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root/group/branches/no-template-branch/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 2003 UTC vs.
Revision 432 by chuckv, Thu Mar 27 23:33:40 2003 UTC

# 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 + #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 +      molIndex++;
318 +    }
319 +  }
320 +
321 + #else // is_mpi
322 +  
323 +  molIndex = 0;
324 +  for(i=0; i<n_components; i++){
325 +    for(j=0; j<components_nmol[i]; j++ ){
326 +      the_molecules[molIndex].setStampID( i );
327 +      molIndex++;
328 +    }
329 +  }
330 +    
331 +
332 + #endif // is_mpi
333 +
334 +
335    if( simnfo->n_SRI ){
336 <    the_sris = new SRI*[simnfo->n_SRI];
337 <    the_excludes = new int[2 * simnfo->n_SRI];
336 >    
337 >    std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
338 >    
339 >    Exclude::createArray(simnfo->n_SRI);
340 >    the_excludes = new Exclude*[simnfo->n_SRI];
341 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
342      simnfo->globalExcludes = new int;
343      simnfo->n_exclude = tot_SRI;
344    }
345    else{
346      
347 <    the_excludes = new int[2];
348 <    the_excludes[0] = 0;
349 <    the_excludes[1] = 0;
347 >    Exclude::createArray( 1 );
348 >    the_excludes = new Exclude*;
349 >    the_excludes[0] = new Exclude(0);
350 >    the_excludes[0]->setPair( 0,0 );
351      simnfo->globalExcludes = new int;
352      simnfo->globalExcludes[0] = 0;
353 <
323 <    simnfo->n_exclude = 1;
353 >    simnfo->n_exclude = 0;
354    }
355  
356    // set the arrays into the SimInfo object
357  
358    simnfo->atoms = the_atoms;
359 <  simnfo->sr_interactions = the_sris;
359 >  simnfo->molecules = the_molecules;
360    simnfo->nGlobalExcludes = 0;
361    simnfo->excludes = the_excludes;
362  
# Line 383 | Line 413 | void SimSetup::createSim( void ){
413  
414    the_ff->setSimInfo( simnfo );
415  
416 <  makeAtoms();
416 >  makeMolecules();
417    simnfo->identArray = new int[simnfo->n_atoms];
418    for(i=0; i<simnfo->n_atoms; i++){
419      simnfo->identArray[i] = the_atoms[i]->getIdent();
420    }
421    
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 –
422    if (the_globals->getUseRF() ) {
423      simnfo->useReactionField = 1;
424    
# Line 638 | Line 655 | void SimSetup::createSim( void ){
655  
656   //   new AllLong( simnfo );
657  
641 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
658    if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
659    if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
660  
661 + #ifdef IS_MPI
662 +  mpiSim->mpiRefresh();
663 + #endif
664  
647 –
665    // initialize the Fortran
666 <  
666 >
667 >
668    simnfo->refreshSim();
669    
670    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 671 | Line 689 | void SimSetup::createSim( void ){
689   #endif // is_mpi
690   }
691  
674 – void SimSetup::makeAtoms( void ){
692  
693 <  int i, j, k, index;
677 <  double ux, uy, uz, uSqr, u;
678 <  AtomStamp* current_atom;
693 > void SimSetup::makeMolecules( void ){
694  
695 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
696 +  molInit info;
697    DirectionalAtom* dAtom;
698 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
698 >  LinkedAssign* extras;
699 >  LinkedAssign* current_extra;
700 >  AtomStamp* currentAtom;
701 >  BondStamp* currentBond;
702 >  BendStamp* currentBend;
703 >  TorsionStamp* currentTorsion;
704  
705 <  lMolIndex = 0;
706 <  molIndex = 0;
707 <  index = 0;
686 <  for( i=0; i<n_components; i++ ){
705 >  bond_pair* theBonds;
706 >  bend_set* theBends;
707 >  torsion_set* theTorsions;
708  
709 <    for( j=0; j<components_nmol[i]; j++ ){
709 >  
710 >  //init the forceField paramters
711  
712 < #ifdef IS_MPI
691 <      if( mpiSim->getMyMolStart() <= molIndex &&
692 <          molIndex <= mpiSim->getMyMolEnd() ){
693 < #endif // is_mpi        
712 >  the_ff->readParams();
713  
714 <        molStart = index;
715 <        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++;
714 >  
715 >  // init the atoms
716  
717 < #ifdef IS_MPI
718 <      }
719 < #endif //is_mpi
720 <      
721 <      molIndex++;
743 <    }
744 <  }
745 <
746 < #ifdef IS_MPI
747 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
717 >  double ux, uy, uz, u, uSqr;
718 >  
719 >  atomOffset = 0;
720 >  excludeOffset = 0;
721 >  for(i=0; i<simnfo->n_mol; i++){
722      
723 <    delete[] globalIndex;
723 >    stampID = the_molecules[i].getStampID();
724  
725 <    mpiSim->mpiRefresh();
726 < #endif //IS_MPI
727 <          
728 <  the_ff->initializeAtoms();
729 < }
725 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
726 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
727 >    info.nBends    = comp_stamps[stampID]->getNBends();
728 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
729 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
730  
731 < void SimSetup::makeBonds( void ){
731 >    info.myAtoms = &the_atoms[atomOffset];
732 >    info.myExcludes = &the_excludes[excludeOffset];
733 >    info.myBonds = new Bond*[info.nBonds];
734 >    info.myBends = new Bend*[info.nBends];
735 >    info.myTorsions = new Torsion*[info.nTorsions];
736  
737 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
738 <  bond_pair* the_bonds;
739 <  BondStamp* current_bond;
740 <
741 <  the_bonds = new bond_pair[tot_bonds];
742 <  index = 0;
743 <  offset = 0;
744 <  molIndex = 0;
745 <
746 <  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        
737 >    theBonds = new bond_pair[info.nBonds];
738 >    theBends = new bend_set[info.nBends];
739 >    theTorsions = new torsion_set[info.nTorsions];
740 >    
741 >    // make the Atoms
742 >    
743 >    for(j=0; j<info.nAtoms; j++){
744 >      
745 >      currentAtom = comp_stamps[stampID]->getAtom( j );
746 >      if( currentAtom->haveOrientation() ){
747          
748 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
749 <          
750 <          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();
748 >        dAtom = new DirectionalAtom(j + atomOffset);
749 >        simnfo->n_oriented++;
750 >        info.myAtoms[j] = dAtom;
751          
752 < #ifdef IS_MPI
752 >        ux = currentAtom->getOrntX();
753 >        uy = currentAtom->getOrntY();
754 >        uz = currentAtom->getOrntZ();
755 >        
756 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
757 >        
758 >        u = sqrt( uSqr );
759 >        ux = ux / u;
760 >        uy = uy / u;
761 >        uz = uz / u;
762 >        
763 >        dAtom->setSUx( ux );
764 >        dAtom->setSUy( uy );
765 >        dAtom->setSUz( uz );
766        }
767 < #endif //is_mpi
767 >      else{
768 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
769 >      }
770 >      info.myAtoms[j]->setType( currentAtom->getType() );
771 >    
772 > #ifdef IS_MPI
773        
774 <      molIndex++;
775 <    }      
776 <  }
774 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
775 >      
776 > #endif // is_mpi
777 >    }
778 >    
779 >    // make the bonds
780 >    for(j=0; j<info.nBonds; j++){
781 >      
782 >      currentBond = comp_stamps[stampID]->getBond( j );
783 >      theBonds[j].a = currentBond->getA() + atomOffset;
784 >      theBonds[j].b = currentBond->getB() + atomOffset;
785  
786 <  the_ff->initializeBonds( the_bonds );
787 < }
823 <
824 < void SimSetup::makeBends( void ){
825 <
826 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
827 <  bend_set* the_bends;
828 <  BendStamp* current_bend;
829 <  LinkedAssign* extras;
830 <  LinkedAssign* current_extra;
831 <  
832 <
833 <  the_bends = new bend_set[tot_bends];
834 <  index = 0;
835 <  offset = 0;
836 <  molIndex = 0;
837 <  for( i=0; i<n_components; i++ ){
838 <
839 <    for( j=0; j<components_nmol[i]; j++ ){
786 >      exI = theBonds[i].a;
787 >      exJ = theBonds[i].b;
788  
789 +      // exclude_I must always be the smaller of the pair
790 +      if( exI > exJ ){
791 +        tempEx = exI;
792 +        exI = exJ;
793 +        exJ = tempEx;
794 +      }
795   #ifdef IS_MPI
796 <      if( mpiSim->getMyMolStart() <= molIndex &&
797 <          molIndex <= mpiSim->getMyMolEnd() ){
798 < #endif // is_mpi        
796 >      tempEx = exI;
797 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
798 >      tempEx = exJ;
799 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
800 >      
801 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
802 > #else  // isn't MPI
803 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
804 > #endif  //is_mpi
805 >    }
806 >    excludeOffset += info.nBonds;
807  
808 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
808 >    //make the bends
809 >    for(j=0; j<info.nBends; j++){
810 >      
811 >      currentBend = comp_stamps[stampID]->getBend( j );
812 >      theBends[j].a = currentBend->getA() + atomOffset;
813 >      theBends[j].b = currentBend->getB() + atomOffset;
814 >      theBends[j].c = currentBend->getC() + atomOffset;
815            
816 <          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() ){
816 >      if( currentBend->haveExtras() ){
817              
818 <            extras = current_bend->getExtras();
819 <            current_extra = extras;
818 >        extras = currentBend->getExtras();
819 >        current_extra = extras;
820              
821 <            while( current_extra != NULL ){
822 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
821 >        while( current_extra != NULL ){
822 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
823                  
824 <                switch( current_extra->getType() ){
824 >            switch( current_extra->getType() ){
825 >              
826 >            case 0:
827 >              theBends[j].ghost =
828 >                current_extra->getInt() + atomOffset;
829 >              theBends[j].isGhost = 1;
830 >              break;
831                    
832 <                case 0:
833 <                  the_bends[index].ghost =
834 <                    current_extra->getInt() + offset;
835 <                  the_bends[index].isGhost = 1;
836 <                  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 <              }
832 >            case 1:
833 >              theBends[j].ghost =
834 >                (int)current_extra->getDouble() + atomOffset;
835 >              theBends[j].isGhost = 1;
836 >              break;
837                
838 <              else{
839 <                
840 <                sprintf( painCave.errMsg,
841 <                         "SimSetup Error: unhandled bend assignment:\n"
842 <                         "    -->%s in Bend[%d] in %s\n",
843 <                         current_extra->getlhs(),
844 <                         k, comp_stamps[i]->getID() );
845 <                painCave.isFatal = 1;
894 <                simError();
895 <              }
896 <              
897 <              current_extra = current_extra->getNext();
838 >            default:
839 >              sprintf( painCave.errMsg,
840 >                       "SimSetup Error: ghostVectorSource was neiter a "
841 >                       "double nor an int.\n"
842 >                       "-->Bend[%d] in %s\n",
843 >                       j, comp_stamps[stampID]->getID() );
844 >              painCave.isFatal = 1;
845 >              simError();
846              }
847            }
848            
901 –          if( !the_bends[index].isGhost ){
902 –            
903 –            exI = the_bends[index].a;
904 –            exJ = the_bends[index].c;
905 –          }
849            else{
850              
851 <            exI = the_bends[index].a;
852 <            exJ = the_bends[index].b;
851 >            sprintf( painCave.errMsg,
852 >                     "SimSetup Error: unhandled bend assignment:\n"
853 >                     "    -->%s in Bend[%d] in %s\n",
854 >                     current_extra->getlhs(),
855 >                     j, comp_stamps[stampID]->getID() );
856 >            painCave.isFatal = 1;
857 >            simError();
858            }
859            
860 <          // 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++;
860 >          current_extra = current_extra->getNext();
861          }
938 –        offset += comp_stamps[i]->getNAtoms();
939 –        
940 – #ifdef IS_MPI
862        }
863 < #endif //is_mpi
864 <
865 <      molIndex++;
866 <    }
867 <  }
868 <
863 >          
864 >      if( !theBends[j].isGhost ){
865 >            
866 >        exI = theBends[j].a;
867 >        exJ = theBends[j].c;
868 >      }
869 >      else{
870 >        
871 >        exI = theBends[j].a;
872 >        exJ = theBends[j].b;
873 >      }
874 >      
875 >      // exclude_I must always be the smaller of the pair
876 >      if( exI > exJ ){
877 >        tempEx = exI;
878 >        exI = exJ;
879 >        exJ = tempEx;
880 >      }
881   #ifdef IS_MPI
882 <  sprintf( checkPointMsg,
883 <           "Successfully created the bends list.\n" );
884 <  MPIcheckPoint();
885 < #endif // is_mpi
886 <  
882 >      tempEx = exI;
883 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
884 >      tempEx = exJ;
885 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
886 >      
887 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
888 > #else  // isn't MPI
889 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
890 > #endif  //is_mpi
891 >    }
892 >    excludeOffset += info.nBends;
893  
894 <  the_ff->initializeBends( the_bends );
895 < }
894 >    for(j=0; j<info.nTorsions; j++){
895 >      
896 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
897 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
898 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
899 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
900 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
901 >      
902 >      exI = theTorsions[j].a;
903 >      exJ = theTorsions[j].d;
904  
905 < void SimSetup::makeTorsions( void ){
906 <
907 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
908 <  torsion_set* the_torsions;
909 <  TorsionStamp* current_torsion;
910 <
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 <
905 >      // exclude_I must always be the smaller of the pair
906 >      if( exI > exJ ){
907 >        tempEx = exI;
908 >        exI = exJ;
909 >        exJ = tempEx;
910 >      }
911   #ifdef IS_MPI
912 <      if( mpiSim->getMyMolStart() <= molIndex &&
913 <          molIndex <= mpiSim->getMyMolEnd() ){
914 < #endif // is_mpi        
915 <
916 <      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
917 <
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 <        
912 >      tempEx = exI;
913 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
914 >      tempEx = exJ;
915 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
916 >      
917 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
918   #else  // isn't MPI
919 <        
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)
919 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
920   #endif  //is_mpi
921 <        
921 >    }
922 >    excludeOffset += info.nTorsions;
923  
924 <        // increment the index and repeat;
925 <        index++;
1014 <      }
1015 <      offset += comp_stamps[i]->getNAtoms();
924 >    
925 >    // send the arrays off to the forceField for init.
926  
927 < #ifdef IS_MPI
928 <      }
929 < #endif //is_mpi      
927 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
928 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
929 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
930 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
931  
932 <      molIndex++;
933 <    }
932 >
933 >    the_molecules[i].initialize( info );
934 >    atomOffset += info.nAtoms;
935 >    delete[] theBonds;
936 >    delete[] theBends;
937 >    delete[] theTorsions;
938    }
939  
940 <  the_ff->initializeTorsions( the_torsions );
940 >  // clean up the forcefield
941 >  the_ff->calcRcut();
942 >  the_ff->cleanMe();
943   }
944  
945   void SimSetup::initFromBass( void ){

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