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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 1611 by gezelter, Thu Aug 4 20:04:35 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 1091 | 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 1116 | 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 1128 | 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 1146 | 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 1155 | 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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