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* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
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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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|
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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 nLocal = snap->getNumberOfAtoms(); |
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int nGroups = snap->getNumberOfCutoffGroups(); |
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|
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< |
int nAtoms; |
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int nGroups; |
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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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< |
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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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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< |
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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< |
|
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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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< |
// more to come |
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> |
|
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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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> |
|
| 80 |
> |
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)); |
| 84 |
> |
|
| 85 |
> |
vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0); |
| 86 |
> |
|
| 87 |
> |
// 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 |
> |
|
| 92 |
> |
AtomCommIntI->gather(identsLocal, identsRow); |
| 93 |
> |
AtomCommIntJ->gather(identsLocal, identsCol); |
| 94 |
> |
|
| 95 |
> |
AtomLocalToGlobal = info_->getLocalToGlobalAtomIndex(); |
| 96 |
> |
AtomCommIntI->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 97 |
> |
AtomCommIntJ->gather(AtomLocalToGlobal, AtomColToGlobal); |
| 98 |
> |
|
| 99 |
> |
cgLocalToGlobal = info_->getLocalToGlobalCutoffGroupIndex(); |
| 100 |
> |
cgCommIntI->gather(cgLocalToGlobal, cgRowToGlobal); |
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> |
cgCommIntJ->gather(cgLocalToGlobal, cgColToGlobal); |
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> |
|
| 103 |
> |
|
| 104 |
> |
|
| 105 |
> |
// still need: |
| 106 |
> |
// topoDist |
| 107 |
> |
// exclude |
| 108 |
|
#endif |
| 109 |
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} |
| 110 |
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|
| 149 |
|
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 150 |
|
|
| 151 |
|
if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) { |
| 152 |
+ |
|
| 153 |
|
AtomCommRealI->scatter(snap->atomIData.density, |
| 154 |
|
snap->atomData.density); |
| 155 |
< |
std::vector<RealType> rho_tmp; |
| 156 |
< |
int n = snap->getNumberOfAtoms(); |
| 157 |
< |
rho_tmp.reserve( n ); |
| 155 |
> |
|
| 156 |
> |
int n = snap->atomData.density.size(); |
| 157 |
> |
std::vector<RealType> rho_tmp(n, 0.0); |
| 158 |
|
AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp); |
| 159 |
|
for (int i = 0; i < n; i++) |
| 160 |
|
snap->atomData.density[i] += rho_tmp[i]; |
| 185 |
|
void ForceDecomposition::collectData() { |
| 186 |
|
#ifdef IS_MPI |
| 187 |
|
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 143 |
– |
int n = snap->getNumberOfAtoms(); |
| 144 |
– |
|
| 145 |
– |
std::vector<Vector3d> frc_tmp; |
| 146 |
– |
frc_tmp.reserve( n ); |
| 188 |
|
|
| 189 |
+ |
int n = snap->atomData.force.size(); |
| 190 |
+ |
vector<Vector3d> frc_tmp(n, V3Zero); |
| 191 |
+ |
|
| 192 |
|
AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp); |
| 193 |
< |
for (int i = 0; i < n; i++) |
| 193 |
> |
for (int i = 0; i < n; i++) { |
| 194 |
|
snap->atomData.force[i] += frc_tmp[i]; |
| 195 |
+ |
frc_tmp[i] = 0.0; |
| 196 |
+ |
} |
| 197 |
|
|
| 198 |
|
AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp); |
| 199 |
|
for (int i = 0; i < n; i++) |
| 201 |
|
|
| 202 |
|
|
| 203 |
|
if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) { |
| 204 |
< |
std::vector<Vector3d> trq_tmp; |
| 205 |
< |
trq_tmp.reserve( n ); |
| 206 |
< |
|
| 204 |
> |
|
| 205 |
> |
int nt = snap->atomData.force.size(); |
| 206 |
> |
vector<Vector3d> trq_tmp(nt, V3Zero); |
| 207 |
> |
|
| 208 |
|
AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp); |
| 209 |
< |
for (int i = 0; i < n; i++) |
| 209 |
> |
for (int i = 0; i < n; i++) { |
| 210 |
|
snap->atomData.torque[i] += trq_tmp[i]; |
| 211 |
+ |
trq_tmp[i] = 0.0; |
| 212 |
+ |
} |
| 213 |
|
|
| 214 |
|
AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp); |
| 215 |
|
for (int i = 0; i < n; i++) |
| 216 |
|
snap->atomData.torque[i] += trq_tmp[i]; |
| 217 |
|
} |
| 218 |
|
|
| 219 |
< |
// Still need pot! |
| 171 |
< |
|
| 219 |
> |
int nLocal = snap->getNumberOfAtoms(); |
| 220 |
|
|
| 221 |
< |
|
| 221 |
> |
vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, |
| 222 |
> |
vector<RealType> (nLocal, 0.0)); |
| 223 |
> |
|
| 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 |
> |
} |
| 230 |
|
#endif |
| 231 |
|
} |
| 232 |
|
|
