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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 1583 by gezelter, Thu Jun 16 22:00:08 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 89 | Line 90 | namespace OpenMD {
90  
91    void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
92  
93 <    sdat.atype = ff_->getAtomType(idents[atom1]);
94 <        
95 <    // Still Missing skippedCharge
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 112 | 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      }
# Line 124 | Line 130 | namespace OpenMD {
130      // if we have changed the group identities or haven't set up the
131      // saved positions we automatically will need a neighbor list update:
132  
133 <    if ( saved_CG_positions_.size() != nGroups ) {
128 <      cerr << "build because size\n";
129 <      return true;
130 <    }
133 >    if ( saved_CG_positions_.size() != nGroups ) return true;
134  
135      RealType dispmax = 0.0;
136      Vector3d disp;    
# Line 146 | Line 149 | namespace OpenMD {
149      dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax);
150  
151  
152 <    if (dispmax > skinThickness_) {
150 <      cerr << "build because movement\n";
152 >    if (dispmax > skinThickness_)
153        return (dispmax > skinThickness_);  
154 <    } else {
153 <      cerr << "not rebuilding\n";
154 <    }
154 >
155      return false;
156    }
157   }

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