| 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" |
| 70 |
|
vScale(i, j) = eta(i, j); |
| 71 |
|
|
| 72 |
|
if (i == j) { |
| 73 |
< |
vScale(i, j) += chi; |
| 73 |
> |
vScale(i, j) += thermostat.first; |
| 74 |
|
} |
| 75 |
|
} |
| 76 |
|
} |
| 104 |
|
} |
| 105 |
|
|
| 106 |
|
scaleMat(2, 2) = exp(dt*eta(2, 2)); |
| 107 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 107 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 108 |
|
hmat = hmat *scaleMat; |
| 109 |
< |
currentSnapshot_->setHmat(hmat); |
| 109 |
> |
snap->setHmat(hmat); |
| 110 |
|
} |
| 111 |
|
|
| 112 |
|
bool NPAT::etaConverged() { |
| 125 |
|
|
| 126 |
|
RealType NPAT::calcConservedQuantity(){ |
| 127 |
|
|
| 128 |
< |
chi= currentSnapshot_->getChi(); |
| 128 |
< |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 128 |
> |
thermostat = snap->getThermostat(); |
| 129 |
|
loadEta(); |
| 130 |
|
|
| 131 |
|
// We need NkBT a lot, so just set it here: This is the RAW number |
| 146 |
|
RealType barostat_potential; |
| 147 |
|
RealType trEta; |
| 148 |
|
|
| 149 |
< |
totalEnergy = thermo.getTotalE(); |
| 149 |
> |
totalEnergy = thermo.getTotalEnergy(); |
| 150 |
|
|
| 151 |
< |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert); |
| 151 |
> |
thermostat_kinetic = fkBT * tt2 * thermostat.first * |
| 152 |
> |
thermostat.first /(2.0 * PhysicalConstants::energyConvert); |
| 153 |
|
|
| 154 |
< |
thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert; |
| 154 |
> |
thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert; |
| 155 |
|
|
| 156 |
|
SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
| 157 |
|
trEta = tmp.trace(); |
| 168 |
|
} |
| 169 |
|
|
| 170 |
|
void NPAT::loadEta() { |
| 171 |
< |
eta= currentSnapshot_->getEta(); |
| 171 |
> |
eta= snap->getBarostat(); |
| 172 |
|
|
| 173 |
|
//if (!eta.isDiagonal()) { |
| 174 |
|
// sprintf( painCave.errMsg, |
| 179 |
|
} |
| 180 |
|
|
| 181 |
|
void NPAT::saveEta() { |
| 182 |
< |
currentSnapshot_->setEta(eta); |
| 182 |
> |
snap->setBarostat(eta); |
| 183 |
|
} |
| 184 |
|
|
| 185 |
|
} |
