| 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 |
|
*/ |
| 679 |
|
snap_->atomData.density[i] += rho_tmp[i]; |
| 680 |
|
} |
| 681 |
|
|
| 682 |
+ |
// this isn't necessary if we don't have polarizable atoms, but |
| 683 |
+ |
// we'll leave it here for now. |
| 684 |
|
if (storageLayout_ & DataStorage::dslElectricField) { |
| 685 |
|
|
| 686 |
|
AtomPlanVectorRow->scatter(atomRowData.electricField, |
| 688 |
|
|
| 689 |
|
int n = snap_->atomData.electricField.size(); |
| 690 |
|
vector<Vector3d> field_tmp(n, V3Zero); |
| 691 |
< |
AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp); |
| 691 |
> |
AtomPlanVectorColumn->scatter(atomColData.electricField, |
| 692 |
> |
field_tmp); |
| 693 |
|
for (int i = 0; i < n; i++) |
| 694 |
|
snap_->atomData.electricField[i] += field_tmp[i]; |
| 695 |
|
} |
| 788 |
|
snap_->atomData.flucQFrc[i] += fqfrc_tmp[i]; |
| 789 |
|
|
| 790 |
|
} |
| 791 |
+ |
|
| 792 |
+ |
if (storageLayout_ & DataStorage::dslElectricField) { |
| 793 |
+ |
|
| 794 |
+ |
int nef = snap_->atomData.electricField.size(); |
| 795 |
+ |
vector<Vector3d> efield_tmp(nef, V3Zero); |
| 796 |
|
|
| 797 |
+ |
AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp); |
| 798 |
+ |
for (int i = 0; i < nef; i++) { |
| 799 |
+ |
snap_->atomData.electricField[i] += efield_tmp[i]; |
| 800 |
+ |
efield_tmp[i] = 0.0; |
| 801 |
+ |
} |
| 802 |
+ |
|
| 803 |
+ |
AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp); |
| 804 |
+ |
for (int i = 0; i < nef; i++) |
| 805 |
+ |
snap_->atomData.electricField[i] += efield_tmp[i]; |
| 806 |
+ |
} |
| 807 |
+ |
|
| 808 |
+ |
|
| 809 |
|
nLocal_ = snap_->getNumberOfAtoms(); |
| 810 |
|
|
| 811 |
|
vector<potVec> pot_temp(nLocal_, |
| 1062 |
|
* the parallel decomposition. |
| 1063 |
|
*/ |
| 1064 |
|
bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) { |
| 1065 |
< |
int unique_id_1, unique_id_2, group1, group2; |
| 1065 |
> |
int unique_id_1, unique_id_2; |
| 1066 |
|
|
| 1067 |
|
#ifdef IS_MPI |
| 1068 |
|
// in MPI, we have to look up the unique IDs for each atom |
| 1069 |
|
unique_id_1 = AtomRowToGlobal[atom1]; |
| 1070 |
|
unique_id_2 = AtomColToGlobal[atom2]; |
| 1071 |
< |
group1 = cgRowToGlobal[cg1]; |
| 1072 |
< |
group2 = cgColToGlobal[cg2]; |
| 1071 |
> |
// group1 = cgRowToGlobal[cg1]; |
| 1072 |
> |
// group2 = cgColToGlobal[cg2]; |
| 1073 |
|
#else |
| 1074 |
|
unique_id_1 = AtomLocalToGlobal[atom1]; |
| 1075 |
|
unique_id_2 = AtomLocalToGlobal[atom2]; |
| 1076 |
< |
group1 = cgLocalToGlobal[cg1]; |
| 1077 |
< |
group2 = cgLocalToGlobal[cg2]; |
| 1076 |
> |
int group1 = cgLocalToGlobal[cg1]; |
| 1077 |
> |
int group2 = cgLocalToGlobal[cg2]; |
| 1078 |
|
#endif |
| 1079 |
|
|
| 1080 |
|
if (unique_id_1 == unique_id_2) return true; |
| 1206 |
|
idat.A2 = &(snap_->atomData.aMat[atom2]); |
| 1207 |
|
} |
| 1208 |
|
|
| 1209 |
+ |
RealType ct = dot(idat.A1->getColumn(2), idat.A2->getColumn(2)); |
| 1210 |
+ |
|
| 1211 |
|
if (storageLayout_ & DataStorage::dslTorque) { |
| 1212 |
|
idat.t1 = &(snap_->atomData.torque[atom1]); |
| 1213 |
|
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 1327 |
|
#endif |
| 1328 |
|
|
| 1329 |
|
RealType rList_ = (largestRcut_ + skinThickness_); |
| 1308 |
– |
RealType rl2 = rList_ * rList_; |
| 1330 |
|
Snapshot* snap_ = sman_->getCurrentSnapshot(); |
| 1331 |
|
Mat3x3d Hmat = snap_->getHmat(); |
| 1332 |
|
Vector3d Hx = Hmat.getColumn(0); |
