# | Line 61 | Line 61 | namespace OpenMD { | |
---|---|---|
61 | nGroups_ = info_->getNLocalCutoffGroups(); | |
62 | cerr << "in dId, nGroups = " << nGroups_ << "\n"; | |
63 | // gather the information for atomtype IDs (atids): | |
64 | < | identsLocal = info_->getIdentArray(); |
64 | > | idents = info_->getIdentArray(); |
65 | AtomLocalToGlobal = info_->getGlobalAtomIndices(); | |
66 | cgLocalToGlobal = info_->getGlobalGroupIndices(); | |
67 | vector<int> globalGroupMembership = info_->getGlobalGroupMembership(); | |
# | Line 108 | Line 108 | namespace OpenMD { | |
108 | identsRow.resize(nAtomsInRow_); | |
109 | identsCol.resize(nAtomsInCol_); | |
110 | ||
111 | < | AtomCommIntRow->gather(identsLocal, identsRow); |
112 | < | AtomCommIntColumn->gather(identsLocal, identsCol); |
111 | > | AtomCommIntRow->gather(idents, identsRow); |
112 | > | AtomCommIntColumn->gather(idents, identsCol); |
113 | ||
114 | AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); | |
115 | AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); | |
# | Line 232 | Line 232 | namespace OpenMD { | |
232 | set<AtomType*> atypes = info_->getSimulatedAtomTypes(); | |
233 | vector<RealType> atypeCutoff; | |
234 | atypeCutoff.resize( atypes.size() ); | |
235 | < | |
235 | > | |
236 | for (set<AtomType*>::iterator at = atypes.begin(); | |
237 | at != atypes.end(); ++at){ | |
238 | – | rc = interactionMan_->getSuggestedCutoffRadius(*at); |
238 | atid = (*at)->getIdent(); | |
239 | < | atypeCutoff[atid] = rc; |
239 | > | |
240 | > | if (userChoseCutoff_) |
241 | > | atypeCutoff[atid] = userCutoff_; |
242 | > | else |
243 | > | atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at); |
244 | } | |
245 | ||
246 | vector<RealType> gTypeCutoffs; | |
# | Line 309 | Line 312 | namespace OpenMD { | |
312 | for (vector<int>::iterator ia = atomList.begin(); | |
313 | ia != atomList.end(); ++ia) { | |
314 | int atom1 = (*ia); | |
315 | < | atid = identsLocal[atom1]; |
315 | > | atid = idents[atom1]; |
316 | if (atypeCutoff[atid] > groupCutoff[cg1]) { | |
317 | groupCutoff[cg1] = atypeCutoff[atid]; | |
318 | } | |
# | Line 378 | Line 381 | namespace OpenMD { | |
381 | if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) { | |
382 | sprintf(painCave.errMsg, | |
383 | "ForceMatrixDecomposition::createGtypeCutoffMap " | |
384 | < | "user-specified rCut does not match computed group Cutoff\n"); |
384 | > | "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_); |
385 | painCave.severity = OPENMD_ERROR; | |
386 | painCave.isFatal = 1; | |
387 | simError(); | |
# | Line 410 | Line 413 | namespace OpenMD { | |
413 | } | |
414 | ||
415 | void ForceMatrixDecomposition::zeroWorkArrays() { | |
416 | < | |
417 | < | for (int j = 0; j < N_INTERACTION_FAMILIES; j++) { |
415 | < | longRangePot_[j] = 0.0; |
416 | < | } |
416 | > | pairwisePot = 0.0; |
417 | > | embeddingPot = 0.0; |
418 | ||
419 | #ifdef IS_MPI | |
420 | if (storageLayout_ & DataStorage::dslForce) { | |
# | Line 430 | Line 431 | namespace OpenMD { | |
431 | Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); | |
432 | ||
433 | fill(pot_col.begin(), pot_col.end(), | |
434 | < | Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
434 | < | |
435 | < | pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0); |
434 | > | Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
435 | ||
436 | if (storageLayout_ & DataStorage::dslParticlePot) { | |
437 | fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0); | |
# | Line 606 | Line 605 | namespace OpenMD { | |
605 | AtomCommPotRow->scatter(pot_row, pot_temp); | |
606 | ||
607 | for (int ii = 0; ii < pot_temp.size(); ii++ ) | |
608 | < | pot_local += pot_temp[ii]; |
608 | > | pairwisePot += pot_temp[ii]; |
609 | ||
610 | fill(pot_temp.begin(), pot_temp.end(), | |
611 | Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); | |
# | Line 614 | Line 613 | namespace OpenMD { | |
613 | AtomCommPotColumn->scatter(pot_col, pot_temp); | |
614 | ||
615 | for (int ii = 0; ii < pot_temp.size(); ii++ ) | |
616 | < | pot_local += pot_temp[ii]; |
618 | < | |
616 | > | pairwisePot += pot_temp[ii]; |
617 | #endif | |
618 | + | |
619 | } | |
620 | ||
621 | int ForceMatrixDecomposition::getNAtomsInRow() { | |
# | Line 754 | Line 753 | namespace OpenMD { | |
753 | for (vector<int>::iterator i = skipsForAtom[atom1].begin(); | |
754 | i != skipsForAtom[atom1].end(); ++i) { | |
755 | if ( (*i) == unique_id_2 ) return true; | |
756 | < | } |
756 | > | } |
757 | ||
758 | + | return false; |
759 | } | |
760 | ||
761 | ||
# | Line 776 | Line 776 | namespace OpenMD { | |
776 | } | |
777 | ||
778 | // filling interaction blocks with pointers | |
779 | < | void ForceMatrixDecomposition::fillInteractionData(InteractionData idat, |
779 | > | void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, |
780 | int atom1, int atom2) { | |
781 | #ifdef IS_MPI | |
782 | ||
# | Line 820 | Line 820 | namespace OpenMD { | |
820 | ||
821 | #else | |
822 | ||
823 | < | idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]), |
824 | < | ff_->getAtomType(identsLocal[atom2]) ); |
823 | > | idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
824 | > | ff_->getAtomType(idents[atom2]) ); |
825 | ||
826 | if (storageLayout_ & DataStorage::dslAmat) { | |
827 | idat.A1 = &(snap_->atomData.aMat[atom1]); | |
# | Line 838 | Line 838 | namespace OpenMD { | |
838 | idat.t2 = &(snap_->atomData.torque[atom2]); | |
839 | } | |
840 | ||
841 | < | if (storageLayout_ & DataStorage::dslDensity) { |
841 | > | if (storageLayout_ & DataStorage::dslDensity) { |
842 | idat.rho1 = &(snap_->atomData.density[atom1]); | |
843 | idat.rho2 = &(snap_->atomData.density[atom2]); | |
844 | } | |
# | Line 862 | Line 862 | namespace OpenMD { | |
862 | } | |
863 | ||
864 | ||
865 | < | void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) { |
865 | > | void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) { |
866 | #ifdef IS_MPI | |
867 | pot_row[atom1] += 0.5 * *(idat.pot); | |
868 | pot_col[atom2] += 0.5 * *(idat.pot); | |
# | Line 870 | Line 870 | namespace OpenMD { | |
870 | atomRowData.force[atom1] += *(idat.f1); | |
871 | atomColData.force[atom2] -= *(idat.f1); | |
872 | #else | |
873 | < | longRangePot_ += *(idat.pot); |
874 | < | |
873 | > | pairwisePot += *(idat.pot); |
874 | > | |
875 | snap_->atomData.force[atom1] += *(idat.f1); | |
876 | snap_->atomData.force[atom2] -= *(idat.f1); | |
877 | #endif | |
# | Line 879 | Line 879 | namespace OpenMD { | |
879 | } | |
880 | ||
881 | ||
882 | < | void ForceMatrixDecomposition::fillSkipData(InteractionData idat, |
882 | > | void ForceMatrixDecomposition::fillSkipData(InteractionData &idat, |
883 | int atom1, int atom2) { | |
884 | + | // Still Missing:: skippedCharge fill must be added to DataStorage |
885 | #ifdef IS_MPI | |
886 | idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), | |
887 | ff_->getAtomType(identsCol[atom2]) ); | |
# | Line 894 | Line 895 | namespace OpenMD { | |
895 | idat.t2 = &(atomColData.torque[atom2]); | |
896 | } | |
897 | #else | |
898 | < | idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]), |
899 | < | ff_->getAtomType(identsLocal[atom2]) ); |
898 | > | idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
899 | > | ff_->getAtomType(idents[atom2]) ); |
900 | ||
901 | if (storageLayout_ & DataStorage::dslElectroFrame) { | |
902 | idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); | |
# | Line 908 | Line 909 | namespace OpenMD { | |
909 | #endif | |
910 | } | |
911 | ||
912 | + | |
913 | + | void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) { |
914 | + | #ifdef IS_MPI |
915 | + | pot_row[atom1] += 0.5 * *(idat.pot); |
916 | + | pot_col[atom2] += 0.5 * *(idat.pot); |
917 | + | #else |
918 | + | pairwisePot += *(idat.pot); |
919 | + | #endif |
920 | + | |
921 | + | } |
922 | + | |
923 | + | |
924 | /* | |
925 | * buildNeighborList | |
926 | * | |
# | Line 943 | Line 956 | namespace OpenMD { | |
956 | int cellIndex; | |
957 | int nCtot = nCells_.x() * nCells_.y() * nCells_.z(); | |
958 | ||
946 | – | cerr << "flag1\n"; |
959 | #ifdef IS_MPI | |
960 | cellListRow_.resize(nCtot); | |
961 | cellListCol_.resize(nCtot); | |
962 | #else | |
963 | cellList_.resize(nCtot); | |
964 | #endif | |
965 | < | cerr << "flag2\n"; |
965 | > | |
966 | #ifdef IS_MPI | |
967 | for (int i = 0; i < nGroupsInRow_; i++) { | |
968 | rs = cgRowData.position[i]; | |
# | Line 1111 | Line 1123 | namespace OpenMD { | |
1123 | saved_CG_positions_.clear(); | |
1124 | for (int i = 0; i < nGroups_; i++) | |
1125 | saved_CG_positions_.push_back(snap_->cgData.position[i]); | |
1126 | < | |
1126 | > | |
1127 | return neighborList; | |
1128 | } | |
1129 | } //end namespace OpenMD |
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