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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 469 by mmeineke, Mon Apr 7 20:06:31 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 <
111 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
112 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
113 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
114 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
109 >  int usesDipoles = 0;
110 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
111 >    the_ff = new TraPPE_ExFF();
112 >    usesDipoles = 1;
113 >  }
114 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
115    else{
116      sprintf( painCave.errMsg,
117               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 242 | Line 262 | void SimSetup::createSim( void ){
262  
263    globalIndex = mpiSim->divideLabor();
264  
245 –
246 –
265    // set up the local variables
266    
267    int localMol, allMol;
268    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
269 +
270 +  int* mol2proc = mpiSim->getMolToProcMap();
271 +  int* molCompType = mpiSim->getMolComponentType();
272    
273    allMol = 0;
274    localMol = 0;
# Line 259 | Line 280 | void SimSetup::createSim( void ){
280  
281      for( j=0; j<components_nmol[i]; j++ ){
282        
283 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
283 >      if( mol2proc[j] == worldRank ){
284          
285          local_atoms +=    comp_stamps[i]->getNAtoms();
286          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 299 | void SimSetup::createSim( void ){
299    if( local_atoms != simnfo->n_atoms ){
300      sprintf( painCave.errMsg,
301               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
302 <             " localAtom (%d) are note equal.\n",
302 >             " localAtom (%d) are not equal.\n",
303               simnfo->n_atoms,
304               local_atoms );
305      painCave.isFatal = 1;
# Line 304 | Line 324 | void SimSetup::createSim( void ){
324    Atom::createArrays(simnfo->n_atoms);
325    the_atoms = new Atom*[simnfo->n_atoms];
326    the_molecules = new Molecule[simnfo->n_mol];
327 +  int molIndex;
328  
329 +  // initialize the molecule's stampID's
330  
331 <  if( simnfo->n_SRI ){
332 <    the_sris = new SRI*[simnfo->n_SRI];
333 <    the_excludes = new int[2 * simnfo->n_SRI];
331 > #ifdef IS_MPI
332 >  
333 >
334 >  molIndex = 0;
335 >  for(i=0; i<mpiSim->getTotNmol(); i++){
336 >    
337 >    if(mol2proc[i] == worldRank ){
338 >      the_molecules[molIndex].setStampID( molCompType[i] );
339 >      the_molecules[molIndex].setMyIndex( molIndex );
340 >      molIndex++;
341 >    }
342 >  }
343 >
344 > #else // is_mpi
345 >  
346 >  molIndex = 0;
347 >  for(i=0; i<n_components; i++){
348 >    for(j=0; j<components_nmol[i]; j++ ){
349 >      the_molecules[molIndex].setStampID( i );
350 >      the_molecules[molIndex].setMyIndex( molIndex );
351 >      molIndex++;
352 >    }
353 >  }
354 >    
355 >
356 > #endif // is_mpi
357 >
358 >
359 >  if( simnfo->n_SRI ){
360 >    
361 >    Exclude::createArray(simnfo->n_SRI);
362 >    the_excludes = new Exclude*[simnfo->n_SRI];
363 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
364      simnfo->globalExcludes = new int;
365 <    simnfo->n_exclude = tot_SRI;
365 >    simnfo->n_exclude = simnfo->n_SRI;
366    }
367    else{
368      
369 <    the_excludes = new int[2];
370 <    the_excludes[0] = 0;
371 <    the_excludes[1] = 0;
369 >    Exclude::createArray( 1 );
370 >    the_excludes = new Exclude*;
371 >    the_excludes[0] = new Exclude(0);
372 >    the_excludes[0]->setPair( 0,0 );
373      simnfo->globalExcludes = new int;
374      simnfo->globalExcludes[0] = 0;
375 <
323 <    simnfo->n_exclude = 1;
375 >    simnfo->n_exclude = 0;
376    }
377  
378    // set the arrays into the SimInfo object
379  
380    simnfo->atoms = the_atoms;
381 <  simnfo->sr_interactions = the_sris;
381 >  simnfo->molecules = the_molecules;
382    simnfo->nGlobalExcludes = 0;
383    simnfo->excludes = the_excludes;
384  
# Line 383 | Line 435 | void SimSetup::createSim( void ){
435  
436    the_ff->setSimInfo( simnfo );
437  
438 <  makeAtoms();
438 >  makeMolecules();
439    simnfo->identArray = new int[simnfo->n_atoms];
440    for(i=0; i<simnfo->n_atoms; i++){
441      simnfo->identArray[i] = the_atoms[i]->getIdent();
442    }
443    
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 –
444    if (the_globals->getUseRF() ) {
445      simnfo->useReactionField = 1;
446    
# Line 443 | Line 482 | void SimSetup::createSim( void ){
482      }
483      simnfo->dielectric = the_globals->getDielectric();  
484    } else {
485 <    if (simnfo->n_dipoles) {
485 >    if (usesDipoles) {
486        
487        if( !the_globals->haveECR() ){
488          sprintf( painCave.errMsg,
489 <                 "SimSetup Warning: using default value of 1/2 the smallest"
489 >                 "SimSetup Warning: using default value of 1/2 the smallest "
490                   "box length for the electrostaticCutoffRadius.\n"
491                   "I hope you have a very fast processor!\n");
492          painCave.isFatal = 0;
# Line 463 | Line 502 | void SimSetup::createSim( void ){
502        
503        if( !the_globals->haveEST() ){
504          sprintf( painCave.errMsg,
505 <                 "SimSetup Warning: using default value of 5% of the"
505 >                 "SimSetup Warning: using default value of 5%% of the "
506                   "electrostaticCutoffRadius for the "
507                   "electrostaticSkinThickness\n"
508                   );
# Line 638 | Line 677 | void SimSetup::createSim( void ){
677  
678   //   new AllLong( simnfo );
679  
641 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643 –  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644 –  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
680  
681 <
681 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
682 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
683 >    std::cerr << "called new Symplecic\n";
684 >    fprintf( stderr, "called new Symplectic. stderr\n" );
685 >  }
686 >  else if( !strcmp( force_field, "LJ" ) ){
687 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
688 >    std::cerr << "called new Verlet\n";
689 >    fprintf( stderr, "called new Verlet. stderr\n" );
690 >  }
691 >  else {
692 >    std::cerr << "I'm a bug.\n";
693 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
694 >  }
695 > #ifdef IS_MPI
696 >  mpiSim->mpiRefresh();
697 > #endif
698  
699    // initialize the Fortran
700 <  
700 >
701 >
702    simnfo->refreshSim();
703    
704    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 671 | Line 723 | void SimSetup::makeAtoms( void ){
723   #endif // is_mpi
724   }
725  
674 – void SimSetup::makeAtoms( void ){
726  
727 <  int i, j, k, index;
677 <  double ux, uy, uz, uSqr, u;
678 <  AtomStamp* current_atom;
727 > void SimSetup::makeMolecules( void ){
728  
729 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
730 +  molInit info;
731    DirectionalAtom* dAtom;
732 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
732 >  LinkedAssign* extras;
733 >  LinkedAssign* current_extra;
734 >  AtomStamp* currentAtom;
735 >  BondStamp* currentBond;
736 >  BendStamp* currentBend;
737 >  TorsionStamp* currentTorsion;
738  
739 <  lMolIndex = 0;
740 <  molIndex = 0;
741 <  index = 0;
686 <  for( i=0; i<n_components; i++ ){
739 >  bond_pair* theBonds;
740 >  bend_set* theBends;
741 >  torsion_set* theTorsions;
742  
743 <    for( j=0; j<components_nmol[i]; j++ ){
743 >  
744 >  //init the forceField paramters
745  
746 < #ifdef IS_MPI
691 <      if( mpiSim->getMyMolStart() <= molIndex &&
692 <          molIndex <= mpiSim->getMyMolEnd() ){
693 < #endif // is_mpi        
746 >  the_ff->readParams();
747  
748 <        molStart = index;
749 <        nMemb = comp_stamps[i]->getNAtoms();
697 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
698 <          
699 <          current_atom = comp_stamps[i]->getAtom( k );
700 <          if( current_atom->haveOrientation() ){
701 <            
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++;
748 >  
749 >  // init the atoms
750  
751 < #ifdef IS_MPI
752 <      }
753 < #endif //is_mpi
754 <      
755 <      molIndex++;
743 <    }
744 <  }
745 <
746 < #ifdef IS_MPI
747 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
751 >  double ux, uy, uz, u, uSqr;
752 >  
753 >  atomOffset = 0;
754 >  excludeOffset = 0;
755 >  for(i=0; i<simnfo->n_mol; i++){
756      
757 <    delete[] globalIndex;
757 >    stampID = the_molecules[i].getStampID();
758  
759 <    mpiSim->mpiRefresh();
760 < #endif //IS_MPI
761 <          
762 <  the_ff->initializeAtoms();
763 < }
759 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
760 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
761 >    info.nBends    = comp_stamps[stampID]->getNBends();
762 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
763 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
764  
765 < void SimSetup::makeBonds( void ){
765 >    info.myAtoms = &the_atoms[atomOffset];
766 >    info.myExcludes = &the_excludes[excludeOffset];
767 >    info.myBonds = new Bond*[info.nBonds];
768 >    info.myBends = new Bend*[info.nBends];
769 >    info.myTorsions = new Torsion*[info.nTorsions];
770  
771 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
772 <  bond_pair* the_bonds;
773 <  BondStamp* current_bond;
774 <
775 <  the_bonds = new bond_pair[tot_bonds];
776 <  index = 0;
777 <  offset = 0;
778 <  molIndex = 0;
779 <
780 <  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        
771 >    theBonds = new bond_pair[info.nBonds];
772 >    theBends = new bend_set[info.nBends];
773 >    theTorsions = new torsion_set[info.nTorsions];
774 >    
775 >    // make the Atoms
776 >    
777 >    for(j=0; j<info.nAtoms; j++){
778 >      
779 >      currentAtom = comp_stamps[stampID]->getAtom( j );
780 >      if( currentAtom->haveOrientation() ){
781          
782 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
783 <          
784 <          current_bond = comp_stamps[i]->getBond( k );
785 <          the_bonds[index].a = current_bond->getA() + offset;
786 <          the_bonds[index].b = current_bond->getB() + offset;
787 <
788 <          exI = the_bonds[index].a;
789 <          exJ = the_bonds[index].b;
790 <
791 <          // exclude_I must always be the smaller of the pair
792 <          if( exI > exJ ){
793 <            tempEx = exI;
794 <            exI = exJ;
795 <            exJ = tempEx;
796 <          }
797 <
798 <          
782 >        dAtom = new DirectionalAtom(j + atomOffset);
783 >        simnfo->n_oriented++;
784 >        info.myAtoms[j] = dAtom;
785 >        
786 >        ux = currentAtom->getOrntX();
787 >        uy = currentAtom->getOrntY();
788 >        uz = currentAtom->getOrntZ();
789 >        
790 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
791 >        
792 >        u = sqrt( uSqr );
793 >        ux = ux / u;
794 >        uy = uy / u;
795 >        uz = uz / u;
796 >        
797 >        dAtom->setSUx( ux );
798 >        dAtom->setSUy( uy );
799 >        dAtom->setSUz( uz );
800 >      }
801 >      else{
802 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
803 >      }
804 >      info.myAtoms[j]->setType( currentAtom->getType() );
805 >    
806   #ifdef IS_MPI
807 +      
808 +      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
809 +      
810 + #endif // is_mpi
811 +    }
812 +    
813 +    // make the bonds
814 +    for(j=0; j<info.nBonds; j++){
815 +      
816 +      currentBond = comp_stamps[stampID]->getBond( j );
817 +      theBonds[j].a = currentBond->getA() + atomOffset;
818 +      theBonds[j].b = currentBond->getB() + atomOffset;
819  
820 <          the_excludes[index*2] =    
821 <            the_atoms[exI]->getGlobalIndex() + 1;
798 <          the_excludes[index*2 + 1] =
799 <            the_atoms[exJ]->getGlobalIndex() + 1;
820 >      exI = theBonds[j].a;
821 >      exJ = theBonds[j].b;
822  
823 +      // exclude_I must always be the smaller of the pair
824 +      if( exI > exJ ){
825 +        tempEx = exI;
826 +        exI = exJ;
827 +        exJ = tempEx;
828 +      }
829 + #ifdef IS_MPI
830 +      tempEx = exI;
831 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
832 +      tempEx = exJ;
833 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
834 +      
835 +      the_excludes[j+excludeOffset]->setPair( exI, exJ );
836   #else  // isn't MPI
837 <          
838 <          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)
837 >
838 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
839   #endif  //is_mpi
840 <          
841 <          // 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 <  }
840 >    }
841 >    excludeOffset += info.nBonds;
842  
843 <  the_ff->initializeBonds( the_bonds );
844 < }
845 <
846 < void SimSetup::makeBends( void ){
847 <
848 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
849 <  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++ ){
843 >    //make the bends
844 >    for(j=0; j<info.nBends; j++){
845 >      
846 >      currentBend = comp_stamps[stampID]->getBend( j );
847 >      theBends[j].a = currentBend->getA() + atomOffset;
848 >      theBends[j].b = currentBend->getB() + atomOffset;
849 >      theBends[j].c = currentBend->getC() + atomOffset;
850            
851 <          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() ){
851 >      if( currentBend->haveExtras() ){
852              
853 <            extras = current_bend->getExtras();
854 <            current_extra = extras;
853 >        extras = currentBend->getExtras();
854 >        current_extra = extras;
855              
856 <            while( current_extra != NULL ){
857 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
856 >        while( current_extra != NULL ){
857 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
858                  
859 <                switch( current_extra->getType() ){
859 >            switch( current_extra->getType() ){
860 >              
861 >            case 0:
862 >              theBends[j].ghost =
863 >                current_extra->getInt() + atomOffset;
864 >              theBends[j].isGhost = 1;
865 >              break;
866                    
867 <                case 0:
868 <                  the_bends[index].ghost =
869 <                    current_extra->getInt() + offset;
870 <                  the_bends[index].isGhost = 1;
871 <                  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 <              }
867 >            case 1:
868 >              theBends[j].ghost =
869 >                (int)current_extra->getDouble() + atomOffset;
870 >              theBends[j].isGhost = 1;
871 >              break;
872                
873 <              else{
874 <                
875 <                sprintf( painCave.errMsg,
876 <                         "SimSetup Error: unhandled bend assignment:\n"
877 <                         "    -->%s in Bend[%d] in %s\n",
878 <                         current_extra->getlhs(),
879 <                         k, comp_stamps[i]->getID() );
880 <                painCave.isFatal = 1;
894 <                simError();
895 <              }
896 <              
897 <              current_extra = current_extra->getNext();
873 >            default:
874 >              sprintf( painCave.errMsg,
875 >                       "SimSetup Error: ghostVectorSource was neither a "
876 >                       "double nor an int.\n"
877 >                       "-->Bend[%d] in %s\n",
878 >                       j, comp_stamps[stampID]->getID() );
879 >              painCave.isFatal = 1;
880 >              simError();
881              }
882            }
883            
901 –          if( !the_bends[index].isGhost ){
902 –            
903 –            exI = the_bends[index].a;
904 –            exJ = the_bends[index].c;
905 –          }
884            else{
885              
886 <            exI = the_bends[index].a;
887 <            exJ = the_bends[index].b;
886 >            sprintf( painCave.errMsg,
887 >                     "SimSetup Error: unhandled bend assignment:\n"
888 >                     "    -->%s in Bend[%d] in %s\n",
889 >                     current_extra->getlhs(),
890 >                     j, comp_stamps[stampID]->getID() );
891 >            painCave.isFatal = 1;
892 >            simError();
893            }
894            
895 <          // 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++;
895 >          current_extra = current_extra->getNext();
896          }
897 <        offset += comp_stamps[i]->getNAtoms();
897 >      }
898 >          
899 >      if( !theBends[j].isGhost ){
900 >            
901 >        exI = theBends[j].a;
902 >        exJ = theBends[j].c;
903 >      }
904 >      else{
905          
906 < #ifdef IS_MPI
906 >        exI = theBends[j].a;
907 >        exJ = theBends[j].b;
908        }
909 < #endif //is_mpi
909 >      
910 >      // exclude_I must always be the smaller of the pair
911 >      if( exI > exJ ){
912 >        tempEx = exI;
913 >        exI = exJ;
914 >        exJ = tempEx;
915 >      }
916 > #ifdef IS_MPI
917 >      tempEx = exI;
918 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
919 >      tempEx = exJ;
920 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
921 >      
922 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
923 > #else  // isn't MPI
924 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
925 > #endif  //is_mpi
926 >    }
927 >    excludeOffset += info.nBends;
928  
929 <      molIndex++;
929 >    for(j=0; j<info.nTorsions; j++){
930 >      
931 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
932 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
933 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
934 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
935 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
936 >      
937 >      exI = theTorsions[j].a;
938 >      exJ = theTorsions[j].d;
939 >
940 >      // exclude_I must always be the smaller of the pair
941 >      if( exI > exJ ){
942 >        tempEx = exI;
943 >        exI = exJ;
944 >        exJ = tempEx;
945 >      }
946 > #ifdef IS_MPI
947 >      tempEx = exI;
948 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
949 >      tempEx = exJ;
950 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
951 >      
952 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
953 > #else  // isn't MPI
954 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
955 > #endif  //is_mpi
956      }
957 +    excludeOffset += info.nTorsions;
958 +
959 +    
960 +    // send the arrays off to the forceField for init.
961 +
962 +    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
963 +    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
964 +    the_ff->initializeBends( info.nBends, info.myBends, theBends );
965 +    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
966 +
967 +
968 +    the_molecules[i].initialize( info );
969 +
970 +
971 +    atomOffset += info.nAtoms;
972 +    delete[] theBonds;
973 +    delete[] theBends;
974 +    delete[] theTorsions;
975    }
976  
977   #ifdef IS_MPI
978 <  sprintf( checkPointMsg,
950 <           "Successfully created the bends list.\n" );
978 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
979    MPIcheckPoint();
980   #endif // is_mpi
953 –  
981  
982 <  the_ff->initializeBends( the_bends );
983 < }
982 >  // clean up the forcefield
983 >  the_ff->calcRcut();
984 >  the_ff->cleanMe();
985  
958 – void SimSetup::makeTorsions( void ){
959 –
960 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
961 –  torsion_set* the_torsions;
962 –  TorsionStamp* current_torsion;
963 –
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++ ){
969 –
970 –    for( j=0; j<components_nmol[i]; j++ ){
971 –
972 – #ifdef IS_MPI
973 –      if( mpiSim->getMyMolStart() <= molIndex &&
974 –          molIndex <= mpiSim->getMyMolEnd() ){
975 – #endif // is_mpi        
976 –
977 –      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
978 –
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 );
986   }
987  
988   void SimSetup::initFromBass( void ){

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