgs = &(top->cgs);
1686 int *cginfo = fr->cginfo;
1687 /* int *i_atoms,*cgsindex=cgs->index; */
1688 ivec sh0, sh1, shp;
1689 int cell_x, cell_y, cell_z;
1690 int d, tx, ty, tz, dx, dy, dz, cj;
1691 #ifdef ALLOW_OFFDIAG_LT_HALFDIAG
1692 int zsh_ty, zsh_tx, ysh_tx;
1693 #endif
1694 int dx0, dx1, dy0, dy1, dz0, dz1;
1695 int Nx, Ny, Nz, shift = -1, j, nrj, nns, nn = -1;
1696 real gridx, gridy, gridz, grid_x, grid_y;
1697 real *dcx2, *dcy2, *dcz2;
1698 int zgi, ygi, xgi;
1699 int cg0, cg1, icg = -1, cgsnr, i0, igid, naaj, max_jcg;
1700 int jcg0, jcg1, jjcg, cgj0, jgid;
1701 int *grida, *gridnra, *gridind;
1702 rvec *cgcm, grid_offset;
1703 real r2, rs2, XI, YI, ZI, tmp1, tmp2;
1704 int *i_egp_flags;
1705 gmx_bool bDomDec, bTriclinicX, bTriclinicY;
1706 ivec ncpddc;
1707
1708 ns = fr->ns;
1709
1710 bDomDec = DOMAINDECOMP(cr);
1711 dd = cr->dd;
1712
1713 bTriclinicX = ((YY < grid->npbcdim &&
1714 (!bDomDec || dd->nc[YY] == 1) && box[YY][XX] != 0) ||
1715 (ZZ < grid->npbcdim &&
1716 (!bDomDec || dd->nc[ZZ] == 1) && box[ZZ][XX] != 0));
1717 bTriclinicY = (ZZ < grid->npbcdim &&
1718 (!bDomDec || dd->nc[ZZ] == 1) && box[ZZ][YY] != 0);
1719
1720 cgsnr = cgs->nr;
1721
1722 get_cutoff2(fr, &rs2);
1723
1724 nl_sr = ns->nl_sr;
1725 nsr = ns->nsr;
1726
1727 /* Unpack arrays */
1728 cgcm = fr->cg_cm;
1729 Nx = grid->n[XX];
1730 Ny = grid->n[YY];
1731 Nz = grid->n[ZZ];
1732 grida = grid->a;
1733 gridind = grid->index;
1734 gridnra = grid->nra;
1735 nns = 0;
1736
1737 gridx = grid->cell_size[XX];
1738 gridy = grid->cell_size[YY];
1739 gridz = grid->cell_size[ZZ];
1740 grid_x = 1/gridx;
1741 grid_y = 1/gridy;
1742 copy_rvec(grid->cell_offset, grid_offset);
1743 copy_ivec(grid->ncpddc, ncpddc);
1744 dcx2 = grid->dcx2;
1745 dcy2 = grid->dcy2;
1746 dcz2 = grid->dcz2;
1747
1748 #ifdef ALLOW_OFFDIAG_LT_HALFDIAG
1749 zsh_ty = floor(-box[ZZ][YY]/box[YY][YY]+0.5);
1750 zsh_tx = floor(-box[ZZ][XX]/box[XX][XX]+0.5);
1751 ysh_tx = floor(-box[YY][XX]/box[XX][XX]+0.5);
1752 if (zsh_tx != 0 && ysh_tx != 0)
1753 {
1754 /* This could happen due to rounding, when both ratios are 0.5 */
1755 ysh_tx = 0;
1756 }
1757 #endif
1758
1759 if (fr->n_tpi)
1760 {
1761 /* We only want a list for the test particle */
1762 cg0 = cgsnr - 1;
1763 }
1764 else
1765 {
1766 cg0 = grid->icg0;
1767 }
1768 cg1 = grid->icg1;
1769
1770 /* Set the shift range */
1771 for (d = 0; d < DIM; d++)
1772 {
1773 sh0[d] = -1;
1774 sh1[d] = 1;
1775 /* Check if we need periodicity shifts.
1776 * Without PBC or with domain decomposition we don't need them.
1777 */
1778 if (d >= ePBC2npbcdim(fr->ePBC) || (bDomDec && dd->nc[d] > 1))
1779 {
1780 shp[d] = 0;
1781 }
1782 else
1783 {
1784 if (d == XX &&
1785 box[XX][XX] - std::abs(box[YY][XX]) - std::abs(box[ZZ][XX]) < std::sqrt(rs2))
1786 {
1787 shp[d] = 2;
1788 }
1789 else
1790 {
1791 shp[d] = 1;
1792 }
1793 }
1794 }
1795
1796 /* Loop over charge groups */
1797 for (icg = cg0; (icg < cg1); icg++)
1798 {
1799 igid = GET_CGINFO_GID(cginfo[icg]);
1800 /* Skip this charge group if all energy groups are excluded! */
1801 if (bExcludeAlleg[igid])
1802 {
1803 continue;
1804 }
1805
1806 i0 = cgs->index[icg];
1807
1808 if (bMakeQMMMnblist)
1809 {
1810 /* Skip this charge group if it is not a QM atom while making a
1811 * QM/MM neighbourlist
1812 */
1813 if (md->bQM[i0] == FALSE)
1814 {
1815 continue; /* MM particle, go to next particle */
1816 }
1817
1818 /* Compute the number of charge groups that fall within the control
1819 * of this one (icg)
1820 */
1821 naaj = calc_naaj(icg, cgsnr);
1822 jcg0 = icg;
1823 jcg1 = icg + naaj;
1824 max_jcg = cgsnr;
1825 }
1826 else
1827 {
1828 /* make a normal neighbourlist */
1829
1830 if (bDomDec)
1831 {
1832 /* Get the j charge-group and dd cell shift ranges */
1833 dd_get_ns_ranges(cr->dd, icg, &jcg0, &jcg1, sh0, sh1);
1834 max_jcg = 0;
1835 }
1836 else
1837 {
1838 /* Compute the number of charge groups that fall within the control
1839 * of this one (icg)
1840 */
1841 naaj = calc_naaj(icg, cgsnr);
1842 jcg0 = icg;
1843 jcg1 = icg + naaj;
1844
1845 if (fr->n_tpi)
1846 {
1847 /* The i-particle is awlways the test particle,
1848 * so we want all j-particles
1849 */
1850 max_jcg = cgsnr - 1;
1851 }
1852 else
1853 {
1854 max_jcg = jcg1 - cgsnr;
1855 }
1856 }
1857 }
1858
1859 i_egp_flags = fr->egp_flags + igid*ngid;
1860
1861 /* Set the exclusions for the atoms in charge group icg using a bitmask */
1862 setexcl(i0, cgs->index[icg+1], &top->excls, TRUE, bexcl);
1863
1864 ci2xyz(grid, icg, &cell_x, &cell_y, &cell_z);
1865
1866 /* Changed iicg to icg, DvdS 990115
1867 * (but see consistency check above, DvdS 990330)
1868 */
1869 #ifdef NS5DB
1870 fprintf(log, "icg=%5d, naaj=%5d, cell %d %d %d\n",
1871 icg, naaj, cell_x, cell_y, cell_z);
1872 #endif
1873 /* Loop over shift vectors in three dimensions */
1874 for (tz = -shp[ZZ]; tz <= shp[ZZ]; tz++)
1875 {
1876 ZI = cgcm[icg][ZZ]+tz*box[ZZ][ZZ];
1877 /* Calculate range of cells in Z direction that have the shift tz */
1878 zgi = cell_z + tz*Nz;
1879 get_dx_dd(Nz, gridz, rs2, zgi, ZI-grid_offset[ZZ],
1880 ncpddc[ZZ], sh0[ZZ], sh1[ZZ], &dz0, &dz1, dcz2);
1881 if (dz0 > dz1)
1882 {
1883 continue;
1884 }
1885 for (ty = -shp[YY]; ty <= shp[YY]; ty++)
1886 {
1887 YI = cgcm[icg][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
1888 /* Calculate range of cells in Y direction that have the shift ty */
1889 if (bTriclinicY)
1890 {
1891 ygi = (int)(Ny + (YI - grid_offset[YY])*grid_y) - Ny;
1892 }
1893 else
1894 {
1895 ygi = cell_y + ty*Ny;
1896 }
1897 get_dx_dd(Ny, gridy, rs2, ygi, YI-grid_offset[YY],
1898 ncpddc[YY], sh0[YY], sh1[YY], &dy0, &dy1, dcy2);
1899 if (dy0 > dy1)
1900 {
1901 continue;
1902 }
1903 for (tx = -shp[XX]; tx <= shp[XX]; tx++)
1904 {
1905 XI = cgcm[icg][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
1906 /* Calculate range of cells in X direction that have the shift tx */
1907 if (bTriclinicX)
1908 {
1909 xgi = (int)(Nx + (XI - grid_offset[XX])*grid_x) - Nx;
1910 }
1911 else
1912 {
1913 xgi = cell_x + tx*Nx;
1914 }
1915 get_dx_dd(Nx, gridx, rs2, xgi, XI-grid_offset[XX],
1916 ncpddc[XX], sh0[XX], sh1[XX], &dx0, &dx1, dcx2);
1917 if (dx0 > dx1)
1918 {
1919 continue;
1920 }
1921 /* Get shift vector */
1922 shift = XYZ2IS(tx, ty, tz);
1923 #ifdef NS5DB
1924 range_check(shift, 0, SHIFTS);
1925 #endif
1926 for (nn = 0; (nn < ngid); nn++)
1927 {
1928 nsr[nn] = 0;
1929 }
1930 #ifdef NS5DB
1931 fprintf(log, "shift: %2d, dx0,1: %2d,%2d, dy0,1: %2d,%2d, dz0,1: %2d,%2d\n",
1932 shift, dx0, dx1, dy0, dy1, dz0, dz1);
1933 fprintf(log, "cgcm: %8.3f %8.3f %8.3f\n", cgcm[icg][XX],
1934 cgcm[icg][YY], cgcm[icg][ZZ]);
1935 fprintf(log, "xi: %8.3f %8.3f %8.3f\n", XI, YI, ZI);
1936 #endif
1937 for (dx = dx0; (dx <= dx1); dx++)
1938 {
1939 tmp1 = rs2 - dcx2[dx];
1940 for (dy = dy0; (dy <= dy1); dy++)
1941 {
1942 tmp2 = tmp1 - dcy2[dy];
1943 if (tmp2 > 0)
1944 {
1945 for (dz = dz0; (dz <= dz1); dz++)
1946 {
1947 if (tmp2 > dcz2[dz])
1948 {
1949 /* Find grid-cell cj in which possible neighbours are */
1950 cj = xyz2ci(Ny, Nz, dx, dy, dz);
1951
1952 /* Check out how many cgs (nrj) there in this cell */
1953 nrj = gridnra[cj];
1954
1955 /* Find the offset in the cg list */
1956 cgj0 = gridind[cj];
1957
1958 /* Check if all j's are out of range so we
1959 * can skip the whole cell.
1960 * Should save some time, especially with DD.
1961 */
1962 if (nrj == 0 ||
1963 (grida[cgj0] >= max_jcg &&
1964 (grida[cgj0] >= jcg1 || grida[cgj0+nrj-1] < jcg0)))
1965 {
1966 continue;
1967 }
1968
1969 /* Loop over cgs */
1970 for (j = 0; (j < nrj); j++)
1971 {
1972 jjcg = grida[cgj0+j];
1973
1974 /* check whether this guy is in range! */
1975 if ((jjcg >= jcg0 && jjcg < jcg1) ||
1976 (jjcg < max_jcg))
1977 {
1978 r2 = calc_dx2(XI, YI, ZI, cgcm[jjcg]);
1979 if (r2 < rs2)
1980 {
1981 /* jgid = gid[cgsatoms[cgsindex[jjcg]]]; */
1982 jgid = GET_CGINFO_GID(cginfo[jjcg]);
1983 /* check energy group exclusions */
1984 if (!(i_egp_flags[jgid] & EGP_EXCL))
1985 {
1986 if (nsr[jgid] >= MAX_CG)
1987 {
1988 /* Add to short-range list */
1989 put_in_list(bHaveVdW, ngid, md, icg, jgid,
1990 nsr[jgid], nl_sr[jgid],
1991 cgs->index, /* cgsatoms, */ bexcl,
1992 shift, fr, TRUE, TRUE, fr->solvent_opt);
1993 nsr[jgid] = 0;
1994 }
1995 nl_sr[jgid][nsr[jgid]++] = jjcg;
1996 }
1997 }
1998 nns++;
1999 }
2000 }
2001 }
2002 }
2003 }
2004 }
2005 }
2006 /* CHECK whether there is anything left in the buffers */
2007 for (nn = 0; (nn < ngid); nn++)
2008 {
2009 if (nsr[nn] > 0)
2010 {
2011 put_in_list(bHaveVdW, ngid, md, icg, nn, nsr[nn], nl_sr[nn],
2012 cgs->index, /* cgsatoms, */ bexcl,
2013 shift, fr, TRUE, TRUE, fr->solvent_opt);
2014 }
2015 }
2016 }
2017 }
2018 }
2019 setexcl(cgs->index[icg], cgs->index[icg+1], &top->excls, FALSE, bexcl);
2020 }
2021 /* No need to perform any left-over force calculations anymore (as we used to do here)
2022 * since we now save the proper long-range lists for later evaluation.
2023 */
2024
2025 /* Close neighbourlists */
2026 close_neighbor_lists(fr, bMakeQMMMnblist);
2027
2028 return nns;
2029 }
2030
2031 static void ns_realloc_natoms(gmx_ns_t *ns, int natoms)
2032 {
2033 int i;
2034
2035 if (natoms > ns->nra_alloc)
2036 {
2037 ns->nra_alloc = over_alloc_dd(natoms);
2038 srenew(ns->bexcl, ns->nra_alloc);
2039 for (i = 0; i < ns->nra_alloc; i++)
2040 {
2041 ns->bexcl[i] = 0;
2042 }
2043 }
2044 }
2045
2046 void init_ns(FILE *fplog, const t_commrec *cr,
2047 gmx_ns_t *ns, t_forcerec *fr,
2048 const gmx_mtop_t *mtop)
2049 {
2050 int icg, nr_in_cg, maxcg, i, j, jcg, ngid, ncg;
2051
2052 /* Compute largest charge groups size (# atoms) */
2053 nr_in_cg = 1;
2054 for (const gmx_moltype_t &molt : mtop->moltype)
2055 {
2056 const t_block *cgs = &molt.cgs;
2057 for (icg = 0; (icg < cgs->nr); icg++)
2058 {
2059 nr_in_cg = std::max(nr_in_cg, (int)(cgs->index[icg+1]-cgs->index[icg]));
2060 }
2061 }
2062
2063 /* Verify whether largest charge group is <= max cg.
2064 * This is determined by the type of the local exclusion type
2065 * Exclusions are stored in bits. (If the type is not large
2066 * enough, enlarge it, unsigned char -> unsigned short -> unsigned long)
2067 */
2068 maxcg = sizeof(t_excl)*8;
2069 if (nr_in_cg > maxcg)
2070 {
2071 gmx_fatal(FARGS, "Max #atoms in a charge group: %d > %d\n",
2072 nr_in_cg, maxcg);
2073 }
2074
2075 ngid = mtop->groups.grps[egcENER].nr;
2076 snew(ns->bExcludeAlleg, ngid);
2077 for (i = 0; i < ngid; i++)
2078 {
2079 ns->bExcludeAlleg[i] = TRUE;
2080 for (j = 0; j < ngid; j++)
2081 {
2082 if (!(fr->egp_flags[i*ngid+j] & EGP_EXCL))
2083 {
2084 ns->bExcludeAlleg[i] = FALSE;
2085 }
2086 }
2087 }
2088
2089 if (fr->bGrid)
2090 {
2091 /* Grid search */
2092 ns->grid = init_grid(fplog, fr);
2093 init_nsgrid_lists(fr, ngid, ns);
2094 }
2095 else
2096 {
2097 /* Simple search */
2098 snew(ns->ns_buf, ngid);
2099 for (i = 0; (i < ngid); i++)
2100 {
2101 snew(ns->ns_buf[i], SHIFTS);
2102 }
2103 ncg = ncg_mtop(mtop);
2104 snew(ns->simple_aaj, 2*ncg);
2105 for (jcg = 0; (jcg < ncg); jcg++)
2106 {
2107 ns->simple_aaj[jcg] = jcg;
2108 ns->simple_aaj[jcg+ncg] = jcg;
2109 }
2110 }
2111
2112 /* Create array that determines whether or not atoms have VdW */
2113 snew(ns->bHaveVdW, fr->ntype);
2114 for (i = 0; (i < fr->ntype); i++)
2115 {
2116 for (j = 0; (j < fr->ntype); j++)
2117 {
2118 ns->bHaveVdW[i] = (ns->bHaveVdW[i] ||
2119 (fr->bBHAM ?
2120 ((BHAMA(fr->nbfp, fr->ntype, i, j) != 0) ||
2121 (BHAMB(fr->nbfp, fr->ntype, i, j) != 0) ||
2122 (BHAMC(fr->nbfp, fr->ntype, i, j) != 0)) :
2123 ((C6(fr->nbfp, fr->ntype, i, j) != 0) ||
2124 (C12(fr->nbfp, fr->ntype, i, j) != 0))));
2125 }
2126 }
2127 if (debug)
2128 {
2129 pr_bvec(debug, 0, "bHaveVdW", ns->bHaveVdW, fr->ntype, TRUE);
2130 }
2131
2132 ns->nra_alloc = 0;
2133 ns->bexcl = nullptr;
2134 if (!DOMAINDECOMP(cr))
2135 {
2136 ns_realloc_natoms(ns, mtop->natoms);
2137 }
2138
2139 ns->nblist_initialized = FALSE;
2140
2141 /* nbr list debug dump */
2142 {
2143 char *ptr = getenv("GMX_DUMP_NL");
2144 if (ptr)
2145 {
2146 ns->dump_nl = strtol(ptr, nullptr, 10);
2147 if (fplog)
2148 {
2149 fprintf(fplog, "GMX_DUMP_NL = %d", ns->dump_nl);
2150 }
2151 }
2152 else
2153 {
2154 ns->dump_nl = 0;
2155 }
2156 }
2157 }
2158
2159 void done_ns(gmx_ns_t *ns, int numEnergyGroups)
2160 {
2161 sfree(ns->bExcludeAlleg);
2162 if (ns->ns_buf)
2163 {
2164 for (int i = 0; i < numEnergyGroups; i++)
2165 {
2166 sfree(ns->ns_buf[i]);
2167 }
2168 sfree(ns->ns_buf);
2169 }
2170 sfree(ns->simple_aaj);
2171 sfree(ns->bHaveVdW);
2172 done_grid(ns->grid);
2173 sfree(ns);
2174 }
2175
2176 int search_neighbours(FILE *log, t_forcerec *fr,
2177 matrix box,
2178 gmx_localtop_t *top,
2179 gmx_groups_t *groups,
2180 const t_commrec *cr,
2181 t_nrnb *nrnb, t_mdatoms *md,
2182 gmx_bool bFillGrid)
2183 {
2184 t_block *cgs = &(top->cgs);
2185 rvec box_size, grid_x0, grid_x1;
2186 int m, ngid;
2187 real min_size, grid_dens;
2188 int nsearch;
2189 gmx_bool bGrid;
2190 int start, end;
2191 gmx_ns_t *ns;
2192 t_grid *grid;
2193 gmx_domdec_zones_t *dd_zones;
2194 put_in_list_t *put_in_list;
2195
2196 ns = fr->ns;
2197
2198 /* Set some local variables */
2199 bGrid = fr->bGrid;
2200 ngid = groups->grps[egcENER].nr;
2201
2202 for (m = 0; (m < DIM); m++)
2203 {
2204 box_size[m] = box[m][m];
2205 }
2206
2207 if (fr->ePBC != epbcNONE)
2208 {
2209 if (gmx::square(fr->rlist) >= max_cutoff2(fr->ePBC, box))
2210 {
2211 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.");
2212 }
2213 if (!bGrid)
2214 {
2215 min_size = std::min(box_size[XX], std::min(box_size[YY], box_size[ZZ]));
2216 if (2*fr->rlist >= min_size)
2217 {
2218 gmx_fatal(FARGS, "One of the box diagonal elements has become smaller than twice the cut-off length.");
2219 }
2220 }
2221 }
2222
2223 if (DOMAINDECOMP(cr))
2224 {
2225 ns_realloc_natoms(ns, cgs->index[cgs->nr]);
2226 }
2227
2228 /* Reset the neighbourlists */
2229 reset_neighbor_lists(fr);
2230
2231 if (bGrid && bFillGrid)
2232 {
2233
2234 grid = ns->grid;
2235 if (DOMAINDECOMP(cr))
2236 {
2237 dd_zones = domdec_zones(cr->dd);
2238 }
2239 else
2240 {
2241 dd_zones = nullptr;
2242
2243 get_nsgrid_boundaries(grid->nboundeddim, box, nullptr, nullptr, nullptr, nullptr,
2244 cgs->nr, fr->cg_cm, grid_x0, grid_x1, &grid_dens);
2245
2246 grid_first(log, grid, nullptr, nullptr, box, grid_x0, grid_x1,
2247 fr->rlist, grid_dens);
2248 }
2249
2250 start = 0;
2251 end = cgs->nr;
2252
2253 if (DOMAINDECOMP(cr))
2254 {
2255 end = cgs->nr;
2256 fill_grid(dd_zones, grid, end, -1, end, fr->cg_cm);
2257 grid->icg0 = 0;
2258 grid->icg1 = dd_zones->izone[dd_zones->nizone-1].cg1;
2259 }
2260 else
2261 {
2262 fill_grid(nullptr, grid, cgs->nr, fr->cg0, fr->hcg, fr->cg_cm);
2263 grid->icg0 = fr->cg0;
2264 grid->icg1 = fr->hcg;
2265 }
2266
2267 calc_elemnr(grid, start, end, cgs->nr);
2268 calc_ptrs(grid);
2269 grid_last(grid, start, end, cgs->nr);
2270
2271 if (gmx_debug_at)
2272 {
2273 check_grid(grid);
2274 print_grid(debug, grid);
2275 }
2276 }
2277 else if (fr->n_tpi)
2278 {
2279 /* Set the grid cell index for the test particle only.
2280 * The cell to cg index is not corrected, but that does not matter.
2281 */
2282 fill_grid(nullptr, ns->grid, fr->hcg, fr->hcg-1, fr->hcg, fr->cg_cm);
2283 }
2284
2285 if (!fr->ns->bCGlist)
2286 {
2287 put_in_list = put_in_list_at;
2288 }
2289 else
2290 {
2291 put_in_list = put_in_list_cg;
2292 }
2293
2294 /* Do the core! */
2295 if (bGrid)
2296 {
2297 grid = ns->grid;
2298 nsearch = nsgrid_core(cr, fr, box, ngid, top,
2299 grid, ns->bexcl, ns->bExcludeAlleg,
2300 md, put_in_list, ns->bHaveVdW,
2301 FALSE);
2302
2303 /* neighbour searching withouth QMMM! QM atoms have zero charge in
2304 * the classical calculation. The charge-charge interaction
2305 * between QM and MM atoms is handled in the QMMM core calculation
2306 * (see QMMM.c). The VDW however, we'd like to compute classically
2307 * and the QM MM atom pairs have just been put in the
2308 * corresponding neighbourlists. in case of QMMM we still need to
2309 * fill a special QMMM neighbourlist that contains all neighbours
2310 * of the QM atoms. If bQMMM is true, this list will now be made:
2311 */
2312 if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
2313 {
2314 nsearch += nsgrid_core(cr, fr, box, ngid, top,
2315 grid, ns->bexcl, ns->bExcludeAlleg,
2316 md, put_in_list_qmmm, ns->bHaveVdW,
2317 TRUE);
2318 }
2319 }
2320 else
2321 {
2322 nsearch = ns_simple_core(fr, top, md, box, box_size,
2323 ns->bexcl, ns->simple_aaj,
2324 ngid, ns->ns_buf, put_in_list, ns->bHaveVdW);
2325 }
2326
2327 inc_nrnb(nrnb, eNR_NS, nsearch);
2328
2329 return nsearch;
2330 }
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