# | Line 73 | Line 73 | void SimSetup::createSim( void ){ | |
---|---|---|
73 | ||
74 | MakeStamps *the_stamps; | |
75 | Globals* the_globals; | |
76 | < | int i; |
76 | > | int i, j; |
77 | ||
78 | // get the stamps and globals; | |
79 | the_stamps = stamps; | |
# | Line 213 | Line 213 | void SimSetup::createSim( void ){ | |
213 | tot_bends = 0; | |
214 | tot_torsions = 0; | |
215 | for( i=0; i<n_components; i++ ){ | |
216 | < | |
217 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
218 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
219 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
216 | > | |
217 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
218 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
219 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
220 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
221 | } | |
222 | ||
# | Line 234 | Line 234 | void SimSetup::createSim( void ){ | |
234 | ||
235 | // divide the molecules among processors here. | |
236 | ||
237 | < | new mpiSimulation( simnfo ); |
237 | > | mpiSimulation* mpiSim = new mpiSimulation( simnfo ); |
238 | ||
239 | < | simnfo->mpiSim->divideLabor( n_components, comp_stamps, components_nmol ); |
239 | > | mpiSim->divideLabor(); |
240 | > | |
241 | > | // set up the local variables |
242 | > | |
243 | > | int localMol, allMol; |
244 | > | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
245 | > | |
246 | > | allMol = 0; |
247 | > | localMol = 0; |
248 | > | local_atoms = 0; |
249 | > | local_bonds = 0; |
250 | > | local_bends = 0; |
251 | > | local_torsions = 0; |
252 | > | for( i=0; i<n_components; i++ ){ |
253 | > | |
254 | > | for( j=0; j<components_nmol[i]; j++ ){ |
255 | > | |
256 | > | if( mpiSim->getMyMolStart() <= allMol && |
257 | > | allMol <= mpiSim->getMyMolEnd() ){ |
258 | > | |
259 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
260 | > | local_bonds += comp_stamps[i]->getNBonds(); |
261 | > | local_bends += comp_stamps[i]->getNBends(); |
262 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
263 | > | localMol++; |
264 | > | } |
265 | > | allMol++; |
266 | > | } |
267 | > | } |
268 | > | local_SRI = local_bonds + local_bends + local_torsions; |
269 | > | |
270 | ||
271 | + | simnfo->n_atoms = mpiSim->getMyNlocal(); |
272 | + | |
273 | + | if( local_atoms != simnfo->n_atoms ){ |
274 | + | sprintf( painCave.errMsg, |
275 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
276 | + | " localAtom (%d) are note equal.\n", |
277 | + | simnfo->n_atoms, |
278 | + | local_atoms ); |
279 | + | painCave.isFatal = 1; |
280 | + | simError(); |
281 | + | } |
282 | + | |
283 | + | simnfo->n_bonds = local_bonds; |
284 | + | simnfo->n_bends = local_bends; |
285 | + | simnfo->n_torsions = local_torsions; |
286 | + | simnfo->n_SRI = local_SRI; |
287 | + | simnfo->n_mol = localMol; |
288 | + | |
289 | + | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
290 | + | MPIcheckPoint(); |
291 | + | |
292 | + | |
293 | #endif // is_mpi | |
294 | ||
295 | ||
# | Line 513 | Line 565 | void SimSetup::makeAtoms( void ){ | |
565 | double ux, uy, uz, uSqr, u; | |
566 | AtomStamp* current_atom; | |
567 | DirectionalAtom* dAtom; | |
568 | < | int molIndex, molStart, molEnd, nMemb; |
568 | > | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
569 | ||
570 | < | |
570 | > | lMolIndex = 0; |
571 | molIndex = 0; | |
572 | index = 0; | |
573 | for( i=0; i<n_components; i++ ){ | |
574 | ||
575 | for( j=0; j<components_nmol[i]; j++ ){ | |
576 | ||
577 | < | molStart = index; |
578 | < | nMemb = comp_stamps[i]->getNAtoms(); |
579 | < | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
577 | > | #ifdef IS_MPI |
578 | > | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
579 | > | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
580 | > | #endif // is_mpi |
581 | ||
582 | < | current_atom = comp_stamps[i]->getAtom( k ); |
583 | < | if( current_atom->haveOrientation() ){ |
584 | < | |
585 | < | dAtom = new DirectionalAtom(index); |
586 | < | simnfo->n_oriented++; |
587 | < | the_atoms[index] = dAtom; |
588 | < | |
589 | < | ux = current_atom->getOrntX(); |
590 | < | uy = current_atom->getOrntY(); |
591 | < | uz = current_atom->getOrntZ(); |
592 | < | |
593 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
594 | < | |
595 | < | u = sqrt( uSqr ); |
596 | < | ux = ux / u; |
597 | < | uy = uy / u; |
598 | < | uz = uz / u; |
599 | < | |
600 | < | dAtom->setSUx( ux ); |
601 | < | dAtom->setSUy( uy ); |
602 | < | dAtom->setSUz( uz ); |
603 | < | } |
604 | < | else{ |
605 | < | the_atoms[index] = new GeneralAtom(index); |
606 | < | } |
607 | < | the_atoms[index]->setType( current_atom->getType() ); |
608 | < | the_atoms[index]->setIndex( index ); |
609 | < | |
610 | < | // increment the index and repeat; |
611 | < | index++; |
612 | < | } |
582 | > | molStart = index; |
583 | > | nMemb = comp_stamps[i]->getNAtoms(); |
584 | > | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
585 | > | |
586 | > | current_atom = comp_stamps[i]->getAtom( k ); |
587 | > | if( current_atom->haveOrientation() ){ |
588 | > | |
589 | > | dAtom = new DirectionalAtom(index); |
590 | > | simnfo->n_oriented++; |
591 | > | the_atoms[index] = dAtom; |
592 | > | |
593 | > | ux = current_atom->getOrntX(); |
594 | > | uy = current_atom->getOrntY(); |
595 | > | uz = current_atom->getOrntZ(); |
596 | > | |
597 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
598 | > | |
599 | > | u = sqrt( uSqr ); |
600 | > | ux = ux / u; |
601 | > | uy = uy / u; |
602 | > | uz = uz / u; |
603 | > | |
604 | > | dAtom->setSUx( ux ); |
605 | > | dAtom->setSUy( uy ); |
606 | > | dAtom->setSUz( uz ); |
607 | > | } |
608 | > | else{ |
609 | > | the_atoms[index] = new GeneralAtom(index); |
610 | > | } |
611 | > | the_atoms[index]->setType( current_atom->getType() ); |
612 | > | the_atoms[index]->setIndex( index ); |
613 | > | |
614 | > | // increment the index and repeat; |
615 | > | index++; |
616 | > | } |
617 | > | |
618 | > | molEnd = index -1; |
619 | > | the_molecules[lMolIndex].setNMembers( nMemb ); |
620 | > | the_molecules[lMolIndex].setStartAtom( molStart ); |
621 | > | the_molecules[lMolIndex].setEndAtom( molEnd ); |
622 | > | the_molecules[lMolIndex].setStampID( i ); |
623 | > | lMolIndex++; |
624 | ||
625 | < | molEnd = index -1; |
626 | < | the_molecules[molIndex].setNMembers( nMemb ); |
627 | < | the_molecules[molIndex].setStartAtom( molStart ); |
628 | < | the_molecules[molIndex].setEndAtom( molEnd ); |
625 | > | #ifdef IS_MPI |
626 | > | } |
627 | > | #endif //is_mpi |
628 | > | |
629 | molIndex++; | |
566 | – | |
630 | } | |
631 | } | |
632 | ||
# | Line 572 | Line 635 | void SimSetup::makeBonds( void ){ | |
635 | ||
636 | void SimSetup::makeBonds( void ){ | |
637 | ||
638 | < | int i, j, k, index, offset; |
638 | > | int i, j, k, index, offset, molIndex; |
639 | bond_pair* the_bonds; | |
640 | BondStamp* current_bond; | |
641 | ||
642 | the_bonds = new bond_pair[tot_bonds]; | |
643 | index = 0; | |
644 | offset = 0; | |
645 | + | molIndex = 0; |
646 | for( i=0; i<n_components; i++ ){ | |
647 | ||
648 | for( j=0; j<components_nmol[i]; j++ ){ | |
649 | ||
650 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
651 | < | |
652 | < | current_bond = comp_stamps[i]->getBond( k ); |
653 | < | the_bonds[index].a = current_bond->getA() + offset; |
654 | < | the_bonds[index].b = current_bond->getB() + offset; |
655 | < | |
656 | < | the_excludes[index].i = the_bonds[index].a; |
657 | < | the_excludes[index].j = the_bonds[index].b; |
658 | < | |
659 | < | // increment the index and repeat; |
660 | < | index++; |
650 | > | #ifdef IS_MPI |
651 | > | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
652 | > | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
653 | > | #endif // is_mpi |
654 | > | |
655 | > | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
656 | > | |
657 | > | current_bond = comp_stamps[i]->getBond( k ); |
658 | > | the_bonds[index].a = current_bond->getA() + offset; |
659 | > | the_bonds[index].b = current_bond->getB() + offset; |
660 | > | |
661 | > | the_excludes[index].i = the_bonds[index].a; |
662 | > | the_excludes[index].j = the_bonds[index].b; |
663 | > | |
664 | > | // increment the index and repeat; |
665 | > | index++; |
666 | > | } |
667 | > | offset += comp_stamps[i]->getNAtoms(); |
668 | > | |
669 | > | #ifdef IS_MPI |
670 | } | |
671 | < | offset += comp_stamps[i]->getNAtoms(); |
672 | < | } |
671 | > | #endif is_mpi |
672 | > | |
673 | > | molIndex++; |
674 | > | } |
675 | } | |
676 | ||
677 | the_ff->initializeBonds( the_bonds ); | |
# | Line 604 | Line 679 | void SimSetup::makeBends( void ){ | |
679 | ||
680 | void SimSetup::makeBends( void ){ | |
681 | ||
682 | < | int i, j, k, index, offset; |
682 | > | int i, j, k, index, offset, molIndex; |
683 | bend_set* the_bends; | |
684 | BendStamp* current_bend; | |
685 | ||
686 | the_bends = new bend_set[tot_bends]; | |
687 | index = 0; | |
688 | offset = 0; | |
689 | + | molIndex = 0; |
690 | for( i=0; i<n_components; i++ ){ | |
691 | ||
692 | for( j=0; j<components_nmol[i]; j++ ){ | |
693 | ||
694 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
694 | > | #ifdef IS_MPI |
695 | > | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
696 | > | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
697 | > | #endif // is_mpi |
698 | ||
699 | < | current_bend = comp_stamps[i]->getBend( k ); |
700 | < | the_bends[index].a = current_bend->getA() + offset; |
701 | < | the_bends[index].b = current_bend->getB() + offset; |
702 | < | the_bends[index].c = current_bend->getC() + offset; |
703 | < | |
704 | < | the_excludes[index + tot_bonds].i = the_bends[index].a; |
705 | < | the_excludes[index + tot_bonds].j = the_bends[index].c; |
706 | < | |
707 | < | // increment the index and repeat; |
708 | < | index++; |
699 | > | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
700 | > | |
701 | > | current_bend = comp_stamps[i]->getBend( k ); |
702 | > | the_bends[index].a = current_bend->getA() + offset; |
703 | > | the_bends[index].b = current_bend->getB() + offset; |
704 | > | the_bends[index].c = current_bend->getC() + offset; |
705 | > | |
706 | > | the_excludes[index + tot_bonds].i = the_bends[index].a; |
707 | > | the_excludes[index + tot_bonds].j = the_bends[index].c; |
708 | > | |
709 | > | // increment the index and repeat; |
710 | > | index++; |
711 | > | } |
712 | > | offset += comp_stamps[i]->getNAtoms(); |
713 | > | |
714 | > | #ifdef IS_MPI |
715 | } | |
716 | < | offset += comp_stamps[i]->getNAtoms(); |
716 | > | #endif //is_mpi |
717 | > | |
718 | > | molIndex++; |
719 | } | |
720 | } | |
721 | ||
# | Line 637 | Line 724 | void SimSetup::makeTorsions( void ){ | |
724 | ||
725 | void SimSetup::makeTorsions( void ){ | |
726 | ||
727 | < | int i, j, k, index, offset; |
727 | > | int i, j, k, index, offset, molIndex; |
728 | torsion_set* the_torsions; | |
729 | TorsionStamp* current_torsion; | |
730 | ||
731 | the_torsions = new torsion_set[tot_torsions]; | |
732 | index = 0; | |
733 | offset = 0; | |
734 | + | molIndex = 0; |
735 | for( i=0; i<n_components; i++ ){ | |
736 | ||
737 | for( j=0; j<components_nmol[i]; j++ ){ | |
738 | ||
739 | + | #ifdef IS_MPI |
740 | + | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
741 | + | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
742 | + | #endif // is_mpi |
743 | + | |
744 | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ | |
745 | ||
746 | current_torsion = comp_stamps[i]->getTorsion( k ); | |
# | Line 663 | Line 756 | void SimSetup::makeTorsions( void ){ | |
756 | index++; | |
757 | } | |
758 | offset += comp_stamps[i]->getNAtoms(); | |
759 | + | |
760 | + | #ifdef IS_MPI |
761 | + | } |
762 | + | #endif //is_mpi |
763 | + | |
764 | + | molIndex++; |
765 | } | |
766 | } | |
767 |
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