| 38 |
|
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
|
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
< |
#include "parallel/ForceDecomposition.hpp" |
| 42 |
< |
#include "parallel/Communicator.hpp" |
| 41 |
> |
#include "parallel/ForceMatrixDecomposition.hpp" |
| 42 |
|
#include "math/SquareMatrix3.hpp" |
| 43 |
+ |
#include "nonbonded/NonBondedInteraction.hpp" |
| 44 |
+ |
#include "brains/SnapshotManager.hpp" |
| 45 |
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|
| 46 |
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using namespace std; |
| 47 |
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namespace OpenMD { |
| 48 |
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|
| 49 |
< |
void ForceDecomposition::distributeInitialData() { |
| 50 |
< |
#ifdef IS_MPI |
| 49 |
> |
/** |
| 50 |
> |
* distributeInitialData is essentially a copy of the older fortran |
| 51 |
> |
* SimulationSetup |
| 52 |
> |
*/ |
| 53 |
> |
|
| 54 |
> |
void ForceMatrixDecomposition::distributeInitialData() { |
| 55 |
> |
#ifdef IS_MPI |
| 56 |
|
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 57 |
< |
int nAtoms = snap->getNumberOfAtoms(); |
| 57 |
> |
int nLocal = snap->getNumberOfAtoms(); |
| 58 |
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int nGroups = snap->getNumberOfCutoffGroups(); |
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|
| 60 |
< |
AtomCommRealI = new Communicator<Row,RealType>(nAtoms); |
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< |
AtomCommVectorI = new Communicator<Row,Vector3d>(nAtoms); |
| 62 |
< |
AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nAtoms); |
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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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< |
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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> |
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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< |
cgCommVectorI = new Communicator<Row,Vector3d>(nGroups); |
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< |
cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups); |
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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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< |
int nInRow = AtomCommRealI.getSize(); |
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< |
int nInCol = AtomCommRealJ.getSize(); |
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> |
int nAtomsInRow = AtomCommIntRow->getSize(); |
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> |
int nAtomsInCol = AtomCommIntColumn->getSize(); |
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> |
int nGroupsInRow = cgCommIntRow->getSize(); |
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> |
int nGroupsInCol = cgCommIntColumn->getSize(); |
| 79 |
> |
|
| 80 |
> |
vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES, |
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> |
vector<RealType> (nAtomsInRow, 0.0)); |
| 82 |
> |
vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES, |
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> |
vector<RealType> (nAtomsInCol, 0.0)); |
| 84 |
> |
|
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> |
vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0); |
| 86 |
> |
|
| 87 |
> |
// gather the information for atomtype IDs (atids): |
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> |
vector<int> identsLocal = info_->getIdentArray(); |
| 89 |
> |
identsRow.reserve(nAtomsInRow); |
| 90 |
> |
identsCol.reserve(nAtomsInCol); |
| 91 |
> |
|
| 92 |
> |
AtomCommIntRow->gather(identsLocal, identsRow); |
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> |
AtomCommIntColumn->gather(identsLocal, identsCol); |
| 94 |
> |
|
| 95 |
> |
AtomLocalToGlobal = info_->getGlobalAtomIndices(); |
| 96 |
> |
AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 97 |
> |
AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
| 98 |
> |
|
| 99 |
> |
cgLocalToGlobal = info_->getGlobalGroupIndices(); |
| 100 |
> |
cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
| 101 |
> |
cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
| 102 |
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|
| 103 |
< |
vector<vector<RealType> > pot_row(LR_POT_TYPES, |
| 104 |
< |
vector<RealType> (nInRow, 0.0)); |
| 105 |
< |
vector<vector<RealType> > pot_col(LR_POT_TYPES, |
| 71 |
< |
vector<RealType> (nInCol, 0.0)); |
| 72 |
< |
|
| 73 |
< |
vector<vector<RealType> > pot_local(LR_POT_TYPES, |
| 74 |
< |
vector<RealType> (nAtoms, 0.0)); |
| 75 |
< |
|
| 103 |
> |
// still need: |
| 104 |
> |
// topoDist |
| 105 |
> |
// exclude |
| 106 |
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#endif |
| 107 |
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} |
| 108 |
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|
| 109 |
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|
| 110 |
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|
| 111 |
< |
void ForceDecomposition::distributeData() { |
| 111 |
> |
void ForceMatrixDecomposition::distributeData() { |
| 112 |
|
#ifdef IS_MPI |
| 113 |
|
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 114 |
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|
| 115 |
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// gather up the atomic positions |
| 116 |
< |
AtomCommVectorI->gather(snap->atomData.position, |
| 116 |
> |
AtomCommVectorRow->gather(snap->atomData.position, |
| 117 |
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snap->atomIData.position); |
| 118 |
< |
AtomCommVectorJ->gather(snap->atomData.position, |
| 118 |
> |
AtomCommVectorColumn->gather(snap->atomData.position, |
| 119 |
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snap->atomJData.position); |
| 120 |
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|
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// gather up the cutoff group positions |
| 122 |
< |
cgCommVectorI->gather(snap->cgData.position, |
| 122 |
> |
cgCommVectorRow->gather(snap->cgData.position, |
| 123 |
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snap->cgIData.position); |
| 124 |
< |
cgCommVectorJ->gather(snap->cgData.position, |
| 124 |
> |
cgCommVectorColumn->gather(snap->cgData.position, |
| 125 |
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snap->cgJData.position); |
| 126 |
|
|
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// if needed, gather the atomic rotation matrices |
| 128 |
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if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) { |
| 129 |
< |
AtomCommMatrixI->gather(snap->atomData.aMat, |
| 129 |
> |
AtomCommMatrixRow->gather(snap->atomData.aMat, |
| 130 |
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snap->atomIData.aMat); |
| 131 |
< |
AtomCommMatrixJ->gather(snap->atomData.aMat, |
| 131 |
> |
AtomCommMatrixColumn->gather(snap->atomData.aMat, |
| 132 |
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snap->atomJData.aMat); |
| 133 |
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} |
| 134 |
|
|
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|
// if needed, gather the atomic eletrostatic frames |
| 136 |
|
if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) { |
| 137 |
< |
AtomCommMatrixI->gather(snap->atomData.electroFrame, |
| 137 |
> |
AtomCommMatrixRow->gather(snap->atomData.electroFrame, |
| 138 |
|
snap->atomIData.electroFrame); |
| 139 |
< |
AtomCommMatrixJ->gather(snap->atomData.electroFrame, |
| 139 |
> |
AtomCommMatrixColumn->gather(snap->atomData.electroFrame, |
| 140 |
|
snap->atomJData.electroFrame); |
| 141 |
|
} |
| 142 |
|
#endif |
| 143 |
|
} |
| 144 |
|
|
| 145 |
< |
void ForceDecomposition::collectIntermediateData() { |
| 145 |
> |
void ForceMatrixDecomposition::collectIntermediateData() { |
| 146 |
|
#ifdef IS_MPI |
| 147 |
|
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 148 |
|
|
| 149 |
|
if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) { |
| 150 |
|
|
| 151 |
< |
AtomCommRealI->scatter(snap->atomIData.density, |
| 151 |
> |
AtomCommRealRow->scatter(snap->atomIData.density, |
| 152 |
|
snap->atomData.density); |
| 153 |
|
|
| 154 |
|
int n = snap->atomData.density.size(); |
| 155 |
|
std::vector<RealType> rho_tmp(n, 0.0); |
| 156 |
< |
AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp); |
| 156 |
> |
AtomCommRealColumn->scatter(snap->atomJData.density, rho_tmp); |
| 157 |
|
for (int i = 0; i < n; i++) |
| 158 |
|
snap->atomData.density[i] += rho_tmp[i]; |
| 159 |
|
} |
| 160 |
|
#endif |
| 161 |
|
} |
| 162 |
|
|
| 163 |
< |
void ForceDecomposition::distributeIntermediateData() { |
| 163 |
> |
void ForceMatrixDecomposition::distributeIntermediateData() { |
| 164 |
|
#ifdef IS_MPI |
| 165 |
|
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 166 |
|
if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) { |
| 167 |
< |
AtomCommRealI->gather(snap->atomData.functional, |
| 167 |
> |
AtomCommRealRow->gather(snap->atomData.functional, |
| 168 |
|
snap->atomIData.functional); |
| 169 |
< |
AtomCommRealJ->gather(snap->atomData.functional, |
| 169 |
> |
AtomCommRealColumn->gather(snap->atomData.functional, |
| 170 |
|
snap->atomJData.functional); |
| 171 |
|
} |
| 172 |
|
|
| 173 |
|
if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) { |
| 174 |
< |
AtomCommRealI->gather(snap->atomData.functionalDerivative, |
| 174 |
> |
AtomCommRealRow->gather(snap->atomData.functionalDerivative, |
| 175 |
|
snap->atomIData.functionalDerivative); |
| 176 |
< |
AtomCommRealJ->gather(snap->atomData.functionalDerivative, |
| 176 |
> |
AtomCommRealColumn->gather(snap->atomData.functionalDerivative, |
| 177 |
|
snap->atomJData.functionalDerivative); |
| 178 |
|
} |
| 179 |
|
#endif |
| 180 |
|
} |
| 181 |
|
|
| 182 |
|
|
| 183 |
< |
void ForceDecomposition::collectData() { |
| 183 |
> |
void ForceMatrixDecomposition::collectData() { |
| 184 |
|
#ifdef IS_MPI |
| 185 |
|
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 186 |
|
|
| 187 |
|
int n = snap->atomData.force.size(); |
| 188 |
< |
std::vector<Vector3d> frc_tmp(n, 0.0); |
| 188 |
> |
vector<Vector3d> frc_tmp(n, V3Zero); |
| 189 |
|
|
| 190 |
< |
AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp); |
| 190 |
> |
AtomCommVectorRow->scatter(snap->atomIData.force, frc_tmp); |
| 191 |
|
for (int i = 0; i < n; i++) { |
| 192 |
|
snap->atomData.force[i] += frc_tmp[i]; |
| 193 |
|
frc_tmp[i] = 0.0; |
| 194 |
|
} |
| 195 |
|
|
| 196 |
< |
AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp); |
| 196 |
> |
AtomCommVectorColumn->scatter(snap->atomJData.force, frc_tmp); |
| 197 |
|
for (int i = 0; i < n; i++) |
| 198 |
|
snap->atomData.force[i] += frc_tmp[i]; |
| 199 |
|
|
| 201 |
|
if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) { |
| 202 |
|
|
| 203 |
|
int nt = snap->atomData.force.size(); |
| 204 |
< |
std::vector<Vector3d> trq_tmp(nt, 0.0); |
| 204 |
> |
vector<Vector3d> trq_tmp(nt, V3Zero); |
| 205 |
|
|
| 206 |
< |
AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp); |
| 206 |
> |
AtomCommVectorRow->scatter(snap->atomIData.torque, trq_tmp); |
| 207 |
|
for (int i = 0; i < n; i++) { |
| 208 |
|
snap->atomData.torque[i] += trq_tmp[i]; |
| 209 |
|
trq_tmp[i] = 0.0; |
| 210 |
|
} |
| 211 |
|
|
| 212 |
< |
AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp); |
| 212 |
> |
AtomCommVectorColumn->scatter(snap->atomJData.torque, trq_tmp); |
| 213 |
|
for (int i = 0; i < n; i++) |
| 214 |
|
snap->atomData.torque[i] += trq_tmp[i]; |
| 215 |
|
} |
| 216 |
|
|
| 217 |
+ |
int nLocal = snap->getNumberOfAtoms(); |
| 218 |
+ |
|
| 219 |
+ |
vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, |
| 220 |
+ |
vector<RealType> (nLocal, 0.0)); |
| 221 |
|
|
| 222 |
< |
vector<vector<RealType> > pot_temp(LR_POT_TYPES, |
| 223 |
< |
vector<RealType> (nAtoms, 0.0)); |
| 190 |
< |
|
| 191 |
< |
for (int i = 0; i < LR_POT_TYPES; i++) { |
| 192 |
< |
AtomCommRealI->scatter(pot_row[i], pot_temp[i]); |
| 222 |
> |
for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
| 223 |
> |
AtomCommRealRow->scatter(pot_row[i], pot_temp[i]); |
| 224 |
|
for (int ii = 0; ii < pot_temp[i].size(); ii++ ) { |
| 225 |
|
pot_local[i] += pot_temp[i][ii]; |
| 226 |
|
} |
| 227 |
|
} |
| 197 |
– |
|
| 198 |
– |
|
| 199 |
– |
|
| 228 |
|
#endif |
| 229 |
|
} |
| 230 |
|
|
