Class for holding a set of ItoSolvers. More...

#include <CD_ItoLayout.H>

Public Member Functions
	ItoLayout ()=delete
	Disallowed weak construction.

	ItoLayout (const Vector< RefCountedPtr< ItoSpecies >> &a_species)
	Full constructor. Calls the define function (but does not generate solvers). More...

virtual	~ItoLayout ()
	Destructor (does nothing).

virtual phase::which_phase	getPhase () const
	Return phase where the solvers are defined.

virtual ItoIterator< T >	iterator ()
	Return a fresh iterator. The iterator is a simple random access object that can iterate through the solvers.

virtual const std::string	getRealm () const
	Get the realm name where the solvers are defined.

virtual void	setRealm (const std::string a_realm)
	Set the realm where the solvers are defined. More...

virtual void	define (const Vector< RefCountedPtr< ItoSpecies >> &a_species)
	Define function. More...

virtual void	parseOptions ()
	Utility function – parse options for all solvers.

virtual void	parseRuntimeOptions ()
	Utility function – parse runtime options for all solvers.

virtual void	allocate ()
	Allocate internals for all solvers. More...

virtual void	addSolver (RefCountedPtr< T > &a_solver)
	Add solver to the list of solvers. More...

virtual void	preRegrid (const int a_lbase, const int a_finestLevel)
	Utility function which caches states before regrid step. More...

virtual void	initialData ()
	Fill all solvers with initial data. More...

virtual void	depositParticles ()
	All solvers deposit their particles. More...

virtual void	depositParticles (const ItoSolver::WhichContainer a_whichContainer)
	Deposit particles for each solver. Input argument determines which container is deposited. More...

virtual void	remap ()
	Remap function – calls remap(ItoSolver::WhichContainer::bulk) for each solver.

virtual void	remap (const ItoSolver::WhichContainer a_whichContainer)
	Remap function – all solves remap the input container. More...

virtual void	interpolateVelocities ()
	Interpolate velocities. More...

virtual void	regrid (const int a_lmin, const int a_oldFinestLevel, const int a_newFinestLevel)
	Regrid method – calls the regrid method for each solver. More...

virtual void	registerOperators ()
	Register operators. Calls registerOperators for each solver.

virtual void	setAmr (const RefCountedPtr< AmrMesh > &a_amr)
	Set AmrMesh object for each solver. More...

virtual void	setComputationalGeometry (const RefCountedPtr< ComputationalGeometry > &a_computationalGeometry)
	Set the computational geometry. This sets the computational geometry for each solver. More...

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

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

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

virtual void	organizeParticlesByCell (const ItoSolver::WhichContainer a_whichContainer)
	Sort ItoSolver particles by cell – this is done for all solvers. More...

virtual void	organizeParticlesByPatch (const ItoSolver::WhichContainer a_whichContainer)
	Sort ItoSolver particles by patch – this is done for all solvers. More...

virtual void	makeSuperparticles (const ItoSolver::WhichContainer a_whichContainer, const int a_ppc)
	Rearrange the input container particle into new superparticles – this is done for all solvers. More...

virtual void	makeSuperparticles (const ItoSolver::WhichContainer a_whichContainer, const Vector< int > a_ppc)
	Rearrange the input container particle into new superparticles – this is done for all solvers. More...

virtual Real	computeDt ()
	Compute smallest possible time step. More...

virtual Real	computeAdvectiveDt ()
	Compute the classical advection time step for all solvers. This returns dt = dx/max(v) where max(v) takes the largest component. More...

virtual Real	computeHopDt (const Real a_maxCellsToMove)
	Compute the largest dt which restricts all particles to move less than a_maxCellsToMove. More...

virtual Real	computeDiffusiveDt ()
	Compute the classical diffusive time step dt = dxdx/(2D) where D is the diffusion coefficient (not dimensional dependence here) More...

virtual size_t	getNumParticles (const ItoSolver::WhichContainer a_ptype, const bool a_localOnly)
	Get total number of particles. More...

virtual Vector< RefCountedPtr< T > > &	getSolvers ()
	Get solvers all solvers. More...

virtual Vector< RefCountedPtr< ItoSpecies > > &	getSpecies ()
	Get species. More...

virtual Vector< EBAMRCellData * >	getVelocityFunctions ()
	Get all velocity functions. More...

virtual Vector< EBAMRCellData * >	getDensities ()
	Get all densities. More...

virtual Vector< EBAMRCellData * >	getDiffusionFunctions ()
	Get all diffusion coefficients. More...

virtual Vector< EBAMRCellData * >	getMobilityFunctions ()
	Get all mobility mesh functions. More...

virtual Vector< ParticleContainer< ItoParticle > * >	getParticles (const ItoSolver::WhichContainer a_whichContainer)
	Get particle containers of a particular container type. More...

Protected Attributes
std::string	m_realm
	Realm where all the solvers are registered.

Vector< RefCountedPtr< T > >	m_solvers
	ItoSolver solvers.

Vector< RefCountedPtr< ItoSpecies > >	m_species
	ItoSolver species.

int	m_verbosity
	Verbosity level.

phase::which_phase	m_phase
	Phase where solvers live.

bool	m_isDefined
	Layout is defined or not.

Detailed Description

template<class T>
class ItoLayout< T >

Class for holding a set of ItoSolvers.

This is primarily a utility class just cuts down on typing when there are multiple species being advected/diffused. This class just stores a set of such solvers and contains an "iterator" for going through them. Fundamentally, there is no difference between this class and a vector of ItoSolvers. This class can be constructed through a factory method.

Constructor & Destructor Documentation

◆ ItoLayout()

template<class T >

ItoLayout< T >::ItoLayout ( const Vector< RefCountedPtr< ItoSpecies >> & a_species )

Full constructor. Calls the define function (but does not generate solvers).

Parameters

[in] a_species List of ItoSpecies.

Member Function Documentation

◆ addSolver()

template<class T >

void ItoLayout< T >::addSolver ( RefCountedPtr< T > & a_solver )

virtual

Add solver to the list of solvers.

Parameters

[in] a_solver New solver.

◆ allocate()

template<class T >

void ItoLayout< T >::allocate

virtual

Allocate internals for all solvers.

This will call allocate for each ItoSolver.

◆ computeAdvectiveDt()

template<class T >

Real ItoLayout< T >::computeAdvectiveDt

virtual

Compute the classical advection time step for all solvers. This returns dt = dx/max(v) where max(v) takes the largest component.

This calls computeAdvectionDt() for each ItoSolver and minimizes the result over the solvers (i.e. it returns the smallest time step)

Note: See ItoSolver::computeAdvectionDt() to see how the time step is computed.

◆ computeDiffusiveDt()

template<class T >

Real ItoLayout< T >::computeDiffusiveDt

virtual

Compute the classical diffusive time step dt = dx*dx/(2*D) where D is the diffusion coefficient (not dimensional dependence here)

This calls computeDiffusiveDt for all solvers and minimizes the result over all solvers.

◆ computeDt()

template<class T >

Real ItoLayout< T >::computeDt

virtual

Compute smallest possible time step.

This calls computeDt() for each ItoSolver and minimizes the result over the solvers (i.e. it returns the smallest time step)

◆ computeHopDt()

template<class T >

Real ItoLayout< T >::computeHopDt ( const Real a_maxCellsToMove )

virtual

Compute the largest dt which restricts all particles to move less than a_maxCellsToMove.

This calls computeHopDt for all solvers – that function uses the maximum permitted diffusion hop to restrict the time step (the user will have restricted the normal distribution to some value). So, the result of this value will depend strongly on the user input for the ItoSolvers.

Parameters

[in] a_maxCellsToMove Maximum number of cells to move.

◆ define()

template<class T >

void ItoLayout< T >::define ( const Vector< RefCountedPtr< ItoSpecies >> & a_species )

virtual

Define function.

Parameters

[in] a_species List of species (for which we generate solvers).

◆ depositParticles() [1/2]

template<class T >

void ItoLayout< T >::depositParticles

virtual

All solvers deposit their particles.

Calls depositParticles for each solver.

◆ depositParticles() [2/2]

template<class T >

void ItoLayout< T >::depositParticles ( const ItoSolver::WhichContainer a_whichContainer )

virtual

Deposit particles for each solver. Input argument determines which container is deposited.

Calls depositParticles(ItoSolver::WhichContainer) for each solver.

Parameters

[in] a_whichContainer Container type (e.g., ItoSolver::WhichContainer::bulk)

◆ getDensities()

template<class T >

Vector< EBAMRCellData * > ItoLayout< T >::getDensities

virtual

Get all densities.

This accumulates a pointer to the density mesh data for each solver.

◆ getDiffusionFunctions()

template<class T >

Vector< EBAMRCellData * > ItoLayout< T >::getDiffusionFunctions

virtual

Get all diffusion coefficients.

This accumulates a pointer to diffusion coefficient mesh data for each solver.

◆ getMobilityFunctions()

template<class T >

Vector< EBAMRCellData * > ItoLayout< T >::getMobilityFunctions

virtual

Get all mobility mesh functions.

This accumulates a pointer to mobility coefficient mesh data for each solver.

◆ getNumParticles()

template<class T >

size_t ItoLayout< T >::getNumParticles	(	const ItoSolver::WhichContainer	a_ptype,
		const bool	a_localOnly
	)

virtual

Get total number of particles.

This returns the total number of particles in a specified container. The result is accumulated over all solvers.

Parameters

[in]	a_whichContainer	Container type in ItoSolver
[in]	a_localOnly	If true, only count particles locally. If false, compute globally.

◆ getParticles()

template<class T >

Vector< ParticleContainer< ItoParticle > * > ItoLayout< T >::getParticles ( const ItoSolver::WhichContainer a_whichContainer )

virtual

Get particle containers of a particular container type.

Parameters

[in] a_whichContainer Which ItoSolver container

◆ getSolvers()

template<class T >

Vector< RefCountedPtr< T > > & ItoLayout< T >::getSolvers

virtual

Get solvers all solvers.

Returns: Returns m_solvers

◆ getSpecies()

template<class T >

Vector< RefCountedPtr< ItoSpecies > > & ItoLayout< T >::getSpecies

virtual

Get species.

Returns: Returns m_species

◆ getVelocityFunctions()

template<class T >

Vector< EBAMRCellData * > ItoLayout< T >::getVelocityFunctions

virtual

Get all velocity functions.

This accumulates a pointer to the velocity mesh data for each solver.

◆ initialData()

template<class T >

void ItoLayout< T >::initialData

virtual

Fill all solvers with initial data.

Calls initialData() for each solver.

◆ interpolateVelocities()

template<class T >

void ItoLayout< T >::interpolateVelocities

virtual

Interpolate velocities.

Calls interpolateVelocities() for each solver.

◆ makeSuperparticles() [1/2]

template<class T >

void ItoLayout< T >::makeSuperparticles	(	const ItoSolver::WhichContainer	a_whichContainer,
		const int	a_ppc
	)

virtual

Rearrange the input container particle into new superparticles – this is done for all solvers.

Parameters

[in]	a_whichContainer	Which ItoSolver container to sort by cell.
[in]	a_ppc	Target particle-per-cell (ppc)

◆ makeSuperparticles() [2/2]

template<class T >

void ItoLayout< T >::makeSuperparticles	(	const ItoSolver::WhichContainer	a_whichContainer,
		const Vector< int >	a_ppc
	)

virtual

Rearrange the input container particle into new superparticles – this is done for all solvers.

Parameters

[in]	a_whichContainer	Which ItoSolver container to sort by cell.
[in]	a_ppc	Target particle-per-cell (ppc) per level

◆ organizeParticlesByCell()

template<class T >

void ItoLayout< T >::organizeParticlesByCell ( const ItoSolver::WhichContainer a_whichContainer )

virtual

Sort ItoSolver particles by cell – this is done for all solvers.

Parameters

[in] a_whichContainer Which ItoSolver container to sort by cell.

◆ organizeParticlesByPatch()

template<class T >

void ItoLayout< T >::organizeParticlesByPatch ( const ItoSolver::WhichContainer a_whichContainer )

virtual

Sort ItoSolver particles by patch – this is done for all solvers.

Parameters

[in] a_whichContainer Which ItoSolver container to sort by cell.

◆ preRegrid()

template<class T >

void ItoLayout< T >::preRegrid	(	const int	a_lbase,
		const int	a_finestLevel
	)

virtual

Utility function which caches states before regrid step.

Calls the preRegrid function for each solver.

Parameters

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

◆ regrid()

template<class T >

void ItoLayout< T >::regrid	(	const int	a_lmin,
		const int	a_oldFinestLevel,
		const int	a_newFinestLevel
	)

virtual

Regrid method – calls the regrid method for each 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.

◆ remap()

template<class T >

void ItoLayout< T >::remap ( const ItoSolver::WhichContainer a_whichContainer )

virtual

Remap function – all solves remap the input container.

Parameters

[in] a_whichContainer Container type (e.g., ItoSolver::WhichContainer::bulk)

◆ setAmr()

template<class T >

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

virtual

Set AmrMesh object for each solver.

Parameters

[in] a_amrMesh AmrMesh object

◆ setComputationalGeometry()

template<class T >

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

virtual

Set the computational geometry. This sets the computational geometry for each solver.

Parameters

[in] a_computationalGeometry Computational geometry.

◆ setPhase()

template<class T >

void ItoLayout< T >::setPhase ( phase::which_phase a_phase )

virtual

Set phase for each solver.

Parameters

[in] a_phase Phase

◆ setRealm()

template<class T >

void ItoLayout< T >::setRealm ( const std::string a_realm )

virtual

Set the realm where the solvers are defined.

Parameters

[in] a_realm Realm name.

◆ setTime()

template<class T >

void ItoLayout< T >::setTime	(	const int	a_step,
		const Real	a_time,
		const Real	a_dt
	)

virtual

Set time for each 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

◆ setVerbosity()

template<class T >

void ItoLayout< T >::setVerbosity ( const int a_verbosity )

virtual

Set verbosity for each solver.

Parameters

[in] a_verbosity Verbosity level.

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

Source/ItoDiffusion/CD_ItoLayout.H
Source/ItoDiffusion/CD_ItoLayoutImplem.H

Public Member Functions

Protected Attributes

Detailed Description

template<class T> class ItoLayout< T >

Constructor & Destructor Documentation

◆ ItoLayout()

Member Function Documentation

◆ addSolver()

◆ allocate()

◆ computeAdvectiveDt()

◆ computeDiffusiveDt()

◆ computeDt()

◆ computeHopDt()

◆ define()

◆ depositParticles() [1/2]

◆ depositParticles() [2/2]

◆ getDensities()

◆ getDiffusionFunctions()

◆ getMobilityFunctions()

◆ getNumParticles()

◆ getParticles()

◆ getSolvers()

◆ getSpecies()

◆ getVelocityFunctions()

◆ initialData()

◆ interpolateVelocities()

◆ makeSuperparticles() [1/2]

◆ makeSuperparticles() [2/2]

◆ organizeParticlesByCell()

◆ organizeParticlesByPatch()

◆ preRegrid()

◆ regrid()

◆ remap()

◆ setAmr()

◆ setComputationalGeometry()

◆ setPhase()

◆ setRealm()

◆ setTime()

◆ setVerbosity()

template<class T>
class ItoLayout< T >