| 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), 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 |
|
if (simParams_->havePrintHeatFlux()) { |
| 64 |
|
if (simParams_->getPrintHeatFlux()) { |
| 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 |
|
} |
| 143 |
|
} |
| 144 |
|
|
| 145 |
|
if (storageLayout_ & DataStorage::dslFlucQForce) { |
| 146 |
< |
sdat.dVdFQ = &(snap_->atomData.flucQFrc[atom1]); |
| 146 |
> |
sdat.flucQfrc = &(snap_->atomData.flucQFrc[atom1]); |
| 147 |
|
} |
| 148 |
|
} |
| 149 |
|
|
| 168 |
|
} |
| 169 |
|
|
| 170 |
|
#ifdef IS_MPI |
| 171 |
< |
MPI::COMM_WORLD.Allreduce(&dispmax, &dispmax, 1, MPI::REALTYPE, MPI::MAX); |
| 171 |
> |
MPI_Allreduce(&dispmax, &dispmax, 1, MPI_REALTYPE, MPI_MAX, MPI_COMM_WORLD); |
| 172 |
|
#endif |
| 173 |
|
|
| 174 |
|
// a conservative test of list skin crossings |
| 182 |
|
} |
| 183 |
|
|
| 184 |
|
void ForceDecomposition::addToHeatFlux(Vector3d hf) { |
| 185 |
< |
snap_->frameData.conductiveHeatFlux += hf; |
| 185 |
> |
Vector3d chf = snap_->getConductiveHeatFlux(); |
| 186 |
> |
chf += hf; |
| 187 |
> |
snap_->setConductiveHeatFlux(chf); |
| 188 |
|
} |
| 189 |
|
void ForceDecomposition::setHeatFlux(Vector3d hf) { |
| 190 |
< |
snap_->frameData.conductiveHeatFlux = hf; |
| 190 |
> |
snap_->setConductiveHeatFlux(hf); |
| 191 |
|
} |
| 192 |
|
|
| 193 |
|
} |
