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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 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC

# Line 66 | Line 66 | void SimSetup::createSim( void ){
66  
67    MakeStamps *the_stamps;
68    Globals* the_globals;
69 +  ExtendedSystem* the_extendedsystem;
70    int i, j;
71  
72    // get the stamps and globals;
# Line 80 | Line 81 | void SimSetup::createSim( void ){
81    // get the ones we know are there, yet still may need some work.
82    n_components = the_globals->getNComponents();
83    strcpy( force_field, the_globals->getForceField() );
84 +
85 +  // get the ensemble and set up an extended system if we need it:
86    strcpy( ensemble, the_globals->getEnsemble() );
87 +  if( !strcasecmp( ensemble, "NPT" ) ) {
88 +    the_extendedsystem = new ExtendedSystem( simnfo );
89 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90 +    the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
91 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
92 +    the_extendedsystem = new ExtendedSystem( simnfo );
93 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
94 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
95 +  } else {
96 +    sprintf( painCave.errMsg,
97 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
98 +             "reverting to NVE for this simulation.\n",
99 +             ensemble );
100 +    painCave.isFatal = 0;
101 +    simError();
102 +    strcpy( ensemble, "NVE" );
103 +  }  
104    strcpy( simnfo->ensemble, ensemble );
105  
106    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
107    simnfo->usePBC = the_globals->getPBC();
108            
109 <
110 <
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();
94 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
109 >  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
110 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
111    else{
112      sprintf( painCave.errMsg,
113               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 242 | Line 258 | void SimSetup::createSim( void ){
258  
259    globalIndex = mpiSim->divideLabor();
260  
245 –
246 –
261    // set up the local variables
262    
263    int localMol, allMol;
264    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
265 +
266 +  int* mol2proc = mpiSim->getMolToProcMap();
267 +  int* molCompType = mpiSim->getMolComponentType();
268    
269    allMol = 0;
270    localMol = 0;
# Line 259 | Line 276 | void SimSetup::createSim( void ){
276  
277      for( j=0; j<components_nmol[i]; j++ ){
278        
279 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
279 >      if( mol2proc[j] == worldRank ){
280          
281          local_atoms +=    comp_stamps[i]->getNAtoms();
282          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 295 | void SimSetup::createSim( void ){
295    if( local_atoms != simnfo->n_atoms ){
296      sprintf( painCave.errMsg,
297               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
298 <             " localAtom (%d) are note equal.\n",
298 >             " localAtom (%d) are not equal.\n",
299               simnfo->n_atoms,
300               local_atoms );
301      painCave.isFatal = 1;
# Line 304 | Line 320 | void SimSetup::createSim( void ){
320    Atom::createArrays(simnfo->n_atoms);
321    the_atoms = new Atom*[simnfo->n_atoms];
322    the_molecules = new Molecule[simnfo->n_mol];
323 +  int molIndex;
324  
325 +  // initialize the molecule's stampID's
326  
327 <  if( simnfo->n_SRI ){
328 <    the_sris = new SRI*[simnfo->n_SRI];
329 <    the_excludes = new int[2 * simnfo->n_SRI];
327 > #ifdef IS_MPI
328 >  
329 >
330 >  molIndex = 0;
331 >  for(i=0; i<mpiSim->getTotNmol(); i++){
332 >    
333 >    if(mol2proc[i] == worldRank ){
334 >      the_molecules[molIndex].setStampID( molCompType[i] );
335 >      the_molecules[molIndex].setMyIndex( molIndex );
336 >      molIndex++;
337 >    }
338 >  }
339 >
340 > #else // is_mpi
341 >  
342 >  molIndex = 0;
343 >  for(i=0; i<n_components; i++){
344 >    for(j=0; j<components_nmol[i]; j++ ){
345 >      the_molecules[molIndex].setStampID( i );
346 >      the_molecules[molIndex].setMyIndex( molIndex );
347 >      molIndex++;
348 >    }
349 >  }
350 >    
351 >
352 > #endif // is_mpi
353 >
354 >
355 >  if( simnfo->n_SRI ){
356 >    
357 >    Exclude::createArray(simnfo->n_SRI);
358 >    the_excludes = new Exclude*[simnfo->n_SRI];
359 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
360      simnfo->globalExcludes = new int;
361 <    simnfo->n_exclude = tot_SRI;
361 >    simnfo->n_exclude = simnfo->n_SRI;
362    }
363    else{
364      
365 <    the_excludes = new int[2];
366 <    the_excludes[0] = 0;
367 <    the_excludes[1] = 0;
365 >    Exclude::createArray( 1 );
366 >    the_excludes = new Exclude*;
367 >    the_excludes[0] = new Exclude(0);
368 >    the_excludes[0]->setPair( 0,0 );
369      simnfo->globalExcludes = new int;
370      simnfo->globalExcludes[0] = 0;
371 <
323 <    simnfo->n_exclude = 1;
371 >    simnfo->n_exclude = 0;
372    }
373  
374    // set the arrays into the SimInfo object
375  
376    simnfo->atoms = the_atoms;
377 <  simnfo->sr_interactions = the_sris;
377 >  simnfo->molecules = the_molecules;
378    simnfo->nGlobalExcludes = 0;
379    simnfo->excludes = the_excludes;
380  
# Line 383 | Line 431 | void SimSetup::createSim( void ){
431  
432    the_ff->setSimInfo( simnfo );
433  
434 <  makeAtoms();
434 >  makeMolecules();
435    simnfo->identArray = new int[simnfo->n_atoms];
436    for(i=0; i<simnfo->n_atoms; i++){
437      simnfo->identArray[i] = the_atoms[i]->getIdent();
438    }
439    
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 –
440    if (the_globals->getUseRF() ) {
441      simnfo->useReactionField = 1;
442    
# Line 638 | Line 673 | void SimSetup::createSim( void ){
673  
674   //   new AllLong( simnfo );
675  
676 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
677 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
678 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
679 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
680 <
676 >  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo,
677 >                                                           the_ff,
678 >                                                           the_extendedsystem);
679 >  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo,
680 >                                                 the_ff,
681 >                                                 the_extendedsystem );
682  
683 + #ifdef IS_MPI
684 +  mpiSim->mpiRefresh();
685 + #endif
686  
687    // initialize the Fortran
688 <  
688 >
689 >
690    simnfo->refreshSim();
691    
692    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 674 | Line 714 | void SimSetup::makeMolecules( void ){
714  
715   void SimSetup::makeMolecules( void ){
716  
717 <  int i, j, exI, exJ, tempEx, stampID, atomOffset;
717 >  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
718    molInit info;
719    DirectionalAtom* dAtom;
720 +  LinkedAssign* extras;
721 +  LinkedAssign* current_extra;
722    AtomStamp* currentAtom;
723    BondStamp* currentBond;
724    BendStamp* currentBend;
725    TorsionStamp* currentTorsion;
726 +
727 +  bond_pair* theBonds;
728 +  bend_set* theBends;
729 +  torsion_set* theTorsions;
730 +
731    
732    //init the forceField paramters
733  
734    the_ff->readParams();
735  
736    
737 <  // init the molecules
737 >  // init the atoms
738  
739 +  double ux, uy, uz, u, uSqr;
740 +  
741    atomOffset = 0;
742 +  excludeOffset = 0;
743    for(i=0; i<simnfo->n_mol; i++){
744      
745      stampID = the_molecules[i].getStampID();
# Line 698 | Line 748 | void SimSetup::makeMolecules( void ){
748      info.nBonds    = comp_stamps[stampID]->getNBonds();
749      info.nBends    = comp_stamps[stampID]->getNBends();
750      info.nTorsions = comp_stamps[stampID]->getNTorsions();
751 <    
751 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
752 >
753      info.myAtoms = &the_atoms[atomOffset];
754 +    info.myExcludes = &the_excludes[excludeOffset];
755      info.myBonds = new Bond*[info.nBonds];
756      info.myBends = new Bend*[info.nBends];
757 <    info.myTorsions = new Torsions*[info.nTorsions];
757 >    info.myTorsions = new Torsion*[info.nTorsions];
758  
759      theBonds = new bond_pair[info.nBonds];
760      theBends = new bend_set[info.nBends];
# Line 712 | Line 764 | void SimSetup::makeMolecules( void ){
764      
765      for(j=0; j<info.nAtoms; j++){
766        
767 <      currentAtom = theComponents[stampID]->getAtom( j );
767 >      currentAtom = comp_stamps[stampID]->getAtom( j );
768        if( currentAtom->haveOrientation() ){
769          
770          dAtom = new DirectionalAtom(j + atomOffset);
# Line 747 | Line 799 | void SimSetup::makeMolecules( void ){
799      }
800      
801      // make the bonds
802 <    for(j=0; j<nBonds; j++){
802 >    for(j=0; j<info.nBonds; j++){
803        
804        currentBond = comp_stamps[stampID]->getBond( j );
805        theBonds[j].a = currentBond->getA() + atomOffset;
806        theBonds[j].b = currentBond->getB() + atomOffset;
807  
808 <      exI = theBonds[i].a;
809 <      exJ = theBonds[i].b;
808 >      exI = theBonds[j].a;
809 >      exJ = theBonds[j].b;
810  
811        // exclude_I must always be the smaller of the pair
812        if( exI > exJ ){
# Line 763 | Line 815 | void SimSetup::makeMolecules( void ){
815          exJ = tempEx;
816        }
817   #ifdef IS_MPI
818 +      tempEx = exI;
819 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
820 +      tempEx = exJ;
821 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
822        
823 <      the_excludes[index*2] =    
768 <        the_atoms[exI]->getGlobalIndex() + 1;
769 <      the_excludes[index*2 + 1] =
770 <        the_atoms[exJ]->getGlobalIndex() + 1;
771 <      
823 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
824   #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)
825  
826 +      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
827   #endif  //is_mpi
828 <    
829 <  }
781 <
782 <
783 <
784 <
785 <
828 >    }
829 >    excludeOffset += info.nBonds;
830  
831 <
832 <
833 <
834 <
835 <
836 <
837 <
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++ ){
831 >    //make the bends
832 >    for(j=0; j<info.nBends; j++){
833 >      
834 >      currentBend = comp_stamps[stampID]->getBend( j );
835 >      theBends[j].a = currentBend->getA() + atomOffset;
836 >      theBends[j].b = currentBend->getB() + atomOffset;
837 >      theBends[j].c = currentBend->getC() + atomOffset;
838            
839 <          current_atom = comp_stamps[i]->getAtom( k );
822 <          if( current_atom->haveOrientation() ){
839 >      if( currentBend->haveExtras() ){
840              
841 <            dAtom = new DirectionalAtom(index);
842 <            simnfo->n_oriented++;
826 <            the_atoms[index] = dAtom;
841 >        extras = currentBend->getExtras();
842 >        current_extra = extras;
843              
844 <            ux = current_atom->getOrntX();
845 <            uy = current_atom->getOrntY();
846 <            uz = current_atom->getOrntZ();
847 <            
848 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
849 <            
850 <            u = sqrt( uSqr );
851 <            ux = ux / u;
852 <            uy = uy / u;
853 <            uz = uz / u;
854 <            
855 <            dAtom->setSUx( ux );
856 <            dAtom->setSUy( uy );
857 <            dAtom->setSUz( uz );
844 >        while( current_extra != NULL ){
845 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
846 >                
847 >            switch( current_extra->getType() ){
848 >              
849 >            case 0:
850 >              theBends[j].ghost =
851 >                current_extra->getInt() + atomOffset;
852 >              theBends[j].isGhost = 1;
853 >              break;
854 >                  
855 >            case 1:
856 >              theBends[j].ghost =
857 >                (int)current_extra->getDouble() + atomOffset;
858 >              theBends[j].isGhost = 1;
859 >              break;
860 >              
861 >            default:
862 >              sprintf( painCave.errMsg,
863 >                       "SimSetup Error: ghostVectorSource was neither a "
864 >                       "double nor an int.\n"
865 >                       "-->Bend[%d] in %s\n",
866 >                       j, comp_stamps[stampID]->getID() );
867 >              painCave.isFatal = 1;
868 >              simError();
869 >            }
870            }
871 +          
872            else{
873 <            the_atoms[index] = new GeneralAtom(index);
873 >            
874 >            sprintf( painCave.errMsg,
875 >                     "SimSetup Error: unhandled bend assignment:\n"
876 >                     "    -->%s in Bend[%d] in %s\n",
877 >                     current_extra->getlhs(),
878 >                     j, comp_stamps[stampID]->getID() );
879 >            painCave.isFatal = 1;
880 >            simError();
881            }
846 –          the_atoms[index]->setType( current_atom->getType() );
847 –          the_atoms[index]->setIndex( index );
882            
883 <          // increment the index and repeat;
850 <          index++;
883 >          current_extra = current_extra->getNext();
884          }
885 +      }
886 +          
887 +      if( !theBends[j].isGhost ){
888 +            
889 +        exI = theBends[j].a;
890 +        exJ = theBends[j].c;
891 +      }
892 +      else{
893          
894 <        molEnd = index -1;
895 <        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
894 >        exI = theBends[j].a;
895 >        exJ = theBends[j].b;
896        }
862 – #endif //is_mpi
897        
898 <      molIndex++;
898 >      // exclude_I must always be the smaller of the pair
899 >      if( exI > exJ ){
900 >        tempEx = exI;
901 >        exI = exJ;
902 >        exJ = tempEx;
903 >      }
904 > #ifdef IS_MPI
905 >      tempEx = exI;
906 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
907 >      tempEx = exJ;
908 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
909 >      
910 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
911 > #else  // isn't MPI
912 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
913 > #endif  //is_mpi
914      }
915 <  }
915 >    excludeOffset += info.nBends;
916  
917 < #ifdef IS_MPI
918 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
919 <    
920 <    delete[] globalIndex;
917 >    for(j=0; j<info.nTorsions; j++){
918 >      
919 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
920 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
921 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
922 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
923 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
924 >      
925 >      exI = theTorsions[j].a;
926 >      exJ = theTorsions[j].d;
927  
928 <    mpiSim->mpiRefresh();
929 < #endif //IS_MPI
930 <          
931 <  the_ff->initializeAtoms();
932 < }
933 <
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 <
928 >      // exclude_I must always be the smaller of the pair
929 >      if( exI > exJ ){
930 >        tempEx = exI;
931 >        exI = exJ;
932 >        exJ = tempEx;
933 >      }
934   #ifdef IS_MPI
935 <      if( mpiSim->getMyMolStart() <= molIndex &&
936 <          molIndex <= mpiSim->getMyMolEnd() ){
937 < #endif // is_mpi        
938 <        
939 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
940 <          
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 <
935 >      tempEx = exI;
936 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
937 >      tempEx = exJ;
938 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
939 >      
940 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
941   #else  // isn't MPI
942 <          
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)
942 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
943   #endif  //is_mpi
944 <          
945 <          // 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 <  }
944 >    }
945 >    excludeOffset += info.nTorsions;
946  
947 <  the_ff->initializeBonds( the_bonds );
948 < }
947 >    
948 >    // send the arrays off to the forceField for init.
949  
950 < void SimSetup::makeBends( void ){
950 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
951 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
952 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
953 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
954  
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 –  
955  
956 <  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 <          }
956 >    the_molecules[i].initialize( info );
957  
958  
959 < #ifdef IS_MPI
960 <
961 <          the_excludes[(index + tot_bonds)*2] =    
962 <            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 <    }
959 >    atomOffset += info.nAtoms;
960 >    delete[] theBonds;
961 >    delete[] theBends;
962 >    delete[] theTorsions;
963    }
964  
965   #ifdef IS_MPI
966 <  sprintf( checkPointMsg,
1072 <           "Successfully created the bends list.\n" );
966 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
967    MPIcheckPoint();
968   #endif // is_mpi
969 <  
969 >
970 >  // clean up the forcefield
971 >  the_ff->calcRcut();
972 >  the_ff->cleanMe();
973  
1077 –  the_ff->initializeBends( the_bends );
974   }
975  
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;
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 );
1148 – }
1149 –
976   void SimSetup::initFromBass( void ){
977  
978    int i, j, k;

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