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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 487 by mmeineke, Thu Apr 10 16:27:21 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 +    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 242 | Line 310 | void SimSetup::createSim( void ){
310  
311    globalIndex = mpiSim->divideLabor();
312  
245 –
246 –
313    // set up the local variables
314    
315    int localMol, allMol;
316    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
317 +
318 +  int* mol2proc = mpiSim->getMolToProcMap();
319 +  int* molCompType = mpiSim->getMolComponentType();
320    
321    allMol = 0;
322    localMol = 0;
# Line 259 | Line 328 | void SimSetup::createSim( void ){
328  
329      for( j=0; j<components_nmol[i]; j++ ){
330        
331 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
331 >      if( mol2proc[allMol] == worldRank ){
332          
333          local_atoms +=    comp_stamps[i]->getNAtoms();
334          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 347 | void SimSetup::createSim( void ){
347    if( local_atoms != simnfo->n_atoms ){
348      sprintf( painCave.errMsg,
349               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
350 <             " localAtom (%d) are note equal.\n",
350 >             " localAtom (%d) are not equal.\n",
351               simnfo->n_atoms,
352               local_atoms );
353      painCave.isFatal = 1;
# Line 304 | Line 372 | void SimSetup::createSim( void ){
372    Atom::createArrays(simnfo->n_atoms);
373    the_atoms = new Atom*[simnfo->n_atoms];
374    the_molecules = new Molecule[simnfo->n_mol];
375 +  int molIndex;
376  
377 +  // initialize the molecule's stampID's
378  
379 + #ifdef IS_MPI
380 +  
381 +
382 +  molIndex = 0;
383 +  for(i=0; i<mpiSim->getTotNmol(); i++){
384 +    
385 +    if(mol2proc[i] == worldRank ){
386 +      the_molecules[molIndex].setStampID( molCompType[i] );
387 +      the_molecules[molIndex].setMyIndex( molIndex );
388 +      molIndex++;
389 +    }
390 +  }
391 +
392 + #else // is_mpi
393 +  
394 +  molIndex = 0;
395 +  for(i=0; i<n_components; i++){
396 +    for(j=0; j<components_nmol[i]; j++ ){
397 +      the_molecules[molIndex].setStampID( i );
398 +      the_molecules[molIndex].setMyIndex( molIndex );
399 +      molIndex++;
400 +    }
401 +  }
402 +    
403 +
404 + #endif // is_mpi
405 +
406 +
407    if( simnfo->n_SRI ){
408 <    the_sris = new SRI*[simnfo->n_SRI];
409 <    the_excludes = new int[2 * simnfo->n_SRI];
408 >    
409 >    Exclude::createArray(simnfo->n_SRI);
410 >    the_excludes = new Exclude*[simnfo->n_SRI];
411 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
412      simnfo->globalExcludes = new int;
413 <    simnfo->n_exclude = tot_SRI;
413 >    simnfo->n_exclude = simnfo->n_SRI;
414    }
415    else{
416      
417 <    the_excludes = new int[2];
418 <    the_excludes[0] = 0;
419 <    the_excludes[1] = 0;
417 >    Exclude::createArray( 1 );
418 >    the_excludes = new Exclude*;
419 >    the_excludes[0] = new Exclude(0);
420 >    the_excludes[0]->setPair( 0,0 );
421      simnfo->globalExcludes = new int;
422      simnfo->globalExcludes[0] = 0;
423 <
323 <    simnfo->n_exclude = 1;
423 >    simnfo->n_exclude = 0;
424    }
425  
426    // set the arrays into the SimInfo object
427  
428    simnfo->atoms = the_atoms;
429 <  simnfo->sr_interactions = the_sris;
429 >  simnfo->molecules = the_molecules;
430    simnfo->nGlobalExcludes = 0;
431    simnfo->excludes = the_excludes;
432  
# Line 383 | Line 483 | void SimSetup::createSim( void ){
483  
484    the_ff->setSimInfo( simnfo );
485  
486 <  makeAtoms();
486 >  makeMolecules();
487    simnfo->identArray = new int[simnfo->n_atoms];
488 +  simnfo->molMembershipArray = new int[simnfo->n_atoms];
489    for(i=0; i<simnfo->n_atoms; i++){
490      simnfo->identArray[i] = the_atoms[i]->getIdent();
491    }
492 <  
493 <  if( tot_bonds ){
393 <    makeBonds();
492 >  for(i=0; i< simnfo->n_mol; i++) {
493 >    the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
494    }
495 <
396 <  if( tot_bends ){
397 <    makeBends();
398 <  }
399 <
400 <  if( tot_torsions ){
401 <    makeTorsions();
402 <  }
403 <
404 <
495 >  
496    if (the_globals->getUseRF() ) {
497      simnfo->useReactionField = 1;
498    
# Line 443 | Line 534 | void SimSetup::createSim( void ){
534      }
535      simnfo->dielectric = the_globals->getDielectric();  
536    } else {
537 <    if (simnfo->n_dipoles) {
537 >    if (usesDipoles) {
538        
539        if( !the_globals->haveECR() ){
540          sprintf( painCave.errMsg,
541 <                 "SimSetup Warning: using default value of 1/2 the smallest"
541 >                 "SimSetup Warning: using default value of 1/2 the smallest "
542                   "box length for the electrostaticCutoffRadius.\n"
543                   "I hope you have a very fast processor!\n");
544          painCave.isFatal = 0;
# Line 463 | Line 554 | void SimSetup::createSim( void ){
554        
555        if( !the_globals->haveEST() ){
556          sprintf( painCave.errMsg,
557 <                 "SimSetup Warning: using default value of 5% of the"
557 >                 "SimSetup Warning: using default value of 5%% of the "
558                   "electrostaticCutoffRadius for the "
559                   "electrostaticSkinThickness\n"
560                   );
# Line 638 | Line 729 | void SimSetup::createSim( void ){
729  
730   //   new AllLong( simnfo );
731  
641 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643 –  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644 –  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
732  
733 <
733 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
734 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
735 >  }
736 >  else if( !strcmp( force_field, "LJ" ) ){
737 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
738 >  }
739 >  else {
740 >    std::cerr << "I'm a bug.\n";
741 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
742 >  }
743 > #ifdef IS_MPI
744 >  mpiSim->mpiRefresh();
745 > #endif
746  
747    // initialize the Fortran
748 <  
748 >
749 >
750    simnfo->refreshSim();
751    
752    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 674 | Line 774 | void SimSetup::makeMolecules( void ){
774  
775   void SimSetup::makeMolecules( void ){
776  
777 <  int i, j, exI, exJ, tempEx, stampID, atomOffset;
777 >  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
778    molInit info;
779    DirectionalAtom* dAtom;
780 +  LinkedAssign* extras;
781 +  LinkedAssign* current_extra;
782    AtomStamp* currentAtom;
783    BondStamp* currentBond;
784    BendStamp* currentBend;
785    TorsionStamp* currentTorsion;
786 +
787 +  bond_pair* theBonds;
788 +  bend_set* theBends;
789 +  torsion_set* theTorsions;
790 +
791    
792    //init the forceField paramters
793  
794    the_ff->readParams();
795  
796    
797 <  // init the molecules
797 >  // init the atoms
798  
799 +  double ux, uy, uz, u, uSqr;
800 +  
801    atomOffset = 0;
802 +  excludeOffset = 0;
803    for(i=0; i<simnfo->n_mol; i++){
804      
805      stampID = the_molecules[i].getStampID();
# Line 698 | Line 808 | void SimSetup::makeMolecules( void ){
808      info.nBonds    = comp_stamps[stampID]->getNBonds();
809      info.nBends    = comp_stamps[stampID]->getNBends();
810      info.nTorsions = comp_stamps[stampID]->getNTorsions();
811 <    
811 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
812 >
813      info.myAtoms = &the_atoms[atomOffset];
814 +    info.myExcludes = &the_excludes[excludeOffset];
815      info.myBonds = new Bond*[info.nBonds];
816      info.myBends = new Bend*[info.nBends];
817 <    info.myTorsions = new Torsions*[info.nTorsions];
817 >    info.myTorsions = new Torsion*[info.nTorsions];
818  
819      theBonds = new bond_pair[info.nBonds];
820      theBends = new bend_set[info.nBends];
# Line 712 | Line 824 | void SimSetup::makeMolecules( void ){
824      
825      for(j=0; j<info.nAtoms; j++){
826        
827 <      currentAtom = theComponents[stampID]->getAtom( j );
827 >      currentAtom = comp_stamps[stampID]->getAtom( j );
828        if( currentAtom->haveOrientation() ){
829          
830          dAtom = new DirectionalAtom(j + atomOffset);
# Line 747 | Line 859 | void SimSetup::makeMolecules( void ){
859      }
860      
861      // make the bonds
862 <    for(j=0; j<nBonds; j++){
862 >    for(j=0; j<info.nBonds; j++){
863        
864        currentBond = comp_stamps[stampID]->getBond( j );
865        theBonds[j].a = currentBond->getA() + atomOffset;
866        theBonds[j].b = currentBond->getB() + atomOffset;
867  
868 <      exI = theBonds[i].a;
869 <      exJ = theBonds[i].b;
868 >      exI = theBonds[j].a;
869 >      exJ = theBonds[j].b;
870  
871        // exclude_I must always be the smaller of the pair
872        if( exI > exJ ){
# Line 763 | Line 875 | void SimSetup::makeMolecules( void ){
875          exJ = tempEx;
876        }
877   #ifdef IS_MPI
878 +      tempEx = exI;
879 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
880 +      tempEx = exJ;
881 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
882        
883 <      the_excludes[index*2] =    
768 <        the_atoms[exI]->getGlobalIndex() + 1;
769 <      the_excludes[index*2 + 1] =
770 <        the_atoms[exJ]->getGlobalIndex() + 1;
771 <      
883 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
884   #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)
885  
886 +      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
887   #endif  //is_mpi
888 <    
889 <  }
888 >    }
889 >    excludeOffset += info.nBonds;
890  
891 <
892 <
893 <
894 <
895 <
896 <
897 <
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++ ){
891 >    //make the bends
892 >    for(j=0; j<info.nBends; j++){
893 >      
894 >      currentBend = comp_stamps[stampID]->getBend( j );
895 >      theBends[j].a = currentBend->getA() + atomOffset;
896 >      theBends[j].b = currentBend->getB() + atomOffset;
897 >      theBends[j].c = currentBend->getC() + atomOffset;
898            
899 <          current_atom = comp_stamps[i]->getAtom( k );
822 <          if( current_atom->haveOrientation() ){
899 >      if( currentBend->haveExtras() ){
900              
901 <            dAtom = new DirectionalAtom(index);
902 <            simnfo->n_oriented++;
826 <            the_atoms[index] = dAtom;
901 >        extras = currentBend->getExtras();
902 >        current_extra = extras;
903              
904 <            ux = current_atom->getOrntX();
905 <            uy = current_atom->getOrntY();
906 <            uz = current_atom->getOrntZ();
907 <            
908 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
909 <            
910 <            u = sqrt( uSqr );
911 <            ux = ux / u;
912 <            uy = uy / u;
913 <            uz = uz / u;
914 <            
915 <            dAtom->setSUx( ux );
916 <            dAtom->setSUy( uy );
917 <            dAtom->setSUz( uz );
918 <          }
919 <          else{
920 <            the_atoms[index] = new GeneralAtom(index);
921 <          }
922 <          the_atoms[index]->setType( current_atom->getType() );
923 <          the_atoms[index]->setIndex( index );
924 <          
925 <          // increment the index and repeat;
926 <          index++;
927 <        }
928 <        
929 <        molEnd = index -1;
930 <        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++ ){
904 >        while( current_extra != NULL ){
905 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
906 >                
907 >            switch( current_extra->getType() ){
908 >              
909 >            case 0:
910 >              theBends[j].ghost =
911 >                current_extra->getInt() + atomOffset;
912 >              theBends[j].isGhost = 1;
913 >              break;
914 >                  
915 >            case 1:
916 >              theBends[j].ghost =
917 >                (int)current_extra->getDouble() + atomOffset;
918 >              theBends[j].isGhost = 1;
919 >              break;
920 >              
921 >            default:
922 >              sprintf( painCave.errMsg,
923 >                       "SimSetup Error: ghostVectorSource was neither a "
924 >                       "double nor an int.\n"
925 >                       "-->Bend[%d] in %s\n",
926 >                       j, comp_stamps[stampID]->getID() );
927 >              painCave.isFatal = 1;
928 >              simError();
929 >            }
930 >          }
931            
932 <          current_bond = comp_stamps[i]->getBond( k );
933 <          the_bonds[index].a = current_bond->getA() + offset;
934 <          the_bonds[index].b = current_bond->getB() + offset;
935 <
936 <          exI = the_bonds[index].a;
937 <          exJ = the_bonds[index].b;
938 <
939 <          // exclude_I must always be the smaller of the pair
940 <          if( exI > exJ ){
910 <            tempEx = exI;
911 <            exI = exJ;
912 <            exJ = tempEx;
932 >          else{
933 >            
934 >            sprintf( painCave.errMsg,
935 >                     "SimSetup Error: unhandled bend assignment:\n"
936 >                     "    -->%s in Bend[%d] in %s\n",
937 >                     current_extra->getlhs(),
938 >                     j, comp_stamps[stampID]->getID() );
939 >            painCave.isFatal = 1;
940 >            simError();
941            }
914 –
942            
943 < #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++;
943 >          current_extra = current_extra->getNext();
944          }
945 <        offset += comp_stamps[i]->getNAtoms();
945 >      }
946 >          
947 >      if( !theBends[j].isGhost ){
948 >            
949 >        exI = theBends[j].a;
950 >        exJ = theBends[j].c;
951 >      }
952 >      else{
953          
954 < #ifdef IS_MPI
954 >        exI = theBends[j].a;
955 >        exJ = theBends[j].b;
956        }
937 – #endif //is_mpi
957        
958 <      molIndex++;
959 <    }      
960 <  }
958 >      // exclude_I must always be the smaller of the pair
959 >      if( exI > exJ ){
960 >        tempEx = exI;
961 >        exI = exJ;
962 >        exJ = tempEx;
963 >      }
964 > #ifdef IS_MPI
965 >      tempEx = exI;
966 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
967 >      tempEx = exJ;
968 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
969 >      
970 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
971 > #else  // isn't MPI
972 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
973 > #endif  //is_mpi
974 >    }
975 >    excludeOffset += info.nBends;
976  
977 <  the_ff->initializeBonds( the_bonds );
978 < }
977 >    for(j=0; j<info.nTorsions; j++){
978 >      
979 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
980 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
981 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
982 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
983 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
984 >      
985 >      exI = theTorsions[j].a;
986 >      exJ = theTorsions[j].d;
987  
988 < void SimSetup::makeBends( void ){
988 >      // exclude_I must always be the smaller of the pair
989 >      if( exI > exJ ){
990 >        tempEx = exI;
991 >        exI = exJ;
992 >        exJ = tempEx;
993 >      }
994 > #ifdef IS_MPI
995 >      tempEx = exI;
996 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
997 >      tempEx = exJ;
998 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
999 >      
1000 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1001 > #else  // isn't MPI
1002 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1003 > #endif  //is_mpi
1004 >    }
1005 >    excludeOffset += info.nTorsions;
1006  
1007 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1008 <  bend_set* the_bends;
950 <  BendStamp* current_bend;
951 <  LinkedAssign* extras;
952 <  LinkedAssign* current_extra;
953 <  
1007 >    
1008 >    // send the arrays off to the forceField for init.
1009  
1010 <  the_bends = new bend_set[tot_bends];
1011 <  index = 0;
1012 <  offset = 0;
1013 <  molIndex = 0;
959 <  for( i=0; i<n_components; i++ ){
1010 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1011 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1012 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1013 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1014  
961 –    for( j=0; j<components_nmol[i]; j++ ){
1015  
1016 < #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 <          }
1016 >    the_molecules[i].initialize( info );
1017  
1041 –
1042 – #ifdef IS_MPI
1043 –
1044 –          the_excludes[(index + tot_bonds)*2] =    
1045 –            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
1018  
1019 <      molIndex++;
1020 <    }
1019 >    atomOffset += info.nAtoms;
1020 >    delete[] theBonds;
1021 >    delete[] theBends;
1022 >    delete[] theTorsions;
1023    }
1024  
1025   #ifdef IS_MPI
1026 <  sprintf( checkPointMsg,
1072 <           "Successfully created the bends list.\n" );
1026 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1027    MPIcheckPoint();
1028   #endif // is_mpi
1075 –  
1029  
1030 <  the_ff->initializeBends( the_bends );
1031 < }
1030 >  // clean up the forcefield
1031 >  the_ff->calcRcut();
1032 >  the_ff->cleanMe();
1033  
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 );
1034   }
1035  
1036   void SimSetup::initFromBass( void ){

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