--- branches/development/src/parallel/ForceDecomposition.cpp	2011/06/08 16:05:07	1576
+++ trunk/src/parallel/ForceDecomposition.cpp	2015/03/07 21:41:51	2071
@@ -35,26 +35,36 @@
  *                                                                      
  * [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).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [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 {
 
-  ForceDecomposition::ForceDecomposition(SimInfo* info) : info_(info) {
+  ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan), needVelocities_(false) {
+
     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()) {
+        needVelocities_ = true;
+      }
+    }
+
     if (simParams_->haveSkinThickness()) {
       skinThickness_ = simParams_->getSkinThickness();
     } else {      
@@ -87,13 +97,27 @@ namespace OpenMD {
     cellOffsets_.push_back( Vector3i(1, -1,1) );
   }
 
-  SelfData ForceDecomposition::fillSelfData(int atom1) {
-    SelfData sdat;
-    // Still Missing atype, skippedCharge, potVec pot,
-    if (storageLayout_ & DataStorage::dslElectroFrame) {
-      sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
+  void ForceDecomposition::setCutoffRadius(RealType rcut) {
+    rCut_ = rcut;
+    rList_ = rCut_ + skinThickness_;
+    rListSq_ = rList_ * rList_;
+  }
+
+  void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
+
+    sdat.atid = idents[atom1];
+
+    sdat.pot = &embeddingPot;
+    sdat.excludedPot = &excludedSelfPot;
+
+    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]);
     }
@@ -110,38 +134,58 @@ namespace OpenMD {
       sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
     }
 
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {
+      sdat.skippedCharge = &(snap_->atomData.skippedCharge[atom1]);
+    }
+
     if (storageLayout_ & DataStorage::dslParticlePot) {
       sdat.particlePot = &(snap_->atomData.particlePot[atom1]);
     }
-
-    return sdat;    
+    
+    if (storageLayout_ & DataStorage::dslFlucQPosition) {
+      sdat.flucQ = &(snap_->atomData.flucQPos[atom1]);
+    }
+    
+    if (storageLayout_ & DataStorage::dslFlucQForce) {
+      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);
+    
     // 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);
+    return (dispmax > st2) ? true : false;
+  }
 
-    return (dispmax > skinThickness_);    
+  void ForceDecomposition::addToHeatFlux(Vector3d hf) {
+    Vector3d chf = snap_->getConductiveHeatFlux();
+    chf += hf;
+    snap_->setConductiveHeatFlux(chf);
   }
+  void ForceDecomposition::setHeatFlux(Vector3d hf) {
+    snap_->setConductiveHeatFlux(hf);
+  }
+
 }