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44 #include "types/commrec.h"
46 #include "gromacs/fileio/pdbio.h"
48 #include "gromacs/math/units.h"
51 #include "gromacs/topology/mtop_util.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/pbcutil/ishift.h"
57 #include "gromacs/pbcutil/mshift.h"
58 #include "gromacs/pbcutil/pbc.h"
59 #include "gromacs/utility/fatalerror.h"
60 #include "gromacs/utility/gmxmpi.h"
61 #include "gromacs/utility/smalloc.h"
63 #ifdef GMX_SIMD_X86_SSE2_OR_HIGHER
65 # include "genborn_sse2_double.h"
66 # include "genborn_allvsall_sse2_double.h"
68 # include "genborn_sse2_single.h"
69 # include "genborn_allvsall_sse2_single.h"
70 # endif /* GMX_DOUBLE */
71 #endif /* SSE or AVX present */
73 #include "genborn_allvsall.h"
75 /*#define DISABLE_SSE*/
84 typedef struct gbtmpnbls {
90 /* This function is exactly the same as the one in bondfree.c. The reason
91 * it is copied here is that the bonded gb-interactions are evaluated
92 * not in calc_bonds, but rather in calc_gb_forces
94 static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
98 return pbc_dx_aiuc(pbc, xi, xj, dx);
102 rvec_sub(xi, xj, dx);
107 static int init_gb_nblist(int natoms, t_nblist *nl)
109 nl->maxnri = natoms*4;
118 /*nl->nltype = nltype;*/
120 srenew(nl->iinr, nl->maxnri);
121 srenew(nl->gid, nl->maxnri);
122 srenew(nl->shift, nl->maxnri);
123 srenew(nl->jindex, nl->maxnri+1);
131 static int init_gb_still(const t_atomtypes *atype, t_idef *idef, t_atoms *atoms,
132 gmx_genborn_t *born, int natoms)
135 int i, j, i1, i2, k, m, nbond, nang, ia, ib, ic, id, nb, idx, idx2, at;
139 real r, ri, rj, ri2, ri3, rj2, r2, r3, r4, rk, ratio, term, h, doffset;
140 real p1, p2, p3, factor, cosine, rab, rbc;
147 snew(born->gpol_still_work, natoms+3);
152 doffset = born->gb_doffset;
154 for (i = 0; i < natoms; i++)
156 born->gpol_globalindex[i] = born->vsolv_globalindex[i] =
157 born->gb_radius_globalindex[i] = 0;
160 /* Compute atomic solvation volumes for Still method */
161 for (i = 0; i < natoms; i++)
163 ri = atype->gb_radius[atoms->atom[i].type];
164 born->gb_radius_globalindex[i] = ri;
166 born->vsolv_globalindex[i] = (4*M_PI/3)*r3;
169 for (j = 0; j < idef->il[F_GB12].nr; j += 3)
171 m = idef->il[F_GB12].iatoms[j];
172 ia = idef->il[F_GB12].iatoms[j+1];
173 ib = idef->il[F_GB12].iatoms[j+2];
175 r = 1.01*idef->iparams[m].gb.st;
177 ri = atype->gb_radius[atoms->atom[ia].type];
178 rj = atype->gb_radius[atoms->atom[ib].type];
184 ratio = (rj2-ri2-r*r)/(2*ri*r);
186 term = (M_PI/3.0)*h*h*(3.0*ri-h);
188 born->vsolv_globalindex[ia] -= term;
190 ratio = (ri2-rj2-r*r)/(2*rj*r);
192 term = (M_PI/3.0)*h*h*(3.0*rj-h);
194 born->vsolv_globalindex[ib] -= term;
197 /* Get the self-, 1-2 and 1-3 polarization energies for analytical Still
200 for (j = 0; j < natoms; j++)
202 if (born->use_globalindex[j] == 1)
204 born->gpol_globalindex[j] = -0.5*ONE_4PI_EPS0/
205 (atype->gb_radius[atoms->atom[j].type]-doffset+STILL_P1);
210 for (j = 0; j < idef->il[F_GB12].nr; j += 3)
212 m = idef->il[F_GB12].iatoms[j];
213 ia = idef->il[F_GB12].iatoms[j+1];
214 ib = idef->il[F_GB12].iatoms[j+2];
216 r = idef->iparams[m].gb.st;
220 born->gpol_globalindex[ia] = born->gpol_globalindex[ia]+
221 STILL_P2*born->vsolv_globalindex[ib]/r4;
222 born->gpol_globalindex[ib] = born->gpol_globalindex[ib]+
223 STILL_P2*born->vsolv_globalindex[ia]/r4;
227 for (j = 0; j < idef->il[F_GB13].nr; j += 3)
229 m = idef->il[F_GB13].iatoms[j];
230 ia = idef->il[F_GB13].iatoms[j+1];
231 ib = idef->il[F_GB13].iatoms[j+2];
233 r = idef->iparams[m].gb.st;
236 born->gpol_globalindex[ia] = born->gpol_globalindex[ia]+
237 STILL_P3*born->vsolv_globalindex[ib]/r4;
238 born->gpol_globalindex[ib] = born->gpol_globalindex[ib]+
239 STILL_P3*born->vsolv_globalindex[ia]/r4;
248 /* Initialize all GB datastructs and compute polarization energies */
249 int init_gb(gmx_genborn_t **p_born,
250 t_forcerec *fr, const t_inputrec *ir,
251 const gmx_mtop_t *mtop, int gb_algorithm)
253 int i, j, m, ai, aj, jj, natoms, nalloc;
254 real rai, sk, p, doffset;
258 gmx_localtop_t *localtop;
260 natoms = mtop->natoms;
262 atoms = gmx_mtop_global_atoms(mtop);
263 localtop = gmx_mtop_generate_local_top(mtop, ir);
270 snew(born->drobc, natoms);
271 snew(born->bRad, natoms);
273 /* Allocate memory for the global data arrays */
274 snew(born->param_globalindex, natoms+3);
275 snew(born->gpol_globalindex, natoms+3);
276 snew(born->vsolv_globalindex, natoms+3);
277 snew(born->gb_radius_globalindex, natoms+3);
278 snew(born->use_globalindex, natoms+3);
280 snew(fr->invsqrta, natoms);
281 snew(fr->dvda, natoms);
284 fr->dadx_rawptr = NULL;
286 born->gpol_still_work = NULL;
287 born->gpol_hct_work = NULL;
289 /* snew(born->asurf,natoms); */
290 /* snew(born->dasurf,natoms); */
292 /* Initialize the gb neighbourlist */
293 init_gb_nblist(natoms, &(fr->gblist));
295 /* Do the Vsites exclusions (if any) */
296 for (i = 0; i < natoms; i++)
298 jj = atoms.atom[i].type;
299 if (mtop->atomtypes.gb_radius[atoms.atom[i].type] > 0)
301 born->use_globalindex[i] = 1;
305 born->use_globalindex[i] = 0;
308 /* If we have a Vsite, put vs_globalindex[i]=0 */
309 if (C6 (fr->nbfp, fr->ntype, jj, jj) == 0 &&
310 C12(fr->nbfp, fr->ntype, jj, jj) == 0 &&
311 atoms.atom[i].q == 0)
313 born->use_globalindex[i] = 0;
317 /* Copy algorithm parameters from inputrecord to local structure */
318 born->obc_alpha = ir->gb_obc_alpha;
319 born->obc_beta = ir->gb_obc_beta;
320 born->obc_gamma = ir->gb_obc_gamma;
321 born->gb_doffset = ir->gb_dielectric_offset;
322 born->gb_epsilon_solvent = ir->gb_epsilon_solvent;
323 born->epsilon_r = ir->epsilon_r;
325 doffset = born->gb_doffset;
327 /* Set the surface tension */
328 born->sa_surface_tension = ir->sa_surface_tension;
330 /* If Still model, initialise the polarisation energies */
331 if (gb_algorithm == egbSTILL)
333 init_gb_still(&(mtop->atomtypes), &(localtop->idef), &atoms,
338 /* If HCT/OBC, precalculate the sk*atype->S_hct factors */
339 else if (gb_algorithm == egbHCT || gb_algorithm == egbOBC)
342 snew(born->gpol_hct_work, natoms+3);
344 for (i = 0; i < natoms; i++)
346 if (born->use_globalindex[i] == 1)
348 rai = mtop->atomtypes.gb_radius[atoms.atom[i].type]-doffset;
349 sk = rai * mtop->atomtypes.S_hct[atoms.atom[i].type];
350 born->param_globalindex[i] = sk;
351 born->gb_radius_globalindex[i] = rai;
355 born->param_globalindex[i] = 0;
356 born->gb_radius_globalindex[i] = 0;
361 /* Allocate memory for work arrays for temporary use */
362 snew(born->work, natoms+4);
363 snew(born->count, natoms);
364 snew(born->nblist_work, natoms);
366 /* Domain decomposition specific stuff */
375 calc_gb_rad_still(t_commrec *cr, t_forcerec *fr, gmx_localtop_t *top,
376 rvec x[], t_nblist *nl,
377 gmx_genborn_t *born, t_mdatoms *md)
379 int i, k, n, nj0, nj1, ai, aj, type;
382 real gpi, dr, dr2, dr4, idr4, rvdw, ratio, ccf, theta, term, rai, raj;
383 real ix1, iy1, iz1, jx1, jy1, jz1, dx11, dy11, dz11;
384 real rinv, idr2, idr6, vaj, dccf, cosq, sinq, prod, gpi2;
386 real vai, prod_ai, icf4, icf6;
388 factor = 0.5*ONE_4PI_EPS0;
391 for (i = 0; i < born->nr; i++)
393 born->gpol_still_work[i] = 0;
396 for (i = 0; i < nl->nri; i++)
401 nj1 = nl->jindex[i+1];
403 /* Load shifts for this list */
404 shift = nl->shift[i];
405 shX = fr->shift_vec[shift][0];
406 shY = fr->shift_vec[shift][1];
407 shZ = fr->shift_vec[shift][2];
411 rai = top->atomtypes.gb_radius[md->typeA[ai]];
412 vai = born->vsolv[ai];
413 prod_ai = STILL_P4*vai;
415 /* Load atom i coordinates, add shift vectors */
416 ix1 = shX + x[ai][0];
417 iy1 = shY + x[ai][1];
418 iz1 = shZ + x[ai][2];
420 for (k = nj0; k < nj1 && nl->jjnr[k] >= 0; k++)
431 dr2 = dx11*dx11+dy11*dy11+dz11*dz11;
432 rinv = gmx_invsqrt(dr2);
437 raj = top->atomtypes.gb_radius[md->typeA[aj]];
441 ratio = dr2 / (rvdw * rvdw);
442 vaj = born->vsolv[aj];
444 if (ratio > STILL_P5INV)
451 theta = ratio*STILL_PIP5;
453 term = 0.5*(1.0-cosq);
455 sinq = 1.0 - cosq*cosq;
456 dccf = 2.0*term*sinq*gmx_invsqrt(sinq)*theta;
461 icf6 = (4*ccf-dccf)*idr6;
462 born->gpol_still_work[aj] += prod_ai*icf4;
465 /* Save ai->aj and aj->ai chain rule terms */
466 fr->dadx[n++] = prod*icf6;
467 fr->dadx[n++] = prod_ai*icf6;
469 born->gpol_still_work[ai] += gpi;
472 /* Parallel summations */
473 if (DOMAINDECOMP(cr))
475 dd_atom_sum_real(cr->dd, born->gpol_still_work);
478 /* Calculate the radii */
479 for (i = 0; i < fr->natoms_force; i++) /* PELA born->nr */
481 if (born->use[i] != 0)
483 gpi = born->gpol[i]+born->gpol_still_work[i];
485 born->bRad[i] = factor*gmx_invsqrt(gpi2);
486 fr->invsqrta[i] = gmx_invsqrt(born->bRad[i]);
490 /* Extra communication required for DD */
491 if (DOMAINDECOMP(cr))
493 dd_atom_spread_real(cr->dd, born->bRad);
494 dd_atom_spread_real(cr->dd, fr->invsqrta);
503 calc_gb_rad_hct(t_commrec *cr, t_forcerec *fr, gmx_localtop_t *top,
504 rvec x[], t_nblist *nl,
505 gmx_genborn_t *born, t_mdatoms *md)
507 int i, k, n, ai, aj, nj0, nj1, at0, at1;
510 real rai, raj, gpi, dr2, dr, sk, sk_ai, sk2, sk2_ai, lij, uij, diff2, tmp, sum_ai;
511 real rad, min_rad, rinv, rai_inv;
512 real ix1, iy1, iz1, jx1, jy1, jz1, dx11, dy11, dz11;
513 real lij2, uij2, lij3, uij3, t1, t2, t3;
514 real lij_inv, dlij, duij, sk2_rinv, prod, log_term;
515 real doffset, raj_inv, dadx_val;
518 doffset = born->gb_doffset;
519 gb_radius = born->gb_radius;
521 for (i = 0; i < born->nr; i++)
523 born->gpol_hct_work[i] = 0;
526 /* Keep the compiler happy */
530 for (i = 0; i < nl->nri; i++)
535 nj1 = nl->jindex[i+1];
537 /* Load shifts for this list */
538 shift = nl->shift[i];
539 shX = fr->shift_vec[shift][0];
540 shY = fr->shift_vec[shift][1];
541 shZ = fr->shift_vec[shift][2];
546 sk_ai = born->param[ai];
547 sk2_ai = sk_ai*sk_ai;
549 /* Load atom i coordinates, add shift vectors */
550 ix1 = shX + x[ai][0];
551 iy1 = shY + x[ai][1];
552 iz1 = shZ + x[ai][2];
556 for (k = nj0; k < nj1 && nl->jjnr[k] >= 0; k++)
568 dr2 = dx11*dx11+dy11*dy11+dz11*dz11;
569 rinv = gmx_invsqrt(dr2);
572 sk = born->param[aj];
575 /* aj -> ai interaction */
596 lij_inv = gmx_invsqrt(lij2);
599 prod = 0.25*sk2_rinv;
601 log_term = log(uij*lij_inv);
603 tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term +
608 tmp = tmp + 2.0 * (rai_inv-lij);
611 t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
612 t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
613 t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
615 dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
616 /* fr->dadx[n++] = (dlij*t1+duij*t2+t3)*rinv; */
617 /* rb2 is moved to chainrule */
625 fr->dadx[n++] = dadx_val;
628 /* ai -> aj interaction */
629 if (raj < dr + sk_ai)
631 lij = 1.0/(dr-sk_ai);
644 uij = 1.0/(dr+sk_ai);
650 lij_inv = gmx_invsqrt(lij2);
651 sk2 = sk2_ai; /* sk2_ai = sk_ai * sk_ai in i loop above */
653 prod = 0.25 * sk2_rinv;
655 /* log_term = table_log(uij*lij_inv,born->log_table,
656 LOG_TABLE_ACCURACY); */
657 log_term = log(uij*lij_inv);
659 tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term +
664 tmp = tmp + 2.0 * (raj_inv-lij);
668 t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
669 t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
670 t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
672 dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
673 /* fr->dadx[n++] = (dlij*t1+duij*t2+t3)*rinv; */ /* rb2 is moved to chainrule */
675 born->gpol_hct_work[aj] += 0.5*tmp;
681 fr->dadx[n++] = dadx_val;
684 born->gpol_hct_work[ai] += sum_ai;
687 /* Parallel summations */
688 if (DOMAINDECOMP(cr))
690 dd_atom_sum_real(cr->dd, born->gpol_hct_work);
693 for (i = 0; i < fr->natoms_force; i++) /* PELA born->nr */
695 if (born->use[i] != 0)
697 rai = top->atomtypes.gb_radius[md->typeA[i]]-doffset;
698 sum_ai = 1.0/rai - born->gpol_hct_work[i];
699 min_rad = rai + doffset;
702 born->bRad[i] = rad > min_rad ? rad : min_rad;
703 fr->invsqrta[i] = gmx_invsqrt(born->bRad[i]);
707 /* Extra communication required for DD */
708 if (DOMAINDECOMP(cr))
710 dd_atom_spread_real(cr->dd, born->bRad);
711 dd_atom_spread_real(cr->dd, fr->invsqrta);
719 calc_gb_rad_obc(t_commrec *cr, t_forcerec *fr, gmx_localtop_t *top,
720 rvec x[], t_nblist *nl, gmx_genborn_t *born, t_mdatoms *md)
722 int i, k, ai, aj, nj0, nj1, n, at0, at1;
725 real rai, raj, gpi, dr2, dr, sk, sk2, lij, uij, diff2, tmp, sum_ai;
726 real rad, min_rad, sum_ai2, sum_ai3, tsum, tchain, rinv, rai_inv, lij_inv, rai_inv2;
727 real log_term, prod, sk2_rinv, sk_ai, sk2_ai;
728 real ix1, iy1, iz1, jx1, jy1, jz1, dx11, dy11, dz11;
729 real lij2, uij2, lij3, uij3, dlij, duij, t1, t2, t3;
730 real doffset, raj_inv, dadx_val;
733 /* Keep the compiler happy */
738 doffset = born->gb_doffset;
739 gb_radius = born->gb_radius;
741 for (i = 0; i < born->nr; i++)
743 born->gpol_hct_work[i] = 0;
746 for (i = 0; i < nl->nri; i++)
751 nj1 = nl->jindex[i+1];
753 /* Load shifts for this list */
754 shift = nl->shift[i];
755 shX = fr->shift_vec[shift][0];
756 shY = fr->shift_vec[shift][1];
757 shZ = fr->shift_vec[shift][2];
762 sk_ai = born->param[ai];
763 sk2_ai = sk_ai*sk_ai;
765 /* Load atom i coordinates, add shift vectors */
766 ix1 = shX + x[ai][0];
767 iy1 = shY + x[ai][1];
768 iz1 = shZ + x[ai][2];
772 for (k = nj0; k < nj1 && nl->jjnr[k] >= 0; k++)
784 dr2 = dx11*dx11+dy11*dy11+dz11*dz11;
785 rinv = gmx_invsqrt(dr2);
788 /* sk is precalculated in init_gb() */
789 sk = born->param[aj];
792 /* aj -> ai interaction */
812 lij_inv = gmx_invsqrt(lij2);
815 prod = 0.25*sk2_rinv;
817 log_term = log(uij*lij_inv);
819 tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2);
823 tmp = tmp + 2.0 * (rai_inv-lij);
827 t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
828 t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
829 t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
831 dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
839 fr->dadx[n++] = dadx_val;
841 /* ai -> aj interaction */
842 if (raj < dr + sk_ai)
844 lij = 1.0/(dr-sk_ai);
857 uij = 1.0/(dr+sk_ai);
863 lij_inv = gmx_invsqrt(lij2);
864 sk2 = sk2_ai; /* sk2_ai = sk_ai * sk_ai in i loop above */
866 prod = 0.25 * sk2_rinv;
868 /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */
869 log_term = log(uij*lij_inv);
871 tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2);
875 tmp = tmp + 2.0 * (raj_inv-lij);
878 t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
879 t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
880 t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
882 dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
884 born->gpol_hct_work[aj] += 0.5*tmp;
891 fr->dadx[n++] = dadx_val;
894 born->gpol_hct_work[ai] += sum_ai;
898 /* Parallel summations */
899 if (DOMAINDECOMP(cr))
901 dd_atom_sum_real(cr->dd, born->gpol_hct_work);
904 for (i = 0; i < fr->natoms_force; i++) /* PELA born->nr */
906 if (born->use[i] != 0)
908 rai = top->atomtypes.gb_radius[md->typeA[i]];
912 sum_ai = rai * born->gpol_hct_work[i];
913 sum_ai2 = sum_ai * sum_ai;
914 sum_ai3 = sum_ai2 * sum_ai;
916 tsum = tanh(born->obc_alpha*sum_ai-born->obc_beta*sum_ai2+born->obc_gamma*sum_ai3);
917 born->bRad[i] = rai_inv - tsum*rai_inv2;
918 born->bRad[i] = 1.0 / born->bRad[i];
920 fr->invsqrta[i] = gmx_invsqrt(born->bRad[i]);
922 tchain = rai * (born->obc_alpha-2*born->obc_beta*sum_ai+3*born->obc_gamma*sum_ai2);
923 born->drobc[i] = (1.0-tsum*tsum)*tchain*rai_inv2;
927 /* Extra (local) communication required for DD */
928 if (DOMAINDECOMP(cr))
930 dd_atom_spread_real(cr->dd, born->bRad);
931 dd_atom_spread_real(cr->dd, fr->invsqrta);
932 dd_atom_spread_real(cr->dd, born->drobc);
941 int calc_gb_rad(t_commrec *cr, t_forcerec *fr, t_inputrec *ir, gmx_localtop_t *top,
942 rvec x[], t_nblist *nl, gmx_genborn_t *born, t_mdatoms *md, t_nrnb *nrnb)
948 if (fr->bAllvsAll && fr->dadx == NULL)
950 /* We might need up to 8 atoms of padding before and after,
951 * and another 4 units to guarantee SSE alignment.
953 fr->nalloc_dadx = 2*(md->homenr+12)*(md->nr/2+1+12);
954 snew(fr->dadx_rawptr, fr->nalloc_dadx);
955 fr->dadx = (real *) (((size_t) fr->dadx_rawptr + 16) & (~((size_t) 15)));
959 /* In the SSE-enabled gb-loops, when writing to dadx, we
960 * always write 2*4 elements at a time, even in the case with only
961 * 1-3 j particles, where we only really need to write 2*(1-3)
962 * elements. This is because we want dadx to be aligned to a 16-
963 * byte boundary, and being able to use _mm_store/load_ps
965 ndadx = 2 * (nl->nrj + 3*nl->nri);
967 /* First, reallocate the dadx array, we need 3 extra for SSE */
968 if (ndadx + 3 > fr->nalloc_dadx)
970 fr->nalloc_dadx = over_alloc_large(ndadx) + 3;
971 srenew(fr->dadx_rawptr, fr->nalloc_dadx);
972 fr->dadx = (real *) (((size_t) fr->dadx_rawptr + 16) & (~((size_t) 15)));
978 cnt = md->homenr*(md->nr/2+1);
980 if (ir->gb_algorithm == egbSTILL)
982 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
983 if (fr->use_simd_kernels)
986 genborn_allvsall_calc_still_radii_sse2_double(fr, md, born, top, x[0], cr, &fr->AllvsAll_workgb);
988 genborn_allvsall_calc_still_radii_sse2_single(fr, md, born, top, x[0], cr, &fr->AllvsAll_workgb);
993 genborn_allvsall_calc_still_radii(fr, md, born, top, x[0], cr, &fr->AllvsAll_workgb);
996 genborn_allvsall_calc_still_radii(fr, md, born, top, x[0], &fr->AllvsAll_workgb);
998 /* 13 flops in outer loop, 47 flops in inner loop */
999 inc_nrnb(nrnb, eNR_BORN_AVA_RADII_STILL, md->homenr*13+cnt*47);
1001 else if (ir->gb_algorithm == egbHCT || ir->gb_algorithm == egbOBC)
1003 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
1004 if (fr->use_simd_kernels)
1007 genborn_allvsall_calc_hct_obc_radii_sse2_double(fr, md, born, ir->gb_algorithm, top, x[0], cr, &fr->AllvsAll_workgb);
1009 genborn_allvsall_calc_hct_obc_radii_sse2_single(fr, md, born, ir->gb_algorithm, top, x[0], cr, &fr->AllvsAll_workgb);
1014 genborn_allvsall_calc_hct_obc_radii(fr, md, born, ir->gb_algorithm, top, x[0], cr, &fr->AllvsAll_workgb);
1017 genborn_allvsall_calc_hct_obc_radii(fr, md, born, ir->gb_algorithm, top, x[0], &fr->AllvsAll_workgb);
1019 /* 24 flops in outer loop, 183 in inner */
1020 inc_nrnb(nrnb, eNR_BORN_AVA_RADII_HCT_OBC, md->homenr*24+cnt*183);
1024 gmx_fatal(FARGS, "Bad gb algorithm for all-vs-all interactions");
1029 /* Switch for determining which algorithm to use for Born radii calculation */
1032 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
1033 /* x86 or x86-64 with GCC inline assembly and/or SSE intrinsics */
1034 switch (ir->gb_algorithm)
1037 if (fr->use_simd_kernels)
1039 calc_gb_rad_still_sse2_double(cr, fr, born->nr, top, atype, x[0], nl, born);
1043 calc_gb_rad_still(cr, fr, top, x, nl, born, md);
1047 if (fr->use_simd_kernels)
1049 calc_gb_rad_hct_obc_sse2_double(cr, fr, born->nr, top, atype, x[0], nl, born, md, ir->gb_algorithm);
1053 calc_gb_rad_hct(cr, fr, top, x, nl, born, md);
1057 if (fr->use_simd_kernels)
1059 calc_gb_rad_hct_obc_sse2_double(cr, fr, born->nr, top, atype, x[0], nl, born, md, ir->gb_algorithm);
1063 calc_gb_rad_obc(cr, fr, born->nr, top, x, nl, born, md);
1068 gmx_fatal(FARGS, "Unknown double precision sse-enabled algorithm for Born radii calculation: %d", ir->gb_algorithm);
1071 switch (ir->gb_algorithm)
1074 calc_gb_rad_still(cr, fr, top, x, nl, born, md);
1077 calc_gb_rad_hct(cr, fr, top, x, nl, born, md);
1080 calc_gb_rad_obc(cr, fr, top, x, nl, born, md);
1084 gmx_fatal(FARGS, "Unknown double precision algorithm for Born radii calculation: %d", ir->gb_algorithm);
1091 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
1092 /* x86 or x86-64 with GCC inline assembly and/or SSE intrinsics */
1093 switch (ir->gb_algorithm)
1096 if (fr->use_simd_kernels)
1098 calc_gb_rad_still_sse2_single(cr, fr, born->nr, top, x[0], nl, born);
1102 calc_gb_rad_still(cr, fr, top, x, nl, born, md);
1106 if (fr->use_simd_kernels)
1108 calc_gb_rad_hct_obc_sse2_single(cr, fr, born->nr, top, x[0], nl, born, md, ir->gb_algorithm);
1112 calc_gb_rad_hct(cr, fr, top, x, nl, born, md);
1117 if (fr->use_simd_kernels)
1119 calc_gb_rad_hct_obc_sse2_single(cr, fr, born->nr, top, x[0], nl, born, md, ir->gb_algorithm);
1123 calc_gb_rad_obc(cr, fr, born->nr, top, x, nl, born, md);
1128 gmx_fatal(FARGS, "Unknown sse-enabled algorithm for Born radii calculation: %d", ir->gb_algorithm);
1132 switch (ir->gb_algorithm)
1135 calc_gb_rad_still(cr, fr, top, x, nl, born, md);
1138 calc_gb_rad_hct(cr, fr, top, x, nl, born, md);
1141 calc_gb_rad_obc(cr, fr, top, x, nl, born, md);
1145 gmx_fatal(FARGS, "Unknown algorithm for Born radii calculation: %d", ir->gb_algorithm);
1148 #endif /* Single precision sse */
1150 #endif /* Double or single precision */
1152 if (fr->bAllvsAll == FALSE)
1154 switch (ir->gb_algorithm)
1157 /* 17 flops per outer loop iteration, 47 flops per inner loop */
1158 inc_nrnb(nrnb, eNR_BORN_RADII_STILL, nl->nri*17+nl->nrj*47);
1162 /* 61 (assuming 10 for tanh) flops for outer loop iteration, 183 flops per inner loop */
1163 inc_nrnb(nrnb, eNR_BORN_RADII_HCT_OBC, nl->nri*61+nl->nrj*183);
1176 real gb_bonds_tab(rvec x[], rvec f[], rvec fshift[], real *charge, real *p_gbtabscale,
1177 real *invsqrta, real *dvda, real *GBtab, t_idef *idef, real epsilon_r,
1178 real gb_epsilon_solvent, real facel, const t_pbc *pbc, const t_graph *graph)
1180 int i, j, n0, m, nnn, type, ai, aj;
1186 real isaprod, qq, gbscale, gbtabscale, Y, F, Geps, Heps2, Fp, VV, FF, rt, eps, eps2;
1187 real vgb, fgb, vcoul, fijC, dvdatmp, fscal, dvdaj;
1193 t_iatom *forceatoms;
1195 /* Scale the electrostatics by gb_epsilon_solvent */
1196 facel = facel * ((1.0/epsilon_r) - 1.0/gb_epsilon_solvent);
1198 gbtabscale = *p_gbtabscale;
1201 for (j = F_GB12; j <= F_GB14; j++)
1203 forceatoms = idef->il[j].iatoms;
1205 for (i = 0; i < idef->il[j].nr; )
1207 /* To avoid reading in the interaction type, we just increment i to pass over
1208 * the types in the forceatoms array, this saves some memory accesses
1211 ai = forceatoms[i++];
1212 aj = forceatoms[i++];
1214 ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx);
1215 rsq11 = iprod(dx, dx);
1217 isai = invsqrta[ai];
1218 iq = (-1)*facel*charge[ai];
1220 rinv11 = gmx_invsqrt(rsq11);
1221 isaj = invsqrta[aj];
1222 isaprod = isai*isaj;
1223 qq = isaprod*iq*charge[aj];
1224 gbscale = isaprod*gbtabscale;
1233 Geps = eps*GBtab[nnn+2];
1234 Heps2 = eps2*GBtab[nnn+3];
1237 FF = Fp+Geps+2.0*Heps2;
1239 fijC = qq*FF*gbscale;
1240 dvdatmp = -(vgb+fijC*r)*0.5;
1241 dvda[aj] = dvda[aj] + dvdatmp*isaj*isaj;
1242 dvda[ai] = dvda[ai] + dvdatmp*isai*isai;
1243 vctot = vctot + vgb;
1244 fgb = -(fijC)*rinv11;
1248 ivec_sub(SHIFT_IVEC(graph, ai), SHIFT_IVEC(graph, aj), dt);
1252 for (m = 0; (m < DIM); m++) /* 15 */
1257 fshift[ki][m] += fscal;
1258 fshift[CENTRAL][m] -= fscal;
1266 real calc_gb_selfcorrections(t_commrec *cr, int natoms,
1267 real *charge, gmx_genborn_t *born, real *dvda, double facel)
1269 int i, ai, at0, at1;
1270 real rai, e, derb, q, q2, fi, rai_inv, vtot;
1272 if (DOMAINDECOMP(cr))
1275 at1 = cr->dd->nat_home;
1284 /* Scale the electrostatics by gb_epsilon_solvent */
1285 facel = facel * ((1.0/born->epsilon_r) - 1.0/born->gb_epsilon_solvent);
1289 /* Apply self corrections */
1290 for (i = at0; i < at1; i++)
1294 if (born->use[ai] == 1)
1296 rai = born->bRad[ai];
1302 derb = 0.5*e*rai_inv*rai_inv;
1303 dvda[ai] += derb*rai;
1312 real calc_gb_nonpolar(t_commrec *cr, t_forcerec *fr, int natoms, gmx_genborn_t *born, gmx_localtop_t *top,
1313 real *dvda, t_mdatoms *md)
1315 int ai, i, at0, at1;
1316 real e, es, rai, rbi, term, probe, tmp, factor;
1317 real rbi_inv, rbi_inv2;
1319 /* To keep the compiler happy */
1322 if (DOMAINDECOMP(cr))
1325 at1 = cr->dd->nat_home;
1333 /* factor is the surface tension */
1334 factor = born->sa_surface_tension;
1337 // The surface tension factor is 0.0049 for Still model, 0.0054 for HCT/OBC
1338 if(gb_algorithm==egbSTILL)
1340 factor=0.0049*100*CAL2JOULE;
1344 factor=0.0054*100*CAL2JOULE;
1347 /* if(gb_algorithm==egbHCT || gb_algorithm==egbOBC) */
1353 for (i = at0; i < at1; i++)
1357 if (born->use[ai] == 1)
1359 rai = top->atomtypes.gb_radius[md->typeA[ai]];
1360 rbi_inv = fr->invsqrta[ai];
1361 rbi_inv2 = rbi_inv * rbi_inv;
1362 tmp = (rai*rbi_inv2)*(rai*rbi_inv2);
1364 e = factor*term*(rai+probe)*(rai+probe)*tmp;
1365 dvda[ai] = dvda[ai] - 6*e*rbi_inv2;
1375 real calc_gb_chainrule(int natoms, t_nblist *nl, real *dadx, real *dvda, rvec x[], rvec t[], rvec fshift[],
1376 rvec shift_vec[], int gb_algorithm, gmx_genborn_t *born)
1378 int i, k, n, ai, aj, nj0, nj1, n0, n1;
1381 real fgb, fij, rb2, rbi, fix1, fiy1, fiz1;
1382 real ix1, iy1, iz1, jx1, jy1, jz1, dx11, dy11, dz11, rsq11;
1383 real rinv11, tx, ty, tz, rbai, rbaj, fgb_ai;
1393 if (gb_algorithm == egbSTILL)
1395 for (i = n0; i < n1; i++)
1397 rbi = born->bRad[i];
1398 rb[i] = (2 * rbi * rbi * dvda[i])/ONE_4PI_EPS0;
1401 else if (gb_algorithm == egbHCT)
1403 for (i = n0; i < n1; i++)
1405 rbi = born->bRad[i];
1406 rb[i] = rbi * rbi * dvda[i];
1409 else if (gb_algorithm == egbOBC)
1411 for (i = n0; i < n1; i++)
1413 rbi = born->bRad[i];
1414 rb[i] = rbi * rbi * born->drobc[i] * dvda[i];
1418 for (i = 0; i < nl->nri; i++)
1422 nj0 = nl->jindex[i];
1423 nj1 = nl->jindex[i+1];
1425 /* Load shifts for this list */
1426 shift = nl->shift[i];
1427 shX = shift_vec[shift][0];
1428 shY = shift_vec[shift][1];
1429 shZ = shift_vec[shift][2];
1431 /* Load atom i coordinates, add shift vectors */
1432 ix1 = shX + x[ai][0];
1433 iy1 = shY + x[ai][1];
1434 iz1 = shZ + x[ai][2];
1442 for (k = nj0; k < nj1 && nl->jjnr[k] >= 0; k++)
1456 fgb = rbai*dadx[n++];
1457 fgb_ai = rbaj*dadx[n++];
1459 /* Total force between ai and aj is the sum of ai->aj and aj->ai */
1470 /* Update force on atom aj */
1471 t[aj][0] = t[aj][0] - tx;
1472 t[aj][1] = t[aj][1] - ty;
1473 t[aj][2] = t[aj][2] - tz;
1476 /* Update force and shift forces on atom ai */
1477 t[ai][0] = t[ai][0] + fix1;
1478 t[ai][1] = t[ai][1] + fiy1;
1479 t[ai][2] = t[ai][2] + fiz1;
1481 fshift[shift][0] = fshift[shift][0] + fix1;
1482 fshift[shift][1] = fshift[shift][1] + fiy1;
1483 fshift[shift][2] = fshift[shift][2] + fiz1;
1492 calc_gb_forces(t_commrec *cr, t_mdatoms *md, gmx_genborn_t *born, gmx_localtop_t *top,
1493 rvec x[], rvec f[], t_forcerec *fr, t_idef *idef, int gb_algorithm, int sa_algorithm, t_nrnb *nrnb,
1494 const t_pbc *pbc, const t_graph *graph, gmx_enerdata_t *enerd)
1501 const t_pbc *pbc_null;
1512 if (sa_algorithm == esaAPPROX)
1514 /* Do a simple ACE type approximation for the non-polar solvation */
1515 enerd->term[F_NPSOLVATION] += calc_gb_nonpolar(cr, fr, born->nr, born, top, fr->dvda, md);
1518 /* Calculate the bonded GB-interactions using either table or analytical formula */
1519 enerd->term[F_GBPOL] += gb_bonds_tab(x, f, fr->fshift, md->chargeA, &(fr->gbtabscale),
1520 fr->invsqrta, fr->dvda, fr->gbtab.data, idef, born->epsilon_r, born->gb_epsilon_solvent, fr->epsfac, pbc_null, graph);
1522 /* Calculate self corrections to the GB energies - currently only A state used! (FIXME) */
1523 enerd->term[F_GBPOL] += calc_gb_selfcorrections(cr, born->nr, md->chargeA, born, fr->dvda, fr->epsfac);
1525 /* If parallel, sum the derivative of the potential w.r.t the born radii */
1526 if (DOMAINDECOMP(cr))
1528 dd_atom_sum_real(cr->dd, fr->dvda);
1529 dd_atom_spread_real(cr->dd, fr->dvda);
1534 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
1535 if (fr->use_simd_kernels)
1538 genborn_allvsall_calc_chainrule_sse2_double(fr, md, born, x[0], f[0], gb_algorithm, fr->AllvsAll_workgb);
1540 genborn_allvsall_calc_chainrule_sse2_single(fr, md, born, x[0], f[0], gb_algorithm, fr->AllvsAll_workgb);
1545 genborn_allvsall_calc_chainrule(fr, md, born, x[0], f[0], gb_algorithm, fr->AllvsAll_workgb);
1548 genborn_allvsall_calc_chainrule(fr, md, born, x[0], f[0], gb_algorithm, fr->AllvsAll_workgb);
1550 cnt = md->homenr*(md->nr/2+1);
1551 /* 9 flops for outer loop, 15 for inner */
1552 inc_nrnb(nrnb, eNR_BORN_AVA_CHAINRULE, md->homenr*9+cnt*15);
1556 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
1557 if (fr->use_simd_kernels)
1560 calc_gb_chainrule_sse2_double(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda, x[0],
1561 f[0], fr->fshift[0], fr->shift_vec[0], gb_algorithm, born, md);
1563 calc_gb_chainrule_sse2_single(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda, x[0],
1564 f[0], fr->fshift[0], fr->shift_vec[0], gb_algorithm, born, md);
1569 calc_gb_chainrule(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda,
1570 x, f, fr->fshift, fr->shift_vec, gb_algorithm, born, md);
1573 calc_gb_chainrule(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda,
1574 x, f, fr->fshift, fr->shift_vec, gb_algorithm, born);
1579 /* 9 flops for outer loop, 15 for inner */
1580 inc_nrnb(nrnb, eNR_BORN_CHAINRULE, fr->gblist.nri*9+fr->gblist.nrj*15);
1584 static void add_j_to_gblist(gbtmpnbl_t *list, int aj)
1586 if (list->naj >= list->aj_nalloc)
1588 list->aj_nalloc = over_alloc_large(list->naj+1);
1589 srenew(list->aj, list->aj_nalloc);
1592 list->aj[list->naj++] = aj;
1595 static gbtmpnbl_t *find_gbtmplist(struct gbtmpnbls *lists, int shift)
1599 /* Search the list with the same shift, if there is one */
1601 while (ind < lists->nlist && shift != lists->list[ind].shift)
1605 if (ind == lists->nlist)
1607 if (lists->nlist == lists->list_nalloc)
1609 lists->list_nalloc++;
1610 srenew(lists->list, lists->list_nalloc);
1611 for (i = lists->nlist; i < lists->list_nalloc; i++)
1613 lists->list[i].aj = NULL;
1614 lists->list[i].aj_nalloc = 0;
1619 lists->list[lists->nlist].shift = shift;
1620 lists->list[lists->nlist].naj = 0;
1624 return &lists->list[ind];
1627 static void add_bondeds_to_gblist(t_ilist *il,
1628 gmx_bool bMolPBC, t_pbc *pbc, t_graph *g, rvec *x,
1629 struct gbtmpnbls *nls)
1631 int ind, j, ai, aj, shift, found;
1637 for (ind = 0; ind < il->nr; ind += 3)
1639 ai = il->iatoms[ind+1];
1640 aj = il->iatoms[ind+2];
1645 rvec_sub(x[ai], x[aj], dx);
1646 ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
1647 shift = IVEC2IS(dt);
1651 shift = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
1654 /* Find the list for this shift or create one */
1655 list = find_gbtmplist(&nls[ai], shift);
1659 /* So that we do not add the same bond twice.
1660 * This happens with some constraints between 1-3 atoms
1661 * that are in the bond-list but should not be in the GB nb-list */
1662 for (j = 0; j < list->naj; j++)
1664 if (list->aj[j] == aj)
1674 gmx_incons("ai == aj");
1677 add_j_to_gblist(list, aj);
1683 compare_int (const void * a, const void * b)
1685 return ( *(int*)a - *(int*)b );
1690 int make_gb_nblist(t_commrec *cr, int gb_algorithm,
1691 rvec x[], matrix box,
1692 t_forcerec *fr, t_idef *idef, t_graph *graph, gmx_genborn_t *born)
1694 int i, l, ii, j, k, n, nj0, nj1, ai, aj, at0, at1, found, shift, s;
1699 struct gbtmpnbls *nls;
1700 gbtmpnbl_t *list = NULL;
1702 set_pbc(&pbc, fr->ePBC, box);
1703 nls = born->nblist_work;
1705 for (i = 0; i < born->nr; i++)
1712 set_pbc_dd(&pbc, fr->ePBC, cr->dd, TRUE, box);
1715 switch (gb_algorithm)
1719 /* Loop over 1-2, 1-3 and 1-4 interactions */
1720 for (j = F_GB12; j <= F_GB14; j++)
1722 add_bondeds_to_gblist(&idef->il[j], fr->bMolPBC, &pbc, graph, x, nls);
1726 /* Loop over 1-4 interactions */
1727 add_bondeds_to_gblist(&idef->il[F_GB14], fr->bMolPBC, &pbc, graph, x, nls);
1730 gmx_incons("Unknown GB algorithm");
1733 /* Loop over the VDWQQ and VDW nblists to set up the nonbonded part of the GB list */
1734 for (n = 0; (n < fr->nnblists); n++)
1736 for (i = 0; (i < eNL_NR); i++)
1738 nblist = &(fr->nblists[n].nlist_sr[i]);
1740 if (nblist->nri > 0 && (i == eNL_VDWQQ || i == eNL_QQ))
1742 for (j = 0; j < nblist->nri; j++)
1744 ai = nblist->iinr[j];
1745 shift = nblist->shift[j];
1747 /* Find the list for this shift or create one */
1748 list = find_gbtmplist(&nls[ai], shift);
1750 nj0 = nblist->jindex[j];
1751 nj1 = nblist->jindex[j+1];
1753 /* Add all the j-atoms in the non-bonded list to the GB list */
1754 for (k = nj0; k < nj1; k++)
1756 add_j_to_gblist(list, nblist->jjnr[k]);
1763 /* Zero out some counters */
1767 fr->gblist.jindex[0] = fr->gblist.nri;
1769 for (i = 0; i < fr->natoms_force; i++)
1771 for (s = 0; s < nls[i].nlist; s++)
1773 list = &nls[i].list[s];
1775 /* Only add those atoms that actually have neighbours */
1776 if (born->use[i] != 0)
1778 fr->gblist.iinr[fr->gblist.nri] = i;
1779 fr->gblist.shift[fr->gblist.nri] = list->shift;
1782 for (k = 0; k < list->naj; k++)
1784 /* Memory allocation for jjnr */
1785 if (fr->gblist.nrj >= fr->gblist.maxnrj)
1787 fr->gblist.maxnrj += over_alloc_large(fr->gblist.maxnrj);
1791 fprintf(debug, "Increasing GB neighbourlist j size to %d\n", fr->gblist.maxnrj);
1794 srenew(fr->gblist.jjnr, fr->gblist.maxnrj);
1798 if (i == list->aj[k])
1800 gmx_incons("i == list->aj[k]");
1802 fr->gblist.jjnr[fr->gblist.nrj++] = list->aj[k];
1805 fr->gblist.jindex[fr->gblist.nri] = fr->gblist.nrj;
1812 for (i = 0; i < fr->gblist.nri; i++)
1814 nj0 = fr->gblist.jindex[i];
1815 nj1 = fr->gblist.jindex[i+1];
1816 ai = fr->gblist.iinr[i];
1819 for (j = nj0; j < nj1; j++)
1821 if (fr->gblist.jjnr[j] < ai)
1823 fr->gblist.jjnr[j] += fr->natoms_force;
1826 qsort(fr->gblist.jjnr+nj0, nj1-nj0, sizeof(int), compare_int);
1828 for (j = nj0; j < nj1; j++)
1830 if (fr->gblist.jjnr[j] >= fr->natoms_force)
1832 fr->gblist.jjnr[j] -= fr->natoms_force;
1842 void make_local_gb(const t_commrec *cr, gmx_genborn_t *born, int gb_algorithm)
1845 gmx_domdec_t *dd = NULL;
1847 if (DOMAINDECOMP(cr))
1855 /* Single node, just copy pointers and return */
1856 if (gb_algorithm == egbSTILL)
1858 born->gpol = born->gpol_globalindex;
1859 born->vsolv = born->vsolv_globalindex;
1860 born->gb_radius = born->gb_radius_globalindex;
1864 born->param = born->param_globalindex;
1865 born->gb_radius = born->gb_radius_globalindex;
1868 born->use = born->use_globalindex;
1873 /* Reallocation of local arrays if necessary */
1874 /* fr->natoms_force is equal to dd->nat_tot */
1875 if (DOMAINDECOMP(cr) && dd->nat_tot > born->nalloc)
1879 nalloc = dd->nat_tot;
1881 /* Arrays specific to different gb algorithms */
1882 if (gb_algorithm == egbSTILL)
1884 srenew(born->gpol, nalloc+3);
1885 srenew(born->vsolv, nalloc+3);
1886 srenew(born->gb_radius, nalloc+3);
1887 for (i = born->nalloc; (i < nalloc+3); i++)
1891 born->gb_radius[i] = 0;
1896 srenew(born->param, nalloc+3);
1897 srenew(born->gb_radius, nalloc+3);
1898 for (i = born->nalloc; (i < nalloc+3); i++)
1901 born->gb_radius[i] = 0;
1905 /* All gb-algorithms use the array for vsites exclusions */
1906 srenew(born->use, nalloc+3);
1907 for (i = born->nalloc; (i < nalloc+3); i++)
1912 born->nalloc = nalloc;
1915 /* With dd, copy algorithm specific arrays */
1916 if (gb_algorithm == egbSTILL)
1918 for (i = at0; i < at1; i++)
1920 born->gpol[i] = born->gpol_globalindex[dd->gatindex[i]];
1921 born->vsolv[i] = born->vsolv_globalindex[dd->gatindex[i]];
1922 born->gb_radius[i] = born->gb_radius_globalindex[dd->gatindex[i]];
1923 born->use[i] = born->use_globalindex[dd->gatindex[i]];
1928 for (i = at0; i < at1; i++)
1930 born->param[i] = born->param_globalindex[dd->gatindex[i]];
1931 born->gb_radius[i] = born->gb_radius_globalindex[dd->gatindex[i]];
1932 born->use[i] = born->use_globalindex[dd->gatindex[i]];