| 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 |
|
|
| 46 |
+ |
using namespace std; |
| 47 |
|
namespace OpenMD { |
| 48 |
|
|
| 49 |
< |
void ForceDecomposition::distributeInitialData() { |
| 49 |
> |
/** |
| 50 |
> |
* distributeInitialData is essentially a copy of the older fortran |
| 51 |
> |
* SimulationSetup |
| 52 |
> |
*/ |
| 53 |
> |
|
| 54 |
> |
void ForceMatrixDecomposition::distributeInitialData() { |
| 55 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 56 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 57 |
> |
nLocal_ = snap_->getNumberOfAtoms(); |
| 58 |
> |
nGroups_ = snap_->getNumberOfCutoffGroups(); |
| 59 |
> |
|
| 60 |
|
#ifdef IS_MPI |
| 61 |
+ |
|
| 62 |
+ |
AtomCommIntRow = new Communicator<Row,int>(nLocal_); |
| 63 |
+ |
AtomCommRealRow = new Communicator<Row,RealType>(nLocal_); |
| 64 |
+ |
AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_); |
| 65 |
+ |
AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_); |
| 66 |
|
|
| 67 |
< |
int nAtoms; |
| 68 |
< |
int nGroups; |
| 67 |
> |
AtomCommIntColumn = new Communicator<Column,int>(nLocal_); |
| 68 |
> |
AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_); |
| 69 |
> |
AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_); |
| 70 |
> |
AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_); |
| 71 |
|
|
| 72 |
< |
AtomCommRealI = new Communicator<Row,RealType>(nAtoms); |
| 73 |
< |
AtomCommVectorI = new Communicator<Row,Vector3d>(nAtoms); |
| 74 |
< |
AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nAtoms); |
| 72 |
> |
cgCommIntRow = new Communicator<Row,int>(nGroups_); |
| 73 |
> |
cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_); |
| 74 |
> |
cgCommIntColumn = new Communicator<Column,int>(nGroups_); |
| 75 |
> |
cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_); |
| 76 |
|
|
| 77 |
< |
AtomCommRealJ = new Communicator<Column,RealType>(nAtoms); |
| 78 |
< |
AtomCommVectorJ = new Communicator<Column,Vector3d>(nAtoms); |
| 79 |
< |
AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nAtoms); |
| 77 |
> |
nAtomsInRow_ = AtomCommIntRow->getSize(); |
| 78 |
> |
nAtomsInCol_ = AtomCommIntColumn->getSize(); |
| 79 |
> |
nGroupsInRow_ = cgCommIntRow->getSize(); |
| 80 |
> |
nGroupsInCol_ = cgCommIntColumn->getSize(); |
| 81 |
|
|
| 82 |
< |
cgCommVectorI = new Communicator<Row,Vector3d>(nGroups); |
| 83 |
< |
cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups); |
| 84 |
< |
// more to come |
| 82 |
> |
// Modify the data storage objects with the correct layouts and sizes: |
| 83 |
> |
atomRowData.resize(nAtomsInRow_); |
| 84 |
> |
atomRowData.setStorageLayout(storageLayout_); |
| 85 |
> |
atomColData.resize(nAtomsInCol_); |
| 86 |
> |
atomColData.setStorageLayout(storageLayout_); |
| 87 |
> |
cgRowData.resize(nGroupsInRow_); |
| 88 |
> |
cgRowData.setStorageLayout(DataStorage::dslPosition); |
| 89 |
> |
cgColData.resize(nGroupsInCol_); |
| 90 |
> |
cgColData.setStorageLayout(DataStorage::dslPosition); |
| 91 |
> |
|
| 92 |
> |
vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES, |
| 93 |
> |
vector<RealType> (nAtomsInRow_, 0.0)); |
| 94 |
> |
vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES, |
| 95 |
> |
vector<RealType> (nAtomsInCol_, 0.0)); |
| 96 |
> |
|
| 97 |
> |
|
| 98 |
> |
vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0); |
| 99 |
> |
|
| 100 |
> |
// gather the information for atomtype IDs (atids): |
| 101 |
> |
vector<int> identsLocal = info_->getIdentArray(); |
| 102 |
> |
identsRow.reserve(nAtomsInRow_); |
| 103 |
> |
identsCol.reserve(nAtomsInCol_); |
| 104 |
> |
|
| 105 |
> |
AtomCommIntRow->gather(identsLocal, identsRow); |
| 106 |
> |
AtomCommIntColumn->gather(identsLocal, identsCol); |
| 107 |
> |
|
| 108 |
> |
AtomLocalToGlobal = info_->getGlobalAtomIndices(); |
| 109 |
> |
AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 110 |
> |
AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
| 111 |
> |
|
| 112 |
> |
cgLocalToGlobal = info_->getGlobalGroupIndices(); |
| 113 |
> |
cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
| 114 |
> |
cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
| 115 |
> |
|
| 116 |
> |
// still need: |
| 117 |
> |
// topoDist |
| 118 |
> |
// exclude |
| 119 |
|
#endif |
| 120 |
|
} |
| 121 |
|
|
| 122 |
|
|
| 123 |
|
|
| 124 |
< |
void ForceDecomposition::distributeData() { |
| 124 |
> |
void ForceMatrixDecomposition::distributeData() { |
| 125 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 126 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 127 |
|
#ifdef IS_MPI |
| 71 |
– |
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 128 |
|
|
| 129 |
|
// gather up the atomic positions |
| 130 |
< |
AtomCommVectorI->gather(snap->atomData.position, |
| 131 |
< |
snap->atomIData.position); |
| 132 |
< |
AtomCommVectorJ->gather(snap->atomData.position, |
| 133 |
< |
snap->atomJData.position); |
| 130 |
> |
AtomCommVectorRow->gather(snap_->atomData.position, |
| 131 |
> |
atomRowData.position); |
| 132 |
> |
AtomCommVectorColumn->gather(snap_->atomData.position, |
| 133 |
> |
atomColData.position); |
| 134 |
|
|
| 135 |
|
// gather up the cutoff group positions |
| 136 |
< |
cgCommVectorI->gather(snap->cgData.position, |
| 137 |
< |
snap->cgIData.position); |
| 138 |
< |
cgCommVectorJ->gather(snap->cgData.position, |
| 139 |
< |
snap->cgJData.position); |
| 136 |
> |
cgCommVectorRow->gather(snap_->cgData.position, |
| 137 |
> |
cgRowData.position); |
| 138 |
> |
cgCommVectorColumn->gather(snap_->cgData.position, |
| 139 |
> |
cgColData.position); |
| 140 |
|
|
| 141 |
|
// if needed, gather the atomic rotation matrices |
| 142 |
< |
if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) { |
| 143 |
< |
AtomCommMatrixI->gather(snap->atomData.aMat, |
| 144 |
< |
snap->atomIData.aMat); |
| 145 |
< |
AtomCommMatrixJ->gather(snap->atomData.aMat, |
| 146 |
< |
snap->atomJData.aMat); |
| 142 |
> |
if (storageLayout_ & DataStorage::dslAmat) { |
| 143 |
> |
AtomCommMatrixRow->gather(snap_->atomData.aMat, |
| 144 |
> |
atomRowData.aMat); |
| 145 |
> |
AtomCommMatrixColumn->gather(snap_->atomData.aMat, |
| 146 |
> |
atomColData.aMat); |
| 147 |
|
} |
| 148 |
|
|
| 149 |
|
// if needed, gather the atomic eletrostatic frames |
| 150 |
< |
if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) { |
| 151 |
< |
AtomCommMatrixI->gather(snap->atomData.electroFrame, |
| 152 |
< |
snap->atomIData.electroFrame); |
| 153 |
< |
AtomCommMatrixJ->gather(snap->atomData.electroFrame, |
| 154 |
< |
snap->atomJData.electroFrame); |
| 150 |
> |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 151 |
> |
AtomCommMatrixRow->gather(snap_->atomData.electroFrame, |
| 152 |
> |
atomRowData.electroFrame); |
| 153 |
> |
AtomCommMatrixColumn->gather(snap_->atomData.electroFrame, |
| 154 |
> |
atomColData.electroFrame); |
| 155 |
|
} |
| 156 |
|
#endif |
| 157 |
|
} |
| 158 |
|
|
| 159 |
< |
void ForceDecomposition::collectIntermediateData() { |
| 159 |
> |
void ForceMatrixDecomposition::collectIntermediateData() { |
| 160 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 161 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 162 |
|
#ifdef IS_MPI |
| 105 |
– |
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 163 |
|
|
| 164 |
< |
if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) { |
| 165 |
< |
AtomCommRealI->scatter(snap->atomIData.density, |
| 166 |
< |
snap->atomData.density); |
| 167 |
< |
std::vector<RealType> rho_tmp; |
| 168 |
< |
int n = snap->getNumberOfAtoms(); |
| 169 |
< |
rho_tmp.reserve( n ); |
| 170 |
< |
AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp); |
| 164 |
> |
if (storageLayout_ & DataStorage::dslDensity) { |
| 165 |
> |
|
| 166 |
> |
AtomCommRealRow->scatter(atomRowData.density, |
| 167 |
> |
snap_->atomData.density); |
| 168 |
> |
|
| 169 |
> |
int n = snap_->atomData.density.size(); |
| 170 |
> |
std::vector<RealType> rho_tmp(n, 0.0); |
| 171 |
> |
AtomCommRealColumn->scatter(atomColData.density, rho_tmp); |
| 172 |
|
for (int i = 0; i < n; i++) |
| 173 |
< |
snap->atomData.density[i] += rho_tmp[i]; |
| 173 |
> |
snap_->atomData.density[i] += rho_tmp[i]; |
| 174 |
|
} |
| 175 |
|
#endif |
| 176 |
|
} |
| 177 |
|
|
| 178 |
< |
void ForceDecomposition::distributeIntermediateData() { |
| 178 |
> |
void ForceMatrixDecomposition::distributeIntermediateData() { |
| 179 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 180 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 181 |
|
#ifdef IS_MPI |
| 182 |
< |
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 183 |
< |
if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) { |
| 184 |
< |
AtomCommRealI->gather(snap->atomData.functional, |
| 185 |
< |
snap->atomIData.functional); |
| 186 |
< |
AtomCommRealJ->gather(snap->atomData.functional, |
| 127 |
< |
snap->atomJData.functional); |
| 182 |
> |
if (storageLayout_ & DataStorage::dslFunctional) { |
| 183 |
> |
AtomCommRealRow->gather(snap_->atomData.functional, |
| 184 |
> |
atomRowData.functional); |
| 185 |
> |
AtomCommRealColumn->gather(snap_->atomData.functional, |
| 186 |
> |
atomColData.functional); |
| 187 |
|
} |
| 188 |
|
|
| 189 |
< |
if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) { |
| 190 |
< |
AtomCommRealI->gather(snap->atomData.functionalDerivative, |
| 191 |
< |
snap->atomIData.functionalDerivative); |
| 192 |
< |
AtomCommRealJ->gather(snap->atomData.functionalDerivative, |
| 193 |
< |
snap->atomJData.functionalDerivative); |
| 189 |
> |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 190 |
> |
AtomCommRealRow->gather(snap_->atomData.functionalDerivative, |
| 191 |
> |
atomRowData.functionalDerivative); |
| 192 |
> |
AtomCommRealColumn->gather(snap_->atomData.functionalDerivative, |
| 193 |
> |
atomColData.functionalDerivative); |
| 194 |
|
} |
| 195 |
|
#endif |
| 196 |
|
} |
| 197 |
|
|
| 198 |
|
|
| 199 |
< |
void ForceDecomposition::collectData() { |
| 200 |
< |
#ifdef IS_MPI |
| 201 |
< |
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 202 |
< |
int n = snap->getNumberOfAtoms(); |
| 203 |
< |
|
| 204 |
< |
std::vector<Vector3d> frc_tmp; |
| 146 |
< |
frc_tmp.reserve( n ); |
| 199 |
> |
void ForceMatrixDecomposition::collectData() { |
| 200 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 201 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 202 |
> |
#ifdef IS_MPI |
| 203 |
> |
int n = snap_->atomData.force.size(); |
| 204 |
> |
vector<Vector3d> frc_tmp(n, V3Zero); |
| 205 |
|
|
| 206 |
< |
AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp); |
| 207 |
< |
for (int i = 0; i < n; i++) |
| 208 |
< |
snap->atomData.force[i] += frc_tmp[i]; |
| 206 |
> |
AtomCommVectorRow->scatter(atomRowData.force, frc_tmp); |
| 207 |
> |
for (int i = 0; i < n; i++) { |
| 208 |
> |
snap_->atomData.force[i] += frc_tmp[i]; |
| 209 |
> |
frc_tmp[i] = 0.0; |
| 210 |
> |
} |
| 211 |
|
|
| 212 |
< |
AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp); |
| 212 |
> |
AtomCommVectorColumn->scatter(atomColData.force, frc_tmp); |
| 213 |
|
for (int i = 0; i < n; i++) |
| 214 |
< |
snap->atomData.force[i] += frc_tmp[i]; |
| 214 |
> |
snap_->atomData.force[i] += frc_tmp[i]; |
| 215 |
|
|
| 216 |
|
|
| 217 |
< |
if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) { |
| 218 |
< |
std::vector<Vector3d> trq_tmp; |
| 219 |
< |
trq_tmp.reserve( n ); |
| 217 |
> |
if (storageLayout_ & DataStorage::dslTorque) { |
| 218 |
> |
|
| 219 |
> |
int nt = snap_->atomData.force.size(); |
| 220 |
> |
vector<Vector3d> trq_tmp(nt, V3Zero); |
| 221 |
> |
|
| 222 |
> |
AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp); |
| 223 |
> |
for (int i = 0; i < n; i++) { |
| 224 |
> |
snap_->atomData.torque[i] += trq_tmp[i]; |
| 225 |
> |
trq_tmp[i] = 0.0; |
| 226 |
> |
} |
| 227 |
|
|
| 228 |
< |
AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp); |
| 228 |
> |
AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp); |
| 229 |
|
for (int i = 0; i < n; i++) |
| 230 |
< |
snap->atomData.torque[i] += trq_tmp[i]; |
| 164 |
< |
|
| 165 |
< |
AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp); |
| 166 |
< |
for (int i = 0; i < n; i++) |
| 167 |
< |
snap->atomData.torque[i] += trq_tmp[i]; |
| 230 |
> |
snap_->atomData.torque[i] += trq_tmp[i]; |
| 231 |
|
} |
| 232 |
|
|
| 233 |
< |
// Still need pot! |
| 233 |
> |
nLocal_ = snap_->getNumberOfAtoms(); |
| 234 |
> |
|
| 235 |
> |
vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, |
| 236 |
> |
vector<RealType> (nLocal_, 0.0)); |
| 237 |
|
|
| 238 |
+ |
for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
| 239 |
+ |
AtomCommRealRow->scatter(pot_row[i], pot_temp[i]); |
| 240 |
+ |
for (int ii = 0; ii < pot_temp[i].size(); ii++ ) { |
| 241 |
+ |
pot_local[i] += pot_temp[i][ii]; |
| 242 |
+ |
} |
| 243 |
+ |
} |
| 244 |
+ |
#endif |
| 245 |
+ |
} |
| 246 |
|
|
| 247 |
+ |
|
| 248 |
+ |
Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){ |
| 249 |
+ |
Vector3d d; |
| 250 |
+ |
|
| 251 |
+ |
#ifdef IS_MPI |
| 252 |
+ |
d = cgColData.position[cg2] - cgRowData.position[cg1]; |
| 253 |
+ |
#else |
| 254 |
+ |
d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1]; |
| 255 |
+ |
#endif |
| 256 |
+ |
|
| 257 |
+ |
snap_->wrapVector(d); |
| 258 |
+ |
return d; |
| 259 |
+ |
} |
| 260 |
|
|
| 261 |
+ |
|
| 262 |
+ |
Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){ |
| 263 |
+ |
|
| 264 |
+ |
Vector3d d; |
| 265 |
+ |
|
| 266 |
+ |
#ifdef IS_MPI |
| 267 |
+ |
d = cgRowData.position[cg1] - atomRowData.position[atom1]; |
| 268 |
+ |
#else |
| 269 |
+ |
d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1]; |
| 270 |
|
#endif |
| 271 |
+ |
|
| 272 |
+ |
snap_->wrapVector(d); |
| 273 |
+ |
return d; |
| 274 |
|
} |
| 275 |
|
|
| 276 |
+ |
Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){ |
| 277 |
+ |
Vector3d d; |
| 278 |
+ |
|
| 279 |
+ |
#ifdef IS_MPI |
| 280 |
+ |
d = cgColData.position[cg2] - atomColData.position[atom2]; |
| 281 |
+ |
#else |
| 282 |
+ |
d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2]; |
| 283 |
+ |
#endif |
| 284 |
+ |
|
| 285 |
+ |
snap_->wrapVector(d); |
| 286 |
+ |
return d; |
| 287 |
+ |
} |
| 288 |
+ |
|
| 289 |
+ |
Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){ |
| 290 |
+ |
Vector3d d; |
| 291 |
+ |
|
| 292 |
+ |
#ifdef IS_MPI |
| 293 |
+ |
d = atomColData.position[atom2] - atomRowData.position[atom1]; |
| 294 |
+ |
#else |
| 295 |
+ |
d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1]; |
| 296 |
+ |
#endif |
| 297 |
+ |
|
| 298 |
+ |
snap_->wrapVector(d); |
| 299 |
+ |
return d; |
| 300 |
+ |
} |
| 301 |
+ |
|
| 302 |
+ |
void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){ |
| 303 |
+ |
#ifdef IS_MPI |
| 304 |
+ |
atomRowData.force[atom1] += fg; |
| 305 |
+ |
#else |
| 306 |
+ |
snap_->atomData.force[atom1] += fg; |
| 307 |
+ |
#endif |
| 308 |
+ |
} |
| 309 |
+ |
|
| 310 |
+ |
void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){ |
| 311 |
+ |
#ifdef IS_MPI |
| 312 |
+ |
atomColData.force[atom2] += fg; |
| 313 |
+ |
#else |
| 314 |
+ |
snap_->atomData.force[atom2] += fg; |
| 315 |
+ |
#endif |
| 316 |
+ |
} |
| 317 |
+ |
|
| 318 |
+ |
// filling interaction blocks with pointers |
| 319 |
+ |
InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) { |
| 320 |
+ |
InteractionData idat; |
| 321 |
+ |
|
| 322 |
+ |
#ifdef IS_MPI |
| 323 |
+ |
if (storageLayout_ & DataStorage::dslAmat) { |
| 324 |
+ |
idat.A1 = &(atomRowData.aMat[atom1]); |
| 325 |
+ |
idat.A2 = &(atomColData.aMat[atom2]); |
| 326 |
+ |
} |
| 327 |
+ |
|
| 328 |
+ |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 329 |
+ |
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 330 |
+ |
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 331 |
+ |
} |
| 332 |
+ |
|
| 333 |
+ |
if (storageLayout_ & DataStorage::dslTorque) { |
| 334 |
+ |
idat.t1 = &(atomRowData.torque[atom1]); |
| 335 |
+ |
idat.t2 = &(atomColData.torque[atom2]); |
| 336 |
+ |
} |
| 337 |
+ |
|
| 338 |
+ |
if (storageLayout_ & DataStorage::dslDensity) { |
| 339 |
+ |
idat.rho1 = &(atomRowData.density[atom1]); |
| 340 |
+ |
idat.rho2 = &(atomColData.density[atom2]); |
| 341 |
+ |
} |
| 342 |
+ |
|
| 343 |
+ |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 344 |
+ |
idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]); |
| 345 |
+ |
idat.dfrho2 = &(atomColData.functionalDerivative[atom2]); |
| 346 |
+ |
} |
| 347 |
+ |
#else |
| 348 |
+ |
if (storageLayout_ & DataStorage::dslAmat) { |
| 349 |
+ |
idat.A1 = &(snap_->atomData.aMat[atom1]); |
| 350 |
+ |
idat.A2 = &(snap_->atomData.aMat[atom2]); |
| 351 |
+ |
} |
| 352 |
+ |
|
| 353 |
+ |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 354 |
+ |
idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
| 355 |
+ |
idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
| 356 |
+ |
} |
| 357 |
+ |
|
| 358 |
+ |
if (storageLayout_ & DataStorage::dslTorque) { |
| 359 |
+ |
idat.t1 = &(snap_->atomData.torque[atom1]); |
| 360 |
+ |
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 361 |
+ |
} |
| 362 |
+ |
|
| 363 |
+ |
if (storageLayout_ & DataStorage::dslDensity) { |
| 364 |
+ |
idat.rho1 = &(snap_->atomData.density[atom1]); |
| 365 |
+ |
idat.rho2 = &(snap_->atomData.density[atom2]); |
| 366 |
+ |
} |
| 367 |
+ |
|
| 368 |
+ |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 369 |
+ |
idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]); |
| 370 |
+ |
idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]); |
| 371 |
+ |
} |
| 372 |
+ |
#endif |
| 373 |
+ |
return idat; |
| 374 |
+ |
} |
| 375 |
+ |
|
| 376 |
+ |
InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){ |
| 377 |
+ |
|
| 378 |
+ |
InteractionData idat; |
| 379 |
+ |
#ifdef IS_MPI |
| 380 |
+ |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 381 |
+ |
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 382 |
+ |
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 383 |
+ |
} |
| 384 |
+ |
if (storageLayout_ & DataStorage::dslTorque) { |
| 385 |
+ |
idat.t1 = &(atomRowData.torque[atom1]); |
| 386 |
+ |
idat.t2 = &(atomColData.torque[atom2]); |
| 387 |
+ |
} |
| 388 |
+ |
if (storageLayout_ & DataStorage::dslForce) { |
| 389 |
+ |
idat.t1 = &(atomRowData.force[atom1]); |
| 390 |
+ |
idat.t2 = &(atomColData.force[atom2]); |
| 391 |
+ |
} |
| 392 |
+ |
#else |
| 393 |
+ |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 394 |
+ |
idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
| 395 |
+ |
idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
| 396 |
+ |
} |
| 397 |
+ |
if (storageLayout_ & DataStorage::dslTorque) { |
| 398 |
+ |
idat.t1 = &(snap_->atomData.torque[atom1]); |
| 399 |
+ |
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 400 |
+ |
} |
| 401 |
+ |
if (storageLayout_ & DataStorage::dslForce) { |
| 402 |
+ |
idat.t1 = &(snap_->atomData.force[atom1]); |
| 403 |
+ |
idat.t2 = &(snap_->atomData.force[atom2]); |
| 404 |
+ |
} |
| 405 |
+ |
#endif |
| 406 |
+ |
|
| 407 |
+ |
} |
| 408 |
+ |
|
| 409 |
+ |
SelfData ForceMatrixDecomposition::fillSelfData(int atom1) { |
| 410 |
+ |
SelfData sdat; |
| 411 |
+ |
// Still Missing atype, skippedCharge, potVec pot, |
| 412 |
+ |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 413 |
+ |
sdat.eFrame = &(snap_->atomData.electroFrame[atom1]); |
| 414 |
+ |
} |
| 415 |
+ |
|
| 416 |
+ |
if (storageLayout_ & DataStorage::dslTorque) { |
| 417 |
+ |
sdat.t = &(snap_->atomData.torque[atom1]); |
| 418 |
+ |
} |
| 419 |
+ |
|
| 420 |
+ |
if (storageLayout_ & DataStorage::dslDensity) { |
| 421 |
+ |
sdat.rho = &(snap_->atomData.density[atom1]); |
| 422 |
+ |
} |
| 423 |
+ |
|
| 424 |
+ |
if (storageLayout_ & DataStorage::dslFunctional) { |
| 425 |
+ |
sdat.frho = &(snap_->atomData.functional[atom1]); |
| 426 |
+ |
} |
| 427 |
+ |
|
| 428 |
+ |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 429 |
+ |
sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]); |
| 430 |
+ |
} |
| 431 |
+ |
|
| 432 |
+ |
return sdat; |
| 433 |
+ |
} |
| 434 |
+ |
|
| 435 |
+ |
|
| 436 |
+ |
|
| 437 |
+ |
/* |
| 438 |
+ |
* buildNeighborList |
| 439 |
+ |
* |
| 440 |
+ |
* first element of pair is row-indexed CutoffGroup |
| 441 |
+ |
* second element of pair is column-indexed CutoffGroup |
| 442 |
+ |
*/ |
| 443 |
+ |
vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() { |
| 444 |
+ |
|
| 445 |
+ |
vector<pair<int, int> > neighborList; |
| 446 |
+ |
#ifdef IS_MPI |
| 447 |
+ |
CellListRow.clear(); |
| 448 |
+ |
CellListCol.clear(); |
| 449 |
+ |
#else |
| 450 |
+ |
CellList.clear(); |
| 451 |
+ |
#endif |
| 452 |
+ |
|
| 453 |
+ |
// dangerous to not do error checking. |
| 454 |
+ |
RealType skinThickness_ = info_->getSimParams()->getSkinThickness(); |
| 455 |
+ |
RealType rCut_; |
| 456 |
+ |
|
| 457 |
+ |
RealType rList_ = (rCut_ + skinThickness_); |
| 458 |
+ |
RealType rl2 = rList_ * rList_; |
| 459 |
+ |
Snapshot* snap_ = sman_->getCurrentSnapshot(); |
| 460 |
+ |
Mat3x3d Hmat = snap_->getHmat(); |
| 461 |
+ |
Vector3d Hx = Hmat.getColumn(0); |
| 462 |
+ |
Vector3d Hy = Hmat.getColumn(1); |
| 463 |
+ |
Vector3d Hz = Hmat.getColumn(2); |
| 464 |
+ |
Vector3i nCells; |
| 465 |
+ |
|
| 466 |
+ |
nCells.x() = (int) ( Hx.length() )/ rList_; |
| 467 |
+ |
nCells.y() = (int) ( Hy.length() )/ rList_; |
| 468 |
+ |
nCells.z() = (int) ( Hz.length() )/ rList_; |
| 469 |
+ |
|
| 470 |
+ |
Mat3x3d invHmat = snap_->getInvHmat(); |
| 471 |
+ |
Vector3d rs, scaled, dr; |
| 472 |
+ |
Vector3i whichCell; |
| 473 |
+ |
int cellIndex; |
| 474 |
+ |
|
| 475 |
+ |
#ifdef IS_MPI |
| 476 |
+ |
for (int i = 0; i < nGroupsInRow_; i++) { |
| 477 |
+ |
rs = cgRowData.position[i]; |
| 478 |
+ |
// scaled positions relative to the box vectors |
| 479 |
+ |
scaled = invHmat * rs; |
| 480 |
+ |
// wrap the vector back into the unit box by subtracting integer box |
| 481 |
+ |
// numbers |
| 482 |
+ |
for (int j = 0; j < 3; j++) |
| 483 |
+ |
scaled[j] -= roundMe(scaled[j]); |
| 484 |
+ |
|
| 485 |
+ |
// find xyz-indices of cell that cutoffGroup is in. |
| 486 |
+ |
whichCell.x() = nCells.x() * scaled.x(); |
| 487 |
+ |
whichCell.y() = nCells.y() * scaled.y(); |
| 488 |
+ |
whichCell.z() = nCells.z() * scaled.z(); |
| 489 |
+ |
|
| 490 |
+ |
// find single index of this cell: |
| 491 |
+ |
cellIndex = Vlinear(whichCell, nCells); |
| 492 |
+ |
// add this cutoff group to the list of groups in this cell; |
| 493 |
+ |
CellListRow[cellIndex].push_back(i); |
| 494 |
+ |
} |
| 495 |
+ |
|
| 496 |
+ |
for (int i = 0; i < nGroupsInCol_; i++) { |
| 497 |
+ |
rs = cgColData.position[i]; |
| 498 |
+ |
// scaled positions relative to the box vectors |
| 499 |
+ |
scaled = invHmat * rs; |
| 500 |
+ |
// wrap the vector back into the unit box by subtracting integer box |
| 501 |
+ |
// numbers |
| 502 |
+ |
for (int j = 0; j < 3; j++) |
| 503 |
+ |
scaled[j] -= roundMe(scaled[j]); |
| 504 |
+ |
|
| 505 |
+ |
// find xyz-indices of cell that cutoffGroup is in. |
| 506 |
+ |
whichCell.x() = nCells.x() * scaled.x(); |
| 507 |
+ |
whichCell.y() = nCells.y() * scaled.y(); |
| 508 |
+ |
whichCell.z() = nCells.z() * scaled.z(); |
| 509 |
+ |
|
| 510 |
+ |
// find single index of this cell: |
| 511 |
+ |
cellIndex = Vlinear(whichCell, nCells); |
| 512 |
+ |
// add this cutoff group to the list of groups in this cell; |
| 513 |
+ |
CellListCol[cellIndex].push_back(i); |
| 514 |
+ |
} |
| 515 |
+ |
#else |
| 516 |
+ |
for (int i = 0; i < nGroups_; i++) { |
| 517 |
+ |
rs = snap_->cgData.position[i]; |
| 518 |
+ |
// scaled positions relative to the box vectors |
| 519 |
+ |
scaled = invHmat * rs; |
| 520 |
+ |
// wrap the vector back into the unit box by subtracting integer box |
| 521 |
+ |
// numbers |
| 522 |
+ |
for (int j = 0; j < 3; j++) |
| 523 |
+ |
scaled[j] -= roundMe(scaled[j]); |
| 524 |
+ |
|
| 525 |
+ |
// find xyz-indices of cell that cutoffGroup is in. |
| 526 |
+ |
whichCell.x() = nCells.x() * scaled.x(); |
| 527 |
+ |
whichCell.y() = nCells.y() * scaled.y(); |
| 528 |
+ |
whichCell.z() = nCells.z() * scaled.z(); |
| 529 |
+ |
|
| 530 |
+ |
// find single index of this cell: |
| 531 |
+ |
cellIndex = Vlinear(whichCell, nCells); |
| 532 |
+ |
// add this cutoff group to the list of groups in this cell; |
| 533 |
+ |
CellList[cellIndex].push_back(i); |
| 534 |
+ |
} |
| 535 |
+ |
#endif |
| 536 |
+ |
|
| 537 |
+ |
|
| 538 |
+ |
|
| 539 |
+ |
for (int m1z = 0; m1z < nCells.z(); m1z++) { |
| 540 |
+ |
for (int m1y = 0; m1y < nCells.y(); m1y++) { |
| 541 |
+ |
for (int m1x = 0; m1x < nCells.x(); m1x++) { |
| 542 |
+ |
Vector3i m1v(m1x, m1y, m1z); |
| 543 |
+ |
int m1 = Vlinear(m1v, nCells); |
| 544 |
+ |
for (int offset = 0; offset < nOffset_; offset++) { |
| 545 |
+ |
Vector3i m2v = m1v + cellOffsets_[offset]; |
| 546 |
+ |
|
| 547 |
+ |
if (m2v.x() >= nCells.x()) { |
| 548 |
+ |
m2v.x() = 0; |
| 549 |
+ |
} else if (m2v.x() < 0) { |
| 550 |
+ |
m2v.x() = nCells.x() - 1; |
| 551 |
+ |
} |
| 552 |
+ |
|
| 553 |
+ |
if (m2v.y() >= nCells.y()) { |
| 554 |
+ |
m2v.y() = 0; |
| 555 |
+ |
} else if (m2v.y() < 0) { |
| 556 |
+ |
m2v.y() = nCells.y() - 1; |
| 557 |
+ |
} |
| 558 |
+ |
|
| 559 |
+ |
if (m2v.z() >= nCells.z()) { |
| 560 |
+ |
m2v.z() = 0; |
| 561 |
+ |
} else if (m2v.z() < 0) { |
| 562 |
+ |
m2v.z() = nCells.z() - 1; |
| 563 |
+ |
} |
| 564 |
+ |
|
| 565 |
+ |
int m2 = Vlinear (m2v, nCells); |
| 566 |
+ |
|
| 567 |
+ |
#ifdef IS_MPI |
| 568 |
+ |
for (vector<int>::iterator j1 = CellListRow[m1].begin(); |
| 569 |
+ |
j1 != CellListRow[m1].end(); ++j1) { |
| 570 |
+ |
for (vector<int>::iterator j2 = CellListCol[m2].begin(); |
| 571 |
+ |
j2 != CellListCol[m2].end(); ++j2) { |
| 572 |
+ |
|
| 573 |
+ |
// Always do this if we're in different cells or if |
| 574 |
+ |
// we're in the same cell and the global index of the |
| 575 |
+ |
// j2 cutoff group is less than the j1 cutoff group |
| 576 |
+ |
|
| 577 |
+ |
if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { |
| 578 |
+ |
dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
| 579 |
+ |
snap_->wrapVector(dr); |
| 580 |
+ |
if (dr.lengthSquare() < rl2) { |
| 581 |
+ |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 582 |
+ |
} |
| 583 |
+ |
} |
| 584 |
+ |
} |
| 585 |
+ |
} |
| 586 |
+ |
#else |
| 587 |
+ |
for (vector<int>::iterator j1 = CellList[m1].begin(); |
| 588 |
+ |
j1 != CellList[m1].end(); ++j1) { |
| 589 |
+ |
for (vector<int>::iterator j2 = CellList[m2].begin(); |
| 590 |
+ |
j2 != CellList[m2].end(); ++j2) { |
| 591 |
+ |
|
| 592 |
+ |
// Always do this if we're in different cells or if |
| 593 |
+ |
// we're in the same cell and the global index of the |
| 594 |
+ |
// j2 cutoff group is less than the j1 cutoff group |
| 595 |
+ |
|
| 596 |
+ |
if (m2 != m1 || (*j2) < (*j1)) { |
| 597 |
+ |
dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
| 598 |
+ |
snap_->wrapVector(dr); |
| 599 |
+ |
if (dr.lengthSquare() < rl2) { |
| 600 |
+ |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 601 |
+ |
} |
| 602 |
+ |
} |
| 603 |
+ |
} |
| 604 |
+ |
} |
| 605 |
+ |
#endif |
| 606 |
+ |
} |
| 607 |
+ |
} |
| 608 |
+ |
} |
| 609 |
+ |
} |
| 610 |
+ |
return neighborList; |
| 611 |
+ |
} |
| 612 |
|
} //end namespace OpenMD |
