| 36 |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
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* [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 |
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|
| 43 |
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#include "brains/SimInfo.hpp" |
| 63 |
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| 64 |
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} |
| 65 |
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void NgammaT::evolveEtaA() { |
| 66 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 66 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 67 |
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RealType hz = hmat(2, 2); |
| 68 |
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RealType Axy = hmat(0,0) * hmat(1, 1); |
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RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert); |
| 75 |
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} |
| 76 |
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|
| 77 |
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void NgammaT::evolveEtaB() { |
| 78 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 78 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 79 |
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RealType hz = hmat(2, 2); |
| 80 |
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RealType Axy = hmat(0,0) * hmat(1, 1); |
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prevEta = eta; |
| 93 |
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vScale(i, j) = eta(i, j); |
| 94 |
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| 95 |
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if (i == j) { |
| 96 |
< |
vScale(i, j) += chi; |
| 96 |
> |
vScale(i, j) += thermostat.first; |
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} |
| 98 |
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} |
| 99 |
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} |
| 120 |
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scaleMat(0, 0) = exp(dt*eta(0, 0)); |
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scaleMat(1, 1) = exp(dt*eta(1, 1)); |
| 122 |
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scaleMat(2, 2) = exp(dt*eta(2, 2)); |
| 123 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 123 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 124 |
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hmat = hmat *scaleMat; |
| 125 |
< |
currentSnapshot_->setHmat(hmat); |
| 125 |
> |
snap->setHmat(hmat); |
| 126 |
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| 127 |
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} |
| 128 |
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| 142 |
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| 143 |
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RealType NgammaT::calcConservedQuantity(){ |
| 144 |
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| 145 |
< |
chi= currentSnapshot_->getChi(); |
| 145 |
< |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 145 |
> |
thermostat = snap->getThermostat(); |
| 146 |
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loadEta(); |
| 147 |
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// We need NkBT a lot, so just set it here: This is the RAW number |
| 156 |
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fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp; |
| 157 |
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| 158 |
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| 159 |
< |
RealType totalEnergy = thermo.getTotalE(); |
| 159 |
> |
RealType totalEnergy = thermo.getTotalEnergy(); |
| 160 |
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|
| 161 |
< |
RealType thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert); |
| 161 |
> |
RealType thermostat_kinetic = fkBT * tt2 * thermostat.first * |
| 162 |
> |
thermostat.first /(2.0 * PhysicalConstants::energyConvert); |
| 163 |
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|
| 164 |
< |
RealType thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert; |
| 164 |
> |
RealType thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert; |
| 165 |
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|
| 166 |
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SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
| 167 |
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RealType trEta = tmp.trace(); |
| 170 |
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|
| 171 |
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RealType barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert; |
| 172 |
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|
| 173 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 173 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 174 |
|
RealType hz = hmat(2, 2); |
| 175 |
|
RealType area = hmat(0,0) * hmat(1, 1); |
| 176 |
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| 182 |
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} |
| 183 |
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| 184 |
|
void NgammaT::loadEta() { |
| 185 |
< |
eta= currentSnapshot_->getEta(); |
| 185 |
> |
eta= snap->getBarostat(); |
| 186 |
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|
| 187 |
|
//if (!eta.isDiagonal()) { |
| 188 |
|
// sprintf( painCave.errMsg, |
| 193 |
|
} |
| 194 |
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|
| 195 |
|
void NgammaT::saveEta() { |
| 196 |
< |
currentSnapshot_->setEta(eta); |
| 196 |
> |
snap->setBarostat(eta); |
| 197 |
|
} |
| 198 |
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| 199 |
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} |
