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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 1929 by gezelter, Mon Aug 19 13:12:00 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 96 | Line 99 | namespace OpenMD {
99    void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
100  
101      sdat.atype = atypesLocal[atom1];
102 +    sdat.atid = idents[atom1];
103  
104      sdat.pot = &embeddingPot;
105 +    sdat.excludedPot = &excludedSelfPot;
106  
107 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
108 <      sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
107 >    if (storageLayout_ & DataStorage::dslDipole) {
108 >      sdat.dipole = &(snap_->atomData.dipole[atom1]);
109      }
110 <    
110 >
111 >    if (storageLayout_ & DataStorage::dslQuadrupole) {
112 >      sdat.quadrupole = &(snap_->atomData.quadrupole[atom1]);
113 >    }
114 >
115      if (storageLayout_ & DataStorage::dslTorque) {
116        sdat.t = &(snap_->atomData.torque[atom1]);
117      }
# Line 132 | Line 141 | namespace OpenMD {
141      }
142      
143      if (storageLayout_ & DataStorage::dslFlucQForce) {
144 <      sdat.dVdFQ = &(snap_->atomData.flucQFrc[atom1]);
144 >      sdat.flucQfrc = &(snap_->atomData.flucQFrc[atom1]);
145      }
146    }
147  
# Line 171 | Line 180 | namespace OpenMD {
180    }
181  
182    void ForceDecomposition::addToHeatFlux(Vector3d hf) {
183 <    snap_->frameData.conductiveHeatFlux += hf;
183 >    Vector3d chf = snap_->getConductiveHeatFlux();
184 >    chf += hf;
185 >    snap_->setConductiveHeatFlux(chf);
186    }
187    void ForceDecomposition::setHeatFlux(Vector3d hf) {
188 <    snap_->frameData.conductiveHeatFlux = hf;
188 >    snap_->setConductiveHeatFlux(hf);
189    }
190  
191   }

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