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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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#include "parallel/ForceDecomposition.hpp" |
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#include "parallel/Communicator.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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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 ForceDecomposition::distributeInitialData() { |
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#ifdef IS_MPI |
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> |
#ifdef IS_MPI |
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Snapshot* snap = sman_->getCurrentSnapshot(); |
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int nAtoms = snap->getNumberOfAtoms(); |
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> |
int nLocal = snap->getNumberOfAtoms(); |
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int nGroups = snap->getNumberOfCutoffGroups(); |
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|
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< |
AtomCommRealI = new Communicator<Row,RealType>(nAtoms); |
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AtomCommVectorI = new Communicator<Row,Vector3d>(nAtoms); |
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AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nAtoms); |
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AtomCommIntI = new Communicator<Row,int>(nLocal); |
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> |
AtomCommRealI = new Communicator<Row,RealType>(nLocal); |
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> |
AtomCommVectorI = new Communicator<Row,Vector3d>(nLocal); |
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> |
AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nLocal); |
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|
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< |
AtomCommRealJ = new Communicator<Column,RealType>(nAtoms); |
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< |
AtomCommVectorJ = new Communicator<Column,Vector3d>(nAtoms); |
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< |
AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nAtoms); |
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> |
AtomCommIntJ = new Communicator<Column,int>(nLocal); |
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> |
AtomCommRealJ = new Communicator<Column,RealType>(nLocal); |
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> |
AtomCommVectorJ = new Communicator<Column,Vector3d>(nLocal); |
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> |
AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nLocal); |
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|
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+ |
cgCommIntI = new Communicator<Row,int>(nGroups); |
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cgCommVectorI = new Communicator<Row,Vector3d>(nGroups); |
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cgCommIntJ = new Communicator<Column,int>(nGroups); |
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cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups); |
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|
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< |
int nInRow = AtomCommRealI.getSize(); |
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< |
int nInCol = AtomCommRealJ.getSize(); |
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> |
int nAtomsInRow = AtomCommIntI->getSize(); |
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> |
int nAtomsInCol = AtomCommIntJ->getSize(); |
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> |
int nGroupsInRow = cgCommIntI->getSize(); |
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> |
int nGroupsInCol = cgCommIntJ->getSize(); |
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|
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< |
vector<vector<RealType> > pot_row(LR_POT_TYPES, |
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< |
vector<RealType> (nInRow, 0.0)); |
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< |
vector<vector<RealType> > pot_col(LR_POT_TYPES, |
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< |
vector<RealType> (nInCol, 0.0)); |
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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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> |
|
| 85 |
> |
vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0); |
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|
| 87 |
< |
vector<vector<RealType> > pot_local(LR_POT_TYPES, |
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< |
vector<RealType> (nAtoms, 0.0)); |
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> |
// gather the information for atomtype IDs (atids): |
| 88 |
> |
vector<int> identsLocal = info_->getIdentArray(); |
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> |
identsRow.reserve(nAtomsInRow); |
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> |
identsCol.reserve(nAtomsInCol); |
| 91 |
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|
| 92 |
+ |
AtomCommIntI->gather(identsLocal, identsRow); |
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+ |
AtomCommIntJ->gather(identsLocal, identsCol); |
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+ |
|
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+ |
AtomLocalToGlobal = info_->getLocalToGlobalAtomIndex(); |
| 96 |
+ |
AtomCommIntI->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 97 |
+ |
AtomCommIntJ->gather(AtomLocalToGlobal, AtomColToGlobal); |
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+ |
|
| 99 |
+ |
cgLocalToGlobal = info_->getLocalToGlobalCutoffGroupIndex(); |
| 100 |
+ |
cgCommIntI->gather(cgLocalToGlobal, cgRowToGlobal); |
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+ |
cgCommIntJ->gather(cgLocalToGlobal, cgColToGlobal); |
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+ |
|
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+ |
|
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+ |
|
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+ |
// still need: |
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+ |
// topoDist |
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// exclude |
| 108 |
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#endif |
| 109 |
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} |
| 110 |
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|
| 187 |
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Snapshot* snap = sman_->getCurrentSnapshot(); |
| 188 |
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|
| 189 |
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int n = snap->atomData.force.size(); |
| 190 |
< |
std::vector<Vector3d> frc_tmp(n, 0.0); |
| 190 |
> |
vector<Vector3d> frc_tmp(n, V3Zero); |
| 191 |
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|
| 192 |
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AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp); |
| 193 |
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for (int i = 0; i < n; i++) { |
| 203 |
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if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) { |
| 204 |
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|
| 205 |
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int nt = snap->atomData.force.size(); |
| 206 |
< |
std::vector<Vector3d> trq_tmp(nt, 0.0); |
| 206 |
> |
vector<Vector3d> trq_tmp(nt, V3Zero); |
| 207 |
|
|
| 208 |
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AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp); |
| 209 |
|
for (int i = 0; i < n; i++) { |
| 216 |
|
snap->atomData.torque[i] += trq_tmp[i]; |
| 217 |
|
} |
| 218 |
|
|
| 219 |
+ |
int nLocal = snap->getNumberOfAtoms(); |
| 220 |
+ |
|
| 221 |
+ |
vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, |
| 222 |
+ |
vector<RealType> (nLocal, 0.0)); |
| 223 |
|
|
| 224 |
< |
vector<vector<RealType> > pot_temp(LR_POT_TYPES, |
| 189 |
< |
vector<RealType> (nAtoms, 0.0)); |
| 190 |
< |
|
| 191 |
< |
for (int i = 0; i < LR_POT_TYPES; i++) { |
| 224 |
> |
for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
| 225 |
|
AtomCommRealI->scatter(pot_row[i], pot_temp[i]); |
| 226 |
|
for (int ii = 0; ii < pot_temp[i].size(); ii++ ) { |
| 227 |
|
pot_local[i] += pot_temp[i][ii]; |
| 228 |
|
} |
| 229 |
|
} |
| 197 |
– |
|
| 198 |
– |
|
| 199 |
– |
|
| 230 |
|
#endif |
| 231 |
|
} |
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|
