| 70 |
|
for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) { |
| 71 |
|
for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
| 72 |
|
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 73 |
< |
|
| 73 |
> |
|
| 74 |
|
double mass = integrableObject->getMass(); |
| 75 |
|
Vector3d vel = integrableObject->getVel(); |
| 76 |
< |
|
| 76 |
> |
|
| 77 |
|
kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); |
| 78 |
< |
|
| 78 |
> |
|
| 79 |
|
if (integrableObject->isDirectional()) { |
| 80 |
|
angMom = integrableObject->getJ(); |
| 81 |
|
I = integrableObject->getI(); |
| 110 |
|
double Thermo::getPotential() { |
| 111 |
|
double potential = 0.0; |
| 112 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 113 |
< |
double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] + |
| 114 |
< |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ; |
| 113 |
> |
double shortRangePot_local = curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ; |
| 114 |
|
|
| 115 |
|
// Get total potential for entire system from MPI. |
| 116 |
|
|
| 117 |
|
#ifdef IS_MPI |
| 118 |
|
|
| 119 |
< |
MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM, |
| 119 |
> |
MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_DOUBLE, MPI_SUM, |
| 120 |
|
MPI_COMM_WORLD); |
| 121 |
+ |
potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL]; |
| 122 |
|
|
| 123 |
|
#else |
| 124 |
|
|
| 125 |
< |
potential = potential_local; |
| 125 |
> |
potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL]; |
| 126 |
|
|
| 127 |
|
#endif // is_mpi |
| 128 |
|
|
| 162 |
|
return pressure; |
| 163 |
|
} |
| 164 |
|
|
| 165 |
+ |
double Thermo::getPressure(int direction) { |
| 166 |
+ |
|
| 167 |
+ |
// Relies on the calculation of the full molecular pressure tensor |
| 168 |
+ |
|
| 169 |
+ |
|
| 170 |
+ |
Mat3x3d tensor; |
| 171 |
+ |
double pressure; |
| 172 |
+ |
|
| 173 |
+ |
tensor = getPressureTensor(); |
| 174 |
+ |
|
| 175 |
+ |
pressure = OOPSEConstant::pressureConvert * tensor(direction, direction); |
| 176 |
+ |
|
| 177 |
+ |
return pressure; |
| 178 |
+ |
} |
| 179 |
+ |
|
| 180 |
+ |
|
| 181 |
+ |
|
| 182 |
|
Mat3x3d Thermo::getPressureTensor() { |
| 183 |
|
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
| 184 |
|
// routine derived via viral theorem description in: |
| 227 |
|
stat[Stats::PRESSURE] = getPressure(); |
| 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); |
| 234 |
+ |
|
| 235 |
+ |
|
| 236 |
|
/**@todo need refactorying*/ |
| 237 |
|
//Conserved Quantity is set by integrator and time is set by setTime |
| 238 |
|
|
