Abstract base class coupling Kinetic Monte Carlo chemistry to Ito/CDR plasma solvers. More...

#include <CD_ItoKMCPhysics.H>

Inheritance diagram for Physics::ItoKMC::ItoKMCPhysics:

Collaboration diagram for Physics::ItoKMC::ItoKMCPhysics:

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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	getNeutralDensity (const RealVect &a_pos) const noexcept=0
	Get the neutral density at a position in space.

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

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

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 for all Ito species.

virtual Vector< std::string >	getPlotVariableNames () const noexcept
	Get plot variable names.

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.

virtual int	getNumberOfPlotVariables () const noexcept
	Get number of extra plot variables contributed by this physics model.

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 if the physics model requires species density gradients.

virtual bool	needGradient (const int a_plasmaIndex) const noexcept
	Return true if the physics model reads the density gradient of one particular plasma species.

const std::map< int, std::pair< SpeciesType, int > > &	getSpeciesMap () const noexcept
	Get the internal mapping from plasma-species index to solver type and solver index.

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.

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

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

virtual void	secondaryEmissionEB (Vector< ParticleSoA< ItoParticle > > &a_secondaryParticles, Vector< Real > &a_cdrFluxes, Vector< ParticleSoA< Photon > > &a_secondaryPhotons, const Vector< ParticleSoA< ItoParticle > > &a_primaryParticles, const Vector< Real > &a_cdrFluxesExtrap, const Vector< ParticleSoA< 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.

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< ParticleSoA< 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< ParticleSoA< 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< ParticleSoA< ItoParticle > * > &a_itoParticles, Vector< ParticleSoA< NoPayload > * > &a_cdrParticles, const Vector< ParticleSoA< Photon > * > &a_absorbedPhotons) const noexcept
	Reconcile photoionization reactions.

void	reconcileCdrParticles (Vector< ParticleSoA< NoPayload > * > &a_cdrParticles, const Vector< ParticleSoA< ItoParticle > * > &a_itoParticles, const Vector< long long > &a_numNewParticles, 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
	Turn the CDR mass created by the reaction network into particles.

Protected Types
enum class	Algorithm { SSA , ExplicitEuler , Midpoint , PRC , ImplicitEuler , HybridExplicitEuler , HybridMidpoint , HybridPRC , HybridImplicitEuler }
	KMC time-stepping algorithms available for advancing the reaction network. More...

enum class	ParticlePlacement { Random , Centroid , Downstream , Parent }
	Strategies for placing secondary particles created during the KMC advance. More...

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.

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_dt, const Real a_dx, const Real a_kappa) const noexcept=0
	Update reaction rates.

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

RealVect	drawNewParticlePosition (const bool a_hasParent, const bool a_hasDownstream, const RealVect a_parentPos, const RealVect a_upstreamPos, const RealVect a_upstreamLo, const RealVect a_upstreamHi, const RealVect a_downstreamDirection, 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
	Draw a position for a particle created by the reaction network in a grid cell.

bool	sampleParentPosition (RealVect &a_pos, const ParticleSoA< ItoParticle > &a_particles, const std::vector< Real > &a_cumulativeWeights) const noexcept
	Draw the position of a parent particle, with probability proportional to particle weight.

void	buildParentWeights (std::vector< Real > &a_cumulativeWeights, const ParticleSoA< ItoParticle > &a_particles, const std::size_t a_numEligible) const noexcept
	Build the running weight sum that sampleParentPosition() draws from.

bool	computeUpstreamPosition (RealVect &a_pos, RealVect &a_lo, RealVect &a_hi, const int &a_Z, const ParticleSoA< 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
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::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.

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 KMCState	m_kmcStateScratch
	Perturbed KMC state used by the time step tail of advanceKMC.

static thread_local std::vector< Real >	m_kmcPropensityScratch
	Propensity buffer used by the time step tail of advanceKMC.

static thread_local std::vector< long long >	m_weightScratch
	Reusable buffer for ParticleManagement::partitionParticleWeights.

static thread_local std::vector< Real >	m_parentWeightScratch
	Running sum of the eligible parent weights in a grid cell, used by ParticlePlacement::Parent.

static thread_local std::vector< std::shared_ptr< const KMCReaction > >	m_kmcReactionsThreadLocal
	Thread-local copies of KMC reactions used in advanceReactionNetwork.

static thread_local std::vector< std::shared_ptr< const KMCReaction > >	m_kmcReactionsDt
	The subset of m_kmcReactionsThreadLocal that takes part in the physics time step calculation.

static thread_local std::vector< Real >	m_reactiveDtFactorsDt
	Time-step scaling factors for m_kmcReactionsDt, parallel to it.

static thread_local std::vector< Real >	m_kmcPropensityScratchDt
	Propensity buffer for m_kmcReactionsDt, parallel to it.

Detailed Description

Abstract base class coupling Kinetic Monte Carlo chemistry to Ito/CDR plasma solvers.

Subclasses must implement updateReactionRates(), computeMobilities(), computeDiffusionCoefficients(), secondaryEmissionEB(), computeAlpha(), computeEta(), and getNeutralDensity(). The reaction network is specified by populating m_kmcReactions and (optionally) m_photoReactions and m_surfaceReactions in the subclass constructor.

Member Enumeration Documentation

◆ Algorithm

enum class Physics::ItoKMC::ItoKMCPhysics::Algorithm

strongprotected

KMC time-stepping algorithms available for advancing the reaction network.

Enumerator
SSA	Gillespie's Stochastic Simulation Algorithm (exact).
ExplicitEuler	Explicit tau-leaping with Euler steps.
Midpoint	Explicit tau-leaping with midpoint (second-order) steps.
PRC	Partially-rejected corrections tau-leaping.
ImplicitEuler	Implicit tau-leaping with Euler steps.
HybridExplicitEuler	Hybrid SSA / explicit Euler (Cao et al.).
HybridMidpoint	Hybrid SSA / midpoint (Cao et al.).
HybridPRC	Hybrid SSA / PRC (Cao et al.).
HybridImplicitEuler	Hybrid SSA / implicit Euler (Cao et al.).

◆ ParticlePlacement

enum class Physics::ItoKMC::ItoKMCPhysics::ParticlePlacement

strongprotected

Strategies for placing secondary particles created during the KMC advance.

Enumerator
Random	Place particles at a uniformly random position within the cell.
Centroid	Place particles at the cell centroid.
Downstream	Place particles in the downstream region relative to the primary particle drift.
Parent	Place particles on an existing particle, drawn with probability proportional to its weight.

Member Function Documentation

◆ advanceKMC()

void ItoKMCPhysics::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

inline

Advance the reaction network using the KMC algorithm.

Parameters

[in,out]	a_numParticles	Number of physical particles
[out]	a_numNewPhotons	Number of new physical photons to generate (of each type)
[out]	a_physicsDt	Reasonable KMC time step computed at end of integration with eps = 1
[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.

◆ buildParentWeights()

void ItoKMCPhysics::buildParentWeights	(	std::vector< Real > &	a_cumulativeWeights,
		const ParticleSoA< ItoParticle > &	a_particles,
		const std::size_t	a_numEligible
	)		const

inlineprotectednoexcept

Build the running weight sum that sampleParentPosition() draws from.

Only the leading a_numEligible entries are eligible parents: the reconciliation appends to the same container, and a freshly created particle must not become a parent for its siblings.

Parameters

[out]	a_cumulativeWeights	Receives one running sum per eligible particle; cleared first.
[in]	a_particles	Candidate parents.
[in]	a_numEligible	Number of leading entries of a_particles that may be drawn.

◆ 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 void Physics::ItoKMC::ItoKMCPhysics::computeDiffusionCoefficients	(	Vector< Real > &	a_diffusionCoefficients,
		const Real	a_time,
		const RealVect &	a_pos,
		const RealVect &	a_E
	)		const

pure virtualnoexcept

Compute the Ito solver diffusion coefficients.

Fills a caller-owned buffer; see computeMobilities() for why.

Parameters

[out]	a_diffusionCoefficients	Non-negative diffusion coefficient per plasma species. Resized by the callee.
[in]	a_time	Time
[in]	a_pos	Position
[in]	a_E	Electric field

Implemented 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 void Physics::ItoKMC::ItoKMCPhysics::computeMobilities	(	Vector< Real > &	a_mobilities,
		const Real	a_time,
		const RealVect &	a_pos,
		const RealVect &	a_E
	)		const

pure virtualnoexcept

Compute the Ito solver mobilities.

Fills a caller-owned buffer rather than returning one. This is called once per grid cell, so a returned Vector<Real> was a heap allocation and a free per cell – pure overhead, and (with Chombo memory tracking compiled in) a pair of counter updates on top. The caller hoists one buffer per patch instead.

Implementations must size a_mobilities to the number of plasma species and fill every entry; a species that is not mobile should be given zero rather than skipped, so the indexing stays dense.

Parameters

[out]	a_mobilities	Non-negative mobility coefficient per plasma species. Resized by the callee.
[in]	a_time	Time
[in]	a_pos	Position
[in]	a_E	Electric field

Implemented in Physics::ItoKMC::ItoKMCJSON.

◆ computeUpstreamPosition()

bool ItoKMCPhysics::computeUpstreamPosition	(	RealVect &	a_pos,
		RealVect &	a_lo,
		RealVect &	a_hi,
		const int &	a_Z,
		const ParticleSoA< ItoParticle > &	a_particles,
		const RealVect &	a_electricField,
		const RealVect &	a_cellPos,
		const Real &	a_dx
	)		const

inlineprotectednoexcept

Compute the upstream position in a grid cell. Returns false if an upstream position was undefinable.

This routine will compute the position of the "most upstream" particle in the input list. For all particles we assume that they advect in the direction of Z*E, where Z is the charge number. This routine also computes the minimum bounding box (in unit coordinates) that encloses the downstreamn region within the grid cell.

Parameters

[out]	a_pos	Upstream position.
[out]	a_lo	Minimum coordinate of the downstream region (relative to the unit cell)
[out]	a_hi	Maximum coordinate of the downstream region (relative to the unit cell)
[in]	a_Z	Particle charge number
[in]	a_particles	Particles where we look for an upstream position.
[in]	a_electricField	Electric field vector
[in]	a_cellPos	Physical location of the cell center
[in]	a_dx	Grid resolution

Returns: Computed upstream position

◆ 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.

◆ drawNewParticlePosition()

RealVect ItoKMCPhysics::drawNewParticlePosition	(	const bool	a_hasParent,
		const bool	a_hasDownstream,
		const RealVect	a_parentPos,
		const RealVect	a_upstreamPos,
		const RealVect	a_upstreamLo,
		const RealVect	a_upstreamHi,
		const RealVect	a_downstreamDirection,
		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

inlineprotectednoexcept

Draw a position for a particle created by the reaction network in a grid cell.

The single implementation of ParticlePlacement, shared by the Ito and CDR products. The caller supplies the sampled parent (Parent) and the downstream region (Downstream); either may be flagged absent, in which case that mode falls back to a uniformly random position within the cell.

Parameters

[in]	a_hasParent	True if a_parentPos holds a usable parent position.
[in]	a_hasDownstream	True if the downstream region below is defined.
[in]	a_parentPos	Position of the sampled parent particle. Only read for ParticlePlacement::Parent.
[in]	a_upstreamPos	Upstream position within the cell, in unit coordinates.
[in]	a_upstreamLo	Lower corner of the downstream region, in unit coordinates.
[in]	a_upstreamHi	Upper corner of the downstream region, in unit coordinates.
[in]	a_downstreamDirection	Normalized drift direction of the downstream species.
[in]	a_cellPos	Cell center position
[in]	a_centroidPos	Cell centroid position
[in]	a_lo	Lower corner of the valid region of the cell, in unit coordinates
[in]	a_hi	Upper corner of the valid region of the cell, in unit coordinates
[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

Returns: Physical position for the new particle.

◆ forwardIsotropicDiffusion()

RealVect ItoKMCPhysics::forwardIsotropicDiffusion	(	const ItoParticle &	a_particle,
		const Real	a_dt
	)		const

inlineprotectednoexcept

Quasi-isotropic diffusion function for a particle which does not permit backward diffusion.

Parameters

[in]	a_particle	Particle to diffuse
[in]	a_dt	Time step

Returns: Same as isotropic diffusion, but ensures that the particle cannot diffuse backward

◆ getCdrSpecies()

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

inline

Get all fluid drift-diffusion species.

Returns: m_cdrSpecies

◆ getItoDiffusionFunctions()

const Vector< DiffusionFunction > & ItoKMCPhysics::getItoDiffusionFunctions ( ) const

inlinenoexcept

Get diffusion functions for all Ito species.

Returns: Vector of per-species diffusion displacement functors.

◆ getItoSpecies()

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

inline

Get all particle drift-diffusion species.

Returns: m_itoSpecies

◆ getNeutralDensity()

virtual Real Physics::ItoKMC::ItoKMCPhysics::getNeutralDensity ( const RealVect & a_pos ) const

pure virtualnoexcept

Get the neutral density at a position in space.

Parameters

[in] a_pos Physical position

Returns: Neutral density

Implemented in Physics::ItoKMC::ItoKMCJSON.

◆ getNumberOfPlotVariables()

int ItoKMCPhysics::getNumberOfPlotVariables ( ) const

virtualnoexcept

Get number of extra plot variables contributed by this physics model.

Returns: Number of diagnostic plot variables.

Reimplemented in Physics::ItoKMC::ItoKMCJSON.

◆ getNumCdrSpecies()

int ItoKMCPhysics::getNumCdrSpecies ( ) const

inline

Return number of CDR solvers.

Returns: Num cdr species

◆ getNumItoSpecies()

int ItoKMCPhysics::getNumItoSpecies ( ) const

inline

Return number of Ito solvers.

Returns: Num ito species

◆ getNumPhotonSpecies()

int ItoKMCPhysics::getNumPhotonSpecies ( ) const

inline

Return number of RTE solvers.

Returns: Num photon species

◆ getNumPlasmaSpecies()

int ItoKMCPhysics::getNumPlasmaSpecies ( ) const

inline

Return total number of plasma species.

Returns: Num plasma species

◆ getPlotVariableNames()

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

virtualnoexcept

Get plot variable names.

Returns: Vector of variable name strings for extra diagnostic quantities.

Reimplemented in Physics::ItoKMC::ItoKMCJSON.

◆ 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

Returns: Plot variables

Reimplemented in Physics::ItoKMC::ItoKMCJSON.

◆ getRtSpecies()

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

inline

Get all photon species.

Returns: m_rtSpecies

◆ getSpeciesMap()

const std::map< int, std::pair< SpeciesType, int > > & ItoKMCPhysics::getSpeciesMap ( ) const

inlinenoexcept

Get the internal mapping from plasma-species index to solver type and solver index.

Returns: Map from plasma species index to (SpeciesType, solver index) pair.

◆ 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

Returns: Return value

◆ isotropicDiffusion()

RealVect ItoKMCPhysics::isotropicDiffusion	(	const ItoParticle &	a_particle,
		const Real	a_dt
	)		const

inlineprotectednoexcept

Isotropic diffusion function for a particle.

This is the stochastic hop alone; it carries no drift. In particular it does not contain the grad(D) correction that makes the Ito update transport v*n - D*grad(n) rather than v*n - grad(D*n) – that term is deterministic and is added to the particle displacement by the time stepper.

Parameters

[in]	a_particle	Particle to diffuse
[in]	a_dt	Time step

Returns: Returns sqrt(2 * D * a_dt) * N(0,1), where N(0,1) is a normal distribution

◆ needGradient()

bool ItoKMCPhysics::needGradient ( const int a_plasmaIndex ) const

inlinevirtualnoexcept

Return true if the physics model reads the density gradient of one particular plasma species.

Refinement of needGradients(), which answers the same question for the whole model at once. Computing a gradient costs a cross-realm copy, a coarsening and a ghost interpolation over the whole AMR hierarchy, per species – so a model that consults one species' gradient pays for every species' unless it can say which one it meant.

The default is the conservative answer: whatever needGradients() says, for every species. A model that knows better should override this; one that does not keeps working unchanged.

Parameters

[in] a_plasmaIndex Plasma species index, in the ordering used by updateReactionRates()'s density argument: the Ito species first, then the CDR species.

Returns: True if this species' gradient must be computed.

Reimplemented in Physics::ItoKMC::ItoKMCJSON.

◆ needGradients()

bool ItoKMCPhysics::needGradients ( ) const

virtualnoexcept

Return true if the physics model requires species density gradients.

Returns: True if density gradients must be computed and passed to updateReactionRates().

Reimplemented in Physics::ItoKMC::ItoKMCJSON.

◆ noDiffusion()

RealVect ItoKMCPhysics::noDiffusion	(	const ItoParticle &	a_particle,
		const Real	a_dt
	)		const

inlineprotectednoexcept

No diffusion function for a particle.

Parameters

[in]	a_particle	Particle to diffuse
[in]	a_dt	Time step

Returns: Returns the zero vector.

◆ parseRuntimeOptions()

void ItoKMCPhysics::parseRuntimeOptions ( )

inlinevirtualnoexcept

Parse run-time options.

Reimplemented in Physics::ItoKMC::ItoKMCJSON.

◆ reconcileCdrParticles()

void ItoKMCPhysics::reconcileCdrParticles	(	Vector< ParticleSoA< NoPayload > * > &	a_cdrParticles,
		const Vector< ParticleSoA< ItoParticle > * > &	a_itoParticles,
		const Vector< long long > &	a_numNewParticles,
		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

inlinenoexcept

Turn the CDR mass created by the reaction network into particles.

Emitting the production as particles lets the stepper deposit it with the Ito solvers' deposition, so both halves of a reaction reach the mesh the same way. The production is partitioned into at most m_maxNewParticles computational particles of integer weight, exactly as the Ito products are.

Note: Only production is handled here. Mass removed from a CDR species carries no sub-cell information, so the stepper subtracts it in the cell it was taken from.; ParticlePlacement::Parent does not apply to these particles – a CDR product has no parents in the cell, its container holding only what the current step created – and falls back to a uniformly random position.

Parameters

[in,out]	a_cdrParticles	Particle products placed in the CDR solvers.
[in]	a_itoParticles	Ito particles in the cell, used by ParticlePlacement::Downstream.
[in]	a_numNewParticles	Number of physical particles produced per CDR species. Must be >= 0.
[in]	a_electricField	Electric field in cell
[in]	a_cellPos	Cell center position
[in]	a_centroidPos	Cell centroid position
[in]	a_lo	Lower corner of the valid region of the cell, in unit coordinates
[in]	a_hi	Upper corner of the valid region of the cell, in unit coordinates
[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

◆ reconcileParticles()

void ItoKMCPhysics::reconcileParticles	(	Vector< ParticleSoA< 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

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_electricField	Electric field in cell
[in]	a_cellPos	Cell center position
[in]	a_centroidPos	Cell centroid position
[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

Parameters

[in]	a_lo	Lo
[in]	a_hi	Hi

◆ reconcilePhotoionization()

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

inlinenoexcept

Reconcile photoionization reactions.

Parameters

[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.

Parameters

[in] a_itoParticles Ito particles

◆ reconcilePhotons()

void ItoKMCPhysics::reconcilePhotons	(	Vector< ParticleSoA< 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_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

Parameters

[in]	a_lo	Lo
[in]	a_hi	Hi

◆ removeParticles()

void ItoKMCPhysics::removeParticles	(	ParticleSoA< 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

◆ sampleParentPosition()

bool ItoKMCPhysics::sampleParentPosition	(	RealVect &	a_pos,
		const ParticleSoA< ItoParticle > &	a_particles,
		const std::vector< Real > &	a_cumulativeWeights
	)		const

inlineprotectednoexcept

Draw the position of a parent particle, with probability proportional to particle weight.

Used by ParticlePlacement::Parent. The caller passes the running weight sum, built by buildParentWeights(), so that a draw is a binary search rather than another walk over the cell's particles.

Parameters

[out]	a_pos	Position of the drawn parent.
[in]	a_particles	Candidate parents.
[in]	a_cumulativeWeights	Running weight sum of the eligible leading entries of a_particles.

Returns: True if a parent was drawn, false if there was nothing to draw from.

◆ secondaryEmissionEB()

virtual void Physics::ItoKMC::ItoKMCPhysics::secondaryEmissionEB	(	Vector< ParticleSoA< ItoParticle > > &	a_secondaryParticles,
		Vector< Real > &	a_cdrFluxes,
		Vector< ParticleSoA< Photon > > &	a_secondaryPhotons,
		const Vector< ParticleSoA< ItoParticle > > &	a_primaryParticles,
		const Vector< Real > &	a_cdrFluxesExtrap,
		const Vector< ParticleSoA< 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_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).
[in]	a_E	E

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_dt,
		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_dt	Time step
[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_downstreamSpecies

int Physics::ItoKMC::ItoKMCPhysics::m_downstreamSpecies

protected

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

This is used by the particle reconciliation routine when only placing secondary particles in the downstream region of the primary particles.

◆ 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_kmcPropensityScratch

thread_local std::vector< Real > ItoKMCPhysics::m_kmcPropensityScratch

staticprotected

Propensity buffer used by the time step tail of advanceKMC.

Reused across the tail's probes so the propensities are not returned by value, which allocated once per probe, i.e. once per reaction per grid cell.

◆ m_kmcReactionsDt

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

staticprotected

The subset of m_kmcReactionsThreadLocal that takes part in the physics time step calculation.

Holds the same objects as m_kmcReactionsThreadLocal, not copies, so the per-cell rate updates written through that list are seen here. Built by defineKMC() from m_reactiveDtFactors; see the comment there for why the compaction leaves the computed time step unchanged.

◆ m_kmcReactionsThreadLocal

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

staticprotected

Thread-local copies of KMC reactions used in advanceReactionNetwork.

Set up via defineKMC() to ensure OpenMP thread safety; depopulated by killKMC().

◆ m_kmcStateScratch

thread_local KMCState ItoKMCPhysics::m_kmcStateScratch

staticprotected

Perturbed KMC state used by the time step tail of advanceKMC.

The tail probes each reaction by firing it to its critical number and re-evaluating the time step on the result. It needs a state to perturb without disturbing m_kmcState, and reuses this one so that the probe does not allocate once per reaction per grid cell.

◆ 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_parentWeightScratch

thread_local std::vector< Real > ItoKMCPhysics::m_parentWeightScratch

staticprotected

Running sum of the eligible parent weights in a grid cell, used by ParticlePlacement::Parent.

Built once per cell and species, so that each of the up to m_maxNewParticles draws is a binary search rather than another walk over the cell's particles. Thread-local for the same reason as m_weightScratch.

◆ 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

◆ m_weightScratch

thread_local std::vector< long long > ItoKMCPhysics::m_weightScratch

staticprotected

Reusable buffer for ParticleManagement::partitionParticleWeights.

Reconciliation calls that function once per grid cell per species, from inside an OpenMP region; the vector-returning form allocates every one of those calls. Thread-local because the cell loop is threaded, and never shrunk, so the allocation is paid once per thread rather than once per cell.

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

◆ ParticlePlacement

Member Function Documentation

◆ advanceKMC()

◆ buildParentWeights()

◆ computeAlpha()

◆ computeDiffusionCoefficients()

◆ computeEta()

◆ computeMobilities()

◆ computeUpstreamPosition()

◆ defineSpeciesMap()

◆ drawNewParticlePosition()

◆ forwardIsotropicDiffusion()

◆ getCdrSpecies()

◆ getItoDiffusionFunctions()

◆ getItoSpecies()

◆ getNeutralDensity()

◆ getNumberOfPlotVariables()

◆ getNumCdrSpecies()

◆ getNumItoSpecies()

◆ getNumPhotonSpecies()

◆ getNumPlasmaSpecies()

◆ getPlotVariableNames()

◆ getPlotVariables()

◆ getRtSpecies()

◆ getSpeciesMap()

◆ initialSigma()

◆ isotropicDiffusion()

◆ needGradient()

◆ needGradients()

◆ noDiffusion()

◆ parseRuntimeOptions()

◆ reconcileCdrParticles()

◆ reconcileParticles()

◆ reconcilePhotoionization()

◆ reconcilePhotons()

◆ removeParticles()

◆ sampleParentPosition()

◆ secondaryEmissionEB()

◆ updateReactionRates()

Member Data Documentation

◆ m_downstreamSpecies

◆ m_eps

◆ m_kmcPropensityScratch

◆ m_kmcReactionsDt

◆ m_kmcReactionsThreadLocal

◆ m_kmcStateScratch

◆ m_Ncrit

◆ m_NSSA

◆ m_parentWeightScratch

◆ m_photoPathways

◆ m_SSAlim

◆ m_weightScratch