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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 1592 by gezelter, Tue Jul 12 20:33:14 2011 UTC vs.
Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC

# Line 47 | Line 47 | namespace OpenMD {
47   using namespace std;
48   namespace OpenMD {
49  
50 +  ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
51 +
52 +    // In a parallel computation, row and colum scans must visit all
53 +    // surrounding cells (not just the 14 upper triangular blocks that
54 +    // are used when the processor can see all pairs)
55 + #ifdef IS_MPI
56 +    cellOffsets_.clear();
57 +    cellOffsets_.push_back( Vector3i(-1,-1,-1) );
58 +    cellOffsets_.push_back( Vector3i( 0,-1,-1) );
59 +    cellOffsets_.push_back( Vector3i( 1,-1,-1) );                          
60 +    cellOffsets_.push_back( Vector3i(-1, 0,-1) );
61 +    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
62 +    cellOffsets_.push_back( Vector3i( 1, 0,-1) );
63 +    cellOffsets_.push_back( Vector3i(-1, 1,-1) );
64 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );      
65 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
66 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
67 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
68 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
69 +    cellOffsets_.push_back( Vector3i(-1, 0, 0) );      
70 +    cellOffsets_.push_back( Vector3i( 0, 0, 0) );
71 +    cellOffsets_.push_back( Vector3i( 1, 0, 0) );
72 +    cellOffsets_.push_back( Vector3i(-1, 1, 0) );
73 +    cellOffsets_.push_back( Vector3i( 0, 1, 0) );
74 +    cellOffsets_.push_back( Vector3i( 1, 1, 0) );
75 +    cellOffsets_.push_back( Vector3i(-1,-1, 1) );
76 +    cellOffsets_.push_back( Vector3i( 0,-1, 1) );
77 +    cellOffsets_.push_back( Vector3i( 1,-1, 1) );
78 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
79 +    cellOffsets_.push_back( Vector3i( 0, 0, 1) );
80 +    cellOffsets_.push_back( Vector3i( 1, 0, 1) );
81 +    cellOffsets_.push_back( Vector3i(-1, 1, 1) );
82 +    cellOffsets_.push_back( Vector3i( 0, 1, 1) );
83 +    cellOffsets_.push_back( Vector3i( 1, 1, 1) );
84 + #endif    
85 +  }
86 +
87 +
88    /**
89     * distributeInitialData is essentially a copy of the older fortran
90     * SimulationSetup
91     */
54 –  
92    void ForceMatrixDecomposition::distributeInitialData() {
93      snap_ = sman_->getCurrentSnapshot();
94      storageLayout_ = sman_->getStorageLayout();
# Line 74 | Line 111 | namespace OpenMD {
111  
112   #ifdef IS_MPI
113  
114 <    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
115 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
79 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
80 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
81 <    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
114 >    MPI::Intracomm row = rowComm.getComm();
115 >    MPI::Intracomm col = colComm.getComm();
116  
117 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
118 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
119 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
120 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
121 <    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
117 >    AtomPlanIntRow = new Plan<int>(row, nLocal_);
118 >    AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
119 >    AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
120 >    AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
121 >    AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
122  
123 <    cgCommIntRow = new Communicator<Row,int>(nGroups_);
124 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
125 <    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
126 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
123 >    AtomPlanIntColumn = new Plan<int>(col, nLocal_);
124 >    AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
125 >    AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
126 >    AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
127 >    AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
128  
129 <    nAtomsInRow_ = AtomCommIntRow->getSize();
130 <    nAtomsInCol_ = AtomCommIntColumn->getSize();
131 <    nGroupsInRow_ = cgCommIntRow->getSize();
132 <    nGroupsInCol_ = cgCommIntColumn->getSize();
129 >    cgPlanIntRow = new Plan<int>(row, nGroups_);
130 >    cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
131 >    cgPlanIntColumn = new Plan<int>(col, nGroups_);
132 >    cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
133  
134 +    nAtomsInRow_ = AtomPlanIntRow->getSize();
135 +    nAtomsInCol_ = AtomPlanIntColumn->getSize();
136 +    nGroupsInRow_ = cgPlanIntRow->getSize();
137 +    nGroupsInCol_ = cgPlanIntColumn->getSize();
138 +
139      // Modify the data storage objects with the correct layouts and sizes:
140      atomRowData.resize(nAtomsInRow_);
141      atomRowData.setStorageLayout(storageLayout_);
# Line 109 | Line 149 | namespace OpenMD {
149      identsRow.resize(nAtomsInRow_);
150      identsCol.resize(nAtomsInCol_);
151      
152 <    AtomCommIntRow->gather(idents, identsRow);
153 <    AtomCommIntColumn->gather(idents, identsCol);
152 >    AtomPlanIntRow->gather(idents, identsRow);
153 >    AtomPlanIntColumn->gather(idents, identsCol);
154      
155      // allocate memory for the parallel objects
156      atypesRow.resize(nAtomsInRow_);
# Line 126 | Line 166 | namespace OpenMD {
166  
167      AtomRowToGlobal.resize(nAtomsInRow_);
168      AtomColToGlobal.resize(nAtomsInCol_);
169 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
170 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
171 <    
169 >    AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
170 >    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
171 >
172      cgRowToGlobal.resize(nGroupsInRow_);
173      cgColToGlobal.resize(nGroupsInCol_);
174 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
175 <    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
174 >    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
175 >    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
176  
177      massFactorsRow.resize(nAtomsInRow_);
178      massFactorsCol.resize(nAtomsInCol_);
179 <    AtomCommRealRow->gather(massFactors, massFactorsRow);
180 <    AtomCommRealColumn->gather(massFactors, massFactorsCol);
179 >    AtomPlanRealRow->gather(massFactors, massFactorsRow);
180 >    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
181  
182      groupListRow_.clear();
183      groupListRow_.resize(nGroupsInRow_);
# Line 193 | Line 233 | namespace OpenMD {
233        }      
234      }
235  
236 < #endif
197 <
198 <    // allocate memory for the parallel objects
199 <    atypesLocal.resize(nLocal_);
200 <
201 <    for (int i = 0; i < nLocal_; i++)
202 <      atypesLocal[i] = ff_->getAtomType(idents[i]);
203 <
204 <    groupList_.clear();
205 <    groupList_.resize(nGroups_);
206 <    for (int i = 0; i < nGroups_; i++) {
207 <      int gid = cgLocalToGlobal[i];
208 <      for (int j = 0; j < nLocal_; j++) {
209 <        int aid = AtomLocalToGlobal[j];
210 <        if (globalGroupMembership[aid] == gid) {
211 <          groupList_[i].push_back(j);
212 <        }
213 <      }      
214 <    }
215 <
236 > #else
237      excludesForAtom.clear();
238      excludesForAtom.resize(nLocal_);
239      toposForAtom.clear();
# Line 226 | Line 247 | namespace OpenMD {
247        for (int j = 0; j < nLocal_; j++) {
248          int jglob = AtomLocalToGlobal[j];
249  
250 <        if (excludes->hasPair(iglob, jglob))
250 >        if (excludes->hasPair(iglob, jglob))          
251            excludesForAtom[i].push_back(j);              
252          
253 +        
254          if (oneTwo->hasPair(iglob, jglob)) {
255            toposForAtom[i].push_back(j);
256            topoDist[i].push_back(1);
# Line 245 | Line 267 | namespace OpenMD {
267          }
268        }      
269      }
270 <    
270 > #endif
271 >
272 >    // allocate memory for the parallel objects
273 >    atypesLocal.resize(nLocal_);
274 >
275 >    for (int i = 0; i < nLocal_; i++)
276 >      atypesLocal[i] = ff_->getAtomType(idents[i]);
277 >
278 >    groupList_.clear();
279 >    groupList_.resize(nGroups_);
280 >    for (int i = 0; i < nGroups_; i++) {
281 >      int gid = cgLocalToGlobal[i];
282 >      for (int j = 0; j < nLocal_; j++) {
283 >        int aid = AtomLocalToGlobal[j];
284 >        if (globalGroupMembership[aid] == gid) {
285 >          groupList_[i].push_back(j);
286 >        }
287 >      }      
288 >    }
289 >
290 >
291      createGtypeCutoffMap();
292  
293    }
# Line 517 | Line 559 | namespace OpenMD {
559   #ifdef IS_MPI
560      
561      // gather up the atomic positions
562 <    AtomCommVectorRow->gather(snap_->atomData.position,
562 >    AtomPlanVectorRow->gather(snap_->atomData.position,
563                                atomRowData.position);
564 <    AtomCommVectorColumn->gather(snap_->atomData.position,
564 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
565                                   atomColData.position);
566      
567      // gather up the cutoff group positions
568 <    cgCommVectorRow->gather(snap_->cgData.position,
568 >
569 >    cgPlanVectorRow->gather(snap_->cgData.position,
570                              cgRowData.position);
571 <    cgCommVectorColumn->gather(snap_->cgData.position,
571 >
572 >    cgPlanVectorColumn->gather(snap_->cgData.position,
573                                 cgColData.position);
574 +
575      
576      // if needed, gather the atomic rotation matrices
577      if (storageLayout_ & DataStorage::dslAmat) {
578 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
578 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
579                                  atomRowData.aMat);
580 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
580 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
581                                     atomColData.aMat);
582      }
583      
584      // if needed, gather the atomic eletrostatic frames
585      if (storageLayout_ & DataStorage::dslElectroFrame) {
586 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
586 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
587                                  atomRowData.electroFrame);
588 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
588 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
589                                     atomColData.electroFrame);
590      }
591  
# Line 557 | Line 602 | namespace OpenMD {
602      
603      if (storageLayout_ & DataStorage::dslDensity) {
604        
605 <      AtomCommRealRow->scatter(atomRowData.density,
605 >      AtomPlanRealRow->scatter(atomRowData.density,
606                                 snap_->atomData.density);
607        
608        int n = snap_->atomData.density.size();
609        vector<RealType> rho_tmp(n, 0.0);
610 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
610 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
611        for (int i = 0; i < n; i++)
612          snap_->atomData.density[i] += rho_tmp[i];
613      }
# Line 578 | Line 623 | namespace OpenMD {
623      storageLayout_ = sman_->getStorageLayout();
624   #ifdef IS_MPI
625      if (storageLayout_ & DataStorage::dslFunctional) {
626 <      AtomCommRealRow->gather(snap_->atomData.functional,
626 >      AtomPlanRealRow->gather(snap_->atomData.functional,
627                                atomRowData.functional);
628 <      AtomCommRealColumn->gather(snap_->atomData.functional,
628 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
629                                   atomColData.functional);
630      }
631      
632      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
633 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
633 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
634                                atomRowData.functionalDerivative);
635 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
635 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
636                                   atomColData.functionalDerivative);
637      }
638   #endif
# Line 601 | Line 646 | namespace OpenMD {
646      int n = snap_->atomData.force.size();
647      vector<Vector3d> frc_tmp(n, V3Zero);
648      
649 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
649 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
650      for (int i = 0; i < n; i++) {
651        snap_->atomData.force[i] += frc_tmp[i];
652        frc_tmp[i] = 0.0;
653      }
654      
655 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
656 <    for (int i = 0; i < n; i++)
655 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
656 >    for (int i = 0; i < n; i++) {
657        snap_->atomData.force[i] += frc_tmp[i];
658 +    }
659          
660      if (storageLayout_ & DataStorage::dslTorque) {
661  
662        int nt = snap_->atomData.torque.size();
663        vector<Vector3d> trq_tmp(nt, V3Zero);
664  
665 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
665 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
666        for (int i = 0; i < nt; i++) {
667          snap_->atomData.torque[i] += trq_tmp[i];
668          trq_tmp[i] = 0.0;
669        }
670        
671 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
671 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
672        for (int i = 0; i < nt; i++)
673          snap_->atomData.torque[i] += trq_tmp[i];
674      }
# Line 632 | Line 678 | namespace OpenMD {
678        int ns = snap_->atomData.skippedCharge.size();
679        vector<RealType> skch_tmp(ns, 0.0);
680  
681 <      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
681 >      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
682        for (int i = 0; i < ns; i++) {
683          snap_->atomData.skippedCharge[i] += skch_tmp[i];
684          skch_tmp[i] = 0.0;
685        }
686        
687 <      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
688 <      for (int i = 0; i < ns; i++)
687 >      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
688 >      for (int i = 0; i < ns; i++)
689          snap_->atomData.skippedCharge[i] += skch_tmp[i];
690 +            
691      }
692      
693      nLocal_ = snap_->getNumberOfAtoms();
# Line 650 | Line 697 | namespace OpenMD {
697  
698      // scatter/gather pot_row into the members of my column
699            
700 <    AtomCommPotRow->scatter(pot_row, pot_temp);
700 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
701  
702      for (int ii = 0;  ii < pot_temp.size(); ii++ )
703        pairwisePot += pot_temp[ii];
# Line 658 | Line 705 | namespace OpenMD {
705      fill(pot_temp.begin(), pot_temp.end(),
706           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
707        
708 <    AtomCommPotColumn->scatter(pot_col, pot_temp);    
708 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
709      
710      for (int ii = 0;  ii < pot_temp.size(); ii++ )
711        pairwisePot += pot_temp[ii];    
712 +    
713 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
714 +      RealType ploc1 = pairwisePot[ii];
715 +      RealType ploc2 = 0.0;
716 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
717 +      pairwisePot[ii] = ploc2;
718 +    }
719 +
720 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
721 +      RealType ploc1 = embeddingPot[ii];
722 +      RealType ploc2 = 0.0;
723 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
724 +      embeddingPot[ii] = ploc2;
725 +    }
726 +
727   #endif
728  
729    }
# Line 774 | Line 836 | namespace OpenMD {
836     */
837    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
838      int unique_id_1, unique_id_2;
839 <
839 >    
840   #ifdef IS_MPI
841      // in MPI, we have to look up the unique IDs for each atom
842      unique_id_1 = AtomRowToGlobal[atom1];
# Line 803 | Line 865 | namespace OpenMD {
865     * field) must still be handled for these pairs.
866     */
867    bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
868 <    int unique_id_2;
868 >
869 >    // excludesForAtom was constructed to use row/column indices in the MPI
870 >    // version, and to use local IDs in the non-MPI version:
871      
808 – #ifdef IS_MPI
809 –    // in MPI, we have to look up the unique IDs for the row atom.
810 –    unique_id_2 = AtomColToGlobal[atom2];
811 – #else
812 –    // in the normal loop, the atom numbers are unique
813 –    unique_id_2 = atom2;
814 – #endif
815 –    
872      for (vector<int>::iterator i = excludesForAtom[atom1].begin();
873           i != excludesForAtom[atom1].end(); ++i) {
874 <      if ( (*i) == unique_id_2 ) return true;
874 >      if ( (*i) == atom2 )  return true;
875      }
876  
877      return false;
# Line 1031 | Line 1087 | namespace OpenMD {
1087          // add this cutoff group to the list of groups in this cell;
1088          cellListRow_[cellIndex].push_back(i);
1089        }
1034 –      
1090        for (int i = 0; i < nGroupsInCol_; i++) {
1091          rs = cgColData.position[i];
1092          
# Line 1056 | Line 1111 | namespace OpenMD {
1111          // add this cutoff group to the list of groups in this cell;
1112          cellListCol_[cellIndex].push_back(i);
1113        }
1114 +    
1115   #else
1116        for (int i = 0; i < nGroups_; i++) {
1117          rs = snap_->cgData.position[i];
# Line 1076 | Line 1132 | namespace OpenMD {
1132          whichCell.z() = nCells_.z() * scaled.z();
1133          
1134          // find single index of this cell:
1135 <        cellIndex = Vlinear(whichCell, nCells_);      
1135 >        cellIndex = Vlinear(whichCell, nCells_);
1136          
1137          // add this cutoff group to the list of groups in this cell;
1138          cellList_[cellIndex].push_back(i);
1139        }
1140 +
1141   #endif
1142  
1143        for (int m1z = 0; m1z < nCells_.z(); m1z++) {
# Line 1093 | Line 1150 | namespace OpenMD {
1150                   os != cellOffsets_.end(); ++os) {
1151                
1152                Vector3i m2v = m1v + (*os);
1153 <              
1153 >            
1154 >
1155                if (m2v.x() >= nCells_.x()) {
1156                  m2v.x() = 0;          
1157                } else if (m2v.x() < 0) {
# Line 1111 | Line 1169 | namespace OpenMD {
1169                } else if (m2v.z() < 0) {
1170                  m2v.z() = nCells_.z() - 1;
1171                }
1172 <              
1172 >
1173                int m2 = Vlinear (m2v, nCells_);
1174                
1175   #ifdef IS_MPI
# Line 1120 | Line 1178 | namespace OpenMD {
1178                  for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1179                       j2 != cellListCol_[m2].end(); ++j2) {
1180                    
1181 <                  // Always do this if we're in different cells or if
1182 <                  // we're in the same cell and the global index of the
1183 <                  // j2 cutoff group is less than the j1 cutoff group
1184 <                  
1185 <                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1186 <                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1187 <                    snap_->wrapVector(dr);
1188 <                    cuts = getGroupCutoffs( (*j1), (*j2) );
1189 <                    if (dr.lengthSquare() < cuts.third) {
1132 <                      neighborList.push_back(make_pair((*j1), (*j2)));
1133 <                    }
1134 <                  }
1181 >                  // In parallel, we need to visit *all* pairs of row
1182 >                  // & column indicies and will divide labor in the
1183 >                  // force evaluation later.
1184 >                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1185 >                  snap_->wrapVector(dr);
1186 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1187 >                  if (dr.lengthSquare() < cuts.third) {
1188 >                    neighborList.push_back(make_pair((*j1), (*j2)));
1189 >                  }                  
1190                  }
1191                }
1192   #else

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