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root/OpenMD/trunk/src/parallel/ForceDecomposition.cpp
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Comparing:
branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1736 by jmichalk, Tue Jun 5 17:51:31 2012 UTC vs.
trunk/src/parallel/ForceDecomposition.cpp (file contents), Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 49 | Line 49 | namespace OpenMD {
49   namespace OpenMD {
50  
51    ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan), needVelocities_(false) {
52 +
53      sman_ = info_->getSnapshotManager();
54      storageLayout_ = sman_->getStorageLayout();
55      ff_ = info_->getForceField();
56      userChoseCutoff_ = false;
57  
58 +    usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions();
59 +
60      Globals* simParams_ = info_->getSimParams();    
61      if (simParams_->havePrintHeatFlux()) {
62        if (simParams_->getPrintHeatFlux()) {
# Line 98 | Line 101 | namespace OpenMD {
101      sdat.atype = atypesLocal[atom1];
102  
103      sdat.pot = &embeddingPot;
104 +    sdat.excludedPot = &excludedSelfPot;
105  
106 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
107 <      sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
106 >    if (storageLayout_ & DataStorage::dslDipole) {
107 >      sdat.dipole = &(snap_->atomData.dipole[atom1]);
108      }
109 <    
109 >
110 >    if (storageLayout_ & DataStorage::dslQuadrupole) {
111 >      sdat.quadrupole = &(snap_->atomData.quadrupole[atom1]);
112 >    }
113 >
114      if (storageLayout_ & DataStorage::dslTorque) {
115        sdat.t = &(snap_->atomData.torque[atom1]);
116      }
# Line 171 | Line 179 | namespace OpenMD {
179    }
180  
181    void ForceDecomposition::addToHeatFlux(Vector3d hf) {
182 <    snap_->frameData.conductiveHeatFlux += hf;
182 >    Vector3d chf = snap_->getConductiveHeatFlux();
183 >    chf += hf;
184 >    snap_->setConductiveHeatFlux(chf);
185    }
186    void ForceDecomposition::setHeatFlux(Vector3d hf) {
187 <    snap_->frameData.conductiveHeatFlux = hf;
187 >    snap_->setConductiveHeatFlux(hf);
188    }
189  
190   }

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