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root/OpenMD/branches/development/src/parallel/ForceMatrixDecomposition.cpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC vs.
Revision 1858 by gezelter, Wed Apr 3 21:32:13 2013 UTC

# Line 975 | Line 975 | namespace OpenMD {
975      d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
976   #endif
977      
978 <    snap_->wrapVector(d);
978 >    if (usePeriodicBoundaryConditions_) {
979 >      snap_->wrapVector(d);
980 >    }
981      return d;    
982    }
983  
# Line 1005 | Line 1007 | namespace OpenMD {
1007   #else
1008      d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1009   #endif
1010 <
1011 <    snap_->wrapVector(d);
1010 >    if (usePeriodicBoundaryConditions_) {
1011 >      snap_->wrapVector(d);
1012 >    }
1013      return d;    
1014    }
1015    
# Line 1018 | Line 1021 | namespace OpenMD {
1021   #else
1022      d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1023   #endif
1024 <    
1025 <    snap_->wrapVector(d);
1024 >    if (usePeriodicBoundaryConditions_) {
1025 >      snap_->wrapVector(d);
1026 >    }
1027      return d;    
1028    }
1029  
# Line 1048 | Line 1052 | namespace OpenMD {
1052   #else
1053      d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1054   #endif
1055 <
1056 <    snap_->wrapVector(d);
1055 >    if (usePeriodicBoundaryConditions_) {
1056 >      snap_->wrapVector(d);
1057 >    }
1058      return d;    
1059    }
1060  
# Line 1206 | Line 1211 | namespace OpenMD {
1211        idat.A2 = &(snap_->atomData.aMat[atom2]);
1212      }
1213  
1209 –    RealType ct = dot(idat.A1->getColumn(2), idat.A2->getColumn(2));
1210 –
1214      if (storageLayout_ & DataStorage::dslTorque) {
1215        idat.t1 = &(snap_->atomData.torque[atom1]);
1216        idat.t2 = &(snap_->atomData.torque[atom2]);
# Line 1319 | Line 1322 | namespace OpenMD {
1322      groupCutoffs cuts;
1323      bool doAllPairs = false;
1324  
1325 +    RealType rList_ = (largestRcut_ + skinThickness_);
1326 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
1327 +    Mat3x3d box;
1328 +    Mat3x3d invBox;
1329 +
1330 +    Vector3d rs, scaled, dr;
1331 +    Vector3i whichCell;
1332 +    int cellIndex;
1333 +
1334   #ifdef IS_MPI
1335      cellListRow_.clear();
1336      cellListCol_.clear();
1337   #else
1338      cellList_.clear();
1339   #endif
1340 <
1341 <    RealType rList_ = (largestRcut_ + skinThickness_);
1342 <    Snapshot* snap_ = sman_->getCurrentSnapshot();
1343 <    Mat3x3d Hmat = snap_->getHmat();
1344 <    Vector3d Hx = Hmat.getColumn(0);
1345 <    Vector3d Hy = Hmat.getColumn(1);
1346 <    Vector3d Hz = Hmat.getColumn(2);
1347 <
1348 <    nCells_.x() = (int) ( Hx.length() )/ rList_;
1349 <    nCells_.y() = (int) ( Hy.length() )/ rList_;
1350 <    nCells_.z() = (int) ( Hz.length() )/ rList_;
1351 <
1340 >    
1341 >    if (!usePeriodicBoundaryConditions_) {
1342 >      box = snap_->getBoundingBox();
1343 >      invBox = snap_->getInvBoundingBox();
1344 >    } else {
1345 >      box = snap_->getHmat();
1346 >      invBox = snap_->getInvHmat();
1347 >    }
1348 >    
1349 >    Vector3d boxX = box.getColumn(0);
1350 >    Vector3d boxY = box.getColumn(1);
1351 >    Vector3d boxZ = box.getColumn(2);
1352 >    
1353 >    nCells_.x() = (int) ( boxX.length() )/ rList_;
1354 >    nCells_.y() = (int) ( boxY.length() )/ rList_;
1355 >    nCells_.z() = (int) ( boxZ.length() )/ rList_;
1356 >    
1357      // handle small boxes where the cell offsets can end up repeating cells
1358      
1359      if (nCells_.x() < 3) doAllPairs = true;
1360      if (nCells_.y() < 3) doAllPairs = true;
1361      if (nCells_.z() < 3) doAllPairs = true;
1362 <
1346 <    Mat3x3d invHmat = snap_->getInvHmat();
1347 <    Vector3d rs, scaled, dr;
1348 <    Vector3i whichCell;
1349 <    int cellIndex;
1362 >    
1363      int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1364 <
1364 >    
1365   #ifdef IS_MPI
1366      cellListRow_.resize(nCtot);
1367      cellListCol_.resize(nCtot);
1368   #else
1369      cellList_.resize(nCtot);
1370   #endif
1371 <
1371 >    
1372      if (!doAllPairs) {
1373   #ifdef IS_MPI
1374 <
1374 >      
1375        for (int i = 0; i < nGroupsInRow_; i++) {
1376          rs = cgRowData.position[i];
1377          
1378          // scaled positions relative to the box vectors
1379 <        scaled = invHmat * rs;
1379 >        scaled = invBox * rs;
1380          
1381          // wrap the vector back into the unit box by subtracting integer box
1382          // numbers
# Line 1391 | Line 1404 | namespace OpenMD {
1404          rs = cgColData.position[i];
1405          
1406          // scaled positions relative to the box vectors
1407 <        scaled = invHmat * rs;
1407 >        scaled = invBox * rs;
1408          
1409          // wrap the vector back into the unit box by subtracting integer box
1410          // numbers
# Line 1415 | Line 1428 | namespace OpenMD {
1428          // add this cutoff group to the list of groups in this cell;
1429          cellListCol_[cellIndex].push_back(i);
1430        }
1431 <    
1431 >      
1432   #else
1433        for (int i = 0; i < nGroups_; i++) {
1434          rs = snap_->cgData.position[i];
1435          
1436          // scaled positions relative to the box vectors
1437 <        scaled = invHmat * rs;
1437 >        scaled = invBox * rs;
1438          
1439          // wrap the vector back into the unit box by subtracting integer box
1440          // numbers
# Line 1490 | Line 1503 | namespace OpenMD {
1503                    // & column indicies and will divide labor in the
1504                    // force evaluation later.
1505                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1506 <                  snap_->wrapVector(dr);
1506 >                  if (usePeriodicBoundaryConditions_) {
1507 >                    snap_->wrapVector(dr);
1508 >                  }
1509                    cuts = getGroupCutoffs( (*j1), (*j2) );
1510                    if (dr.lengthSquare() < cuts.third) {
1511                      neighborList.push_back(make_pair((*j1), (*j2)));
# Line 1512 | Line 1527 | namespace OpenMD {
1527                    // allows atoms within a single cutoff group to
1528                    // interact with each other.
1529  
1515 –
1516 –
1530                    if (m2 != m1 || (*j2) >= (*j1) ) {
1531  
1532                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1533 <                    snap_->wrapVector(dr);
1533 >                    if (usePeriodicBoundaryConditions_) {
1534 >                      snap_->wrapVector(dr);
1535 >                    }
1536                      cuts = getGroupCutoffs( (*j1), (*j2) );
1537                      if (dr.lengthSquare() < cuts.third) {
1538                        neighborList.push_back(make_pair((*j1), (*j2)));
# Line 1536 | Line 1551 | namespace OpenMD {
1551        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1552          for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1553            dr = cgColData.position[j2] - cgRowData.position[j1];
1554 <          snap_->wrapVector(dr);
1554 >          if (usePeriodicBoundaryConditions_) {
1555 >            snap_->wrapVector(dr);
1556 >          }
1557            cuts = getGroupCutoffs( j1, j2 );
1558            if (dr.lengthSquare() < cuts.third) {
1559              neighborList.push_back(make_pair(j1, j2));
# Line 1549 | Line 1566 | namespace OpenMD {
1566          // include self group interactions j2 == j1
1567          for (int j2 = j1; j2 < nGroups_; j2++) {
1568            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1569 <          snap_->wrapVector(dr);
1569 >          if (usePeriodicBoundaryConditions_) {
1570 >            snap_->wrapVector(dr);
1571 >          }
1572            cuts = getGroupCutoffs( j1, j2 );
1573            if (dr.lengthSquare() < cuts.third) {
1574              neighborList.push_back(make_pair(j1, j2));

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