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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 558 by mmeineke, Thu Jun 19 19:21:23 2003 UTC

# Line 12 | Line 12 | SimSetup::SimSetup(){
12   #include "mpiSimulation.hpp"
13   #endif
14  
15 + // some defines for ensemble and Forcefield  cases
16 +
17 + #define NVE_ENS 0
18 + #define NVT_ENS 1
19 + #define NPT_ENS 2
20 +
21 + #define FF_DUFF 0
22 + #define FF_LJ   1
23 +
24 +
25   SimSetup::SimSetup(){
26    stamps = new MakeStamps();
27    globals = new Globals();
# Line 66 | Line 76 | void SimSetup::createSim( void ){
76  
77    MakeStamps *the_stamps;
78    Globals* the_globals;
79 <  int i, j;
79 >  int i, j, k, globalAtomIndex;
80 >  
81 >  int ensembleCase;
82 >  int ffCase;
83 >  
84 >  ensembleCase = -1;
85 >  ffCase = -1;
86  
87    // get the stamps and globals;
88    the_stamps = stamps;
# Line 80 | Line 96 | void SimSetup::createSim( void ){
96    // get the ones we know are there, yet still may need some work.
97    n_components = the_globals->getNComponents();
98    strcpy( force_field, the_globals->getForceField() );
99 +
100 +  if( !strcasecmp( force_field, "DUFF" ))    ffCase = FF_DUFF;
101 +  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102 +  else{
103 +    sprintf( painCave.errMsg,
104 +             "SimSetup Error. Unrecognized force field -> %s\n",
105 +             force_field );
106 +    painCave.isFatal = 1;
107 +    simError();
108 +  }
109 +
110 +  // get the ensemble:
111    strcpy( ensemble, the_globals->getEnsemble() );
112 +
113 +  if( !strcasecmp( ensemble, "NVE" ))      ffCase = NVE_ENS;
114 +  else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS;
115 +  else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS;
116 +  else{
117 +    sprintf( painCave.errMsg,
118 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
119 +             "reverting to NVE for this simulation.\n",
120 +             ensemble );
121 +    painCave.isFatal = 0;
122 +    simError();
123 +    strcpy( ensemble, "NVE" );
124 +    ensembleCase = NVE_ENS;
125 +  }  
126    strcpy( simnfo->ensemble, ensemble );
127  
128 +
129 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
130 + //     the_extendedsystem = new ExtendedSystem( simnfo );
131 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132 + //     if (the_globals->haveTargetPressure())
133 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134 + //     else {
135 + //       sprintf( painCave.errMsg,
136 + //                "SimSetup error: If you use the constant pressure\n"
137 + //                "    ensemble, you must set targetPressure.\n"
138 + //                "    This was found in the BASS file.\n");
139 + //       painCave.isFatal = 1;
140 + //       simError();
141 + //     }
142 +
143 + //     if (the_globals->haveTauThermostat())
144 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145 + //     else if (the_globals->haveQmass())
146 + //       the_extendedsystem->setQmass(the_globals->getQmass());
147 + //     else {
148 + //       sprintf( painCave.errMsg,
149 + //                "SimSetup error: If you use one of the constant temperature\n"
150 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
151 + //                "    Neither of these was found in the BASS file.\n");
152 + //       painCave.isFatal = 1;
153 + //       simError();
154 + //     }
155 +
156 + //     if (the_globals->haveTauBarostat())
157 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158 + //     else {
159 + //       sprintf( painCave.errMsg,
160 + //                "SimSetup error: If you use the constant pressure\n"
161 + //                "    ensemble, you must set tauBarostat.\n"
162 + //                "    This was found in the BASS file.\n");
163 + //       painCave.isFatal = 1;
164 + //       simError();
165 + //     }
166 +
167 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
168 + //     the_extendedsystem = new ExtendedSystem( simnfo );
169 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
170 +
171 + //     if (the_globals->haveTauThermostat())
172 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173 + //     else if (the_globals->haveQmass())
174 + //       the_extendedsystem->setQmass(the_globals->getQmass());
175 + //     else {
176 + //       sprintf( painCave.errMsg,
177 + //                "SimSetup error: If you use one of the constant temperature\n"
178 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
179 + //                "    Neither of these was found in the BASS file.\n");
180 + //       painCave.isFatal = 1;
181 + //       simError();
182 + //     }
183 +
184    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185    simnfo->usePBC = the_globals->getPBC();
186            
187 +  int usesDipoles = 0;
188 +  switch( ffCase ){
189  
190 <
191 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
192 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
193 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
194 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
195 <  else{
190 >  case FF_DUFF:
191 >    the_ff = new DUFF();
192 >    usesDipoles = 1;
193 >    break;
194 >
195 >  case FF_LJ:
196 >    the_ff = LJFF();
197 >    break;
198 >
199 >  default:
200      sprintf( painCave.errMsg,
201 <             "SimSetup Error. Unrecognized force field -> %s\n",
98 <             force_field );
201 >             "SimSetup Error. Unrecognized force field in case statement.\n");
202      painCave.isFatal = 1;
203      simError();
204    }
# Line 105 | Line 208 | void SimSetup::createSim( void ){
208    MPIcheckPoint();
209   #endif // is_mpi
210  
108 –  
109 –
211    // get the components and calculate the tot_nMol and indvidual n_mol
212    the_components = the_globals->getComponents();
213    components_nmol = new int[n_components];
# Line 230 | Line 331 | void SimSetup::createSim( void ){
331    simnfo->n_torsions = tot_torsions;
332    simnfo->n_SRI = tot_SRI;
333    simnfo->n_mol = tot_nmol;
233 –
334    
335 +  simnfo->molMembershipArray = new int[tot_atoms];
336 +
337   #ifdef IS_MPI
338  
339    // divide the molecules among processors here.
340    
341    mpiSim = new mpiSimulation( simnfo );
342    
241 –  
242 –
343    globalIndex = mpiSim->divideLabor();
344  
245 –
246 –
345    // set up the local variables
346    
347    int localMol, allMol;
348    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
349 +
350 +  int* mol2proc = mpiSim->getMolToProcMap();
351 +  int* molCompType = mpiSim->getMolComponentType();
352    
353    allMol = 0;
354    localMol = 0;
# Line 255 | Line 356 | void SimSetup::createSim( void ){
356    local_bonds = 0;
357    local_bends = 0;
358    local_torsions = 0;
359 +  globalAtomIndex = 0;
360 +
361 +
362    for( i=0; i<n_components; i++ ){
363  
364      for( j=0; j<components_nmol[i]; j++ ){
365        
366 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
366 >      if( mol2proc[allMol] == worldRank ){
367          
368          local_atoms +=    comp_stamps[i]->getNAtoms();
369          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 371 | void SimSetup::createSim( void ){
371          local_torsions += comp_stamps[i]->getNTorsions();
372          localMol++;
373        }      
374 <      allMol++;
374 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
376 >        globalAtomIndex++;
377 >      }
378 >
379 >      allMol++;      
380      }
381    }
382    local_SRI = local_bonds + local_bends + local_torsions;
383    
276 –
384    simnfo->n_atoms = mpiSim->getMyNlocal();  
385    
386    if( local_atoms != simnfo->n_atoms ){
387      sprintf( painCave.errMsg,
388               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389 <             " localAtom (%d) are note equal.\n",
389 >             " localAtom (%d) are not equal.\n",
390               simnfo->n_atoms,
391               local_atoms );
392      painCave.isFatal = 1;
# Line 304 | Line 411 | void SimSetup::createSim( void ){
411    Atom::createArrays(simnfo->n_atoms);
412    the_atoms = new Atom*[simnfo->n_atoms];
413    the_molecules = new Molecule[simnfo->n_mol];
414 +  int molIndex;
415  
416 +  // initialize the molecule's stampID's
417  
418 <  if( simnfo->n_SRI ){
419 <    the_sris = new SRI*[simnfo->n_SRI];
420 <    the_excludes = new int[2 * simnfo->n_SRI];
418 > #ifdef IS_MPI
419 >  
420 >
421 >  molIndex = 0;
422 >  for(i=0; i<mpiSim->getTotNmol(); i++){
423 >    
424 >    if(mol2proc[i] == worldRank ){
425 >      the_molecules[molIndex].setStampID( molCompType[i] );
426 >      the_molecules[molIndex].setMyIndex( molIndex );
427 >      the_molecules[molIndex].setGlobalIndex( i );
428 >      molIndex++;
429 >    }
430 >  }
431 >
432 > #else // is_mpi
433 >  
434 >  molIndex = 0;
435 >  globalAtomIndex = 0;
436 >  for(i=0; i<n_components; i++){
437 >    for(j=0; j<components_nmol[i]; j++ ){
438 >      the_molecules[molIndex].setStampID( i );
439 >      the_molecules[molIndex].setMyIndex( molIndex );
440 >      the_molecules[molIndex].setGlobalIndex( molIndex );
441 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442 >        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443 >        globalAtomIndex++;
444 >      }
445 >      molIndex++;
446 >    }
447 >  }
448 >    
449 >
450 > #endif // is_mpi
451 >
452 >
453 >  if( simnfo->n_SRI ){
454 >    
455 >    Exclude::createArray(simnfo->n_SRI);
456 >    the_excludes = new Exclude*[simnfo->n_SRI];
457 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
458      simnfo->globalExcludes = new int;
459 <    simnfo->n_exclude = tot_SRI;
459 >    simnfo->n_exclude = simnfo->n_SRI;
460    }
461    else{
462      
463 <    the_excludes = new int[2];
464 <    the_excludes[0] = 0;
465 <    the_excludes[1] = 0;
463 >    Exclude::createArray( 1 );
464 >    the_excludes = new Exclude*;
465 >    the_excludes[0] = new Exclude(0);
466 >    the_excludes[0]->setPair( 0,0 );
467      simnfo->globalExcludes = new int;
468      simnfo->globalExcludes[0] = 0;
469 <
323 <    simnfo->n_exclude = 1;
469 >    simnfo->n_exclude = 0;
470    }
471  
472    // set the arrays into the SimInfo object
473  
474    simnfo->atoms = the_atoms;
475 <  simnfo->sr_interactions = the_sris;
475 >  simnfo->molecules = the_molecules;
476    simnfo->nGlobalExcludes = 0;
477    simnfo->excludes = the_excludes;
478  
# Line 383 | Line 529 | void SimSetup::createSim( void ){
529  
530    the_ff->setSimInfo( simnfo );
531  
532 <  makeAtoms();
532 >  makeMolecules();
533    simnfo->identArray = new int[simnfo->n_atoms];
534    for(i=0; i<simnfo->n_atoms; i++){
535      simnfo->identArray[i] = the_atoms[i]->getIdent();
536    }
537    
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 –
538    if (the_globals->getUseRF() ) {
539      simnfo->useReactionField = 1;
540    
# Line 443 | Line 576 | void SimSetup::createSim( void ){
576      }
577      simnfo->dielectric = the_globals->getDielectric();  
578    } else {
579 <    if (simnfo->n_dipoles) {
579 >    if (usesDipoles) {
580        
581        if( !the_globals->haveECR() ){
582          sprintf( painCave.errMsg,
583 <                 "SimSetup Warning: using default value of 1/2 the smallest"
583 >                 "SimSetup Warning: using default value of 1/2 the smallest "
584                   "box length for the electrostaticCutoffRadius.\n"
585                   "I hope you have a very fast processor!\n");
586          painCave.isFatal = 0;
# Line 463 | Line 596 | void SimSetup::createSim( void ){
596        
597        if( !the_globals->haveEST() ){
598          sprintf( painCave.errMsg,
599 <                 "SimSetup Warning: using default value of 5% of the"
599 >                 "SimSetup Warning: using default value of 5%% of the "
600                   "electrostaticCutoffRadius for the "
601                   "electrostaticSkinThickness\n"
602                   );
# Line 634 | Line 767 | void SimSetup::createSim( void ){
767    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
768  
769  
770 < //   // make the longe range forces and the integrator
770 >  // make the integrator
771  
772 < //   new AllLong( simnfo );
772 >  switch( ensembleCase ){
773  
774 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
775 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
776 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
777 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
774 >  case NVE_ENS:
775 >    new NVE( simnfo, the_ff );
776 >    break;
777 >
778 >  default:
779 >    sprintf( painCave.errMsg,
780 >             "SimSetup Error. Unrecognized ensemble in case statement.\n");
781 >    painCave.isFatal = 1;
782 >    simError();
783 >  }
784  
785  
786 + #ifdef IS_MPI
787 +  mpiSim->mpiRefresh();
788 + #endif
789  
790    // initialize the Fortran
791 <  
791 >
792 >
793    simnfo->refreshSim();
794    
795    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 671 | Line 814 | void SimSetup::makeAtoms( void ){
814   #endif // is_mpi
815   }
816  
674 – void SimSetup::makeAtoms( void ){
817  
818 <  int i, j, k, index;
677 <  double ux, uy, uz, uSqr, u;
678 <  AtomStamp* current_atom;
818 > void SimSetup::makeMolecules( void ){
819  
820 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
821 +  molInit info;
822    DirectionalAtom* dAtom;
823 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
824 <
825 <  lMolIndex = 0;
826 <  molIndex = 0;
827 <  index = 0;
828 <  for( i=0; i<n_components; i++ ){
687 <
688 <    for( j=0; j<components_nmol[i]; j++ ){
823 >  LinkedAssign* extras;
824 >  LinkedAssign* current_extra;
825 >  AtomStamp* currentAtom;
826 >  BondStamp* currentBond;
827 >  BendStamp* currentBend;
828 >  TorsionStamp* currentTorsion;
829  
830 < #ifdef IS_MPI
831 <      if( mpiSim->getMyMolStart() <= molIndex &&
832 <          molIndex <= mpiSim->getMyMolEnd() ){
693 < #endif // is_mpi        
830 >  bond_pair* theBonds;
831 >  bend_set* theBends;
832 >  torsion_set* theTorsions;
833  
834 <        molStart = index;
835 <        nMemb = comp_stamps[i]->getNAtoms();
836 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
837 <          
838 <          current_atom = comp_stamps[i]->getAtom( k );
839 <          if( current_atom->haveOrientation() ){
840 <            
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++;
834 >  
835 >  //init the forceField paramters
836 >
837 >  the_ff->readParams();
838 >
839 >  
840 >  // init the atoms
841  
842 < #ifdef IS_MPI
843 <      }
844 < #endif //is_mpi
845 <      
846 <      molIndex++;
743 <    }
744 <  }
745 <
746 < #ifdef IS_MPI
747 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
842 >  double ux, uy, uz, u, uSqr;
843 >  
844 >  atomOffset = 0;
845 >  excludeOffset = 0;
846 >  for(i=0; i<simnfo->n_mol; i++){
847      
848 <    delete[] globalIndex;
848 >    stampID = the_molecules[i].getStampID();
849  
850 <    mpiSim->mpiRefresh();
851 < #endif //IS_MPI
852 <          
853 <  the_ff->initializeAtoms();
854 < }
850 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
851 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
852 >    info.nBends    = comp_stamps[stampID]->getNBends();
853 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
854 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
855  
856 < void SimSetup::makeBonds( void ){
856 >    info.myAtoms = &the_atoms[atomOffset];
857 >    info.myExcludes = &the_excludes[excludeOffset];
858 >    info.myBonds = new Bond*[info.nBonds];
859 >    info.myBends = new Bend*[info.nBends];
860 >    info.myTorsions = new Torsion*[info.nTorsions];
861  
862 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
863 <  bond_pair* the_bonds;
864 <  BondStamp* current_bond;
865 <
866 <  the_bonds = new bond_pair[tot_bonds];
867 <  index = 0;
868 <  offset = 0;
869 <  molIndex = 0;
870 <
871 <  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        
776 <        
777 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
778 <          
779 <          current_bond = comp_stamps[i]->getBond( k );
780 <          the_bonds[index].a = current_bond->getA() + offset;
781 <          the_bonds[index].b = current_bond->getB() + offset;
782 <
783 <          exI = the_bonds[index].a;
784 <          exJ = the_bonds[index].b;
785 <
786 <          // exclude_I must always be the smaller of the pair
787 <          if( exI > exJ ){
788 <            tempEx = exI;
789 <            exI = exJ;
790 <            exJ = tempEx;
791 <          }
792 <
793 <          
794 < #ifdef IS_MPI
795 <
796 <          the_excludes[index*2] =    
797 <            the_atoms[exI]->getGlobalIndex() + 1;
798 <          the_excludes[index*2 + 1] =
799 <            the_atoms[exJ]->getGlobalIndex() + 1;
800 <
801 < #else  // isn't MPI
802 <          
803 <          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)
806 < #endif  //is_mpi
807 <          
808 <          // increment the index and repeat;
809 <          index++;
810 <        }
811 <        offset += comp_stamps[i]->getNAtoms();
862 >    theBonds = new bond_pair[info.nBonds];
863 >    theBends = new bend_set[info.nBends];
864 >    theTorsions = new torsion_set[info.nTorsions];
865 >    
866 >    // make the Atoms
867 >    
868 >    for(j=0; j<info.nAtoms; j++){
869 >      
870 >      currentAtom = comp_stamps[stampID]->getAtom( j );
871 >      if( currentAtom->haveOrientation() ){
872          
873 < #ifdef IS_MPI
873 >        dAtom = new DirectionalAtom(j + atomOffset);
874 >        simnfo->n_oriented++;
875 >        info.myAtoms[j] = dAtom;
876 >        
877 >        ux = currentAtom->getOrntX();
878 >        uy = currentAtom->getOrntY();
879 >        uz = currentAtom->getOrntZ();
880 >        
881 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
882 >        
883 >        u = sqrt( uSqr );
884 >        ux = ux / u;
885 >        uy = uy / u;
886 >        uz = uz / u;
887 >        
888 >        dAtom->setSUx( ux );
889 >        dAtom->setSUy( uy );
890 >        dAtom->setSUz( uz );
891        }
892 < #endif //is_mpi
892 >      else{
893 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
894 >      }
895 >      info.myAtoms[j]->setType( currentAtom->getType() );
896 >    
897 > #ifdef IS_MPI
898        
899 <      molIndex++;
900 <    }      
901 <  }
899 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
900 >      
901 > #endif // is_mpi
902 >    }
903 >    
904 >    // make the bonds
905 >    for(j=0; j<info.nBonds; j++){
906 >      
907 >      currentBond = comp_stamps[stampID]->getBond( j );
908 >      theBonds[j].a = currentBond->getA() + atomOffset;
909 >      theBonds[j].b = currentBond->getB() + atomOffset;
910  
911 <  the_ff->initializeBonds( the_bonds );
912 < }
911 >      exI = theBonds[j].a;
912 >      exJ = theBonds[j].b;
913  
914 < void SimSetup::makeBends( void ){
915 <
916 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
917 <  bend_set* the_bends;
918 <  BendStamp* current_bend;
919 <  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 <
914 >      // exclude_I must always be the smaller of the pair
915 >      if( exI > exJ ){
916 >        tempEx = exI;
917 >        exI = exJ;
918 >        exJ = tempEx;
919 >      }
920   #ifdef IS_MPI
921 <      if( mpiSim->getMyMolStart() <= molIndex &&
922 <          molIndex <= mpiSim->getMyMolEnd() ){
923 < #endif // is_mpi        
921 >      tempEx = exI;
922 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
923 >      tempEx = exJ;
924 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
925 >      
926 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
927 > #else  // isn't MPI
928  
929 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
929 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
930 > #endif  //is_mpi
931 >    }
932 >    excludeOffset += info.nBonds;
933 >
934 >    //make the bends
935 >    for(j=0; j<info.nBends; j++){
936 >      
937 >      currentBend = comp_stamps[stampID]->getBend( j );
938 >      theBends[j].a = currentBend->getA() + atomOffset;
939 >      theBends[j].b = currentBend->getB() + atomOffset;
940 >      theBends[j].c = currentBend->getC() + atomOffset;
941            
942 <          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() ){
942 >      if( currentBend->haveExtras() ){
943              
944 <            extras = current_bend->getExtras();
945 <            current_extra = extras;
944 >        extras = currentBend->getExtras();
945 >        current_extra = extras;
946              
947 <            while( current_extra != NULL ){
948 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
947 >        while( current_extra != NULL ){
948 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
949                  
950 <                switch( current_extra->getType() ){
950 >            switch( current_extra->getType() ){
951 >              
952 >            case 0:
953 >              theBends[j].ghost =
954 >                current_extra->getInt() + atomOffset;
955 >              theBends[j].isGhost = 1;
956 >              break;
957                    
958 <                case 0:
959 <                  the_bends[index].ghost =
960 <                    current_extra->getInt() + offset;
961 <                  the_bends[index].isGhost = 1;
962 <                  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 <              }
958 >            case 1:
959 >              theBends[j].ghost =
960 >                (int)current_extra->getDouble() + atomOffset;
961 >              theBends[j].isGhost = 1;
962 >              break;
963                
964 <              else{
965 <                
966 <                sprintf( painCave.errMsg,
967 <                         "SimSetup Error: unhandled bend assignment:\n"
968 <                         "    -->%s in Bend[%d] in %s\n",
969 <                         current_extra->getlhs(),
970 <                         k, comp_stamps[i]->getID() );
971 <                painCave.isFatal = 1;
894 <                simError();
895 <              }
896 <              
897 <              current_extra = current_extra->getNext();
964 >            default:
965 >              sprintf( painCave.errMsg,
966 >                       "SimSetup Error: ghostVectorSource was neither a "
967 >                       "double nor an int.\n"
968 >                       "-->Bend[%d] in %s\n",
969 >                       j, comp_stamps[stampID]->getID() );
970 >              painCave.isFatal = 1;
971 >              simError();
972              }
973            }
974            
901 –          if( !the_bends[index].isGhost ){
902 –            
903 –            exI = the_bends[index].a;
904 –            exJ = the_bends[index].c;
905 –          }
975            else{
976              
977 <            exI = the_bends[index].a;
978 <            exJ = the_bends[index].b;
979 <          }
980 <          
981 <          // exclude_I must always be the smaller of the pair
982 <          if( exI > exJ ){
983 <            tempEx = exI;
915 <            exI = exJ;
916 <            exJ = tempEx;
977 >            sprintf( painCave.errMsg,
978 >                     "SimSetup Error: unhandled bend assignment:\n"
979 >                     "    -->%s in Bend[%d] in %s\n",
980 >                     current_extra->getlhs(),
981 >                     j, comp_stamps[stampID]->getID() );
982 >            painCave.isFatal = 1;
983 >            simError();
984            }
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;
985            
986 < #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++;
986 >          current_extra = current_extra->getNext();
987          }
988 <        offset += comp_stamps[i]->getNAtoms();
988 >      }
989 >          
990 >      if( !theBends[j].isGhost ){
991 >            
992 >        exI = theBends[j].a;
993 >        exJ = theBends[j].c;
994 >      }
995 >      else{
996          
997 < #ifdef IS_MPI
997 >        exI = theBends[j].a;
998 >        exJ = theBends[j].b;
999        }
1000 < #endif //is_mpi
1000 >      
1001 >      // exclude_I must always be the smaller of the pair
1002 >      if( exI > exJ ){
1003 >        tempEx = exI;
1004 >        exI = exJ;
1005 >        exJ = tempEx;
1006 >      }
1007 > #ifdef IS_MPI
1008 >      tempEx = exI;
1009 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1010 >      tempEx = exJ;
1011 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1012 >      
1013 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1014 > #else  // isn't MPI
1015 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1016 > #endif  //is_mpi
1017 >    }
1018 >    excludeOffset += info.nBends;
1019  
1020 <      molIndex++;
1020 >    for(j=0; j<info.nTorsions; j++){
1021 >      
1022 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
1023 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
1024 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
1025 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
1026 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
1027 >      
1028 >      exI = theTorsions[j].a;
1029 >      exJ = theTorsions[j].d;
1030 >
1031 >      // exclude_I must always be the smaller of the pair
1032 >      if( exI > exJ ){
1033 >        tempEx = exI;
1034 >        exI = exJ;
1035 >        exJ = tempEx;
1036 >      }
1037 > #ifdef IS_MPI
1038 >      tempEx = exI;
1039 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1040 >      tempEx = exJ;
1041 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1042 >      
1043 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1044 > #else  // isn't MPI
1045 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1046 > #endif  //is_mpi
1047      }
1048 <  }
1048 >    excludeOffset += info.nTorsions;
1049 >
1050 >    
1051 >    // send the arrays off to the forceField for init.
1052 >
1053 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1054 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1055 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1056 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1057  
948 – #ifdef IS_MPI
949 –  sprintf( checkPointMsg,
950 –           "Successfully created the bends list.\n" );
951 –  MPIcheckPoint();
952 – #endif // is_mpi
953 –  
1058  
1059 <  the_ff->initializeBends( the_bends );
956 < }
1059 >    the_molecules[i].initialize( info );
1060  
958 – void SimSetup::makeTorsions( void ){
1061  
1062 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1063 <  torsion_set* the_torsions;
1064 <  TorsionStamp* current_torsion;
1062 >    atomOffset += info.nAtoms;
1063 >    delete[] theBonds;
1064 >    delete[] theBends;
1065 >    delete[] theTorsions;
1066 >  }
1067  
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 –
1068   #ifdef IS_MPI
1069 <      if( mpiSim->getMyMolStart() <= molIndex &&
1070 <          molIndex <= mpiSim->getMyMolEnd() ){
1071 < #endif // is_mpi        
1069 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1070 >  MPIcheckPoint();
1071 > #endif // is_mpi
1072  
1073 <      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1073 >  // clean up the forcefield
1074 >  the_ff->calcRcut();
1075 >  the_ff->cleanMe();
1076  
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 );
1077   }
1078  
1079   void SimSetup::initFromBass( void ){

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