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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 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 );
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 <
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 671 | Line 711 | void SimSetup::makeAtoms( void ){
711   #endif // is_mpi
712   }
713  
674 – void SimSetup::makeAtoms( void ){
714  
715 <  int i, j, k, index;
677 <  double ux, uy, uz, uSqr, u;
678 <  AtomStamp* current_atom;
715 > void SimSetup::makeMolecules( void ){
716  
717 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
718 +  molInit info;
719    DirectionalAtom* dAtom;
720 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
721 <
722 <  lMolIndex = 0;
723 <  molIndex = 0;
724 <  index = 0;
725 <  for( i=0; i<n_components; i++ ){
687 <
688 <    for( j=0; j<components_nmol[i]; j++ ){
720 >  LinkedAssign* extras;
721 >  LinkedAssign* current_extra;
722 >  AtomStamp* currentAtom;
723 >  BondStamp* currentBond;
724 >  BendStamp* currentBend;
725 >  TorsionStamp* currentTorsion;
726  
727 < #ifdef IS_MPI
728 <      if( mpiSim->getMyMolStart() <= molIndex &&
729 <          molIndex <= mpiSim->getMyMolEnd() ){
693 < #endif // is_mpi        
727 >  bond_pair* theBonds;
728 >  bend_set* theBends;
729 >  torsion_set* theTorsions;
730  
731 <        molStart = index;
732 <        nMemb = comp_stamps[i]->getNAtoms();
733 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
734 <          
735 <          current_atom = comp_stamps[i]->getAtom( k );
736 <          if( current_atom->haveOrientation() ){
737 <            
702 <            dAtom = new DirectionalAtom(index);
703 <            simnfo->n_oriented++;
704 <            the_atoms[index] = dAtom;
705 <            
706 <            ux = current_atom->getOrntX();
707 <            uy = current_atom->getOrntY();
708 <            uz = current_atom->getOrntZ();
709 <            
710 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
711 <            
712 <            u = sqrt( uSqr );
713 <            ux = ux / u;
714 <            uy = uy / u;
715 <            uz = uz / u;
716 <            
717 <            dAtom->setSUx( ux );
718 <            dAtom->setSUy( uy );
719 <            dAtom->setSUz( uz );
720 <          }
721 <          else{
722 <            the_atoms[index] = new GeneralAtom(index);
723 <          }
724 <          the_atoms[index]->setType( current_atom->getType() );
725 <          the_atoms[index]->setIndex( index );
726 <          
727 <          // increment the index and repeat;
728 <          index++;
729 <        }
730 <        
731 <        molEnd = index -1;
732 <        the_molecules[lMolIndex].setNMembers( nMemb );
733 <        the_molecules[lMolIndex].setStartAtom( molStart );
734 <        the_molecules[lMolIndex].setEndAtom( molEnd );
735 <        the_molecules[lMolIndex].setStampID( i );
736 <        lMolIndex++;
731 >  
732 >  //init the forceField paramters
733 >
734 >  the_ff->readParams();
735 >
736 >  
737 >  // init the atoms
738  
739 < #ifdef IS_MPI
740 <      }
741 < #endif //is_mpi
742 <      
743 <      molIndex++;
743 <    }
744 <  }
745 <
746 < #ifdef IS_MPI
747 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
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 <    delete[] globalIndex;
745 >    stampID = the_molecules[i].getStampID();
746  
747 <    mpiSim->mpiRefresh();
748 < #endif //IS_MPI
749 <          
750 <  the_ff->initializeAtoms();
751 < }
747 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
748 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
749 >    info.nBends    = comp_stamps[stampID]->getNBends();
750 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
751 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
752  
753 < void SimSetup::makeBonds( void ){
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 Torsion*[info.nTorsions];
758  
759 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
760 <  bond_pair* the_bonds;
761 <  BondStamp* current_bond;
762 <
763 <  the_bonds = new bond_pair[tot_bonds];
764 <  index = 0;
765 <  offset = 0;
766 <  molIndex = 0;
767 <
768 <  for( i=0; i<n_components; i++ ){
769 <
770 <    for( j=0; j<components_nmol[i]; j++ ){
771 <
772 < #ifdef IS_MPI
773 <      if( mpiSim->getMyMolStart() <= molIndex &&
774 <          molIndex <= mpiSim->getMyMolEnd() ){
775 < #endif // is_mpi        
759 >    theBonds = new bond_pair[info.nBonds];
760 >    theBends = new bend_set[info.nBends];
761 >    theTorsions = new torsion_set[info.nTorsions];
762 >    
763 >    // make the Atoms
764 >    
765 >    for(j=0; j<info.nAtoms; j++){
766 >      
767 >      currentAtom = comp_stamps[stampID]->getAtom( j );
768 >      if( currentAtom->haveOrientation() ){
769          
770 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
771 <          
772 <          current_bond = comp_stamps[i]->getBond( k );
773 <          the_bonds[index].a = current_bond->getA() + offset;
774 <          the_bonds[index].b = current_bond->getB() + offset;
775 <
776 <          exI = the_bonds[index].a;
777 <          exJ = the_bonds[index].b;
778 <
779 <          // exclude_I must always be the smaller of the pair
780 <          if( exI > exJ ){
781 <            tempEx = exI;
782 <            exI = exJ;
783 <            exJ = tempEx;
784 <          }
785 <
786 <          
770 >        dAtom = new DirectionalAtom(j + atomOffset);
771 >        simnfo->n_oriented++;
772 >        info.myAtoms[j] = dAtom;
773 >        
774 >        ux = currentAtom->getOrntX();
775 >        uy = currentAtom->getOrntY();
776 >        uz = currentAtom->getOrntZ();
777 >        
778 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
779 >        
780 >        u = sqrt( uSqr );
781 >        ux = ux / u;
782 >        uy = uy / u;
783 >        uz = uz / u;
784 >        
785 >        dAtom->setSUx( ux );
786 >        dAtom->setSUy( uy );
787 >        dAtom->setSUz( uz );
788 >      }
789 >      else{
790 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
791 >      }
792 >      info.myAtoms[j]->setType( currentAtom->getType() );
793 >    
794   #ifdef IS_MPI
795 +      
796 +      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
797 +      
798 + #endif // is_mpi
799 +    }
800 +    
801 +    // make the bonds
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 <          the_excludes[index*2] =    
809 <            the_atoms[exI]->getGlobalIndex() + 1;
798 <          the_excludes[index*2 + 1] =
799 <            the_atoms[exJ]->getGlobalIndex() + 1;
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 ){
813 +        tempEx = exI;
814 +        exI = exJ;
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[j+excludeOffset]->setPair( exI, exJ );
824   #else  // isn't MPI
825 <          
826 <          the_excludes[index*2] =     exI + 1;
804 <          the_excludes[index*2 + 1] = exJ + 1;
805 <          // 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 <          // increment the index and repeat;
809 <          index++;
810 <        }
811 <        offset += comp_stamps[i]->getNAtoms();
812 <        
813 < #ifdef IS_MPI
814 <      }
815 < #endif //is_mpi
816 <      
817 <      molIndex++;
818 <    }      
819 <  }
828 >    }
829 >    excludeOffset += info.nBonds;
830  
831 <  the_ff->initializeBonds( the_bonds );
832 < }
833 <
834 < void SimSetup::makeBends( void ){
835 <
836 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
837 <  bend_set* the_bends;
828 <  BendStamp* current_bend;
829 <  LinkedAssign* extras;
830 <  LinkedAssign* current_extra;
831 <  
832 <
833 <  the_bends = new bend_set[tot_bends];
834 <  index = 0;
835 <  offset = 0;
836 <  molIndex = 0;
837 <  for( i=0; i<n_components; i++ ){
838 <
839 <    for( j=0; j<components_nmol[i]; j++ ){
840 <
841 < #ifdef IS_MPI
842 <      if( mpiSim->getMyMolStart() <= molIndex &&
843 <          molIndex <= mpiSim->getMyMolEnd() ){
844 < #endif // is_mpi        
845 <
846 <        for( k=0; k<comp_stamps[i]->getNBends(); 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_bend = comp_stamps[i]->getBend( k );
849 <          the_bends[index].a = current_bend->getA() + offset;
850 <          the_bends[index].b = current_bend->getB() + offset;
851 <          the_bends[index].c = current_bend->getC() + offset;
852 <          
853 <          if( current_bend->haveExtras() ){
839 >      if( currentBend->haveExtras() ){
840              
841 <            extras = current_bend->getExtras();
842 <            current_extra = extras;
841 >        extras = currentBend->getExtras();
842 >        current_extra = extras;
843              
844 <            while( current_extra != NULL ){
845 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
844 >        while( current_extra != NULL ){
845 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
846                  
847 <                switch( current_extra->getType() ){
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 0:
856 <                  the_bends[index].ghost =
857 <                    current_extra->getInt() + offset;
858 <                  the_bends[index].isGhost = 1;
859 <                  break;
868 <                  
869 <                case 1:
870 <                  the_bends[index].ghost =
871 <                    (int)current_extra->getDouble() + offset;
872 <                  the_bends[index].isGhost = 1;
873 <                  break;
874 <                  
875 <                default:
876 <                  sprintf( painCave.errMsg,
877 <                           "SimSetup Error: ghostVectorSource was neiter a "
878 <                           "double nor an int.\n"
879 <                           "-->Bend[%d] in %s\n",
880 <                           k, comp_stamps[i]->getID() );
881 <                  painCave.isFatal = 1;
882 <                  simError();
883 <                }
884 <              }
855 >            case 1:
856 >              theBends[j].ghost =
857 >                (int)current_extra->getDouble() + atomOffset;
858 >              theBends[j].isGhost = 1;
859 >              break;
860                
861 <              else{
862 <                
863 <                sprintf( painCave.errMsg,
864 <                         "SimSetup Error: unhandled bend assignment:\n"
865 <                         "    -->%s in Bend[%d] in %s\n",
866 <                         current_extra->getlhs(),
867 <                         k, comp_stamps[i]->getID() );
868 <                painCave.isFatal = 1;
894 <                simError();
895 <              }
896 <              
897 <              current_extra = current_extra->getNext();
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            
901 –          if( !the_bends[index].isGhost ){
902 –            
903 –            exI = the_bends[index].a;
904 –            exJ = the_bends[index].c;
905 –          }
872            else{
873              
874 <            exI = the_bends[index].a;
875 <            exJ = the_bends[index].b;
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            }
882            
883 <          // exclude_I must always be the smaller of the pair
913 <          if( exI > exJ ){
914 <            tempEx = exI;
915 <            exI = exJ;
916 <            exJ = tempEx;
917 <          }
918 <
919 <
920 < #ifdef IS_MPI
921 <
922 <          the_excludes[(index + tot_bonds)*2] =    
923 <            the_atoms[exI]->getGlobalIndex() + 1;
924 <          the_excludes[(index + tot_bonds)*2 + 1] =
925 <            the_atoms[exJ]->getGlobalIndex() + 1;
926 <          
927 < #else  // isn't MPI
928 <          
929 <          the_excludes[(index + tot_bonds)*2] =     exI + 1;
930 <          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
931 <          // fortran index from 1 (hence the +1 in the indexing)
932 < #endif  //is_mpi
933 <          
934 <          
935 <          // increment the index and repeat;
936 <          index++;
883 >          current_extra = current_extra->getNext();
884          }
885 <        offset += comp_stamps[i]->getNAtoms();
885 >      }
886 >          
887 >      if( !theBends[j].isGhost ){
888 >            
889 >        exI = theBends[j].a;
890 >        exJ = theBends[j].c;
891 >      }
892 >      else{
893          
894 < #ifdef IS_MPI
894 >        exI = theBends[j].a;
895 >        exJ = theBends[j].b;
896        }
897 < #endif //is_mpi
898 <
899 <      molIndex++;
897 >      
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 +    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 +      // 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 <  sprintf( checkPointMsg,
936 <           "Successfully created the bends list.\n" );
937 <  MPIcheckPoint();
938 < #endif // is_mpi
939 <  
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 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
943 > #endif  //is_mpi
944 >    }
945 >    excludeOffset += info.nTorsions;
946  
947 <  the_ff->initializeBends( the_bends );
948 < }
947 >    
948 >    // send the arrays off to the forceField for init.
949  
950 < void SimSetup::makeTorsions( 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  
955 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
956 <  torsion_set* the_torsions;
962 <  TorsionStamp* current_torsion;
955 >
956 >    the_molecules[i].initialize( info );
957  
964 –  the_torsions = new torsion_set[tot_torsions];
965 –  index = 0;
966 –  offset = 0;
967 –  molIndex = 0;
968 –  for( i=0; i<n_components; i++ ){
958  
959 <    for( j=0; j<components_nmol[i]; j++ ){
959 >    atomOffset += info.nAtoms;
960 >    delete[] theBonds;
961 >    delete[] theBends;
962 >    delete[] theTorsions;
963 >  }
964  
965   #ifdef IS_MPI
966 <      if( mpiSim->getMyMolStart() <= molIndex &&
967 <          molIndex <= mpiSim->getMyMolEnd() ){
968 < #endif // is_mpi        
966 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
967 >  MPIcheckPoint();
968 > #endif // is_mpi
969  
970 <      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
970 >  // clean up the forcefield
971 >  the_ff->calcRcut();
972 >  the_ff->cleanMe();
973  
979 –        current_torsion = comp_stamps[i]->getTorsion( k );
980 –        the_torsions[index].a = current_torsion->getA() + offset;
981 –        the_torsions[index].b = current_torsion->getB() + offset;
982 –        the_torsions[index].c = current_torsion->getC() + offset;
983 –        the_torsions[index].d = current_torsion->getD() + offset;
984 –
985 –        exI = the_torsions[index].a;
986 –        exJ = the_torsions[index].d;
987 –
988 –        
989 –        // exclude_I must always be the smaller of the pair
990 –        if( exI > exJ ){
991 –          tempEx = exI;
992 –          exI = exJ;
993 –          exJ = tempEx;
994 –        }
995 –
996 –
997 – #ifdef IS_MPI
998 –        
999 –        the_excludes[(index + tot_bonds + tot_bends)*2] =    
1000 –          the_atoms[exI]->getGlobalIndex() + 1;
1001 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1002 –          the_atoms[exJ]->getGlobalIndex() + 1;
1003 –        
1004 – #else  // isn't MPI
1005 –        
1006 –        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1007 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1008 –        // fortran indexes from 1 (hence the +1 in the indexing)
1009 – #endif  //is_mpi
1010 –        
1011 –
1012 –        // increment the index and repeat;
1013 –        index++;
1014 –      }
1015 –      offset += comp_stamps[i]->getNAtoms();
1016 –
1017 – #ifdef IS_MPI
1018 –      }
1019 – #endif //is_mpi      
1020 –
1021 –      molIndex++;
1022 –    }
1023 –  }
1024 –
1025 –  the_ff->initializeTorsions( the_torsions );
974   }
975  
976   void SimSetup::initFromBass( void ){

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