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44 #include "gromacs/utility/smalloc.h"
46 #include "gromacs/math/utilities.h"
48 #include "types/commrec.h"
52 #include "nonbonded.h"
56 #include "gmx_fatal.h"
59 #include "mtop_util.h"
66 * E X C L U S I O N H A N D L I N G
70 static void SETEXCL_(t_excl e[], atom_id i, atom_id j)
74 static void RMEXCL_(t_excl e[], atom_id i, atom_id j)
76 e[j] = e[j] & ~(1<<i);
78 static gmx_bool ISEXCL_(t_excl e[], atom_id i, atom_id j)
80 return (gmx_bool)(e[j] & (1<<i));
82 static gmx_bool NOTEXCL_(t_excl e[], atom_id i, atom_id j)
84 return !(ISEXCL(e, i, j));
87 #define SETEXCL(e, i, j) (e)[((atom_id) (j))] |= (1<<((atom_id) (i)))
88 #define RMEXCL(e, i, j) (e)[((atom_id) (j))] &= (~(1<<((atom_id) (i))))
89 #define ISEXCL(e, i, j) (gmx_bool) ((e)[((atom_id) (j))] & (1<<((atom_id) (i))))
90 #define NOTEXCL(e, i, j) !(ISEXCL(e, i, j))
94 round_up_to_simd_width(int length, int simd_width)
96 int offset, newlength;
98 offset = (simd_width > 0) ? length % simd_width : 0;
100 return (offset == 0) ? length : length-offset+simd_width;
102 /************************************************
104 * U T I L I T I E S F O R N S
106 ************************************************/
108 void reallocate_nblist(t_nblist *nl)
112 fprintf(debug, "reallocating neigborlist (ielec=%d, ivdw=%d, igeometry=%d, type=%d), maxnri=%d\n",
113 nl->ielec, nl->ivdw, nl->igeometry, nl->type, nl->maxnri);
115 srenew(nl->iinr, nl->maxnri);
116 if (nl->igeometry == GMX_NBLIST_GEOMETRY_CG_CG)
118 srenew(nl->iinr_end, nl->maxnri);
120 srenew(nl->gid, nl->maxnri);
121 srenew(nl->shift, nl->maxnri);
122 srenew(nl->jindex, nl->maxnri+1);
126 static void init_nblist(FILE *log, t_nblist *nl_sr, t_nblist *nl_lr,
127 int maxsr, int maxlr,
128 int ivdw, int ivdwmod,
129 int ielec, int ielecmod,
130 int igeometry, int type)
136 for (i = 0; (i < 2); i++)
138 nl = (i == 0) ? nl_sr : nl_lr;
139 homenr = (i == 0) ? maxsr : maxlr;
147 /* Set coul/vdw in neighborlist, and for the normal loops we determine
148 * an index of which one to call.
151 nl->ivdwmod = ivdwmod;
153 nl->ielecmod = ielecmod;
155 nl->igeometry = igeometry;
157 if (nl->type == GMX_NBLIST_INTERACTION_FREE_ENERGY)
159 nl->igeometry = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
162 /* This will also set the simd_padding_width field */
163 gmx_nonbonded_set_kernel_pointers( (i == 0) ? log : NULL, nl);
165 /* maxnri is influenced by the number of shifts (maximum is 8)
166 * and the number of energy groups.
167 * If it is not enough, nl memory will be reallocated during the run.
168 * 4 seems to be a reasonable factor, which only causes reallocation
169 * during runs with tiny and many energygroups.
171 nl->maxnri = homenr*4;
181 reallocate_nblist(nl);
186 fprintf(debug, "Initiating neighbourlist (ielec=%d, ivdw=%d, type=%d) for %s interactions,\nwith %d SR, %d LR atoms.\n",
187 nl->ielec, nl->ivdw, nl->type, gmx_nblist_geometry_names[nl->igeometry], maxsr, maxlr);
192 void init_neighbor_list(FILE *log, t_forcerec *fr, int homenr)
194 /* Make maxlr tunable! (does not seem to be a big difference though)
195 * This parameter determines the number of i particles in a long range
196 * neighbourlist. Too few means many function calls, too many means
199 int maxsr, maxsr_wat, maxlr, maxlr_wat;
200 int ielec, ielecf, ivdw, ielecmod, ielecmodf, ivdwmod, type;
202 int igeometry_def, igeometry_w, igeometry_ww;
206 /* maxsr = homenr-fr->nWatMol*3; */
211 gmx_fatal(FARGS, "%s, %d: Negative number of short range atoms.\n"
212 "Call your Gromacs dealer for assistance.", __FILE__, __LINE__);
214 /* This is just for initial allocation, so we do not reallocate
215 * all the nlist arrays many times in a row.
216 * The numbers seem very accurate, but they are uncritical.
218 maxsr_wat = min(fr->nWatMol, (homenr+2)/3);
222 maxlr_wat = min(maxsr_wat, maxlr);
226 maxlr = maxlr_wat = 0;
229 /* Determine the values for ielec/ivdw. */
230 ielec = fr->nbkernel_elec_interaction;
231 ivdw = fr->nbkernel_vdw_interaction;
232 ielecmod = fr->nbkernel_elec_modifier;
233 ivdwmod = fr->nbkernel_vdw_modifier;
234 type = GMX_NBLIST_INTERACTION_STANDARD;
236 fr->ns.bCGlist = (getenv("GMX_NBLISTCG") != 0);
239 igeometry_def = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
243 igeometry_def = GMX_NBLIST_GEOMETRY_CG_CG;
246 fprintf(log, "\nUsing charge-group - charge-group neighbor lists and kernels\n\n");
250 if (fr->solvent_opt == esolTIP4P)
252 igeometry_w = GMX_NBLIST_GEOMETRY_WATER4_PARTICLE;
253 igeometry_ww = GMX_NBLIST_GEOMETRY_WATER4_WATER4;
257 igeometry_w = GMX_NBLIST_GEOMETRY_WATER3_PARTICLE;
258 igeometry_ww = GMX_NBLIST_GEOMETRY_WATER3_WATER3;
261 for (i = 0; i < fr->nnblists; i++)
263 nbl = &(fr->nblists[i]);
265 if ((fr->adress_type != eAdressOff) && (i >= fr->nnblists/2))
267 type = GMX_NBLIST_INTERACTION_ADRESS;
269 init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ], &nbl->nlist_lr[eNL_VDWQQ],
270 maxsr, maxlr, ivdw, ivdwmod, ielec, ielecmod, igeometry_def, type);
271 init_nblist(log, &nbl->nlist_sr[eNL_VDW], &nbl->nlist_lr[eNL_VDW],
272 maxsr, maxlr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, igeometry_def, type);
273 init_nblist(log, &nbl->nlist_sr[eNL_QQ], &nbl->nlist_lr[eNL_QQ],
274 maxsr, maxlr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_def, type);
275 init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_WATER], &nbl->nlist_lr[eNL_VDWQQ_WATER],
276 maxsr_wat, maxlr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_w, type);
277 init_nblist(log, &nbl->nlist_sr[eNL_QQ_WATER], &nbl->nlist_lr[eNL_QQ_WATER],
278 maxsr_wat, maxlr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_w, type);
279 init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_WATERWATER], &nbl->nlist_lr[eNL_VDWQQ_WATERWATER],
280 maxsr_wat, maxlr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_ww, type);
281 init_nblist(log, &nbl->nlist_sr[eNL_QQ_WATERWATER], &nbl->nlist_lr[eNL_QQ_WATERWATER],
282 maxsr_wat, maxlr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_ww, type);
284 /* Did we get the solvent loops so we can use optimized water kernels? */
285 if (nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf == NULL
286 || nbl->nlist_sr[eNL_QQ_WATER].kernelptr_vf == NULL
287 #ifndef DISABLE_WATERWATER_NLIST
288 || nbl->nlist_sr[eNL_VDWQQ_WATERWATER].kernelptr_vf == NULL
289 || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == NULL
293 fr->solvent_opt = esolNO;
296 fprintf(log, "Note: The available nonbonded kernels do not support water optimization - disabling.\n");
300 if (fr->efep != efepNO)
302 if ((fr->bEwald) && (fr->sc_alphacoul > 0)) /* need to handle long range differently if using softcore */
304 ielecf = GMX_NBKERNEL_ELEC_EWALD;
305 ielecmodf = eintmodNONE;
310 ielecmodf = ielecmod;
313 init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_FREE], &nbl->nlist_lr[eNL_VDWQQ_FREE],
314 maxsr, maxlr, ivdw, ivdwmod, ielecf, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
315 init_nblist(log, &nbl->nlist_sr[eNL_VDW_FREE], &nbl->nlist_lr[eNL_VDW_FREE],
316 maxsr, maxlr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
317 init_nblist(log, &nbl->nlist_sr[eNL_QQ_FREE], &nbl->nlist_lr[eNL_QQ_FREE],
318 maxsr, maxlr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielecf, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
322 if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
324 init_nblist(log, &fr->QMMMlist, NULL,
325 maxsr, maxlr, 0, 0, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_STANDARD);
333 fr->ns.nblist_initialized = TRUE;
336 static void reset_nblist(t_nblist *nl)
346 static void reset_neighbor_lists(t_forcerec *fr, gmx_bool bResetSR, gmx_bool bResetLR)
352 /* only reset the short-range nblist */
353 reset_nblist(&(fr->QMMMlist));
356 for (n = 0; n < fr->nnblists; n++)
358 for (i = 0; i < eNL_NR; i++)
362 reset_nblist( &(fr->nblists[n].nlist_sr[i]) );
366 reset_nblist( &(fr->nblists[n].nlist_lr[i]) );
375 static gmx_inline void new_i_nblist(t_nblist *nlist, atom_id i_atom, int shift, int gid)
377 int i, k, nri, nshift;
381 /* Check whether we have to increase the i counter */
383 (nlist->iinr[nri] != i_atom) ||
384 (nlist->shift[nri] != shift) ||
385 (nlist->gid[nri] != gid))
387 /* This is something else. Now see if any entries have
388 * been added in the list of the previous atom.
391 ((nlist->jindex[nri+1] > nlist->jindex[nri]) &&
392 (nlist->gid[nri] != -1)))
394 /* If so increase the counter */
397 if (nlist->nri >= nlist->maxnri)
399 nlist->maxnri += over_alloc_large(nlist->nri);
400 reallocate_nblist(nlist);
403 /* Set the number of neighbours and the atom number */
404 nlist->jindex[nri+1] = nlist->jindex[nri];
405 nlist->iinr[nri] = i_atom;
406 nlist->gid[nri] = gid;
407 nlist->shift[nri] = shift;
411 /* Adding to previous list. First remove possible previous padding */
412 if (nlist->simd_padding_width > 1)
414 while (nlist->nrj > 0 && nlist->jjnr[nlist->nrj-1] < 0)
422 static gmx_inline void close_i_nblist(t_nblist *nlist)
424 int nri = nlist->nri;
429 /* Add elements up to padding. Since we allocate memory in units
430 * of the simd_padding width, we do not have to check for possible
431 * list reallocation here.
433 while ((nlist->nrj % nlist->simd_padding_width) != 0)
435 /* Use -4 here, so we can write forces for 4 atoms before real data */
436 nlist->jjnr[nlist->nrj++] = -4;
438 nlist->jindex[nri+1] = nlist->nrj;
440 len = nlist->nrj - nlist->jindex[nri];
444 static gmx_inline void close_nblist(t_nblist *nlist)
446 /* Only close this nblist when it has been initialized.
447 * Avoid the creation of i-lists with no j-particles.
451 /* Some assembly kernels do not support empty lists,
452 * make sure here that we don't generate any empty lists.
453 * With the current ns code this branch is taken in two cases:
454 * No i-particles at all: nri=-1 here
455 * There are i-particles, but no j-particles; nri=0 here
461 /* Close list number nri by incrementing the count */
466 static gmx_inline void close_neighbor_lists(t_forcerec *fr, gmx_bool bMakeQMMMnblist)
472 close_nblist(&(fr->QMMMlist));
475 for (n = 0; n < fr->nnblists; n++)
477 for (i = 0; (i < eNL_NR); i++)
479 close_nblist(&(fr->nblists[n].nlist_sr[i]));
480 close_nblist(&(fr->nblists[n].nlist_lr[i]));
486 static gmx_inline void add_j_to_nblist(t_nblist *nlist, atom_id j_atom, gmx_bool bLR)
488 int nrj = nlist->nrj;
490 if (nlist->nrj >= nlist->maxnrj)
492 nlist->maxnrj = round_up_to_simd_width(over_alloc_small(nlist->nrj + 1), nlist->simd_padding_width);
496 fprintf(debug, "Increasing %s nblist (ielec=%d,ivdw=%d,type=%d,igeometry=%d) j size to %d\n",
497 bLR ? "LR" : "SR", nlist->ielec, nlist->ivdw, nlist->type, nlist->igeometry, nlist->maxnrj);
500 srenew(nlist->jjnr, nlist->maxnrj);
503 nlist->jjnr[nrj] = j_atom;
507 static gmx_inline void add_j_to_nblist_cg(t_nblist *nlist,
508 atom_id j_start, int j_end,
509 t_excl *bexcl, gmx_bool i_is_j,
512 int nrj = nlist->nrj;
515 if (nlist->nrj >= nlist->maxnrj)
517 nlist->maxnrj = over_alloc_small(nlist->nrj + 1);
520 fprintf(debug, "Increasing %s nblist (ielec=%d,ivdw=%d,type=%d,igeometry=%d) j size to %d\n",
521 bLR ? "LR" : "SR", nlist->ielec, nlist->ivdw, nlist->type, nlist->igeometry, nlist->maxnrj);
524 srenew(nlist->jjnr, nlist->maxnrj);
525 srenew(nlist->jjnr_end, nlist->maxnrj);
526 srenew(nlist->excl, nlist->maxnrj*MAX_CGCGSIZE);
529 nlist->jjnr[nrj] = j_start;
530 nlist->jjnr_end[nrj] = j_end;
532 if (j_end - j_start > MAX_CGCGSIZE)
534 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);
537 /* Set the exclusions */
538 for (j = j_start; j < j_end; j++)
540 nlist->excl[nrj*MAX_CGCGSIZE + j - j_start] = bexcl[j];
544 /* Avoid double counting of intra-cg interactions */
545 for (j = 1; j < j_end-j_start; j++)
547 nlist->excl[nrj*MAX_CGCGSIZE + j] |= (1<<j) - 1;
555 put_in_list_t (gmx_bool bHaveVdW[],
572 put_in_list_at(gmx_bool bHaveVdW[],
588 /* The a[] index has been removed,
589 * to put it back in i_atom should be a[i0] and jj should be a[jj].
594 t_nblist * vdwc_free = NULL;
595 t_nblist * vdw_free = NULL;
596 t_nblist * coul_free = NULL;
597 t_nblist * vdwc_ww = NULL;
598 t_nblist * coul_ww = NULL;
600 int i, j, jcg, igid, gid, nbl_ind, ind_ij;
601 atom_id jj, jj0, jj1, i_atom;
606 real *charge, *chargeB;
607 real qi, qiB, qq, rlj;
608 gmx_bool bFreeEnergy, bFree, bFreeJ, bNotEx, *bPert;
609 gmx_bool bDoVdW_i, bDoCoul_i, bDoCoul_i_sol;
613 /* Copy some pointers */
615 charge = md->chargeA;
616 chargeB = md->chargeB;
619 bPert = md->bPerturbed;
623 nicg = index[icg+1]-i0;
625 /* Get the i charge group info */
626 igid = GET_CGINFO_GID(cginfo[icg]);
628 iwater = (solvent_opt != esolNO) ? GET_CGINFO_SOLOPT(cginfo[icg]) : esolNO;
633 /* Check if any of the particles involved are perturbed.
634 * If not we can do the cheaper normal put_in_list
635 * and use more solvent optimization.
637 for (i = 0; i < nicg; i++)
639 bFreeEnergy |= bPert[i0+i];
641 /* Loop over the j charge groups */
642 for (j = 0; (j < nj && !bFreeEnergy); j++)
647 /* Finally loop over the atoms in the j-charge group */
648 for (jj = jj0; jj < jj1; jj++)
650 bFreeEnergy |= bPert[jj];
655 /* Unpack pointers to neighbourlist structs */
656 if (fr->nnblists == 1)
662 nbl_ind = fr->gid2nblists[GID(igid, jgid, ngid)];
666 nlist = fr->nblists[nbl_ind].nlist_lr;
670 nlist = fr->nblists[nbl_ind].nlist_sr;
673 if (iwater != esolNO)
675 vdwc = &nlist[eNL_VDWQQ_WATER];
676 vdw = &nlist[eNL_VDW];
677 coul = &nlist[eNL_QQ_WATER];
678 #ifndef DISABLE_WATERWATER_NLIST
679 vdwc_ww = &nlist[eNL_VDWQQ_WATERWATER];
680 coul_ww = &nlist[eNL_QQ_WATERWATER];
685 vdwc = &nlist[eNL_VDWQQ];
686 vdw = &nlist[eNL_VDW];
687 coul = &nlist[eNL_QQ];
692 if (iwater != esolNO)
694 /* Loop over the atoms in the i charge group */
696 gid = GID(igid, jgid, ngid);
697 /* Create new i_atom for each energy group */
698 if (bDoCoul && bDoVdW)
700 new_i_nblist(vdwc, i_atom, shift, gid);
701 #ifndef DISABLE_WATERWATER_NLIST
702 new_i_nblist(vdwc_ww, i_atom, shift, gid);
707 new_i_nblist(vdw, i_atom, shift, gid);
711 new_i_nblist(coul, i_atom, shift, gid);
712 #ifndef DISABLE_WATERWATER_NLIST
713 new_i_nblist(coul_ww, i_atom, shift, gid);
716 /* Loop over the j charge groups */
717 for (j = 0; (j < nj); j++)
727 jwater = GET_CGINFO_SOLOPT(cginfo[jcg]);
729 if (iwater == esolSPC && jwater == esolSPC)
731 /* Interaction between two SPC molecules */
734 /* VdW only - only first atoms in each water interact */
735 add_j_to_nblist(vdw, jj0, bLR);
739 #ifdef DISABLE_WATERWATER_NLIST
740 /* Add entries for the three atoms - only do VdW if we need to */
743 add_j_to_nblist(coul, jj0, bLR);
747 add_j_to_nblist(vdwc, jj0, bLR);
749 add_j_to_nblist(coul, jj0+1, bLR);
750 add_j_to_nblist(coul, jj0+2, bLR);
752 /* One entry for the entire water-water interaction */
755 add_j_to_nblist(coul_ww, jj0, bLR);
759 add_j_to_nblist(vdwc_ww, jj0, bLR);
764 else if (iwater == esolTIP4P && jwater == esolTIP4P)
766 /* Interaction between two TIP4p molecules */
769 /* VdW only - only first atoms in each water interact */
770 add_j_to_nblist(vdw, jj0, bLR);
774 #ifdef DISABLE_WATERWATER_NLIST
775 /* Add entries for the four atoms - only do VdW if we need to */
778 add_j_to_nblist(vdw, jj0, bLR);
780 add_j_to_nblist(coul, jj0+1, bLR);
781 add_j_to_nblist(coul, jj0+2, bLR);
782 add_j_to_nblist(coul, jj0+3, bLR);
784 /* One entry for the entire water-water interaction */
787 add_j_to_nblist(coul_ww, jj0, bLR);
791 add_j_to_nblist(vdwc_ww, jj0, bLR);
798 /* j charge group is not water, but i is.
799 * Add entries to the water-other_atom lists; the geometry of the water
800 * molecule doesn't matter - that is taken care of in the nonbonded kernel,
801 * so we don't care if it is SPC or TIP4P...
808 for (jj = jj0; (jj < jj1); jj++)
812 add_j_to_nblist(coul, jj, bLR);
818 for (jj = jj0; (jj < jj1); jj++)
820 if (bHaveVdW[type[jj]])
822 add_j_to_nblist(vdw, jj, bLR);
828 /* _charge_ _groups_ interact with both coulomb and LJ */
829 /* Check which atoms we should add to the lists! */
830 for (jj = jj0; (jj < jj1); jj++)
832 if (bHaveVdW[type[jj]])
836 add_j_to_nblist(vdwc, jj, bLR);
840 add_j_to_nblist(vdw, jj, bLR);
843 else if (charge[jj] != 0)
845 add_j_to_nblist(coul, jj, bLR);
852 close_i_nblist(coul);
853 close_i_nblist(vdwc);
854 #ifndef DISABLE_WATERWATER_NLIST
855 close_i_nblist(coul_ww);
856 close_i_nblist(vdwc_ww);
861 /* no solvent as i charge group */
862 /* Loop over the atoms in the i charge group */
863 for (i = 0; i < nicg; i++)
866 gid = GID(igid, jgid, ngid);
869 /* Create new i_atom for each energy group */
870 if (bDoVdW && bDoCoul)
872 new_i_nblist(vdwc, i_atom, shift, gid);
876 new_i_nblist(vdw, i_atom, shift, gid);
880 new_i_nblist(coul, i_atom, shift, gid);
882 bDoVdW_i = (bDoVdW && bHaveVdW[type[i_atom]]);
883 bDoCoul_i = (bDoCoul && qi != 0);
885 if (bDoVdW_i || bDoCoul_i)
887 /* Loop over the j charge groups */
888 for (j = 0; (j < nj); j++)
892 /* Check for large charge groups */
903 /* Finally loop over the atoms in the j-charge group */
904 for (jj = jj0; jj < jj1; jj++)
906 bNotEx = NOTEXCL(bExcl, i, jj);
914 add_j_to_nblist(coul, jj, bLR);
919 if (bHaveVdW[type[jj]])
921 add_j_to_nblist(vdw, jj, bLR);
926 if (bHaveVdW[type[jj]])
930 add_j_to_nblist(vdwc, jj, bLR);
934 add_j_to_nblist(vdw, jj, bLR);
937 else if (charge[jj] != 0)
939 add_j_to_nblist(coul, jj, bLR);
947 close_i_nblist(coul);
948 close_i_nblist(vdwc);
954 /* we are doing free energy */
955 vdwc_free = &nlist[eNL_VDWQQ_FREE];
956 vdw_free = &nlist[eNL_VDW_FREE];
957 coul_free = &nlist[eNL_QQ_FREE];
958 /* Loop over the atoms in the i charge group */
959 for (i = 0; i < nicg; i++)
962 gid = GID(igid, jgid, ngid);
964 qiB = chargeB[i_atom];
966 /* Create new i_atom for each energy group */
967 if (bDoVdW && bDoCoul)
969 new_i_nblist(vdwc, i_atom, shift, gid);
973 new_i_nblist(vdw, i_atom, shift, gid);
977 new_i_nblist(coul, i_atom, shift, gid);
980 new_i_nblist(vdw_free, i_atom, shift, gid);
981 new_i_nblist(coul_free, i_atom, shift, gid);
982 new_i_nblist(vdwc_free, i_atom, shift, gid);
984 bDoVdW_i = (bDoVdW &&
985 (bHaveVdW[type[i_atom]] || bHaveVdW[typeB[i_atom]]));
986 bDoCoul_i = (bDoCoul && (qi != 0 || qiB != 0));
987 /* For TIP4P the first atom does not have a charge,
988 * but the last three do. So we should still put an atom
989 * without LJ but with charge in the water-atom neighborlist
990 * for a TIP4p i charge group.
991 * For SPC type water the first atom has LJ and charge,
992 * so there is no such problem.
994 if (iwater == esolNO)
996 bDoCoul_i_sol = bDoCoul_i;
1000 bDoCoul_i_sol = bDoCoul;
1003 if (bDoVdW_i || bDoCoul_i_sol)
1005 /* Loop over the j charge groups */
1006 for (j = 0; (j < nj); j++)
1010 /* Check for large charge groups */
1021 /* Finally loop over the atoms in the j-charge group */
1022 bFree = bPert[i_atom];
1023 for (jj = jj0; (jj < jj1); jj++)
1025 bFreeJ = bFree || bPert[jj];
1026 /* Complicated if, because the water H's should also
1027 * see perturbed j-particles
1029 if (iwater == esolNO || i == 0 || bFreeJ)
1031 bNotEx = NOTEXCL(bExcl, i, jj);
1039 if (charge[jj] != 0 || chargeB[jj] != 0)
1041 add_j_to_nblist(coul_free, jj, bLR);
1044 else if (!bDoCoul_i)
1046 if (bHaveVdW[type[jj]] || bHaveVdW[typeB[jj]])
1048 add_j_to_nblist(vdw_free, jj, bLR);
1053 if (bHaveVdW[type[jj]] || bHaveVdW[typeB[jj]])
1055 if (charge[jj] != 0 || chargeB[jj] != 0)
1057 add_j_to_nblist(vdwc_free, jj, bLR);
1061 add_j_to_nblist(vdw_free, jj, bLR);
1064 else if (charge[jj] != 0 || chargeB[jj] != 0)
1066 add_j_to_nblist(coul_free, jj, bLR);
1072 /* This is done whether or not bWater is set */
1073 if (charge[jj] != 0)
1075 add_j_to_nblist(coul, jj, bLR);
1078 else if (!bDoCoul_i_sol)
1080 if (bHaveVdW[type[jj]])
1082 add_j_to_nblist(vdw, jj, bLR);
1087 if (bHaveVdW[type[jj]])
1089 if (charge[jj] != 0)
1091 add_j_to_nblist(vdwc, jj, bLR);
1095 add_j_to_nblist(vdw, jj, bLR);
1098 else if (charge[jj] != 0)
1100 add_j_to_nblist(coul, jj, bLR);
1108 close_i_nblist(vdw);
1109 close_i_nblist(coul);
1110 close_i_nblist(vdwc);
1111 close_i_nblist(vdw_free);
1112 close_i_nblist(coul_free);
1113 close_i_nblist(vdwc_free);
1119 put_in_list_adress(gmx_bool bHaveVdW[],
1135 /* The a[] index has been removed,
1136 * to put it back in i_atom should be a[i0] and jj should be a[jj].
1141 t_nblist * vdwc_adress = NULL;
1142 t_nblist * vdw_adress = NULL;
1143 t_nblist * coul_adress = NULL;
1144 t_nblist * vdwc_ww = NULL;
1145 t_nblist * coul_ww = NULL;
1147 int i, j, jcg, igid, gid, nbl_ind, nbl_ind_adress;
1148 atom_id jj, jj0, jj1, i_atom;
1153 real *charge, *chargeB;
1155 real qi, qiB, qq, rlj;
1156 gmx_bool bFreeEnergy, bFree, bFreeJ, bNotEx, *bPert;
1157 gmx_bool bDoVdW_i, bDoCoul_i, bDoCoul_i_sol;
1159 gmx_bool j_all_atom;
1161 t_nblist *nlist, *nlist_adress;
1162 gmx_bool bEnergyGroupCG;
1164 /* Copy some pointers */
1165 cginfo = fr->cginfo;
1166 charge = md->chargeA;
1167 chargeB = md->chargeB;
1170 bPert = md->bPerturbed;
1173 /* Get atom range */
1175 nicg = index[icg+1]-i0;
1177 /* Get the i charge group info */
1178 igid = GET_CGINFO_GID(cginfo[icg]);
1180 iwater = (solvent_opt != esolNO) ? GET_CGINFO_SOLOPT(cginfo[icg]) : esolNO;
1184 gmx_fatal(FARGS, "AdResS does not support free energy pertubation\n");
1187 /* Unpack pointers to neighbourlist structs */
1188 if (fr->nnblists == 2)
1195 nbl_ind = fr->gid2nblists[GID(igid, jgid, ngid)];
1196 nbl_ind_adress = nbl_ind+fr->nnblists/2;
1200 nlist = fr->nblists[nbl_ind].nlist_lr;
1201 nlist_adress = fr->nblists[nbl_ind_adress].nlist_lr;
1205 nlist = fr->nblists[nbl_ind].nlist_sr;
1206 nlist_adress = fr->nblists[nbl_ind_adress].nlist_sr;
1210 vdwc = &nlist[eNL_VDWQQ];
1211 vdw = &nlist[eNL_VDW];
1212 coul = &nlist[eNL_QQ];
1214 vdwc_adress = &nlist_adress[eNL_VDWQQ];
1215 vdw_adress = &nlist_adress[eNL_VDW];
1216 coul_adress = &nlist_adress[eNL_QQ];
1218 /* We do not support solvent optimization with AdResS for now.
1219 For this we would need hybrid solvent-other kernels */
1221 /* no solvent as i charge group */
1222 /* Loop over the atoms in the i charge group */
1223 for (i = 0; i < nicg; i++)
1226 gid = GID(igid, jgid, ngid);
1227 qi = charge[i_atom];
1229 /* Create new i_atom for each energy group */
1230 if (bDoVdW && bDoCoul)
1232 new_i_nblist(vdwc, i_atom, shift, gid);
1233 new_i_nblist(vdwc_adress, i_atom, shift, gid);
1238 new_i_nblist(vdw, i_atom, shift, gid);
1239 new_i_nblist(vdw_adress, i_atom, shift, gid);
1244 new_i_nblist(coul, i_atom, shift, gid);
1245 new_i_nblist(coul_adress, i_atom, shift, gid);
1247 bDoVdW_i = (bDoVdW && bHaveVdW[type[i_atom]]);
1248 bDoCoul_i = (bDoCoul && qi != 0);
1250 /* Here we find out whether the energy groups interaction belong to a
1251 * coarse-grained (vsite) or atomistic interaction. Note that, beacuse
1252 * interactions between coarse-grained and other (atomistic) energygroups
1253 * are excluded automatically by grompp, it is sufficient to check for
1254 * the group id of atom i (igid) */
1255 bEnergyGroupCG = !egp_explicit(fr, igid);
1257 if (bDoVdW_i || bDoCoul_i)
1259 /* Loop over the j charge groups */
1260 for (j = 0; (j < nj); j++)
1264 /* Check for large charge groups */
1275 /* Finally loop over the atoms in the j-charge group */
1276 for (jj = jj0; jj < jj1; jj++)
1278 bNotEx = NOTEXCL(bExcl, i, jj);
1280 /* Now we have to exclude interactions which will be zero
1281 * anyway due to the AdResS weights (in previous implementations
1282 * this was done in the force kernel). This is necessary as
1283 * pure interactions (those with b_hybrid=false, i.e. w_i*w_j==1 or 0)
1284 * are put into neighbour lists which will be passed to the
1285 * standard (optimized) kernels for speed. The interactions with
1286 * b_hybrid=true are placed into the _adress neighbour lists and
1287 * processed by the generic AdResS kernel.
1289 if ( (bEnergyGroupCG &&
1290 wf[i_atom] >= 1-GMX_REAL_EPS && wf[jj] >= 1-GMX_REAL_EPS ) ||
1291 ( !bEnergyGroupCG && wf[jj] <= GMX_REAL_EPS ) )
1296 b_hybrid = !((wf[i_atom] >= 1-GMX_REAL_EPS && wf[jj] >= 1-GMX_REAL_EPS) ||
1297 (wf[i_atom] <= GMX_REAL_EPS && wf[jj] <= GMX_REAL_EPS));
1303 if (charge[jj] != 0)
1307 add_j_to_nblist(coul, jj, bLR);
1311 add_j_to_nblist(coul_adress, jj, bLR);
1315 else if (!bDoCoul_i)
1317 if (bHaveVdW[type[jj]])
1321 add_j_to_nblist(vdw, jj, bLR);
1325 add_j_to_nblist(vdw_adress, jj, bLR);
1331 if (bHaveVdW[type[jj]])
1333 if (charge[jj] != 0)
1337 add_j_to_nblist(vdwc, jj, bLR);
1341 add_j_to_nblist(vdwc_adress, jj, bLR);
1348 add_j_to_nblist(vdw, jj, bLR);
1352 add_j_to_nblist(vdw_adress, jj, bLR);
1357 else if (charge[jj] != 0)
1361 add_j_to_nblist(coul, jj, bLR);
1365 add_j_to_nblist(coul_adress, jj, bLR);
1374 close_i_nblist(vdw);
1375 close_i_nblist(coul);
1376 close_i_nblist(vdwc);
1377 close_i_nblist(vdw_adress);
1378 close_i_nblist(coul_adress);
1379 close_i_nblist(vdwc_adress);
1385 put_in_list_qmmm(gmx_bool gmx_unused bHaveVdW[],
1387 t_mdatoms gmx_unused * md,
1397 gmx_bool gmx_unused bDoVdW,
1398 gmx_bool gmx_unused bDoCoul,
1399 int gmx_unused solvent_opt)
1402 int i, j, jcg, igid, gid;
1403 atom_id jj, jj0, jj1, i_atom;
1407 /* Get atom range */
1409 nicg = index[icg+1]-i0;
1411 /* Get the i charge group info */
1412 igid = GET_CGINFO_GID(fr->cginfo[icg]);
1414 coul = &fr->QMMMlist;
1416 /* Loop over atoms in the ith charge group */
1417 for (i = 0; i < nicg; i++)
1420 gid = GID(igid, jgid, ngid);
1421 /* Create new i_atom for each energy group */
1422 new_i_nblist(coul, i_atom, shift, gid);
1424 /* Loop over the j charge groups */
1425 for (j = 0; j < nj; j++)
1429 /* Charge groups cannot have QM and MM atoms simultaneously */
1434 /* Finally loop over the atoms in the j-charge group */
1435 for (jj = jj0; jj < jj1; jj++)
1437 bNotEx = NOTEXCL(bExcl, i, jj);
1440 add_j_to_nblist(coul, jj, bLR);
1445 close_i_nblist(coul);
1450 put_in_list_cg(gmx_bool gmx_unused bHaveVdW[],
1452 t_mdatoms gmx_unused * md,
1462 gmx_bool gmx_unused bDoVdW,
1463 gmx_bool gmx_unused bDoCoul,
1464 int gmx_unused solvent_opt)
1467 int igid, gid, nbl_ind;
1471 cginfo = fr->cginfo[icg];
1473 igid = GET_CGINFO_GID(cginfo);
1474 gid = GID(igid, jgid, ngid);
1476 /* Unpack pointers to neighbourlist structs */
1477 if (fr->nnblists == 1)
1483 nbl_ind = fr->gid2nblists[gid];
1487 vdwc = &fr->nblists[nbl_ind].nlist_lr[eNL_VDWQQ];
1491 vdwc = &fr->nblists[nbl_ind].nlist_sr[eNL_VDWQQ];
1494 /* Make a new neighbor list for charge group icg.
1495 * Currently simply one neighbor list is made with LJ and Coulomb.
1496 * If required, zero interactions could be removed here
1497 * or in the force loop.
1499 new_i_nblist(vdwc, index[icg], shift, gid);
1500 vdwc->iinr_end[vdwc->nri] = index[icg+1];
1502 for (j = 0; (j < nj); j++)
1505 /* Skip the icg-icg pairs if all self interactions are excluded */
1506 if (!(jcg == icg && GET_CGINFO_EXCL_INTRA(cginfo)))
1508 /* Here we add the j charge group jcg to the list,
1509 * exclusions are also added to the list.
1511 add_j_to_nblist_cg(vdwc, index[jcg], index[jcg+1], bExcl, icg == jcg, bLR);
1515 close_i_nblist(vdwc);
1518 static void setexcl(atom_id start, atom_id end, t_blocka *excl, gmx_bool b,
1525 for (i = start; i < end; i++)
1527 for (k = excl->index[i]; k < excl->index[i+1]; k++)
1529 SETEXCL(bexcl, i-start, excl->a[k]);
1535 for (i = start; i < end; i++)
1537 for (k = excl->index[i]; k < excl->index[i+1]; k++)
1539 RMEXCL(bexcl, i-start, excl->a[k]);
1545 int calc_naaj(int icg, int cgtot)
1549 if ((cgtot % 2) == 1)
1551 /* Odd number of charge groups, easy */
1552 naaj = 1 + (cgtot/2);
1554 else if ((cgtot % 4) == 0)
1556 /* Multiple of four is hard */
1593 fprintf(log, "naaj=%d\n", naaj);
1599 /************************************************
1601 * S I M P L E C O R E S T U F F
1603 ************************************************/
1605 static real calc_image_tric(rvec xi, rvec xj, matrix box,
1606 rvec b_inv, int *shift)
1608 /* This code assumes that the cut-off is smaller than
1609 * a half times the smallest diagonal element of the box.
1611 const real h25 = 2.5;
1616 /* Compute diff vector */
1617 dz = xj[ZZ] - xi[ZZ];
1618 dy = xj[YY] - xi[YY];
1619 dx = xj[XX] - xi[XX];
1621 /* Perform NINT operation, using trunc operation, therefore
1622 * we first add 2.5 then subtract 2 again
1624 tz = dz*b_inv[ZZ] + h25;
1626 dz -= tz*box[ZZ][ZZ];
1627 dy -= tz*box[ZZ][YY];
1628 dx -= tz*box[ZZ][XX];
1630 ty = dy*b_inv[YY] + h25;
1632 dy -= ty*box[YY][YY];
1633 dx -= ty*box[YY][XX];
1635 tx = dx*b_inv[XX]+h25;
1637 dx -= tx*box[XX][XX];
1639 /* Distance squared */
1640 r2 = (dx*dx) + (dy*dy) + (dz*dz);
1642 *shift = XYZ2IS(tx, ty, tz);
1647 static real calc_image_rect(rvec xi, rvec xj, rvec box_size,
1648 rvec b_inv, int *shift)
1650 const real h15 = 1.5;
1656 /* Compute diff vector */
1657 dx = xj[XX] - xi[XX];
1658 dy = xj[YY] - xi[YY];
1659 dz = xj[ZZ] - xi[ZZ];
1661 /* Perform NINT operation, using trunc operation, therefore
1662 * we first add 1.5 then subtract 1 again
1664 tx = dx*b_inv[XX] + h15;
1665 ty = dy*b_inv[YY] + h15;
1666 tz = dz*b_inv[ZZ] + h15;
1671 /* Correct diff vector for translation */
1672 ddx = tx*box_size[XX] - dx;
1673 ddy = ty*box_size[YY] - dy;
1674 ddz = tz*box_size[ZZ] - dz;
1676 /* Distance squared */
1677 r2 = (ddx*ddx) + (ddy*ddy) + (ddz*ddz);
1679 *shift = XYZ2IS(tx, ty, tz);
1684 static void add_simple(t_ns_buf *nsbuf, int nrj, atom_id cg_j,
1685 gmx_bool bHaveVdW[], int ngid, t_mdatoms *md,
1686 int icg, int jgid, t_block *cgs, t_excl bexcl[],
1687 int shift, t_forcerec *fr, put_in_list_t *put_in_list)
1689 if (nsbuf->nj + nrj > MAX_CG)
1691 put_in_list(bHaveVdW, ngid, md, icg, jgid, nsbuf->ncg, nsbuf->jcg,
1692 cgs->index, bexcl, shift, fr, FALSE, TRUE, TRUE, fr->solvent_opt);
1693 /* Reset buffer contents */
1694 nsbuf->ncg = nsbuf->nj = 0;
1696 nsbuf->jcg[nsbuf->ncg++] = cg_j;
1700 static void ns_inner_tric(rvec x[], int icg, int *i_egp_flags,
1701 int njcg, atom_id jcg[],
1702 matrix box, rvec b_inv, real rcut2,
1703 t_block *cgs, t_ns_buf **ns_buf,
1704 gmx_bool bHaveVdW[], int ngid, t_mdatoms *md,
1705 t_excl bexcl[], t_forcerec *fr,
1706 put_in_list_t *put_in_list)
1710 int *cginfo = fr->cginfo;
1711 atom_id cg_j, *cgindex;
1714 cgindex = cgs->index;
1716 for (j = 0; (j < njcg); j++)
1719 nrj = cgindex[cg_j+1]-cgindex[cg_j];
1720 if (calc_image_tric(x[icg], x[cg_j], box, b_inv, &shift) < rcut2)
1722 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1723 if (!(i_egp_flags[jgid] & EGP_EXCL))
1725 add_simple(&ns_buf[jgid][shift], nrj, cg_j,
1726 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, shift, fr,
1733 static void ns_inner_rect(rvec x[], int icg, int *i_egp_flags,
1734 int njcg, atom_id jcg[],
1735 gmx_bool bBox, rvec box_size, rvec b_inv, real rcut2,
1736 t_block *cgs, t_ns_buf **ns_buf,
1737 gmx_bool bHaveVdW[], int ngid, t_mdatoms *md,
1738 t_excl bexcl[], t_forcerec *fr,
1739 put_in_list_t *put_in_list)
1743 int *cginfo = fr->cginfo;
1744 atom_id cg_j, *cgindex;
1747 cgindex = cgs->index;
1751 for (j = 0; (j < njcg); j++)
1754 nrj = cgindex[cg_j+1]-cgindex[cg_j];
1755 if (calc_image_rect(x[icg], x[cg_j], box_size, b_inv, &shift) < rcut2)
1757 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1758 if (!(i_egp_flags[jgid] & EGP_EXCL))
1760 add_simple(&ns_buf[jgid][shift], nrj, cg_j,
1761 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, shift, fr,
1769 for (j = 0; (j < njcg); j++)
1772 nrj = cgindex[cg_j+1]-cgindex[cg_j];
1773 if ((rcut2 == 0) || (distance2(x[icg], x[cg_j]) < rcut2))
1775 jgid = GET_CGINFO_GID(cginfo[cg_j]);
1776 if (!(i_egp_flags[jgid] & EGP_EXCL))
1778 add_simple(&ns_buf[jgid][CENTRAL], nrj, cg_j,
1779 bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, CENTRAL, fr,
1787 /* ns_simple_core needs to be adapted for QMMM still 2005 */
1789 static int ns_simple_core(t_forcerec *fr,
1790 gmx_localtop_t *top,
1792 matrix box, rvec box_size,
1793 t_excl bexcl[], atom_id *aaj,
1794 int ngid, t_ns_buf **ns_buf,
1795 put_in_list_t *put_in_list, gmx_bool bHaveVdW[])
1799 int nsearch, icg, jcg, igid, i0, nri, nn;
1802 /* atom_id *i_atoms; */
1803 t_block *cgs = &(top->cgs);
1804 t_blocka *excl = &(top->excls);
1807 gmx_bool bBox, bTriclinic;
1810 rlist2 = sqr(fr->rlist);
1812 bBox = (fr->ePBC != epbcNONE);
1815 for (m = 0; (m < DIM); m++)
1817 b_inv[m] = divide_err(1.0, box_size[m]);
1819 bTriclinic = TRICLINIC(box);
1826 cginfo = fr->cginfo;
1829 for (icg = fr->cg0; (icg < fr->hcg); icg++)
1832 i0 = cgs->index[icg];
1833 nri = cgs->index[icg+1]-i0;
1834 i_atoms = &(cgs->a[i0]);
1835 i_eg_excl = fr->eg_excl + ngid*md->cENER[*i_atoms];
1836 setexcl(nri,i_atoms,excl,TRUE,bexcl);
1838 igid = GET_CGINFO_GID(cginfo[icg]);
1839 i_egp_flags = fr->egp_flags + ngid*igid;
1840 setexcl(cgs->index[icg], cgs->index[icg+1], excl, TRUE, bexcl);
1842 naaj = calc_naaj(icg, cgs->nr);
1845 ns_inner_tric(fr->cg_cm, icg, i_egp_flags, naaj, &(aaj[icg]),
1846 box, b_inv, rlist2, cgs, ns_buf,
1847 bHaveVdW, ngid, md, bexcl, fr, put_in_list);
1851 ns_inner_rect(fr->cg_cm, icg, i_egp_flags, naaj, &(aaj[icg]),
1852 bBox, box_size, b_inv, rlist2, cgs, ns_buf,
1853 bHaveVdW, ngid, md, bexcl, fr, put_in_list);
1857 for (nn = 0; (nn < ngid); nn++)
1859 for (k = 0; (k < SHIFTS); k++)
1861 nsbuf = &(ns_buf[nn][k]);
1864 put_in_list(bHaveVdW, ngid, md, icg, nn, nsbuf->ncg, nsbuf->jcg,
1865 cgs->index, bexcl, k, fr, FALSE, TRUE, TRUE, fr->solvent_opt);
1866 nsbuf->ncg = nsbuf->nj = 0;
1870 /* setexcl(nri,i_atoms,excl,FALSE,bexcl); */
1871 setexcl(cgs->index[icg], cgs->index[icg+1], excl, FALSE, bexcl);
1873 close_neighbor_lists(fr, FALSE);
1878 /************************************************
1880 * N S 5 G R I D S T U F F
1882 ************************************************/
1884 static gmx_inline void get_dx(int Nx, real gridx, real rc2, int xgi, real x,
1885 int *dx0, int *dx1, real *dcx2)
1913 for (i = xgi0; i >= 0; i--)
1915 dcx = (i+1)*gridx-x;
1924 for (i = xgi1; i < Nx; i++)
1937 static gmx_inline void get_dx_dd(int Nx, real gridx, real rc2, int xgi, real x,
1938 int ncpddc, int shift_min, int shift_max,
1939 int *g0, int *g1, real *dcx2)
1942 int g_min, g_max, shift_home;
1975 g_min = (shift_min == shift_home ? 0 : ncpddc);
1976 g_max = (shift_max == shift_home ? ncpddc - 1 : Nx - 1);
1983 else if (shift_max < 0)
1998 /* Check one grid cell down */
1999 dcx = ((*g0 - 1) + 1)*gridx - x;
2011 /* Check one grid cell up */
2012 dcx = (*g1 + 1)*gridx - x;
2024 #define sqr(x) ((x)*(x))
2025 #define calc_dx2(XI, YI, ZI, y) (sqr(XI-y[XX]) + sqr(YI-y[YY]) + sqr(ZI-y[ZZ]))
2026 #define calc_cyl_dx2(XI, YI, y) (sqr(XI-y[XX]) + sqr(YI-y[YY]))
2027 /****************************************************
2029 * F A S T N E I G H B O R S E A R C H I N G
2031 * Optimized neighboursearching routine using grid
2032 * at least 1x1x1, see GROMACS manual
2034 ****************************************************/
2037 static void get_cutoff2(t_forcerec *fr, gmx_bool bDoLongRange,
2038 real *rvdw2, real *rcoul2,
2039 real *rs2, real *rm2, real *rl2)
2041 *rs2 = sqr(fr->rlist);
2043 if (bDoLongRange && fr->bTwinRange)
2045 /* With plain cut-off or RF we need to make the list exactly
2046 * up to the cut-off and the cut-off's can be different,
2047 * so we can not simply set them to rlistlong.
2048 * To keep this code compatible with (exotic) old cases,
2049 * we also create lists up to rvdw/rcoulomb for PME and Ewald.
2050 * The interaction check should correspond to:
2051 * !ir_vdw/coulomb_might_be_zero_at_cutoff from inputrec.c.
2053 if (((fr->vdwtype == evdwCUT || fr->vdwtype == evdwPME) &&
2054 fr->vdw_modifier == eintmodNONE) ||
2055 fr->rvdw <= fr->rlist)
2057 *rvdw2 = sqr(fr->rvdw);
2061 *rvdw2 = sqr(fr->rlistlong);
2063 if (((fr->eeltype == eelCUT ||
2064 (EEL_RF(fr->eeltype) && fr->eeltype != eelRF_ZERO) ||
2065 fr->eeltype == eelPME ||
2066 fr->eeltype == eelEWALD) &&
2067 fr->coulomb_modifier == eintmodNONE) ||
2068 fr->rcoulomb <= fr->rlist)
2070 *rcoul2 = sqr(fr->rcoulomb);
2074 *rcoul2 = sqr(fr->rlistlong);
2079 /* Workaround for a gcc -O3 or -ffast-math problem */
2083 *rm2 = min(*rvdw2, *rcoul2);
2084 *rl2 = max(*rvdw2, *rcoul2);
2087 static void init_nsgrid_lists(t_forcerec *fr, int ngid, gmx_ns_t *ns)
2089 real rvdw2, rcoul2, rs2, rm2, rl2;
2092 get_cutoff2(fr, TRUE, &rvdw2, &rcoul2, &rs2, &rm2, &rl2);
2094 /* Short range buffers */
2095 snew(ns->nl_sr, ngid);
2097 snew(ns->nsr, ngid);
2098 snew(ns->nlr_ljc, ngid);
2099 snew(ns->nlr_one, ngid);
2101 /* Always allocate both list types, since rcoulomb might now change with PME load balancing */
2102 /* Long range VdW and Coul buffers */
2103 snew(ns->nl_lr_ljc, ngid);
2104 /* Long range VdW or Coul only buffers */
2105 snew(ns->nl_lr_one, ngid);
2107 for (j = 0; (j < ngid); j++)
2109 snew(ns->nl_sr[j], MAX_CG);
2110 snew(ns->nl_lr_ljc[j], MAX_CG);
2111 snew(ns->nl_lr_one[j], MAX_CG);
2116 "ns5_core: rs2 = %g, rm2 = %g, rl2 = %g (nm^2)\n",
2121 static int nsgrid_core(t_commrec *cr, t_forcerec *fr,
2122 matrix box, int ngid,
2123 gmx_localtop_t *top,
2125 t_excl bexcl[], gmx_bool *bExcludeAlleg,
2127 put_in_list_t *put_in_list,
2128 gmx_bool bHaveVdW[],
2129 gmx_bool bDoLongRange, gmx_bool bMakeQMMMnblist)
2132 atom_id **nl_lr_ljc, **nl_lr_one, **nl_sr;
2133 int *nlr_ljc, *nlr_one, *nsr;
2134 gmx_domdec_t *dd = NULL;
2135 t_block *cgs = &(top->cgs);
2136 int *cginfo = fr->cginfo;
2137 /* atom_id *i_atoms,*cgsindex=cgs->index; */
2139 int cell_x, cell_y, cell_z;
2140 int d, tx, ty, tz, dx, dy, dz, cj;
2141 #ifdef ALLOW_OFFDIAG_LT_HALFDIAG
2142 int zsh_ty, zsh_tx, ysh_tx;
2144 int dx0, dx1, dy0, dy1, dz0, dz1;
2145 int Nx, Ny, Nz, shift = -1, j, nrj, nns, nn = -1;
2146 real gridx, gridy, gridz, grid_x, grid_y, grid_z;
2147 real *dcx2, *dcy2, *dcz2;
2149 int cg0, cg1, icg = -1, cgsnr, i0, igid, nri, naaj, max_jcg;
2150 int jcg0, jcg1, jjcg, cgj0, jgid;
2151 int *grida, *gridnra, *gridind;
2152 gmx_bool rvdw_lt_rcoul, rcoul_lt_rvdw;
2153 rvec xi, *cgcm, grid_offset;
2154 real r2, rs2, rvdw2, rcoul2, rm2, rl2, XI, YI, ZI, dcx, dcy, dcz, tmp1, tmp2;
2156 gmx_bool bDomDec, bTriclinicX, bTriclinicY;
2161 bDomDec = DOMAINDECOMP(cr);
2167 bTriclinicX = ((YY < grid->npbcdim &&
2168 (!bDomDec || dd->nc[YY] == 1) && box[YY][XX] != 0) ||
2169 (ZZ < grid->npbcdim &&
2170 (!bDomDec || dd->nc[ZZ] == 1) && box[ZZ][XX] != 0));
2171 bTriclinicY = (ZZ < grid->npbcdim &&
2172 (!bDomDec || dd->nc[ZZ] == 1) && box[ZZ][YY] != 0);
2176 get_cutoff2(fr, bDoLongRange, &rvdw2, &rcoul2, &rs2, &rm2, &rl2);
2178 rvdw_lt_rcoul = (rvdw2 >= rcoul2);
2179 rcoul_lt_rvdw = (rcoul2 >= rvdw2);
2181 if (bMakeQMMMnblist)
2189 nl_lr_ljc = ns->nl_lr_ljc;
2190 nl_lr_one = ns->nl_lr_one;
2191 nlr_ljc = ns->nlr_ljc;
2192 nlr_one = ns->nlr_one;
2200 gridind = grid->index;
2201 gridnra = grid->nra;
2204 gridx = grid->cell_size[XX];
2205 gridy = grid->cell_size[YY];
2206 gridz = grid->cell_size[ZZ];
2210 copy_rvec(grid->cell_offset, grid_offset);
2211 copy_ivec(grid->ncpddc, ncpddc);
2216 #ifdef ALLOW_OFFDIAG_LT_HALFDIAG
2217 zsh_ty = floor(-box[ZZ][YY]/box[YY][YY]+0.5);
2218 zsh_tx = floor(-box[ZZ][XX]/box[XX][XX]+0.5);
2219 ysh_tx = floor(-box[YY][XX]/box[XX][XX]+0.5);
2220 if (zsh_tx != 0 && ysh_tx != 0)
2222 /* This could happen due to rounding, when both ratios are 0.5 */
2231 /* We only want a list for the test particle */
2240 /* Set the shift range */
2241 for (d = 0; d < DIM; d++)
2245 /* Check if we need periodicity shifts.
2246 * Without PBC or with domain decomposition we don't need them.
2248 if (d >= ePBC2npbcdim(fr->ePBC) || (bDomDec && dd->nc[d] > 1))
2255 box[XX][XX] - fabs(box[YY][XX]) - fabs(box[ZZ][XX]) < sqrt(rl2))
2266 /* Loop over charge groups */
2267 for (icg = cg0; (icg < cg1); icg++)
2269 igid = GET_CGINFO_GID(cginfo[icg]);
2270 /* Skip this charge group if all energy groups are excluded! */
2271 if (bExcludeAlleg[igid])
2276 i0 = cgs->index[icg];
2278 if (bMakeQMMMnblist)
2280 /* Skip this charge group if it is not a QM atom while making a
2281 * QM/MM neighbourlist
2283 if (md->bQM[i0] == FALSE)
2285 continue; /* MM particle, go to next particle */
2288 /* Compute the number of charge groups that fall within the control
2291 naaj = calc_naaj(icg, cgsnr);
2298 /* make a normal neighbourlist */
2302 /* Get the j charge-group and dd cell shift ranges */
2303 dd_get_ns_ranges(cr->dd, icg, &jcg0, &jcg1, sh0, sh1);
2308 /* Compute the number of charge groups that fall within the control
2311 naaj = calc_naaj(icg, cgsnr);
2317 /* The i-particle is awlways the test particle,
2318 * so we want all j-particles
2320 max_jcg = cgsnr - 1;
2324 max_jcg = jcg1 - cgsnr;
2329 i_egp_flags = fr->egp_flags + igid*ngid;
2331 /* Set the exclusions for the atoms in charge group icg using a bitmask */
2332 setexcl(i0, cgs->index[icg+1], &top->excls, TRUE, bexcl);
2334 ci2xyz(grid, icg, &cell_x, &cell_y, &cell_z);
2336 /* Changed iicg to icg, DvdS 990115
2337 * (but see consistency check above, DvdS 990330)
2340 fprintf(log, "icg=%5d, naaj=%5d, cell %d %d %d\n",
2341 icg, naaj, cell_x, cell_y, cell_z);
2343 /* Loop over shift vectors in three dimensions */
2344 for (tz = -shp[ZZ]; tz <= shp[ZZ]; tz++)
2346 ZI = cgcm[icg][ZZ]+tz*box[ZZ][ZZ];
2347 /* Calculate range of cells in Z direction that have the shift tz */
2348 zgi = cell_z + tz*Nz;
2351 get_dx(Nz, gridz, rl2, zgi, ZI, &dz0, &dz1, dcz2);
2353 get_dx_dd(Nz, gridz, rl2, zgi, ZI-grid_offset[ZZ],
2354 ncpddc[ZZ], sh0[ZZ], sh1[ZZ], &dz0, &dz1, dcz2);
2360 for (ty = -shp[YY]; ty <= shp[YY]; ty++)
2362 YI = cgcm[icg][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
2363 /* Calculate range of cells in Y direction that have the shift ty */
2366 ygi = (int)(Ny + (YI - grid_offset[YY])*grid_y) - Ny;
2370 ygi = cell_y + ty*Ny;
2373 get_dx(Ny, gridy, rl2, ygi, YI, &dy0, &dy1, dcy2);
2375 get_dx_dd(Ny, gridy, rl2, ygi, YI-grid_offset[YY],
2376 ncpddc[YY], sh0[YY], sh1[YY], &dy0, &dy1, dcy2);
2382 for (tx = -shp[XX]; tx <= shp[XX]; tx++)
2384 XI = cgcm[icg][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
2385 /* Calculate range of cells in X direction that have the shift tx */
2388 xgi = (int)(Nx + (XI - grid_offset[XX])*grid_x) - Nx;
2392 xgi = cell_x + tx*Nx;
2395 get_dx(Nx, gridx, rl2, xgi*Nx, XI, &dx0, &dx1, dcx2);
2397 get_dx_dd(Nx, gridx, rl2, xgi, XI-grid_offset[XX],
2398 ncpddc[XX], sh0[XX], sh1[XX], &dx0, &dx1, dcx2);
2404 /* Adress: an explicit cg that has a weigthing function of 0 is excluded
2405 * from the neigbour list as it will not interact */
2406 if (fr->adress_type != eAdressOff)
2408 if (md->wf[cgs->index[icg]] <= GMX_REAL_EPS && egp_explicit(fr, igid))
2413 /* Get shift vector */
2414 shift = XYZ2IS(tx, ty, tz);
2416 range_check(shift, 0, SHIFTS);
2418 for (nn = 0; (nn < ngid); nn++)
2425 fprintf(log, "shift: %2d, dx0,1: %2d,%2d, dy0,1: %2d,%2d, dz0,1: %2d,%2d\n",
2426 shift, dx0, dx1, dy0, dy1, dz0, dz1);
2427 fprintf(log, "cgcm: %8.3f %8.3f %8.3f\n", cgcm[icg][XX],
2428 cgcm[icg][YY], cgcm[icg][ZZ]);
2429 fprintf(log, "xi: %8.3f %8.3f %8.3f\n", XI, YI, ZI);
2431 for (dx = dx0; (dx <= dx1); dx++)
2433 tmp1 = rl2 - dcx2[dx];
2434 for (dy = dy0; (dy <= dy1); dy++)
2436 tmp2 = tmp1 - dcy2[dy];
2439 for (dz = dz0; (dz <= dz1); dz++)
2441 if (tmp2 > dcz2[dz])
2443 /* Find grid-cell cj in which possible neighbours are */
2444 cj = xyz2ci(Ny, Nz, dx, dy, dz);
2446 /* Check out how many cgs (nrj) there in this cell */
2449 /* Find the offset in the cg list */
2452 /* Check if all j's are out of range so we
2453 * can skip the whole cell.
2454 * Should save some time, especially with DD.
2457 (grida[cgj0] >= max_jcg &&
2458 (grida[cgj0] >= jcg1 || grida[cgj0+nrj-1] < jcg0)))
2464 for (j = 0; (j < nrj); j++)
2466 jjcg = grida[cgj0+j];
2468 /* check whether this guy is in range! */
2469 if ((jjcg >= jcg0 && jjcg < jcg1) ||
2472 r2 = calc_dx2(XI, YI, ZI, cgcm[jjcg]);
2475 /* jgid = gid[cgsatoms[cgsindex[jjcg]]]; */
2476 jgid = GET_CGINFO_GID(cginfo[jjcg]);
2477 /* check energy group exclusions */
2478 if (!(i_egp_flags[jgid] & EGP_EXCL))
2482 if (nsr[jgid] >= MAX_CG)
2484 /* Add to short-range list */
2485 put_in_list(bHaveVdW, ngid, md, icg, jgid,
2486 nsr[jgid], nl_sr[jgid],
2487 cgs->index, /* cgsatoms, */ bexcl,
2488 shift, fr, FALSE, TRUE, TRUE, fr->solvent_opt);
2491 nl_sr[jgid][nsr[jgid]++] = jjcg;
2495 if (nlr_ljc[jgid] >= MAX_CG)
2497 /* Add to LJ+coulomb long-range list */
2498 put_in_list(bHaveVdW, ngid, md, icg, jgid,
2499 nlr_ljc[jgid], nl_lr_ljc[jgid], top->cgs.index,
2500 bexcl, shift, fr, TRUE, TRUE, TRUE, fr->solvent_opt);
2503 nl_lr_ljc[jgid][nlr_ljc[jgid]++] = jjcg;
2507 if (nlr_one[jgid] >= MAX_CG)
2509 /* Add to long-range list with only coul, or only LJ */
2510 put_in_list(bHaveVdW, ngid, md, icg, jgid,
2511 nlr_one[jgid], nl_lr_one[jgid], top->cgs.index,
2512 bexcl, shift, fr, TRUE, rvdw_lt_rcoul, rcoul_lt_rvdw, fr->solvent_opt);
2515 nl_lr_one[jgid][nlr_one[jgid]++] = jjcg;
2527 /* CHECK whether there is anything left in the buffers */
2528 for (nn = 0; (nn < ngid); nn++)
2532 put_in_list(bHaveVdW, ngid, md, icg, nn, nsr[nn], nl_sr[nn],
2533 cgs->index, /* cgsatoms, */ bexcl,
2534 shift, fr, FALSE, TRUE, TRUE, fr->solvent_opt);
2537 if (nlr_ljc[nn] > 0)
2539 put_in_list(bHaveVdW, ngid, md, icg, nn, nlr_ljc[nn],
2540 nl_lr_ljc[nn], top->cgs.index,
2541 bexcl, shift, fr, TRUE, TRUE, TRUE, fr->solvent_opt);
2544 if (nlr_one[nn] > 0)
2546 put_in_list(bHaveVdW, ngid, md, icg, nn, nlr_one[nn],
2547 nl_lr_one[nn], top->cgs.index,
2548 bexcl, shift, fr, TRUE, rvdw_lt_rcoul, rcoul_lt_rvdw, fr->solvent_opt);
2554 /* setexcl(nri,i_atoms,&top->atoms.excl,FALSE,bexcl); */
2555 setexcl(cgs->index[icg], cgs->index[icg+1], &top->excls, FALSE, bexcl);
2557 /* No need to perform any left-over force calculations anymore (as we used to do here)
2558 * since we now save the proper long-range lists for later evaluation.
2563 /* Close neighbourlists */
2564 close_neighbor_lists(fr, bMakeQMMMnblist);
2569 void ns_realloc_natoms(gmx_ns_t *ns, int natoms)
2573 if (natoms > ns->nra_alloc)
2575 ns->nra_alloc = over_alloc_dd(natoms);
2576 srenew(ns->bexcl, ns->nra_alloc);
2577 for (i = 0; i < ns->nra_alloc; i++)
2584 void init_ns(FILE *fplog, const t_commrec *cr,
2585 gmx_ns_t *ns, t_forcerec *fr,
2586 const gmx_mtop_t *mtop)
2588 int mt, icg, nr_in_cg, maxcg, i, j, jcg, ngid, ncg;
2592 /* Compute largest charge groups size (# atoms) */
2594 for (mt = 0; mt < mtop->nmoltype; mt++)
2596 cgs = &mtop->moltype[mt].cgs;
2597 for (icg = 0; (icg < cgs->nr); icg++)
2599 nr_in_cg = max(nr_in_cg, (int)(cgs->index[icg+1]-cgs->index[icg]));
2603 /* Verify whether largest charge group is <= max cg.
2604 * This is determined by the type of the local exclusion type
2605 * Exclusions are stored in bits. (If the type is not large
2606 * enough, enlarge it, unsigned char -> unsigned short -> unsigned long)
2608 maxcg = sizeof(t_excl)*8;
2609 if (nr_in_cg > maxcg)
2611 gmx_fatal(FARGS, "Max #atoms in a charge group: %d > %d\n",
2615 ngid = mtop->groups.grps[egcENER].nr;
2616 snew(ns->bExcludeAlleg, ngid);
2617 for (i = 0; i < ngid; i++)
2619 ns->bExcludeAlleg[i] = TRUE;
2620 for (j = 0; j < ngid; j++)
2622 if (!(fr->egp_flags[i*ngid+j] & EGP_EXCL))
2624 ns->bExcludeAlleg[i] = FALSE;
2632 ns->grid = init_grid(fplog, fr);
2633 init_nsgrid_lists(fr, ngid, ns);
2638 snew(ns->ns_buf, ngid);
2639 for (i = 0; (i < ngid); i++)
2641 snew(ns->ns_buf[i], SHIFTS);
2643 ncg = ncg_mtop(mtop);
2644 snew(ns->simple_aaj, 2*ncg);
2645 for (jcg = 0; (jcg < ncg); jcg++)
2647 ns->simple_aaj[jcg] = jcg;
2648 ns->simple_aaj[jcg+ncg] = jcg;
2652 /* Create array that determines whether or not atoms have VdW */
2653 snew(ns->bHaveVdW, fr->ntype);
2654 for (i = 0; (i < fr->ntype); i++)
2656 for (j = 0; (j < fr->ntype); j++)
2658 ns->bHaveVdW[i] = (ns->bHaveVdW[i] ||
2660 ((BHAMA(fr->nbfp, fr->ntype, i, j) != 0) ||
2661 (BHAMB(fr->nbfp, fr->ntype, i, j) != 0) ||
2662 (BHAMC(fr->nbfp, fr->ntype, i, j) != 0)) :
2663 ((C6(fr->nbfp, fr->ntype, i, j) != 0) ||
2664 (C12(fr->nbfp, fr->ntype, i, j) != 0))));
2669 pr_bvec(debug, 0, "bHaveVdW", ns->bHaveVdW, fr->ntype, TRUE);
2674 if (!DOMAINDECOMP(cr))
2676 ns_realloc_natoms(ns, mtop->natoms);
2679 ns->nblist_initialized = FALSE;
2681 /* nbr list debug dump */
2683 char *ptr = getenv("GMX_DUMP_NL");
2686 ns->dump_nl = strtol(ptr, NULL, 10);
2689 fprintf(fplog, "GMX_DUMP_NL = %d", ns->dump_nl);
2700 int search_neighbours(FILE *log, t_forcerec *fr,
2702 gmx_localtop_t *top,
2703 gmx_groups_t *groups,
2705 t_nrnb *nrnb, t_mdatoms *md,
2707 gmx_bool bDoLongRangeNS)
2709 t_block *cgs = &(top->cgs);
2710 rvec box_size, grid_x0, grid_x1;
2712 real min_size, grid_dens;
2716 gmx_bool *i_egp_flags;
2717 int cg_start, cg_end, start, end;
2720 gmx_domdec_zones_t *dd_zones;
2721 put_in_list_t *put_in_list;
2725 /* Set some local variables */
2727 ngid = groups->grps[egcENER].nr;
2729 for (m = 0; (m < DIM); m++)
2731 box_size[m] = box[m][m];
2734 if (fr->ePBC != epbcNONE)
2736 if (sqr(fr->rlistlong) >= max_cutoff2(fr->ePBC, box))
2738 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.");
2742 min_size = min(box_size[XX], min(box_size[YY], box_size[ZZ]));
2743 if (2*fr->rlistlong >= min_size)
2745 gmx_fatal(FARGS, "One of the box diagonal elements has become smaller than twice the cut-off length.");
2750 if (DOMAINDECOMP(cr))
2752 ns_realloc_natoms(ns, cgs->index[cgs->nr]);
2756 /* Reset the neighbourlists */
2757 reset_neighbor_lists(fr, TRUE, TRUE);
2759 if (bGrid && bFillGrid)
2763 if (DOMAINDECOMP(cr))
2765 dd_zones = domdec_zones(cr->dd);
2771 get_nsgrid_boundaries(grid->nboundeddim, box, NULL, NULL, NULL, NULL,
2772 cgs->nr, fr->cg_cm, grid_x0, grid_x1, &grid_dens);
2774 grid_first(log, grid, NULL, NULL, box, grid_x0, grid_x1,
2775 fr->rlistlong, grid_dens);
2782 if (DOMAINDECOMP(cr))
2785 fill_grid(dd_zones, grid, end, -1, end, fr->cg_cm);
2787 grid->icg1 = dd_zones->izone[dd_zones->nizone-1].cg1;
2791 fill_grid(NULL, grid, cgs->nr, fr->cg0, fr->hcg, fr->cg_cm);
2792 grid->icg0 = fr->cg0;
2793 grid->icg1 = fr->hcg;
2797 calc_elemnr(grid, start, end, cgs->nr);
2799 grid_last(grid, start, end, cgs->nr);
2804 print_grid(debug, grid);
2809 /* Set the grid cell index for the test particle only.
2810 * The cell to cg index is not corrected, but that does not matter.
2812 fill_grid(NULL, ns->grid, fr->hcg, fr->hcg-1, fr->hcg, fr->cg_cm);
2816 if (fr->adress_type == eAdressOff)
2818 if (!fr->ns.bCGlist)
2820 put_in_list = put_in_list_at;
2824 put_in_list = put_in_list_cg;
2829 put_in_list = put_in_list_adress;
2836 nsearch = nsgrid_core(cr, fr, box, ngid, top,
2837 grid, ns->bexcl, ns->bExcludeAlleg,
2838 md, put_in_list, ns->bHaveVdW,
2839 bDoLongRangeNS, FALSE);
2841 /* neighbour searching withouth QMMM! QM atoms have zero charge in
2842 * the classical calculation. The charge-charge interaction
2843 * between QM and MM atoms is handled in the QMMM core calculation
2844 * (see QMMM.c). The VDW however, we'd like to compute classically
2845 * and the QM MM atom pairs have just been put in the
2846 * corresponding neighbourlists. in case of QMMM we still need to
2847 * fill a special QMMM neighbourlist that contains all neighbours
2848 * of the QM atoms. If bQMMM is true, this list will now be made:
2850 if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
2852 nsearch += nsgrid_core(cr, fr, box, ngid, top,
2853 grid, ns->bexcl, ns->bExcludeAlleg,
2854 md, put_in_list_qmmm, ns->bHaveVdW,
2855 bDoLongRangeNS, TRUE);
2860 nsearch = ns_simple_core(fr, top, md, box, box_size,
2861 ns->bexcl, ns->simple_aaj,
2862 ngid, ns->ns_buf, put_in_list, ns->bHaveVdW);
2870 inc_nrnb(nrnb, eNR_NS, nsearch);
2871 /* inc_nrnb(nrnb,eNR_LR,fr->nlr); */
2876 int natoms_beyond_ns_buffer(t_inputrec *ir, t_forcerec *fr, t_block *cgs,
2877 matrix scale_tot, rvec *x)
2879 int cg0, cg1, cg, a0, a1, a, i, j;
2880 real rint, hbuf2, scale;
2882 gmx_bool bIsotropic;
2887 rint = max(ir->rcoulomb, ir->rvdw);
2888 if (ir->rlist < rint)
2890 gmx_fatal(FARGS, "The neighbor search buffer has negative size: %f nm",
2898 if (!EI_DYNAMICS(ir->eI) || !DYNAMIC_BOX(*ir))
2900 hbuf2 = sqr(0.5*(ir->rlist - rint));
2901 for (cg = cg0; cg < cg1; cg++)
2903 a0 = cgs->index[cg];
2904 a1 = cgs->index[cg+1];
2905 for (a = a0; a < a1; a++)
2907 if (distance2(cg_cm[cg], x[a]) > hbuf2)
2917 scale = scale_tot[0][0];
2918 for (i = 1; i < DIM; i++)
2920 /* With anisotropic scaling, the original spherical ns volumes become
2921 * ellipsoids. To avoid costly transformations we use the minimum
2922 * eigenvalue of the scaling matrix for determining the buffer size.
2923 * Since the lower half is 0, the eigenvalues are the diagonal elements.
2925 scale = min(scale, scale_tot[i][i]);
2926 if (scale_tot[i][i] != scale_tot[i-1][i-1])
2930 for (j = 0; j < i; j++)
2932 if (scale_tot[i][j] != 0)
2938 hbuf2 = sqr(0.5*(scale*ir->rlist - rint));
2941 for (cg = cg0; cg < cg1; cg++)
2943 svmul(scale, cg_cm[cg], cgsc);
2944 a0 = cgs->index[cg];
2945 a1 = cgs->index[cg+1];
2946 for (a = a0; a < a1; a++)
2948 if (distance2(cgsc, x[a]) > hbuf2)
2957 /* Anistropic scaling */
2958 for (cg = cg0; cg < cg1; cg++)
2960 /* Since scale_tot contains the transpose of the scaling matrix,
2961 * we need to multiply with the transpose.
2963 tmvmul_ur0(scale_tot, cg_cm[cg], cgsc);
2964 a0 = cgs->index[cg];
2965 a1 = cgs->index[cg+1];
2966 for (a = a0; a < a1; a++)
2968 if (distance2(cgsc, x[a]) > hbuf2)