# | 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 241 | Line 239 | void SimSetup::createSim( void ){ | |
239 | ||
240 | ||
241 | globalIndex = mpiSim->divideLabor(); | |
244 | – | |
245 | – | |
242 | ||
243 | // set up the local variables | |
244 | ||
245 | int localMol, allMol; | |
246 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
247 | + | |
248 | + | int* mol2proc = mpiSim->getMolToProcMap(); |
249 | + | int* molCompType = mpiSim->getMolComponentType(); |
250 | ||
251 | allMol = 0; | |
252 | localMol = 0; | |
# | Line 259 | Line 258 | void SimSetup::createSim( void ){ | |
258 | ||
259 | for( j=0; j<components_nmol[i]; j++ ){ | |
260 | ||
261 | < | if( mpiSim->getMyMolStart() <= allMol && |
263 | < | allMol <= mpiSim->getMyMolEnd() ){ |
261 | > | if( mol2proc[j] == worldRank ){ |
262 | ||
263 | local_atoms += comp_stamps[i]->getNAtoms(); | |
264 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 279 | Line 277 | void SimSetup::createSim( void ){ | |
277 | if( local_atoms != simnfo->n_atoms ){ | |
278 | sprintf( painCave.errMsg, | |
279 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
280 | < | " localAtom (%d) are note equal.\n", |
280 | > | " localAtom (%d) are not equal.\n", |
281 | simnfo->n_atoms, | |
282 | local_atoms ); | |
283 | painCave.isFatal = 1; | |
# | Line 304 | Line 302 | void SimSetup::createSim( void ){ | |
302 | Atom::createArrays(simnfo->n_atoms); | |
303 | the_atoms = new Atom*[simnfo->n_atoms]; | |
304 | the_molecules = new Molecule[simnfo->n_mol]; | |
305 | + | int molIndex; |
306 | ||
307 | + | // initialize the molecule's stampID's |
308 | ||
309 | < | if( simnfo->n_SRI ){ |
310 | < | the_sris = new SRI*[simnfo->n_SRI]; |
311 | < | the_excludes = new int[2 * simnfo->n_SRI]; |
309 | > | #ifdef IS_MPI |
310 | > | |
311 | > | |
312 | > | molIndex = 0; |
313 | > | for(i=0; i<mpiSim->getTotNmol(); i++){ |
314 | > | |
315 | > | if(mol2proc[i] == worldRank ){ |
316 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
317 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
318 | > | molIndex++; |
319 | > | } |
320 | > | } |
321 | > | |
322 | > | #else // is_mpi |
323 | > | |
324 | > | molIndex = 0; |
325 | > | for(i=0; i<n_components; i++){ |
326 | > | for(j=0; j<components_nmol[i]; j++ ){ |
327 | > | the_molecules[molIndex].setStampID( i ); |
328 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
329 | > | molIndex++; |
330 | > | } |
331 | > | } |
332 | > | |
333 | > | |
334 | > | #endif // is_mpi |
335 | > | |
336 | > | |
337 | > | if( simnfo->n_SRI ){ |
338 | > | |
339 | > | std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
340 | > | |
341 | > | Exclude::createArray(simnfo->n_SRI); |
342 | > | the_excludes = new Exclude*[simnfo->n_SRI]; |
343 | > | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
344 | simnfo->globalExcludes = new int; | |
345 | < | simnfo->n_exclude = tot_SRI; |
345 | > | simnfo->n_exclude = simnfo->n_SRI; |
346 | } | |
347 | else{ | |
348 | ||
349 | < | the_excludes = new int[2]; |
350 | < | the_excludes[0] = 0; |
351 | < | the_excludes[1] = 0; |
349 | > | Exclude::createArray( 1 ); |
350 | > | the_excludes = new Exclude*; |
351 | > | the_excludes[0] = new Exclude(0); |
352 | > | the_excludes[0]->setPair( 0,0 ); |
353 | simnfo->globalExcludes = new int; | |
354 | simnfo->globalExcludes[0] = 0; | |
355 | < | |
323 | < | simnfo->n_exclude = 1; |
355 | > | simnfo->n_exclude = 0; |
356 | } | |
357 | ||
358 | // set the arrays into the SimInfo object | |
359 | ||
360 | simnfo->atoms = the_atoms; | |
361 | < | simnfo->sr_interactions = the_sris; |
361 | > | simnfo->molecules = the_molecules; |
362 | simnfo->nGlobalExcludes = 0; | |
363 | simnfo->excludes = the_excludes; | |
364 | ||
# | Line 383 | Line 415 | void SimSetup::createSim( void ){ | |
415 | ||
416 | the_ff->setSimInfo( simnfo ); | |
417 | ||
418 | < | makeAtoms(); |
418 | > | makeMolecules(); |
419 | simnfo->identArray = new int[simnfo->n_atoms]; | |
420 | for(i=0; i<simnfo->n_atoms; i++){ | |
421 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
422 | } | |
423 | ||
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 | – | |
424 | if (the_globals->getUseRF() ) { | |
425 | simnfo->useReactionField = 1; | |
426 | ||
# | Line 638 | Line 657 | void SimSetup::createSim( void ){ | |
657 | ||
658 | // new AllLong( simnfo ); | |
659 | ||
641 | – | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 | – | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
660 | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); | |
661 | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); | |
662 | ||
663 | + | #ifdef IS_MPI |
664 | + | mpiSim->mpiRefresh(); |
665 | + | #endif |
666 | ||
647 | – | |
667 | // initialize the Fortran | |
668 | < | |
668 | > | |
669 | > | |
670 | simnfo->refreshSim(); | |
671 | ||
672 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 674 | Line 694 | void SimSetup::makeMolecules( void ){ | |
694 | ||
695 | void SimSetup::makeMolecules( void ){ | |
696 | ||
697 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset; |
697 | > | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
698 | molInit info; | |
699 | DirectionalAtom* dAtom; | |
700 | + | LinkedAssign* extras; |
701 | + | LinkedAssign* current_extra; |
702 | AtomStamp* currentAtom; | |
703 | BondStamp* currentBond; | |
704 | BendStamp* currentBend; | |
705 | TorsionStamp* currentTorsion; | |
706 | + | |
707 | + | bond_pair* theBonds; |
708 | + | bend_set* theBends; |
709 | + | torsion_set* theTorsions; |
710 | + | |
711 | ||
712 | //init the forceField paramters | |
713 | ||
714 | the_ff->readParams(); | |
715 | ||
716 | ||
717 | < | // init the molecules |
717 | > | // init the atoms |
718 | ||
719 | + | double ux, uy, uz, u, uSqr; |
720 | + | |
721 | atomOffset = 0; | |
722 | + | excludeOffset = 0; |
723 | for(i=0; i<simnfo->n_mol; i++){ | |
724 | ||
725 | stampID = the_molecules[i].getStampID(); | |
# | Line 698 | Line 728 | void SimSetup::makeMolecules( void ){ | |
728 | info.nBonds = comp_stamps[stampID]->getNBonds(); | |
729 | info.nBends = comp_stamps[stampID]->getNBends(); | |
730 | info.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
731 | < | |
731 | > | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
732 | > | |
733 | info.myAtoms = &the_atoms[atomOffset]; | |
734 | + | info.myExcludes = &the_excludes[excludeOffset]; |
735 | info.myBonds = new Bond*[info.nBonds]; | |
736 | info.myBends = new Bend*[info.nBends]; | |
737 | < | info.myTorsions = new Torsions*[info.nTorsions]; |
737 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
738 | ||
739 | theBonds = new bond_pair[info.nBonds]; | |
740 | theBends = new bend_set[info.nBends]; | |
# | Line 712 | Line 744 | void SimSetup::makeMolecules( void ){ | |
744 | ||
745 | for(j=0; j<info.nAtoms; j++){ | |
746 | ||
747 | < | currentAtom = theComponents[stampID]->getAtom( j ); |
747 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
748 | if( currentAtom->haveOrientation() ){ | |
749 | ||
750 | dAtom = new DirectionalAtom(j + atomOffset); | |
# | Line 747 | Line 779 | void SimSetup::makeMolecules( void ){ | |
779 | } | |
780 | ||
781 | // make the bonds | |
782 | < | for(j=0; j<nBonds; j++){ |
782 | > | for(j=0; j<info.nBonds; j++){ |
783 | ||
784 | currentBond = comp_stamps[stampID]->getBond( j ); | |
785 | theBonds[j].a = currentBond->getA() + atomOffset; | |
786 | theBonds[j].b = currentBond->getB() + atomOffset; | |
787 | ||
788 | < | exI = theBonds[i].a; |
789 | < | exJ = theBonds[i].b; |
788 | > | exI = theBonds[j].a; |
789 | > | exJ = theBonds[j].b; |
790 | ||
791 | // exclude_I must always be the smaller of the pair | |
792 | if( exI > exJ ){ | |
# | Line 763 | Line 795 | void SimSetup::makeMolecules( void ){ | |
795 | exJ = tempEx; | |
796 | } | |
797 | #ifdef IS_MPI | |
798 | + | tempEx = exI; |
799 | + | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
800 | + | tempEx = exJ; |
801 | + | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
802 | ||
803 | < | the_excludes[index*2] = |
768 | < | the_atoms[exI]->getGlobalIndex() + 1; |
769 | < | the_excludes[index*2 + 1] = |
770 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
771 | < | |
803 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
804 | #else // isn't MPI | |
773 | – | |
774 | – | the_excludes[index*2] = exI + 1; |
775 | – | the_excludes[index*2 + 1] = exJ + 1; |
776 | – | // fortran index from 1 (hence the +1 in the indexing) |
805 | ||
806 | + | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
807 | #endif //is_mpi | |
808 | < | |
809 | < | } |
781 | < | |
782 | < | |
783 | < | |
784 | < | |
785 | < | |
786 | < | |
787 | < | |
788 | < | |
789 | < | |
790 | < | |
791 | < | |
792 | < | |
793 | < | |
794 | < | |
795 | < | |
796 | < | void SimSetup::makeAtoms( void ){ |
797 | < | |
798 | < | int i, j, k, index; |
799 | < | double ux, uy, uz, uSqr, u; |
800 | < | AtomStamp* current_atom; |
801 | < | |
802 | < | DirectionalAtom* dAtom; |
803 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
804 | < | |
805 | < | lMolIndex = 0; |
806 | < | molIndex = 0; |
807 | < | index = 0; |
808 | < | for( i=0; i<n_components; i++ ){ |
808 | > | } |
809 | > | excludeOffset += info.nBonds; |
810 | ||
811 | < | for( j=0; j<components_nmol[i]; j++ ){ |
812 | < | |
813 | < | #ifdef IS_MPI |
814 | < | if( mpiSim->getMyMolStart() <= molIndex && |
815 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
816 | < | #endif // is_mpi |
817 | < | |
817 | < | molStart = index; |
818 | < | nMemb = comp_stamps[i]->getNAtoms(); |
819 | < | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
811 | > | //make the bends |
812 | > | for(j=0; j<info.nBends; j++){ |
813 | > | |
814 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
815 | > | theBends[j].a = currentBend->getA() + atomOffset; |
816 | > | theBends[j].b = currentBend->getB() + atomOffset; |
817 | > | theBends[j].c = currentBend->getC() + atomOffset; |
818 | ||
819 | < | current_atom = comp_stamps[i]->getAtom( k ); |
822 | < | if( current_atom->haveOrientation() ){ |
819 | > | if( currentBend->haveExtras() ){ |
820 | ||
821 | < | dAtom = new DirectionalAtom(index); |
822 | < | simnfo->n_oriented++; |
826 | < | the_atoms[index] = dAtom; |
821 | > | extras = currentBend->getExtras(); |
822 | > | current_extra = extras; |
823 | ||
824 | < | ux = current_atom->getOrntX(); |
825 | < | uy = current_atom->getOrntY(); |
826 | < | uz = current_atom->getOrntZ(); |
827 | < | |
828 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
829 | < | |
830 | < | u = sqrt( uSqr ); |
831 | < | ux = ux / u; |
832 | < | uy = uy / u; |
833 | < | uz = uz / u; |
834 | < | |
835 | < | dAtom->setSUx( ux ); |
836 | < | dAtom->setSUy( uy ); |
837 | < | dAtom->setSUz( uz ); |
824 | > | while( current_extra != NULL ){ |
825 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
826 | > | |
827 | > | switch( current_extra->getType() ){ |
828 | > | |
829 | > | case 0: |
830 | > | theBends[j].ghost = |
831 | > | current_extra->getInt() + atomOffset; |
832 | > | theBends[j].isGhost = 1; |
833 | > | break; |
834 | > | |
835 | > | case 1: |
836 | > | theBends[j].ghost = |
837 | > | (int)current_extra->getDouble() + atomOffset; |
838 | > | theBends[j].isGhost = 1; |
839 | > | break; |
840 | > | |
841 | > | default: |
842 | > | sprintf( painCave.errMsg, |
843 | > | "SimSetup Error: ghostVectorSource was neither a " |
844 | > | "double nor an int.\n" |
845 | > | "-->Bend[%d] in %s\n", |
846 | > | j, comp_stamps[stampID]->getID() ); |
847 | > | painCave.isFatal = 1; |
848 | > | simError(); |
849 | > | } |
850 | } | |
851 | + | |
852 | else{ | |
853 | < | the_atoms[index] = new GeneralAtom(index); |
853 | > | |
854 | > | sprintf( painCave.errMsg, |
855 | > | "SimSetup Error: unhandled bend assignment:\n" |
856 | > | " -->%s in Bend[%d] in %s\n", |
857 | > | current_extra->getlhs(), |
858 | > | j, comp_stamps[stampID]->getID() ); |
859 | > | painCave.isFatal = 1; |
860 | > | simError(); |
861 | } | |
846 | – | the_atoms[index]->setType( current_atom->getType() ); |
847 | – | the_atoms[index]->setIndex( index ); |
862 | ||
863 | < | // increment the index and repeat; |
850 | < | index++; |
863 | > | current_extra = current_extra->getNext(); |
864 | } | |
865 | + | } |
866 | + | |
867 | + | if( !theBends[j].isGhost ){ |
868 | + | |
869 | + | exI = theBends[j].a; |
870 | + | exJ = theBends[j].c; |
871 | + | } |
872 | + | else{ |
873 | ||
874 | < | molEnd = index -1; |
875 | < | the_molecules[lMolIndex].setNMembers( nMemb ); |
855 | < | the_molecules[lMolIndex].setStartAtom( molStart ); |
856 | < | the_molecules[lMolIndex].setEndAtom( molEnd ); |
857 | < | the_molecules[lMolIndex].setStampID( i ); |
858 | < | lMolIndex++; |
859 | < | |
860 | < | #ifdef IS_MPI |
874 | > | exI = theBends[j].a; |
875 | > | exJ = theBends[j].b; |
876 | } | |
862 | – | #endif //is_mpi |
877 | ||
878 | < | molIndex++; |
879 | < | } |
880 | < | } |
881 | < | |
878 | > | // exclude_I must always be the smaller of the pair |
879 | > | if( exI > exJ ){ |
880 | > | tempEx = exI; |
881 | > | exI = exJ; |
882 | > | exJ = tempEx; |
883 | > | } |
884 | #ifdef IS_MPI | |
885 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
886 | < | |
887 | < | delete[] globalIndex; |
888 | < | |
889 | < | mpiSim->mpiRefresh(); |
890 | < | #endif //IS_MPI |
891 | < | |
892 | < | the_ff->initializeAtoms(); |
893 | < | } |
894 | < | |
895 | < | void SimSetup::makeBonds( void ){ |
880 | < | |
881 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
882 | < | bond_pair* the_bonds; |
883 | < | BondStamp* current_bond; |
884 | < | |
885 | < | the_bonds = new bond_pair[tot_bonds]; |
886 | < | index = 0; |
887 | < | offset = 0; |
888 | < | molIndex = 0; |
889 | < | |
890 | < | for( i=0; i<n_components; i++ ){ |
891 | < | |
892 | < | for( j=0; j<components_nmol[i]; j++ ){ |
885 | > | tempEx = exI; |
886 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
887 | > | tempEx = exJ; |
888 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
889 | > | |
890 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
891 | > | #else // isn't MPI |
892 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
893 | > | #endif //is_mpi |
894 | > | } |
895 | > | excludeOffset += info.nBends; |
896 | ||
897 | < | #ifdef IS_MPI |
898 | < | if( mpiSim->getMyMolStart() <= molIndex && |
899 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
900 | < | #endif // is_mpi |
901 | < | |
902 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
903 | < | |
904 | < | current_bond = comp_stamps[i]->getBond( k ); |
905 | < | the_bonds[index].a = current_bond->getA() + offset; |
906 | < | the_bonds[index].b = current_bond->getB() + offset; |
897 | > | for(j=0; j<info.nTorsions; j++){ |
898 | > | |
899 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
900 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
901 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
902 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
903 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
904 | > | |
905 | > | exI = theTorsions[j].a; |
906 | > | exJ = theTorsions[j].d; |
907 | ||
908 | < | exI = the_bonds[index].a; |
909 | < | exJ = the_bonds[index].b; |
910 | < | |
911 | < | // exclude_I must always be the smaller of the pair |
912 | < | if( exI > exJ ){ |
913 | < | tempEx = exI; |
911 | < | exI = exJ; |
912 | < | exJ = tempEx; |
913 | < | } |
914 | < | |
915 | < | |
908 | > | // exclude_I must always be the smaller of the pair |
909 | > | if( exI > exJ ){ |
910 | > | tempEx = exI; |
911 | > | exI = exJ; |
912 | > | exJ = tempEx; |
913 | > | } |
914 | #ifdef IS_MPI | |
915 | < | |
916 | < | the_excludes[index*2] = |
917 | < | the_atoms[exI]->getGlobalIndex() + 1; |
918 | < | the_excludes[index*2 + 1] = |
919 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
920 | < | |
915 | > | tempEx = exI; |
916 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
917 | > | tempEx = exJ; |
918 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
919 | > | |
920 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
921 | #else // isn't MPI | |
922 | < | |
925 | < | the_excludes[index*2] = exI + 1; |
926 | < | the_excludes[index*2 + 1] = exJ + 1; |
927 | < | // fortran index from 1 (hence the +1 in the indexing) |
922 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
923 | #endif //is_mpi | |
924 | < | |
925 | < | // increment the index and repeat; |
931 | < | index++; |
932 | < | } |
933 | < | offset += comp_stamps[i]->getNAtoms(); |
934 | < | |
935 | < | #ifdef IS_MPI |
936 | < | } |
937 | < | #endif //is_mpi |
938 | < | |
939 | < | molIndex++; |
940 | < | } |
941 | < | } |
924 | > | } |
925 | > | excludeOffset += info.nTorsions; |
926 | ||
927 | < | the_ff->initializeBonds( the_bonds ); |
928 | < | } |
927 | > | |
928 | > | // send the arrays off to the forceField for init. |
929 | ||
930 | < | void SimSetup::makeBends( void ){ |
930 | > | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
931 | > | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
932 | > | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
933 | > | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
934 | ||
948 | – | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
949 | – | bend_set* the_bends; |
950 | – | BendStamp* current_bend; |
951 | – | LinkedAssign* extras; |
952 | – | LinkedAssign* current_extra; |
953 | – | |
935 | ||
936 | < | the_bends = new bend_set[tot_bends]; |
956 | < | index = 0; |
957 | < | offset = 0; |
958 | < | molIndex = 0; |
959 | < | for( i=0; i<n_components; i++ ){ |
960 | < | |
961 | < | for( j=0; j<components_nmol[i]; j++ ){ |
962 | < | |
963 | < | #ifdef IS_MPI |
964 | < | if( mpiSim->getMyMolStart() <= molIndex && |
965 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
966 | < | #endif // is_mpi |
967 | < | |
968 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
969 | < | |
970 | < | current_bend = comp_stamps[i]->getBend( k ); |
971 | < | the_bends[index].a = current_bend->getA() + offset; |
972 | < | the_bends[index].b = current_bend->getB() + offset; |
973 | < | the_bends[index].c = current_bend->getC() + offset; |
974 | < | |
975 | < | if( current_bend->haveExtras() ){ |
976 | < | |
977 | < | extras = current_bend->getExtras(); |
978 | < | current_extra = extras; |
979 | < | |
980 | < | while( current_extra != NULL ){ |
981 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
982 | < | |
983 | < | switch( current_extra->getType() ){ |
984 | < | |
985 | < | case 0: |
986 | < | the_bends[index].ghost = |
987 | < | current_extra->getInt() + offset; |
988 | < | the_bends[index].isGhost = 1; |
989 | < | break; |
990 | < | |
991 | < | case 1: |
992 | < | the_bends[index].ghost = |
993 | < | (int)current_extra->getDouble() + offset; |
994 | < | the_bends[index].isGhost = 1; |
995 | < | break; |
996 | < | |
997 | < | default: |
998 | < | sprintf( painCave.errMsg, |
999 | < | "SimSetup Error: ghostVectorSource was neiter a " |
1000 | < | "double nor an int.\n" |
1001 | < | "-->Bend[%d] in %s\n", |
1002 | < | k, comp_stamps[i]->getID() ); |
1003 | < | painCave.isFatal = 1; |
1004 | < | simError(); |
1005 | < | } |
1006 | < | } |
1007 | < | |
1008 | < | else{ |
1009 | < | |
1010 | < | sprintf( painCave.errMsg, |
1011 | < | "SimSetup Error: unhandled bend assignment:\n" |
1012 | < | " -->%s in Bend[%d] in %s\n", |
1013 | < | current_extra->getlhs(), |
1014 | < | k, comp_stamps[i]->getID() ); |
1015 | < | painCave.isFatal = 1; |
1016 | < | simError(); |
1017 | < | } |
1018 | < | |
1019 | < | current_extra = current_extra->getNext(); |
1020 | < | } |
1021 | < | } |
1022 | < | |
1023 | < | if( !the_bends[index].isGhost ){ |
1024 | < | |
1025 | < | exI = the_bends[index].a; |
1026 | < | exJ = the_bends[index].c; |
1027 | < | } |
1028 | < | else{ |
1029 | < | |
1030 | < | exI = the_bends[index].a; |
1031 | < | exJ = the_bends[index].b; |
1032 | < | } |
1033 | < | |
1034 | < | // exclude_I must always be the smaller of the pair |
1035 | < | if( exI > exJ ){ |
1036 | < | tempEx = exI; |
1037 | < | exI = exJ; |
1038 | < | exJ = tempEx; |
1039 | < | } |
936 | > | the_molecules[i].initialize( info ); |
937 | ||
938 | ||
939 | < | #ifdef IS_MPI |
940 | < | |
941 | < | the_excludes[(index + tot_bonds)*2] = |
942 | < | the_atoms[exI]->getGlobalIndex() + 1; |
1046 | < | the_excludes[(index + tot_bonds)*2 + 1] = |
1047 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1048 | < | |
1049 | < | #else // isn't MPI |
1050 | < | |
1051 | < | the_excludes[(index + tot_bonds)*2] = exI + 1; |
1052 | < | the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
1053 | < | // fortran index from 1 (hence the +1 in the indexing) |
1054 | < | #endif //is_mpi |
1055 | < | |
1056 | < | |
1057 | < | // increment the index and repeat; |
1058 | < | index++; |
1059 | < | } |
1060 | < | offset += comp_stamps[i]->getNAtoms(); |
1061 | < | |
1062 | < | #ifdef IS_MPI |
1063 | < | } |
1064 | < | #endif //is_mpi |
1065 | < | |
1066 | < | molIndex++; |
1067 | < | } |
939 | > | atomOffset += info.nAtoms; |
940 | > | delete[] theBonds; |
941 | > | delete[] theBends; |
942 | > | delete[] theTorsions; |
943 | } | |
944 | ||
945 | #ifdef IS_MPI | |
946 | < | sprintf( checkPointMsg, |
1072 | < | "Successfully created the bends list.\n" ); |
946 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
947 | MPIcheckPoint(); | |
948 | #endif // is_mpi | |
1075 | – | |
1076 | – | |
1077 | – | the_ff->initializeBends( the_bends ); |
1078 | – | } |
949 | ||
950 | < | void SimSetup::makeTorsions( void ){ |
950 | > | // clean up the forcefield |
951 | > | the_ff->calcRcut(); |
952 | > | the_ff->cleanMe(); |
953 | ||
1082 | – | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1083 | – | torsion_set* the_torsions; |
1084 | – | TorsionStamp* current_torsion; |
1085 | – | |
1086 | – | the_torsions = new torsion_set[tot_torsions]; |
1087 | – | index = 0; |
1088 | – | offset = 0; |
1089 | – | molIndex = 0; |
1090 | – | for( i=0; i<n_components; i++ ){ |
1091 | – | |
1092 | – | for( j=0; j<components_nmol[i]; j++ ){ |
1093 | – | |
1094 | – | #ifdef IS_MPI |
1095 | – | if( mpiSim->getMyMolStart() <= molIndex && |
1096 | – | molIndex <= mpiSim->getMyMolEnd() ){ |
1097 | – | #endif // is_mpi |
1098 | – | |
1099 | – | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1100 | – | |
1101 | – | current_torsion = comp_stamps[i]->getTorsion( k ); |
1102 | – | the_torsions[index].a = current_torsion->getA() + offset; |
1103 | – | the_torsions[index].b = current_torsion->getB() + offset; |
1104 | – | the_torsions[index].c = current_torsion->getC() + offset; |
1105 | – | the_torsions[index].d = current_torsion->getD() + offset; |
1106 | – | |
1107 | – | exI = the_torsions[index].a; |
1108 | – | exJ = the_torsions[index].d; |
1109 | – | |
1110 | – | |
1111 | – | // exclude_I must always be the smaller of the pair |
1112 | – | if( exI > exJ ){ |
1113 | – | tempEx = exI; |
1114 | – | exI = exJ; |
1115 | – | exJ = tempEx; |
1116 | – | } |
1117 | – | |
1118 | – | |
1119 | – | #ifdef IS_MPI |
1120 | – | |
1121 | – | the_excludes[(index + tot_bonds + tot_bends)*2] = |
1122 | – | the_atoms[exI]->getGlobalIndex() + 1; |
1123 | – | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1124 | – | the_atoms[exJ]->getGlobalIndex() + 1; |
1125 | – | |
1126 | – | #else // isn't MPI |
1127 | – | |
1128 | – | the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1129 | – | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1130 | – | // fortran indexes from 1 (hence the +1 in the indexing) |
1131 | – | #endif //is_mpi |
1132 | – | |
1133 | – | |
1134 | – | // increment the index and repeat; |
1135 | – | index++; |
1136 | – | } |
1137 | – | offset += comp_stamps[i]->getNAtoms(); |
1138 | – | |
1139 | – | #ifdef IS_MPI |
1140 | – | } |
1141 | – | #endif //is_mpi |
1142 | – | |
1143 | – | molIndex++; |
1144 | – | } |
1145 | – | } |
1146 | – | |
1147 | – | the_ff->initializeTorsions( the_torsions ); |
954 | } | |
955 | ||
956 | void SimSetup::initFromBass( void ){ |
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