--- trunk/src/parallel/ForceMatrixDecomposition.cpp	2013/07/02 20:02:31	1896
+++ trunk/src/parallel/ForceMatrixDecomposition.cpp	2013/10/31 18:18:57	1939
@@ -99,6 +99,7 @@ namespace OpenMD {
     nGroups_ = info_->getNLocalCutoffGroups();
     // gather the information for atomtype IDs (atids):
     idents = info_->getIdentArray();
+    regions = info_->getRegions();
     AtomLocalToGlobal = info_->getGlobalAtomIndices();
     cgLocalToGlobal = info_->getGlobalGroupIndices();
     vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
@@ -163,7 +164,13 @@ namespace OpenMD {
     
     AtomPlanIntRow->gather(idents, identsRow);
     AtomPlanIntColumn->gather(idents, identsCol);
+
+    regionsRow.resize(nAtomsInRow_);
+    regionsCol.resize(nAtomsInCol_);
     
+    AtomPlanIntRow->gather(regions, regionsRow);
+    AtomPlanIntColumn->gather(regions, regionsCol);
+    
     // allocate memory for the parallel objects
     atypesRow.resize(nAtomsInRow_);
     atypesCol.resize(nAtomsInCol_);
@@ -1168,12 +1175,16 @@ namespace OpenMD {
     idat.excluded = excludeAtomPair(atom1, atom2);
    
 #ifdef IS_MPI
-    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
+    //idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
     idat.atid1 = identsRow[atom1];
     idat.atid2 = identsCol[atom2];
-    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), 
-    //                         ff_->getAtomType(identsCol[atom2]) );
-    
+
+    if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
+      idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
+    } else {
+      idat.sameRegion = false;
+    }
+
     if (storageLayout_ & DataStorage::dslAmat) {
       idat.A1 = &(atomRowData.aMat[atom1]);
       idat.A2 = &(atomColData.aMat[atom2]);
@@ -1226,10 +1237,16 @@ namespace OpenMD {
 
 #else
     
-    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
+    //idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
     idat.atid1 = idents[atom1];
     idat.atid2 = idents[atom2];
 
+    if (regions[atom1] >= 0 && regions[atom2] >= 0) {
+      idat.sameRegion = (regions[atom1] == regions[atom2]);
+    } else {
+      idat.sameRegion = false;
+    }
+
     if (storageLayout_ & DataStorage::dslAmat) {
       idat.A1 = &(snap_->atomData.aMat[atom1]);
       idat.A2 = &(snap_->atomData.aMat[atom2]);
@@ -1375,9 +1392,9 @@ namespace OpenMD {
     Vector3d boxY = box.getColumn(1);
     Vector3d boxZ = box.getColumn(2);
     
-    nCells_.x() = (int) ( boxX.length() )/ rList_;
-    nCells_.y() = (int) ( boxY.length() )/ rList_;
-    nCells_.z() = (int) ( boxZ.length() )/ rList_;
+    nCells_.x() = int( boxX.length() / rList_ );
+    nCells_.y() = int( boxY.length() / rList_ );
+    nCells_.z() = int( boxZ.length() / rList_ );
     
     // handle small boxes where the cell offsets can end up repeating cells
     
@@ -1473,9 +1490,9 @@ namespace OpenMD {
         }
         
         // find xyz-indices of cell that cutoffGroup is in.
-        whichCell.x() = nCells_.x() * scaled.x();
-        whichCell.y() = nCells_.y() * scaled.y();
-        whichCell.z() = nCells_.z() * scaled.z();
+        whichCell.x() = int(nCells_.x() * scaled.x());
+        whichCell.y() = int(nCells_.y() * scaled.y());
+        whichCell.z() = int(nCells_.z() * scaled.z());
         
         // find single index of this cell:
         cellIndex = Vlinear(whichCell, nCells_);