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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1736 by jmichalk, Tue Jun 5 17:51:31 2012 UTC vs.
Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

# Line 175 | Line 175 | namespace OpenMD {
175  
176      pot_row.resize(nAtomsInRow_);
177      pot_col.resize(nAtomsInCol_);
178 +
179 +    expot_row.resize(nAtomsInRow_);
180 +    expot_col.resize(nAtomsInCol_);
181  
182      AtomRowToGlobal.resize(nAtomsInRow_);
183      AtomColToGlobal.resize(nAtomsInCol_);
# Line 307 | Line 310 | namespace OpenMD {
310      
311      RealType tol = 1e-6;
312      largestRcut_ = 0.0;
310 –    RealType rc;
313      int atid;
314      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315      
# Line 392 | 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 417 | 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 461 | Line 463 | namespace OpenMD {
463      }
464    }
465  
464 –
466    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467      int i, j;  
468   #ifdef IS_MPI
# Line 475 | 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 485 | Line 486 | namespace OpenMD {
486    void ForceMatrixDecomposition::zeroWorkArrays() {
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 503 | Line 506 | namespace OpenMD {
506      fill(pot_col.begin(), pot_col.end(),
507           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
508  
509 +    fill(expot_row.begin(), expot_row.end(),
510 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
511 +
512 +    fill(expot_col.begin(), expot_col.end(),
513 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
514 +
515      if (storageLayout_ & DataStorage::dslParticlePot) {    
516        fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
517             0.0);
# Line 550 | Line 559 | namespace OpenMD {
559             atomColData.electricField.end(), V3Zero);
560      }
561  
553 –    if (storageLayout_ & DataStorage::dslFlucQForce) {    
554 –      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
555 –           0.0);
556 –      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
557 –           0.0);
558 –    }
559 –
562   #endif
563      // even in parallel, we need to zero out the local arrays:
564  
# Line 630 | 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 677 | 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 781 | Line 791 | namespace OpenMD {
791  
792      vector<potVec> pot_temp(nLocal_,
793                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
794 +    vector<potVec> expot_temp(nLocal_,
795 +                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
796  
797      // scatter/gather pot_row into the members of my column
798            
799      AtomPlanPotRow->scatter(pot_row, pot_temp);
800 +    AtomPlanPotRow->scatter(expot_row, expot_temp);
801  
802 <    for (int ii = 0;  ii < pot_temp.size(); ii++ )
802 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
803        pairwisePot += pot_temp[ii];
804 +
805 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
806 +      excludedPot += expot_temp[ii];
807          
808      if (storageLayout_ & DataStorage::dslParticlePot) {
809        // This is the pairwise contribution to the particle pot.  The
# Line 805 | Line 821 | namespace OpenMD {
821  
822      fill(pot_temp.begin(), pot_temp.end(),
823           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
824 +    fill(expot_temp.begin(), expot_temp.end(),
825 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
826        
827      AtomPlanPotColumn->scatter(pot_col, pot_temp);    
828 +    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
829      
830      for (int ii = 0;  ii < pot_temp.size(); ii++ )
831        pairwisePot += pot_temp[ii];    
832  
833 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
834 +      excludedPot += expot_temp[ii];    
835 +
836      if (storageLayout_ & DataStorage::dslParticlePot) {
837        // This is the pairwise contribution to the particle pot.  The
838        // embedding contribution is added in each of the low level
# Line 853 | Line 875 | namespace OpenMD {
875      }
876  
877      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
878 <      RealType ploc1 = embeddingPot[ii];
878 >      RealType ploc1 = excludedPot[ii];
879        RealType ploc2 = 0.0;
880        MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
881 <      embeddingPot[ii] = ploc2;
881 >      excludedPot[ii] = ploc2;
882      }
883 <    
883 >
884      // Here be dragons.
885      MPI::Intracomm col = colComm.getComm();
886  
# Line 869 | Line 891 | namespace OpenMD {
891  
892   #endif
893  
894 +  }
895 +
896 +  /**
897 +   * Collects information obtained during the post-pair (and embedding
898 +   * functional) loops onto local data structures.
899 +   */
900 +  void ForceMatrixDecomposition::collectSelfData() {
901 +    snap_ = sman_->getCurrentSnapshot();
902 +    storageLayout_ = sman_->getStorageLayout();
903 +
904 + #ifdef IS_MPI
905 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
906 +      RealType ploc1 = embeddingPot[ii];
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 +    
919    }
920  
921 +
922 +
923    int ForceMatrixDecomposition::getNAtomsInRow() {  
924   #ifdef IS_MPI
925      return nAtomsInRow_;
# Line 993 | Line 1042 | namespace OpenMD {
1042     * We need to exclude some overcounted interactions that result from
1043     * the parallel decomposition.
1044     */
1045 <  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1045 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
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];
1054   #else
1055      unique_id_1 = AtomLocalToGlobal[atom1];
1056      unique_id_2 = AtomLocalToGlobal[atom2];
1057 +    int group1 = cgLocalToGlobal[cg1];
1058 +    int group2 = cgLocalToGlobal[cg2];
1059   #endif  
1060  
1061      if (unique_id_1 == unique_id_2) return true;
# Line 1014 | Line 1067 | namespace OpenMD {
1067      } else {
1068        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1069      }
1070 + #endif    
1071 +
1072 + #ifndef IS_MPI
1073 +    if (group1 == group2) {
1074 +      if (unique_id_1 < unique_id_2) return true;
1075 +    }
1076   #endif
1077      
1078      return false;
# Line 1074 | Line 1133 | namespace OpenMD {
1133        idat.A2 = &(atomColData.aMat[atom2]);
1134      }
1135      
1077 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1078 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1079 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1080 –    }
1081 –
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) {
# Line 1116 | Line 1180 | namespace OpenMD {
1180  
1181   #else
1182      
1119 –
1120 –    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1121 –    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1122 –    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1123 –
1183      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1125 –    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1126 –    //                         ff_->getAtomType(idents[atom2]) );
1184  
1185      if (storageLayout_ & DataStorage::dslAmat) {
1186        idat.A1 = &(snap_->atomData.aMat[atom1]);
1187        idat.A2 = &(snap_->atomData.aMat[atom2]);
1188      }
1189  
1190 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1134 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1135 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1136 <    }
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 1178 | Line 1242 | namespace OpenMD {
1242   #ifdef IS_MPI
1243      pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1244      pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1245 +    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1246 +    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1247  
1248      atomRowData.force[atom1] += *(idat.f1);
1249      atomColData.force[atom2] -= *(idat.f1);
# Line 1194 | Line 1260 | namespace OpenMD {
1260  
1261   #else
1262      pairwisePot += *(idat.pot);
1263 +    excludedPot += *(idat.excludedPot);
1264  
1265      snap_->atomData.force[atom1] += *(idat.f1);
1266      snap_->atomData.force[atom2] -= *(idat.f1);
# Line 1241 | Line 1308 | namespace OpenMD {
1308   #endif
1309  
1310      RealType rList_ = (largestRcut_ + skinThickness_);
1244 –    RealType rl2 = rList_ * rList_;
1311      Snapshot* snap_ = sman_->getCurrentSnapshot();
1312      Mat3x3d Hmat = snap_->getHmat();
1313      Vector3d Hx = Hmat.getColumn(0);
# Line 1285 | Line 1351 | namespace OpenMD {
1351          for (int j = 0; j < 3; j++) {
1352            scaled[j] -= roundMe(scaled[j]);
1353            scaled[j] += 0.5;
1354 +          // Handle the special case when an object is exactly on the
1355 +          // boundary (a scaled coordinate of 1.0 is the same as
1356 +          // scaled coordinate of 0.0)
1357 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1358          }
1359          
1360          // find xyz-indices of cell that cutoffGroup is in.
# Line 1309 | Line 1379 | namespace OpenMD {
1379          for (int j = 0; j < 3; j++) {
1380            scaled[j] -= roundMe(scaled[j]);
1381            scaled[j] += 0.5;
1382 +          // Handle the special case when an object is exactly on the
1383 +          // boundary (a scaled coordinate of 1.0 is the same as
1384 +          // scaled coordinate of 0.0)
1385 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1386          }
1387          
1388          // find xyz-indices of cell that cutoffGroup is in.
# Line 1335 | Line 1409 | namespace OpenMD {
1409          for (int j = 0; j < 3; j++) {
1410            scaled[j] -= roundMe(scaled[j]);
1411            scaled[j] += 0.5;
1412 +          // Handle the special case when an object is exactly on the
1413 +          // boundary (a scaled coordinate of 1.0 is the same as
1414 +          // scaled coordinate of 0.0)
1415 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1416          }
1417          
1418          // find xyz-indices of cell that cutoffGroup is in.

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