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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 474 by gezelter, Mon Apr 7 21:42:19 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 +    the_extendedsystem->setQmass(the_globals->getQmass());
92 +    the_extendedsystem->setTauRelax(the_globals->getTauRelax());
93 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
94 +    the_extendedsystem = new ExtendedSystem( simnfo );
95 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
96 +    the_extendedsystem->setQmass(the_globals->getQmass());    
97 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
98 +  } else {
99 +    sprintf( painCave.errMsg,
100 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
101 +             "reverting to NVE for this simulation.\n",
102 +             ensemble );
103 +    painCave.isFatal = 0;
104 +    simError();
105 +    strcpy( ensemble, "NVE" );
106 +  }  
107    strcpy( simnfo->ensemble, ensemble );
108  
109    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
110    simnfo->usePBC = the_globals->getPBC();
111            
112 <
113 <
114 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
115 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
116 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
117 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
112 >  int usesDipoles = 0;
113 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
114 >    the_ff = new TraPPE_ExFF();
115 >    usesDipoles = 1;
116 >  }
117 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
118    else{
119      sprintf( painCave.errMsg,
120               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 242 | Line 265 | void SimSetup::createSim( void ){
265  
266    globalIndex = mpiSim->divideLabor();
267  
245 –
246 –
268    // set up the local variables
269    
270    int localMol, allMol;
271    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
272 +
273 +  int* mol2proc = mpiSim->getMolToProcMap();
274 +  int* molCompType = mpiSim->getMolComponentType();
275    
276    allMol = 0;
277    localMol = 0;
# Line 259 | Line 283 | void SimSetup::createSim( void ){
283  
284      for( j=0; j<components_nmol[i]; j++ ){
285        
286 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
286 >      if( mol2proc[j] == worldRank ){
287          
288          local_atoms +=    comp_stamps[i]->getNAtoms();
289          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 302 | void SimSetup::createSim( void ){
302    if( local_atoms != simnfo->n_atoms ){
303      sprintf( painCave.errMsg,
304               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
305 <             " localAtom (%d) are note equal.\n",
305 >             " localAtom (%d) are not equal.\n",
306               simnfo->n_atoms,
307               local_atoms );
308      painCave.isFatal = 1;
# Line 304 | Line 327 | void SimSetup::createSim( void ){
327    Atom::createArrays(simnfo->n_atoms);
328    the_atoms = new Atom*[simnfo->n_atoms];
329    the_molecules = new Molecule[simnfo->n_mol];
330 +  int molIndex;
331  
332 +  // initialize the molecule's stampID's
333  
334 + #ifdef IS_MPI
335 +  
336 +
337 +  molIndex = 0;
338 +  for(i=0; i<mpiSim->getTotNmol(); i++){
339 +    
340 +    if(mol2proc[i] == worldRank ){
341 +      the_molecules[molIndex].setStampID( molCompType[i] );
342 +      the_molecules[molIndex].setMyIndex( molIndex );
343 +      molIndex++;
344 +    }
345 +  }
346 +
347 + #else // is_mpi
348 +  
349 +  molIndex = 0;
350 +  for(i=0; i<n_components; i++){
351 +    for(j=0; j<components_nmol[i]; j++ ){
352 +      the_molecules[molIndex].setStampID( i );
353 +      the_molecules[molIndex].setMyIndex( molIndex );
354 +      molIndex++;
355 +    }
356 +  }
357 +    
358 +
359 + #endif // is_mpi
360 +
361 +
362    if( simnfo->n_SRI ){
363 +    
364      Exclude::createArray(simnfo->n_SRI);
365      the_excludes = new Exclude*[simnfo->n_SRI];
366 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
367      simnfo->globalExcludes = new int;
368 <    simnfo->n_exclude = tot_SRI;
368 >    simnfo->n_exclude = simnfo->n_SRI;
369    }
370    else{
371      
# Line 326 | Line 381 | void SimSetup::createSim( void ){
381    // set the arrays into the SimInfo object
382  
383    simnfo->atoms = the_atoms;
384 <  simnfo->sr_interactions = the_sris;
384 >  simnfo->molecules = the_molecules;
385    simnfo->nGlobalExcludes = 0;
386    simnfo->excludes = the_excludes;
387  
# Line 383 | Line 438 | void SimSetup::createSim( void ){
438  
439    the_ff->setSimInfo( simnfo );
440  
441 <  makeAtoms();
441 >  makeMolecules();
442    simnfo->identArray = new int[simnfo->n_atoms];
443    for(i=0; i<simnfo->n_atoms; i++){
444      simnfo->identArray[i] = the_atoms[i]->getIdent();
445    }
446    
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 –
447    if (the_globals->getUseRF() ) {
448      simnfo->useReactionField = 1;
449    
# Line 443 | Line 485 | void SimSetup::createSim( void ){
485      }
486      simnfo->dielectric = the_globals->getDielectric();  
487    } else {
488 <    if (simnfo->n_dipoles) {
488 >    if (usesDipoles) {
489        
490        if( !the_globals->haveECR() ){
491          sprintf( painCave.errMsg,
492 <                 "SimSetup Warning: using default value of 1/2 the smallest"
492 >                 "SimSetup Warning: using default value of 1/2 the smallest "
493                   "box length for the electrostaticCutoffRadius.\n"
494                   "I hope you have a very fast processor!\n");
495          painCave.isFatal = 0;
# Line 463 | Line 505 | void SimSetup::createSim( void ){
505        
506        if( !the_globals->haveEST() ){
507          sprintf( painCave.errMsg,
508 <                 "SimSetup Warning: using default value of 5% of the"
508 >                 "SimSetup Warning: using default value of 5%% of the "
509                   "electrostaticCutoffRadius for the "
510                   "electrostaticSkinThickness\n"
511                   );
# Line 638 | Line 680 | void SimSetup::createSim( void ){
680  
681   //   new AllLong( simnfo );
682  
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 );
683  
684 +  if( !strcmp( force_field, "TraPPE_Ex" ) ){
685 +    new Symplectic(simnfo, the_ff, the_extendedsystem);
686 +    std::cerr << "called new Symplecic\n";
687 +    fprintf( stderr, "called new Symplectic. stderr\n" );
688 +  }
689 +  else if( !strcmp( force_field, "LJ" ) ){
690 +    new Verlet( *simnfo, the_ff, the_extendedsystem );
691 +    std::cerr << "called new Verlet\n";
692 +    fprintf( stderr, "called new Verlet. stderr\n" );
693 +  }
694 +  else {
695 +    std::cerr << "I'm a bug.\n";
696 +    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
697 +  }
698 + #ifdef IS_MPI
699 +  mpiSim->mpiRefresh();
700 + #endif
701  
647 –
702    // initialize the Fortran
703 <  
703 >
704 >
705    simnfo->refreshSim();
706    
707    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 738 | void SimSetup::makeMolecules( void ){
738    BondStamp* currentBond;
739    BendStamp* currentBend;
740    TorsionStamp* currentTorsion;
741 +
742 +  bond_pair* theBonds;
743 +  bend_set* theBends;
744 +  torsion_set* theTorsions;
745 +
746    
747    //init the forceField paramters
748  
749    the_ff->readParams();
750  
751    
752 <  // init the molecules
752 >  // init the atoms
753  
754 +  double ux, uy, uz, u, uSqr;
755 +  
756    atomOffset = 0;
757    excludeOffset = 0;
758    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 769 | void SimSetup::makeMolecules( void ){
769      info.myExcludes = &the_excludes[excludeOffset];
770      info.myBonds = new Bond*[info.nBonds];
771      info.myBends = new Bend*[info.nBends];
772 <    info.myTorsions = new Torsions*[info.nTorsions];
772 >    info.myTorsions = new Torsion*[info.nTorsions];
773  
774      theBonds = new bond_pair[info.nBonds];
775      theBends = new bend_set[info.nBends];
# Line 717 | Line 779 | void SimSetup::makeMolecules( void ){
779      
780      for(j=0; j<info.nAtoms; j++){
781        
782 <      currentAtom = theComponents[stampID]->getAtom( j );
782 >      currentAtom = comp_stamps[stampID]->getAtom( j );
783        if( currentAtom->haveOrientation() ){
784          
785          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 820 | void SimSetup::makeMolecules( void ){
820        theBonds[j].a = currentBond->getA() + atomOffset;
821        theBonds[j].b = currentBond->getB() + atomOffset;
822  
823 <      exI = theBonds[i].a;
824 <      exJ = theBonds[i].b;
823 >      exI = theBonds[j].a;
824 >      exJ = theBonds[j].b;
825  
826        // exclude_I must always be the smaller of the pair
827        if( exI > exJ ){
# Line 775 | Line 837 | void SimSetup::makeMolecules( void ){
837        
838        the_excludes[j+excludeOffset]->setPair( exI, exJ );
839   #else  // isn't MPI
840 +
841        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
842   #endif  //is_mpi
843      }
# Line 790 | Line 853 | void SimSetup::makeMolecules( void ){
853            
854        if( currentBend->haveExtras() ){
855              
856 <        extras = current_bend->getExtras();
856 >        extras = currentBend->getExtras();
857          current_extra = extras;
858              
859          while( current_extra != NULL ){
# Line 812 | Line 875 | void SimSetup::makeMolecules( void ){
875                
876              default:
877                sprintf( painCave.errMsg,
878 <                       "SimSetup Error: ghostVectorSource was neiter a "
878 >                       "SimSetup Error: ghostVectorSource was neither a "
879                         "double nor an int.\n"
880                         "-->Bend[%d] in %s\n",
881                         j, comp_stamps[stampID]->getID() );
# Line 906 | Line 969 | void SimSetup::makeMolecules( void ){
969  
970  
971      the_molecules[i].initialize( info );
909 –    atomOffset += info.nAtoms;
910 –  }
911 –
912 –  // clean up the forcefield
913 –
914 –  the_ff->cleanMe();
915 – }
916 –
917 –
918 –
919 – void SimSetup::makeAtoms( void ){
920 –
921 –  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;
972  
1028 –          exI = the_bonds[index].a;
1029 –          exJ = the_bonds[index].b;
973  
974 <          // exclude_I must always be the smaller of the pair
975 <          if( exI > exJ ){
976 <            tempEx = exI;
977 <            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 <    }
974 >    atomOffset += info.nAtoms;
975 >    delete[] theBonds;
976 >    delete[] theBends;
977 >    delete[] theTorsions;
978    }
979  
980   #ifdef IS_MPI
981 <  sprintf( checkPointMsg,
1195 <           "Successfully created the bends list.\n" );
981 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
982    MPIcheckPoint();
983   #endif // is_mpi
1198 –  
984  
985 <  the_ff->initializeBends( the_bends );
986 < }
985 >  // clean up the forcefield
986 >  the_ff->calcRcut();
987 >  the_ff->cleanMe();
988  
1203 – void SimSetup::makeTorsions( void ){
1204 –
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 );
989   }
990  
991   void SimSetup::initFromBass( void ){

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