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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 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC

# Line 66 | Line 66 | void SimSetup::createSim( void ){
66  
67    MakeStamps *the_stamps;
68    Globals* the_globals;
69 +  ExtendedSystem* the_extendedsystem;
70    int i, j;
71  
72    // get the stamps and globals;
# Line 80 | Line 81 | void SimSetup::createSim( void ){
81    // get the ones we know are there, yet still may need some work.
82    n_components = the_globals->getNComponents();
83    strcpy( force_field, the_globals->getForceField() );
84 +
85 +  // get the ensemble and set up an extended system if we need it:
86    strcpy( ensemble, the_globals->getEnsemble() );
87 +  if( !strcasecmp( ensemble, "NPT" ) ) {
88 +    the_extendedsystem = new ExtendedSystem( simnfo );
89 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90 +    the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
91 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
92 +    the_extendedsystem = new ExtendedSystem( simnfo );
93 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
94 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
95 +  } else {
96 +    sprintf( painCave.errMsg,
97 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
98 +             "reverting to NVE for this simulation.\n",
99 +             ensemble );
100 +    painCave.isFatal = 0;
101 +    simError();
102 +    strcpy( ensemble, "NVE" );
103 +  }  
104    strcpy( simnfo->ensemble, ensemble );
105  
106    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
107    simnfo->usePBC = the_globals->getPBC();
108            
109 <
110 <
91 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
109 >  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
110 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
111    else{
112      sprintf( painCave.errMsg,
113               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 242 | Line 258 | void SimSetup::createSim( void ){
258  
259    globalIndex = mpiSim->divideLabor();
260  
245 –
246 –
261    // set up the local variables
262    
263    int localMol, allMol;
264    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
265 +
266 +  int* mol2proc = mpiSim->getMolToProcMap();
267 +  int* molCompType = mpiSim->getMolComponentType();
268    
269    allMol = 0;
270    localMol = 0;
# Line 259 | Line 276 | void SimSetup::createSim( void ){
276  
277      for( j=0; j<components_nmol[i]; j++ ){
278        
279 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
279 >      if( mol2proc[j] == worldRank ){
280          
281          local_atoms +=    comp_stamps[i]->getNAtoms();
282          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 295 | void SimSetup::createSim( void ){
295    if( local_atoms != simnfo->n_atoms ){
296      sprintf( painCave.errMsg,
297               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
298 <             " localAtom (%d) are note equal.\n",
298 >             " localAtom (%d) are not equal.\n",
299               simnfo->n_atoms,
300               local_atoms );
301      painCave.isFatal = 1;
# Line 304 | Line 320 | void SimSetup::createSim( void ){
320    Atom::createArrays(simnfo->n_atoms);
321    the_atoms = new Atom*[simnfo->n_atoms];
322    the_molecules = new Molecule[simnfo->n_mol];
323 +  int molIndex;
324  
325 +  // initialize the molecule's stampID's
326  
327 + #ifdef IS_MPI
328 +  
329 +
330 +  molIndex = 0;
331 +  for(i=0; i<mpiSim->getTotNmol(); i++){
332 +    
333 +    if(mol2proc[i] == worldRank ){
334 +      the_molecules[molIndex].setStampID( molCompType[i] );
335 +      the_molecules[molIndex].setMyIndex( molIndex );
336 +      molIndex++;
337 +    }
338 +  }
339 +
340 + #else // is_mpi
341 +  
342 +  molIndex = 0;
343 +  for(i=0; i<n_components; i++){
344 +    for(j=0; j<components_nmol[i]; j++ ){
345 +      the_molecules[molIndex].setStampID( i );
346 +      the_molecules[molIndex].setMyIndex( molIndex );
347 +      molIndex++;
348 +    }
349 +  }
350 +    
351 +
352 + #endif // is_mpi
353 +
354 +
355    if( simnfo->n_SRI ){
356 +    
357      Exclude::createArray(simnfo->n_SRI);
358      the_excludes = new Exclude*[simnfo->n_SRI];
359 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
360      simnfo->globalExcludes = new int;
361 <    simnfo->n_exclude = tot_SRI;
361 >    simnfo->n_exclude = simnfo->n_SRI;
362    }
363    else{
364      
# Line 326 | Line 374 | void SimSetup::createSim( void ){
374    // set the arrays into the SimInfo object
375  
376    simnfo->atoms = the_atoms;
377 <  simnfo->sr_interactions = the_sris;
377 >  simnfo->molecules = the_molecules;
378    simnfo->nGlobalExcludes = 0;
379    simnfo->excludes = the_excludes;
380  
# Line 383 | Line 431 | void SimSetup::createSim( void ){
431  
432    the_ff->setSimInfo( simnfo );
433  
434 <  makeAtoms();
434 >  makeMolecules();
435    simnfo->identArray = new int[simnfo->n_atoms];
436    for(i=0; i<simnfo->n_atoms; i++){
437      simnfo->identArray[i] = the_atoms[i]->getIdent();
438    }
439    
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 –
440    if (the_globals->getUseRF() ) {
441      simnfo->useReactionField = 1;
442    
# Line 638 | Line 673 | void SimSetup::createSim( void ){
673  
674   //   new AllLong( simnfo );
675  
676 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
677 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
678 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
679 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
680 <
676 >  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo,
677 >                                                           the_ff,
678 >                                                           the_extendedsystem);
679 >  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo,
680 >                                                 the_ff,
681 >                                                 the_extendedsystem );
682  
683 + #ifdef IS_MPI
684 +  mpiSim->mpiRefresh();
685 + #endif
686  
687    // initialize the Fortran
688 <  
688 >
689 >
690    simnfo->refreshSim();
691    
692    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 723 | void SimSetup::makeMolecules( void ){
723    BondStamp* currentBond;
724    BendStamp* currentBend;
725    TorsionStamp* currentTorsion;
726 +
727 +  bond_pair* theBonds;
728 +  bend_set* theBends;
729 +  torsion_set* theTorsions;
730 +
731    
732    //init the forceField paramters
733  
734    the_ff->readParams();
735  
736    
737 <  // init the molecules
737 >  // init the atoms
738  
739 +  double ux, uy, uz, u, uSqr;
740 +  
741    atomOffset = 0;
742    excludeOffset = 0;
743    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 754 | void SimSetup::makeMolecules( void ){
754      info.myExcludes = &the_excludes[excludeOffset];
755      info.myBonds = new Bond*[info.nBonds];
756      info.myBends = new Bend*[info.nBends];
757 <    info.myTorsions = new Torsions*[info.nTorsions];
757 >    info.myTorsions = new Torsion*[info.nTorsions];
758  
759      theBonds = new bond_pair[info.nBonds];
760      theBends = new bend_set[info.nBends];
# Line 717 | Line 764 | void SimSetup::makeMolecules( void ){
764      
765      for(j=0; j<info.nAtoms; j++){
766        
767 <      currentAtom = theComponents[stampID]->getAtom( j );
767 >      currentAtom = comp_stamps[stampID]->getAtom( j );
768        if( currentAtom->haveOrientation() ){
769          
770          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 805 | void SimSetup::makeMolecules( void ){
805        theBonds[j].a = currentBond->getA() + atomOffset;
806        theBonds[j].b = currentBond->getB() + atomOffset;
807  
808 <      exI = theBonds[i].a;
809 <      exJ = theBonds[i].b;
808 >      exI = theBonds[j].a;
809 >      exJ = theBonds[j].b;
810  
811        // exclude_I must always be the smaller of the pair
812        if( exI > exJ ){
# Line 775 | Line 822 | void SimSetup::makeMolecules( void ){
822        
823        the_excludes[j+excludeOffset]->setPair( exI, exJ );
824   #else  // isn't MPI
825 +
826        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
827   #endif  //is_mpi
828      }
# Line 790 | Line 838 | void SimSetup::makeMolecules( void ){
838            
839        if( currentBend->haveExtras() ){
840              
841 <        extras = current_bend->getExtras();
841 >        extras = currentBend->getExtras();
842          current_extra = extras;
843              
844          while( current_extra != NULL ){
# Line 812 | Line 860 | void SimSetup::makeMolecules( void ){
860                
861              default:
862                sprintf( painCave.errMsg,
863 <                       "SimSetup Error: ghostVectorSource was neiter a "
863 >                       "SimSetup Error: ghostVectorSource was neither a "
864                         "double nor an int.\n"
865                         "-->Bend[%d] in %s\n",
866                         j, comp_stamps[stampID]->getID() );
# Line 897 | Line 945 | void SimSetup::makeMolecules( void ){
945      excludeOffset += info.nTorsions;
946  
947      
948 +    // send the arrays off to the forceField for init.
949  
950 +    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
951 +    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
952 +    the_ff->initializeBends( info.nBends, info.myBends, theBends );
953 +    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
954  
902 –
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++;
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;
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;
955  
956 <          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 <          }
956 >    the_molecules[i].initialize( info );
957  
958  
959 < #ifdef IS_MPI
960 <
961 <          the_excludes[(index + tot_bonds)*2] =    
962 <            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 <    }
959 >    atomOffset += info.nAtoms;
960 >    delete[] theBonds;
961 >    delete[] theBends;
962 >    delete[] theTorsions;
963    }
964  
965   #ifdef IS_MPI
966 <  sprintf( checkPointMsg,
1182 <           "Successfully created the bends list.\n" );
966 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
967    MPIcheckPoint();
968   #endif // is_mpi
1185 –  
969  
970 <  the_ff->initializeBends( the_bends );
971 < }
970 >  // clean up the forcefield
971 >  the_ff->calcRcut();
972 >  the_ff->cleanMe();
973  
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 );
974   }
975  
976   void SimSetup::initFromBass( void ){

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