| 57 |
|
storageLayout_ = sman_->getStorageLayout(); |
| 58 |
|
ff_ = info_->getForceField(); |
| 59 |
|
nLocal_ = snap_->getNumberOfAtoms(); |
| 60 |
< |
|
| 60 |
> |
|
| 61 |
|
nGroups_ = info_->getNLocalCutoffGroups(); |
| 62 |
– |
cerr << "in dId, nGroups = " << nGroups_ << "\n"; |
| 62 |
|
// gather the information for atomtype IDs (atids): |
| 63 |
|
idents = info_->getIdentArray(); |
| 64 |
|
AtomLocalToGlobal = info_->getGlobalAtomIndices(); |
| 65 |
|
cgLocalToGlobal = info_->getGlobalGroupIndices(); |
| 66 |
|
vector<int> globalGroupMembership = info_->getGlobalGroupMembership(); |
| 67 |
+ |
|
| 68 |
|
massFactors = info_->getMassFactors(); |
| 69 |
|
|
| 70 |
< |
PairList excludes = info_->getExcludedInteractions(); |
| 71 |
< |
PairList oneTwo = info_->getOneTwoInteractions(); |
| 72 |
< |
PairList oneThree = info_->getOneThreeInteractions(); |
| 73 |
< |
PairList oneFour = info_->getOneFourInteractions(); |
| 70 |
> |
PairList* excludes = info_->getExcludedInteractions(); |
| 71 |
> |
PairList* oneTwo = info_->getOneTwoInteractions(); |
| 72 |
> |
PairList* oneThree = info_->getOneThreeInteractions(); |
| 73 |
> |
PairList* oneFour = info_->getOneFourInteractions(); |
| 74 |
|
|
| 75 |
|
#ifdef IS_MPI |
| 76 |
|
|
| 112 |
|
AtomCommIntRow->gather(idents, identsRow); |
| 113 |
|
AtomCommIntColumn->gather(idents, identsCol); |
| 114 |
|
|
| 115 |
+ |
vector<int>::iterator it; |
| 116 |
+ |
for (it = AtomLocalToGlobal.begin(); it != AtomLocalToGlobal.end(); ++it) { |
| 117 |
+ |
cerr << "my AtomLocalToGlobal = " << (*it) << "\n"; |
| 118 |
+ |
} |
| 119 |
|
AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 120 |
|
AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
| 121 |
|
|
| 147 |
|
} |
| 148 |
|
} |
| 149 |
|
|
| 150 |
< |
skipsForAtom.clear(); |
| 151 |
< |
skipsForAtom.resize(nAtomsInRow_); |
| 150 |
> |
excludesForAtom.clear(); |
| 151 |
> |
excludesForAtom.resize(nAtomsInRow_); |
| 152 |
|
toposForAtom.clear(); |
| 153 |
|
toposForAtom.resize(nAtomsInRow_); |
| 154 |
|
topoDist.clear(); |
| 159 |
|
for (int j = 0; j < nAtomsInCol_; j++) { |
| 160 |
|
int jglob = AtomColToGlobal[j]; |
| 161 |
|
|
| 162 |
< |
if (excludes.hasPair(iglob, jglob)) |
| 163 |
< |
skipsForAtom[i].push_back(j); |
| 162 |
> |
if (excludes->hasPair(iglob, jglob)) |
| 163 |
> |
excludesForAtom[i].push_back(j); |
| 164 |
|
|
| 165 |
< |
if (oneTwo.hasPair(iglob, jglob)) { |
| 165 |
> |
if (oneTwo->hasPair(iglob, jglob)) { |
| 166 |
|
toposForAtom[i].push_back(j); |
| 167 |
|
topoDist[i].push_back(1); |
| 168 |
|
} else { |
| 169 |
< |
if (oneThree.hasPair(iglob, jglob)) { |
| 169 |
> |
if (oneThree->hasPair(iglob, jglob)) { |
| 170 |
|
toposForAtom[i].push_back(j); |
| 171 |
|
topoDist[i].push_back(2); |
| 172 |
|
} else { |
| 173 |
< |
if (oneFour.hasPair(iglob, jglob)) { |
| 173 |
> |
if (oneFour->hasPair(iglob, jglob)) { |
| 174 |
|
toposForAtom[i].push_back(j); |
| 175 |
|
topoDist[i].push_back(3); |
| 176 |
|
} |
| 193 |
|
} |
| 194 |
|
} |
| 195 |
|
|
| 196 |
< |
skipsForAtom.clear(); |
| 197 |
< |
skipsForAtom.resize(nLocal_); |
| 196 |
> |
excludesForAtom.clear(); |
| 197 |
> |
excludesForAtom.resize(nLocal_); |
| 198 |
|
toposForAtom.clear(); |
| 199 |
|
toposForAtom.resize(nLocal_); |
| 200 |
|
topoDist.clear(); |
| 206 |
|
for (int j = 0; j < nLocal_; j++) { |
| 207 |
|
int jglob = AtomLocalToGlobal[j]; |
| 208 |
|
|
| 209 |
< |
if (excludes.hasPair(iglob, jglob)) |
| 210 |
< |
skipsForAtom[i].push_back(j); |
| 209 |
> |
if (excludes->hasPair(iglob, jglob)) |
| 210 |
> |
excludesForAtom[i].push_back(j); |
| 211 |
|
|
| 212 |
< |
if (oneTwo.hasPair(iglob, jglob)) { |
| 212 |
> |
if (oneTwo->hasPair(iglob, jglob)) { |
| 213 |
|
toposForAtom[i].push_back(j); |
| 214 |
|
topoDist[i].push_back(1); |
| 215 |
|
} else { |
| 216 |
< |
if (oneThree.hasPair(iglob, jglob)) { |
| 216 |
> |
if (oneThree->hasPair(iglob, jglob)) { |
| 217 |
|
toposForAtom[i].push_back(j); |
| 218 |
|
topoDist[i].push_back(2); |
| 219 |
|
} else { |
| 220 |
< |
if (oneFour.hasPair(iglob, jglob)) { |
| 220 |
> |
if (oneFour->hasPair(iglob, jglob)) { |
| 221 |
|
toposForAtom[i].push_back(j); |
| 222 |
|
topoDist[i].push_back(3); |
| 223 |
|
} |
| 227 |
|
} |
| 228 |
|
|
| 229 |
|
createGtypeCutoffMap(); |
| 230 |
+ |
|
| 231 |
|
} |
| 232 |
|
|
| 233 |
|
void ForceMatrixDecomposition::createGtypeCutoffMap() { |
| 234 |
< |
|
| 234 |
> |
|
| 235 |
|
RealType tol = 1e-6; |
| 236 |
|
RealType rc; |
| 237 |
|
int atid; |
| 238 |
|
set<AtomType*> atypes = info_->getSimulatedAtomTypes(); |
| 239 |
< |
vector<RealType> atypeCutoff; |
| 235 |
< |
atypeCutoff.resize( atypes.size() ); |
| 239 |
> |
map<int, RealType> atypeCutoff; |
| 240 |
|
|
| 241 |
|
for (set<AtomType*>::iterator at = atypes.begin(); |
| 242 |
|
at != atypes.end(); ++at){ |
| 243 |
|
atid = (*at)->getIdent(); |
| 244 |
< |
|
| 241 |
< |
if (userChoseCutoff_) |
| 244 |
> |
if (userChoseCutoff_) |
| 245 |
|
atypeCutoff[atid] = userCutoff_; |
| 246 |
< |
else |
| 246 |
> |
else |
| 247 |
|
atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at); |
| 248 |
|
} |
| 249 |
|
|
| 250 |
|
vector<RealType> gTypeCutoffs; |
| 248 |
– |
|
| 251 |
|
// first we do a single loop over the cutoff groups to find the |
| 252 |
|
// largest cutoff for any atypes present in this group. |
| 253 |
|
#ifdef IS_MPI |
| 305 |
|
|
| 306 |
|
vector<RealType> groupCutoff(nGroups_, 0.0); |
| 307 |
|
groupToGtype.resize(nGroups_); |
| 306 |
– |
|
| 307 |
– |
cerr << "nGroups = " << nGroups_ << "\n"; |
| 308 |
|
for (int cg1 = 0; cg1 < nGroups_; cg1++) { |
| 309 |
|
|
| 310 |
|
groupCutoff[cg1] = 0.0; |
| 333 |
|
} |
| 334 |
|
#endif |
| 335 |
|
|
| 336 |
– |
cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n"; |
| 336 |
|
// Now we find the maximum group cutoff value present in the simulation |
| 337 |
|
|
| 338 |
|
RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end()); |
| 453 |
|
atomRowData.functionalDerivative.end(), 0.0); |
| 454 |
|
fill(atomColData.functionalDerivative.begin(), |
| 455 |
|
atomColData.functionalDerivative.end(), 0.0); |
| 456 |
+ |
} |
| 457 |
+ |
|
| 458 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 459 |
+ |
fill(atomRowData.skippedCharge.begin(), |
| 460 |
+ |
atomRowData.skippedCharge.end(), 0.0); |
| 461 |
+ |
fill(atomColData.skippedCharge.begin(), |
| 462 |
+ |
atomColData.skippedCharge.end(), 0.0); |
| 463 |
|
} |
| 464 |
|
|
| 465 |
|
#else |
| 481 |
|
fill(snap_->atomData.functionalDerivative.begin(), |
| 482 |
|
snap_->atomData.functionalDerivative.end(), 0.0); |
| 483 |
|
} |
| 484 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 485 |
+ |
fill(snap_->atomData.skippedCharge.begin(), |
| 486 |
+ |
snap_->atomData.skippedCharge.end(), 0.0); |
| 487 |
+ |
} |
| 488 |
|
#endif |
| 489 |
|
|
| 490 |
|
} |
| 592 |
|
|
| 593 |
|
if (storageLayout_ & DataStorage::dslTorque) { |
| 594 |
|
|
| 595 |
< |
int nt = snap_->atomData.force.size(); |
| 595 |
> |
int nt = snap_->atomData.torque.size(); |
| 596 |
|
vector<Vector3d> trq_tmp(nt, V3Zero); |
| 597 |
|
|
| 598 |
|
AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp); |
| 599 |
< |
for (int i = 0; i < n; i++) { |
| 599 |
> |
for (int i = 0; i < nt; i++) { |
| 600 |
|
snap_->atomData.torque[i] += trq_tmp[i]; |
| 601 |
|
trq_tmp[i] = 0.0; |
| 602 |
|
} |
| 603 |
|
|
| 604 |
|
AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp); |
| 605 |
< |
for (int i = 0; i < n; i++) |
| 605 |
> |
for (int i = 0; i < nt; i++) |
| 606 |
|
snap_->atomData.torque[i] += trq_tmp[i]; |
| 607 |
|
} |
| 608 |
+ |
|
| 609 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 610 |
+ |
|
| 611 |
+ |
int ns = snap_->atomData.skippedCharge.size(); |
| 612 |
+ |
vector<RealType> skch_tmp(ns, 0.0); |
| 613 |
+ |
|
| 614 |
+ |
AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp); |
| 615 |
+ |
for (int i = 0; i < ns; i++) { |
| 616 |
+ |
snap_->atomData.skippedCharge[i] = skch_tmp[i]; |
| 617 |
+ |
skch_tmp[i] = 0.0; |
| 618 |
+ |
} |
| 619 |
+ |
|
| 620 |
+ |
AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp); |
| 621 |
+ |
for (int i = 0; i < ns; i++) |
| 622 |
+ |
snap_->atomData.skippedCharge[i] += skch_tmp[i]; |
| 623 |
+ |
} |
| 624 |
|
|
| 625 |
|
nLocal_ = snap_->getNumberOfAtoms(); |
| 626 |
|
|
| 717 |
|
#ifdef IS_MPI |
| 718 |
|
return massFactorsRow[atom1]; |
| 719 |
|
#else |
| 694 |
– |
cerr << "mfs = " << massFactors.size() << " atom1 = " << atom1 << "\n"; |
| 720 |
|
return massFactors[atom1]; |
| 721 |
|
#endif |
| 722 |
|
} |
| 743 |
|
return d; |
| 744 |
|
} |
| 745 |
|
|
| 746 |
< |
vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) { |
| 747 |
< |
return skipsForAtom[atom1]; |
| 746 |
> |
vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) { |
| 747 |
> |
return excludesForAtom[atom1]; |
| 748 |
|
} |
| 749 |
|
|
| 750 |
|
/** |
| 751 |
< |
* There are a number of reasons to skip a pair or a |
| 727 |
< |
* particle. Mostly we do this to exclude atoms who are involved in |
| 728 |
< |
* short range interactions (bonds, bends, torsions), but we also |
| 729 |
< |
* need to exclude some overcounted interactions that result from |
| 751 |
> |
* We need to exclude some overcounted interactions that result from |
| 752 |
|
* the parallel decomposition. |
| 753 |
|
*/ |
| 754 |
|
bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { |
| 768 |
|
} else { |
| 769 |
|
if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
| 770 |
|
} |
| 771 |
+ |
#endif |
| 772 |
+ |
return false; |
| 773 |
+ |
} |
| 774 |
+ |
|
| 775 |
+ |
/** |
| 776 |
+ |
* We need to handle the interactions for atoms who are involved in |
| 777 |
+ |
* the same rigid body as well as some short range interactions |
| 778 |
+ |
* (bonds, bends, torsions) differently from other interactions. |
| 779 |
+ |
* We'll still visit the pairwise routines, but with a flag that |
| 780 |
+ |
* tells those routines to exclude the pair from direct long range |
| 781 |
+ |
* interactions. Some indirect interactions (notably reaction |
| 782 |
+ |
* field) must still be handled for these pairs. |
| 783 |
+ |
*/ |
| 784 |
+ |
bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) { |
| 785 |
+ |
int unique_id_2; |
| 786 |
+ |
|
| 787 |
+ |
#ifdef IS_MPI |
| 788 |
+ |
// in MPI, we have to look up the unique IDs for the row atom. |
| 789 |
+ |
unique_id_2 = AtomColToGlobal[atom2]; |
| 790 |
|
#else |
| 791 |
|
// in the normal loop, the atom numbers are unique |
| 751 |
– |
unique_id_1 = atom1; |
| 792 |
|
unique_id_2 = atom2; |
| 793 |
|
#endif |
| 794 |
|
|
| 795 |
< |
for (vector<int>::iterator i = skipsForAtom[atom1].begin(); |
| 796 |
< |
i != skipsForAtom[atom1].end(); ++i) { |
| 795 |
> |
for (vector<int>::iterator i = excludesForAtom[atom1].begin(); |
| 796 |
> |
i != excludesForAtom[atom1].end(); ++i) { |
| 797 |
|
if ( (*i) == unique_id_2 ) return true; |
| 798 |
|
} |
| 799 |
|
|
| 819 |
|
|
| 820 |
|
// filling interaction blocks with pointers |
| 821 |
|
void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, |
| 822 |
< |
int atom1, int atom2) { |
| 822 |
> |
int atom1, int atom2) { |
| 823 |
> |
|
| 824 |
> |
idat.excluded = excludeAtomPair(atom1, atom2); |
| 825 |
> |
|
| 826 |
|
#ifdef IS_MPI |
| 827 |
|
|
| 828 |
|
idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
| 863 |
|
idat.particlePot2 = &(atomColData.particlePot[atom2]); |
| 864 |
|
} |
| 865 |
|
|
| 866 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 867 |
+ |
idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]); |
| 868 |
+ |
idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); |
| 869 |
+ |
} |
| 870 |
+ |
|
| 871 |
|
#else |
| 872 |
|
|
| 873 |
|
idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
| 908 |
|
idat.particlePot2 = &(snap_->atomData.particlePot[atom2]); |
| 909 |
|
} |
| 910 |
|
|
| 911 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 912 |
+ |
idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]); |
| 913 |
+ |
idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]); |
| 914 |
+ |
} |
| 915 |
|
#endif |
| 916 |
|
} |
| 917 |
|
|
| 929 |
|
snap_->atomData.force[atom1] += *(idat.f1); |
| 930 |
|
snap_->atomData.force[atom2] -= *(idat.f1); |
| 931 |
|
#endif |
| 932 |
< |
|
| 932 |
> |
|
| 933 |
|
} |
| 934 |
|
|
| 883 |
– |
|
| 884 |
– |
void ForceMatrixDecomposition::fillSkipData(InteractionData &idat, |
| 885 |
– |
int atom1, int atom2) { |
| 886 |
– |
#ifdef IS_MPI |
| 887 |
– |
idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
| 888 |
– |
ff_->getAtomType(identsCol[atom2]) ); |
| 889 |
– |
|
| 890 |
– |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 891 |
– |
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 892 |
– |
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 893 |
– |
} |
| 894 |
– |
|
| 895 |
– |
if (storageLayout_ & DataStorage::dslTorque) { |
| 896 |
– |
idat.t1 = &(atomRowData.torque[atom1]); |
| 897 |
– |
idat.t2 = &(atomColData.torque[atom2]); |
| 898 |
– |
} |
| 899 |
– |
|
| 900 |
– |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 901 |
– |
idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]); |
| 902 |
– |
idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); |
| 903 |
– |
} |
| 904 |
– |
#else |
| 905 |
– |
idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
| 906 |
– |
ff_->getAtomType(idents[atom2]) ); |
| 907 |
– |
|
| 908 |
– |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 909 |
– |
idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
| 910 |
– |
idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
| 911 |
– |
} |
| 912 |
– |
|
| 913 |
– |
if (storageLayout_ & DataStorage::dslTorque) { |
| 914 |
– |
idat.t1 = &(snap_->atomData.torque[atom1]); |
| 915 |
– |
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 916 |
– |
} |
| 917 |
– |
|
| 918 |
– |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 919 |
– |
idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]); |
| 920 |
– |
idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]); |
| 921 |
– |
} |
| 922 |
– |
#endif |
| 923 |
– |
} |
| 924 |
– |
|
| 925 |
– |
|
| 926 |
– |
void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) { |
| 927 |
– |
#ifdef IS_MPI |
| 928 |
– |
pot_row[atom1] += 0.5 * *(idat.pot); |
| 929 |
– |
pot_col[atom2] += 0.5 * *(idat.pot); |
| 930 |
– |
#else |
| 931 |
– |
pairwisePot += *(idat.pot); |
| 932 |
– |
#endif |
| 933 |
– |
|
| 934 |
– |
} |
| 935 |
– |
|
| 936 |
– |
|
| 935 |
|
/* |
| 936 |
|
* buildNeighborList |
| 937 |
|
* |
| 942 |
|
|
| 943 |
|
vector<pair<int, int> > neighborList; |
| 944 |
|
groupCutoffs cuts; |
| 945 |
+ |
bool doAllPairs = false; |
| 946 |
+ |
|
| 947 |
|
#ifdef IS_MPI |
| 948 |
|
cellListRow_.clear(); |
| 949 |
|
cellListCol_.clear(); |
| 963 |
|
nCells_.y() = (int) ( Hy.length() )/ rList_; |
| 964 |
|
nCells_.z() = (int) ( Hz.length() )/ rList_; |
| 965 |
|
|
| 966 |
+ |
// handle small boxes where the cell offsets can end up repeating cells |
| 967 |
+ |
|
| 968 |
+ |
if (nCells_.x() < 3) doAllPairs = true; |
| 969 |
+ |
if (nCells_.y() < 3) doAllPairs = true; |
| 970 |
+ |
if (nCells_.z() < 3) doAllPairs = true; |
| 971 |
+ |
|
| 972 |
|
Mat3x3d invHmat = snap_->getInvHmat(); |
| 973 |
|
Vector3d rs, scaled, dr; |
| 974 |
|
Vector3i whichCell; |
| 982 |
|
cellList_.resize(nCtot); |
| 983 |
|
#endif |
| 984 |
|
|
| 985 |
+ |
if (!doAllPairs) { |
| 986 |
|
#ifdef IS_MPI |
| 980 |
– |
for (int i = 0; i < nGroupsInRow_; i++) { |
| 981 |
– |
rs = cgRowData.position[i]; |
| 987 |
|
|
| 988 |
< |
// scaled positions relative to the box vectors |
| 989 |
< |
scaled = invHmat * rs; |
| 990 |
< |
|
| 991 |
< |
// wrap the vector back into the unit box by subtracting integer box |
| 992 |
< |
// numbers |
| 993 |
< |
for (int j = 0; j < 3; j++) { |
| 994 |
< |
scaled[j] -= roundMe(scaled[j]); |
| 995 |
< |
scaled[j] += 0.5; |
| 996 |
< |
} |
| 997 |
< |
|
| 998 |
< |
// find xyz-indices of cell that cutoffGroup is in. |
| 999 |
< |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1000 |
< |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1001 |
< |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1002 |
< |
|
| 1003 |
< |
// find single index of this cell: |
| 1004 |
< |
cellIndex = Vlinear(whichCell, nCells_); |
| 1005 |
< |
|
| 1006 |
< |
// add this cutoff group to the list of groups in this cell; |
| 1007 |
< |
cellListRow_[cellIndex].push_back(i); |
| 1008 |
< |
} |
| 1009 |
< |
|
| 1010 |
< |
for (int i = 0; i < nGroupsInCol_; i++) { |
| 1011 |
< |
rs = cgColData.position[i]; |
| 1012 |
< |
|
| 1013 |
< |
// scaled positions relative to the box vectors |
| 1014 |
< |
scaled = invHmat * rs; |
| 1015 |
< |
|
| 1016 |
< |
// wrap the vector back into the unit box by subtracting integer box |
| 1017 |
< |
// numbers |
| 1018 |
< |
for (int j = 0; j < 3; j++) { |
| 1019 |
< |
scaled[j] -= roundMe(scaled[j]); |
| 1020 |
< |
scaled[j] += 0.5; |
| 1021 |
< |
} |
| 1022 |
< |
|
| 1023 |
< |
// find xyz-indices of cell that cutoffGroup is in. |
| 1024 |
< |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1025 |
< |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1026 |
< |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1027 |
< |
|
| 1028 |
< |
// find single index of this cell: |
| 1029 |
< |
cellIndex = Vlinear(whichCell, nCells_); |
| 1030 |
< |
|
| 1031 |
< |
// add this cutoff group to the list of groups in this cell; |
| 1032 |
< |
cellListCol_[cellIndex].push_back(i); |
| 1033 |
< |
} |
| 988 |
> |
for (int i = 0; i < nGroupsInRow_; i++) { |
| 989 |
> |
rs = cgRowData.position[i]; |
| 990 |
> |
|
| 991 |
> |
// scaled positions relative to the box vectors |
| 992 |
> |
scaled = invHmat * rs; |
| 993 |
> |
|
| 994 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 995 |
> |
// numbers |
| 996 |
> |
for (int j = 0; j < 3; j++) { |
| 997 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 998 |
> |
scaled[j] += 0.5; |
| 999 |
> |
} |
| 1000 |
> |
|
| 1001 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1002 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1003 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1004 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1005 |
> |
|
| 1006 |
> |
// find single index of this cell: |
| 1007 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1008 |
> |
|
| 1009 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1010 |
> |
cellListRow_[cellIndex].push_back(i); |
| 1011 |
> |
} |
| 1012 |
> |
|
| 1013 |
> |
for (int i = 0; i < nGroupsInCol_; i++) { |
| 1014 |
> |
rs = cgColData.position[i]; |
| 1015 |
> |
|
| 1016 |
> |
// scaled positions relative to the box vectors |
| 1017 |
> |
scaled = invHmat * rs; |
| 1018 |
> |
|
| 1019 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 1020 |
> |
// numbers |
| 1021 |
> |
for (int j = 0; j < 3; j++) { |
| 1022 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 1023 |
> |
scaled[j] += 0.5; |
| 1024 |
> |
} |
| 1025 |
> |
|
| 1026 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1027 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1028 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1029 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1030 |
> |
|
| 1031 |
> |
// find single index of this cell: |
| 1032 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1033 |
> |
|
| 1034 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1035 |
> |
cellListCol_[cellIndex].push_back(i); |
| 1036 |
> |
} |
| 1037 |
|
#else |
| 1038 |
< |
for (int i = 0; i < nGroups_; i++) { |
| 1039 |
< |
rs = snap_->cgData.position[i]; |
| 1040 |
< |
|
| 1041 |
< |
// scaled positions relative to the box vectors |
| 1042 |
< |
scaled = invHmat * rs; |
| 1043 |
< |
|
| 1044 |
< |
// wrap the vector back into the unit box by subtracting integer box |
| 1045 |
< |
// numbers |
| 1046 |
< |
for (int j = 0; j < 3; j++) { |
| 1047 |
< |
scaled[j] -= roundMe(scaled[j]); |
| 1048 |
< |
scaled[j] += 0.5; |
| 1038 |
> |
for (int i = 0; i < nGroups_; i++) { |
| 1039 |
> |
rs = snap_->cgData.position[i]; |
| 1040 |
> |
|
| 1041 |
> |
// scaled positions relative to the box vectors |
| 1042 |
> |
scaled = invHmat * rs; |
| 1043 |
> |
|
| 1044 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 1045 |
> |
// numbers |
| 1046 |
> |
for (int j = 0; j < 3; j++) { |
| 1047 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 1048 |
> |
scaled[j] += 0.5; |
| 1049 |
> |
} |
| 1050 |
> |
|
| 1051 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1052 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1053 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1054 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1055 |
> |
|
| 1056 |
> |
// find single index of this cell: |
| 1057 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1058 |
> |
|
| 1059 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1060 |
> |
cellList_[cellIndex].push_back(i); |
| 1061 |
|
} |
| 1042 |
– |
|
| 1043 |
– |
// find xyz-indices of cell that cutoffGroup is in. |
| 1044 |
– |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1045 |
– |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1046 |
– |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1047 |
– |
|
| 1048 |
– |
// find single index of this cell: |
| 1049 |
– |
cellIndex = Vlinear(whichCell, nCells_); |
| 1050 |
– |
|
| 1051 |
– |
// add this cutoff group to the list of groups in this cell; |
| 1052 |
– |
cellList_[cellIndex].push_back(i); |
| 1053 |
– |
} |
| 1062 |
|
#endif |
| 1063 |
|
|
| 1064 |
< |
for (int m1z = 0; m1z < nCells_.z(); m1z++) { |
| 1065 |
< |
for (int m1y = 0; m1y < nCells_.y(); m1y++) { |
| 1066 |
< |
for (int m1x = 0; m1x < nCells_.x(); m1x++) { |
| 1067 |
< |
Vector3i m1v(m1x, m1y, m1z); |
| 1068 |
< |
int m1 = Vlinear(m1v, nCells_); |
| 1061 |
< |
|
| 1062 |
< |
for (vector<Vector3i>::iterator os = cellOffsets_.begin(); |
| 1063 |
< |
os != cellOffsets_.end(); ++os) { |
| 1064 |
> |
for (int m1z = 0; m1z < nCells_.z(); m1z++) { |
| 1065 |
> |
for (int m1y = 0; m1y < nCells_.y(); m1y++) { |
| 1066 |
> |
for (int m1x = 0; m1x < nCells_.x(); m1x++) { |
| 1067 |
> |
Vector3i m1v(m1x, m1y, m1z); |
| 1068 |
> |
int m1 = Vlinear(m1v, nCells_); |
| 1069 |
|
|
| 1070 |
< |
Vector3i m2v = m1v + (*os); |
| 1071 |
< |
|
| 1072 |
< |
if (m2v.x() >= nCells_.x()) { |
| 1073 |
< |
m2v.x() = 0; |
| 1074 |
< |
} else if (m2v.x() < 0) { |
| 1075 |
< |
m2v.x() = nCells_.x() - 1; |
| 1076 |
< |
} |
| 1077 |
< |
|
| 1078 |
< |
if (m2v.y() >= nCells_.y()) { |
| 1079 |
< |
m2v.y() = 0; |
| 1080 |
< |
} else if (m2v.y() < 0) { |
| 1081 |
< |
m2v.y() = nCells_.y() - 1; |
| 1082 |
< |
} |
| 1083 |
< |
|
| 1084 |
< |
if (m2v.z() >= nCells_.z()) { |
| 1085 |
< |
m2v.z() = 0; |
| 1086 |
< |
} else if (m2v.z() < 0) { |
| 1087 |
< |
m2v.z() = nCells_.z() - 1; |
| 1088 |
< |
} |
| 1089 |
< |
|
| 1090 |
< |
int m2 = Vlinear (m2v, nCells_); |
| 1091 |
< |
|
| 1070 |
> |
for (vector<Vector3i>::iterator os = cellOffsets_.begin(); |
| 1071 |
> |
os != cellOffsets_.end(); ++os) { |
| 1072 |
> |
|
| 1073 |
> |
Vector3i m2v = m1v + (*os); |
| 1074 |
> |
|
| 1075 |
> |
if (m2v.x() >= nCells_.x()) { |
| 1076 |
> |
m2v.x() = 0; |
| 1077 |
> |
} else if (m2v.x() < 0) { |
| 1078 |
> |
m2v.x() = nCells_.x() - 1; |
| 1079 |
> |
} |
| 1080 |
> |
|
| 1081 |
> |
if (m2v.y() >= nCells_.y()) { |
| 1082 |
> |
m2v.y() = 0; |
| 1083 |
> |
} else if (m2v.y() < 0) { |
| 1084 |
> |
m2v.y() = nCells_.y() - 1; |
| 1085 |
> |
} |
| 1086 |
> |
|
| 1087 |
> |
if (m2v.z() >= nCells_.z()) { |
| 1088 |
> |
m2v.z() = 0; |
| 1089 |
> |
} else if (m2v.z() < 0) { |
| 1090 |
> |
m2v.z() = nCells_.z() - 1; |
| 1091 |
> |
} |
| 1092 |
> |
|
| 1093 |
> |
int m2 = Vlinear (m2v, nCells_); |
| 1094 |
> |
|
| 1095 |
|
#ifdef IS_MPI |
| 1096 |
< |
for (vector<int>::iterator j1 = cellListRow_[m1].begin(); |
| 1097 |
< |
j1 != cellListRow_[m1].end(); ++j1) { |
| 1098 |
< |
for (vector<int>::iterator j2 = cellListCol_[m2].begin(); |
| 1099 |
< |
j2 != cellListCol_[m2].end(); ++j2) { |
| 1100 |
< |
|
| 1101 |
< |
// Always do this if we're in different cells or if |
| 1102 |
< |
// we're in the same cell and the global index of the |
| 1103 |
< |
// j2 cutoff group is less than the j1 cutoff group |
| 1104 |
< |
|
| 1105 |
< |
if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { |
| 1106 |
< |
dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
| 1107 |
< |
snap_->wrapVector(dr); |
| 1108 |
< |
cuts = getGroupCutoffs( (*j1), (*j2) ); |
| 1109 |
< |
if (dr.lengthSquare() < cuts.third) { |
| 1110 |
< |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 1096 |
> |
for (vector<int>::iterator j1 = cellListRow_[m1].begin(); |
| 1097 |
> |
j1 != cellListRow_[m1].end(); ++j1) { |
| 1098 |
> |
for (vector<int>::iterator j2 = cellListCol_[m2].begin(); |
| 1099 |
> |
j2 != cellListCol_[m2].end(); ++j2) { |
| 1100 |
> |
|
| 1101 |
> |
// Always do this if we're in different cells or if |
| 1102 |
> |
// we're in the same cell and the global index of the |
| 1103 |
> |
// j2 cutoff group is less than the j1 cutoff group |
| 1104 |
> |
|
| 1105 |
> |
if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { |
| 1106 |
> |
dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
| 1107 |
> |
snap_->wrapVector(dr); |
| 1108 |
> |
cuts = getGroupCutoffs( (*j1), (*j2) ); |
| 1109 |
> |
if (dr.lengthSquare() < cuts.third) { |
| 1110 |
> |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 1111 |
> |
} |
| 1112 |
|
} |
| 1113 |
|
} |
| 1114 |
|
} |
| 1106 |
– |
} |
| 1115 |
|
#else |
| 1116 |
< |
|
| 1117 |
< |
for (vector<int>::iterator j1 = cellList_[m1].begin(); |
| 1118 |
< |
j1 != cellList_[m1].end(); ++j1) { |
| 1119 |
< |
for (vector<int>::iterator j2 = cellList_[m2].begin(); |
| 1120 |
< |
j2 != cellList_[m2].end(); ++j2) { |
| 1121 |
< |
|
| 1122 |
< |
// Always do this if we're in different cells or if |
| 1123 |
< |
// we're in the same cell and the global index of the |
| 1124 |
< |
// j2 cutoff group is less than the j1 cutoff group |
| 1125 |
< |
|
| 1126 |
< |
if (m2 != m1 || (*j2) < (*j1)) { |
| 1127 |
< |
dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
| 1128 |
< |
snap_->wrapVector(dr); |
| 1129 |
< |
cuts = getGroupCutoffs( (*j1), (*j2) ); |
| 1130 |
< |
if (dr.lengthSquare() < cuts.third) { |
| 1131 |
< |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 1116 |
> |
|
| 1117 |
> |
for (vector<int>::iterator j1 = cellList_[m1].begin(); |
| 1118 |
> |
j1 != cellList_[m1].end(); ++j1) { |
| 1119 |
> |
for (vector<int>::iterator j2 = cellList_[m2].begin(); |
| 1120 |
> |
j2 != cellList_[m2].end(); ++j2) { |
| 1121 |
> |
|
| 1122 |
> |
// Always do this if we're in different cells or if |
| 1123 |
> |
// we're in the same cell and the global index of the |
| 1124 |
> |
// j2 cutoff group is less than the j1 cutoff group |
| 1125 |
> |
|
| 1126 |
> |
if (m2 != m1 || (*j2) < (*j1)) { |
| 1127 |
> |
dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
| 1128 |
> |
snap_->wrapVector(dr); |
| 1129 |
> |
cuts = getGroupCutoffs( (*j1), (*j2) ); |
| 1130 |
> |
if (dr.lengthSquare() < cuts.third) { |
| 1131 |
> |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 1132 |
> |
} |
| 1133 |
|
} |
| 1134 |
|
} |
| 1135 |
|
} |
| 1127 |
– |
} |
| 1136 |
|
#endif |
| 1137 |
+ |
} |
| 1138 |
|
} |
| 1139 |
|
} |
| 1140 |
|
} |
| 1141 |
+ |
} else { |
| 1142 |
+ |
// branch to do all cutoff group pairs |
| 1143 |
+ |
#ifdef IS_MPI |
| 1144 |
+ |
for (int j1 = 0; j1 < nGroupsInRow_; j1++) { |
| 1145 |
+ |
for (int j2 = 0; j2 < nGroupsInCol_; j2++) { |
| 1146 |
+ |
dr = cgColData.position[j2] - cgRowData.position[j1]; |
| 1147 |
+ |
snap_->wrapVector(dr); |
| 1148 |
+ |
cuts = getGroupCutoffs( j1, j2 ); |
| 1149 |
+ |
if (dr.lengthSquare() < cuts.third) { |
| 1150 |
+ |
neighborList.push_back(make_pair(j1, j2)); |
| 1151 |
+ |
} |
| 1152 |
+ |
} |
| 1153 |
+ |
} |
| 1154 |
+ |
#else |
| 1155 |
+ |
for (int j1 = 0; j1 < nGroups_ - 1; j1++) { |
| 1156 |
+ |
for (int j2 = j1 + 1; j2 < nGroups_; j2++) { |
| 1157 |
+ |
dr = snap_->cgData.position[j2] - snap_->cgData.position[j1]; |
| 1158 |
+ |
snap_->wrapVector(dr); |
| 1159 |
+ |
cuts = getGroupCutoffs( j1, j2 ); |
| 1160 |
+ |
if (dr.lengthSquare() < cuts.third) { |
| 1161 |
+ |
neighborList.push_back(make_pair(j1, j2)); |
| 1162 |
+ |
} |
| 1163 |
+ |
} |
| 1164 |
+ |
} |
| 1165 |
+ |
#endif |
| 1166 |
|
} |
| 1167 |
< |
|
| 1167 |
> |
|
| 1168 |
|
// save the local cutoff group positions for the check that is |
| 1169 |
|
// done on each loop: |
| 1170 |
|
saved_CG_positions_.clear(); |
| 1171 |
|
for (int i = 0; i < nGroups_; i++) |
| 1172 |
|
saved_CG_positions_.push_back(snap_->cgData.position[i]); |
| 1173 |
< |
|
| 1173 |
> |
|
| 1174 |
|
return neighborList; |
| 1175 |
|
} |
| 1176 |
|
} //end namespace OpenMD |
