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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 424 by mmeineke, Thu Mar 27 20:36:16 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 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;
# Line 690 | Line 704 | void SimSetup::makeMolecules( void ){
704    // init the molecules
705  
706    atomOffset = 0;
707 +  excludeOffset = 0;
708    for(i=0; i<simnfo->n_mol; i++){
709      
710      stampID = the_molecules[i].getStampID();
# Line 698 | Line 713 | void SimSetup::makeMolecules( void ){
713      info.nBonds    = comp_stamps[stampID]->getNBonds();
714      info.nBends    = comp_stamps[stampID]->getNBends();
715      info.nTorsions = comp_stamps[stampID]->getNTorsions();
716 <    
716 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
717 >
718      info.myAtoms = &the_atoms[atomOffset];
719 +    info.myExcludes = &the_excludes[excludeOffset];
720      info.myBonds = new Bond*[info.nBonds];
721      info.myBends = new Bend*[info.nBends];
722      info.myTorsions = new Torsions*[info.nTorsions];
# Line 747 | Line 764 | void SimSetup::makeMolecules( void ){
764      }
765      
766      // make the bonds
767 <    for(j=0; j<nBonds; j++){
767 >    for(j=0; j<info.nBonds; j++){
768        
769        currentBond = comp_stamps[stampID]->getBond( j );
770        theBonds[j].a = currentBond->getA() + atomOffset;
# Line 763 | Line 780 | void SimSetup::makeMolecules( void ){
780          exJ = tempEx;
781        }
782   #ifdef IS_MPI
783 +      tempEx = exI;
784 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
785 +      tempEx = exJ;
786 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
787        
788 <      the_excludes[index*2] =    
768 <        the_atoms[exI]->getGlobalIndex() + 1;
769 <      the_excludes[index*2 + 1] =
770 <        the_atoms[exJ]->getGlobalIndex() + 1;
771 <      
788 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
789   #else  // isn't MPI
790 <      
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 <
790 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
791   #endif  //is_mpi
792 <    
793 <  }
792 >    }
793 >    excludeOffset += info.nBonds;
794  
795 <
796 <
797 <
798 <
799 <
800 <
801 <
802 <
803 <
804 <
805 <
806 <
807 <
808 <
809 < void SimSetup::makeAtoms( void ){
810 <
811 <  int i, j, k, index;
812 <  double ux, uy, uz, uSqr, u;
813 <  AtomStamp* current_atom;
814 <
815 <  DirectionalAtom* dAtom;
816 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
817 <
818 <  lMolIndex = 0;
819 <  molIndex = 0;
820 <  index = 0;
821 <  for( i=0; i<n_components; i++ ){
822 <
823 <    for( j=0; j<components_nmol[i]; j++ ){
824 <
825 < #ifdef IS_MPI
826 <      if( mpiSim->getMyMolStart() <= molIndex &&
827 <          molIndex <= mpiSim->getMyMolEnd() ){
828 < #endif // is_mpi        
829 <
830 <        molStart = index;
831 <        nMemb = comp_stamps[i]->getNAtoms();
832 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
795 >    //make the bends
796 >    for(j=0; j<info.nBends; j++){
797 >      
798 >      currentBend = comp_stamps[stampID]->getBend( j );
799 >      theBends[j].a = currentBend->getA() + atomOffset;
800 >      theBends[j].b = currentBend->getB() + atomOffset;
801 >      theBends[j].c = currentBend->getC() + atomOffset;
802 >          
803 >      if( currentBend->haveExtras() ){
804 >            
805 >        extras = current_bend->getExtras();
806 >        current_extra = extras;
807 >            
808 >        while( current_extra != NULL ){
809 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
810 >                
811 >            switch( current_extra->getType() ){
812 >              
813 >            case 0:
814 >              theBends[j].ghost =
815 >                current_extra->getInt() + atomOffset;
816 >              theBends[j].isGhost = 1;
817 >              break;
818 >                  
819 >            case 1:
820 >              theBends[j].ghost =
821 >                (int)current_extra->getDouble() + atomOffset;
822 >              theBends[j].isGhost = 1;
823 >              break;
824 >              
825 >            default:
826 >              sprintf( painCave.errMsg,
827 >                       "SimSetup Error: ghostVectorSource was neiter a "
828 >                       "double nor an int.\n"
829 >                       "-->Bend[%d] in %s\n",
830 >                       j, comp_stamps[stampID]->getID() );
831 >              painCave.isFatal = 1;
832 >              simError();
833 >            }
834 >          }
835            
836 <          current_atom = comp_stamps[i]->getAtom( k );
822 <          if( current_atom->haveOrientation() ){
836 >          else{
837              
838 <            dAtom = new DirectionalAtom(index);
839 <            simnfo->n_oriented++;
840 <            the_atoms[index] = dAtom;
841 <            
842 <            ux = current_atom->getOrntX();
843 <            uy = current_atom->getOrntY();
844 <            uz = current_atom->getOrntZ();
831 <            
832 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
833 <            
834 <            u = sqrt( uSqr );
835 <            ux = ux / u;
836 <            uy = uy / u;
837 <            uz = uz / u;
838 <            
839 <            dAtom->setSUx( ux );
840 <            dAtom->setSUy( uy );
841 <            dAtom->setSUz( uz );
838 >            sprintf( painCave.errMsg,
839 >                     "SimSetup Error: unhandled bend assignment:\n"
840 >                     "    -->%s in Bend[%d] in %s\n",
841 >                     current_extra->getlhs(),
842 >                     j, comp_stamps[stampID]->getID() );
843 >            painCave.isFatal = 1;
844 >            simError();
845            }
843 –          else{
844 –            the_atoms[index] = new GeneralAtom(index);
845 –          }
846 –          the_atoms[index]->setType( current_atom->getType() );
847 –          the_atoms[index]->setIndex( index );
846            
847 <          // increment the index and repeat;
850 <          index++;
847 >          current_extra = current_extra->getNext();
848          }
849 +      }
850 +          
851 +      if( !theBends[j].isGhost ){
852 +            
853 +        exI = theBends[j].a;
854 +        exJ = theBends[j].c;
855 +      }
856 +      else{
857          
858 <        molEnd = index -1;
859 <        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
858 >        exI = theBends[j].a;
859 >        exJ = theBends[j].b;
860        }
862 – #endif //is_mpi
861        
862 <      molIndex++;
862 >      // exclude_I must always be the smaller of the pair
863 >      if( exI > exJ ){
864 >        tempEx = exI;
865 >        exI = exJ;
866 >        exJ = tempEx;
867 >      }
868 > #ifdef IS_MPI
869 >      tempEx = exI;
870 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
871 >      tempEx = exJ;
872 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
873 >      
874 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
875 > #else  // isn't MPI
876 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
877 > #endif  //is_mpi
878      }
879 <  }
879 >    excludeOffset += info.nBends;
880  
881 +    for(j=0; j<info.nTorsions; j++){
882 +      
883 +      currentTorsion = comp_stamps[stampID]->getTorsion( j );
884 +      theTorsions[j].a = currentTorsion->getA() + atomOffset;
885 +      theTorsions[j].b = currentTorsion->getB() + atomOffset;
886 +      theTorsions[j].c = currentTorsion->getC() + atomOffset;
887 +      theTorsions[j].d = currentTorsion->getD() + atomOffset;
888 +      
889 +      exI = theTorsions[j].a;
890 +      exJ = theTorsions[j].d;
891 +
892 +      // exclude_I must always be the smaller of the pair
893 +      if( exI > exJ ){
894 +        tempEx = exI;
895 +        exI = exJ;
896 +        exJ = tempEx;
897 +      }
898   #ifdef IS_MPI
899 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
899 >      tempEx = exI;
900 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
901 >      tempEx = exJ;
902 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
903 >      
904 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
905 > #else  // isn't MPI
906 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
907 > #endif  //is_mpi
908 >    }
909 >    excludeOffset += info.nTorsions;
910 >
911      
912 <    delete[] globalIndex;
912 >    // send the arrays off to the forceField for init.
913  
914 <    mpiSim->mpiRefresh();
915 < #endif //IS_MPI
916 <          
917 <  the_ff->initializeAtoms();
877 < }
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++ ){
893 <
894 < #ifdef IS_MPI
895 <      if( mpiSim->getMyMolStart() <= molIndex &&
896 <          molIndex <= mpiSim->getMyMolEnd() ){
897 < #endif // is_mpi        
898 <        
899 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
900 <          
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 <
923 < #else  // isn't MPI
924 <          
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)
928 < #endif  //is_mpi
929 <          
930 <          // 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 <  }
942 <
943 <  the_ff->initializeBonds( the_bonds );
944 < }
945 <
946 < void SimSetup::makeBends( void ){
947 <
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 <  
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;
914 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
915 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
916 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
917 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
918  
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++ ){
919  
920 <    for( j=0; j<components_nmol[i]; j++ ){
921 <
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 <    }
920 >    the_molecules[i].initialize( info );
921 >    atomOffset += info.nAtoms;
922    }
923  
924 <  the_ff->initializeTorsions( the_torsions );
924 >  // clean up the forcefield
925 >  the_ff->calcRcut();
926 >  the_ff->cleanMe();
927   }
928  
929   void SimSetup::initFromBass( void ){

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