# | Line 88 | Line 88 | void SimSetup::createSim( void ){ | |
---|---|---|
88 | ||
89 | ||
90 | ||
91 | < | if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
92 | < | else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
93 | < | else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
91 | > | if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
92 | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); | |
93 | else{ | |
94 | sprintf( painCave.errMsg, | |
# | Line 248 | Line 246 | void SimSetup::createSim( void ){ | |
246 | ||
247 | int localMol, allMol; | |
248 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
249 | + | |
250 | + | int* mol2proc = mpiSim->getMolToProcMap(); |
251 | + | int* molCompType = mpiSim->getMolComponentType(); |
252 | ||
253 | allMol = 0; | |
254 | localMol = 0; | |
# | Line 259 | Line 260 | void SimSetup::createSim( void ){ | |
260 | ||
261 | for( j=0; j<components_nmol[i]; j++ ){ | |
262 | ||
263 | < | if( mpiSim->getMyMolStart() <= allMol && |
263 | < | allMol <= mpiSim->getMyMolEnd() ){ |
263 | > | if( mol2proc[j] == worldRank ){ |
264 | ||
265 | local_atoms += comp_stamps[i]->getNAtoms(); | |
266 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 279 | Line 279 | void SimSetup::createSim( void ){ | |
279 | if( local_atoms != simnfo->n_atoms ){ | |
280 | sprintf( painCave.errMsg, | |
281 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
282 | < | " localAtom (%d) are note equal.\n", |
282 | > | " localAtom (%d) are not equal.\n", |
283 | simnfo->n_atoms, | |
284 | local_atoms ); | |
285 | painCave.isFatal = 1; | |
# | Line 304 | Line 304 | void SimSetup::createSim( void ){ | |
304 | Atom::createArrays(simnfo->n_atoms); | |
305 | the_atoms = new Atom*[simnfo->n_atoms]; | |
306 | the_molecules = new Molecule[simnfo->n_mol]; | |
307 | + | int molIndex; |
308 | + | |
309 | + | // initialize the molecule's stampID's |
310 | + | |
311 | + | #ifdef IS_MPI |
312 | + | |
313 | + | |
314 | + | molIndex = 0; |
315 | + | for(i=0; i<mpiSim->getTotNmol(); i++){ |
316 | + | |
317 | + | if(mol2proc[i] == worldRank ){ |
318 | + | the_molecules[molIndex].setStampID( molCompType[i] ); |
319 | + | molIndex++; |
320 | + | } |
321 | + | } |
322 | ||
323 | + | #else // is_mpi |
324 | + | |
325 | + | molIndex = 0; |
326 | + | for(i=0; i<n_components; i++){ |
327 | + | for(j=0; j<components_nmol[i]; j++ ){ |
328 | + | the_molecules[molIndex].setStampID( i ); |
329 | + | molIndex++; |
330 | + | } |
331 | + | } |
332 | + | |
333 | ||
334 | + | #endif // is_mpi |
335 | + | |
336 | + | |
337 | if( simnfo->n_SRI ){ | |
338 | < | the_sris = new SRI*[simnfo->n_SRI]; |
339 | < | the_excludes = new int[2 * simnfo->n_SRI]; |
338 | > | Exclude::createArray(simnfo->n_SRI); |
339 | > | the_excludes = new Exclude*[simnfo->n_SRI]; |
340 | simnfo->globalExcludes = new int; | |
341 | simnfo->n_exclude = tot_SRI; | |
342 | } | |
343 | else{ | |
344 | ||
345 | < | the_excludes = new int[2]; |
346 | < | the_excludes[0] = 0; |
347 | < | the_excludes[1] = 0; |
345 | > | Exclude::createArray( 1 ); |
346 | > | the_excludes = new Exclude*; |
347 | > | the_excludes[0] = new Exclude(0); |
348 | > | the_excludes[0]->setPair( 0,0 ); |
349 | simnfo->globalExcludes = new int; | |
350 | simnfo->globalExcludes[0] = 0; | |
351 | < | |
323 | < | simnfo->n_exclude = 1; |
351 | > | simnfo->n_exclude = 0; |
352 | } | |
353 | ||
354 | // set the arrays into the SimInfo object | |
355 | ||
356 | simnfo->atoms = the_atoms; | |
357 | < | simnfo->sr_interactions = the_sris; |
357 | > | simnfo->molecules = the_molecules; |
358 | simnfo->nGlobalExcludes = 0; | |
359 | simnfo->excludes = the_excludes; | |
360 | ||
361 | ||
362 | // get some of the tricky things that may still be in the globals | |
363 | ||
336 | – | if( simnfo->n_dipoles ){ |
337 | – | |
338 | – | if( !the_globals->haveRRF() ){ |
339 | – | sprintf( painCave.errMsg, |
340 | – | "SimSetup Error, system has dipoles, but no rRF was set.\n"); |
341 | – | painCave.isFatal = 1; |
342 | – | simError(); |
343 | – | } |
344 | – | if( !the_globals->haveDielectric() ){ |
345 | – | sprintf( painCave.errMsg, |
346 | – | "SimSetup Error, system has dipoles, but no" |
347 | – | " dielectric was set.\n" ); |
348 | – | painCave.isFatal = 1; |
349 | – | simError(); |
350 | – | } |
351 | – | |
352 | – | simnfo->rRF = the_globals->getRRF(); |
353 | – | simnfo->dielectric = the_globals->getDielectric(); |
354 | – | } |
355 | – | |
356 | – | #ifdef IS_MPI |
357 | – | strcpy( checkPointMsg, "rRf and dielectric check out" ); |
358 | – | MPIcheckPoint(); |
359 | – | #endif // is_mpi |
364 | ||
365 | if( the_globals->haveBox() ){ | |
366 | simnfo->box_x = the_globals->getBox(); | |
# | Line 407 | Line 411 | void SimSetup::createSim( void ){ | |
411 | ||
412 | the_ff->setSimInfo( simnfo ); | |
413 | ||
414 | < | makeAtoms(); |
414 | > | makeMolecules(); |
415 | simnfo->identArray = new int[simnfo->n_atoms]; | |
416 | for(i=0; i<simnfo->n_atoms; i++){ | |
417 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
418 | } | |
419 | ||
420 | < | if( tot_bonds ){ |
421 | < | makeBonds(); |
422 | < | } |
423 | < | |
424 | < | if( tot_bends ){ |
425 | < | makeBends(); |
426 | < | } |
427 | < | |
428 | < | if( tot_torsions ){ |
429 | < | makeTorsions(); |
430 | < | } |
431 | < | |
420 | > | if (the_globals->getUseRF() ) { |
421 | > | simnfo->useReactionField = 1; |
422 | > | |
423 | > | if( !the_globals->haveECR() ){ |
424 | > | sprintf( painCave.errMsg, |
425 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
426 | > | "box length for the electrostaticCutoffRadius.\n" |
427 | > | "I hope you have a very fast processor!\n"); |
428 | > | painCave.isFatal = 0; |
429 | > | simError(); |
430 | > | double smallest; |
431 | > | smallest = simnfo->box_x; |
432 | > | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
433 | > | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
434 | > | simnfo->ecr = 0.5 * smallest; |
435 | > | } else { |
436 | > | simnfo->ecr = the_globals->getECR(); |
437 | > | } |
438 | ||
439 | + | if( !the_globals->haveEST() ){ |
440 | + | sprintf( painCave.errMsg, |
441 | + | "SimSetup Warning: using default value of 0.05 * the " |
442 | + | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
443 | + | ); |
444 | + | painCave.isFatal = 0; |
445 | + | simError(); |
446 | + | simnfo->est = 0.05 * simnfo->ecr; |
447 | + | } else { |
448 | + | simnfo->est = the_globals->getEST(); |
449 | + | } |
450 | + | |
451 | + | if(!the_globals->haveDielectric() ){ |
452 | + | sprintf( painCave.errMsg, |
453 | + | "SimSetup Error: You are trying to use Reaction Field without" |
454 | + | "setting a dielectric constant!\n" |
455 | + | ); |
456 | + | painCave.isFatal = 1; |
457 | + | simError(); |
458 | + | } |
459 | + | simnfo->dielectric = the_globals->getDielectric(); |
460 | + | } else { |
461 | + | if (simnfo->n_dipoles) { |
462 | + | |
463 | + | if( !the_globals->haveECR() ){ |
464 | + | sprintf( painCave.errMsg, |
465 | + | "SimSetup Warning: using default value of 1/2 the smallest" |
466 | + | "box length for the electrostaticCutoffRadius.\n" |
467 | + | "I hope you have a very fast processor!\n"); |
468 | + | painCave.isFatal = 0; |
469 | + | simError(); |
470 | + | double smallest; |
471 | + | smallest = simnfo->box_x; |
472 | + | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
473 | + | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
474 | + | simnfo->ecr = 0.5 * smallest; |
475 | + | } else { |
476 | + | simnfo->ecr = the_globals->getECR(); |
477 | + | } |
478 | + | |
479 | + | if( !the_globals->haveEST() ){ |
480 | + | sprintf( painCave.errMsg, |
481 | + | "SimSetup Warning: using default value of 5% of the" |
482 | + | "electrostaticCutoffRadius for the " |
483 | + | "electrostaticSkinThickness\n" |
484 | + | ); |
485 | + | painCave.isFatal = 0; |
486 | + | simError(); |
487 | + | simnfo->est = 0.05 * simnfo->ecr; |
488 | + | } else { |
489 | + | simnfo->est = the_globals->getEST(); |
490 | + | } |
491 | + | } |
492 | + | } |
493 | ||
494 | + | #ifdef IS_MPI |
495 | + | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
496 | + | MPIcheckPoint(); |
497 | + | #endif // is_mpi |
498 | ||
431 | – | |
432 | – | |
499 | if( the_globals->haveInitialConfig() ){ | |
500 | ||
501 | InitializeFromFile* fileInit; | |
# | Line 587 | Line 653 | void SimSetup::createSim( void ){ | |
653 | ||
654 | // new AllLong( simnfo ); | |
655 | ||
590 | – | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
591 | – | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
656 | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); | |
657 | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); | |
658 | ||
# | Line 620 | Line 684 | void SimSetup::createSim( void ){ | |
684 | #endif // is_mpi | |
685 | } | |
686 | ||
623 | – | void SimSetup::makeAtoms( void ){ |
687 | ||
688 | < | int i, j, k, index; |
626 | < | double ux, uy, uz, uSqr, u; |
627 | < | AtomStamp* current_atom; |
688 | > | void SimSetup::makeMolecules( void ){ |
689 | ||
690 | + | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
691 | + | molInit info; |
692 | DirectionalAtom* dAtom; | |
693 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
693 | > | LinkedAssign* extras; |
694 | > | LinkedAssign* current_extra; |
695 | > | AtomStamp* currentAtom; |
696 | > | BondStamp* currentBond; |
697 | > | BendStamp* currentBend; |
698 | > | TorsionStamp* currentTorsion; |
699 | ||
700 | < | lMolIndex = 0; |
701 | < | molIndex = 0; |
702 | < | index = 0; |
635 | < | for( i=0; i<n_components; i++ ){ |
700 | > | bond_pair* theBonds; |
701 | > | bend_set* theBends; |
702 | > | torsion_set* theTorsions; |
703 | ||
704 | < | for( j=0; j<components_nmol[i]; j++ ){ |
704 | > | |
705 | > | //init the forceField paramters |
706 | ||
707 | < | #ifdef IS_MPI |
640 | < | if( mpiSim->getMyMolStart() <= molIndex && |
641 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
642 | < | #endif // is_mpi |
707 | > | the_ff->readParams(); |
708 | ||
709 | < | molStart = index; |
710 | < | nMemb = comp_stamps[i]->getNAtoms(); |
646 | < | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
647 | < | |
648 | < | current_atom = comp_stamps[i]->getAtom( k ); |
649 | < | if( current_atom->haveOrientation() ){ |
650 | < | |
651 | < | dAtom = new DirectionalAtom(index); |
652 | < | simnfo->n_oriented++; |
653 | < | the_atoms[index] = dAtom; |
654 | < | |
655 | < | ux = current_atom->getOrntX(); |
656 | < | uy = current_atom->getOrntY(); |
657 | < | uz = current_atom->getOrntZ(); |
658 | < | |
659 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
660 | < | |
661 | < | u = sqrt( uSqr ); |
662 | < | ux = ux / u; |
663 | < | uy = uy / u; |
664 | < | uz = uz / u; |
665 | < | |
666 | < | dAtom->setSUx( ux ); |
667 | < | dAtom->setSUy( uy ); |
668 | < | dAtom->setSUz( uz ); |
669 | < | } |
670 | < | else{ |
671 | < | the_atoms[index] = new GeneralAtom(index); |
672 | < | } |
673 | < | the_atoms[index]->setType( current_atom->getType() ); |
674 | < | the_atoms[index]->setIndex( index ); |
675 | < | |
676 | < | // increment the index and repeat; |
677 | < | index++; |
678 | < | } |
679 | < | |
680 | < | molEnd = index -1; |
681 | < | the_molecules[lMolIndex].setNMembers( nMemb ); |
682 | < | the_molecules[lMolIndex].setStartAtom( molStart ); |
683 | < | the_molecules[lMolIndex].setEndAtom( molEnd ); |
684 | < | the_molecules[lMolIndex].setStampID( i ); |
685 | < | lMolIndex++; |
709 | > | |
710 | > | // init the atoms |
711 | ||
712 | < | #ifdef IS_MPI |
713 | < | } |
714 | < | #endif //is_mpi |
715 | < | |
716 | < | molIndex++; |
692 | < | } |
693 | < | } |
694 | < | |
695 | < | #ifdef IS_MPI |
696 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
712 | > | double ux, uy, uz, u, uSqr; |
713 | > | |
714 | > | atomOffset = 0; |
715 | > | excludeOffset = 0; |
716 | > | for(i=0; i<simnfo->n_mol; i++){ |
717 | ||
718 | < | delete[] globalIndex; |
718 | > | stampID = the_molecules[i].getStampID(); |
719 | ||
720 | < | mpiSim->mpiRefresh(); |
721 | < | #endif //IS_MPI |
722 | < | |
723 | < | the_ff->initializeAtoms(); |
724 | < | } |
720 | > | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
721 | > | info.nBonds = comp_stamps[stampID]->getNBonds(); |
722 | > | info.nBends = comp_stamps[stampID]->getNBends(); |
723 | > | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
724 | > | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
725 | ||
726 | < | void SimSetup::makeBonds( void ){ |
726 | > | info.myAtoms = &the_atoms[atomOffset]; |
727 | > | info.myExcludes = &the_excludes[excludeOffset]; |
728 | > | info.myBonds = new Bond*[info.nBonds]; |
729 | > | info.myBends = new Bend*[info.nBends]; |
730 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
731 | ||
732 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
733 | < | bond_pair* the_bonds; |
734 | < | BondStamp* current_bond; |
735 | < | |
736 | < | the_bonds = new bond_pair[tot_bonds]; |
737 | < | index = 0; |
738 | < | offset = 0; |
739 | < | molIndex = 0; |
740 | < | |
741 | < | for( i=0; i<n_components; i++ ){ |
718 | < | |
719 | < | for( j=0; j<components_nmol[i]; j++ ){ |
720 | < | |
721 | < | #ifdef IS_MPI |
722 | < | if( mpiSim->getMyMolStart() <= molIndex && |
723 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
724 | < | #endif // is_mpi |
732 | > | theBonds = new bond_pair[info.nBonds]; |
733 | > | theBends = new bend_set[info.nBends]; |
734 | > | theTorsions = new torsion_set[info.nTorsions]; |
735 | > | |
736 | > | // make the Atoms |
737 | > | |
738 | > | for(j=0; j<info.nAtoms; j++){ |
739 | > | |
740 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
741 | > | if( currentAtom->haveOrientation() ){ |
742 | ||
743 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
744 | < | |
745 | < | current_bond = comp_stamps[i]->getBond( k ); |
746 | < | the_bonds[index].a = current_bond->getA() + offset; |
747 | < | the_bonds[index].b = current_bond->getB() + offset; |
748 | < | |
749 | < | exI = the_bonds[index].a; |
750 | < | exJ = the_bonds[index].b; |
751 | < | |
752 | < | // exclude_I must always be the smaller of the pair |
753 | < | if( exI > exJ ){ |
754 | < | tempEx = exI; |
755 | < | exI = exJ; |
756 | < | exJ = tempEx; |
757 | < | } |
758 | < | |
759 | < | |
743 | > | dAtom = new DirectionalAtom(j + atomOffset); |
744 | > | simnfo->n_oriented++; |
745 | > | info.myAtoms[j] = dAtom; |
746 | > | |
747 | > | ux = currentAtom->getOrntX(); |
748 | > | uy = currentAtom->getOrntY(); |
749 | > | uz = currentAtom->getOrntZ(); |
750 | > | |
751 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
752 | > | |
753 | > | u = sqrt( uSqr ); |
754 | > | ux = ux / u; |
755 | > | uy = uy / u; |
756 | > | uz = uz / u; |
757 | > | |
758 | > | dAtom->setSUx( ux ); |
759 | > | dAtom->setSUy( uy ); |
760 | > | dAtom->setSUz( uz ); |
761 | > | } |
762 | > | else{ |
763 | > | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
764 | > | } |
765 | > | info.myAtoms[j]->setType( currentAtom->getType() ); |
766 | > | |
767 | #ifdef IS_MPI | |
768 | < | |
769 | < | the_excludes[index*2] = |
770 | < | the_atoms[exI]->getGlobalIndex() + 1; |
771 | < | the_excludes[index*2 + 1] = |
772 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
773 | < | |
774 | < | #else // isn't MPI |
775 | < | |
752 | < | the_excludes[index*2] = exI + 1; |
753 | < | the_excludes[index*2 + 1] = exJ + 1; |
754 | < | // fortran index from 1 (hence the +1 in the indexing) |
755 | < | #endif //is_mpi |
756 | < | |
757 | < | // increment the index and repeat; |
758 | < | index++; |
759 | < | } |
760 | < | offset += comp_stamps[i]->getNAtoms(); |
761 | < | |
762 | < | #ifdef IS_MPI |
763 | < | } |
764 | < | #endif //is_mpi |
768 | > | |
769 | > | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
770 | > | |
771 | > | #endif // is_mpi |
772 | > | } |
773 | > | |
774 | > | // make the bonds |
775 | > | for(j=0; j<info.nBonds; j++){ |
776 | ||
777 | < | molIndex++; |
778 | < | } |
779 | < | } |
777 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
778 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
779 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
780 | ||
781 | < | the_ff->initializeBonds( the_bonds ); |
782 | < | } |
781 | > | exI = theBonds[i].a; |
782 | > | exJ = theBonds[i].b; |
783 | ||
784 | < | void SimSetup::makeBends( void ){ |
785 | < | |
786 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
787 | < | bend_set* the_bends; |
788 | < | BendStamp* current_bend; |
789 | < | LinkedAssign* extras; |
779 | < | LinkedAssign* current_extra; |
780 | < | |
781 | < | |
782 | < | the_bends = new bend_set[tot_bends]; |
783 | < | index = 0; |
784 | < | offset = 0; |
785 | < | molIndex = 0; |
786 | < | for( i=0; i<n_components; i++ ){ |
787 | < | |
788 | < | for( j=0; j<components_nmol[i]; j++ ){ |
789 | < | |
784 | > | // exclude_I must always be the smaller of the pair |
785 | > | if( exI > exJ ){ |
786 | > | tempEx = exI; |
787 | > | exI = exJ; |
788 | > | exJ = tempEx; |
789 | > | } |
790 | #ifdef IS_MPI | |
791 | < | if( mpiSim->getMyMolStart() <= molIndex && |
792 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
793 | < | #endif // is_mpi |
791 | > | tempEx = exI; |
792 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
793 | > | tempEx = exJ; |
794 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
795 | > | |
796 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
797 | > | #else // isn't MPI |
798 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
799 | > | #endif //is_mpi |
800 | > | } |
801 | > | excludeOffset += info.nBonds; |
802 | ||
803 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
803 | > | //make the bends |
804 | > | for(j=0; j<info.nBends; j++){ |
805 | > | |
806 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
807 | > | theBends[j].a = currentBend->getA() + atomOffset; |
808 | > | theBends[j].b = currentBend->getB() + atomOffset; |
809 | > | theBends[j].c = currentBend->getC() + atomOffset; |
810 | ||
811 | < | current_bend = comp_stamps[i]->getBend( k ); |
798 | < | the_bends[index].a = current_bend->getA() + offset; |
799 | < | the_bends[index].b = current_bend->getB() + offset; |
800 | < | the_bends[index].c = current_bend->getC() + offset; |
801 | < | |
802 | < | if( current_bend->haveExtras() ){ |
811 | > | if( currentBend->haveExtras() ){ |
812 | ||
813 | < | extras = current_bend->getExtras(); |
814 | < | current_extra = extras; |
813 | > | extras = currentBend->getExtras(); |
814 | > | current_extra = extras; |
815 | ||
816 | < | while( current_extra != NULL ){ |
817 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
816 | > | while( current_extra != NULL ){ |
817 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
818 | ||
819 | < | switch( current_extra->getType() ){ |
819 | > | switch( current_extra->getType() ){ |
820 | > | |
821 | > | case 0: |
822 | > | theBends[j].ghost = |
823 | > | current_extra->getInt() + atomOffset; |
824 | > | theBends[j].isGhost = 1; |
825 | > | break; |
826 | ||
827 | < | case 0: |
828 | < | the_bends[index].ghost = |
829 | < | current_extra->getInt() + offset; |
830 | < | the_bends[index].isGhost = 1; |
831 | < | break; |
817 | < | |
818 | < | case 1: |
819 | < | the_bends[index].ghost = |
820 | < | (int)current_extra->getDouble() + offset; |
821 | < | the_bends[index].isGhost = 1; |
822 | < | break; |
823 | < | |
824 | < | default: |
825 | < | sprintf( painCave.errMsg, |
826 | < | "SimSetup Error: ghostVectorSource was neiter a " |
827 | < | "double nor an int.\n" |
828 | < | "-->Bend[%d] in %s\n", |
829 | < | k, comp_stamps[i]->getID() ); |
830 | < | painCave.isFatal = 1; |
831 | < | simError(); |
832 | < | } |
833 | < | } |
827 | > | case 1: |
828 | > | theBends[j].ghost = |
829 | > | (int)current_extra->getDouble() + atomOffset; |
830 | > | theBends[j].isGhost = 1; |
831 | > | break; |
832 | ||
833 | < | else{ |
834 | < | |
835 | < | sprintf( painCave.errMsg, |
836 | < | "SimSetup Error: unhandled bend assignment:\n" |
837 | < | " -->%s in Bend[%d] in %s\n", |
838 | < | current_extra->getlhs(), |
839 | < | k, comp_stamps[i]->getID() ); |
840 | < | painCave.isFatal = 1; |
843 | < | simError(); |
844 | < | } |
845 | < | |
846 | < | current_extra = current_extra->getNext(); |
833 | > | default: |
834 | > | sprintf( painCave.errMsg, |
835 | > | "SimSetup Error: ghostVectorSource was neiter a " |
836 | > | "double nor an int.\n" |
837 | > | "-->Bend[%d] in %s\n", |
838 | > | j, comp_stamps[stampID]->getID() ); |
839 | > | painCave.isFatal = 1; |
840 | > | simError(); |
841 | } | |
842 | } | |
843 | ||
850 | – | if( !the_bends[index].isGhost ){ |
851 | – | |
852 | – | exI = the_bends[index].a; |
853 | – | exJ = the_bends[index].c; |
854 | – | } |
844 | else{ | |
845 | ||
846 | < | exI = the_bends[index].a; |
847 | < | exJ = the_bends[index].b; |
846 | > | sprintf( painCave.errMsg, |
847 | > | "SimSetup Error: unhandled bend assignment:\n" |
848 | > | " -->%s in Bend[%d] in %s\n", |
849 | > | current_extra->getlhs(), |
850 | > | j, comp_stamps[stampID]->getID() ); |
851 | > | painCave.isFatal = 1; |
852 | > | simError(); |
853 | } | |
854 | ||
855 | < | // exclude_I must always be the smaller of the pair |
856 | < | if( exI > exJ ){ |
857 | < | tempEx = exI; |
858 | < | exI = exJ; |
859 | < | exJ = tempEx; |
860 | < | } |
855 | > | current_extra = current_extra->getNext(); |
856 | > | } |
857 | > | } |
858 | > | |
859 | > | if( !theBends[j].isGhost ){ |
860 | > | |
861 | > | exI = theBends[j].a; |
862 | > | exJ = theBends[j].c; |
863 | > | } |
864 | > | else{ |
865 | > | |
866 | > | exI = theBends[j].a; |
867 | > | exJ = theBends[j].b; |
868 | > | } |
869 | > | |
870 | > | // exclude_I must always be the smaller of the pair |
871 | > | if( exI > exJ ){ |
872 | > | tempEx = exI; |
873 | > | exI = exJ; |
874 | > | exJ = tempEx; |
875 | > | } |
876 | > | #ifdef IS_MPI |
877 | > | tempEx = exI; |
878 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
879 | > | tempEx = exJ; |
880 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
881 | > | |
882 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
883 | > | #else // isn't MPI |
884 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
885 | > | #endif //is_mpi |
886 | > | } |
887 | > | excludeOffset += info.nBends; |
888 | ||
889 | + | for(j=0; j<info.nTorsions; j++){ |
890 | + | |
891 | + | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
892 | + | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
893 | + | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
894 | + | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
895 | + | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
896 | + | |
897 | + | exI = theTorsions[j].a; |
898 | + | exJ = theTorsions[j].d; |
899 | ||
900 | + | // exclude_I must always be the smaller of the pair |
901 | + | if( exI > exJ ){ |
902 | + | tempEx = exI; |
903 | + | exI = exJ; |
904 | + | exJ = tempEx; |
905 | + | } |
906 | #ifdef IS_MPI | |
907 | < | |
908 | < | the_excludes[(index + tot_bonds)*2] = |
909 | < | the_atoms[exI]->getGlobalIndex() + 1; |
910 | < | the_excludes[(index + tot_bonds)*2 + 1] = |
911 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
912 | < | |
907 | > | tempEx = exI; |
908 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
909 | > | tempEx = exJ; |
910 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
911 | > | |
912 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
913 | #else // isn't MPI | |
914 | < | |
878 | < | the_excludes[(index + tot_bonds)*2] = exI + 1; |
879 | < | the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
880 | < | // fortran index from 1 (hence the +1 in the indexing) |
914 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
915 | #endif //is_mpi | |
882 | – | |
883 | – | |
884 | – | // increment the index and repeat; |
885 | – | index++; |
886 | – | } |
887 | – | offset += comp_stamps[i]->getNAtoms(); |
888 | – | |
889 | – | #ifdef IS_MPI |
890 | – | } |
891 | – | #endif //is_mpi |
892 | – | |
893 | – | molIndex++; |
916 | } | |
917 | < | } |
917 | > | excludeOffset += info.nTorsions; |
918 | ||
919 | < | #ifdef IS_MPI |
920 | < | sprintf( checkPointMsg, |
899 | < | "Successfully created the bends list.\n" ); |
900 | < | MPIcheckPoint(); |
901 | < | #endif // is_mpi |
902 | < | |
919 | > | |
920 | > | // send the arrays off to the forceField for init. |
921 | ||
922 | < | the_ff->initializeBends( the_bends ); |
923 | < | } |
922 | > | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
923 | > | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
924 | > | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
925 | > | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
926 | ||
907 | – | void SimSetup::makeTorsions( void ){ |
927 | ||
928 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
929 | < | torsion_set* the_torsions; |
930 | < | TorsionStamp* current_torsion; |
931 | < | |
932 | < | the_torsions = new torsion_set[tot_torsions]; |
914 | < | index = 0; |
915 | < | offset = 0; |
916 | < | molIndex = 0; |
917 | < | for( i=0; i<n_components; i++ ){ |
918 | < | |
919 | < | for( j=0; j<components_nmol[i]; j++ ){ |
920 | < | |
921 | < | #ifdef IS_MPI |
922 | < | if( mpiSim->getMyMolStart() <= molIndex && |
923 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
924 | < | #endif // is_mpi |
925 | < | |
926 | < | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
927 | < | |
928 | < | current_torsion = comp_stamps[i]->getTorsion( k ); |
929 | < | the_torsions[index].a = current_torsion->getA() + offset; |
930 | < | the_torsions[index].b = current_torsion->getB() + offset; |
931 | < | the_torsions[index].c = current_torsion->getC() + offset; |
932 | < | the_torsions[index].d = current_torsion->getD() + offset; |
933 | < | |
934 | < | exI = the_torsions[index].a; |
935 | < | exJ = the_torsions[index].d; |
936 | < | |
937 | < | |
938 | < | // exclude_I must always be the smaller of the pair |
939 | < | if( exI > exJ ){ |
940 | < | tempEx = exI; |
941 | < | exI = exJ; |
942 | < | exJ = tempEx; |
943 | < | } |
944 | < | |
945 | < | |
946 | < | #ifdef IS_MPI |
947 | < | |
948 | < | the_excludes[(index + tot_bonds + tot_bends)*2] = |
949 | < | the_atoms[exI]->getGlobalIndex() + 1; |
950 | < | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
951 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
952 | < | |
953 | < | #else // isn't MPI |
954 | < | |
955 | < | the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
956 | < | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
957 | < | // fortran indexes from 1 (hence the +1 in the indexing) |
958 | < | #endif //is_mpi |
959 | < | |
960 | < | |
961 | < | // increment the index and repeat; |
962 | < | index++; |
963 | < | } |
964 | < | offset += comp_stamps[i]->getNAtoms(); |
965 | < | |
966 | < | #ifdef IS_MPI |
967 | < | } |
968 | < | #endif //is_mpi |
969 | < | |
970 | < | molIndex++; |
971 | < | } |
928 | > | the_molecules[i].initialize( info ); |
929 | > | atomOffset += info.nAtoms; |
930 | > | delete[] theBonds; |
931 | > | delete[] theBends; |
932 | > | delete[] theTorsions; |
933 | } | |
934 | ||
935 | < | the_ff->initializeTorsions( the_torsions ); |
935 | > | // clean up the forcefield |
936 | > | the_ff->calcRcut(); |
937 | > | the_ff->cleanMe(); |
938 | } | |
939 | ||
940 | void SimSetup::initFromBass( void ){ |
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