| 64 |
|
int i; |
| 65 |
|
int j; |
| 66 |
|
int k; |
| 67 |
+ |
RealType mass; |
| 68 |
|
RealType kinetic = 0.0; |
| 69 |
|
RealType kinetic_global = 0.0; |
| 70 |
|
|
| 72 |
|
for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
| 73 |
|
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 74 |
|
|
| 75 |
< |
RealType mass = integrableObject->getMass(); |
| 76 |
< |
Vector3d vel = integrableObject->getVel(); |
| 75 |
> |
mass = integrableObject->getMass(); |
| 76 |
> |
vel = integrableObject->getVel(); |
| 77 |
|
|
| 78 |
|
kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); |
| 79 |
|
|
| 178 |
|
return pressure; |
| 179 |
|
} |
| 180 |
|
|
| 180 |
– |
|
| 181 |
– |
|
| 181 |
|
Mat3x3d Thermo::getPressureTensor() { |
| 182 |
|
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
| 183 |
|
// routine derived via viral theorem description in: |
| 211 |
|
Mat3x3d tau = curSnapshot->statData.getTau(); |
| 212 |
|
|
| 213 |
|
pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume; |
| 214 |
< |
|
| 214 |
> |
|
| 215 |
|
return pressureTensor; |
| 216 |
|
} |
| 217 |
|
|
| 218 |
+ |
|
| 219 |
|
void Thermo::saveStat(){ |
| 220 |
|
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 221 |
|
Stats& stat = currSnapshot->statData; |
| 228 |
|
stat[Stats::VOLUME] = getVolume(); |
| 229 |
|
|
| 230 |
|
Mat3x3d tensor =getPressureTensor(); |
| 231 |
< |
stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0); |
| 232 |
< |
stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1); |
| 233 |
< |
stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2); |
| 231 |
> |
stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0); |
| 232 |
> |
stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1); |
| 233 |
> |
stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2); |
| 234 |
> |
stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0); |
| 235 |
> |
stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1); |
| 236 |
> |
stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2); |
| 237 |
> |
stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0); |
| 238 |
> |
stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1); |
| 239 |
> |
stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2); |
| 240 |
> |
|
| 241 |
> |
|
| 242 |
> |
Globals* simParams = info_->getSimParams(); |
| 243 |
> |
|
| 244 |
> |
if (simParams->haveTaggedAtomPair() && |
| 245 |
> |
simParams->havePrintTaggedPairDistance()) { |
| 246 |
> |
if ( simParams->getPrintTaggedPairDistance()) { |
| 247 |
> |
|
| 248 |
> |
std::pair<int, int> tap = simParams->getTaggedAtomPair(); |
| 249 |
> |
Vector3d pos1, pos2, rab; |
| 250 |
> |
|
| 251 |
> |
#ifdef IS_MPI |
| 252 |
> |
std::cerr << "tap = " << tap.first << " " << tap.second << std::endl; |
| 253 |
> |
|
| 254 |
> |
int mol1 = info_->getGlobalMolMembership(tap.first); |
| 255 |
> |
int mol2 = info_->getGlobalMolMembership(tap.second); |
| 256 |
> |
std::cerr << "mols = " << mol1 << " " << mol2 << std::endl; |
| 257 |
> |
|
| 258 |
> |
int proc1 = info_->getMolToProc(mol1); |
| 259 |
> |
int proc2 = info_->getMolToProc(mol2); |
| 260 |
|
|
| 261 |
+ |
std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl; |
| 262 |
|
|
| 263 |
+ |
RealType data[3]; |
| 264 |
+ |
if (proc1 == worldRank) { |
| 265 |
+ |
StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first); |
| 266 |
+ |
std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl; |
| 267 |
+ |
pos1 = sd1->getPos(); |
| 268 |
+ |
data[0] = pos1.x(); |
| 269 |
+ |
data[1] = pos1.y(); |
| 270 |
+ |
data[2] = pos1.z(); |
| 271 |
+ |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
| 272 |
+ |
} else { |
| 273 |
+ |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
| 274 |
+ |
pos1 = Vector3d(data); |
| 275 |
+ |
} |
| 276 |
+ |
|
| 277 |
+ |
|
| 278 |
+ |
if (proc2 == worldRank) { |
| 279 |
+ |
StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second); |
| 280 |
+ |
std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl; |
| 281 |
+ |
pos2 = sd2->getPos(); |
| 282 |
+ |
data[0] = pos2.x(); |
| 283 |
+ |
data[1] = pos2.y(); |
| 284 |
+ |
data[2] = pos2.z(); |
| 285 |
+ |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
| 286 |
+ |
} else { |
| 287 |
+ |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
| 288 |
+ |
pos2 = Vector3d(data); |
| 289 |
+ |
} |
| 290 |
+ |
#else |
| 291 |
+ |
StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first); |
| 292 |
+ |
StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second); |
| 293 |
+ |
pos1 = at1->getPos(); |
| 294 |
+ |
pos2 = at2->getPos(); |
| 295 |
+ |
#endif |
| 296 |
+ |
rab = pos2 - pos1; |
| 297 |
+ |
currSnapshot->wrapVector(rab); |
| 298 |
+ |
stat[Stats::TAGGED_PAIR_DISTANCE] = rab.length(); |
| 299 |
+ |
} |
| 300 |
+ |
} |
| 301 |
+ |
|
| 302 |
|
/**@todo need refactorying*/ |
| 303 |
|
//Conserved Quantity is set by integrator and time is set by setTime |
| 304 |
|
|
