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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 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# 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 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 670 | Line 679 | namespace OpenMD {
679          snap_->atomData.density[i] += rho_tmp[i];
680      }
681  
682 +    // this isn't necessary if we don't have polarizable atoms, but
683 +    // we'll leave it here for now.
684      if (storageLayout_ & DataStorage::dslElectricField) {
685        
686        AtomPlanVectorRow->scatter(atomRowData.electricField,
# Line 677 | Line 688 | namespace OpenMD {
688        
689        int n = snap_->atomData.electricField.size();
690        vector<Vector3d> field_tmp(n, V3Zero);
691 <      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
691 >      AtomPlanVectorColumn->scatter(atomColData.electricField,
692 >                                    field_tmp);
693        for (int i = 0; i < n; i++)
694          snap_->atomData.electricField[i] += field_tmp[i];
695      }
# Line 777 | Line 789 | namespace OpenMD {
789              
790      }
791  
792 +    if (storageLayout_ & DataStorage::dslElectricField) {
793 +
794 +      int nef = snap_->atomData.electricField.size();
795 +      vector<Vector3d> efield_tmp(nef, V3Zero);
796 +
797 +      AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
798 +      for (int i = 0; i < nef; i++) {
799 +        snap_->atomData.electricField[i] += efield_tmp[i];
800 +        efield_tmp[i] = 0.0;
801 +      }
802 +      
803 +      AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
804 +      for (int i = 0; i < nef; i++)
805 +        snap_->atomData.electricField[i] += efield_tmp[i];
806 +    }
807 +
808 +
809      nLocal_ = snap_->getNumberOfAtoms();
810  
811      vector<potVec> pot_temp(nLocal_,
812                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
813 +    vector<potVec> expot_temp(nLocal_,
814 +                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
815  
816      // scatter/gather pot_row into the members of my column
817            
818      AtomPlanPotRow->scatter(pot_row, pot_temp);
819 +    AtomPlanPotRow->scatter(expot_row, expot_temp);
820  
821 <    for (int ii = 0;  ii < pot_temp.size(); ii++ )
821 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
822        pairwisePot += pot_temp[ii];
823 +
824 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
825 +      excludedPot += expot_temp[ii];
826          
827      if (storageLayout_ & DataStorage::dslParticlePot) {
828        // This is the pairwise contribution to the particle pot.  The
# Line 805 | Line 840 | namespace OpenMD {
840  
841      fill(pot_temp.begin(), pot_temp.end(),
842           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
843 +    fill(expot_temp.begin(), expot_temp.end(),
844 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
845        
846      AtomPlanPotColumn->scatter(pot_col, pot_temp);    
847 +    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
848      
849      for (int ii = 0;  ii < pot_temp.size(); ii++ )
850        pairwisePot += pot_temp[ii];    
851  
852 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
853 +      excludedPot += expot_temp[ii];    
854 +
855      if (storageLayout_ & DataStorage::dslParticlePot) {
856        // This is the pairwise contribution to the particle pot.  The
857        // embedding contribution is added in each of the low level
# Line 853 | Line 894 | namespace OpenMD {
894      }
895  
896      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
897 <      RealType ploc1 = embeddingPot[ii];
897 >      RealType ploc1 = excludedPot[ii];
898        RealType ploc2 = 0.0;
899        MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
900 <      embeddingPot[ii] = ploc2;
900 >      excludedPot[ii] = ploc2;
901      }
902 <    
902 >
903      // Here be dragons.
904      MPI::Intracomm col = colComm.getComm();
905  
# Line 871 | Line 912 | namespace OpenMD {
912  
913    }
914  
915 +  /**
916 +   * Collects information obtained during the post-pair (and embedding
917 +   * functional) loops onto local data structures.
918 +   */
919 +  void ForceMatrixDecomposition::collectSelfData() {
920 +    snap_ = sman_->getCurrentSnapshot();
921 +    storageLayout_ = sman_->getStorageLayout();
922 +
923 + #ifdef IS_MPI
924 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
925 +      RealType ploc1 = embeddingPot[ii];
926 +      RealType ploc2 = 0.0;
927 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
928 +      embeddingPot[ii] = ploc2;
929 +    }    
930 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
931 +      RealType ploc1 = excludedSelfPot[ii];
932 +      RealType ploc2 = 0.0;
933 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
934 +      excludedSelfPot[ii] = ploc2;
935 +    }    
936 + #endif
937 +    
938 +  }
939 +
940 +
941 +
942    int ForceMatrixDecomposition::getNAtomsInRow() {  
943   #ifdef IS_MPI
944      return nAtomsInRow_;
# Line 993 | Line 1061 | namespace OpenMD {
1061     * We need to exclude some overcounted interactions that result from
1062     * the parallel decomposition.
1063     */
1064 <  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1064 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1065      int unique_id_1, unique_id_2;
1066          
1067   #ifdef IS_MPI
1068      // in MPI, we have to look up the unique IDs for each atom
1069      unique_id_1 = AtomRowToGlobal[atom1];
1070      unique_id_2 = AtomColToGlobal[atom2];
1071 +    // group1 = cgRowToGlobal[cg1];
1072 +    // group2 = cgColToGlobal[cg2];
1073   #else
1074      unique_id_1 = AtomLocalToGlobal[atom1];
1075      unique_id_2 = AtomLocalToGlobal[atom2];
1076 +    int group1 = cgLocalToGlobal[cg1];
1077 +    int group2 = cgLocalToGlobal[cg2];
1078   #endif  
1079  
1080      if (unique_id_1 == unique_id_2) return true;
# Line 1014 | Line 1086 | namespace OpenMD {
1086      } else {
1087        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1088      }
1089 + #endif    
1090 +
1091 + #ifndef IS_MPI
1092 +    if (group1 == group2) {
1093 +      if (unique_id_1 < unique_id_2) return true;
1094 +    }
1095   #endif
1096      
1097      return false;
# Line 1074 | Line 1152 | namespace OpenMD {
1152        idat.A2 = &(atomColData.aMat[atom2]);
1153      }
1154      
1077 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1078 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1079 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1080 –    }
1081 –
1155      if (storageLayout_ & DataStorage::dslTorque) {
1156        idat.t1 = &(atomRowData.torque[atom1]);
1157        idat.t2 = &(atomColData.torque[atom2]);
1158      }
1159  
1160 +    if (storageLayout_ & DataStorage::dslDipole) {
1161 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1162 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1163 +    }
1164 +
1165 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1166 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1167 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1168 +    }
1169 +
1170      if (storageLayout_ & DataStorage::dslDensity) {
1171        idat.rho1 = &(atomRowData.density[atom1]);
1172        idat.rho2 = &(atomColData.density[atom2]);
# Line 1116 | Line 1199 | namespace OpenMD {
1199  
1200   #else
1201      
1119 –
1120 –    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1121 –    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1122 –    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1123 –
1202      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1125 –    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1126 –    //                         ff_->getAtomType(idents[atom2]) );
1203  
1204      if (storageLayout_ & DataStorage::dslAmat) {
1205        idat.A1 = &(snap_->atomData.aMat[atom1]);
1206        idat.A2 = &(snap_->atomData.aMat[atom2]);
1207      }
1208  
1209 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1134 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1135 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1136 <    }
1209 >    RealType ct = dot(idat.A1->getColumn(2), idat.A2->getColumn(2));
1210  
1211      if (storageLayout_ & DataStorage::dslTorque) {
1212        idat.t1 = &(snap_->atomData.torque[atom1]);
1213        idat.t2 = &(snap_->atomData.torque[atom2]);
1214      }
1215  
1216 +    if (storageLayout_ & DataStorage::dslDipole) {
1217 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1218 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1219 +    }
1220 +
1221 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1222 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1223 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1224 +    }
1225 +
1226      if (storageLayout_ & DataStorage::dslDensity) {    
1227        idat.rho1 = &(snap_->atomData.density[atom1]);
1228        idat.rho2 = &(snap_->atomData.density[atom2]);
# Line 1178 | Line 1261 | namespace OpenMD {
1261   #ifdef IS_MPI
1262      pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1263      pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1264 +    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1265 +    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1266  
1267      atomRowData.force[atom1] += *(idat.f1);
1268      atomColData.force[atom2] -= *(idat.f1);
# Line 1194 | Line 1279 | namespace OpenMD {
1279  
1280   #else
1281      pairwisePot += *(idat.pot);
1282 +    excludedPot += *(idat.excludedPot);
1283  
1284      snap_->atomData.force[atom1] += *(idat.f1);
1285      snap_->atomData.force[atom2] -= *(idat.f1);
# Line 1241 | Line 1327 | namespace OpenMD {
1327   #endif
1328  
1329      RealType rList_ = (largestRcut_ + skinThickness_);
1244 –    RealType rl2 = rList_ * rList_;
1330      Snapshot* snap_ = sman_->getCurrentSnapshot();
1331      Mat3x3d Hmat = snap_->getHmat();
1332      Vector3d Hx = Hmat.getColumn(0);
# Line 1285 | Line 1370 | namespace OpenMD {
1370          for (int j = 0; j < 3; j++) {
1371            scaled[j] -= roundMe(scaled[j]);
1372            scaled[j] += 0.5;
1373 +          // Handle the special case when an object is exactly on the
1374 +          // boundary (a scaled coordinate of 1.0 is the same as
1375 +          // scaled coordinate of 0.0)
1376 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1377          }
1378          
1379          // find xyz-indices of cell that cutoffGroup is in.
# Line 1309 | Line 1398 | namespace OpenMD {
1398          for (int j = 0; j < 3; j++) {
1399            scaled[j] -= roundMe(scaled[j]);
1400            scaled[j] += 0.5;
1401 +          // Handle the special case when an object is exactly on the
1402 +          // boundary (a scaled coordinate of 1.0 is the same as
1403 +          // scaled coordinate of 0.0)
1404 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1405          }
1406          
1407          // find xyz-indices of cell that cutoffGroup is in.
# Line 1335 | Line 1428 | namespace OpenMD {
1428          for (int j = 0; j < 3; j++) {
1429            scaled[j] -= roundMe(scaled[j]);
1430            scaled[j] += 0.5;
1431 +          // Handle the special case when an object is exactly on the
1432 +          // boundary (a scaled coordinate of 1.0 is the same as
1433 +          // scaled coordinate of 0.0)
1434 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1435          }
1436          
1437          // find xyz-indices of cell that cutoffGroup is in.

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