| 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 "NPTi.hpp" |
| 78 |
|
} |
| 79 |
|
|
| 80 |
|
void NPTi::calcVelScale() { |
| 81 |
< |
vScale = chi + eta; |
| 81 |
> |
vScale = thermostat.first + eta; |
| 82 |
|
} |
| 83 |
|
|
| 84 |
|
void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) { |
| 112 |
|
painCave.isFatal = 1; |
| 113 |
|
simError(); |
| 114 |
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} else { |
| 115 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 115 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 116 |
|
hmat *= scaleFactor; |
| 117 |
< |
currentSnapshot_->setHmat(hmat); |
| 117 |
> |
snap->setHmat(hmat); |
| 118 |
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} |
| 119 |
|
|
| 120 |
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} |
| 126 |
|
|
| 127 |
|
RealType NPTi::calcConservedQuantity(){ |
| 128 |
|
|
| 129 |
< |
chi= currentSnapshot_->getChi(); |
| 129 |
< |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 129 |
> |
thermostat = snap->getThermostat(); |
| 130 |
|
loadEta(); |
| 131 |
|
// We need NkBT a lot, so just set it here: This is the RAW number |
| 132 |
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// of integrableObjects, so no subtraction or addition of constraints or |
| 145 |
|
RealType barostat_kinetic; |
| 146 |
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RealType barostat_potential; |
| 147 |
|
|
| 148 |
< |
Energy =thermo.getTotalE(); |
| 148 |
> |
Energy =thermo.getTotalEnergy(); |
| 149 |
|
|
| 150 |
< |
thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * PhysicalConstants::energyConvert); |
| 150 |
> |
thermostat_kinetic = fkBT* tt2 * thermostat.first * |
| 151 |
> |
thermostat.first / (2.0 * PhysicalConstants::energyConvert); |
| 152 |
|
|
| 153 |
< |
thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert; |
| 153 |
> |
thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert; |
| 154 |
|
|
| 155 |
|
|
| 156 |
|
barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * PhysicalConstants::energyConvert); |
| 165 |
|
} |
| 166 |
|
|
| 167 |
|
void NPTi::loadEta() { |
| 168 |
< |
Mat3x3d etaMat = currentSnapshot_->getEta(); |
| 168 |
> |
Mat3x3d etaMat = snap->getBarostat(); |
| 169 |
|
eta = etaMat(0,0); |
| 170 |
|
//if (fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || !etaMat.isDiagonal()) { |
| 171 |
|
// sprintf( painCave.errMsg, |
| 180 |
|
etaMat(0, 0) = eta; |
| 181 |
|
etaMat(1, 1) = eta; |
| 182 |
|
etaMat(2, 2) = eta; |
| 183 |
< |
currentSnapshot_->setEta(etaMat); |
| 183 |
> |
snap->setBarostat(etaMat); |
| 184 |
|
} |
| 185 |
|
} |
