| 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" |
| 48 |
|
using namespace std; |
| 49 |
|
namespace OpenMD { |
| 50 |
|
|
| 51 |
< |
ForceDecomposition::ForceDecomposition(SimInfo* info) : info_(info) { |
| 51 |
> |
ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan) { |
| 52 |
|
sman_ = info_->getSnapshotManager(); |
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|
storageLayout_ = sman_->getStorageLayout(); |
| 54 |
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ff_ = info_->getForceField(); |
| 55 |
+ |
userChoseCutoff_ = false; |
| 56 |
|
|
| 57 |
|
Globals* simParams_ = info_->getSimParams(); |
| 58 |
|
|
| 88 |
|
cellOffsets_.push_back( Vector3i(1, -1,1) ); |
| 89 |
|
} |
| 90 |
|
|
| 91 |
< |
SelfData ForceDecomposition::fillSelfData(int atom1) { |
| 92 |
< |
SelfData sdat; |
| 93 |
< |
// Still Missing atype, skippedCharge, potVec pot, |
| 91 |
> |
void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) { |
| 92 |
> |
|
| 93 |
> |
sdat.atype = atypesLocal[atom1]; |
| 94 |
> |
|
| 95 |
> |
sdat.pot = &embeddingPot; |
| 96 |
> |
|
| 97 |
|
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 98 |
|
sdat.eFrame = &(snap_->atomData.electroFrame[atom1]); |
| 99 |
|
} |
| 114 |
|
sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]); |
| 115 |
|
} |
| 116 |
|
|
| 117 |
< |
return sdat; |
| 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 |
> |
} |
| 124 |
|
} |
| 125 |
|
|
| 126 |
|
bool ForceDecomposition::checkNeighborList() { |
| 148 |
|
// a conservative test of list skin crossings |
| 149 |
|
dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax); |
| 150 |
|
|
| 151 |
< |
return (dispmax > skinThickness_); |
| 151 |
> |
|
| 152 |
> |
if (dispmax > skinThickness_) |
| 153 |
> |
return (dispmax > skinThickness_); |
| 154 |
> |
|
| 155 |
> |
return false; |
| 156 |
|
} |
| 157 |
|
} |
