Implementation of ItoKMCPhysics which parses input data from a JSON file. More...

#include <CD_ItoKMCJSON.H>

Inheritance diagram for Physics::ItoKMC::ItoKMCJSON:

Collaboration diagram for Physics::ItoKMC::ItoKMCJSON:

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

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.

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

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.

using	FunctionEVXTP = std::function< Real(const Real E, const Real V, const Real dx, const Real dt, const RealVect x, const Vector< Real > &phi)>
	Function for encapsulating a function f = f(E, V, x) where E is the electric field at physical coordinates x, and V is a grid cell volume.

using	FunctionDXP = std::function< Real(const Real dx, const Vector< Real > &phi)>
	Function which encapsulates.

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.

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.

Public Member Functions
	ItoKMCJSON ()
	Default constructor.

virtual	~ItoKMCJSON () noexcept
	Destructor.

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

virtual Real	getNeutralDensity (const RealVect a_pos) const noexcept override
	Get the neutral density at a position in space.

virtual Real	computeAlpha (const Real a_E, const RealVect a_pos) const noexcept override
	Compute Townsend ionization coefficient.

virtual Real	computeEta (const Real a_E, const RealVect a_pos) const noexcept override
	Compute Townsend attachment coefficient.

virtual Vector< std::string >	getPlotVariableNames () const noexcept override
	Get number of plot variables.

virtual Vector< Real >	getPlotVariables (const RealVect a_E, const RealVect a_pos, const Vector< Real > &a_phi, const Vector< RealVect > &a_gradPhi, const Real a_dx, const Real a_kappa) const noexcept override
	Get plot variables.

virtual int	getNumberOfPlotVariables () const noexcept override
	Get number of plot variables.

virtual bool	needGradients () const noexcept override
	Return true/false if physics model needs species gradients.

virtual Vector< Real >	computeMobilities (const Real a_time, const RealVect a_pos, const RealVect a_E) const noexcept override
	Compute the Ito solver mobilities.

virtual Vector< Real >	computeDiffusionCoefficients (const Real a_time, const RealVect a_pos, const RealVect a_E) const noexcept override
	Compute the Ito solver diffusion coefficients.

virtual void	secondaryEmissionEB (Vector< List< ItoParticle > > &a_secondaryParticles, Vector< Real > &a_secondaryCDRFluxes, Vector< List< Photon > > &a_secondaryPhotons, const Vector< List< ItoParticle > > &a_primaryParticles, const Vector< Real > &a_primaryCDRFluxes, const Vector< List< Photon > > &a_primaryPhotons, const RealVect &a_E, const RealVect &a_cellCenter, const RealVect &a_cellCentroid, const RealVect &a_bndryCentroid, const RealVect &a_bndryNormal, const Real a_bndryArea, const Real a_dx, const Real a_dt, const bool a_isDielectric, const int a_matIndex) const noexcept override
	Resolve secondary emission at the EB.

Public Member Functions inherited from Physics::ItoKMC::ItoKMCPhysics
	ItoKMCPhysics () noexcept
	Constructor. Does nothing.

virtual	~ItoKMCPhysics () noexcept
	Destructor. Does nothing.

void	defineKMC () const noexcept
	Define the KMC solver and state.

void	killKMC () const noexcept
	Kill the KMC solver.

const Vector< RefCountedPtr< ItoSpecies > > &	getItoSpecies () const
	Get all particle drift-diffusion species.

const Vector< RefCountedPtr< CdrSpecies > > &	getCdrSpecies () const
	Get all fluid drift-diffusion species.

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

const Vector< DiffusionFunction > &	getItoDiffusionFunctions () const noexcept
	Get diffusion functions.

int	getNumItoSpecies () const
	Return number of Ito solvers.

int	getNumCdrSpecies () const
	Return number of CDR solvers.

int	getNumPlasmaSpecies () const
	Return total number of plasma species.

int	getNumPhotonSpecies () const
	Return number of RTE solvers.

const std::map< int, std::pair< SpeciesType, int > > &	getSpeciesMap () const noexcept
	Get the internal mapping between plasma species and Ito solvers.

virtual Real	initialSigma (const Real a_time, const RealVect a_pos) const
	Set initial surface charge. Default is 0, override if you want.

void	advanceKMC (Vector< FPR > &a_numParticles, Vector< FPR > &a_numNewPhotons, Real &a_physicsDt, const Vector< Real > &a_phi, const Vector< RealVect > &a_gradPhi, const Real a_dt, const RealVect a_E, const RealVect a_pos, const Real a_dx, const Real a_kappa) const
	Advance the reaction network using the KMC algorithm.

void	reconcileParticles (Vector< List< ItoParticle > * > &a_particles, const Vector< FPR > &a_newNumParticles, const Vector< FPR > &a_oldNumParticles, const RealVect a_electricField, const RealVect a_cellPos, const RealVect a_centroidPos, const RealVect a_lo, const RealVect a_hi, const RealVect a_bndryCentroid, const RealVect a_bndryNormal, const Real a_dx, const Real a_kappa) const noexcept
	Reconcile the number of particles.

void	reconcilePhotons (Vector< List< Photon > * > &a_newPhotons, const Vector< FPR > &a_numNewPhotons, const RealVect a_cellPos, const RealVect a_centroidPos, const RealVect a_lo, const RealVect a_hi, const RealVect a_bndryCentroid, const RealVect a_bndryNormal, const Real a_dx, const Real a_kappa) const noexcept
	Generate new photons.

void	reconcilePhotoionization (Vector< List< ItoParticle > * > &a_itoParticles, Vector< List< PointParticle > * > &a_cdrParticles, const Vector< List< Photon > * > &a_absorbedPhotons) const noexcept
	Reconcile photoionization reactions.

Protected Member Functions
virtual std::string	trim (const std::string &a_string) const noexcept
	Trim a string. This removes whitespace before/after.

virtual void	parseJSON ()
	Parse the JSON file.

virtual void	parseVerbose () noexcept
	Parse chattiness.

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

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

virtual bool	doesFileExist (const std::string a_filename) const noexcept
	Check if a file exists.

virtual bool	isBackgroundSpecies (const std::string &a_name) const noexcept
	Return true if species is a background species.

virtual bool	isPlasmaSpecies (const std::string &a_name) const noexcept
	Return true if species is a plasma species.

virtual bool	isPhotonSpecies (const std::string &a_name) const noexcept
	Return true if species is a photon species.

virtual bool	containsWildcard (const std::string a_str) const noexcept
	Check if a string contains the wildcard @ and return true if it does.

virtual bool	containsBracket (const std::string a_str) const noexcept
	Check if a string contains standard brackets.

virtual bool	isBracketed (const std::string a_str) const noexcept
	Check if a string contains starts with '(' and ends with ')'.

virtual void	checkMolarFraction (const RealVect a_position) const noexcept
	Check that molar fraction is one. Throws a warning if it isn't.

virtual void	sanctifyPlasmaReaction (const std::vector< std::string > &a_reactants, const std::vector< std::string > &a_products, const std::string &a_reaction) const noexcept
	Check that a plasma reaction makes sense. I.e. that all species are properly defined and that it conserves charge.

virtual void	sanctifyPhotoReaction (const std::vector< std::string > &a_reactants, const std::vector< std::string > &a_products, const std::string &a_reaction) const noexcept
	Check that a photo-reaction makes sense. I.e. that all species are properly defined and that it conserves charge.

virtual void	initializeGasLaw ()
	Initialize gas law.

virtual void	initializeBackgroundSpecies ()
	Initialize the background species.

virtual void	initializeTownsendCoefficient (const std::string a_coeff)
	Parse one of the Townsend coefficients.

virtual void	initializeAutomaticTownsend (const std::string a_coeff)
	Initialize automatic Townsend coefficient (ionizatino or attachment) from the reaction rates.

virtual void	previewFunctionEX (const nlohmann::json &a_json, const FunctionEX &a_function) const
	Simple function for previewing a rate/coefficient defined as a function f = f(E,x)

virtual void	printFluidRates () const noexcept
	Print the fluid-representation of the reaction rates.

virtual void	initializePlasmaSpecies ()
	Initialize the plasma species.

virtual void	initializeParticles ()
	Parse initial particles.

virtual void	initializeDensities ()
	Parse initial densities for CDR and Ito species.

virtual void	initializeMobilities ()
	Initialize mobility functions.

virtual void	initializeDiffusionCoefficients ()
	Initialize diffusion coefficients.

virtual void	initializeTemperatures ()
	Initialize the plasma species temperatures.

virtual void	initializePhotonSpecies ()
	Initialize the photon species.

virtual void	initializePlasmaReactions ()
	Initialize plasma reactions.

virtual void	initializePhotoReactions ()
	Initialize photo-reactions.

virtual void	initializeSurfaceEmission (const std::string a_surface)
	Initialize surface reactions.

virtual void	initializeFieldEmission ()
	Initialize field emission reactions.

virtual void	initializeParticlePlacement ()
	Initialize the particle placement algorithm.

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

virtual void	getReactionSpecies (std::list< size_t > &a_backgroundReactants, std::list< size_t > &a_plasmaReactants, std::list< size_t > &a_photonReactants, std::list< size_t > &a_backgroundProducts, std::list< size_t > &a_plasmaProducts, std::list< size_t > &a_photonProducts, const std::vector< std::string > &a_reactants, const std::vector< std::string > &a_products) const noexcept
	Turn reactants and products strings into indices.

virtual std::pair< FunctionEVXTP, FunctionEX >	parsePlasmaReactionRate (const nlohmann::json &a_reactionJSON, const std::list< size_t > &a_backgroundReactants, const std::list< size_t > &a_plasmaReactants) const
	Parse a plasma reaction rate and turn it into a function.

virtual std::pair< bool, std::string >	parsePlasmaReactionPlot (const nlohmann::json &a_reactionJSON) const
	Parse whether or not a reaction rate should be plotted.

virtual std::pair< bool, std::string >	parsePlasmaReactionGradientCorrection (const nlohmann::json &a_reactionJSON) const
	Parse whether or not a reaction uses a gradient correction for the rate.

virtual Real	parsePlasmaReactionDt (const nlohmann::json &a_reactionJSON) const
	Parse whether or not a reaction should be a part of the time step calculation. Returns 1 if the reaction is a part of it.

virtual LookupTable1D< Real, 1 >	parseTableEByN (const nlohmann::json &a_tableEntry, const std::string &a_dataID) const
	Parse a table which is stored in E/N format.

virtual std::vector< 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 nlohmann::json &a_reactionJSON) const noexcept
	Make a reaction set into a superset. This parses wildcards '@' in reaction string.

virtual void	updateReactionRates (std::vector< std::shared_ptr< const KMCReaction > > &a_kmcReactions, const RealVect a_E, const RealVect a_pos, const Vector< Real > &a_phi, const Vector< RealVect > &a_gradPhi, const Real a_dt, const Real a_dx, const Real a_kappa) const noexcept override
	Update reaction rates.

std::vector< size_t >	multinomial (const size_t N, const std::discrete_distribution< size_t > &a_distribution) const noexcept
	Sample a multinomial distribution with N samples.

Protected Member Functions inherited from Physics::ItoKMC::ItoKMCPhysics
void	define () noexcept
	Define method – defines all the internal machinery.

void	defineSpeciesMap () noexcept
	Build internal representation of how we distinguish the Ito and CDR solvers.

void	definePhotoPathways () noexcept
	Define pathways for photo-reactions.

void	parsePPC () noexcept
	Parse the maximum number of particles generated per cell.

void	parseDebug () noexcept
	Parse the maximum number of particles generated per cell.

void	parseAlgorithm () noexcept
	Parse reaction algorithm.

void	removeParticles (List< ItoParticle > &a_particles, const long long a_numToRemove) const
	Remove particles from the input list.

bool	computeUpstreamPosition (RealVect &a_pos, RealVect &a_lo, RealVect &a_hi, const int &a_Z, const List< ItoParticle > &a_particles, const RealVect &a_electricField, const RealVect &a_cellPos, const Real &a_dx) const noexcept
	Compute the upstream position in a grid cell. Returns false if an upstream position was undefinable.

RealVect	noDiffusion (const ItoParticle &a_particle, const Real a_dt) const noexcept
	No diffusion function for a particle.

RealVect	isotropicDiffusion (const ItoParticle &a_particle, const Real a_dt) const noexcept
	Isotropic diffusion function for a particle.

RealVect	forwardIsotropicDiffusion (const ItoParticle &a_particle, const Real a_dt) const noexcept
	Quasi-isotropic diffusion function for a particle which does not permit backward diffusion.

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_skipReactions
	A flag for skipping reactions completely.

bool	m_previewRates
	Preview rates or not.

int	m_numPlasmaSpecies
	Total number of plasma species.

int	m_numPhotonSpecies
	Total number of photon species.

nlohmann::json	m_json
	Nohmanns implementation of JSON files.

std::string	m_jsonFile
	Input JSON file name.

std::set< std::string >	m_allSpecies
	All species that have been defined.

std::map< std::string, int >	m_backgroundSpeciesMap
	Map of string-int identifiers for background species.

std::map< int, std::string >	m_backgroundSpeciesMapInverse
	Map of int-string identifiers for background species.

std::vector< ItoKMCBackgroundSpecies >	m_backgroundSpecies
	Map of background species.

std::vector< bool >	m_backgroundSpeciesPlot
	Plot background species or not.

std::map< std::string, SpeciesType >	m_plasmaSpeciesTypes
	Map for identifying a species name with a solver type.

std::map< std::string, int >	m_itoSpeciesMap
	Map for indexing from an ID to an Ito solver index.

std::map< std::string, int >	m_cdrSpeciesMap
	Map for indexing from an ID to an Ito solver index.

std::map< std::string, int >	m_plasmaIndexMap
	Map for indexing a plasma species name to a global index in the solver vectors.

std::map< std::string, int >	m_photonIndexMap
	Map for indexing a photon species name to a global index in the solver vectors.

std::vector< FunctionEX >	m_mobilityFunctions
	Mobilities for the various species.

std::vector< FunctionEX >	m_diffusionCoefficients
	Diffusion coefficients for the various species.

std::vector< FunctionEX >	m_plasmaTemperatures
	Plasma species temperatures.

std::vector< FunctionEVXTP >	m_kmcReactionRates
	Function-based plasma reaction rates. Same index as the actual reactions.

std::vector< FunctionEX >	m_fluidRates
	Function-based plasma reaction rates as if they appeared in the reaction rate equation. Same index as actual reactions.

std::vector< std::list< size_t > >	m_plasmaReactionBackgroundReactants
	List of background species involved in a reaction.

std::vector< std::list< size_t > >	m_plasmaReactionPlasmaReactants
	List of plasma species on the left-hand side of a reaction.

std::vector< std::list< size_t > >	m_plasmaReactionPlasmaProducts
	List of plasma species on the right-hand side of a reaction.

std::vector< std::list< size_t > >	m_plasmaReactionPhotonProducts
	List of photon species on the right-hand side of a reaction.

std::vector< std::pair< bool, std::string > >	m_kmcReactionGradientCorrections
	Whether or not a reaction uses a gradient correction for the rate (Soloviev et. al. paper)

std::vector< std::pair< bool, std::string > >	m_kmcReactionRatePlots
	Map of reactions that will be plotted.

std::map< int, std::pair< bool, int > >	m_plasmaReactionSolovievCorrection
	Map of reactions that will be plotted.

std::pair< bool, std::string >	m_autoAlpha
	Flag if the user wants to compute the alpha coefficient from the reactions.

std::pair< bool, std::string >	m_autoEta
	Flag if the user wants to compute the alpha coefficient from the reactions.

std::vector< std::pair< int, FunctionEN > >	m_dielectricFieldEmission
	List of dielectric field emission reactions.

std::vector< std::pair< int, FunctionEN > >	m_electrodeFieldEmission
	List of electrode field emission reactions.

FunctionEX	m_alpha
	Townsend ionization coefficient. Defined during parseAlpha.

FunctionEX	m_eta
	Townsend attachment coefficient. Defined during parseEta.

FunctionX	m_gasPressure
	Background gas pressure.

FunctionX	m_gasTemperature
	Background gas temperature.

FunctionX	m_gasNumberDensity
	Background gas number density.

Protected Attributes inherited from Physics::ItoKMC::ItoKMCPhysics
Algorithm	m_algorithm
	Algorithm to use for KMC advance.

ParticlePlacement	m_particlePlacement
	Particle placement algorithm.

std::map< int, std::pair< SpeciesType, int > >	m_speciesMap
	Map for associating a plasma species with an Ito solver or CDR solver.

std::string	m_className
	Class name. Used for options parsing.

bool	m_debug
	Turn on/off debugging.

bool	m_isDefined
	Is defined or not.

bool	m_incrementNewParticles
	If true, increment onto existing particles rather than creating new ones.

std::vector< KMCReaction >	m_kmcReactions
	List of reactions for the KMC solver.

std::vector< ItoKMCPhotoReaction >	m_photoReactions
	List of photoionization reactions.

std::vector< Real >	m_reactiveDtFactors
	List of reactions that are a part of the time step limitation.

std::map< int, std::pair< std::discrete_distribution< int >, std::map< int, int > > >	m_photoPathways
	Random number generators for photoionization pathways.

ItoKMCSurfaceReactionSet	m_surfaceReactions
	Surface reactions.

Vector< DiffusionFunction >	m_itoDiffusionFunctions
	Diffusion functions for the various Ito species.

Vector< RefCountedPtr< ItoSpecies > >	m_itoSpecies
	List of solver-tracked particle drift-diffusion species.

Vector< RefCountedPtr< CdrSpecies > >	m_cdrSpecies
	List of solver-tracked fluid drift-diffusion species.

Vector< RefCountedPtr< RtSpecies > >	m_rtSpecies
	List of solver-tracked photon species.

int	m_downstreamSpecies
	An internal integer describing which species is the "ionizing" species.

int	m_maxNewParticles
	Maximum new number of particles generated by the chemistry advance.

int	m_maxNewPhotons
	Maximum new number of photons generated by the chemistry advance.

int	m_Ncrit
	Solver setting for the Cao et. al algorithm.

int	m_NSSA
	Solver setting for the Cao et. al algorithm.

int	m_maxIter
	Maximum number of iterations for implicit KMC-leaping algorithms.

Real	m_SSAlim
	Solver setting for the Cao et. al. algorithm.

Real	m_eps
	Solver setting for the Cao et. al. algorithm.

Real	m_exitTol
	Exit tolerance for implicit KMC-leaping algorithms.

Additional Inherited Members
Protected Types inherited from Physics::ItoKMC::ItoKMCPhysics
enum class	Algorithm { SSA , ExplicitEuler , Midpoint , PRC , ImplicitEuler , HybridExplicitEuler , HybridMidpoint , HybridPRC , HybridImplicitEuler }
	Enum for switching between KMC algorithms. More...

enum class	ParticlePlacement { Random , Centroid , Downstream }
	Enum for switching between various particle placement algorithms.

Static Protected Attributes inherited from Physics::ItoKMC::ItoKMCPhysics
static thread_local bool	m_hasKMCSolver
	Is the KMC solver defined or not.

static thread_local KMCSolverType	m_kmcSolver
	Kinetic Monte Carlo solver used in advanceReactionNetwork.

static thread_local KMCState	m_kmcState
	KMC state used in advanceReactionNetwork.

static thread_local std::vector< std::shared_ptr< const KMCReaction > >	m_kmcReactionsThreadLocal
	KMC reactions used in advanceReactionNetowkr.

Detailed Description

Implementation of ItoKMCPhysics which parses input data from a JSON file.

Member Typedef Documentation

◆ FunctionDXP

using Physics::ItoKMC::ItoKMCJSON::FunctionDXP = std::function<Real(const Real dx, const Vector<Real>& phi)>

Function which encapsulates.

Parameters

[in]	dx	Grid resolution
[in]	dx	List of plasma species densities.

◆ FunctionEN

using Physics::ItoKMC::ItoKMCJSON::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.

◆ FunctionEVXTP

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

Parameters

[in]	E	Electric field magnitude in SI units.
[in]	V	Volume
[in]	dx	Grid resolution
[in]	dt	Time step
[in]	x	Physical coordinate
[in]	phi	List of plasma species densities

◆ FunctionEX

using Physics::ItoKMC::ItoKMCJSON::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::ItoKMC::ItoKMCJSON::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::ItoKMC::ItoKMCJSON::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::ItoKMC::ItoKMCJSON::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)

◆ FunctionXt

using Physics::ItoKMC::ItoKMCJSON::FunctionXt = std::function<Real(const RealVect a_position, const Real a_time)>

Function alias for e.g. initial data.

Parameters

[in]	a_position	Physical coordinates
[in]	a_time	Time

Member Function Documentation

◆ checkMolarFraction()

void ItoKMCJSON::checkMolarFraction ( const RealVect a_position ) const

protectedvirtualnoexcept

Check that molar fraction is one. Throws a warning if it isn't.

Parameters

[in] a_position Physical coordinates

◆ computeAlpha()

Real ItoKMCJSON::computeAlpha	(	const Real	a_E,
		const RealVect	a_pos
	)		const

overridevirtualnoexcept

Compute Townsend ionization coefficient.

Parameters

[in]	a_E	Electric field.
[in]	a_pos	Physical coordinates

Implements Physics::ItoKMC::ItoKMCPhysics.

◆ computeDiffusionCoefficients()

Vector< Real > ItoKMCJSON::computeDiffusionCoefficients	(	const Real	a_time,
		const RealVect	a_pos,
		const RealVect	a_E
	)		const

overridevirtualnoexcept

Compute the Ito solver diffusion coefficients.

Parameters

[in]	a_time	Time
[in]	a_pos	Position
[in]	a_E	Electric field

Implements Physics::ItoKMC::ItoKMCPhysics.

◆ computeEta()

Real ItoKMCJSON::computeEta	(	const Real	a_E,
		const RealVect	a_pos
	)		const

overridevirtualnoexcept

Compute Townsend attachment coefficient.

Parameters

[in]	a_E	Electric field.
[in]	a_pos	Physical coordinates

Implements Physics::ItoKMC::ItoKMCPhysics.

◆ computeMobilities()

Vector< Real > ItoKMCJSON::computeMobilities	(	const Real	a_time,
		const RealVect	a_pos,
		const RealVect	a_E
	)		const

overridevirtualnoexcept

Compute the Ito solver mobilities.

Parameters

[in]	a_time	Time
[in]	a_pos	Position
[in]	a_E	Electric field

Implements Physics::ItoKMC::ItoKMCPhysics.

◆ containsBracket()

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

protectedvirtualnoexcept

Check if a string contains standard brackets.

Parameters

[in] a_str Input string

◆ containsWildcard()

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

protectedvirtualnoexcept

Check if a string contains the wildcard @ and return true if it does.

Parameters

[in] a_str Input string

◆ doesFileExist()

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

protectedvirtualnoexcept

Check if a file exists.

Parameters

[in] a_filename File name

◆ getNeutralDensity()

Real ItoKMCJSON::getNeutralDensity ( const RealVect a_pos ) const

overridevirtualnoexcept

Get the neutral density at a position in space.

Parameters

[in] a_pos Physical position

Returns: Neutral density

Implements Physics::ItoKMC::ItoKMCPhysics.

◆ getNumberOfPlotVariables()

int ItoKMCJSON::getNumberOfPlotVariables ( ) const

overridevirtualnoexcept

Get number of plot variables.

Reimplemented from Physics::ItoKMC::ItoKMCPhysics.

◆ getPlotVariableNames()

Vector< std::string > ItoKMCJSON::getPlotVariableNames ( ) const

overridevirtualnoexcept

Get number of plot variables.

Reimplemented from Physics::ItoKMC::ItoKMCPhysics.

◆ getPlotVariables()

Vector< Real > ItoKMCJSON::getPlotVariables	(	const RealVect	a_E,
		const RealVect	a_pos,
		const Vector< Real > &	a_phi,
		const Vector< RealVect > &	a_gradPhi,
		const Real	a_dx,
		const Real	a_kappa
	)		const

overridevirtualnoexcept

Get plot variables.

Parameters

[in]	a_E	Electric field
[in]	a_pos	Physical position
[in]	a_phi	Plasma species densities
[in]	a_gradPhi	Density gradients for plasma species.
[in]	a_dx	Grid resolution
[in]	a_kappa	Cut-cell volume fraction

Reimplemented from Physics::ItoKMC::ItoKMCPhysics.

◆ getReactionSpecies()

void ItoKMCJSON::getReactionSpecies	(	std::list< size_t > &	a_backgroundReactants,
		std::list< size_t > &	a_plasmaReactants,
		std::list< size_t > &	a_photonReactants,
		std::list< size_t > &	a_backgroundProducts,
		std::list< size_t > &	a_plasmaProducts,
		std::list< size_t > &	a_photonProducts,
		const std::vector< std::string > &	a_reactants,
		const std::vector< std::string > &	a_products
	)		const

protectedvirtualnoexcept

Turn reactants and products strings into indices.

Parameters

[out]	a_backgroundReactants	Background reactant indices
[out]	a_plasmaReactants	Plasma reactant indices
[out]	a_photonReactants	Photon reactant indices
[out]	a_backgroundProducts	Background product indices
[out]	a_plasmaProducts	Plasma product indices
[out]	a_photonProducts	Photon product indices
[in]	a_reactants	Reactants
[in]	a_products	Products

◆ initializeAutomaticTownsend()

void ItoKMCJSON::initializeAutomaticTownsend ( const std::string a_coeff )

protectedvirtual

Initialize automatic Townsend coefficient (ionizatino or attachment) from the reaction rates.

Parameters

[in] a_coeff Which coefficient. Must be "alpha" or "eta"

◆ initializeSurfaceEmission()

void ItoKMCJSON::initializeSurfaceEmission ( const std::string a_surface )

protectedvirtual

Initialize surface reactions.

Parameters

[in] a_surface Surface type

◆ initializeTownsendCoefficient()

void ItoKMCJSON::initializeTownsendCoefficient ( const std::string a_coeff )

protectedvirtual

Parse one of the Townsend coefficients.

Parameters

[in] a_coeff Which coefficient. Must be "alpha" or "eta"

◆ isBackgroundSpecies()

bool ItoKMCJSON::isBackgroundSpecies ( const std::string & a_name ) const

protectedvirtualnoexcept

Return true if species is a background species.

Parameters

[in] a_name Species name

◆ isBracketed()

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

protectedvirtualnoexcept

Check if a string contains starts with '(' and ends with ')'.

Parameters

[in] a_str Input string

◆ isPhotonSpecies()

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

protectedvirtualnoexcept

Return true if species is a photon species.

Parameters

[in] a_name Species name

◆ isPlasmaSpecies()

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

protectedvirtualnoexcept

Return true if species is a plasma species.

Parameters

[in] a_name Species name

◆ multinomial()

std::vector< size_t > ItoKMCJSON::multinomial	(	const size_t	N,
		const std::discrete_distribution< size_t > &	a_distribution
	)		const

protectednoexcept

Sample a multinomial distribution with N samples.

Parameters

[in]	a_N	Number of samples
[in]	a_distribution	Discrete distribution

◆ needGradients()

bool ItoKMCJSON::needGradients ( ) const

overridevirtualnoexcept

Return true/false if physics model needs species gradients.

Reimplemented from Physics::ItoKMC::ItoKMCPhysics.

◆ parsePlasmaReactionGradientCorrection()

std::pair< bool, std::string > ItoKMCJSON::parsePlasmaReactionGradientCorrection ( const nlohmann::json & a_reactionJSON ) const

protectedvirtual

Parse whether or not a reaction uses a gradient correction for the rate.

Parameters

[in] a_reactionJSON Reaction entry in JSON file

◆ parsePlasmaReactionPlot()

std::pair< bool, std::string > ItoKMCJSON::parsePlasmaReactionPlot ( const nlohmann::json & a_reactionJSON ) const

protectedvirtual

Parse whether or not a reaction rate should be plotted.

Parameters

[in] a_reactionJSON Reaction entry in JSON file

◆ parsePlasmaReactionRate()

std::pair< std::function< Real(const Real E, const Real V, const Real dx, const Real dt, const RealVect x, const Vector< Real > &phi)>, std::function< Real(const Real E, const RealVect x)> > ItoKMCJSON::parsePlasmaReactionRate	(	const nlohmann::json &	a_reactionJSON,
		const std::list< size_t > &	a_backgroundReactants,
		const std::list< size_t > &	a_plasmaReactants
	)		const

protectedvirtual

Parse a plasma reaction rate and turn it into a function.

Parameters

[in]	a_reactionJSON	Reaction entry in JSON file
[in]	a_backgroundReactants	List of background species appearing on the left hand side of the reaction
[in]	a_plasmaReactants	List of plasma species appearing on the left-hand side of the reaction

Returns: This should return a tuple of KMC and fluid rates. The KMC rate will also be multiplied by background species on the left hand side of the reaction.

◆ parseReactionString()

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

protectedvirtualnoexcept

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::vector< std::tuple< std::string, std::vector< std::string >, std::vector< std::string > > > ItoKMCJSON::parseReactionWildcards	(	const std::vector< std::string > &	a_reactants,
		const std::vector< std::string > &	a_products,
		const nlohmann::json &	a_reactionJSON
	)		const

protectedvirtualnoexcept

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_reactionJSON	JSON reaction entry.

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

◆ parseRuntimeOptions()

void ItoKMCJSON::parseRuntimeOptions ( )

overridevirtualnoexcept

Parse run-time options.

Reimplemented from Physics::ItoKMC::ItoKMCPhysics.

◆ parseTableEByN()

LookupTable1D< Real, 1 > ItoKMCJSON::parseTableEByN	(	const nlohmann::json &	a_tableEntry,
		const std::string &	a_dataID
	)		const

protectedvirtual

Parse a table which is stored in E/N format.

Parameters

[in]	a_tableEntry	Table entry in JSON format.
[in]	a_dataID	Data identifier

◆ previewFunctionEX()

void ItoKMCJSON::previewFunctionEX	(	const nlohmann::json &	a_json,
		const FunctionEX &	a_function
	)		const

protectedvirtual

Simple function for previewing a rate/coefficient defined as a function f = f(E,x)

Parameters

[in]	a_json	JSON entry containing the previewing information.
[in]	a_function	Function to be previewed.

◆ sanctifyPhotoReaction()

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

protectedvirtualnoexcept

Check that a photo-reaction makes sense. I.e. that all species are properly defined and that it conserves charge.

Parameters

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

◆ sanctifyPlasmaReaction()

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

protectedvirtualnoexcept

Check that a plasma reaction makes sense. I.e. that all species are properly defined and that it conserves charge.

Parameters

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

◆ secondaryEmissionEB()

void ItoKMCJSON::secondaryEmissionEB	(	Vector< List< ItoParticle > > &	a_secondaryParticles,
		Vector< Real > &	a_secondaryCDRFluxes,
		Vector< List< Photon > > &	a_secondaryPhotons,
		const Vector< List< ItoParticle > > &	a_primaryParticles,
		const Vector< Real > &	a_primaryCDRFluxes,
		const Vector< List< Photon > > &	a_primaryPhotons,
		const RealVect &	a_E,
		const RealVect &	a_cellCenter,
		const RealVect &	a_cellCentroid,
		const RealVect &	a_bndryCentroid,
		const RealVect &	a_bndryNormal,
		const Real	a_bndryArea,
		const Real	a_dx,
		const Real	a_dt,
		const bool	a_isDielectric,
		const int	a_matIndex
	)		const

overridevirtualnoexcept

Resolve secondary emission at the EB.

Routine is here to handle charge injection, secondary emission etc.

Parameters

[out]	a_secondaryParticles	Outgoing plasma species particles.
[out]	a_secondaryCDRFluxes	Outgoing plasma species CDR fluxes
[out]	a_secondaryPhotons	Photons injected through the EB
[in]	a_primaryParticles	Particles that left the computational domain through the EB
[in]	a_primaryCDRFluxes	CDR fluxes leaving the computational domain through the EB
[in]	a_primaryPhotons	Photons that left the computational domain through the EB
[in]	a_newNumParticles	Total number of particles in the cut-cell AFTER the transport step
[in]	a_oldNumParticles	Total number of particles in the cut-cell BEFORE the transport step
[in]	a_electricField	Electric field
[in]	a_cellCenter	Physical position of the cell center.
[in]	a_cellCentroid	Cell centroid relative to the cell center (not multiplied by dx)
[in]	a_bndryCentroid	EB face centroid relative to the cell center (not multiplied by dx)
[in]	a_bndryNormal	Cut-cell normal vector.
[in]	a_bndryArea	Cut-cell boundary area - not multiplied by dx (2D) or dx^2 (3D)
[in]	a_dx	Grid resolution on this level.
[in]	a_dt	Time step
[in]	a_isDielectric	Dielectric or electrode.
[in]	a_matIndex	Material index (taken from computationalGeometry)

Implements Physics::ItoKMC::ItoKMCPhysics.

◆ throwParserError()

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

protectedvirtualnoexcept

Throw a parser error.

Parameters

[in] a_error Error code.

◆ throwParserWarning()

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

protectedvirtualnoexcept

Throw a parser wearning.

Parameters

[in] a_error Warning

◆ trim()

std::string ItoKMCJSON::trim ( const std::string & a_string ) const

protectedvirtualnoexcept

Trim a string. This removes whitespace before/after.

Parameters

[in] a_string String to be trimmed

◆ updateReactionRates()

void ItoKMCJSON::updateReactionRates	(	std::vector< std::shared_ptr< const KMCReaction > > &	a_kmcReactions,
		const RealVect	a_E,
		const RealVect	a_pos,
		const Vector< Real > &	a_phi,
		const Vector< RealVect > &	a_gradPhi,
		const Real	a_dt,
		const Real	a_dx,
		const Real	a_kappa
	)		const

overrideprotectedvirtualnoexcept

Update reaction rates.

Parameters

[out]	a_kmcReactions	Reaction rates to be set.
[in]	a_E	Electric field
[in]	a_pos	Physical position
[in]	a_phi	Plasma species densities
[in]	a_gradPhi	Density gradients for plasma species.
[in]	a_dt	Time step
[in]	a_dx	Grid resolution
[in]	a_kappa	Cut-cell volume fraction

Implements Physics::ItoKMC::ItoKMCPhysics.

Member Data Documentation

◆ m_allSpecies

std::set<std::string> Physics::ItoKMC::ItoKMCJSON::m_allSpecies

protected

All species that have been defined.

Only used to make sure we're not doubly defining some species

◆ m_backgroundSpecies

std::vector<ItoKMCBackgroundSpecies> Physics::ItoKMC::ItoKMCJSON::m_backgroundSpecies

protected

Map of background species.

Built in initialization order but can look up arbitrary species name but using the maps.

◆ m_backgroundSpeciesPlot

std::vector<bool> Physics::ItoKMC::ItoKMCJSON::m_backgroundSpeciesPlot

protected

Plot background species or not.

Built in initialization order but can look up arbitrary species name but using the maps.

◆ m_fluidRates

std::vector<FunctionEX> Physics::ItoKMC::ItoKMCJSON::m_fluidRates

protected

Function-based plasma reaction rates as if they appeared in the reaction rate equation. Same index as actual reactions.

If S = k * n_1 * n_2 * n_3 where n_1, n_2, n_3 is any species, then this contains 'k'.

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

Physics/ItoKMC/PlasmaModels/ItoKMCJSON/CD_ItoKMCJSON.H
Physics/ItoKMC/PlasmaModels/ItoKMCJSON/CD_ItoKMCJSON.cpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ FunctionDXP

◆ FunctionEN

◆ FunctionEVXTP

◆ FunctionEX

◆ FunctionT

◆ FunctionTT

◆ FunctionX

◆ FunctionXt

Member Function Documentation

◆ checkMolarFraction()

◆ computeAlpha()

◆ computeDiffusionCoefficients()

◆ computeEta()

◆ computeMobilities()

◆ containsBracket()

◆ containsWildcard()

◆ doesFileExist()

◆ getNeutralDensity()

◆ getNumberOfPlotVariables()

◆ getPlotVariableNames()

◆ getPlotVariables()

◆ getReactionSpecies()

◆ initializeAutomaticTownsend()

◆ initializeSurfaceEmission()

◆ initializeTownsendCoefficient()

◆ isBackgroundSpecies()

◆ isBracketed()

◆ isPhotonSpecies()

◆ isPlasmaSpecies()

◆ multinomial()

◆ needGradients()

◆ parsePlasmaReactionGradientCorrection()

◆ parsePlasmaReactionPlot()

◆ parsePlasmaReactionRate()

◆ parseReactionString()

◆ parseReactionWildcards()

◆ parseRuntimeOptions()

◆ parseTableEByN()

◆ previewFunctionEX()

◆ sanctifyPhotoReaction()

◆ sanctifyPlasmaReaction()

◆ secondaryEmissionEB()

◆ throwParserError()

◆ throwParserWarning()

◆ trim()

◆ updateReactionRates()

Member Data Documentation

◆ m_allSpecies

◆ m_backgroundSpecies

◆ m_backgroundSpeciesPlot

◆ m_fluidRates