--- branches/development/src/parallel/ForceDecomposition.cpp	2012/06/14 01:58:35	1755
+++ trunk/src/parallel/ForceDecomposition.cpp	2015/03/07 21:41:51	2071
@@ -35,16 +35,18 @@
  *                                                                      
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
- * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
  * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
  * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
-#include "parallel/ForceDecomposition.hpp"
-#include "math/Vector3.hpp"
+
 #ifdef IS_MPI
 #include <mpi.h>
 #endif
 
+#include "parallel/ForceDecomposition.hpp"
+#include "math/Vector3.hpp"
+
 using namespace std;
 namespace OpenMD {
 
@@ -53,8 +55,9 @@ namespace OpenMD {
     sman_ = info_->getSnapshotManager();
     storageLayout_ = sman_->getStorageLayout();
     ff_ = info_->getForceField();
-    userChoseCutoff_ = false;
 
+    usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions();
+
     Globals* simParams_ = info_->getSimParams();    
     if (simParams_->havePrintHeatFlux()) {
       if (simParams_->getPrintHeatFlux()) {
@@ -94,16 +97,27 @@ namespace OpenMD {
     cellOffsets_.push_back( Vector3i(1, -1,1) );
   }
 
+  void ForceDecomposition::setCutoffRadius(RealType rcut) {
+    rCut_ = rcut;
+    rList_ = rCut_ + skinThickness_;
+    rListSq_ = rList_ * rList_;
+  }
+
   void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
 
-    sdat.atype = atypesLocal[atom1];
+    sdat.atid = idents[atom1];
 
     sdat.pot = &embeddingPot;
+    sdat.excludedPot = &excludedSelfPot;
 
-    if (storageLayout_ & DataStorage::dslElectroFrame) {
-      sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
+    if (storageLayout_ & DataStorage::dslDipole) {
+      sdat.dipole = &(snap_->atomData.dipole[atom1]);
     }
-    
+
+    if (storageLayout_ & DataStorage::dslQuadrupole) {
+      sdat.quadrupole = &(snap_->atomData.quadrupole[atom1]);
+    }
+
     if (storageLayout_ & DataStorage::dslTorque) {
       sdat.t = &(snap_->atomData.torque[atom1]);
     }
@@ -133,42 +147,36 @@ namespace OpenMD {
     }
     
     if (storageLayout_ & DataStorage::dslFlucQForce) {
-      sdat.dVdFQ = &(snap_->atomData.flucQFrc[atom1]);
+      sdat.flucQfrc = &(snap_->atomData.flucQFrc[atom1]);
     }
   }
 
   bool ForceDecomposition::checkNeighborList() {
-
-    int nGroups = snap_->cgData.position.size();
+    RealType st2 = pow( skinThickness_ / 2.0, 2);
+    std::size_t nGroups = snap_->cgData.position.size();
     if (needVelocities_) 
-      snap_->cgData.setStorageLayout(DataStorage::dslPosition | DataStorage::dslVelocity);
+      snap_->cgData.setStorageLayout(DataStorage::dslPosition |
+                                     DataStorage::dslVelocity);
     
     // if we have changed the group identities or haven't set up the
     // saved positions we automatically will need a neighbor list update:
-
+    
     if ( saved_CG_positions_.size() != nGroups ) return true;
 
     RealType dispmax = 0.0;
     Vector3d disp;    
 
-    for (int i = 0; i < nGroups; i++) {
+    for (std::size_t i = 0; i < nGroups; i++) {
       disp = snap_->cgData.position[i]  - saved_CG_positions_[i];
-      for (int j = 0; j < 3; j++)
-        dispmax = max( abs(disp[j]), dispmax);
+      dispmax = max(dispmax, disp.lengthSquare());
     }
 
 #ifdef IS_MPI
-    MPI::COMM_WORLD.Allreduce(&dispmax, &dispmax, 1, MPI::REALTYPE, MPI::MAX);
+    MPI_Allreduce(MPI_IN_PLACE, &dispmax, 1, MPI_REALTYPE, MPI_MAX, 
+                  MPI_COMM_WORLD);
 #endif
 
-    // a conservative test of list skin crossings
-    dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax);
-
-
-    if (dispmax > skinThickness_) 
-      return (dispmax > skinThickness_);   
-
-    return false;
+    return (dispmax > st2) ? true : false;
   }
 
   void ForceDecomposition::addToHeatFlux(Vector3d hf) {