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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 422 by mmeineke, Thu Mar 27 19:21:42 2003 UTC

# Line 248 | Line 248 | void SimSetup::createSim( void ){
248    
249    int localMol, allMol;
250    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251 +
252 +  int* mol2proc = mpiSim->getMolToProcMap();
253 +  int* molCompType = mpiSim->getMolComponentType();
254    
255    allMol = 0;
256    localMol = 0;
# Line 259 | Line 262 | void SimSetup::createSim( void ){
262  
263      for( j=0; j<components_nmol[i]; j++ ){
264        
265 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
265 >      if( mol2proc[j] == worldRank ){
266          
267          local_atoms +=    comp_stamps[i]->getNAtoms();
268          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 281 | void SimSetup::createSim( void ){
281    if( local_atoms != simnfo->n_atoms ){
282      sprintf( painCave.errMsg,
283               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
284 <             " localAtom (%d) are note equal.\n",
284 >             " localAtom (%d) are not equal.\n",
285               simnfo->n_atoms,
286               local_atoms );
287      painCave.isFatal = 1;
# Line 304 | Line 306 | void SimSetup::createSim( void ){
306    Atom::createArrays(simnfo->n_atoms);
307    the_atoms = new Atom*[simnfo->n_atoms];
308    the_molecules = new Molecule[simnfo->n_mol];
309 +  int molIndex;
310 +
311 +  // initialize the molecule's stampID's
312  
313 + #ifdef IS_MPI
314 +  
315  
316 +  molIndex = 0;
317 +  for(i=0; i<mpiSim->getTotNmol(); i++){
318 +    
319 +    if(mol2proc[i] == worldRank ){
320 +      the_molecules[molIndex].setStampID( molCompType[i] );
321 +      molIndex++;
322 +    }
323 +  }
324 +
325 + #else // is_mpi
326 +  
327 +  molIndex = 0;
328 +  for(i=0; i<n_components; i++){
329 +    for(j=0; j<components_nmol[i]; j++ ){
330 +      the_molecules[molIndex].setStampID( i );
331 +      molIndex++;
332 +    }
333 +  }
334 +    
335 +
336 + #endif // is_mpi
337 +
338 +
339    if( simnfo->n_SRI ){
340 <    the_sris = new SRI*[simnfo->n_SRI];
341 <    the_excludes = new int[2 * simnfo->n_SRI];
340 >    Exclude::createArray(simnfo->n_SRI);
341 >    the_excludes = new Exclude*[simnfo->n_SRI];
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;
329 –  simnfo->sr_interactions = the_sris;
359    simnfo->nGlobalExcludes = 0;
360    simnfo->excludes = the_excludes;
361  
# Line 383 | Line 412 | void SimSetup::createSim( void ){
412  
413    the_ff->setSimInfo( simnfo );
414  
415 <  makeAtoms();
415 >  makeMolecules();
416    simnfo->identArray = new int[simnfo->n_atoms];
417    for(i=0; i<simnfo->n_atoms; i++){
418      simnfo->identArray[i] = the_atoms[i]->getIdent();
419    }
420    
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 –
421    if (the_globals->getUseRF() ) {
422      simnfo->useReactionField = 1;
423    
# Line 674 | Line 690 | void SimSetup::makeMolecules( void ){
690  
691   void SimSetup::makeMolecules( void ){
692  
693 <  int i, j, exI, exJ, tempEx, stampID, atomOffset;
693 >  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
694    molInit info;
695    DirectionalAtom* dAtom;
696 +  LinkedAssign* extras;
697 +  LinkedAssign* current_extra;
698    AtomStamp* currentAtom;
699    BondStamp* currentBond;
700    BendStamp* currentBend;
# Line 690 | Line 708 | void SimSetup::makeMolecules( void ){
708    // init the molecules
709  
710    atomOffset = 0;
711 +  excludeOffset = 0;
712    for(i=0; i<simnfo->n_mol; i++){
713      
714      stampID = the_molecules[i].getStampID();
# Line 698 | Line 717 | void SimSetup::makeMolecules( void ){
717      info.nBonds    = comp_stamps[stampID]->getNBonds();
718      info.nBends    = comp_stamps[stampID]->getNBends();
719      info.nTorsions = comp_stamps[stampID]->getNTorsions();
720 <    
720 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
721 >
722      info.myAtoms = &the_atoms[atomOffset];
723 +    info.myExcludes = &the_excludes[excludeOffset];
724      info.myBonds = new Bond*[info.nBonds];
725      info.myBends = new Bend*[info.nBends];
726      info.myTorsions = new Torsions*[info.nTorsions];
# Line 747 | Line 768 | void SimSetup::makeMolecules( void ){
768      }
769      
770      // make the bonds
771 <    for(j=0; j<nBonds; j++){
771 >    for(j=0; j<info.nBonds; j++){
772        
773        currentBond = comp_stamps[stampID]->getBond( j );
774        theBonds[j].a = currentBond->getA() + atomOffset;
# Line 763 | Line 784 | void SimSetup::makeMolecules( void ){
784          exJ = tempEx;
785        }
786   #ifdef IS_MPI
787 +      tempEx = exI;
788 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
789 +      tempEx = exJ;
790 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
791        
792 <      the_excludes[index*2] =    
768 <        the_atoms[exI]->getGlobalIndex() + 1;
769 <      the_excludes[index*2 + 1] =
770 <        the_atoms[exJ]->getGlobalIndex() + 1;
771 <      
792 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
793   #else  // isn't MPI
794 <      
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 <
794 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
795   #endif  //is_mpi
796 <    
797 <  }
796 >    }
797 >    excludeOffset += info.nBonds;
798  
799 <
800 <
801 <
802 <
803 <
804 <
805 <
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++ ){
799 >    //make the bends
800 >    for(j=0; j<info.nBends; j++){
801 >      
802 >      currentBend = comp_stamps[stampID]->getBend( j );
803 >      theBends[j].a = currentBend->getA() + atomOffset;
804 >      theBends[j].b = currentBend->getB() + atomOffset;
805 >      theBends[j].c = currentBend->getC() + atomOffset;
806            
807 <          current_atom = comp_stamps[i]->getAtom( k );
822 <          if( current_atom->haveOrientation() ){
807 >      if( currentBend->haveExtras() ){
808              
809 <            dAtom = new DirectionalAtom(index);
810 <            simnfo->n_oriented++;
826 <            the_atoms[index] = dAtom;
809 >        extras = current_bend->getExtras();
810 >        current_extra = extras;
811              
812 <            ux = current_atom->getOrntX();
813 <            uy = current_atom->getOrntY();
814 <            uz = current_atom->getOrntZ();
815 <            
816 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
817 <            
818 <            u = sqrt( uSqr );
819 <            ux = ux / u;
820 <            uy = uy / u;
821 <            uz = uz / u;
822 <            
823 <            dAtom->setSUx( ux );
824 <            dAtom->setSUy( uy );
825 <            dAtom->setSUz( uz );
812 >        while( current_extra != NULL ){
813 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
814 >                
815 >            switch( current_extra->getType() ){
816 >              
817 >            case 0:
818 >              theBends[j].ghost =
819 >                current_extra->getInt() + atomOffset;
820 >              theBends[j].isGhost = 1;
821 >              break;
822 >                  
823 >            case 1:
824 >              theBends[j].ghost =
825 >                (int)current_extra->getDouble() + atomOffset;
826 >              theBends[j].isGhost = 1;
827 >              break;
828 >              
829 >            default:
830 >              sprintf( painCave.errMsg,
831 >                       "SimSetup Error: ghostVectorSource was neiter a "
832 >                       "double nor an int.\n"
833 >                       "-->Bend[%d] in %s\n",
834 >                       j, comp_stamps[stampID]->getID() );
835 >              painCave.isFatal = 1;
836 >              simError();
837 >            }
838            }
839 +          
840            else{
841 <            the_atoms[index] = new GeneralAtom(index);
841 >            
842 >            sprintf( painCave.errMsg,
843 >                     "SimSetup Error: unhandled bend assignment:\n"
844 >                     "    -->%s in Bend[%d] in %s\n",
845 >                     current_extra->getlhs(),
846 >                     j, comp_stamps[stampID]->getID() );
847 >            painCave.isFatal = 1;
848 >            simError();
849            }
846 –          the_atoms[index]->setType( current_atom->getType() );
847 –          the_atoms[index]->setIndex( index );
850            
851 <          // increment the index and repeat;
850 <          index++;
851 >          current_extra = current_extra->getNext();
852          }
853 +      }
854 +          
855 +      if( !theBends[j].isGhost ){
856 +            
857 +        exI = theBends[j].a;
858 +        exJ = theBends[j].c;
859 +      }
860 +      else{
861          
862 <        molEnd = index -1;
863 <        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
862 >        exI = theBends[j].a;
863 >        exJ = theBends[j].b;
864        }
862 – #endif //is_mpi
865        
866 <      molIndex++;
866 >      // exclude_I must always be the smaller of the pair
867 >      if( exI > exJ ){
868 >        tempEx = exI;
869 >        exI = exJ;
870 >        exJ = tempEx;
871 >      }
872 > #ifdef IS_MPI
873 >      tempEx = exI;
874 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
875 >      tempEx = exJ;
876 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
877 >      
878 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
879 > #else  // isn't MPI
880 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
881 > #endif  //is_mpi
882      }
883 <  }
883 >    excludeOffset += info.nBends;
884  
885 +    for(j=0; j<info.nTorsions; j++){
886 +      
887 +      currentTorsion = comp_stamps[stampID]->getTorsion( j );
888 +      theTorsions[j].a = currentTorsion->getA() + atomOffset;
889 +      theTorsions[j].b = currentTorsion->getB() + atomOffset;
890 +      theTorsions[j].c = currentTorsion->getC() + atomOffset;
891 +      theTorsions[j].d = currentTorsion->getD() + atomOffset;
892 +      
893 +      exI = theTorsions[j].a;
894 +      exJ = theTorsions[j].d;
895 +
896 +      // exclude_I must always be the smaller of the pair
897 +      if( exI > exJ ){
898 +        tempEx = exI;
899 +        exI = exJ;
900 +        exJ = tempEx;
901 +      }
902   #ifdef IS_MPI
903 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
903 >      tempEx = exI;
904 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
905 >      tempEx = exJ;
906 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
907 >      
908 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
909 > #else  // isn't MPI
910 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
911 > #endif  //is_mpi
912 >    }
913 >    excludeOffset += info.nTorsions;
914 >
915      
916 <    delete[] globalIndex;
916 >    // send the arrays off to the forceField for init.
917  
918 <    mpiSim->mpiRefresh();
919 < #endif //IS_MPI
920 <          
921 <  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;
918 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
919 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
920 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
921 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
922  
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++ ){
923  
924 <    for( j=0; j<components_nmol[i]; j++ ){
925 <
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 <    }
924 >    the_molecules[i].initialize( info );
925 >    atomOffset += info.nAtoms;
926    }
927  
928 <  the_ff->initializeTorsions( the_torsions );
928 >  // clean up the forcefield
929 >  the_ff->calcRcut();
930 >  the_ff->cleanMe();
931   }
932  
933   void SimSetup::initFromBass( void ){

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