| 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 <stdlib.h> |
| 91 |
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DefineOptionalParameter(DampingAlpha, "dampingAlpha"); |
| 92 |
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DefineOptionalParameter(SurfaceTension, "surfaceTension"); |
| 93 |
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DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); |
| 94 |
+ |
DefineOptionalParameter(PrintHeatFlux, "printHeatFlux"); |
| 95 |
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DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair"); |
| 96 |
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DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance"); |
| 95 |
– |
DefineOptionalParameter(CutoffPolicy, "cutoffPolicy"); |
| 97 |
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DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); |
| 98 |
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DefineOptionalParameter(HydroPropFile, "HydroPropFile"); |
| 99 |
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DefineOptionalParameter(Viscosity, "viscosity"); |
| 102 |
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DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius"); |
| 103 |
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DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors"); |
| 104 |
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DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod"); |
| 105 |
+ |
DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod"); |
| 106 |
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DefineOptionalParameter(MTM_Ce, "MTM_Ce"); |
| 107 |
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DefineOptionalParameter(MTM_G, "MTM_G"); |
| 108 |
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DefineOptionalParameter(MTM_Io, "MTM_Io"); |
| 116 |
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DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false); |
| 117 |
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DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false); |
| 118 |
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DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6); |
| 119 |
< |
DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE"); |
| 119 |
> |
DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE"); |
| 120 |
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DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED"); |
| 121 |
< |
DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5); |
| 122 |
< |
DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); |
| 123 |
< |
DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); |
| 121 |
> |
DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0); |
| 122 |
> |
DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false); |
| 123 |
> |
DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false); |
| 124 |
> |
DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false); |
| 125 |
> |
DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false); |
| 126 |
> |
DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false); |
| 127 |
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DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0); |
| 128 |
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DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY"); |
| 129 |
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DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false); |
| 135 |
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DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16); |
| 136 |
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DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale"); |
| 137 |
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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 |
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DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all"); |
| 143 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false); |
| 144 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_outputTemperature, "RNEMD_outputTemperature", false); |
| 145 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false); |
| 146 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", false); |
| 147 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false); |
| 148 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", false); |
| 149 |
+ |
|
| 150 |
|
DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false); |
| 151 |
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DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in"); |
| 152 |
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DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false); |
| 153 |
|
DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex"); |
| 154 |
+ |
DefineOptionalParameterWithDefaultValue(FlucQPropagator, "flucQ.propagator", "NVT"); |
| 155 |
+ |
DefineOptionalParameterWithDefaultValue(FlucQFriction, "flucQ.friction", 1600.0); |
| 156 |
+ |
DefineOptionalParameterWithDefaultValue(FlucQTolerance, "flucQ.tolerance", 1.0e-6); |
| 157 |
+ |
DefineOptionalParameterWithDefaultValue(FlucQMaxIterations, "flucQ.maxIterations", 100); |
| 158 |
+ |
DefineOptionalParameterWithDefaultValue(FlucQTargetTemp, "flucQ.targetTemp", 1.0e-6); |
| 159 |
+ |
DefineOptionalParameterWithDefaultValue(FlucQtauThermostat, "flucQ.tauThermostat", 10.0); |
| 160 |
|
|
| 139 |
– |
|
| 161 |
|
deprecatedKeywords_.insert("nComponents"); |
| 162 |
|
deprecatedKeywords_.insert("nZconstraints"); |
| 163 |
|
deprecatedKeywords_.insert("initialConfig"); |
| 180 |
|
|
| 181 |
|
CheckParameter(ForceField, isNotEmpty()); |
| 182 |
|
CheckParameter(TargetTemp, isPositive()); |
| 183 |
< |
CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT") || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("SMIPD")); |
| 183 |
> |
CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT") || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("LANGEVINHULL") || isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD")); |
| 184 |
|
CheckParameter(Dt, isPositive()); |
| 185 |
|
CheckParameter(RunTime, isPositive()); |
| 186 |
|
CheckParameter(FinalConfig, isNotEmpty()); |
| 210 |
|
CheckParameter(ThermodynamicIntegrationK, isPositive()); |
| 211 |
|
CheckParameter(ForceFieldVariant, isNotEmpty()); |
| 212 |
|
CheckParameter(ForceFieldFileName, isNotEmpty()); |
| 213 |
< |
CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD")); |
| 193 |
< |
CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); |
| 213 |
> |
CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE")); |
| 214 |
|
CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL")); |
| 215 |
+ |
CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD")); |
| 216 |
+ |
CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); |
| 217 |
|
CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL")); |
| 196 |
– |
//CheckParameter(StatFileFormat,); |
| 218 |
|
CheckParameter(OrthoBoxTolerance, isPositive()); |
| 219 |
|
CheckParameter(DampingAlpha,isNonNegative()); |
| 220 |
|
CheckParameter(SkinThickness, isPositive()); |
| 225 |
|
CheckParameter(NeighborListNeighbors, isPositive()); |
| 226 |
|
CheckParameter(RNEMD_exchangeTime, isPositive()); |
| 227 |
|
CheckParameter(RNEMD_nBins, isPositive() && isEven()); |
| 228 |
< |
CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale")); |
| 208 |
< |
CheckParameter(RNEMD_targetFlux, isNonNegative()); |
| 228 |
> |
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")); |
| 229 |
|
CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape")); |
| 230 |
|
CheckParameter(Alpha, isPositive()); |
| 231 |
< |
|
| 231 |
> |
CheckParameter(FlucQPropagator, isEqualIgnoreCase("NVT") || isEqualIgnoreCase("Langevin") || isEqualIgnoreCase("Minimizer") || isEqualIgnoreCase("Exact") ); |
| 232 |
> |
CheckParameter(FlucQFriction, isNonNegative()); |
| 233 |
> |
CheckParameter(FlucQTolerance, isPositive()); |
| 234 |
> |
CheckParameter(FlucQMaxIterations, isPositive()); |
| 235 |
> |
CheckParameter(FlucQTargetTemp, isNonNegative()); |
| 236 |
> |
CheckParameter(FlucQtauThermostat, isPositive()); |
| 237 |
|
|
| 238 |
|
for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) { |
| 239 |
|
if (!(*i)->findMoleculeStamp(moleculeStamps_)) { |
| 243 |
|
} |
| 244 |
|
} |
| 245 |
|
} |
| 246 |
< |
|
| 246 |
> |
|
| 247 |
|
bool Globals::addComponent(Component* comp) { |
| 248 |
|
components_.push_back(comp); |
| 249 |
|
return true; |
