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root/group/branches/no-template-branch/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 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  
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 );
683  
684 <
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 <  
703 >
704 >
705    simnfo->refreshSim();
706    
707    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 674 | Line 729 | void SimSetup::makeMolecules( void ){
729  
730   void SimSetup::makeMolecules( void ){
731  
732 <  int i, j, exI, exJ, tempEx, stampID, atomOffset;
732 >  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
733    molInit info;
734    DirectionalAtom* dAtom;
735 +  LinkedAssign* extras;
736 +  LinkedAssign* current_extra;
737    AtomStamp* currentAtom;
738    BondStamp* currentBond;
739    BendStamp* currentBend;
740    TorsionStamp* currentTorsion;
741 +
742 +  bond_pair* theBonds;
743 +  bend_set* theBends;
744 +  torsion_set* theTorsions;
745 +
746    
747    //init the forceField paramters
748  
749    the_ff->readParams();
750  
751    
752 <  // init the molecules
752 >  // init the atoms
753  
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      stampID = the_molecules[i].getStampID();
# Line 698 | Line 763 | void SimSetup::makeMolecules( void ){
763      info.nBonds    = comp_stamps[stampID]->getNBonds();
764      info.nBends    = comp_stamps[stampID]->getNBends();
765      info.nTorsions = comp_stamps[stampID]->getNTorsions();
766 <    
766 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
767 >
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 Torsions*[info.nTorsions];
772 >    info.myTorsions = new Torsion*[info.nTorsions];
773  
774      theBonds = new bond_pair[info.nBonds];
775      theBends = new bend_set[info.nBends];
# Line 712 | Line 779 | void SimSetup::makeMolecules( void ){
779      
780      for(j=0; j<info.nAtoms; j++){
781        
782 <      currentAtom = theComponents[stampID]->getAtom( j );
782 >      currentAtom = comp_stamps[stampID]->getAtom( j );
783        if( currentAtom->haveOrientation() ){
784          
785          dAtom = new DirectionalAtom(j + atomOffset);
# Line 747 | Line 814 | void SimSetup::makeMolecules( void ){
814      }
815      
816      // make the bonds
817 <    for(j=0; j<nBonds; j++){
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 <      exI = theBonds[i].a;
824 <      exJ = theBonds[i].b;
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 ){
# Line 763 | Line 830 | void SimSetup::makeMolecules( void ){
830          exJ = tempEx;
831        }
832   #ifdef IS_MPI
833 <      
834 <      the_excludes[index*2] =    
835 <        the_atoms[exI]->getGlobalIndex() + 1;
836 <      the_excludes[index*2 + 1] =
770 <        the_atoms[exJ]->getGlobalIndex() + 1;
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
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)
840  
841 +      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
842   #endif  //is_mpi
843 <    
844 <  }
843 >    }
844 >    excludeOffset += info.nBonds;
845  
846 <
847 <
848 <
849 <
850 <
851 <
852 <
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++ ){
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_atom = comp_stamps[i]->getAtom( k );
822 <          if( current_atom->haveOrientation() ){
854 >      if( currentBend->haveExtras() ){
855              
856 <            dAtom = new DirectionalAtom(index);
857 <            simnfo->n_oriented++;
826 <            the_atoms[index] = dAtom;
856 >        extras = currentBend->getExtras();
857 >        current_extra = extras;
858              
859 <            ux = current_atom->getOrntX();
860 <            uy = current_atom->getOrntY();
861 <            uz = current_atom->getOrntZ();
862 <            
863 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
864 <            
865 <            u = sqrt( uSqr );
866 <            ux = ux / u;
867 <            uy = uy / u;
868 <            uz = uz / u;
869 <            
870 <            dAtom->setSUx( ux );
871 <            dAtom->setSUy( uy );
872 <            dAtom->setSUz( uz );
859 >        while( current_extra != NULL ){
860 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
861 >                
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 1:
871 >              theBends[j].ghost =
872 >                (int)current_extra->getDouble() + atomOffset;
873 >              theBends[j].isGhost = 1;
874 >              break;
875 >              
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 +          
887            else{
888 <            the_atoms[index] = new GeneralAtom(index);
888 >            
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            }
846 –          the_atoms[index]->setType( current_atom->getType() );
847 –          the_atoms[index]->setIndex( index );
897            
898 <          // increment the index and repeat;
850 <          index++;
898 >          current_extra = current_extra->getNext();
899          }
900 +      }
901 +          
902 +      if( !theBends[j].isGhost ){
903 +            
904 +        exI = theBends[j].a;
905 +        exJ = theBends[j].c;
906 +      }
907 +      else{
908          
909 <        molEnd = index -1;
910 <        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
909 >        exI = theBends[j].a;
910 >        exJ = theBends[j].b;
911        }
862 – #endif //is_mpi
912        
913 <      molIndex++;
914 <    }
915 <  }
916 <
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 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
921 <    
922 <    delete[] globalIndex;
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 <    mpiSim->mpiRefresh();
933 < #endif //IS_MPI
934 <          
935 <  the_ff->initializeAtoms();
936 < }
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 < void SimSetup::makeBonds( void ){
944 <
945 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
946 <  bond_pair* the_bonds;
947 <  BondStamp* current_bond;
948 <
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 <
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 <      if( mpiSim->getMyMolStart() <= molIndex &&
951 <          molIndex <= mpiSim->getMyMolEnd() ){
952 < #endif // is_mpi        
953 <        
954 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
955 <          
901 <          current_bond = comp_stamps[i]->getBond( k );
902 <          the_bonds[index].a = current_bond->getA() + offset;
903 <          the_bonds[index].b = current_bond->getB() + offset;
904 <
905 <          exI = the_bonds[index].a;
906 <          exJ = the_bonds[index].b;
907 <
908 <          // exclude_I must always be the smaller of the pair
909 <          if( exI > exJ ){
910 <            tempEx = exI;
911 <            exI = exJ;
912 <            exJ = tempEx;
913 <          }
914 <
915 <          
916 < #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 <
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 <          
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)
957 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
958   #endif  //is_mpi
959 <          
960 <          // increment the index and repeat;
931 <          index++;
932 <        }
933 <        offset += comp_stamps[i]->getNAtoms();
934 <        
935 < #ifdef IS_MPI
936 <      }
937 < #endif //is_mpi
938 <      
939 <      molIndex++;
940 <    }      
941 <  }
959 >    }
960 >    excludeOffset += info.nTorsions;
961  
962 <  the_ff->initializeBonds( the_bonds );
963 < }
962 >    
963 >    // send the arrays off to the forceField for init.
964  
965 < void SimSetup::makeBends( void ){
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  
948 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
949 –  bend_set* the_bends;
950 –  BendStamp* current_bend;
951 –  LinkedAssign* extras;
952 –  LinkedAssign* current_extra;
953 –  
970  
971 <  the_bends = new bend_set[tot_bends];
956 <  index = 0;
957 <  offset = 0;
958 <  molIndex = 0;
959 <  for( i=0; i<n_components; i++ ){
960 <
961 <    for( j=0; j<components_nmol[i]; j++ ){
962 <
963 < #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 <          }
971 >    the_molecules[i].initialize( info );
972  
973  
974 < #ifdef IS_MPI
975 <
976 <          the_excludes[(index + tot_bonds)*2] =    
977 <            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 <    }
974 >    atomOffset += info.nAtoms;
975 >    delete[] theBonds;
976 >    delete[] theBends;
977 >    delete[] theTorsions;
978    }
979  
980   #ifdef IS_MPI
981 <  sprintf( checkPointMsg,
1072 <           "Successfully created the bends list.\n" );
981 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
982    MPIcheckPoint();
983   #endif // is_mpi
1075 –  
984  
985 <  the_ff->initializeBends( the_bends );
986 < }
985 >  // clean up the forcefield
986 >  the_ff->calcRcut();
987 >  the_ff->cleanMe();
988  
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 );
989   }
990  
991   void SimSetup::initFromBass( void ){

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