| 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(); |
| 54 |
– |
userChoseCutoff_ = false; |
| 58 |
|
|
| 59 |
+ |
usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions(); |
| 60 |
+ |
|
| 61 |
|
Globals* simParams_ = info_->getSimParams(); |
| 62 |
< |
|
| 62 |
> |
if (simParams_->havePrintHeatFlux()) { |
| 63 |
> |
if (simParams_->getPrintHeatFlux()) { |
| 64 |
> |
needVelocities_ = true; |
| 65 |
> |
} |
| 66 |
> |
} |
| 67 |
> |
|
| 68 |
|
if (simParams_->haveSkinThickness()) { |
| 69 |
|
skinThickness_ = simParams_->getSkinThickness(); |
| 70 |
|
} else { |
| 97 |
|
cellOffsets_.push_back( Vector3i(1, -1,1) ); |
| 98 |
|
} |
| 99 |
|
|
| 100 |
+ |
void ForceDecomposition::setCutoffRadius(RealType rcut) { |
| 101 |
+ |
rCut_ = rcut; |
| 102 |
+ |
rList_ = rCut_ + skinThickness_; |
| 103 |
+ |
rListSq_ = rList_ * rList_; |
| 104 |
+ |
} |
| 105 |
+ |
|
| 106 |
|
void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) { |
| 107 |
< |
|
| 108 |
< |
// Still Missing atype, skippedCharge, potVec pot, |
| 109 |
< |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 110 |
< |
sdat.eFrame = &(snap_->atomData.electroFrame[atom1]); |
| 107 |
> |
|
| 108 |
> |
sdat.atid = idents[atom1]; |
| 109 |
> |
|
| 110 |
> |
sdat.pot = &embeddingPot; |
| 111 |
> |
sdat.excludedPot = &excludedSelfPot; |
| 112 |
> |
|
| 113 |
> |
if (storageLayout_ & DataStorage::dslDipole) { |
| 114 |
> |
sdat.dipole = &(snap_->atomData.dipole[atom1]); |
| 115 |
|
} |
| 116 |
< |
|
| 116 |
> |
|
| 117 |
> |
if (storageLayout_ & DataStorage::dslQuadrupole) { |
| 118 |
> |
sdat.quadrupole = &(snap_->atomData.quadrupole[atom1]); |
| 119 |
> |
} |
| 120 |
> |
|
| 121 |
|
if (storageLayout_ & DataStorage::dslTorque) { |
| 122 |
|
sdat.t = &(snap_->atomData.torque[atom1]); |
| 123 |
|
} |
| 134 |
|
sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]); |
| 135 |
|
} |
| 136 |
|
|
| 137 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 138 |
+ |
sdat.skippedCharge = &(snap_->atomData.skippedCharge[atom1]); |
| 139 |
+ |
} |
| 140 |
+ |
|
| 141 |
|
if (storageLayout_ & DataStorage::dslParticlePot) { |
| 142 |
|
sdat.particlePot = &(snap_->atomData.particlePot[atom1]); |
| 143 |
|
} |
| 144 |
+ |
|
| 145 |
+ |
if (storageLayout_ & DataStorage::dslFlucQPosition) { |
| 146 |
+ |
sdat.flucQ = &(snap_->atomData.flucQPos[atom1]); |
| 147 |
+ |
} |
| 148 |
+ |
|
| 149 |
+ |
if (storageLayout_ & DataStorage::dslFlucQForce) { |
| 150 |
+ |
sdat.flucQfrc = &(snap_->atomData.flucQFrc[atom1]); |
| 151 |
+ |
} |
| 152 |
|
} |
| 153 |
|
|
| 154 |
|
bool ForceDecomposition::checkNeighborList() { |
| 155 |
< |
|
| 155 |
> |
RealType st2 = pow( skinThickness_ / 2.0, 2); |
| 156 |
|
int nGroups = snap_->cgData.position.size(); |
| 157 |
< |
|
| 157 |
> |
if (needVelocities_) |
| 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 |
+ |
|
| 164 |
+ |
if ( saved_CG_positions_.size() != nGroups ) return true; |
| 165 |
|
|
| 125 |
– |
if ( saved_CG_positions_.size() != nGroups ) { |
| 126 |
– |
cerr << "build because size\n"; |
| 127 |
– |
return true; |
| 128 |
– |
} |
| 129 |
– |
|
| 166 |
|
RealType dispmax = 0.0; |
| 167 |
|
Vector3d disp; |
| 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++) |
| 136 |
< |
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 |
| 180 |
< |
dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax); |
| 179 |
> |
return (dispmax > st2) ? true : false; |
| 180 |
> |
} |
| 181 |
|
|
| 182 |
< |
|
| 183 |
< |
if (dispmax > skinThickness_) { |
| 184 |
< |
cerr << "build because movement\n"; |
| 185 |
< |
return (dispmax > skinThickness_); |
| 150 |
< |
} |
| 151 |
< |
return false; |
| 182 |
> |
void ForceDecomposition::addToHeatFlux(Vector3d hf) { |
| 183 |
> |
Vector3d chf = snap_->getConductiveHeatFlux(); |
| 184 |
> |
chf += hf; |
| 185 |
> |
snap_->setConductiveHeatFlux(chf); |
| 186 |
|
} |
| 187 |
+ |
void ForceDecomposition::setHeatFlux(Vector3d hf) { |
| 188 |
+ |
snap_->setConductiveHeatFlux(hf); |
| 189 |
+ |
} |
| 190 |
+ |
|
| 191 |
|
} |
