| 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" |
| 57 |
|
*/ |
| 58 |
|
RealType NPTsz::calcConservedQuantity(){ |
| 59 |
|
|
| 60 |
< |
chi= currentSnapshot_->getChi(); |
| 60 |
< |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 60 |
> |
thermostat = snap->getThermostat(); |
| 61 |
|
loadEta(); |
| 62 |
|
|
| 63 |
|
// We need NkBT a lot, so just set it here: This is the RAW number |
| 79 |
|
RealType barostat_potential; |
| 80 |
|
RealType trEta; |
| 81 |
|
|
| 82 |
< |
totalEnergy = thermo.getTotalE(); |
| 82 |
> |
totalEnergy = thermo.getTotalEnergy(); |
| 83 |
|
|
| 84 |
< |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
| 84 |
> |
thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first / |
| 85 |
|
(2.0 * PhysicalConstants::energyConvert); |
| 86 |
|
|
| 87 |
< |
thermostat_potential = fkBT* integralOfChidt / |
| 87 |
> |
thermostat_potential = fkBT* thermostat.second / |
| 88 |
|
PhysicalConstants::energyConvert; |
| 89 |
|
|
| 90 |
|
SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
| 106 |
|
|
| 107 |
|
void NPTsz::scaleSimBox(){ |
| 108 |
|
|
| 109 |
< |
int i,j,k; |
| 109 |
> |
int i, j; |
| 110 |
|
Mat3x3d scaleMat; |
| 111 |
< |
RealType eta2ij, scaleFactor; |
| 111 |
> |
RealType scaleFactor; |
| 112 |
|
RealType bigScale, smallScale, offDiagMax; |
| 113 |
|
Mat3x3d hm; |
| 114 |
|
Mat3x3d hmnew; |
| 161 |
|
simError(); |
| 162 |
|
} else { |
| 163 |
|
|
| 164 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 164 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 165 |
|
hmat = hmat *scaleMat; |
| 166 |
< |
currentSnapshot_->setHmat(hmat); |
| 166 |
> |
snap->setHmat(hmat); |
| 167 |
|
} |
| 168 |
|
} |
| 169 |
|
|
| 170 |
|
void NPTsz::loadEta() { |
| 171 |
< |
eta= currentSnapshot_->getEta(); |
| 171 |
> |
eta= snap->getBarostat(); |
| 172 |
|
} |
| 173 |
|
} |
