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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 434 by chuckv, Fri Mar 28 19:30:59 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 <
661 > #ifdef IS_MPI
662 >  mpiSim->mpiRefresh();
663 > #endif
664  
665    // initialize the Fortran
666 <  
666 >
667 >
668    simnfo->refreshSim();
669    
670    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 674 | Line 692 | void SimSetup::makeMolecules( void ){
692  
693   void SimSetup::makeMolecules( void ){
694  
695 <  int i, j, exI, exJ, tempEx, stampID, atomOffset;
695 >  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
696    molInit info;
697    DirectionalAtom* dAtom;
698 +  LinkedAssign* extras;
699 +  LinkedAssign* current_extra;
700    AtomStamp* currentAtom;
701    BondStamp* currentBond;
702    BendStamp* currentBend;
703    TorsionStamp* currentTorsion;
704 +
705 +  bond_pair* theBonds;
706 +  bend_set* theBends;
707 +  torsion_set* theTorsions;
708 +
709    
710    //init the forceField paramters
711  
712    the_ff->readParams();
713  
714    
715 <  // init the molecules
715 >  // init the atoms
716  
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      stampID = the_molecules[i].getStampID();
# Line 698 | Line 726 | void SimSetup::makeMolecules( void ){
726      info.nBonds    = comp_stamps[stampID]->getNBonds();
727      info.nBends    = comp_stamps[stampID]->getNBends();
728      info.nTorsions = comp_stamps[stampID]->getNTorsions();
729 <    
729 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
730 >
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 Torsions*[info.nTorsions];
735 >    info.myTorsions = new Torsion*[info.nTorsions];
736  
737      theBonds = new bond_pair[info.nBonds];
738      theBends = new bend_set[info.nBends];
# Line 712 | Line 742 | void SimSetup::makeMolecules( void ){
742      
743      for(j=0; j<info.nAtoms; j++){
744        
745 <      currentAtom = theComponents[stampID]->getAtom( j );
745 >      currentAtom = comp_stamps[stampID]->getAtom( j );
746        if( currentAtom->haveOrientation() ){
747          
748          dAtom = new DirectionalAtom(j + atomOffset);
# Line 747 | Line 777 | void SimSetup::makeMolecules( void ){
777      }
778      
779      // make the bonds
780 <    for(j=0; j<nBonds; j++){
780 >    for(j=0; j<info.nBonds; j++){
781        
782        currentBond = comp_stamps[stampID]->getBond( j );
783        theBonds[j].a = currentBond->getA() + atomOffset;
# Line 763 | Line 793 | void SimSetup::makeMolecules( void ){
793          exJ = tempEx;
794        }
795   #ifdef 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[index*2] =    
768 <        the_atoms[exI]->getGlobalIndex() + 1;
769 <      the_excludes[index*2 + 1] =
770 <        the_atoms[exJ]->getGlobalIndex() + 1;
771 <      
801 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
802   #else  // isn't MPI
803 <      
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 <
803 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
804   #endif  //is_mpi
805 <    
806 <  }
805 >    }
806 >    excludeOffset += info.nBonds;
807  
808 <
809 <
810 <
811 <
812 <
813 <
814 <
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++ ){
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_atom = comp_stamps[i]->getAtom( k );
822 <          if( current_atom->haveOrientation() ){
816 >      if( currentBend->haveExtras() ){
817              
818 <            dAtom = new DirectionalAtom(index);
819 <            simnfo->n_oriented++;
826 <            the_atoms[index] = dAtom;
818 >        extras = currentBend->getExtras();
819 >        current_extra = extras;
820              
821 <            ux = current_atom->getOrntX();
822 <            uy = current_atom->getOrntY();
823 <            uz = current_atom->getOrntZ();
824 <            
825 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
826 <            
827 <            u = sqrt( uSqr );
828 <            ux = ux / u;
829 <            uy = uy / u;
830 <            uz = uz / u;
831 <            
832 <            dAtom->setSUx( ux );
833 <            dAtom->setSUy( uy );
834 <            dAtom->setSUz( uz );
821 >        while( current_extra != NULL ){
822 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
823 >                
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 1:
833 >              theBends[j].ghost =
834 >                (int)current_extra->getDouble() + atomOffset;
835 >              theBends[j].isGhost = 1;
836 >              break;
837 >              
838 >            default:
839 >              sprintf( painCave.errMsg,
840 >                       "SimSetup Error: ghostVectorSource was neither 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 +          
849            else{
850 <            the_atoms[index] = new GeneralAtom(index);
850 >            
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            }
846 –          the_atoms[index]->setType( current_atom->getType() );
847 –          the_atoms[index]->setIndex( index );
859            
860 <          // increment the index and repeat;
850 <          index++;
860 >          current_extra = current_extra->getNext();
861          }
862 +      }
863 +          
864 +      if( !theBends[j].isGhost ){
865 +            
866 +        exI = theBends[j].a;
867 +        exJ = theBends[j].c;
868 +      }
869 +      else{
870          
871 <        molEnd = index -1;
872 <        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
871 >        exI = theBends[j].a;
872 >        exJ = theBends[j].b;
873        }
862 – #endif //is_mpi
874        
875 <      molIndex++;
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 >      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 <  }
892 >    excludeOffset += info.nBends;
893  
894 < #ifdef IS_MPI
895 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
896 <    
897 <    delete[] globalIndex;
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 <    mpiSim->mpiRefresh();
906 < #endif //IS_MPI
907 <          
908 <  the_ff->initializeAtoms();
909 < }
910 <
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 <
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]->getNBonds(); k++ ){
917 <          
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 <
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 <          
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)
919 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
920   #endif  //is_mpi
921 <          
922 <          // 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 <  }
921 >    }
922 >    excludeOffset += info.nTorsions;
923  
924 <  the_ff->initializeBonds( the_bonds );
925 < }
924 >    
925 >    // send the arrays off to the forceField for init.
926  
927 < void SimSetup::makeBends( void ){
928 <
929 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
930 <  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 <          }
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  
933 < #ifdef IS_MPI
934 <
935 <          the_excludes[(index + tot_bonds)*2] =    
936 <            the_atoms[exI]->getGlobalIndex() + 1;
937 <          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 <    }
933 >    the_molecules[i].initialize( info );
934 >    atomOffset += info.nAtoms;
935 >    delete[] theBonds;
936 >    delete[] theBends;
937 >    delete[] theTorsions;
938    }
939  
940   #ifdef IS_MPI
941 <  sprintf( checkPointMsg,
1072 <           "Successfully created the bends list.\n" );
941 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
942    MPIcheckPoint();
943   #endif // is_mpi
1075 –  
944  
945 <  the_ff->initializeBends( the_bends );
946 < }
947 <
1080 < void SimSetup::makeTorsions( void ){
945 >  // clean up the forcefield
946 >  the_ff->calcRcut();
947 >  the_ff->cleanMe();
948  
1082 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1083 –  torsion_set* the_torsions;
1084 –  TorsionStamp* current_torsion;
1085 –
1086 –  the_torsions = new torsion_set[tot_torsions];
1087 –  index = 0;
1088 –  offset = 0;
1089 –  molIndex = 0;
1090 –  for( i=0; i<n_components; i++ ){
1091 –
1092 –    for( j=0; j<components_nmol[i]; j++ ){
1093 –
1094 – #ifdef IS_MPI
1095 –      if( mpiSim->getMyMolStart() <= molIndex &&
1096 –          molIndex <= mpiSim->getMyMolEnd() ){
1097 – #endif // is_mpi        
1098 –
1099 –      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1100 –
1101 –        current_torsion = comp_stamps[i]->getTorsion( k );
1102 –        the_torsions[index].a = current_torsion->getA() + offset;
1103 –        the_torsions[index].b = current_torsion->getB() + offset;
1104 –        the_torsions[index].c = current_torsion->getC() + offset;
1105 –        the_torsions[index].d = current_torsion->getD() + offset;
1106 –
1107 –        exI = the_torsions[index].a;
1108 –        exJ = the_torsions[index].d;
1109 –
1110 –        
1111 –        // exclude_I must always be the smaller of the pair
1112 –        if( exI > exJ ){
1113 –          tempEx = exI;
1114 –          exI = exJ;
1115 –          exJ = tempEx;
1116 –        }
1117 –
1118 –
1119 – #ifdef IS_MPI
1120 –        
1121 –        the_excludes[(index + tot_bonds + tot_bends)*2] =    
1122 –          the_atoms[exI]->getGlobalIndex() + 1;
1123 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1124 –          the_atoms[exJ]->getGlobalIndex() + 1;
1125 –        
1126 – #else  // isn't MPI
1127 –        
1128 –        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1129 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1130 –        // fortran indexes from 1 (hence the +1 in the indexing)
1131 – #endif  //is_mpi
1132 –        
1133 –
1134 –        // increment the index and repeat;
1135 –        index++;
1136 –      }
1137 –      offset += comp_stamps[i]->getNAtoms();
1138 –
1139 – #ifdef IS_MPI
1140 –      }
1141 – #endif //is_mpi      
1142 –
1143 –      molIndex++;
1144 –    }
1145 –  }
1146 –
1147 –  the_ff->initializeTorsions( the_torsions );
949   }
950  
951   void SimSetup::initFromBass( void ){

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