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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 414 by mmeineke, Wed Mar 26 22:02:36 2003 UTC vs.
Revision 504 by mmeineke, Thu Apr 17 21:54:18 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;
233 –
301    
302 +  simnfo->molMembershipArray = new int[tot_atoms];
303 +
304   #ifdef IS_MPI
305  
306    // divide the molecules among processors here.
307    
308    mpiSim = new mpiSimulation( simnfo );
309    
241 –  
242 –
310    globalIndex = mpiSim->divideLabor();
311  
245 –
246 –
312    // set up the local variables
313    
314    int localMol, allMol;
315    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
316 +
317 +  int* mol2proc = mpiSim->getMolToProcMap();
318 +  int* molCompType = mpiSim->getMolComponentType();
319    
320    allMol = 0;
321    localMol = 0;
# Line 255 | Line 323 | void SimSetup::createSim( void ){
323    local_bonds = 0;
324    local_bends = 0;
325    local_torsions = 0;
326 +  globalAtomIndex = 0;
327 +
328 +
329    for( i=0; i<n_components; i++ ){
330  
331      for( j=0; j<components_nmol[i]; j++ ){
332        
333 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
333 >      if( mol2proc[allMol] == worldRank ){
334          
335          local_atoms +=    comp_stamps[i]->getNAtoms();
336          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 338 | void SimSetup::createSim( void ){
338          local_torsions += comp_stamps[i]->getNTorsions();
339          localMol++;
340        }      
341 <      allMol++;
341 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
342 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
343 >        globalAtomIndex++;
344 >      }
345 >
346 >      allMol++;      
347      }
348    }
349    local_SRI = local_bonds + local_bends + local_torsions;
350    
276 –
351    simnfo->n_atoms = mpiSim->getMyNlocal();  
352    
353    if( local_atoms != simnfo->n_atoms ){
354      sprintf( painCave.errMsg,
355               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
356 <             " localAtom (%d) are note equal.\n",
356 >             " localAtom (%d) are not equal.\n",
357               simnfo->n_atoms,
358               local_atoms );
359      painCave.isFatal = 1;
# Line 304 | Line 378 | void SimSetup::createSim( void ){
378    Atom::createArrays(simnfo->n_atoms);
379    the_atoms = new Atom*[simnfo->n_atoms];
380    the_molecules = new Molecule[simnfo->n_mol];
381 +  int molIndex;
382  
383 +  // initialize the molecule's stampID's
384  
385 + #ifdef IS_MPI
386 +  
387 +
388 +  molIndex = 0;
389 +  for(i=0; i<mpiSim->getTotNmol(); i++){
390 +    
391 +    if(mol2proc[i] == worldRank ){
392 +      the_molecules[molIndex].setStampID( molCompType[i] );
393 +      the_molecules[molIndex].setMyIndex( molIndex );
394 +      the_molecules[molIndex].setGlobalIndex( i );
395 +      molIndex++;
396 +    }
397 +  }
398 +
399 + #else // is_mpi
400 +  
401 +  molIndex = 0;
402 +  globalAtomIndex = 0;
403 +  for(i=0; i<n_components; i++){
404 +    for(j=0; j<components_nmol[i]; j++ ){
405 +      the_molecules[molIndex].setStampID( i );
406 +      the_molecules[molIndex].setMyIndex( molIndex );
407 +      the_molecules[molIndex].setGlobalIndex( molIndex );
408 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
409 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
410 +        globalAtomIndex++;
411 +      }
412 +      molIndex++;
413 +    }
414 +  }
415 +    
416 +
417 + #endif // is_mpi
418 +
419 +
420    if( simnfo->n_SRI ){
421 +    
422      Exclude::createArray(simnfo->n_SRI);
423      the_excludes = new Exclude*[simnfo->n_SRI];
424 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
425      simnfo->globalExcludes = new int;
426 <    simnfo->n_exclude = tot_SRI;
426 >    simnfo->n_exclude = simnfo->n_SRI;
427    }
428    else{
429      
# Line 326 | Line 439 | void SimSetup::createSim( void ){
439    // set the arrays into the SimInfo object
440  
441    simnfo->atoms = the_atoms;
442 <  simnfo->sr_interactions = the_sris;
442 >  simnfo->molecules = the_molecules;
443    simnfo->nGlobalExcludes = 0;
444    simnfo->excludes = the_excludes;
445  
# Line 383 | Line 496 | void SimSetup::createSim( void ){
496  
497    the_ff->setSimInfo( simnfo );
498  
499 <  makeAtoms();
499 >  makeMolecules();
500    simnfo->identArray = new int[simnfo->n_atoms];
501    for(i=0; i<simnfo->n_atoms; i++){
502      simnfo->identArray[i] = the_atoms[i]->getIdent();
503    }
504    
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 –
505    if (the_globals->getUseRF() ) {
506      simnfo->useReactionField = 1;
507    
# Line 443 | Line 543 | void SimSetup::createSim( void ){
543      }
544      simnfo->dielectric = the_globals->getDielectric();  
545    } else {
546 <    if (simnfo->n_dipoles) {
546 >    if (usesDipoles) {
547        
548        if( !the_globals->haveECR() ){
549          sprintf( painCave.errMsg,
550 <                 "SimSetup Warning: using default value of 1/2 the smallest"
550 >                 "SimSetup Warning: using default value of 1/2 the smallest "
551                   "box length for the electrostaticCutoffRadius.\n"
552                   "I hope you have a very fast processor!\n");
553          painCave.isFatal = 0;
# Line 463 | Line 563 | void SimSetup::createSim( void ){
563        
564        if( !the_globals->haveEST() ){
565          sprintf( painCave.errMsg,
566 <                 "SimSetup Warning: using default value of 5% of the"
566 >                 "SimSetup Warning: using default value of 5%% of the "
567                   "electrostaticCutoffRadius for the "
568                   "electrostaticSkinThickness\n"
569                   );
# Line 638 | Line 738 | void SimSetup::createSim( void ){
738  
739   //   new AllLong( simnfo );
740  
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 );
741  
742 +  if( !strcmp( force_field, "TraPPE_Ex" ) ){
743 +    new Symplectic(simnfo, the_ff, the_extendedsystem);
744 +  }
745 +  else if( !strcmp( force_field, "LJ" ) ){
746 +    new Verlet( *simnfo, the_ff, the_extendedsystem );
747 +  }
748  
749 + #ifdef IS_MPI
750 +  mpiSim->mpiRefresh();
751 + #endif
752  
753    // initialize the Fortran
754 <  
754 >
755 >
756    simnfo->refreshSim();
757    
758    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 789 | void SimSetup::makeMolecules( void ){
789    BondStamp* currentBond;
790    BendStamp* currentBend;
791    TorsionStamp* currentTorsion;
792 +
793 +  bond_pair* theBonds;
794 +  bend_set* theBends;
795 +  torsion_set* theTorsions;
796 +
797    
798    //init the forceField paramters
799  
800    the_ff->readParams();
801  
802    
803 <  // init the molecules
803 >  // init the atoms
804  
805 +  double ux, uy, uz, u, uSqr;
806 +  
807    atomOffset = 0;
808    excludeOffset = 0;
809    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 820 | void SimSetup::makeMolecules( void ){
820      info.myExcludes = &the_excludes[excludeOffset];
821      info.myBonds = new Bond*[info.nBonds];
822      info.myBends = new Bend*[info.nBends];
823 <    info.myTorsions = new Torsions*[info.nTorsions];
823 >    info.myTorsions = new Torsion*[info.nTorsions];
824  
825      theBonds = new bond_pair[info.nBonds];
826      theBends = new bend_set[info.nBends];
# Line 717 | Line 830 | void SimSetup::makeMolecules( void ){
830      
831      for(j=0; j<info.nAtoms; j++){
832        
833 <      currentAtom = theComponents[stampID]->getAtom( j );
833 >      currentAtom = comp_stamps[stampID]->getAtom( j );
834        if( currentAtom->haveOrientation() ){
835          
836          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 871 | void SimSetup::makeMolecules( void ){
871        theBonds[j].a = currentBond->getA() + atomOffset;
872        theBonds[j].b = currentBond->getB() + atomOffset;
873  
874 <      exI = theBonds[i].a;
875 <      exJ = theBonds[i].b;
874 >      exI = theBonds[j].a;
875 >      exJ = theBonds[j].b;
876  
877        // exclude_I must always be the smaller of the pair
878        if( exI > exJ ){
# Line 775 | Line 888 | void SimSetup::makeMolecules( void ){
888        
889        the_excludes[j+excludeOffset]->setPair( exI, exJ );
890   #else  // isn't MPI
891 +
892        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
893   #endif  //is_mpi
894      }
# Line 790 | Line 904 | void SimSetup::makeMolecules( void ){
904            
905        if( currentBend->haveExtras() ){
906              
907 <        extras = current_bend->getExtras();
907 >        extras = currentBend->getExtras();
908          current_extra = extras;
909              
910          while( current_extra != NULL ){
# Line 812 | Line 926 | void SimSetup::makeMolecules( void ){
926                
927              default:
928                sprintf( painCave.errMsg,
929 <                       "SimSetup Error: ghostVectorSource was neiter a "
929 >                       "SimSetup Error: ghostVectorSource was neither a "
930                         "double nor an int.\n"
931                         "-->Bend[%d] in %s\n",
932                         j, comp_stamps[stampID]->getID() );
# Line 906 | Line 1020 | void SimSetup::makeMolecules( void ){
1020  
1021  
1022      the_molecules[i].initialize( info );
909 –    atomOffset += info.nAtoms;
910 –  }
911 –
912 –  // clean up the forcefield
913 –
914 –  the_ff->cleanMe();
915 – }
1023  
1024  
1025 <
1026 < void SimSetup::makeAtoms( void ){
1027 <
1028 <  int i, j, k, index;
922 <  double ux, uy, uz, uSqr, u;
923 <  AtomStamp* current_atom;
924 <
925 <  DirectionalAtom* dAtom;
926 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
927 <
928 <  lMolIndex = 0;
929 <  molIndex = 0;
930 <  index = 0;
931 <  for( i=0; i<n_components; i++ ){
932 <
933 <    for( j=0; j<components_nmol[i]; j++ ){
934 <
935 < #ifdef IS_MPI
936 <      if( mpiSim->getMyMolStart() <= molIndex &&
937 <          molIndex <= mpiSim->getMyMolEnd() ){
938 < #endif // is_mpi        
939 <
940 <        molStart = index;
941 <        nMemb = comp_stamps[i]->getNAtoms();
942 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
943 <          
944 <          current_atom = comp_stamps[i]->getAtom( k );
945 <          if( current_atom->haveOrientation() ){
946 <            
947 <            dAtom = new DirectionalAtom(index);
948 <            simnfo->n_oriented++;
949 <            the_atoms[index] = dAtom;
950 <            
951 <            ux = current_atom->getOrntX();
952 <            uy = current_atom->getOrntY();
953 <            uz = current_atom->getOrntZ();
954 <            
955 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
956 <            
957 <            u = sqrt( uSqr );
958 <            ux = ux / u;
959 <            uy = uy / u;
960 <            uz = uz / u;
961 <            
962 <            dAtom->setSUx( ux );
963 <            dAtom->setSUy( uy );
964 <            dAtom->setSUz( uz );
965 <          }
966 <          else{
967 <            the_atoms[index] = new GeneralAtom(index);
968 <          }
969 <          the_atoms[index]->setType( current_atom->getType() );
970 <          the_atoms[index]->setIndex( index );
971 <          
972 <          // increment the index and repeat;
973 <          index++;
974 <        }
975 <        
976 <        molEnd = index -1;
977 <        the_molecules[lMolIndex].setNMembers( nMemb );
978 <        the_molecules[lMolIndex].setStartAtom( molStart );
979 <        the_molecules[lMolIndex].setEndAtom( molEnd );
980 <        the_molecules[lMolIndex].setStampID( i );
981 <        lMolIndex++;
982 <
983 < #ifdef IS_MPI
984 <      }
985 < #endif //is_mpi
986 <      
987 <      molIndex++;
988 <    }
989 <  }
990 <
991 < #ifdef IS_MPI
992 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
993 <    
994 <    delete[] globalIndex;
995 <
996 <    mpiSim->mpiRefresh();
997 < #endif //IS_MPI
998 <          
999 <  the_ff->initializeAtoms();
1000 < }
1001 <
1002 < void SimSetup::makeBonds( void ){
1003 <
1004 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1005 <  bond_pair* the_bonds;
1006 <  BondStamp* current_bond;
1007 <
1008 <  the_bonds = new bond_pair[tot_bonds];
1009 <  index = 0;
1010 <  offset = 0;
1011 <  molIndex = 0;
1012 <
1013 <  for( i=0; i<n_components; i++ ){
1014 <
1015 <    for( j=0; j<components_nmol[i]; j++ ){
1016 <
1017 < #ifdef IS_MPI
1018 <      if( mpiSim->getMyMolStart() <= molIndex &&
1019 <          molIndex <= mpiSim->getMyMolEnd() ){
1020 < #endif // is_mpi        
1021 <        
1022 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1023 <          
1024 <          current_bond = comp_stamps[i]->getBond( k );
1025 <          the_bonds[index].a = current_bond->getA() + offset;
1026 <          the_bonds[index].b = current_bond->getB() + offset;
1027 <
1028 <          exI = the_bonds[index].a;
1029 <          exJ = the_bonds[index].b;
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 <
1038 <          
1039 < #ifdef IS_MPI
1040 <
1041 <          the_excludes[index*2] =    
1042 <            the_atoms[exI]->getGlobalIndex() + 1;
1043 <          the_excludes[index*2 + 1] =
1044 <            the_atoms[exJ]->getGlobalIndex() + 1;
1045 <
1046 < #else  // isn't MPI
1047 <          
1048 <          the_excludes[index*2] =     exI + 1;
1049 <          the_excludes[index*2 + 1] = exJ + 1;
1050 <          // fortran index from 1 (hence the +1 in the indexing)
1051 < #endif  //is_mpi
1052 <          
1053 <          // increment the index and repeat;
1054 <          index++;
1055 <        }
1056 <        offset += comp_stamps[i]->getNAtoms();
1057 <        
1058 < #ifdef IS_MPI
1059 <      }
1060 < #endif //is_mpi
1061 <      
1062 <      molIndex++;
1063 <    }      
1064 <  }
1065 <
1066 <  the_ff->initializeBonds( the_bonds );
1067 < }
1068 <
1069 < void SimSetup::makeBends( void ){
1070 <
1071 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1072 <  bend_set* the_bends;
1073 <  BendStamp* current_bend;
1074 <  LinkedAssign* extras;
1075 <  LinkedAssign* current_extra;
1076 <  
1077 <
1078 <  the_bends = new bend_set[tot_bends];
1079 <  index = 0;
1080 <  offset = 0;
1081 <  molIndex = 0;
1082 <  for( i=0; i<n_components; i++ ){
1083 <
1084 <    for( j=0; j<components_nmol[i]; j++ ){
1085 <
1086 < #ifdef IS_MPI
1087 <      if( mpiSim->getMyMolStart() <= molIndex &&
1088 <          molIndex <= mpiSim->getMyMolEnd() ){
1089 < #endif // is_mpi        
1090 <
1091 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1092 <          
1093 <          current_bend = comp_stamps[i]->getBend( k );
1094 <          the_bends[index].a = current_bend->getA() + offset;
1095 <          the_bends[index].b = current_bend->getB() + offset;
1096 <          the_bends[index].c = current_bend->getC() + offset;
1097 <          
1098 <          if( current_bend->haveExtras() ){
1099 <            
1100 <            extras = current_bend->getExtras();
1101 <            current_extra = extras;
1102 <            
1103 <            while( current_extra != NULL ){
1104 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1105 <                
1106 <                switch( current_extra->getType() ){
1107 <                  
1108 <                case 0:
1109 <                  the_bends[index].ghost =
1110 <                    current_extra->getInt() + offset;
1111 <                  the_bends[index].isGhost = 1;
1112 <                  break;
1113 <                  
1114 <                case 1:
1115 <                  the_bends[index].ghost =
1116 <                    (int)current_extra->getDouble() + offset;
1117 <                  the_bends[index].isGhost = 1;
1118 <                  break;
1119 <                  
1120 <                default:
1121 <                  sprintf( painCave.errMsg,
1122 <                           "SimSetup Error: ghostVectorSource was neiter a "
1123 <                           "double nor an int.\n"
1124 <                           "-->Bend[%d] in %s\n",
1125 <                           k, comp_stamps[i]->getID() );
1126 <                  painCave.isFatal = 1;
1127 <                  simError();
1128 <                }
1129 <              }
1130 <              
1131 <              else{
1132 <                
1133 <                sprintf( painCave.errMsg,
1134 <                         "SimSetup Error: unhandled bend assignment:\n"
1135 <                         "    -->%s in Bend[%d] in %s\n",
1136 <                         current_extra->getlhs(),
1137 <                         k, comp_stamps[i]->getID() );
1138 <                painCave.isFatal = 1;
1139 <                simError();
1140 <              }
1141 <              
1142 <              current_extra = current_extra->getNext();
1143 <            }
1144 <          }
1145 <          
1146 <          if( !the_bends[index].isGhost ){
1147 <            
1148 <            exI = the_bends[index].a;
1149 <            exJ = the_bends[index].c;
1150 <          }
1151 <          else{
1152 <            
1153 <            exI = the_bends[index].a;
1154 <            exJ = the_bends[index].b;
1155 <          }
1156 <          
1157 <          // exclude_I must always be the smaller of the pair
1158 <          if( exI > exJ ){
1159 <            tempEx = exI;
1160 <            exI = exJ;
1161 <            exJ = tempEx;
1162 <          }
1163 <
1164 <
1165 < #ifdef IS_MPI
1166 <
1167 <          the_excludes[(index + tot_bonds)*2] =    
1168 <            the_atoms[exI]->getGlobalIndex() + 1;
1169 <          the_excludes[(index + tot_bonds)*2 + 1] =
1170 <            the_atoms[exJ]->getGlobalIndex() + 1;
1171 <          
1172 < #else  // isn't MPI
1173 <          
1174 <          the_excludes[(index + tot_bonds)*2] =     exI + 1;
1175 <          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1176 <          // fortran index from 1 (hence the +1 in the indexing)
1177 < #endif  //is_mpi
1178 <          
1179 <          
1180 <          // increment the index and repeat;
1181 <          index++;
1182 <        }
1183 <        offset += comp_stamps[i]->getNAtoms();
1184 <        
1185 < #ifdef IS_MPI
1186 <      }
1187 < #endif //is_mpi
1188 <
1189 <      molIndex++;
1190 <    }
1025 >    atomOffset += info.nAtoms;
1026 >    delete[] theBonds;
1027 >    delete[] theBends;
1028 >    delete[] theTorsions;
1029    }
1030  
1031   #ifdef IS_MPI
1032 <  sprintf( checkPointMsg,
1195 <           "Successfully created the bends list.\n" );
1032 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1033    MPIcheckPoint();
1034   #endif // is_mpi
1198 –  
1199 –
1200 –  the_ff->initializeBends( the_bends );
1201 – }
1035  
1036 < void SimSetup::makeTorsions( void ){
1036 >  // clean up the forcefield
1037 >  the_ff->calcRcut();
1038 >  the_ff->cleanMe();
1039  
1205 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1206 –  torsion_set* the_torsions;
1207 –  TorsionStamp* current_torsion;
1208 –
1209 –  the_torsions = new torsion_set[tot_torsions];
1210 –  index = 0;
1211 –  offset = 0;
1212 –  molIndex = 0;
1213 –  for( i=0; i<n_components; i++ ){
1214 –
1215 –    for( j=0; j<components_nmol[i]; j++ ){
1216 –
1217 – #ifdef IS_MPI
1218 –      if( mpiSim->getMyMolStart() <= molIndex &&
1219 –          molIndex <= mpiSim->getMyMolEnd() ){
1220 – #endif // is_mpi        
1221 –
1222 –      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1223 –
1224 –        current_torsion = comp_stamps[i]->getTorsion( k );
1225 –        the_torsions[index].a = current_torsion->getA() + offset;
1226 –        the_torsions[index].b = current_torsion->getB() + offset;
1227 –        the_torsions[index].c = current_torsion->getC() + offset;
1228 –        the_torsions[index].d = current_torsion->getD() + offset;
1229 –
1230 –        exI = the_torsions[index].a;
1231 –        exJ = the_torsions[index].d;
1232 –
1233 –        
1234 –        // exclude_I must always be the smaller of the pair
1235 –        if( exI > exJ ){
1236 –          tempEx = exI;
1237 –          exI = exJ;
1238 –          exJ = tempEx;
1239 –        }
1240 –
1241 –
1242 – #ifdef IS_MPI
1243 –        
1244 –        the_excludes[(index + tot_bonds + tot_bends)*2] =    
1245 –          the_atoms[exI]->getGlobalIndex() + 1;
1246 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1247 –          the_atoms[exJ]->getGlobalIndex() + 1;
1248 –        
1249 – #else  // isn't MPI
1250 –        
1251 –        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1252 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1253 –        // fortran indexes from 1 (hence the +1 in the indexing)
1254 – #endif  //is_mpi
1255 –        
1256 –
1257 –        // increment the index and repeat;
1258 –        index++;
1259 –      }
1260 –      offset += comp_stamps[i]->getNAtoms();
1261 –
1262 – #ifdef IS_MPI
1263 –      }
1264 – #endif //is_mpi      
1265 –
1266 –      molIndex++;
1267 –    }
1268 –  }
1269 –
1270 –  the_ff->initializeTorsions( the_torsions );
1040   }
1041  
1042   void SimSetup::initFromBass( void ){

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