Base class for solving convection-diffusion-reaction equations. More...

#include <CD_CdrSolver.H>

Inheritance diagram for CdrSolver:

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Collaboration diagram for CdrSolver:

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Public Member Functions
	CdrSolver ()
	Default constructor. More...

	CdrSolver (const CdrSolver &a_other)=delete
	Disallowed copy constructor. More...

	CdrSolver (const CdrSolver &&a_other)=delete
	Disallowed move constructor. More...

CdrSolver &	operator= (const CdrSolver &a_other)=delete
	Disallowed assignment operator. More...

CdrSolver &	operator= (const CdrSolver &&a_other)=delete
	Disallowed move assignement operator. More...

virtual	~CdrSolver ()
	Constructor.

virtual void	parseOptions ()=0
	Parse class options.

virtual void	parseRuntimeOptions ()=0
	Parse runtime options.

void	setDefaultDomainBC ()
	This sets default boundary conditions (wall type). More...

void	setDomainBcType (const CdrDomainBC::DomainSide a_domainSide, const CdrDomainBC::BcType a_bcType)
	Set domain bc type on domain side. More...

void	setDomainBcFunction (const CdrDomainBC::DomainSide a_domainSide, const CdrDomainBC::FluxFunction a_fluxFunction)
	Set domain bc function on particular domain side. More...

virtual void	advanceEuler (EBAMRCellData &a_newPhi, const EBAMRCellData &a_oldPhi, const Real a_dt)
	Implicit diffusion Euler advance without source term. More...

virtual void	advanceEuler (EBAMRCellData &a_newPhi, const EBAMRCellData &a_oldPhi, const EBAMRCellData &a_source, const Real a_dt)=0
	Implicit diffusion Euler advance with source term. More...

virtual void	advanceCrankNicholson (EBAMRCellData &a_newPhi, const EBAMRCellData &a_oldPhi, const Real a_dt)
	Implicit diffusion Crank-Nicholson advance without source term. More...

virtual void	advanceCrankNicholson (EBAMRCellData &a_newPhi, const EBAMRCellData &a_oldPhi, const EBAMRCellData &a_source, const Real a_dt)=0
	Implicit diffusion Crank-Nicholson advance with source term. More...

virtual void	computeDivJ (EBAMRCellData &a_divJ, EBAMRCellData &a_phi, const Real a_extrapDt, const bool a_conservativeOnly, const bool a_ebFlux, const bool a_domainFlux)=0
	Compute div(J) explicitly, where J = nV - D*grad(n) More...

virtual void	computeDivF (EBAMRCellData &a_divF, EBAMRCellData &a_phi, const Real a_extrapDt, const bool a_conservativeOnly, const bool a_ebFlux, const bool a_domainFlux)=0
	Compute div(v*phi) explicitly. More...

virtual void	computeDivD (EBAMRCellData &a_divD, EBAMRCellData &a_phi, const bool a_conservativeOnly, const bool a_ebFlux, const bool a_domainFlux)=0
	Compute div(D*grad(phi)) explicitly. More...

virtual void	computeDivG (EBAMRCellData &a_divG, EBAMRFluxData &a_G, const EBAMRIVData &a_ebFlux, const bool a_conservativeOnly)
	Compute div(G) where G is a general face-centered flux on face centers and EB centers. This can involve mass redistribution. More...

virtual void	gwnDiffusionSource (EBAMRCellData &a_noiseSource, const EBAMRCellData &a_cellPhi)
	Compute a random gaussian white noise source term. More...

virtual void	averageVelocityToFaces ()
	Average velocities to faces. More...

virtual void	preRegrid (const int a_lbase, const int a_oldFinestLevel)
	Perform pre-regrid operations. More...

virtual void	deallocate ()
	Deallocate internal storage. More...

virtual void	registerOperators ()
	Register operators for AMR operations. More...

virtual void	setRealm (const std::string a_realm)
	Set the realm for this solver. More...

virtual RefCountedPtr< CdrSpecies > &	getSpecies () noexcept
	Get the CDR species.

virtual const RefCountedPtr< CdrSpecies > &	getSpecies () const noexcept
	Get the CDR species.

virtual void	setSpecies (const RefCountedPtr< CdrSpecies > &a_species)
	Set species. More...

virtual void	setComputationalGeometry (const RefCountedPtr< ComputationalGeometry > &a_computationalGeometry)
	Set computational geometry. More...

virtual void	setAmr (const RefCountedPtr< AmrMesh > &a_amr)
	Set the amr object. More...

virtual void	setPhase (phase::which_phase a_phase)
	Set phase. More...

virtual void	setVerbosity (const int a_verbosity)
	Set verbosity. More...

virtual void	setTime (const int a_step, const Real a_time, const Real a_dt)
	Set the time for this solver. More...

virtual void	setVelocity (const EBAMRCellData &a_velocity)
	Set velocity from data holder. More...

virtual void	setVelocity (const RealVect a_velocity)
	Set constant velocity. More...

virtual void	setVelocity (const std::function< RealVect(const RealVect a_pos)> &a_velocity)
	Set velocity using a polymorphic function. More...

virtual void	setDiffusionCoefficient (const EBAMRFluxData &a_diffusionCoefficient, const EBAMRIVData &a_ebDiffusionCoefficient)
	Data-based version of setting diffusion coefficients (which are stored on faces) More...

virtual void	setDiffusionCoefficient (const Real a_diffusionCoefficient)
	Set diffusion coefficient to be constant everywhere (they are stored on faces) More...

virtual void	setDiffusionCoefficient (const std::function< Real(const RealVect a_position)> &a_diffusionCoefficient)
	Polymorphic way of setting diffusion coefficients every. More...

virtual void	setSource (const EBAMRCellData &a_source)
	Data based version of setting source terms. More...

virtual void	setSource (const Real a_source)
	Set constant source terms everywhere. More...

virtual void	setSource (const std::function< Real(const RealVect a_position)> a_source)
	Polymorphic way of setting source terms. More...

virtual void	setEbFlux (const EBAMRIVData &a_ebFlux)
	Data-based version of setting the EB flux. More...

virtual void	setEbFlux (const Real a_ebFlux)
	Set the eb flux to a constant. More...

virtual void	initialData ()
	Fill m_phi state with initial data from m_species. More...

virtual void	allocate ()
	Allocate internal storage. More...

virtual void	writePlotFile ()
	Write plot file. More...

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

virtual void	regrid (const int a_lmin, const int a_oldFinestLevel, const int a_newFinestLevel)
	Write checkpoint data into HDF5 file. @paramo[out] a_handle HDF5 file. More...

virtual std::string	getRealm () const
	Get the realm where this solver is registered. More...

virtual std::string	getName () const
	Get solver name. More...

virtual Vector< std::string >	getPlotVariableNames () const
	Get output plot names. More...

virtual int	getNumberOfPlotVariables () const
	Get number of output fields. More...

virtual Real	computeAdvectionDt ()
	Compute the largest possible diffusive time step (for explicit methods) More...

virtual Real	computeDiffusionDt ()
	Compute the largest possible diffusive time step (for explicit methods) More...

virtual Real	computeAdvectionDiffusionDt ()
	Compute the largest possible diffusive time step (for explicit methods) More...

virtual Real	computeSourceDt (const Real a_max, const Real a_tolerance)
	Compute the largest possible source time step (for explicit methods. More...

virtual void	weightedUpwind (EBAMRCellData &a_weightedUpwindPhi, const int a_pow)
	Compute an upwind-weighted version of phi. More...

virtual Real	computeMass ()
	Compute the "physical mass" in m_phi. More...

virtual Real	computeMass (const EBAMRCellData &a_phi, const bool a_kappaScale=true)
	Compute the "physical mass" in the input argument. More...

virtual Real	computeCharge ()
	Compute the total charge in m_phi. More...

virtual bool	isDiffusive ()
	Return true if the solver is diffusive and false otherwise.

virtual bool	isMobile ()
	Return true if the solver is mobile and false otherwise.

virtual EBAMRCellData &	getPhi ()
	Get the cell-centered phi. More...

virtual EBAMRCellData &	getSource ()
	Get the source term. More...

virtual EBAMRCellData &	getCellCenteredVelocity ()
	Get the cell-centered velocity. More...

virtual EBAMRFluxData &	getFaceCenteredVelocity ()
	Get the face-centered velocities. More...

virtual EBAMRIVData &	getEbCenteredVelocity ()
	Get the eb-centered velocities. More...

virtual EBAMRCellData &	getCellCenteredDiffusionCoefficient ()
	Get the cell-centered diffusion coefficient.

virtual EBAMRFluxData &	getFaceCenteredDiffusionCoefficient ()
	Get the face-centered diffusion coefficient. More...

virtual EBAMRIVData &	getEbCenteredDiffusionCoefficient ()
	Get the EB-centered diffusion coefficient. More...

virtual EBAMRIVData &	getEbFlux ()
	Get the eb flux data holder. More...

virtual EBAMRIFData &	getDomainFlux ()
	Get the domain flux data holder. More...

virtual void	extrapolateAdvectiveFluxToEB () noexcept
	Extrapolate advective flux to EB. More...

virtual void	extrapolateAdvectiveFluxToEB (EBAMRIVData &a_ebFlux) const noexcept
	Extrapolate advective flux to EB. More...

virtual void	redistribute (EBAMRCellData &a_phi, const EBAMRIVData &a_delta) const noexcept
	Add data through redistribution into cell-centered holders. More...

Protected Types
enum class	Redistribution { VolumeWeighted , None }
	Redistribution method.

Protected Member Functions
virtual void	averageVelocityToFaces (EBAMRFluxData &a_faceVelocity, const EBAMRCellData &a_cellVelocity)
	Average cell-centered velocities to face centers. More...

virtual void	advectToFaces (EBAMRFluxData &a_facePhi, const EBAMRCellData &a_phi, const Real a_extrapDt)=0
	Advection-only extrapolation to faces. More...

virtual void	computeAdvectionFlux (EBAMRFluxData &a_flux, const EBAMRFluxData &a_facePhi, const EBAMRFluxData &a_faceVelocity, const bool a_addDomainFlux=true)
	Set up face-centered advection flux. More...

virtual void	computeAdvectionFlux (LevelData< EBFluxFAB > &a_flux, const LevelData< EBFluxFAB > &a_facePhi, const LevelData< EBFluxFAB > &a_faceVelocity, const int a_lvl)
	Set up face-centered advection flux on a grid level. More...

virtual void	computeDiffusionFlux (EBAMRFluxData &a_flux, const EBAMRCellData &a_phi, const bool a_addDomainFlux)
	Compute the face-centered diffusion flux. More...

virtual void	computeDiffusionFlux (LevelData< EBFluxFAB > &a_flux, const LevelData< EBCellFAB > &a_phi, const int a_lvl)
	Compute the face-centered diffusion flux. More...

virtual void	computeAdvectionDiffusionFlux (EBAMRFluxData &a_flux, const EBAMRCellData &a_cellStates, const EBAMRFluxData &a_faceStates, const EBAMRFluxData &a_faceVelocities, const EBAMRFluxData &a_faceDiffCo, const bool a_addDomainFlux)
	Compute the full advection-diffusion flux. This assumes that the solver is mobile and diffusive. More...

virtual void	resetDomainFlux (EBAMRFluxData &a_flux)
	Set flux to zero on domain boundaries. More...

virtual void	fillDomainFlux (EBAMRFluxData &a_flux)
	Set domain in data holder. This sets the flux on the boundary to either zero or to m_domainFlux. More...

virtual void	fillDomainFlux (LevelData< EBFluxFAB > &a_flux, const int a_level)
	Set domain in data holder. This sets the flux on the boundary to either zero or to m_domainFlux. More...

virtual void	conservativeDivergenceNoKappaDivision (EBAMRCellData &a_conservativeDivergence, EBAMRFluxData &a_flux, const EBAMRIVData &a_ebFlux)
	Compute conservative divergence from fluxes. More...

virtual void	nonConservativeDivergence (EBAMRIVData &a_nonConservativeDivergence, const EBAMRCellData &a_divG)
	Compute the non-conservative divergence. More...

virtual void	hybridDivergence (EBAMRCellData &a_hybridDivergence, EBAMRIVData &a_massDifference, const EBAMRIVData &a_nonConservativeDivergence)
	Use the non-conservative divergence to make the conservative divergence hold the hybrid divergence. More...

virtual void	hybridDivergence (LevelData< EBCellFAB > &a_hybridDivergence, LevelData< BaseIVFAB< Real >> &a_massDifference, const LevelData< BaseIVFAB< Real >> &a_nonConservativeDivergence, const int a_lvl)
	Make the hybrid divergence. On the way in, a_hybridDivergence must hold the conservative divergence. More...

virtual void	conservativeDivergenceRegular (LevelData< EBCellFAB > &a_divJ, const LevelData< EBFluxFAB > &a_flux, const int a_lvl)
	Compute the conservative divergence over regular cells. More...

virtual void	interpolateFluxToFaceCentroids (EBAMRFluxData &a_flux)
	Interpolate flux to centroids. More...

virtual void	interpolateFluxToFaceCentroids (LevelData< EBFluxFAB > &a_flux, const int a_lvl)
	Interpolate flux to centroids. More...

virtual void	computeDivergenceIrregular (LevelData< EBCellFAB > &a_divG, const LevelData< EBFluxFAB > &a_centroidFluxes, const LevelData< BaseIVFAB< Real >> &a_ebFlux, const int a_lvl)
	Compute conservative divergence on irregular cells (not kappa divided) More...

virtual void	initialDataDistribution ()
	Fill initial data from a distribution function. More...

virtual void	initialDataParticles ()
	Fill initial data from particles. More...

virtual void	defineInterpolationStencils ()
	Define stencils for doing face-centered to face-centroid-centered states. More...

virtual void	parseDomainBc ()
	Parses domain BC options.

virtual void	parsePlotVariables ()
	Parses plot variables.

virtual void	parsePlotMode ()
	Parse plot mode.

virtual void	parseDivergenceComputation ()
	Parse the conservation.

virtual void	parseRegridSlopes ()
	Parse slope regrid.

virtual std::string	makeBcString (const int a_dir, const Side::LoHiSide a_side) const
	Shortcut for making a boundary condition string. More...

virtual void	fillGwn (EBAMRFluxData &a_noise, const Real a_sigma)
	Gaussian noise field. More...

virtual void	smoothHeavisideFaces (EBAMRFluxData &a_facePhi, const EBAMRCellData &a_cellPhi)
	Use Heaviside smoothing for computing face-centered states. More...

virtual void	writeData (LevelData< EBCellFAB > &a_output, int &a_comp, const EBAMRCellData &a_data, const std::string a_outputRealm, const int a_level, const bool a_interpToCentroids, const bool a_interpGhost) const noexcept
	Write data to output. Convenience function. More...

Protected Attributes
RefCountedPtr< CdrSpecies >	m_species
	Species through which e.g. mobility/diffusion and initial conditions is passed.

RefCountedPtr< ComputationalGeometry >	m_computationalGeometry
	Computational geometry.

RefCountedPtr< AmrMesh >	m_amr
	AMR; needed for grid stuff.

Vector< RefCountedPtr< LayoutData< BaseIFFAB< FaceStencil > > > >	m_interpStencils [SpaceDim]
	Stencils for interpolating face-centered fluxes to face centroids.

phase::which_phase	m_phase
	Phase.

std::string	m_name
	Solver name.

std::string	m_className
	Class name. More...

std::string	m_realm
	Realm where this solver is registered.

CdrDomainBC	m_domainBC
	Domain BCs.

EBAMRCellData	m_phi
	Cell-centered data (i.e. the advected-diffused quantity)

EBAMRCellData	m_source
	Source term.

EBAMRCellData	m_cellVelocity
	Cell-centered velocities. More...

EBAMRFluxData	m_faceStates
	Holder for face centered states. More...

EBAMRFluxData	m_faceVelocity
	Face-centered velocities (only normal components) More...

EBAMRIVData	m_nonConservativeDivG
	Scratch storage for the non-conservative divergence.

EBAMRIVData	m_massDifference
	Scratch storage for the mass difference.

EBAMRIVData	m_ebZero
	Scratch storage for the EB flux.

EBAMRCellData	m_cachePhi
	Cached state vector for regrid.

EBAMRCellData	m_cacheSource
	Cached source term for regrids.

EBAMRIVData	m_ebVelocity
	EB-centered velocities.

EBAMRIVData	m_ebFlux
	Flux through the embedded boundary.

EBAMRIFData	m_domainFlux
	Domain flux.

EBAMRCellData	m_cellCenteredDiffusionCoefficient
	Diffusion coefficients on cell centers. More...

EBAMRFluxData	m_faceCenteredDiffusionCoefficient
	Diffusion coefficients on face centers. More...

EBAMRIVData	m_ebCenteredDiffusionCoefficient
	Diffusion coefficients on EB faces. More...

std::map< CdrDomainBC::DomainSide, CdrDomainBC::FluxFunction >	m_domainFluxFunctions
	Domain flux functions. More...

int	m_verbosity
	Solver verbosity. More...

int	m_timeStep
	Time step.

Real	m_time
	Current time.

Real	m_dt
	Last time step increment.

Redistribution	m_whichRedistribution
	Which type of redistribution to use.

bool	m_blendConservation
	Flag for blending the hybrid divergence.

bool	m_isDiffusive
	Is the solver diffusive or not.

bool	m_isMobile
	Solve for advection/convection or not.

bool	m_plotPhi
	If true, m_phi is added to plot files.

bool	m_plotVelocity
	Output velocities.

bool	m_plotDiffusionCoefficient
	Output diffusion coefficients.

bool	m_plotEbFlux
	Output EB fluxes.

bool	m_plotSource
	Output source term.

bool	m_plotNumbers
	Plot numbers or densities.

bool	m_regridSlopes
	Use slopes when regridding.

int	m_seed
	RNG seed.

Static Protected Attributes
static constexpr int	m_comp = 0
	Component number in data holder.

static constexpr int	m_nComp = 1
	Number of components that this solver solves for.

Detailed Description

Base class for solving convection-diffusion-reaction equations.

On embedded boundaries, users must always set the flux directly (but possibly via a function, if desired).

On domain edges/faces, the user can select between various ways of setting the domain boundary conditions (e.g. wall, data-based, function-based, outflow).

Constructor & Destructor Documentation

◆ CdrSolver() [1/3]

CdrSolver::CdrSolver ( )

Default constructor.

Note: This sets the realm to primal and populates the domain flux functions (with zero-fluxes, i.e. wall BCs)

◆ CdrSolver() [2/3]

CdrSolver::CdrSolver ( const CdrSolver & a_other )

delete

Disallowed copy constructor.

Parameters

[in] a_other Other solver

◆ CdrSolver() [3/3]

CdrSolver::CdrSolver ( const CdrSolver && a_other )

delete

Disallowed move constructor.

Parameters

[in] a_other Other solver

Member Function Documentation

◆ advanceCrankNicholson() [1/2]

virtual void CdrSolver::advanceCrankNicholson	(	EBAMRCellData &	a_newPhi,
		const EBAMRCellData &	a_oldPhi,
		const EBAMRCellData &	a_source,
		const Real	a_dt
	)

pure virtual

Implicit diffusion Crank-Nicholson advance with source term.

Parameters

[in,out]	a_newPhi	Solution at time t + dt
[in]	a_oldPhi	Solution at time t
[in]	a_source	Source term.
[in]	a_dt	Time step

Implemented in CdrMultigrid.

◆ advanceCrankNicholson() [2/2]

void CdrSolver::advanceCrankNicholson	(	EBAMRCellData &	a_newPhi,
		const EBAMRCellData &	a_oldPhi,
		const Real	a_dt
	)

virtual

Implicit diffusion Crank-Nicholson advance without source term.

Parameters

[in,out]	a_newPhi	Solution at time t + dt
[in]	a_oldPhi	Solution at time t
[in]	a_dt	Time step

Note: This calls the other version with a zero source term.

◆ advanceEuler() [1/2]

virtual void CdrSolver::advanceEuler	(	EBAMRCellData &	a_newPhi,
		const EBAMRCellData &	a_oldPhi,
		const EBAMRCellData &	a_source,
		const Real	a_dt
	)

pure virtual

Implicit diffusion Euler advance with source term.

Parameters

[in,out]	a_newPhi	Solution at time t + dt
[in]	a_oldPhi	Solution at time t
[in]	a_source	Source term.
[in]	a_dt	Time step

Note: For purely implicit Euler the source term should be centered at t+dt (otherwise it's an implicit-explicit method)

This solves the implicit diffusion equation equation a_newPhi - a_oldPhi = dt*Laplacian(a_newPhi) + dt*a_source.

Implemented in CdrMultigrid.

◆ advanceEuler() [2/2]

void CdrSolver::advanceEuler	(	EBAMRCellData &	a_newPhi,
		const EBAMRCellData &	a_oldPhi,
		const Real	a_dt
	)

virtual

Implicit diffusion Euler advance without source term.

Parameters

[in,out]	a_newPhi	Solution at time t + dt
[in]	a_oldPhi	Solution at time t
[in]	a_dt	Time step

Note: This calls the other version with a zero source term.

◆ advectToFaces()

virtual void CdrSolver::advectToFaces	(	EBAMRFluxData &	a_facePhi,
		const EBAMRCellData &	a_phi,
		const Real	a_extrapDt
	)

protectedpure virtual

Advection-only extrapolation to faces.

Parameters

[out]	a_facePhi	Phi on faces
[in]	a_phi	Phi on cell center
[in]	a_extrapDt	Time centering/extrapolation (if the advective integrator can do it)

Implemented in CdrMultigrid, CdrGodunov, and CdrCTU.

◆ allocate()

void CdrSolver::allocate ( )

virtual

Allocate internal storage.

Note: This allocates a bunch of storage – if the solver is not diffusive or mobile then we do our best to trim memory.

Reimplemented in CdrMultigrid, and CdrGodunov.

◆ averageVelocityToFaces() [1/2]

void CdrSolver::averageVelocityToFaces ( )

virtual

Average velocities to faces.

Note: This takes the cell-centered velocities in m_cellVelocity and averages them onto m_faceVelocity. Only the velocity component normal to the face is stored in m_faceVelocity.

◆ averageVelocityToFaces() [2/2]

void CdrSolver::averageVelocityToFaces	(	EBAMRFluxData &	a_faceVelocity,
		const EBAMRCellData &	a_cellVelocity
	)

protectedvirtual

Average cell-centered velocities to face centers.

Parameters

[out]	a_faceVelocity	Face-centered velocities
[in]	a_cellVelocity	Cell-centered velocities

Note: This sets the velocity component normal to the face to be the arithmetic average of the cell center velocities on the low/high side of the face.; Virtual because some solvers might want to do this differently.

◆ computeAdvectionDiffusionDt()

Real CdrSolver::computeAdvectionDiffusionDt ( )

virtual

Compute the largest possible diffusive time step (for explicit methods)

This computes dt = 1/[ dx/(|vx|+|vy|+|vz|) + (dx*dx)/(2*D*d) ] and minimizes the result over all grid levels and patches.

Note: This is the appropriate time step routine for explicit advection-diffusion solvers.

◆ computeAdvectionDiffusionFlux()

void CdrSolver::computeAdvectionDiffusionFlux	(	EBAMRFluxData &	a_flux,
		const EBAMRCellData &	a_cellStates,
		const EBAMRFluxData &	a_faceStates,
		const EBAMRFluxData &	a_faceVelocities,
		const EBAMRFluxData &	a_faceDiffCo,
		const bool	a_addDomainFlux
	)

protectedvirtual

Compute the full advection-diffusion flux. This assumes that the solver is mobile and diffusive.

Parameters

[out]	a_flux	Face-centered flux.
[in]	a_cellStates	Cell-centered states.
[in]	a_faceVelocities	Face-centered velocities.
[in]	a_faceStates	Face-centered (advected) states.
[in]	a_faceDiffCo	Face-centered diffusion coefficients.
[in]	a_addDomainFlux	Add domain flux or not.

◆ computeAdvectionDt()

Real CdrSolver::computeAdvectionDt ( )

virtual

Compute the largest possible diffusive time step (for explicit methods)

This computes dt = dx/sum(|vx| + |vy| + |vz|), minimized over all grid levels and patches.

Note: This is the appropriate time step routine for explicit advection solvers.

Reimplemented in CdrGodunov, and CdrCTU.

◆ computeAdvectionFlux() [1/2]

void CdrSolver::computeAdvectionFlux	(	EBAMRFluxData &	a_flux,
		const EBAMRFluxData &	a_facePhi,
		const EBAMRFluxData &	a_faceVelocity,
		const bool	a_addDomainFlux = `true`
	)

protectedvirtual

Set up face-centered advection flux.

Parameters

[out]	a_flux	Face-centered fluxes
[in]	a_facePhi	Face-centered state
[in]	a_faceVelocity	Face-centered velocities
[in]	a_addDomainFlux	Add the domain flux

Note: This computes flux = phi*vel on all face centers. If a_addDomainFlux is true, we enforce BC fluxes on the domain sides. Otherwise, the flux on the domain sides is set to zero.

◆ computeAdvectionFlux() [2/2]

void CdrSolver::computeAdvectionFlux	(	LevelData< EBFluxFAB > &	a_flux,
		const LevelData< EBFluxFAB > &	a_facePhi,
		const LevelData< EBFluxFAB > &	a_faceVelocity,
		const int	a_lvl
	)

protectedvirtual

Set up face-centered advection flux on a grid level.

Parameters

[out]	a_flux	Face-centered fluxes
[in]	a_facePhi	Face-centered state
[in]	a_faceVelocity	Face-centered velocities
[in]	a_domainFlux	Domain flux
[in]	a_level	Grid level

Note: This computes flux = v*phi on all face centers. If a_addDomainFlux is true, we enforce BC fluxes on the domain sides. Otherwise, the flux on the domain sides is set to zero.

◆ computeCharge()

Real CdrSolver::computeCharge ( )

virtual

Compute the total charge in m_phi.

Calls computeMass and multiplies by charge

◆ computeDiffusionDt()

Real CdrSolver::computeDiffusionDt ( )

virtual

Compute the largest possible diffusive time step (for explicit methods)

This computes dt = (dx*dx)/(2*D*d) where D is the diffusion coefficient. The result is minimized over all grid levels and patches.

Note: This is the appropriate time step routine for explicit diffusion solvers.

◆ computeDiffusionFlux() [1/2]

void CdrSolver::computeDiffusionFlux	(	EBAMRFluxData &	a_flux,
		const EBAMRCellData &	a_phi,
		const bool	a_addDomainFlux
	)

protectedvirtual

Compute the face-centered diffusion flux.

Parameters

[out]	a_flux	Face-centered flux
[in]	a_phi	Cell centered phi
[in]	a_addDomainFlux	Add domain flux or not

Note: This computes flux = D*grad(phi) on all face centers. If a_addDomainFlux is true, we enforce BC fluxes on the domain sides. Otherwise, the flux on the domain sides is set to zero.

◆ computeDiffusionFlux() [2/2]

void CdrSolver::computeDiffusionFlux	(	LevelData< EBFluxFAB > &	a_flux,
		const LevelData< EBCellFAB > &	a_phi,
		const int	a_lvl
	)

protectedvirtual

Compute the face-centered diffusion flux.

Parameters

[out]	a_flux	Face-centered flux
[in]	a_phi	Cell centered phi
[in]	a_lvl	Grid level

Note: This computes flux = D*grad(phi) on all face centers. The flux is set to zero on domain edges/faces

◆ computeDivD()

virtual void CdrSolver::computeDivD	(	EBAMRCellData &	a_divD,
		EBAMRCellData &	a_phi,
		const bool	a_conservativeOnly,
		const bool	a_ebFlux,
		const bool	a_domainFlux
	)

pure virtual

Compute div(D*grad(phi)) explicitly.

Parameters

[out]	a_divF	Divergence term, i.e. finite volume approximation to Div(D*Grad(phi)).
[in]	a_phi	Cell-centered state
[in]	a_domainBc	Flag for setting domain boundary conditions
[in]	a_conservativeOnly	If true, we compute div(D) = 1/dx*sum(fluxes), which does not involve redistribution.
[in]	a_useEbFlux	If true, the embedded boundary flux will be injected and included in div(D)
[in]	a_domainFlux	If true, the domain flux will injected and included in div(D)

Note: a_phi is non-const because ghost cells will be interpolated in this routine. Valid data in a_phi is not touched.

Implemented in CdrMultigrid.

◆ computeDivergenceIrregular()

void CdrSolver::computeDivergenceIrregular	(	LevelData< EBCellFAB > &	a_divG,
		const LevelData< EBFluxFAB > &	a_centroidFluxes,
		const LevelData< BaseIVFAB< Real >> &	a_ebFlux,
		const int	a_lvl
	)

protectedvirtual

Compute conservative divergence on irregular cells (not kappa divided)

Parameters

[out]	a_divG	Conservative divergence (not kappa divided)
[out]	a_centroidFlux	Face centroid centered fluxes
[in]	a_ebFlux	EB flux
[in]	a_lvl	Grid level

Note: This overwrites the result of divG in cut-cells, using the eb flux and face centroid fluxes to compute kappa*div(G) = sum(fluxes)/dx

◆ computeDivF()

virtual void CdrSolver::computeDivF	(	EBAMRCellData &	a_divF,
		EBAMRCellData &	a_phi,
		const Real	a_extrapDt,
		const bool	a_conservativeOnly,
		const bool	a_ebFlux,
		const bool	a_domainFlux
	)

pure virtual

Compute div(v*phi) explicitly.

Parameters

[out]	a_divF	Divergence term, i.e. finite volume approximation to Div(v*phi), including redistribution magic.
[in]	a_phi	Cell-centered state
[in]	a_extrapDt	Extrapolation in time, i.e. shifting of div(F) towards e.g. half time step. Only affects the advective term.
[in]	a_conservativeOnly	If true, we compute div(F)=1/dx*sum(fluxes), which does not involve redistribution.
[in]	a_domainBc	How to set domain fluxes
[in]	a_ebFlux	If true, the embedded boundary flux will injected be included in div(F)
[in]	a_domainFlux	If true, the domain flux will injected and included in div(F)

Note: a_phi is non-const because ghost cells will be interpolated in this routine. Valid data in a_phi is not touched.

Implemented in CdrMultigrid.

◆ computeDivG()

void CdrSolver::computeDivG	(	EBAMRCellData &	a_divG,
		EBAMRFluxData &	a_G,
		const EBAMRIVData &	a_ebFlux,
		const bool	a_conservativeOnly
	)

virtual

Compute div(G) where G is a general face-centered flux on face centers and EB centers. This can involve mass redistribution.

Parameters

[in]	a_divG	div(G) or kappa*div(G).
[in,out]	a_G	Vector field which contains face-centered fluxes on input. Contains face-centroid fluxes on output.
[in]	a_ebFlux	Flux on the EB centroids
[in]	a_conservativeOnly	If true, we compute div(G)=1/dx*sum(fluxes), which does not involve redistribution.

◆ computeDivJ()

virtual void CdrSolver::computeDivJ	(	EBAMRCellData &	a_divJ,
		EBAMRCellData &	a_phi,
		const Real	a_extrapDt,
		const bool	a_conservativeOnly,
		const bool	a_ebFlux,
		const bool	a_domainFlux
	)

pure virtual

Compute div(J) explicitly, where J = nV - D*grad(n)

Parameters

[out]	a_divJ	Divergence term, i.e. finite volume approximation to
[in]	a_phi	Cell-centered state
[in]	a_extrapDt	Extrapolation in time, i.e. shifting of div(J) towards e.g. half time step. Only affects the advective term.
[in]	a_conservativeOnly	If true, we compute div(J) = 1/dx*sum(fluxes), which does not involve redistribution.
[in]	a_ebFlux	If true, the embedded boundary flux will injected and included in div(J)
[in]	a_domainFlux	If true, the domain flux will injected and included in div(J)

Note: a_phi is non-const because ghost cells will be re-filled

Implemented in CdrMultigrid.

◆ computeMass() [1/2]

Real CdrSolver::computeMass ( )

virtual

Compute the "physical mass" in m_phi.

This conservatively coarsens the solution and computes on the coarsest level only

◆ computeMass() [2/2]

Real CdrSolver::computeMass	(	const EBAMRCellData &	a_phi,
		const bool	a_kappaScale = `true`
	)

virtual

Compute the "physical mass" in the input argument.

This conservatively coarsens the solution and computes on the coarsest level only

Parameters

[in]	a_phi	Cell-centered data.
[in]	a_kappaScale	Multiply by kappa in irregular cells.

◆ computeSourceDt()

Real CdrSolver::computeSourceDt	(	const Real	a_max,
		const Real	a_tolerance
	)

virtual

Compute the largest possible source time step (for explicit methods.

Parameters

[in]	a_max	Maximum value of m_phi
[in]	a_tolerance	Tolerance

This computes dt = phi/source, but only for cells where phi lies within a_tolerance*a_max (and source > 0)

Todo:: An old routine which we could (probably) remove.

◆ conservativeDivergenceNoKappaDivision()

void CdrSolver::conservativeDivergenceNoKappaDivision	(	EBAMRCellData &	a_conservativeDivergence,
		EBAMRFluxData &	a_flux,
		const EBAMRIVData &	a_ebFlux
	)

protectedvirtual

Compute conservative divergence from fluxes.

Parameters

[out]	a_conservativeDivergence	Conservative divergence computed as div(F) using finite volumes. Not divided by kappa.
[in]	a_flux	Face-centered fluxes. Includes domain fluxes.
[in]	a_ebFlux	EB flux.

Note: This computes the conservative divergence kappa*div(F) = sum(fluxes).

◆ conservativeDivergenceRegular()

void CdrSolver::conservativeDivergenceRegular	(	LevelData< EBCellFAB > &	a_divJ,
		const LevelData< EBFluxFAB > &	a_flux,
		const int	a_lvl
	)

protectedvirtual

Compute the conservative divergence over regular cells.

Parameters

[out]	a_divJ	Conservative divergence. Not kappa-divided.
[in]	a_flux	Face-centered fluxes
[in]	a_lvl	Grid level

Note: This computes the finite volume approximation to div(J) in regular cells – cut-cells (in a_divJ are set to zero)

◆ deallocate()

void CdrSolver::deallocate ( )

virtual

Deallocate internal storage.

Note: This deallocates a bunch of storage which is not needed (during regrids). It can be used to trim memory during Berger-Rigoutsous regrids (which EAT memory).

◆ defineInterpolationStencils()

void CdrSolver::defineInterpolationStencils ( )

protectedvirtual

Define stencils for doing face-centered to face-centroid-centered states.

Note: This computes standard finite-difference stencils for interpolating from face centers to face centroids.

◆ extrapolateAdvectiveFluxToEB() [1/2]

void CdrSolver::extrapolateAdvectiveFluxToEB ( )

virtualnoexcept

Extrapolate advective flux to EB.

This does not use any slope limiting (derived classes might want to redo this routine). The returned flux is equal to -n.(phi * v) where n is the normal vector pointing into the solution domain.

Note: Calls the other version with m_ebFlux as argument

◆ extrapolateAdvectiveFluxToEB() [2/2]

void CdrSolver::extrapolateAdvectiveFluxToEB ( EBAMRIVData & a_ebFlux ) const

virtualnoexcept

Extrapolate advective flux to EB.

This does not use any slope limiting (derived classes might want to redo this routine). The returned flux is equal to -n.(phi * v) where n is the normal vector pointing into the solution domain.

Parameters

[out] a_ebFlux Projected flux on the EB.

◆ fillDomainFlux() [1/2]

void CdrSolver::fillDomainFlux ( EBAMRFluxData & a_flux )

protectedvirtual

Set domain in data holder. This sets the flux on the boundary to either zero or to m_domainFlux.

Parameters

[in,out] a_flux Flux to be modified.

◆ fillDomainFlux() [2/2]

void CdrSolver::fillDomainFlux	(	LevelData< EBFluxFAB > &	a_flux,
		const int	a_level
	)

protectedvirtual

Set domain in data holder. This sets the flux on the boundary to either zero or to m_domainFlux.

Parameters

[in,out]	a_flux	Flux to be modified.
[in]	a_level	Grid level

◆ fillGwn()

void CdrSolver::fillGwn	(	EBAMRFluxData &	a_noise,
		const Real	a_sigma
	)

protectedvirtual

Gaussian noise field.

Parameters

[out]	a_noise	Gaussian white nosie
[out]	a_sigma	Standard deviation

◆ getCellCenteredVelocity()

EBAMRCellData & CdrSolver::getCellCenteredVelocity ( )

virtual

Get the cell-centered velocity.

Returns: m_cellVelocity

◆ getDomainFlux()

EBAMRIFData & CdrSolver::getDomainFlux ( )

virtual

Get the domain flux data holder.

Returns: m_domainFlux

◆ getEbCenteredDiffusionCoefficient()

EBAMRIVData & CdrSolver::getEbCenteredDiffusionCoefficient ( )

virtual

Get the EB-centered diffusion coefficient.

Returns: m_ebCentereDiffusionCoefficient

◆ getEbCenteredVelocity()

EBAMRIVData & CdrSolver::getEbCenteredVelocity ( )

virtual

Get the eb-centered velocities.

Returns: m_ebVelocity

◆ getEbFlux()

EBAMRIVData & CdrSolver::getEbFlux ( )

virtual

Get the eb flux data holder.

Returns: m_ebFlux

◆ getFaceCenteredDiffusionCoefficient()

EBAMRFluxData & CdrSolver::getFaceCenteredDiffusionCoefficient ( )

virtual

Get the face-centered diffusion coefficient.

Returns: m_faceCentereDiffusionCoefficient

◆ getFaceCenteredVelocity()

EBAMRFluxData & CdrSolver::getFaceCenteredVelocity ( )

virtual

Get the face-centered velocities.

Returns: m_faceVelocity

◆ getName()

std::string CdrSolver::getName ( ) const

virtual

Get solver name.

Note: Not necessarily equal to class name (we can have many CdrSolvers instantiated).

◆ getNumberOfPlotVariables()

int CdrSolver::getNumberOfPlotVariables ( ) const

virtual

Get number of output fields.

Returns: Returns number of plot variables include in writePlotFile() and writePlotData()

◆ getPhi()

EBAMRCellData & CdrSolver::getPhi ( )

virtual

Get the cell-centered phi.

Returns: m_phi

◆ getPlotVariableNames()

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

virtual

Get output plot names.

Returns: Return a list of plot variable names.

◆ getRealm()

std::string CdrSolver::getRealm ( ) const

virtual

Get the realm where this solver is registered.

Returns: Returns realm name.

◆ getSource()

EBAMRCellData & CdrSolver::getSource ( )

virtual

Get the source term.

Returns: m_source

◆ gwnDiffusionSource()

void CdrSolver::gwnDiffusionSource	(	EBAMRCellData &	a_noiseSource,
		const EBAMRCellData &	a_cellPhi
	)

virtual

Compute a random gaussian white noise source term.

Parameters

[out]	a_noiseSource	Source term
[in]	a_cellPhi	Cell-centered states

Note: Used e.g. for fluctuating hydrodynamics.

◆ hybridDivergence() [1/2]

void CdrSolver::hybridDivergence	(	EBAMRCellData &	a_hybridDivergence,
		EBAMRIVData &	a_massDifference,
		const EBAMRIVData &	a_nonConservativeDivergence
	)

protectedvirtual

Use the non-conservative divergence to make the conservative divergence hold the hybrid divergence.

Parameters

[in,out]	a_hybridDivergence	On input, contains the conservative divergence (without kappa division). Contains hybrid divergence on output.
[out]	a_massDifference	Mass difference between updating with hybrid divergence and true divergence
[in]	a_nonConservativeDivergence	Non-conservative divergence.

◆ hybridDivergence() [2/2]

void CdrSolver::hybridDivergence	(	LevelData< EBCellFAB > &	a_hybridDivergence,
		LevelData< BaseIVFAB< Real >> &	a_massDifference,
		const LevelData< BaseIVFAB< Real >> &	a_nonConservativeDivergence,
		const int	a_lvl
	)

protectedvirtual

Make the hybrid divergence. On the way in, a_hybridDivergence must hold the conservative divergence.

Parameters

[in,out]	a_hybridDivergence	On input, contains the conservative divergence (without kappa division). Contains hybrid divergence on output.
[out]	a_massDifference	Mass difference between updating with hybrid divergence and true divergence
[in]	a_nonConservativeDivergence	Non-conservative divergence.
[in]	a_lvl	Grid level.

◆ initialData()

void CdrSolver::initialData ( )

virtual

Fill m_phi state with initial data from m_species.

Note: This will call initialDataParticles() and initialDataFunction().

◆ initialDataDistribution()

void CdrSolver::initialDataDistribution ( )

protectedvirtual

Fill initial data from a distribution function.

Note: This increments m_phi on the mesh with data from m_species->initialData().

◆ initialDataParticles()

void CdrSolver::initialDataParticles ( )

protectedvirtual

Fill initial data from particles.

Note: This will set m_phi to zero before depositing the particles (which are deposited with an NGP scheme, ignoring modifactions near cut-cells)

◆ interpolateFluxToFaceCentroids() [1/2]

void CdrSolver::interpolateFluxToFaceCentroids ( EBAMRFluxData & a_flux )

protectedvirtual

Interpolate flux to centroids.

Parameters

[in,out] a_flux On input, contains centered fluxes. Output contains centroid fluxes

This interpolates face fluxes to centroids.

◆ interpolateFluxToFaceCentroids() [2/2]

void CdrSolver::interpolateFluxToFaceCentroids	(	LevelData< EBFluxFAB > &	a_flux,
		const int	a_lvl
	)

protectedvirtual

Interpolate flux to centroids.

Parameters

[in,out]	a_flux	On input, contains centered fluxes. Output contains centroid fluxes
[in]	a_lvl	Grid level

This interpolates face fluxes to centroids.

◆ makeBcString()

std::string CdrSolver::makeBcString	(	const int	a_dir,
		const Side::LoHiSide	a_side
	)		const

protectedvirtual

Shortcut for making a boundary condition string.

Parameters

[in]	a_dir	Direction.
[in]	a_side	Coordinate side.

Returns: Returns string of type m_className.bc.direction.side.

◆ nonConservativeDivergence()

void CdrSolver::nonConservativeDivergence	(	EBAMRIVData &	a_nonConservativeDivergence,
		const EBAMRCellData &	a_divG
	)

protectedvirtual

Compute the non-conservative divergence.

Parameters

[out]	a_nonConservativeDivergence	Non-conservative divergence.
[in]	a_divG	Conservative divergence.

Note: This will compute the non-conservative divergence as divNC(G) = sum(kappa*div(G))/sum(kappa) in the cut-cell neighborhood.

◆ operator=() [1/2]

CdrSolver& CdrSolver::operator= ( const CdrSolver && a_other )

delete

Disallowed move assignement operator.

Parameters

[in] a_other Other solver

◆ operator=() [2/2]

CdrSolver& CdrSolver::operator= ( const CdrSolver & a_other )

delete

Disallowed assignment operator.

Parameters

[in] a_other Other solver

◆ preRegrid()

void CdrSolver::preRegrid	(	const int	a_lbase,
		const int	a_oldFinestLevel
	)

virtual

Perform pre-regrid operations.

Parameters

[in]	a_lbase	Coarsest level that changed during regrid.
[in]	a_oldFinestLevel	Finest grid level before the regrid operation.

Note: This stores m_phi and m_source.

Reimplemented in CdrMultigrid.

◆ redistribute()

void CdrSolver::redistribute	(	EBAMRCellData &	a_phi,
		const EBAMRIVData &	a_delta
	)		const

virtualnoexcept

Add data through redistribution into cell-centered holders.

Parameters

[in,out]	a_phi	Target data
[in]	a_delta	Data to be redistributed

◆ registerOperators()

void CdrSolver::registerOperators ( )

virtual

Register operators for AMR operations.

Note: This includes operators for redistribution, flux registers, regridding, ghost cell interpolation, and conservative coarsening.

Reimplemented in CdrMultigrid.

◆ regrid()

void CdrSolver::regrid	(	const int	a_lmin,
		const int	a_oldFinestLevel,
		const int	a_newFinestLevel
	)

virtual

Write checkpoint data into HDF5 file. @paramo[out] a_handle HDF5 file.

Parameters

[in] a_level Grid level

Read checkpoint data from HDF5 file.

Parameters

[in]	a_handle	HDF5 handle.
[in]	const	int a_level Grid level

Regrid this solver.

Parameters

[in]	a_lmin	Coarsest level where grids did not change.
[in]	a_oldFinestLevel	Finest AMR level before the regrid.
[in]	a_newFinestLevel	Finest AMR level after the regrid.

This linearly interpolates (with limiters) m_state to the new grids. Velocities are left undefined.

◆ resetDomainFlux()

void CdrSolver::resetDomainFlux ( EBAMRFluxData & a_flux )

protectedvirtual

Set flux to zero on domain boundaries.

Parameters

[in] a_flux Flux data holder – on domain edges this is modified so the flux is zero.

◆ setAmr()

void CdrSolver::setAmr ( const RefCountedPtr< AmrMesh > & a_amr )

virtual

Set the amr object.

Parameters

[in] a_amr AmrMesh object.

◆ setComputationalGeometry()

void CdrSolver::setComputationalGeometry ( const RefCountedPtr< ComputationalGeometry > & a_computationalGeometry )

virtual

Set computational geometry.

Parameters

[in] a_computationalGeometry The computational geometry.

◆ setDefaultDomainBC()

void CdrSolver::setDefaultDomainBC ( )

This sets default boundary conditions (wall type).

Called in constructor for setting domain BCs.

Note: This sets the domain boundary condition to be a wall BC (no incoming/outgoing mass). This is the default behavior – if the user wants different BCs he can call setDomainBcType and setDomainBcFunction.

◆ setDiffusionCoefficient() [1/3]

void CdrSolver::setDiffusionCoefficient	(	const EBAMRFluxData &	a_diffusionCoefficient,
		const EBAMRIVData &	a_ebDiffusionCoefficient
	)

virtual

Data-based version of setting diffusion coefficients (which are stored on faces)

Parameters

[in]	a_diffusionCoefficient	Face-centered diffusion coefficient.
[in]	a_ebDiffusionCoefficient	EB-centered diffusion coefficient.

Note: Realms do not have to be the same.

◆ setDiffusionCoefficient() [2/3]

void CdrSolver::setDiffusionCoefficient ( const Real a_diffusionCoefficient )

virtual

Set diffusion coefficient to be constant everywhere (they are stored on faces)

Parameters

[in] a_diffusionCoefficient Global diffusion coefficient.

This sets the diffusion coefficient to be constant on both faces and EB faces.

◆ setDiffusionCoefficient() [3/3]

void CdrSolver::setDiffusionCoefficient ( const std::function< Real(const RealVect a_position)> & a_diffusionCoefficient )

virtual

Polymorphic way of setting diffusion coefficients every.

Parameters

[in] a_diffusionCoefficient Diffusion coefficient.

Note: This will evaluate the function in all grid cells and set the diffusion coefficient

◆ setDomainBcFunction()

void CdrSolver::setDomainBcFunction	(	const CdrDomainBC::DomainSide	a_domainSide,
		const CdrDomainBC::FluxFunction	a_fluxFunction
	)

Set domain bc function on particular domain side.

Parameters

[in]	a_domainSide	Domain side
[in]	a_fluxFunction	Flux function

Note: This only associates a function with a domain side – to use it one must also call setDomainBcType(a_domainSide, BcType::Function)

◆ setDomainBcType()

void CdrSolver::setDomainBcType	(	const CdrDomainBC::DomainSide	a_domainSide,
		const CdrDomainBC::BcType	a_bcType
	)

Set domain bc type on domain side.

Parameters

[in]	a_domainSide	Domain side
[in]	a_bcType	Boundary condition type

◆ setEbFlux() [1/2]

void CdrSolver::setEbFlux ( const EBAMRIVData & a_ebFlux )

virtual

Data-based version of setting the EB flux.

Parameters

[in] a_ebFlux Flux on EB centroids.

Note: a_ebFlux does not have to be the same realm as in the solver.

◆ setEbFlux() [2/2]

void CdrSolver::setEbFlux ( const Real a_ebFlux )

virtual

Set the eb flux to a constant.

Parameters

[in] a_ebFlux Flux on EB centroids.

This sets a constant EB-flux on all EBs.

◆ setPhase()

void CdrSolver::setPhase ( phase::which_phase a_phase )

virtual

Set phase.

Parameters

[in] a_phase Phase.

◆ setRealm()

void CdrSolver::setRealm ( const std::string a_realm )

virtual

Set the realm for this solver.

Parameters

[in] a_realm Realm identifier

◆ setSource() [1/3]

void CdrSolver::setSource ( const EBAMRCellData & a_source )

virtual

Data based version of setting source terms.

Parameters

[in] a_source Source term.

This sets m_source to be equal to a_source

◆ setSource() [2/3]

void CdrSolver::setSource ( const Real a_source )

virtual

Set constant source terms everywhere.

Parameters

[in] a_source Source term.

Note: This sets m_source to a_source everywhere

◆ setSource() [3/3]

void CdrSolver::setSource ( const std::function< Real(const RealVect a_position)> a_source )

virtual

Polymorphic way of setting source terms.

Parameters

[in] a_source Source term.

Note: This fills m_source with the evaluation of a_source

◆ setSpecies()

void CdrSolver::setSpecies ( const RefCountedPtr< CdrSpecies > & a_species )

virtual

Set species.

Parameters

[in] a_species Species (where this solver gets its name, charge, initial conditions etc).

◆ setTime()

void CdrSolver::setTime	(	const int	a_step,
		const Real	a_time,
		const Real	a_dt
	)

virtual

Set the time for this solver.

Parameters

[in]	a_step	Time step number
[in]	a_time	Time (in seconds)
[in]	a_dt	Time step increment

Note: This sets m_step=a_step, m_time=a_time, m_dt=a_dt

◆ setVelocity() [1/3]

void CdrSolver::setVelocity ( const EBAMRCellData & a_velocity )

virtual

Set velocity from data holder.

Parameters

[in] a_velocity Cell centered velocities.

This copies a_velo onto m_cellVelocity.

◆ setVelocity() [2/3]

void CdrSolver::setVelocity ( const RealVect a_velocity )

virtual

Set constant velocity.

Parameters

[in] a_velocity Velocity

This sets the cell centered velocity to be a_velo in every grid cell.

◆ setVelocity() [3/3]

void CdrSolver::setVelocity ( const std::function< RealVect(const RealVect a_pos)> & a_velocity )

virtual

Set velocity using a polymorphic function.

Parameters

[in] a_velocity Velocity to be set. You can use e.g. a lambda to set it.

◆ setVerbosity()

void CdrSolver::setVerbosity ( const int a_verbosity )

virtual

Set verbosity.

Parameters

[in] a_verbosity Verbosity level.

◆ smoothHeavisideFaces()

void CdrSolver::smoothHeavisideFaces	(	EBAMRFluxData &	a_facePhi,
		const EBAMRCellData &	a_cellPhi
	)

protectedvirtual

Use Heaviside smoothing for computing face-centered states.

Parameters

[out]	a_facePhi	Face centered state
[in]	a_cellPhi	Cell-centered states

Note: This is only intended to be used with FHD functionality.

◆ weightedUpwind()

void CdrSolver::weightedUpwind	(	EBAMRCellData &	a_weightedUpwindPhi,
		const int	a_pow
	)

virtual

Compute an upwind-weighted version of phi.

This is equal to sum(alpha * v^p * phi)/sum(alpha * v^p) where alpha is the face aperture and v is the face velocity. phi is taken as the upwind value.

Parameters

[out]	a_weightedUpwindPhi	Weighted upwind phi
[in]	a_pow	Weighting factor

◆ writeData()

void CdrSolver::writeData	(	LevelData< EBCellFAB > &	a_output,
		int &	a_comp,
		const EBAMRCellData &	a_data,
		const std::string	a_outputRealm,
		const int	a_level,
		const bool	a_interpToCentroids,
		const bool	a_interpGhost
	)		const

protectedvirtualnoexcept

Write data to output. Convenience function.

Parameters

[in,out]	a_output	Output data holder.
[in,out]	a_icomp	Starting component where this solver begins writing the output.
[in]	a_data	Data to write.
[in]	a_outputRealm	Realm where a_output belongs
[in]	a_level	Grid level
[in]	a_interpToCentroids	If true, a_data will be interpolated to cell centroids before writing to a_output.
[in]	a_interpGhost	If true, interpolate ghost cells

◆ writePlotData()

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

virtualnoexcept

Write output data to a_output.

Parameters

[in,out]	a_output	Output data holder.
[in,out]	a_icomp	Starting component where this solver begins writing the output.
[in]	a_outputRealm	Realm where a_output belongs
[in]	a_level	Grid level

Note: This will write the plot data in this solver to a_output, starting on a_comp; This routine writes m_phi on centroids (and not cell-centers).

◆ writePlotFile()

void CdrSolver::writePlotFile ( )

virtual

Write plot file.

The name of the plot file is m_name.stepXXXXX.DIM.hdf5

Note: This calls writePlotData(...)

Member Data Documentation

◆ m_cellCenteredDiffusionCoefficient

EBAMRCellData CdrSolver::m_cellCenteredDiffusionCoefficient

protected

Diffusion coefficients on cell centers.

Note: Memory is only allocated if the solver is diffusive

◆ m_cellVelocity

EBAMRCellData CdrSolver::m_cellVelocity

protected

Cell-centered velocities.

Note: Memory is only allocated if the solver is mobile.

◆ m_className

std::string CdrSolver::m_className

protected

Class name.

This will be different for different implementations of CdrSolver

◆ m_domainFluxFunctions

std::map<CdrDomainBC::DomainSide, CdrDomainBC::FluxFunction> CdrSolver::m_domainFluxFunctions

protected

Domain flux functions.

Used when the user specifies that the domain flux is function-based

◆ m_ebCenteredDiffusionCoefficient

EBAMRIVData CdrSolver::m_ebCenteredDiffusionCoefficient

protected

Diffusion coefficients on EB faces.

Note: Memory is only allocated if the solver is diffusive

◆ m_faceCenteredDiffusionCoefficient

EBAMRFluxData CdrSolver::m_faceCenteredDiffusionCoefficient

protected

Diffusion coefficients on face centers.

Note: Memory is only allocated if the solver is diffusive

◆ m_faceStates

EBAMRFluxData CdrSolver::m_faceStates

protected

Holder for face centered states.

Note: Memory is only allocated if the solver is mobile.

◆ m_faceVelocity

EBAMRFluxData CdrSolver::m_faceVelocity

protected

Face-centered velocities (only normal components)

Note: Memory is only allocated if the solver is mobile.

◆ m_verbosity

int CdrSolver::m_verbosity

protected

Solver verbosity.

A high number gives lots of output

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

Source/ConvectionDiffusionReaction/CD_CdrSolver.H
Source/ConvectionDiffusionReaction/CD_CdrSolver.cpp

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CdrSolver() [1/3]

◆ CdrSolver() [2/3]

◆ CdrSolver() [3/3]

Member Function Documentation

◆ advanceCrankNicholson() [1/2]

◆ advanceCrankNicholson() [2/2]

◆ advanceEuler() [1/2]

◆ advanceEuler() [2/2]

◆ advectToFaces()

◆ allocate()

◆ averageVelocityToFaces() [1/2]

◆ averageVelocityToFaces() [2/2]

◆ computeAdvectionDiffusionDt()

◆ computeAdvectionDiffusionFlux()

◆ computeAdvectionDt()

◆ computeAdvectionFlux() [1/2]

◆ computeAdvectionFlux() [2/2]

◆ computeCharge()

◆ computeDiffusionDt()

◆ computeDiffusionFlux() [1/2]

◆ computeDiffusionFlux() [2/2]

◆ computeDivD()

◆ computeDivergenceIrregular()

◆ computeDivF()

◆ computeDivG()

◆ computeDivJ()

◆ computeMass() [1/2]

◆ computeMass() [2/2]

◆ computeSourceDt()

◆ conservativeDivergenceNoKappaDivision()

◆ conservativeDivergenceRegular()

◆ deallocate()

◆ defineInterpolationStencils()

◆ extrapolateAdvectiveFluxToEB() [1/2]

◆ extrapolateAdvectiveFluxToEB() [2/2]

◆ fillDomainFlux() [1/2]

◆ fillDomainFlux() [2/2]

◆ fillGwn()

◆ getCellCenteredVelocity()

◆ getDomainFlux()

◆ getEbCenteredDiffusionCoefficient()

◆ getEbCenteredVelocity()

◆ getEbFlux()

◆ getFaceCenteredDiffusionCoefficient()

◆ getFaceCenteredVelocity()

◆ getName()

◆ getNumberOfPlotVariables()

◆ getPhi()

◆ getPlotVariableNames()

◆ getRealm()

◆ getSource()

◆ gwnDiffusionSource()

◆ hybridDivergence() [1/2]

◆ hybridDivergence() [2/2]

◆ initialData()

◆ initialDataDistribution()

◆ initialDataParticles()

◆ interpolateFluxToFaceCentroids() [1/2]

◆ interpolateFluxToFaceCentroids() [2/2]

◆ makeBcString()

◆ nonConservativeDivergence()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ preRegrid()

◆ redistribute()

◆ registerOperators()

◆ regrid()

◆ resetDomainFlux()

◆ setAmr()

◆ setComputationalGeometry()

◆ setDefaultDomainBC()

◆ setDiffusionCoefficient() [1/3]

◆ setDiffusionCoefficient() [2/3]