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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 491 by mmeineke, Fri Apr 11 18:46:37 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 638 | Line 738 | void SimSetup::createSim( void ){
738  
739   //   new AllLong( simnfo );
740  
741 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
742 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
743 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
744 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
741 >
742 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
743 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
744 >  }
745 >  else if( !strcmp( force_field, "LJ" ) ){
746 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
747 >  }
748 >  else {
749 >    std::cerr << "I'm a bug.\n";
750 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
751 >  }
752 > #ifdef IS_MPI
753 >  mpiSim->mpiRefresh();
754 > #endif
755  
756 +  // initialize the Fortran
757  
758  
648 –  // initialize the Fortran
649 –  
759    simnfo->refreshSim();
760    
761    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 674 | Line 783 | void SimSetup::makeMolecules( void ){
783  
784   void SimSetup::makeMolecules( void ){
785  
786 <  int i, j, exI, exJ, tempEx, stampID, atomOffset;
786 >  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
787    molInit info;
788    DirectionalAtom* dAtom;
789 +  LinkedAssign* extras;
790 +  LinkedAssign* current_extra;
791    AtomStamp* currentAtom;
792    BondStamp* currentBond;
793    BendStamp* currentBend;
794    TorsionStamp* currentTorsion;
795 +
796 +  bond_pair* theBonds;
797 +  bend_set* theBends;
798 +  torsion_set* theTorsions;
799 +
800    
801    //init the forceField paramters
802  
803    the_ff->readParams();
804  
805    
806 <  // init the molecules
806 >  // init the atoms
807  
808 +  double ux, uy, uz, u, uSqr;
809 +  
810    atomOffset = 0;
811 +  excludeOffset = 0;
812    for(i=0; i<simnfo->n_mol; i++){
813      
814      stampID = the_molecules[i].getStampID();
# Line 698 | Line 817 | void SimSetup::makeMolecules( void ){
817      info.nBonds    = comp_stamps[stampID]->getNBonds();
818      info.nBends    = comp_stamps[stampID]->getNBends();
819      info.nTorsions = comp_stamps[stampID]->getNTorsions();
820 <    
820 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
821 >
822      info.myAtoms = &the_atoms[atomOffset];
823 +    info.myExcludes = &the_excludes[excludeOffset];
824      info.myBonds = new Bond*[info.nBonds];
825      info.myBends = new Bend*[info.nBends];
826 <    info.myTorsions = new Torsions*[info.nTorsions];
826 >    info.myTorsions = new Torsion*[info.nTorsions];
827  
828      theBonds = new bond_pair[info.nBonds];
829      theBends = new bend_set[info.nBends];
# Line 712 | Line 833 | void SimSetup::makeMolecules( void ){
833      
834      for(j=0; j<info.nAtoms; j++){
835        
836 <      currentAtom = theComponents[stampID]->getAtom( j );
836 >      currentAtom = comp_stamps[stampID]->getAtom( j );
837        if( currentAtom->haveOrientation() ){
838          
839          dAtom = new DirectionalAtom(j + atomOffset);
# Line 747 | Line 868 | void SimSetup::makeMolecules( void ){
868      }
869      
870      // make the bonds
871 <    for(j=0; j<nBonds; j++){
871 >    for(j=0; j<info.nBonds; j++){
872        
873        currentBond = comp_stamps[stampID]->getBond( j );
874        theBonds[j].a = currentBond->getA() + atomOffset;
875        theBonds[j].b = currentBond->getB() + atomOffset;
876  
877 <      exI = theBonds[i].a;
878 <      exJ = theBonds[i].b;
877 >      exI = theBonds[j].a;
878 >      exJ = theBonds[j].b;
879  
880        // exclude_I must always be the smaller of the pair
881        if( exI > exJ ){
# Line 763 | Line 884 | void SimSetup::makeMolecules( void ){
884          exJ = tempEx;
885        }
886   #ifdef IS_MPI
887 +      tempEx = exI;
888 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
889 +      tempEx = exJ;
890 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
891        
892 <      the_excludes[index*2] =    
768 <        the_atoms[exI]->getGlobalIndex() + 1;
769 <      the_excludes[index*2 + 1] =
770 <        the_atoms[exJ]->getGlobalIndex() + 1;
771 <      
892 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
893   #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)
894  
895 +      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
896   #endif  //is_mpi
897 <    
898 <  }
897 >    }
898 >    excludeOffset += info.nBonds;
899  
900 <
901 <
902 <
903 <
904 <
905 <
906 <
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++ ){
900 >    //make the bends
901 >    for(j=0; j<info.nBends; j++){
902 >      
903 >      currentBend = comp_stamps[stampID]->getBend( j );
904 >      theBends[j].a = currentBend->getA() + atomOffset;
905 >      theBends[j].b = currentBend->getB() + atomOffset;
906 >      theBends[j].c = currentBend->getC() + atomOffset;
907            
908 <          current_atom = comp_stamps[i]->getAtom( k );
822 <          if( current_atom->haveOrientation() ){
908 >      if( currentBend->haveExtras() ){
909              
910 <            dAtom = new DirectionalAtom(index);
911 <            simnfo->n_oriented++;
826 <            the_atoms[index] = dAtom;
910 >        extras = currentBend->getExtras();
911 >        current_extra = extras;
912              
913 <            ux = current_atom->getOrntX();
914 <            uy = current_atom->getOrntY();
915 <            uz = current_atom->getOrntZ();
916 <            
917 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
918 <            
919 <            u = sqrt( uSqr );
920 <            ux = ux / u;
921 <            uy = uy / u;
922 <            uz = uz / u;
923 <            
924 <            dAtom->setSUx( ux );
925 <            dAtom->setSUy( uy );
926 <            dAtom->setSUz( uz );
927 <          }
928 <          else{
929 <            the_atoms[index] = new GeneralAtom(index);
930 <          }
931 <          the_atoms[index]->setType( current_atom->getType() );
932 <          the_atoms[index]->setIndex( index );
933 <          
934 <          // increment the index and repeat;
935 <          index++;
936 <        }
937 <        
938 <        molEnd = index -1;
939 <        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++ ){
913 >        while( current_extra != NULL ){
914 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
915 >                
916 >            switch( current_extra->getType() ){
917 >              
918 >            case 0:
919 >              theBends[j].ghost =
920 >                current_extra->getInt() + atomOffset;
921 >              theBends[j].isGhost = 1;
922 >              break;
923 >                  
924 >            case 1:
925 >              theBends[j].ghost =
926 >                (int)current_extra->getDouble() + atomOffset;
927 >              theBends[j].isGhost = 1;
928 >              break;
929 >              
930 >            default:
931 >              sprintf( painCave.errMsg,
932 >                       "SimSetup Error: ghostVectorSource was neither a "
933 >                       "double nor an int.\n"
934 >                       "-->Bend[%d] in %s\n",
935 >                       j, comp_stamps[stampID]->getID() );
936 >              painCave.isFatal = 1;
937 >              simError();
938 >            }
939 >          }
940            
941 <          current_bond = comp_stamps[i]->getBond( k );
942 <          the_bonds[index].a = current_bond->getA() + offset;
943 <          the_bonds[index].b = current_bond->getB() + offset;
944 <
945 <          exI = the_bonds[index].a;
946 <          exJ = the_bonds[index].b;
947 <
948 <          // exclude_I must always be the smaller of the pair
949 <          if( exI > exJ ){
910 <            tempEx = exI;
911 <            exI = exJ;
912 <            exJ = tempEx;
941 >          else{
942 >            
943 >            sprintf( painCave.errMsg,
944 >                     "SimSetup Error: unhandled bend assignment:\n"
945 >                     "    -->%s in Bend[%d] in %s\n",
946 >                     current_extra->getlhs(),
947 >                     j, comp_stamps[stampID]->getID() );
948 >            painCave.isFatal = 1;
949 >            simError();
950            }
914 –
951            
952 < #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++;
952 >          current_extra = current_extra->getNext();
953          }
954 <        offset += comp_stamps[i]->getNAtoms();
954 >      }
955 >          
956 >      if( !theBends[j].isGhost ){
957 >            
958 >        exI = theBends[j].a;
959 >        exJ = theBends[j].c;
960 >      }
961 >      else{
962          
963 < #ifdef IS_MPI
963 >        exI = theBends[j].a;
964 >        exJ = theBends[j].b;
965        }
937 – #endif //is_mpi
966        
967 <      molIndex++;
968 <    }      
969 <  }
967 >      // exclude_I must always be the smaller of the pair
968 >      if( exI > exJ ){
969 >        tempEx = exI;
970 >        exI = exJ;
971 >        exJ = tempEx;
972 >      }
973 > #ifdef IS_MPI
974 >      tempEx = exI;
975 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
976 >      tempEx = exJ;
977 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
978 >      
979 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
980 > #else  // isn't MPI
981 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
982 > #endif  //is_mpi
983 >    }
984 >    excludeOffset += info.nBends;
985  
986 <  the_ff->initializeBonds( the_bonds );
987 < }
986 >    for(j=0; j<info.nTorsions; j++){
987 >      
988 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
989 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
990 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
991 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
992 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
993 >      
994 >      exI = theTorsions[j].a;
995 >      exJ = theTorsions[j].d;
996  
997 < void SimSetup::makeBends( void ){
997 >      // exclude_I must always be the smaller of the pair
998 >      if( exI > exJ ){
999 >        tempEx = exI;
1000 >        exI = exJ;
1001 >        exJ = tempEx;
1002 >      }
1003 > #ifdef IS_MPI
1004 >      tempEx = exI;
1005 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1006 >      tempEx = exJ;
1007 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1008 >      
1009 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1010 > #else  // isn't MPI
1011 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1012 > #endif  //is_mpi
1013 >    }
1014 >    excludeOffset += info.nTorsions;
1015  
1016 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1017 <  bend_set* the_bends;
950 <  BendStamp* current_bend;
951 <  LinkedAssign* extras;
952 <  LinkedAssign* current_extra;
953 <  
1016 >    
1017 >    // send the arrays off to the forceField for init.
1018  
1019 <  the_bends = new bend_set[tot_bends];
1020 <  index = 0;
1021 <  offset = 0;
1022 <  molIndex = 0;
959 <  for( i=0; i<n_components; i++ ){
1019 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1020 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1021 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1022 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1023  
961 –    for( j=0; j<components_nmol[i]; j++ ){
1024  
1025 < #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 <          }
1025 >    the_molecules[i].initialize( info );
1026  
1027  
1028 < #ifdef IS_MPI
1029 <
1030 <          the_excludes[(index + tot_bonds)*2] =    
1031 <            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 <    }
1028 >    atomOffset += info.nAtoms;
1029 >    delete[] theBonds;
1030 >    delete[] theBends;
1031 >    delete[] theTorsions;
1032    }
1033  
1034   #ifdef IS_MPI
1035 <  sprintf( checkPointMsg,
1072 <           "Successfully created the bends list.\n" );
1035 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1036    MPIcheckPoint();
1037   #endif // is_mpi
1075 –  
1038  
1039 <  the_ff->initializeBends( the_bends );
1040 < }
1039 >  // clean up the forcefield
1040 >  the_ff->calcRcut();
1041 >  the_ff->cleanMe();
1042  
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 );
1043   }
1044  
1045   void SimSetup::initFromBass( void ){

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