3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
11 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
12 * Copyright (c) 2001-2004, The GROMACS development team,
13 * check out http://www.gromacs.org for more information.
15 * This program is free software; you can redistribute it and/or
16 * modify it under the terms of the GNU General Public License
17 * as published by the Free Software Foundation; either version 2
18 * of the License, or (at your option) any later version.
20 * If you want to redistribute modifications, please consider that
21 * scientific software is very special. Version control is crucial -
22 * bugs must be traceable. We will be happy to consider code for
23 * inclusion in the official distribution, but derived work must not
24 * be called official GROMACS. Details are found in the README & COPYING
25 * files - if they are missing, get the official version at www.gromacs.org.
27 * To help us fund GROMACS development, we humbly ask that you cite
28 * the papers on the package - you can find them in the top README file.
30 * For more info, check our website at http://www.gromacs.org
33 * GROwing Monsters And Cloning Shrimps
63 #include "gmx_fatal.h"
66 #include "mtop_util.h"
69 /* declarations of the interfaces to the QM packages. The _SH indicate
70 * the QM interfaces can be used for Surface Hopping simulations
72 #ifdef GMX_QMMM_GAMESS
73 /* GAMESS interface */
76 init_gamess(t_commrec *cr, t_QMrec *qm, t_MMrec *mm);
79 call_gamess(t_commrec *cr,t_forcerec *fr,
80 t_QMrec *qm, t_MMrec *mm,rvec f[], rvec fshift[]);
82 #elif defined GMX_QMMM_MOPAC
86 init_mopac(t_commrec *cr, t_QMrec *qm, t_MMrec *mm);
89 call_mopac(t_commrec *cr,t_forcerec *fr, t_QMrec *qm,
90 t_MMrec *mm,rvec f[], rvec fshift[]);
93 call_mopac_SH(t_commrec *cr,t_forcerec *fr,t_QMrec *qm,
94 t_MMrec *mm,rvec f[], rvec fshift[]);
96 #elif defined GMX_QMMM_GAUSSIAN
97 /* GAUSSIAN interface */
100 init_gaussian(t_commrec *cr ,t_QMrec *qm, t_MMrec *mm);
103 call_gaussian_SH(t_commrec *cr,t_forcerec *fr,t_QMrec *qm,
104 t_MMrec *mm,rvec f[], rvec fshift[]);
107 call_gaussian(t_commrec *cr,t_forcerec *fr, t_QMrec *qm,
108 t_MMrec *mm,rvec f[], rvec fshift[]);
110 #elif defined GMX_QMMM_ORCA
114 init_orca(t_commrec *cr ,t_QMrec *qm, t_MMrec *mm);
117 call_orca(t_commrec *cr,t_forcerec *fr, t_QMrec *qm,
118 t_MMrec *mm,rvec f[], rvec fshift[]);
125 /* this struct and these comparison functions are needed for creating
126 * a QMMM input for the QM routines from the QMMM neighbor list.
134 static int struct_comp(const void *a, const void *b){
136 return (int)(((t_j_particle *)a)->j)-(int)(((t_j_particle *)b)->j);
140 static int int_comp(const void *a,const void *b){
142 return (*(int *)a) - (*(int *)b);
146 static int QMlayer_comp(const void *a, const void *b){
148 return (int)(((t_QMrec *)a)->nrQMatoms)-(int)(((t_QMrec *)b)->nrQMatoms);
152 real call_QMroutine(t_commrec *cr, t_forcerec *fr, t_QMrec *qm,
153 t_MMrec *mm, rvec f[], rvec fshift[])
155 /* makes a call to the requested QM routine (qm->QMmethod)
156 * Note that f is actually the gradient, i.e. -f
161 /* do a semi-empiprical calculation */
163 if (qm->QMmethod<eQMmethodRHF && !(mm->nrMMatoms))
165 #ifdef GMX_QMMM_MOPAC
167 QMener = call_mopac_SH(cr,fr,qm,mm,f,fshift);
169 QMener = call_mopac(cr,fr,qm,mm,f,fshift);
171 gmx_fatal(FARGS,"Semi-empirical QM only supported with Mopac.");
176 /* do an ab-initio calculation */
177 if (qm->bSH && qm->QMmethod==eQMmethodCASSCF)
179 #ifdef GMX_QMMM_GAUSSIAN
180 QMener = call_gaussian_SH(cr,fr,qm,mm,f,fshift);
182 gmx_fatal(FARGS,"Ab-initio Surface-hopping only supported with Gaussian.");
187 #ifdef GMX_QMMM_GAMESS
188 QMener = call_gamess(cr,fr,qm,mm,f,fshift);
189 #elif defined GMX_QMMM_GAUSSIAN
190 QMener = call_gaussian(cr,fr,qm,mm,f,fshift);
191 #elif defined GMX_QMMM_ORCA
192 QMener = call_orca(cr,fr,qm,mm,f,fshift);
194 gmx_fatal(FARGS,"Ab-initio calculation only supported with Gamess, Gaussian or ORCA.");
201 void init_QMroutine(t_commrec *cr, t_QMrec *qm, t_MMrec *mm)
203 /* makes a call to the requested QM routine (qm->QMmethod)
205 if (qm->QMmethod<eQMmethodRHF){
206 #ifdef GMX_QMMM_MOPAC
207 /* do a semi-empiprical calculation */
208 init_mopac(cr,qm,mm);
210 gmx_fatal(FARGS,"Semi-empirical QM only supported with Mopac.");
215 /* do an ab-initio calculation */
216 #ifdef GMX_QMMM_GAMESS
217 init_gamess(cr,qm,mm);
218 #elif defined GMX_QMMM_GAUSSIAN
219 init_gaussian(cr,qm,mm);
220 #elif defined GMX_QMMM_ORCA
223 gmx_fatal(FARGS,"Ab-initio calculation only supported with Gamess, Gaussian or ORCA.");
226 } /* init_QMroutine */
228 void update_QMMM_coord(rvec x[],t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
230 /* shifts the QM and MM particles into the central box and stores
231 * these shifted coordinates in the coordinate arrays of the
232 * QMMMrec. These coordinates are passed on the QM subroutines.
237 /* shift the QM atoms into the central box
239 for(i=0;i<qm->nrQMatoms;i++){
240 rvec_sub(x[qm->indexQM[i]],fr->shift_vec[qm->shiftQM[i]],qm->xQM[i]);
242 /* also shift the MM atoms into the central box, if any
244 for(i=0;i<mm->nrMMatoms;i++){
245 rvec_sub(x[mm->indexMM[i]],fr->shift_vec[mm->shiftMM[i]],mm->xMM[i]);
247 } /* update_QMMM_coord */
249 static void punch_QMMM_excl(t_QMrec *qm,t_MMrec *mm,t_blocka *excls)
251 /* punch a file containing the bonded interactions of each QM
252 * atom with MM atoms. These need to be excluded in the QM routines
253 * Only needed in case of QM/MM optimizations
258 i,j,k,nrexcl=0,*excluded=NULL,max=0;
261 out = fopen("QMMMexcl.dat","w");
263 /* this can be done more efficiently I think
265 for(i=0;i<qm->nrQMatoms;i++){
267 for(j=excls->index[qm->indexQM[i]];
268 j<excls->index[qm->indexQM[i]+1];
270 for(k=0;k<mm->nrMMatoms;k++){
271 if(mm->indexMM[k]==excls->a[j]){/* the excluded MM atom */
274 srenew(excluded,max);
276 excluded[nrexcl++]=k;
282 fprintf(out,"%5d %5d\n",i+1,nrexcl);
283 for(j=0;j<nrexcl;j++){
284 fprintf(out,"%5d ",excluded[j]);
290 } /* punch_QMMM_excl */
293 /* end of QMMM subroutines */
295 /* QMMM core routines */
297 t_QMrec *mk_QMrec(void){
303 t_MMrec *mk_MMrec(void){
309 static void init_QMrec(int grpnr, t_QMrec *qm,int nr, int *atomarray,
310 gmx_mtop_t *mtop, t_inputrec *ir)
312 /* fills the t_QMrec struct of QM group grpnr
315 gmx_mtop_atomlookup_t alook;
321 snew(qm->indexQM,nr);
322 snew(qm->shiftQM,nr); /* the shifts */
324 qm->indexQM[i]=atomarray[i];
327 alook = gmx_mtop_atomlookup_init(mtop);
329 snew(qm->atomicnumberQM,nr);
330 for (i=0;i<qm->nrQMatoms;i++){
331 gmx_mtop_atomnr_to_atom(alook,qm->indexQM[i],&atom);
332 qm->nelectrons += mtop->atomtypes.atomnumber[atom->type];
333 qm->atomicnumberQM[i] = mtop->atomtypes.atomnumber[atom->type];
336 gmx_mtop_atomlookup_destroy(alook);
338 qm->QMcharge = ir->opts.QMcharge[grpnr];
339 qm->multiplicity = ir->opts.QMmult[grpnr];
340 qm->nelectrons -= ir->opts.QMcharge[grpnr];
342 qm->QMmethod = ir->opts.QMmethod[grpnr];
343 qm->QMbasis = ir->opts.QMbasis[grpnr];
344 /* trajectory surface hopping setup (Gaussian only) */
345 qm->bSH = ir->opts.bSH[grpnr];
346 qm->CASorbitals = ir->opts.CASorbitals[grpnr];
347 qm->CASelectrons = ir->opts.CASelectrons[grpnr];
348 qm->SAsteps = ir->opts.SAsteps[grpnr];
349 qm->SAon = ir->opts.SAon[grpnr];
350 qm->SAoff = ir->opts.SAoff[grpnr];
351 /* hack to prevent gaussian from reinitializing all the time */
352 qm->nQMcpus = 0; /* number of CPU's to be used by g01, is set
353 * upon initializing gaussian
356 /* print the current layer to allow users to check their input */
357 fprintf(stderr,"Layer %d\nnr of QM atoms %d\n",grpnr,nr);
358 fprintf(stderr,"QMlevel: %s/%s\n\n",
359 eQMmethod_names[qm->QMmethod],eQMbasis_names[qm->QMbasis]);
362 snew(qm->frontatoms,nr);
363 /* Lennard-Jones coefficients */
366 /* do we optimize the QM separately using the algorithms of the QM program??
368 qm->bTS = ir->opts.bTS[grpnr];
369 qm->bOPT = ir->opts.bOPT[grpnr];
373 t_QMrec *copy_QMrec(t_QMrec *qm)
375 /* copies the contents of qm into a new t_QMrec struct */
382 qmcopy->nrQMatoms = qm->nrQMatoms;
383 snew(qmcopy->xQM,qmcopy->nrQMatoms);
384 snew(qmcopy->indexQM,qmcopy->nrQMatoms);
385 snew(qmcopy->atomicnumberQM,qm->nrQMatoms);
386 snew(qmcopy->shiftQM,qmcopy->nrQMatoms); /* the shifts */
387 for (i=0;i<qmcopy->nrQMatoms;i++){
388 qmcopy->shiftQM[i] = qm->shiftQM[i];
389 qmcopy->indexQM[i] = qm->indexQM[i];
390 qmcopy->atomicnumberQM[i] = qm->atomicnumberQM[i];
392 qmcopy->nelectrons = qm->nelectrons;
393 qmcopy->multiplicity = qm->multiplicity;
394 qmcopy->QMcharge = qm->QMcharge;
395 qmcopy->nelectrons = qm->nelectrons;
396 qmcopy->QMmethod = qm->QMmethod;
397 qmcopy->QMbasis = qm->QMbasis;
398 /* trajectory surface hopping setup (Gaussian only) */
399 qmcopy->bSH = qm->bSH;
400 qmcopy->CASorbitals = qm->CASorbitals;
401 qmcopy->CASelectrons = qm->CASelectrons;
402 qmcopy->SAsteps = qm->SAsteps;
403 qmcopy->SAon = qm->SAon;
404 qmcopy->SAoff = qm->SAoff;
405 qmcopy->bOPT = qm->bOPT;
407 /* Gaussian init. variables */
408 qmcopy->nQMcpus = qm->nQMcpus;
410 qmcopy->SHbasis[i] = qm->SHbasis[i];
411 qmcopy->QMmem = qm->QMmem;
412 qmcopy->accuracy = qm->accuracy;
413 qmcopy->cpmcscf = qm->cpmcscf;
414 qmcopy->SAstep = qm->SAstep;
415 snew(qmcopy->frontatoms,qm->nrQMatoms);
416 snew(qmcopy->c12,qmcopy->nrQMatoms);
417 snew(qmcopy->c6,qmcopy->nrQMatoms);
418 if(qmcopy->bTS||qmcopy->bOPT){
419 for(i=1;i<qmcopy->nrQMatoms;i++){
420 qmcopy->frontatoms[i] = qm->frontatoms[i];
421 qmcopy->c12[i] = qm->c12[i];
422 qmcopy->c6[i] = qm->c6[i];
430 t_QMMMrec *mk_QMMMrec(void)
441 void init_QMMMrec(t_commrec *cr,
447 /* we put the atomsnumbers of atoms that belong to the QMMM group in
448 * an array that will be copied later to QMMMrec->indexQM[..]. Also
449 * it will be used to create an QMMMrec->bQMMM index array that
450 * simply contains true/false for QM and MM (the other) atoms.
453 gmx_groups_t *groups;
454 atom_id *qm_arr=NULL,vsite,ai,aj;
455 int qm_max=0,qm_nr=0,i,j,jmax,k,l,nrvsite2=0;
460 gmx_mtop_atomloop_all_t aloop;
462 gmx_mtop_ilistloop_all_t iloop;
465 gmx_mtop_atomlookup_t alook;
467 c6au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,6));
468 c12au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,12));
469 /* issue a fatal if the user wants to run with more than one node */
470 if ( PAR(cr)) gmx_fatal(FARGS,"QM/MM does not work in parallel, use a single node instead\n");
472 /* Make a local copy of the QMMMrec */
475 /* bQMMM[..] is an array containing TRUE/FALSE for atoms that are
476 * QM/not QM. We first set all elemenst at false. Afterwards we use
477 * the qm_arr (=MMrec->indexQM) to changes the elements
478 * corresponding to the QM atoms at TRUE. */
480 qr->QMMMscheme = ir->QMMMscheme;
482 /* we take the possibility into account that a user has
483 * defined more than one QM group:
485 /* an ugly work-around in case there is only one group In this case
486 * the whole system is treated as QM. Otherwise the second group is
487 * always the rest of the total system and is treated as MM.
490 /* small problem if there is only QM.... so no MM */
492 jmax = ir->opts.ngQM;
494 if(qr->QMMMscheme==eQMMMschemeoniom)
495 qr->nrQMlayers = jmax;
499 groups = &mtop->groups;
501 /* there are jmax groups of QM atoms. In case of multiple QM groups
502 * I assume that the users wants to do ONIOM. However, maybe it
503 * should also be possible to define more than one QM subsystem with
504 * independent neighbourlists. I have to think about
510 aloop = gmx_mtop_atomloop_all_init(mtop);
511 while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
514 srenew(qm_arr,qm_max);
516 if (ggrpnr(groups,egcQMMM ,i) == j) {
521 if(qr->QMMMscheme==eQMMMschemeoniom){
522 /* add the atoms to the bQMMM array
525 /* I assume that users specify the QM groups from small to
526 * big(ger) in the mdp file
528 qr->qm[j] = mk_QMrec();
529 /* we need to throw out link atoms that in the previous layer
530 * existed to separate this QMlayer from the previous
531 * QMlayer. We use the iatoms array in the idef for that
532 * purpose. If all atoms defining the current Link Atom (Dummy2)
533 * are part of the current QM layer it needs to be removed from
536 iloop = gmx_mtop_ilistloop_all_init(mtop);
537 while (gmx_mtop_ilistloop_all_next(iloop,&ilist_mol,&a_offset)) {
538 nrvsite2 = ilist_mol[F_VSITE2].nr;
539 iatoms = ilist_mol[F_VSITE2].iatoms;
541 for(k=0; k<nrvsite2; k+=4) {
542 vsite = a_offset + iatoms[k+1]; /* the vsite */
543 ai = a_offset + iatoms[k+2]; /* constructing atom */
544 aj = a_offset + iatoms[k+3]; /* constructing atom */
545 if (ggrpnr(groups, egcQMMM, vsite) == ggrpnr(groups, egcQMMM, ai)
547 ggrpnr(groups, egcQMMM, vsite) == ggrpnr(groups, egcQMMM, aj)) {
548 /* this dummy link atom needs to be removed from the qm_arr
549 * before making the QMrec of this layer!
551 for(i=0;i<qm_nr;i++){
552 if(qm_arr[i]==vsite){
553 /* drop the element */
554 for(l=i;l<qm_nr;l++){
555 qm_arr[l]=qm_arr[l+1];
564 /* store QM atoms in this layer in the QMrec and initialise layer
566 init_QMrec(j,qr->qm[j],qm_nr,qm_arr,mtop,ir);
568 /* we now store the LJ C6 and C12 parameters in QM rec in case
569 * we need to do an optimization
571 if(qr->qm[j]->bOPT || qr->qm[j]->bTS)
575 /* nbfp now includes the 6.0/12.0 derivative prefactors */
576 qr->qm[j]->c6[i] = C6(fr->nbfp,mtop->ffparams.atnr,atom->type,atom->type)/c6au/6.0;
577 qr->qm[j]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,atom->type,atom->type)/c12au/12.0;
580 /* now we check for frontier QM atoms. These occur in pairs that
581 * construct the vsite
583 iloop = gmx_mtop_ilistloop_all_init(mtop);
584 while (gmx_mtop_ilistloop_all_next(iloop,&ilist_mol,&a_offset)) {
585 nrvsite2 = ilist_mol[F_VSITE2].nr;
586 iatoms = ilist_mol[F_VSITE2].iatoms;
588 for(k=0; k<nrvsite2; k+=4){
589 vsite = a_offset + iatoms[k+1]; /* the vsite */
590 ai = a_offset + iatoms[k+2]; /* constructing atom */
591 aj = a_offset + iatoms[k+3]; /* constructing atom */
592 if(ggrpnr(groups,egcQMMM,ai) < (groups->grps[egcQMMM].nr-1) &&
593 (ggrpnr(groups,egcQMMM,aj) >= (groups->grps[egcQMMM].nr-1))){
594 /* mark ai as frontier atom */
595 for(i=0;i<qm_nr;i++){
596 if( (qm_arr[i]==ai) || (qm_arr[i]==vsite) ){
597 qr->qm[j]->frontatoms[i]=TRUE;
601 else if(ggrpnr(groups,egcQMMM,aj) < (groups->grps[egcQMMM].nr-1) &&
602 (ggrpnr(groups,egcQMMM,ai) >= (groups->grps[egcQMMM].nr-1))){
603 /* mark aj as frontier atom */
604 for(i=0;i<qm_nr;i++){
605 if( (qm_arr[i]==aj) || (qm_arr[i]==vsite)){
606 qr->qm[j]->frontatoms[i]=TRUE;
614 if(qr->QMMMscheme!=eQMMMschemeoniom){
616 /* standard QMMM, all layers are merged together so there is one QM
617 * subsystem and one MM subsystem.
618 * Also we set the charges to zero in the md->charge arrays to prevent
619 * the innerloops from doubly counting the electostatic QM MM interaction
622 alook = gmx_mtop_atomlookup_init(mtop);
624 for (k=0;k<qm_nr;k++){
625 gmx_mtop_atomnr_to_atom(alook,qm_arr[k],&atom);
629 qr->qm[0] = mk_QMrec();
630 /* store QM atoms in the QMrec and initialise
632 init_QMrec(0,qr->qm[0],qm_nr,qm_arr,mtop,ir);
633 if(qr->qm[0]->bOPT || qr->qm[0]->bTS)
637 gmx_mtop_atomnr_to_atom(alook,qm_arr[i],&atom);
638 /* nbfp now includes the 6.0/12.0 derivative prefactors */
639 qr->qm[0]->c6[i] = C6(fr->nbfp,mtop->ffparams.atnr,atom->type,atom->type)/c6au/6.0;
640 qr->qm[0]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,atom->type,atom->type)/c12au/12.0;
644 /* find frontier atoms and mark them true in the frontieratoms array.
646 for(i=0;i<qm_nr;i++) {
647 gmx_mtop_atomnr_to_ilist(alook,qm_arr[i],&ilist_mol,&a_offset);
648 nrvsite2 = ilist_mol[F_VSITE2].nr;
649 iatoms = ilist_mol[F_VSITE2].iatoms;
651 for(k=0;k<nrvsite2;k+=4){
652 vsite = a_offset + iatoms[k+1]; /* the vsite */
653 ai = a_offset + iatoms[k+2]; /* constructing atom */
654 aj = a_offset + iatoms[k+3]; /* constructing atom */
655 if(ggrpnr(groups,egcQMMM,ai) < (groups->grps[egcQMMM].nr-1) &&
656 (ggrpnr(groups,egcQMMM,aj) >= (groups->grps[egcQMMM].nr-1))){
657 /* mark ai as frontier atom */
658 if ( (qm_arr[i]==ai) || (qm_arr[i]==vsite) ){
659 qr->qm[0]->frontatoms[i]=TRUE;
662 else if (ggrpnr(groups,egcQMMM,aj) < (groups->grps[egcQMMM].nr-1) &&
663 (ggrpnr(groups,egcQMMM,ai) >=(groups->grps[egcQMMM].nr-1))) {
664 /* mark aj as frontier atom */
665 if ( (qm_arr[i]==aj) || (qm_arr[i]==vsite) ){
666 qr->qm[0]->frontatoms[i]=TRUE;
672 gmx_mtop_atomlookup_destroy(alook);
674 /* MM rec creation */
676 mm->scalefactor = ir->scalefactor;
677 mm->nrMMatoms = (mtop->natoms)-(qr->qm[0]->nrQMatoms); /* rest of the atoms */
680 /* MM rec creation */
682 mm->scalefactor = ir->scalefactor;
687 /* these variables get updated in the update QMMMrec */
689 if(qr->nrQMlayers==1){
690 /* with only one layer there is only one initialisation
691 * needed. Multilayer is a bit more complicated as it requires
692 * re-initialisation at every step of the simulation. This is due
693 * to the use of COMMON blocks in the fortran QM subroutines.
695 if (qr->qm[0]->QMmethod<eQMmethodRHF)
697 #ifdef GMX_QMMM_MOPAC
698 /* semi-empiprical 1-layer ONIOM calculation requested (mopac93) */
699 init_mopac(cr,qr->qm[0],qr->mm);
701 gmx_fatal(FARGS,"Semi-empirical QM only supported with Mopac.");
706 /* ab initio calculation requested (gamess/gaussian/ORCA) */
707 #ifdef GMX_QMMM_GAMESS
708 init_gamess(cr,qr->qm[0],qr->mm);
709 #elif defined GMX_QMMM_GAUSSIAN
710 init_gaussian(cr,qr->qm[0],qr->mm);
711 #elif defined GMX_QMMM_ORCA
712 init_orca(cr,qr->qm[0],qr->mm);
714 gmx_fatal(FARGS,"Ab-initio calculation only supported with Gamess, Gaussian or ORCA.");
720 void update_QMMMrec(t_commrec *cr,
727 /* updates the coordinates of both QM atoms and MM atoms and stores
728 * them in the QMMMrec.
730 * NOTE: is NOT yet working if there are no PBC. Also in ns.c, simple
731 * ns needs to be fixed!
734 mm_max=0,mm_nr=0,mm_nr_new,i,j,is,k,shift;
736 *mm_j_particles=NULL,*qm_i_particles=NULL;
752 *parallelMMarray=NULL;
756 c6au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,6));
757 c12au = (HARTREE2KJ*AVOGADRO*pow(BOHR2NM,12));
759 /* every cpu has this array. On every processor we fill this array
760 * with 1's and 0's. 1's indicate the atoms is a QM atom on the
761 * current cpu in a later stage these arrays are all summed. indexes
762 * > 0 indicate the atom is a QM atom. Every node therefore knows
763 * whcih atoms are part of the QM subsystem.
765 /* copy some pointers */
768 QMMMlist = fr->QMMMlist;
772 /* init_pbc(box); needs to be called first, see pbc.h */
773 set_pbc_dd(&pbc,fr->ePBC,DOMAINDECOMP(cr) ? cr->dd : NULL,FALSE,box);
774 /* only in standard (normal) QMMM we need the neighbouring MM
775 * particles to provide a electric field of point charges for the QM
778 if(qr->QMMMscheme==eQMMMschemenormal){ /* also implies 1 QM-layer */
779 /* we NOW create/update a number of QMMMrec entries:
781 * 1) the shiftQM, containing the shifts of the QM atoms
783 * 2) the indexMM array, containing the index of the MM atoms
785 * 3) the shiftMM, containing the shifts of the MM atoms
787 * 4) the shifted coordinates of the MM atoms
789 * the shifts are used for computing virial of the QM/MM particles.
791 qm = qr->qm[0]; /* in case of normal QMMM, there is only one group */
792 snew(qm_i_particles,QMMMlist.nri);
794 qm_i_particles[0].shift = XYZ2IS(0,0,0);
795 for(i=0;i<QMMMlist.nri;i++){
796 qm_i_particles[i].j = QMMMlist.iinr[i];
799 qm_i_particles[i].shift = pbc_dx_aiuc(&pbc,x[QMMMlist.iinr[0]],
800 x[QMMMlist.iinr[i]],dx);
803 /* However, since nri >= nrQMatoms, we do a quicksort, and throw
804 * out double, triple, etc. entries later, as we do for the MM
808 /* compute the shift for the MM j-particles with respect to
809 * the QM i-particle and store them.
812 crd[0] = IS2X(QMMMlist.shift[i]) + IS2X(qm_i_particles[i].shift);
813 crd[1] = IS2Y(QMMMlist.shift[i]) + IS2Y(qm_i_particles[i].shift);
814 crd[2] = IS2Z(QMMMlist.shift[i]) + IS2Z(qm_i_particles[i].shift);
815 is = XYZ2IS(crd[0],crd[1],crd[2]);
816 for(j=QMMMlist.jindex[i];
817 j<QMMMlist.jindex[i+1];
821 srenew(mm_j_particles,mm_max);
824 mm_j_particles[mm_nr].j = QMMMlist.jjnr[j];
825 mm_j_particles[mm_nr].shift = is;
830 /* quicksort QM and MM shift arrays and throw away multiple entries */
834 qsort(qm_i_particles,QMMMlist.nri,
835 (size_t)sizeof(qm_i_particles[0]),
837 qsort(mm_j_particles,mm_nr,
838 (size_t)sizeof(mm_j_particles[0]),
840 /* remove multiples in the QM shift array, since in init_QMMM() we
841 * went through the atom numbers from 0 to md.nr, the order sorted
842 * here matches the one of QMindex already.
845 for(i=0;i<QMMMlist.nri;i++){
846 if (i==0 || qm_i_particles[i].j!=qm_i_particles[i-1].j){
847 qm_i_particles[j++] = qm_i_particles[i];
851 if(qm->bTS||qm->bOPT){
852 /* only remove double entries for the MM array */
853 for(i=0;i<mm_nr;i++){
854 if((i==0 || mm_j_particles[i].j!=mm_j_particles[i-1].j)
855 && !md->bQM[mm_j_particles[i].j]){
856 mm_j_particles[mm_nr_new++] = mm_j_particles[i];
860 /* we also remove mm atoms that have no charges!
861 * actually this is already done in the ns.c
864 for(i=0;i<mm_nr;i++){
865 if((i==0 || mm_j_particles[i].j!=mm_j_particles[i-1].j)
866 && !md->bQM[mm_j_particles[i].j]
867 && (md->chargeA[mm_j_particles[i].j]
868 || (md->chargeB && md->chargeB[mm_j_particles[i].j]))) {
869 mm_j_particles[mm_nr_new++] = mm_j_particles[i];
874 /* store the data retrieved above into the QMMMrec
877 /* Keep the compiler happy,
878 * shift will always be set in the loop for i=0
881 for(i=0;i<qm->nrQMatoms;i++){
882 /* not all qm particles might have appeared as i
883 * particles. They might have been part of the same charge
884 * group for instance.
886 if (qm->indexQM[i] == qm_i_particles[k].j) {
887 shift = qm_i_particles[k++].shift;
889 /* use previous shift, assuming they belong the same charge
893 qm->shiftQM[i] = shift;
896 /* parallel excecution */
898 snew(parallelMMarray,2*(md->nr));
899 /* only MM particles have a 1 at their atomnumber. The second part
900 * of the array contains the shifts. Thus:
901 * p[i]=1/0 depending on wether atomnumber i is a MM particle in the QM
902 * step or not. p[i+md->nr] is the shift of atomnumber i.
904 for(i=0;i<2*(md->nr);i++){
905 parallelMMarray[i]=0;
908 for(i=0;i<mm_nr;i++){
909 parallelMMarray[mm_j_particles[i].j]=1;
910 parallelMMarray[mm_j_particles[i].j+(md->nr)]=mm_j_particles[i].shift;
912 gmx_sumi(md->nr,parallelMMarray,cr);
916 for(i=0;i<md->nr;i++){
917 if(parallelMMarray[i]){
920 srenew(mm->indexMM,mm_max);
921 srenew(mm->shiftMM,mm_max);
923 mm->indexMM[mm_nr] = i;
924 mm->shiftMM[mm_nr++]= parallelMMarray[i+md->nr]/parallelMMarray[i];
928 free(parallelMMarray);
930 /* serial execution */
932 mm->nrMMatoms = mm_nr;
933 srenew(mm->shiftMM,mm_nr);
934 srenew(mm->indexMM,mm_nr);
935 for(i=0;i<mm_nr;i++){
936 mm->indexMM[i]=mm_j_particles[i].j;
937 mm->shiftMM[i]=mm_j_particles[i].shift;
941 /* (re) allocate memory for the MM coordiate array. The QM
942 * coordinate array was already allocated in init_QMMM, and is
943 * only (re)filled in the update_QMMM_coordinates routine
945 srenew(mm->xMM,mm->nrMMatoms);
946 /* now we (re) fill the array that contains the MM charges with
947 * the forcefield charges. If requested, these charges will be
950 srenew(mm->MMcharges,mm->nrMMatoms);
951 for(i=0;i<mm->nrMMatoms;i++){/* no free energy yet */
952 mm->MMcharges[i]=md->chargeA[mm->indexMM[i]]*mm->scalefactor;
954 if(qm->bTS||qm->bOPT){
955 /* store (copy) the c6 and c12 parameters into the MMrec struct
957 srenew(mm->c6,mm->nrMMatoms);
958 srenew(mm->c12,mm->nrMMatoms);
959 for (i=0;i<mm->nrMMatoms;i++)
961 /* nbfp now includes the 6.0/12.0 derivative prefactors */
962 mm->c6[i] = C6(fr->nbfp,top->idef.atnr,md->typeA[mm->indexMM[i]],md->typeA[mm->indexMM[i]])/c6au/6.0;
963 mm->c12[i] =C12(fr->nbfp,top->idef.atnr,md->typeA[mm->indexMM[i]],md->typeA[mm->indexMM[i]])/c12au/12.0;
965 punch_QMMM_excl(qr->qm[0],mm,&(top->excls));
967 /* the next routine fills the coordinate fields in the QMMM rec of
968 * both the qunatum atoms and the MM atoms, using the shifts
972 update_QMMM_coord(x,fr,qr->qm[0],qr->mm);
973 free(qm_i_particles);
974 free(mm_j_particles);
976 else { /* ONIOM */ /* ????? */
978 /* do for each layer */
979 for (j=0;j<qr->nrQMlayers;j++){
981 qm->shiftQM[0]=XYZ2IS(0,0,0);
982 for(i=1;i<qm->nrQMatoms;i++){
983 qm->shiftQM[i] = pbc_dx_aiuc(&pbc,x[qm->indexQM[0]],x[qm->indexQM[i]],
986 update_QMMM_coord(x,fr,qm,mm);
989 } /* update_QMMM_rec */
992 real calculate_QMMM(t_commrec *cr,
999 /* a selection for the QM package depending on which is requested
1000 * (Gaussian, GAMESS-UK, MOPAC or ORCA) needs to be implemented here. Now
1001 * it works through defines.... Not so nice yet
1010 *forces=NULL,*fshift=NULL,
1011 *forces2=NULL, *fshift2=NULL; /* needed for multilayer ONIOM */
1014 /* make a local copy the QMMMrec pointer
1019 /* now different procedures are carried out for one layer ONION and
1020 * normal QMMM on one hand and multilayer oniom on the other
1022 if(qr->QMMMscheme==eQMMMschemenormal || qr->nrQMlayers==1){
1024 snew(forces,(qm->nrQMatoms+mm->nrMMatoms));
1025 snew(fshift,(qm->nrQMatoms+mm->nrMMatoms));
1026 QMener = call_QMroutine(cr,fr,qm,mm,forces,fshift);
1027 for(i=0;i<qm->nrQMatoms;i++){
1029 f[qm->indexQM[i]][j] -= forces[i][j];
1030 fr->fshift[qm->shiftQM[i]][j] += fshift[i][j];
1033 for(i=0;i<mm->nrMMatoms;i++){
1035 f[mm->indexMM[i]][j] -= forces[qm->nrQMatoms+i][j];
1036 fr->fshift[mm->shiftMM[i]][j] += fshift[qm->nrQMatoms+i][j];
1043 else{ /* Multi-layer ONIOM */
1044 for(i=0;i<qr->nrQMlayers-1;i++){ /* last layer is special */
1046 qm2 = copy_QMrec(qr->qm[i+1]);
1048 qm2->nrQMatoms = qm->nrQMatoms;
1050 for(j=0;j<qm2->nrQMatoms;j++){
1052 qm2->xQM[j][k] = qm->xQM[j][k];
1053 qm2->indexQM[j] = qm->indexQM[j];
1054 qm2->atomicnumberQM[j] = qm->atomicnumberQM[j];
1055 qm2->shiftQM[j] = qm->shiftQM[j];
1058 qm2->QMcharge = qm->QMcharge;
1059 /* this layer at the higher level of theory */
1060 srenew(forces,qm->nrQMatoms);
1061 srenew(fshift,qm->nrQMatoms);
1062 /* we need to re-initialize the QMroutine every step... */
1063 init_QMroutine(cr,qm,mm);
1064 QMener += call_QMroutine(cr,fr,qm,mm,forces,fshift);
1066 /* this layer at the lower level of theory */
1067 srenew(forces2,qm->nrQMatoms);
1068 srenew(fshift2,qm->nrQMatoms);
1069 init_QMroutine(cr,qm2,mm);
1070 QMener -= call_QMroutine(cr,fr,qm2,mm,forces2,fshift2);
1071 /* E = E1high-E1low The next layer includes the current layer at
1072 * the lower level of theory, which provides + E2low
1073 * this is similar for gradients
1075 for(i=0;i<qm->nrQMatoms;i++){
1077 f[qm->indexQM[i]][j] -= (forces[i][j]-forces2[i][j]);
1078 fr->fshift[qm->shiftQM[i]][j] += (fshift[i][j]-fshift2[i][j]);
1083 /* now the last layer still needs to be done: */
1084 qm = qr->qm[qr->nrQMlayers-1]; /* C counts from 0 */
1085 init_QMroutine(cr,qm,mm);
1086 srenew(forces,qm->nrQMatoms);
1087 srenew(fshift,qm->nrQMatoms);
1088 QMener += call_QMroutine(cr,fr,qm,mm,forces,fshift);
1089 for(i=0;i<qm->nrQMatoms;i++){
1091 f[qm->indexQM[i]][j] -= forces[i][j];
1092 fr->fshift[qm->shiftQM[i]][j] += fshift[i][j];
1100 if(qm->bTS||qm->bOPT){
1101 /* qm[0] still contains the largest ONIOM QM subsystem
1102 * we take the optimized coordiates and put the in x[]
1104 for(i=0;i<qm->nrQMatoms;i++){
1106 x[qm->indexQM[i]][j] = qm->xQM[i][j];
1111 } /* calculate_QMMM */
1113 /* end of QMMM core routines */