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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 483 by gezelter, Wed Apr 9 04:06:43 2003 UTC

# Line 66 | Line 66 | void SimSetup::createSim( void ){
66  
67    MakeStamps *the_stamps;
68    Globals* the_globals;
69 +  ExtendedSystem* the_extendedsystem;
70    int i, j;
71  
72    // get the stamps and globals;
# Line 80 | Line 81 | void SimSetup::createSim( void ){
81    // get the ones we know are there, yet still may need some work.
82    n_components = the_globals->getNComponents();
83    strcpy( force_field, the_globals->getForceField() );
84 +
85 +  // get the ensemble and set up an extended system if we need it:
86    strcpy( ensemble, the_globals->getEnsemble() );
87 +  if( !strcasecmp( ensemble, "NPT" ) ) {
88 +    the_extendedsystem = new ExtendedSystem( simnfo );
89 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90 +    if (the_globals->haveTargetPressure())
91 +      the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92 +    else {
93 +      sprintf( painCave.errMsg,
94 +               "SimSetup error: If you use the constant pressure\n"
95 +               "    ensemble, you must set targetPressure.\n"
96 +               "    This was found in the BASS file.\n");
97 +      painCave.isFatal = 1;
98 +      simError();
99 +    }
100 +
101 +    if (the_globals->haveTauThermostat())
102 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103 +    else if (the_globals->haveQmass())
104 +      the_extendedsystem->setQmass(the_globals->getQmass());
105 +    else {
106 +      sprintf( painCave.errMsg,
107 +               "SimSetup error: If you use one of the constant temperature\n"
108 +               "    ensembles, you must set either tauThermostat or qMass.\n"
109 +               "    Neither of these was found in the BASS file.\n");
110 +      painCave.isFatal = 1;
111 +      simError();
112 +    }
113 +
114 +    if (the_globals->haveTauBarostat())
115 +      the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116 +    else {
117 +      sprintf( painCave.errMsg,
118 +               "SimSetup error: If you use the constant pressure\n"
119 +               "    ensemble, you must set tauBarostat.\n"
120 +               "    This was found in the BASS file.\n");
121 +      painCave.isFatal = 1;
122 +      simError();
123 +    }
124 +
125 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
126 +    the_extendedsystem = new ExtendedSystem( simnfo );
127 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
128 +
129 +    if (the_globals->haveTauThermostat())
130 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131 +    else if (the_globals->haveQmass())
132 +      the_extendedsystem->setQmass(the_globals->getQmass());
133 +    else {
134 +      sprintf( painCave.errMsg,
135 +               "SimSetup error: If you use one of the constant temperature\n"
136 +               "    ensembles, you must set either tauThermostat or qMass.\n"
137 +               "    Neither of these was found in the BASS file.\n");
138 +      painCave.isFatal = 1;
139 +      simError();
140 +    }
141 +
142 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
143 +  } else {
144 +    sprintf( painCave.errMsg,
145 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
146 +             "reverting to NVE for this simulation.\n",
147 +             ensemble );
148 +    painCave.isFatal = 0;
149 +    simError();
150 +    strcpy( ensemble, "NVE" );
151 +  }  
152    strcpy( simnfo->ensemble, ensemble );
153  
154    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155    simnfo->usePBC = the_globals->getPBC();
156            
157 <
158 <
159 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
160 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
161 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
162 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
157 >  int usesDipoles = 0;
158 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
159 >    the_ff = new TraPPE_ExFF();
160 >    usesDipoles = 1;
161 >  }
162 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163    else{
164      sprintf( painCave.errMsg,
165               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 242 | Line 310 | void SimSetup::createSim( void ){
310  
311    globalIndex = mpiSim->divideLabor();
312  
245 –
246 –
313    // set up the local variables
314    
315    int localMol, allMol;
316    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
317 +
318 +  int* mol2proc = mpiSim->getMolToProcMap();
319 +  int* molCompType = mpiSim->getMolComponentType();
320    
321    allMol = 0;
322    localMol = 0;
# Line 259 | Line 328 | void SimSetup::createSim( void ){
328  
329      for( j=0; j<components_nmol[i]; j++ ){
330        
331 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
331 >      if( mol2proc[j] == worldRank ){
332          
333          local_atoms +=    comp_stamps[i]->getNAtoms();
334          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 347 | void SimSetup::createSim( void ){
347    if( local_atoms != simnfo->n_atoms ){
348      sprintf( painCave.errMsg,
349               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
350 <             " localAtom (%d) are note equal.\n",
350 >             " localAtom (%d) are not equal.\n",
351               simnfo->n_atoms,
352               local_atoms );
353      painCave.isFatal = 1;
# Line 304 | Line 372 | void SimSetup::createSim( void ){
372    Atom::createArrays(simnfo->n_atoms);
373    the_atoms = new Atom*[simnfo->n_atoms];
374    the_molecules = new Molecule[simnfo->n_mol];
375 +  int molIndex;
376  
377 +  // initialize the molecule's stampID's
378  
379 + #ifdef IS_MPI
380 +  
381 +
382 +  molIndex = 0;
383 +  for(i=0; i<mpiSim->getTotNmol(); i++){
384 +    
385 +    if(mol2proc[i] == worldRank ){
386 +      the_molecules[molIndex].setStampID( molCompType[i] );
387 +      the_molecules[molIndex].setMyIndex( molIndex );
388 +      molIndex++;
389 +    }
390 +  }
391 +
392 + #else // is_mpi
393 +  
394 +  molIndex = 0;
395 +  for(i=0; i<n_components; i++){
396 +    for(j=0; j<components_nmol[i]; j++ ){
397 +      the_molecules[molIndex].setStampID( i );
398 +      the_molecules[molIndex].setMyIndex( molIndex );
399 +      molIndex++;
400 +    }
401 +  }
402 +    
403 +
404 + #endif // is_mpi
405 +
406 +
407    if( simnfo->n_SRI ){
408 +    
409      Exclude::createArray(simnfo->n_SRI);
410      the_excludes = new Exclude*[simnfo->n_SRI];
411 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
412      simnfo->globalExcludes = new int;
413 <    simnfo->n_exclude = tot_SRI;
413 >    simnfo->n_exclude = simnfo->n_SRI;
414    }
415    else{
416      
# Line 326 | Line 426 | void SimSetup::createSim( void ){
426    // set the arrays into the SimInfo object
427  
428    simnfo->atoms = the_atoms;
429 <  simnfo->sr_interactions = the_sris;
429 >  simnfo->molecules = the_molecules;
430    simnfo->nGlobalExcludes = 0;
431    simnfo->excludes = the_excludes;
432  
# Line 383 | Line 483 | void SimSetup::createSim( void ){
483  
484    the_ff->setSimInfo( simnfo );
485  
486 <  makeAtoms();
486 >  makeMolecules();
487    simnfo->identArray = new int[simnfo->n_atoms];
488 +  simnfo->molMembershipArray = new int[simnfo->n_atoms];
489    for(i=0; i<simnfo->n_atoms; i++){
490      simnfo->identArray[i] = the_atoms[i]->getIdent();
491    }
492 <  
493 <  if( tot_bonds ){
393 <    makeBonds();
394 <  }
395 <
396 <  if( tot_bends ){
397 <    makeBends();
398 <  }
399 <
400 <  if( tot_torsions ){
401 <    makeTorsions();
492 >  for(i=0; i< simnfo->n_mol; i++) {
493 >    the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
494    }
495 <
404 <
495 >  
496    if (the_globals->getUseRF() ) {
497      simnfo->useReactionField = 1;
498    
# Line 443 | Line 534 | void SimSetup::createSim( void ){
534      }
535      simnfo->dielectric = the_globals->getDielectric();  
536    } else {
537 <    if (simnfo->n_dipoles) {
537 >    if (usesDipoles) {
538        
539        if( !the_globals->haveECR() ){
540          sprintf( painCave.errMsg,
541 <                 "SimSetup Warning: using default value of 1/2 the smallest"
541 >                 "SimSetup Warning: using default value of 1/2 the smallest "
542                   "box length for the electrostaticCutoffRadius.\n"
543                   "I hope you have a very fast processor!\n");
544          painCave.isFatal = 0;
# Line 463 | Line 554 | void SimSetup::createSim( void ){
554        
555        if( !the_globals->haveEST() ){
556          sprintf( painCave.errMsg,
557 <                 "SimSetup Warning: using default value of 5% of the"
557 >                 "SimSetup Warning: using default value of 5%% of the "
558                   "electrostaticCutoffRadius for the "
559                   "electrostaticSkinThickness\n"
560                   );
# Line 638 | Line 729 | void SimSetup::createSim( void ){
729  
730   //   new AllLong( simnfo );
731  
641 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643 –  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644 –  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
732  
733 <
733 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
734 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
735 >  }
736 >  else if( !strcmp( force_field, "LJ" ) ){
737 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
738 >  }
739 >  else {
740 >    std::cerr << "I'm a bug.\n";
741 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
742 >  }
743 > #ifdef IS_MPI
744 >  mpiSim->mpiRefresh();
745 > #endif
746  
747    // initialize the Fortran
748 <  
748 >
749 >
750    simnfo->refreshSim();
751    
752    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 783 | void SimSetup::makeMolecules( void ){
783    BondStamp* currentBond;
784    BendStamp* currentBend;
785    TorsionStamp* currentTorsion;
786 +
787 +  bond_pair* theBonds;
788 +  bend_set* theBends;
789 +  torsion_set* theTorsions;
790 +
791    
792    //init the forceField paramters
793  
794    the_ff->readParams();
795  
796    
797 <  // init the molecules
797 >  // init the atoms
798  
799 +  double ux, uy, uz, u, uSqr;
800 +  
801    atomOffset = 0;
802    excludeOffset = 0;
803    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 814 | void SimSetup::makeMolecules( void ){
814      info.myExcludes = &the_excludes[excludeOffset];
815      info.myBonds = new Bond*[info.nBonds];
816      info.myBends = new Bend*[info.nBends];
817 <    info.myTorsions = new Torsions*[info.nTorsions];
817 >    info.myTorsions = new Torsion*[info.nTorsions];
818  
819      theBonds = new bond_pair[info.nBonds];
820      theBends = new bend_set[info.nBends];
# Line 717 | Line 824 | void SimSetup::makeMolecules( void ){
824      
825      for(j=0; j<info.nAtoms; j++){
826        
827 <      currentAtom = theComponents[stampID]->getAtom( j );
827 >      currentAtom = comp_stamps[stampID]->getAtom( j );
828        if( currentAtom->haveOrientation() ){
829          
830          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 865 | void SimSetup::makeMolecules( void ){
865        theBonds[j].a = currentBond->getA() + atomOffset;
866        theBonds[j].b = currentBond->getB() + atomOffset;
867  
868 <      exI = theBonds[i].a;
869 <      exJ = theBonds[i].b;
868 >      exI = theBonds[j].a;
869 >      exJ = theBonds[j].b;
870  
871        // exclude_I must always be the smaller of the pair
872        if( exI > exJ ){
# Line 775 | Line 882 | void SimSetup::makeMolecules( void ){
882        
883        the_excludes[j+excludeOffset]->setPair( exI, exJ );
884   #else  // isn't MPI
885 +
886        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
887   #endif  //is_mpi
888      }
# Line 790 | Line 898 | void SimSetup::makeMolecules( void ){
898            
899        if( currentBend->haveExtras() ){
900              
901 <        extras = current_bend->getExtras();
901 >        extras = currentBend->getExtras();
902          current_extra = extras;
903              
904          while( current_extra != NULL ){
# Line 812 | Line 920 | void SimSetup::makeMolecules( void ){
920                
921              default:
922                sprintf( painCave.errMsg,
923 <                       "SimSetup Error: ghostVectorSource was neiter a "
923 >                       "SimSetup Error: ghostVectorSource was neither a "
924                         "double nor an int.\n"
925                         "-->Bend[%d] in %s\n",
926                         j, comp_stamps[stampID]->getID() );
# Line 897 | Line 1005 | void SimSetup::makeMolecules( void ){
1005      excludeOffset += info.nTorsions;
1006  
1007      
1008 +    // send the arrays off to the forceField for init.
1009  
1010 <
1011 <
1012 <
1013 <
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++ ){
1010 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1011 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1012 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1013 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1014  
920 –    for( j=0; j<components_nmol[i]; j++ ){
1015  
1016 < #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++;
969 <
970 < #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;
1016 >    the_molecules[i].initialize( info );
1017  
983 –    mpiSim->mpiRefresh();
984 – #endif //IS_MPI
985 –          
986 –  the_ff->initializeAtoms();
987 – }
1018  
1019 < void SimSetup::makeBonds( void ){
1020 <
1021 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1022 <  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 <          }
1150 <
1151 <
1152 < #ifdef IS_MPI
1153 <
1154 <          the_excludes[(index + tot_bonds)*2] =    
1155 <            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 <    }
1019 >    atomOffset += info.nAtoms;
1020 >    delete[] theBonds;
1021 >    delete[] theBends;
1022 >    delete[] theTorsions;
1023    }
1024  
1025   #ifdef IS_MPI
1026 <  sprintf( checkPointMsg,
1182 <           "Successfully created the bends list.\n" );
1026 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1027    MPIcheckPoint();
1028   #endif // is_mpi
1185 –  
1186 –
1187 –  the_ff->initializeBends( the_bends );
1188 – }
1189 –
1190 – void SimSetup::makeTorsions( void ){
1029  
1030 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1031 <  torsion_set* the_torsions;
1032 <  TorsionStamp* current_torsion;
1030 >  // clean up the forcefield
1031 >  the_ff->calcRcut();
1032 >  the_ff->cleanMe();
1033  
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 );
1034   }
1035  
1036   void SimSetup::initFromBass( void ){

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