# | 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; | |
329 | – | simnfo->sr_interactions = the_sris; |
357 | simnfo->nGlobalExcludes = 0; | |
358 | simnfo->excludes = the_excludes; | |
359 | ||
# | Line 383 | Line 410 | void SimSetup::createSim( void ){ | |
410 | ||
411 | the_ff->setSimInfo( simnfo ); | |
412 | ||
413 | < | makeAtoms(); |
413 | > | makeMolecules(); |
414 | simnfo->identArray = new int[simnfo->n_atoms]; | |
415 | for(i=0; i<simnfo->n_atoms; i++){ | |
416 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
417 | } | |
418 | ||
392 | – | if( tot_bonds ){ |
393 | – | makeBonds(); |
394 | – | } |
395 | – | |
396 | – | if( tot_bends ){ |
397 | – | makeBends(); |
398 | – | } |
399 | – | |
400 | – | if( tot_torsions ){ |
401 | – | makeTorsions(); |
402 | – | } |
403 | – | |
404 | – | |
419 | if (the_globals->getUseRF() ) { | |
420 | simnfo->useReactionField = 1; | |
421 | ||
# | Line 638 | Line 652 | void SimSetup::createSim( void ){ | |
652 | ||
653 | // new AllLong( simnfo ); | |
654 | ||
641 | – | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 | – | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
655 | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); | |
656 | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); | |
657 | ||
# | Line 671 | Line 683 | void SimSetup::createSim( void ){ | |
683 | #endif // is_mpi | |
684 | } | |
685 | ||
674 | – | void SimSetup::makeAtoms( void ){ |
686 | ||
687 | < | int i, j, k, index; |
677 | < | double ux, uy, uz, uSqr, u; |
678 | < | AtomStamp* current_atom; |
687 | > | void SimSetup::makeMolecules( void ){ |
688 | ||
689 | + | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
690 | + | molInit info; |
691 | DirectionalAtom* dAtom; | |
692 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
692 | > | LinkedAssign* extras; |
693 | > | LinkedAssign* current_extra; |
694 | > | AtomStamp* currentAtom; |
695 | > | BondStamp* currentBond; |
696 | > | BendStamp* currentBend; |
697 | > | TorsionStamp* currentTorsion; |
698 | ||
699 | < | lMolIndex = 0; |
700 | < | molIndex = 0; |
701 | < | index = 0; |
686 | < | for( i=0; i<n_components; i++ ){ |
699 | > | bond_pair* theBonds; |
700 | > | bend_set* theBends; |
701 | > | torsion_set* theTorsions; |
702 | ||
703 | < | for( j=0; j<components_nmol[i]; j++ ){ |
703 | > | |
704 | > | //init the forceField paramters |
705 | ||
706 | < | #ifdef IS_MPI |
691 | < | if( mpiSim->getMyMolStart() <= molIndex && |
692 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
693 | < | #endif // is_mpi |
706 | > | the_ff->readParams(); |
707 | ||
708 | < | molStart = index; |
709 | < | nMemb = comp_stamps[i]->getNAtoms(); |
697 | < | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
698 | < | |
699 | < | current_atom = comp_stamps[i]->getAtom( k ); |
700 | < | if( current_atom->haveOrientation() ){ |
701 | < | |
702 | < | dAtom = new DirectionalAtom(index); |
703 | < | simnfo->n_oriented++; |
704 | < | the_atoms[index] = dAtom; |
705 | < | |
706 | < | ux = current_atom->getOrntX(); |
707 | < | uy = current_atom->getOrntY(); |
708 | < | uz = current_atom->getOrntZ(); |
709 | < | |
710 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
711 | < | |
712 | < | u = sqrt( uSqr ); |
713 | < | ux = ux / u; |
714 | < | uy = uy / u; |
715 | < | uz = uz / u; |
716 | < | |
717 | < | dAtom->setSUx( ux ); |
718 | < | dAtom->setSUy( uy ); |
719 | < | dAtom->setSUz( uz ); |
720 | < | } |
721 | < | else{ |
722 | < | the_atoms[index] = new GeneralAtom(index); |
723 | < | } |
724 | < | the_atoms[index]->setType( current_atom->getType() ); |
725 | < | the_atoms[index]->setIndex( index ); |
726 | < | |
727 | < | // increment the index and repeat; |
728 | < | index++; |
729 | < | } |
730 | < | |
731 | < | molEnd = index -1; |
732 | < | the_molecules[lMolIndex].setNMembers( nMemb ); |
733 | < | the_molecules[lMolIndex].setStartAtom( molStart ); |
734 | < | the_molecules[lMolIndex].setEndAtom( molEnd ); |
735 | < | the_molecules[lMolIndex].setStampID( i ); |
736 | < | lMolIndex++; |
708 | > | |
709 | > | // init the atoms |
710 | ||
711 | < | #ifdef IS_MPI |
712 | < | } |
713 | < | #endif //is_mpi |
714 | < | |
715 | < | molIndex++; |
716 | < | } |
717 | < | } |
711 | > | double ux, uy, uz, u, uSqr; |
712 | > | |
713 | > | atomOffset = 0; |
714 | > | excludeOffset = 0; |
715 | > | for(i=0; i<simnfo->n_mol; i++){ |
716 | > | |
717 | > | stampID = the_molecules[i].getStampID(); |
718 | > | |
719 | > | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
720 | > | info.nBonds = comp_stamps[stampID]->getNBonds(); |
721 | > | info.nBends = comp_stamps[stampID]->getNBends(); |
722 | > | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
723 | > | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
724 | ||
725 | < | #ifdef IS_MPI |
726 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
727 | < | |
728 | < | delete[] globalIndex; |
725 | > | info.myAtoms = &the_atoms[atomOffset]; |
726 | > | info.myExcludes = &the_excludes[excludeOffset]; |
727 | > | info.myBonds = new Bond*[info.nBonds]; |
728 | > | info.myBends = new Bend*[info.nBends]; |
729 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
730 | ||
731 | < | mpiSim->mpiRefresh(); |
732 | < | #endif //IS_MPI |
733 | < | |
734 | < | the_ff->initializeAtoms(); |
735 | < | } |
736 | < | |
737 | < | void SimSetup::makeBonds( void ){ |
738 | < | |
739 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
740 | < | bond_pair* the_bonds; |
761 | < | BondStamp* current_bond; |
762 | < | |
763 | < | the_bonds = new bond_pair[tot_bonds]; |
764 | < | index = 0; |
765 | < | offset = 0; |
766 | < | molIndex = 0; |
767 | < | |
768 | < | for( i=0; i<n_components; i++ ){ |
769 | < | |
770 | < | for( j=0; j<components_nmol[i]; j++ ){ |
771 | < | |
772 | < | #ifdef IS_MPI |
773 | < | if( mpiSim->getMyMolStart() <= molIndex && |
774 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
775 | < | #endif // is_mpi |
731 | > | theBonds = new bond_pair[info.nBonds]; |
732 | > | theBends = new bend_set[info.nBends]; |
733 | > | theTorsions = new torsion_set[info.nTorsions]; |
734 | > | |
735 | > | // make the Atoms |
736 | > | |
737 | > | for(j=0; j<info.nAtoms; j++){ |
738 | > | |
739 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
740 | > | if( currentAtom->haveOrientation() ){ |
741 | ||
742 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
743 | < | |
744 | < | current_bond = comp_stamps[i]->getBond( k ); |
780 | < | the_bonds[index].a = current_bond->getA() + offset; |
781 | < | the_bonds[index].b = current_bond->getB() + offset; |
782 | < | |
783 | < | exI = the_bonds[index].a; |
784 | < | exJ = the_bonds[index].b; |
785 | < | |
786 | < | // exclude_I must always be the smaller of the pair |
787 | < | if( exI > exJ ){ |
788 | < | tempEx = exI; |
789 | < | exI = exJ; |
790 | < | exJ = tempEx; |
791 | < | } |
792 | < | |
793 | < | |
794 | < | #ifdef IS_MPI |
795 | < | |
796 | < | the_excludes[index*2] = |
797 | < | the_atoms[exI]->getGlobalIndex() + 1; |
798 | < | the_excludes[index*2 + 1] = |
799 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
800 | < | |
801 | < | #else // isn't MPI |
802 | < | |
803 | < | the_excludes[index*2] = exI + 1; |
804 | < | the_excludes[index*2 + 1] = exJ + 1; |
805 | < | // fortran index from 1 (hence the +1 in the indexing) |
806 | < | #endif //is_mpi |
807 | < | |
808 | < | // increment the index and repeat; |
809 | < | index++; |
810 | < | } |
811 | < | offset += comp_stamps[i]->getNAtoms(); |
742 | > | dAtom = new DirectionalAtom(j + atomOffset); |
743 | > | simnfo->n_oriented++; |
744 | > | info.myAtoms[j] = dAtom; |
745 | ||
746 | < | #ifdef IS_MPI |
746 | > | ux = currentAtom->getOrntX(); |
747 | > | uy = currentAtom->getOrntY(); |
748 | > | uz = currentAtom->getOrntZ(); |
749 | > | |
750 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
751 | > | |
752 | > | u = sqrt( uSqr ); |
753 | > | ux = ux / u; |
754 | > | uy = uy / u; |
755 | > | uz = uz / u; |
756 | > | |
757 | > | dAtom->setSUx( ux ); |
758 | > | dAtom->setSUy( uy ); |
759 | > | dAtom->setSUz( uz ); |
760 | } | |
761 | < | #endif //is_mpi |
761 | > | else{ |
762 | > | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
763 | > | } |
764 | > | info.myAtoms[j]->setType( currentAtom->getType() ); |
765 | > | |
766 | > | #ifdef IS_MPI |
767 | ||
768 | < | molIndex++; |
769 | < | } |
770 | < | } |
768 | > | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
769 | > | |
770 | > | #endif // is_mpi |
771 | > | } |
772 | > | |
773 | > | // make the bonds |
774 | > | for(j=0; j<info.nBonds; j++){ |
775 | > | |
776 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
777 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
778 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
779 | ||
780 | < | the_ff->initializeBonds( the_bonds ); |
781 | < | } |
780 | > | exI = theBonds[i].a; |
781 | > | exJ = theBonds[i].b; |
782 | ||
783 | < | void SimSetup::makeBends( void ){ |
784 | < | |
785 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
786 | < | bend_set* the_bends; |
787 | < | BendStamp* current_bend; |
788 | < | LinkedAssign* extras; |
789 | < | LinkedAssign* current_extra; |
790 | < | |
791 | < | |
792 | < | the_bends = new bend_set[tot_bends]; |
793 | < | index = 0; |
794 | < | offset = 0; |
795 | < | molIndex = 0; |
796 | < | for( i=0; i<n_components; i++ ){ |
797 | < | |
798 | < | for( j=0; j<components_nmol[i]; j++ ){ |
799 | < | |
800 | < | #ifdef IS_MPI |
842 | < | if( mpiSim->getMyMolStart() <= molIndex && |
843 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
844 | < | #endif // is_mpi |
783 | > | // exclude_I must always be the smaller of the pair |
784 | > | if( exI > exJ ){ |
785 | > | tempEx = exI; |
786 | > | exI = exJ; |
787 | > | exJ = tempEx; |
788 | > | } |
789 | > | #ifdef IS_MPI |
790 | > | tempEx = exI; |
791 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
792 | > | tempEx = exJ; |
793 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
794 | > | |
795 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
796 | > | #else // isn't MPI |
797 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
798 | > | #endif //is_mpi |
799 | > | } |
800 | > | excludeOffset += info.nBonds; |
801 | ||
802 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
802 | > | //make the bends |
803 | > | for(j=0; j<info.nBends; j++){ |
804 | > | |
805 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
806 | > | theBends[j].a = currentBend->getA() + atomOffset; |
807 | > | theBends[j].b = currentBend->getB() + atomOffset; |
808 | > | theBends[j].c = currentBend->getC() + atomOffset; |
809 | ||
810 | < | current_bend = comp_stamps[i]->getBend( k ); |
849 | < | the_bends[index].a = current_bend->getA() + offset; |
850 | < | the_bends[index].b = current_bend->getB() + offset; |
851 | < | the_bends[index].c = current_bend->getC() + offset; |
852 | < | |
853 | < | if( current_bend->haveExtras() ){ |
810 | > | if( currentBend->haveExtras() ){ |
811 | ||
812 | < | extras = current_bend->getExtras(); |
813 | < | current_extra = extras; |
812 | > | extras = currentBend->getExtras(); |
813 | > | current_extra = extras; |
814 | ||
815 | < | while( current_extra != NULL ){ |
816 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
815 | > | while( current_extra != NULL ){ |
816 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
817 | ||
818 | < | switch( current_extra->getType() ){ |
818 | > | switch( current_extra->getType() ){ |
819 | > | |
820 | > | case 0: |
821 | > | theBends[j].ghost = |
822 | > | current_extra->getInt() + atomOffset; |
823 | > | theBends[j].isGhost = 1; |
824 | > | break; |
825 | ||
826 | < | case 0: |
827 | < | the_bends[index].ghost = |
828 | < | current_extra->getInt() + offset; |
829 | < | the_bends[index].isGhost = 1; |
830 | < | break; |
868 | < | |
869 | < | case 1: |
870 | < | the_bends[index].ghost = |
871 | < | (int)current_extra->getDouble() + offset; |
872 | < | the_bends[index].isGhost = 1; |
873 | < | break; |
874 | < | |
875 | < | default: |
876 | < | sprintf( painCave.errMsg, |
877 | < | "SimSetup Error: ghostVectorSource was neiter a " |
878 | < | "double nor an int.\n" |
879 | < | "-->Bend[%d] in %s\n", |
880 | < | k, comp_stamps[i]->getID() ); |
881 | < | painCave.isFatal = 1; |
882 | < | simError(); |
883 | < | } |
884 | < | } |
826 | > | case 1: |
827 | > | theBends[j].ghost = |
828 | > | (int)current_extra->getDouble() + atomOffset; |
829 | > | theBends[j].isGhost = 1; |
830 | > | break; |
831 | ||
832 | < | else{ |
833 | < | |
834 | < | sprintf( painCave.errMsg, |
835 | < | "SimSetup Error: unhandled bend assignment:\n" |
836 | < | " -->%s in Bend[%d] in %s\n", |
837 | < | current_extra->getlhs(), |
838 | < | k, comp_stamps[i]->getID() ); |
839 | < | painCave.isFatal = 1; |
894 | < | simError(); |
895 | < | } |
896 | < | |
897 | < | current_extra = current_extra->getNext(); |
832 | > | default: |
833 | > | sprintf( painCave.errMsg, |
834 | > | "SimSetup Error: ghostVectorSource was neiter a " |
835 | > | "double nor an int.\n" |
836 | > | "-->Bend[%d] in %s\n", |
837 | > | j, comp_stamps[stampID]->getID() ); |
838 | > | painCave.isFatal = 1; |
839 | > | simError(); |
840 | } | |
841 | } | |
842 | ||
901 | – | if( !the_bends[index].isGhost ){ |
902 | – | |
903 | – | exI = the_bends[index].a; |
904 | – | exJ = the_bends[index].c; |
905 | – | } |
843 | else{ | |
844 | ||
845 | < | exI = the_bends[index].a; |
846 | < | exJ = the_bends[index].b; |
845 | > | sprintf( painCave.errMsg, |
846 | > | "SimSetup Error: unhandled bend assignment:\n" |
847 | > | " -->%s in Bend[%d] in %s\n", |
848 | > | current_extra->getlhs(), |
849 | > | j, comp_stamps[stampID]->getID() ); |
850 | > | painCave.isFatal = 1; |
851 | > | simError(); |
852 | } | |
853 | ||
854 | < | // exclude_I must always be the smaller of the pair |
913 | < | if( exI > exJ ){ |
914 | < | tempEx = exI; |
915 | < | exI = exJ; |
916 | < | exJ = tempEx; |
917 | < | } |
918 | < | |
919 | < | |
920 | < | #ifdef IS_MPI |
921 | < | |
922 | < | the_excludes[(index + tot_bonds)*2] = |
923 | < | the_atoms[exI]->getGlobalIndex() + 1; |
924 | < | the_excludes[(index + tot_bonds)*2 + 1] = |
925 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
926 | < | |
927 | < | #else // isn't MPI |
928 | < | |
929 | < | the_excludes[(index + tot_bonds)*2] = exI + 1; |
930 | < | the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
931 | < | // fortran index from 1 (hence the +1 in the indexing) |
932 | < | #endif //is_mpi |
933 | < | |
934 | < | |
935 | < | // increment the index and repeat; |
936 | < | index++; |
854 | > | current_extra = current_extra->getNext(); |
855 | } | |
938 | – | offset += comp_stamps[i]->getNAtoms(); |
939 | – | |
940 | – | #ifdef IS_MPI |
856 | } | |
857 | < | #endif //is_mpi |
858 | < | |
859 | < | molIndex++; |
860 | < | } |
861 | < | } |
862 | < | |
857 | > | |
858 | > | if( !theBends[j].isGhost ){ |
859 | > | |
860 | > | exI = theBends[j].a; |
861 | > | exJ = theBends[j].c; |
862 | > | } |
863 | > | else{ |
864 | > | |
865 | > | exI = theBends[j].a; |
866 | > | exJ = theBends[j].b; |
867 | > | } |
868 | > | |
869 | > | // exclude_I must always be the smaller of the pair |
870 | > | if( exI > exJ ){ |
871 | > | tempEx = exI; |
872 | > | exI = exJ; |
873 | > | exJ = tempEx; |
874 | > | } |
875 | #ifdef IS_MPI | |
876 | < | sprintf( checkPointMsg, |
877 | < | "Successfully created the bends list.\n" ); |
878 | < | MPIcheckPoint(); |
879 | < | #endif // is_mpi |
880 | < | |
876 | > | tempEx = exI; |
877 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
878 | > | tempEx = exJ; |
879 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
880 | > | |
881 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
882 | > | #else // isn't MPI |
883 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
884 | > | #endif //is_mpi |
885 | > | } |
886 | > | excludeOffset += info.nBends; |
887 | ||
888 | < | the_ff->initializeBends( the_bends ); |
889 | < | } |
888 | > | for(j=0; j<info.nTorsions; j++){ |
889 | > | |
890 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
891 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
892 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
893 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
894 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
895 | > | |
896 | > | exI = theTorsions[j].a; |
897 | > | exJ = theTorsions[j].d; |
898 | ||
899 | < | void SimSetup::makeTorsions( void ){ |
900 | < | |
901 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
902 | < | torsion_set* the_torsions; |
903 | < | TorsionStamp* current_torsion; |
904 | < | |
964 | < | the_torsions = new torsion_set[tot_torsions]; |
965 | < | index = 0; |
966 | < | offset = 0; |
967 | < | molIndex = 0; |
968 | < | for( i=0; i<n_components; i++ ){ |
969 | < | |
970 | < | for( j=0; j<components_nmol[i]; j++ ){ |
971 | < | |
899 | > | // exclude_I must always be the smaller of the pair |
900 | > | if( exI > exJ ){ |
901 | > | tempEx = exI; |
902 | > | exI = exJ; |
903 | > | exJ = tempEx; |
904 | > | } |
905 | #ifdef IS_MPI | |
906 | < | if( mpiSim->getMyMolStart() <= molIndex && |
907 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
908 | < | #endif // is_mpi |
909 | < | |
910 | < | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
911 | < | |
979 | < | current_torsion = comp_stamps[i]->getTorsion( k ); |
980 | < | the_torsions[index].a = current_torsion->getA() + offset; |
981 | < | the_torsions[index].b = current_torsion->getB() + offset; |
982 | < | the_torsions[index].c = current_torsion->getC() + offset; |
983 | < | the_torsions[index].d = current_torsion->getD() + offset; |
984 | < | |
985 | < | exI = the_torsions[index].a; |
986 | < | exJ = the_torsions[index].d; |
987 | < | |
988 | < | |
989 | < | // exclude_I must always be the smaller of the pair |
990 | < | if( exI > exJ ){ |
991 | < | tempEx = exI; |
992 | < | exI = exJ; |
993 | < | exJ = tempEx; |
994 | < | } |
995 | < | |
996 | < | |
997 | < | #ifdef IS_MPI |
998 | < | |
999 | < | the_excludes[(index + tot_bonds + tot_bends)*2] = |
1000 | < | the_atoms[exI]->getGlobalIndex() + 1; |
1001 | < | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1002 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1003 | < | |
906 | > | tempEx = exI; |
907 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
908 | > | tempEx = exJ; |
909 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
910 | > | |
911 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
912 | #else // isn't MPI | |
913 | < | |
1006 | < | the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1007 | < | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1008 | < | // fortran indexes from 1 (hence the +1 in the indexing) |
913 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
914 | #endif //is_mpi | |
915 | < | |
915 | > | } |
916 | > | excludeOffset += info.nTorsions; |
917 | ||
918 | < | // increment the index and repeat; |
919 | < | index++; |
1014 | < | } |
1015 | < | offset += comp_stamps[i]->getNAtoms(); |
918 | > | |
919 | > | // send the arrays off to the forceField for init. |
920 | ||
921 | < | #ifdef IS_MPI |
922 | < | } |
923 | < | #endif //is_mpi |
921 | > | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
922 | > | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
923 | > | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
924 | > | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
925 | ||
926 | < | molIndex++; |
927 | < | } |
926 | > | |
927 | > | the_molecules[i].initialize( info ); |
928 | > | atomOffset += info.nAtoms; |
929 | > | delete[] theBonds; |
930 | > | delete[] theBends; |
931 | > | delete[] theTorsions; |
932 | } | |
933 | ||
934 | < | the_ff->initializeTorsions( the_torsions ); |
934 | > | // clean up the forcefield |
935 | > | the_ff->calcRcut(); |
936 | > | the_ff->cleanMe(); |
937 | } | |
938 | ||
939 | void SimSetup::initFromBass( void ){ |
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