# | Line 35 | Line 35 | |
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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 | */ | |
42 | < | #include "parallel/ForceDecomposition.hpp" |
43 | < | #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 90 | Line 100 | namespace OpenMD { | |
100 | ||
101 | void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) { | |
102 | ||
103 | < | sdat.atype = atypesLocal[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::dslElectroFrame) { |
110 | < | sdat.eFrame = &(snap_->atomData.electroFrame[atom1]); |
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 121 | 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 | ||
# | Line 154 | Line 180 | namespace OpenMD { | |
180 | ||
181 | return false; | |
182 | } | |
183 | + | |
184 | + | void ForceDecomposition::addToHeatFlux(Vector3d hf) { |
185 | + | Vector3d chf = snap_->getConductiveHeatFlux(); |
186 | + | chf += hf; |
187 | + | snap_->setConductiveHeatFlux(chf); |
188 | + | } |
189 | + | void ForceDecomposition::setHeatFlux(Vector3d hf) { |
190 | + | snap_->setConductiveHeatFlux(hf); |
191 | + | } |
192 | + | |
193 | } |
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