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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 1586 by gezelter, Tue Jun 21 06:34:35 2011 UTC vs.
trunk/src/parallel/ForceDecomposition.cpp (file contents), Revision 1971 by gezelter, Fri Feb 28 13:25:13 2014 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"
42 < #include "math/Vector3.hpp"
42 >
43   #ifdef IS_MPI
44   #include <mpi.h>
45   #endif
46  
47 + #include "parallel/ForceDecomposition.hpp"
48 + #include "math/Vector3.hpp"
49 +
50   using namespace std;
51   namespace OpenMD {
52  
53 <  ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan) {
53 >  ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan), needVelocities_(false) {
54 >
55      sman_ = info_->getSnapshotManager();
56      storageLayout_ = sman_->getStorageLayout();
57      ff_ = info_->getForceField();
58      userChoseCutoff_ = false;
59  
60 +    usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions();
61 +
62      Globals* simParams_ = info_->getSimParams();    
63 <  
63 >    if (simParams_->havePrintHeatFlux()) {
64 >      if (simParams_->getPrintHeatFlux()) {
65 >        needVelocities_ = true;
66 >      }
67 >    }
68 >
69      if (simParams_->haveSkinThickness()) {
70        skinThickness_ = simParams_->getSkinThickness();
71      } else {      
# Line 89 | Line 100 | namespace OpenMD {
100  
101    void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
102  
103 <    sdat.atype = ff_->getAtomType(idents[atom1]);
104 <        
105 <    // Still Missing skippedCharge
106 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
107 <      sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
103 >    //sdat.atype = atypesLocal[atom1];
104 >    sdat.atid = idents[atom1];
105 >
106 >    sdat.pot = &embeddingPot;
107 >    sdat.excludedPot = &excludedSelfPot;
108 >
109 >    if (storageLayout_ & DataStorage::dslDipole) {
110 >      sdat.dipole = &(snap_->atomData.dipole[atom1]);
111      }
112 <    
112 >
113 >    if (storageLayout_ & DataStorage::dslQuadrupole) {
114 >      sdat.quadrupole = &(snap_->atomData.quadrupole[atom1]);
115 >    }
116 >
117      if (storageLayout_ & DataStorage::dslTorque) {
118        sdat.t = &(snap_->atomData.torque[atom1]);
119      }
# Line 119 | Line 137 | namespace OpenMD {
137      if (storageLayout_ & DataStorage::dslParticlePot) {
138        sdat.particlePot = &(snap_->atomData.particlePot[atom1]);
139      }
140 +    
141 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {
142 +      sdat.flucQ = &(snap_->atomData.flucQPos[atom1]);
143 +    }
144 +    
145 +    if (storageLayout_ & DataStorage::dslFlucQForce) {
146 +      sdat.flucQfrc = &(snap_->atomData.flucQFrc[atom1]);
147 +    }
148    }
149  
150    bool ForceDecomposition::checkNeighborList() {
151  
152      int nGroups = snap_->cgData.position.size();
153 <
153 >    if (needVelocities_)
154 >      snap_->cgData.setStorageLayout(DataStorage::dslPosition | DataStorage::dslVelocity);
155 >    
156      // if we have changed the group identities or haven't set up the
157      // saved positions we automatically will need a neighbor list update:
158  
159 <    if ( saved_CG_positions_.size() != nGroups ) {
132 <      cerr << "build because size\n";
133 <      return true;
134 <    }
159 >    if ( saved_CG_positions_.size() != nGroups ) return true;
160  
161      RealType dispmax = 0.0;
162      Vector3d disp;    
# Line 143 | Line 168 | namespace OpenMD {
168      }
169  
170   #ifdef IS_MPI
171 <    MPI::COMM_WORLD.Allreduce(&dispmax, &dispmax, 1, MPI::REALTYPE, MPI::MAX);
171 >    MPI_Allreduce(MPI_IN_PLACE, &dispmax, 1, MPI_REALTYPE, MPI_MAX,
172 >                  MPI_COMM_WORLD);
173   #endif
174  
175      // a conservative test of list skin crossings
176      dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax);
177  
178  
179 <    if (dispmax > skinThickness_) {
154 <      cerr << "build because movement\n";
179 >    if (dispmax > skinThickness_)
180        return (dispmax > skinThickness_);  
181 <    } else {
157 <      cerr << "not rebuilding\n";
158 <    }
181 >
182      return false;
183    }
184 +
185 +  void ForceDecomposition::addToHeatFlux(Vector3d hf) {
186 +    Vector3d chf = snap_->getConductiveHeatFlux();
187 +    chf += hf;
188 +    snap_->setConductiveHeatFlux(chf);
189 +  }
190 +  void ForceDecomposition::setHeatFlux(Vector3d hf) {
191 +    snap_->setConductiveHeatFlux(hf);
192 +  }
193 +
194   }

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