Abstract Class which implements CellTagger for the CDR plasma physics module. More...

#include <CD_CdrPlasmaTagger.H>

Inheritance diagram for Physics::CdrPlasma::CdrPlasmaTagger:

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Collaboration diagram for Physics::CdrPlasma::CdrPlasmaTagger:

Public Member Functions
	CdrPlasmaTagger ()
	Weak constructor. Must subsequently call define.

	CdrPlasmaTagger (const RefCountedPtr< CdrPlasmaPhysics > &a_physics, const RefCountedPtr< CdrPlasmaStepper > &a_timeStepper, const RefCountedPtr< AmrMesh > &a_amr, const RefCountedPtr< ComputationalGeometry > &a_computationalGeometry)
	Full constructor. Leaves object in usable state.

virtual	~CdrPlasmaTagger ()
	Destructor.

void	define (const RefCountedPtr< CdrPlasmaPhysics > &a_physics, const RefCountedPtr< CdrPlasmaStepper > &a_timeStepper, const RefCountedPtr< AmrMesh > &a_amr, const RefCountedPtr< ComputationalGeometry > &a_computationalGeometry)
	Define function constructor. Leaves object in usable state.

virtual void	computeTracers () const =0
	Compute tracer fields.

virtual void	parseOptions () override=0
	Parse class options – must be implemented by user.

virtual void	prePlot () const noexcept override
	Pre-plot magic for Driver.

virtual void	preRegrid () noexcept override
	Perform pre-regrid operations.

virtual void	regrid () override final
	Regrid method – used for reallocating storage for the tracer fields.

virtual bool	tagCells (EBAMRTags &a_tags) override final
	Tag cells for refinement.

virtual int	getNumberOfPlotVariables () const override final
	Get number of plot variables. This is fetched by Driver and can be used.

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

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

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

virtual	~CellTagger ()
	Destructor (does nothing).

virtual void	parseRuntimeOptions ()
	Parse runtime class options.

virtual int	getBuffer () const
	Get tag buffer.

Protected Member Functions
virtual void	refineCellsBox (DenseIntVectSet &a_refinedCells, const Vector< EBCellFAB * > &a_tracers, const Vector< EBCellFAB * > &a_gradTracers, 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)
	Per-box refinement method.

virtual void	coarsenCellsBox (DenseIntVectSet &a_coarsenedCells, const Vector< EBCellFAB * > &a_tracers, const Vector< EBCellFAB * > &a_gradTracers, 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)
	Per-box coarsening method.

virtual bool	coarsenCell (const RealVect a_pos, const Real a_time, const Real a_dx, const int a_lvl, const Vector< Real > a_tracers, const Vector< RealVect > a_gradTracers) const =0
	Coarsen a cell based on a tracer field.

virtual bool	refineCell (const RealVect a_pos, const Real a_time, const Real a_dx, const int a_lvl, const Vector< Real > a_tracers, const Vector< RealVect > a_gradTracers) const =0
	Refine a cell based on a tracer field.

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
std::string	m_realm
	Realm where this cell tagger allocates its data.

phase::which_phase	m_phase
	Phase where this cell tagger allocates its data.

RefCountedPtr< CdrPlasmaPhysics >	m_physics
	Plasma physics.

RefCountedPtr< CdrPlasmaStepper >	m_timeStepper
	Time stepper.

RefCountedPtr< AmrMesh >	m_amr
	AmrMesh. Needed for computing tracer stuff.

RefCountedPtr< ComputationalGeometry >	m_computationalGeometry
	Computational geometry. Not needed but useful to have.

int	m_numTracers
	Number of tracer fields.

Vector< EBAMRCellData >	m_tracers
	Tracer fields.

Vector< EBAMRCellData >	m_gradTracers
	Gradient of tracer 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

Abstract Class which implements CellTagger for the CDR plasma physics module.

This class exposes a number of mesh data holders which can be used for flagging cells for refinement. It is only meant to be used as an interface, providing the user access to solver data and physics through the constructor. From that, users can fetch the necessary data from the solvers (or the physics class) and more easily use the data to flag cells for refinement and coarsening.

This class uses 'tracer fields' for flagging cells for refinement and coarsening. It is up to the user to compute these fields by implementing the routine CdrPlasmaTagger::computeTracerFields. These fields can then be used in the other routines CdrPlasmaTagger::refineCell and CdrPlasmaTagger::coarsenCell

Constructor & Destructor Documentation

◆ CdrPlasmaTagger()

CdrPlasmaTagger::CdrPlasmaTagger	(	const RefCountedPtr< CdrPlasmaPhysics > &	a_physics,
		const RefCountedPtr< CdrPlasmaStepper > &	a_timeStepper,
		const RefCountedPtr< AmrMesh > &	a_amr,
		const RefCountedPtr< ComputationalGeometry > &	a_computationalGeometry
	)

Full constructor. Leaves object in usable state.

Parameters

[in]	a_physics	Reference to CdrPlasmaPhysics.
[in]	a_timeStepper	Reference to the TimeStepper being used.
[in]	a_amr	Reference to AmrMesh.
[in]	a_computationalGeometry	Computational geometry

Member Function Documentation

◆ coarsenCell()

virtual bool Physics::CdrPlasma::CdrPlasmaTagger::coarsenCell	(	const RealVect	a_pos,
		const Real	a_time,
		const Real	a_dx,
		const int	a_lvl,
		const Vector< Real >	a_tracers,
		const Vector< RealVect >	a_gradTracers
	)		const

protectedpure virtual

Coarsen a cell based on a tracer field.

Parameters

[in]	a_pos	Physical position
[in]	a_time	Current time
[in]	a_dx	Grid resolution
[in]	a_lvl	Grid level
[in]	a_tracers	Tracer fields
[in]	a_gradTracers	Gradient of tracer fields

Returns: Return true if the cell should be coarsened and false otherwise.

Implemented in Physics::CdrPlasma::CdrPlasmaStreamerTagger, and Physics::CdrPlasma::CdrPlasmaFieldTagger.

◆ coarsenCellsBox()

void CdrPlasmaTagger::coarsenCellsBox	(	DenseIntVectSet &	a_coarsenedCells,
		const Vector< EBCellFAB * > &	a_tracers,
		const Vector< EBCellFAB * > &	a_gradTracers,
		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
	)

protectedvirtual

Per-box coarsening method.

Iterates through all cells and check if they need coarsening.

Parameters

[out]	a_coarsenedCells	Cells flagged for coarsening.
[in]	a_tracers	Tracer fields on this grid patch.
[in]	a_gradTracers	Gradient of tracer fields on this grid patch.
[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 simulation domain.

◆ computeTracers()

virtual void Physics::CdrPlasma::CdrPlasmaTagger::computeTracers ( ) const

pure virtual

Compute tracer fields.

This should fill m_tracers – user must implement it.

Implemented in Physics::CdrPlasma::CdrPlasmaFieldTagger.

◆ define()

void CdrPlasmaTagger::define	(	const RefCountedPtr< CdrPlasmaPhysics > &	a_physics,
		const RefCountedPtr< CdrPlasmaStepper > &	a_timeStepper,
		const RefCountedPtr< AmrMesh > &	a_amr,
		const RefCountedPtr< ComputationalGeometry > &	a_computationalGeometry
	)

Define function constructor. Leaves object in usable state.

Parameters

[in]	a_physics	Reference to CdrPlasmaPhysics.
[in]	a_timeStepper	Reference to the TimeStepper being used.
[in]	a_amr	Reference to AmrMesh.
[in]	a_computationalGeometry	Computational geometry

◆ getNumberOfPlotVariables()

int CdrPlasmaTagger::getNumberOfPlotVariables ( ) const

finaloverridevirtual

Get number of plot variables. This is fetched by Driver and can be used.

Reimplemented from CellTagger.

◆ getPlotVariableNames()

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

finaloverridevirtual

Get plot variable names.

Reimplemented from CellTagger.

◆ parseOptions()

virtual void Physics::CdrPlasma::CdrPlasmaTagger::parseOptions ( )

overridepure virtual

Parse class options – must be implemented by user.

Implements CellTagger.

Implemented in Physics::CdrPlasma::CdrPlasmaStreamerTagger, and Physics::CdrPlasma::CdrPlasmaFieldTagger.

◆ prePlot()

void CdrPlasmaTagger::prePlot ( ) const

overridevirtualnoexcept

Pre-plot magic for Driver.

Reimplemented from CellTagger.

◆ preRegrid()

void CdrPlasmaTagger::preRegrid ( )

overridevirtualnoexcept

Perform pre-regrid operations.

Reimplemented from CellTagger.

◆ refineCell()

virtual bool Physics::CdrPlasma::CdrPlasmaTagger::refineCell	(	const RealVect	a_pos,
		const Real	a_time,
		const Real	a_dx,
		const int	a_lvl,
		const Vector< Real >	a_tracers,
		const Vector< RealVect >	a_gradTracers
	)		const

protectedpure virtual

Refine a cell based on a tracer field.

Parameters

[in]	a_pos	Physical position
[in]	a_time	Current time
[in]	a_dx	Grid resolution
[in]	a_lvl	Grid level
[in]	a_tracers	Tracer fields
[in]	a_gradTracers	Gradient of tracer fields

Returns: True if the cell should be refined and false otherwise.

Implemented in Physics::CdrPlasma::CdrPlasmaStreamerTagger, and Physics::CdrPlasma::CdrPlasmaFieldTagger.

◆ refineCellsBox()

void CdrPlasmaTagger::refineCellsBox	(	DenseIntVectSet &	a_refinedCells,
		const Vector< EBCellFAB * > &	a_tracers,
		const Vector< EBCellFAB * > &	a_gradTracers,
		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
	)

protectedvirtual

Per-box refinement method.

Iterates through all cells and check if they need refinement.

Parameters

[out]	a_refinedCells	Cells flagged for refinement
[in]	a_tracers	Tracer fields on this grid patch.
[in]	a_gradTracers	Gradient of tracer fields on this grid patch.
[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 simulation domain.

◆ regrid()

void CdrPlasmaTagger::regrid ( )

finaloverridevirtual

Regrid method – used for reallocating storage for the tracer fields.

Implements CellTagger.

◆ tagCells()

bool CdrPlasmaTagger::tagCells ( EBAMRTags & a_tags )

finaloverridevirtual

Tag cells for refinement.

Parameters

[in,out] a_tags Tags on grid levels

EBAMRTags is a data-type Vector<RefCountedPtr<LayoutData<DenseIntVectSet> > >. The vector indicates the grid level, the LayoutData indicates data ownership (in much the same way as LevelData. The DenseIntVectSet is essentially an IntVectSet restricted to the patch (i.e. one cannot add IntVects that are outside the patch). This function cells for refinement or coarsening. The user's responsibility is to add (or remove) tags from a_tags.

Implements CellTagger.

◆ writePlotData()

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

finaloverridevirtual

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. πaram[in] a_outputRealm Realm where a_output lives
[in]	a_level	Grid level

Reimplemented from CellTagger.

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

Physics/CdrPlasma/CD_CdrPlasmaTagger.H
Physics/CdrPlasma/CD_CdrPlasmaTagger.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CdrPlasmaTagger()

Member Function Documentation

◆ coarsenCell()

◆ coarsenCellsBox()

◆ computeTracers()

◆ define()

◆ getNumberOfPlotVariables()

◆ getPlotVariableNames()

◆ parseOptions()

◆ prePlot()

◆ preRegrid()

◆ refineCell()

◆ refineCellsBox()

◆ regrid()

◆ tagCells()

◆ writePlotData()