| 36 |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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< |
* [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 |
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*/ |
| 42 |
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| 43 |
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#include <stdlib.h> |
| 118 |
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DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE"); |
| 119 |
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DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED"); |
| 120 |
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DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0); |
| 121 |
< |
DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); |
| 122 |
< |
DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); |
| 123 |
< |
DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", 0); |
| 121 |
> |
DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false); |
| 122 |
> |
DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false); |
| 123 |
> |
DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false); |
| 124 |
> |
DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false); |
| 125 |
> |
DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false); |
| 126 |
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DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0); |
| 127 |
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DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY"); |
| 128 |
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DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false); |
| 141 |
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DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in"); |
| 142 |
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DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false); |
| 143 |
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DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex"); |
| 144 |
< |
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| 145 |
< |
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| 144 |
> |
DefineOptionalParameterWithDefaultValue(FlucQPropagator, "flucQ.propagator", "NVT"); |
| 145 |
> |
DefineOptionalParameterWithDefaultValue(FlucQFriction, "flucQ.friction", 1600.0); |
| 146 |
> |
DefineOptionalParameterWithDefaultValue(FlucQTolerance, "flucQ.tolerance", 1.0e-6); |
| 147 |
> |
DefineOptionalParameterWithDefaultValue(FlucQMaxIterations, "flucQ.maxIterations", 100); |
| 148 |
> |
DefineOptionalParameterWithDefaultValue(FlucQTargetTemp, "flucQ.targetTemp", 1.0e-6); |
| 149 |
> |
DefineOptionalParameterWithDefaultValue(FlucQtauThermostat, "flucQ.tauThermostat", 10.0); |
| 150 |
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| 151 |
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deprecatedKeywords_.insert("nComponents"); |
| 152 |
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deprecatedKeywords_.insert("nZconstraints"); |
| 218 |
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CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale")); |
| 219 |
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CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape")); |
| 220 |
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CheckParameter(Alpha, isPositive()); |
| 221 |
< |
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| 221 |
> |
CheckParameter(FlucQPropagator, isEqualIgnoreCase("NVT") || isEqualIgnoreCase("Langevin") || isEqualIgnoreCase("Minimizer") || isEqualIgnoreCase("Exact") ); |
| 222 |
> |
CheckParameter(FlucQFriction, isNonNegative()); |
| 223 |
> |
CheckParameter(FlucQTolerance, isPositive()); |
| 224 |
> |
CheckParameter(FlucQMaxIterations, isPositive()); |
| 225 |
> |
CheckParameter(FlucQTargetTemp, isNonNegative()); |
| 226 |
> |
CheckParameter(FlucQtauThermostat, isPositive()); |
| 227 |
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| 228 |
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for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) { |
| 229 |
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if (!(*i)->findMoleculeStamp(moleculeStamps_)) { |
