| 36 |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [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 |
|
*/ |
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|
#include "parallel/ForceDecomposition.hpp" |
| 43 |
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#include "math/Vector3.hpp" |
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|
using namespace std; |
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namespace OpenMD { |
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|
| 51 |
< |
ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan) { |
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> |
ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan), needVelocities_(false) { |
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sman_ = info_->getSnapshotManager(); |
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storageLayout_ = sman_->getStorageLayout(); |
| 54 |
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ff_ = info_->getForceField(); |
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userChoseCutoff_ = false; |
| 56 |
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|
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Globals* simParams_ = info_->getSimParams(); |
| 58 |
< |
|
| 58 |
> |
if (simParams_->havePrintHeatFlux()) { |
| 59 |
> |
if (simParams_->getPrintHeatFlux()) { |
| 60 |
> |
needVelocities_ = true; |
| 61 |
> |
} |
| 62 |
> |
} |
| 63 |
> |
|
| 64 |
|
if (simParams_->haveSkinThickness()) { |
| 65 |
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skinThickness_ = simParams_->getSkinThickness(); |
| 66 |
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} else { |
| 95 |
|
|
| 96 |
|
void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) { |
| 97 |
|
|
| 98 |
< |
sdat.atype = ff_->getAtomType(idents[atom1]); |
| 99 |
< |
|
| 100 |
< |
// Still Missing skippedCharge |
| 98 |
> |
sdat.atype = atypesLocal[atom1]; |
| 99 |
> |
|
| 100 |
> |
sdat.pot = &embeddingPot; |
| 101 |
> |
|
| 102 |
|
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 103 |
|
sdat.eFrame = &(snap_->atomData.electroFrame[atom1]); |
| 104 |
|
} |
| 131 |
|
bool ForceDecomposition::checkNeighborList() { |
| 132 |
|
|
| 133 |
|
int nGroups = snap_->cgData.position.size(); |
| 134 |
< |
|
| 134 |
> |
if (needVelocities_) |
| 135 |
> |
snap_->cgData.setStorageLayout(DataStorage::dslPosition | DataStorage::dslVelocity); |
| 136 |
> |
|
| 137 |
|
// if we have changed the group identities or haven't set up the |
| 138 |
|
// saved positions we automatically will need a neighbor list update: |
| 139 |
|
|
| 140 |
< |
if ( saved_CG_positions_.size() != nGroups ) { |
| 132 |
< |
cerr << "build because size\n"; |
| 133 |
< |
return true; |
| 134 |
< |
} |
| 140 |
> |
if ( saved_CG_positions_.size() != nGroups ) return true; |
| 141 |
|
|
| 142 |
|
RealType dispmax = 0.0; |
| 143 |
|
Vector3d disp; |
| 156 |
|
dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax); |
| 157 |
|
|
| 158 |
|
|
| 159 |
< |
if (dispmax > skinThickness_) { |
| 154 |
< |
cerr << "build because movement\n"; |
| 159 |
> |
if (dispmax > skinThickness_) |
| 160 |
|
return (dispmax > skinThickness_); |
| 161 |
< |
} else { |
| 157 |
< |
cerr << "not rebuilding\n"; |
| 158 |
< |
} |
| 161 |
> |
|
| 162 |
|
return false; |
| 163 |
|
} |
| 164 |
+ |
|
| 165 |
+ |
void ForceDecomposition::addToHeatFlux(Vector3d hf) { |
| 166 |
+ |
snap_->frameData.conductiveHeatFlux += hf; |
| 167 |
+ |
} |
| 168 |
+ |
void ForceDecomposition::setHeatFlux(Vector3d hf) { |
| 169 |
+ |
snap_->frameData.conductiveHeatFlux = hf; |
| 170 |
+ |
} |
| 171 |
+ |
|
| 172 |
|
} |
