1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
4 * This file is part of Gromacs Copyright (c) 1991-2008
5 * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
7 * This program is free software; you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation; either version 2
10 * of the License, or (at your option) any later version.
12 * To help us fund GROMACS development, we humbly ask that you cite
13 * the research papers on the package. Check out http://www.gromacs.org
16 * Gnomes, ROck Monsters And Chili Sauce
28 #include "domdec_network.h"
29 #include "mtop_util.h"
30 #include "gmx_ga2la.h"
32 #include "gmx_omp_nthreads.h"
48 typedef struct gmx_domdec_specat_comm {
49 /* The number of indices to receive during the setup */
51 /* The atoms to send */
52 gmx_specatsend_t spas[DIM][2];
62 /* The range in the local buffer(s) for received atoms */
66 /* The atom indices we need from the surrounding cells.
67 * We can gather the indices over nthread threads.
71 } gmx_domdec_specat_comm_t;
73 typedef struct gmx_domdec_constraints {
76 /* The fully local and connected constraints */
78 /* The global constraint number, only required for clearing gc_req */
82 /* Boolean that tells if a global constraint index has been requested */
84 /* Global to local communicated constraint atom only index */
87 /* Multi-threading stuff */
90 } gmx_domdec_constraints_t;
93 static void dd_move_f_specat(gmx_domdec_t *dd,gmx_domdec_specat_comm_t *spac,
96 gmx_specatsend_t *spas;
98 int n,n0,n1,d,dim,dir,i;
101 gmx_bool bPBC,bScrew;
104 for(d=dd->ndim-1; d>=0; d--)
109 /* Pulse the grid forward and backward */
110 spas = spac->spas[d];
115 /* Send and receive the coordinates */
116 dd_sendrecv2_rvec(dd,d,
117 f+n+n1,n0,vbuf ,spas[0].nsend,
118 f+n ,n1,vbuf+spas[0].nsend,spas[1].nsend);
119 for(dir=0; dir<2; dir++)
121 bPBC = ((dir == 0 && dd->ci[dim] == 0) ||
122 (dir == 1 && dd->ci[dim] == dd->nc[dim]-1));
123 bScrew = (bPBC && dd->bScrewPBC && dim == XX);
125 spas = &spac->spas[d][dir];
126 /* Sum the buffer into the required forces */
127 if (!bPBC || (!bScrew && fshift == NULL))
129 for(i=0; i<spas->nsend; i++)
131 rvec_inc(f[spas->a[i]],*vbuf);
138 vis[dim] = (dir==0 ? 1 : -1);
142 /* Sum and add to shift forces */
143 for(i=0; i<spas->nsend; i++)
145 rvec_inc(f[spas->a[i]],*vbuf);
146 rvec_inc(fshift[is],*vbuf);
152 /* Rotate the forces */
153 for(i=0; i<spas->nsend; i++)
155 f[spas->a[i]][XX] += (*vbuf)[XX];
156 f[spas->a[i]][YY] -= (*vbuf)[YY];
157 f[spas->a[i]][ZZ] -= (*vbuf)[ZZ];
160 rvec_inc(fshift[is],*vbuf);
170 /* Two cells, so we only need to communicate one way */
171 spas = &spac->spas[d][0];
173 /* Send and receive the coordinates */
174 dd_sendrecv_rvec(dd,d,dddirForward,
175 f+n,spas->nrecv,spac->vbuf,spas->nsend);
176 /* Sum the buffer into the required forces */
177 if (dd->bScrewPBC && dim == XX &&
179 dd->ci[dim] == dd->nc[dim]-1))
181 for(i=0; i<spas->nsend; i++)
183 /* Rotate the force */
184 f[spas->a[i]][XX] += spac->vbuf[i][XX];
185 f[spas->a[i]][YY] -= spac->vbuf[i][YY];
186 f[spas->a[i]][ZZ] -= spac->vbuf[i][ZZ];
191 for(i=0; i<spas->nsend; i++)
193 rvec_inc(f[spas->a[i]],spac->vbuf[i]);
200 void dd_move_f_vsites(gmx_domdec_t *dd,rvec *f,rvec *fshift)
204 dd_move_f_specat(dd,dd->vsite_comm,f,fshift);
208 void dd_clear_f_vsites(gmx_domdec_t *dd,rvec *f)
214 for(i=dd->vsite_comm->at_start; i<dd->vsite_comm->at_end; i++)
221 static void dd_move_x_specat(gmx_domdec_t *dd,gmx_domdec_specat_comm_t *spac,
222 matrix box,rvec *x0,rvec *x1)
224 gmx_specatsend_t *spas;
226 int nvec,v,n,nn,ns0,ns1,nr0,nr1,nr,d,dim,dir,i;
227 gmx_bool bPBC,bScrew=FALSE;
237 for(d=0; d<dd->ndim; d++)
242 /* Pulse the grid forward and backward */
244 for(dir=0; dir<2; dir++)
246 if (dir == 0 && dd->ci[dim] == 0)
249 bScrew = (dd->bScrewPBC && dim == XX);
250 copy_rvec(box[dim],shift);
252 else if (dir == 1 && dd->ci[dim] == dd->nc[dim]-1)
255 bScrew = (dd->bScrewPBC && dim == XX);
258 shift[i] = -box[dim][i];
266 spas = &spac->spas[d][dir];
267 for(v=0; v<nvec; v++)
269 x = (v == 0 ? x0 : x1);
270 /* Copy the required coordinates to the send buffer */
274 for(i=0; i<spas->nsend; i++)
276 copy_rvec(x[spas->a[i]],*vbuf);
282 /* Shift coordinates */
283 for(i=0; i<spas->nsend; i++)
285 rvec_add(x[spas->a[i]],shift,*vbuf);
291 /* Shift and rotate coordinates */
292 for(i=0; i<spas->nsend; i++)
294 (*vbuf)[XX] = x[spas->a[i]][XX] + shift[XX];
295 (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY] + shift[YY];
296 (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ] + shift[ZZ];
302 /* Send and receive the coordinates */
303 spas = spac->spas[d];
310 dd_sendrecv2_rvec(dd,d,
311 spac->vbuf+ns0,ns1,x0+n ,nr1,
312 spac->vbuf ,ns0,x0+n+nr1,nr0);
316 /* Communicate both vectors in one buffer */
318 dd_sendrecv2_rvec(dd,d,
319 spac->vbuf+2*ns0,2*ns1,rbuf ,2*nr1,
320 spac->vbuf ,2*ns0,rbuf+2*nr1,2*nr0);
321 /* Split the buffer into the two vectors */
323 for(dir=1; dir>=0; dir--)
325 nr = spas[dir].nrecv;
328 x = (v == 0 ? x0 : x1);
331 copy_rvec(*rbuf,x[nn+i]);
342 spas = &spac->spas[d][0];
343 /* Copy the required coordinates to the send buffer */
345 for(v=0; v<nvec; v++)
347 x = (v == 0 ? x0 : x1);
348 if (dd->bScrewPBC && dim == XX &&
349 (dd->ci[XX] == 0 || dd->ci[XX] == dd->nc[XX]-1))
351 /* Here we only perform the rotation, the rest of the pbc
352 * is handled in the constraint or viste routines.
354 for(i=0; i<spas->nsend; i++)
356 (*vbuf)[XX] = x[spas->a[i]][XX];
357 (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY];
358 (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ];
364 for(i=0; i<spas->nsend; i++)
366 copy_rvec(x[spas->a[i]],*vbuf);
371 /* Send and receive the coordinates */
374 dd_sendrecv_rvec(dd,d,dddirBackward,
375 spac->vbuf,spas->nsend,x0+n,spas->nrecv);
379 /* Communicate both vectors in one buffer */
381 dd_sendrecv_rvec(dd,d,dddirBackward,
382 spac->vbuf,2*spas->nsend,rbuf,2*spas->nrecv);
383 /* Split the buffer into the two vectors */
387 x = (v == 0 ? x0 : x1);
390 copy_rvec(*rbuf,x[n+i]);
400 void dd_move_x_constraints(gmx_domdec_t *dd,matrix box,rvec *x0,rvec *x1)
402 if (dd->constraint_comm)
404 dd_move_x_specat(dd,dd->constraint_comm,box,x0,x1);
408 void dd_move_x_vsites(gmx_domdec_t *dd,matrix box,rvec *x)
412 dd_move_x_specat(dd,dd->vsite_comm,box,x,NULL);
416 int *dd_constraints_nlocalatoms(gmx_domdec_t *dd)
420 return dd->constraints->con_nlocat;
428 void dd_clear_local_constraint_indices(gmx_domdec_t *dd)
430 gmx_domdec_constraints_t *dc;
433 dc = dd->constraints;
435 for(i=0; i<dc->ncon; i++)
437 dc->gc_req[dc->con_gl[i]] = 0;
440 if (dd->constraint_comm)
442 gmx_hash_clear_and_optimize(dc->ga2la);
446 void dd_clear_local_vsite_indices(gmx_domdec_t *dd)
452 gmx_hash_clear_and_optimize(dd->ga2la_vsite);
456 static int setup_specat_communication(gmx_domdec_t *dd,
458 gmx_domdec_specat_comm_t *spac,
459 gmx_hash_t ga2la_specat,
462 const char *specat_type,
465 int nsend[2],nlast,nsend_zero[2]={0,0},*nsend_ptr;
466 int d,dim,ndir,dir,nr,ns,i,nrecv_local,n0,start,indr,ind,buf[2];
467 int nat_tot_specat,nat_tot_prev,nalloc_old;
468 gmx_bool bPBC,bFirst;
469 gmx_specatsend_t *spas;
473 fprintf(debug,"Begin setup_specat_communication for %s\n",specat_type);
476 /* nsend[0]: the number of atoms requested by this node only,
477 * we communicate this for more efficients checks
478 * nsend[1]: the total number of requested atoms
483 for(d=dd->ndim-1; d>=0; d--)
485 /* Pulse the grid forward and backward */
487 bPBC = (dim < dd->npbcdim);
488 if (dd->nc[dim] == 2)
490 /* Only 2 cells, so we only need to communicate once */
497 for(dir=0; dir<ndir; dir++)
501 ((dir == 0 && dd->ci[dim] == dd->nc[dim] - 1) ||
502 (dir == 1 && dd->ci[dim] == 0)))
504 /* No pbc: the fist/last cell should not request atoms */
505 nsend_ptr = nsend_zero;
511 /* Communicate the number of indices */
512 dd_sendrecv_int(dd,d,dir==0 ? dddirForward : dddirBackward,
513 nsend_ptr,2,spac->nreq[d][dir],2);
514 nr = spac->nreq[d][dir][1];
515 if (nlast+nr > ireq->nalloc)
517 ireq->nalloc = over_alloc_dd(nlast+nr);
518 srenew(ireq->ind,ireq->nalloc);
520 /* Communicate the indices */
521 dd_sendrecv_int(dd,d,dir==0 ? dddirForward : dddirBackward,
522 ireq->ind,nsend_ptr[1],ireq->ind+nlast,nr);
529 fprintf(debug,"Communicated the counts\n");
532 /* Search for the requested atoms and communicate the indices we have */
533 nat_tot_specat = at_start;
535 for(d=0; d<dd->ndim; d++)
538 /* Pulse the grid forward and backward */
539 if (dd->dim[d] >= dd->npbcdim || dd->nc[dd->dim[d]] > 2)
547 nat_tot_prev = nat_tot_specat;
548 for(dir=ndir-1; dir>=0; dir--)
550 if (nat_tot_specat > spac->bSendAtom_nalloc)
552 nalloc_old = spac->bSendAtom_nalloc;
553 spac->bSendAtom_nalloc = over_alloc_dd(nat_tot_specat);
554 srenew(spac->bSendAtom,spac->bSendAtom_nalloc);
555 for(i=nalloc_old; i<spac->bSendAtom_nalloc; i++)
557 spac->bSendAtom[i] = FALSE;
560 spas = &spac->spas[d][dir];
561 n0 = spac->nreq[d][dir][0];
562 nr = spac->nreq[d][dir][1];
565 fprintf(debug,"dim=%d, dir=%d, searching for %d atoms\n",
573 indr = ireq->ind[start+i];
575 /* Check if this is a home atom and if so ind will be set */
576 if (!ga2la_get_home(dd->ga2la,indr,&ind))
578 /* Search in the communicated atoms */
579 ind = gmx_hash_get_minone(ga2la_specat,indr);
583 if (i < n0 || !spac->bSendAtom[ind])
585 if (spas->nsend+1 > spas->a_nalloc)
587 spas->a_nalloc = over_alloc_large(spas->nsend+1);
588 srenew(spas->a,spas->a_nalloc);
590 /* Store the local index so we know which coordinates
593 spas->a[spas->nsend] = ind;
594 spac->bSendAtom[ind] = TRUE;
595 if (spas->nsend+1 > spac->ibuf_nalloc)
597 spac->ibuf_nalloc = over_alloc_large(spas->nsend+1);
598 srenew(spac->ibuf,spac->ibuf_nalloc);
600 /* Store the global index so we can send it now */
601 spac->ibuf[spas->nsend] = indr;
611 /* Clear the local flags */
612 for(i=0; i<spas->nsend; i++)
614 spac->bSendAtom[spas->a[i]] = FALSE;
616 /* Send and receive the number of indices to communicate */
617 nsend[1] = spas->nsend;
618 dd_sendrecv_int(dd,d,dir==0 ? dddirBackward : dddirForward,
622 fprintf(debug,"Send to node %d, %d (%d) indices, "
623 "receive from node %d, %d (%d) indices\n",
624 dd->neighbor[d][1-dir],nsend[1],nsend[0],
625 dd->neighbor[d][dir],buf[1],buf[0]);
628 for(i=0; i<spas->nsend; i++)
630 fprintf(debug," %d",spac->ibuf[i]+1);
635 nrecv_local += buf[0];
636 spas->nrecv = buf[1];
637 if (nat_tot_specat + spas->nrecv > dd->gatindex_nalloc)
639 dd->gatindex_nalloc =
640 over_alloc_dd(nat_tot_specat + spas->nrecv);
641 srenew(dd->gatindex,dd->gatindex_nalloc);
643 /* Send and receive the indices */
644 dd_sendrecv_int(dd,d,dir==0 ? dddirBackward : dddirForward,
645 spac->ibuf,spas->nsend,
646 dd->gatindex+nat_tot_specat,spas->nrecv);
647 nat_tot_specat += spas->nrecv;
650 /* Allocate the x/f communication buffers */
651 ns = spac->spas[d][0].nsend;
652 nr = spac->spas[d][0].nrecv;
655 ns += spac->spas[d][1].nsend;
656 nr += spac->spas[d][1].nrecv;
658 if (vbuf_fac*ns > spac->vbuf_nalloc)
660 spac->vbuf_nalloc = over_alloc_dd(vbuf_fac*ns);
661 srenew(spac->vbuf,spac->vbuf_nalloc);
663 if (vbuf_fac == 2 && vbuf_fac*nr > spac->vbuf2_nalloc)
665 spac->vbuf2_nalloc = over_alloc_dd(vbuf_fac*nr);
666 srenew(spac->vbuf2,spac->vbuf2_nalloc);
669 /* Make a global to local index for the communication atoms */
670 for(i=nat_tot_prev; i<nat_tot_specat; i++)
672 gmx_hash_change_or_set(ga2la_specat,dd->gatindex[i],i);
676 /* Check that in the end we got the number of atoms we asked for */
677 if (nrecv_local != ireq->n)
681 fprintf(debug,"Requested %d, received %d (tot recv %d)\n",
682 ireq->n,nrecv_local,nat_tot_specat-at_start);
685 for(i=0; i<ireq->n; i++)
687 ind = gmx_hash_get_minone(ga2la_specat,ireq->ind[i]);
688 fprintf(debug," %s%d",
689 (ind >= 0) ? "" : "!",
695 fprintf(stderr,"\nDD cell %d %d %d: Neighboring cells do not have atoms:",
696 dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
697 for(i=0; i<ireq->n; i++)
699 if (gmx_hash_get_minone(ga2la_specat,ireq->ind[i]) < 0)
701 fprintf(stderr," %d",ireq->ind[i]+1);
704 fprintf(stderr,"\n");
705 gmx_fatal(FARGS,"DD cell %d %d %d could only obtain %d of the %d atoms that are connected via %ss from the neighboring cells. This probably means your %s lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells%s%s.",
706 dd->ci[XX],dd->ci[YY],dd->ci[ZZ],
707 nrecv_local,ireq->n,specat_type,
709 dd->bGridJump ? " or use the -rcon option of mdrun" : "");
712 spac->at_start = at_start;
713 spac->at_end = nat_tot_specat;
717 fprintf(debug,"Done setup_specat_communication\n");
720 return nat_tot_specat;
723 static void walk_out(int con,int con_offset,int a,int offset,int nrec,
724 int ncon1,const t_iatom *ia1,const t_iatom *ia2,
725 const t_blocka *at2con,
726 const gmx_ga2la_t ga2la,gmx_bool bHomeConnect,
727 gmx_domdec_constraints_t *dc,
728 gmx_domdec_specat_comm_t *dcc,
732 int a1_gl,a2_gl,a_loc,i,coni,b;
735 if (dc->gc_req[con_offset+con] == 0)
737 /* Add this non-home constraint to the list */
738 if (dc->ncon+1 > dc->con_nalloc)
740 dc->con_nalloc = over_alloc_large(dc->ncon+1);
741 srenew(dc->con_gl,dc->con_nalloc);
742 srenew(dc->con_nlocat,dc->con_nalloc);
744 dc->con_gl[dc->ncon] = con_offset + con;
745 dc->con_nlocat[dc->ncon] = (bHomeConnect ? 1 : 0);
746 dc->gc_req[con_offset+con] = 1;
747 if (il_local->nr + 3 > il_local->nalloc)
749 il_local->nalloc = over_alloc_dd(il_local->nr+3);
750 srenew(il_local->iatoms,il_local->nalloc);
752 iap = constr_iatomptr(ncon1,ia1,ia2,con);
753 il_local->iatoms[il_local->nr++] = iap[0];
754 a1_gl = offset + iap[1];
755 a2_gl = offset + iap[2];
756 /* The following indexing code can probably be optizimed */
757 if (ga2la_get_home(ga2la,a1_gl,&a_loc))
759 il_local->iatoms[il_local->nr++] = a_loc;
763 /* We set this index later */
764 il_local->iatoms[il_local->nr++] = -a1_gl - 1;
766 if (ga2la_get_home(ga2la,a2_gl,&a_loc))
768 il_local->iatoms[il_local->nr++] = a_loc;
772 /* We set this index later */
773 il_local->iatoms[il_local->nr++] = -a2_gl - 1;
777 /* Check to not ask for the same atom more than once */
778 if (gmx_hash_get_minone(dc->ga2la,offset+a) == -1)
781 /* Add this non-home atom to the list */
782 if (ireq->n+1 > ireq->nalloc)
784 ireq->nalloc = over_alloc_large(ireq->n+1);
785 srenew(ireq->ind,ireq->nalloc);
787 ireq->ind[ireq->n++] = offset + a;
788 /* Temporarily mark with -2, we get the index later */
789 gmx_hash_set(dc->ga2la,offset+a,-2);
794 for(i=at2con->index[a]; i<at2con->index[a+1]; i++)
800 iap = constr_iatomptr(ncon1,ia1,ia2,coni);
809 if (!ga2la_get_home(ga2la,offset+b,&a_loc))
811 walk_out(coni,con_offset,b,offset,nrec-1,
812 ncon1,ia1,ia2,at2con,
813 ga2la,FALSE,dc,dcc,il_local,ireq);
820 static void atoms_to_settles(gmx_domdec_t *dd,
821 const gmx_mtop_t *mtop,
823 const int **at2settle_mt,
824 int cg_start,int cg_end,
829 gmx_mtop_atomlookup_t alook;
832 int cg,a,a_gl,a_glsa,a_gls[3],a_locs[3];
833 int mb,molnr,a_mol,offset;
834 const gmx_molblock_t *molb;
842 alook = gmx_mtop_atomlookup_settle_init(mtop);
844 nral = NRAL(F_SETTLE);
846 for(cg=cg_start; cg<cg_end; cg++)
848 if (GET_CGINFO_SETTLE(cginfo[cg]))
850 for(a=dd->cgindex[cg]; a<dd->cgindex[cg+1]; a++)
852 a_gl = dd->gatindex[a];
854 gmx_mtop_atomnr_to_molblock_ind(alook,a_gl,&mb,&molnr,&a_mol);
855 molb = &mtop->molblock[mb];
857 settle = at2settle_mt[molb->type][a_mol];
861 offset = a_gl - a_mol;
863 ia1 = mtop->moltype[molb->type].ilist[F_SETTLE].iatoms;
867 for(sa=0; sa<nral; sa++)
869 a_glsa = offset + ia1[settle*(1+nral)+1+sa];
871 a_home[sa] = ga2la_get_home(ga2la,a_glsa,&a_locs[sa]);
874 if (nlocal == 0 && a_gl == a_glsa)
884 if (ils_local->nr+1+nral > ils_local->nalloc)
886 ils_local->nalloc = over_alloc_dd(ils_local->nr+1+nral);
887 srenew(ils_local->iatoms,ils_local->nalloc);
890 ils_local->iatoms[ils_local->nr++] = ia1[settle*4];
892 for(sa=0; sa<nral; sa++)
894 if (ga2la_get_home(ga2la,a_gls[sa],&a_locs[sa]))
896 ils_local->iatoms[ils_local->nr++] = a_locs[sa];
900 ils_local->iatoms[ils_local->nr++] = -a_gls[sa] - 1;
901 /* Add this non-home atom to the list */
902 if (ireq->n+1 > ireq->nalloc)
904 ireq->nalloc = over_alloc_large(ireq->n+1);
905 srenew(ireq->ind,ireq->nalloc);
907 ireq->ind[ireq->n++] = a_gls[sa];
908 /* A check on double atom requests is
909 * not required for settle.
919 gmx_mtop_atomlookup_destroy(alook);
922 static void atoms_to_constraints(gmx_domdec_t *dd,
923 const gmx_mtop_t *mtop,
925 const t_blocka *at2con_mt,int nrec,
929 const t_blocka *at2con;
931 gmx_mtop_atomlookup_t alook;
933 gmx_molblock_t *molb;
934 t_iatom *ia1,*ia2,*iap;
935 int nhome,cg,a,a_gl,a_mol,a_loc,b_lo,offset,mb,molnr,b_mol,i,con,con_offset;
936 gmx_domdec_constraints_t *dc;
937 gmx_domdec_specat_comm_t *dcc;
939 dc = dd->constraints;
940 dcc = dd->constraint_comm;
944 alook = gmx_mtop_atomlookup_init(mtop);
947 for(cg=0; cg<dd->ncg_home; cg++)
949 if (GET_CGINFO_CONSTR(cginfo[cg]))
951 for(a=dd->cgindex[cg]; a<dd->cgindex[cg+1]; a++)
953 a_gl = dd->gatindex[a];
955 gmx_mtop_atomnr_to_molblock_ind(alook,a_gl,&mb,&molnr,&a_mol);
956 molb = &mtop->molblock[mb];
958 ncon1 = mtop->moltype[molb->type].ilist[F_CONSTR].nr/NRAL(F_SETTLE);
960 ia1 = mtop->moltype[molb->type].ilist[F_CONSTR].iatoms;
961 ia2 = mtop->moltype[molb->type].ilist[F_CONSTRNC].iatoms;
963 /* Calculate the global constraint number offset for the molecule.
964 * This is only required for the global index to make sure
965 * that we use each constraint only once.
968 dc->molb_con_offset[mb] + molnr*dc->molb_ncon_mol[mb];
970 /* The global atom number offset for this molecule */
971 offset = a_gl - a_mol;
972 at2con = &at2con_mt[molb->type];
973 for(i=at2con->index[a_mol]; i<at2con->index[a_mol+1]; i++)
976 iap = constr_iatomptr(ncon1,ia1,ia2,con);
985 if (ga2la_get_home(ga2la,offset+b_mol,&a_loc))
987 /* Add this fully home constraint at the first atom */
990 if (dc->ncon+1 > dc->con_nalloc)
992 dc->con_nalloc = over_alloc_large(dc->ncon+1);
993 srenew(dc->con_gl,dc->con_nalloc);
994 srenew(dc->con_nlocat,dc->con_nalloc);
996 dc->con_gl[dc->ncon] = con_offset + con;
997 dc->con_nlocat[dc->ncon] = 2;
998 if (ilc_local->nr + 3 > ilc_local->nalloc)
1000 ilc_local->nalloc = over_alloc_dd(ilc_local->nr + 3);
1001 srenew(ilc_local->iatoms,ilc_local->nalloc);
1004 ilc_local->iatoms[ilc_local->nr++] = iap[0];
1005 ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? a : b_lo);
1006 ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? b_lo : a );
1013 /* We need the nrec constraints coupled to this constraint,
1014 * so we need to walk out of the home cell by nrec+1 atoms,
1015 * since already atom bg is not locally present.
1016 * Therefore we call walk_out with nrec recursions to go
1017 * after this first call.
1019 walk_out(con,con_offset,b_mol,offset,nrec,
1020 ncon1,ia1,ia2,at2con,
1021 dd->ga2la,TRUE,dc,dcc,ilc_local,ireq);
1028 gmx_mtop_atomlookup_destroy(alook);
1033 "Constraints: home %3d border %3d atoms: %3d\n",
1034 nhome,dc->ncon-nhome,
1035 dd->constraint_comm ? ireq->n : 0);
1039 int dd_make_local_constraints(gmx_domdec_t *dd,int at_start,
1040 const gmx_mtop_t *mtop,
1042 gmx_constr_t constr,int nrec,
1045 gmx_domdec_constraints_t *dc;
1046 t_ilist *ilc_local,*ils_local;
1048 const t_blocka *at2con_mt;
1049 const int **at2settle_mt;
1050 gmx_hash_t ga2la_specat;
1054 dc = dd->constraints;
1056 ilc_local = &il_local[F_CONSTR];
1057 ils_local = &il_local[F_SETTLE];
1061 if (dd->constraint_comm)
1063 at2con_mt = atom2constraints_moltype(constr);
1064 ireq = &dd->constraint_comm->ireq[0];
1073 if (dd->bInterCGsettles)
1075 at2settle_mt = atom2settle_moltype(constr);
1080 /* Settle works inside charge groups, we assigned them already */
1081 at2settle_mt = NULL;
1084 if (at2settle_mt == NULL)
1086 atoms_to_constraints(dd,mtop,cginfo,at2con_mt,nrec,
1094 /* Do the constraints, if present, on the first thread.
1095 * Do the settles on all other threads.
1097 t0_set = ((at2con_mt != NULL && dc->nthread > 1) ? 1 : 0);
1099 #pragma omp parallel for num_threads(dc->nthread) schedule(static)
1100 for(thread=0; thread<dc->nthread; thread++)
1102 if (at2con_mt && thread == 0)
1104 atoms_to_constraints(dd,mtop,cginfo,at2con_mt,nrec,
1108 if (thread >= t0_set)
1114 /* Distribute the settle check+assignments over
1115 * dc->nthread or dc->nthread-1 threads.
1117 cg0 = (dd->ncg_home*(thread-t0_set ))/(dc->nthread-t0_set);
1118 cg1 = (dd->ncg_home*(thread-t0_set+1))/(dc->nthread-t0_set);
1120 if (thread == t0_set)
1126 ilst = &dc->ils[thread];
1130 ireqt = &dd->constraint_comm->ireq[thread];
1136 atoms_to_settles(dd,mtop,cginfo,at2settle_mt,
1142 /* Combine the generate settles and requested indices */
1143 for(thread=1; thread<dc->nthread; thread++)
1149 if (thread > t0_set)
1151 ilst = &dc->ils[thread];
1152 if (ils_local->nr + ilst->nr > ils_local->nalloc)
1154 ils_local->nalloc = over_alloc_large(ils_local->nr + ilst->nr);
1155 srenew(ils_local->iatoms,ils_local->nalloc);
1157 for(ia=0; ia<ilst->nr; ia++)
1159 ils_local->iatoms[ils_local->nr+ia] = ilst->iatoms[ia];
1161 ils_local->nr += ilst->nr;
1164 ireqt = &dd->constraint_comm->ireq[thread];
1165 if (ireq->n+ireqt->n > ireq->nalloc)
1167 ireq->nalloc = over_alloc_large(ireq->n+ireqt->n);
1168 srenew(ireq->ind,ireq->nalloc);
1170 for(ia=0; ia<ireqt->n; ia++)
1172 ireq->ind[ireq->n+ia] = ireqt->ind[ia];
1174 ireq->n += ireqt->n;
1179 fprintf(debug,"Settles: total %3d\n",ils_local->nr/4);
1183 if (dd->constraint_comm) {
1187 setup_specat_communication(dd,ireq,dd->constraint_comm,
1188 dd->constraints->ga2la,
1190 "constraint"," or lincs-order");
1192 /* Fill in the missing indices */
1193 ga2la_specat = dd->constraints->ga2la;
1195 nral1 = 1 + NRAL(F_CONSTR);
1196 for(i=0; i<ilc_local->nr; i+=nral1)
1198 iap = ilc_local->iatoms + i;
1199 for(j=1; j<nral1; j++)
1203 iap[j] = gmx_hash_get_minone(ga2la_specat,-iap[j]-1);
1208 nral1 = 1 + NRAL(F_SETTLE);
1209 for(i=0; i<ils_local->nr; i+=nral1)
1211 iap = ils_local->iatoms + i;
1212 for(j=1; j<nral1; j++)
1216 iap[j] = gmx_hash_get_minone(ga2la_specat,-iap[j]-1);
1229 int dd_make_local_vsites(gmx_domdec_t *dd,int at_start,t_ilist *lil)
1231 gmx_domdec_specat_comm_t *spac;
1233 gmx_hash_t ga2la_specat;
1234 int ftype,nral,i,j,gat,a;
1239 spac = dd->vsite_comm;
1240 ireq = &spac->ireq[0];
1241 ga2la_specat = dd->ga2la_vsite;
1244 /* Loop over all the home vsites */
1245 for(ftype=0; ftype<F_NRE; ftype++)
1247 if (interaction_function[ftype].flags & IF_VSITE)
1251 for(i=0; i<lilf->nr; i+=1+nral)
1253 iatoms = lilf->iatoms + i;
1254 /* Check if we have the other atoms */
1255 for(j=1; j<1+nral; j++)
1257 if (iatoms[j] < 0) {
1258 /* This is not a home atom,
1259 * we need to ask our neighbors.
1262 /* Check to not ask for the same atom more than once */
1263 if (gmx_hash_get_minone(dd->ga2la_vsite,a) == -1)
1265 /* Add this non-home atom to the list */
1266 if (ireq->n+1 > ireq->nalloc)
1268 ireq->nalloc = over_alloc_large(ireq->n+1);
1269 srenew(ireq->ind,ireq->nalloc);
1271 ireq->ind[ireq->n++] = a;
1272 /* Temporarily mark with -2,
1273 * we get the index later.
1275 gmx_hash_set(ga2la_specat,a,-2);
1283 at_end = setup_specat_communication(dd,ireq,dd->vsite_comm,ga2la_specat,
1284 at_start,1,"vsite","");
1286 /* Fill in the missing indices */
1287 for(ftype=0; ftype<F_NRE; ftype++)
1289 if (interaction_function[ftype].flags & IF_VSITE)
1293 for(i=0; i<lilf->nr; i+=1+nral)
1295 iatoms = lilf->iatoms + i;
1296 for(j=1; j<1+nral; j++)
1300 iatoms[j] = gmx_hash_get_minone(ga2la_specat,-iatoms[j]-1);
1310 static gmx_domdec_specat_comm_t *specat_comm_init(int nthread)
1312 gmx_domdec_specat_comm_t *spac;
1315 spac->nthread = nthread;
1316 snew(spac->ireq,spac->nthread);
1321 void init_domdec_constraints(gmx_domdec_t *dd,
1323 gmx_constr_t constr)
1325 gmx_domdec_constraints_t *dc;
1326 gmx_molblock_t *molb;
1331 fprintf(debug,"Begin init_domdec_constraints\n");
1334 snew(dd->constraints,1);
1335 dc = dd->constraints;
1337 snew(dc->molb_con_offset,mtop->nmolblock);
1338 snew(dc->molb_ncon_mol,mtop->nmolblock);
1341 for(mb=0; mb<mtop->nmolblock; mb++)
1343 molb = &mtop->molblock[mb];
1344 dc->molb_con_offset[mb] = ncon;
1345 dc->molb_ncon_mol[mb] =
1346 mtop->moltype[molb->type].ilist[F_CONSTR].nr/3 +
1347 mtop->moltype[molb->type].ilist[F_CONSTRNC].nr/3;
1348 ncon += molb->nmol*dc->molb_ncon_mol[mb];
1353 snew(dc->gc_req,ncon);
1354 for(c=0; c<ncon; c++)
1360 /* Use a hash table for the global to local index.
1361 * The number of keys is a rough estimate, it will be optimized later.
1363 dc->ga2la = gmx_hash_init(min(mtop->natoms/20,
1364 mtop->natoms/(2*dd->nnodes)));
1366 dc->nthread = gmx_omp_nthreads_get(emntDomdec);
1367 snew(dc->ils,dc->nthread);
1369 dd->constraint_comm = specat_comm_init(dc->nthread);
1372 void init_domdec_vsites(gmx_domdec_t *dd,int n_intercg_vsite)
1375 gmx_domdec_constraints_t *dc;
1379 fprintf(debug,"Begin init_domdec_vsites\n");
1382 /* Use a hash table for the global to local index.
1383 * The number of keys is a rough estimate, it will be optimized later.
1385 dd->ga2la_vsite = gmx_hash_init(min(n_intercg_vsite/20,
1386 n_intercg_vsite/(2*dd->nnodes)));
1388 dd->vsite_comm = specat_comm_init(1);