Class which implements CdrPlasmaPhysics and parses plasma chemistry from a JSON input file. More...

#include <CD_CdrPlasmaJSON.H>

Inheritance diagram for Physics::CdrPlasma::CdrPlasmaJSON:

Collaboration diagram for Physics::CdrPlasma::CdrPlasmaJSON:

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Public Types
using	InitialDataFunction = std::function< Real(const RealVect a_position, const Real a_time)>
	Function alias for initial data function. More...

using	FunctionEN = std::function< Real(const Real a_E, const Real a_N)>
	Function for encapsulating operations f = f(E,N). field in Townsend units. More...

using	FunctionX = std::function< Real(const RealVect a_position)>
	Function for encapsulating a function f = f(x) where x is the physical coordinates. More...

using	FunctionEX = std::function< Real(const Real E, const RealVect x)>
	Function for encapsulating a function f = f(E, x) where E is the electric field at physical coordinates x. More...

using	FunctionT = std::function< Real(const Real a_T)>
	Function for encapsulating a function f = f(T) where T is the temperature of some species. More...

using	FunctionTT = std::function< Real(const Real a_T1, const Real a_T2)>
	Function for encapsulating a function f = f(T1, T2) where T1/T2 are temperatures of two species. More...

Public Member Functions
	CdrPlasmaJSON ()
	Default constructor.

virtual	~CdrPlasmaJSON ()
	Destructor.

virtual void	parseRuntimeOptions () override
	Parse run-time class options.

virtual int	getNumberOfPlotVariables () const override
	Get number of plot variables for this physics class. More...

virtual Vector< std::string >	getPlotVariableNames () const override
	Get plot variable names. The names and positions between this routine and getPlotVariables must be consistent!

virtual Vector< Real >	getPlotVariables (const Vector< Real > a_cdrDensities, const Vector< RealVect > a_cdrGradients, const Vector< Real > a_rteDensities, const RealVect a_E, const RealVect a_position, const Real a_dx, const Real a_dt, const Real a_time, const Real a_kappa) const override
	Provide plot variables. This is used by CdrPlasmaStepper when writing plot files. More...

virtual Real	computeAlpha (const Real E, const RealVect a_position) const override
	Compute alpha. Should return Townsend ionization coefficient. More...

virtual Real	computeEta (const Real a_E, const RealVect a_position) const override
	Compute eta. Should return Townsend attachment coefficient. More...

virtual void	advanceReactionNetwork (Vector< Real > &a_cdrSources, Vector< Real > &a_rteSources, const Vector< Real > a_cdrDensities, const Vector< RealVect > a_cdrGradients, const Vector< Real > a_rteDensities, const RealVect a_E, const RealVect a_pos, const Real a_dx, const Real a_dt, const Real a_time, const Real a_kappa) const override
	Routine intended for advancing a reaction network over a time a_dt. More...

virtual Vector< RealVect >	computeCdrDriftVelocities (const Real a_time, const RealVect a_pos, const RealVect a_E, const Vector< Real > a_cdrDensities) const override
	Compute velocities for the CDR equations. More...

virtual Vector< Real >	computeCdrDiffusionCoefficients (const Real a_time, const RealVect a_pos, const RealVect a_E, const Vector< Real > a_cdrDensities) const override
	Compute diffusion coefficients for the CDR equations. More...

virtual Vector< Real >	computeCdrElectrodeFluxes (const Real a_time, const RealVect a_pos, const RealVect a_normal, const RealVect a_E, const Vector< Real > a_cdrDensities, const Vector< Real > a_cdrVelocities, const Vector< Real > a_cdrGradients, const Vector< Real > a_rteFluxes, const Vector< Real > a_extrapCdrFluxes) const override
	Compute CDR fluxes on electrode-gas interfaces. This is used as a boundary condition in the CDR equations. More...

virtual Vector< Real >	computeCdrDielectricFluxes (const Real a_time, const RealVect a_pos, const RealVect a_normal, const RealVect a_E, const Vector< Real > a_cdrDensities, const Vector< Real > a_cdrVelocities, const Vector< Real > a_cdrGradients, const Vector< Real > a_rteFluxes, const Vector< Real > a_extrapCdrFluxes) const override
	Compute CDR fluxes on dielectric-gas interfaces. This is used as a boundary condition in the CDR equations. More...

virtual Vector< Real >	computeCdrDomainFluxes (const Real a_time, const RealVect a_pos, const int a_dir, const Side::LoHiSide a_side, const RealVect a_E, const Vector< Real > a_cdrDensities, const Vector< Real > a_cdrVelocities, const Vector< Real > a_cdrGradients, const Vector< Real > a_rteFluxes, const Vector< Real > a_extrapCdrFluxes) const override
	Compute CDR fluxes through domain sides. This is used as a boundary condition in the CDR equations. More...

virtual Real	initialSigma (const Real a_time, const RealVect a_pos) const override
	Set the initial surface charge. More...

Public Member Functions inherited from Physics::CdrPlasma::CdrPlasmaPhysics
	CdrPlasmaPhysics ()
	Default constructor. Does nothing.

virtual	~CdrPlasmaPhysics ()
	Base destructor. Does nothing.

const Vector< RefCountedPtr< CdrSpecies > > &	getCdrSpecies () const
	Get all CDR species.

const Vector< RefCountedPtr< RtSpecies > > &	getRtSpecies () const
	Get all RTE species.

int	getNumCdrSpecies () const
	Return number of CDR species that we solve for.

int	getNumRtSpecies () const
	Return number of RTE equations that we solve for.

Protected Types
enum class	LookupMethod { Constant , FunctionX , FunctionT , FunctionTT , FunctionEN , FunctionEX , TableEN , TableEnergy , AlphaV , EtaV }
	Enum class for distinguishing types of computation methods when computing transport data stuff.

enum class	ReactionIntegrator { None , ExplicitEuler , ExplicitTrapezoidal , ExplicitMidpoint , ExplicitRK4 }
	Enum for distinguishing integration methods. Note that 'None' just fills directly with source terms.

enum class	ReactiveEnergyLoss { AddMean , SubtractMean , AddDirect , SubtractDirect , External }
	Enum class for distinguishing how we add/lose energy when running LEA-based models. The user will specify how to do this in the chemistry file, where 'AddMean' means that we add the mean energy to the equation. Likewise, 'SubtractMean' implies removing the mean energy, and 'External' is a user-specified energy to be added/removed.

Protected Member Functions
virtual void	parseOptions ()
	Parse class options.

virtual void	parseIntegrator ()
	Parse the reactive integrator.

virtual void	parseJSON ()
	Parse the JSON file.

virtual void	initializeSigma ()
	Initialize surface charge. More...

virtual void	initializeNeutralSpecies ()
	Initialize neutral species.

virtual void	initializePlasmaSpecies ()
	Initialize species. More...

virtual void	initializePhotonSpecies ()
	Initialize photon species. More...

virtual void	parseMobilities ()
	Initialize species mobilities.

virtual void	parseDiffusion ()
	Initialize species diffusion coefficients.

virtual void	parseTemperatures ()
	Initialize species temperatures.

virtual void	parseAlpha ()
	Parse the Townsend ionization coefficient.

virtual void	parseEta ()
	Parse the Townsend attachment coefficient.

virtual void	parsePlasmaReactions ()
	Parse plasma reactions.

virtual InitialDataFunction	parsePlasmaSpeciesInitialData (const json &a_json) const
	Generate an initial data function for a given plasma species. More...

virtual List< PointParticle >	parsePlasmaSpeciesInitialParticles (const json &a_json) const
	Generate initial particles for a given plasma species. More...

virtual std::list< std::tuple< std::string, std::vector< std::string >, std::vector< std::string > > >	parseReactionWildcards (const std::vector< std::string > &a_reactants, const std::vector< std::string > &a_products, const json &a_reaction)
	Make a reaction set into a superset. This parses wildcards '@' in reaction string. More...

virtual void	parseReactionString (std::vector< std::string > &a_reactants, std::vector< std::string > &a_products, const std::string &a_reaction) const
	Parses a reaction string into reactangs and products. More...

virtual void	sanctifyPlasmaReaction (const std::vector< std::string > &a_reactants, const std::vector< std::string > &a_products, const std::string a_reaction) const
	Check if a plasma-reaction makes sense in terms of the species that have been defined. More...

virtual void	getReactionSpecies (std::list< int > &a_plasmaReactants, std::list< int > &a_neutralReactants, std::list< int > &a_photonReactants, std::list< int > &a_plasmaProducts, std::list< int > &a_neutralProducts, std::list< int > &a_photonProducts, const std::vector< std::string > &a_reactants, const std::vector< std::string > &a_products) const
	Get the int-encoding corresponding to species involved in some reaction. More...

virtual void	parsePlasmaReactionRate (const int a_reactionIndex, const json &a_reactionJSON)
	Parse reaction rate for plasma reaction. More...

virtual void	parsePlasmaReactionScaling (const int a_reactionIndex, const json &a_reactionJSON)
	Parse scaling factors for reactions. More...

virtual void	parsePlasmaReactionPlot (const int a_reactionIndex, const json &a_reactionJSON)
	Parse reaction plotting. More...

virtual void	parsePlasmaReactionDescription (const int a_reactionIndex, const json &a_reactionJSON, const std::string a_wildcard)
	Parse plasma reaction descriptions. More...

virtual void	parsePlasmaReactionSoloviev (const int a_reactionIndex, const json &a_reactionJSON)
	Parse plasma reaction energy correction. More...

virtual void	parsePlasmaReactionEnergyLosses (const int a_reactionIndex, const json &a_reactionJSON)
	Parse plasma reaction energy losses. More...

virtual void	parsePhotoReactions ()
	Parse photo-reactions.

virtual void	parsePhotoReactionScaling (const int a_reactionIndex, const json &a_reactionJSON)
	Parse scaling for photo-reactions. Includes Helmholtz corrections if doing Helmholtz reconstruction of photoionization profiles. More...

virtual void	parsePhotoReactionEnergyLosses (const int a_reactionIndex, const json &a_reactionJSON)
	Parse photo-reaction energy losses. More...

virtual void	sanityCheckSpecies () const
	Do a species sanity check. More...

virtual void	sanctifyPhotoReaction (const std::vector< std::string > &a_reactants, const std::vector< std::string > &a_products, const std::string a_reaction) const
	Check if a photo-reaction makes sense in terms of the species that have been defined. More...

virtual void	parseElectrodeReactions ()
	Parse secondary emission on electrodes.

virtual void	parseElectrodeReactionRate (const int a_reactionIndex, const json &a_reactionJSON)
	Parse reaction rate for electrode surface reactions. More...

virtual void	parseElectrodeReactionScaling (const int a_reactionIndex, const json &a_reactionJSON)
	Parse electrode reaction scaling for a specific reaction. More...

virtual void	parseElectrodeReactionEnergyLosses (const int a_reactionIndex, const json &a_reactionJSON)
	Parse electrode-reaction energy losses. More...

virtual void	parseDielectricReactions ()
	Parse secondary emission on dielectrics.

virtual void	parseDielectricReactionRate (const int a_reactionIndex, const json &a_reactionJSON)
	Parse reaction rate for dielectric surface reactions. More...

virtual void	parseDielectricReactionScaling (const int a_reactionIndex, const json &a_reactionJSON)
	Parse dielectric electrode reaction scaling for a specific reaction. More...

virtual void	parseDielectricReactionEnergyLosses (const int a_reactionIndex, const json &a_reactionJSON)
	Parse dielectric-reaction energy losses. More...

virtual void	parseDomainReactions ()
	Parse secondary emission on domain.

virtual void	parseDomainReactionRate (const int a_reactionIndex, const json &a_reactionJSON, const std::vector< std::string > &a_sides)
	Parse reaction rate for domain reactions. More...

virtual void	parseDomainReactionScaling (const int a_reactionIndex, const json &a_reactionJSON, const std::vector< std::string > &a_sides)
	Parse domain reaction scaling for a specific reaction. More...

virtual void	sanctifySurfaceReaction (const std::vector< std::string > &a_reactants, const std::vector< std::string > &a_products, const std::string a_reaction) const
	Check if a surface-reaction makes sense in terms of the species that have been defined. More...

virtual std::vector< Real >	computePlasmaSpeciesTemperatures (const RealVect &a_position, const RealVect &a_E, const std::vector< Real > &a_cdrDensities) const
	Compute the various plasma species temperatures. More...

virtual std::vector< Real >	computePlasmaSpeciesEnergies (const RealVect &a_position, const RealVect &a_E, const std::vector< Real > &a_cdrDensities) const
	Compute the various plasma species energies. Returns a list of energies in electron-volts. We assume that temperature-energy relations are e = 3/2 * kB * T. More...

virtual std::vector< Real >	computePlasmaSpeciesMobilities (const RealVect &a_position, const RealVect &a_E, const std::vector< Real > &a_cdrDensities) const
	Compute the various plasma species mobilities. More...

virtual std::vector< Real >	computePlasmaSpeciesDiffusion (const RealVect a_position, const RealVect a_E, const std::vector< Real > a_cdrDensities) const
	Compute the various plasma species diffusion coefficients. More...

virtual Real	computePlasmaReactionRate (const int &a_reactionIndex, const std::vector< Real > &a_cdrDensities, const std::vector< Real > &a_cdrMobilities, const std::vector< Real > &a_cdrDiffusionCoefficients, const std::vector< Real > &a_cdrTemperatures, const std::vector< Real > &a_cdrEnergies, const std::vector< RealVect > &a_cdrGradients, const RealVect &a_pos, const RealVect &a_vectorE, const Real &a_E, const Real &a_Etd, const Real &a_N, const Real &a_alpha, const Real &a_eta, const Real &a_time) const
	Compute the reaction rate for a plasma reaction. More...

void	throwParserError (const std::string a_error) const
	Throw a parser error. More...

void	throwParserWarning (const std::string a_warning) const
	Throw a parser wearning. More...

bool	containsWildcard (const std::string a_str) const
	Protect the @ character in a string. More...

bool	containsBracket (const std::string a_str) const
	Protect all kinds of brackets in a string. More...

bool	isBracketed (const std::string a_str) const
	Return true if string starts and ends with a paranthesis. More...

std::string	trim (const std::string &a_string) const
	Remove whitespace from string.

bool	isNeutralSpecies (const std::string &a_name) const
	Return true if species exists in map and false otherwise. More...

bool	isPlasmaSpecies (const std::string &a_name) const
	Return true if species exists in map and false otherwise. More...

bool	isPhotonSpecies (const std::string &a_name) const
	Return true if species exists in map and false otherwise. More...

bool	doesFileExist (const std::string a_filename) const
	Check if file exists. More...

virtual void	addPhotoIonization (std::vector< Real > &a_cdrSources, const std::vector< Real > &a_rteDensities, const RealVect a_position, const Real a_E, const Real a_dt, const Real a_dx) const
	Add photoionization products to transport equations source terms. More...

virtual void	integrateReactions (std::vector< Real > &a_cdrDensities, std::vector< Real > &a_photonProduction, const std::vector< RealVect > a_cdrGradients, const RealVect a_E, const RealVect a_pos, const Real a_dx, const Real a_dt, const Real a_time, const Real a_kappa) const
	Routine for integrating the reactive-only problem using various algorithms. More...

void	fillSourceTerms (std::vector< Real > &a_cdrSources, std::vector< Real > &a_rteSources, const std::vector< Real > a_cdrDensities, const std::vector< RealVect > a_cdrGradients, const RealVect a_E, const RealVect a_pos, const Real a_dx, const Real a_time, const Real a_kappa) const
	Routine for filling the source terms in the reactive problem. More...

void	integrateReactionsExplicitEuler (std::vector< Real > &a_cdrDensities, std::vector< Real > &a_photonProduction, const std::vector< RealVect > a_cdrGradients, const RealVect a_E, const RealVect a_pos, const Real a_dx, const Real a_dt, const Real a_time, const Real a_kappa) const
	Routine for integrating the reactive-only problem using the explicit Euler rule. More...

void	integrateReactionsImplicitEuler (std::vector< Real > &a_cdrDensities, std::vector< Real > &a_photonProduction, const std::vector< RealVect > a_cdrGradients, const RealVect a_E, const RealVect a_pos, const Real a_dx, const Real a_dt, const Real a_time, const Real a_kappa) const
	Routine for integrating the reactive-only problem using the implicit Euler rule. More...

void	integrateReactionsExplicitRK2 (std::vector< Real > &a_cdrDensities, std::vector< Real > &a_photonProduction, const std::vector< RealVect > a_cdrGradients, const RealVect a_E, const RealVect a_pos, const Real a_dx, const Real a_dt, const Real a_time, const Real a_kappa, const Real a_tableuAlpha) const
	Routine for integrating the reactive-only problem using a second order Runge-Kutta method. More...

void	integrateReactionsExplicitRK4 (std::vector< Real > &a_cdrDensities, std::vector< Real > &a_photonProduction, const std::vector< RealVect > a_cdrGradients, const RealVect a_E, const RealVect a_pos, const Real a_dx, const Real a_dt, const Real a_time, const Real a_kappa) const
	Routine for integrating the reactive-only problem using the foruth order Runge-Kutta method. More...

Protected Attributes
bool	m_verbose
	Verbose or not.

bool	m_plotGas
	Plot gas pressure, density, and temperature.

bool	m_plotAlpha
	Plot Townsend ionization coefficient.

bool	m_plotEta
	Plot Townsend attachment coefficient.

bool	m_discretePhotons
	Using discrete photons or not.

bool	m_skipReactions
	A flag for skipping reactions completely.

json	m_json
	JSON definition. This is populated when calling parseJSON.

ReactionIntegrator	m_reactionIntegrator
	Reaction integrator.

std::string	m_jsonFile
	Input JSON file name.

std::vector< json >	m_cdrSpeciesJSON
	JSON entries for species in the defined field 'plasma species'.

std::vector< json >	m_rteSpeciesJSON
	JSON entries for species in photon_species.

std::function< Real(const RealVect a_position, const Real a_time)>	m_initialSigma
	Initial surface charge.

FunctionX	m_gasPressure
	Gas pressure (in Pascal).

FunctionX	m_gasTemperature
	Gas temperature (in Kelvin)

FunctionX	m_gasDensity
	Gas number density (in m^(-3))

Real	m_chemistryDt
	Chemistry time step.

std::vector< FunctionX >	m_neutralSpeciesDensities
	Neutral species densities.

std::vector< std::shared_ptr< NeutralSpeciesJSON > >	m_neutralSpecies
	These are the neutral species.

std::map< std::string, int >	m_neutralSpeciesMap
	Map for figuring out which where in m_neutralSpecies a neutral species is found.

std::map< int, std::string >	m_neutralSpeciesInverseMap
	Inverse of m_neutralSpeciesMap.

std::map< std::string, int >	m_cdrSpeciesMap
	string-int encoding of the CDr species. More...

std::map< int, std::string >	m_cdrSpeciesInverseMap
	int-string encoding of the CDR species. More...

std::map< int, bool >	m_cdrIsEnergySolver
	int-bool encoding for determining if a solver is an energy solver.

std::map< int, bool >	m_cdrHasEnergySolver
	int-bool encoding for determining if a CDR solver HAS an associated energy solver.

std::map< int, std::tuple< Real, Real, Real > >	m_cdrEnergyComputation
	Parameters for computing the mean energy from energy density and density. More...

std::map< int, int >	m_cdrTransportEnergyMap
	int-int encoding for associating a transport solver with an energy solver. More...

std::map< int, Real >	m_cdrMasses
	Map of the species masses. This is needed for imposing BCs on the energy equations. More...

std::map< std::string, int >	m_rteSpeciesMap
	string-int encoding of the RTE species. More...

std::map< int, std::string >	m_rteSpeciesInverseMap
	int-string encoding of the RTE species. More...

LookupMethod	m_alphaLookup
	Lookup method for Townsend ionization coefficient.

LookupMethod	m_etaLookup
	Lookup method for Townsend attachment coefficient.

Real	m_alphaConstant
	For when we can use alpha = constant.

Real	m_etaConstant
	For when we can use eta = constant.

FunctionEN	m_alphaFunctionEN
	For when we can put alpha = alpha(E,N) as an analytic function.

FunctionEN	m_etaFunctionEN
	For when we can put eta = eta(E,N) as an analytic function.

LookupTable1D< Real, 1 >	m_alphaTableEN
	For when we can put alpha = table(E,N)

LookupTable1D< Real, 1 >	m_etaTableEN
	For when we can put eta = table(E,N)

std::map< int, LookupMethod >	m_mobilityLookup
	Mobility lookup method for each species.

std::map< int, Real >	m_mobilityConstants
	Map for constant mobilities.

std::map< int, FunctionEN >	m_mobilityFunctionsEN
	Map for function-based mobilities mu = mu(E,N)

std::map< int, FunctionEX >	m_mobilityFunctionsEX
	Map for function-based mobilities mu = mu(E,x)

std::map< int, LookupTable1D< Real, 1 > >	m_mobilityTablesEN
	Map for table-based mobilities. Stored as tables (E/N, mu*N)

std::map< int, LookupTable1D< Real, 1 > >	m_mobilityTablesEnergy
	Map for table-based mobilities as function of energy. More...

std::map< int, LookupMethod >	m_diffusionLookup
	Diffusion lookup method.

std::map< int, Real >	m_diffusionConstants
	Map for constant diffusion coefficients.

std::map< int, FunctionEN >	m_diffusionFunctionsEN
	Map for function-based diffusion coefficients. .

std::map< int, LookupTable1D< Real, 1 > >	m_diffusionTablesEN
	Map for table-based diffusion coefficients D = D(E,N). More...

std::map< int, LookupTable1D< Real, 1 > >	m_diffusionTablesEnergy
	Map for table-based diffusion coefficients as function of energy. More...

std::map< int, LookupMethod >	m_temperatureLookup
	Temperature lookup method.

std::map< int, FunctionX >	m_temperatureConstants
	Constant temperatures.

std::map< int, LookupTable1D< Real, 1 > >	m_temperatureTablesEN
	Temperatures as functions of E/N.

std::map< int, std::string >	m_plasmaReactionDescriptions
	Description of plasma reactions. Only used for I/O.

std::map< int, LookupMethod >	m_plasmaReactionLookup
	Map for figuring out how to look up the rate for a certain plasma reaction.

std::map< int, Real >	m_plasmaReactionConstants
	Constant plasma reaction rates.

std::map< int, int >	m_plasmaReactionAlphaV
	Plasma reaction rates that are alpha*\|v\|.

std::map< int, int >	m_plasmaReactionEtaV
	Plasma reaction rates that are eta*\|v\|.

std::map< int, std::pair< int, FunctionT > >	m_plasmaReactionFunctionsT
	Maps for functions of the type k = f(T) where T is the temperature of some species. More...

std::map< int, std::tuple< int, int, FunctionTT > >	m_plasmaReactionFunctionsTT
	Maps for functions of the type k = f(T1,T2) where T1 and T2 are the temperatures of some species. More...

std::map< int, FunctionEN >	m_plasmaReactionFunctionsEN
	Function-based plasma reaction rates.

std::map< int, LookupTable1D< Real, 1 > >	m_plasmaReactionTablesEN
	Map for table-based reaction coefficients, where k = k(E,N).

std::map< int, std::pair< int, LookupTable1D< Real, 1 > > >	m_plasmaReactionTablesEnergy
	Map for table-based reaction coefficients where k = k(energy). More...

std::map< int, FunctionEX >	m_plasmaReactionEfficiencies
	Scaled plasma reactions. These account for e.g. reaction efficiencies, collisional quenching, etc.

std::vector< CdrPlasmaReactionJSON >	m_plasmaReactions
	Plasma reactions.

std::map< int, bool >	m_plasmaReactionPlot
	Plot plasma reaction or not.

std::map< int, std::pair< bool, int > >	m_plasmaReactionSolovievCorrection
	Flag for whether or not reaction includes Soloviev energy correction. More...

std::map< int, std::map< int, std::pair< ReactiveEnergyLoss, Real > > >	m_plasmaReactionEnergyLosses
	For mapping reactive energy losses for all reactions. More...

std::map< int, bool >	m_plasmaReactionHasEnergyLoss
	Associative container for determining if a reaction is associated with an energy loss/gain.

std::map< int, FunctionEX >	m_photoReactionEfficiencies
	Flag for photo-reaction efficiencies. Includes Helmholtz corrections, if present.

std::map< int, bool >	m_photoReactionUseHelmholtz
	Map over the Helmholtz reconstructions.

std::vector< CdrPlasmaPhotoReactionJSON >	m_photoReactions
	Photo-reactions.

std::map< int, std::list< std::pair< int, Real > > >	m_photoReactionEnergyLosses
	Associated energy losses for a photo-reaction. More...

std::map< int, bool >	m_photoReactionHasEnergyLoss
	Associative container for determining if a reaction is associated with an energy loss/gain.

std::map< int, LookupMethod >	m_electrodeReactionLookup
	Lookup method for the electrode surface reaction rates.

std::map< int, Real >	m_electrodeReactionConstants
	Constant electrode reaction rate.

std::map< int, FunctionEX >	m_electrodeReactionEfficiencies
	Electrode reaction effiencies. Used for scaling reactions on electrodes in a "generic" way.

std::vector< CdrPlasmaSurfaceReactionJSON >	m_electrodeReactions
	List of electrode reactions.

std::map< int, std::list< std::pair< int, Real > > >	m_electrodeReactionEnergyLosses
	Associated energy losses for a surface reaction on electrodes. More...

std::map< int, bool >	m_electrodeReactionHasEnergyLoss
	Associative container for determining if a reaction is associated with an energy loss/gain.

std::map< int, bool >	m_electrodeExtrapBC
	A container which determines if we should add the extrapolated flux as an inflow condition.

std::map< int, LookupMethod >	m_dielectricReactionLookup
	Lookup method for the dielectric surface reaction rates.

std::map< int, Real >	m_dielectricReactionConstants
	Constant dielectric reaction rate.

std::map< int, FunctionEX >	m_dielectricReactionEfficiencies
	Dielectric reaction effiencies. Used for scaling reactions on dielectrics in a "generic" way.

std::vector< CdrPlasmaSurfaceReactionJSON >	m_dielectricReactions
	List of dielectric reactions.

std::map< int, std::list< std::pair< int, Real > > >	m_dielectricReactionEnergyLosses
	Associated energy losses for a surface reaction on dielectrics. More...

std::map< int, bool >	m_dielectricReactionHasEnergyLoss
	Associative container for determining if a reaction is associated with an energy loss/gain.

std::map< int, bool >	m_dielectricExtrapBC
	A container which determines if we should add the extrapolated flux as an inflow condition.

std::map< std::pair< int, Side::LoHiSide >, std::map< int, LookupMethod > >	m_domainReactionLookup
	Lookup method for the domain reaction rates. The pair is made up of an int representing direction (0=x, 1=y, 2=z) and a Side::LoHiSide representing side (Side::Lo, Side::Hi)

std::map< std::pair< int, Side::LoHiSide >, std::map< int, Real > >	m_domainReactionConstants
	Constant domain reaction rate. The pair is made up of an int representing direction (0=x, 1=y, 2=z) and a Side::LoHiSide representing side (Side::Lo, Side::Hi)

std::map< std::pair< int, Side::LoHiSide >, std::map< int, FunctionEX > >	m_domainReactionEfficiencies
	Domain reaction effiencies. Used for scaling reactions on domains in a "generic" way. The pair is made up of an int representing direction (0=x, 1=y, 2=z) and a Side::LoHiSide representing side (Side::Lo, Side::Hi)

std::map< std::pair< int, Side::LoHiSide >, std::vector< CdrPlasmaSurfaceReactionJSON > >	m_domainReactions
	List of domain reactions. The pair is made up of an int representing direction (0=x, 1=y, 2=z) and a Side::LoHiSide representing side (Side::Lo, Side::Hi)

const std::map< char, int >	m_dirCharToInt {{'x', 0}, {'y', 1}, {'z', 2}}
	map to translate dir from char to int

const std::map< std::string, Side::LoHiSide >	m_sideStringToSide {{"lo", Side::Lo}, {"hi", Side::Hi}}
	map to translate side from std::string to Side::LoHiSide

std::map< std::tuple< int, Side::LoHiSide, int >, bool >	m_domainExtrapBC
	A container which determines if we should add the extrapolated flux as an inflow condition. More...

Protected Attributes inherited from Physics::CdrPlasma::CdrPlasmaPhysics
Vector< RefCountedPtr< CdrSpecies > >	m_cdrSpecies
	List of species.

Vector< RefCountedPtr< RtSpecies > >	m_rtSpecies
	List of optical transitions between species.

int	m_numCdrSpecies
	Number of species.

int	m_numRtSpecies
	Number of RTE species.

Detailed Description

Class which implements CdrPlasmaPhysics and parses plasma chemistry from a JSON input file.

Member Typedef Documentation

◆ FunctionEN

using Physics::CdrPlasma::CdrPlasmaJSON::FunctionEN = std::function<Real(const Real a_E, const Real a_N)>

Function for encapsulating operations f = f(E,N). field in Townsend units.

Parameters

[in]	a_E	Electric field in SI units.
[in]	a_N	Neutral density.

Returns: Returns f = f(E,N).

Note: a_E is in SI units and the neutral density is in m^-3.

◆ FunctionEX

using Physics::CdrPlasma::CdrPlasmaJSON::FunctionEX = std::function<Real(const Real E, const RealVect x)>

Function for encapsulating a function f = f(E, x) where E is the electric field at physical coordinates x.

Parameters

[in]	E	Electric field magnitude in SI units.
[in]	x	Physical coordinates

◆ FunctionT

using Physics::CdrPlasma::CdrPlasmaJSON::FunctionT = std::function<Real(const Real a_T)>

Function for encapsulating a function f = f(T) where T is the temperature of some species.

Parameters

[in] a_T Some temperature.

◆ FunctionTT

using Physics::CdrPlasma::CdrPlasmaJSON::FunctionTT = std::function<Real(const Real a_T1, const Real a_T2)>

Function for encapsulating a function f = f(T1, T2) where T1/T2 are temperatures of two species.

Parameters

[in]	a_T1	Some species temperature.
[in]	a_T2	Some other species temperature.

◆ FunctionX

using Physics::CdrPlasma::CdrPlasmaJSON::FunctionX = std::function<Real(const RealVect a_position)>

Function for encapsulating a function f = f(x) where x is the physical coordinates.

Parameters

[in] a_position Physical coordinates

Returns: Returns f(x)

◆ InitialDataFunction

using Physics::CdrPlasma::CdrPlasmaJSON::InitialDataFunction = std::function<Real(const RealVect a_position, const Real a_time)>

Function alias for initial data function.

Parameters

[in]	a_position	Physical coordinates
[in]	a_time	Time

Member Function Documentation

◆ addPhotoIonization()

void CdrPlasmaJSON::addPhotoIonization	(	std::vector< Real > &	a_cdrSources,
		const std::vector< Real > &	a_rteDensities,
		const RealVect	a_position,
		const Real	a_E,
		const Real	a_dt,
		const Real	a_dx
	)		const

protectedvirtual

Add photoionization products to transport equations source terms.

Parameters

[in,out]	a_cdrSources	Source terms for CDR densities.
[in]	a_rteDensities	RTE mesh densities.
[in]	a_position	Physical coordinates
[in]	a_E	Electric field (SI units)
[in]	a_dt	Time step
[in]	a_dx	Grid resolution.

◆ advanceReactionNetwork()

void CdrPlasmaJSON::advanceReactionNetwork	(	Vector< Real > &	a_cdrSources,
		Vector< Real > &	a_rteSources,
		const Vector< Real >	a_cdrDensities,
		const Vector< RealVect >	a_cdrGradients,
		const Vector< Real >	a_rteDensities,
		const RealVect	a_E,
		const RealVect	a_pos,
		const Real	a_dx,
		const Real	a_dt,
		const Real	a_time,
		const Real	a_kappa
	)		const

overridevirtual

Routine intended for advancing a reaction network over a time a_dt.

This routine assumes that the subsequent advance is in the form phi^(k+1) = phi^k + S*a_dt. Thus, this routine exists such that users can EITHER fill a_cdrSources and a_rteSources directly with an explicit rule, OR they can perform a fully implicit advance within this routine and set S from that.

Parameters

[out]	a_cdrSources	Source terms for CDR equations.
[out]	a_rteSources	Source terms for RTE equations.
[in]	a_cdrDensities	Grid-based density for particle species.
[in]	a_cdrGradients	Grid-based gradients for particle species.
[in]	a_rteDensities	Grid-based densities for photons.
[in]	a_E	Electric field.
[in]	a_pos	Position in space.
[in]	a_dx	Grid resolution.
[in]	a_dt	Advanced time.
[in]	a_time	Current time.
[in]	a_kappa	Grid cell unit volume.

Implements Physics::CdrPlasma::CdrPlasmaPhysics.

◆ computeAlpha()

Real CdrPlasmaJSON::computeAlpha	(	const Real	E,
		const RealVect	a_position
	)		const

overridevirtual

Compute alpha. Should return Townsend ionization coefficient.

This function is mostly used for the cell tagging classes, but can be used for reactions as well.

Parameters

[in] a_E Electric field.

Implements Physics::CdrPlasma::CdrPlasmaPhysics.

◆ computeCdrDielectricFluxes()

Vector< Real > CdrPlasmaJSON::computeCdrDielectricFluxes	(	const Real	a_time,
		const RealVect	a_pos,
		const RealVect	a_normal,
		const RealVect	a_E,
		const Vector< Real >	a_cdrDensities,
		const Vector< Real >	a_cdrVelocities,
		const Vector< Real >	a_cdrGradients,
		const Vector< Real >	a_rteFluxes,
		const Vector< Real >	a_extrapCdrFluxes
	)		const

overridevirtual

Compute CDR fluxes on dielectric-gas interfaces. This is used as a boundary condition in the CDR equations.

Parameters

[in]	a_time	Time
[in]	a_pos	Position
[in]	a_normal	Normal vector. This points into the gas phase.
[in]	a_E	Electric field
[in]	a_cdrDensities	CDR densities (on the EB)
[in]	a_cdrVelocities	Normal component of CDR velocities (on the EB).
[in]	a_cdrGradients	Normal gradients of cdr densities
[in]	a_rteFluxes	RTE fluxes (normal component only)
[in]	a_extrapCdrFluxes	Extrapolated fluxes from the gas side.

Returns: Returns the flux on a dielectric interface cell. The vector ordering must be the same as m_cdrSpecies.

Implements Physics::CdrPlasma::CdrPlasmaPhysics.

◆ computeCdrDiffusionCoefficients()

Vector< Real > CdrPlasmaJSON::computeCdrDiffusionCoefficients	(	const Real	a_time,
		const RealVect	a_pos,
		const RealVect	a_E,
		const Vector< Real >	a_cdrDensities
	)		const

overridevirtual

Compute diffusion coefficients for the CDR equations.

Parameters

[in]	a_time	Time
[in]	a_pos	Position
[in]	a_E	Electric field
[in]	a_cdrDensities	CDR densities

Returns: Returns the diffusion coefficients for each CDR species. The vector ordering is the same as m_cdrSpecies.

Implements Physics::CdrPlasma::CdrPlasmaPhysics.

◆ computeCdrDomainFluxes()

Vector< Real > CdrPlasmaJSON::computeCdrDomainFluxes	(	const Real	a_time,
		const RealVect	a_pos,
		const int	a_dir,
		const Side::LoHiSide	a_side,
		const RealVect	a_E,
		const Vector< Real >	a_cdrDensities,
		const Vector< Real >	a_cdrVelocities,
		const Vector< Real >	a_cdrGradients,
		const Vector< Real >	a_rteFluxes,
		const Vector< Real >	a_extrapCdrFluxes
	)		const

overridevirtual

Compute CDR fluxes through domain sides. This is used as a boundary condition in the CDR equations.

Parameters

[in]	a_time	Time
[in]	a_pos	Position
[in]	a_dir	Direction (0 = x, 1=y etc)
[in]	a_side	Side (low or high side)
[in]	a_E	Electric field
[in]	a_cdrDensities	CDR densities.
[in]	a_cdrVelocities	CDR velocities (normal component only).
[in]	a_cdrGradients	CDR gradients (normal component only)
[in]	a_rteFluxes	RTE fluxes (normal component only)
[in]	a_extrapCdrFluxes	Extrapolated fluxes from the gas side.

Implements Physics::CdrPlasma::CdrPlasmaPhysics.

◆ computeCdrDriftVelocities()

Vector< RealVect > CdrPlasmaJSON::computeCdrDriftVelocities	(	const Real	a_time,
		const RealVect	a_pos,
		const RealVect	a_E,
		const Vector< Real >	a_cdrDensities
	)		const

overridevirtual

Compute velocities for the CDR equations.

Parameters

[in]	a_time	Time
[in]	a_pos	Position
[in]	a_E	Electric field
[in]	a_cdrDensities	CDR densities

Returns: Returns the drift velocities for each CDR species. The vector ordering is the same as m_cdrSpecies.

Implements Physics::CdrPlasma::CdrPlasmaPhysics.

◆ computeCdrElectrodeFluxes()

Vector< Real > CdrPlasmaJSON::computeCdrElectrodeFluxes	(	const Real	a_time,
		const RealVect	a_pos,
		const RealVect	a_normal,
		const RealVect	a_E,
		const Vector< Real >	a_cdrDensities,
		const Vector< Real >	a_cdrVelocities,
		const Vector< Real >	a_cdrGradients,
		const Vector< Real >	a_rteFluxes,
		const Vector< Real >	a_extrapCdrFluxes
	)		const

overridevirtual

Compute CDR fluxes on electrode-gas interfaces. This is used as a boundary condition in the CDR equations.

Parameters

[in]	a_time	Time
[in]	a_pos	Position
[in]	a_normal	Boundary normal vector. This points into the gas phase.
[in]	a_E	Electric field
[in]	a_cdrVelocities	CDR velocities. Normal component only.
[in]	a_cdrDensities	CDR densities.
[in]	a_cdrGradients	Normal gradients of cdr densities
[in]	a_rteFluxes	RTE fluxes (normal component only)
[in]	a_extrapCdrFluxes	Extrapolated fluxes from the gas side.

Returns: Returns the flux on an electrode interface cell. The vector ordering must be the same as m_cdrSpecies.

Implements Physics::CdrPlasma::CdrPlasmaPhysics.

◆ computeEta()

Real CdrPlasmaJSON::computeEta	(	const Real	a_E,
		const RealVect	a_position
	)		const

overridevirtual

Compute eta. Should return Townsend attachment coefficient.

This function is mostly used for the cell tagging classes, but can be used for reactions as well.

Parameters

[in]	a_E	Electric field.
[in]	a_position	Position

Implements Physics::CdrPlasma::CdrPlasmaPhysics.

◆ computePlasmaReactionRate()

Real CdrPlasmaJSON::computePlasmaReactionRate	(	const int &	a_reactionIndex,
		const std::vector< Real > &	a_cdrDensities,
		const std::vector< Real > &	a_cdrMobilities,
		const std::vector< Real > &	a_cdrDiffusionCoefficients,
		const std::vector< Real > &	a_cdrTemperatures,
		const std::vector< Real > &	a_cdrEnergies,
		const std::vector< RealVect > &	a_cdrGradients,
		const RealVect &	a_pos,
		const RealVect &	a_vectorE,
		const Real &	a_E,
		const Real &	a_Etd,
		const Real &	a_N,
		const Real &	a_alpha,
		const Real &	a_eta,
		const Real &	a_time
	)		const

protectedvirtual

Compute the reaction rate for a plasma reaction.

This routine exists because we need to compute the rates both in advanceReactionNetwork and getPlotVariables. This function reduces code duplication.

Parameters

[in]	a_reactionIndex	Reaction index
[in]	a_cdrDensities	Plasma species densities.
[in]	a_cdrMobilities	Plasma species mobilities.
[in]	a_cdrDiffusionCoefficients	Plasma species diffusion coefficients.
[in]	a_cdrTemperatures	Plasma species temperatures.
[in]	a_cdrEnergies	Plasma species energies.
[in]	a_cdrGradients	Plasma species gradients.
[in]	a_pos	Position (physical coordinates)
[in]	a_vectorE	Electric field (vector)
[in]	a_E	Electric field magnitude (SI units)
[in]	a_Etd	Electric field magnitude (Townsend units)
[in]	a_N	Neutral density
[in]	a_alpha	Townsend ionization coefficient
[in]	a_eta	Townsend attachment coefficient
[in]	a_time	Time

◆ computePlasmaSpeciesDiffusion()

std::vector< Real > CdrPlasmaJSON::computePlasmaSpeciesDiffusion	(	const RealVect	a_position,
		const RealVect	a_E,
		const std::vector< Real >	a_cdrDensities
	)		const

protectedvirtual

Compute the various plasma species diffusion coefficients.

Parameters

[in]	a_position	Physical coordinates
[in]	a_E	Electric field (SI units)
[in]	a_cdrDensities	List of plasma species densities

Returns: Returns the diffusion coefficients for each CDR species. The vector ordering is the same as m_cdrSpecies.

◆ computePlasmaSpeciesEnergies()

std::vector< Real > CdrPlasmaJSON::computePlasmaSpeciesEnergies	(	const RealVect &	a_position,
		const RealVect &	a_E,
		const std::vector< Real > &	a_cdrDensities
	)		const

protectedvirtual

Compute the various plasma species energies. Returns a list of energies in electron-volts. We assume that temperature-energy relations are e = 3/2 * kB * T.

If a transported species is associated with an energy solver the energy is computed from e = (n_eps)/ne. Otherwise, we compute the energy and returns 3/2 * kB * T.

Parameters

[in]	a_position	Physical coordinates
[in]	a_E	Electric field (SI units)
[in]	a_cdrDensities	List of plasma species densities.

◆ computePlasmaSpeciesMobilities()

std::vector< Real > CdrPlasmaJSON::computePlasmaSpeciesMobilities	(	const RealVect &	a_position,
		const RealVect &	a_E,
		const std::vector< Real > &	a_cdrDensities
	)		const

protectedvirtual

Compute the various plasma species mobilities.

Parameters

[in]	a_position	Physical coordinates
[in]	a_E	Electric field (SI units)
[in]	a_cdrDensities	List of plasma species densities.

◆ computePlasmaSpeciesTemperatures()

std::vector< Real > CdrPlasmaJSON::computePlasmaSpeciesTemperatures	(	const RealVect &	a_position,
		const RealVect &	a_E,
		const std::vector< Real > &	a_cdrDensities
	)		const

protectedvirtual

Compute the various plasma species temperatures.

Parameters

[in]	a_position	Physical coordinates
[in]	a_E	Electric field (SI units)
[in]	a_cdrDensities	List of plasma species densities.

◆ containsBracket()

bool CdrPlasmaJSON::containsBracket ( const std::string a_str ) const

protected

Protect all kinds of brackets in a string.

Parameters

[in] a_str Input string. If it contains any bracket we throw an error.

◆ containsWildcard()

bool CdrPlasmaJSON::containsWildcard ( const std::string a_str ) const

protected

Protect the @ character in a string.

Parameters

[in] a_str Input string. If it contains the at character we throw an error.

◆ doesFileExist()

bool CdrPlasmaJSON::doesFileExist ( const std::string a_filename ) const

protected

Check if file exists.

Parameters

[in] a_filename File name

◆ fillSourceTerms()

void CdrPlasmaJSON::fillSourceTerms	(	std::vector< Real > &	a_cdrSources,
		std::vector< Real > &	a_rteSources,
		const std::vector< Real >	a_cdrDensities,
		const std::vector< RealVect >	a_cdrGradients,
		const RealVect	a_E,
		const RealVect	a_pos,
		const Real	a_dx,
		const Real	a_time,
		const Real	a_kappa
	)		const

protected

Routine for filling the source terms in the reactive problem.

Parameters

[out]	a_cdrSources	Contains source term for CDR equations.
[out]	a_rteSources	Contains source terms for RTE equations.
[in]	a_cdrDensities	CDR densities
[in]	a_cdrGradients	CDR gradients at time a_time
[in]	a_E	Electric field
[in]	a_pos	Physical coordinates
[in]	a_dx	Grid resolution
[in]	a_time	Time
[in]	a_kappa	Volume fraction

◆ getNumberOfPlotVariables()

int CdrPlasmaJSON::getNumberOfPlotVariables ( ) const

overridevirtual

Get number of plot variables for this physics class.

This is used by CdrPlasmaStepper for pre-allocating data that will be put in a plot file. The current implementation plots the gas pressure, temperature, and density

Reimplemented from Physics::CdrPlasma::CdrPlasmaPhysics.

◆ getPlotVariables()

Vector< Real > CdrPlasmaJSON::getPlotVariables	(	const Vector< Real >	a_cdrDensities,
		const Vector< RealVect >	a_cdrGradients,
		const Vector< Real >	a_rteDensities,
		const RealVect	a_E,
		const RealVect	a_position,
		const Real	a_dx,
		const Real	a_dt,
		const Real	a_time,
		const Real	a_kappa
	)		const

overridevirtual

Provide plot variables. This is used by CdrPlasmaStepper when writing plot files.

The plot variables should have length this->getNumberOfPlotVariables (as should getPlotVariableNames)

Parameters

[in]	a_cdrDensities	Grid-based density for particle species.
[in]	a_cdrGradients	Grid-based gradients for particle species.
[in]	a_rteDensities	Grid-based densities for photons.
[in]	a_E	Electric field.
[in]	a_pos	Position in space.
[in]	a_dx	Grid resolution.
[in]	a_dt	Advanced time.
[in]	a_time	Current time.
[in]	a_kappa	Grid cell unit volume.

Reimplemented from Physics::CdrPlasma::CdrPlasmaPhysics.

◆ getReactionSpecies()

void CdrPlasmaJSON::getReactionSpecies	(	std::list< int > &	a_plasmaReactants,
		std::list< int > &	a_neutralReactants,
		std::list< int > &	a_photonReactants,
		std::list< int > &	a_plasmaProducts,
		std::list< int > &	a_neutralProducts,
		std::list< int > &	a_photonProducts,
		const std::vector< std::string > &	a_reactants,
		const std::vector< std::string > &	a_products
	)		const

protectedvirtual

Get the int-encoding corresponding to species involved in some reaction.

Parameters

[out]	a_plasmaReactants	Plasma reactants
[out]	a_neutralReactants	Neutral reactants
[out]	a_photonReactants	Photon reactants
[out]	a_plasmaProducts	Plasma products
[out]	a_neutralProducts	Neutral products
[out]	a_photonProducts	Photon products
[in]	a_reactants	Reactant names
[in]	a_products	Reaction names

◆ initializePhotonSpecies()

void CdrPlasmaJSON::initializePhotonSpecies ( )

protectedvirtual

Initialize photon species.

This will initialize the radiative transfer species absed on the "photon_species" field in the JSON file.

◆ initializePlasmaSpecies()

void CdrPlasmaJSON::initializePlasmaSpecies ( )

protectedvirtual

Initialize species.

This will initialize the species based on the "plasma_species" field in the JSON file.

◆ initializeSigma()

void CdrPlasmaJSON::initializeSigma ( )

protectedvirtual

Initialize surface charge.

This will initialize the surface charge based on the "sigma" field in the JSON file. If you want more complex initial surface charges, you will have to either extend this routine or overwrite it.

◆ initialSigma()

Real CdrPlasmaJSON::initialSigma	(	const Real	a_time,
		const RealVect	a_pos
	)		const

overridevirtual

Set the initial surface charge.

Parameters

[in]	a_time	Time
[in]	a_pos	Position

Implements Physics::CdrPlasma::CdrPlasmaPhysics.

◆ integrateReactions()

void CdrPlasmaJSON::integrateReactions	(	std::vector< Real > &	a_cdrDensities,
		std::vector< Real > &	a_photonProduction,
		const std::vector< RealVect >	a_cdrGradients,
		const RealVect	a_E,
		const RealVect	a_pos,
		const Real	a_dx,
		const Real	a_dt,
		const Real	a_time,
		const Real	a_kappa
	)		const

protectedvirtual

Routine for integrating the reactive-only problem using various algorithms.

Parameters

[in,out]	a_cdrDensities	On input, contains n(t). On output it contains n(t+dt).
[out]	a_photonProduction	On input, should be equal to zero. On output it will contain the number of photons produced during the time step.
[in]	a_cdrGradients	CDR gradients at time a_time
[in]	a_E	Electric field
[in]	a_pos	Physical coordinates
[in]	a_dx	Grid resolution
[in]	a_dt	Time step
[in]	a_kappa	Volume fraction

◆ integrateReactionsExplicitEuler()

void CdrPlasmaJSON::integrateReactionsExplicitEuler	(	std::vector< Real > &	a_cdrDensities,
		std::vector< Real > &	a_photonProduction,
		const std::vector< RealVect >	a_cdrGradients,
		const RealVect	a_E,
		const RealVect	a_pos,
		const Real	a_dx,
		const Real	a_dt,
		const Real	a_time,
		const Real	a_kappa
	)		const

protected

Routine for integrating the reactive-only problem using the explicit Euler rule.

Parameters

[in,out]	a_cdrDensities	On input, contains n(t). On output it contains n(t+dt).
[out]	a_photonProduction	On input, should be equal to zero. On output it will contain the number of photons produced during the time step.
[in]	a_cdrGradients	CDR gradients at time a_time
[in]	a_E	Electric field
[in]	a_pos	Physical coordinates
[in]	a_dx	Grid resolution
[in]	a_dt	Time step
[in]	a_time	Time
[in]	a_kappa	Volume fraction

◆ integrateReactionsExplicitRK2()

void CdrPlasmaJSON::integrateReactionsExplicitRK2	(	std::vector< Real > &	a_cdrDensities,
		std::vector< Real > &	a_photonProduction,
		const std::vector< RealVect >	a_cdrGradients,
		const RealVect	a_E,
		const RealVect	a_pos,
		const Real	a_dx,
		const Real	a_dt,
		const Real	a_time,
		const Real	a_kappa,
		const Real	a_tableuAlpha
	)		const

protected

Routine for integrating the reactive-only problem using a second order Runge-Kutta method.

This includes the tableu through the a_tableuAlpha parameter.

Parameters

[in,out]	a_cdrDensities	On input, contains n(t). On output it contains n(t+dt).
[out]	a_photonProduction	On input, should be equal to zero. On output it will contain the number of photons produced during the time step.
[in]	a_cdrGradients	CDR gradients at time a_time
[in]	a_E	Electric field
[in]	a_pos	Physical coordinates
[in]	a_dx	Grid resolution
[in]	a_dt	Time step
[in]	a_time	Time
[in]	a_kappa	Volume fraction
[in]	a_tableuAlpha	RK2 tableu alpha. Use 0.5 for midpoint and 1.0 for trapezoidal (Heun's method)

◆ integrateReactionsExplicitRK4()

void CdrPlasmaJSON::integrateReactionsExplicitRK4	(	std::vector< Real > &	a_cdrDensities,
		std::vector< Real > &	a_photonProduction,
		const std::vector< RealVect >	a_cdrGradients,
		const RealVect	a_E,
		const RealVect	a_pos,
		const Real	a_dx,
		const Real	a_dt,
		const Real	a_time,
		const Real	a_kappa
	)		const

protected

Routine for integrating the reactive-only problem using the foruth order Runge-Kutta method.

Parameters

[in,out]	a_cdrDensities	On input, contains n(t). On output it contains n(t+dt).
[out]	a_photonProduction	On input, should be equal to zero. On output it will contain the number of photons produced during the time step.
[in]	a_cdrGradients	CDR gradients at time a_time
[in]	a_E	Electric field
[in]	a_pos	Physical coordinates
[in]	a_dx	Grid resolution
[in]	a_dt	Time step
[in]	a_time	Time
[in]	a_kappa	Volume fraction

◆ integrateReactionsImplicitEuler()

void Physics::CdrPlasma::CdrPlasmaJSON::integrateReactionsImplicitEuler	(	std::vector< Real > &	a_cdrDensities,
		std::vector< Real > &	a_photonProduction,
		const std::vector< RealVect >	a_cdrGradients,
		const RealVect	a_E,
		const RealVect	a_pos,
		const Real	a_dx,
		const Real	a_dt,
		const Real	a_time,
		const Real	a_kappa
	)		const

protected

Routine for integrating the reactive-only problem using the implicit Euler rule.

Parameters

[in,out]	a_cdrDensities	On input, contains n(t). On output it contains n(t+dt).
[out]	a_photonProduction	On input, should be equal to zero. On output it will contain the number of photons produced during the time step.
[in]	a_cdrGradients	CDR gradients at time a_time
[in]	a_E	Electric field
[in]	a_pos	Physical coordinates
[in]	a_dx	Grid resolution
[in]	a_dt	Time step
[in]	a_time	Time
[in]	a_kappa	Volume fraction

◆ isBracketed()

bool CdrPlasmaJSON::isBracketed ( const std::string a_str ) const

protected

Return true if string starts and ends with a paranthesis.

Parameters

[in] a_str Input string.

Returns: True if the first character in the string is ( and the last character is )

◆ isNeutralSpecies()

bool CdrPlasmaJSON::isNeutralSpecies ( const std::string & a_name ) const

protected

Return true if species exists in map and false otherwise.

Parameters

[in] a_name Neutral species name

◆ isPhotonSpecies()

bool CdrPlasmaJSON::isPhotonSpecies ( const std::string & a_name ) const

protected

Return true if species exists in map and false otherwise.

Parameters

[in] a_name Rte species name

◆ isPlasmaSpecies()

bool CdrPlasmaJSON::isPlasmaSpecies ( const std::string & a_name ) const

protected

Return true if species exists in map and false otherwise.

Parameters

[in] a_name Cdr species name

◆ parseDielectricReactionEnergyLosses()

void CdrPlasmaJSON::parseDielectricReactionEnergyLosses	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse dielectric-reaction energy losses.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'dielectric reactions' array.

◆ parseDielectricReactionRate()

void CdrPlasmaJSON::parseDielectricReactionRate	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse reaction rate for dielectric surface reactions.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'electrode reactions' array.

◆ parseDielectricReactionScaling()

void CdrPlasmaJSON::parseDielectricReactionScaling	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse dielectric electrode reaction scaling for a specific reaction.

This can be used to adjust for e.g. positional or field dependence.

Parameters

[in]	a_reactionIndex	Reaction index (this is the array index in the dielectric reaction array supplied in the JSON file)
[in]	a_reactionJSON	JSON entry for the reaction in the JSON input file.

◆ parseDomainReactionRate()

void CdrPlasmaJSON::parseDomainReactionRate	(	const int	a_reactionIndex,
		const json &	a_reactionJSON,
		const std::vector< std::string > &	a_sides
	)

protectedvirtual

Parse reaction rate for domain reactions.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'domain reactions' array.
[in]	a_sides	List of the domain sides that this occurs at

◆ parseDomainReactionScaling()

void CdrPlasmaJSON::parseDomainReactionScaling	(	const int	a_reactionIndex,
		const json &	a_reactionJSON,
		const std::vector< std::string > &	a_sides
	)

protectedvirtual

Parse domain reaction scaling for a specific reaction.

This can be used to adjust for e.g. positional or field dependence.

Parameters

[in]	a_reactionIndex	Reaction index (this is the array index in the domain reaction array supplied in the JSON file)
[in]	a_reactionJSON	JSON entry for the reaction in the JSON input file.
[in]	a_sides	List of the domain sides that this occurs at

◆ parseElectrodeReactionEnergyLosses()

void CdrPlasmaJSON::parseElectrodeReactionEnergyLosses	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse electrode-reaction energy losses.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'electrode reactions' array.

◆ parseElectrodeReactionRate()

void CdrPlasmaJSON::parseElectrodeReactionRate	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse reaction rate for electrode surface reactions.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'electrode reactions' array.

◆ parseElectrodeReactionScaling()

void CdrPlasmaJSON::parseElectrodeReactionScaling	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse electrode reaction scaling for a specific reaction.

This can be used to adjust for e.g. positional or field dependence.

Parameters

[in]	a_reactionIndex	Reaction index (this is the array index in the reaction array supplied in the JSON file)
[in]	a_reactionJSON	JSON entry for the reaction in the JSON input file.

◆ parsePhotoReactionEnergyLosses()

void CdrPlasmaJSON::parsePhotoReactionEnergyLosses	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse photo-reaction energy losses.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'photo reactions' array.

◆ parsePhotoReactionScaling()

void CdrPlasmaJSON::parsePhotoReactionScaling	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse scaling for photo-reactions. Includes Helmholtz corrections if doing Helmholtz reconstruction of photoionization profiles.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'photo reactions' array.

◆ parsePlasmaReactionDescription()

void CdrPlasmaJSON::parsePlasmaReactionDescription	(	const int	a_reactionIndex,
		const json &	a_reactionJSON,
		const std::string	a_wildcard
	)

protectedvirtual

Parse plasma reaction descriptions.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'plasma reactions' array.

◆ parsePlasmaReactionEnergyLosses()

void CdrPlasmaJSON::parsePlasmaReactionEnergyLosses	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse plasma reaction energy losses.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'plasma reactions' array.

◆ parsePlasmaReactionPlot()

void CdrPlasmaJSON::parsePlasmaReactionPlot	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse reaction plotting.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'plasma reactions' array.

◆ parsePlasmaReactionRate()

void CdrPlasmaJSON::parsePlasmaReactionRate	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse reaction rate for plasma reaction.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'plasma reactions' array.

Add the rate and lookup method.

◆ parsePlasmaReactionScaling()

void CdrPlasmaJSON::parsePlasmaReactionScaling	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse scaling factors for reactions.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'plasma reactions' array.

◆ parsePlasmaReactionSoloviev()

void CdrPlasmaJSON::parsePlasmaReactionSoloviev	(	const int	a_reactionIndex,
		const json &	a_reactionJSON
	)

protectedvirtual

Parse plasma reaction energy correction.

Parameters

[in]	a_reactionIndex	Reaction index.
[in]	a_reactionJSON	Input reaction. Must be one of the entries in the 'plasma reactions' array.

◆ parsePlasmaSpeciesInitialData()

CdrPlasmaJSON::InitialDataFunction CdrPlasmaJSON::parsePlasmaSpeciesInitialData ( const json & a_json ) const

protectedvirtual

Generate an initial data function for a given plasma species.

Parameters

[in] a_json JSON field, usually (always?) describing one of the objects in the 'plasma species' field.

◆ parsePlasmaSpeciesInitialParticles()

List< PointParticle > CdrPlasmaJSON::parsePlasmaSpeciesInitialParticles ( const json & a_json ) const

protectedvirtual

Generate initial particles for a given plasma species.

Parameters

[in] a_json JSON field, usually (always?) describing one of the objects in the 'plasma species' field.

◆ parseReactionString()

void CdrPlasmaJSON::parseReactionString	(	std::vector< std::string > &	a_reactants,
		std::vector< std::string > &	a_products,
		const std::string &	a_reaction
	)		const

protectedvirtual

Parses a reaction string into reactangs and products.

Parameters

[out]	a_reactants	Left-hand side of reaction
[out]	a_products	Right-hand side of reaction
[in]	a_reaction	Reaction string. Must be in format "a + b + c -> e + f + g".

◆ parseReactionWildcards()

std::list< std::tuple< std::string, std::vector< std::string >, std::vector< std::string > > > CdrPlasmaJSON::parseReactionWildcards	(	const std::vector< std::string > &	a_reactants,
		const std::vector< std::string > &	a_products,
		const json &	a_reaction
	)

protectedvirtual

Make a reaction set into a superset. This parses wildcards '@' in reaction string.

Parameters

[in]	a_reactants	List of reactants. Can contain wildcard.
[in]	a_products	List of products. Can contain wildcard.
[in]	a_reaction	JSON reaction entry.

Returns: Returns a list of reactants and products with wilcards replaced. The tuple entries are: <wildcard, reactants, products>

◆ sanctifyPhotoReaction()

void CdrPlasmaJSON::sanctifyPhotoReaction	(	const std::vector< std::string > &	a_reactants,
		const std::vector< std::string > &	a_products,
		const std::string	a_reaction
	)		const

protectedvirtual

Check if a photo-reaction makes sense in terms of the species that have been defined.

This will throw errors if the species do not exist or charge is not conserved.

Parameters

[in]	a_reactants	Reactants
[in]	a_products	Reaction products
[in]	a_reaction	Reaction string

◆ sanctifyPlasmaReaction()

void CdrPlasmaJSON::sanctifyPlasmaReaction	(	const std::vector< std::string > &	a_reactants,
		const std::vector< std::string > &	a_products,
		const std::string	a_reaction
	)		const

protectedvirtual

Check if a plasma-reaction makes sense in terms of the species that have been defined.

This will throw errors if the species do not exist or charge is not conserved.

Parameters

[in]	a_reactants	Reactants
[in]	a_products	Reaction products
[in]	a_reaction	Reaction string

◆ sanctifySurfaceReaction()

void CdrPlasmaJSON::sanctifySurfaceReaction	(	const std::vector< std::string > &	a_reactants,
		const std::vector< std::string > &	a_products,
		const std::string	a_reaction
	)		const

protectedvirtual

Check if a surface-reaction makes sense in terms of the species that have been defined.

Parameters

[in]	a_reactants	Reactants
[in]	a_products	Reaction products
[in]	a_reaction	Reaction string

◆ sanityCheckSpecies()

void CdrPlasmaJSON::sanityCheckSpecies ( ) const

protectedvirtual

Do a species sanity check.

This will make sure that species names are not duplicates.

◆ throwParserError()

void CdrPlasmaJSON::throwParserError ( const std::string a_error ) const

protected

Throw a parser error.

Parameters

[in] a_error Error code.

◆ throwParserWarning()

void CdrPlasmaJSON::throwParserWarning ( const std::string a_warning ) const

protected

Throw a parser wearning.

Parameters

[in] a_error Warning

Member Data Documentation

◆ m_cdrEnergyComputation

std::map<int, std::tuple<Real, Real, Real> > Physics::CdrPlasma::CdrPlasmaJSON::m_cdrEnergyComputation

protected

Parameters for computing the mean energy from energy density and density.

The energy is computed as e = max(Emin, min(Emax, E)) where E = n_energy/(min(n_density, safety));

◆ m_cdrMasses

std::map<int, Real> Physics::CdrPlasma::CdrPlasmaJSON::m_cdrMasses

protected

Map of the species masses. This is needed for imposing BCs on the energy equations.

This is populated in initializePlasmaSpecies.

◆ m_cdrSpeciesInverseMap

std::map<int, std::string> Physics::CdrPlasma::CdrPlasmaJSON::m_cdrSpeciesInverseMap

protected

int-string encoding of the CDR species.

This is needed because we sometimes need to use the species name for indexing in the vector.

Note: This is the inverse of m_cdrSpeciesMap

◆ m_cdrSpeciesMap

std::map<std::string, int> Physics::CdrPlasma::CdrPlasmaJSON::m_cdrSpeciesMap

protected

string-int encoding of the CDr species.

This is needed because we sometimes need to use the species name for indexing in the vector.

◆ m_cdrTransportEnergyMap

std::map<int, int> Physics::CdrPlasma::CdrPlasmaJSON::m_cdrTransportEnergyMap

protected

int-int encoding for associating a transport solver with an energy solver.

This is only defined for the species that has/is an energy solver. The first index is the transport solver index and the second index is the energy solver index.

◆ m_dielectricReactionEnergyLosses

std::map<int, std::list<std::pair<int, Real> > > Physics::CdrPlasma::CdrPlasmaJSON::m_dielectricReactionEnergyLosses

protected

Associated energy losses for a surface reaction on dielectrics.

The list is a list of species and the corresponding energy losses for a reaction. Note that although we write 'loss', this can also be an energy 'gain'.

◆ m_diffusionTablesEN

std::map<int, LookupTable1D<Real, 1> > Physics::CdrPlasma::CdrPlasmaJSON::m_diffusionTablesEN

protected

Map for table-based diffusion coefficients D = D(E,N).

Tables stored as (E/N, D*N)

◆ m_diffusionTablesEnergy

std::map<int, LookupTable1D<Real, 1> > Physics::CdrPlasma::CdrPlasmaJSON::m_diffusionTablesEnergy

protected

Map for table-based diffusion coefficients as function of energy.

Stored as tables (eV, D*N)

◆ m_domainExtrapBC

std::map<std::tuple<int, Side::LoHiSide, int>, bool> Physics::CdrPlasma::CdrPlasmaJSON::m_domainExtrapBC

protected

A container which determines if we should add the extrapolated flux as an inflow condition.

The first entry in the map is the species integer index. The tuple indicates (coordinate_direction, side, doExtrap).

◆ m_electrodeReactionEnergyLosses

std::map<int, std::list<std::pair<int, Real> > > Physics::CdrPlasma::CdrPlasmaJSON::m_electrodeReactionEnergyLosses

protected

Associated energy losses for a surface reaction on electrodes.

The list is a list of species and the corresponding energy losses for a reaction. Note that although we write 'loss', this can also be an energy 'gain'.

◆ m_mobilityTablesEnergy

std::map<int, LookupTable1D<Real, 1> > Physics::CdrPlasma::CdrPlasmaJSON::m_mobilityTablesEnergy

protected

Map for table-based mobilities as function of energy.

Stored as tables (eV, mu*N)

◆ m_photoReactionEnergyLosses

std::map<int, std::list<std::pair<int, Real> > > Physics::CdrPlasma::CdrPlasmaJSON::m_photoReactionEnergyLosses

protected

Associated energy losses for a photo-reaction.

The list is a list of species and the corresponding energy losses for a reaction. Note that although we write 'loss', this can also be an energy 'gain'.

◆ m_plasmaReactionEnergyLosses

std::map<int, std::map<int, std::pair<ReactiveEnergyLoss, Real> > > Physics::CdrPlasma::CdrPlasmaJSON::m_plasmaReactionEnergyLosses

protected

For mapping reactive energy losses for all reactions.

The index in the first map is the reaction (i.e., index in m_plasmaReactions). The second map determines how reactive energy losses/gains are computed for each species. The first index in the second map indicates the species which will add/lose energy, and the std::pair indicates how this loss is computed.

◆ m_plasmaReactionFunctionsT

std::map<int, std::pair<int, FunctionT> > Physics::CdrPlasma::CdrPlasmaJSON::m_plasmaReactionFunctionsT

protected

Maps for functions of the type k = f(T) where T is the temperature of some species.

In the tuple the first index in the pair indicates the species we are talking about here. A special rule is enforced when this index is < 0 in which case the temperature is replaced by the background gas temperature.

◆ m_plasmaReactionFunctionsTT

std::map<int, std::tuple<int, int, FunctionTT> > Physics::CdrPlasma::CdrPlasmaJSON::m_plasmaReactionFunctionsTT

protected

Maps for functions of the type k = f(T1,T2) where T1 and T2 are the temperatures of some species.

This signature is absolute horrific – what it means is that we have a reaction which should be evaluated as f(T1, T2), but we need to know which species are involved. By design, this should be general so that T1 and T2 can be the temperatures of any species, including neutral species. So, we make a tuple for indicating which species we are talking about. The first index in the tuple is the first species, the second is the second species and the third entry in the tuple is the actual function. A special rule occurs if one of the first two indices is < 0 in which case the temperature is replaced by the background gas temperature.

◆ m_plasmaReactionSolovievCorrection

std::map<int, std::pair<bool, int> > Physics::CdrPlasma::CdrPlasmaJSON::m_plasmaReactionSolovievCorrection

protected

Flag for whether or not reaction includes Soloviev energy correction.

If this is true, the rate for a reaction (in the local field approximation) will be modified as k * (1 + E.(D * grad(phi))/n *

◆ m_plasmaReactionTablesEnergy

std::map<int, std::pair<int, LookupTable1D<Real, 1> > > Physics::CdrPlasma::CdrPlasmaJSON::m_plasmaReactionTablesEnergy

protected

Map for table-based reaction coefficients where k = k(energy).

The first index is the reaction index, while the pair describes which species energy and the tabulated data.

◆ m_rteSpeciesInverseMap

std::map<int, std::string> Physics::CdrPlasma::CdrPlasmaJSON::m_rteSpeciesInverseMap

protected

int-string encoding of the RTE species.

This is needed because we sometimes need to use the species name for indexing in the vector.

Note: This is the inverse of m_rteSpeciesMap

◆ m_rteSpeciesMap

std::map<std::string, int> Physics::CdrPlasma::CdrPlasmaJSON::m_rteSpeciesMap

protected

string-int encoding of the RTE species.

This is needed because we sometimes need to use the species name for indexing in the vector.

The documentation for this class was generated from the following files:

Physics/CdrPlasma/PlasmaModels/CdrPlasmaJSON/CD_CdrPlasmaJSON.H
Physics/CdrPlasma/PlasmaModels/CdrPlasmaJSON/CD_CdrPlasmaJSON.cpp

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ FunctionEN

◆ FunctionEX

◆ FunctionT

◆ FunctionTT

◆ FunctionX

◆ InitialDataFunction

Member Function Documentation

◆ addPhotoIonization()

◆ advanceReactionNetwork()

◆ computeAlpha()

◆ computeCdrDielectricFluxes()

◆ computeCdrDiffusionCoefficients()

◆ computeCdrDomainFluxes()

◆ computeCdrDriftVelocities()

◆ computeCdrElectrodeFluxes()

◆ computeEta()

◆ computePlasmaReactionRate()

◆ computePlasmaSpeciesDiffusion()

◆ computePlasmaSpeciesEnergies()

◆ computePlasmaSpeciesMobilities()

◆ computePlasmaSpeciesTemperatures()

◆ containsBracket()

◆ containsWildcard()

◆ doesFileExist()

◆ fillSourceTerms()

◆ getNumberOfPlotVariables()

◆ getPlotVariables()

◆ getReactionSpecies()

◆ initializePhotonSpecies()

◆ initializePlasmaSpecies()

◆ initializeSigma()

◆ initialSigma()

◆ integrateReactions()

◆ integrateReactionsExplicitEuler()

◆ integrateReactionsExplicitRK2()

◆ integrateReactionsExplicitRK4()

◆ integrateReactionsImplicitEuler()

◆ isBracketed()

◆ isNeutralSpecies()

◆ isPhotonSpecies()

◆ isPlasmaSpecies()

◆ parseDielectricReactionEnergyLosses()

◆ parseDielectricReactionRate()

◆ parseDielectricReactionScaling()

◆ parseDomainReactionRate()

◆ parseDomainReactionScaling()

◆ parseElectrodeReactionEnergyLosses()

◆ parseElectrodeReactionRate()

◆ parseElectrodeReactionScaling()

◆ parsePhotoReactionEnergyLosses()

◆ parsePhotoReactionScaling()

◆ parsePlasmaReactionDescription()

◆ parsePlasmaReactionEnergyLosses()

◆ parsePlasmaReactionPlot()

◆ parsePlasmaReactionRate()

◆ parsePlasmaReactionScaling()

◆ parsePlasmaReactionSoloviev()

◆ parsePlasmaSpeciesInitialData()

◆ parsePlasmaSpeciesInitialParticles()

◆ parseReactionString()

◆ parseReactionWildcards()

◆ sanctifyPhotoReaction()

◆ sanctifyPlasmaReaction()

◆ sanctifySurfaceReaction()

◆ sanityCheckSpecies()

◆ throwParserError()

◆ throwParserWarning()

Member Data Documentation

◆ m_cdrEnergyComputation

◆ m_cdrMasses

◆ m_cdrSpeciesInverseMap

◆ m_cdrSpeciesMap

◆ m_cdrTransportEnergyMap