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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 443 by mmeineke, Wed Apr 2 22:19:03 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 <  if( simnfo->n_SRI ){
310 <    the_sris = new SRI*[simnfo->n_SRI];
311 <    the_excludes = new int[2 * simnfo->n_SRI];
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 >      the_molecules[molIndex].setMyIndex( molIndex );
318 >      molIndex++;
319 >    }
320 >  }
321 >
322 > #else // is_mpi
323 >  
324 >  molIndex = 0;
325 >  for(i=0; i<n_components; i++){
326 >    for(j=0; j<components_nmol[i]; j++ ){
327 >      the_molecules[molIndex].setStampID( i );
328 >      the_molecules[molIndex].setMyIndex( molIndex );
329 >      molIndex++;
330 >    }
331 >  }
332 >    
333 >
334 > #endif // is_mpi
335 >
336 >
337 >  if( simnfo->n_SRI ){
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;
343 >    simnfo->n_exclude = simnfo->n_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 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;
784        theBonds[j].b = currentBond->getB() + atomOffset;
785  
786 <      exI = theBonds[i].a;
787 <      exJ = theBonds[i].b;
786 >      exI = theBonds[j].a;
787 >      exJ = theBonds[j].b;
788  
789        // exclude_I must always be the smaller of the pair
790        if( exI > exJ ){
# 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
773 –      
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)
803  
804 +      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
805   #endif  //is_mpi
806 <    
807 <  }
806 >    }
807 >    excludeOffset += info.nBonds;
808  
809 <
810 <
811 <
812 <
813 <
814 <
815 <
816 <
817 <
818 <
819 <
820 <
821 <
822 <
823 < void SimSetup::makeAtoms( void ){
824 <
825 <  int i, j, k, index;
826 <  double ux, uy, uz, uSqr, u;
827 <  AtomStamp* current_atom;
828 <
829 <  DirectionalAtom* dAtom;
830 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
831 <
832 <  lMolIndex = 0;
833 <  molIndex = 0;
834 <  index = 0;
835 <  for( i=0; i<n_components; i++ ){
836 <
837 <    for( j=0; j<components_nmol[i]; j++ ){
838 <
839 < #ifdef IS_MPI
840 <      if( mpiSim->getMyMolStart() <= molIndex &&
841 <          molIndex <= mpiSim->getMyMolEnd() ){
842 < #endif // is_mpi        
843 <
844 <        molStart = index;
845 <        nMemb = comp_stamps[i]->getNAtoms();
846 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
809 >    //make the bends
810 >    for(j=0; j<info.nBends; j++){
811 >      
812 >      currentBend = comp_stamps[stampID]->getBend( j );
813 >      theBends[j].a = currentBend->getA() + atomOffset;
814 >      theBends[j].b = currentBend->getB() + atomOffset;
815 >      theBends[j].c = currentBend->getC() + atomOffset;
816 >          
817 >      if( currentBend->haveExtras() ){
818 >            
819 >        extras = currentBend->getExtras();
820 >        current_extra = extras;
821 >            
822 >        while( current_extra != NULL ){
823 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
824 >                
825 >            switch( current_extra->getType() ){
826 >              
827 >            case 0:
828 >              theBends[j].ghost =
829 >                current_extra->getInt() + atomOffset;
830 >              theBends[j].isGhost = 1;
831 >              break;
832 >                  
833 >            case 1:
834 >              theBends[j].ghost =
835 >                (int)current_extra->getDouble() + atomOffset;
836 >              theBends[j].isGhost = 1;
837 >              break;
838 >              
839 >            default:
840 >              sprintf( painCave.errMsg,
841 >                       "SimSetup Error: ghostVectorSource was neither a "
842 >                       "double nor an int.\n"
843 >                       "-->Bend[%d] in %s\n",
844 >                       j, comp_stamps[stampID]->getID() );
845 >              painCave.isFatal = 1;
846 >              simError();
847 >            }
848 >          }
849            
850 <          current_atom = comp_stamps[i]->getAtom( k );
822 <          if( current_atom->haveOrientation() ){
850 >          else{
851              
852 <            dAtom = new DirectionalAtom(index);
853 <            simnfo->n_oriented++;
854 <            the_atoms[index] = dAtom;
855 <            
856 <            ux = current_atom->getOrntX();
857 <            uy = current_atom->getOrntY();
858 <            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 );
852 >            sprintf( painCave.errMsg,
853 >                     "SimSetup Error: unhandled bend assignment:\n"
854 >                     "    -->%s in Bend[%d] in %s\n",
855 >                     current_extra->getlhs(),
856 >                     j, comp_stamps[stampID]->getID() );
857 >            painCave.isFatal = 1;
858 >            simError();
859            }
843 –          else{
844 –            the_atoms[index] = new GeneralAtom(index);
845 –          }
846 –          the_atoms[index]->setType( current_atom->getType() );
847 –          the_atoms[index]->setIndex( index );
860            
861 <          // increment the index and repeat;
850 <          index++;
861 >          current_extra = current_extra->getNext();
862          }
863 +      }
864 +          
865 +      if( !theBends[j].isGhost ){
866 +            
867 +        exI = theBends[j].a;
868 +        exJ = theBends[j].c;
869 +      }
870 +      else{
871          
872 <        molEnd = index -1;
873 <        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
872 >        exI = theBends[j].a;
873 >        exJ = theBends[j].b;
874        }
862 – #endif //is_mpi
875        
876 <      molIndex++;
876 >      // exclude_I must always be the smaller of the pair
877 >      if( exI > exJ ){
878 >        tempEx = exI;
879 >        exI = exJ;
880 >        exJ = tempEx;
881 >      }
882 > #ifdef IS_MPI
883 >      tempEx = exI;
884 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
885 >      tempEx = exJ;
886 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
887 >      
888 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
889 > #else  // isn't MPI
890 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
891 > #endif  //is_mpi
892      }
893 <  }
893 >    excludeOffset += info.nBends;
894  
895 +    for(j=0; j<info.nTorsions; j++){
896 +      
897 +      currentTorsion = comp_stamps[stampID]->getTorsion( j );
898 +      theTorsions[j].a = currentTorsion->getA() + atomOffset;
899 +      theTorsions[j].b = currentTorsion->getB() + atomOffset;
900 +      theTorsions[j].c = currentTorsion->getC() + atomOffset;
901 +      theTorsions[j].d = currentTorsion->getD() + atomOffset;
902 +      
903 +      exI = theTorsions[j].a;
904 +      exJ = theTorsions[j].d;
905 +
906 +      // exclude_I must always be the smaller of the pair
907 +      if( exI > exJ ){
908 +        tempEx = exI;
909 +        exI = exJ;
910 +        exJ = tempEx;
911 +      }
912   #ifdef IS_MPI
913 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
914 <    
915 <    delete[] globalIndex;
916 <
917 <    mpiSim->mpiRefresh();
918 < #endif //IS_MPI
875 <          
876 <  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 <
913 >      tempEx = exI;
914 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
915 >      tempEx = exJ;
916 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
917 >      
918 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
919   #else  // isn't MPI
920 <          
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)
920 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
921   #endif  //is_mpi
922 <          
923 <          // 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 <  }
922 >    }
923 >    excludeOffset += info.nTorsions;
924  
925 <  the_ff->initializeBonds( the_bonds );
926 < }
925 >    
926 >    // send the arrays off to the forceField for init.
927  
928 < void SimSetup::makeBends( void ){
928 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
929 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
930 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
931 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
932  
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 –  
933  
934 <  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 <          }
934 >    the_molecules[i].initialize( info );
935  
936  
937 < #ifdef IS_MPI
938 <
939 <          the_excludes[(index + tot_bonds)*2] =    
940 <            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 <    }
937 >    atomOffset += info.nAtoms;
938 >    delete[] theBonds;
939 >    delete[] theBends;
940 >    delete[] theTorsions;
941    }
942  
943   #ifdef IS_MPI
944 <  sprintf( checkPointMsg,
1072 <           "Successfully created the bends list.\n" );
944 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
945    MPIcheckPoint();
946   #endif // is_mpi
1075 –  
947  
948 <  the_ff->initializeBends( the_bends );
949 < }
950 <
1080 < void SimSetup::makeTorsions( void ){
948 >  // clean up the forcefield
949 >  the_ff->calcRcut();
950 >  the_ff->cleanMe();
951  
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 );
952   }
953  
954   void SimSetup::initFromBass( void ){

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