Zapdos-only Input File Syntax

Listed below are the input parameter options for a Zapdos input file for code contained solely within Zapdos (not within Squirrel, CRANE, or MOOSE and its modules). Click the blue link to see more detailed information about the usage of each object.

To return to the complete code syntax, please click here.

Adaptivity

Adaptivity/Indicators

Zapdos App
AnalyticalDiffIndicatorReturns the difference between the function of the analytic solution vs the computed solution

AuxKernels

Zapdos App
ADCurrentReturns the electric current associated with the flux of the specified species
ADDiffusiveFluxReturns the diffusive flux of the specified species
ADEFieldAdvAuxReturns the electric field driven advective flux of the specified species
ADPowerDepAmount of power deposited into a user specified specie by Joule Heating
ADProcRateReaction rate for electron impact collisions in units of #/m $var element = document.getElementById("moose-equation-a7b4e398-a9bf-487e-861a-0cabb7988d71");katex.render("^{3}", element, {displayMode:false,throwOnError:false});$ s. User can pass choice of elastic, excitation, or ionization Townsend coefficients
ADProcRateForRateCoeffReaction rate for two body collisions in units of #/m $var element = document.getElementById("moose-equation-866dee86-443d-4f4e-9d0e-8e002fd37bb4");katex.render("^{3}", element, {displayMode:false,throwOnError:false});$ s. User can pass choice of elastic, excitation, or ionization reaction rate coefficients
ADProcRateForRateCoeffThreeBodyReaction rate for three body collisions in units of #/m $var element = document.getElementById("moose-equation-a3248640-b9ec-473c-a6c6-6055507fddec");katex.render("^{3}", element, {displayMode:false,throwOnError:false});$ s. User can pass choice of elastic, excitation, or ionization reaction rate coefficients
ADTotalFluxReturns the total flux of the specified species
AbsValueAuxReturns the absolute value of the specified variable
CurrentReturns the electric current associated with the flux of the specified species
DensityMolesReturns physical densities in units of #/m $var element = document.getElementById("moose-equation-4a5689ef-ecbc-493a-b5b4-56852683f550");katex.render("^3", element, {displayMode:false,throwOnError:false});$
DensityNormalizationSimilar to NormalizationAux except meant to normalize variables expressed in log form
DiffusiveFluxReturns the diffusive flux of the specified species
DriftDiffusionFluxAuxReturns the drift-diffusion flux of the specified species
EFieldAdvAuxReturns the electric field driven advective flux of the specified species
EfieldReturns the defined component of the electric field (0 = x, 1 = y, 2 = z)
ElectronTemperatureReturns the electron temperature
LinearCombinationAuxKernelLinearly combine coupled variables with user provided weights and a bias
PositionProduces an elemental auxiliary variable useful for plotting against other elemental auxiliary variables. Mesh points automatically output by Zapdos only work for plotting nodal variables. Since almost all auxiliary variables are elemental, this AuxKernel is very important
PowerDepAmount of power deposited into a user specified specie by Joule Heating
ProcRateReaction rate for electron impact collisions in units of #/m $var element = document.getElementById("moose-equation-56dbf2dc-63ec-49d2-b850-6d1da3e498f4");katex.render("^{3}", element, {displayMode:false,throwOnError:false});$ s. User can pass choice of elastic, excitation, or ionization Townsend coefficients
ProcRateForRateCoeffReaction rate for two body collisions in units of #/m $var element = document.getElementById("moose-equation-08a2a82f-adea-47a8-8274-c0cfe5749410");katex.render("^{3}", element, {displayMode:false,throwOnError:false});$ s. User can pass choice of elastic, excitation, or ionization reaction rate coefficients
ProcRateForRateCoeffThreeBodyReaction rate for three body collisions in units of #/m $var element = document.getElementById("moose-equation-9bde8885-4409-4225-9425-09c2fc033aa6");katex.render("^{3}", element, {displayMode:false,throwOnError:false});$ s. User can pass choice of elastic, excitation, or ionization reaction rate coefficients
SigmaCalculates the surface charge due to a simplified version of the ion flux to a boundary.
TM0CylindricalErAuxCalculates the radial E-field for an axisymmetric TM $var element = document.getElementById("moose-equation-9f59b3dd-d196-428d-80ab-930b9fe40325");katex.render("_{0}", element, {displayMode:false,throwOnError:false});$ wave.
TM0CylindricalEzAuxCalculates the axial E-field for an axisymmetric TM $var element = document.getElementById("moose-equation-fdab07d6-1c3c-4436-9c97-745c50f9772a");katex.render("_{0}", element, {displayMode:false,throwOnError:false});$ wave.
TotalFluxReturns the total flux of the specified species

AuxVariables

BCs

Zapdos App
CircuitDirichletPotentialDirichlet circuit boundary condition for potential (The current is given through a UserObject)
DCIonBCElectric field driven outflow boundary condition (Based on Hagelaar et al. (2000))
DriftDiffusionDoNothingBCBoundary condition where the flux at the boundary is equal to the bulk dift-diffusion equation
EconomouDielectricBCDielectric boundary condition (Based on Lymberopoulos and Economou (1994))
ElectronAdvectionDoNothingBCBoundary condition where the electron advection flux at the boundary is equal to the bulk electron advection equation
ElectronDiffusionDoNothingBCBoundary condition where the electron diffusion flux at the boundary is equal to the bulk electron diffusion equation
ElectronTemperatureDirichletBCElectron temperature boundary condition
FieldEmissionBCThe electron flux boundary condition due to field emission (Based on Forbes (2006) and Forbes (2008))
HagelaarElectronAdvectionBCKinetic advective electron boundary condition (Based on Hagelaar et al. (2000))
HagelaarElectronBCKinetic electron boundary condition (Based on Hagelaar et al. (2000))
HagelaarEnergyAdvectionBCKinetic advective electron energy boundary condition (Based on Hagelaar et al. (2000))
HagelaarEnergyBCKinetic electron mean energy boundary condition (Based on Hagelaar et al. (2000))
HagelaarIonAdvectionBCKinetic advective ion boundary condition (Based on Hagelaar et al. (2000))
HagelaarIonDiffusionBCKinetic electron boundary condition (Based on Hagelaar et al. (2000))
LogDensityDirichletBCDensity Dirichlet boundary condition (Densities must be in log form and in moles/m $var element = document.getElementById("moose-equation-52110448-c43a-4e8f-98a6-2aa1f075dac9");katex.render("^3", element, {displayMode:false,throwOnError:false});$ )
LymberopoulosElectronBCSimpified kinetic electron boundary condition (Based on Lymberopoulos and Economou (1993))
LymberopoulosIonBCSimpified kinetic ion boundary condition (Based on Lymberopoulos and Economou (1993))
MatchedValueLogBCHenry’s Law like thermodynamic boundary condition for specifying a species concentration ratio at the gas-liquid interface
NeumannCircuitVoltageMoles_KVA Neumann boundary condition based on Kirchhoff's law of voltage
PenaltyCircuitPotentialCircuit boundary condition for potential multiplied by a penalty term
PotentialDriftOutflowBCThe drift flux boundary condition
SakiyamaElectronDiffusionBCKinetic electron boundary condition (Based on Sakiyama and Graves (2006))
SakiyamaEnergyDiffusionBCKinetic advective electron energy boundary condition (Based on Sakiyama and Graves (2007))
SakiyamaEnergySecondaryElectronBCKinetic secondary electron for mean electron energy boundary condition (Based on Sakiyama and Graves (2007))
SakiyamaIonAdvectionBCKinetic advective ion boundary condition (Based on Sakiyama and Graves (2006))
SakiyamaSecondaryElectronBCKinetic secondary electron boundary condition (Based on Sakiyama and Graves (2006))
SchottkyEmissionBCThe electron flux boundary condition due to field ehanced thermionic emission (Schottky emission) (Based on Go (2012))
SecondaryElectronBCKinetic secondary electron boundary condition
SecondaryElectronEnergyBCKinetic secondary electron for mean electron energy boundary condition
TM0AntennaVertBCA simple vertical antenna BC of the azimuthal component of the magnetizing field.
TM0PECVertBCA perfect electric conductor BC of the azimuthal component of the magnetizing field.

Constraints

Zapdos App
ArbitrarilyTiedValueConstraint

DGKernels

Zapdos App
DGCoeffDiffusionThe discontinuous Galerkin form of the generic diffusion term(Densities must be in log form)
DGEFieldAdvectionThe discontinuous Galerkin form of the generic electric field driven advection term(Densities must be in log form)

DriftDiffusionAction

Zapdos App
AddDriftDiffusionActionAdd a non-linear variable to the simulation.

InterfaceKernels

Zapdos App
HphiRadialInterface
InterfaceAdvectionUsed to include the electric field driven advective flux of speciesinto or out of a neighboring subdomain. Currently this interface kernelis specific to electrons because the transport coefficients are assumedto be a function of the mean electron energy. A generic interfacekernel with constant transport coefficients will have a much simpler Jacobian
InterfaceLogDiffusionElectronsUsed to include the diffusive flux of species into or out of a neighboringsubdomain. Currently specific to electrons.
PotentialSurfaceCharge

Kernels

Zapdos App
AccelerationByAveragingAn acceleration scheme based on averaging a density over a periodic cycle
AxisymmetricCurlZThe Z-component of an axisymmetric curl.
ChargeSourceMoles_KVUsed for adding charged sources to Poisson’s equation. This kernel assumes that densities are measured in units of mol/m $var element = document.getElementById("moose-equation-9605f937-985d-43b6-9bb4-c8ed4a9dc6b0");katex.render("^{3}", element, {displayMode:false,throwOnError:false});$ as opposed to #/m $var element = document.getElementById("moose-equation-a9082be0-76b2-4a9d-b501-f50c491fedf9");katex.render("^{3}", element, {displayMode:false,throwOnError:false});$
CoeffDiffusionGeneric diffusion term (densities must be in logarithmic form), where the Jacobian is computed using forward automatic differentiation.
CoeffDiffusionForShootMethodThe derivative of the generic diffusion term used to calculate the sensitivity value for the shoothing method.(Densities must be in logarithmic form)
CoeffDiffusionLinGeneric linear diffusion term (Values are NOT in logarithmic form), where the Jacobian is computed using forward automatic differentiation.
DriftDiffusionGeneric drift-diffusion equation that contains both an electric field driven advection term and a diffusion term (Densities must be in logarithmic form)
EEDFReactionLogForShootMethodThe derivative of an EEDF reaction term used to calculate the sensitivity variable for the shoothing method.(Densities must be in logarithmic form)
EFieldAdvectionGeneric electric field driven advection term. (Densities must be in logarithmic form.)
EFieldArtDiffGeneric artificial electric field driven advection term (Densities must be in logarithmic form)
EFieldMagnitudeSourceElectric field magnitude term based on the electrostatic approximation
ElectronEnergyLossFromElasticElectron energy loss term for elastic collisions using Townsend coefficient (Densities must be in logarithmic form)
ElectronEnergyLossFromExcitationElectron energy loss term for inelastic excitation collisions using Townsend coefficient, the energy lost in Volts in a single excitation collision (Densities must be in logarithmic form)
ElectronEnergyLossFromIonizationElectron energy loss term for inelastic ionization collisions using Townsend coefficients, the energy lost in Volts in a single ionization collision (Densities must be in logarithmic form)
ElectronEnergyTermElasticRateElectron energy loss term for elastic collisions using reaction rate coefficients (Densities must be in logarithmic form)
ElectronEnergyTermRateElectron energy loss term for inelastic collisions using reaction rate coefficients. Threshold energy is the energy lost in Volts in a single collision (Densities must be in logarithmic form)
ElectronTimeDerivativeGeneric accumulation term for variables in logarithmic form.
ElectronsFromIonizationRate of production of electrons from ionization using Townsend coefficients (Electron density must be in logarithmic form)
ExcitationReactionRate of production of metastables from excitation using Townsend coefficients (Densities must be in logarithmic form)
IonsFromIonizationRate of production of ions from ionization using Townsend coefficients (Ion density must be in logarithmic form)
JouleHeatingJoule heating term for electrons (densities must be in logarithmic form), where the Jacobian is computed using forward automatic differentiation.
LogStabilizationMolesKernel stabilizes solution variable u in places where u → 0; b is the offset valuespecified by the user. A typical value for b is 20.
ProductAABBRxnGeneric second order reaction source term in which two molecules of v are produced from two molecules of u (Densities must be in logarithmic form)
ProductFirstOrderRxnGeneric first order reaction source term for u (v is the reactant and densities must be in logarithmic form)
ReactantAARxnGeneric second order reaction sink term for u in which twomolecules of u are consumed(Densities must be in logarithmic form)
ReactantFirstOrderRxnGeneric first order reaction sink term for u (u is the reactant)(Densities must be in logarithmic form)
ReactionSecondOrderLogForShootMethodThe derivative of a second order reaction term used to calculate the sensitivity variable for the shoothing method. (Densities must be in logarithmic form)
ReactionThirdOrderLogForShootMethodThe derivative of a third order reaction term used to calculate the sensitivity variable for the shoothing method. (Densities must be in logarithmic form)
ScaledReactionThe multiple of a given variable (Used for calculating the effective ion potential for a given collision frequency)
ShootMethodLogAn acceleration scheme based on the shooting method
TM0CylindricalThe axisymmetric wave equation for the azimuthal component of the magnetizing field.
TM0CylindricalErThe axisymmetric wave equation for the radial component of the electric field.
TM0CylindricalEzThe axisymmetric wave equation for the axial component of the electric field.
UserSourceUser defined source term

Materials

Zapdos App
ADGasElectronMomentsMaterial properties of electrons(Defines reaction properties with rate coefficients)
ADHeavySpecies
ADSurfaceChargeAdds a surface charge material property based on the rate of change of the total charged flux to a boundary. (NOTE: this material is meant to be boundary-restricted.)
GasMaterial properties of electron and ions for argon gas(Defines reaction properties with Townsend coefficients)
GasBaseMaterial properties of electrons(Defines reaction properties with Townsend coefficients)
GasElectronMomentsMaterial properties of electrons(Defines reaction properties with rate coefficients)
HeavySpecies
WaterMaterial properties of water species

PeriodicControllers

Zapdos App
AddPeriodicControllersThis Action automatically adds multiply 'TimePeriod' controllers forthe purpose of enabling and disabling multiple objects during multiple cycles.(Ideally for periodic accelerations)

PeriodicRelativeNodalDifference

Zapdos App
AddPeriodicRelativeNodalDifferenceThis Action automatically adds the necessary objects to calculate the relative periodic difference. Relative Difference will be outputted as an Postprocessor named: 'var'_periodic_difference

Postprocessors

Zapdos App
AverageNodalDensitySimilar to AverageNodalVariableValue except meant to average variables expressed in log form
AverageNodalDifferenceReturns the average nodal differences between two variables
BlockAverageValueReturns the average value of a defined variable for a given domain
MultiPeriodAveragerCalculate the average value of a post processor over multiple periods
MultipliedTimeIntegratedPostprocessorIntegrate a Postprocessor value over time using trapezoidal rule.
PeriodicAmplitudeRegulatorPostprocessor that will modify its value by the ratio of anotherpostprocessor to the provided reference value
PeriodicComparisonCounterCompares two Postprocessors or values and keeps countof how many cycles in a row that comparision is true.
PeriodicTimeIntegratedPostprocessorIntegrate a Postprocessor value over a period in time using trapezoidal rule.
PlasmaFrequencyInverseReturns the inverse of the peak electron frequency
RelativeElementL2DifferenceComputes the element-wise relative L2 difference between the current variable and a coupled variable: i.e. ||u-v||/||u||
SideCurrentComputes a surface integral of the specified variable
SideTotFluxIntegralReturns the flux of a defined species at a boundary

UserObjects

Zapdos App
CurrentDensityShapeSideUserObjectCalculates the total current at a boundary
ProvideMobilityDefines ballast resistance and the area of an electrode(Used with Circuit BCs)

References

Richard G Forbes. Simple good approximations for the special elliptic functions in standard fowler-nordheim tunneling theory for a schottky-nordheim barrier. Applied physics letters, 2006. doi:10.1063/1.2354582.

@article{forbes2006simple,
    author = "Forbes, Richard G",
    title = "Simple good approximations for the special elliptic functions in standard Fowler-Nordheim tunneling theory for a Schottky-Nordheim barrier",
    journal = "Applied physics letters",
    volume = "89",
    number = "11",
    year = "2006",
    publisher = "AIP Publishing",
    doi = "10.1063/1.2354582"
}

Richard G Forbes. Physics of generalized fowler-nordheim-type equations. Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures Processing, Measurement, and Phenomena, 26(2):788–793, 2008. doi:10.1116/1.2827505.

@article{forbes2008physics,
    author = "Forbes, Richard G",
    title = "Physics of generalized Fowler-Nordheim-type equations",
    journal = "Journal of Vacuum Science \\& Technology B: Microelectronics and Nanometer Structures Processing, Measurement, and Phenomena",
    volume = "26",
    number = "2",
    pages = "788--793",
    year = "2008",
    publisher = "AIP Publishing",
    doi = "10.1116/1.2827505"
}

David B Go. Theoretical analysis of ion-enhanced thermionic emission for low-temperature, non-equilibrium gas discharges. Journal of Physics D: Applied Physics, 46(3):035202, 2012. doi:10.1088/0022-3727/46/3/035202.

@article{go2012theoretical,
    author = "Go, David B",
    title = "Theoretical analysis of ion-enhanced thermionic emission for low-temperature, non-equilibrium gas discharges",
    journal = "Journal of Physics D: Applied Physics",
    volume = "46",
    number = "3",
    pages = "035202",
    year = "2012",
    publisher = "IOP Publishing",
    doi = "10.1088/0022-3727/46/3/035202"
}

GJM Hagelaar, FJ De Hoog, and GMW Kroesen. Boundary conditions in fluid models of gas discharges. Physical Review E, 62(1):1452, 2000. doi:10.1103/PhysRevE.62.1452.

@article{hagelaar2000boundary,
    author = "Hagelaar, GJM and De Hoog, FJ and Kroesen, GMW",
    title = "Boundary conditions in fluid models of gas discharges",
    journal = "Physical Review E",
    volume = "62",
    number = "1",
    pages = "1452",
    year = "2000",
    publisher = "APS",
    doi = "10.1103/PhysRevE.62.1452"
}

Dimitris P Lymberopoulos and Demetre J Economou. Modeling and simulation of glow discharge plasma reactors. Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films, 12(4):1229–1236, 1994. doi:10.1116/1.579300.

@article{lymberopoulos1994modeling,
    author = "Lymberopoulos, Dimitris P and Economou, Demetre J",
    title = "Modeling and simulation of glow discharge plasma reactors",
    journal = "Journal of Vacuum Science \\& Technology A: Vacuum, Surfaces, and Films",
    volume = "12",
    number = "4",
    pages = "1229--1236",
    year = "1994",
    publisher = "American Vacuum Society",
    doi = "10.1116/1.579300"
}

Dimitris P. Lymberopoulos and Demetre J. Economou. Fluid simulations of glow discharges: effect of metastable atoms in argon. Journal of Applied Physics, 73(8):3668–3679, 04 1993. doi:10.1063/1.352926.

@article{Lymberopoulos1993,
    author = "Lymberopoulos, Dimitris P. and Economou, Demetre J.",
    title = "Fluid simulations of glow discharges: Effect of metastable atoms in argon",
    journal = "Journal of Applied Physics",
    volume = "73",
    number = "8",
    pages = "3668-3679",
    year = "1993",
    month = "04",
    issn = "0021-8979",
    doi = "10.1063/1.352926"
}

Y Sakiyama and David B Graves. Corona-glow transition in the atmospheric pressure rf-excited plasma needle. Journal of Physics D: Applied Physics, 39(16):3644, 2006. doi:10.1088/0022-3727/39/16/018.

@article{sakiyama2006corona,
    author = "Sakiyama, Y and Graves, David B",
    title = "Corona-glow transition in the atmospheric pressure RF-excited plasma needle",
    journal = "Journal of Physics D: Applied Physics",
    volume = "39",
    number = "16",
    pages = "3644",
    year = "2006",
    publisher = "IOP Publishing",
    doi = "10.1088/0022-3727/39/16/018"
}

Yukinori Sakiyama and David B Graves. Nonthermal atmospheric rf plasma in one-dimensional spherical coordinates: asymmetric sheath structure and the discharge mechanism. Journal of applied physics, 2007. doi:https://doi.org/10.1063/1.2715745.

@article{sakiyama2007nonthermal,
    author = "Sakiyama, Yukinori and Graves, David B",
    title = "Nonthermal atmospheric rf plasma in one-dimensional spherical coordinates: asymmetric sheath structure and the discharge mechanism",
    journal = "Journal of applied physics",
    volume = "101",
    number = "7",
    year = "2007",
    publisher = "AIP Publishing",
    doi = "https://doi.org/10.1063/1.2715745"
}

Adaptivity
AuxKernels
AuxVariables
BCs
Constraints
DGKernels
DriftDiffusionAction
InterfaceKernels
Kernels
Materials
PeriodicControllers
PeriodicRelativeNodalDifference
Postprocessors
UserObjects
References