CellTagger for the ItoKMC module that refines on the ionization coefficient and field curvature. More...

#include <CD_ItoKMCStreamerTagger.H>

Inheritance diagram for Physics::ItoKMC::ItoKMCStreamerTagger< S >:

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Collaboration diagram for Physics::ItoKMC::ItoKMCStreamerTagger< S >:

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Public Member Functions
	ItoKMCStreamerTagger () noexcept
	Constructor. Must subsequently call the define function.

	ItoKMCStreamerTagger (const RefCountedPtr< ItoKMCPhysics > &a_physics, const RefCountedPtr< S > &a_timeStepper, const RefCountedPtr< AmrMesh > &a_amr) noexcept
	Full constructor.

virtual	~ItoKMCStreamerTagger () noexcept
	Destructor.

virtual void	parseOptions () noexcept override
	Parse class options.

virtual void	parseRuntimeOptions () noexcept override
	Parse runtime-configurable class options.

Public Member Functions inherited from Physics::ItoKMC::ItoKMCFieldTagger< S >
	ItoKMCFieldTagger () noexcept
	Weak constructor. User MUST subsequently call define.

virtual	~ItoKMCFieldTagger () noexcept
	Destructor.

virtual void	computeTagFields () const noexcept override
	Compute tagging fields.

Public Member Functions inherited from Physics::ItoKMC::ItoKMCTagger< S >
	ItoKMCTagger ()
	Weak constructor. User MUST subsequently call the define function.

	ItoKMCTagger (const RefCountedPtr< ItoKMCPhysics > &a_physics, const RefCountedPtr< S > &a_timeStepper, const RefCountedPtr< AmrMesh > &a_amr) noexcept
	Full constructor.

virtual	~ItoKMCTagger () noexcept
	Destructor.

virtual void	define (const RefCountedPtr< ItoKMCPhysics > &a_physics, const RefCountedPtr< S > &a_timeStepper, const RefCountedPtr< AmrMesh > &a_amr) noexcept
	Define function.

virtual int	getNumberOfPlotVariables () const noexcept override
	Get number of plot variables that will be written to file (by Driver).

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

virtual void	writePlotData (LevelData< EBCellFAB > &a_output, int &a_icomp, const std::string &a_outputRealm, const int a_level) const noexcept override
	Write plot data.

virtual void	regrid () noexcept override
	Regrid this class. Note that there is no preRegrid method.

virtual bool	tagCells (EBAMRTags &a_tags) noexcept override
	Tag cells for refinement and coarsening.

virtual void	setPhase (const phase::which_phase a_phase) noexcept
	Set the phase where we do the tagging.

virtual Vector< EBAMRCellData > &	getTagFields () noexcept
	Get the tagging fields (mutable reference).

Public Member Functions inherited from CellTagger
	CellTagger ()
	Weak constructor (does nothing)

virtual	~CellTagger ()
	Destructor (does nothing).

virtual void	preRegrid () noexcept
	Pre-regrid function for cell-tagger.

virtual void	prePlot () const noexcept
	Perform pre-plotting operations (if necessary)

virtual int	getBuffer () const
	Get tag buffer.

Protected Member Functions
virtual Vector< Real >	computeTagFields (const RealVect &a_pos, const Real a_time, const Real a_dx, const RealVect &a_E, const Real a_minE, const Real a_maxE, const RealVect &a_gradE, const Real a_minGradE, const Real a_maxGradE) const noexcept override
	Compute per-cell tagging fields from the electric field and its gradient.

virtual bool	coarsenCell (const RealVect &a_pos, const Real a_time, const Real a_dx, const int a_lvl, const Vector< Real > &a_tagFields, const Vector< RealVect > &a_gradTagFields) const noexcept override
	Determine if a particular cell should be coarsened.

virtual bool	refineCell (const RealVect &a_pos, const Real a_time, const Real a_dx, const int a_lvl, const Vector< Real > &a_tagFields, const Vector< RealVect > &a_gradTagFields) const noexcept override
	Determine if a particular cell should be refined.

Protected Member Functions inherited from Physics::ItoKMC::ItoKMCFieldTagger< S >
virtual void	allocateStorage () const noexcept
	Allocate memory for scratch, electric field, and gradient of electric field.

virtual void	deallocateStorage () const noexcept
	Deallocate memory.

virtual void	computeElectricField (EBAMRCellData &a_E, EBAMRCellData &a_gradE) const noexcept
	Compute the electric field and its gradient magnitude.

Protected Member Functions inherited from Physics::ItoKMC::ItoKMCTagger< S >
virtual void	tagCellsBox (DenseIntVectSet &a_refinedCells, DenseIntVectSet &a_coarsenedCells, const Vector< EBCellFAB * > &a_tagFields, const Vector< EBCellFAB * > &a_gradTagFields, const int a_lvl, const DataIndex a_dit, const Box a_box, const EBISBox &a_ebisbox, const Real a_time, const Real a_dx, const RealVect a_probLo) const noexcept
	Per-box refinement tagging routine.

Protected Member Functions inherited from CellTagger
bool	insideTagBox (const RealVect &a_pos) const
	Check if a point is inside a tagging box.

int	getManualRefinementLevel (const RealVect &a_pos) const
	Get the specified level for this position when doing manual refinement.

virtual void	parseTagBoxes ()
	Parse boxes.

virtual void	parseRefinementBoxes ()
	Parse refinement boxes.

virtual void	parseBuffer ()
	Parse refinement buffer.

virtual void	parseVerbosity ()
	Parse the verbosity from the input file or command line.

Protected Attributes
Real	m_coarsenCurvature
	Threshold for coarsening based on curvature.

Real	m_refineCurvature
	Threshold for refinement based on curvature.

Real	m_refineAlpha
	Threshold for ionization refinement.

Real	m_coarsenAlpha
	Threshold for ionization coarsening.

int	m_maxCoarsenLevel
	Set coarsening level.

Protected Attributes inherited from Physics::ItoKMC::ItoKMCFieldTagger< S >
EBAMRCellData	m_scratch
	Scratch storage.

EBAMRCellData	m_E
	Storage for the electric field E.

EBAMRCellData	m_gradE
	Storage for grad(\|E\|)

Protected Attributes inherited from Physics::ItoKMC::ItoKMCTagger< S >
bool	m_isDefined
	Defined or not.

bool	m_plotData
	Plot data or not.

std::string	m_realm
	Realm where data is allocated.

phase::which_phase	m_phase
	Phase where data is allocated.

RefCountedPtr< ItoKMCPhysics >	m_physics
	Physics implementation.

RefCountedPtr< S >	m_timeStepper
	Time stepper.

RefCountedPtr< AmrMesh >	m_amr
	AmrMesh. Needed for allocating memory and things like that.

int	m_numTagFields
	Number of tagging fields.

Vector< EBAMRCellData >	m_tagFields
	Tagging fields.

Vector< EBAMRCellData >	m_gradTagFields
	Gradient of tagging fields.

Protected Attributes inherited from CellTagger
std::string	m_name
	Cell tagger class name (default is CellTagger).

int	m_verbosity
	Class verbosity.

int	m_buffer
	Tag buffer. Grow tags by this amount (finest level only)

Vector< RealBox >	m_tagBoxes
	Boxes that can be used to restrict tagging.

std::vector< std::pair< RealBox, int > >	m_refBoxes
	Refinement boxes for adding manual refinement.

Detailed Description

template<typename S>
class Physics::ItoKMC::ItoKMCStreamerTagger< S >

CellTagger for the ItoKMC module that refines on the ionization coefficient and field curvature.

Refinement is triggered when \( \alpha \cdot \Delta x \) exceeds a user-specified threshold or when the normalised curvature of |E| exceeds another threshold. Coarsening uses the same fields with separate (lower) thresholds.

Constructor & Destructor Documentation

◆ ItoKMCStreamerTagger()

template<typename S >

ItoKMCStreamerTagger::ItoKMCStreamerTagger	(	const RefCountedPtr< ItoKMCPhysics > &	a_physics,
		const RefCountedPtr< S > &	a_timeStepper,
		const RefCountedPtr< AmrMesh > &	a_amr
	)

noexcept

Full constructor.

Parameters

[in]	a_physics	Physics implementation.
[in]	a_timeStepper	Time integrator.
[in]	a_amr	Reference to AmrMesh

Member Function Documentation

◆ coarsenCell()

template<typename S >

bool ItoKMCStreamerTagger::coarsenCell	(	const RealVect &	a_pos,
		const Real	a_time,
		const Real	a_dx,
		const int	a_lvl,
		const Vector< Real > &	a_tagFields,
		const Vector< RealVect > &	a_gradTagFields
	)		const

overrideprotectedvirtualnoexcept

Determine if a particular cell should be coarsened.

Parameters

[in]	a_pos	Physical position.
[in]	a_time	Current simulation time.
[in]	a_dx	Grid resolution.
[in]	a_lvl	Grid level.
[in]	a_tagFields	Cell tagging field values.
[in]	a_gradTagFields	Gradient of cell tagging fields.

Returns: True if the cell should be coarsened.

Implements Physics::ItoKMC::ItoKMCFieldTagger< S >.

◆ computeTagFields()

template<typename S >

Vector< Real > ItoKMCStreamerTagger::computeTagFields	(	const RealVect &	a_pos,
		const Real	a_time,
		const Real	a_dx,
		const RealVect &	a_E,
		const Real	a_minE,
		const Real	a_maxE,
		const RealVect &	a_gradE,
		const Real	a_minGradE,
		const Real	a_maxGradE
	)		const

overrideprotectedvirtualnoexcept

Compute per-cell tagging fields from the electric field and its gradient.

Parameters

[in]	a_pos	Physical coordinates.
[in]	a_time	Current simulation time.
[in]	a_dx	Grid resolution.
[in]	a_E	Electric field vector at this cell.
[in]	a_minE	Minimum \|E\| over the domain.
[in]	a_maxE	Maximum \|E\| over the domain.
[in]	a_gradE	grad(\|E\|) at this cell.
[in]	a_minGradE	Minimum \|grad(\|E\|)\| over the domain.
[in]	a_maxGradE	Maximum \|grad(\|E\|)\| over the domain.

Returns: Per-cell tagging fields [normalised curvature, normalised alpha*dx].

Implements Physics::ItoKMC::ItoKMCFieldTagger< S >.

◆ parseOptions()

template<typename S >

void ItoKMCStreamerTagger::parseOptions ( )

overridevirtualnoexcept

Parse class options.

Implements Physics::ItoKMC::ItoKMCFieldTagger< S >.

◆ parseRuntimeOptions()

template<typename S >

void ItoKMCStreamerTagger::parseRuntimeOptions ( )

overridevirtualnoexcept

Parse runtime-configurable class options.

Implements Physics::ItoKMC::ItoKMCFieldTagger< S >.

◆ refineCell()

template<typename S >

bool ItoKMCStreamerTagger::refineCell	(	const RealVect &	a_pos,
		const Real	a_time,
		const Real	a_dx,
		const int	a_lvl,
		const Vector< Real > &	a_tagFields,
		const Vector< RealVect > &	a_gradTagFields
	)		const

overrideprotectedvirtualnoexcept

Determine if a particular cell should be refined.

Parameters

[in]	a_pos	Physical position.
[in]	a_time	Current simulation time.
[in]	a_dx	Grid resolution.
[in]	a_lvl	Grid level.
[in]	a_tagFields	Cell tagging field values.
[in]	a_gradTagFields	Gradient of cell tagging fields.

Returns: True if the cell should be refined.

Implements Physics::ItoKMC::ItoKMCFieldTagger< S >.

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

Physics/ItoKMC/CellTaggers/ItoKMCStreamerTagger/CD_ItoKMCStreamerTagger.H
Physics/ItoKMC/CellTaggers/ItoKMCStreamerTagger/CD_ItoKMCStreamerTaggerImplem.H

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ItoKMCStreamerTagger()

Member Function Documentation

◆ coarsenCell()

◆ computeTagFields()

◆ parseOptions()

◆ parseRuntimeOptions()

◆ refineCell()