| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
|
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "brains/SimInfo.hpp" |
| 62 |
|
|
| 63 |
|
|
| 64 |
|
RealType NPTxyz::calcConservedQuantity(){ |
| 65 |
+ |
thermostat = snap->getThermostat(); |
| 66 |
+ |
loadEta(); |
| 67 |
|
|
| 68 |
|
// We need NkBT a lot, so just set it here: This is the RAW number |
| 69 |
|
// of integrableObjects, so no subtraction or addition of constraints or |
| 83 |
|
RealType barostat_potential; |
| 84 |
|
RealType trEta; |
| 85 |
|
|
| 86 |
< |
totalEnergy = thermo.getTotalE(); |
| 86 |
> |
totalEnergy = thermo.getTotalEnergy(); |
| 87 |
|
|
| 88 |
< |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert); |
| 88 |
> |
thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first |
| 89 |
> |
/ (2.0 * PhysicalConstants::energyConvert); |
| 90 |
|
|
| 91 |
< |
thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert; |
| 91 |
> |
thermostat_potential = fkBT* thermostat.second |
| 92 |
> |
/ PhysicalConstants::energyConvert; |
| 93 |
|
|
| 94 |
|
SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
| 95 |
|
trEta = tmp.trace(); |
| 167 |
|
simError(); |
| 168 |
|
} else { |
| 169 |
|
|
| 170 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 170 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 171 |
|
hmat = hmat *scaleMat; |
| 172 |
< |
currentSnapshot_->setHmat(hmat); |
| 172 |
> |
snap->setHmat(hmat); |
| 173 |
|
} |
| 174 |
|
} |
| 175 |
|
|
| 176 |
|
void NPTxyz::loadEta() { |
| 177 |
< |
eta= currentSnapshot_->getEta(); |
| 177 |
> |
eta= snap->getBarostat(); |
| 178 |
|
} |
| 179 |
|
|
| 180 |
|
} |
