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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 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs.
Revision 1586 by gezelter, Tue Jun 21 06:34:35 2011 UTC

# Line 59 | Line 59 | namespace OpenMD {
59      nLocal_ = snap_->getNumberOfAtoms();
60  
61      nGroups_ = info_->getNLocalCutoffGroups();
62 –    cerr << "in dId, nGroups = " << nGroups_ << "\n";
62      // gather the information for atomtype IDs (atids):
63 <    identsLocal = info_->getIdentArray();
63 >    idents = info_->getIdentArray();
64      AtomLocalToGlobal = info_->getGlobalAtomIndices();
65      cgLocalToGlobal = info_->getGlobalGroupIndices();
66      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67 <    vector<RealType> massFactorsLocal = info_->getMassFactors();
67 >
68 >    massFactors = info_->getMassFactors();
69 >
70      PairList excludes = info_->getExcludedInteractions();
71      PairList oneTwo = info_->getOneTwoInteractions();
72      PairList oneThree = info_->getOneThreeInteractions();
# Line 108 | Line 109 | namespace OpenMD {
109      identsRow.resize(nAtomsInRow_);
110      identsCol.resize(nAtomsInCol_);
111      
112 <    AtomCommIntRow->gather(identsLocal, identsRow);
113 <    AtomCommIntColumn->gather(identsLocal, identsCol);
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
115      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
# Line 117 | Line 118 | namespace OpenMD {
118      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
120  
121 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
122 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
121 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
122 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
123  
124      groupListRow_.clear();
125      groupListRow_.resize(nGroupsInRow_);
# Line 225 | Line 226 | namespace OpenMD {
226    }
227    
228    void ForceMatrixDecomposition::createGtypeCutoffMap() {
229 <
229 >    
230      RealType tol = 1e-6;
231      RealType rc;
232      int atid;
233      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
234      vector<RealType> atypeCutoff;
235      atypeCutoff.resize( atypes.size() );
236 <
236 >      
237      for (set<AtomType*>::iterator at = atypes.begin();
238           at != atypes.end(); ++at){
238 –      rc = interactionMan_->getSuggestedCutoffRadius(*at);
239        atid = (*at)->getIdent();
240 <      atypeCutoff[atid] = rc;
240 >
241 >      if (userChoseCutoff_)
242 >        atypeCutoff[atid] = userCutoff_;
243 >      else
244 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
245      }
246  
247      vector<RealType> gTypeCutoffs;
# Line 300 | Line 304 | namespace OpenMD {
304      vector<RealType> groupCutoff(nGroups_, 0.0);
305      groupToGtype.resize(nGroups_);
306  
303 –    cerr << "nGroups = " << nGroups_ << "\n";
307      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
308  
309        groupCutoff[cg1] = 0.0;
# Line 309 | Line 312 | namespace OpenMD {
312        for (vector<int>::iterator ia = atomList.begin();
313             ia != atomList.end(); ++ia) {            
314          int atom1 = (*ia);
315 <        atid = identsLocal[atom1];
315 >        atid = idents[atom1];
316          if (atypeCutoff[atid] > groupCutoff[cg1]) {
317            groupCutoff[cg1] = atypeCutoff[atid];
318          }
# Line 329 | Line 332 | namespace OpenMD {
332      }
333   #endif
334  
332 –    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
335      // Now we find the maximum group cutoff value present in the simulation
336  
337      RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
# Line 378 | Line 380 | namespace OpenMD {
380            if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
381              sprintf(painCave.errMsg,
382                      "ForceMatrixDecomposition::createGtypeCutoffMap "
383 <                    "user-specified rCut does not match computed group Cutoff\n");
383 >                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
384              painCave.severity = OPENMD_ERROR;
385              painCave.isFatal = 1;
386              simError();            
# Line 410 | Line 412 | namespace OpenMD {
412    }
413  
414    void ForceMatrixDecomposition::zeroWorkArrays() {
415 +    pairwisePot = 0.0;
416 +    embeddingPot = 0.0;
417  
414 –    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
415 –      longRangePot_[j] = 0.0;
416 –    }
417 –
418   #ifdef IS_MPI
419      if (storageLayout_ & DataStorage::dslForce) {
420        fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
# Line 430 | Line 430 | namespace OpenMD {
430           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
431  
432      fill(pot_col.begin(), pot_col.end(),
433 <         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
434 <    
435 <    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
433 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
434  
435      if (storageLayout_ & DataStorage::dslParticlePot) {    
436        fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
# Line 456 | Line 454 | namespace OpenMD {
454             atomColData.functionalDerivative.end(), 0.0);
455      }
456  
457 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
458 +      fill(atomRowData.skippedCharge.begin(), atomRowData.skippedCharge.end(), 0.0);
459 +      fill(atomColData.skippedCharge.begin(), atomColData.skippedCharge.end(), 0.0);
460 +    }
461 +
462   #else
463      
464      if (storageLayout_ & DataStorage::dslParticlePot) {      
# Line 475 | Line 478 | namespace OpenMD {
478        fill(snap_->atomData.functionalDerivative.begin(),
479             snap_->atomData.functionalDerivative.end(), 0.0);
480      }
481 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
482 +      fill(snap_->atomData.skippedCharge.begin(),
483 +           snap_->atomData.skippedCharge.end(), 0.0);
484 +    }
485   #endif
486      
487    }
# Line 606 | Line 613 | namespace OpenMD {
613      AtomCommPotRow->scatter(pot_row, pot_temp);
614  
615      for (int ii = 0;  ii < pot_temp.size(); ii++ )
616 <      pot_local += pot_temp[ii];
616 >      pairwisePot += pot_temp[ii];
617      
618      fill(pot_temp.begin(), pot_temp.end(),
619           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
# Line 614 | Line 621 | namespace OpenMD {
621      AtomCommPotColumn->scatter(pot_col, pot_temp);    
622      
623      for (int ii = 0;  ii < pot_temp.size(); ii++ )
624 <      pot_local += pot_temp[ii];
618 <    
624 >      pairwisePot += pot_temp[ii];    
625   #endif
626 +
627    }
628  
629    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 691 | Line 698 | namespace OpenMD {
698   #ifdef IS_MPI
699      return massFactorsRow[atom1];
700   #else
701 <    return massFactorsLocal[atom1];
701 >    return massFactors[atom1];
702   #endif
703    }
704  
# Line 699 | Line 706 | namespace OpenMD {
706   #ifdef IS_MPI
707      return massFactorsCol[atom2];
708   #else
709 <    return massFactorsLocal[atom2];
709 >    return massFactors[atom2];
710   #endif
711  
712    }
# Line 754 | Line 761 | namespace OpenMD {
761      for (vector<int>::iterator i = skipsForAtom[atom1].begin();
762           i != skipsForAtom[atom1].end(); ++i) {
763        if ( (*i) == unique_id_2 ) return true;
764 <    }    
764 >    }
765  
766 +    return false;
767    }
768  
769  
# Line 776 | Line 784 | namespace OpenMD {
784    }
785  
786      // filling interaction blocks with pointers
787 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
788 <    InteractionData idat;
781 <
787 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
788 >                                                     int atom1, int atom2) {    
789   #ifdef IS_MPI
790      
791      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
792                               ff_->getAtomType(identsCol[atom2]) );
786 –
793      
794      if (storageLayout_ & DataStorage::dslAmat) {
795        idat.A1 = &(atomRowData.aMat[atom1]);
# Line 822 | Line 828 | namespace OpenMD {
828  
829   #else
830  
831 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
832 <                             ff_->getAtomType(identsLocal[atom2]) );
831 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
832 >                             ff_->getAtomType(idents[atom2]) );
833  
834      if (storageLayout_ & DataStorage::dslAmat) {
835        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 840 | Line 846 | namespace OpenMD {
846        idat.t2 = &(snap_->atomData.torque[atom2]);
847      }
848  
849 <    if (storageLayout_ & DataStorage::dslDensity) {
849 >    if (storageLayout_ & DataStorage::dslDensity) {    
850        idat.rho1 = &(snap_->atomData.density[atom1]);
851        idat.rho2 = &(snap_->atomData.density[atom2]);
852      }
# Line 861 | Line 867 | namespace OpenMD {
867      }
868  
869   #endif
864 –    return idat;
870    }
871  
872    
873 <  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
873 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
874   #ifdef IS_MPI
875      pot_row[atom1] += 0.5 *  *(idat.pot);
876      pot_col[atom2] += 0.5 *  *(idat.pot);
# Line 873 | Line 878 | namespace OpenMD {
878      atomRowData.force[atom1] += *(idat.f1);
879      atomColData.force[atom2] -= *(idat.f1);
880   #else
881 <    longRangePot_ += *(idat.pot);
882 <    
881 >    pairwisePot += *(idat.pot);
882 >
883      snap_->atomData.force[atom1] += *(idat.f1);
884      snap_->atomData.force[atom2] -= *(idat.f1);
885   #endif
886 <
886 >    
887    }
888  
889  
890 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
891 <
887 <    InteractionData idat;
890 >  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
891 >                                              int atom1, int atom2) {
892   #ifdef IS_MPI
893      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
894                               ff_->getAtomType(identsCol[atom2]) );
# Line 893 | Line 897 | namespace OpenMD {
897        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
898        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
899      }
900 +
901      if (storageLayout_ & DataStorage::dslTorque) {
902        idat.t1 = &(atomRowData.torque[atom1]);
903        idat.t2 = &(atomColData.torque[atom2]);
904      }
905 +
906 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
907 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
908 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
909 +    }
910   #else
911 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
912 <                             ff_->getAtomType(identsLocal[atom2]) );
911 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
912 >                             ff_->getAtomType(idents[atom2]) );
913  
914      if (storageLayout_ & DataStorage::dslElectroFrame) {
915        idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
916        idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
917      }
918 +
919      if (storageLayout_ & DataStorage::dslTorque) {
920        idat.t1 = &(snap_->atomData.torque[atom1]);
921        idat.t2 = &(snap_->atomData.torque[atom2]);
922      }
923 +
924 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
925 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
926 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
927 +    }
928   #endif    
929    }
930  
931 +
932 +  void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {    
933 + #ifdef IS_MPI
934 +    pot_row[atom1] += 0.5 *  *(idat.pot);
935 +    pot_col[atom2] += 0.5 *  *(idat.pot);
936 + #else
937 +    pairwisePot += *(idat.pot);  
938 + #endif
939 +
940 +  }
941 +
942 +
943    /*
944     * buildNeighborList
945     *
# Line 957 | Line 985 | namespace OpenMD {
985   #ifdef IS_MPI
986      for (int i = 0; i < nGroupsInRow_; i++) {
987        rs = cgRowData.position[i];
988 +
989        // scaled positions relative to the box vectors
990        scaled = invHmat * rs;
991 +
992        // wrap the vector back into the unit box by subtracting integer box
993        // numbers
994 <      for (int j = 0; j < 3; j++)
994 >      for (int j = 0; j < 3; j++) {
995          scaled[j] -= roundMe(scaled[j]);
996 +        scaled[j] += 0.5;
997 +      }
998      
999        // find xyz-indices of cell that cutoffGroup is in.
1000        whichCell.x() = nCells_.x() * scaled.x();
# Line 971 | Line 1003 | namespace OpenMD {
1003  
1004        // find single index of this cell:
1005        cellIndex = Vlinear(whichCell, nCells_);
1006 +
1007        // add this cutoff group to the list of groups in this cell;
1008        cellListRow_[cellIndex].push_back(i);
1009      }
1010  
1011      for (int i = 0; i < nGroupsInCol_; i++) {
1012        rs = cgColData.position[i];
1013 +
1014        // scaled positions relative to the box vectors
1015        scaled = invHmat * rs;
1016 +
1017        // wrap the vector back into the unit box by subtracting integer box
1018        // numbers
1019 <      for (int j = 0; j < 3; j++)
1019 >      for (int j = 0; j < 3; j++) {
1020          scaled[j] -= roundMe(scaled[j]);
1021 +        scaled[j] += 0.5;
1022 +      }
1023  
1024        // find xyz-indices of cell that cutoffGroup is in.
1025        whichCell.x() = nCells_.x() * scaled.x();
# Line 991 | Line 1028 | namespace OpenMD {
1028  
1029        // find single index of this cell:
1030        cellIndex = Vlinear(whichCell, nCells_);
1031 +
1032        // add this cutoff group to the list of groups in this cell;
1033        cellListCol_[cellIndex].push_back(i);
1034      }
1035   #else
1036      for (int i = 0; i < nGroups_; i++) {
1037        rs = snap_->cgData.position[i];
1038 +
1039        // scaled positions relative to the box vectors
1040        scaled = invHmat * rs;
1041 +
1042        // wrap the vector back into the unit box by subtracting integer box
1043        // numbers
1044 <      for (int j = 0; j < 3; j++)
1044 >      for (int j = 0; j < 3; j++) {
1045          scaled[j] -= roundMe(scaled[j]);
1046 +        scaled[j] += 0.5;
1047 +      }
1048  
1049        // find xyz-indices of cell that cutoffGroup is in.
1050        whichCell.x() = nCells_.x() * scaled.x();
# Line 1010 | Line 1052 | namespace OpenMD {
1052        whichCell.z() = nCells_.z() * scaled.z();
1053  
1054        // find single index of this cell:
1055 <      cellIndex = Vlinear(whichCell, nCells_);
1055 >      cellIndex = Vlinear(whichCell, nCells_);      
1056 >
1057        // add this cutoff group to the list of groups in this cell;
1058        cellList_[cellIndex].push_back(i);
1059      }
# Line 1068 | Line 1111 | namespace OpenMD {
1111                }
1112              }
1113   #else
1114 +
1115              for (vector<int>::iterator j1 = cellList_[m1].begin();
1116                   j1 != cellList_[m1].end(); ++j1) {
1117                for (vector<int>::iterator j2 = cellList_[m2].begin();
1118                     j2 != cellList_[m2].end(); ++j2) {
1119 <                              
1119 >
1120                  // Always do this if we're in different cells or if
1121                  // we're in the same cell and the global index of the
1122                  // j2 cutoff group is less than the j1 cutoff group
# Line 1092 | Line 1136 | namespace OpenMD {
1136          }
1137        }
1138      }
1139 <
1139 >    
1140      // save the local cutoff group positions for the check that is
1141      // done on each loop:
1142      saved_CG_positions_.clear();
1143      for (int i = 0; i < nGroups_; i++)
1144        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1145 <
1145 >  
1146      return neighborList;
1147    }
1148   } //end namespace OpenMD

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