# | 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 353 | Line 405 | void SimSetup::createSim( void ){ | |
405 | ||
406 | ||
407 | ||
408 | < | // if( the_globals->haveInitialConfig() ){ |
409 | < | // InitializeFromFile* fileInit; |
410 | < | // fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
411 | < | |
412 | < | // fileInit->read_xyz( simnfo ); // default velocities on |
408 | > | if( the_globals->haveInitialConfig() ){ |
409 | > | |
410 | > | InitializeFromFile* fileInit; |
411 | > | #ifdef IS_MPI // is_mpi |
412 | > | if( worldRank == 0 ){ |
413 | > | #endif //is_mpi |
414 | > | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
415 | > | #ifdef IS_MPI |
416 | > | }else fileInit = new InitializeFromFile( NULL ); |
417 | > | #endif |
418 | > | fileInit->read_xyz( simnfo ); // default velocities on |
419 | ||
420 | < | // delete fileInit; |
421 | < | // } |
422 | < | // else{ |
420 | > | delete fileInit; |
421 | > | } |
422 | > | else{ |
423 | ||
424 | #ifdef IS_MPI | |
425 | ||
# | Line 376 | Line 434 | void SimSetup::createSim( void ){ | |
434 | ||
435 | initFromBass(); | |
436 | ||
437 | < | #endif // is_mpi |
438 | < | |
437 | > | |
438 | > | #endif |
439 | > | } |
440 | > | |
441 | #ifdef IS_MPI | |
442 | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); | |
443 | MPIcheckPoint(); | |
# | Line 387 | Line 447 | void SimSetup::createSim( void ){ | |
447 | ||
448 | ||
449 | ||
450 | < | // } |
450 | > | |
451 | ||
452 | #ifdef IS_MPI | |
453 | if( worldRank == 0 ){ | |
# | Line 513 | Line 573 | void SimSetup::makeAtoms( void ){ | |
573 | double ux, uy, uz, uSqr, u; | |
574 | AtomStamp* current_atom; | |
575 | DirectionalAtom* dAtom; | |
576 | < | int molIndex, molStart, molEnd, nMemb; |
576 | > | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
577 | ||
578 | < | |
578 | > | lMolIndex = 0; |
579 | molIndex = 0; | |
580 | index = 0; | |
581 | for( i=0; i<n_components; i++ ){ | |
582 | ||
583 | for( j=0; j<components_nmol[i]; j++ ){ | |
584 | ||
585 | < | molStart = index; |
586 | < | nMemb = comp_stamps[i]->getNAtoms(); |
587 | < | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
585 | > | #ifdef IS_MPI |
586 | > | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
587 | > | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
588 | > | #endif // is_mpi |
589 | ||
590 | < | current_atom = comp_stamps[i]->getAtom( k ); |
591 | < | if( current_atom->haveOrientation() ){ |
592 | < | |
593 | < | dAtom = new DirectionalAtom(index); |
594 | < | simnfo->n_oriented++; |
595 | < | the_atoms[index] = dAtom; |
596 | < | |
597 | < | ux = current_atom->getOrntX(); |
598 | < | uy = current_atom->getOrntY(); |
599 | < | uz = current_atom->getOrntZ(); |
600 | < | |
601 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
602 | < | |
603 | < | u = sqrt( uSqr ); |
604 | < | ux = ux / u; |
605 | < | uy = uy / u; |
606 | < | uz = uz / u; |
607 | < | |
608 | < | dAtom->setSUx( ux ); |
609 | < | dAtom->setSUy( uy ); |
610 | < | dAtom->setSUz( uz ); |
611 | < | } |
612 | < | else{ |
613 | < | the_atoms[index] = new GeneralAtom(index); |
614 | < | } |
615 | < | the_atoms[index]->setType( current_atom->getType() ); |
616 | < | the_atoms[index]->setIndex( index ); |
617 | < | |
618 | < | // increment the index and repeat; |
619 | < | index++; |
620 | < | } |
590 | > | molStart = index; |
591 | > | nMemb = comp_stamps[i]->getNAtoms(); |
592 | > | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
593 | > | |
594 | > | current_atom = comp_stamps[i]->getAtom( k ); |
595 | > | if( current_atom->haveOrientation() ){ |
596 | > | |
597 | > | dAtom = new DirectionalAtom(index); |
598 | > | simnfo->n_oriented++; |
599 | > | the_atoms[index] = dAtom; |
600 | > | |
601 | > | ux = current_atom->getOrntX(); |
602 | > | uy = current_atom->getOrntY(); |
603 | > | uz = current_atom->getOrntZ(); |
604 | > | |
605 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
606 | > | |
607 | > | u = sqrt( uSqr ); |
608 | > | ux = ux / u; |
609 | > | uy = uy / u; |
610 | > | uz = uz / u; |
611 | > | |
612 | > | dAtom->setSUx( ux ); |
613 | > | dAtom->setSUy( uy ); |
614 | > | dAtom->setSUz( uz ); |
615 | > | } |
616 | > | else{ |
617 | > | the_atoms[index] = new GeneralAtom(index); |
618 | > | } |
619 | > | the_atoms[index]->setType( current_atom->getType() ); |
620 | > | the_atoms[index]->setIndex( index ); |
621 | > | |
622 | > | // increment the index and repeat; |
623 | > | index++; |
624 | > | } |
625 | > | |
626 | > | molEnd = index -1; |
627 | > | the_molecules[lMolIndex].setNMembers( nMemb ); |
628 | > | the_molecules[lMolIndex].setStartAtom( molStart ); |
629 | > | the_molecules[lMolIndex].setEndAtom( molEnd ); |
630 | > | the_molecules[lMolIndex].setStampID( i ); |
631 | > | lMolIndex++; |
632 | ||
633 | < | molEnd = index -1; |
634 | < | the_molecules[molIndex].setNMembers( nMemb ); |
635 | < | the_molecules[molIndex].setStartAtom( molStart ); |
636 | < | the_molecules[molIndex].setEndAtom( molEnd ); |
633 | > | #ifdef IS_MPI |
634 | > | } |
635 | > | #endif //is_mpi |
636 | > | |
637 | molIndex++; | |
566 | – | |
638 | } | |
639 | } | |
640 | ||
# | Line 572 | Line 643 | void SimSetup::makeBonds( void ){ | |
643 | ||
644 | void SimSetup::makeBonds( void ){ | |
645 | ||
646 | < | int i, j, k, index, offset; |
646 | > | int i, j, k, index, offset, molIndex; |
647 | bond_pair* the_bonds; | |
648 | BondStamp* current_bond; | |
649 | ||
650 | the_bonds = new bond_pair[tot_bonds]; | |
651 | index = 0; | |
652 | offset = 0; | |
653 | + | molIndex = 0; |
654 | for( i=0; i<n_components; i++ ){ | |
655 | ||
656 | for( j=0; j<components_nmol[i]; j++ ){ | |
657 | ||
658 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
659 | < | |
660 | < | current_bond = comp_stamps[i]->getBond( k ); |
661 | < | the_bonds[index].a = current_bond->getA() + offset; |
662 | < | the_bonds[index].b = current_bond->getB() + offset; |
663 | < | |
664 | < | the_excludes[index].i = the_bonds[index].a; |
665 | < | the_excludes[index].j = the_bonds[index].b; |
666 | < | |
667 | < | // increment the index and repeat; |
668 | < | index++; |
658 | > | #ifdef IS_MPI |
659 | > | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
660 | > | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
661 | > | #endif // is_mpi |
662 | > | |
663 | > | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
664 | > | |
665 | > | current_bond = comp_stamps[i]->getBond( k ); |
666 | > | the_bonds[index].a = current_bond->getA() + offset; |
667 | > | the_bonds[index].b = current_bond->getB() + offset; |
668 | > | |
669 | > | the_excludes[index].i = the_bonds[index].a; |
670 | > | the_excludes[index].j = the_bonds[index].b; |
671 | > | |
672 | > | // increment the index and repeat; |
673 | > | index++; |
674 | > | } |
675 | > | offset += comp_stamps[i]->getNAtoms(); |
676 | > | |
677 | > | #ifdef IS_MPI |
678 | } | |
679 | < | offset += comp_stamps[i]->getNAtoms(); |
680 | < | } |
679 | > | #endif is_mpi |
680 | > | |
681 | > | molIndex++; |
682 | > | } |
683 | } | |
684 | ||
685 | the_ff->initializeBonds( the_bonds ); | |
# | Line 604 | Line 687 | void SimSetup::makeBends( void ){ | |
687 | ||
688 | void SimSetup::makeBends( void ){ | |
689 | ||
690 | < | int i, j, k, index, offset; |
690 | > | int i, j, k, index, offset, molIndex; |
691 | bend_set* the_bends; | |
692 | BendStamp* current_bend; | |
693 | ||
694 | the_bends = new bend_set[tot_bends]; | |
695 | index = 0; | |
696 | offset = 0; | |
697 | + | molIndex = 0; |
698 | for( i=0; i<n_components; i++ ){ | |
699 | ||
700 | for( j=0; j<components_nmol[i]; j++ ){ | |
701 | ||
702 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
702 | > | #ifdef IS_MPI |
703 | > | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
704 | > | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
705 | > | #endif // is_mpi |
706 | ||
707 | < | current_bend = comp_stamps[i]->getBend( k ); |
708 | < | the_bends[index].a = current_bend->getA() + offset; |
709 | < | the_bends[index].b = current_bend->getB() + offset; |
710 | < | the_bends[index].c = current_bend->getC() + offset; |
711 | < | |
712 | < | the_excludes[index + tot_bonds].i = the_bends[index].a; |
713 | < | the_excludes[index + tot_bonds].j = the_bends[index].c; |
714 | < | |
715 | < | // increment the index and repeat; |
716 | < | index++; |
707 | > | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
708 | > | |
709 | > | current_bend = comp_stamps[i]->getBend( k ); |
710 | > | the_bends[index].a = current_bend->getA() + offset; |
711 | > | the_bends[index].b = current_bend->getB() + offset; |
712 | > | the_bends[index].c = current_bend->getC() + offset; |
713 | > | |
714 | > | the_excludes[index + tot_bonds].i = the_bends[index].a; |
715 | > | the_excludes[index + tot_bonds].j = the_bends[index].c; |
716 | > | |
717 | > | // increment the index and repeat; |
718 | > | index++; |
719 | > | } |
720 | > | offset += comp_stamps[i]->getNAtoms(); |
721 | > | |
722 | > | #ifdef IS_MPI |
723 | } | |
724 | < | offset += comp_stamps[i]->getNAtoms(); |
724 | > | #endif //is_mpi |
725 | > | |
726 | > | molIndex++; |
727 | } | |
728 | } | |
729 | ||
# | Line 637 | Line 732 | void SimSetup::makeTorsions( void ){ | |
732 | ||
733 | void SimSetup::makeTorsions( void ){ | |
734 | ||
735 | < | int i, j, k, index, offset; |
735 | > | int i, j, k, index, offset, molIndex; |
736 | torsion_set* the_torsions; | |
737 | TorsionStamp* current_torsion; | |
738 | ||
739 | the_torsions = new torsion_set[tot_torsions]; | |
740 | index = 0; | |
741 | offset = 0; | |
742 | + | molIndex = 0; |
743 | for( i=0; i<n_components; i++ ){ | |
744 | ||
745 | for( j=0; j<components_nmol[i]; j++ ){ | |
746 | ||
747 | + | #ifdef IS_MPI |
748 | + | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
749 | + | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
750 | + | #endif // is_mpi |
751 | + | |
752 | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ | |
753 | ||
754 | current_torsion = comp_stamps[i]->getTorsion( k ); | |
# | Line 663 | Line 764 | void SimSetup::makeTorsions( void ){ | |
764 | index++; | |
765 | } | |
766 | offset += comp_stamps[i]->getNAtoms(); | |
767 | + | |
768 | + | #ifdef IS_MPI |
769 | + | } |
770 | + | #endif //is_mpi |
771 | + | |
772 | + | molIndex++; |
773 | } | |
774 | } | |
775 |
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