| 113 |
|
AtomCommIntColumn->gather(idents, identsCol); |
| 114 |
|
|
| 115 |
|
// allocate memory for the parallel objects |
| 116 |
< |
AtomRowToGlobal.resize(nAtomsInRow_); |
| 117 |
< |
AtomColToGlobal.resize(nAtomsInCol_); |
| 118 |
< |
cgRowToGlobal.resize(nGroupsInRow_); |
| 119 |
< |
cgColToGlobal.resize(nGroupsInCol_); |
| 120 |
< |
massFactorsRow.resize(nAtomsInRow_); |
| 121 |
< |
massFactorsCol.resize(nAtomsInCol_); |
| 116 |
> |
atypesRow.resize(nAtomsInRow_); |
| 117 |
> |
atypesCol.resize(nAtomsInCol_); |
| 118 |
> |
|
| 119 |
> |
for (int i = 0; i < nAtomsInRow_; i++) |
| 120 |
> |
atypesRow[i] = ff_->getAtomType(identsRow[i]); |
| 121 |
> |
for (int i = 0; i < nAtomsInCol_; i++) |
| 122 |
> |
atypesCol[i] = ff_->getAtomType(identsCol[i]); |
| 123 |
> |
|
| 124 |
|
pot_row.resize(nAtomsInRow_); |
| 125 |
|
pot_col.resize(nAtomsInCol_); |
| 126 |
|
|
| 127 |
+ |
AtomRowToGlobal.resize(nAtomsInRow_); |
| 128 |
+ |
AtomColToGlobal.resize(nAtomsInCol_); |
| 129 |
|
AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 130 |
|
AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
| 131 |
|
|
| 132 |
+ |
cgRowToGlobal.resize(nGroupsInRow_); |
| 133 |
+ |
cgColToGlobal.resize(nGroupsInCol_); |
| 134 |
|
cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
| 135 |
|
cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
| 136 |
|
|
| 137 |
+ |
massFactorsRow.resize(nAtomsInRow_); |
| 138 |
+ |
massFactorsCol.resize(nAtomsInCol_); |
| 139 |
|
AtomCommRealRow->gather(massFactors, massFactorsRow); |
| 140 |
|
AtomCommRealColumn->gather(massFactors, massFactorsCol); |
| 141 |
|
|
| 195 |
|
|
| 196 |
|
#endif |
| 197 |
|
|
| 198 |
+ |
// allocate memory for the parallel objects |
| 199 |
+ |
atypesLocal.resize(nLocal_); |
| 200 |
+ |
|
| 201 |
+ |
for (int i = 0; i < nLocal_; i++) |
| 202 |
+ |
atypesLocal[i] = ff_->getAtomType(idents[i]); |
| 203 |
+ |
|
| 204 |
|
groupList_.clear(); |
| 205 |
|
groupList_.resize(nGroups_); |
| 206 |
|
for (int i = 0; i < nGroups_; i++) { |
| 850 |
|
idat.excluded = excludeAtomPair(atom1, atom2); |
| 851 |
|
|
| 852 |
|
#ifdef IS_MPI |
| 853 |
< |
|
| 854 |
< |
idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
| 855 |
< |
ff_->getAtomType(identsCol[atom2]) ); |
| 853 |
> |
idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]); |
| 854 |
> |
//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
| 855 |
> |
// ff_->getAtomType(identsCol[atom2]) ); |
| 856 |
|
|
| 857 |
|
if (storageLayout_ & DataStorage::dslAmat) { |
| 858 |
|
idat.A1 = &(atomRowData.aMat[atom1]); |
| 896 |
|
|
| 897 |
|
#else |
| 898 |
|
|
| 899 |
< |
idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
| 900 |
< |
ff_->getAtomType(idents[atom2]) ); |
| 899 |
> |
idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]); |
| 900 |
> |
//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
| 901 |
> |
// ff_->getAtomType(idents[atom2]) ); |
| 902 |
|
|
| 903 |
|
if (storageLayout_ & DataStorage::dslAmat) { |
| 904 |
|
idat.A1 = &(snap_->atomData.aMat[atom1]); |
