Abstract CellTagger base class 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 ()
	Default constructor. Sets default realm and phase.

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

virtual void	computeTracers () const =0
	Compute tracer fields on the AMR hierarchy. Must be implemented by subclasses.

virtual void	parseOptions () override=0
	Parse class options from ParmParse. Must be implemented by subclasses.

virtual void	prePlot () const noexcept override
	Pre-plot hook. Computes tracer fields so they appear in plot output.

virtual void	preRegrid () noexcept override
	Pre-regrid hook. Clears tracer field storage before the grid changes.

virtual void	regrid () override final
	Regrid hook. Reallocates tracer field and gradient storage on the new mesh.

virtual bool	tagCells (EBAMRTags &a_tags) override final
	Flag cells for refinement and coarsening using the tracer-field approach.

virtual int	getNumberOfPlotVariables () const override final
	Return the number of plot variables (one per tracer field).

virtual Vector< std::string >	getPlotVariableNames () const override final
	Return the names of the tracer field plot variables.

virtual void	writePlotData (LevelData< EBCellFAB > &a_output, int &a_icomp, const std::string &a_outputRealm, const int a_level) const override final
	Write tracer field data into the output holder.

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)
	Flag cells for refinement within a single grid patch.

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)
	Flag cells for coarsening within a single grid patch.

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
	Decide whether a single cell should be coarsened. Must be implemented by subclasses.

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
	Decide whether a single cell should be refined. Must be implemented by subclasses.

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 on which tracer field storage is allocated.

phase::which_phase	m_phase
	Phase on which tracer field storage is allocated.

RefCountedPtr< CdrPlasmaPhysics >	m_physics
	Plasma kinetics interface.

RefCountedPtr< CdrPlasmaStepper >	m_timeStepper
	Time stepper providing access to solver data and electric field.

RefCountedPtr< AmrMesh >	m_amr
	AMR mesh for grid iteration, gradient computation, and interpolation.

RefCountedPtr< ComputationalGeometry >	m_computationalGeometry
	Computational geometry providing electrode and dielectric information.

int	m_numTracers
	Number of scalar tracer fields used for tagging decisions.

Vector< EBAMRCellData >	m_tracers
	Tracer fields on the AMR hierarchy. Allocated and filled by computeTracers().

Vector< EBAMRCellData >	m_gradTracers
	Gradients of the tracer fields on the AMR hierarchy.

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 CellTagger base class for the CDR plasma physics module.

This class provides subclasses with access to solver data and plasma physics through references to CdrPlasmaStepper, AmrMesh, CdrPlasmaPhysics, and ComputationalGeometry. It implements the CellTagger interface using a tracer-field approach: subclasses compute one or more scalar tracer fields via computeTracers(), and the base class then calls the per-cell refineCell() and coarsenCell() methods to determine which cells should be flagged.

Subclasses must implement computeTracers(), parseOptions(), refineCell(), and coarsenCell(). The number of tracer fields is controlled by setting m_numTracers in the subclass constructor.

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 the object in a usable state.

Parameters

[in]	a_physics	Plasma kinetics interface.
[in]	a_timeStepper	Time stepper providing solver data.
[in]	a_amr	AMR mesh for grid iteration and operators.
[in]	a_computationalGeometry	Computational geometry (electrodes and dielectrics).

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

Decide whether a single cell should be coarsened. Must be implemented by subclasses.

Parameters

[in]	a_pos	Cell centroid position.
[in]	a_time	Current simulation time.
[in]	a_dx	Grid cell spacing.
[in]	a_lvl	AMR level of this cell.
[in]	a_tracers	Tracer field values at this cell.
[in]	a_gradTracers	Gradient of tracer fields at this cell.

Returns: True if the cell should be coarsened.

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

Flag cells for coarsening within a single grid patch.

Parameters

[out]	a_coarsenedCells	Cells flagged for coarsening on this patch.
[in]	a_tracers	Tracer field data on this patch.
[in]	a_gradTracers	Gradient of tracer fields on this patch.
[in]	a_lvl	AMR level.
[in]	a_dit	Grid patch index.
[in]	a_box	Cell-centered box for this patch.
[in]	a_ebisbox	EB geometry information for this patch.
[in]	a_time	Current simulation time.
[in]	a_dx	Grid cell spacing.
[in]	a_probLo	Lower-left corner of the simulation domain.

◆ computeTracers()

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

pure virtual

Compute tracer fields on the AMR hierarchy. Must be implemented by subclasses.

Results are stored in m_tracers. The number of tracer fields must equal m_numTracers.

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. Leaves the object in a usable state.

Parameters

[in]	a_physics	Plasma kinetics interface.
[in]	a_timeStepper	Time stepper providing solver data.
[in]	a_amr	AMR mesh for grid iteration and operators.
[in]	a_computationalGeometry	Computational geometry.

◆ getNumberOfPlotVariables()

int CdrPlasmaTagger::getNumberOfPlotVariables ( ) const

finaloverridevirtual

Return the number of plot variables (one per tracer field).

Returns: Number of tracer fields (m_numTracers).

Reimplemented from CellTagger.

◆ getPlotVariableNames()

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

finaloverridevirtual

Return the names of the tracer field plot variables.

Returns: Vector of names of the form "Tracer field-i".

Reimplemented from CellTagger.

◆ parseOptions()

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

overridepure virtual

Parse class options from ParmParse. Must be implemented by subclasses.

Implements CellTagger.

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

◆ prePlot()

void CdrPlasmaTagger::prePlot ( ) const

overridevirtualnoexcept

Pre-plot hook. Computes tracer fields so they appear in plot output.

Reimplemented from CellTagger.

◆ preRegrid()

void CdrPlasmaTagger::preRegrid ( )

overridevirtualnoexcept

Pre-regrid hook. Clears tracer field storage before the grid changes.

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

Decide whether a single cell should be refined. Must be implemented by subclasses.

Parameters

[in]	a_pos	Cell centroid position.
[in]	a_time	Current simulation time.
[in]	a_dx	Grid cell spacing.
[in]	a_lvl	AMR level of this cell.
[in]	a_tracers	Tracer field values at this cell.
[in]	a_gradTracers	Gradient of tracer fields at this cell.

Returns: True if the cell should be refined.

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

Flag cells for refinement within a single grid patch.

Parameters

[out]	a_refinedCells	Cells flagged for refinement on this patch.
[in]	a_tracers	Tracer field data on this patch.
[in]	a_gradTracers	Gradient of tracer fields on this patch.
[in]	a_lvl	AMR level.
[in]	a_dit	Grid patch index.
[in]	a_box	Cell-centered box for this patch.
[in]	a_ebisbox	EB geometry information for this patch.
[in]	a_time	Current simulation time.
[in]	a_dx	Grid cell spacing.
[in]	a_probLo	Lower-left corner of the simulation domain.

◆ regrid()

void CdrPlasmaTagger::regrid ( )

finaloverridevirtual

Regrid hook. Reallocates tracer field and gradient storage on the new mesh.

Implements CellTagger.

◆ tagCells()

bool CdrPlasmaTagger::tagCells ( EBAMRTags & a_tags )

finaloverridevirtual

Flag cells for refinement and coarsening using the tracer-field approach.

Calls computeTracers(), then iterates over grid cells calling refineCell() and coarsenCell() on each. Returns true if the tag set changed on any MPI rank.

Parameters

[in,out] a_tags Cell tags across the AMR hierarchy.

Returns: True if any new tags were added or removed.

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 tracer field data into the output holder.

Parameters

[in,out]	a_output	Output data holder.
[in,out]	a_icomp	Starting component index; incremented on return.
[in]	a_outputRealm	Realm that owns a_output.
[in]	a_level	AMR level to write.

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()