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34 * GROwing Monsters And Cloning Shrimps
49 #include "nonbonded.h"
63 #include "mtop_util.h"
67 /* MSVC definition for __cpuid() */
73 t_forcerec *mk_forcerec(void)
83 static void pr_nbfp(FILE *fp,real *nbfp,gmx_bool bBHAM,int atnr)
87 for(i=0; (i<atnr); i++) {
88 for(j=0; (j<atnr); j++) {
89 fprintf(fp,"%2d - %2d",i,j);
91 fprintf(fp," a=%10g, b=%10g, c=%10g\n",BHAMA(nbfp,atnr,i,j),
92 BHAMB(nbfp,atnr,i,j),BHAMC(nbfp,atnr,i,j));
94 fprintf(fp," c6=%10g, c12=%10g\n",C6(nbfp,atnr,i,j),
101 static real *mk_nbfp(const gmx_ffparams_t *idef,gmx_bool bBHAM)
108 snew(nbfp,3*atnr*atnr);
109 for(i=k=0; (i<atnr); i++) {
110 for(j=0; (j<atnr); j++,k++) {
111 BHAMA(nbfp,atnr,i,j) = idef->iparams[k].bham.a;
112 BHAMB(nbfp,atnr,i,j) = idef->iparams[k].bham.b;
113 BHAMC(nbfp,atnr,i,j) = idef->iparams[k].bham.c;
118 snew(nbfp,2*atnr*atnr);
119 for(i=k=0; (i<atnr); i++) {
120 for(j=0; (j<atnr); j++,k++) {
121 C6(nbfp,atnr,i,j) = idef->iparams[k].lj.c6;
122 C12(nbfp,atnr,i,j) = idef->iparams[k].lj.c12;
129 /* This routine sets fr->solvent_opt to the most common solvent in the
130 * system, e.g. esolSPC or esolTIP4P. It will also mark each charge group in
131 * the fr->solvent_type array with the correct type (or esolNO).
133 * Charge groups that fulfill the conditions but are not identical to the
134 * most common one will be marked as esolNO in the solvent_type array.
136 * TIP3p is identical to SPC for these purposes, so we call it
137 * SPC in the arrays (Apologies to Bill Jorgensen ;-)
139 * NOTE: QM particle should not
140 * become an optimized solvent. Not even if there is only one charge
150 } solvent_parameters_t;
153 check_solvent_cg(const gmx_moltype_t *molt,
156 const unsigned char *qm_grpnr,
157 const t_grps *qm_grps,
159 int *n_solvent_parameters,
160 solvent_parameters_t **solvent_parameters_p,
164 const t_blocka * excl;
175 solvent_parameters_t *solvent_parameters;
177 /* We use a list with parameters for each solvent type.
178 * Every time we discover a new molecule that fulfills the basic
179 * conditions for a solvent we compare with the previous entries
180 * in these lists. If the parameters are the same we just increment
181 * the counter for that type, and otherwise we create a new type
182 * based on the current molecule.
184 * Once we've finished going through all molecules we check which
185 * solvent is most common, and mark all those molecules while we
186 * clear the flag on all others.
189 solvent_parameters = *solvent_parameters_p;
191 /* Mark the cg first as non optimized */
194 /* Check if this cg has no exclusions with atoms in other charge groups
195 * and all atoms inside the charge group excluded.
196 * We only have 3 or 4 atom solvent loops.
198 if (GET_CGINFO_EXCL_INTER(cginfo) ||
199 !GET_CGINFO_EXCL_INTRA(cginfo))
204 /* Get the indices of the first atom in this charge group */
205 j0 = molt->cgs.index[cg0];
206 j1 = molt->cgs.index[cg0+1];
208 /* Number of atoms in our molecule */
213 "Moltype '%s': there are %d atoms in this charge group\n",
217 /* Check if it could be an SPC (3 atoms) or TIP4p (4) water,
225 /* Check if we are doing QM on this group */
227 if (qm_grpnr != NULL)
229 for(j=j0 ; j<j1 && !qm; j++)
231 qm = (qm_grpnr[j] < qm_grps->nr - 1);
234 /* Cannot use solvent optimization with QM */
240 atom = molt->atoms.atom;
242 /* Still looks like a solvent, time to check parameters */
244 /* If it is perturbed (free energy) we can't use the solvent loops,
245 * so then we just skip to the next molecule.
249 for(j=j0; j<j1 && !perturbed; j++)
251 perturbed = PERTURBED(atom[j]);
259 /* Now it's only a question if the VdW and charge parameters
260 * are OK. Before doing the check we compare and see if they are
261 * identical to a possible previous solvent type.
262 * First we assign the current types and charges.
266 tmp_vdwtype[j] = atom[j0+j].type;
267 tmp_charge[j] = atom[j0+j].q;
270 /* Does it match any previous solvent type? */
271 for(k=0 ; k<*n_solvent_parameters; k++)
276 /* We can only match SPC with 3 atoms and TIP4p with 4 atoms */
277 if( (solvent_parameters[k].model==esolSPC && nj!=3) ||
278 (solvent_parameters[k].model==esolTIP4P && nj!=4) )
281 /* Check that types & charges match for all atoms in molecule */
282 for(j=0 ; j<nj && match==TRUE; j++)
284 if (tmp_vdwtype[j] != solvent_parameters[k].vdwtype[j])
288 if(tmp_charge[j] != solvent_parameters[k].charge[j])
295 /* Congratulations! We have a matched solvent.
296 * Flag it with this type for later processing.
299 solvent_parameters[k].count += nmol;
301 /* We are done with this charge group */
306 /* If we get here, we have a tentative new solvent type.
307 * Before we add it we must check that it fulfills the requirements
308 * of the solvent optimized loops. First determine which atoms have
314 tjA = tmp_vdwtype[j];
316 /* Go through all other tpes and see if any have non-zero
317 * VdW parameters when combined with this one.
319 for(k=0; k<fr->ntype && (has_vdw[j]==FALSE); k++)
321 /* We already checked that the atoms weren't perturbed,
322 * so we only need to check state A now.
326 has_vdw[j] = (has_vdw[j] ||
327 (BHAMA(fr->nbfp,fr->ntype,tjA,k) != 0.0) ||
328 (BHAMB(fr->nbfp,fr->ntype,tjA,k) != 0.0) ||
329 (BHAMC(fr->nbfp,fr->ntype,tjA,k) != 0.0));
334 has_vdw[j] = (has_vdw[j] ||
335 (C6(fr->nbfp,fr->ntype,tjA,k) != 0.0) ||
336 (C12(fr->nbfp,fr->ntype,tjA,k) != 0.0));
341 /* Now we know all we need to make the final check and assignment. */
345 * For this we require thatn all atoms have charge,
346 * the charges on atom 2 & 3 should be the same, and only
347 * atom 1 should have VdW.
349 if (has_vdw[0] == TRUE &&
350 has_vdw[1] == FALSE &&
351 has_vdw[2] == FALSE &&
352 tmp_charge[0] != 0 &&
353 tmp_charge[1] != 0 &&
354 tmp_charge[2] == tmp_charge[1])
356 srenew(solvent_parameters,*n_solvent_parameters+1);
357 solvent_parameters[*n_solvent_parameters].model = esolSPC;
358 solvent_parameters[*n_solvent_parameters].count = nmol;
361 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
362 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
365 *cg_sp = *n_solvent_parameters;
366 (*n_solvent_parameters)++;
371 /* Or could it be a TIP4P?
372 * For this we require thatn atoms 2,3,4 have charge, but not atom 1.
373 * Only atom 1 should have VdW.
375 if(has_vdw[0] == TRUE &&
376 has_vdw[1] == FALSE &&
377 has_vdw[2] == FALSE &&
378 has_vdw[3] == FALSE &&
379 tmp_charge[0] == 0 &&
380 tmp_charge[1] != 0 &&
381 tmp_charge[2] == tmp_charge[1] &&
384 srenew(solvent_parameters,*n_solvent_parameters+1);
385 solvent_parameters[*n_solvent_parameters].model = esolTIP4P;
386 solvent_parameters[*n_solvent_parameters].count = nmol;
389 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
390 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
393 *cg_sp = *n_solvent_parameters;
394 (*n_solvent_parameters)++;
398 *solvent_parameters_p = solvent_parameters;
402 check_solvent(FILE * fp,
403 const gmx_mtop_t * mtop,
405 cginfo_mb_t *cginfo_mb)
408 const t_block * mols;
409 const gmx_moltype_t *molt;
410 int mb,mol,cg_mol,at_offset,cg_offset,am,cgm,i,nmol_ch,nmol;
411 int n_solvent_parameters;
412 solvent_parameters_t *solvent_parameters;
418 fprintf(debug,"Going to determine what solvent types we have.\n");
423 n_solvent_parameters = 0;
424 solvent_parameters = NULL;
425 /* Allocate temporary array for solvent type */
426 snew(cg_sp,mtop->nmolblock);
430 for(mb=0; mb<mtop->nmolblock; mb++)
432 molt = &mtop->moltype[mtop->molblock[mb].type];
434 /* Here we have to loop over all individual molecules
435 * because we need to check for QMMM particles.
437 snew(cg_sp[mb],cginfo_mb[mb].cg_mod);
438 nmol_ch = cginfo_mb[mb].cg_mod/cgs->nr;
439 nmol = mtop->molblock[mb].nmol/nmol_ch;
440 for(mol=0; mol<nmol_ch; mol++)
443 am = mol*cgs->index[cgs->nr];
444 for(cg_mol=0; cg_mol<cgs->nr; cg_mol++)
446 check_solvent_cg(molt,cg_mol,nmol,
447 mtop->groups.grpnr[egcQMMM] ?
448 mtop->groups.grpnr[egcQMMM]+at_offset+am : 0,
449 &mtop->groups.grps[egcQMMM],
451 &n_solvent_parameters,&solvent_parameters,
452 cginfo_mb[mb].cginfo[cgm+cg_mol],
453 &cg_sp[mb][cgm+cg_mol]);
456 cg_offset += cgs->nr;
457 at_offset += cgs->index[cgs->nr];
460 /* Puh! We finished going through all charge groups.
461 * Now find the most common solvent model.
464 /* Most common solvent this far */
466 for(i=0;i<n_solvent_parameters;i++)
469 solvent_parameters[i].count > solvent_parameters[bestsp].count)
477 bestsol = solvent_parameters[bestsp].model;
484 #ifdef DISABLE_WATER_NLIST
489 for(mb=0; mb<mtop->nmolblock; mb++)
491 cgs = &mtop->moltype[mtop->molblock[mb].type].cgs;
492 nmol = (mtop->molblock[mb].nmol*cgs->nr)/cginfo_mb[mb].cg_mod;
493 for(i=0; i<cginfo_mb[mb].cg_mod; i++)
495 if (cg_sp[mb][i] == bestsp)
497 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i],bestsol);
502 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i],esolNO);
509 if (bestsol != esolNO && fp!=NULL)
511 fprintf(fp,"\nEnabling %s-like water optimization for %d molecules.\n\n",
513 solvent_parameters[bestsp].count);
516 sfree(solvent_parameters);
517 fr->solvent_opt = bestsol;
520 static cginfo_mb_t *init_cginfo_mb(FILE *fplog,const gmx_mtop_t *mtop,
521 t_forcerec *fr,gmx_bool bNoSolvOpt)
524 const t_blocka *excl;
525 const gmx_moltype_t *molt;
526 const gmx_molblock_t *molb;
527 cginfo_mb_t *cginfo_mb;
529 int cg_offset,a_offset,cgm,am;
530 int mb,m,ncg_tot,cg,a0,a1,gid,ai,j,aj,excl_nalloc;
531 gmx_bool bId,*bExcl,bExclIntraAll,bExclInter;
533 ncg_tot = ncg_mtop(mtop);
534 snew(cginfo_mb,mtop->nmolblock);
537 snew(bExcl,excl_nalloc);
540 for(mb=0; mb<mtop->nmolblock; mb++)
542 molb = &mtop->molblock[mb];
543 molt = &mtop->moltype[molb->type];
547 /* Check if the cginfo is identical for all molecules in this block.
548 * If so, we only need an array of the size of one molecule.
549 * Otherwise we make an array of #mol times #cgs per molecule.
553 for(m=0; m<molb->nmol; m++)
555 am = m*cgs->index[cgs->nr];
556 for(cg=0; cg<cgs->nr; cg++)
559 a1 = cgs->index[cg+1];
560 if (ggrpnr(&mtop->groups,egcENER,a_offset+am+a0) !=
561 ggrpnr(&mtop->groups,egcENER,a_offset +a0))
565 if (mtop->groups.grpnr[egcQMMM] != NULL)
567 for(ai=a0; ai<a1; ai++)
569 if (mtop->groups.grpnr[egcQMMM][a_offset+am+ai] !=
570 mtop->groups.grpnr[egcQMMM][a_offset +ai])
579 cginfo_mb[mb].cg_start = cg_offset;
580 cginfo_mb[mb].cg_end = cg_offset + molb->nmol*cgs->nr;
581 cginfo_mb[mb].cg_mod = (bId ? 1 : molb->nmol)*cgs->nr;
582 snew(cginfo_mb[mb].cginfo,cginfo_mb[mb].cg_mod);
583 cginfo = cginfo_mb[mb].cginfo;
585 for(m=0; m<(bId ? 1 : molb->nmol); m++)
588 am = m*cgs->index[cgs->nr];
589 for(cg=0; cg<cgs->nr; cg++)
592 a1 = cgs->index[cg+1];
594 /* Store the energy group in cginfo */
595 gid = ggrpnr(&mtop->groups,egcENER,a_offset+am+a0);
596 SET_CGINFO_GID(cginfo[cgm+cg],gid);
598 /* Check the intra/inter charge group exclusions */
599 if (a1-a0 > excl_nalloc) {
600 excl_nalloc = a1 - a0;
601 srenew(bExcl,excl_nalloc);
603 /* bExclIntraAll: all intra cg interactions excluded
604 * bExclInter: any inter cg interactions excluded
606 bExclIntraAll = TRUE;
608 for(ai=a0; ai<a1; ai++) {
609 /* Clear the exclusion list for atom ai */
610 for(aj=a0; aj<a1; aj++) {
611 bExcl[aj-a0] = FALSE;
613 /* Loop over all the exclusions of atom ai */
614 for(j=excl->index[ai]; j<excl->index[ai+1]; j++)
617 if (aj < a0 || aj >= a1)
626 /* Check if ai excludes a0 to a1 */
627 for(aj=a0; aj<a1; aj++)
631 bExclIntraAll = FALSE;
637 SET_CGINFO_EXCL_INTRA(cginfo[cgm+cg]);
641 SET_CGINFO_EXCL_INTER(cginfo[cgm+cg]);
643 if (a1 - a0 > MAX_CHARGEGROUP_SIZE)
645 /* The size in cginfo is currently only read with DD */
646 gmx_fatal(FARGS,"A charge group has size %d which is larger than the limit of %d atoms",a1-a0,MAX_CHARGEGROUP_SIZE);
648 SET_CGINFO_NATOMS(cginfo[cgm+cg],a1-a0);
651 cg_offset += molb->nmol*cgs->nr;
652 a_offset += molb->nmol*cgs->index[cgs->nr];
656 /* the solvent optimizer is called after the QM is initialized,
657 * because we don't want to have the QM subsystemto become an
661 check_solvent(fplog,mtop,fr,cginfo_mb);
663 if (getenv("GMX_NO_SOLV_OPT"))
667 fprintf(fplog,"Found environment variable GMX_NO_SOLV_OPT.\n"
668 "Disabling all solvent optimization\n");
670 fr->solvent_opt = esolNO;
674 fr->solvent_opt = esolNO;
676 if (!fr->solvent_opt)
678 for(mb=0; mb<mtop->nmolblock; mb++)
680 for(cg=0; cg<cginfo_mb[mb].cg_mod; cg++)
682 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[cg],esolNO);
690 static int *cginfo_expand(int nmb,cginfo_mb_t *cgi_mb)
695 ncg = cgi_mb[nmb-1].cg_end;
698 for(cg=0; cg<ncg; cg++)
700 while (cg >= cgi_mb[mb].cg_end)
705 cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
711 static void set_chargesum(FILE *log,t_forcerec *fr,const gmx_mtop_t *mtop)
715 const t_atoms *atoms;
718 for(mb=0; mb<mtop->nmolblock; mb++)
720 nmol = mtop->molblock[mb].nmol;
721 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
722 for(i=0; i<atoms->nr; i++)
724 qsum += nmol*atoms->atom[i].q;
728 if (fr->efep != efepNO)
731 for(mb=0; mb<mtop->nmolblock; mb++)
733 nmol = mtop->molblock[mb].nmol;
734 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
735 for(i=0; i<atoms->nr; i++)
737 qsum += nmol*atoms->atom[i].qB;
744 fr->qsum[1] = fr->qsum[0];
747 if (fr->efep == efepNO)
748 fprintf(log,"System total charge: %.3f\n",fr->qsum[0]);
750 fprintf(log,"System total charge, top. A: %.3f top. B: %.3f\n",
751 fr->qsum[0],fr->qsum[1]);
755 void update_forcerec(FILE *log,t_forcerec *fr,matrix box)
757 if (fr->eeltype == eelGRF)
759 calc_rffac(NULL,fr->eeltype,fr->epsilon_r,fr->epsilon_rf,
760 fr->rcoulomb,fr->temp,fr->zsquare,box,
761 &fr->kappa,&fr->k_rf,&fr->c_rf);
765 void set_avcsixtwelve(FILE *fplog,t_forcerec *fr,const gmx_mtop_t *mtop)
767 const t_atoms *atoms,*atoms_tpi;
768 const t_blocka *excl;
769 int mb,nmol,nmolc,i,j,tpi,tpj,j1,j2,k,n,nexcl,q;
770 #if (defined SIZEOF_LONG_LONG_INT) && (SIZEOF_LONG_LONG_INT >= 8)
771 long long int npair,npair_ij,tmpi,tmpj;
773 double npair, npair_ij,tmpi,tmpj;
784 for(q=0; q<(fr->efep==efepNO ? 1 : 2); q++) {
790 /* Count the types so we avoid natoms^2 operations */
792 for(mb=0; mb<mtop->nmolblock; mb++) {
793 nmol = mtop->molblock[mb].nmol;
794 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
795 for(i=0; i<atoms->nr; i++) {
798 tpi = atoms->atom[i].type;
802 tpi = atoms->atom[i].typeB;
804 typecount[tpi] += nmol;
807 for(tpi=0; tpi<ntp; tpi++) {
808 for(tpj=tpi; tpj<ntp; tpj++) {
809 tmpi = typecount[tpi];
810 tmpj = typecount[tpj];
813 npair_ij = tmpi*tmpj;
817 npair_ij = tmpi*(tmpi - 1)/2;
820 csix += npair_ij*BHAMC(nbfp,ntp,tpi,tpj);
822 csix += npair_ij* C6(nbfp,ntp,tpi,tpj);
823 ctwelve += npair_ij* C12(nbfp,ntp,tpi,tpj);
829 /* Subtract the excluded pairs.
830 * The main reason for substracting exclusions is that in some cases
831 * some combinations might never occur and the parameters could have
832 * any value. These unused values should not influence the dispersion
835 for(mb=0; mb<mtop->nmolblock; mb++) {
836 nmol = mtop->molblock[mb].nmol;
837 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
838 excl = &mtop->moltype[mtop->molblock[mb].type].excls;
839 for(i=0; (i<atoms->nr); i++) {
842 tpi = atoms->atom[i].type;
846 tpi = atoms->atom[i].typeB;
849 j2 = excl->index[i+1];
850 for(j=j1; j<j2; j++) {
856 tpj = atoms->atom[k].type;
860 tpj = atoms->atom[k].typeB;
863 csix -= nmol*BHAMC(nbfp,ntp,tpi,tpj);
865 csix -= nmol*C6 (nbfp,ntp,tpi,tpj);
866 ctwelve -= nmol*C12(nbfp,ntp,tpi,tpj);
874 /* Only correct for the interaction of the test particle
875 * with the rest of the system.
878 &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].atoms;
881 for(mb=0; mb<mtop->nmolblock; mb++) {
882 nmol = mtop->molblock[mb].nmol;
883 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
884 for(j=0; j<atoms->nr; j++) {
886 /* Remove the interaction of the test charge group
889 if (mb == mtop->nmolblock-1)
893 if (mb == 0 && nmol == 1)
895 gmx_fatal(FARGS,"Old format tpr with TPI, please generate a new tpr file");
900 tpj = atoms->atom[j].type;
904 tpj = atoms->atom[j].typeB;
906 for(i=0; i<fr->n_tpi; i++)
910 tpi = atoms_tpi->atom[i].type;
914 tpi = atoms_tpi->atom[i].typeB;
918 csix += nmolc*BHAMC(nbfp,ntp,tpi,tpj);
922 csix += nmolc*C6 (nbfp,ntp,tpi,tpj);
923 ctwelve += nmolc*C12(nbfp,ntp,tpi,tpj);
930 if (npair - nexcl <= 0 && fplog) {
931 fprintf(fplog,"\nWARNING: There are no atom pairs for dispersion correction\n\n");
935 csix /= npair - nexcl;
936 ctwelve /= npair - nexcl;
939 fprintf(debug,"Counted %d exclusions\n",nexcl);
940 fprintf(debug,"Average C6 parameter is: %10g\n",(double)csix);
941 fprintf(debug,"Average C12 parameter is: %10g\n",(double)ctwelve);
943 fr->avcsix[q] = csix;
944 fr->avctwelve[q] = ctwelve;
948 if (fr->eDispCorr == edispcAllEner ||
949 fr->eDispCorr == edispcAllEnerPres)
951 fprintf(fplog,"Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
952 fr->avcsix[0],fr->avctwelve[0]);
956 fprintf(fplog,"Long Range LJ corr.: <C6> %10.4e\n",fr->avcsix[0]);
962 static void set_bham_b_max(FILE *fplog,t_forcerec *fr,
963 const gmx_mtop_t *mtop)
965 const t_atoms *at1,*at2;
966 int mt1,mt2,i,j,tpi,tpj,ntypes;
972 fprintf(fplog,"Determining largest Buckingham b parameter for table\n");
979 for(mt1=0; mt1<mtop->nmoltype; mt1++)
981 at1 = &mtop->moltype[mt1].atoms;
982 for(i=0; (i<at1->nr); i++)
984 tpi = at1->atom[i].type;
986 gmx_fatal(FARGS,"Atomtype[%d] = %d, maximum = %d",i,tpi,ntypes);
988 for(mt2=mt1; mt2<mtop->nmoltype; mt2++)
990 at2 = &mtop->moltype[mt2].atoms;
991 for(j=0; (j<at2->nr); j++) {
992 tpj = at2->atom[j].type;
995 gmx_fatal(FARGS,"Atomtype[%d] = %d, maximum = %d",j,tpj,ntypes);
997 b = BHAMB(nbfp,ntypes,tpi,tpj);
998 if (b > fr->bham_b_max)
1002 if ((b < bmin) || (bmin==-1))
1012 fprintf(fplog,"Buckingham b parameters, min: %g, max: %g\n",
1013 bmin,fr->bham_b_max);
1017 static void make_nbf_tables(FILE *fp,const output_env_t oenv,
1018 t_forcerec *fr,real rtab,
1019 const t_commrec *cr,
1020 const char *tabfn,char *eg1,char *eg2,
1026 if (tabfn == NULL) {
1028 fprintf(debug,"No table file name passed, can not read table, can not do non-bonded interactions\n");
1032 sprintf(buf,"%s",tabfn);
1034 /* Append the two energy group names */
1035 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1,"_%s_%s.%s",
1036 eg1,eg2,ftp2ext(efXVG));
1037 nbl->tab = make_tables(fp,oenv,fr,MASTER(cr),buf,rtab,0);
1038 /* Copy the contents of the table to separate coulomb and LJ tables too,
1039 * to improve cache performance.
1042 /* For performance reasons we want
1043 * the table data to be aligned to 16-byte. The pointer could be freed
1044 * but currently isn't.
1046 snew_aligned(nbl->vdwtab,8*(nbl->tab.n+1),16);
1047 snew_aligned(nbl->coultab,4*(nbl->tab.n+1),16);
1049 for(i=0; i<=nbl->tab.n; i++) {
1051 nbl->coultab[4*i+j] = nbl->tab.tab[12*i+j];
1053 nbl->vdwtab [8*i+j] = nbl->tab.tab[12*i+4+j];
1057 static void count_tables(int ftype1,int ftype2,const gmx_mtop_t *mtop,
1058 int *ncount,int **count)
1060 const gmx_moltype_t *molt;
1062 int mt,ftype,stride,i,j,tabnr;
1064 for(mt=0; mt<mtop->nmoltype; mt++)
1066 molt = &mtop->moltype[mt];
1067 for(ftype=0; ftype<F_NRE; ftype++)
1069 if (ftype == ftype1 || ftype == ftype2) {
1070 il = &molt->ilist[ftype];
1071 stride = 1 + NRAL(ftype);
1072 for(i=0; i<il->nr; i+=stride) {
1073 tabnr = mtop->ffparams.iparams[il->iatoms[i]].tab.table;
1075 gmx_fatal(FARGS,"A bonded table number is smaller than 0: %d\n",tabnr);
1076 if (tabnr >= *ncount) {
1077 srenew(*count,tabnr+1);
1078 for(j=*ncount; j<tabnr+1; j++)
1089 static bondedtable_t *make_bonded_tables(FILE *fplog,
1090 int ftype1,int ftype2,
1091 const gmx_mtop_t *mtop,
1092 const char *basefn,const char *tabext)
1094 int i,ncount,*count;
1102 count_tables(ftype1,ftype2,mtop,&ncount,&count);
1106 for(i=0; i<ncount; i++) {
1108 sprintf(tabfn,"%s",basefn);
1109 sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1,"_%s%d.%s",
1110 tabext,i,ftp2ext(efXVG));
1111 tab[i] = make_bonded_table(fplog,tabfn,NRAL(ftype1)-2);
1120 void forcerec_set_ranges(t_forcerec *fr,
1121 int ncg_home,int ncg_force,
1123 int natoms_force_constr,int natoms_f_novirsum)
1128 /* fr->ncg_force is unused in the standard code,
1129 * but it can be useful for modified code dealing with charge groups.
1131 fr->ncg_force = ncg_force;
1132 fr->natoms_force = natoms_force;
1133 fr->natoms_force_constr = natoms_force_constr;
1135 if (fr->natoms_force_constr > fr->nalloc_force)
1137 fr->nalloc_force = over_alloc_dd(fr->natoms_force_constr);
1141 srenew(fr->f_twin,fr->nalloc_force);
1145 if (fr->bF_NoVirSum)
1147 fr->f_novirsum_n = natoms_f_novirsum;
1148 if (fr->f_novirsum_n > fr->f_novirsum_nalloc)
1150 fr->f_novirsum_nalloc = over_alloc_dd(fr->f_novirsum_n);
1151 srenew(fr->f_novirsum_alloc,fr->f_novirsum_nalloc);
1156 fr->f_novirsum_n = 0;
1160 static real cutoff_inf(real cutoff)
1164 cutoff = GMX_CUTOFF_INF;
1170 static void make_adress_tf_tables(FILE *fp,const output_env_t oenv,
1171 t_forcerec *fr,const t_inputrec *ir,
1172 const char *tabfn, const gmx_mtop_t *mtop,
1178 if (tabfn == NULL) {
1179 gmx_fatal(FARGS,"No thermoforce table file given. Use -tabletf to specify a file\n");
1183 snew(fr->atf_tabs, ir->adress->n_tf_grps);
1185 for (i=0; i<ir->adress->n_tf_grps; i++){
1186 j = ir->adress->tf_table_index[i]; /* get energy group index */
1187 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1,"tf_%s.%s",
1188 *(mtop->groups.grpname[mtop->groups.grps[egcENER].nm_ind[j]]) ,ftp2ext(efXVG));
1189 printf("loading tf table for energygrp index %d from %s\n", ir->adress->tf_table_index[j], buf);
1190 fr->atf_tabs[i] = make_atf_table(fp,oenv,fr,buf, box);
1195 gmx_bool can_use_allvsall(const t_inputrec *ir, const gmx_mtop_t *mtop,
1196 gmx_bool bPrintNote,t_commrec *cr,FILE *fp)
1205 ir->ePBC==epbcNONE &&
1206 ir->vdwtype==evdwCUT &&
1207 ir->coulombtype==eelCUT &&
1209 (ir->implicit_solvent == eisNO ||
1210 (ir->implicit_solvent==eisGBSA && (ir->gb_algorithm==egbSTILL ||
1211 ir->gb_algorithm==egbHCT ||
1212 ir->gb_algorithm==egbOBC))) &&
1213 getenv("GMX_NO_ALLVSALL") == NULL
1216 if (bAllvsAll && ir->opts.ngener > 1)
1218 const char *note="NOTE: Can not use all-vs-all force loops, because there are multiple energy monitor groups; you might get significantly higher performance when using only a single energy monitor group.\n";
1224 fprintf(stderr,"\n%s\n",note);
1228 fprintf(fp,"\n%s\n",note);
1234 if(bAllvsAll && fp && MASTER(cr))
1236 fprintf(fp,"\nUsing accelerated all-vs-all kernels.\n\n");
1243 /* Return 1 if SSE2 support is present, otherwise 0. */
1245 forcerec_check_sse2()
1247 #if ( defined(GMX_IA32_SSE2) || defined(GMX_X86_64_SSE2) || defined(GMX_IA32_SSE) || defined(GMX_X86_64_SSE)|| defined(GMX_SSE2) )
1249 unsigned int _eax,_ebx,_ecx,_edx;
1262 #elif defined(__x86_64__)
1263 /* GCC 64-bit inline asm */
1264 __asm__ ("push %%rbx\n\tcpuid\n\tpop %%rbx\n" \
1265 : "=a" (_eax), "=S" (_ebx), "=c" (_ecx), "=d" (_edx) \
1267 #elif defined(__i386__)
1268 __asm__ ("push %%ebx\n\tcpuid\n\tpop %%ebx\n" \
1269 : "=a" (_eax), "=S" (_ebx), "=c" (_ecx), "=d" (_edx) \
1272 _eax=_ebx=_ecx=_edx=0;
1277 * SSE Bit 25 of edx should be set
1278 * SSE2 Bit 26 of edx should be set
1279 * SSE3 Bit 0 of ecx should be set
1280 * SSE4.1 Bit 19 of ecx should be set
1282 status = (_edx & (1 << 26)) != 0;
1287 /* Return SSE2 status */
1294 void init_forcerec(FILE *fp,
1295 const output_env_t oenv,
1298 const t_inputrec *ir,
1299 const gmx_mtop_t *mtop,
1300 const t_commrec *cr,
1307 gmx_bool bNoSolvOpt,
1310 int i,j,m,natoms,ngrp,negp_pp,negptable,egi,egj;
1316 gmx_bool bGenericKernelOnly;
1317 gmx_bool bTab,bSep14tab,bNormalnblists;
1319 int *nm_ind,egp_flags;
1321 fr->bDomDec = DOMAINDECOMP(cr);
1323 natoms = mtop->natoms;
1325 if (check_box(ir->ePBC,box))
1327 gmx_fatal(FARGS,check_box(ir->ePBC,box));
1330 /* Test particle insertion ? */
1331 if (EI_TPI(ir->eI)) {
1332 /* Set to the size of the molecule to be inserted (the last one) */
1333 /* Because of old style topologies, we have to use the last cg
1334 * instead of the last molecule type.
1336 cgs = &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].cgs;
1337 fr->n_tpi = cgs->index[cgs->nr] - cgs->index[cgs->nr-1];
1338 if (fr->n_tpi != mtop->mols.index[mtop->mols.nr] - mtop->mols.index[mtop->mols.nr-1]) {
1339 gmx_fatal(FARGS,"The molecule to insert can not consist of multiple charge groups.\nMake it a single charge group.");
1345 /* Copy AdResS parameters */
1347 fr->adress_type = ir->adress->type;
1348 fr->adress_const_wf = ir->adress->const_wf;
1349 fr->adress_ex_width = ir->adress->ex_width;
1350 fr->adress_hy_width = ir->adress->hy_width;
1351 fr->adress_icor = ir->adress->icor;
1352 fr->adress_site = ir->adress->site;
1353 fr->adress_ex_forcecap = ir->adress->ex_forcecap;
1354 fr->adress_do_hybridpairs = ir->adress->do_hybridpairs;
1357 snew(fr->adress_group_explicit , ir->adress->n_energy_grps);
1358 for (i=0; i< ir->adress->n_energy_grps; i++){
1359 fr->adress_group_explicit[i]= ir->adress->group_explicit[i];
1362 fr->n_adress_tf_grps = ir->adress->n_tf_grps;
1363 snew(fr->adress_tf_table_index, fr->n_adress_tf_grps);
1364 for (i=0; i< fr->n_adress_tf_grps; i++){
1365 fr->adress_tf_table_index[i]= ir->adress->tf_table_index[i];
1367 copy_rvec(ir->adress->refs,fr->adress_refs);
1369 fr->adress_type = eAdressOff;
1370 fr->adress_do_hybridpairs = FALSE;
1373 /* Copy the user determined parameters */
1374 fr->userint1 = ir->userint1;
1375 fr->userint2 = ir->userint2;
1376 fr->userint3 = ir->userint3;
1377 fr->userint4 = ir->userint4;
1378 fr->userreal1 = ir->userreal1;
1379 fr->userreal2 = ir->userreal2;
1380 fr->userreal3 = ir->userreal3;
1381 fr->userreal4 = ir->userreal4;
1384 fr->fc_stepsize = ir->fc_stepsize;
1387 fr->efep = ir->efep;
1388 fr->sc_alphavdw = ir->fepvals->sc_alpha;
1389 if (ir->fepvals->bScCoul)
1391 fr->sc_alphacoul = ir->fepvals->sc_alpha;
1392 fr->sc_sigma6_min = pow(ir->fepvals->sc_sigma_min,6);
1396 fr->sc_alphacoul = 0;
1397 fr->sc_sigma6_min = 0; /* only needed when bScCoul is on */
1399 fr->sc_power = ir->fepvals->sc_power;
1400 fr->sc_r_power = ir->fepvals->sc_r_power;
1401 fr->sc_sigma6_def = pow(ir->fepvals->sc_sigma,6);
1403 env = getenv("GMX_SCSIGMA_MIN");
1407 sscanf(env,"%lf",&dbl);
1408 fr->sc_sigma6_min = pow(dbl,6);
1411 fprintf(fp,"Setting the minimum soft core sigma to %g nm\n",dbl);
1415 bGenericKernelOnly = FALSE;
1416 if (getenv("GMX_NB_GENERIC") != NULL)
1421 "Found environment variable GMX_NB_GENERIC.\n"
1422 "Disabling interaction-specific nonbonded kernels.\n\n");
1424 bGenericKernelOnly = TRUE;
1428 fr->UseOptimizedKernels = (getenv("GMX_NOOPTIMIZEDKERNELS") == NULL);
1429 if(fp && fr->UseOptimizedKernels==FALSE)
1432 "\nFound environment variable GMX_NOOPTIMIZEDKERNELS.\n"
1433 "Disabling SSE/SSE2/Altivec/ia64/Power6/Bluegene specific kernels.\n\n");
1436 #if ( defined(GMX_IA32_SSE2) || defined(GMX_X86_64_SSE2) || defined(GMX_IA32_SSE) || defined(GMX_X86_64_SSE)|| defined(GMX_SSE2) )
1437 if( forcerec_check_sse2() == 0 )
1439 fr->UseOptimizedKernels = FALSE;
1443 /* Check if we can/should do all-vs-all kernels */
1444 fr->bAllvsAll = can_use_allvsall(ir,mtop,FALSE,NULL,NULL);
1445 fr->AllvsAll_work = NULL;
1446 fr->AllvsAll_workgb = NULL;
1450 /* Neighbour searching stuff */
1451 fr->bGrid = (ir->ns_type == ensGRID);
1452 fr->ePBC = ir->ePBC;
1453 fr->bMolPBC = ir->bPeriodicMols;
1454 fr->rc_scaling = ir->refcoord_scaling;
1455 copy_rvec(ir->posres_com,fr->posres_com);
1456 copy_rvec(ir->posres_comB,fr->posres_comB);
1457 fr->rlist = cutoff_inf(ir->rlist);
1458 fr->rlistlong = cutoff_inf(ir->rlistlong);
1459 fr->eeltype = ir->coulombtype;
1460 fr->vdwtype = ir->vdwtype;
1462 fr->bTwinRange = fr->rlistlong > fr->rlist;
1463 fr->bEwald = (EEL_PME(fr->eeltype) || fr->eeltype==eelEWALD);
1465 fr->reppow = mtop->ffparams.reppow;
1466 fr->bvdwtab = (fr->vdwtype != evdwCUT ||
1467 !gmx_within_tol(fr->reppow,12.0,10*GMX_DOUBLE_EPS));
1468 fr->bcoultab = (!(fr->eeltype == eelCUT || EEL_RF(fr->eeltype)) ||
1469 fr->eeltype == eelRF_ZERO);
1471 if (getenv("GMX_FORCE_TABLES"))
1474 fr->bcoultab = TRUE;
1478 fprintf(fp,"Table routines are used for coulomb: %s\n",bool_names[fr->bcoultab]);
1479 fprintf(fp,"Table routines are used for vdw: %s\n",bool_names[fr->bvdwtab ]);
1482 /* Tables are used for direct ewald sum */
1485 if (EEL_PME(ir->coulombtype))
1488 fprintf(fp,"Will do PME sum in reciprocal space.\n");
1489 if (ir->coulombtype == eelP3M_AD)
1491 please_cite(fp,"Hockney1988");
1492 please_cite(fp,"Ballenegger2012");
1496 please_cite(fp,"Essmann95a");
1499 if (ir->ewald_geometry == eewg3DC)
1503 fprintf(fp,"Using the Ewald3DC correction for systems with a slab geometry.\n");
1505 please_cite(fp,"In-Chul99a");
1508 fr->ewaldcoeff=calc_ewaldcoeff(ir->rcoulomb, ir->ewald_rtol);
1509 init_ewald_tab(&(fr->ewald_table), cr, ir, fp);
1512 fprintf(fp,"Using a Gaussian width (1/beta) of %g nm for Ewald\n",
1517 /* Electrostatics */
1518 fr->epsilon_r = ir->epsilon_r;
1519 fr->epsilon_rf = ir->epsilon_rf;
1520 fr->fudgeQQ = mtop->ffparams.fudgeQQ;
1521 fr->rcoulomb_switch = ir->rcoulomb_switch;
1522 fr->rcoulomb = cutoff_inf(ir->rcoulomb);
1524 /* Parameters for generalized RF */
1528 if (fr->eeltype == eelGRF)
1530 init_generalized_rf(fp,mtop,ir,fr);
1532 else if (fr->eeltype == eelSHIFT)
1534 for(m=0; (m<DIM); m++)
1535 box_size[m]=box[m][m];
1537 if ((fr->eeltype == eelSHIFT && fr->rcoulomb > fr->rcoulomb_switch))
1538 set_shift_consts(fp,fr->rcoulomb_switch,fr->rcoulomb,box_size,fr);
1541 fr->bF_NoVirSum = (EEL_FULL(fr->eeltype) ||
1542 gmx_mtop_ftype_count(mtop,F_POSRES) > 0 ||
1543 IR_ELEC_FIELD(*ir) ||
1544 (fr->adress_icor != eAdressICOff)
1547 /* Mask that says whether or not this NBF list should be computed */
1548 /* if (fr->bMask == NULL) {
1549 ngrp = ir->opts.ngener*ir->opts.ngener;
1550 snew(fr->bMask,ngrp);*/
1551 /* Defaults to always */
1552 /* for(i=0; (i<ngrp); i++)
1553 fr->bMask[i] = TRUE;
1556 if (ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr)) {
1557 /* Count the total number of charge groups */
1558 fr->cg_nalloc = ncg_mtop(mtop);
1559 srenew(fr->cg_cm,fr->cg_nalloc);
1561 if (fr->shift_vec == NULL)
1562 snew(fr->shift_vec,SHIFTS);
1564 if (fr->fshift == NULL)
1565 snew(fr->fshift,SHIFTS);
1567 if (fr->nbfp == NULL) {
1568 fr->ntype = mtop->ffparams.atnr;
1569 fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
1570 fr->nbfp = mk_nbfp(&mtop->ffparams,fr->bBHAM);
1573 /* Copy the energy group exclusions */
1574 fr->egp_flags = ir->opts.egp_flags;
1576 /* Van der Waals stuff */
1577 fr->rvdw = cutoff_inf(ir->rvdw);
1578 fr->rvdw_switch = ir->rvdw_switch;
1579 if ((fr->vdwtype != evdwCUT) && (fr->vdwtype != evdwUSER) && !fr->bBHAM) {
1580 if (fr->rvdw_switch >= fr->rvdw)
1581 gmx_fatal(FARGS,"rvdw_switch (%f) must be < rvdw (%f)",
1582 fr->rvdw_switch,fr->rvdw);
1584 fprintf(fp,"Using %s Lennard-Jones, switch between %g and %g nm\n",
1585 (fr->eeltype==eelSWITCH) ? "switched":"shifted",
1586 fr->rvdw_switch,fr->rvdw);
1589 if (fr->bBHAM && (fr->vdwtype == evdwSHIFT || fr->vdwtype == evdwSWITCH))
1590 gmx_fatal(FARGS,"Switch/shift interaction not supported with Buckingham");
1593 fprintf(fp,"Cut-off's: NS: %g Coulomb: %g %s: %g\n",
1594 fr->rlist,fr->rcoulomb,fr->bBHAM ? "BHAM":"LJ",fr->rvdw);
1596 fr->eDispCorr = ir->eDispCorr;
1597 if (ir->eDispCorr != edispcNO)
1599 set_avcsixtwelve(fp,fr,mtop);
1604 set_bham_b_max(fp,fr,mtop);
1607 fr->bGB = (ir->implicit_solvent == eisGBSA);
1608 fr->gb_epsilon_solvent = ir->gb_epsilon_solvent;
1610 /* Copy the GBSA data (radius, volume and surftens for each
1611 * atomtype) from the topology atomtype section to forcerec.
1613 snew(fr->atype_radius,fr->ntype);
1614 snew(fr->atype_vol,fr->ntype);
1615 snew(fr->atype_surftens,fr->ntype);
1616 snew(fr->atype_gb_radius,fr->ntype);
1617 snew(fr->atype_S_hct,fr->ntype);
1619 if (mtop->atomtypes.nr > 0)
1621 for(i=0;i<fr->ntype;i++)
1622 fr->atype_radius[i] =mtop->atomtypes.radius[i];
1623 for(i=0;i<fr->ntype;i++)
1624 fr->atype_vol[i] = mtop->atomtypes.vol[i];
1625 for(i=0;i<fr->ntype;i++)
1626 fr->atype_surftens[i] = mtop->atomtypes.surftens[i];
1627 for(i=0;i<fr->ntype;i++)
1628 fr->atype_gb_radius[i] = mtop->atomtypes.gb_radius[i];
1629 for(i=0;i<fr->ntype;i++)
1630 fr->atype_S_hct[i] = mtop->atomtypes.S_hct[i];
1633 /* Generate the GB table if needed */
1637 fr->gbtabscale=2000;
1643 fr->gbtab=make_gb_table(fp,oenv,fr,tabpfn,fr->gbtabscale);
1645 init_gb(&fr->born,cr,fr,ir,mtop,ir->rgbradii,ir->gb_algorithm);
1647 /* Copy local gb data (for dd, this is done in dd_partition_system) */
1648 if (!DOMAINDECOMP(cr))
1650 make_local_gb(cr,fr->born,ir->gb_algorithm);
1654 /* Set the charge scaling */
1655 if (fr->epsilon_r != 0)
1656 fr->epsfac = ONE_4PI_EPS0/fr->epsilon_r;
1658 /* eps = 0 is infinite dieletric: no coulomb interactions */
1661 /* Reaction field constants */
1662 if (EEL_RF(fr->eeltype))
1663 calc_rffac(fp,fr->eeltype,fr->epsilon_r,fr->epsilon_rf,
1664 fr->rcoulomb,fr->temp,fr->zsquare,box,
1665 &fr->kappa,&fr->k_rf,&fr->c_rf);
1667 set_chargesum(fp,fr,mtop);
1669 /* if we are using LR electrostatics, and they are tabulated,
1670 * the tables will contain modified coulomb interactions.
1671 * Since we want to use the non-shifted ones for 1-4
1672 * coulombic interactions, we must have an extra set of tables.
1675 /* Construct tables.
1676 * A little unnecessary to make both vdw and coul tables sometimes,
1677 * but what the heck... */
1679 bTab = fr->bcoultab || fr->bvdwtab;
1681 bSep14tab = ((!bTab || fr->eeltype!=eelCUT || fr->vdwtype!=evdwCUT ||
1683 (gmx_mtop_ftype_count(mtop,F_LJ14) > 0 ||
1684 gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0 ||
1685 gmx_mtop_ftype_count(mtop,F_LJC_PAIRS_NB) > 0));
1687 negp_pp = ir->opts.ngener - ir->nwall;
1690 bNormalnblists = TRUE;
1693 bNormalnblists = (ir->eDispCorr != edispcNO);
1694 for(egi=0; egi<negp_pp; egi++) {
1695 for(egj=egi; egj<negp_pp; egj++) {
1696 egp_flags = ir->opts.egp_flags[GID(egi,egj,ir->opts.ngener)];
1697 if (!(egp_flags & EGP_EXCL)) {
1698 if (egp_flags & EGP_TABLE) {
1701 bNormalnblists = TRUE;
1706 if (bNormalnblists) {
1707 fr->nnblists = negptable + 1;
1709 fr->nnblists = negptable;
1711 if (fr->nnblists > 1)
1712 snew(fr->gid2nblists,ir->opts.ngener*ir->opts.ngener);
1714 snew(fr->nblists,fr->nnblists);
1716 /* This code automatically gives table length tabext without cut-off's,
1717 * in that case grompp should already have checked that we do not need
1718 * normal tables and we only generate tables for 1-4 interactions.
1720 rtab = ir->rlistlong + ir->tabext;
1723 /* make tables for ordinary interactions */
1724 if (bNormalnblists) {
1725 make_nbf_tables(fp,oenv,fr,rtab,cr,tabfn,NULL,NULL,&fr->nblists[0]);
1727 fr->tab14 = fr->nblists[0].tab;
1732 if (negptable > 0) {
1733 /* Read the special tables for certain energy group pairs */
1734 nm_ind = mtop->groups.grps[egcENER].nm_ind;
1735 for(egi=0; egi<negp_pp; egi++) {
1736 for(egj=egi; egj<negp_pp; egj++) {
1737 egp_flags = ir->opts.egp_flags[GID(egi,egj,ir->opts.ngener)];
1738 if ((egp_flags & EGP_TABLE) && !(egp_flags & EGP_EXCL)) {
1739 nbl = &(fr->nblists[m]);
1740 if (fr->nnblists > 1) {
1741 fr->gid2nblists[GID(egi,egj,ir->opts.ngener)] = m;
1743 /* Read the table file with the two energy groups names appended */
1744 make_nbf_tables(fp,oenv,fr,rtab,cr,tabfn,
1745 *mtop->groups.grpname[nm_ind[egi]],
1746 *mtop->groups.grpname[nm_ind[egj]],
1749 } else if (fr->nnblists > 1) {
1750 fr->gid2nblists[GID(egi,egj,ir->opts.ngener)] = 0;
1758 /* generate extra tables with plain Coulomb for 1-4 interactions only */
1759 fr->tab14 = make_tables(fp,oenv,fr,MASTER(cr),tabpfn,rtab,
1760 GMX_MAKETABLES_14ONLY);
1763 /* Read AdResS Thermo Force table if needed */
1764 if(fr->adress_icor == eAdressICThermoForce)
1766 /* old todo replace */
1768 if (ir->adress->n_tf_grps > 0){
1769 make_adress_tf_tables(fp,oenv,fr,ir,tabfn, mtop, box);
1772 /* load the default table */
1773 snew(fr->atf_tabs, 1);
1774 fr->atf_tabs[DEFAULT_TF_TABLE] = make_atf_table(fp,oenv,fr,tabafn, box);
1779 fr->nwall = ir->nwall;
1780 if (ir->nwall && ir->wall_type==ewtTABLE)
1782 make_wall_tables(fp,oenv,ir,tabfn,&mtop->groups,fr);
1785 if (fcd && tabbfn) {
1786 fcd->bondtab = make_bonded_tables(fp,
1787 F_TABBONDS,F_TABBONDSNC,
1789 fcd->angletab = make_bonded_tables(fp,
1792 fcd->dihtab = make_bonded_tables(fp,
1797 fprintf(debug,"No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
1800 if (ir->eDispCorr != edispcNO)
1802 calc_enervirdiff(fp,ir->eDispCorr,fr);
1805 /* QM/MM initialization if requested
1809 fprintf(stderr,"QM/MM calculation requested.\n");
1812 fr->bQMMM = ir->bQMMM;
1813 fr->qr = mk_QMMMrec();
1815 /* Set all the static charge group info */
1816 fr->cginfo_mb = init_cginfo_mb(fp,mtop,fr,bNoSolvOpt);
1818 if (DOMAINDECOMP(cr)) {
1821 fr->cginfo = cginfo_expand(mtop->nmolblock,fr->cginfo_mb);
1824 if (!DOMAINDECOMP(cr))
1826 /* When using particle decomposition, the effect of the second argument,
1827 * which sets fr->hcg, is corrected later in do_md and init_em.
1829 forcerec_set_ranges(fr,ncg_mtop(mtop),ncg_mtop(mtop),
1830 mtop->natoms,mtop->natoms,mtop->natoms);
1833 fr->print_force = print_force;
1836 /* coarse load balancing vars */
1841 /* Initialize neighbor search */
1842 init_ns(fp,cr,&fr->ns,fr,mtop,box);
1844 if (cr->duty & DUTY_PP){
1845 gmx_setup_kernels(fp,bGenericKernelOnly);
1847 gmx_setup_adress_kernels(fp,bGenericKernelOnly);
1851 #define pr_real(fp,r) fprintf(fp,"%s: %e\n",#r,r)
1852 #define pr_int(fp,i) fprintf((fp),"%s: %d\n",#i,i)
1853 #define pr_bool(fp,b) fprintf((fp),"%s: %s\n",#b,bool_names[b])
1855 void pr_forcerec(FILE *fp,t_forcerec *fr,t_commrec *cr)
1859 pr_real(fp,fr->rlist);
1860 pr_real(fp,fr->rcoulomb);
1861 pr_real(fp,fr->fudgeQQ);
1862 pr_bool(fp,fr->bGrid);
1863 pr_bool(fp,fr->bTwinRange);
1864 /*pr_int(fp,fr->cg0);
1865 pr_int(fp,fr->hcg);*/
1866 for(i=0; i<fr->nnblists; i++)
1867 pr_int(fp,fr->nblists[i].tab.n);
1868 pr_real(fp,fr->rcoulomb_switch);
1869 pr_real(fp,fr->rcoulomb);