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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 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 460 | Line 462 | namespace OpenMD {
462        }
463      }
464    }
463 –
465  
466    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467      int i, j;  
# 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 548 | Line 557 | namespace OpenMD {
557             atomRowData.electricField.end(), V3Zero);
558        fill(atomColData.electricField.begin(),
559             atomColData.electricField.end(), V3Zero);
551 –    }
552 –
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);
560      }
561  
562   #endif
# 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 781 | Line 790 | namespace OpenMD {
790  
791      vector<potVec> pot_temp(nLocal_,
792                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
793 +    vector<potVec> expot_temp(nLocal_,
794 +                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
795  
796      // scatter/gather pot_row into the members of my column
797            
798      AtomPlanPotRow->scatter(pot_row, pot_temp);
799 +    AtomPlanPotRow->scatter(expot_row, expot_temp);
800  
801 <    for (int ii = 0;  ii < pot_temp.size(); ii++ )
801 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
802        pairwisePot += pot_temp[ii];
803 +
804 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
805 +      excludedPot += expot_temp[ii];
806          
807      if (storageLayout_ & DataStorage::dslParticlePot) {
808        // This is the pairwise contribution to the particle pot.  The
# Line 805 | Line 820 | namespace OpenMD {
820  
821      fill(pot_temp.begin(), pot_temp.end(),
822           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
823 +    fill(expot_temp.begin(), expot_temp.end(),
824 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
825        
826      AtomPlanPotColumn->scatter(pot_col, pot_temp);    
827 +    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
828      
829      for (int ii = 0;  ii < pot_temp.size(); ii++ )
830        pairwisePot += pot_temp[ii];    
831  
832 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
833 +      excludedPot += expot_temp[ii];    
834 +
835      if (storageLayout_ & DataStorage::dslParticlePot) {
836        // This is the pairwise contribution to the particle pot.  The
837        // embedding contribution is added in each of the low level
# Line 853 | Line 874 | namespace OpenMD {
874      }
875  
876      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
877 <      RealType ploc1 = embeddingPot[ii];
877 >      RealType ploc1 = excludedPot[ii];
878        RealType ploc2 = 0.0;
879        MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
880 <      embeddingPot[ii] = ploc2;
880 >      excludedPot[ii] = ploc2;
881      }
882 <    
882 >
883      // Here be dragons.
884      MPI::Intracomm col = colComm.getComm();
885  
# Line 869 | Line 890 | namespace OpenMD {
890  
891   #endif
892  
893 +  }
894 +
895 +  /**
896 +   * Collects information obtained during the post-pair (and embedding
897 +   * functional) loops onto local data structures.
898 +   */
899 +  void ForceMatrixDecomposition::collectSelfData() {
900 +    snap_ = sman_->getCurrentSnapshot();
901 +    storageLayout_ = sman_->getStorageLayout();
902 +
903 + #ifdef IS_MPI
904 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
905 +      RealType ploc1 = embeddingPot[ii];
906 +      RealType ploc2 = 0.0;
907 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
908 +      embeddingPot[ii] = ploc2;
909 +    }    
910 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
911 +      RealType ploc1 = excludedSelfPot[ii];
912 +      RealType ploc2 = 0.0;
913 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
914 +      excludedSelfPot[ii] = ploc2;
915 +    }    
916 + #endif
917 +    
918    }
919  
920 +
921 +
922    int ForceMatrixDecomposition::getNAtomsInRow() {  
923   #ifdef IS_MPI
924      return nAtomsInRow_;
# Line 993 | Line 1041 | namespace OpenMD {
1041     * We need to exclude some overcounted interactions that result from
1042     * the parallel decomposition.
1043     */
1044 <  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1045 <    int unique_id_1, unique_id_2;
1044 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1045 >    int unique_id_1, unique_id_2, group1, group2;
1046          
1047   #ifdef IS_MPI
1048      // in MPI, we have to look up the unique IDs for each atom
1049      unique_id_1 = AtomRowToGlobal[atom1];
1050      unique_id_2 = AtomColToGlobal[atom2];
1051 +    group1 = cgRowToGlobal[cg1];
1052 +    group2 = cgColToGlobal[cg2];
1053   #else
1054      unique_id_1 = AtomLocalToGlobal[atom1];
1055      unique_id_2 = AtomLocalToGlobal[atom2];
1056 +    group1 = cgLocalToGlobal[cg1];
1057 +    group2 = cgLocalToGlobal[cg2];
1058   #endif  
1059  
1060      if (unique_id_1 == unique_id_2) return true;
# Line 1014 | Line 1066 | namespace OpenMD {
1066      } else {
1067        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1068      }
1069 + #endif    
1070 +
1071 + #ifndef IS_MPI
1072 +    if (group1 == group2) {
1073 +      if (unique_id_1 < unique_id_2) return true;
1074 +    }
1075   #endif
1076      
1077      return false;
# Line 1074 | Line 1132 | namespace OpenMD {
1132        idat.A2 = &(atomColData.aMat[atom2]);
1133      }
1134      
1077 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1078 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1079 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1080 –    }
1081 –
1135      if (storageLayout_ & DataStorage::dslTorque) {
1136        idat.t1 = &(atomRowData.torque[atom1]);
1137        idat.t2 = &(atomColData.torque[atom2]);
1138      }
1139  
1140 +    if (storageLayout_ & DataStorage::dslDipole) {
1141 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1142 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1143 +    }
1144 +
1145 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1146 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1147 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1148 +    }
1149 +
1150      if (storageLayout_ & DataStorage::dslDensity) {
1151        idat.rho1 = &(atomRowData.density[atom1]);
1152        idat.rho2 = &(atomColData.density[atom2]);
# Line 1116 | Line 1179 | namespace OpenMD {
1179  
1180   #else
1181      
1119 –
1120 –    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1121 –    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1122 –    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1123 –
1182      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1125 –    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1126 –    //                         ff_->getAtomType(idents[atom2]) );
1183  
1184      if (storageLayout_ & DataStorage::dslAmat) {
1185        idat.A1 = &(snap_->atomData.aMat[atom1]);
1186        idat.A2 = &(snap_->atomData.aMat[atom2]);
1187      }
1188  
1133 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1134 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1135 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1136 –    }
1137 –
1189      if (storageLayout_ & DataStorage::dslTorque) {
1190        idat.t1 = &(snap_->atomData.torque[atom1]);
1191        idat.t2 = &(snap_->atomData.torque[atom2]);
1192      }
1193  
1194 +    if (storageLayout_ & DataStorage::dslDipole) {
1195 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1196 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1197 +    }
1198 +
1199 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1200 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1201 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1202 +    }
1203 +
1204      if (storageLayout_ & DataStorage::dslDensity) {    
1205        idat.rho1 = &(snap_->atomData.density[atom1]);
1206        idat.rho2 = &(snap_->atomData.density[atom2]);
# Line 1178 | Line 1239 | namespace OpenMD {
1239   #ifdef IS_MPI
1240      pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1241      pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1242 +    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1243 +    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1244  
1245      atomRowData.force[atom1] += *(idat.f1);
1246      atomColData.force[atom2] -= *(idat.f1);
1247  
1248      if (storageLayout_ & DataStorage::dslFlucQForce) {              
1249 <      atomRowData.flucQFrc[atom1] += *(idat.dVdFQ1);
1250 <      atomColData.flucQFrc[atom2] += *(idat.dVdFQ2);
1249 >      atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1250 >      atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1251      }
1252  
1253      if (storageLayout_ & DataStorage::dslElectricField) {              
# Line 1194 | Line 1257 | namespace OpenMD {
1257  
1258   #else
1259      pairwisePot += *(idat.pot);
1260 +    excludedPot += *(idat.excludedPot);
1261  
1262      snap_->atomData.force[atom1] += *(idat.f1);
1263      snap_->atomData.force[atom2] -= *(idat.f1);
# Line 1208 | Line 1272 | namespace OpenMD {
1272      }
1273      
1274      if (storageLayout_ & DataStorage::dslFlucQForce) {              
1275 <      snap_->atomData.flucQFrc[atom1] += *(idat.dVdFQ1);
1275 >      snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1276        snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1277      }
1278  
# Line 1285 | Line 1349 | namespace OpenMD {
1349          for (int j = 0; j < 3; j++) {
1350            scaled[j] -= roundMe(scaled[j]);
1351            scaled[j] += 0.5;
1352 +          // Handle the special case when an object is exactly on the
1353 +          // boundary (a scaled coordinate of 1.0 is the same as
1354 +          // scaled coordinate of 0.0)
1355 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1356          }
1357          
1358          // find xyz-indices of cell that cutoffGroup is in.
# Line 1309 | Line 1377 | namespace OpenMD {
1377          for (int j = 0; j < 3; j++) {
1378            scaled[j] -= roundMe(scaled[j]);
1379            scaled[j] += 0.5;
1380 +          // Handle the special case when an object is exactly on the
1381 +          // boundary (a scaled coordinate of 1.0 is the same as
1382 +          // scaled coordinate of 0.0)
1383 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1384          }
1385          
1386          // find xyz-indices of cell that cutoffGroup is in.
# Line 1335 | Line 1407 | namespace OpenMD {
1407          for (int j = 0; j < 3; j++) {
1408            scaled[j] -= roundMe(scaled[j]);
1409            scaled[j] += 0.5;
1410 +          // Handle the special case when an object is exactly on the
1411 +          // boundary (a scaled coordinate of 1.0 is the same as
1412 +          // scaled coordinate of 0.0)
1413 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1414          }
1415          
1416          // find xyz-indices of cell that cutoffGroup is in.

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