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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1721 by gezelter, Thu May 24 14:17:42 2012 UTC vs.
Revision 1772 by gezelter, Tue Jul 31 14:00:05 2012 UTC

# Line 95 | Line 95 | namespace OpenMD {
95      storageLayout_ = sman_->getStorageLayout();
96      ff_ = info_->getForceField();
97      nLocal_ = snap_->getNumberOfAtoms();
98 <    
98 >  
99      nGroups_ = info_->getNLocalCutoffGroups();
100      // gather the information for atomtype IDs (atids):
101      idents = info_->getIdentArray();
# Line 109 | Line 109 | namespace OpenMD {
109      PairList* oneTwo = info_->getOneTwoInteractions();
110      PairList* oneThree = info_->getOneThreeInteractions();
111      PairList* oneFour = info_->getOneFourInteractions();
112 <
112 >    
113 >    if (needVelocities_)
114 >      snap_->cgData.setStorageLayout(DataStorage::dslPosition |
115 >                                     DataStorage::dslVelocity);
116 >    else
117 >      snap_->cgData.setStorageLayout(DataStorage::dslPosition);
118 >    
119   #ifdef IS_MPI
120  
121      MPI::Intracomm row = rowComm.getComm();
# Line 145 | Line 151 | namespace OpenMD {
151      cgRowData.resize(nGroupsInRow_);
152      cgRowData.setStorageLayout(DataStorage::dslPosition);
153      cgColData.resize(nGroupsInCol_);
154 <    cgColData.setStorageLayout(DataStorage::dslPosition);
155 <        
154 >    if (needVelocities_)
155 >      // we only need column velocities if we need them.
156 >      cgColData.setStorageLayout(DataStorage::dslPosition |
157 >                                 DataStorage::dslVelocity);
158 >    else    
159 >      cgColData.setStorageLayout(DataStorage::dslPosition);
160 >      
161      identsRow.resize(nAtomsInRow_);
162      identsCol.resize(nAtomsInCol_);
163      
# Line 165 | Line 176 | namespace OpenMD {
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_);
184      AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
# Line 296 | Line 310 | namespace OpenMD {
310      
311      RealType tol = 1e-6;
312      largestRcut_ = 0.0;
299 –    RealType rc;
313      int atid;
314      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315      
# Line 381 | 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 406 | 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 450 | Line 463 | namespace OpenMD {
463      }
464    }
465  
453 –
466    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467      int i, j;  
468   #ifdef IS_MPI
# Line 464 | 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 474 | 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 492 | 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 600 | Line 620 | namespace OpenMD {
620      cgPlanVectorColumn->gather(snap_->cgData.position,
621                                 cgColData.position);
622  
623 +
624 +
625 +    if (needVelocities_) {
626 +      // gather up the atomic velocities
627 +      AtomPlanVectorColumn->gather(snap_->atomData.velocity,
628 +                                   atomColData.velocity);
629 +      
630 +      cgPlanVectorColumn->gather(snap_->cgData.velocity,
631 +                                 cgColData.velocity);
632 +    }
633 +
634      
635      // if needed, gather the atomic rotation matrices
636      if (storageLayout_ & DataStorage::dslAmat) {
# Line 759 | 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 <    
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
809 >      // embedding contribution is added in each of the low level
810 >      // non-bonded routines.  In single processor, this is done in
811 >      // unpackInteractionData, not in collectData.
812 >      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
813 >        for (int i = 0; i < nLocal_; i++) {
814 >          // factor of two is because the total potential terms are divided
815 >          // by 2 in parallel due to row/ column scatter      
816 >          snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
817 >        }
818 >      }
819 >    }
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
838 +      // non-bonded routines.  In single processor, this is done in
839 +      // unpackInteractionData, not in collectData.
840 +      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
841 +        for (int i = 0; i < nLocal_; i++) {
842 +          // factor of two is because the total potential terms are divided
843 +          // by 2 in parallel due to row/ column scatter      
844 +          snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
845 +        }
846 +      }
847 +    }
848      
849 +    if (storageLayout_ & DataStorage::dslParticlePot) {
850 +      int npp = snap_->atomData.particlePot.size();
851 +      vector<RealType> ppot_temp(npp, 0.0);
852 +
853 +      // This is the direct or embedding contribution to the particle
854 +      // pot.
855 +      
856 +      AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
857 +      for (int i = 0; i < npp; i++) {
858 +        snap_->atomData.particlePot[i] += ppot_temp[i];
859 +      }
860 +
861 +      fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
862 +      
863 +      AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
864 +      for (int i = 0; i < npp; i++) {
865 +        snap_->atomData.particlePot[i] += ppot_temp[i];
866 +      }
867 +    }
868 +
869      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
870        RealType ploc1 = pairwisePot[ii];
871        RealType ploc2 = 0.0;
# Line 783 | 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  
883 +    // Here be dragons.
884 +    MPI::Intracomm col = colComm.getComm();
885 +
886 +    col.Allreduce(MPI::IN_PLACE,
887 +                  &snap_->frameData.conductiveHeatFlux[0], 3,
888 +                  MPI::REALTYPE, MPI::SUM);
889 +
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 833 | Line 959 | namespace OpenMD {
959      return d;    
960    }
961  
962 +  Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
963 + #ifdef IS_MPI
964 +    return cgColData.velocity[cg2];
965 + #else
966 +    return snap_->cgData.velocity[cg2];
967 + #endif
968 +  }
969  
970 +  Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
971 + #ifdef IS_MPI
972 +    return atomColData.velocity[atom2];
973 + #else
974 +    return snap_->atomData.velocity[atom2];
975 + #endif
976 +  }
977 +
978 +
979    Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
980  
981      Vector3d d;
# Line 899 | 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 920 | 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 1022 | Line 1174 | namespace OpenMD {
1174  
1175   #else
1176      
1025 –
1026 –    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1027 –    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1028 –    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1029 –
1177      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1031 –    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1032 –    //                         ff_->getAtomType(idents[atom2]) );
1178  
1179      if (storageLayout_ & DataStorage::dslAmat) {
1180        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 1084 | Line 1229 | namespace OpenMD {
1229   #ifdef IS_MPI
1230      pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1231      pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1232 +    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1233 +    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1234  
1235      atomRowData.force[atom1] += *(idat.f1);
1236      atomColData.force[atom2] -= *(idat.f1);
1237  
1238      if (storageLayout_ & DataStorage::dslFlucQForce) {              
1239 <      atomRowData.flucQFrc[atom1] += *(idat.dVdFQ1);
1240 <      atomColData.flucQFrc[atom2] += *(idat.dVdFQ2);
1239 >      atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1240 >      atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1241      }
1242  
1243      if (storageLayout_ & DataStorage::dslElectricField) {              
# Line 1098 | Line 1245 | namespace OpenMD {
1245        atomColData.electricField[atom2] += *(idat.eField2);
1246      }
1247  
1101 –    // should particle pot be done here also?
1248   #else
1249      pairwisePot += *(idat.pot);
1250 +    excludedPot += *(idat.excludedPot);
1251  
1252      snap_->atomData.force[atom1] += *(idat.f1);
1253      snap_->atomData.force[atom2] -= *(idat.f1);
1254  
1255      if (idat.doParticlePot) {
1256 +      // This is the pairwise contribution to the particle pot.  The
1257 +      // embedding contribution is added in each of the low level
1258 +      // non-bonded routines.  In parallel, this calculation is done
1259 +      // in collectData, not in unpackInteractionData.
1260        snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1261 <      snap_->atomData.particlePot[atom2] -= *(idat.vpair) * *(idat.sw);
1261 >      snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1262      }
1263      
1264      if (storageLayout_ & DataStorage::dslFlucQForce) {              
1265 <      snap_->atomData.flucQFrc[atom1] += *(idat.dVdFQ1);
1265 >      snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1266        snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1267      }
1268  
# Line 1188 | Line 1339 | namespace OpenMD {
1339          for (int j = 0; j < 3; j++) {
1340            scaled[j] -= roundMe(scaled[j]);
1341            scaled[j] += 0.5;
1342 +          // Handle the special case when an object is exactly on the
1343 +          // boundary (a scaled coordinate of 1.0 is the same as
1344 +          // scaled coordinate of 0.0)
1345 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1346          }
1347          
1348          // find xyz-indices of cell that cutoffGroup is in.
# Line 1212 | Line 1367 | namespace OpenMD {
1367          for (int j = 0; j < 3; j++) {
1368            scaled[j] -= roundMe(scaled[j]);
1369            scaled[j] += 0.5;
1370 +          // Handle the special case when an object is exactly on the
1371 +          // boundary (a scaled coordinate of 1.0 is the same as
1372 +          // scaled coordinate of 0.0)
1373 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1374          }
1375          
1376          // find xyz-indices of cell that cutoffGroup is in.
# Line 1238 | Line 1397 | namespace OpenMD {
1397          for (int j = 0; j < 3; j++) {
1398            scaled[j] -= roundMe(scaled[j]);
1399            scaled[j] += 0.5;
1400 +          // Handle the special case when an object is exactly on the
1401 +          // boundary (a scaled coordinate of 1.0 is the same as
1402 +          // scaled coordinate of 0.0)
1403 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1404          }
1405          
1406          // find xyz-indices of cell that cutoffGroup is in.

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