176 |
|
pot_row.resize(nAtomsInRow_); |
177 |
|
pot_col.resize(nAtomsInCol_); |
178 |
|
|
179 |
+ |
expot_row.resize(nAtomsInRow_); |
180 |
+ |
expot_col.resize(nAtomsInCol_); |
181 |
+ |
|
182 |
|
AtomRowToGlobal.resize(nAtomsInRow_); |
183 |
|
AtomColToGlobal.resize(nAtomsInCol_); |
184 |
|
AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
464 |
|
} |
465 |
|
} |
466 |
|
|
464 |
– |
|
467 |
|
groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) { |
468 |
|
int i, j; |
469 |
|
#ifdef IS_MPI |
487 |
|
void ForceMatrixDecomposition::zeroWorkArrays() { |
488 |
|
pairwisePot = 0.0; |
489 |
|
embeddingPot = 0.0; |
490 |
+ |
excludedPot = 0.0; |
491 |
|
|
492 |
|
#ifdef IS_MPI |
493 |
|
if (storageLayout_ & DataStorage::dslForce) { |
504 |
|
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
505 |
|
|
506 |
|
fill(pot_col.begin(), pot_col.end(), |
507 |
+ |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
508 |
+ |
|
509 |
+ |
fill(expot_row.begin(), expot_row.end(), |
510 |
+ |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
511 |
+ |
|
512 |
+ |
fill(expot_col.begin(), expot_col.end(), |
513 |
|
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
514 |
|
|
515 |
|
if (storageLayout_ & DataStorage::dslParticlePot) { |
790 |
|
|
791 |
|
vector<potVec> pot_temp(nLocal_, |
792 |
|
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
793 |
+ |
vector<potVec> expot_temp(nLocal_, |
794 |
+ |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
795 |
|
|
796 |
|
// scatter/gather pot_row into the members of my column |
797 |
|
|
798 |
|
AtomPlanPotRow->scatter(pot_row, pot_temp); |
799 |
+ |
AtomPlanPotRow->scatter(expot_row, expot_temp); |
800 |
|
|
801 |
< |
for (int ii = 0; ii < pot_temp.size(); ii++ ) |
801 |
> |
for (int ii = 0; ii < pot_temp.size(); ii++ ) |
802 |
|
pairwisePot += pot_temp[ii]; |
803 |
+ |
|
804 |
+ |
for (int ii = 0; ii < expot_temp.size(); ii++ ) |
805 |
+ |
excludedPot += expot_temp[ii]; |
806 |
|
|
807 |
|
if (storageLayout_ & DataStorage::dslParticlePot) { |
808 |
|
// This is the pairwise contribution to the particle pot. The |
819 |
|
} |
820 |
|
|
821 |
|
fill(pot_temp.begin(), pot_temp.end(), |
822 |
+ |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
823 |
+ |
fill(expot_temp.begin(), expot_temp.end(), |
824 |
|
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
825 |
|
|
826 |
|
AtomPlanPotColumn->scatter(pot_col, pot_temp); |
827 |
+ |
AtomPlanPotColumn->scatter(expot_col, expot_temp); |
828 |
|
|
829 |
|
for (int ii = 0; ii < pot_temp.size(); ii++ ) |
830 |
|
pairwisePot += pot_temp[ii]; |
831 |
|
|
832 |
+ |
for (int ii = 0; ii < expot_temp.size(); ii++ ) |
833 |
+ |
excludedPot += expot_temp[ii]; |
834 |
+ |
|
835 |
|
if (storageLayout_ & DataStorage::dslParticlePot) { |
836 |
|
// This is the pairwise contribution to the particle pot. The |
837 |
|
// embedding contribution is added in each of the low level |
874 |
|
} |
875 |
|
|
876 |
|
for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { |
877 |
< |
RealType ploc1 = embeddingPot[ii]; |
877 |
> |
RealType ploc1 = excludedPot[ii]; |
878 |
|
RealType ploc2 = 0.0; |
879 |
|
MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); |
880 |
< |
embeddingPot[ii] = ploc2; |
880 |
> |
excludedPot[ii] = ploc2; |
881 |
|
} |
882 |
< |
|
882 |
> |
|
883 |
|
// Here be dragons. |
884 |
|
MPI::Intracomm col = colComm.getComm(); |
885 |
|
|
889 |
|
|
890 |
|
|
891 |
|
#endif |
892 |
+ |
|
893 |
+ |
} |
894 |
+ |
|
895 |
+ |
/** |
896 |
+ |
* Collects information obtained during the post-pair (and embedding |
897 |
+ |
* functional) loops onto local data structures. |
898 |
+ |
*/ |
899 |
+ |
void ForceMatrixDecomposition::collectSelfData() { |
900 |
+ |
snap_ = sman_->getCurrentSnapshot(); |
901 |
+ |
storageLayout_ = sman_->getStorageLayout(); |
902 |
|
|
903 |
+ |
#ifdef IS_MPI |
904 |
+ |
for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { |
905 |
+ |
RealType ploc1 = embeddingPot[ii]; |
906 |
+ |
RealType ploc2 = 0.0; |
907 |
+ |
MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); |
908 |
+ |
embeddingPot[ii] = ploc2; |
909 |
+ |
} |
910 |
+ |
#endif |
911 |
+ |
|
912 |
|
} |
913 |
|
|
914 |
+ |
|
915 |
+ |
|
916 |
|
int ForceMatrixDecomposition::getNAtomsInRow() { |
917 |
|
#ifdef IS_MPI |
918 |
|
return nAtomsInRow_; |
1035 |
|
* We need to exclude some overcounted interactions that result from |
1036 |
|
* the parallel decomposition. |
1037 |
|
*/ |
1038 |
< |
bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { |
1039 |
< |
int unique_id_1, unique_id_2; |
1038 |
> |
bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) { |
1039 |
> |
int unique_id_1, unique_id_2, group1, group2; |
1040 |
|
|
1041 |
|
#ifdef IS_MPI |
1042 |
|
// in MPI, we have to look up the unique IDs for each atom |
1043 |
|
unique_id_1 = AtomRowToGlobal[atom1]; |
1044 |
|
unique_id_2 = AtomColToGlobal[atom2]; |
1045 |
+ |
group1 = cgRowToGlobal[cg1]; |
1046 |
+ |
group2 = cgColToGlobal[cg2]; |
1047 |
|
#else |
1048 |
|
unique_id_1 = AtomLocalToGlobal[atom1]; |
1049 |
|
unique_id_2 = AtomLocalToGlobal[atom2]; |
1050 |
+ |
group1 = cgLocalToGlobal[cg1]; |
1051 |
+ |
group2 = cgLocalToGlobal[cg2]; |
1052 |
|
#endif |
1053 |
|
|
1054 |
|
if (unique_id_1 == unique_id_2) return true; |
1060 |
|
} else { |
1061 |
|
if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
1062 |
|
} |
1063 |
+ |
#endif |
1064 |
+ |
|
1065 |
+ |
#ifndef IS_MPI |
1066 |
+ |
if (group1 == group2) { |
1067 |
+ |
if (unique_id_1 < unique_id_2) return true; |
1068 |
+ |
} |
1069 |
|
#endif |
1070 |
|
|
1071 |
|
return false; |
1168 |
|
|
1169 |
|
#else |
1170 |
|
|
1119 |
– |
|
1120 |
– |
// cerr << "atoms = " << atom1 << " " << atom2 << "\n"; |
1121 |
– |
// cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n"; |
1122 |
– |
// cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n"; |
1123 |
– |
|
1171 |
|
idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]); |
1125 |
– |
//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
1126 |
– |
// ff_->getAtomType(idents[atom2]) ); |
1172 |
|
|
1173 |
|
if (storageLayout_ & DataStorage::dslAmat) { |
1174 |
|
idat.A1 = &(snap_->atomData.aMat[atom1]); |
1223 |
|
#ifdef IS_MPI |
1224 |
|
pot_row[atom1] += RealType(0.5) * *(idat.pot); |
1225 |
|
pot_col[atom2] += RealType(0.5) * *(idat.pot); |
1226 |
+ |
expot_row[atom1] += RealType(0.5) * *(idat.excludedPot); |
1227 |
+ |
expot_col[atom2] += RealType(0.5) * *(idat.excludedPot); |
1228 |
|
|
1229 |
|
atomRowData.force[atom1] += *(idat.f1); |
1230 |
|
atomColData.force[atom2] -= *(idat.f1); |
1241 |
|
|
1242 |
|
#else |
1243 |
|
pairwisePot += *(idat.pot); |
1244 |
+ |
excludedPot += *(idat.excludedPot); |
1245 |
|
|
1246 |
|
snap_->atomData.force[atom1] += *(idat.f1); |
1247 |
|
snap_->atomData.force[atom2] -= *(idat.f1); |