| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
| 42 |
< |
#include "parallel/ForceDecomposition.hpp" |
| 43 |
< |
#include "math/Vector3.hpp" |
| 42 |
> |
|
| 43 |
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#ifdef IS_MPI |
| 44 |
|
#include <mpi.h> |
| 45 |
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#endif |
| 46 |
|
|
| 47 |
+ |
#include "parallel/ForceDecomposition.hpp" |
| 48 |
+ |
#include "math/Vector3.hpp" |
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+ |
|
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using namespace std; |
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namespace OpenMD { |
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|
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sman_ = info_->getSnapshotManager(); |
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storageLayout_ = sman_->getStorageLayout(); |
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ff_ = info_->getForceField(); |
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– |
userChoseCutoff_ = false; |
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|
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usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions(); |
| 60 |
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|
| 97 |
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cellOffsets_.push_back( Vector3i(1, -1,1) ); |
| 98 |
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} |
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|
| 100 |
+ |
void ForceDecomposition::setCutoffRadius(RealType rcut) { |
| 101 |
+ |
rCut_ = rcut; |
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+ |
rList_ = rCut_ + skinThickness_; |
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+ |
rListSq_ = rList_ * rList_; |
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+ |
} |
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+ |
|
| 106 |
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void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) { |
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|
| 108 |
< |
sdat.atype = atypesLocal[atom1]; |
| 108 |
> |
sdat.atid = idents[atom1]; |
| 109 |
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|
| 110 |
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sdat.pot = &embeddingPot; |
| 111 |
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sdat.excludedPot = &excludedSelfPot; |
| 147 |
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} |
| 148 |
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|
| 149 |
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if (storageLayout_ & DataStorage::dslFlucQForce) { |
| 150 |
< |
sdat.dVdFQ = &(snap_->atomData.flucQFrc[atom1]); |
| 150 |
> |
sdat.flucQfrc = &(snap_->atomData.flucQFrc[atom1]); |
| 151 |
|
} |
| 152 |
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} |
| 153 |
|
|
| 154 |
|
bool ForceDecomposition::checkNeighborList() { |
| 155 |
< |
|
| 155 |
> |
RealType st2 = pow( skinThickness_ / 2.0, 2); |
| 156 |
|
int nGroups = snap_->cgData.position.size(); |
| 157 |
|
if (needVelocities_) |
| 158 |
< |
snap_->cgData.setStorageLayout(DataStorage::dslPosition | DataStorage::dslVelocity); |
| 158 |
> |
snap_->cgData.setStorageLayout(DataStorage::dslPosition | |
| 159 |
> |
DataStorage::dslVelocity); |
| 160 |
|
|
| 161 |
|
// if we have changed the group identities or haven't set up the |
| 162 |
|
// saved positions we automatically will need a neighbor list update: |
| 163 |
< |
|
| 163 |
> |
|
| 164 |
|
if ( saved_CG_positions_.size() != nGroups ) return true; |
| 165 |
|
|
| 166 |
|
RealType dispmax = 0.0; |
| 168 |
|
|
| 169 |
|
for (int i = 0; i < nGroups; i++) { |
| 170 |
|
disp = snap_->cgData.position[i] - saved_CG_positions_[i]; |
| 171 |
< |
for (int j = 0; j < 3; j++) |
| 164 |
< |
dispmax = max( abs(disp[j]), dispmax); |
| 171 |
> |
dispmax = max(dispmax, disp.lengthSquare()); |
| 172 |
|
} |
| 173 |
|
|
| 174 |
|
#ifdef IS_MPI |
| 175 |
< |
MPI::COMM_WORLD.Allreduce(&dispmax, &dispmax, 1, MPI::REALTYPE, MPI::MAX); |
| 175 |
> |
MPI_Allreduce(MPI_IN_PLACE, &dispmax, 1, MPI_REALTYPE, MPI_MAX, |
| 176 |
> |
MPI_COMM_WORLD); |
| 177 |
|
#endif |
| 178 |
|
|
| 179 |
< |
// a conservative test of list skin crossings |
| 172 |
< |
dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax); |
| 173 |
< |
|
| 174 |
< |
|
| 175 |
< |
if (dispmax > skinThickness_) |
| 176 |
< |
return (dispmax > skinThickness_); |
| 177 |
< |
|
| 178 |
< |
return false; |
| 179 |
> |
return (dispmax > st2) ? true : false; |
| 180 |
|
} |
| 181 |
|
|
| 182 |
|
void ForceDecomposition::addToHeatFlux(Vector3d hf) { |
