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root/OpenMD/trunk/src/parallel/ForceDecomposition.cpp
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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1582 by gezelter, Tue Jun 14 20:41:44 2011 UTC vs.
trunk/src/parallel/ForceDecomposition.cpp (file contents), Revision 1895 by gezelter, Mon Jul 1 21:09:37 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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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   */
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, InteractionManager* iMan) : info_(info), interactionMan_(iMan) {
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 <  
61 >    if (simParams_->havePrintHeatFlux()) {
62 >      if (simParams_->getPrintHeatFlux()) {
63 >        needVelocities_ = true;
64 >      }
65 >    }
66 >
67      if (simParams_->haveSkinThickness()) {
68        skinThickness_ = simParams_->getSkinThickness();
69      } else {      
# Line 88 | Line 97 | namespace OpenMD {
97    }
98  
99    void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
100 <    
101 <    // Still Missing atype, skippedCharge, potVec pot,
102 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
103 <      sdat.eFrame = &(snap_->atomData.electroFrame[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::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 110 | Line 128 | namespace OpenMD {
128        sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
129      }
130  
131 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
132 +      sdat.skippedCharge = &(snap_->atomData.skippedCharge[atom1]);
133 +    }
134 +
135      if (storageLayout_ & DataStorage::dslParticlePot) {
136        sdat.particlePot = &(snap_->atomData.particlePot[atom1]);
137      }
138 +    
139 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {
140 +      sdat.flucQ = &(snap_->atomData.flucQPos[atom1]);
141 +    }
142 +    
143 +    if (storageLayout_ & DataStorage::dslFlucQForce) {
144 +      sdat.dVdFQ = &(snap_->atomData.flucQFrc[atom1]);
145 +    }
146    }
147  
148    bool ForceDecomposition::checkNeighborList() {
149  
150      int nGroups = snap_->cgData.position.size();
151 <
151 >    if (needVelocities_)
152 >      snap_->cgData.setStorageLayout(DataStorage::dslPosition | DataStorage::dslVelocity);
153 >    
154      // if we have changed the group identities or haven't set up the
155      // saved positions we automatically will need a neighbor list update:
156  
157 <    if ( saved_CG_positions_.size() != nGroups ) {
126 <      cerr << "build because size\n";
127 <      return true;
128 <    }
157 >    if ( saved_CG_positions_.size() != nGroups ) return true;
158  
159      RealType dispmax = 0.0;
160      Vector3d disp;    
# Line 144 | Line 173 | namespace OpenMD {
173      dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax);
174  
175  
176 <    if (dispmax > skinThickness_) {
148 <      cerr << "build because movement\n";
176 >    if (dispmax > skinThickness_)
177        return (dispmax > skinThickness_);  
178 <    }
178 >
179      return false;
180    }
181 +
182 +  void ForceDecomposition::addToHeatFlux(Vector3d hf) {
183 +    Vector3d chf = snap_->getConductiveHeatFlux();
184 +    chf += hf;
185 +    snap_->setConductiveHeatFlux(chf);
186 +  }
187 +  void ForceDecomposition::setHeatFlux(Vector3d hf) {
188 +    snap_->setConductiveHeatFlux(hf);
189 +  }
190 +
191   }

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