Base class for interaction between Kinetic Monte Carlo and Ito-based plasma solvers. More...

#include <CD_ItoKMCPhysics.H>

Inheritance diagram for Physics::ItoKMC::ItoKMCPhysics:

Collaboration diagram for Physics::ItoKMC::ItoKMCPhysics:

[legend]

Public Member Functions
	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.

virtual Real	computeDt (const RealVect a_E, const RealVect a_pos, const Vector< FPR > a_numParticles) const noexcept
	Compute a time step to use. More...

virtual Real	computeAlpha (const Real a_E, const RealVect a_x) const =0
	Compute Townsend ionization coefficient. More...

virtual Real	computeEta (const Real a_E, const RealVect a_x) const =0
	Compute Townsend attachment coefficient. More...

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

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

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

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

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

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.

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

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

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

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

virtual Vector< Real >	computeMobilities (const Real a_time, const RealVect a_pos, const RealVect a_E) const noexcept=0
	Compute the Ito solver mobilities. More...

virtual Vector< Real >	computeDiffusionCoefficients (const Real a_time, const RealVect a_pos, const RealVect a_E) const noexcept=0
	Compute the Ito solver diffusion coefficients. More...

virtual void	secondaryEmissionEB (Vector< List< ItoParticle >> &a_secondaryParticles, Vector< Real > &a_cdrFluxes, Vector< List< Photon >> &a_secondaryPhotons, const Vector< List< ItoParticle >> &a_primaryParticles, const Vector< Real > &a_cdrFluxesExtrap, const Vector< List< Photon >> &a_primaryPhotons, const RealVect &a_E, const RealVect &a_physicalCellCenter, 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=0
	Resolve secondary emission at the EB. More...

void	advanceKMC (Vector< FPR > &a_numParticles, Vector< FPR > &a_numNewPhotons, 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 particles. More...

void	reconcileParticles (Vector< List< ItoParticle > * > &a_particles, const Vector< FPR > &a_newNumParticles, const Vector< FPR > &a_oldNumParticles, 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. More...

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. More...

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

Protected Types
enum class	Algorithm { SSA , TauPlain , TauMidpoint , HybridPlain , HybridMidpoint }
	Enum for switching between KMC algorithms. More...

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

Protected Member Functions
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. More...

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.

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_dx, const Real a_kappa) const noexcept=0
	Update reaction rates. More...

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

Protected Attributes
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.

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

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

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

ItoKMCSurfaceReactionSet	m_surfaceReactions
	Surface reactions.

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_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. More...

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

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

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

Static Protected Attributes
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. More...

Detailed Description

Base class for interaction between Kinetic Monte Carlo and Ito-based plasma solvers.

When using this class, the user should populate m_kmcReactions with the appropriate reactions AND implement routines for computing the mobility/diffusion coefficeints.

Member Enumeration Documentation

◆ Algorithm

enum Physics::ItoKMC::ItoKMCPhysics::Algorithm

strongprotected

Enum for switching between KMC algorithms.

'SSA' is the Gillespie algorithm, 'Tau' is tau-leaping and 'Hybrid' is the Cao et. al. algorithm.

Member Function Documentation

◆ advanceKMC()

void ItoKMCPhysics::advanceKMC	(	Vector< FPR > &	a_numParticles,
		Vector< FPR > &	a_numNewPhotons,
		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

inline

Advance particles.

Parameters

[in,out]	a_numParticles	Number of physical particles
[out]	a_numNewPhotons	Number of new physical photons to generate (of each type)
[in]	a_phi	Plasma species densities.
[in]	a_gradPhi	Plasma species density gradients.
[in]	a_dt	Time step
[in]	a_E	Electric field
[in]	a_pos	Physical position
[in]	a_dx	Grid resolution
[in]	a_kappa	Cut-cell volume fraction.

◆ computeAlpha()

virtual Real Physics::ItoKMC::ItoKMCPhysics::computeAlpha	(	const Real	a_E,
		const RealVect	a_x
	)		const

pure virtual

Compute Townsend ionization coefficient.

Parameters

[in]	a_E	Electric field magnitude
[in]	a_x	Physical coordinate

Returns: Should return the Townsend ionization coefficient.

Implemented in Physics::ItoKMC::ItoKMCJSON.

◆ computeDiffusionCoefficients()

virtual Vector<Real> Physics::ItoKMC::ItoKMCPhysics::computeDiffusionCoefficients	(	const Real	a_time,
		const RealVect	a_pos,
		const RealVect	a_E
	)		const

pure virtualnoexcept

Compute the Ito solver diffusion coefficients.

Parameters

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

Returns: Must return a vector of non-negative diffusion coefficients for the plasma species

Implemented in Physics::ItoKMC::ItoKMCJSON.

◆ computeDt()

Real ItoKMCPhysics::computeDt	(	const RealVect	a_E,
		const RealVect	a_pos,
		const Vector< FPR >	a_numParticles
	)		const

inlinevirtualnoexcept

Compute a time step to use.

Parameters

[in]	a_E	Electric field.
[in]	a_pos	Position
[in]	a_numParticles	Number of reactive particles of each species

Returns: Default returns infinity but user can implement a physics based time step.

Reimplemented in Physics::ItoKMC::ItoKMCJSON.

◆ computeEta()

virtual Real Physics::ItoKMC::ItoKMCPhysics::computeEta	(	const Real	a_E,
		const RealVect	a_x
	)		const

pure virtual

Compute Townsend attachment coefficient.

Parameters

[in]	a_E	Electric field magnitude
[in]	a_x	Physical coordinate

Returns: Should return the Townsend attachment coefficient.

Implemented in Physics::ItoKMC::ItoKMCJSON.

◆ computeMobilities()

virtual Vector<Real> Physics::ItoKMC::ItoKMCPhysics::computeMobilities	(	const Real	a_time,
		const RealVect	a_pos,
		const RealVect	a_E
	)		const

pure virtualnoexcept

Compute the Ito solver mobilities.

Parameters

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

Returns: Must return a vector of non-negative mobility coefficients for the plasma species

Implemented in Physics::ItoKMC::ItoKMCJSON.

◆ defineSpeciesMap()

void ItoKMCPhysics::defineSpeciesMap ( )

inlineprotectednoexcept

Build internal representation of how we distinguish the Ito and CDR solvers.

Note: This should ALWAYS be called after initializing the species since ItoKMCStepper will rely on it.

◆ getCdrSpecies()

const Vector< RefCountedPtr< CdrSpecies > > & ItoKMCPhysics::getCdrSpecies ( ) const

inline

Get all fluid drift-diffusion species.

Returns: m_cdrSpecies

◆ getItoSpecies()

const Vector< RefCountedPtr< ItoSpecies > > & ItoKMCPhysics::getItoSpecies ( ) const

inline

Get all particle drift-diffusion species.

Returns: m_itoSpecies

◆ getPlotVariables()

Vector< Real > ItoKMCPhysics::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

virtualnoexcept

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 in Physics::ItoKMC::ItoKMCJSON.

◆ getRtSpecies()

const Vector< RefCountedPtr< RtSpecies > > & ItoKMCPhysics::getRtSpecies ( ) const

inline

Get all photon species.

Returns: m_rtSpecies

◆ initialSigma()

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

inlinevirtual

Set initial surface charge. Default is 0, override if you want.

Parameters

[in]	a_time	Simulation time
[in]	a_pos	Physical coordinate

◆ reconcileParticles()

void ItoKMCPhysics::reconcileParticles	(	Vector< List< ItoParticle > * > &	a_particles,
		const Vector< FPR > &	a_newNumParticles,
		const Vector< FPR > &	a_oldNumParticles,
		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

inlinenoexcept

Reconcile the number of particles.

This will add/remove particles and potentially also adjust the particle weights.

Parameters

[in,out]	a_particles	Computational particles
[in]	a_newNumParticles	New number of particles (i.e., after the KMC advance)
[in]	a_oldNumParticles	Previous number of particles (i.e., before the KMC advance)
[in]	a_cellPos	Cell center position
[in]	a_centroidPos	Cell centroid position
[in]	a_loCorner	Low corner of minimum box enclosing the cut-cell
[in]	a_hiCorner	High corner of minimum box enclosing the cut-cell
[in]	a_bndryCentroid	Cut-cell boundary centroid
[in]	a_bndryNormal	Cut-cell normal (pointing into the domain)
[in]	a_dx	Grid resolution
[in]	a_kappa	Cut-cell volume fraction.

Note: Public because this is called by ItoKMCStepper

◆ reconcilePhotoionization()

void ItoKMCPhysics::reconcilePhotoionization	(	Vector< List< ItoParticle > * > &	a_itoParticles,
		Vector< List< PointParticle > * > &	a_cdrParticles,
		const Vector< List< Photon > * > &	a_absorbedPhotons
	)		const

inlinenoexcept

Reconcile photoionization reactions.

Parameters

[in,out]	a_itoPrticles	Particle products placed in Ito solvers.
[in,out]	a_cdrParticles	Particle products placed in CDR solvers.
[in]	a_absorbedPhotons	Photons absorbed on the mesh.

This runs through the photo-reactions and associates photo-ionization products.

◆ reconcilePhotons()

void ItoKMCPhysics::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

inlinenoexcept

Generate new photons.

This will add photons

Parameters

[in]	a_newPhotons	New photons
[in]	a_numNewPhotons	Number of physical photons to be generated.
[in]	a_cellPos	Cell center position
[in]	a_centroidPos	Cell centroid position
[in]	a_loCorner	Low corner of minimum box enclosing the cut-cell
[in]	a_hiCorner	High corner of minimum box enclosing the cut-cell
[in]	a_bndryCentroid	Cut-cell boundary centroid
[in]	a_bndryNormal	Cut-cell normal (pointing into the domain)
[in]	a_dx	Grid resolution
[in]	a_kappa	Cut-cell volume fraction.

Note: Public because this is called by ItoKMCStepper

◆ removeParticles()

void ItoKMCPhysics::removeParticles	(	List< ItoParticle > &	a_particles,
		const long long	a_numToRemove
	)		const

inlineprotected

Remove particles from the input list.

This will remove weight from the input particles if we can. Otherwise we remove full particles.

Parameters

[in,out]	a_particles	List of (super-)particles to remove from.
[in]	a_numToRemove	Number of physical particles to remove from the input list

◆ secondaryEmissionEB()

virtual void Physics::ItoKMC::ItoKMCPhysics::secondaryEmissionEB	(	Vector< List< ItoParticle >> &	a_secondaryParticles,
		Vector< Real > &	a_cdrFluxes,
		Vector< List< Photon >> &	a_secondaryPhotons,
		const Vector< List< ItoParticle >> &	a_primaryParticles,
		const Vector< Real > &	a_cdrFluxesExtrap,
		const Vector< List< Photon >> &	a_primaryPhotons,
		const RealVect &	a_E,
		const RealVect &	a_physicalCellCenter,
		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

pure virtualnoexcept

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_cdrFluxes	CDR fluxes for CDR species.
[out]	a_secondaryPhotons	Photons injected through the EB.
[in]	a_primaryParticles	Particles that left the computational domain through the EB.
[in]	a_cdrFluxesExtrap	Extrapolated CDR fluxes.
[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_physicalCellCenter	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).

Implemented in Physics::ItoKMC::ItoKMCJSON.

◆ updateReactionRates()

virtual void Physics::ItoKMC::ItoKMCPhysics::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_dx,
		const Real	a_kappa
	)		const

protectedpure virtualnoexcept

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_dx	Grid resolution
[in]	a_kappa	Cut-cell volume fraction

Note: Must be implemented by the user.

Implemented in Physics::ItoKMC::ItoKMCJSON.

Member Data Documentation

◆ m_eps

Real Physics::ItoKMC::ItoKMCPhysics::m_eps

protected

Solver setting for the Cao et. al. algorithm.

Equal to the maximum permitted change in the relative propensity for non-critical reactions

◆ m_kmcReactionsThreadLocal

thread_local std::vector< std::shared_ptr< const KMCReaction > > ItoKMCPhysics::m_kmcReactionsThreadLocal

staticprotected

KMC reactions used in advanceReactionNetowkr.

Note: This is set up via setupKMC in order toi ensure OpenMP thread safety when calling advanceReactionNetwork. The vector is later depopulated in killKMC().

◆ m_Ncrit

int Physics::ItoKMC::ItoKMCPhysics::m_Ncrit

protected

Solver setting for the Cao et. al algorithm.

Determines critical reactions. A reaction is critical if it is m_Ncrit firings away from depleting a reactant.

◆ m_NSSA

int Physics::ItoKMC::ItoKMCPhysics::m_NSSA

protected

Solver setting for the Cao et. al algorithm.

Maximum number of SSA steps to run when switching into SSA-based advancement for non-critical reactions.

◆ m_photoPathways

std::map<int, std::pair<std::discrete_distribution<int>, std::map<int, int> > > Physics::ItoKMC::ItoKMCPhysics::m_photoPathways

protected

Random number generators for photoionization pathways.

The first index is the photon index, i.e. entry in m_photonSpecies. The second index in the map is an RNG generator for selecting photo-reactions, and a map which associates the returned reaction from the RNG generator with an index in m_photoReactions.

◆ m_SSAlim

Real Physics::ItoKMC::ItoKMCPhysics::m_SSAlim

protected

Solver setting for the Cao et. al. algorithm.

Equal to the maximum permitted change in the relative propensity for non-critical reactions

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

Physics/ItoKMC/CD_ItoKMCPhysics.H
Physics/ItoKMC/CD_ItoKMCPhysics.cpp
Physics/ItoKMC/CD_ItoKMCPhysicsImplem.H

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ Algorithm

Member Function Documentation

◆ advanceKMC()

◆ computeAlpha()

◆ computeDiffusionCoefficients()

◆ computeDt()

◆ computeEta()

◆ computeMobilities()

◆ defineSpeciesMap()

◆ getCdrSpecies()

◆ getItoSpecies()

◆ getPlotVariables()

◆ getRtSpecies()

◆ initialSigma()

◆ reconcileParticles()

◆ reconcilePhotoionization()

◆ reconcilePhotons()

◆ removeParticles()

◆ secondaryEmissionEB()

◆ updateReactionRates()

Member Data Documentation

◆ m_eps

◆ m_kmcReactionsThreadLocal

◆ m_Ncrit

◆ m_NSSA

◆ m_photoPathways

◆ m_SSAlim