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54 #include "gmx_fatal.h"
55 #include "mtop_util.h"
69 # include "genborn_sse2_double.h"
70 # include "genborn_allvsall_sse2_double.h"
72 # include "genborn_sse2_single.h"
73 # include "genborn_allvsall_sse2_single.h"
74 # endif /* GMX_DOUBLE */
75 #endif /* SSE or AVX present */
77 #include "genborn_allvsall.h"
79 /*#define DISABLE_SSE*/
88 typedef struct gbtmpnbls {
94 /* This function is exactly the same as the one in bondfree.c. The reason
95 * it is copied here is that the bonded gb-interactions are evaluated
96 * not in calc_bonds, but rather in calc_gb_forces
98 static int pbc_rvec_sub(const t_pbc *pbc,const rvec xi,const rvec xj,rvec dx)
101 return pbc_dx_aiuc(pbc,xi,xj,dx);
109 int init_gb_nblist(int natoms, t_nblist *nl)
111 nl->maxnri = natoms*4;
121 /*nl->nltype = nltype;*/
123 srenew(nl->iinr, nl->maxnri);
124 srenew(nl->gid, nl->maxnri);
125 srenew(nl->shift, nl->maxnri);
126 srenew(nl->jindex, nl->maxnri+1);
133 void gb_pd_send(t_commrec *cr, real *send_data, int nr)
137 int *index,*sendc,*disp;
139 snew(sendc,cr->nnodes);
140 snew(disp,cr->nnodes);
142 index = pd_index(cr);
145 /* Setup count/index arrays */
146 for(i=0;i<cr->nnodes;i++)
148 sendc[i] = index[i+1]-index[i];
152 /* Do communication */
153 MPI_Gatherv(send_data+index[cur],sendc[cur],GMX_MPI_REAL,send_data,sendc,
154 disp,GMX_MPI_REAL,0,cr->mpi_comm_mygroup);
155 MPI_Bcast(send_data,nr,GMX_MPI_REAL,0,cr->mpi_comm_mygroup);
161 int init_gb_plist(t_params *p_list)
164 p_list->param = NULL;
171 int init_gb_still(const t_commrec *cr, t_forcerec *fr,
172 const t_atomtypes *atype, t_idef *idef, t_atoms *atoms,
173 gmx_genborn_t *born,int natoms)
176 int i,j,i1,i2,k,m,nbond,nang,ia,ib,ic,id,nb,idx,idx2,at;
180 real r,ri,rj,ri2,ri3,rj2,r2,r3,r4,rk,ratio,term,h,doffset;
181 real p1,p2,p3,factor,cosine,rab,rbc;
188 snew(born->gpol_still_work,natoms+3);
194 pd_at_range(cr,&at0,&at1);
196 for(i=0;i<natoms;i++)
213 doffset = born->gb_doffset;
215 for(i=0;i<natoms;i++)
217 born->gpol_globalindex[i]=born->vsolv_globalindex[i]=
218 born->gb_radius_globalindex[i]=0;
221 /* Compute atomic solvation volumes for Still method */
222 for(i=0;i<natoms;i++)
224 ri=atype->gb_radius[atoms->atom[i].type];
225 born->gb_radius_globalindex[i] = ri;
227 born->vsolv_globalindex[i]=(4*M_PI/3)*r3;
230 for(j=0;j<idef->il[F_GB12].nr;j+=3)
232 m=idef->il[F_GB12].iatoms[j];
233 ia=idef->il[F_GB12].iatoms[j+1];
234 ib=idef->il[F_GB12].iatoms[j+2];
236 r=1.01*idef->iparams[m].gb.st;
238 ri = atype->gb_radius[atoms->atom[ia].type];
239 rj = atype->gb_radius[atoms->atom[ib].type];
245 ratio = (rj2-ri2-r*r)/(2*ri*r);
247 term = (M_PI/3.0)*h*h*(3.0*ri-h);
255 born->vsolv_globalindex[ia] -= term;
258 ratio = (ri2-rj2-r*r)/(2*rj*r);
260 term = (M_PI/3.0)*h*h*(3.0*rj-h);
268 born->vsolv_globalindex[ib] -= term;
274 gmx_sum(natoms,vsol,cr);
276 for(i=0;i<natoms;i++)
278 born->vsolv_globalindex[i]=born->vsolv_globalindex[i]-vsol[i];
282 /* Get the self-, 1-2 and 1-3 polarization energies for analytical Still
285 for(j=0;j<natoms;j++)
287 if(born->use_globalindex[j]==1)
289 born->gpol_globalindex[j]=-0.5*ONE_4PI_EPS0/
290 (atype->gb_radius[atoms->atom[j].type]-doffset+STILL_P1);
295 for(j=0;j<idef->il[F_GB12].nr;j+=3)
297 m=idef->il[F_GB12].iatoms[j];
298 ia=idef->il[F_GB12].iatoms[j+1];
299 ib=idef->il[F_GB12].iatoms[j+2];
301 r=idef->iparams[m].gb.st;
307 gp[ia]+=STILL_P2*born->vsolv_globalindex[ib]/r4;
308 gp[ib]+=STILL_P2*born->vsolv_globalindex[ia]/r4;
312 born->gpol_globalindex[ia]=born->gpol_globalindex[ia]+
313 STILL_P2*born->vsolv_globalindex[ib]/r4;
314 born->gpol_globalindex[ib]=born->gpol_globalindex[ib]+
315 STILL_P2*born->vsolv_globalindex[ia]/r4;
320 for(j=0;j<idef->il[F_GB13].nr;j+=3)
322 m=idef->il[F_GB13].iatoms[j];
323 ia=idef->il[F_GB13].iatoms[j+1];
324 ib=idef->il[F_GB13].iatoms[j+2];
326 r=idef->iparams[m].gb.st;
331 gp[ia]+=STILL_P3*born->vsolv[ib]/r4;
332 gp[ib]+=STILL_P3*born->vsolv[ia]/r4;
336 born->gpol_globalindex[ia]=born->gpol_globalindex[ia]+
337 STILL_P3*born->vsolv_globalindex[ib]/r4;
338 born->gpol_globalindex[ib]=born->gpol_globalindex[ib]+
339 STILL_P3*born->vsolv_globalindex[ia]/r4;
345 gmx_sum(natoms,gp,cr);
347 for(i=0;i<natoms;i++)
349 born->gpol_globalindex[i]=born->gpol_globalindex[i]+gp[i];
359 /* Initialize all GB datastructs and compute polarization energies */
360 int init_gb(gmx_genborn_t **p_born,
361 const t_commrec *cr, t_forcerec *fr, const t_inputrec *ir,
362 const gmx_mtop_t *mtop, real rgbradii, int gb_algorithm)
364 int i,j,m,ai,aj,jj,natoms,nalloc;
365 real rai,sk,p,doffset;
369 gmx_localtop_t *localtop;
371 natoms = mtop->natoms;
373 atoms = gmx_mtop_global_atoms(mtop);
374 localtop = gmx_mtop_generate_local_top(mtop,ir);
381 snew(born->drobc, natoms);
382 snew(born->bRad, natoms);
384 /* Allocate memory for the global data arrays */
385 snew(born->param_globalindex, natoms+3);
386 snew(born->gpol_globalindex, natoms+3);
387 snew(born->vsolv_globalindex, natoms+3);
388 snew(born->gb_radius_globalindex, natoms+3);
389 snew(born->use_globalindex, natoms+3);
391 snew(fr->invsqrta, natoms);
392 snew(fr->dvda, natoms);
395 fr->dadx_rawptr = NULL;
397 born->gpol_still_work = NULL;
398 born->gpol_hct_work = NULL;
400 /* snew(born->asurf,natoms); */
401 /* snew(born->dasurf,natoms); */
403 /* Initialize the gb neighbourlist */
404 init_gb_nblist(natoms,&(fr->gblist));
406 /* Do the Vsites exclusions (if any) */
407 for(i=0;i<natoms;i++)
409 jj = atoms.atom[i].type;
410 if (mtop->atomtypes.gb_radius[atoms.atom[i].type] > 0)
412 born->use_globalindex[i] = 1;
416 born->use_globalindex[i] = 0;
419 /* If we have a Vsite, put vs_globalindex[i]=0 */
420 if (C6 (fr->nbfp,fr->ntype,jj,jj) == 0 &&
421 C12(fr->nbfp,fr->ntype,jj,jj) == 0 &&
422 atoms.atom[i].q == 0)
424 born->use_globalindex[i]=0;
428 /* Copy algorithm parameters from inputrecord to local structure */
429 born->obc_alpha = ir->gb_obc_alpha;
430 born->obc_beta = ir->gb_obc_beta;
431 born->obc_gamma = ir->gb_obc_gamma;
432 born->gb_doffset = ir->gb_dielectric_offset;
433 born->gb_epsilon_solvent = ir->gb_epsilon_solvent;
434 born->epsilon_r = ir->epsilon_r;
436 doffset = born->gb_doffset;
438 /* Set the surface tension */
439 born->sa_surface_tension = ir->sa_surface_tension;
441 /* If Still model, initialise the polarisation energies */
442 if(gb_algorithm==egbSTILL)
444 init_gb_still(cr, fr,&(mtop->atomtypes), &(localtop->idef), &atoms,
449 /* If HCT/OBC, precalculate the sk*atype->S_hct factors */
450 else if(gb_algorithm==egbHCT || gb_algorithm==egbOBC)
453 snew(born->gpol_hct_work, natoms+3);
455 for(i=0;i<natoms;i++)
457 if(born->use_globalindex[i]==1)
459 rai = mtop->atomtypes.gb_radius[atoms.atom[i].type]-doffset;
460 sk = rai * mtop->atomtypes.S_hct[atoms.atom[i].type];
461 born->param_globalindex[i] = sk;
462 born->gb_radius_globalindex[i] = rai;
466 born->param_globalindex[i] = 0;
467 born->gb_radius_globalindex[i] = 0;
472 /* Allocate memory for work arrays for temporary use */
473 snew(born->work,natoms+4);
474 snew(born->count,natoms);
475 snew(born->nblist_work,natoms);
477 /* Domain decomposition specific stuff */
486 calc_gb_rad_still(t_commrec *cr, t_forcerec *fr,int natoms, gmx_localtop_t *top,
487 const t_atomtypes *atype, rvec x[], t_nblist *nl,
488 gmx_genborn_t *born,t_mdatoms *md)
490 int i,k,n,nj0,nj1,ai,aj,type;
493 real gpi,dr,dr2,dr4,idr4,rvdw,ratio,ccf,theta,term,rai,raj;
494 real ix1,iy1,iz1,jx1,jy1,jz1,dx11,dy11,dz11;
495 real rinv,idr2,idr6,vaj,dccf,cosq,sinq,prod,gpi2;
497 real vai, prod_ai, icf4,icf6;
499 factor = 0.5*ONE_4PI_EPS0;
502 for(i=0;i<born->nr;i++)
504 born->gpol_still_work[i]=0;
507 for(i=0;i<nl->nri;i++ )
512 nj1 = nl->jindex[i+1];
514 /* Load shifts for this list */
515 shift = nl->shift[i];
516 shX = fr->shift_vec[shift][0];
517 shY = fr->shift_vec[shift][1];
518 shZ = fr->shift_vec[shift][2];
522 rai = top->atomtypes.gb_radius[md->typeA[ai]];
523 vai = born->vsolv[ai];
524 prod_ai = STILL_P4*vai;
526 /* Load atom i coordinates, add shift vectors */
527 ix1 = shX + x[ai][0];
528 iy1 = shY + x[ai][1];
529 iz1 = shZ + x[ai][2];
542 dr2 = dx11*dx11+dy11*dy11+dz11*dz11;
543 rinv = gmx_invsqrt(dr2);
548 raj = top->atomtypes.gb_radius[md->typeA[aj]];
552 ratio = dr2 / (rvdw * rvdw);
553 vaj = born->vsolv[aj];
555 if(ratio>STILL_P5INV)
562 theta = ratio*STILL_PIP5;
564 term = 0.5*(1.0-cosq);
566 sinq = 1.0 - cosq*cosq;
567 dccf = 2.0*term*sinq*gmx_invsqrt(sinq)*theta;
572 icf6 = (4*ccf-dccf)*idr6;
574 born->gpol_still_work[aj] += prod_ai*icf4;
577 /* Save ai->aj and aj->ai chain rule terms */
578 fr->dadx[n++] = prod*icf6;
579 fr->dadx[n++] = prod_ai*icf6;
581 born->gpol_still_work[ai]+=gpi;
584 /* Parallel summations */
587 gmx_sum(natoms, born->gpol_still_work, cr);
589 else if(DOMAINDECOMP(cr))
591 dd_atom_sum_real(cr->dd, born->gpol_still_work);
594 /* Calculate the radii */
595 for(i=0;i<fr->natoms_force;i++) /* PELA born->nr */
597 if(born->use[i] != 0)
600 gpi = born->gpol[i]+born->gpol_still_work[i];
602 born->bRad[i] = factor*gmx_invsqrt(gpi2);
603 fr->invsqrta[i] = gmx_invsqrt(born->bRad[i]);
607 /* Extra communication required for DD */
610 dd_atom_spread_real(cr->dd, born->bRad);
611 dd_atom_spread_real(cr->dd, fr->invsqrta);
620 calc_gb_rad_hct(t_commrec *cr,t_forcerec *fr,int natoms, gmx_localtop_t *top,
621 const t_atomtypes *atype, rvec x[], t_nblist *nl,
622 gmx_genborn_t *born,t_mdatoms *md)
624 int i,k,n,ai,aj,nj0,nj1,at0,at1;
627 real rai,raj,gpi,dr2,dr,sk,sk_ai,sk2,sk2_ai,lij,uij,diff2,tmp,sum_ai;
628 real rad,min_rad,rinv,rai_inv;
629 real ix1,iy1,iz1,jx1,jy1,jz1,dx11,dy11,dz11;
630 real lij2, uij2, lij3, uij3, t1,t2,t3;
631 real lij_inv,dlij,duij,sk2_rinv,prod,log_term;
632 real doffset,raj_inv,dadx_val;
635 doffset = born->gb_doffset;
636 gb_radius = born->gb_radius;
638 for(i=0;i<born->nr;i++)
640 born->gpol_hct_work[i] = 0;
643 /* Keep the compiler happy */
647 for(i=0;i<nl->nri;i++)
652 nj1 = nl->jindex[i+1];
654 /* Load shifts for this list */
655 shift = nl->shift[i];
656 shX = fr->shift_vec[shift][0];
657 shY = fr->shift_vec[shift][1];
658 shZ = fr->shift_vec[shift][2];
663 sk_ai = born->param[ai];
664 sk2_ai = sk_ai*sk_ai;
666 /* Load atom i coordinates, add shift vectors */
667 ix1 = shX + x[ai][0];
668 iy1 = shY + x[ai][1];
669 iz1 = shZ + x[ai][2];
685 dr2 = dx11*dx11+dy11*dy11+dz11*dz11;
686 rinv = gmx_invsqrt(dr2);
689 sk = born->param[aj];
692 /* aj -> ai interaction */
713 lij_inv = gmx_invsqrt(lij2);
716 prod = 0.25*sk2_rinv;
718 log_term = log(uij*lij_inv);
720 tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term +
725 tmp = tmp + 2.0 * (rai_inv-lij);
728 t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
729 t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
730 t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
732 dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
733 /* fr->dadx[n++] = (dlij*t1+duij*t2+t3)*rinv; */
734 /* rb2 is moved to chainrule */
742 fr->dadx[n++] = dadx_val;
745 /* ai -> aj interaction */
748 lij = 1.0/(dr-sk_ai);
761 uij = 1.0/(dr+sk_ai);
767 lij_inv = gmx_invsqrt(lij2);
768 sk2 = sk2_ai; /* sk2_ai = sk_ai * sk_ai in i loop above */
770 prod = 0.25 * sk2_rinv;
772 /* log_term = table_log(uij*lij_inv,born->log_table,
773 LOG_TABLE_ACCURACY); */
774 log_term = log(uij*lij_inv);
776 tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term +
781 tmp = tmp + 2.0 * (raj_inv-lij);
785 t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
786 t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
787 t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
789 dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
790 /* fr->dadx[n++] = (dlij*t1+duij*t2+t3)*rinv; */ /* rb2 is moved to chainrule */
792 born->gpol_hct_work[aj] += 0.5*tmp;
798 fr->dadx[n++] = dadx_val;
801 born->gpol_hct_work[ai] += sum_ai;
804 /* Parallel summations */
807 gmx_sum(natoms, born->gpol_hct_work, cr);
809 else if(DOMAINDECOMP(cr))
811 dd_atom_sum_real(cr->dd, born->gpol_hct_work);
814 for(i=0;i<fr->natoms_force;i++) /* PELA born->nr */
816 if(born->use[i] != 0)
818 rai = top->atomtypes.gb_radius[md->typeA[i]]-doffset;
819 sum_ai = 1.0/rai - born->gpol_hct_work[i];
820 min_rad = rai + doffset;
823 born->bRad[i] = rad > min_rad ? rad : min_rad;
824 fr->invsqrta[i] = gmx_invsqrt(born->bRad[i]);
828 /* Extra communication required for DD */
831 dd_atom_spread_real(cr->dd, born->bRad);
832 dd_atom_spread_real(cr->dd, fr->invsqrta);
840 calc_gb_rad_obc(t_commrec *cr, t_forcerec *fr, int natoms, gmx_localtop_t *top,
841 const t_atomtypes *atype, rvec x[], t_nblist *nl, gmx_genborn_t *born,t_mdatoms *md)
843 int i,k,ai,aj,nj0,nj1,n,at0,at1;
846 real rai,raj,gpi,dr2,dr,sk,sk2,lij,uij,diff2,tmp,sum_ai;
847 real rad, min_rad,sum_ai2,sum_ai3,tsum,tchain,rinv,rai_inv,lij_inv,rai_inv2;
848 real log_term,prod,sk2_rinv,sk_ai,sk2_ai;
849 real ix1,iy1,iz1,jx1,jy1,jz1,dx11,dy11,dz11;
850 real lij2,uij2,lij3,uij3,dlij,duij,t1,t2,t3;
851 real doffset,raj_inv,dadx_val;
854 /* Keep the compiler happy */
859 doffset = born->gb_doffset;
860 gb_radius = born->gb_radius;
862 for(i=0;i<born->nr;i++)
864 born->gpol_hct_work[i] = 0;
867 for(i=0;i<nl->nri;i++)
872 nj1 = nl->jindex[i+1];
874 /* Load shifts for this list */
875 shift = nl->shift[i];
876 shX = fr->shift_vec[shift][0];
877 shY = fr->shift_vec[shift][1];
878 shZ = fr->shift_vec[shift][2];
883 sk_ai = born->param[ai];
884 sk2_ai = sk_ai*sk_ai;
886 /* Load atom i coordinates, add shift vectors */
887 ix1 = shX + x[ai][0];
888 iy1 = shY + x[ai][1];
889 iz1 = shZ + x[ai][2];
905 dr2 = dx11*dx11+dy11*dy11+dz11*dz11;
906 rinv = gmx_invsqrt(dr2);
909 /* sk is precalculated in init_gb() */
910 sk = born->param[aj];
913 /* aj -> ai interaction */
933 lij_inv = gmx_invsqrt(lij2);
936 prod = 0.25*sk2_rinv;
938 log_term = log(uij*lij_inv);
940 tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2);
944 tmp = tmp + 2.0 * (rai_inv-lij);
948 t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
949 t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
950 t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
952 dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
960 fr->dadx[n++] = dadx_val;
962 /* ai -> aj interaction */
965 lij = 1.0/(dr-sk_ai);
978 uij = 1.0/(dr+sk_ai);
984 lij_inv = gmx_invsqrt(lij2);
985 sk2 = sk2_ai; /* sk2_ai = sk_ai * sk_ai in i loop above */
987 prod = 0.25 * sk2_rinv;
989 /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */
990 log_term = log(uij*lij_inv);
992 tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2);
996 tmp = tmp + 2.0 * (raj_inv-lij);
999 t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
1000 t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
1001 t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
1003 dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
1005 born->gpol_hct_work[aj] += 0.5*tmp;
1012 fr->dadx[n++] = dadx_val;
1015 born->gpol_hct_work[ai] += sum_ai;
1019 /* Parallel summations */
1022 gmx_sum(natoms, born->gpol_hct_work, cr);
1024 else if(DOMAINDECOMP(cr))
1026 dd_atom_sum_real(cr->dd, born->gpol_hct_work);
1029 for(i=0;i<fr->natoms_force;i++) /* PELA born->nr */
1031 if(born->use[i] != 0)
1033 rai = top->atomtypes.gb_radius[md->typeA[i]];
1037 sum_ai = rai * born->gpol_hct_work[i];
1038 sum_ai2 = sum_ai * sum_ai;
1039 sum_ai3 = sum_ai2 * sum_ai;
1041 tsum = tanh(born->obc_alpha*sum_ai-born->obc_beta*sum_ai2+born->obc_gamma*sum_ai3);
1042 born->bRad[i] = rai_inv - tsum*rai_inv2;
1043 born->bRad[i] = 1.0 / born->bRad[i];
1045 fr->invsqrta[i] = gmx_invsqrt(born->bRad[i]);
1047 tchain = rai * (born->obc_alpha-2*born->obc_beta*sum_ai+3*born->obc_gamma*sum_ai2);
1048 born->drobc[i] = (1.0-tsum*tsum)*tchain*rai_inv2;
1052 /* Extra (local) communication required for DD */
1053 if(DOMAINDECOMP(cr))
1055 dd_atom_spread_real(cr->dd, born->bRad);
1056 dd_atom_spread_real(cr->dd, fr->invsqrta);
1057 dd_atom_spread_real(cr->dd, born->drobc);
1066 int calc_gb_rad(t_commrec *cr, t_forcerec *fr, t_inputrec *ir,gmx_localtop_t *top,
1067 const t_atomtypes *atype, rvec x[], t_nblist *nl, gmx_genborn_t *born,t_mdatoms *md,t_nrnb *nrnb)
1073 if(fr->bAllvsAll && fr->dadx==NULL)
1075 /* We might need up to 8 atoms of padding before and after,
1076 * and another 4 units to guarantee SSE alignment.
1078 fr->nalloc_dadx = 2*(md->homenr+12)*(md->nr/2+1+12);
1079 snew(fr->dadx_rawptr,fr->nalloc_dadx);
1080 fr->dadx = (real *) (((size_t) fr->dadx_rawptr + 16) & (~((size_t) 15)));
1084 /* In the SSE-enabled gb-loops, when writing to dadx, we
1085 * always write 2*4 elements at a time, even in the case with only
1086 * 1-3 j particles, where we only really need to write 2*(1-3)
1087 * elements. This is because we want dadx to be aligned to a 16-
1088 * byte boundary, and being able to use _mm_store/load_ps
1090 ndadx = 2 * (nl->nrj + 3*nl->nri);
1092 /* First, reallocate the dadx array, we need 3 extra for SSE */
1093 if (ndadx + 3 > fr->nalloc_dadx)
1095 fr->nalloc_dadx = over_alloc_large(ndadx) + 3;
1096 srenew(fr->dadx_rawptr,fr->nalloc_dadx);
1097 fr->dadx = (real *) (((size_t) fr->dadx_rawptr + 16) & (~((size_t) 15)));
1103 cnt = md->homenr*(md->nr/2+1);
1105 if(ir->gb_algorithm==egbSTILL)
1107 #if 0 && defined (GMX_X86_SSE2)
1108 if(fr->use_acceleration)
1111 genborn_allvsall_calc_still_radii_sse2_double(fr,md,born,top,x[0],cr,&fr->AllvsAll_workgb);
1113 genborn_allvsall_calc_still_radii_sse2_single(fr,md,born,top,x[0],cr,&fr->AllvsAll_workgb);
1118 genborn_allvsall_calc_still_radii(fr,md,born,top,x[0],cr,&fr->AllvsAll_workgb);
1121 genborn_allvsall_calc_still_radii(fr,md,born,top,x[0],cr,&fr->AllvsAll_workgb);
1123 inc_nrnb(nrnb,eNR_BORN_AVA_RADII_STILL,cnt);
1125 else if(ir->gb_algorithm==egbHCT || ir->gb_algorithm==egbOBC)
1127 #if 0 && defined (GMX_X86_SSE2)
1128 if(fr->use_acceleration)
1131 genborn_allvsall_calc_hct_obc_radii_sse2_double(fr,md,born,ir->gb_algorithm,top,x[0],cr,&fr->AllvsAll_workgb);
1133 genborn_allvsall_calc_hct_obc_radii_sse2_single(fr,md,born,ir->gb_algorithm,top,x[0],cr,&fr->AllvsAll_workgb);
1138 genborn_allvsall_calc_hct_obc_radii(fr,md,born,ir->gb_algorithm,top,x[0],cr,&fr->AllvsAll_workgb);
1141 genborn_allvsall_calc_hct_obc_radii(fr,md,born,ir->gb_algorithm,top,x[0],cr,&fr->AllvsAll_workgb);
1143 inc_nrnb(nrnb,eNR_BORN_AVA_RADII_HCT_OBC,cnt);
1147 gmx_fatal(FARGS,"Bad gb algorithm for all-vs-all interactions");
1149 inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,md->homenr);
1154 /* Switch for determining which algorithm to use for Born radii calculation */
1157 #if 0 && defined (GMX_X86_SSE2)
1158 /* x86 or x86-64 with GCC inline assembly and/or SSE intrinsics */
1159 switch(ir->gb_algorithm)
1162 if(fr->use_acceleration)
1164 calc_gb_rad_still_sse2_double(cr,fr,born->nr,top, atype, x[0], nl, born);
1168 calc_gb_rad_still(cr,fr,born->nr,top,atype,x,nl,born,md);
1172 if(fr->use_acceleration)
1174 calc_gb_rad_hct_obc_sse2_double(cr,fr,born->nr,top, atype, x[0], nl, born, md, ir->gb_algorithm);
1178 calc_gb_rad_hct(cr,fr,born->nr,top,atype,x,nl,born,md);
1182 if(fr->use_acceleration)
1184 calc_gb_rad_hct_obc_sse2_double(cr,fr,born->nr,top, atype, x[0], nl, born, md, ir->gb_algorithm);
1188 calc_gb_rad_obc(cr,fr,born->nr,top,atype,x,nl,born,md);
1193 gmx_fatal(FARGS, "Unknown double precision sse-enabled algorithm for Born radii calculation: %d",ir->gb_algorithm);
1196 switch(ir->gb_algorithm)
1199 calc_gb_rad_still(cr,fr,born->nr,top,atype,x,nl,born,md);
1202 calc_gb_rad_hct(cr,fr,born->nr,top,atype,x,nl,born,md);
1205 calc_gb_rad_obc(cr,fr,born->nr,top,atype,x,nl,born,md);
1209 gmx_fatal(FARGS, "Unknown double precision algorithm for Born radii calculation: %d",ir->gb_algorithm);
1216 #if 0 && defined (GMX_X86_SSE2)
1217 /* x86 or x86-64 with GCC inline assembly and/or SSE intrinsics */
1218 switch(ir->gb_algorithm)
1221 if(fr->use_acceleration)
1223 calc_gb_rad_still_sse2_single(cr,fr,born->nr,top, atype, x[0], nl, born);
1227 calc_gb_rad_still(cr,fr,born->nr,top,atype,x,nl,born,md);
1231 if(fr->use_acceleration)
1233 calc_gb_rad_hct_obc_sse2_single(cr,fr,born->nr,top, atype, x[0], nl, born, md, ir->gb_algorithm);
1237 calc_gb_rad_hct(cr,fr,born->nr,top,atype,x,nl,born,md);
1242 if(fr->use_acceleration)
1244 calc_gb_rad_hct_obc_sse2_single(cr,fr,born->nr,top, atype, x[0], nl, born, md, ir->gb_algorithm);
1248 calc_gb_rad_obc(cr,fr,born->nr,top,atype,x,nl,born,md);
1253 gmx_fatal(FARGS, "Unknown sse-enabled algorithm for Born radii calculation: %d",ir->gb_algorithm);
1257 switch(ir->gb_algorithm)
1260 calc_gb_rad_still(cr,fr,born->nr,top,atype,x,nl,born,md);
1263 calc_gb_rad_hct(cr,fr,born->nr,top,atype,x,nl,born,md);
1266 calc_gb_rad_obc(cr,fr,born->nr,top,atype,x,nl,born,md);
1270 gmx_fatal(FARGS, "Unknown algorithm for Born radii calculation: %d",ir->gb_algorithm);
1273 #endif /* Single precision sse */
1275 #endif /* Double or single precision */
1277 if(fr->bAllvsAll==FALSE)
1279 switch(ir->gb_algorithm)
1282 inc_nrnb(nrnb,eNR_BORN_RADII_STILL,nl->nrj);
1286 inc_nrnb(nrnb,eNR_BORN_RADII_HCT_OBC,nl->nrj);
1292 inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,nl->nri);
1300 real gb_bonds_tab(rvec x[], rvec f[], rvec fshift[], real *charge, real *p_gbtabscale,
1301 real *invsqrta, real *dvda, real *GBtab, t_idef *idef, real epsilon_r,
1302 real gb_epsilon_solvent, real facel, const t_pbc *pbc, const t_graph *graph)
1304 int i,j,n0,m,nnn,type,ai,aj;
1310 real isaprod,qq,gbscale,gbtabscale,Y,F,Geps,Heps2,Fp,VV,FF,rt,eps,eps2;
1311 real vgb,fgb,vcoul,fijC,dvdatmp,fscal,dvdaj;
1317 t_iatom *forceatoms;
1319 /* Scale the electrostatics by gb_epsilon_solvent */
1320 facel = facel * ((1.0/epsilon_r) - 1.0/gb_epsilon_solvent);
1322 gbtabscale=*p_gbtabscale;
1325 for(j=F_GB12;j<=F_GB14;j++)
1327 forceatoms = idef->il[j].iatoms;
1329 for(i=0;i<idef->il[j].nr; )
1331 /* To avoid reading in the interaction type, we just increment i to pass over
1332 * the types in the forceatoms array, this saves some memory accesses
1335 ai = forceatoms[i++];
1336 aj = forceatoms[i++];
1338 ki = pbc_rvec_sub(pbc,x[ai],x[aj],dx);
1339 rsq11 = iprod(dx,dx);
1341 isai = invsqrta[ai];
1342 iq = (-1)*facel*charge[ai];
1344 rinv11 = gmx_invsqrt(rsq11);
1345 isaj = invsqrta[aj];
1346 isaprod = isai*isaj;
1347 qq = isaprod*iq*charge[aj];
1348 gbscale = isaprod*gbtabscale;
1357 Geps = eps*GBtab[nnn+2];
1358 Heps2 = eps2*GBtab[nnn+3];
1361 FF = Fp+Geps+2.0*Heps2;
1363 fijC = qq*FF*gbscale;
1364 dvdatmp = -(vgb+fijC*r)*0.5;
1365 dvda[aj] = dvda[aj] + dvdatmp*isaj*isaj;
1366 dvda[ai] = dvda[ai] + dvdatmp*isai*isai;
1367 vctot = vctot + vgb;
1368 fgb = -(fijC)*rinv11;
1371 ivec_sub(SHIFT_IVEC(graph,ai),SHIFT_IVEC(graph,aj),dt);
1375 for (m=0; (m<DIM); m++) { /* 15 */
1379 fshift[ki][m]+=fscal;
1380 fshift[CENTRAL][m]-=fscal;
1388 real calc_gb_selfcorrections(t_commrec *cr, int natoms,
1389 real *charge, gmx_genborn_t *born, real *dvda, t_mdatoms *md, double facel)
1392 real rai,e,derb,q,q2,fi,rai_inv,vtot;
1396 pd_at_range(cr,&at0,&at1);
1398 else if(DOMAINDECOMP(cr))
1401 at1=cr->dd->nat_home;
1410 /* Scale the electrostatics by gb_epsilon_solvent */
1411 facel = facel * ((1.0/born->epsilon_r) - 1.0/born->gb_epsilon_solvent);
1415 /* Apply self corrections */
1416 for(i=at0;i<at1;i++)
1420 if(born->use[ai]==1)
1422 rai = born->bRad[ai];
1428 derb = 0.5*e*rai_inv*rai_inv;
1429 dvda[ai] += derb*rai;
1438 real calc_gb_nonpolar(t_commrec *cr, t_forcerec *fr,int natoms,gmx_genborn_t *born, gmx_localtop_t *top,
1439 const t_atomtypes *atype, real *dvda,int gb_algorithm, t_mdatoms *md)
1442 real e,es,rai,rbi,term,probe,tmp,factor;
1443 real rbi_inv,rbi_inv2;
1445 /* To keep the compiler happy */
1450 pd_at_range(cr,&at0,&at1);
1452 else if(DOMAINDECOMP(cr))
1455 at1 = cr->dd->nat_home;
1463 /* factor is the surface tension */
1464 factor = born->sa_surface_tension;
1467 // The surface tension factor is 0.0049 for Still model, 0.0054 for HCT/OBC
1468 if(gb_algorithm==egbSTILL)
1470 factor=0.0049*100*CAL2JOULE;
1474 factor=0.0054*100*CAL2JOULE;
1477 /* if(gb_algorithm==egbHCT || gb_algorithm==egbOBC) */
1483 for(i=at0;i<at1;i++)
1487 if(born->use[ai]==1)
1489 rai = top->atomtypes.gb_radius[md->typeA[ai]];
1490 rbi_inv = fr->invsqrta[ai];
1491 rbi_inv2 = rbi_inv * rbi_inv;
1492 tmp = (rai*rbi_inv2)*(rai*rbi_inv2);
1494 e = factor*term*(rai+probe)*(rai+probe)*tmp;
1495 dvda[ai] = dvda[ai] - 6*e*rbi_inv2;
1505 real calc_gb_chainrule(int natoms, t_nblist *nl, real *dadx, real *dvda, rvec x[], rvec t[], rvec fshift[],
1506 rvec shift_vec[], int gb_algorithm, gmx_genborn_t *born, t_mdatoms *md)
1508 int i,k,n,ai,aj,nj0,nj1,n0,n1;
1511 real fgb,fij,rb2,rbi,fix1,fiy1,fiz1;
1512 real ix1,iy1,iz1,jx1,jy1,jz1,dx11,dy11,dz11,rsq11;
1513 real rinv11,tx,ty,tz,rbai,rbaj,fgb_ai;
1523 if(gb_algorithm==egbSTILL)
1527 rbi = born->bRad[i];
1528 rb[i] = (2 * rbi * rbi * dvda[i])/ONE_4PI_EPS0;
1531 else if(gb_algorithm==egbHCT)
1535 rbi = born->bRad[i];
1536 rb[i] = rbi * rbi * dvda[i];
1539 else if(gb_algorithm==egbOBC)
1543 rbi = born->bRad[i];
1544 rb[i] = rbi * rbi * born->drobc[i] * dvda[i];
1548 for(i=0;i<nl->nri;i++)
1552 nj0 = nl->jindex[i];
1553 nj1 = nl->jindex[i+1];
1555 /* Load shifts for this list */
1556 shift = nl->shift[i];
1557 shX = shift_vec[shift][0];
1558 shY = shift_vec[shift][1];
1559 shZ = shift_vec[shift][2];
1561 /* Load atom i coordinates, add shift vectors */
1562 ix1 = shX + x[ai][0];
1563 iy1 = shY + x[ai][1];
1564 iz1 = shZ + x[ai][2];
1572 for(k=nj0;k<nj1;k++)
1586 fgb = rbai*dadx[n++];
1587 fgb_ai = rbaj*dadx[n++];
1589 /* Total force between ai and aj is the sum of ai->aj and aj->ai */
1600 /* Update force on atom aj */
1601 t[aj][0] = t[aj][0] - tx;
1602 t[aj][1] = t[aj][1] - ty;
1603 t[aj][2] = t[aj][2] - tz;
1606 /* Update force and shift forces on atom ai */
1607 t[ai][0] = t[ai][0] + fix1;
1608 t[ai][1] = t[ai][1] + fiy1;
1609 t[ai][2] = t[ai][2] + fiz1;
1611 fshift[shift][0] = fshift[shift][0] + fix1;
1612 fshift[shift][1] = fshift[shift][1] + fiy1;
1613 fshift[shift][2] = fshift[shift][2] + fiz1;
1622 calc_gb_forces(t_commrec *cr, t_mdatoms *md, gmx_genborn_t *born, gmx_localtop_t *top, const t_atomtypes *atype,
1623 rvec x[], rvec f[], t_forcerec *fr, t_idef *idef, int gb_algorithm, int sa_algorithm, t_nrnb *nrnb, gmx_bool bRad,
1624 const t_pbc *pbc, const t_graph *graph, gmx_enerdata_t *enerd)
1631 const t_pbc *pbc_null;
1638 if(sa_algorithm == esaAPPROX)
1640 /* Do a simple ACE type approximation for the non-polar solvation */
1641 enerd->term[F_NPSOLVATION] += calc_gb_nonpolar(cr, fr,born->nr, born, top, atype, fr->dvda, gb_algorithm,md);
1644 /* Calculate the bonded GB-interactions using either table or analytical formula */
1645 enerd->term[F_GBPOL] += gb_bonds_tab(x,f,fr->fshift, md->chargeA,&(fr->gbtabscale),
1646 fr->invsqrta,fr->dvda,fr->gbtab.tab,idef,born->epsilon_r,born->gb_epsilon_solvent, fr->epsfac, pbc_null, graph);
1648 /* Calculate self corrections to the GB energies - currently only A state used! (FIXME) */
1649 enerd->term[F_GBPOL] += calc_gb_selfcorrections(cr,born->nr,md->chargeA, born, fr->dvda, md, fr->epsfac);
1651 /* If parallel, sum the derivative of the potential w.r.t the born radii */
1654 gmx_sum(md->nr,fr->dvda, cr);
1656 else if(DOMAINDECOMP(cr))
1658 dd_atom_sum_real(cr->dd,fr->dvda);
1659 dd_atom_spread_real(cr->dd,fr->dvda);
1664 #if 0 && defined (GMX_X86_SSE2)
1665 if(fr->use_acceleration)
1668 genborn_allvsall_calc_chainrule_sse2_double(fr,md,born,x[0],f[0],gb_algorithm,fr->AllvsAll_workgb);
1670 genborn_allvsall_calc_chainrule_sse2_single(fr,md,born,x[0],f[0],gb_algorithm,fr->AllvsAll_workgb);
1675 genborn_allvsall_calc_chainrule(fr,md,born,x[0],f[0],gb_algorithm,fr->AllvsAll_workgb);
1678 genborn_allvsall_calc_chainrule(fr,md,born,x[0],f[0],gb_algorithm,fr->AllvsAll_workgb);
1680 cnt = md->homenr*(md->nr/2+1);
1681 inc_nrnb(nrnb,eNR_BORN_AVA_CHAINRULE,cnt);
1682 inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,md->homenr);
1686 #if 0 && defined (GMX_X86_SSE2)
1687 if(fr->use_acceleration)
1690 calc_gb_chainrule_sse2_double(fr->natoms_force, &(fr->gblist),fr->dadx,fr->dvda,x[0],
1691 f[0],fr->fshift[0],fr->shift_vec[0],gb_algorithm,born,md);
1693 calc_gb_chainrule_sse2_single(fr->natoms_force, &(fr->gblist),fr->dadx,fr->dvda,x[0],
1694 f[0],fr->fshift[0],fr->shift_vec[0],gb_algorithm,born,md);
1699 calc_gb_chainrule(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda,
1700 x, f, fr->fshift, fr->shift_vec, gb_algorithm, born, md);
1703 calc_gb_chainrule(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda,
1704 x, f, fr->fshift, fr->shift_vec, gb_algorithm, born, md);
1709 inc_nrnb(nrnb,eNR_BORN_CHAINRULE,fr->gblist.nrj);
1710 inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,fr->gblist.nri);
1715 static void add_j_to_gblist(gbtmpnbl_t *list,int aj)
1717 if (list->naj >= list->aj_nalloc)
1719 list->aj_nalloc = over_alloc_large(list->naj+1);
1720 srenew(list->aj,list->aj_nalloc);
1723 list->aj[list->naj++] = aj;
1726 static gbtmpnbl_t *find_gbtmplist(struct gbtmpnbls *lists,int shift)
1730 /* Search the list with the same shift, if there is one */
1732 while (ind < lists->nlist && shift != lists->list[ind].shift)
1736 if (ind == lists->nlist)
1738 if (lists->nlist == lists->list_nalloc)
1740 lists->list_nalloc++;
1741 srenew(lists->list,lists->list_nalloc);
1742 for(i=lists->nlist; i<lists->list_nalloc; i++)
1744 lists->list[i].aj = NULL;
1745 lists->list[i].aj_nalloc = 0;
1750 lists->list[lists->nlist].shift = shift;
1751 lists->list[lists->nlist].naj = 0;
1755 return &lists->list[ind];
1758 static void add_bondeds_to_gblist(t_ilist *il,
1759 gmx_bool bMolPBC,t_pbc *pbc,t_graph *g,rvec *x,
1760 struct gbtmpnbls *nls)
1762 int ind,j,ai,aj,shift,found;
1768 for(ind=0; ind<il->nr; ind+=3)
1770 ai = il->iatoms[ind+1];
1771 aj = il->iatoms[ind+2];
1776 rvec_sub(x[ai],x[aj],dx);
1777 ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
1778 shift = IVEC2IS(dt);
1782 shift = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
1785 /* Find the list for this shift or create one */
1786 list = find_gbtmplist(&nls[ai],shift);
1790 /* So that we do not add the same bond twice.
1791 * This happens with some constraints between 1-3 atoms
1792 * that are in the bond-list but should not be in the GB nb-list */
1793 for(j=0;j<list->naj;j++)
1795 if (list->aj[j] == aj)
1805 gmx_incons("ai == aj");
1808 add_j_to_gblist(list,aj);
1814 compare_int (const void * a, const void * b)
1816 return ( *(int*)a - *(int*)b );
1821 int make_gb_nblist(t_commrec *cr, int gb_algorithm, real gbcut,
1822 rvec x[], matrix box,
1823 t_forcerec *fr, t_idef *idef, t_graph *graph, gmx_genborn_t *born)
1825 int i,l,ii,j,k,n,nj0,nj1,ai,aj,at0,at1,found,shift,s;
1830 struct gbtmpnbls *nls;
1831 gbtmpnbl_t *list =NULL;
1833 set_pbc(&pbc,fr->ePBC,box);
1834 nls = born->nblist_work;
1836 for(i=0;i<born->nr;i++)
1843 set_pbc_dd(&pbc,fr->ePBC,cr->dd,TRUE,box);
1846 switch (gb_algorithm)
1850 /* Loop over 1-2, 1-3 and 1-4 interactions */
1851 for(j=F_GB12;j<=F_GB14;j++)
1853 add_bondeds_to_gblist(&idef->il[j],fr->bMolPBC,&pbc,graph,x,nls);
1857 /* Loop over 1-4 interactions */
1858 add_bondeds_to_gblist(&idef->il[F_GB14],fr->bMolPBC,&pbc,graph,x,nls);
1861 gmx_incons("Unknown GB algorithm");
1864 /* Loop over the VDWQQ and VDW nblists to set up the nonbonded part of the GB list */
1865 for(n=0; (n<fr->nnblists); n++)
1867 for(i=0; (i<eNL_NR); i++)
1869 nblist=&(fr->nblists[n].nlist_sr[i]);
1871 if (nblist->nri > 0 && (i==eNL_VDWQQ || i==eNL_QQ))
1873 for(j=0;j<nblist->nri;j++)
1875 ai = nblist->iinr[j];
1876 shift = nblist->shift[j];
1878 /* Find the list for this shift or create one */
1879 list = find_gbtmplist(&nls[ai],shift);
1881 nj0 = nblist->jindex[j];
1882 nj1 = nblist->jindex[j+1];
1884 /* Add all the j-atoms in the non-bonded list to the GB list */
1885 for(k=nj0;k<nj1;k++)
1887 add_j_to_gblist(list,nblist->jjnr[k]);
1894 /* Zero out some counters */
1898 fr->gblist.jindex[0] = fr->gblist.nri;
1900 for(i=0;i<fr->natoms_force;i++)
1902 for(s=0; s<nls[i].nlist; s++)
1904 list = &nls[i].list[s];
1906 /* Only add those atoms that actually have neighbours */
1907 if (born->use[i] != 0)
1909 fr->gblist.iinr[fr->gblist.nri] = i;
1910 fr->gblist.shift[fr->gblist.nri] = list->shift;
1913 for(k=0; k<list->naj; k++)
1915 /* Memory allocation for jjnr */
1916 if(fr->gblist.nrj >= fr->gblist.maxnrj)
1918 fr->gblist.maxnrj += over_alloc_large(fr->gblist.maxnrj);
1922 fprintf(debug,"Increasing GB neighbourlist j size to %d\n",fr->gblist.maxnrj);
1925 srenew(fr->gblist.jjnr,fr->gblist.maxnrj);
1929 if(i == list->aj[k])
1931 gmx_incons("i == list->aj[k]");
1933 fr->gblist.jjnr[fr->gblist.nrj++] = list->aj[k];
1936 fr->gblist.jindex[fr->gblist.nri] = fr->gblist.nrj;
1943 for(i=0;i<fr->gblist.nri;i++)
1945 nj0 = fr->gblist.jindex[i];
1946 nj1 = fr->gblist.jindex[i+1];
1947 ai = fr->gblist.iinr[i];
1950 for(j=nj0;j<nj1;j++)
1952 if(fr->gblist.jjnr[j]<ai)
1953 fr->gblist.jjnr[j]+=fr->natoms_force;
1955 qsort(fr->gblist.jjnr+nj0,nj1-nj0,sizeof(int),compare_int);
1957 for(j=nj0;j<nj1;j++)
1959 if(fr->gblist.jjnr[j]>=fr->natoms_force)
1960 fr->gblist.jjnr[j]-=fr->natoms_force;
1969 void make_local_gb(const t_commrec *cr, gmx_genborn_t *born, int gb_algorithm)
1972 gmx_domdec_t *dd=NULL;
1974 if(DOMAINDECOMP(cr))
1982 /* Single node or particle decomp (global==local), just copy pointers and return */
1983 if(gb_algorithm==egbSTILL)
1985 born->gpol = born->gpol_globalindex;
1986 born->vsolv = born->vsolv_globalindex;
1987 born->gb_radius = born->gb_radius_globalindex;
1991 born->param = born->param_globalindex;
1992 born->gb_radius = born->gb_radius_globalindex;
1995 born->use = born->use_globalindex;
2000 /* Reallocation of local arrays if necessary */
2001 /* fr->natoms_force is equal to dd->nat_tot */
2002 if (DOMAINDECOMP(cr) && dd->nat_tot > born->nalloc)
2006 nalloc = dd->nat_tot;
2008 /* Arrays specific to different gb algorithms */
2009 if (gb_algorithm == egbSTILL)
2011 srenew(born->gpol, nalloc+3);
2012 srenew(born->vsolv, nalloc+3);
2013 srenew(born->gb_radius, nalloc+3);
2014 for(i=born->nalloc; (i<nalloc+3); i++)
2018 born->gb_radius[i] = 0;
2023 srenew(born->param, nalloc+3);
2024 srenew(born->gb_radius, nalloc+3);
2025 for(i=born->nalloc; (i<nalloc+3); i++)
2028 born->gb_radius[i] = 0;
2032 /* All gb-algorithms use the array for vsites exclusions */
2033 srenew(born->use, nalloc+3);
2034 for(i=born->nalloc; (i<nalloc+3); i++)
2039 born->nalloc = nalloc;
2042 /* With dd, copy algorithm specific arrays */
2043 if(gb_algorithm==egbSTILL)
2045 for(i=at0;i<at1;i++)
2047 born->gpol[i] = born->gpol_globalindex[dd->gatindex[i]];
2048 born->vsolv[i] = born->vsolv_globalindex[dd->gatindex[i]];
2049 born->gb_radius[i] = born->gb_radius_globalindex[dd->gatindex[i]];
2050 born->use[i] = born->use_globalindex[dd->gatindex[i]];
2055 for(i=at0;i<at1;i++)
2057 born->param[i] = born->param_globalindex[dd->gatindex[i]];
2058 born->gb_radius[i] = born->gb_radius_globalindex[dd->gatindex[i]];
2059 born->use[i] = born->use_globalindex[dd->gatindex[i]];