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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 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

# Line 36 | Line 36
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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42   #include "parallel/ForceDecomposition.hpp"
43   #include "math/Vector3.hpp"
# Line 47 | Line 48 | namespace OpenMD {
48   using namespace std;
49   namespace OpenMD {
50  
51 <  ForceDecomposition::ForceDecomposition(SimInfo* info) : info_(info) {
51 >  ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan) {
52      sman_ = info_->getSnapshotManager();
53      storageLayout_ = sman_->getStorageLayout();
54      ff_ = info_->getForceField();
# Line 87 | Line 88 | namespace OpenMD {
88      cellOffsets_.push_back( Vector3i(1, -1,1) );
89    }
90  
91 <  SelfData ForceDecomposition::fillSelfData(int atom1) {
92 <    SelfData sdat;
93 <    // Still Missing atype, skippedCharge, potVec pot,
91 >  void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
92 >
93 >    sdat.atype = atypesLocal[atom1];
94 >
95 >    sdat.pot = &embeddingPot;
96 >
97      if (storageLayout_ & DataStorage::dslElectroFrame) {
98        sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
99      }
# Line 110 | Line 114 | namespace OpenMD {
114        sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
115      }
116  
117 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
118 +      sdat.skippedCharge = &(snap_->atomData.skippedCharge[atom1]);
119 +    }
120 +
121      if (storageLayout_ & DataStorage::dslParticlePot) {
122        sdat.particlePot = &(snap_->atomData.particlePot[atom1]);
123      }
116 –
117 –    return sdat;    
124    }
125  
126    bool ForceDecomposition::checkNeighborList() {
# Line 142 | Line 148 | namespace OpenMD {
148      // a conservative test of list skin crossings
149      dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax);
150  
151 <    return (dispmax > skinThickness_);    
151 >
152 >    if (dispmax > skinThickness_)
153 >      return (dispmax > skinThickness_);  
154 >
155 >    return false;
156    }
157   }

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