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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 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

# Line 1042 | Line 1042 | namespace OpenMD {
1042     * the parallel decomposition.
1043     */
1044    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1045 <    int unique_id_1, unique_id_2, group1, group2;
1045 >    int unique_id_1, unique_id_2;
1046          
1047   #ifdef IS_MPI
1048      // in MPI, we have to look up the unique IDs for each atom
1049      unique_id_1 = AtomRowToGlobal[atom1];
1050      unique_id_2 = AtomColToGlobal[atom2];
1051 <    group1 = cgRowToGlobal[cg1];
1052 <    group2 = cgColToGlobal[cg2];
1051 >    // group1 = cgRowToGlobal[cg1];
1052 >    // group2 = cgColToGlobal[cg2];
1053   #else
1054      unique_id_1 = AtomLocalToGlobal[atom1];
1055      unique_id_2 = AtomLocalToGlobal[atom2];
1056 <    group1 = cgLocalToGlobal[cg1];
1057 <    group2 = cgLocalToGlobal[cg2];
1056 >    int group1 = cgLocalToGlobal[cg1];
1057 >    int group2 = cgLocalToGlobal[cg2];
1058   #endif  
1059  
1060      if (unique_id_1 == unique_id_2) return true;
# Line 1295 | Line 1295 | namespace OpenMD {
1295   #endif
1296  
1297      RealType rList_ = (largestRcut_ + skinThickness_);
1298 –    RealType rl2 = rList_ * rList_;
1298      Snapshot* snap_ = sman_->getCurrentSnapshot();
1299      Mat3x3d Hmat = snap_->getHmat();
1300      Vector3d Hx = Hmat.getColumn(0);
# Line 1339 | Line 1338 | namespace OpenMD {
1338          for (int j = 0; j < 3; j++) {
1339            scaled[j] -= roundMe(scaled[j]);
1340            scaled[j] += 0.5;
1341 +          // Handle the special case when an object is exactly on the
1342 +          // boundary (a scaled coordinate of 1.0 is the same as
1343 +          // scaled coordinate of 0.0)
1344 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1345          }
1346          
1347          // find xyz-indices of cell that cutoffGroup is in.
# Line 1363 | Line 1366 | namespace OpenMD {
1366          for (int j = 0; j < 3; j++) {
1367            scaled[j] -= roundMe(scaled[j]);
1368            scaled[j] += 0.5;
1369 +          // Handle the special case when an object is exactly on the
1370 +          // boundary (a scaled coordinate of 1.0 is the same as
1371 +          // scaled coordinate of 0.0)
1372 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1373          }
1374          
1375          // find xyz-indices of cell that cutoffGroup is in.
# Line 1389 | Line 1396 | namespace OpenMD {
1396          for (int j = 0; j < 3; j++) {
1397            scaled[j] -= roundMe(scaled[j]);
1398            scaled[j] += 0.5;
1399 +          // Handle the special case when an object is exactly on the
1400 +          // boundary (a scaled coordinate of 1.0 is the same as
1401 +          // scaled coordinate of 0.0)
1402 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1403          }
1404          
1405          // find xyz-indices of cell that cutoffGroup is in.

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