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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/nsgrid.h"
58 #include "gromacs/mdlib/qmmm.h"
59 #include "gromacs/mdtypes/commrec.h"
60 #include "gromacs/mdtypes/forcerec.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"
71 * E X C L U S I O N H A N D L I N G
75 static void SETEXCL_(t_excl e[], int i, int j)
79 static void RMEXCL_(t_excl e[], int i, int j)
81 e[j] = e[j] & ~(1<<i);
83 static gmx_bool ISEXCL_(t_excl e[], int i, int j)
85 return (gmx_bool)(e[j] & (1<<i));
87 static gmx_bool NOTEXCL_(t_excl e[], int i, int j)
89 return !(ISEXCL(e, i, j));
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))
99 round_up_to_simd_width(int length, int simd_width)
103 offset = (simd_width > 0) ? length % simd_width : 0;
105 return (offset == 0) ? length : length-offset+simd_width;
107 /************************************************
109 * U T I L I T I E S F O R N S
111 ************************************************/
113 void reallocate_nblist(t_nblist *nl)
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);
120 srenew(nl->iinr, nl->maxnri);
121 if (nl->igeometry == GMX_NBLIST_GEOMETRY_CG_CG)
123 srenew(nl->iinr_end, nl->maxnri);
125 srenew(nl->gid, nl->maxnri);
126 srenew(nl->shift, nl->maxnri);
127 srenew(nl->jindex, nl->maxnri+1);
131 static void init_nblist(FILE *log, t_nblist *nl_sr,
133 int ivdw, int ivdwmod,
134 int ielec, int ielecmod,
135 int igeometry, int type,
136 gmx_bool bElecAndVdwSwitchDiffers)
151 /* Set coul/vdw in neighborlist, and for the normal loops we determine
152 * an index of which one to call.
155 nl->ivdwmod = ivdwmod;
157 nl->ielecmod = ielecmod;
159 nl->igeometry = igeometry;
161 if (nl->type == GMX_NBLIST_INTERACTION_FREE_ENERGY)
163 nl->igeometry = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
166 /* This will also set the simd_padding_width field */
167 gmx_nonbonded_set_kernel_pointers(log, nl, bElecAndVdwSwitchDiffers);
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.
175 nl->maxnri = homenr*4;
182 nl->jindex = nullptr;
184 nl->excl_fep = nullptr;
185 reallocate_nblist(nl);
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);
196 void init_neighbor_list(FILE *log, t_forcerec *fr, int homenr)
198 int maxsr, maxsr_wat;
199 int ielec, ivdw, ielecmod, ivdwmod, type;
200 int igeometry_def, igeometry_w, igeometry_ww;
202 gmx_bool bElecAndVdwSwitchDiffers;
205 /* maxsr = homenr-fr->nWatMol*3; */
210 gmx_fatal(FARGS, "%s, %d: Negative number of short range atoms.\n"
211 "Call your GROMACS dealer for assistance.", __FILE__, __LINE__);
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.
217 maxsr_wat = std::min(fr->nWatMol, (homenr+2)/3);
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));
227 fr->ns->bCGlist = (getenv("GMX_NBLISTCG") != nullptr);
228 if (!fr->ns->bCGlist)
230 igeometry_def = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
234 igeometry_def = GMX_NBLIST_GEOMETRY_CG_CG;
237 fprintf(log, "\nUsing charge-group - charge-group neighbor lists and kernels\n\n");
241 if (fr->solvent_opt == esolTIP4P)
243 igeometry_w = GMX_NBLIST_GEOMETRY_WATER4_PARTICLE;
244 igeometry_ww = GMX_NBLIST_GEOMETRY_WATER4_WATER4;
248 igeometry_w = GMX_NBLIST_GEOMETRY_WATER3_PARTICLE;
249 igeometry_ww = GMX_NBLIST_GEOMETRY_WATER3_WATER3;
252 for (i = 0; i < fr->nnblists; i++)
254 nbl = &(fr->nblists[i]);
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);
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)
277 fr->solvent_opt = esolNO;
280 fprintf(log, "Note: The available nonbonded kernels do not support water optimization - disabling.\n");
284 if (fr->efep != efepNO)
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);
295 if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
297 if (nullptr == fr->QMMMlist)
299 snew(fr->QMMMlist, 1);
301 init_nblist(log, fr->QMMMlist,
302 maxsr, 0, 0, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_STANDARD, bElecAndVdwSwitchDiffers);
310 fr->ns->nblist_initialized = TRUE;
313 static void reset_nblist(t_nblist *nl)
323 static void reset_neighbor_lists(t_forcerec *fr)
329 /* only reset the short-range nblist */
330 reset_nblist(fr->QMMMlist);
333 for (n = 0; n < fr->nnblists; n++)
335 for (i = 0; i < eNL_NR; i++)
337 reset_nblist( &(fr->nblists[n].nlist_sr[i]) );
345 static inline void new_i_nblist(t_nblist *nlist, int i_atom, int shift, int gid)
347 int nri = nlist->nri;
349 /* Check whether we have to increase the i counter */
351 (nlist->iinr[nri] != i_atom) ||
352 (nlist->shift[nri] != shift) ||
353 (nlist->gid[nri] != gid))
355 /* This is something else. Now see if any entries have
356 * been added in the list of the previous atom.
359 ((nlist->jindex[nri+1] > nlist->jindex[nri]) &&
360 (nlist->gid[nri] != -1)))
362 /* If so increase the counter */
365 if (nlist->nri >= nlist->maxnri)
367 nlist->maxnri += over_alloc_large(nlist->nri);
368 reallocate_nblist(nlist);
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;
379 /* Adding to previous list. First remove possible previous padding */
380 if (nlist->simd_padding_width > 1)
382 while (nlist->nrj > 0 && nlist->jjnr[nlist->nrj-1] < 0)
390 static inline void close_i_nblist(t_nblist *nlist)
392 int nri = nlist->nri;
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.
401 while ((nlist->nrj % nlist->simd_padding_width) != 0)
403 /* Use -4 here, so we can write forces for 4 atoms before real data */
404 nlist->jjnr[nlist->nrj++] = -4;
406 nlist->jindex[nri+1] = nlist->nrj;
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
413 if ((len == 0) && (nlist->nri > 0))
420 static inline void close_nblist(t_nblist *nlist)
422 /* Only close this nblist when it has been initialized.
423 * Avoid the creation of i-lists with no j-particles.
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
437 /* Close list number nri by incrementing the count */
442 static inline void close_neighbor_lists(t_forcerec *fr, gmx_bool bMakeQMMMnblist)
448 close_nblist(fr->QMMMlist);
451 for (n = 0; n < fr->nnblists; n++)
453 for (i = 0; (i < eNL_NR); i++)
455 close_nblist(&(fr->nblists[n].nlist_sr[i]));
461 static inline void add_j_to_nblist(t_nblist *nlist, int j_atom)
463 int nrj = nlist->nrj;
465 if (nlist->nrj >= nlist->maxnrj)
467 nlist->maxnrj = round_up_to_simd_width(over_alloc_small(nlist->nrj + 1), nlist->simd_padding_width);
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);
475 srenew(nlist->jjnr, nlist->maxnrj);
478 nlist->jjnr[nrj] = j_atom;
482 static inline void add_j_to_nblist_cg(t_nblist *nlist,
483 int j_start, int j_end,
484 const t_excl *bexcl, gmx_bool i_is_j)
486 int nrj = nlist->nrj;
489 if (nlist->nrj >= nlist->maxnrj)
491 nlist->maxnrj = over_alloc_small(nlist->nrj + 1);
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);
498 srenew(nlist->jjnr, nlist->maxnrj);
499 srenew(nlist->jjnr_end, nlist->maxnrj);
500 srenew(nlist->excl, nlist->maxnrj*MAX_CGCGSIZE);
503 nlist->jjnr[nrj] = j_start;
504 nlist->jjnr_end[nrj] = j_end;
506 if (j_end - j_start > MAX_CGCGSIZE)
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);
511 /* Set the exclusions */
512 for (j = j_start; j < j_end; j++)
514 nlist->excl[nrj*MAX_CGCGSIZE + j - j_start] = bexcl[j];
518 /* Avoid double counting of intra-cg interactions */
519 for (j = 1; j < j_end-j_start; j++)
521 nlist->excl[nrj*MAX_CGCGSIZE + j] |= (1<<j) - 1;
529 put_in_list_t (const gmx_bool bHaveVdW[],
537 const t_excl bExcl[],
545 put_in_list_at(const gmx_bool bHaveVdW[],
553 const t_excl bExcl[],
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].
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;
572 int i, j, jcg, igid, gid, nbl_ind;
573 int jj, jj0, jj1, i_atom;
578 real *charge, *chargeB;
580 gmx_bool bFreeEnergy, bFree, bFreeJ, bNotEx, *bPert;
581 gmx_bool bDoVdW_i, bDoCoul_i, bDoCoul_i_sol;
585 /* Copy some pointers */
587 charge = md->chargeA;
588 chargeB = md->chargeB;
591 bPert = md->bPerturbed;
595 nicg = index[icg+1]-i0;
597 /* Get the i charge group info */
598 igid = GET_CGINFO_GID(cginfo[icg]);
600 iwater = (solvent_opt != esolNO) ? GET_CGINFO_SOLOPT(cginfo[icg]) : esolNO;
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.
609 for (i = 0; i < nicg; i++)
611 bFreeEnergy |= bPert[i0+i];
613 /* Loop over the j charge groups */
614 for (j = 0; (j < nj && !bFreeEnergy); j++)
619 /* Finally loop over the atoms in the j-charge group */
620 for (jj = jj0; jj < jj1; jj++)
622 bFreeEnergy |= bPert[jj];
627 /* Unpack pointers to neighbourlist structs */
628 if (fr->nnblists == 1)
634 nbl_ind = fr->gid2nblists[GID(igid, jgid, ngid)];
636 nlist = fr->nblists[nbl_ind].nlist_sr;
638 if (iwater != esolNO)
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];
648 vdwc = &nlist[eNL_VDWQQ];
649 vdw = &nlist[eNL_VDW];
650 coul = &nlist[eNL_QQ];
655 if (iwater != esolNO)
657 /* Loop over the atoms in the i charge group */
659 gid = GID(igid, jgid, ngid);
660 /* Create new i_atom for each energy group */
661 if (bDoCoul && bDoVdW)
663 new_i_nblist(vdwc, i_atom, shift, gid);
664 new_i_nblist(vdwc_ww, i_atom, shift, gid);
668 new_i_nblist(vdw, i_atom, shift, gid);
672 new_i_nblist(coul, i_atom, shift, gid);
673 new_i_nblist(coul_ww, i_atom, shift, gid);
675 /* Loop over the j charge groups */
676 for (j = 0; (j < nj); j++)
686 jwater = GET_CGINFO_SOLOPT(cginfo[jcg]);
688 if (iwater == esolSPC && jwater == esolSPC)
690 /* Interaction between two SPC molecules */
693 /* VdW only - only first atoms in each water interact */
694 add_j_to_nblist(vdw, jj0);
698 /* One entry for the entire water-water interaction */
701 add_j_to_nblist(coul_ww, jj0);
705 add_j_to_nblist(vdwc_ww, jj0);
709 else if (iwater == esolTIP4P && jwater == esolTIP4P)
711 /* Interaction between two TIP4p molecules */
714 /* VdW only - only first atoms in each water interact */
715 add_j_to_nblist(vdw, jj0);
719 /* One entry for the entire water-water interaction */
722 add_j_to_nblist(coul_ww, jj0);
726 add_j_to_nblist(vdwc_ww, jj0);
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...
742 for (jj = jj0; (jj < jj1); jj++)
746 add_j_to_nblist(coul, jj);
752 for (jj = jj0; (jj < jj1); jj++)
754 if (bHaveVdW[type[jj]])
756 add_j_to_nblist(vdw, jj);
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++)
766 if (bHaveVdW[type[jj]])
770 add_j_to_nblist(vdwc, jj);
774 add_j_to_nblist(vdw, jj);
777 else if (charge[jj] != 0)
779 add_j_to_nblist(coul, jj);
786 close_i_nblist(coul);
787 close_i_nblist(vdwc);
788 close_i_nblist(coul_ww);
789 close_i_nblist(vdwc_ww);
793 /* no solvent as i charge group */
794 /* Loop over the atoms in the i charge group */
795 for (i = 0; i < nicg; i++)
798 gid = GID(igid, jgid, ngid);
801 /* Create new i_atom for each energy group */
802 if (bDoVdW && bDoCoul)
804 new_i_nblist(vdwc, i_atom, shift, gid);
808 new_i_nblist(vdw, i_atom, shift, gid);
812 new_i_nblist(coul, i_atom, shift, gid);
814 bDoVdW_i = (bDoVdW && bHaveVdW[type[i_atom]]);
815 bDoCoul_i = (bDoCoul && qi != 0);
817 if (bDoVdW_i || bDoCoul_i)
819 /* Loop over the j charge groups */
820 for (j = 0; (j < nj); j++)
824 /* Check for large charge groups */
835 /* Finally loop over the atoms in the j-charge group */
836 for (jj = jj0; jj < jj1; jj++)
838 bNotEx = NOTEXCL(bExcl, i, jj);
846 add_j_to_nblist(coul, jj);
851 if (bHaveVdW[type[jj]])
853 add_j_to_nblist(vdw, jj);
858 if (bHaveVdW[type[jj]])
862 add_j_to_nblist(vdwc, jj);
866 add_j_to_nblist(vdw, jj);
869 else if (charge[jj] != 0)
871 add_j_to_nblist(coul, jj);
879 close_i_nblist(coul);
880 close_i_nblist(vdwc);
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++)
894 gid = GID(igid, jgid, ngid);
896 qiB = chargeB[i_atom];
898 /* Create new i_atom for each energy group */
899 if (bDoVdW && bDoCoul)
901 new_i_nblist(vdwc, i_atom, shift, gid);
905 new_i_nblist(vdw, i_atom, shift, gid);
909 new_i_nblist(coul, i_atom, shift, gid);
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);
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.
926 if (iwater == esolNO)
928 bDoCoul_i_sol = bDoCoul_i;
932 bDoCoul_i_sol = bDoCoul;
935 if (bDoVdW_i || bDoCoul_i_sol)
937 /* Loop over the j charge groups */
938 for (j = 0; (j < nj); j++)
942 /* Check for large charge groups */
953 /* Finally loop over the atoms in the j-charge group */
954 bFree = bPert[i_atom];
955 for (jj = jj0; (jj < jj1); jj++)
957 bFreeJ = bFree || bPert[jj];
958 /* Complicated if, because the water H's should also
959 * see perturbed j-particles
961 if (iwater == esolNO || i == 0 || bFreeJ)
963 bNotEx = NOTEXCL(bExcl, i, jj);
971 if (charge[jj] != 0 || chargeB[jj] != 0)
973 add_j_to_nblist(coul_free, jj);
978 if (bHaveVdW[type[jj]] || bHaveVdW[typeB[jj]])
980 add_j_to_nblist(vdw_free, jj);
985 if (bHaveVdW[type[jj]] || bHaveVdW[typeB[jj]])
987 if (charge[jj] != 0 || chargeB[jj] != 0)
989 add_j_to_nblist(vdwc_free, jj);
993 add_j_to_nblist(vdw_free, jj);
996 else if (charge[jj] != 0 || chargeB[jj] != 0)
998 add_j_to_nblist(coul_free, jj);
1004 /* This is done whether or not bWater is set */
1005 if (charge[jj] != 0)
1007 add_j_to_nblist(coul, jj);
1010 else if (!bDoCoul_i_sol)
1012 if (bHaveVdW[type[jj]])
1014 add_j_to_nblist(vdw, jj);
1019 if (bHaveVdW[type[jj]])
1021 if (charge[jj] != 0)
1023 add_j_to_nblist(vdwc, jj);
1027 add_j_to_nblist(vdw, jj);
1030 else if (charge[jj] != 0)
1032 add_j_to_nblist(coul, jj);
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);
1051 put_in_list_qmmm(const gmx_bool gmx_unused bHaveVdW[],
1053 const t_mdatoms * /* md */,
1059 const t_excl bExcl[],
1062 gmx_bool gmx_unused bDoVdW,
1063 gmx_bool gmx_unused bDoCoul,
1064 int gmx_unused solvent_opt)
1067 int i, j, jcg, igid, gid;
1068 int jj, jj0, jj1, i_atom;
1072 /* Get atom range */
1074 nicg = index[icg+1]-i0;
1076 /* Get the i charge group info */
1077 igid = GET_CGINFO_GID(fr->cginfo[icg]);
1079 coul = fr->QMMMlist;
1081 /* Loop over atoms in the ith charge group */
1082 for (i = 0; i < nicg; 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);
1089 /* Loop over the j charge groups */
1090 for (j = 0; j < nj; j++)
1094 /* Charge groups cannot have QM and MM atoms simultaneously */
1099 /* Finally loop over the atoms in the j-charge group */
1100 for (jj = jj0; jj < jj1; jj++)
1102 bNotEx = NOTEXCL(bExcl, i, jj);
1105 add_j_to_nblist(coul, jj);
1110 close_i_nblist(coul);
1115 put_in_list_cg(const gmx_bool gmx_unused bHaveVdW[],
1117 const t_mdatoms * /* md */,
1123 const t_excl bExcl[],
1126 gmx_bool gmx_unused bDoVdW,
1127 gmx_bool gmx_unused bDoCoul,
1128 int gmx_unused solvent_opt)
1131 int igid, gid, nbl_ind;
1135 cginfo = fr->cginfo[icg];
1137 igid = GET_CGINFO_GID(cginfo);
1138 gid = GID(igid, jgid, ngid);
1140 /* Unpack pointers to neighbourlist structs */
1141 if (fr->nnblists == 1)
1147 nbl_ind = fr->gid2nblists[gid];
1149 vdwc = &fr->nblists[nbl_ind].nlist_sr[eNL_VDWQQ];
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.
1156 new_i_nblist(vdwc, index[icg], shift, gid);
1157 vdwc->iinr_end[vdwc->nri] = index[icg+1];
1159 for (j = 0; (j < nj); j++)
1162 /* Skip the icg-icg pairs if all self interactions are excluded */
1163 if (!(jcg == icg && GET_CGINFO_EXCL_INTRA(cginfo)))
1165 /* Here we add the j charge group jcg to the list,
1166 * exclusions are also added to the list.
1168 add_j_to_nblist_cg(vdwc, index[jcg], index[jcg+1], bExcl, icg == jcg);
1172 close_i_nblist(vdwc);
1175 static void setexcl(int start, int end, t_blocka *excl, gmx_bool b,
1182 for (i = start; i < end; i++)
1184 for (k = excl->index[i]; k < excl->index[i+1]; k++)
1186 SETEXCL(bexcl, i-start, excl->a[k]);
1192 for (i = start; i < end; i++)
1194 for (k = excl->index[i]; k < excl->index[i+1]; k++)
1196 RMEXCL(bexcl, i-start, excl->a[k]);
1202 int calc_naaj(int icg, int cgtot)
1206 if ((cgtot % 2) == 1)
1208 /* Odd number of charge groups, easy */
1209 naaj = 1 + (cgtot/2);
1211 else if ((cgtot % 4) == 0)
1213 /* Multiple of four is hard */
1250 fprintf(log, "naaj=%d\n", naaj);
1256 /************************************************
1258 * S I M P L E C O R E S T U F F
1260 ************************************************/
1262 static real calc_image_tric(const rvec xi, const rvec xj, matrix box,
1263 const rvec b_inv, int *shift)
1265 /* This code assumes that the cut-off is smaller than
1266 * a half times the smallest diagonal element of the box.
1268 const real h25 = 2.5;
1273 /* Compute diff vector */
1274 dz = xj[ZZ] - xi[ZZ];
1275 dy = xj[YY] - xi[YY];
1276 dx = xj[XX] - xi[XX];
1278 /* Perform NINT operation, using trunc operation, therefore
1279 * we first add 2.5 then subtract 2 again
1281 tz = static_cast<int>(dz*b_inv[ZZ] + h25);
1283 dz -= tz*box[ZZ][ZZ];
1284 dy -= tz*box[ZZ][YY];
1285 dx -= tz*box[ZZ][XX];
1287 ty = static_cast<int>(dy*b_inv[YY] + h25);
1289 dy -= ty*box[YY][YY];
1290 dx -= ty*box[YY][XX];
1292 tx = static_cast<int>(dx*b_inv[XX]+h25);
1294 dx -= tx*box[XX][XX];
1296 /* Distance squared */
1297 r2 = (dx*dx) + (dy*dy) + (dz*dz);
1299 *shift = XYZ2IS(tx, ty, tz);
1304 static real calc_image_rect(const rvec xi, const rvec xj, const rvec box_size,
1305 const rvec b_inv, int *shift)
1307 const real h15 = 1.5;
1313 /* Compute diff vector */
1314 dx = xj[XX] - xi[XX];
1315 dy = xj[YY] - xi[YY];
1316 dz = xj[ZZ] - xi[ZZ];
1318 /* Perform NINT operation, using trunc operation, therefore
1319 * we first add 1.5 then subtract 1 again
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);
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;
1333 /* Distance squared */
1334 r2 = (ddx*ddx) + (ddy*ddy) + (ddz*ddz);
1336 *shift = XYZ2IS(tx, ty, tz);
1341 static void add_simple(t_ns_buf * nsbuf,
1344 gmx_bool bHaveVdW[],
1346 const t_mdatoms *md,
1353 put_in_list_t *put_in_list)
1355 if (nsbuf->nj + nrj > MAX_CG)
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;
1362 nsbuf->jcg[nsbuf->ncg++] = cg_j;
1366 static void ns_inner_tric(rvec x[],
1368 const int *i_egp_flags,
1376 gmx_bool bHaveVdW[],
1378 const t_mdatoms *md,
1381 put_in_list_t *put_in_list)
1385 int *cginfo = fr->cginfo;
1388 cgindex = cgs->index;
1390 for (j = 0; (j < njcg); 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)
1396 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1397 if (!(i_egp_flags[jgid] & EGP_EXCL))
1399 add_simple(&ns_buf[jgid][shift], nrj, cg_j,
1400 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, shift, fr,
1407 static void ns_inner_rect(rvec x[],
1409 const int *i_egp_flags,
1418 gmx_bool bHaveVdW[],
1420 const t_mdatoms *md,
1423 put_in_list_t *put_in_list)
1427 int *cginfo = fr->cginfo;
1430 cgindex = cgs->index;
1434 for (j = 0; (j < njcg); 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)
1440 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1441 if (!(i_egp_flags[jgid] & EGP_EXCL))
1443 add_simple(&ns_buf[jgid][shift], nrj, cg_j,
1444 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, shift, fr,
1452 for (j = 0; (j < njcg); j++)
1455 nrj = cgindex[cg_j+1]-cgindex[cg_j];
1456 if ((rcut2 == 0) || (distance2(x[icg], x[cg_j]) < rcut2))
1458 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1459 if (!(i_egp_flags[jgid] & EGP_EXCL))
1461 add_simple(&ns_buf[jgid][CENTRAL], nrj, cg_j,
1462 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, CENTRAL, fr,
1470 /* ns_simple_core needs to be adapted for QMMM still 2005 */
1472 static int ns_simple_core(t_forcerec *fr,
1473 gmx_localtop_t *top,
1474 const t_mdatoms *md,
1481 put_in_list_t *put_in_list,
1482 gmx_bool bHaveVdW[])
1486 int nsearch, icg, igid, nn;
1490 t_block *cgs = &(top->cgs);
1491 t_blocka *excl = &(top->excls);
1494 gmx_bool bBox, bTriclinic;
1497 rlist2 = gmx::square(fr->rlist);
1499 bBox = (fr->ePBC != epbcNONE);
1502 for (m = 0; (m < DIM); m++)
1504 if (gmx_numzero(box_size[m]))
1506 gmx_fatal(FARGS, "Dividing by zero box size!");
1508 b_inv[m] = 1.0/box_size[m];
1510 bTriclinic = TRICLINIC(box);
1517 cginfo = fr->cginfo;
1520 for (icg = fr->cg0; (icg < fr->hcg); icg++)
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);
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);
1533 naaj = calc_naaj(icg, cgs->nr);
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);
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);
1548 for (nn = 0; (nn < ngid); nn++)
1550 for (k = 0; (k < SHIFTS); k++)
1552 nsbuf = &(ns_buf[nn][k]);
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;
1561 /* setexcl(nri,i_atoms,excl,FALSE,bexcl); */
1562 setexcl(cgs->index[icg], cgs->index[icg+1], excl, FALSE, bexcl);
1564 close_neighbor_lists(fr, FALSE);
1569 /************************************************
1571 * N S 5 G R I D S T U F F
1573 ************************************************/
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)
1580 int g_min, g_max, shift_home;
1613 g_min = (shift_min == shift_home ? 0 : ncpddc);
1614 g_max = (shift_max == shift_home ? ncpddc - 1 : Nx - 1);
1621 else if (shift_max < 0)
1636 /* Check one grid cell down */
1637 dcx = ((*g0 - 1) + 1)*gridx - x;
1649 /* Check one grid cell up */
1650 dcx = (*g1 + 1)*gridx - x;
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 /****************************************************
1666 * F A S T N E I G H B O R S E A R C H I N G
1668 * Optimized neighboursearching routine using grid
1669 * at least 1x1x1, see GROMACS manual
1671 ****************************************************/
1674 static void get_cutoff2(t_forcerec *fr, real *rs2)
1676 *rs2 = gmx::square(fr->rlist);
1679 static void init_nsgrid_lists(t_forcerec *fr, int ngid, gmx_ns_t *ns)
1684 get_cutoff2(fr, &rs2);
1686 /* Short range buffers */
1687 snew(ns->nl_sr, ngid);
1689 snew(ns->nsr, ngid);
1691 for (j = 0; (j < ngid); j++)
1693 snew(ns->nl_sr[j], MAX_CG);
1698 "ns5_core: rs2 = %g (nm^2)\n",
1703 static int nsgrid_core(const t_commrec *cr,
1707 gmx_localtop_t *top,
1710 const gmx_bool *bExcludeAlleg,
1711 const t_mdatoms *md,
1712 put_in_list_t *put_in_list,
1713 gmx_bool bHaveVdW[],
1714 gmx_bool bMakeQMMMnblist)
1720 const t_block *cgs = &(top->cgs);
1721 int *cginfo = fr->cginfo;
1722 /* int *i_atoms,*cgsindex=cgs->index; */
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;
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;
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;
1740 gmx_bool bDomDec, bTriclinicX, bTriclinicY;
1745 bDomDec = DOMAINDECOMP(cr);
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);
1757 get_cutoff2(fr, &rs2);
1768 gridind = grid->index;
1769 gridnra = grid->nra;
1772 gridx = grid->cell_size[XX];
1773 gridy = grid->cell_size[YY];
1774 gridz = grid->cell_size[ZZ];
1777 copy_rvec(grid->cell_offset, grid_offset);
1778 copy_ivec(grid->ncpddc, ncpddc);
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)
1789 /* This could happen due to rounding, when both ratios are 0.5 */
1796 /* We only want a list for the test particle */
1805 /* Set the shift range */
1806 for (d = 0; d < DIM; d++)
1810 /* Check if we need periodicity shifts.
1811 * Without PBC or with domain decomposition we don't need them.
1813 if (d >= ePBC2npbcdim(fr->ePBC) || (bDomDec && dd->nc[d] > 1))
1820 box[XX][XX] - std::abs(box[YY][XX]) - std::abs(box[ZZ][XX]) < std::sqrt(rs2))
1831 /* Loop over charge groups */
1832 for (icg = cg0; (icg < cg1); icg++)
1834 igid = GET_CGINFO_GID(cginfo[icg]);
1835 /* Skip this charge group if all energy groups are excluded! */
1836 if (bExcludeAlleg[igid])
1841 i0 = cgs->index[icg];
1843 if (bMakeQMMMnblist)
1845 /* Skip this charge group if it is not a QM atom while making a
1846 * QM/MM neighbourlist
1848 if (md->bQM[i0] == FALSE)
1850 continue; /* MM particle, go to next particle */
1853 /* Compute the number of charge groups that fall within the control
1856 naaj = calc_naaj(icg, cgsnr);
1863 /* make a normal neighbourlist */
1867 /* Get the j charge-group and dd cell shift ranges */
1868 dd_get_ns_ranges(cr->dd, icg, &jcg0, &jcg1, sh0, sh1);
1873 /* Compute the number of charge groups that fall within the control
1876 naaj = calc_naaj(icg, cgsnr);
1882 /* The i-particle is awlways the test particle,
1883 * so we want all j-particles
1885 max_jcg = cgsnr - 1;
1889 max_jcg = jcg1 - cgsnr;
1894 i_egp_flags = fr->egp_flags + igid*ngid;
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);
1899 ci2xyz(grid, icg, &cell_x, &cell_y, &cell_z);
1901 /* Changed iicg to icg, DvdS 990115
1902 * (but see consistency check above, DvdS 990330)
1905 fprintf(log, "icg=%5d, naaj=%5d, cell %d %d %d\n",
1906 icg, naaj, cell_x, cell_y, cell_z);
1908 /* Loop over shift vectors in three dimensions */
1909 for (tz = -shp[ZZ]; tz <= shp[ZZ]; tz++)
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);
1920 for (ty = -shp[YY]; ty <= shp[YY]; ty++)
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 */
1926 ygi = static_cast<int>(Ny + (YI - grid_offset[YY])*grid_y) - Ny;
1930 ygi = cell_y + ty*Ny;
1932 get_dx_dd(Ny, gridy, rs2, ygi, YI-grid_offset[YY],
1933 ncpddc[YY], sh0[YY], sh1[YY], &dy0, &dy1, dcy2);
1938 for (tx = -shp[XX]; tx <= shp[XX]; tx++)
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 */
1944 xgi = static_cast<int>(Nx + (XI - grid_offset[XX])*grid_x) - Nx;
1948 xgi = cell_x + tx*Nx;
1950 get_dx_dd(Nx, gridx, rs2, xgi, XI-grid_offset[XX],
1951 ncpddc[XX], sh0[XX], sh1[XX], &dx0, &dx1, dcx2);
1956 /* Get shift vector */
1957 shift = XYZ2IS(tx, ty, tz);
1959 range_check(shift, 0, SHIFTS);
1961 for (nn = 0; (nn < ngid); nn++)
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);
1972 for (dx = dx0; (dx <= dx1); dx++)
1974 tmp1 = rs2 - dcx2[dx];
1975 for (dy = dy0; (dy <= dy1); dy++)
1977 tmp2 = tmp1 - dcy2[dy];
1980 for (dz = dz0; (dz <= dz1); dz++)
1982 if (tmp2 > dcz2[dz])
1984 /* Find grid-cell cj in which possible neighbours are */
1985 cj = xyz2ci(Ny, Nz, dx, dy, dz);
1987 /* Check out how many cgs (nrj) there in this cell */
1990 /* Find the offset in the cg list */
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.
1998 (grida[cgj0] >= max_jcg &&
1999 (grida[cgj0] >= jcg1 || grida[cgj0+nrj-1] < jcg0)))
2005 for (j = 0; (j < nrj); j++)
2007 jjcg = grida[cgj0+j];
2009 /* check whether this guy is in range! */
2010 if ((jjcg >= jcg0 && jjcg < jcg1) ||
2013 r2 = calc_dx2(XI, YI, ZI, cgcm[jjcg]);
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))
2021 if (nsr[jgid] >= MAX_CG)
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);
2030 nl_sr[jgid][nsr[jgid]++] = jjcg;
2041 /* CHECK whether there is anything left in the buffers */
2042 for (nn = 0; (nn < ngid); nn++)
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);
2054 setexcl(cgs->index[icg], cgs->index[icg+1], &top->excls, FALSE, bexcl);
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.
2060 /* Close neighbourlists */
2061 close_neighbor_lists(fr, bMakeQMMMnblist);
2066 static void ns_realloc_natoms(gmx_ns_t *ns, int natoms)
2070 if (natoms > ns->nra_alloc)
2072 ns->nra_alloc = over_alloc_dd(natoms);
2073 srenew(ns->bexcl, ns->nra_alloc);
2074 for (i = 0; i < ns->nra_alloc; i++)
2081 void init_ns(FILE *fplog, const t_commrec *cr,
2082 gmx_ns_t *ns, t_forcerec *fr,
2083 const gmx_mtop_t *mtop)
2085 int icg, nr_in_cg, maxcg, i, j, jcg, ngid, ncg;
2087 /* Compute largest charge groups size (# atoms) */
2089 for (const gmx_moltype_t &molt : mtop->moltype)
2091 const t_block *cgs = &molt.cgs;
2092 for (icg = 0; (icg < cgs->nr); icg++)
2094 nr_in_cg = std::max(nr_in_cg, (cgs->index[icg+1]-cgs->index[icg]));
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)
2103 maxcg = sizeof(t_excl)*8;
2104 if (nr_in_cg > maxcg)
2106 gmx_fatal(FARGS, "Max #atoms in a charge group: %d > %d\n",
2110 ngid = mtop->groups.grps[egcENER].nr;
2111 snew(ns->bExcludeAlleg, ngid);
2112 for (i = 0; i < ngid; i++)
2114 ns->bExcludeAlleg[i] = TRUE;
2115 for (j = 0; j < ngid; j++)
2117 if (!(fr->egp_flags[i*ngid+j] & EGP_EXCL))
2119 ns->bExcludeAlleg[i] = FALSE;
2127 ns->grid = init_grid(fplog, fr);
2128 init_nsgrid_lists(fr, ngid, ns);
2133 snew(ns->ns_buf, ngid);
2134 for (i = 0; (i < ngid); i++)
2136 snew(ns->ns_buf[i], SHIFTS);
2138 ncg = ncg_mtop(mtop);
2139 snew(ns->simple_aaj, 2*ncg);
2140 for (jcg = 0; (jcg < ncg); jcg++)
2142 ns->simple_aaj[jcg] = jcg;
2143 ns->simple_aaj[jcg+ncg] = jcg;
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++)
2151 for (j = 0; (j < fr->ntype); j++)
2153 ns->bHaveVdW[i] = (ns->bHaveVdW[i] ||
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))));
2164 pr_bvec(debug, 0, "bHaveVdW", ns->bHaveVdW, fr->ntype, TRUE);
2168 ns->bexcl = nullptr;
2169 if (!DOMAINDECOMP(cr))
2171 ns_realloc_natoms(ns, mtop->natoms);
2174 ns->nblist_initialized = FALSE;
2176 /* nbr list debug dump */
2178 char *ptr = getenv("GMX_DUMP_NL");
2181 ns->dump_nl = strtol(ptr, nullptr, 10);
2184 fprintf(fplog, "GMX_DUMP_NL = %d", ns->dump_nl);
2194 void done_ns(gmx_ns_t *ns, int numEnergyGroups)
2196 sfree(ns->bExcludeAlleg);
2199 for (int i = 0; i < numEnergyGroups; i++)
2201 sfree(ns->ns_buf[i]);
2205 sfree(ns->simple_aaj);
2206 sfree(ns->bHaveVdW);
2207 done_grid(ns->grid);
2211 int search_neighbours(FILE *log,
2214 gmx_localtop_t *top,
2215 const gmx_groups_t *groups,
2216 const t_commrec *cr,
2218 const t_mdatoms *md,
2221 const t_block *cgs = &(top->cgs);
2222 rvec box_size, grid_x0, grid_x1;
2224 real min_size, grid_dens;
2230 gmx_domdec_zones_t *dd_zones;
2231 put_in_list_t *put_in_list;
2235 /* Set some local variables */
2237 ngid = groups->grps[egcENER].nr;
2239 for (m = 0; (m < DIM); m++)
2241 box_size[m] = box[m][m];
2244 if (fr->ePBC != epbcNONE)
2246 if (gmx::square(fr->rlist) >= max_cutoff2(fr->ePBC, box))
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.");
2252 min_size = std::min(box_size[XX], std::min(box_size[YY], box_size[ZZ]));
2253 if (2*fr->rlist >= min_size)
2255 gmx_fatal(FARGS, "One of the box diagonal elements has become smaller than twice the cut-off length.");
2260 if (DOMAINDECOMP(cr))
2262 ns_realloc_natoms(ns, cgs->index[cgs->nr]);
2265 /* Reset the neighbourlists */
2266 reset_neighbor_lists(fr);
2268 if (bGrid && bFillGrid)
2272 if (DOMAINDECOMP(cr))
2274 dd_zones = domdec_zones(cr->dd);
2280 get_nsgrid_boundaries(grid->nboundeddim, box, nullptr, nullptr, nullptr, nullptr,
2281 cgs->nr, fr->cg_cm, grid_x0, grid_x1, &grid_dens);
2283 grid_first(log, grid, nullptr, nullptr, box, grid_x0, grid_x1,
2284 fr->rlist, grid_dens);
2290 if (DOMAINDECOMP(cr))
2293 fill_grid(dd_zones, grid, end, -1, end, fr->cg_cm);
2295 grid->icg1 = dd_zones->izone[dd_zones->nizone-1].cg1;
2299 fill_grid(nullptr, grid, cgs->nr, fr->cg0, fr->hcg, fr->cg_cm);
2300 grid->icg0 = fr->cg0;
2301 grid->icg1 = fr->hcg;
2304 calc_elemnr(grid, start, end, cgs->nr);
2306 grid_last(grid, start, end, cgs->nr);
2311 print_grid(debug, grid);
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.
2319 fill_grid(nullptr, ns->grid, fr->hcg, fr->hcg-1, fr->hcg, fr->cg_cm);
2322 if (!fr->ns->bCGlist)
2324 put_in_list = put_in_list_at;
2328 put_in_list = put_in_list_cg;
2335 nsearch = nsgrid_core(cr, fr, box, ngid, top,
2336 grid, ns->bexcl, ns->bExcludeAlleg,
2337 md, put_in_list, ns->bHaveVdW,
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:
2349 if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
2351 nsearch += nsgrid_core(cr, fr, box, ngid, top,
2352 grid, ns->bexcl, ns->bExcludeAlleg,
2353 md, put_in_list_qmmm, ns->bHaveVdW,
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);
2364 inc_nrnb(nrnb, eNR_NS, nsearch);