# | 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 674 | Line 686 | void SimSetup::makeMolecules( void ){ | |
686 | ||
687 | void SimSetup::makeMolecules( void ){ | |
688 | ||
689 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset; |
689 | > | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
690 | molInit info; | |
691 | DirectionalAtom* dAtom; | |
692 | + | LinkedAssign* extras; |
693 | + | LinkedAssign* current_extra; |
694 | AtomStamp* currentAtom; | |
695 | BondStamp* currentBond; | |
696 | BendStamp* currentBend; | |
697 | TorsionStamp* currentTorsion; | |
698 | + | |
699 | + | bond_pair* theBonds; |
700 | + | bend_set* theBends; |
701 | + | torsion_set* theTorsions; |
702 | + | |
703 | ||
704 | //init the forceField paramters | |
705 | ||
706 | the_ff->readParams(); | |
707 | ||
708 | ||
709 | < | // init the molecules |
709 | > | // init the atoms |
710 | ||
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(); | |
# | Line 698 | Line 720 | void SimSetup::makeMolecules( void ){ | |
720 | info.nBonds = comp_stamps[stampID]->getNBonds(); | |
721 | info.nBends = comp_stamps[stampID]->getNBends(); | |
722 | info.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
723 | < | |
723 | > | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
724 | > | |
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 Torsions*[info.nTorsions]; |
729 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
730 | ||
731 | theBonds = new bond_pair[info.nBonds]; | |
732 | theBends = new bend_set[info.nBends]; | |
# | Line 712 | Line 736 | void SimSetup::makeMolecules( void ){ | |
736 | ||
737 | for(j=0; j<info.nAtoms; j++){ | |
738 | ||
739 | < | currentAtom = theComponents[stampID]->getAtom( j ); |
739 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
740 | if( currentAtom->haveOrientation() ){ | |
741 | ||
742 | dAtom = new DirectionalAtom(j + atomOffset); | |
# | Line 747 | Line 771 | void SimSetup::makeMolecules( void ){ | |
771 | } | |
772 | ||
773 | // make the bonds | |
774 | < | for(j=0; j<nBonds; j++){ |
774 | > | for(j=0; j<info.nBonds; j++){ |
775 | ||
776 | currentBond = comp_stamps[stampID]->getBond( j ); | |
777 | theBonds[j].a = currentBond->getA() + atomOffset; | |
# | Line 763 | Line 787 | void SimSetup::makeMolecules( void ){ | |
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[index*2] = |
768 | < | the_atoms[exI]->getGlobalIndex() + 1; |
769 | < | the_excludes[index*2 + 1] = |
770 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
771 | < | |
795 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
796 | #else // isn't MPI | |
797 | < | |
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) |
777 | < | |
797 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
798 | #endif //is_mpi | |
799 | < | |
800 | < | } |
799 | > | } |
800 | > | excludeOffset += info.nBonds; |
801 | ||
802 | < | |
803 | < | |
804 | < | |
805 | < | |
806 | < | |
807 | < | |
808 | < | |
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++ ){ |
809 | < | |
810 | < | for( j=0; j<components_nmol[i]; j++ ){ |
811 | < | |
812 | < | #ifdef IS_MPI |
813 | < | if( mpiSim->getMyMolStart() <= molIndex && |
814 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
815 | < | #endif // is_mpi |
816 | < | |
817 | < | molStart = index; |
818 | < | nMemb = comp_stamps[i]->getNAtoms(); |
819 | < | for( k=0; k<comp_stamps[i]->getNAtoms(); 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_atom = comp_stamps[i]->getAtom( k ); |
822 | < | if( current_atom->haveOrientation() ){ |
810 | > | if( currentBend->haveExtras() ){ |
811 | ||
812 | < | dAtom = new DirectionalAtom(index); |
813 | < | simnfo->n_oriented++; |
826 | < | the_atoms[index] = dAtom; |
812 | > | extras = currentBend->getExtras(); |
813 | > | current_extra = extras; |
814 | ||
815 | < | ux = current_atom->getOrntX(); |
816 | < | uy = current_atom->getOrntY(); |
817 | < | uz = current_atom->getOrntZ(); |
818 | < | |
819 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
820 | < | |
821 | < | u = sqrt( uSqr ); |
822 | < | ux = ux / u; |
823 | < | uy = uy / u; |
824 | < | uz = uz / u; |
825 | < | |
826 | < | dAtom->setSUx( ux ); |
827 | < | dAtom->setSUy( uy ); |
828 | < | dAtom->setSUz( uz ); |
815 | > | while( current_extra != NULL ){ |
816 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
817 | > | |
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 1: |
827 | > | theBends[j].ghost = |
828 | > | (int)current_extra->getDouble() + atomOffset; |
829 | > | theBends[j].isGhost = 1; |
830 | > | break; |
831 | > | |
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 | + | |
843 | else{ | |
844 | < | the_atoms[index] = new GeneralAtom(index); |
844 | > | |
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 | } | |
846 | – | the_atoms[index]->setType( current_atom->getType() ); |
847 | – | the_atoms[index]->setIndex( index ); |
853 | ||
854 | < | // increment the index and repeat; |
850 | < | index++; |
854 | > | current_extra = current_extra->getNext(); |
855 | } | |
856 | + | } |
857 | + | |
858 | + | if( !theBends[j].isGhost ){ |
859 | + | |
860 | + | exI = theBends[j].a; |
861 | + | exJ = theBends[j].c; |
862 | + | } |
863 | + | else{ |
864 | ||
865 | < | molEnd = index -1; |
866 | < | 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 |
865 | > | exI = theBends[j].a; |
866 | > | exJ = theBends[j].b; |
867 | } | |
862 | – | #endif //is_mpi |
868 | ||
869 | < | molIndex++; |
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 | > | 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 | < | } |
886 | > | excludeOffset += info.nBends; |
887 | ||
888 | < | #ifdef IS_MPI |
889 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
890 | < | |
891 | < | delete[] globalIndex; |
892 | < | |
893 | < | mpiSim->mpiRefresh(); |
894 | < | #endif //IS_MPI |
895 | < | |
896 | < | the_ff->initializeAtoms(); |
897 | < | } |
878 | < | |
879 | < | 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++ ){ |
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 | + | // 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]->getNBonds(); k++ ){ |
911 | < | |
901 | < | current_bond = comp_stamps[i]->getBond( k ); |
902 | < | the_bonds[index].a = current_bond->getA() + offset; |
903 | < | the_bonds[index].b = current_bond->getB() + offset; |
904 | < | |
905 | < | exI = the_bonds[index].a; |
906 | < | exJ = the_bonds[index].b; |
907 | < | |
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 | < | |
915 | < | |
916 | < | #ifdef IS_MPI |
917 | < | |
918 | < | the_excludes[index*2] = |
919 | < | the_atoms[exI]->getGlobalIndex() + 1; |
920 | < | the_excludes[index*2 + 1] = |
921 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
922 | < | |
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 | < | |
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) |
913 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
914 | #endif //is_mpi | |
915 | < | |
916 | < | // 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 | < | } |
915 | > | } |
916 | > | excludeOffset += info.nTorsions; |
917 | ||
918 | < | the_ff->initializeBonds( the_bonds ); |
919 | < | } |
918 | > | |
919 | > | // send the arrays off to the forceField for init. |
920 | ||
921 | < | void SimSetup::makeBends( void ){ |
922 | < | |
923 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
924 | < | bend_set* the_bends; |
950 | < | BendStamp* current_bend; |
951 | < | LinkedAssign* extras; |
952 | < | LinkedAssign* current_extra; |
953 | < | |
954 | < | |
955 | < | 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 | < | } |
1040 | < | |
1041 | < | |
1042 | < | #ifdef IS_MPI |
1043 | < | |
1044 | < | the_excludes[(index + tot_bonds)*2] = |
1045 | < | 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 | < | } |
1068 | < | } |
1069 | < | |
1070 | < | #ifdef IS_MPI |
1071 | < | sprintf( checkPointMsg, |
1072 | < | "Successfully created the bends list.\n" ); |
1073 | < | MPIcheckPoint(); |
1074 | < | #endif // is_mpi |
1075 | < | |
1076 | < | |
1077 | < | the_ff->initializeBends( the_bends ); |
1078 | < | } |
1079 | < | |
1080 | < | void SimSetup::makeTorsions( void ){ |
1081 | < | |
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++ ){ |
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 | ||
1092 | – | for( j=0; j<components_nmol[i]; j++ ){ |
926 | ||
927 | < | #ifdef IS_MPI |
928 | < | if( mpiSim->getMyMolStart() <= molIndex && |
929 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
930 | < | #endif // is_mpi |
931 | < | |
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 | < | } |
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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