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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 555 by mmeineke, Tue Jun 17 21:56:15 2003 UTC

# Line 66 | Line 66 | void SimSetup::createSim( void ){
66  
67    MakeStamps *the_stamps;
68    Globals* the_globals;
69 <  int i, j;
69 >  ExtendedSystem* the_extendedsystem;
70 >  int i, j, k, globalAtomIndex;
71  
72    // get the stamps and globals;
73    the_stamps = stamps;
# 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 +    if (the_globals->haveTargetPressure())
91 +      the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92 +    else {
93 +      sprintf( painCave.errMsg,
94 +               "SimSetup error: If you use the constant pressure\n"
95 +               "    ensemble, you must set targetPressure.\n"
96 +               "    This was found in the BASS file.\n");
97 +      painCave.isFatal = 1;
98 +      simError();
99 +    }
100 +
101 +    if (the_globals->haveTauThermostat())
102 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103 +    else if (the_globals->haveQmass())
104 +      the_extendedsystem->setQmass(the_globals->getQmass());
105 +    else {
106 +      sprintf( painCave.errMsg,
107 +               "SimSetup error: If you use one of the constant temperature\n"
108 +               "    ensembles, you must set either tauThermostat or qMass.\n"
109 +               "    Neither of these was found in the BASS file.\n");
110 +      painCave.isFatal = 1;
111 +      simError();
112 +    }
113 +
114 +    if (the_globals->haveTauBarostat())
115 +      the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116 +    else {
117 +      sprintf( painCave.errMsg,
118 +               "SimSetup error: If you use the constant pressure\n"
119 +               "    ensemble, you must set tauBarostat.\n"
120 +               "    This was found in the BASS file.\n");
121 +      painCave.isFatal = 1;
122 +      simError();
123 +    }
124 +
125 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
126 +    the_extendedsystem = new ExtendedSystem( simnfo );
127 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
128 +
129 +    if (the_globals->haveTauThermostat())
130 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131 +    else if (the_globals->haveQmass())
132 +      the_extendedsystem->setQmass(the_globals->getQmass());
133 +    else {
134 +      sprintf( painCave.errMsg,
135 +               "SimSetup error: If you use one of the constant temperature\n"
136 +               "    ensembles, you must set either tauThermostat or qMass.\n"
137 +               "    Neither of these was found in the BASS file.\n");
138 +      painCave.isFatal = 1;
139 +      simError();
140 +    }
141 +
142 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
143 +  } else {
144 +    sprintf( painCave.errMsg,
145 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
146 +             "reverting to NVE for this simulation.\n",
147 +             ensemble );
148 +    painCave.isFatal = 0;
149 +    simError();
150 +    strcpy( ensemble, "NVE" );
151 +  }  
152    strcpy( simnfo->ensemble, ensemble );
153  
154    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155    simnfo->usePBC = the_globals->getPBC();
156            
157 <
158 <
159 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
160 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
161 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
162 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
157 >  int usesDipoles = 0;
158 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
159 >    the_ff = new TraPPE_ExFF();
160 >    usesDipoles = 1;
161 >  }
162 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163    else{
164      sprintf( painCave.errMsg,
165               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 230 | Line 298 | void SimSetup::createSim( void ){
298    simnfo->n_torsions = tot_torsions;
299    simnfo->n_SRI = tot_SRI;
300    simnfo->n_mol = tot_nmol;
233 –
301    
302 +  simnfo->molMembershipArray = new int[tot_atoms];
303 +
304   #ifdef IS_MPI
305  
306    // divide the molecules among processors here.
307    
308    mpiSim = new mpiSimulation( simnfo );
309    
241 –  
242 –
310    globalIndex = mpiSim->divideLabor();
311  
245 –
246 –
312    // set up the local variables
313    
314    int localMol, allMol;
315    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
316 +
317 +  int* mol2proc = mpiSim->getMolToProcMap();
318 +  int* molCompType = mpiSim->getMolComponentType();
319    
320    allMol = 0;
321    localMol = 0;
# Line 255 | Line 323 | void SimSetup::createSim( void ){
323    local_bonds = 0;
324    local_bends = 0;
325    local_torsions = 0;
326 +  globalAtomIndex = 0;
327 +
328 +
329    for( i=0; i<n_components; i++ ){
330  
331      for( j=0; j<components_nmol[i]; j++ ){
332        
333 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
333 >      if( mol2proc[allMol] == worldRank ){
334          
335          local_atoms +=    comp_stamps[i]->getNAtoms();
336          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 338 | void SimSetup::createSim( void ){
338          local_torsions += comp_stamps[i]->getNTorsions();
339          localMol++;
340        }      
341 <      allMol++;
341 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
342 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
343 >        globalAtomIndex++;
344 >      }
345 >
346 >      allMol++;      
347      }
348    }
349    local_SRI = local_bonds + local_bends + local_torsions;
350    
276 –
351    simnfo->n_atoms = mpiSim->getMyNlocal();  
352    
353    if( local_atoms != simnfo->n_atoms ){
354      sprintf( painCave.errMsg,
355               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
356 <             " localAtom (%d) are note equal.\n",
356 >             " localAtom (%d) are not equal.\n",
357               simnfo->n_atoms,
358               local_atoms );
359      painCave.isFatal = 1;
# Line 304 | Line 378 | void SimSetup::createSim( void ){
378    Atom::createArrays(simnfo->n_atoms);
379    the_atoms = new Atom*[simnfo->n_atoms];
380    the_molecules = new Molecule[simnfo->n_mol];
381 +  int molIndex;
382  
383 +  // initialize the molecule's stampID's
384  
385 <  if( simnfo->n_SRI ){
386 <    the_sris = new SRI*[simnfo->n_SRI];
387 <    the_excludes = new int[2 * simnfo->n_SRI];
385 > #ifdef IS_MPI
386 >  
387 >
388 >  molIndex = 0;
389 >  for(i=0; i<mpiSim->getTotNmol(); i++){
390 >    
391 >    if(mol2proc[i] == worldRank ){
392 >      the_molecules[molIndex].setStampID( molCompType[i] );
393 >      the_molecules[molIndex].setMyIndex( molIndex );
394 >      the_molecules[molIndex].setGlobalIndex( i );
395 >      molIndex++;
396 >    }
397 >  }
398 >
399 > #else // is_mpi
400 >  
401 >  molIndex = 0;
402 >  globalAtomIndex = 0;
403 >  for(i=0; i<n_components; i++){
404 >    for(j=0; j<components_nmol[i]; j++ ){
405 >      the_molecules[molIndex].setStampID( i );
406 >      the_molecules[molIndex].setMyIndex( molIndex );
407 >      the_molecules[molIndex].setGlobalIndex( molIndex );
408 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
409 >        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
410 >        globalAtomIndex++;
411 >      }
412 >      molIndex++;
413 >    }
414 >  }
415 >    
416 >
417 > #endif // is_mpi
418 >
419 >
420 >  if( simnfo->n_SRI ){
421 >    
422 >    Exclude::createArray(simnfo->n_SRI);
423 >    the_excludes = new Exclude*[simnfo->n_SRI];
424 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
425      simnfo->globalExcludes = new int;
426 <    simnfo->n_exclude = tot_SRI;
426 >    simnfo->n_exclude = simnfo->n_SRI;
427    }
428    else{
429      
430 <    the_excludes = new int[2];
431 <    the_excludes[0] = 0;
432 <    the_excludes[1] = 0;
430 >    Exclude::createArray( 1 );
431 >    the_excludes = new Exclude*;
432 >    the_excludes[0] = new Exclude(0);
433 >    the_excludes[0]->setPair( 0,0 );
434      simnfo->globalExcludes = new int;
435      simnfo->globalExcludes[0] = 0;
436 <
323 <    simnfo->n_exclude = 1;
436 >    simnfo->n_exclude = 0;
437    }
438  
439    // set the arrays into the SimInfo object
440  
441    simnfo->atoms = the_atoms;
442 <  simnfo->sr_interactions = the_sris;
442 >  simnfo->molecules = the_molecules;
443    simnfo->nGlobalExcludes = 0;
444    simnfo->excludes = the_excludes;
445  
# Line 383 | Line 496 | void SimSetup::createSim( void ){
496  
497    the_ff->setSimInfo( simnfo );
498  
499 <  makeAtoms();
499 >  makeMolecules();
500    simnfo->identArray = new int[simnfo->n_atoms];
501    for(i=0; i<simnfo->n_atoms; i++){
502      simnfo->identArray[i] = the_atoms[i]->getIdent();
503    }
504    
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 –
505    if (the_globals->getUseRF() ) {
506      simnfo->useReactionField = 1;
507    
# Line 443 | Line 543 | void SimSetup::createSim( void ){
543      }
544      simnfo->dielectric = the_globals->getDielectric();  
545    } else {
546 <    if (simnfo->n_dipoles) {
546 >    if (usesDipoles) {
547        
548        if( !the_globals->haveECR() ){
549          sprintf( painCave.errMsg,
550 <                 "SimSetup Warning: using default value of 1/2 the smallest"
550 >                 "SimSetup Warning: using default value of 1/2 the smallest "
551                   "box length for the electrostaticCutoffRadius.\n"
552                   "I hope you have a very fast processor!\n");
553          painCave.isFatal = 0;
# Line 463 | Line 563 | void SimSetup::createSim( void ){
563        
564        if( !the_globals->haveEST() ){
565          sprintf( painCave.errMsg,
566 <                 "SimSetup Warning: using default value of 5% of the"
566 >                 "SimSetup Warning: using default value of 5%% of the "
567                   "electrostaticCutoffRadius for the "
568                   "electrostaticSkinThickness\n"
569                   );
# Line 634 | Line 734 | void SimSetup::createSim( void ){
734    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
735  
736  
737 < //   // make the longe range forces and the integrator
737 >  // make the integrator
738  
739 < //   new AllLong( simnfo );
739 >
740 >  if( !strcmp( ensemble, "TraPPE_Ex" ) ){
741 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
742 >  }
743 >  else if( !strcmp( force_field, "LJ" ) ){
744 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
745 >  }
746  
747 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
748 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
749 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
747 > #ifdef IS_MPI
748 >  mpiSim->mpiRefresh();
749 > #endif
750  
751 +  // initialize the Fortran
752  
753  
648 –  // initialize the Fortran
649 –  
754    simnfo->refreshSim();
755    
756    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 674 | Line 778 | void SimSetup::makeMolecules( void ){
778  
779   void SimSetup::makeMolecules( void ){
780  
781 <  int i, j, exI, exJ, tempEx, stampID, atomOffset;
781 >  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
782    molInit info;
783    DirectionalAtom* dAtom;
784 +  LinkedAssign* extras;
785 +  LinkedAssign* current_extra;
786    AtomStamp* currentAtom;
787    BondStamp* currentBond;
788    BendStamp* currentBend;
789    TorsionStamp* currentTorsion;
790 +
791 +  bond_pair* theBonds;
792 +  bend_set* theBends;
793 +  torsion_set* theTorsions;
794 +
795    
796    //init the forceField paramters
797  
798    the_ff->readParams();
799  
800    
801 <  // init the molecules
801 >  // init the atoms
802  
803 +  double ux, uy, uz, u, uSqr;
804 +  
805    atomOffset = 0;
806 +  excludeOffset = 0;
807    for(i=0; i<simnfo->n_mol; i++){
808      
809      stampID = the_molecules[i].getStampID();
# Line 698 | Line 812 | void SimSetup::makeMolecules( void ){
812      info.nBonds    = comp_stamps[stampID]->getNBonds();
813      info.nBends    = comp_stamps[stampID]->getNBends();
814      info.nTorsions = comp_stamps[stampID]->getNTorsions();
815 <    
815 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
816 >
817      info.myAtoms = &the_atoms[atomOffset];
818 +    info.myExcludes = &the_excludes[excludeOffset];
819      info.myBonds = new Bond*[info.nBonds];
820      info.myBends = new Bend*[info.nBends];
821 <    info.myTorsions = new Torsions*[info.nTorsions];
821 >    info.myTorsions = new Torsion*[info.nTorsions];
822  
823      theBonds = new bond_pair[info.nBonds];
824      theBends = new bend_set[info.nBends];
# Line 712 | Line 828 | void SimSetup::makeMolecules( void ){
828      
829      for(j=0; j<info.nAtoms; j++){
830        
831 <      currentAtom = theComponents[stampID]->getAtom( j );
831 >      currentAtom = comp_stamps[stampID]->getAtom( j );
832        if( currentAtom->haveOrientation() ){
833          
834          dAtom = new DirectionalAtom(j + atomOffset);
# Line 747 | Line 863 | void SimSetup::makeMolecules( void ){
863      }
864      
865      // make the bonds
866 <    for(j=0; j<nBonds; j++){
866 >    for(j=0; j<info.nBonds; j++){
867        
868        currentBond = comp_stamps[stampID]->getBond( j );
869        theBonds[j].a = currentBond->getA() + atomOffset;
870        theBonds[j].b = currentBond->getB() + atomOffset;
871  
872 <      exI = theBonds[i].a;
873 <      exJ = theBonds[i].b;
872 >      exI = theBonds[j].a;
873 >      exJ = theBonds[j].b;
874  
875        // exclude_I must always be the smaller of the pair
876        if( exI > exJ ){
# Line 763 | Line 879 | void SimSetup::makeMolecules( void ){
879          exJ = tempEx;
880        }
881   #ifdef IS_MPI
882 +      tempEx = exI;
883 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
884 +      tempEx = exJ;
885 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
886        
887 <      the_excludes[index*2] =    
768 <        the_atoms[exI]->getGlobalIndex() + 1;
769 <      the_excludes[index*2 + 1] =
770 <        the_atoms[exJ]->getGlobalIndex() + 1;
771 <      
887 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
888   #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)
889  
890 +      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
891   #endif  //is_mpi
892 <    
893 <  }
892 >    }
893 >    excludeOffset += info.nBonds;
894  
895 <
896 <
897 <
898 <
899 <
900 <
901 <
789 <
790 <
791 <
792 <
793 <
794 <
795 <
796 < void SimSetup::makeAtoms( void ){
797 <
798 <  int i, j, k, index;
799 <  double ux, uy, uz, uSqr, u;
800 <  AtomStamp* current_atom;
801 <
802 <  DirectionalAtom* dAtom;
803 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
804 <
805 <  lMolIndex = 0;
806 <  molIndex = 0;
807 <  index = 0;
808 <  for( i=0; i<n_components; i++ ){
809 <
810 <    for( j=0; j<components_nmol[i]; j++ ){
811 <
812 < #ifdef IS_MPI
813 <      if( mpiSim->getMyMolStart() <= molIndex &&
814 <          molIndex <= mpiSim->getMyMolEnd() ){
815 < #endif // is_mpi        
816 <
817 <        molStart = index;
818 <        nMemb = comp_stamps[i]->getNAtoms();
819 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
895 >    //make the bends
896 >    for(j=0; j<info.nBends; j++){
897 >      
898 >      currentBend = comp_stamps[stampID]->getBend( j );
899 >      theBends[j].a = currentBend->getA() + atomOffset;
900 >      theBends[j].b = currentBend->getB() + atomOffset;
901 >      theBends[j].c = currentBend->getC() + atomOffset;
902            
903 <          current_atom = comp_stamps[i]->getAtom( k );
822 <          if( current_atom->haveOrientation() ){
903 >      if( currentBend->haveExtras() ){
904              
905 <            dAtom = new DirectionalAtom(index);
906 <            simnfo->n_oriented++;
826 <            the_atoms[index] = dAtom;
905 >        extras = currentBend->getExtras();
906 >        current_extra = extras;
907              
908 <            ux = current_atom->getOrntX();
909 <            uy = current_atom->getOrntY();
910 <            uz = current_atom->getOrntZ();
911 <            
912 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
913 <            
914 <            u = sqrt( uSqr );
915 <            ux = ux / u;
916 <            uy = uy / u;
917 <            uz = uz / u;
918 <            
919 <            dAtom->setSUx( ux );
920 <            dAtom->setSUy( uy );
921 <            dAtom->setSUz( uz );
922 <          }
923 <          else{
924 <            the_atoms[index] = new GeneralAtom(index);
925 <          }
926 <          the_atoms[index]->setType( current_atom->getType() );
927 <          the_atoms[index]->setIndex( index );
928 <          
929 <          // increment the index and repeat;
930 <          index++;
931 <        }
932 <        
933 <        molEnd = index -1;
934 <        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
861 <      }
862 < #endif //is_mpi
863 <      
864 <      molIndex++;
865 <    }
866 <  }
867 <
868 < #ifdef IS_MPI
869 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
870 <    
871 <    delete[] globalIndex;
872 <
873 <    mpiSim->mpiRefresh();
874 < #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++ ){
908 >        while( current_extra != NULL ){
909 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
910 >                
911 >            switch( current_extra->getType() ){
912 >              
913 >            case 0:
914 >              theBends[j].ghost =
915 >                current_extra->getInt() + atomOffset;
916 >              theBends[j].isGhost = 1;
917 >              break;
918 >                  
919 >            case 1:
920 >              theBends[j].ghost =
921 >                (int)current_extra->getDouble() + atomOffset;
922 >              theBends[j].isGhost = 1;
923 >              break;
924 >              
925 >            default:
926 >              sprintf( painCave.errMsg,
927 >                       "SimSetup Error: ghostVectorSource was neither a "
928 >                       "double nor an int.\n"
929 >                       "-->Bend[%d] in %s\n",
930 >                       j, comp_stamps[stampID]->getID() );
931 >              painCave.isFatal = 1;
932 >              simError();
933 >            }
934 >          }
935            
936 <          current_bond = comp_stamps[i]->getBond( k );
937 <          the_bonds[index].a = current_bond->getA() + offset;
938 <          the_bonds[index].b = current_bond->getB() + offset;
939 <
940 <          exI = the_bonds[index].a;
941 <          exJ = the_bonds[index].b;
942 <
943 <          // exclude_I must always be the smaller of the pair
944 <          if( exI > exJ ){
910 <            tempEx = exI;
911 <            exI = exJ;
912 <            exJ = tempEx;
936 >          else{
937 >            
938 >            sprintf( painCave.errMsg,
939 >                     "SimSetup Error: unhandled bend assignment:\n"
940 >                     "    -->%s in Bend[%d] in %s\n",
941 >                     current_extra->getlhs(),
942 >                     j, comp_stamps[stampID]->getID() );
943 >            painCave.isFatal = 1;
944 >            simError();
945            }
914 –
946            
947 < #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 <
923 < #else  // isn't MPI
924 <          
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)
928 < #endif  //is_mpi
929 <          
930 <          // increment the index and repeat;
931 <          index++;
947 >          current_extra = current_extra->getNext();
948          }
949 <        offset += comp_stamps[i]->getNAtoms();
949 >      }
950 >          
951 >      if( !theBends[j].isGhost ){
952 >            
953 >        exI = theBends[j].a;
954 >        exJ = theBends[j].c;
955 >      }
956 >      else{
957          
958 < #ifdef IS_MPI
958 >        exI = theBends[j].a;
959 >        exJ = theBends[j].b;
960        }
937 – #endif //is_mpi
961        
962 <      molIndex++;
963 <    }      
964 <  }
962 >      // exclude_I must always be the smaller of the pair
963 >      if( exI > exJ ){
964 >        tempEx = exI;
965 >        exI = exJ;
966 >        exJ = tempEx;
967 >      }
968 > #ifdef IS_MPI
969 >      tempEx = exI;
970 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
971 >      tempEx = exJ;
972 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
973 >      
974 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
975 > #else  // isn't MPI
976 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
977 > #endif  //is_mpi
978 >    }
979 >    excludeOffset += info.nBends;
980  
981 <  the_ff->initializeBonds( the_bonds );
982 < }
981 >    for(j=0; j<info.nTorsions; j++){
982 >      
983 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
984 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
985 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
986 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
987 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
988 >      
989 >      exI = theTorsions[j].a;
990 >      exJ = theTorsions[j].d;
991  
992 < void SimSetup::makeBends( void ){
992 >      // exclude_I must always be the smaller of the pair
993 >      if( exI > exJ ){
994 >        tempEx = exI;
995 >        exI = exJ;
996 >        exJ = tempEx;
997 >      }
998 > #ifdef IS_MPI
999 >      tempEx = exI;
1000 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1001 >      tempEx = exJ;
1002 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1003 >      
1004 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1005 > #else  // isn't MPI
1006 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1007 > #endif  //is_mpi
1008 >    }
1009 >    excludeOffset += info.nTorsions;
1010  
1011 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1012 <  bend_set* the_bends;
950 <  BendStamp* current_bend;
951 <  LinkedAssign* extras;
952 <  LinkedAssign* current_extra;
953 <  
1011 >    
1012 >    // send the arrays off to the forceField for init.
1013  
1014 <  the_bends = new bend_set[tot_bends];
1015 <  index = 0;
1016 <  offset = 0;
1017 <  molIndex = 0;
959 <  for( i=0; i<n_components; i++ ){
1014 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1015 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1016 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1017 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1018  
961 –    for( j=0; j<components_nmol[i]; j++ ){
1019  
1020 < #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 <          }
1020 >    the_molecules[i].initialize( info );
1021  
1022  
1023 < #ifdef IS_MPI
1024 <
1025 <          the_excludes[(index + tot_bonds)*2] =    
1026 <            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 <    }
1023 >    atomOffset += info.nAtoms;
1024 >    delete[] theBonds;
1025 >    delete[] theBends;
1026 >    delete[] theTorsions;
1027    }
1028  
1029   #ifdef IS_MPI
1030 <  sprintf( checkPointMsg,
1072 <           "Successfully created the bends list.\n" );
1030 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1031    MPIcheckPoint();
1032   #endif // is_mpi
1075 –  
1033  
1034 <  the_ff->initializeBends( the_bends );
1035 < }
1034 >  // clean up the forcefield
1035 >  the_ff->calcRcut();
1036 >  the_ff->cleanMe();
1037  
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 );
1038   }
1039  
1040   void SimSetup::initFromBass( void ){

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