--- trunk/src/parallel/ForceMatrixDecomposition.cpp	2013/08/19 13:12:00	1929
+++ trunk/src/parallel/ForceMatrixDecomposition.cpp	2014/02/28 13:25:13	1971
@@ -119,8 +119,8 @@ namespace OpenMD {
     
 #ifdef IS_MPI
  
-    MPI::Intracomm row = rowComm.getComm();
-    MPI::Intracomm col = colComm.getComm();
+    MPI_Comm row = rowComm.getComm();
+    MPI_Comm col = colComm.getComm();
 
     AtomPlanIntRow = new Plan<int>(row, nLocal_);
     AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
@@ -424,8 +424,8 @@ namespace OpenMD {
                                      gTypeCutoffs.end());
 
 #ifdef IS_MPI
-    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, 
-                              MPI::MAX);
+    MPI_Allreduce(MPI_IN_PLACE, &groupMax, 1, MPI_REALTYPE, 
+                  MPI_MAX, MPI_COMM_WORLD);
 #endif
     
     RealType tradRcut = groupMax;
@@ -916,23 +916,23 @@ namespace OpenMD {
     for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
       RealType ploc1 = pairwisePot[ii];
       RealType ploc2 = 0.0;
-      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
+      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
       pairwisePot[ii] = ploc2;
     }
 
     for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
       RealType ploc1 = excludedPot[ii];
       RealType ploc2 = 0.0;
-      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
+      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
       excludedPot[ii] = ploc2;
     }
 
     // Here be dragons.
-    MPI::Intracomm col = colComm.getComm();
-
-    col.Allreduce(MPI::IN_PLACE, 
+    MPI_Comm col = colComm.getComm();
+
+    MPI_Allreduce(MPI_IN_PLACE, 
                   &snap_->frameData.conductiveHeatFlux[0], 3, 
-                  MPI::REALTYPE, MPI::SUM);
+                  MPI_REALTYPE, MPI_SUM, col);
 
 
 #endif
@@ -951,13 +951,13 @@ namespace OpenMD {
     for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
       RealType ploc1 = embeddingPot[ii];
       RealType ploc2 = 0.0;
-      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
+      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
       embeddingPot[ii] = ploc2;
     }    
     for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
       RealType ploc1 = excludedSelfPot[ii];
       RealType ploc2 = 0.0;
-      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
+      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
       excludedSelfPot[ii] = ploc2;
     }    
 #endif
@@ -1175,16 +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];
 
-    if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) 
+    if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
       idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
-       
-    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), 
-    //                         ff_->getAtomType(identsCol[atom2]) );
-    
+    } else {
+      idat.sameRegion = false;
+    }
+
     if (storageLayout_ & DataStorage::dslAmat) {
       idat.A1 = &(atomRowData.aMat[atom1]);
       idat.A2 = &(atomColData.aMat[atom2]);
@@ -1237,12 +1237,15 @@ 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) 
+    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]);
@@ -1389,9 +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
     
@@ -1487,9 +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_);