| 91 |
|
DefineOptionalParameter(DampingAlpha, "dampingAlpha"); |
| 92 |
|
DefineOptionalParameter(SurfaceTension, "surfaceTension"); |
| 93 |
|
DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); |
| 94 |
+ |
DefineOptionalParameter(PrintHeatFlux, "printHeatFlux"); |
| 95 |
|
DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair"); |
| 96 |
|
DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance"); |
| 97 |
|
DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); |
| 135 |
|
DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16); |
| 136 |
|
DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale"); |
| 137 |
|
DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0); |
| 138 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_targetJzKE, "RNEMD_targetJzKE", 0.0); |
| 139 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpx, "RNEMD_targetJzpx", 0.0); |
| 140 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpy, "RNEMD_targetJzpy", 0.0); |
| 141 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpz, "RNEMD_targetJzpz", 0.0); |
| 142 |
|
DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all"); |
| 143 |
|
DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false); |
| 144 |
< |
DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false); |
| 144 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_outputTemperature, "RNEMD_outputTemperature", false); |
| 145 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false); |
| 146 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", false); |
| 147 |
> |
// James put this in. |
| 148 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_outputDen, "RNEMD_outputDen", false); |
| 149 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_outputAh, "RNEMD_outputAh", false); |
| 150 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_outputVz, "RNEMD_outputVz", false); |
| 151 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false); |
| 152 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", false); |
| 153 |
> |
|
| 154 |
|
DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false); |
| 155 |
|
DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in"); |
| 156 |
|
DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false); |
| 229 |
|
CheckParameter(NeighborListNeighbors, isPositive()); |
| 230 |
|
CheckParameter(RNEMD_exchangeTime, isPositive()); |
| 231 |
|
CheckParameter(RNEMD_nBins, isPositive() && isEven()); |
| 232 |
< |
CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale")); |
| 232 |
> |
CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("KineticScaleVAM") || isEqualIgnoreCase("KineticScaleAM") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale") || isEqualIgnoreCase("ShiftScaleV") || isEqualIgnoreCase("ShiftScaleVAM")); |
| 233 |
|
CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape")); |
| 234 |
|
CheckParameter(Alpha, isPositive()); |
| 235 |
|
CheckParameter(FlucQPropagator, isEqualIgnoreCase("NVT") || isEqualIgnoreCase("Langevin") || isEqualIgnoreCase("Minimizer") || isEqualIgnoreCase("Exact") ); |
