--- branches/development/src/parallel/ForceDecomposition.cpp	2011/06/21 06:34:35	1586
+++ trunk/src/parallel/ForceDecomposition.cpp	2014/02/28 13:25:13	1971
@@ -35,26 +35,37 @@
  *                                                                      
  * [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, InteractionManager* iMan) : info_(info), interactionMan_(iMan) {
+  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 {      
@@ -89,13 +100,20 @@ namespace OpenMD {
 
   void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
 
-    sdat.atype = ff_->getAtomType(idents[atom1]);
-        
-    // Still Missing skippedCharge
-    if (storageLayout_ & DataStorage::dslElectroFrame) {
-      sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
+    //sdat.atype = atypesLocal[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]);
     }
@@ -119,19 +137,26 @@ namespace OpenMD {
     if (storageLayout_ & DataStorage::dslParticlePot) {
       sdat.particlePot = &(snap_->atomData.particlePot[atom1]);
     }
+    
+    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();
-
+    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 ) {
-      cerr << "build because size\n";
-      return true;
-    }
+    if ( saved_CG_positions_.size() != nGroups ) return true;
 
     RealType dispmax = 0.0;
     Vector3d disp;    
@@ -143,19 +168,27 @@ namespace OpenMD {
     }
 
 #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_) {
-      cerr << "build because movement\n";
+    if (dispmax > skinThickness_) 
       return (dispmax > skinThickness_);   
-    } else {
-      cerr << "not rebuilding\n";
-    }
+
     return false;
   }
+
+  void ForceDecomposition::addToHeatFlux(Vector3d hf) {
+    Vector3d chf = snap_->getConductiveHeatFlux();
+    chf += hf;
+    snap_->setConductiveHeatFlux(chf);
+  }
+  void ForceDecomposition::setHeatFlux(Vector3d hf) {
+    snap_->setConductiveHeatFlux(hf);
+  }
+
 }