Abstract CellTagger for the Ito-KMC-Poisson physics module. More...

#include <CD_ItoKMCTagger.H>

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

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

Public Member Functions
	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	computeTagFields () const noexcept=0
	Compute tagging fields.

virtual void	parseOptions () override=0
	Parse class options.

virtual void	parseRuntimeOptions () override=0
	Parse run-time configurable class options.

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 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.

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=0
	Determine if a particular cell should be coarsened or not.

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=0
	Determine if a particular cell should be refined or not.

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
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::ItoKMCTagger< S >

Abstract CellTagger for the Ito-KMC-Poisson physics module.

The template parameter S is the concrete ItoKMCStepper type. Subclasses implement computeTagFields(), refineCell(), and coarsenCell() to define the refinement criterion. Tag fields are computed on the Primal realm and live on the phase set by setPhase().

Constructor & Destructor Documentation

◆ ItoKMCTagger()

template<typename S >

ItoKMCTagger::ItoKMCTagger	(	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 >

virtual bool Physics::ItoKMC::ItoKMCTagger< S >::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

protectedpure virtualnoexcept

Determine if a particular cell should be coarsened or not.

Parameters

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

Returns: Return value

Implemented in Physics::ItoKMC::ItoKMCStreamerTagger< S >, and Physics::ItoKMC::ItoKMCFieldTagger< S >.

◆ computeTagFields()

template<typename S >

virtual void Physics::ItoKMC::ItoKMCTagger< S >::computeTagFields ( ) const

pure virtualnoexcept

Compute tagging fields.

Implemented in Physics::ItoKMC::ItoKMCFieldTagger< S >.

◆ define()

template<typename S >

void ItoKMCTagger::define	(	const RefCountedPtr< ItoKMCPhysics > &	a_physics,
		const RefCountedPtr< S > &	a_timeStepper,
		const RefCountedPtr< AmrMesh > &	a_amr
	)

virtualnoexcept

Define function.

Parameters

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

◆ getNumberOfPlotVariables()

template<typename S >

int ItoKMCTagger::getNumberOfPlotVariables ( ) const

overridevirtualnoexcept

Get number of plot variables that will be written to file (by Driver).

Returns: Returns number of plot variables that Driver will write to plot files.

Reimplemented from CellTagger.

◆ getPlotVariableNames()

template<typename S >

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

overridevirtualnoexcept

Get plot variable names.

Returns: Vector of variable name strings for the tag fields.

Reimplemented from CellTagger.

◆ getTagFields()

template<typename S >

Vector< EBAMRCellData > & ItoKMCTagger::getTagFields ( )

virtualnoexcept

Get the tagging fields (mutable reference).

Returns: Reference to the vector of cell-centred tagging fields on the Primal realm.

◆ parseOptions()

template<typename S >

virtual void Physics::ItoKMC::ItoKMCTagger< S >::parseOptions ( )

overridepure virtual

Parse class options.

Implements CellTagger.

Implemented in Physics::ItoKMC::ItoKMCStreamerTagger< S >, and Physics::ItoKMC::ItoKMCFieldTagger< S >.

◆ parseRuntimeOptions()

template<typename S >

virtual void Physics::ItoKMC::ItoKMCTagger< S >::parseRuntimeOptions ( )

overridepure virtual

Parse run-time configurable class options.

Reimplemented from CellTagger.

Implemented in Physics::ItoKMC::ItoKMCStreamerTagger< S >, and Physics::ItoKMC::ItoKMCFieldTagger< S >.

◆ refineCell()

template<typename S >

virtual bool Physics::ItoKMC::ItoKMCTagger< S >::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

protectedpure virtualnoexcept

Determine if a particular cell should be refined or not.

Parameters

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

Returns: Return value

Implemented in Physics::ItoKMC::ItoKMCStreamerTagger< S >, and Physics::ItoKMC::ItoKMCFieldTagger< S >.

◆ regrid()

template<typename S >

void ItoKMCTagger::regrid ( )

overridevirtualnoexcept

Regrid this class. Note that there is no preRegrid method.

Implements CellTagger.

◆ setPhase()

template<typename S >

void ItoKMCTagger::setPhase ( const phase::which_phase a_phase )

virtualnoexcept

Set the phase where we do the tagging.

Parameters

[in] a_phase Phase

◆ tagCells()

template<typename S >

bool ItoKMCTagger::tagCells ( EBAMRTags & a_tags )

overridevirtualnoexcept

Tag cells for refinement and coarsening.

Parameters

[in,out] a_tags Cell tags that become the new grids.

Returns: Return value

Implements CellTagger.

◆ tagCellsBox()

template<typename S >

void ItoKMCTagger::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

protectedvirtualnoexcept

Per-box refinement tagging routine.

Parameters

[out]	a_refinedCells	Cells to be refined
[out]	a_coarsenedCells	Cells to be coarsened
[in]	a_tagFields	Tagging fields
[in]	a_gradTagFields	Gradient of tagging fields
[in]	a_lvl	Grid level
[in]	a_dit	Grid index
[in]	a_box	Cell-centered box
[in]	a_ebisbox	EBIS box
[in]	a_time	Current time
[in]	a_dx	Grid resolution
[in]	a_probLo	Lower-left corner of physical domain

◆ writePlotData()

template<typename S >

void ItoKMCTagger::writePlotData	(	LevelData< EBCellFAB > &	a_output,
		int &	a_icomp,
		const std::string &	a_outputRealm,
		const int	a_level
	)		const

overridevirtualnoexcept

Write plot data.

Parameters

[in,out]	a_output	Output data holder
[in,out]	a_icomp	Starting variable in a_output where we begin appending data.
[in]	a_level	Grid level
[in]	a_outputRealm	Description

Reimplemented from CellTagger.

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

Physics/ItoKMC/CD_ItoKMCTagger.H
Physics/ItoKMC/CD_ItoKMCTaggerImplem.H

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ItoKMCTagger()

Member Function Documentation

◆ coarsenCell()

◆ computeTagFields()

◆ define()

◆ getNumberOfPlotVariables()

◆ getPlotVariableNames()

◆ getTagFields()

◆ parseOptions()

◆ parseRuntimeOptions()

◆ refineCell()

◆ regrid()

◆ setPhase()

◆ tagCells()

◆ tagCellsBox()

◆ writePlotData()