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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 474 by gezelter, Mon Apr 7 21:42:19 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 +    the_extendedsystem->setQmass(the_globals->getQmass());
92 +    the_extendedsystem->setTauRelax(the_globals->getTauRelax());
93 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
94 +    the_extendedsystem = new ExtendedSystem( simnfo );
95 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
96 +    the_extendedsystem->setQmass(the_globals->getQmass());    
97 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
98 +  } else {
99 +    sprintf( painCave.errMsg,
100 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
101 +             "reverting to NVE for this simulation.\n",
102 +             ensemble );
103 +    painCave.isFatal = 0;
104 +    simError();
105 +    strcpy( ensemble, "NVE" );
106 +  }  
107    strcpy( simnfo->ensemble, ensemble );
108  
109    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
110    simnfo->usePBC = the_globals->getPBC();
111            
112 <
113 <
114 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
115 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
116 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
117 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
112 >  int usesDipoles = 0;
113 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
114 >    the_ff = new TraPPE_ExFF();
115 >    usesDipoles = 1;
116 >  }
117 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
118    else{
119      sprintf( painCave.errMsg,
120               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 242 | Line 265 | void SimSetup::createSim( void ){
265  
266    globalIndex = mpiSim->divideLabor();
267  
245 –
246 –
268    // set up the local variables
269    
270    int localMol, allMol;
271    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
272 +
273 +  int* mol2proc = mpiSim->getMolToProcMap();
274 +  int* molCompType = mpiSim->getMolComponentType();
275    
276    allMol = 0;
277    localMol = 0;
# Line 259 | Line 283 | void SimSetup::createSim( void ){
283  
284      for( j=0; j<components_nmol[i]; j++ ){
285        
286 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
286 >      if( mol2proc[j] == worldRank ){
287          
288          local_atoms +=    comp_stamps[i]->getNAtoms();
289          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 302 | void SimSetup::createSim( void ){
302    if( local_atoms != simnfo->n_atoms ){
303      sprintf( painCave.errMsg,
304               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
305 <             " localAtom (%d) are note equal.\n",
305 >             " localAtom (%d) are not equal.\n",
306               simnfo->n_atoms,
307               local_atoms );
308      painCave.isFatal = 1;
# Line 304 | Line 327 | void SimSetup::createSim( void ){
327    Atom::createArrays(simnfo->n_atoms);
328    the_atoms = new Atom*[simnfo->n_atoms];
329    the_molecules = new Molecule[simnfo->n_mol];
330 +  int molIndex;
331  
332 +  // initialize the molecule's stampID's
333  
334 + #ifdef IS_MPI
335 +  
336 +
337 +  molIndex = 0;
338 +  for(i=0; i<mpiSim->getTotNmol(); i++){
339 +    
340 +    if(mol2proc[i] == worldRank ){
341 +      the_molecules[molIndex].setStampID( molCompType[i] );
342 +      the_molecules[molIndex].setMyIndex( molIndex );
343 +      molIndex++;
344 +    }
345 +  }
346 +
347 + #else // is_mpi
348 +  
349 +  molIndex = 0;
350 +  for(i=0; i<n_components; i++){
351 +    for(j=0; j<components_nmol[i]; j++ ){
352 +      the_molecules[molIndex].setStampID( i );
353 +      the_molecules[molIndex].setMyIndex( molIndex );
354 +      molIndex++;
355 +    }
356 +  }
357 +    
358 +
359 + #endif // is_mpi
360 +
361 +
362    if( simnfo->n_SRI ){
363 <    the_sris = new SRI*[simnfo->n_SRI];
364 <    the_excludes = new int[2 * simnfo->n_SRI];
363 >    
364 >    Exclude::createArray(simnfo->n_SRI);
365 >    the_excludes = new Exclude*[simnfo->n_SRI];
366 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
367      simnfo->globalExcludes = new int;
368 <    simnfo->n_exclude = tot_SRI;
368 >    simnfo->n_exclude = simnfo->n_SRI;
369    }
370    else{
371      
372 <    the_excludes = new int[2];
373 <    the_excludes[0] = 0;
374 <    the_excludes[1] = 0;
372 >    Exclude::createArray( 1 );
373 >    the_excludes = new Exclude*;
374 >    the_excludes[0] = new Exclude(0);
375 >    the_excludes[0]->setPair( 0,0 );
376      simnfo->globalExcludes = new int;
377      simnfo->globalExcludes[0] = 0;
378 <
323 <    simnfo->n_exclude = 1;
378 >    simnfo->n_exclude = 0;
379    }
380  
381    // set the arrays into the SimInfo object
382  
383    simnfo->atoms = the_atoms;
384 <  simnfo->sr_interactions = the_sris;
384 >  simnfo->molecules = the_molecules;
385    simnfo->nGlobalExcludes = 0;
386    simnfo->excludes = the_excludes;
387  
# Line 383 | Line 438 | void SimSetup::createSim( void ){
438  
439    the_ff->setSimInfo( simnfo );
440  
441 <  makeAtoms();
441 >  makeMolecules();
442    simnfo->identArray = new int[simnfo->n_atoms];
443    for(i=0; i<simnfo->n_atoms; i++){
444      simnfo->identArray[i] = the_atoms[i]->getIdent();
445    }
446    
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 –
447    if (the_globals->getUseRF() ) {
448      simnfo->useReactionField = 1;
449    
# Line 443 | Line 485 | void SimSetup::createSim( void ){
485      }
486      simnfo->dielectric = the_globals->getDielectric();  
487    } else {
488 <    if (simnfo->n_dipoles) {
488 >    if (usesDipoles) {
489        
490        if( !the_globals->haveECR() ){
491          sprintf( painCave.errMsg,
492 <                 "SimSetup Warning: using default value of 1/2 the smallest"
492 >                 "SimSetup Warning: using default value of 1/2 the smallest "
493                   "box length for the electrostaticCutoffRadius.\n"
494                   "I hope you have a very fast processor!\n");
495          painCave.isFatal = 0;
# Line 463 | Line 505 | void SimSetup::createSim( void ){
505        
506        if( !the_globals->haveEST() ){
507          sprintf( painCave.errMsg,
508 <                 "SimSetup Warning: using default value of 5% of the"
508 >                 "SimSetup Warning: using default value of 5%% of the "
509                   "electrostaticCutoffRadius for the "
510                   "electrostaticSkinThickness\n"
511                   );
# Line 638 | Line 680 | void SimSetup::createSim( void ){
680  
681   //   new AllLong( simnfo );
682  
683 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
684 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
685 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
686 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
683 >
684 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
685 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
686 >    std::cerr << "called new Symplecic\n";
687 >    fprintf( stderr, "called new Symplectic. stderr\n" );
688 >  }
689 >  else if( !strcmp( force_field, "LJ" ) ){
690 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
691 >    std::cerr << "called new Verlet\n";
692 >    fprintf( stderr, "called new Verlet. stderr\n" );
693 >  }
694 >  else {
695 >    std::cerr << "I'm a bug.\n";
696 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
697 >  }
698 > #ifdef IS_MPI
699 >  mpiSim->mpiRefresh();
700 > #endif
701  
702 +  // initialize the Fortran
703  
704  
648 –  // initialize the Fortran
649 –  
705    simnfo->refreshSim();
706    
707    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 671 | Line 726 | void SimSetup::makeAtoms( void ){
726   #endif // is_mpi
727   }
728  
674 – void SimSetup::makeAtoms( void ){
729  
730 <  int i, j, k, index;
677 <  double ux, uy, uz, uSqr, u;
678 <  AtomStamp* current_atom;
730 > void SimSetup::makeMolecules( void ){
731  
732 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
733 +  molInit info;
734    DirectionalAtom* dAtom;
735 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
735 >  LinkedAssign* extras;
736 >  LinkedAssign* current_extra;
737 >  AtomStamp* currentAtom;
738 >  BondStamp* currentBond;
739 >  BendStamp* currentBend;
740 >  TorsionStamp* currentTorsion;
741  
742 <  lMolIndex = 0;
743 <  molIndex = 0;
744 <  index = 0;
686 <  for( i=0; i<n_components; i++ ){
742 >  bond_pair* theBonds;
743 >  bend_set* theBends;
744 >  torsion_set* theTorsions;
745  
746 <    for( j=0; j<components_nmol[i]; j++ ){
746 >  
747 >  //init the forceField paramters
748  
749 < #ifdef IS_MPI
691 <      if( mpiSim->getMyMolStart() <= molIndex &&
692 <          molIndex <= mpiSim->getMyMolEnd() ){
693 < #endif // is_mpi        
749 >  the_ff->readParams();
750  
751 <        molStart = index;
752 <        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++;
751 >  
752 >  // init the atoms
753  
754 < #ifdef IS_MPI
755 <      }
756 < #endif //is_mpi
757 <      
758 <      molIndex++;
743 <    }
744 <  }
745 <
746 < #ifdef IS_MPI
747 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
754 >  double ux, uy, uz, u, uSqr;
755 >  
756 >  atomOffset = 0;
757 >  excludeOffset = 0;
758 >  for(i=0; i<simnfo->n_mol; i++){
759      
760 <    delete[] globalIndex;
760 >    stampID = the_molecules[i].getStampID();
761  
762 <    mpiSim->mpiRefresh();
763 < #endif //IS_MPI
764 <          
765 <  the_ff->initializeAtoms();
766 < }
762 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
763 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
764 >    info.nBends    = comp_stamps[stampID]->getNBends();
765 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
766 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
767  
768 < void SimSetup::makeBonds( void ){
768 >    info.myAtoms = &the_atoms[atomOffset];
769 >    info.myExcludes = &the_excludes[excludeOffset];
770 >    info.myBonds = new Bond*[info.nBonds];
771 >    info.myBends = new Bend*[info.nBends];
772 >    info.myTorsions = new Torsion*[info.nTorsions];
773  
774 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
775 <  bond_pair* the_bonds;
776 <  BondStamp* current_bond;
777 <
778 <  the_bonds = new bond_pair[tot_bonds];
779 <  index = 0;
780 <  offset = 0;
781 <  molIndex = 0;
782 <
783 <  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        
774 >    theBonds = new bond_pair[info.nBonds];
775 >    theBends = new bend_set[info.nBends];
776 >    theTorsions = new torsion_set[info.nTorsions];
777 >    
778 >    // make the Atoms
779 >    
780 >    for(j=0; j<info.nAtoms; j++){
781 >      
782 >      currentAtom = comp_stamps[stampID]->getAtom( j );
783 >      if( currentAtom->haveOrientation() ){
784          
785 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
786 <          
787 <          current_bond = comp_stamps[i]->getBond( k );
788 <          the_bonds[index].a = current_bond->getA() + offset;
789 <          the_bonds[index].b = current_bond->getB() + offset;
790 <
791 <          exI = the_bonds[index].a;
792 <          exJ = the_bonds[index].b;
793 <
794 <          // exclude_I must always be the smaller of the pair
795 <          if( exI > exJ ){
796 <            tempEx = exI;
797 <            exI = exJ;
798 <            exJ = tempEx;
799 <          }
800 <
801 <          
785 >        dAtom = new DirectionalAtom(j + atomOffset);
786 >        simnfo->n_oriented++;
787 >        info.myAtoms[j] = dAtom;
788 >        
789 >        ux = currentAtom->getOrntX();
790 >        uy = currentAtom->getOrntY();
791 >        uz = currentAtom->getOrntZ();
792 >        
793 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
794 >        
795 >        u = sqrt( uSqr );
796 >        ux = ux / u;
797 >        uy = uy / u;
798 >        uz = uz / u;
799 >        
800 >        dAtom->setSUx( ux );
801 >        dAtom->setSUy( uy );
802 >        dAtom->setSUz( uz );
803 >      }
804 >      else{
805 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
806 >      }
807 >      info.myAtoms[j]->setType( currentAtom->getType() );
808 >    
809   #ifdef IS_MPI
810 +      
811 +      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
812 +      
813 + #endif // is_mpi
814 +    }
815 +    
816 +    // make the bonds
817 +    for(j=0; j<info.nBonds; j++){
818 +      
819 +      currentBond = comp_stamps[stampID]->getBond( j );
820 +      theBonds[j].a = currentBond->getA() + atomOffset;
821 +      theBonds[j].b = currentBond->getB() + atomOffset;
822  
823 <          the_excludes[index*2] =    
824 <            the_atoms[exI]->getGlobalIndex() + 1;
798 <          the_excludes[index*2 + 1] =
799 <            the_atoms[exJ]->getGlobalIndex() + 1;
823 >      exI = theBonds[j].a;
824 >      exJ = theBonds[j].b;
825  
826 +      // exclude_I must always be the smaller of the pair
827 +      if( exI > exJ ){
828 +        tempEx = exI;
829 +        exI = exJ;
830 +        exJ = tempEx;
831 +      }
832 + #ifdef IS_MPI
833 +      tempEx = exI;
834 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
835 +      tempEx = exJ;
836 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
837 +      
838 +      the_excludes[j+excludeOffset]->setPair( exI, exJ );
839   #else  // isn't MPI
840 <          
841 <          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)
840 >
841 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
842   #endif  //is_mpi
843 <          
844 <          // 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 <  }
843 >    }
844 >    excludeOffset += info.nBonds;
845  
846 <  the_ff->initializeBonds( the_bonds );
847 < }
848 <
849 < void SimSetup::makeBends( void ){
850 <
851 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
852 <  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++ ){
846 >    //make the bends
847 >    for(j=0; j<info.nBends; j++){
848 >      
849 >      currentBend = comp_stamps[stampID]->getBend( j );
850 >      theBends[j].a = currentBend->getA() + atomOffset;
851 >      theBends[j].b = currentBend->getB() + atomOffset;
852 >      theBends[j].c = currentBend->getC() + atomOffset;
853            
854 <          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() ){
854 >      if( currentBend->haveExtras() ){
855              
856 <            extras = current_bend->getExtras();
857 <            current_extra = extras;
856 >        extras = currentBend->getExtras();
857 >        current_extra = extras;
858              
859 <            while( current_extra != NULL ){
860 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
859 >        while( current_extra != NULL ){
860 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
861                  
862 <                switch( current_extra->getType() ){
862 >            switch( current_extra->getType() ){
863 >              
864 >            case 0:
865 >              theBends[j].ghost =
866 >                current_extra->getInt() + atomOffset;
867 >              theBends[j].isGhost = 1;
868 >              break;
869                    
870 <                case 0:
871 <                  the_bends[index].ghost =
872 <                    current_extra->getInt() + offset;
873 <                  the_bends[index].isGhost = 1;
874 <                  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 <              }
870 >            case 1:
871 >              theBends[j].ghost =
872 >                (int)current_extra->getDouble() + atomOffset;
873 >              theBends[j].isGhost = 1;
874 >              break;
875                
876 <              else{
877 <                
878 <                sprintf( painCave.errMsg,
879 <                         "SimSetup Error: unhandled bend assignment:\n"
880 <                         "    -->%s in Bend[%d] in %s\n",
881 <                         current_extra->getlhs(),
882 <                         k, comp_stamps[i]->getID() );
883 <                painCave.isFatal = 1;
894 <                simError();
895 <              }
896 <              
897 <              current_extra = current_extra->getNext();
876 >            default:
877 >              sprintf( painCave.errMsg,
878 >                       "SimSetup Error: ghostVectorSource was neither a "
879 >                       "double nor an int.\n"
880 >                       "-->Bend[%d] in %s\n",
881 >                       j, comp_stamps[stampID]->getID() );
882 >              painCave.isFatal = 1;
883 >              simError();
884              }
885            }
886            
901 –          if( !the_bends[index].isGhost ){
902 –            
903 –            exI = the_bends[index].a;
904 –            exJ = the_bends[index].c;
905 –          }
887            else{
888              
889 <            exI = the_bends[index].a;
890 <            exJ = the_bends[index].b;
889 >            sprintf( painCave.errMsg,
890 >                     "SimSetup Error: unhandled bend assignment:\n"
891 >                     "    -->%s in Bend[%d] in %s\n",
892 >                     current_extra->getlhs(),
893 >                     j, comp_stamps[stampID]->getID() );
894 >            painCave.isFatal = 1;
895 >            simError();
896            }
897            
898 <          // 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++;
898 >          current_extra = current_extra->getNext();
899          }
900 <        offset += comp_stamps[i]->getNAtoms();
900 >      }
901 >          
902 >      if( !theBends[j].isGhost ){
903 >            
904 >        exI = theBends[j].a;
905 >        exJ = theBends[j].c;
906 >      }
907 >      else{
908          
909 < #ifdef IS_MPI
909 >        exI = theBends[j].a;
910 >        exJ = theBends[j].b;
911        }
912 < #endif //is_mpi
912 >      
913 >      // exclude_I must always be the smaller of the pair
914 >      if( exI > exJ ){
915 >        tempEx = exI;
916 >        exI = exJ;
917 >        exJ = tempEx;
918 >      }
919 > #ifdef IS_MPI
920 >      tempEx = exI;
921 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
922 >      tempEx = exJ;
923 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
924 >      
925 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
926 > #else  // isn't MPI
927 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
928 > #endif  //is_mpi
929 >    }
930 >    excludeOffset += info.nBends;
931  
932 <      molIndex++;
932 >    for(j=0; j<info.nTorsions; j++){
933 >      
934 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
935 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
936 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
937 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
938 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
939 >      
940 >      exI = theTorsions[j].a;
941 >      exJ = theTorsions[j].d;
942 >
943 >      // exclude_I must always be the smaller of the pair
944 >      if( exI > exJ ){
945 >        tempEx = exI;
946 >        exI = exJ;
947 >        exJ = tempEx;
948 >      }
949 > #ifdef IS_MPI
950 >      tempEx = exI;
951 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
952 >      tempEx = exJ;
953 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
954 >      
955 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
956 > #else  // isn't MPI
957 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
958 > #endif  //is_mpi
959      }
960 +    excludeOffset += info.nTorsions;
961 +
962 +    
963 +    // send the arrays off to the forceField for init.
964 +
965 +    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
966 +    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
967 +    the_ff->initializeBends( info.nBends, info.myBends, theBends );
968 +    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
969 +
970 +
971 +    the_molecules[i].initialize( info );
972 +
973 +
974 +    atomOffset += info.nAtoms;
975 +    delete[] theBonds;
976 +    delete[] theBends;
977 +    delete[] theTorsions;
978    }
979  
980   #ifdef IS_MPI
981 <  sprintf( checkPointMsg,
950 <           "Successfully created the bends list.\n" );
981 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
982    MPIcheckPoint();
983   #endif // is_mpi
953 –  
984  
985 <  the_ff->initializeBends( the_bends );
986 < }
985 >  // clean up the forcefield
986 >  the_ff->calcRcut();
987 >  the_ff->cleanMe();
988  
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 );
989   }
990  
991   void SimSetup::initFromBass( void ){

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