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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 1593 by gezelter, Fri Jul 15 21:35:14 2011 UTC vs.
Revision 1612 by gezelter, Fri Aug 12 19:59:56 2011 UTC

# Line 53 | Line 53 | namespace OpenMD {
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_.push_back( Vector3i(-1, 0, 0) );
57 <    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
58 <    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
59 <    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
60 <    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
61 <    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
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) );
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) );
66 –    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67 –    cellOffsets_.push_back( Vector3i( 0, 1,-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  
# Line 154 | Line 169 | namespace OpenMD {
169      AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
170      AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
171  
157 –    cerr << "Atoms in Local:\n";
158 –    for (int i = 0; i < AtomLocalToGlobal.size(); i++) {
159 –      cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
160 –    }
161 –    cerr << "Atoms in Row:\n";
162 –    for (int i = 0; i < AtomRowToGlobal.size(); i++) {
163 –      cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
164 –    }
165 –    cerr << "Atoms in Col:\n";
166 –    for (int i = 0; i < AtomColToGlobal.size(); i++) {
167 –      cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
168 –    }
169 –
172      cgRowToGlobal.resize(nGroupsInRow_);
173      cgColToGlobal.resize(nGroupsInCol_);
174      cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
175      cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
176  
175 –    cerr << "Gruops in Local:\n";
176 –    for (int i = 0; i < cgLocalToGlobal.size(); i++) {
177 –      cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
178 –    }
179 –    cerr << "Groups in Row:\n";
180 –    for (int i = 0; i < cgRowToGlobal.size(); i++) {
181 –      cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
182 –    }
183 –    cerr << "Groups in Col:\n";
184 –    for (int i = 0; i < cgColToGlobal.size(); i++) {
185 –      cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
186 –    }
187 –
188 –
177      massFactorsRow.resize(nAtomsInRow_);
178      massFactorsCol.resize(nAtomsInCol_);
179      AtomPlanRealRow->gather(massFactors, massFactorsRow);
# Line 576 | Line 564 | namespace OpenMD {
564      
565      // gather up the cutoff group positions
566  
579 –    cerr  << "before gather\n";
580 –    for (int i = 0; i < snap_->cgData.position.size(); i++) {
581 –      cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
582 –    }
583 –
567      cgPlanVectorRow->gather(snap_->cgData.position,
568                              cgRowData.position);
569  
587 –    cerr  << "after gather\n";
588 –    for (int i = 0; i < cgRowData.position.size(); i++) {
589 –      cerr << "cgRpos = " << cgRowData.position[i] << "\n";
590 –    }
591 –
570      cgPlanVectorColumn->gather(snap_->cgData.position,
571                                 cgColData.position);
594 –    for (int i = 0; i < cgColData.position.size(); i++) {
595 –      cerr << "cgCpos = " << cgColData.position[i] << "\n";
596 –    }
572  
573      
574      // if needed, gather the atomic rotation matrices
# Line 731 | Line 706 | namespace OpenMD {
706      
707      for (int ii = 0;  ii < pot_temp.size(); ii++ )
708        pairwisePot += pot_temp[ii];    
709 +    
710 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
711 +      RealType ploc1 = pairwisePot[ii];
712 +      RealType ploc2 = 0.0;
713 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
714 +      pairwisePot[ii] = ploc2;
715 +    }
716 +
717   #endif
718  
736 –    cerr << "pairwisePot = " <<  pairwisePot << "\n";
719    }
720  
721    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 768 | Line 750 | namespace OpenMD {
750      
751   #ifdef IS_MPI
752      d = cgColData.position[cg2] - cgRowData.position[cg1];
771 –    cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
772 –    cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
753   #else
754      d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
775 –    cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
776 –    cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
755   #endif
756      
757      snap_->wrapVector(d);
# Line 849 | Line 827 | namespace OpenMD {
827    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
828      int unique_id_1, unique_id_2;
829      
852 –
853 –    cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
830   #ifdef IS_MPI
831      // in MPI, we have to look up the unique IDs for each atom
832      unique_id_1 = AtomRowToGlobal[atom1];
833      unique_id_2 = AtomColToGlobal[atom2];
834  
859 –    cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
835      // this situation should only arise in MPI simulations
836      if (unique_id_1 == unique_id_2) return true;
837      
# Line 1131 | Line 1106 | namespace OpenMD {
1106          // add this cutoff group to the list of groups in this cell;
1107          cellListCol_[cellIndex].push_back(i);
1108        }
1109 +    
1110   #else
1111        for (int i = 0; i < nGroups_; i++) {
1112          rs = snap_->cgData.position[i];
# Line 1156 | Line 1132 | namespace OpenMD {
1132          // add this cutoff group to the list of groups in this cell;
1133          cellList_[cellIndex].push_back(i);
1134        }
1135 +
1136   #endif
1137  
1138        for (int m1z = 0; m1z < nCells_.z(); m1z++) {
# Line 1168 | Line 1145 | namespace OpenMD {
1145                   os != cellOffsets_.end(); ++os) {
1146                
1147                Vector3i m2v = m1v + (*os);
1148 <              
1148 >            
1149 >
1150                if (m2v.x() >= nCells_.x()) {
1151                  m2v.x() = 0;          
1152                } else if (m2v.x() < 0) {
# Line 1186 | Line 1164 | namespace OpenMD {
1164                } else if (m2v.z() < 0) {
1165                  m2v.z() = nCells_.z() - 1;
1166                }
1167 <              
1167 >
1168                int m2 = Vlinear (m2v, nCells_);
1169                
1170   #ifdef IS_MPI
# Line 1195 | Line 1173 | namespace OpenMD {
1173                  for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1174                       j2 != cellListCol_[m2].end(); ++j2) {
1175                    
1176 <                  // In parallel, we need to visit *all* pairs of row &
1177 <                  // column indicies and will truncate later on.
1176 >                  // In parallel, we need to visit *all* pairs of row
1177 >                  // & column indicies and will divide labor in the
1178 >                  // force evaluation later.
1179                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1180                    snap_->wrapVector(dr);
1181                    cuts = getGroupCutoffs( (*j1), (*j2) );

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