| 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/ForceMatrixDecomposition.hpp" |
| 43 |
|
#include "math/SquareMatrix3.hpp" |
| 537 |
|
fill(snap_->atomData.density.begin(), |
| 538 |
|
snap_->atomData.density.end(), 0.0); |
| 539 |
|
} |
| 540 |
+ |
|
| 541 |
|
if (storageLayout_ & DataStorage::dslFunctional) { |
| 542 |
|
fill(snap_->atomData.functional.begin(), |
| 543 |
|
snap_->atomData.functional.end(), 0.0); |
| 544 |
|
} |
| 545 |
+ |
|
| 546 |
|
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 547 |
|
fill(snap_->atomData.functionalDerivative.begin(), |
| 548 |
|
snap_->atomData.functionalDerivative.end(), 0.0); |
| 549 |
|
} |
| 550 |
+ |
|
| 551 |
|
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 552 |
|
fill(snap_->atomData.skippedCharge.begin(), |
| 553 |
|
snap_->atomData.skippedCharge.end(), 0.0); |
| 554 |
|
} |
| 551 |
– |
|
| 555 |
|
} |
| 556 |
|
|
| 557 |
|
|
| 953 |
|
} |
| 954 |
|
|
| 955 |
|
#else |
| 956 |
+ |
|
| 957 |
+ |
|
| 958 |
+ |
// cerr << "atoms = " << atom1 << " " << atom2 << "\n"; |
| 959 |
+ |
// cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n"; |
| 960 |
+ |
// cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n"; |
| 961 |
|
|
| 962 |
|
idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]); |
| 963 |
|
//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
| 1008 |
|
|
| 1009 |
|
void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) { |
| 1010 |
|
#ifdef IS_MPI |
| 1011 |
< |
pot_row[atom1] += 0.5 * *(idat.pot); |
| 1012 |
< |
pot_col[atom2] += 0.5 * *(idat.pot); |
| 1011 |
> |
pot_row[atom1] += RealType(0.5) * *(idat.pot); |
| 1012 |
> |
pot_col[atom2] += RealType(0.5) * *(idat.pot); |
| 1013 |
|
|
| 1014 |
|
atomRowData.force[atom1] += *(idat.f1); |
| 1015 |
|
atomColData.force[atom2] -= *(idat.f1); |
