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/** |
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* @file ForceDecomposition.cpp |
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* @author Charles Vardeman <cvardema.at.nd.edu> |
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* @date 08/18/2010 |
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* @time 11:56am |
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* @version 1.0 |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* @section LICENSE |
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* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
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*/ |
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#include "parallel/ForceMatrixDecomposition.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "nonbonded/NonBondedInteraction.hpp" |
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#include "brains/SnapshotManager.hpp" |
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#include "brains/PairList.hpp" |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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/** |
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* distributeInitialData is essentially a copy of the older fortran |
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* SimulationSetup |
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*/ |
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|
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void ForceMatrixDecomposition::distributeInitialData() { |
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snap_ = sman_->getCurrentSnapshot(); |
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storageLayout_ = sman_->getStorageLayout(); |
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nLocal_ = snap_->getNumberOfAtoms(); |
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nGroups_ = snap_->getNumberOfCutoffGroups(); |
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|
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/* -*- c++ -*- */ |
| 62 |
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#include "config.h" |
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#include <stdlib.h> |
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> |
// gather the information for atomtype IDs (atids): |
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> |
vector<int> identsLocal = info_->getIdentArray(); |
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> |
AtomLocalToGlobal = info_->getGlobalAtomIndices(); |
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cgLocalToGlobal = info_->getGlobalGroupIndices(); |
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vector<int> globalGroupMembership = info_->getGlobalGroupMembership(); |
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vector<RealType> massFactorsLocal = info_->getMassFactors(); |
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> |
PairList excludes = info_->getExcludedInteractions(); |
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PairList oneTwo = info_->getOneTwoInteractions(); |
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PairList oneThree = info_->getOneThreeInteractions(); |
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PairList oneFour = info_->getOneFourInteractions(); |
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vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0); |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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|
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AtomCommIntRow = new Communicator<Row,int>(nLocal_); |
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AtomCommRealRow = new Communicator<Row,RealType>(nLocal_); |
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AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_); |
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AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_); |
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|
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#include <iostream> |
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#include <vector> |
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#include <algorithm> |
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#include <cmath> |
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#include "parallel/ForceDecomposition.hpp" |
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AtomCommIntColumn = new Communicator<Column,int>(nLocal_); |
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AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_); |
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AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_); |
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AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_); |
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|
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cgCommIntRow = new Communicator<Row,int>(nGroups_); |
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cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_); |
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cgCommIntColumn = new Communicator<Column,int>(nGroups_); |
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cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_); |
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|
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using namespace std; |
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using namespace OpenMD; |
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nAtomsInRow_ = AtomCommIntRow->getSize(); |
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nAtomsInCol_ = AtomCommIntColumn->getSize(); |
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nGroupsInRow_ = cgCommIntRow->getSize(); |
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nGroupsInCol_ = cgCommIntColumn->getSize(); |
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|
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//__static |
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#ifdef IS_MPI |
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static vector<MPI:Comm> communictors; |
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#endif |
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// Modify the data storage objects with the correct layouts and sizes: |
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atomRowData.resize(nAtomsInRow_); |
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atomRowData.setStorageLayout(storageLayout_); |
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atomColData.resize(nAtomsInCol_); |
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atomColData.setStorageLayout(storageLayout_); |
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cgRowData.resize(nGroupsInRow_); |
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cgRowData.setStorageLayout(DataStorage::dslPosition); |
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cgColData.resize(nGroupsInCol_); |
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cgColData.setStorageLayout(DataStorage::dslPosition); |
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|
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vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES, |
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vector<RealType> (nAtomsInRow_, 0.0)); |
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vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES, |
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vector<RealType> (nAtomsInCol_, 0.0)); |
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|
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identsRow.reserve(nAtomsInRow_); |
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identsCol.reserve(nAtomsInCol_); |
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|
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AtomCommIntRow->gather(identsLocal, identsRow); |
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AtomCommIntColumn->gather(identsLocal, identsCol); |
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|
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AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
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AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
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|
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cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
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cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
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|
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//____ MPITypeTraits |
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template<typename T> |
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struct MPITypeTraits; |
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AtomCommRealRow->gather(massFactorsLocal, massFactorsRow); |
| 123 |
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AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol); |
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|
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#ifdef IS_MPI |
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template<> |
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struct MPITypeTraits<RealType> { |
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static const MPI::Datatype datatype; |
| 129 |
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}; |
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const MPI_Datatype MPITypeTraits<RealType>::datatype = MY_MPI_REAL; |
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> |
groupListRow_.clear(); |
| 126 |
> |
groupListRow_.reserve(nGroupsInRow_); |
| 127 |
> |
for (int i = 0; i < nGroupsInRow_; i++) { |
| 128 |
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int gid = cgRowToGlobal[i]; |
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> |
for (int j = 0; j < nAtomsInRow_; j++) { |
| 130 |
> |
int aid = AtomRowToGlobal[j]; |
| 131 |
> |
if (globalGroupMembership[aid] == gid) |
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groupListRow_[i].push_back(j); |
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} |
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} |
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|
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template<> |
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struct MPITypeTraits<int> { |
| 138 |
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static const MPI::Datatype datatype; |
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}; |
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const MPI::Datatype MPITypeTraits<int>::datatype = MPI_INT; |
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groupListCol_.clear(); |
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> |
groupListCol_.reserve(nGroupsInCol_); |
| 138 |
> |
for (int i = 0; i < nGroupsInCol_; i++) { |
| 139 |
> |
int gid = cgColToGlobal[i]; |
| 140 |
> |
for (int j = 0; j < nAtomsInCol_; j++) { |
| 141 |
> |
int aid = AtomColToGlobal[j]; |
| 142 |
> |
if (globalGroupMembership[aid] == gid) |
| 143 |
> |
groupListCol_[i].push_back(j); |
| 144 |
> |
} |
| 145 |
> |
} |
| 146 |
> |
|
| 147 |
> |
skipsForRowAtom.clear(); |
| 148 |
> |
skipsForRowAtom.reserve(nAtomsInRow_); |
| 149 |
> |
for (int i = 0; i < nAtomsInRow_; i++) { |
| 150 |
> |
int iglob = AtomColToGlobal[i]; |
| 151 |
> |
for (int j = 0; j < nAtomsInCol_; j++) { |
| 152 |
> |
int jglob = AtomRowToGlobal[j]; |
| 153 |
> |
if (excludes.hasPair(iglob, jglob)) |
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> |
skipsForRowAtom[i].push_back(j); |
| 155 |
> |
} |
| 156 |
> |
} |
| 157 |
> |
|
| 158 |
> |
toposForRowAtom.clear(); |
| 159 |
> |
toposForRowAtom.reserve(nAtomsInRow_); |
| 160 |
> |
for (int i = 0; i < nAtomsInRow_; i++) { |
| 161 |
> |
int iglob = AtomColToGlobal[i]; |
| 162 |
> |
int nTopos = 0; |
| 163 |
> |
for (int j = 0; j < nAtomsInCol_; j++) { |
| 164 |
> |
int jglob = AtomRowToGlobal[j]; |
| 165 |
> |
if (oneTwo.hasPair(iglob, jglob)) { |
| 166 |
> |
toposForRowAtom[i].push_back(j); |
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> |
topoDistRow[i][nTopos] = 1; |
| 168 |
> |
nTopos++; |
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> |
} |
| 170 |
> |
if (oneThree.hasPair(iglob, jglob)) { |
| 171 |
> |
toposForRowAtom[i].push_back(j); |
| 172 |
> |
topoDistRow[i][nTopos] = 2; |
| 173 |
> |
nTopos++; |
| 174 |
> |
} |
| 175 |
> |
if (oneFour.hasPair(iglob, jglob)) { |
| 176 |
> |
toposForRowAtom[i].push_back(j); |
| 177 |
> |
topoDistRow[i][nTopos] = 3; |
| 178 |
> |
nTopos++; |
| 179 |
> |
} |
| 180 |
> |
} |
| 181 |
> |
} |
| 182 |
> |
|
| 183 |
|
#endif |
| 184 |
|
|
| 185 |
< |
/** |
| 186 |
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* Constructor for ForceDecomposition Parallel Decomposition Method |
| 187 |
< |
* Will try to construct a symmetric grid of processors. Ideally, the |
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< |
* number of processors will be a square ex: 4, 9, 16, 25. |
| 189 |
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* |
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< |
*/ |
| 185 |
> |
groupList_.clear(); |
| 186 |
> |
groupList_.reserve(nGroups_); |
| 187 |
> |
for (int i = 0; i < nGroups_; i++) { |
| 188 |
> |
int gid = cgLocalToGlobal[i]; |
| 189 |
> |
for (int j = 0; j < nLocal_; j++) { |
| 190 |
> |
int aid = AtomLocalToGlobal[j]; |
| 191 |
> |
if (globalGroupMembership[aid] == gid) |
| 192 |
> |
groupList_[i].push_back(j); |
| 193 |
> |
} |
| 194 |
> |
} |
| 195 |
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|
| 196 |
< |
ForceDecomposition::ForceDecomposition() { |
| 196 |
> |
skipsForLocalAtom.clear(); |
| 197 |
> |
skipsForLocalAtom.reserve(nLocal_); |
| 198 |
|
|
| 199 |
+ |
for (int i = 0; i < nLocal_; i++) { |
| 200 |
+ |
int iglob = AtomLocalToGlobal[i]; |
| 201 |
+ |
for (int j = 0; j < nLocal_; j++) { |
| 202 |
+ |
int jglob = AtomLocalToGlobal[j]; |
| 203 |
+ |
if (excludes.hasPair(iglob, jglob)) |
| 204 |
+ |
skipsForLocalAtom[i].push_back(j); |
| 205 |
+ |
} |
| 206 |
+ |
} |
| 207 |
+ |
|
| 208 |
+ |
toposForLocalAtom.clear(); |
| 209 |
+ |
toposForLocalAtom.reserve(nLocal_); |
| 210 |
+ |
for (int i = 0; i < nLocal_; i++) { |
| 211 |
+ |
int iglob = AtomLocalToGlobal[i]; |
| 212 |
+ |
int nTopos = 0; |
| 213 |
+ |
for (int j = 0; j < nLocal_; j++) { |
| 214 |
+ |
int jglob = AtomLocalToGlobal[j]; |
| 215 |
+ |
if (oneTwo.hasPair(iglob, jglob)) { |
| 216 |
+ |
toposForLocalAtom[i].push_back(j); |
| 217 |
+ |
topoDistLocal[i][nTopos] = 1; |
| 218 |
+ |
nTopos++; |
| 219 |
+ |
} |
| 220 |
+ |
if (oneThree.hasPair(iglob, jglob)) { |
| 221 |
+ |
toposForLocalAtom[i].push_back(j); |
| 222 |
+ |
topoDistLocal[i][nTopos] = 2; |
| 223 |
+ |
nTopos++; |
| 224 |
+ |
} |
| 225 |
+ |
if (oneFour.hasPair(iglob, jglob)) { |
| 226 |
+ |
toposForLocalAtom[i].push_back(j); |
| 227 |
+ |
topoDistLocal[i][nTopos] = 3; |
| 228 |
+ |
nTopos++; |
| 229 |
+ |
} |
| 230 |
+ |
} |
| 231 |
+ |
} |
| 232 |
+ |
} |
| 233 |
+ |
|
| 234 |
+ |
void ForceMatrixDecomposition::distributeData() { |
| 235 |
+ |
snap_ = sman_->getCurrentSnapshot(); |
| 236 |
+ |
storageLayout_ = sman_->getStorageLayout(); |
| 237 |
|
#ifdef IS_MPI |
| 238 |
< |
int nProcs = MPI::COMM_WORLD.Get_size(); |
| 239 |
< |
int worldRank = MPI::COMM_WORLD.Get_rank(); |
| 240 |
< |
#endif |
| 241 |
< |
|
| 242 |
< |
// First time through, construct column stride. |
| 243 |
< |
if (communicators.size() == 0) |
| 244 |
< |
{ |
| 245 |
< |
int nColumnsMax = (int) round(sqrt((float) nProcs)); |
| 246 |
< |
for (int i = 0; i < nProcs; ++i) |
| 247 |
< |
{ |
| 248 |
< |
if (nProcs%i==0) nColumns=i; |
| 238 |
> |
|
| 239 |
> |
// gather up the atomic positions |
| 240 |
> |
AtomCommVectorRow->gather(snap_->atomData.position, |
| 241 |
> |
atomRowData.position); |
| 242 |
> |
AtomCommVectorColumn->gather(snap_->atomData.position, |
| 243 |
> |
atomColData.position); |
| 244 |
> |
|
| 245 |
> |
// gather up the cutoff group positions |
| 246 |
> |
cgCommVectorRow->gather(snap_->cgData.position, |
| 247 |
> |
cgRowData.position); |
| 248 |
> |
cgCommVectorColumn->gather(snap_->cgData.position, |
| 249 |
> |
cgColData.position); |
| 250 |
> |
|
| 251 |
> |
// if needed, gather the atomic rotation matrices |
| 252 |
> |
if (storageLayout_ & DataStorage::dslAmat) { |
| 253 |
> |
AtomCommMatrixRow->gather(snap_->atomData.aMat, |
| 254 |
> |
atomRowData.aMat); |
| 255 |
> |
AtomCommMatrixColumn->gather(snap_->atomData.aMat, |
| 256 |
> |
atomColData.aMat); |
| 257 |
|
} |
| 258 |
< |
|
| 259 |
< |
int nRows = nProcs/nColumns; |
| 260 |
< |
myRank_ = (int) worldRank%nColumns; |
| 258 |
> |
|
| 259 |
> |
// if needed, gather the atomic eletrostatic frames |
| 260 |
> |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 261 |
> |
AtomCommMatrixRow->gather(snap_->atomData.electroFrame, |
| 262 |
> |
atomRowData.electroFrame); |
| 263 |
> |
AtomCommMatrixColumn->gather(snap_->atomData.electroFrame, |
| 264 |
> |
atomColData.electroFrame); |
| 265 |
> |
} |
| 266 |
> |
#endif |
| 267 |
|
} |
| 268 |
< |
else |
| 269 |
< |
{ |
| 270 |
< |
myRank_ = myRank/nColumns; |
| 268 |
> |
|
| 269 |
> |
void ForceMatrixDecomposition::collectIntermediateData() { |
| 270 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 271 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 272 |
> |
#ifdef IS_MPI |
| 273 |
> |
|
| 274 |
> |
if (storageLayout_ & DataStorage::dslDensity) { |
| 275 |
> |
|
| 276 |
> |
AtomCommRealRow->scatter(atomRowData.density, |
| 277 |
> |
snap_->atomData.density); |
| 278 |
> |
|
| 279 |
> |
int n = snap_->atomData.density.size(); |
| 280 |
> |
std::vector<RealType> rho_tmp(n, 0.0); |
| 281 |
> |
AtomCommRealColumn->scatter(atomColData.density, rho_tmp); |
| 282 |
> |
for (int i = 0; i < n; i++) |
| 283 |
> |
snap_->atomData.density[i] += rho_tmp[i]; |
| 284 |
> |
} |
| 285 |
> |
#endif |
| 286 |
|
} |
| 121 |
– |
MPI::Comm newComm = MPI:COMM_WORLD.Split(myRank_,0); |
| 287 |
|
|
| 288 |
< |
isColumn_ = false; |
| 288 |
> |
void ForceMatrixDecomposition::distributeIntermediateData() { |
| 289 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 290 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 291 |
> |
#ifdef IS_MPI |
| 292 |
> |
if (storageLayout_ & DataStorage::dslFunctional) { |
| 293 |
> |
AtomCommRealRow->gather(snap_->atomData.functional, |
| 294 |
> |
atomRowData.functional); |
| 295 |
> |
AtomCommRealColumn->gather(snap_->atomData.functional, |
| 296 |
> |
atomColData.functional); |
| 297 |
> |
} |
| 298 |
> |
|
| 299 |
> |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 300 |
> |
AtomCommRealRow->gather(snap_->atomData.functionalDerivative, |
| 301 |
> |
atomRowData.functionalDerivative); |
| 302 |
> |
AtomCommRealColumn->gather(snap_->atomData.functionalDerivative, |
| 303 |
> |
atomColData.functionalDerivative); |
| 304 |
> |
} |
| 305 |
> |
#endif |
| 306 |
> |
} |
| 307 |
|
|
| 308 |
< |
} |
| 308 |
> |
|
| 309 |
> |
void ForceMatrixDecomposition::collectData() { |
| 310 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 311 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 312 |
> |
#ifdef IS_MPI |
| 313 |
> |
int n = snap_->atomData.force.size(); |
| 314 |
> |
vector<Vector3d> frc_tmp(n, V3Zero); |
| 315 |
> |
|
| 316 |
> |
AtomCommVectorRow->scatter(atomRowData.force, frc_tmp); |
| 317 |
> |
for (int i = 0; i < n; i++) { |
| 318 |
> |
snap_->atomData.force[i] += frc_tmp[i]; |
| 319 |
> |
frc_tmp[i] = 0.0; |
| 320 |
> |
} |
| 321 |
> |
|
| 322 |
> |
AtomCommVectorColumn->scatter(atomColData.force, frc_tmp); |
| 323 |
> |
for (int i = 0; i < n; i++) |
| 324 |
> |
snap_->atomData.force[i] += frc_tmp[i]; |
| 325 |
> |
|
| 326 |
> |
|
| 327 |
> |
if (storageLayout_ & DataStorage::dslTorque) { |
| 328 |
|
|
| 329 |
< |
ForceDecomposition::gather(sendbuf, receivebuf){ |
| 330 |
< |
communicators(myIndex_).Allgatherv(); |
| 129 |
< |
} |
| 329 |
> |
int nt = snap_->atomData.force.size(); |
| 330 |
> |
vector<Vector3d> trq_tmp(nt, V3Zero); |
| 331 |
|
|
| 332 |
+ |
AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp); |
| 333 |
+ |
for (int i = 0; i < n; i++) { |
| 334 |
+ |
snap_->atomData.torque[i] += trq_tmp[i]; |
| 335 |
+ |
trq_tmp[i] = 0.0; |
| 336 |
+ |
} |
| 337 |
+ |
|
| 338 |
+ |
AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp); |
| 339 |
+ |
for (int i = 0; i < n; i++) |
| 340 |
+ |
snap_->atomData.torque[i] += trq_tmp[i]; |
| 341 |
+ |
} |
| 342 |
+ |
|
| 343 |
+ |
nLocal_ = snap_->getNumberOfAtoms(); |
| 344 |
|
|
| 345 |
+ |
vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, |
| 346 |
+ |
vector<RealType> (nLocal_, 0.0)); |
| 347 |
+ |
|
| 348 |
+ |
for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
| 349 |
+ |
AtomCommRealRow->scatter(pot_row[i], pot_temp[i]); |
| 350 |
+ |
for (int ii = 0; ii < pot_temp[i].size(); ii++ ) { |
| 351 |
+ |
pot_local[i] += pot_temp[i][ii]; |
| 352 |
+ |
} |
| 353 |
+ |
} |
| 354 |
+ |
#endif |
| 355 |
+ |
} |
| 356 |
|
|
| 357 |
< |
ForceDecomposition::scatter(sbuffer, rbuffer){ |
| 358 |
< |
communicators(myIndex_).Reduce_scatter(sbuffer, recevbuf. recvcounts, MPI::DOUBLE, MPI::SUM); |
| 359 |
< |
} |
| 357 |
> |
int ForceMatrixDecomposition::getNAtomsInRow() { |
| 358 |
> |
#ifdef IS_MPI |
| 359 |
> |
return nAtomsInRow_; |
| 360 |
> |
#else |
| 361 |
> |
return nLocal_; |
| 362 |
> |
#endif |
| 363 |
> |
} |
| 364 |
|
|
| 365 |
+ |
/** |
| 366 |
+ |
* returns the list of atoms belonging to this group. |
| 367 |
+ |
*/ |
| 368 |
+ |
vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){ |
| 369 |
+ |
#ifdef IS_MPI |
| 370 |
+ |
return groupListRow_[cg1]; |
| 371 |
+ |
#else |
| 372 |
+ |
return groupList_[cg1]; |
| 373 |
+ |
#endif |
| 374 |
+ |
} |
| 375 |
|
|
| 376 |
+ |
vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){ |
| 377 |
+ |
#ifdef IS_MPI |
| 378 |
+ |
return groupListCol_[cg2]; |
| 379 |
+ |
#else |
| 380 |
+ |
return groupList_[cg2]; |
| 381 |
+ |
#endif |
| 382 |
+ |
} |
| 383 |
+ |
|
| 384 |
+ |
Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){ |
| 385 |
+ |
Vector3d d; |
| 386 |
+ |
|
| 387 |
+ |
#ifdef IS_MPI |
| 388 |
+ |
d = cgColData.position[cg2] - cgRowData.position[cg1]; |
| 389 |
+ |
#else |
| 390 |
+ |
d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1]; |
| 391 |
+ |
#endif |
| 392 |
+ |
|
| 393 |
+ |
snap_->wrapVector(d); |
| 394 |
+ |
return d; |
| 395 |
+ |
} |
| 396 |
+ |
|
| 397 |
+ |
|
| 398 |
+ |
Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){ |
| 399 |
+ |
|
| 400 |
+ |
Vector3d d; |
| 401 |
+ |
|
| 402 |
+ |
#ifdef IS_MPI |
| 403 |
+ |
d = cgRowData.position[cg1] - atomRowData.position[atom1]; |
| 404 |
+ |
#else |
| 405 |
+ |
d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1]; |
| 406 |
+ |
#endif |
| 407 |
+ |
|
| 408 |
+ |
snap_->wrapVector(d); |
| 409 |
+ |
return d; |
| 410 |
+ |
} |
| 411 |
+ |
|
| 412 |
+ |
Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){ |
| 413 |
+ |
Vector3d d; |
| 414 |
+ |
|
| 415 |
+ |
#ifdef IS_MPI |
| 416 |
+ |
d = cgColData.position[cg2] - atomColData.position[atom2]; |
| 417 |
+ |
#else |
| 418 |
+ |
d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2]; |
| 419 |
+ |
#endif |
| 420 |
+ |
|
| 421 |
+ |
snap_->wrapVector(d); |
| 422 |
+ |
return d; |
| 423 |
+ |
} |
| 424 |
+ |
|
| 425 |
+ |
RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) { |
| 426 |
+ |
#ifdef IS_MPI |
| 427 |
+ |
return massFactorsRow[atom1]; |
| 428 |
+ |
#else |
| 429 |
+ |
return massFactorsLocal[atom1]; |
| 430 |
+ |
#endif |
| 431 |
+ |
} |
| 432 |
+ |
|
| 433 |
+ |
RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) { |
| 434 |
+ |
#ifdef IS_MPI |
| 435 |
+ |
return massFactorsCol[atom2]; |
| 436 |
+ |
#else |
| 437 |
+ |
return massFactorsLocal[atom2]; |
| 438 |
+ |
#endif |
| 439 |
+ |
|
| 440 |
+ |
} |
| 441 |
+ |
|
| 442 |
+ |
Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){ |
| 443 |
+ |
Vector3d d; |
| 444 |
+ |
|
| 445 |
+ |
#ifdef IS_MPI |
| 446 |
+ |
d = atomColData.position[atom2] - atomRowData.position[atom1]; |
| 447 |
+ |
#else |
| 448 |
+ |
d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1]; |
| 449 |
+ |
#endif |
| 450 |
+ |
|
| 451 |
+ |
snap_->wrapVector(d); |
| 452 |
+ |
return d; |
| 453 |
+ |
} |
| 454 |
+ |
|
| 455 |
+ |
vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) { |
| 456 |
+ |
#ifdef IS_MPI |
| 457 |
+ |
return skipsForRowAtom[atom1]; |
| 458 |
+ |
#else |
| 459 |
+ |
return skipsForLocalAtom[atom1]; |
| 460 |
+ |
#endif |
| 461 |
+ |
} |
| 462 |
+ |
|
| 463 |
+ |
/** |
| 464 |
+ |
* there are a number of reasons to skip a pair or a particle mostly |
| 465 |
+ |
* we do this to exclude atoms who are involved in short range |
| 466 |
+ |
* interactions (bonds, bends, torsions), but we also need to |
| 467 |
+ |
* exclude some overcounted interactions that result from the |
| 468 |
+ |
* parallel decomposition. |
| 469 |
+ |
*/ |
| 470 |
+ |
bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { |
| 471 |
+ |
int unique_id_1, unique_id_2; |
| 472 |
+ |
|
| 473 |
+ |
#ifdef IS_MPI |
| 474 |
+ |
// in MPI, we have to look up the unique IDs for each atom |
| 475 |
+ |
unique_id_1 = AtomRowToGlobal[atom1]; |
| 476 |
+ |
unique_id_2 = AtomColToGlobal[atom2]; |
| 477 |
+ |
|
| 478 |
+ |
// this situation should only arise in MPI simulations |
| 479 |
+ |
if (unique_id_1 == unique_id_2) return true; |
| 480 |
+ |
|
| 481 |
+ |
// this prevents us from doing the pair on multiple processors |
| 482 |
+ |
if (unique_id_1 < unique_id_2) { |
| 483 |
+ |
if ((unique_id_1 + unique_id_2) % 2 == 0) return true; |
| 484 |
+ |
} else { |
| 485 |
+ |
if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
| 486 |
+ |
} |
| 487 |
+ |
#else |
| 488 |
+ |
// in the normal loop, the atom numbers are unique |
| 489 |
+ |
unique_id_1 = atom1; |
| 490 |
+ |
unique_id_2 = atom2; |
| 491 |
+ |
#endif |
| 492 |
+ |
|
| 493 |
+ |
#ifdef IS_MPI |
| 494 |
+ |
for (vector<int>::iterator i = skipsForRowAtom[atom1].begin(); |
| 495 |
+ |
i != skipsForRowAtom[atom1].end(); ++i) { |
| 496 |
+ |
if ( (*i) == unique_id_2 ) return true; |
| 497 |
+ |
} |
| 498 |
+ |
#else |
| 499 |
+ |
for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin(); |
| 500 |
+ |
i != skipsForLocalAtom[atom1].end(); ++i) { |
| 501 |
+ |
if ( (*i) == unique_id_2 ) return true; |
| 502 |
+ |
} |
| 503 |
+ |
#endif |
| 504 |
+ |
} |
| 505 |
+ |
|
| 506 |
+ |
int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) { |
| 507 |
+ |
|
| 508 |
+ |
#ifdef IS_MPI |
| 509 |
+ |
for (int i = 0; i < toposForRowAtom[atom1].size(); i++) { |
| 510 |
+ |
if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i]; |
| 511 |
+ |
} |
| 512 |
+ |
#else |
| 513 |
+ |
for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) { |
| 514 |
+ |
if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i]; |
| 515 |
+ |
} |
| 516 |
+ |
#endif |
| 517 |
+ |
|
| 518 |
+ |
// zero is default for unconnected (i.e. normal) pair interactions |
| 519 |
+ |
return 0; |
| 520 |
+ |
} |
| 521 |
+ |
|
| 522 |
+ |
void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){ |
| 523 |
+ |
#ifdef IS_MPI |
| 524 |
+ |
atomRowData.force[atom1] += fg; |
| 525 |
+ |
#else |
| 526 |
+ |
snap_->atomData.force[atom1] += fg; |
| 527 |
+ |
#endif |
| 528 |
+ |
} |
| 529 |
+ |
|
| 530 |
+ |
void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){ |
| 531 |
+ |
#ifdef IS_MPI |
| 532 |
+ |
atomColData.force[atom2] += fg; |
| 533 |
+ |
#else |
| 534 |
+ |
snap_->atomData.force[atom2] += fg; |
| 535 |
+ |
#endif |
| 536 |
+ |
} |
| 537 |
+ |
|
| 538 |
+ |
// filling interaction blocks with pointers |
| 539 |
+ |
InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) { |
| 540 |
+ |
InteractionData idat; |
| 541 |
+ |
|
| 542 |
+ |
#ifdef IS_MPI |
| 543 |
+ |
if (storageLayout_ & DataStorage::dslAmat) { |
| 544 |
+ |
idat.A1 = &(atomRowData.aMat[atom1]); |
| 545 |
+ |
idat.A2 = &(atomColData.aMat[atom2]); |
| 546 |
+ |
} |
| 547 |
+ |
|
| 548 |
+ |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 549 |
+ |
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 550 |
+ |
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 551 |
+ |
} |
| 552 |
+ |
|
| 553 |
+ |
if (storageLayout_ & DataStorage::dslTorque) { |
| 554 |
+ |
idat.t1 = &(atomRowData.torque[atom1]); |
| 555 |
+ |
idat.t2 = &(atomColData.torque[atom2]); |
| 556 |
+ |
} |
| 557 |
+ |
|
| 558 |
+ |
if (storageLayout_ & DataStorage::dslDensity) { |
| 559 |
+ |
idat.rho1 = &(atomRowData.density[atom1]); |
| 560 |
+ |
idat.rho2 = &(atomColData.density[atom2]); |
| 561 |
+ |
} |
| 562 |
+ |
|
| 563 |
+ |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 564 |
+ |
idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]); |
| 565 |
+ |
idat.dfrho2 = &(atomColData.functionalDerivative[atom2]); |
| 566 |
+ |
} |
| 567 |
+ |
|
| 568 |
+ |
#else |
| 569 |
+ |
if (storageLayout_ & DataStorage::dslAmat) { |
| 570 |
+ |
idat.A1 = &(snap_->atomData.aMat[atom1]); |
| 571 |
+ |
idat.A2 = &(snap_->atomData.aMat[atom2]); |
| 572 |
+ |
} |
| 573 |
+ |
|
| 574 |
+ |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 575 |
+ |
idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
| 576 |
+ |
idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
| 577 |
+ |
} |
| 578 |
+ |
|
| 579 |
+ |
if (storageLayout_ & DataStorage::dslTorque) { |
| 580 |
+ |
idat.t1 = &(snap_->atomData.torque[atom1]); |
| 581 |
+ |
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 582 |
+ |
} |
| 583 |
+ |
|
| 584 |
+ |
if (storageLayout_ & DataStorage::dslDensity) { |
| 585 |
+ |
idat.rho1 = &(snap_->atomData.density[atom1]); |
| 586 |
+ |
idat.rho2 = &(snap_->atomData.density[atom2]); |
| 587 |
+ |
} |
| 588 |
+ |
|
| 589 |
+ |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 590 |
+ |
idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]); |
| 591 |
+ |
idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]); |
| 592 |
+ |
} |
| 593 |
+ |
#endif |
| 594 |
+ |
return idat; |
| 595 |
+ |
} |
| 596 |
+ |
|
| 597 |
+ |
InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){ |
| 598 |
+ |
|
| 599 |
+ |
InteractionData idat; |
| 600 |
+ |
#ifdef IS_MPI |
| 601 |
+ |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 602 |
+ |
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 603 |
+ |
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 604 |
+ |
} |
| 605 |
+ |
if (storageLayout_ & DataStorage::dslTorque) { |
| 606 |
+ |
idat.t1 = &(atomRowData.torque[atom1]); |
| 607 |
+ |
idat.t2 = &(atomColData.torque[atom2]); |
| 608 |
+ |
} |
| 609 |
+ |
if (storageLayout_ & DataStorage::dslForce) { |
| 610 |
+ |
idat.t1 = &(atomRowData.force[atom1]); |
| 611 |
+ |
idat.t2 = &(atomColData.force[atom2]); |
| 612 |
+ |
} |
| 613 |
+ |
#else |
| 614 |
+ |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 615 |
+ |
idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
| 616 |
+ |
idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
| 617 |
+ |
} |
| 618 |
+ |
if (storageLayout_ & DataStorage::dslTorque) { |
| 619 |
+ |
idat.t1 = &(snap_->atomData.torque[atom1]); |
| 620 |
+ |
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 621 |
+ |
} |
| 622 |
+ |
if (storageLayout_ & DataStorage::dslForce) { |
| 623 |
+ |
idat.t1 = &(snap_->atomData.force[atom1]); |
| 624 |
+ |
idat.t2 = &(snap_->atomData.force[atom2]); |
| 625 |
+ |
} |
| 626 |
+ |
#endif |
| 627 |
+ |
|
| 628 |
+ |
} |
| 629 |
+ |
|
| 630 |
+ |
|
| 631 |
+ |
|
| 632 |
+ |
|
| 633 |
+ |
/* |
| 634 |
+ |
* buildNeighborList |
| 635 |
+ |
* |
| 636 |
+ |
* first element of pair is row-indexed CutoffGroup |
| 637 |
+ |
* second element of pair is column-indexed CutoffGroup |
| 638 |
+ |
*/ |
| 639 |
+ |
vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() { |
| 640 |
+ |
|
| 641 |
+ |
vector<pair<int, int> > neighborList; |
| 642 |
+ |
#ifdef IS_MPI |
| 643 |
+ |
cellListRow_.clear(); |
| 644 |
+ |
cellListCol_.clear(); |
| 645 |
+ |
#else |
| 646 |
+ |
cellList_.clear(); |
| 647 |
+ |
#endif |
| 648 |
+ |
|
| 649 |
+ |
// dangerous to not do error checking. |
| 650 |
+ |
RealType rCut_; |
| 651 |
+ |
|
| 652 |
+ |
RealType rList_ = (rCut_ + skinThickness_); |
| 653 |
+ |
RealType rl2 = rList_ * rList_; |
| 654 |
+ |
Snapshot* snap_ = sman_->getCurrentSnapshot(); |
| 655 |
+ |
Mat3x3d Hmat = snap_->getHmat(); |
| 656 |
+ |
Vector3d Hx = Hmat.getColumn(0); |
| 657 |
+ |
Vector3d Hy = Hmat.getColumn(1); |
| 658 |
+ |
Vector3d Hz = Hmat.getColumn(2); |
| 659 |
+ |
|
| 660 |
+ |
nCells_.x() = (int) ( Hx.length() )/ rList_; |
| 661 |
+ |
nCells_.y() = (int) ( Hy.length() )/ rList_; |
| 662 |
+ |
nCells_.z() = (int) ( Hz.length() )/ rList_; |
| 663 |
+ |
|
| 664 |
+ |
Mat3x3d invHmat = snap_->getInvHmat(); |
| 665 |
+ |
Vector3d rs, scaled, dr; |
| 666 |
+ |
Vector3i whichCell; |
| 667 |
+ |
int cellIndex; |
| 668 |
+ |
|
| 669 |
+ |
#ifdef IS_MPI |
| 670 |
+ |
for (int i = 0; i < nGroupsInRow_; i++) { |
| 671 |
+ |
rs = cgRowData.position[i]; |
| 672 |
+ |
// scaled positions relative to the box vectors |
| 673 |
+ |
scaled = invHmat * rs; |
| 674 |
+ |
// wrap the vector back into the unit box by subtracting integer box |
| 675 |
+ |
// numbers |
| 676 |
+ |
for (int j = 0; j < 3; j++) |
| 677 |
+ |
scaled[j] -= roundMe(scaled[j]); |
| 678 |
+ |
|
| 679 |
+ |
// find xyz-indices of cell that cutoffGroup is in. |
| 680 |
+ |
whichCell.x() = nCells_.x() * scaled.x(); |
| 681 |
+ |
whichCell.y() = nCells_.y() * scaled.y(); |
| 682 |
+ |
whichCell.z() = nCells_.z() * scaled.z(); |
| 683 |
+ |
|
| 684 |
+ |
// find single index of this cell: |
| 685 |
+ |
cellIndex = Vlinear(whichCell, nCells_); |
| 686 |
+ |
// add this cutoff group to the list of groups in this cell; |
| 687 |
+ |
cellListRow_[cellIndex].push_back(i); |
| 688 |
+ |
} |
| 689 |
+ |
|
| 690 |
+ |
for (int i = 0; i < nGroupsInCol_; i++) { |
| 691 |
+ |
rs = cgColData.position[i]; |
| 692 |
+ |
// scaled positions relative to the box vectors |
| 693 |
+ |
scaled = invHmat * rs; |
| 694 |
+ |
// wrap the vector back into the unit box by subtracting integer box |
| 695 |
+ |
// numbers |
| 696 |
+ |
for (int j = 0; j < 3; j++) |
| 697 |
+ |
scaled[j] -= roundMe(scaled[j]); |
| 698 |
+ |
|
| 699 |
+ |
// find xyz-indices of cell that cutoffGroup is in. |
| 700 |
+ |
whichCell.x() = nCells_.x() * scaled.x(); |
| 701 |
+ |
whichCell.y() = nCells_.y() * scaled.y(); |
| 702 |
+ |
whichCell.z() = nCells_.z() * scaled.z(); |
| 703 |
+ |
|
| 704 |
+ |
// find single index of this cell: |
| 705 |
+ |
cellIndex = Vlinear(whichCell, nCells_); |
| 706 |
+ |
// add this cutoff group to the list of groups in this cell; |
| 707 |
+ |
cellListCol_[cellIndex].push_back(i); |
| 708 |
+ |
} |
| 709 |
+ |
#else |
| 710 |
+ |
for (int i = 0; i < nGroups_; i++) { |
| 711 |
+ |
rs = snap_->cgData.position[i]; |
| 712 |
+ |
// scaled positions relative to the box vectors |
| 713 |
+ |
scaled = invHmat * rs; |
| 714 |
+ |
// wrap the vector back into the unit box by subtracting integer box |
| 715 |
+ |
// numbers |
| 716 |
+ |
for (int j = 0; j < 3; j++) |
| 717 |
+ |
scaled[j] -= roundMe(scaled[j]); |
| 718 |
+ |
|
| 719 |
+ |
// find xyz-indices of cell that cutoffGroup is in. |
| 720 |
+ |
whichCell.x() = nCells_.x() * scaled.x(); |
| 721 |
+ |
whichCell.y() = nCells_.y() * scaled.y(); |
| 722 |
+ |
whichCell.z() = nCells_.z() * scaled.z(); |
| 723 |
+ |
|
| 724 |
+ |
// find single index of this cell: |
| 725 |
+ |
cellIndex = Vlinear(whichCell, nCells_); |
| 726 |
+ |
// add this cutoff group to the list of groups in this cell; |
| 727 |
+ |
cellList_[cellIndex].push_back(i); |
| 728 |
+ |
} |
| 729 |
+ |
#endif |
| 730 |
+ |
|
| 731 |
+ |
|
| 732 |
+ |
|
| 733 |
+ |
for (int m1z = 0; m1z < nCells_.z(); m1z++) { |
| 734 |
+ |
for (int m1y = 0; m1y < nCells_.y(); m1y++) { |
| 735 |
+ |
for (int m1x = 0; m1x < nCells_.x(); m1x++) { |
| 736 |
+ |
Vector3i m1v(m1x, m1y, m1z); |
| 737 |
+ |
int m1 = Vlinear(m1v, nCells_); |
| 738 |
+ |
|
| 739 |
+ |
for (vector<Vector3i>::iterator os = cellOffsets_.begin(); |
| 740 |
+ |
os != cellOffsets_.end(); ++os) { |
| 741 |
+ |
|
| 742 |
+ |
Vector3i m2v = m1v + (*os); |
| 743 |
+ |
|
| 744 |
+ |
if (m2v.x() >= nCells_.x()) { |
| 745 |
+ |
m2v.x() = 0; |
| 746 |
+ |
} else if (m2v.x() < 0) { |
| 747 |
+ |
m2v.x() = nCells_.x() - 1; |
| 748 |
+ |
} |
| 749 |
+ |
|
| 750 |
+ |
if (m2v.y() >= nCells_.y()) { |
| 751 |
+ |
m2v.y() = 0; |
| 752 |
+ |
} else if (m2v.y() < 0) { |
| 753 |
+ |
m2v.y() = nCells_.y() - 1; |
| 754 |
+ |
} |
| 755 |
+ |
|
| 756 |
+ |
if (m2v.z() >= nCells_.z()) { |
| 757 |
+ |
m2v.z() = 0; |
| 758 |
+ |
} else if (m2v.z() < 0) { |
| 759 |
+ |
m2v.z() = nCells_.z() - 1; |
| 760 |
+ |
} |
| 761 |
+ |
|
| 762 |
+ |
int m2 = Vlinear (m2v, nCells_); |
| 763 |
+ |
|
| 764 |
+ |
#ifdef IS_MPI |
| 765 |
+ |
for (vector<int>::iterator j1 = cellListRow_[m1].begin(); |
| 766 |
+ |
j1 != cellListRow_[m1].end(); ++j1) { |
| 767 |
+ |
for (vector<int>::iterator j2 = cellListCol_[m2].begin(); |
| 768 |
+ |
j2 != cellListCol_[m2].end(); ++j2) { |
| 769 |
+ |
|
| 770 |
+ |
// Always do this if we're in different cells or if |
| 771 |
+ |
// we're in the same cell and the global index of the |
| 772 |
+ |
// j2 cutoff group is less than the j1 cutoff group |
| 773 |
+ |
|
| 774 |
+ |
if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { |
| 775 |
+ |
dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
| 776 |
+ |
snap_->wrapVector(dr); |
| 777 |
+ |
if (dr.lengthSquare() < rl2) { |
| 778 |
+ |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 779 |
+ |
} |
| 780 |
+ |
} |
| 781 |
+ |
} |
| 782 |
+ |
} |
| 783 |
+ |
#else |
| 784 |
+ |
for (vector<int>::iterator j1 = cellList_[m1].begin(); |
| 785 |
+ |
j1 != cellList_[m1].end(); ++j1) { |
| 786 |
+ |
for (vector<int>::iterator j2 = cellList_[m2].begin(); |
| 787 |
+ |
j2 != cellList_[m2].end(); ++j2) { |
| 788 |
+ |
|
| 789 |
+ |
// Always do this if we're in different cells or if |
| 790 |
+ |
// we're in the same cell and the global index of the |
| 791 |
+ |
// j2 cutoff group is less than the j1 cutoff group |
| 792 |
+ |
|
| 793 |
+ |
if (m2 != m1 || (*j2) < (*j1)) { |
| 794 |
+ |
dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
| 795 |
+ |
snap_->wrapVector(dr); |
| 796 |
+ |
if (dr.lengthSquare() < rl2) { |
| 797 |
+ |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 798 |
+ |
} |
| 799 |
+ |
} |
| 800 |
+ |
} |
| 801 |
+ |
} |
| 802 |
+ |
#endif |
| 803 |
+ |
} |
| 804 |
+ |
} |
| 805 |
+ |
} |
| 806 |
+ |
} |
| 807 |
+ |
|
| 808 |
+ |
// save the local cutoff group positions for the check that is |
| 809 |
+ |
// done on each loop: |
| 810 |
+ |
saved_CG_positions_.clear(); |
| 811 |
+ |
for (int i = 0; i < nGroups_; i++) |
| 812 |
+ |
saved_CG_positions_.push_back(snap_->cgData.position[i]); |
| 813 |
+ |
|
| 814 |
+ |
return neighborList; |
| 815 |
+ |
} |
| 816 |
+ |
} //end namespace OpenMD |
