| 35 |
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* |
| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 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 |
|
#include "brains/SimInfo.hpp" |
| 62 |
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|
| 63 |
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| 64 |
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RealType NPTxyz::calcConservedQuantity(){ |
| 65 |
< |
|
| 65 |
< |
chi= currentSnapshot_->getChi(); |
| 66 |
< |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 65 |
> |
thermostat = snap->getThermostat(); |
| 66 |
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loadEta(); |
| 67 |
< |
|
| 67 |
> |
|
| 68 |
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// We need NkBT a lot, so just set it here: This is the RAW number |
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// of integrableObjects, so no subtraction or addition of constraints or |
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// orientational degrees of freedom: |
| 83 |
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RealType barostat_potential; |
| 84 |
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RealType trEta; |
| 85 |
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|
| 86 |
< |
totalEnergy = thermo.getTotalE(); |
| 86 |
> |
totalEnergy = thermo.getTotalEnergy(); |
| 87 |
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|
| 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 |
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|
| 91 |
< |
thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert; |
| 91 |
> |
thermostat_potential = fkBT* thermostat.second |
| 92 |
> |
/ PhysicalConstants::energyConvert; |
| 93 |
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|
| 94 |
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SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
| 95 |
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trEta = tmp.trace(); |
| 109 |
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void NPTxyz::scaleSimBox(){ |
| 111 |
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< |
int i,j,k; |
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> |
int i, j; |
| 113 |
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Mat3x3d scaleMat; |
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< |
RealType eta2ij, scaleFactor; |
| 115 |
< |
RealType bigScale, smallScale, offDiagMax; |
| 114 |
> |
RealType scaleFactor; |
| 115 |
> |
RealType bigScale, smallScale; |
| 116 |
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Mat3x3d hm; |
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Mat3x3d hmnew; |
| 118 |
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|
| 118 |
– |
|
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– |
|
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// Scale the box after all the positions have been moved: |
| 120 |
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// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 123 |
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bigScale = 1.0; |
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smallScale = 1.0; |
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– |
offDiagMax = 0.0; |
| 126 |
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|
| 127 |
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for(i=0; i<3; i++){ |
| 128 |
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for(j=0; j<3; j++){ |
| 164 |
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simError(); |
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} else { |
| 166 |
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|
| 167 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 167 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 168 |
|
hmat = hmat *scaleMat; |
| 169 |
< |
currentSnapshot_->setHmat(hmat); |
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> |
snap->setHmat(hmat); |
| 170 |
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} |
| 171 |
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} |
| 172 |
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|
| 173 |
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void NPTxyz::loadEta() { |
| 174 |
< |
eta= currentSnapshot_->getEta(); |
| 174 |
> |
eta= snap->getBarostat(); |
| 175 |
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} |
| 176 |
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| 177 |
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} |
