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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC vs.
Revision 490 by gezelter, Fri Apr 11 15:16:59 2003 UTC

# Line 66 | Line 66 | void SimSetup::createSim( void ){
66  
67    MakeStamps *the_stamps;
68    Globals* the_globals;
69 <  int i, j;
69 >  ExtendedSystem* the_extendedsystem;
70 >  int i, j, k, globalAtomIndex;
71  
72    // get the stamps and globals;
73    the_stamps = stamps;
# Line 80 | Line 81 | void SimSetup::createSim( void ){
81    // get the ones we know are there, yet still may need some work.
82    n_components = the_globals->getNComponents();
83    strcpy( force_field, the_globals->getForceField() );
84 +
85 +  // get the ensemble and set up an extended system if we need it:
86    strcpy( ensemble, the_globals->getEnsemble() );
87 +  if( !strcasecmp( ensemble, "NPT" ) ) {
88 +    the_extendedsystem = new ExtendedSystem( simnfo );
89 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90 +    if (the_globals->haveTargetPressure())
91 +      the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92 +    else {
93 +      sprintf( painCave.errMsg,
94 +               "SimSetup error: If you use the constant pressure\n"
95 +               "    ensemble, you must set targetPressure.\n"
96 +               "    This was found in the BASS file.\n");
97 +      painCave.isFatal = 1;
98 +      simError();
99 +    }
100 +
101 +    if (the_globals->haveTauThermostat())
102 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103 +    else if (the_globals->haveQmass())
104 +      the_extendedsystem->setQmass(the_globals->getQmass());
105 +    else {
106 +      sprintf( painCave.errMsg,
107 +               "SimSetup error: If you use one of the constant temperature\n"
108 +               "    ensembles, you must set either tauThermostat or qMass.\n"
109 +               "    Neither of these was found in the BASS file.\n");
110 +      painCave.isFatal = 1;
111 +      simError();
112 +    }
113 +
114 +    if (the_globals->haveTauBarostat())
115 +      the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116 +    else {
117 +      sprintf( painCave.errMsg,
118 +               "SimSetup error: If you use the constant pressure\n"
119 +               "    ensemble, you must set tauBarostat.\n"
120 +               "    This was found in the BASS file.\n");
121 +      painCave.isFatal = 1;
122 +      simError();
123 +    }
124 +
125 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
126 +    the_extendedsystem = new ExtendedSystem( simnfo );
127 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
128 +
129 +    if (the_globals->haveTauThermostat())
130 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131 +    else if (the_globals->haveQmass())
132 +      the_extendedsystem->setQmass(the_globals->getQmass());
133 +    else {
134 +      sprintf( painCave.errMsg,
135 +               "SimSetup error: If you use one of the constant temperature\n"
136 +               "    ensembles, you must set either tauThermostat or qMass.\n"
137 +               "    Neither of these was found in the BASS file.\n");
138 +      painCave.isFatal = 1;
139 +      simError();
140 +    }
141 +
142 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
143 +  } else {
144 +    sprintf( painCave.errMsg,
145 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
146 +             "reverting to NVE for this simulation.\n",
147 +             ensemble );
148 +    painCave.isFatal = 0;
149 +    simError();
150 +    strcpy( ensemble, "NVE" );
151 +  }  
152    strcpy( simnfo->ensemble, ensemble );
153  
154    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155    simnfo->usePBC = the_globals->getPBC();
156            
157 <
158 <
159 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
160 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
161 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
162 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
157 >  int usesDipoles = 0;
158 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
159 >    the_ff = new TraPPE_ExFF();
160 >    usesDipoles = 1;
161 >  }
162 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163    else{
164      sprintf( painCave.errMsg,
165               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 230 | Line 298 | void SimSetup::createSim( void ){
298    simnfo->n_torsions = tot_torsions;
299    simnfo->n_SRI = tot_SRI;
300    simnfo->n_mol = tot_nmol;
301 +  simnfo->molMembershipArray = new int[tot_atoms];
302  
234 –  
303   #ifdef IS_MPI
304  
305    // divide the molecules among processors here.
306    
307    mpiSim = new mpiSimulation( simnfo );
308    
241 –  
242 –
309    globalIndex = mpiSim->divideLabor();
310  
245 –
246 –
311    // set up the local variables
312    
313    int localMol, allMol;
314    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
315 +
316 +  int* mol2proc = mpiSim->getMolToProcMap();
317 +  int* molCompType = mpiSim->getMolComponentType();
318    
319    allMol = 0;
320    localMol = 0;
# Line 255 | Line 322 | void SimSetup::createSim( void ){
322    local_bonds = 0;
323    local_bends = 0;
324    local_torsions = 0;
325 +  globalAtomIndex = 0;
326 +
327 +
328    for( i=0; i<n_components; i++ ){
329  
330      for( j=0; j<components_nmol[i]; j++ ){
331        
332 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
332 >      if( mol2proc[allMol] == worldRank ){
333          
334          local_atoms +=    comp_stamps[i]->getNAtoms();
335          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 337 | void SimSetup::createSim( void ){
337          local_torsions += comp_stamps[i]->getNTorsions();
338          localMol++;
339        }      
340 <      allMol++;
340 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
341 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
342 >        globalAtomIndex++;
343 >      }
344 >
345 >      allMol++;      
346      }
347    }
348    local_SRI = local_bonds + local_bends + local_torsions;
349    
350 +  if (worldRank != 0) {
351 +    for (i =0; i < tot_atoms; i++){
352 +      std::cerr << "i = " << i << " molMembershipArray[i] = " << simnfo->molMembershipArray[i] << "\n";
353 +    }
354 +  }
355  
356    simnfo->n_atoms = mpiSim->getMyNlocal();  
357    
358    if( local_atoms != simnfo->n_atoms ){
359      sprintf( painCave.errMsg,
360               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
361 <             " localAtom (%d) are note equal.\n",
361 >             " localAtom (%d) are not equal.\n",
362               simnfo->n_atoms,
363               local_atoms );
364      painCave.isFatal = 1;
# Line 304 | Line 383 | void SimSetup::createSim( void ){
383    Atom::createArrays(simnfo->n_atoms);
384    the_atoms = new Atom*[simnfo->n_atoms];
385    the_molecules = new Molecule[simnfo->n_mol];
386 +  int molIndex;
387 +
388 +  // initialize the molecule's stampID's
389 +
390 + #ifdef IS_MPI
391 +  
392 +
393 +  molIndex = 0;
394 +  for(i=0; i<mpiSim->getTotNmol(); i++){
395 +    
396 +    if(mol2proc[i] == worldRank ){
397 +      the_molecules[molIndex].setStampID( molCompType[i] );
398 +      the_molecules[molIndex].setMyIndex( molIndex );
399 +      the_molecules[molIndex].setGlobalIndex( i );
400 +      molIndex++;
401 +    }
402 +  }
403 +
404 + #else // is_mpi
405 +  
406 +  molIndex = 0;
407 +  globalAtomIndex = 0;
408 +  for(i=0; i<n_components; i++){
409 +    for(j=0; j<components_nmol[i]; j++ ){
410 +      the_molecules[molIndex].setStampID( i );
411 +      the_molecules[molIndex].setMyIndex( molIndex );
412 +      the_molecules[molIndex].setGlobalIndex( molIndex );
413 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
414 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
415 +        globalAtomIndex++;
416 +      }
417 +      molIndex++;
418 +    }
419 +  }
420 +    
421 +
422 + #endif // is_mpi
423  
424  
425    if( simnfo->n_SRI ){
426 +    
427      Exclude::createArray(simnfo->n_SRI);
428      the_excludes = new Exclude*[simnfo->n_SRI];
429 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
430      simnfo->globalExcludes = new int;
431 <    simnfo->n_exclude = tot_SRI;
431 >    simnfo->n_exclude = simnfo->n_SRI;
432    }
433    else{
434      
# Line 326 | Line 444 | void SimSetup::createSim( void ){
444    // set the arrays into the SimInfo object
445  
446    simnfo->atoms = the_atoms;
447 <  simnfo->sr_interactions = the_sris;
447 >  simnfo->molecules = the_molecules;
448    simnfo->nGlobalExcludes = 0;
449    simnfo->excludes = the_excludes;
450  
# Line 383 | Line 501 | void SimSetup::createSim( void ){
501  
502    the_ff->setSimInfo( simnfo );
503  
504 <  makeAtoms();
504 >  makeMolecules();
505    simnfo->identArray = new int[simnfo->n_atoms];
506    for(i=0; i<simnfo->n_atoms; i++){
507      simnfo->identArray[i] = the_atoms[i]->getIdent();
508    }
509    
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 –
510    if (the_globals->getUseRF() ) {
511      simnfo->useReactionField = 1;
512    
# Line 443 | Line 548 | void SimSetup::createSim( void ){
548      }
549      simnfo->dielectric = the_globals->getDielectric();  
550    } else {
551 <    if (simnfo->n_dipoles) {
551 >    if (usesDipoles) {
552        
553        if( !the_globals->haveECR() ){
554          sprintf( painCave.errMsg,
555 <                 "SimSetup Warning: using default value of 1/2 the smallest"
555 >                 "SimSetup Warning: using default value of 1/2 the smallest "
556                   "box length for the electrostaticCutoffRadius.\n"
557                   "I hope you have a very fast processor!\n");
558          painCave.isFatal = 0;
# Line 463 | Line 568 | void SimSetup::createSim( void ){
568        
569        if( !the_globals->haveEST() ){
570          sprintf( painCave.errMsg,
571 <                 "SimSetup Warning: using default value of 5% of the"
571 >                 "SimSetup Warning: using default value of 5%% of the "
572                   "electrostaticCutoffRadius for the "
573                   "electrostaticSkinThickness\n"
574                   );
# Line 638 | Line 743 | void SimSetup::createSim( void ){
743  
744   //   new AllLong( simnfo );
745  
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 );
746  
747 <
747 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
748 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
749 >  }
750 >  else if( !strcmp( force_field, "LJ" ) ){
751 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
752 >  }
753 >  else {
754 >    std::cerr << "I'm a bug.\n";
755 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
756 >  }
757 > #ifdef IS_MPI
758 >  mpiSim->mpiRefresh();
759 > #endif
760  
761    // initialize the Fortran
762 <  
762 >
763 >
764    simnfo->refreshSim();
765    
766    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 797 | void SimSetup::makeMolecules( void ){
797    BondStamp* currentBond;
798    BendStamp* currentBend;
799    TorsionStamp* currentTorsion;
800 +
801 +  bond_pair* theBonds;
802 +  bend_set* theBends;
803 +  torsion_set* theTorsions;
804 +
805    
806    //init the forceField paramters
807  
808    the_ff->readParams();
809  
810    
811 <  // init the molecules
811 >  // init the atoms
812  
813 +  double ux, uy, uz, u, uSqr;
814 +  
815    atomOffset = 0;
816    excludeOffset = 0;
817    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 828 | void SimSetup::makeMolecules( void ){
828      info.myExcludes = &the_excludes[excludeOffset];
829      info.myBonds = new Bond*[info.nBonds];
830      info.myBends = new Bend*[info.nBends];
831 <    info.myTorsions = new Torsions*[info.nTorsions];
831 >    info.myTorsions = new Torsion*[info.nTorsions];
832  
833      theBonds = new bond_pair[info.nBonds];
834      theBends = new bend_set[info.nBends];
# Line 717 | Line 838 | void SimSetup::makeMolecules( void ){
838      
839      for(j=0; j<info.nAtoms; j++){
840        
841 <      currentAtom = theComponents[stampID]->getAtom( j );
841 >      currentAtom = comp_stamps[stampID]->getAtom( j );
842        if( currentAtom->haveOrientation() ){
843          
844          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 879 | void SimSetup::makeMolecules( void ){
879        theBonds[j].a = currentBond->getA() + atomOffset;
880        theBonds[j].b = currentBond->getB() + atomOffset;
881  
882 <      exI = theBonds[i].a;
883 <      exJ = theBonds[i].b;
882 >      exI = theBonds[j].a;
883 >      exJ = theBonds[j].b;
884  
885        // exclude_I must always be the smaller of the pair
886        if( exI > exJ ){
# Line 775 | Line 896 | void SimSetup::makeMolecules( void ){
896        
897        the_excludes[j+excludeOffset]->setPair( exI, exJ );
898   #else  // isn't MPI
899 +
900        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
901   #endif  //is_mpi
902      }
# Line 790 | Line 912 | void SimSetup::makeMolecules( void ){
912            
913        if( currentBend->haveExtras() ){
914              
915 <        extras = current_bend->getExtras();
915 >        extras = currentBend->getExtras();
916          current_extra = extras;
917              
918          while( current_extra != NULL ){
# Line 812 | Line 934 | void SimSetup::makeMolecules( void ){
934                
935              default:
936                sprintf( painCave.errMsg,
937 <                       "SimSetup Error: ghostVectorSource was neiter a "
937 >                       "SimSetup Error: ghostVectorSource was neither a "
938                         "double nor an int.\n"
939                         "-->Bend[%d] in %s\n",
940                         j, comp_stamps[stampID]->getID() );
# Line 897 | Line 1019 | void SimSetup::makeMolecules( void ){
1019      excludeOffset += info.nTorsions;
1020  
1021      
1022 <
1022 >    // send the arrays off to the forceField for init.
1023  
1024 +    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1025 +    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1026 +    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1027 +    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1028  
903 –
904 –
905 –
906 – void SimSetup::makeAtoms( void ){
907 –
908 –  int i, j, k, index;
909 –  double ux, uy, uz, uSqr, u;
910 –  AtomStamp* current_atom;
911 –
912 –  DirectionalAtom* dAtom;
913 –  int molIndex, molStart, molEnd, nMemb, lMolIndex;
914 –
915 –  lMolIndex = 0;
916 –  molIndex = 0;
917 –  index = 0;
918 –  for( i=0; i<n_components; i++ ){
919 –
920 –    for( j=0; j<components_nmol[i]; j++ ){
921 –
922 – #ifdef IS_MPI
923 –      if( mpiSim->getMyMolStart() <= molIndex &&
924 –          molIndex <= mpiSim->getMyMolEnd() ){
925 – #endif // is_mpi        
926 –
927 –        molStart = index;
928 –        nMemb = comp_stamps[i]->getNAtoms();
929 –        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
930 –          
931 –          current_atom = comp_stamps[i]->getAtom( k );
932 –          if( current_atom->haveOrientation() ){
933 –            
934 –            dAtom = new DirectionalAtom(index);
935 –            simnfo->n_oriented++;
936 –            the_atoms[index] = dAtom;
937 –            
938 –            ux = current_atom->getOrntX();
939 –            uy = current_atom->getOrntY();
940 –            uz = current_atom->getOrntZ();
941 –            
942 –            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
943 –            
944 –            u = sqrt( uSqr );
945 –            ux = ux / u;
946 –            uy = uy / u;
947 –            uz = uz / u;
948 –            
949 –            dAtom->setSUx( ux );
950 –            dAtom->setSUy( uy );
951 –            dAtom->setSUz( uz );
952 –          }
953 –          else{
954 –            the_atoms[index] = new GeneralAtom(index);
955 –          }
956 –          the_atoms[index]->setType( current_atom->getType() );
957 –          the_atoms[index]->setIndex( index );
958 –          
959 –          // increment the index and repeat;
960 –          index++;
961 –        }
962 –        
963 –        molEnd = index -1;
964 –        the_molecules[lMolIndex].setNMembers( nMemb );
965 –        the_molecules[lMolIndex].setStartAtom( molStart );
966 –        the_molecules[lMolIndex].setEndAtom( molEnd );
967 –        the_molecules[lMolIndex].setStampID( i );
968 –        lMolIndex++;
1029  
1030 < #ifdef IS_MPI
971 <      }
972 < #endif //is_mpi
973 <      
974 <      molIndex++;
975 <    }
976 <  }
977 <
978 < #ifdef IS_MPI
979 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
980 <    
981 <    delete[] globalIndex;
982 <
983 <    mpiSim->mpiRefresh();
984 < #endif //IS_MPI
985 <          
986 <  the_ff->initializeAtoms();
987 < }
988 <
989 < void SimSetup::makeBonds( void ){
990 <
991 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
992 <  bond_pair* the_bonds;
993 <  BondStamp* current_bond;
994 <
995 <  the_bonds = new bond_pair[tot_bonds];
996 <  index = 0;
997 <  offset = 0;
998 <  molIndex = 0;
999 <
1000 <  for( i=0; i<n_components; i++ ){
1001 <
1002 <    for( j=0; j<components_nmol[i]; j++ ){
1003 <
1004 < #ifdef IS_MPI
1005 <      if( mpiSim->getMyMolStart() <= molIndex &&
1006 <          molIndex <= mpiSim->getMyMolEnd() ){
1007 < #endif // is_mpi        
1008 <        
1009 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1010 <          
1011 <          current_bond = comp_stamps[i]->getBond( k );
1012 <          the_bonds[index].a = current_bond->getA() + offset;
1013 <          the_bonds[index].b = current_bond->getB() + offset;
1014 <
1015 <          exI = the_bonds[index].a;
1016 <          exJ = the_bonds[index].b;
1017 <
1018 <          // exclude_I must always be the smaller of the pair
1019 <          if( exI > exJ ){
1020 <            tempEx = exI;
1021 <            exI = exJ;
1022 <            exJ = tempEx;
1023 <          }
1024 <
1025 <          
1026 < #ifdef IS_MPI
1027 <
1028 <          the_excludes[index*2] =    
1029 <            the_atoms[exI]->getGlobalIndex() + 1;
1030 <          the_excludes[index*2 + 1] =
1031 <            the_atoms[exJ]->getGlobalIndex() + 1;
1032 <
1033 < #else  // isn't MPI
1034 <          
1035 <          the_excludes[index*2] =     exI + 1;
1036 <          the_excludes[index*2 + 1] = exJ + 1;
1037 <          // fortran index from 1 (hence the +1 in the indexing)
1038 < #endif  //is_mpi
1039 <          
1040 <          // increment the index and repeat;
1041 <          index++;
1042 <        }
1043 <        offset += comp_stamps[i]->getNAtoms();
1044 <        
1045 < #ifdef IS_MPI
1046 <      }
1047 < #endif //is_mpi
1048 <      
1049 <      molIndex++;
1050 <    }      
1051 <  }
1052 <
1053 <  the_ff->initializeBonds( the_bonds );
1054 < }
1055 <
1056 < void SimSetup::makeBends( void ){
1057 <
1058 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1059 <  bend_set* the_bends;
1060 <  BendStamp* current_bend;
1061 <  LinkedAssign* extras;
1062 <  LinkedAssign* current_extra;
1063 <  
1064 <
1065 <  the_bends = new bend_set[tot_bends];
1066 <  index = 0;
1067 <  offset = 0;
1068 <  molIndex = 0;
1069 <  for( i=0; i<n_components; i++ ){
1070 <
1071 <    for( j=0; j<components_nmol[i]; j++ ){
1072 <
1073 < #ifdef IS_MPI
1074 <      if( mpiSim->getMyMolStart() <= molIndex &&
1075 <          molIndex <= mpiSim->getMyMolEnd() ){
1076 < #endif // is_mpi        
1077 <
1078 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1079 <          
1080 <          current_bend = comp_stamps[i]->getBend( k );
1081 <          the_bends[index].a = current_bend->getA() + offset;
1082 <          the_bends[index].b = current_bend->getB() + offset;
1083 <          the_bends[index].c = current_bend->getC() + offset;
1084 <          
1085 <          if( current_bend->haveExtras() ){
1086 <            
1087 <            extras = current_bend->getExtras();
1088 <            current_extra = extras;
1089 <            
1090 <            while( current_extra != NULL ){
1091 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092 <                
1093 <                switch( current_extra->getType() ){
1094 <                  
1095 <                case 0:
1096 <                  the_bends[index].ghost =
1097 <                    current_extra->getInt() + offset;
1098 <                  the_bends[index].isGhost = 1;
1099 <                  break;
1100 <                  
1101 <                case 1:
1102 <                  the_bends[index].ghost =
1103 <                    (int)current_extra->getDouble() + offset;
1104 <                  the_bends[index].isGhost = 1;
1105 <                  break;
1106 <                  
1107 <                default:
1108 <                  sprintf( painCave.errMsg,
1109 <                           "SimSetup Error: ghostVectorSource was neiter a "
1110 <                           "double nor an int.\n"
1111 <                           "-->Bend[%d] in %s\n",
1112 <                           k, comp_stamps[i]->getID() );
1113 <                  painCave.isFatal = 1;
1114 <                  simError();
1115 <                }
1116 <              }
1117 <              
1118 <              else{
1119 <                
1120 <                sprintf( painCave.errMsg,
1121 <                         "SimSetup Error: unhandled bend assignment:\n"
1122 <                         "    -->%s in Bend[%d] in %s\n",
1123 <                         current_extra->getlhs(),
1124 <                         k, comp_stamps[i]->getID() );
1125 <                painCave.isFatal = 1;
1126 <                simError();
1127 <              }
1128 <              
1129 <              current_extra = current_extra->getNext();
1130 <            }
1131 <          }
1132 <          
1133 <          if( !the_bends[index].isGhost ){
1134 <            
1135 <            exI = the_bends[index].a;
1136 <            exJ = the_bends[index].c;
1137 <          }
1138 <          else{
1139 <            
1140 <            exI = the_bends[index].a;
1141 <            exJ = the_bends[index].b;
1142 <          }
1143 <          
1144 <          // exclude_I must always be the smaller of the pair
1145 <          if( exI > exJ ){
1146 <            tempEx = exI;
1147 <            exI = exJ;
1148 <            exJ = tempEx;
1149 <          }
1030 >    the_molecules[i].initialize( info );
1031  
1032  
1033 < #ifdef IS_MPI
1034 <
1035 <          the_excludes[(index + tot_bonds)*2] =    
1036 <            the_atoms[exI]->getGlobalIndex() + 1;
1156 <          the_excludes[(index + tot_bonds)*2 + 1] =
1157 <            the_atoms[exJ]->getGlobalIndex() + 1;
1158 <          
1159 < #else  // isn't MPI
1160 <          
1161 <          the_excludes[(index + tot_bonds)*2] =     exI + 1;
1162 <          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1163 <          // fortran index from 1 (hence the +1 in the indexing)
1164 < #endif  //is_mpi
1165 <          
1166 <          
1167 <          // increment the index and repeat;
1168 <          index++;
1169 <        }
1170 <        offset += comp_stamps[i]->getNAtoms();
1171 <        
1172 < #ifdef IS_MPI
1173 <      }
1174 < #endif //is_mpi
1175 <
1176 <      molIndex++;
1177 <    }
1033 >    atomOffset += info.nAtoms;
1034 >    delete[] theBonds;
1035 >    delete[] theBends;
1036 >    delete[] theTorsions;
1037    }
1038  
1039   #ifdef IS_MPI
1040 <  sprintf( checkPointMsg,
1182 <           "Successfully created the bends list.\n" );
1040 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1041    MPIcheckPoint();
1042   #endif // is_mpi
1185 –  
1043  
1044 <  the_ff->initializeBends( the_bends );
1045 < }
1044 >  // clean up the forcefield
1045 >  the_ff->calcRcut();
1046 >  the_ff->cleanMe();
1047  
1190 – void SimSetup::makeTorsions( void ){
1191 –
1192 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1193 –  torsion_set* the_torsions;
1194 –  TorsionStamp* current_torsion;
1195 –
1196 –  the_torsions = new torsion_set[tot_torsions];
1197 –  index = 0;
1198 –  offset = 0;
1199 –  molIndex = 0;
1200 –  for( i=0; i<n_components; i++ ){
1201 –
1202 –    for( j=0; j<components_nmol[i]; j++ ){
1203 –
1204 – #ifdef IS_MPI
1205 –      if( mpiSim->getMyMolStart() <= molIndex &&
1206 –          molIndex <= mpiSim->getMyMolEnd() ){
1207 – #endif // is_mpi        
1208 –
1209 –      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1210 –
1211 –        current_torsion = comp_stamps[i]->getTorsion( k );
1212 –        the_torsions[index].a = current_torsion->getA() + offset;
1213 –        the_torsions[index].b = current_torsion->getB() + offset;
1214 –        the_torsions[index].c = current_torsion->getC() + offset;
1215 –        the_torsions[index].d = current_torsion->getD() + offset;
1216 –
1217 –        exI = the_torsions[index].a;
1218 –        exJ = the_torsions[index].d;
1219 –
1220 –        
1221 –        // exclude_I must always be the smaller of the pair
1222 –        if( exI > exJ ){
1223 –          tempEx = exI;
1224 –          exI = exJ;
1225 –          exJ = tempEx;
1226 –        }
1227 –
1228 –
1229 – #ifdef IS_MPI
1230 –        
1231 –        the_excludes[(index + tot_bonds + tot_bends)*2] =    
1232 –          the_atoms[exI]->getGlobalIndex() + 1;
1233 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1234 –          the_atoms[exJ]->getGlobalIndex() + 1;
1235 –        
1236 – #else  // isn't MPI
1237 –        
1238 –        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1239 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1240 –        // fortran indexes from 1 (hence the +1 in the indexing)
1241 – #endif  //is_mpi
1242 –        
1243 –
1244 –        // increment the index and repeat;
1245 –        index++;
1246 –      }
1247 –      offset += comp_stamps[i]->getNAtoms();
1248 –
1249 – #ifdef IS_MPI
1250 –      }
1251 – #endif //is_mpi      
1252 –
1253 –      molIndex++;
1254 –    }
1255 –  }
1256 –
1257 –  the_ff->initializeTorsions( the_torsions );
1048   }
1049  
1050   void SimSetup::initFromBass( void ){

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