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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC vs.
Revision 1821 by gezelter, Mon Jan 7 20:05:43 2013 UTC

# Line 310 | Line 310 | namespace OpenMD {
310      
311      RealType tol = 1e-6;
312      largestRcut_ = 0.0;
313 –    RealType rc;
313      int atid;
314      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315      
# Line 395 | Line 394 | namespace OpenMD {
394        }
395        
396        bool gTypeFound = false;
397 <      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
397 >      for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
398          if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
399            groupToGtype[cg1] = gt;
400            gTypeFound = true;
# Line 420 | Line 419 | namespace OpenMD {
419      
420      RealType tradRcut = groupMax;
421  
422 <    for (int i = 0; i < gTypeCutoffs.size();  i++) {
423 <      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
422 >    for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
423 >      for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {      
424          RealType thisRcut;
425          switch(cutoffPolicy_) {
426          case TRADITIONAL:
# Line 477 | Line 476 | namespace OpenMD {
476    }
477  
478    int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
479 <    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
479 >    for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
480        if (toposForAtom[atom1][j] == atom2)
481          return topoDist[atom1][j];
482      }
# Line 488 | Line 487 | namespace OpenMD {
487      pairwisePot = 0.0;
488      embeddingPot = 0.0;
489      excludedPot = 0.0;
490 +    excludedSelfPot = 0.0;
491  
492   #ifdef IS_MPI
493      if (storageLayout_ & DataStorage::dslForce) {
# Line 559 | Line 559 | namespace OpenMD {
559             atomColData.electricField.end(), V3Zero);
560      }
561  
562 –    if (storageLayout_ & DataStorage::dslFlucQForce) {    
563 –      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
564 –           0.0);
565 –      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
566 –           0.0);
567 –    }
568 –
562   #endif
563      // even in parallel, we need to zero out the local arrays:
564  
# Line 639 | Line 632 | namespace OpenMD {
632        AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
633                                     atomColData.aMat);
634      }
635 <    
636 <    // if needed, gather the atomic eletrostatic frames
637 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
638 <      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
639 <                                atomRowData.electroFrame);
640 <      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
641 <                                   atomColData.electroFrame);
635 >
636 >    // if needed, gather the atomic eletrostatic information
637 >    if (storageLayout_ & DataStorage::dslDipole) {
638 >      AtomPlanVectorRow->gather(snap_->atomData.dipole,
639 >                                atomRowData.dipole);
640 >      AtomPlanVectorColumn->gather(snap_->atomData.dipole,
641 >                                   atomColData.dipole);
642      }
643  
644 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
645 +      AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
646 +                                atomRowData.quadrupole);
647 +      AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
648 +                                   atomColData.quadrupole);
649 +    }
650 +        
651      // if needed, gather the atomic fluctuating charge values
652      if (storageLayout_ & DataStorage::dslFlucQPosition) {
653        AtomPlanRealRow->gather(snap_->atomData.flucQPos,
# Line 686 | Line 686 | namespace OpenMD {
686        
687        int n = snap_->atomData.electricField.size();
688        vector<Vector3d> field_tmp(n, V3Zero);
689 <      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
689 >      AtomPlanVectorColumn->scatter(atomColData.electricField,
690 >                                    field_tmp);
691        for (int i = 0; i < n; i++)
692          snap_->atomData.electricField[i] += field_tmp[i];
693      }
# Line 906 | Line 907 | namespace OpenMD {
907        RealType ploc2 = 0.0;
908        MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
909        embeddingPot[ii] = ploc2;
910 +    }    
911 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
912 +      RealType ploc1 = excludedSelfPot[ii];
913 +      RealType ploc2 = 0.0;
914 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
915 +      excludedSelfPot[ii] = ploc2;
916      }    
917   #endif
918      
# Line 1036 | Line 1043 | namespace OpenMD {
1043     * the parallel decomposition.
1044     */
1045    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1046 <    int unique_id_1, unique_id_2, group1, group2;
1046 >    int unique_id_1, unique_id_2;
1047          
1048   #ifdef IS_MPI
1049      // in MPI, we have to look up the unique IDs for each atom
1050      unique_id_1 = AtomRowToGlobal[atom1];
1051      unique_id_2 = AtomColToGlobal[atom2];
1052 <    group1 = cgRowToGlobal[cg1];
1053 <    group2 = cgColToGlobal[cg2];
1052 >    // group1 = cgRowToGlobal[cg1];
1053 >    // group2 = cgColToGlobal[cg2];
1054   #else
1055      unique_id_1 = AtomLocalToGlobal[atom1];
1056      unique_id_2 = AtomLocalToGlobal[atom2];
1057 <    group1 = cgLocalToGlobal[cg1];
1058 <    group2 = cgLocalToGlobal[cg2];
1057 >    int group1 = cgLocalToGlobal[cg1];
1058 >    int group2 = cgLocalToGlobal[cg2];
1059   #endif  
1060  
1061      if (unique_id_1 == unique_id_2) return true;
# Line 1126 | Line 1133 | namespace OpenMD {
1133        idat.A2 = &(atomColData.aMat[atom2]);
1134      }
1135      
1129 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1130 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1131 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1132 –    }
1133 –
1136      if (storageLayout_ & DataStorage::dslTorque) {
1137        idat.t1 = &(atomRowData.torque[atom1]);
1138        idat.t2 = &(atomColData.torque[atom2]);
1139      }
1140  
1141 +    if (storageLayout_ & DataStorage::dslDipole) {
1142 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1143 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1144 +    }
1145 +
1146 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1147 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1148 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1149 +    }
1150 +
1151      if (storageLayout_ & DataStorage::dslDensity) {
1152        idat.rho1 = &(atomRowData.density[atom1]);
1153        idat.rho2 = &(atomColData.density[atom2]);
# Line 1175 | Line 1187 | namespace OpenMD {
1187        idat.A2 = &(snap_->atomData.aMat[atom2]);
1188      }
1189  
1190 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1179 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1180 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1181 <    }
1190 >    RealType ct = dot(idat.A1->getColumn(2), idat.A2->getColumn(2));
1191  
1192      if (storageLayout_ & DataStorage::dslTorque) {
1193        idat.t1 = &(snap_->atomData.torque[atom1]);
1194        idat.t2 = &(snap_->atomData.torque[atom2]);
1195      }
1196  
1197 +    if (storageLayout_ & DataStorage::dslDipole) {
1198 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1199 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1200 +    }
1201 +
1202 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1203 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1204 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1205 +    }
1206 +
1207      if (storageLayout_ & DataStorage::dslDensity) {    
1208        idat.rho1 = &(snap_->atomData.density[atom1]);
1209        idat.rho2 = &(snap_->atomData.density[atom2]);
# Line 1333 | Line 1352 | namespace OpenMD {
1352          for (int j = 0; j < 3; j++) {
1353            scaled[j] -= roundMe(scaled[j]);
1354            scaled[j] += 0.5;
1355 +          // Handle the special case when an object is exactly on the
1356 +          // boundary (a scaled coordinate of 1.0 is the same as
1357 +          // scaled coordinate of 0.0)
1358 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1359          }
1360          
1361          // find xyz-indices of cell that cutoffGroup is in.
# Line 1357 | Line 1380 | namespace OpenMD {
1380          for (int j = 0; j < 3; j++) {
1381            scaled[j] -= roundMe(scaled[j]);
1382            scaled[j] += 0.5;
1383 +          // Handle the special case when an object is exactly on the
1384 +          // boundary (a scaled coordinate of 1.0 is the same as
1385 +          // scaled coordinate of 0.0)
1386 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1387          }
1388          
1389          // find xyz-indices of cell that cutoffGroup is in.
# Line 1383 | Line 1410 | namespace OpenMD {
1410          for (int j = 0; j < 3; j++) {
1411            scaled[j] -= roundMe(scaled[j]);
1412            scaled[j] += 0.5;
1413 +          // Handle the special case when an object is exactly on the
1414 +          // boundary (a scaled coordinate of 1.0 is the same as
1415 +          // scaled coordinate of 0.0)
1416 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1417          }
1418          
1419          // find xyz-indices of cell that cutoffGroup is in.

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