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33 * GROwing Monsters And Cloning Shrimps
62 #include "gmx_fatal.h"
65 #include "mtop_util.h"
68 /* declarations of the interfaces to the QM packages. The _SH indicate
69 * the QM interfaces can be used for Surface Hopping simulations
71 #ifdef GMX_QMMM_GAMESS
72 /* GAMESS interface */
75 init_gamess(t_commrec *cr, t_QMrec *qm, t_MMrec *mm);
78 call_gamess(t_commrec *cr,t_forcerec *fr,
79 t_QMrec *qm, t_MMrec *mm,rvec f[], rvec fshift[]);
81 #elif defined GMX_QMMM_MOPAC
85 init_mopac(t_commrec *cr, t_QMrec *qm, t_MMrec *mm);
88 call_mopac(t_commrec *cr,t_forcerec *fr, t_QMrec *qm,
89 t_MMrec *mm,rvec f[], rvec fshift[]);
92 call_mopac_SH(t_commrec *cr,t_forcerec *fr,t_QMrec *qm,
93 t_MMrec *mm,rvec f[], rvec fshift[]);
95 #elif defined GMX_QMMM_GAUSSIAN
96 /* GAUSSIAN interface */
99 init_gaussian(t_commrec *cr ,t_QMrec *qm, t_MMrec *mm);
102 call_gaussian_SH(t_commrec *cr,t_forcerec *fr,t_QMrec *qm,
103 t_MMrec *mm,rvec f[], rvec fshift[]);
106 call_gaussian(t_commrec *cr,t_forcerec *fr, t_QMrec *qm,
107 t_MMrec *mm,rvec f[], rvec fshift[]);
109 #elif defined GMX_QMMM_ORCA
113 init_orca(t_commrec *cr ,t_QMrec *qm, t_MMrec *mm);
116 call_orca(t_commrec *cr,t_forcerec *fr, t_QMrec *qm,
117 t_MMrec *mm,rvec f[], rvec fshift[]);
124 /* this struct and these comparison functions are needed for creating
125 * a QMMM input for the QM routines from the QMMM neighbor list.
133 static int struct_comp(const void *a, const void *b){
135 return (int)(((t_j_particle *)a)->j)-(int)(((t_j_particle *)b)->j);
139 static int int_comp(const void *a,const void *b){
141 return (*(int *)a) - (*(int *)b);
145 static int QMlayer_comp(const void *a, const void *b){
147 return (int)(((t_QMrec *)a)->nrQMatoms)-(int)(((t_QMrec *)b)->nrQMatoms);
151 real call_QMroutine(t_commrec *cr, t_forcerec *fr, t_QMrec *qm,
152 t_MMrec *mm, rvec f[], rvec fshift[])
154 /* makes a call to the requested QM routine (qm->QMmethod)
155 * Note that f is actually the gradient, i.e. -f
160 /* do a semi-empiprical calculation */
162 if (qm->QMmethod<eQMmethodRHF && !(mm->nrMMatoms))
164 #ifdef GMX_QMMM_MOPAC
166 QMener = call_mopac_SH(cr,fr,qm,mm,f,fshift);
168 QMener = call_mopac(cr,fr,qm,mm,f,fshift);
170 gmx_fatal(FARGS,"Semi-empirical QM only supported with Mopac.");
175 /* do an ab-initio calculation */
176 if (qm->bSH && qm->QMmethod==eQMmethodCASSCF)
178 #ifdef GMX_QMMM_GAUSSIAN
179 QMener = call_gaussian_SH(cr,fr,qm,mm,f,fshift);
181 gmx_fatal(FARGS,"Ab-initio Surface-hopping only supported with Gaussian.");
186 #ifdef GMX_QMMM_GAMESS
187 QMener = call_gamess(cr,fr,qm,mm,f,fshift);
188 #elif defined GMX_QMMM_GAUSSIAN
189 QMener = call_gaussian(cr,fr,qm,mm,f,fshift);
190 #elif defined GMX_QMMM_ORCA
191 QMener = call_orca(cr,fr,qm,mm,f,fshift);
193 gmx_fatal(FARGS,"Ab-initio calculation only supported with Gamess, Gaussian or ORCA.");
200 void init_QMroutine(t_commrec *cr, t_QMrec *qm, t_MMrec *mm)
202 /* makes a call to the requested QM routine (qm->QMmethod)
204 if (qm->QMmethod<eQMmethodRHF){
205 #ifdef GMX_QMMM_MOPAC
206 /* do a semi-empiprical calculation */
207 init_mopac(cr,qm,mm);
209 gmx_fatal(FARGS,"Semi-empirical QM only supported with Mopac.");
214 /* do an ab-initio calculation */
215 #ifdef GMX_QMMM_GAMESS
216 init_gamess(cr,qm,mm);
217 #elif defined GMX_QMMM_GAUSSIAN
218 init_gaussian(cr,qm,mm);
219 #elif defined GMX_QMMM_ORCA
222 gmx_fatal(FARGS,"Ab-initio calculation only supported with Gamess, Gaussian or ORCA.");
225 } /* init_QMroutine */
227 void update_QMMM_coord(rvec x[],t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
229 /* shifts the QM and MM particles into the central box and stores
230 * these shifted coordinates in the coordinate arrays of the
231 * QMMMrec. These coordinates are passed on the QM subroutines.
236 /* shift the QM atoms into the central box
238 for(i=0;i<qm->nrQMatoms;i++){
239 rvec_sub(x[qm->indexQM[i]],fr->shift_vec[qm->shiftQM[i]],qm->xQM[i]);
241 /* also shift the MM atoms into the central box, if any
243 for(i=0;i<mm->nrMMatoms;i++){
244 rvec_sub(x[mm->indexMM[i]],fr->shift_vec[mm->shiftMM[i]],mm->xMM[i]);
246 } /* update_QMMM_coord */
248 static void punch_QMMM_excl(t_QMrec *qm,t_MMrec *mm,t_blocka *excls)
250 /* punch a file containing the bonded interactions of each QM
251 * atom with MM atoms. These need to be excluded in the QM routines
252 * Only needed in case of QM/MM optimizations
257 i,j,k,nrexcl=0,*excluded=NULL,max=0;
260 out = fopen("QMMMexcl.dat","w");
262 /* this can be done more efficiently I think
264 for(i=0;i<qm->nrQMatoms;i++){
266 for(j=excls->index[qm->indexQM[i]];
267 j<excls->index[qm->indexQM[i]+1];
269 for(k=0;k<mm->nrMMatoms;k++){
270 if(mm->indexMM[k]==excls->a[j]){/* the excluded MM atom */
273 srenew(excluded,max);
275 excluded[nrexcl++]=k;
281 fprintf(out,"%5d %5d\n",i+1,nrexcl);
282 for(j=0;j<nrexcl;j++){
283 fprintf(out,"%5d ",excluded[j]);
289 } /* punch_QMMM_excl */
292 /* end of QMMM subroutines */
294 /* QMMM core routines */
296 t_QMrec *mk_QMrec(void){
302 t_MMrec *mk_MMrec(void){
308 static void init_QMrec(int grpnr, t_QMrec *qm,int nr, int *atomarray,
309 gmx_mtop_t *mtop, t_inputrec *ir)
311 /* fills the t_QMrec struct of QM group grpnr
319 snew(qm->indexQM,nr);
320 snew(qm->shiftQM,nr); /* the shifts */
322 qm->indexQM[i]=atomarray[i];
325 snew(qm->atomicnumberQM,nr);
326 for (i=0;i<qm->nrQMatoms;i++){
327 gmx_mtop_atomnr_to_atom(mtop,qm->indexQM[i],&atom);
328 qm->nelectrons += mtop->atomtypes.atomnumber[atom->type];
329 qm->atomicnumberQM[i] = mtop->atomtypes.atomnumber[atom->type];
331 qm->QMcharge = ir->opts.QMcharge[grpnr];
332 qm->multiplicity = ir->opts.QMmult[grpnr];
333 qm->nelectrons -= ir->opts.QMcharge[grpnr];
335 qm->QMmethod = ir->opts.QMmethod[grpnr];
336 qm->QMbasis = ir->opts.QMbasis[grpnr];
337 /* trajectory surface hopping setup (Gaussian only) */
338 qm->bSH = ir->opts.bSH[grpnr];
339 qm->CASorbitals = ir->opts.CASorbitals[grpnr];
340 qm->CASelectrons = ir->opts.CASelectrons[grpnr];
341 qm->SAsteps = ir->opts.SAsteps[grpnr];
342 qm->SAon = ir->opts.SAon[grpnr];
343 qm->SAoff = ir->opts.SAoff[grpnr];
344 /* hack to prevent gaussian from reinitializing all the time */
345 qm->nQMcpus = 0; /* number of CPU's to be used by g01, is set
346 * upon initializing gaussian
349 /* print the current layer to allow users to check their input */
350 fprintf(stderr,"Layer %d\nnr of QM atoms %d\n",grpnr,nr);
351 fprintf(stderr,"QMlevel: %s/%s\n\n",
352 eQMmethod_names[qm->QMmethod],eQMbasis_names[qm->QMbasis]);
355 snew(qm->frontatoms,nr);
356 /* Lennard-Jones coefficients */
359 /* do we optimize the QM separately using the algorithms of the QM program??
361 qm->bTS = ir->opts.bTS[grpnr];
362 qm->bOPT = ir->opts.bOPT[grpnr];
366 t_QMrec *copy_QMrec(t_QMrec *qm)
368 /* copies the contents of qm into a new t_QMrec struct */
375 qmcopy->nrQMatoms = qm->nrQMatoms;
376 snew(qmcopy->xQM,qmcopy->nrQMatoms);
377 snew(qmcopy->indexQM,qmcopy->nrQMatoms);
378 snew(qmcopy->atomicnumberQM,qm->nrQMatoms);
379 snew(qmcopy->shiftQM,qmcopy->nrQMatoms); /* the shifts */
380 for (i=0;i<qmcopy->nrQMatoms;i++){
381 qmcopy->shiftQM[i] = qm->shiftQM[i];
382 qmcopy->indexQM[i] = qm->indexQM[i];
383 qmcopy->atomicnumberQM[i] = qm->atomicnumberQM[i];
385 qmcopy->nelectrons = qm->nelectrons;
386 qmcopy->multiplicity = qm->multiplicity;
387 qmcopy->QMcharge = qm->QMcharge;
388 qmcopy->nelectrons = qm->nelectrons;
389 qmcopy->QMmethod = qm->QMmethod;
390 qmcopy->QMbasis = qm->QMbasis;
391 /* trajectory surface hopping setup (Gaussian only) */
392 qmcopy->bSH = qm->bSH;
393 qmcopy->CASorbitals = qm->CASorbitals;
394 qmcopy->CASelectrons = qm->CASelectrons;
395 qmcopy->SAsteps = qm->SAsteps;
396 qmcopy->SAon = qm->SAon;
397 qmcopy->SAoff = qm->SAoff;
398 qmcopy->bOPT = qm->bOPT;
400 /* Gaussian init. variables */
401 qmcopy->nQMcpus = qm->nQMcpus;
403 qmcopy->SHbasis[i] = qm->SHbasis[i];
404 qmcopy->QMmem = qm->QMmem;
405 qmcopy->accuracy = qm->accuracy;
406 qmcopy->cpmcscf = qm->cpmcscf;
407 qmcopy->SAstep = qm->SAstep;
408 snew(qmcopy->frontatoms,qm->nrQMatoms);
409 snew(qmcopy->c12,qmcopy->nrQMatoms);
410 snew(qmcopy->c6,qmcopy->nrQMatoms);
411 if(qmcopy->bTS||qmcopy->bOPT){
412 for(i=1;i<qmcopy->nrQMatoms;i++){
413 qmcopy->frontatoms[i] = qm->frontatoms[i];
414 qmcopy->c12[i] = qm->c12[i];
415 qmcopy->c6[i] = qm->c6[i];
423 t_QMMMrec *mk_QMMMrec(void)
434 void init_QMMMrec(t_commrec *cr,
440 /* we put the atomsnumbers of atoms that belong to the QMMM group in
441 * an array that will be copied later to QMMMrec->indexQM[..]. Also
442 * it will be used to create an QMMMrec->bQMMM index array that
443 * simply contains true/false for QM and MM (the other) atoms.
446 gmx_groups_t *groups;
447 atom_id *qm_arr=NULL,vsite,ai,aj;
448 int qm_max=0,qm_nr=0,i,j,jmax,k,l,nrvsite2=0;
453 gmx_mtop_atomloop_all_t aloop;
455 gmx_mtop_ilistloop_all_t iloop;
459 c6au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,6));
460 c12au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,12));
461 /* issue a fatal if the user wants to run with more than one node */
462 if ( PAR(cr)) gmx_fatal(FARGS,"QM/MM does not work in parallel, use a single node instead\n");
464 /* Make a local copy of the QMMMrec */
467 /* bQMMM[..] is an array containing TRUE/FALSE for atoms that are
468 * QM/not QM. We first set all elemenst at false. Afterwards we use
469 * the qm_arr (=MMrec->indexQM) to changes the elements
470 * corresponding to the QM atoms at TRUE. */
472 qr->QMMMscheme = ir->QMMMscheme;
474 /* we take the possibility into account that a user has
475 * defined more than one QM group:
477 /* an ugly work-around in case there is only one group In this case
478 * the whole system is treated as QM. Otherwise the second group is
479 * always the rest of the total system and is treated as MM.
482 /* small problem if there is only QM.... so no MM */
484 jmax = ir->opts.ngQM;
486 if(qr->QMMMscheme==eQMMMschemeoniom)
487 qr->nrQMlayers = jmax;
491 groups = &mtop->groups;
493 /* there are jmax groups of QM atoms. In case of multiple QM groups
494 * I assume that the users wants to do ONIOM. However, maybe it
495 * should also be possible to define more than one QM subsystem with
496 * independent neighbourlists. I have to think about
502 aloop = gmx_mtop_atomloop_all_init(mtop);
503 while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
506 srenew(qm_arr,qm_max);
508 if (ggrpnr(groups,egcQMMM ,i) == j) {
513 if(qr->QMMMscheme==eQMMMschemeoniom){
514 /* add the atoms to the bQMMM array
517 /* I assume that users specify the QM groups from small to
518 * big(ger) in the mdp file
520 qr->qm[j] = mk_QMrec();
521 /* we need to throw out link atoms that in the previous layer
522 * existed to separate this QMlayer from the previous
523 * QMlayer. We use the iatoms array in the idef for that
524 * purpose. If all atoms defining the current Link Atom (Dummy2)
525 * are part of the current QM layer it needs to be removed from
528 iloop = gmx_mtop_ilistloop_all_init(mtop);
529 while (gmx_mtop_ilistloop_all_next(iloop,&ilist_mol,&a_offset)) {
530 nrvsite2 = ilist_mol[F_VSITE2].nr;
531 iatoms = ilist_mol[F_VSITE2].iatoms;
533 for(k=0; k<nrvsite2; k+=4) {
534 vsite = a_offset + iatoms[k+1]; /* the vsite */
535 ai = a_offset + iatoms[k+2]; /* constructing atom */
536 aj = a_offset + iatoms[k+3]; /* constructing atom */
537 if (ggrpnr(groups, egcQMMM, vsite) == ggrpnr(groups, egcQMMM, ai)
539 ggrpnr(groups, egcQMMM, vsite) == ggrpnr(groups, egcQMMM, aj)) {
540 /* this dummy link atom needs to be removed from the qm_arr
541 * before making the QMrec of this layer!
543 for(i=0;i<qm_nr;i++){
544 if(qm_arr[i]==vsite){
545 /* drop the element */
546 for(l=i;l<qm_nr;l++){
547 qm_arr[l]=qm_arr[l+1];
556 /* store QM atoms in this layer in the QMrec and initialise layer
558 init_QMrec(j,qr->qm[j],qm_nr,qm_arr,mtop,ir);
560 /* we now store the LJ C6 and C12 parameters in QM rec in case
561 * we need to do an optimization
563 if(qr->qm[j]->bOPT || qr->qm[j]->bTS){
564 for(i=0;i<qm_nr;i++){
565 qr->qm[j]->c6[i] = C6(fr->nbfp,mtop->ffparams.atnr,
566 atom->type,atom->type)/c6au;
567 qr->qm[j]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,
568 atom->type,atom->type)/c12au;
571 /* now we check for frontier QM atoms. These occur in pairs that
572 * construct the vsite
574 iloop = gmx_mtop_ilistloop_all_init(mtop);
575 while (gmx_mtop_ilistloop_all_next(iloop,&ilist_mol,&a_offset)) {
576 nrvsite2 = ilist_mol[F_VSITE2].nr;
577 iatoms = ilist_mol[F_VSITE2].iatoms;
579 for(k=0; k<nrvsite2; k+=4){
580 vsite = a_offset + iatoms[k+1]; /* the vsite */
581 ai = a_offset + iatoms[k+2]; /* constructing atom */
582 aj = a_offset + iatoms[k+3]; /* constructing atom */
583 if(ggrpnr(groups,egcQMMM,ai) < (groups->grps[egcQMMM].nr-1) &&
584 (ggrpnr(groups,egcQMMM,aj) >= (groups->grps[egcQMMM].nr-1))){
585 /* mark ai as frontier atom */
586 for(i=0;i<qm_nr;i++){
587 if( (qm_arr[i]==ai) || (qm_arr[i]==vsite) ){
588 qr->qm[j]->frontatoms[i]=TRUE;
592 else if(ggrpnr(groups,egcQMMM,aj) < (groups->grps[egcQMMM].nr-1) &&
593 (ggrpnr(groups,egcQMMM,ai) >= (groups->grps[egcQMMM].nr-1))){
594 /* mark aj as frontier atom */
595 for(i=0;i<qm_nr;i++){
596 if( (qm_arr[i]==aj) || (qm_arr[i]==vsite)){
597 qr->qm[j]->frontatoms[i]=TRUE;
605 if(qr->QMMMscheme!=eQMMMschemeoniom){
607 /* standard QMMM, all layers are merged together so there is one QM
608 * subsystem and one MM subsystem.
609 * Also we set the charges to zero in the md->charge arrays to prevent
610 * the innerloops from doubly counting the electostatic QM MM interaction
612 for (k=0;k<qm_nr;k++){
613 gmx_mtop_atomnr_to_atom(mtop,qm_arr[k],&atom);
617 qr->qm[0] = mk_QMrec();
618 /* store QM atoms in the QMrec and initialise
620 init_QMrec(0,qr->qm[0],qm_nr,qm_arr,mtop,ir);
621 if(qr->qm[0]->bOPT || qr->qm[0]->bTS){
622 for(i=0;i<qm_nr;i++){
623 gmx_mtop_atomnr_to_atom(mtop,qm_arr[i],&atom);
624 qr->qm[0]->c6[i] = C6(fr->nbfp,mtop->ffparams.atnr,
625 atom->type,atom->type)/c6au;
626 qr->qm[0]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,
627 atom->type,atom->type)/c12au;
634 /* find frontier atoms and mark them true in the frontieratoms array.
636 for(i=0;i<qm_nr;i++) {
637 gmx_mtop_atomnr_to_ilist(mtop,qm_arr[i],&ilist_mol,&a_offset);
638 nrvsite2 = ilist_mol[F_VSITE2].nr;
639 iatoms = ilist_mol[F_VSITE2].iatoms;
641 for(k=0;k<nrvsite2;k+=4){
642 vsite = a_offset + iatoms[k+1]; /* the vsite */
643 ai = a_offset + iatoms[k+2]; /* constructing atom */
644 aj = a_offset + iatoms[k+3]; /* constructing atom */
645 if(ggrpnr(groups,egcQMMM,ai) < (groups->grps[egcQMMM].nr-1) &&
646 (ggrpnr(groups,egcQMMM,aj) >= (groups->grps[egcQMMM].nr-1))){
647 /* mark ai as frontier atom */
648 if ( (qm_arr[i]==ai) || (qm_arr[i]==vsite) ){
649 qr->qm[0]->frontatoms[i]=TRUE;
652 else if (ggrpnr(groups,egcQMMM,aj) < (groups->grps[egcQMMM].nr-1) &&
653 (ggrpnr(groups,egcQMMM,ai) >=(groups->grps[egcQMMM].nr-1))) {
654 /* mark aj as frontier atom */
655 if ( (qm_arr[i]==aj) || (qm_arr[i]==vsite) ){
656 qr->qm[0]->frontatoms[i]=TRUE;
662 /* MM rec creation */
664 mm->scalefactor = ir->scalefactor;
665 mm->nrMMatoms = (mtop->natoms)-(qr->qm[0]->nrQMatoms); /* rest of the atoms */
668 /* MM rec creation */
670 mm->scalefactor = ir->scalefactor;
675 /* these variables get updated in the update QMMMrec */
677 if(qr->nrQMlayers==1){
678 /* with only one layer there is only one initialisation
679 * needed. Multilayer is a bit more complicated as it requires
680 * re-initialisation at every step of the simulation. This is due
681 * to the use of COMMON blocks in the fortran QM subroutines.
683 if (qr->qm[0]->QMmethod<eQMmethodRHF)
685 #ifdef GMX_QMMM_MOPAC
686 /* semi-empiprical 1-layer ONIOM calculation requested (mopac93) */
687 init_mopac(cr,qr->qm[0],qr->mm);
689 gmx_fatal(FARGS,"Semi-empirical QM only supported with Mopac.");
694 /* ab initio calculation requested (gamess/gaussian/ORCA) */
695 #ifdef GMX_QMMM_GAMESS
696 init_gamess(cr,qr->qm[0],qr->mm);
697 #elif defined GMX_QMMM_GAUSSIAN
698 init_gaussian(cr,qr->qm[0],qr->mm);
699 #elif defined GMX_QMMM_ORCA
700 init_orca(cr,qr->qm[0],qr->mm);
702 gmx_fatal(FARGS,"Ab-initio calculation only supported with Gamess, Gaussian or ORCA.");
708 void update_QMMMrec(t_commrec *cr,
715 /* updates the coordinates of both QM atoms and MM atoms and stores
716 * them in the QMMMrec.
718 * NOTE: is NOT yet working if there are no PBC. Also in ns.c, simple
719 * ns needs to be fixed!
722 mm_max=0,mm_nr=0,mm_nr_new,i,j,is,k,shift;
724 *mm_j_particles=NULL,*qm_i_particles=NULL;
740 *parallelMMarray=NULL;
744 c6au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,6));
745 c12au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,12));
747 /* every cpu has this array. On every processor we fill this array
748 * with 1's and 0's. 1's indicate the atoms is a QM atom on the
749 * current cpu in a later stage these arrays are all summed. indexes
750 * > 0 indicate the atom is a QM atom. Every node therefore knows
751 * whcih atoms are part of the QM subsystem.
753 /* copy some pointers */
756 QMMMlist = fr->QMMMlist;
760 /* init_pbc(box); needs to be called first, see pbc.h */
761 set_pbc_dd(&pbc,fr->ePBC,DOMAINDECOMP(cr) ? cr->dd : NULL,FALSE,box);
762 /* only in standard (normal) QMMM we need the neighbouring MM
763 * particles to provide a electric field of point charges for the QM
766 if(qr->QMMMscheme==eQMMMschemenormal){ /* also implies 1 QM-layer */
767 /* we NOW create/update a number of QMMMrec entries:
769 * 1) the shiftQM, containing the shifts of the QM atoms
771 * 2) the indexMM array, containing the index of the MM atoms
773 * 3) the shiftMM, containing the shifts of the MM atoms
775 * 4) the shifted coordinates of the MM atoms
777 * the shifts are used for computing virial of the QM/MM particles.
779 qm = qr->qm[0]; /* in case of normal QMMM, there is only one group */
780 snew(qm_i_particles,QMMMlist.nri);
782 qm_i_particles[0].shift = XYZ2IS(0,0,0);
783 for(i=0;i<QMMMlist.nri;i++){
784 qm_i_particles[i].j = QMMMlist.iinr[i];
787 qm_i_particles[i].shift = pbc_dx_aiuc(&pbc,x[QMMMlist.iinr[0]],
788 x[QMMMlist.iinr[i]],dx);
791 /* However, since nri >= nrQMatoms, we do a quicksort, and throw
792 * out double, triple, etc. entries later, as we do for the MM
796 /* compute the shift for the MM j-particles with respect to
797 * the QM i-particle and store them.
800 crd[0] = IS2X(QMMMlist.shift[i]) + IS2X(qm_i_particles[i].shift);
801 crd[1] = IS2Y(QMMMlist.shift[i]) + IS2Y(qm_i_particles[i].shift);
802 crd[2] = IS2Z(QMMMlist.shift[i]) + IS2Z(qm_i_particles[i].shift);
803 is = XYZ2IS(crd[0],crd[1],crd[2]);
804 for(j=QMMMlist.jindex[i];
805 j<QMMMlist.jindex[i+1];
809 srenew(mm_j_particles,mm_max);
812 mm_j_particles[mm_nr].j = QMMMlist.jjnr[j];
813 mm_j_particles[mm_nr].shift = is;
818 /* quicksort QM and MM shift arrays and throw away multiple entries */
822 qsort(qm_i_particles,QMMMlist.nri,
823 (size_t)sizeof(qm_i_particles[0]),
825 qsort(mm_j_particles,mm_nr,
826 (size_t)sizeof(mm_j_particles[0]),
828 /* remove multiples in the QM shift array, since in init_QMMM() we
829 * went through the atom numbers from 0 to md.nr, the order sorted
830 * here matches the one of QMindex already.
833 for(i=0;i<QMMMlist.nri;i++){
834 if (i==0 || qm_i_particles[i].j!=qm_i_particles[i-1].j){
835 qm_i_particles[j++] = qm_i_particles[i];
839 if(qm->bTS||qm->bOPT){
840 /* only remove double entries for the MM array */
841 for(i=0;i<mm_nr;i++){
842 if((i==0 || mm_j_particles[i].j!=mm_j_particles[i-1].j)
843 && !md->bQM[mm_j_particles[i].j]){
844 mm_j_particles[mm_nr_new++] = mm_j_particles[i];
848 /* we also remove mm atoms that have no charges!
849 * actually this is already done in the ns.c
852 for(i=0;i<mm_nr;i++){
853 if((i==0 || mm_j_particles[i].j!=mm_j_particles[i-1].j)
854 && !md->bQM[mm_j_particles[i].j]
855 && (md->chargeA[mm_j_particles[i].j]
856 || (md->chargeB && md->chargeB[mm_j_particles[i].j]))) {
857 mm_j_particles[mm_nr_new++] = mm_j_particles[i];
862 /* store the data retrieved above into the QMMMrec
865 /* Keep the compiler happy,
866 * shift will always be set in the loop for i=0
869 for(i=0;i<qm->nrQMatoms;i++){
870 /* not all qm particles might have appeared as i
871 * particles. They might have been part of the same charge
872 * group for instance.
874 if (qm->indexQM[i] == qm_i_particles[k].j) {
875 shift = qm_i_particles[k++].shift;
877 /* use previous shift, assuming they belong the same charge
881 qm->shiftQM[i] = shift;
884 /* parallel excecution */
886 snew(parallelMMarray,2*(md->nr));
887 /* only MM particles have a 1 at their atomnumber. The second part
888 * of the array contains the shifts. Thus:
889 * p[i]=1/0 depending on wether atomnumber i is a MM particle in the QM
890 * step or not. p[i+md->nr] is the shift of atomnumber i.
892 for(i=0;i<2*(md->nr);i++){
893 parallelMMarray[i]=0;
896 for(i=0;i<mm_nr;i++){
897 parallelMMarray[mm_j_particles[i].j]=1;
898 parallelMMarray[mm_j_particles[i].j+(md->nr)]=mm_j_particles[i].shift;
900 gmx_sumi(md->nr,parallelMMarray,cr);
904 for(i=0;i<md->nr;i++){
905 if(parallelMMarray[i]){
908 srenew(mm->indexMM,mm_max);
909 srenew(mm->shiftMM,mm_max);
911 mm->indexMM[mm_nr] = i;
912 mm->shiftMM[mm_nr++]= parallelMMarray[i+md->nr]/parallelMMarray[i];
916 free(parallelMMarray);
918 /* serial execution */
920 mm->nrMMatoms = mm_nr;
921 srenew(mm->shiftMM,mm_nr);
922 srenew(mm->indexMM,mm_nr);
923 for(i=0;i<mm_nr;i++){
924 mm->indexMM[i]=mm_j_particles[i].j;
925 mm->shiftMM[i]=mm_j_particles[i].shift;
929 /* (re) allocate memory for the MM coordiate array. The QM
930 * coordinate array was already allocated in init_QMMM, and is
931 * only (re)filled in the update_QMMM_coordinates routine
933 srenew(mm->xMM,mm->nrMMatoms);
934 /* now we (re) fill the array that contains the MM charges with
935 * the forcefield charges. If requested, these charges will be
938 srenew(mm->MMcharges,mm->nrMMatoms);
939 for(i=0;i<mm->nrMMatoms;i++){/* no free energy yet */
940 mm->MMcharges[i]=md->chargeA[mm->indexMM[i]]*mm->scalefactor;
942 if(qm->bTS||qm->bOPT){
943 /* store (copy) the c6 and c12 parameters into the MMrec struct
945 srenew(mm->c6,mm->nrMMatoms);
946 srenew(mm->c12,mm->nrMMatoms);
947 for (i=0;i<mm->nrMMatoms;i++){
948 mm->c6[i] = C6(fr->nbfp,top->idef.atnr,
949 md->typeA[mm->indexMM[i]],
950 md->typeA[mm->indexMM[i]])/c6au;
951 mm->c12[i] =C12(fr->nbfp,top->idef.atnr,
952 md->typeA[mm->indexMM[i]],
953 md->typeA[mm->indexMM[i]])/c12au;
955 punch_QMMM_excl(qr->qm[0],mm,&(top->excls));
957 /* the next routine fills the coordinate fields in the QMMM rec of
958 * both the qunatum atoms and the MM atoms, using the shifts
962 update_QMMM_coord(x,fr,qr->qm[0],qr->mm);
963 free(qm_i_particles);
964 free(mm_j_particles);
966 else { /* ONIOM */ /* ????? */
968 /* do for each layer */
969 for (j=0;j<qr->nrQMlayers;j++){
971 qm->shiftQM[0]=XYZ2IS(0,0,0);
972 for(i=1;i<qm->nrQMatoms;i++){
973 qm->shiftQM[i] = pbc_dx_aiuc(&pbc,x[qm->indexQM[0]],x[qm->indexQM[i]],
976 update_QMMM_coord(x,fr,qm,mm);
979 } /* update_QMMM_rec */
982 real calculate_QMMM(t_commrec *cr,
989 /* a selection for the QM package depending on which is requested
990 * (Gaussian, GAMESS-UK, MOPAC or ORCA) needs to be implemented here. Now
991 * it works through defines.... Not so nice yet
1000 *forces=NULL,*fshift=NULL,
1001 *forces2=NULL, *fshift2=NULL; /* needed for multilayer ONIOM */
1004 /* make a local copy the QMMMrec pointer
1009 /* now different procedures are carried out for one layer ONION and
1010 * normal QMMM on one hand and multilayer oniom on the other
1012 if(qr->QMMMscheme==eQMMMschemenormal || qr->nrQMlayers==1){
1014 snew(forces,(qm->nrQMatoms+mm->nrMMatoms));
1015 snew(fshift,(qm->nrQMatoms+mm->nrMMatoms));
1016 QMener = call_QMroutine(cr,fr,qm,mm,forces,fshift);
1017 for(i=0;i<qm->nrQMatoms;i++){
1019 f[qm->indexQM[i]][j] -= forces[i][j];
1020 fr->fshift[qm->shiftQM[i]][j] += fshift[i][j];
1023 for(i=0;i<mm->nrMMatoms;i++){
1025 f[mm->indexMM[i]][j] -= forces[qm->nrQMatoms+i][j];
1026 fr->fshift[mm->shiftMM[i]][j] += fshift[qm->nrQMatoms+i][j];
1033 else{ /* Multi-layer ONIOM */
1034 for(i=0;i<qr->nrQMlayers-1;i++){ /* last layer is special */
1036 qm2 = copy_QMrec(qr->qm[i+1]);
1038 qm2->nrQMatoms = qm->nrQMatoms;
1040 for(j=0;j<qm2->nrQMatoms;j++){
1042 qm2->xQM[j][k] = qm->xQM[j][k];
1043 qm2->indexQM[j] = qm->indexQM[j];
1044 qm2->atomicnumberQM[j] = qm->atomicnumberQM[j];
1045 qm2->shiftQM[j] = qm->shiftQM[j];
1048 qm2->QMcharge = qm->QMcharge;
1049 /* this layer at the higher level of theory */
1050 srenew(forces,qm->nrQMatoms);
1051 srenew(fshift,qm->nrQMatoms);
1052 /* we need to re-initialize the QMroutine every step... */
1053 init_QMroutine(cr,qm,mm);
1054 QMener += call_QMroutine(cr,fr,qm,mm,forces,fshift);
1056 /* this layer at the lower level of theory */
1057 srenew(forces2,qm->nrQMatoms);
1058 srenew(fshift2,qm->nrQMatoms);
1059 init_QMroutine(cr,qm2,mm);
1060 QMener -= call_QMroutine(cr,fr,qm2,mm,forces2,fshift2);
1061 /* E = E1high-E1low The next layer includes the current layer at
1062 * the lower level of theory, which provides + E2low
1063 * this is similar for gradients
1065 for(i=0;i<qm->nrQMatoms;i++){
1067 f[qm->indexQM[i]][j] -= (forces[i][j]-forces2[i][j]);
1068 fr->fshift[qm->shiftQM[i]][j] += (fshift[i][j]-fshift2[i][j]);
1073 /* now the last layer still needs to be done: */
1074 qm = qr->qm[qr->nrQMlayers-1]; /* C counts from 0 */
1075 init_QMroutine(cr,qm,mm);
1076 srenew(forces,qm->nrQMatoms);
1077 srenew(fshift,qm->nrQMatoms);
1078 QMener += call_QMroutine(cr,fr,qm,mm,forces,fshift);
1079 for(i=0;i<qm->nrQMatoms;i++){
1081 f[qm->indexQM[i]][j] -= forces[i][j];
1082 fr->fshift[qm->shiftQM[i]][j] += fshift[i][j];
1090 if(qm->bTS||qm->bOPT){
1091 /* qm[0] still contains the largest ONIOM QM subsystem
1092 * we take the optimized coordiates and put the in x[]
1094 for(i=0;i<qm->nrQMatoms;i++){
1096 x[qm->indexQM[i]][j] = qm->xQM[i][j];
1101 } /* calculate_QMMM */
1103 /* end of QMMM core routines */