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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 429 by mmeineke, Thu Mar 27 21:52:21 2003 UTC

# Line 88 | Line 88 | void SimSetup::createSim( void ){
88            
89  
90  
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();
91 >  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92    else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93    else{
94      sprintf( painCave.errMsg,
# Line 248 | Line 246 | void SimSetup::createSim( void ){
246    
247    int localMol, allMol;
248    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
249 +
250 +  int* mol2proc = mpiSim->getMolToProcMap();
251 +  int* molCompType = mpiSim->getMolComponentType();
252    
253    allMol = 0;
254    localMol = 0;
# Line 259 | Line 260 | void SimSetup::createSim( void ){
260  
261      for( j=0; j<components_nmol[i]; j++ ){
262        
263 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
263 >      if( mol2proc[j] == worldRank ){
264          
265          local_atoms +=    comp_stamps[i]->getNAtoms();
266          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 279 | void SimSetup::createSim( void ){
279    if( local_atoms != simnfo->n_atoms ){
280      sprintf( painCave.errMsg,
281               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282 <             " localAtom (%d) are note equal.\n",
282 >             " localAtom (%d) are not equal.\n",
283               simnfo->n_atoms,
284               local_atoms );
285      painCave.isFatal = 1;
# Line 304 | Line 304 | void SimSetup::createSim( void ){
304    Atom::createArrays(simnfo->n_atoms);
305    the_atoms = new Atom*[simnfo->n_atoms];
306    the_molecules = new Molecule[simnfo->n_mol];
307 +  int molIndex;
308 +
309 +  // initialize the molecule's stampID's
310 +
311 + #ifdef IS_MPI
312 +  
313 +
314 +  molIndex = 0;
315 +  for(i=0; i<mpiSim->getTotNmol(); i++){
316 +    
317 +    if(mol2proc[i] == worldRank ){
318 +      the_molecules[molIndex].setStampID( molCompType[i] );
319 +      molIndex++;
320 +    }
321 +  }
322 +
323 + #else // is_mpi
324 +  
325 +  molIndex = 0;
326 +  for(i=0; i<n_components; i++){
327 +    for(j=0; j<components_nmol[i]; j++ ){
328 +      the_molecules[molIndex].setStampID( i );
329 +      molIndex++;
330 +    }
331 +  }
332 +    
333  
334 + #endif // is_mpi
335  
336 +
337    if( simnfo->n_SRI ){
338      Exclude::createArray(simnfo->n_SRI);
339      the_excludes = new Exclude*[simnfo->n_SRI];
# Line 326 | Line 354 | void SimSetup::createSim( void ){
354    // set the arrays into the SimInfo object
355  
356    simnfo->atoms = the_atoms;
357 <  simnfo->sr_interactions = the_sris;
357 >  simnfo->molecules = the_molecules;
358    simnfo->nGlobalExcludes = 0;
359    simnfo->excludes = the_excludes;
360  
# Line 383 | Line 411 | void SimSetup::createSim( void ){
411  
412    the_ff->setSimInfo( simnfo );
413  
414 <  makeAtoms();
414 >  makeMolecules();
415    simnfo->identArray = new int[simnfo->n_atoms];
416    for(i=0; i<simnfo->n_atoms; i++){
417      simnfo->identArray[i] = the_atoms[i]->getIdent();
418    }
419    
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 –
420    if (the_globals->getUseRF() ) {
421      simnfo->useReactionField = 1;
422    
# Line 638 | Line 653 | void SimSetup::createSim( void ){
653  
654   //   new AllLong( simnfo );
655  
641 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
656    if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
657    if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
658  
# Line 683 | Line 696 | void SimSetup::makeMolecules( void ){
696    BondStamp* currentBond;
697    BendStamp* currentBend;
698    TorsionStamp* currentTorsion;
699 +
700 +  bond_pair* theBonds;
701 +  bend_set* theBends;
702 +  torsion_set* theTorsions;
703 +
704    
705    //init the forceField paramters
706  
707    the_ff->readParams();
708  
709    
710 <  // init the molecules
710 >  // init the atoms
711  
712 +  double ux, uy, uz, u, uSqr;
713 +  
714    atomOffset = 0;
715    excludeOffset = 0;
716    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 727 | void SimSetup::makeMolecules( void ){
727      info.myExcludes = &the_excludes[excludeOffset];
728      info.myBonds = new Bond*[info.nBonds];
729      info.myBends = new Bend*[info.nBends];
730 <    info.myTorsions = new Torsions*[info.nTorsions];
730 >    info.myTorsions = new Torsion*[info.nTorsions];
731  
732      theBonds = new bond_pair[info.nBonds];
733      theBends = new bend_set[info.nBends];
# Line 717 | Line 737 | void SimSetup::makeMolecules( void ){
737      
738      for(j=0; j<info.nAtoms; j++){
739        
740 <      currentAtom = theComponents[stampID]->getAtom( j );
740 >      currentAtom = comp_stamps[stampID]->getAtom( j );
741        if( currentAtom->haveOrientation() ){
742          
743          dAtom = new DirectionalAtom(j + atomOffset);
# Line 790 | Line 810 | void SimSetup::makeMolecules( void ){
810            
811        if( currentBend->haveExtras() ){
812              
813 <        extras = current_bend->getExtras();
813 >        extras = currentBend->getExtras();
814          current_extra = extras;
815              
816          while( current_extra != NULL ){
# Line 897 | Line 917 | void SimSetup::makeMolecules( void ){
917      excludeOffset += info.nTorsions;
918  
919      
920 <
901 <
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++;
920 >    // send the arrays off to the forceField for init.
921  
922 < #ifdef IS_MPI
923 <      }
924 < #endif //is_mpi
925 <      
974 <      molIndex++;
975 <    }
976 <  }
977 <
978 < #ifdef IS_MPI
979 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
980 <    
981 <    delete[] globalIndex;
982 <
983 <    mpiSim->mpiRefresh();
984 < #endif //IS_MPI
985 <          
986 <  the_ff->initializeAtoms();
987 < }
988 <
989 < void SimSetup::makeBonds( void ){
990 <
991 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
992 <  bond_pair* the_bonds;
993 <  BondStamp* current_bond;
994 <
995 <  the_bonds = new bond_pair[tot_bonds];
996 <  index = 0;
997 <  offset = 0;
998 <  molIndex = 0;
999 <
1000 <  for( i=0; i<n_components; i++ ){
1001 <
1002 <    for( j=0; j<components_nmol[i]; j++ ){
1003 <
1004 < #ifdef IS_MPI
1005 <      if( mpiSim->getMyMolStart() <= molIndex &&
1006 <          molIndex <= mpiSim->getMyMolEnd() ){
1007 < #endif // is_mpi        
1008 <        
1009 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1010 <          
1011 <          current_bond = comp_stamps[i]->getBond( k );
1012 <          the_bonds[index].a = current_bond->getA() + offset;
1013 <          the_bonds[index].b = current_bond->getB() + offset;
1014 <
1015 <          exI = the_bonds[index].a;
1016 <          exJ = the_bonds[index].b;
1017 <
1018 <          // exclude_I must always be the smaller of the pair
1019 <          if( exI > exJ ){
1020 <            tempEx = exI;
1021 <            exI = exJ;
1022 <            exJ = tempEx;
1023 <          }
1024 <
1025 <          
1026 < #ifdef IS_MPI
1027 <
1028 <          the_excludes[index*2] =    
1029 <            the_atoms[exI]->getGlobalIndex() + 1;
1030 <          the_excludes[index*2 + 1] =
1031 <            the_atoms[exJ]->getGlobalIndex() + 1;
1032 <
1033 < #else  // isn't MPI
1034 <          
1035 <          the_excludes[index*2] =     exI + 1;
1036 <          the_excludes[index*2 + 1] = exJ + 1;
1037 <          // fortran index from 1 (hence the +1 in the indexing)
1038 < #endif  //is_mpi
1039 <          
1040 <          // increment the index and repeat;
1041 <          index++;
1042 <        }
1043 <        offset += comp_stamps[i]->getNAtoms();
1044 <        
1045 < #ifdef IS_MPI
1046 <      }
1047 < #endif //is_mpi
1048 <      
1049 <      molIndex++;
1050 <    }      
1051 <  }
1052 <
1053 <  the_ff->initializeBonds( the_bonds );
1054 < }
1055 <
1056 < void SimSetup::makeBends( void ){
1057 <
1058 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1059 <  bend_set* the_bends;
1060 <  BendStamp* current_bend;
1061 <  LinkedAssign* extras;
1062 <  LinkedAssign* current_extra;
1063 <  
1064 <
1065 <  the_bends = new bend_set[tot_bends];
1066 <  index = 0;
1067 <  offset = 0;
1068 <  molIndex = 0;
1069 <  for( i=0; i<n_components; i++ ){
1070 <
1071 <    for( j=0; j<components_nmol[i]; j++ ){
1072 <
1073 < #ifdef IS_MPI
1074 <      if( mpiSim->getMyMolStart() <= molIndex &&
1075 <          molIndex <= mpiSim->getMyMolEnd() ){
1076 < #endif // is_mpi        
1077 <
1078 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1079 <          
1080 <          current_bend = comp_stamps[i]->getBend( k );
1081 <          the_bends[index].a = current_bend->getA() + offset;
1082 <          the_bends[index].b = current_bend->getB() + offset;
1083 <          the_bends[index].c = current_bend->getC() + offset;
1084 <          
1085 <          if( current_bend->haveExtras() ){
1086 <            
1087 <            extras = current_bend->getExtras();
1088 <            current_extra = extras;
1089 <            
1090 <            while( current_extra != NULL ){
1091 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092 <                
1093 <                switch( current_extra->getType() ){
1094 <                  
1095 <                case 0:
1096 <                  the_bends[index].ghost =
1097 <                    current_extra->getInt() + offset;
1098 <                  the_bends[index].isGhost = 1;
1099 <                  break;
1100 <                  
1101 <                case 1:
1102 <                  the_bends[index].ghost =
1103 <                    (int)current_extra->getDouble() + offset;
1104 <                  the_bends[index].isGhost = 1;
1105 <                  break;
1106 <                  
1107 <                default:
1108 <                  sprintf( painCave.errMsg,
1109 <                           "SimSetup Error: ghostVectorSource was neiter a "
1110 <                           "double nor an int.\n"
1111 <                           "-->Bend[%d] in %s\n",
1112 <                           k, comp_stamps[i]->getID() );
1113 <                  painCave.isFatal = 1;
1114 <                  simError();
1115 <                }
1116 <              }
1117 <              
1118 <              else{
1119 <                
1120 <                sprintf( painCave.errMsg,
1121 <                         "SimSetup Error: unhandled bend assignment:\n"
1122 <                         "    -->%s in Bend[%d] in %s\n",
1123 <                         current_extra->getlhs(),
1124 <                         k, comp_stamps[i]->getID() );
1125 <                painCave.isFatal = 1;
1126 <                simError();
1127 <              }
1128 <              
1129 <              current_extra = current_extra->getNext();
1130 <            }
1131 <          }
1132 <          
1133 <          if( !the_bends[index].isGhost ){
1134 <            
1135 <            exI = the_bends[index].a;
1136 <            exJ = the_bends[index].c;
1137 <          }
1138 <          else{
1139 <            
1140 <            exI = the_bends[index].a;
1141 <            exJ = the_bends[index].b;
1142 <          }
1143 <          
1144 <          // exclude_I must always be the smaller of the pair
1145 <          if( exI > exJ ){
1146 <            tempEx = exI;
1147 <            exI = exJ;
1148 <            exJ = tempEx;
1149 <          }
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
922 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
923 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
924 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
925 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
926  
1176 –      molIndex++;
1177 –    }
1178 –  }
927  
928 < #ifdef IS_MPI
929 <  sprintf( checkPointMsg,
930 <           "Successfully created the bends list.\n" );
931 <  MPIcheckPoint();
932 < #endif // is_mpi
1185 <  
1186 <
1187 <  the_ff->initializeBends( the_bends );
1188 < }
1189 <
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 <    }
928 >    the_molecules[i].initialize( info );
929 >    atomOffset += info.nAtoms;
930 >    delete[] theBonds;
931 >    delete[] theBends;
932 >    delete[] theTorsions;
933    }
934  
935 <  the_ff->initializeTorsions( the_torsions );
935 >  // clean up the forcefield
936 >  the_ff->calcRcut();
937 >  the_ff->cleanMe();
938   }
939  
940   void SimSetup::initFromBass( void ){

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