Base class for Ito diffusion particle models. More...

#include <CD_ItoSolver.H>

Collaboration diagram for ItoSolver:

[legend]

Public Types
enum class	WhichContainer { Bulk , EB , Domain , Source , Covered , Scratch }
	Enum class for distinguishing various types of particle containers. More...

Public Member Functions
	ItoSolver ()
	Constructor – user must subsequently set the realm and, parse class options, set the species etc.

virtual	~ItoSolver ()
	Destructor (does nothing).

virtual void	setParticleMerger (const ParticleManagement::ParticleMerger< ItoParticle > &a_particleMerger) noexcept
	Set the particle merger. This will get called when merging particles using makeSuperparticles. More...

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

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

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

virtual void	parseOptions ()
	Parse class options.

virtual void	parseRuntimeOptions ()
	Parse class runtime configurable options.

virtual EBIntersection	getIntersectionAlgorithm () const noexcept
	Get the EB-particle intersection algorithm.

virtual void	initialData ()
	Set the initial data. More...

virtual void	regrid (const int a_lmin, const int a_oldFinestLevel, const int a_newFinestLevel)
	Regrid this solver. More...

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

virtual void	clear (const WhichContainer a_container)
	Clear a particle container – this will delete all the particles in the input container. More...

virtual void	clear (ParticleContainer< ItoParticle > &a_particles) const
	Clear a particle container – this will delete all the particles in the input container. More...

virtual void	clear (AMRParticles< ItoParticle > &a_particles) const
	Clear particles – this will deleted all the particles in the input container. More...

virtual void	depositConductivity (EBAMRCellData &a_phi, ParticleContainer< ItoParticle > &a_particles) const
	Deposit conductivities (i.e. mass*mobility / volume) More...

virtual void	depositConductivity (EBAMRCellData &a_phi, ParticleContainer< ItoParticle > &a_particles, const DepositionType a_deposition, const CoarseFineDeposition a_coarseFineDeposition) const
	Deposit conductivities (i.e. mass*mobility / volume) More...

virtual void	depositDiffusivity (EBAMRCellData &a_phi, ParticleContainer< ItoParticle > &a_particles) const
	Deposit diffusivity (i.e. mass*D/volume) More...

virtual void	depositDiffusivity (EBAMRCellData &a_phi, ParticleContainer< ItoParticle > &a_particles, const DepositionType a_deposition, const CoarseFineDeposition a_coarseFineDeposition) const
	Deposit diffusivity (i.e. mass*D/volume) More...

virtual void	depositEnergyDensity (EBAMRCellData &a_phi, ParticleContainer< ItoParticle > &a_particles) const
	Deposit energy densities (i.e. mass*energy/volume => total energy per unit volume) More...

virtual void	depositEnergyDensity (EBAMRCellData &a_phi, ParticleContainer< ItoParticle > &a_particles, const DepositionType a_deposition, const CoarseFineDeposition a_coarseFineDeposition) const
	Deposit energy densities (i.e. mass*energy/volume => total energy per unit volume) More...

virtual void	computeAverageMobility (EBAMRCellData &a_phi, ParticleContainer< ItoParticle > &a_particles) const
	Compute average mobility. More...

virtual void	computeAverageDiffusion (EBAMRCellData &a_phi, ParticleContainer< ItoParticle > &a_particles) const
	Compute average diffusion coefficient. More...

virtual void	computeAverageEnergy (EBAMRCellData &a_phi, ParticleContainer< ItoParticle > &a_particles) const
	Compute average particle energy.. More...

virtual void	depositParticles ()
	Deposit particles onto mesh. More...

virtual void	depositParticles (const WhichContainer a_container)
	Deposit particles on to mesh. More...

template<class P , const Real &(P ::*)() const particleScalarField>
void	depositParticlesNGP (LevelData< EBCellFAB > &a_output, const ParticleContainer< P > &a_particles, const int a_level) const noexcept
	Do an NGP deposit on a specific grid level. Used for IO. More...

template<class P , Real(P ::*)() const particleScalarField>
void	depositParticlesNGP (LevelData< EBCellFAB > &a_output, const ParticleContainer< P > &a_particles, const int a_level) const noexcept
	Do an NGP deposit on a specific grid level. Used for IO. More...

template<class P , const Real &(P::*)() const particleScalarField>
void	depositParticles (EBAMRCellData &a_phi, ParticleContainer< P > &a_particles) const
	Generic deposition function which deposits a particle field onto the mesh using a specified deposition method. More...

template<class P , const Real &(P::*)() const particleScalarField>
void	depositParticles (EBAMRCellData &a_phi, ParticleContainer< P > &a_particles, const DepositionType a_deposition, const CoarseFineDeposition a_coarseFineDeposition) const
	Generic deposition function which deposits a particle field onto the mesh using a specified deposition method. More...

template<class P , Real(P::*)() const particleScalarField>
void	depositParticles (EBAMRCellData &a_phi, ParticleContainer< P > &a_particles, const DepositionType a_deposition, const CoarseFineDeposition a_coarseFineDeposition) const
	Generic deposition function which deposits a particle field onto the mesh using a specified deposition method. More...

virtual void	removeCoveredParticles (const EBRepresentation a_representation, const Real a_tol)
	Remove particles that are inside the EB. More...

virtual void	removeCoveredParticles (const WhichContainer a_container, const EBRepresentation a_representation, const Real a_tol)
	Remove particles that are inside the EB. More...

virtual void	removeCoveredParticles (ParticleContainer< ItoParticle > &a_particles, const EBRepresentation a_representation, const Real a_tol) const
	Remove particles that are inside the EB. More...

virtual void	transferCoveredParticles (const EBRepresentation a_representation, const Real a_tol)
	Transfer particles that are covered (within a_tol distance from EB) to another container. More...

virtual void	transferCoveredParticles (const WhichContainer a_containerFrom, const WhichContainer a_containerTo, const EBRepresentation a_representation, const Real a_tol)
	Transfer particles that are covered (within a_tol distance from EB) to another container. More...

virtual void	transferCoveredParticles (ParticleContainer< ItoParticle > &a_particlesFrom, ParticleContainer< ItoParticle > &a_particlesTo, const EBRepresentation a_representation, const Real a_tol) const
	Transfer particles that are inside the EB to another container. More...

virtual void	intersectParticles (const EBIntersection a_ebIntersection, const bool a_deleteParticles, const std::function< void(ItoParticle &)> a_nonDeletionModifier=[](ItoParticle &) -> void { return;})
	Do boundary intersection tests. More...

virtual void	intersectParticles (const WhichContainer a_particles, const WhichContainer a_ebParticles, const WhichContainer a_domainParticles, const EBIntersection a_ebIntersection, const bool a_deleteParticles, const std::function< void(ItoParticle &)> a_nonDeletionModifier=[](ItoParticle &) -> void { return;})
	Do boundary intersection tests. More...

virtual void	intersectParticles (ParticleContainer< ItoParticle > &a_particles, ParticleContainer< ItoParticle > &a_ebParticles, ParticleContainer< ItoParticle > &a_domainParticles, const EBIntersection a_ebIntersection, const bool a_deleteParticles, const std::function< void(ItoParticle &)> a_nonDeletionModifier=[](ItoParticle &) -> void { return;})
	Do boundary intersection tests. More...

virtual void	computeLoads (Vector< long int > &a_loads, const DisjointBoxLayout &a_dbl, const int a_level)
	Compute particle load on a specific grid level – this will compute the number of particles in each box in the input grids. More...

virtual int	getNumberOfPlotVariables () const
	Get number of plot variables. More...

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

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

virtual unsigned long long	getNumParticles (const WhichContainer a_container, const bool a_localOnly) const
	Get number of particles in a specified particle container. More...

virtual void	registerOperators () const
	Register operators. More...

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

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

virtual void	setPhase (const phase::which_phase a_phase)
	Set phase where the particles will live. More...

virtual void	setVerbosity (const int a_verbosity)
	Set verbosity level for this solver. 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	setSpecies (const RefCountedPtr< ItoSpecies > &a_species)
	Set the species. More...

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

template<ItoSolver::WhichContainer C = WhichContainer::Bulk>
void	addParticles (ListBox< ItoParticle > &a_inputParticles, const int a_lvl, const DataIndex a_dit, const bool a_destructive)
	Add particles to a contain. This adds into a specific grid level and patch. The user can delete the input particles. More...

virtual bool	isMobile () const
	Check if solver is mobile. More...

virtual bool	isDiffusive () const
	Check if solver is diffusive. More...

virtual ParticleContainer< ItoParticle > &	getParticles (const WhichContainer a_container)
	Get a general particle container. More...

virtual const ParticleContainer< ItoParticle > &	getParticles (const WhichContainer a_container) const
	Get a general particle container. More...

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

virtual EBAMRCellData &	getPhi ()
	Get the mesh data. More...

virtual EBAMRCellData &	getVelocityFunction ()
	Get cell-centered velocity mesh data. More...

virtual const EBAMRCellData &	getVelocityFunction () const
	Get cell-centered velocity mesh data. More...

virtual EBAMRCellData &	getDiffusionFunction ()
	Get the diffusion function. More...

virtual const EBAMRCellData &	getDiffusionFunction () const
	Get the diffusion function. More...

virtual EBAMRCellData &	getMobilityFunction ()
	Get mobility function. More...

virtual const EBAMRCellData &	getMobilityFunction () const
	Get mobility function. More...

virtual void	setDiffusionFunction (const Real a_diffusionCoefficient)
	Utility function – set a constant diffusion coefficient. More...

virtual void	setVelocityFunction (const RealVect a_velocity)
	Utility function – set a constant velocity. More...

virtual void	setParticleMobility (const Real a_mobility)
	Sets mobility coefficient for all particles. More...

virtual void	setParticleDiffusion (const Real a_diffusion)
	Sets diffusion coefficient for all particles. More...

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

virtual void	interpolateVelocities (const int a_level, const DataIndex &a_dit)
	Interpolate the particle velocities. More...

virtual void	interpolateMobilities ()
	Interpolate mobilities. More...

virtual void	updateMobilities ()
	Update mobilities parametrically from the particle energy. More...

virtual void	interpolateDiffusion ()
	Interpolate the diffusion field to the particle positions. More...

virtual void	updateDiffusion ()
	Update mobilities parametrically from the particle energy. More...

virtual void	organizeParticlesByCell (const WhichContainer a_container)
	Sort the input particle container by cell. More...

virtual void	organizeParticlesByPatch (const WhichContainer a_container)
	Sort the input particle container by patch. More...

virtual void	makeSuperparticles (const WhichContainer a_container, const int a_particlesPerCell)
	Make superparticles for a full container – this is the AMR version that users will usually call. More...

virtual void	makeSuperparticles (const WhichContainer a_container, const Vector< int > a_particlesPerCell)
	Make superparticles for a full container – this is the AMR version that users will usually call. More...

virtual void	makeSuperparticles (const WhichContainer a_container, const int a_particlesPerCell, const int a_level)
	Make superparticles for a particle container – this is used for a specified grid level. More...

virtual void	makeSuperparticles (const WhichContainer a_container, const int a_particlesPerCell, const int a_level, const DataIndex a_dit)
	Make superparticles for a particle container – this is used for a specified grid level and patch. More...

virtual void	mergeParticles (List< ItoParticle > &a_particles, const CellInfo &a_cellInfo, const int a_particlesPerCell) const noexcept
	General superparticle merging with underlying algorithm through m_particleMerger. More...

virtual void	makeSuperparticlesEqualWeightKD (List< ItoParticle > &a_particles, const CellInfo &a_cellInfo, const int a_particlesPerCell) const noexcept
	Superparticle merging with KD/BVH trees. More...

virtual void	reinitializeParticles (List< ItoParticle > &a_particles, const CellInfo &a_cellInfo, const int a_particlesPerCell) const noexcept
	Particle re-initialization algorithm. More...

virtual void	remap ()
	Remap the bulk particle container.

virtual void	remap (const WhichContainer a_container)
	Remap all particles in the input container. More...

virtual void	remapAll ()
	Remap all particle containers.

RealVect	randomGaussian () const
	Draw a random N-dimensional Gaussian number from a normal distribution with zero with and unit standard deviation. More...

RealVect	randomDirection () const
	Draw a random direction in N-dimensional space. More...

virtual Real	computeDt () const
	Compute a time step for the advance – this calls the level function. More...

virtual Real	computeDt (const int a_lvl) const
	Compute a time step for the advance – this returns the maximum permitted time step on the input grid level. More...

virtual Real	computeDt (const int a_lvl, const DataIndex &a_dit) const
	Compute a time step for the advance – this returns the maximum permitted time step on the input grid patch. More...

virtual Real	computeHopDt (const Real a_maxCellsToMove) const
	Compute the largest possible time step such that the particles does not move more than a specified number of grid cells on any grid level. More...

virtual Real	computeHopDt (const Real a_maxCellsToMove, const int a_lvl) const
	Compute the largest possible time step such that the particles does not move more than a specified number of grid cells on the input grid level. More...

virtual Real	computeHopDt (const Real a_maxCellsToMove, const int a_lvl, const DataIndex &a_dit) const
	Compute the largest possible time step such that the particles does not move more than a specified number of grid cells on the input grid level. More...

virtual Real	computeAdvectiveDt () const
	Compute advection time step dt = dx/vMax where vMax is the largest velocity component of the particle.

virtual Real	computeAdvectiveDt (const int a_lvl) const
	Compute the drift dt. This computes the minimum dt = dx/vMax on the input level. More...

virtual Real	computeAdvectiveDt (const int a_lvl, const DataIndex &a_dit) const
	Compute the drift dt. This computes the minimum dt = dx/vMax on one level and one box. More...

virtual Real	computeDiffusiveDt () const
	Compute the diffusive dt. This computes dt = dxdx/(2D) for all particles.

virtual Real	computeDiffusiveDt (const int a_lvl) const
	Compute the diffusive dt. This computes dt = dxdx/(2D) for all particles on the input level. More...

virtual Real	computeDiffusiveDt (const int a_lvl, const DataIndex &a_dit) const
	Compute the diffusive dt. This computes dt = dxdx/(2D) for all particles on the input grid patch. More...

DepositionType	getDeposition () const
	Get deposition method. More...

CoarseFineDeposition	getCoarseFineDeposition () const
	Get the coarse-fine deposition strategy.

phase::which_phase	getPhase () const
	Return phase. More...

Protected Types
enum class	WhichCheckpoint { Particles , Numbers }
	How to checkpoint files. More...

enum class	WhichMobilityInterpolation { Direct , Velocity }
	Enum for deciding how to interpolate particle mobilities. More...

Protected Member Functions
void	parseRNG ()
	Parse RNG options – this parses the RNG seed and instantiates the distributions.

void	parseTruncation ()
	Parse the normal distribution truncation level.

void	parseDeposition ()
	Parse particle deposition methods.

void	parseParticleMerger ()
	Parse the super-particle merger.

void	parseIntersectionEB ()
	Parse EB intersection algorithms.

void	parseVerbosity ()
	Parse class verbosity.

void	parsePlotVariables ()
	Parse plot variables.

void	parseDiffusionHop ()
	Parse diffusion hop.

void	parseRedistribution ()
	Parse whether or not to use redistribution.

void	parseDivergenceComputation ()
	Parse whether or not to compute a "non-conservative" divergence when redistributing mass.

void	parseCheckpointing ()
	Parse checkpointing method.

void	drawNewParticles (const LevelData< EBCellFAB > &a_particlesPerCell, const int a_level, const int a_newPPC)
	Restart particles from a specified number of particles in the grid cell. More...

template<class P , const Real &(P::*)() const particleScalarField>
void	depositKappaConservative (EBAMRCellData &a_phi, ParticleContainer< P > &a_particles, const DepositionType a_deposition, const CoarseFineDeposition a_coarseFineDeposition) const
	Compute the cell-centered deposition – this is the main deposition function. More...

template<class P , Real(P::*)() const particleScalarField>
void	depositKappaConservative (EBAMRCellData &a_phi, ParticleContainer< P > &a_particles, const DepositionType a_deposition, const CoarseFineDeposition a_coarseFineDeposition) const
	Compute the cell-centered deposition – this is the main deposition function. More...

virtual void	redistributeAMR (EBAMRCellData &a_phi) const
	Redistribute mass in an AMR context. More...

virtual void	depositNonConservative (EBAMRIVData &a_depositionNC, const EBAMRCellData &a_depositionKappaC) const
	Make the "non-conservative" kappa deposition – computing depositionNC = sum(kappa*depositionC)/sum(kappa) in a neighborhood around each vof. More...

virtual void	depositHybrid (EBAMRCellData &a_depositionH, EBAMRIVData &a_massDifference, const EBAMRIVData &a_depositionNC) const
	Make the "hybrid" deposition phiH = kappaphiC + (1-kappa)phiNC. On input, a_depositionH should contain phiC. More...

virtual void	interpolateMobilities (const int a_level, const DataIndex &a_dit, const EBCellFAB &a_velocityMagnitude) noexcept
	Interpolate mobilities – this will switch between the two ways of computing the particle mobility. More...

virtual void	interpolateMobilitiesDirect (const int a_level, const DataIndex &a_dit) noexcept
	Directly interpolate mobilities. Interpolates for all particles in the specified grid patch. More...

virtual void	interpolateMobilitiesVelocity (const int a_level, const DataIndex &a_dit, const EBCellFAB &a_velocityMagnitude) noexcept
	Interpolate mobilities through the velocity. Interpolates for all particles in the specified grid patch. More...

virtual void	updateMobilities (const int a_level, const DataIndex a_dit)
	Update mobilities parametrically from the particle energy. More...

virtual void	interpolateDiffusion (const int a_level, const DataIndex &a_dit)
	Interpolate the diffusion field to the particle positions. More...

virtual void	updateDiffusion (const int a_level, const DataIndex a_dit)
	Update mobilities parametrically from the particle energy. 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
WhichCheckpoint	m_checkpointing
	How to checkpoint files. particles => write particles to HDF5. numbers => write numbers to HDF5.

WhichMobilityInterpolation	m_mobilityInterp
	Switch for deciding how to interpolate mobilities, i.e. interpolating either mu*E or just mu (to the particle position)

ParticleManagement::ParticleMerger< ItoParticle >	m_particleMerger
	Particle merger.

int	m_restartPPC
	Number of particles used when restarting a simulation – this is relevant only when restarting from a "fluid" checkpoint file.

std::string	m_realm
	Realm where this solve lives.

RefCountedPtr< ComputationalGeometry >	m_computationalGeometry
	Computational geometry.

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

RefCountedPtr< ItoSpecies >	m_species
	Species that this solver solves for.

phase::which_phase	m_phase
	Phase where this solver lives.

std::string	m_name
	Solver name.

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

Real	m_normalDistributionTruncation
	Truncation value for normal distribution. More...

Real	m_bisectionStep
	Bisection step size to use for particle intersection tests with EBs.

int	m_verbosity
	Verbosity level for this solver.

int	m_timeStep
	Time step.

int	m_haloBuffer
	Size of refinement boundary halo.

Real	m_time
	Current time.

Real	m_dt
	Time step.

bool	m_forceIrregDepositionNGP
	NGP deposition in cut cells or not.

bool	m_forceIrregInterpolationNGP
	NGP interpolation in cut cells or not.

bool	m_forceHaloNGP
	Force usage of NGP when depositing "halo" particles.

bool	m_useRedistribution
	Use mass redistribution or not.

bool	m_blendConservation
	Flag for blending the deposition clouds with the "non-conservative" divergence.

bool	m_isDiffusive
	If true, solver is diffusive.

bool	m_isMobile
	If true, solver is mobile, i.e. advection is turned on.

bool	m_plotPhi
	Flag for outputting m_phi to plot files.

bool	m_plotVelocity
	Flag for outputting m_velocityFunction to plot files.

bool	m_plotDiffCo
	Flag for outputting m_diffusionFunction to plot files.

bool	m_plotParticles
	Flag for depositing and plotting the bulk particles on the mesh.

bool	m_plotParticlesEB
	Flag for depositing and plotting the EB particles on the mesh.

bool	m_plotParticlesDomain
	Flag for depositing and plotting the domain particles on the mesh.

bool	m_plotParticlesSource
	Flag for depositing and plotting the source particles on the mesh.

bool	m_plotParticlesCovered
	Flag for depositing and plotting the covered particles on the mesh.

bool	m_plotEnergyDensity
	Flag for plotting the energy density on the mesh.

bool	m_plotAverageEnergy
	Flag for plotting the average particle energy on the mesh.

DepositionType	m_deposition
	Deposition method when depositing particles to the mesh.

CoarseFineDeposition	m_coarseFineDeposition
	Coarse-fine deposition strategy.

DepositionType	m_plotDeposition
	Deposition method when depositing particles to mesh during plotting.

EBAMRCellData	m_phi
	Storage for particle mesh data.

EBAMRCellData	m_mobilityFunction
	Mobility function – used when interpolating particle mobilities.

EBAMRCellData	m_velocityFunction
	Cell-centered field used for interpolating velocities.

EBAMRCellData	m_diffusionFunction
	Diffusion-centerer field used for interpolating diffusion coefficients.

EBAMRIVData	m_depositionNC
	Scratch storage for holding the non-conservative deposition.

EBAMRIVData	m_massDiff
	Scratch storage for holding the mass difference when using hybrid deposition.

std::map< WhichContainer, ParticleContainer< ItoParticle > >	m_particleContainers
	Various particle containers with identifiers.

EBIntersection	m_intersectionAlg
	Algorithm for EB intersection.

Static Protected Attributes
static constexpr int	m_comp = 0
	Default component in data holders (do not touch).

static constexpr int	m_nComp = 1
	Default number of component in data holders (do not touch).

Detailed Description

Base class for Ito diffusion particle models.

This is a particle class for solving Ito diffusion problems dX = v*dt + sqrt(2*D)*dW_t (dW_t is a Wiener process over dt) over an AMR hierarchy. The diffusion coefficient is related to the hydrodynamic diffusion coefficient by D(fluid) = sqrt(2*D(Ito)).

Note: To use this class, the user must add a species and set the realm and phase where the solver will live.

Member Enumeration Documentation

◆ WhichCheckpoint

enum ItoSolver::WhichCheckpoint

strongprotected

How to checkpoint files.

Particles => Write particles to HDF5. Numbers => Write particle numbers to HDF5 (and lose information)

◆ WhichContainer

enum ItoSolver::WhichContainer

strong

Enum class for distinguishing various types of particle containers.

This exists because the ItoSolver can partition particles into various containers, which is very useful when one wants to add particles from a source term, remove particles that fall inside the EB, or parse boundary conditions on the EB and domain faces. Here, Bulk = "Active" particles, EB = Particles on the EBs , Domain = Particles on the domain sides, Source = Source particles – used to e.g. add new particles to the bulk particles, Covered = Particles inside the EB, Scratch = Scratch particles

◆ WhichMobilityInterpolation

enum ItoSolver::WhichMobilityInterpolation

strongprotected

Enum for deciding how to interpolate particle mobilities.

Direct => Interpolate particle mobilities from the mesh. Velocity => Set particle mobilitys by computing mu = |v|/|V| where v is the particle velocity and V is the "velocity field".

Member Function Documentation

◆ addParticles()

template<ItoSolver::WhichContainer C>

void ItoSolver::addParticles	(	ListBox< ItoParticle > &	a_inputParticles,
		const int	a_lvl,
		const DataIndex	a_dit,
		const bool	a_destructive
	)

Add particles to a contain. This adds into a specific grid level and patch. The user can delete the input particles.

Parameters

[in,out]	a_inputParticles	Input particles – can be destroyed if a_destructive=true
[in]	a_lvl	Grid level
[in]	a_dit	Grid index
[in]	a_destructive	If true, delete the input particles.

◆ allocate()

void ItoSolver::allocate ( )

virtual

Allocate internal storage.

This will allocate the required mesh data as well as all the particle data holders.

Note: Storage for diffusion and advection fields are only allocate if the species is diffusive/mobile.

◆ clear() [1/3]

void ItoSolver::clear ( AMRParticles< ItoParticle > & a_particles ) const

virtual

Clear particles – this will deleted all the particles in the input container.

Parameters

[in] a_particles Particle container to be emptied.

◆ clear() [2/3]

void ItoSolver::clear ( const WhichContainer a_container )

virtual

Clear a particle container – this will delete all the particles in the input container.

Parameters

[in] a_whichContainer Particle container to be cleared.

◆ clear() [3/3]

void ItoSolver::clear ( ParticleContainer< ItoParticle > & a_particles ) const

virtual

Clear a particle container – this will delete all the particles in the input container.

Parameters

[in] a_particles Particle container to be emptied.

◆ computeAdvectiveDt() [1/2]

Real ItoSolver::computeAdvectiveDt ( const int a_lvl ) const

virtual

Compute the drift dt. This computes the minimum dt = dx/vMax on the input level.

Parameters

[in] a_lvl Grid level

◆ computeAdvectiveDt() [2/2]

Real ItoSolver::computeAdvectiveDt	(	const int	a_lvl,
		const DataIndex &	a_dit
	)		const

virtual

Compute the drift dt. This computes the minimum dt = dx/vMax on one level and one box.

Parameters

[in]	a_lvl	Grid level
[in]	a_dit	Grid index

◆ computeAverageDiffusion()

void ItoSolver::computeAverageDiffusion	(	EBAMRCellData &	a_phi,
		ParticleContainer< ItoParticle > &	a_particles
	)		const

virtual

Compute average diffusion coefficient.

This computes the average diffusion coefficient as D_avg = sum(mass*D)/sum(mass) by depositing on the mesh.

Parameters

[out]	a_phi	Mesh data
[in]	a_particles	Particle data

◆ computeAverageEnergy()

void ItoSolver::computeAverageEnergy	(	EBAMRCellData &	a_phi,
		ParticleContainer< ItoParticle > &	a_particles
	)		const

virtual

Compute average particle energy..

This computes the average energy as E_avg = sum(mass*energy)/sum(mass) by depositing on the mesh.

Parameters

[out]	a_phi	Mesh data
[in]	a_particles	Particle data

◆ computeAverageMobility()

void ItoSolver::computeAverageMobility	(	EBAMRCellData &	a_phi,
		ParticleContainer< ItoParticle > &	a_particles
	)		const

virtual

Compute average mobility.

This computes the average mobility as mu_avg = sum(mass*mu)/sum(mass) by depositing on the mesh.

Parameters

[out]	a_phi	Mesh data
[in]	a_particles	Particle data

◆ computeDiffusiveDt() [1/2]

Real ItoSolver::computeDiffusiveDt ( const int a_lvl ) const

virtual

Compute the diffusive dt. This computes dt = dx*dx/(2*D) for all particles on the input level.

Parameters

[in] a_lvl Grid level

◆ computeDiffusiveDt() [2/2]

Real ItoSolver::computeDiffusiveDt	(	const int	a_lvl,
		const DataIndex &	a_dit
	)		const

virtual

Compute the diffusive dt. This computes dt = dx*dx/(2*D) for all particles on the input grid patch.

Parameters

[in]	a_lvl	Grid level
[in]	a_dit	Grid index

◆ computeDt() [1/3]

Real ItoSolver::computeDt ( ) const

virtual

Compute a time step for the advance – this calls the level function.

This computes the time step differently whether or not diffusion and advection are active. The Ito particle model does not have a fundamental time step limitation, so these limits "replicate" the time step selections in a 1D fluid model. If we only use advection advection the time step is computed as dt = dx/Vmax = dtA, where Vmax is the largest velocity component along any of the directions. If only diffusion is active the time step is computed as dt = (dx*dx)/(2*D) = dtD. If both advection and diffusion are active the time step is computed as dt = 1/(1/dtA + 1/dtD).

◆ computeDt() [2/3]

Real ItoSolver::computeDt ( const int a_lvl ) const

virtual

Compute a time step for the advance – this returns the maximum permitted time step on the input grid level.

This computes the time step differently whether or not diffusion and advection are active. The Ito particle model does not have a fundamental time step limitation, so these limits "replicate" the time step selections in a 1D fluid model. If we only use advection advection the time step is computed as dt = dx/Vmax = dtA, where Vmax is the largest velocity component along any of the directions. If only diffusion is active the time step is computed as dt = (dx*dx)/(2*D) = dtD. If both advection and diffusion are active the time step is computed as dt = 1/(1/dtA + 1/dtD).

Parameters

[in] a_lvl Grid level

◆ computeDt() [3/3]

Real ItoSolver::computeDt	(	const int	a_lvl,
		const DataIndex &	a_dit
	)		const

virtual

Compute a time step for the advance – this returns the maximum permitted time step on the input grid patch.

This computes the time step differently whether or not diffusion and advection are active. The Ito particle model does not have a fundamental time step limitation, so these limits "replicate" the time step selections in a 1D fluid model. If we only use advection advection the time step is computed as dt = dx/Vmax = dtA, where Vmax is the largest velocity component along any of the directions. If only diffusion is active the time step is computed as dt = (dx*dx)/(2*D) = dtD. If both advection and diffusion are active the time step is computed as dt = 1/(1/dtA + 1/dtD).

Parameters

[in]	a_lvl	Grid level
[in]	a_dit	Grid index

◆ computeHopDt() [1/3]

Real ItoSolver::computeHopDt ( const Real a_maxCellsToMove ) const

virtual

Compute the largest possible time step such that the particles does not move more than a specified number of grid cells on any grid level.

This computes the time step differently whether or not diffusion and advection are active. The Ito particle model does not a fundamental time step limitation, so this function does its best at computing a time step such that the particles do not move more than the specified amount of grid cells. If only advection is active the time step is computed as dt = a_maxCellsToMove * dx/vMax where vMax is the largest velocity component. If only diffusion is active the usual kernel is dX = dWt which yields a "hop" of length L_d = sqrt(2*D*dt)*N0 where N0 is the diffusion hop in one of the coordinates. We do not need to worry about SpaceDim-related corrections because the hops in each direction are independent, so solving for dt we find dtD = L_d^2/(2*D*N0^2). If both advectino and diffusion are active then we can move up to L_d = v_d*dt + sqrt(2*D*dt)*N0 in any one coordinate direction (this is the usual Ito kernel). This requires a solution to a quadratic equation. Fortunately, this is easy to solve for.

Parameters

[in] a_maxCellsToMove

◆ computeHopDt() [2/3]

Real ItoSolver::computeHopDt	(	const Real	a_maxCellsToMove,
		const int	a_lvl
	)		const

virtual

Compute the largest possible time step such that the particles does not move more than a specified number of grid cells on the input grid level.

This computes the time step differently whether or not diffusion and advection are active. The Ito particle model does not a fundamental time step limitation, so this function does its best at computing a time step such that the particles do not move more than the specified amount of grid cells. If only advection is active the time step is computed as dt = a_maxCellsToMove * dx/vMax where vMax is the largest velocity component. If only diffusion is active the usual kernel is dX = dWt which yields a "hop" of length L_d = sqrt(2*D*dt)*N0 where N0 is the diffusion hop in one of the coordinates. We do not need to worry about SpaceDim-related corrections because the hops in each direction are independent, so solving for dt we find dtD = L_d^2/(2*D*N0^2). If both advectino and diffusion are active then we can move up to L_d = v_d*dt + sqrt(2*D*dt)*N0 in any one coordinate direction (this is the usual Ito kernel). This requires a solution to a quadratic equation. Fortunately, this is easy to solve for.

Parameters

[in]	a_maxCellsToMove	Maximum number of cells to move with a standard Ito kernel dX = vdt + sqrt(2Ddt)N
[in]	a_lvl	Grid level

◆ computeHopDt() [3/3]

Real ItoSolver::computeHopDt	(	const Real	a_maxCellsToMove,
		const int	a_lvl,
		const DataIndex &	a_dit
	)		const

virtual

Compute the largest possible time step such that the particles does not move more than a specified number of grid cells on the input grid level.

This computes the time step differently whether or not diffusion and advection are active. The Ito particle model does not a fundamental time step limitation, so this function does its best at computing a time step such that the particles do not move more than the specified amount of grid cells. If only advection is active the time step is computed as dt = a_maxCellsToMove * dx/vMax where vMax is the largest velocity component. If only diffusion is active the usual kernel is dX = dWt which yields a "hop" of length L_d = sqrt(2*D*dt)*N0 where N0 is the diffusion hop in one of the coordinates. We do not need to worry about SpaceDim-related corrections because the hops in each direction are independent, so solving for dt we find dtD = L_d^2/(2*D*N0^2). If both advectino and diffusion are active then we can move up to L_d = v_d*dt + sqrt(2*D*dt)*N0 in any one coordinate direction (this is the usual Ito kernel). This requires a solution to a quadratic equation. Fortunately, this is easy to solve for.

Parameters

[in]	a_maxCellsToMove	Maximum number of cells to move with a standard Ito kernel dX = vdt + sqrt(2Ddt)N
[in]	a_lvl	Grid level
[in]	a_dit	Grid index

◆ computeLoads()

void ItoSolver::computeLoads	(	Vector< long int > &	a_loads,
		const DisjointBoxLayout &	a_dbl,
		const int	a_level
	)

virtual

Compute particle load on a specific grid level – this will compute the number of particles in each box in the input grids.

Parameters

[out]	a_loads	Loads on each grid patch. This follows the order from a_dbl.boxArray()
[in]	a_dbl	Grids
[in]	a_level	Grid level

◆ depositConductivity() [1/2]

void ItoSolver::depositConductivity	(	EBAMRCellData &	a_phi,
		ParticleContainer< ItoParticle > &	a_particles
	)		const

virtual

Deposit conductivities (i.e. mass*mobility / volume)

This deposits mass*mobility (not multiplied by charge)

Parameters

[out]	a_phi	Mesh data
[in]	a_particles	Particle data

◆ depositConductivity() [2/2]

void ItoSolver::depositConductivity	(	EBAMRCellData &	a_phi,
		ParticleContainer< ItoParticle > &	a_particles,
		const DepositionType	a_deposition,
		const CoarseFineDeposition	a_coarseFineDeposition
	)		const

virtual

Deposit conductivities (i.e. mass*mobility / volume)

This deposits mass*mobility (not multiplied by charge)

Parameters

[out]	a_phi	Mesh data
[in]	a_particles	Particle data
[in]	a_deposition	Deposition method
[in]	a_coarseFineDeposition	Coarse-fine deposition method.

◆ depositDiffusivity() [1/2]

void ItoSolver::depositDiffusivity	(	EBAMRCellData &	a_phi,
		ParticleContainer< ItoParticle > &	a_particles
	)		const

virtual

Deposit diffusivity (i.e. mass*D/volume)

This deposits mass*diffusion (not multiplied by charge)

Parameters

[out]	a_phi	Mesh data
[in]	a_particles	Particle data

Note: Calls the other versions with a_deposition = m_deposition

◆ depositDiffusivity() [2/2]

void ItoSolver::depositDiffusivity	(	EBAMRCellData &	a_phi,
		ParticleContainer< ItoParticle > &	a_particles,
		const DepositionType	a_deposition,
		const CoarseFineDeposition	a_coarseFineDeposition
	)		const

virtual

Deposit diffusivity (i.e. mass*D/volume)

This deposits mass*mobility (not multiplied by charge)

Parameters

[out]	a_phi	Mesh data
[in]	a_particles	Particle data
[in]	a_deposition	Deposition method
[in]	a_coarseFineDeposition	Coarse-fine deposition method.

◆ depositEnergyDensity() [1/2]

void ItoSolver::depositEnergyDensity	(	EBAMRCellData &	a_phi,
		ParticleContainer< ItoParticle > &	a_particles
	)		const

virtual

Deposit energy densities (i.e. mass*energy/volume => total energy per unit volume)

This deposits mass*energy

Parameters

[out]	a_phi	Mesh data
[in]	a_particles	Particle data

Note: Calls the other versions with a_deposition = m_deposition

◆ depositEnergyDensity() [2/2]

void ItoSolver::depositEnergyDensity	(	EBAMRCellData &	a_phi,
		ParticleContainer< ItoParticle > &	a_particles,
		const DepositionType	a_deposition,
		const CoarseFineDeposition	a_coarseFineDeposition
	)		const

virtual

Deposit energy densities (i.e. mass*energy/volume => total energy per unit volume)

This deposits mass*energy

Parameters

[out]	a_phi	Mesh data
[in]	a_particles	Particle data
[in]	a_deposition	Deposition method
[in]	a_coarseFineDeposition	Coarse-fine deposition method.

◆ depositHybrid()

void ItoSolver::depositHybrid	(	EBAMRCellData &	a_depositionH,
		EBAMRIVData &	a_massDifference,
		const EBAMRIVData &	a_depositionNC
	)		const

protectedvirtual

Make the "hybrid" deposition phiH = kappa*phiC + (1-kappa)*phiNC. On input, a_depositionH should contain phiC.

Parameters

[in,out]	a_depositionH	On input, contains phiC. On output, contain phiH
[out]	a_massDifference	On output, contains mass loss in each cut-cell.
[in]	a_depositionNC	The "non-conservative" deposited variable.

◆ depositKappaConservative() [1/2]

template<class P , Real(P::*)() const particleScalarField>

void ItoSolver::depositKappaConservative	(	EBAMRCellData &	a_phi,
		ParticleContainer< P > &	a_particles,
		const DepositionType	a_deposition,
		const CoarseFineDeposition	a_coarseFineDeposition
	)		const

protected

Compute the cell-centered deposition – this is the main deposition function.

The template parameters indicate the particle type and quantity to be deposited. The second template parameter must be a pointer to a member function in the particle class with signature 'const Real& P::function() const'. E.g. 'const Real& P::mass() const' which is the default quantity to be deposited.

Parameters

[out]	a_phi	Cell-centered mesh data. Must have exactly one component.
[in]	a_particles	Particles to be deposited.
[in]	a_deposition	Deposition type
[in]	a_coarseFineDeposition	Coarse-fine deposition strategy

◆ depositKappaConservative() [2/2]

template<class P , Real(P::*)() const particleScalarField>

void ItoSolver::depositKappaConservative	(	EBAMRCellData &	a_phi,
		ParticleContainer< P > &	a_particles,
		const DepositionType	a_deposition,
		const CoarseFineDeposition	a_coarseFineDeposition
	)		const

protected

Compute the cell-centered deposition – this is the main deposition function.

Just like the version above except that the function signature is Real P::particleScalarField() const.

Parameters

[out]	a_phi	Cell-centered mesh data. Must have exactly one component.
[in]	a_particles	Particles to be deposited.
[in]	a_deposition	Deposition type
[in]	a_coarseFineDeposition	Coarse-fine deposition strategy

◆ depositNonConservative()

void ItoSolver::depositNonConservative	(	EBAMRIVData &	a_depositionNC,
		const EBAMRCellData &	a_depositionKappaC
	)		const

protectedvirtual

Make the "non-conservative" kappa deposition – computing depositionNC = sum(kappa*depositionC)/sum(kappa) in a neighborhood around each vof.

Parameters

[out]	a_depositionNC	Non-conservative deposition
[in]	a_depositionKappaC	Conserved deposition

◆ depositParticles() [1/5]

void ItoSolver::depositParticles ( )

virtual

Deposit particles onto mesh.

This will deposit the mass (i.e., computational weight) "bulk" particles into m_phi.

Note: Cells the other version with a_container = WhichContainer::Bulk

◆ depositParticles() [2/5]

void ItoSolver::depositParticles ( const WhichContainer a_container )

virtual

Deposit particles on to mesh.

Parameters

[in] a_container Which container to deposit.

This will deposit mass (i.e., computational weight) of the the input particle container particles onto the classes member 'm_phi'.

Note: Calls the general version with arguments: m_phi, m_particles.at(a_container), m_deposition.

◆ depositParticles() [3/5]

template<class P , const Real &(P::*)() const particleScalarField>

void ItoSolver::depositParticles	(	EBAMRCellData &	a_phi,
		ParticleContainer< P > &	a_particles
	)		const

Generic deposition function which deposits a particle field onto the mesh using a specified deposition method.

The template parameters indicate the particle type and quantity to be deposited. The second template parameter must be a pointer to a member function in the particle class with signature 'const Real& P::function() const'. E.g. 'const Real& P::mass() const' which is the default quantity to be deposited.

Parameters

[out]	a_phi	Mesh data – must have exactly one component.
[in]	a_particles	Particles to be deposited

◆ depositParticles() [4/5]

template<class P , Real(P::*)() const particleScalarField>

void ItoSolver::depositParticles	(	EBAMRCellData &	a_phi,
		ParticleContainer< P > &	a_particles,
		const DepositionType	a_deposition,
		const CoarseFineDeposition	a_coarseFineDeposition
	)		const

Generic deposition function which deposits a particle field onto the mesh using a specified deposition method.

The template parameters indicate the particle type and quantity to be deposited. The second template parameter must be a pointer to a member function in the particle class with signature 'const Real& P::function() const'. E.g. 'const Real& P::mass() const' which is the default quantity to be deposited.

Parameters

[out]	a_phi	Mesh data – must have exactly one component.
[in]	a_particles	Particles to be deposited
[in]	a_deposition	Deposition method
[in]	a_coarseFineDeposition	Coarse-fine deposition strategy

◆ depositParticles() [5/5]

template<class P , Real(P::*)() const particleScalarField>

void ItoSolver::depositParticles	(	EBAMRCellData &	a_phi,
		ParticleContainer< P > &	a_particles,
		const DepositionType	a_deposition,
		const CoarseFineDeposition	a_coarseFineDeposition
	)		const

Generic deposition function which deposits a particle field onto the mesh using a specified deposition method.

Just like the version above, but with a different function signature.

Parameters

[out]	a_phi	Mesh data – must have exactly one component.
[in]	a_particles	Particles to be deposited
[in]	a_deposition	Deposition method
[in]	a_coarseFineDeposition	Coarse-fine deposition strategy

◆ depositParticlesNGP() [1/2]

template<class P , Real(P ::*)() const particleScalarField>

void ItoSolver::depositParticlesNGP	(	LevelData< EBCellFAB > &	a_output,
		const ParticleContainer< P > &	a_particles,
		const int	a_level
	)		const

noexcept

Do an NGP deposit on a specific grid level. Used for IO.

Parameters

[out]	a_output	Contains NGP deposition of particles. Ignores cut-cells.
[in]	a_particles	Particles
[in]	a_level	Grid level

◆ depositParticlesNGP() [2/2]

template<class P , Real(P ::*)() const particleScalarField>

void ItoSolver::depositParticlesNGP	(	LevelData< EBCellFAB > &	a_output,
		const ParticleContainer< P > &	a_particles,
		const int	a_level
	)		const

noexcept

Do an NGP deposit on a specific grid level. Used for IO.

Parameters

[out]	a_output	Contains NGP deposition of particles. Ignores cut-cells.
[in]	a_particles	Particles
[in]	a_level	Grid level

◆ drawNewParticles()

void ItoSolver::drawNewParticles	(	const LevelData< EBCellFAB > &	a_particlesPerCell,
		const int	a_level,
		const int	a_newPPC
	)

protected

Restart particles from a specified number of particles in the grid cell.

This will instantiate the bulk particles by randomly drawing new particles in each grid cell.

Parameters

[in]	a_particlesPerCell	Mesh data showing how many particles are in each cell.
[in]	a_level	Grid level.
[in]	a_newPPC	Desired number of computational particles per cell

◆ getDeposition()

DepositionType ItoSolver::getDeposition ( ) const

Get deposition method.

Returns: Returns m_deposition

◆ getDiffusionFunction() [1/2]

EBAMRCellData & ItoSolver::getDiffusionFunction ( )

virtual

Get the diffusion function.

Returns: m_diffusionFunction

◆ getDiffusionFunction() [2/2]

const EBAMRCellData & ItoSolver::getDiffusionFunction ( ) const

virtual

Get the diffusion function.

Returns: m_diffusionFunction

◆ getMobilityFunction() [1/2]

EBAMRCellData & ItoSolver::getMobilityFunction ( )

virtual

Get mobility function.

Returns: m_mobilityFunction

◆ getMobilityFunction() [2/2]

const EBAMRCellData & ItoSolver::getMobilityFunction ( ) const

virtual

Get mobility function.

Returns: m_mobilityFunction

◆ getName()

std::string ItoSolver::getName ( ) const

virtual

Get this solver's name.

Returns: Returns m_name

◆ getNumberOfPlotVariables()

int ItoSolver::getNumberOfPlotVariables ( ) const

virtual

Get number of plot variables.

Returns: Returns the number of plot variables (Note: Scalars-> one variable and vectors -> SpaceDim variables).

◆ getNumParticles()

unsigned long long ItoSolver::getNumParticles	(	const WhichContainer	a_container,
		const bool	a_localOnly
	)		const

virtual

Get number of particles in a specified particle container.

Parameters

[in]	a_whichContainer	Which container to count particles in.
[in]	a_localOnly	Only report local particles (i.e. not reduced over MPI ranks)

◆ getParticles() [1/2]

ParticleContainer< ItoParticle > & ItoSolver::getParticles ( const WhichContainer a_container )

virtual

Get a general particle container.

Parameters

[in] a_container Which container to fetch.

◆ getParticles() [2/2]

const ParticleContainer< ItoParticle > & ItoSolver::getParticles ( const WhichContainer a_container ) const

virtual

Get a general particle container.

Parameters

[in] a_container Which container to fetch.

◆ getPhase()

phase::which_phase ItoSolver::getPhase ( ) const

Return phase.

Returns: Returns m_phase

◆ getPhi()

EBAMRCellData & ItoSolver::getPhi ( )

virtual

Get the mesh data.

Returns: Returns m_phi

◆ getPlotVariableNames()

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

virtual

Get output plot names.

Returns: Returns a string of all variables that this solver can add to plot files.

◆ getRealm()

const std::string ItoSolver::getRealm ( ) const

virtual

Get the realm where this solver is registered.

Returns: m_realm

◆ getSpecies()

const RefCountedPtr< ItoSpecies > & ItoSolver::getSpecies ( ) const

virtual

Get the species.

Returns: Returns m_species

◆ getVelocityFunction() [1/2]

EBAMRCellData & ItoSolver::getVelocityFunction ( )

virtual

Get cell-centered velocity mesh data.

Returns: m_velocityFunction

◆ getVelocityFunction() [2/2]

const EBAMRCellData & ItoSolver::getVelocityFunction ( ) const

virtual

Get cell-centered velocity mesh data.

Returns: m_velocityFunction

◆ initialData()

void ItoSolver::initialData ( )

virtual

Set the initial data.

This will add the initial particles and deposit them.

◆ interpolateDiffusion() [1/2]

void ItoSolver::interpolateDiffusion ( )

virtual

Interpolate the diffusion field to the particle positions.

This computes D_p = Df(X_p) where Df is the diffusion field on the mesh.

◆ interpolateDiffusion() [2/2]

void ItoSolver::interpolateDiffusion	(	const int	a_level,
		const DataIndex &	a_dit
	)

protectedvirtual

Interpolate the diffusion field to the particle positions.

This computes D_p = Df(X_p) where Df is the diffusion field on the mesh.

Parameters

[in]	a_level	Grid level
[in]	a_dit	Grid index

◆ interpolateMobilities() [1/2]

void ItoSolver::interpolateMobilities ( )

virtual

Interpolate mobilities.

This will switch between the two ways of computing the particle mobility.

◆ interpolateMobilities() [2/2]

void ItoSolver::interpolateMobilities	(	const int	a_level,
		const DataIndex &	a_dit,
		const EBCellFAB &	a_velocityMagnitude
	)

protectedvirtualnoexcept

Interpolate mobilities – this will switch between the two ways of computing the particle mobility.

Parameters

[in]	a_level	Grid level.
[in]	a_dit	Grid index.
[in]	a_velocityMagnitude	Velocity magnitude.

◆ interpolateMobilitiesDirect()

void ItoSolver::interpolateMobilitiesDirect	(	const int	a_level,
		const DataIndex &	a_dit
	)

protectedvirtualnoexcept

Directly interpolate mobilities. Interpolates for all particles in the specified grid patch.

Parameters

[in]	a_level	Grid level.
[in]	a_dit	Grid index.

◆ interpolateMobilitiesVelocity()

void ItoSolver::interpolateMobilitiesVelocity	(	const int	a_level,
		const DataIndex &	a_dit,
		const EBCellFAB &	a_velocityMagnitude
	)

protectedvirtualnoexcept

Interpolate mobilities through the velocity. Interpolates for all particles in the specified grid patch.

Parameters

[in]	a_level	Grid level.
[in]	a_dit	Grid index.
[in]	a_velocityMagnitude	Velocity magnitude.

◆ interpolateVelocities() [1/2]

void ItoSolver::interpolateVelocities ( )

virtual

Interpolate the particle velocities.

This will compute the particle velocities as v = mu * V(Xp) where mu is the particle mobility and V(Xp) is the interpolation of m_velocityFunction to the particle position.

◆ interpolateVelocities() [2/2]

void ItoSolver::interpolateVelocities	(	const int	a_level,
		const DataIndex &	a_dit
	)

virtual

Interpolate the particle velocities.

This will compute the particle velocities as v = mu * V(Xp) where mu is the particle mobility and V(Xp) is the interpolation of m_velocityFunction to the particle position.

Parameters

[in]	a_level	Grid level
[in]	a_dit	Grid index

◆ intersectParticles() [1/3]

void ItoSolver::intersectParticles	(	const EBIntersection	a_ebIntersection,
		const bool	a_deleteParticles,
		const std::function< void(ItoParticle &)>	a_nonDeletionModifier = `[](ItoParticle&) -> void { return; }`
	)

virtual

Do boundary intersection tests.

This will intersect the particles in the "bulk" particles data holder with the domain faces and EBs. If a particle crossed the EB it will be put into the "EB" particle data holder and likewise for the particles that crossed the domain side.

Parameters

[in]	a_ebIntersection	Enum for switching between various types of intersection tests.
[in]	a_deleteParticles	If true, the origin particle will also be removed from the bulk particle data holder.
[in]	a_nonDeletionModifier	Optional input argument for letting the user manipulate particles that were intersected but not deleted

Note: This will call the other version with WhichContainer::Bulk, WhichContainer::EB, and WhichContainer::Domain.

◆ intersectParticles() [2/3]

void ItoSolver::intersectParticles	(	const WhichContainer	a_particles,
		const WhichContainer	a_ebParticles,
		const WhichContainer	a_domainParticles,
		const EBIntersection	a_ebIntersection,
		const bool	a_deleteParticles,
		const std::function< void(ItoParticle &)>	a_nonDeletionModifier = `[](ItoParticle&) -> void { return; }`
	)

virtual

Do boundary intersection tests.

This will intersect the particles in the a_particles data holder with the domain faces and EBs. If a particle crossed the EB it will be put into the a_eb_particles particle data holder and likewise for the particles that crossed the domain side.

Parameters

[in]	a_particles	Which particle container to use for the "active" particles
[in]	a_ebParticles	Which particle container to put the EB particles
[in]	a_domainParticles	Which particle container to put the domain particles
[in]	a_ebIntersection	Enum for switching between various types of intersection tests.
[in]	a_deleteParticles	If true, the origin particle will also be removed from the bulk particle data holder.
[in]	a_nonDeletionModifier	Optional input argument for letting the user manipulate particles that were intersected but not deleted

Note: This will look up the ParticleContainer and call the other version.

◆ intersectParticles() [3/3]

void ItoSolver::intersectParticles	(	ParticleContainer< ItoParticle > &	a_particles,
		ParticleContainer< ItoParticle > &	a_ebParticles,
		ParticleContainer< ItoParticle > &	a_domainParticles,
		const EBIntersection	a_ebIntersection,
		const bool	a_deleteParticles,
		const std::function< void(ItoParticle &)>	a_nonDeletionModifier = `[](ItoParticle&) -> void { return; }`
	)

virtual

Do boundary intersection tests.

This will intersect the particles in the a_particles data holder with the domain faces and EBs. If a particle crossed the EB it will be put into the a_eb_particles particle data holder and likewise for the particles that crossed the domain side.

Parameters

[in]	a_particles	Which particle container to use for the "active" particles
[in]	a_ebParticles	Which particle container to put the EB particles
[in]	a_domainParticles	Which particle container to put the domain particles
[in]	a_ebIntersection	Enum for switching between various types of intersection tests.
[in]	a_deleteParticles	If true, the origin particle will also be removed from the bulk particle data holder.
[in]	a_nonDeletionModifier	Optional input argument for letting the user manipulate particles that were intersected but not deleted

◆ isDiffusive()

bool ItoSolver::isDiffusive ( ) const

virtual

Check if solver is diffusive.

Returns: Returns m_isDiffusive

◆ isMobile()

bool ItoSolver::isMobile ( ) const

virtual

Check if solver is mobile.

Returns: Returns m_isMobile

◆ makeSuperparticles() [1/4]

void ItoSolver::makeSuperparticles	(	const WhichContainer	a_container,
		const int	a_particlesPerCell
	)

virtual

Make superparticles for a full container – this is the AMR version that users will usually call.

Parameters

[in]	a_container	Which container to repartition into new superparticles
[in]	a_particlesPerCell	Target number of particles per cell

◆ makeSuperparticles() [2/4]

void ItoSolver::makeSuperparticles	(	const WhichContainer	a_container,
		const int	a_particlesPerCell,
		const int	a_level
	)

virtual

Make superparticles for a particle container – this is used for a specified grid level.

Parameters

[in]	a_container	Which container to repartition into new superparticles
[in]	a_particlesPerCell	Target number of particles per cell
[in]	a_level	Grid level

◆ makeSuperparticles() [3/4]

void ItoSolver::makeSuperparticles	(	const WhichContainer	a_container,
		const int	a_particlesPerCell,
		const int	a_level,
		const DataIndex	a_dit
	)

virtual

Make superparticles for a particle container – this is used for a specified grid level and patch.

Parameters

[in]	a_container	Which container to repartition into new superparticles
[in]	a_particlesPerCell	Target number of particles per cell
[in]	a_level	Grid level
[in]	a_dit	Grid index

◆ makeSuperparticles() [4/4]

void ItoSolver::makeSuperparticles	(	const WhichContainer	a_container,
		const Vector< int >	a_particlesPerCell
	)

virtual

Make superparticles for a full container – this is the AMR version that users will usually call.

Parameters

[in]	a_container	Which container to repartition into new superparticles
[in]	a_particlesPerCell	Target number of particles per cell. Vector indicates grid levels.

◆ makeSuperparticlesEqualWeightKD()

void ItoSolver::makeSuperparticlesEqualWeightKD	(	List< ItoParticle > &	a_particles,
		const CellInfo &	a_cellInfo,
		const int	a_particlesPerCell
	)		const

virtualnoexcept

Superparticle merging with KD/BVH trees.

Parameters

[in,out]	a_particles	Particles to be merged/split
[in]	a_cellInfo	Arithmetic information about the current grid cell.
[in]	a_particlesPerCell	Target number of particles per cell

◆ mergeParticles()

void ItoSolver::mergeParticles	(	List< ItoParticle > &	a_particles,
		const CellInfo &	a_cellInfo,
		const int	a_particlesPerCell
	)		const

virtualnoexcept

General superparticle merging with underlying algorithm through m_particleMerger.

Parameters

[in,out]	a_particles	Particles to be merged/split
[in]	a_cellInfo	Arithmetic information about the current grid cell.
[in]	a_particlesPerCell	Target number of particles per cell

◆ organizeParticlesByCell()

void ItoSolver::organizeParticlesByCell ( const WhichContainer a_container )

virtual

Sort the input particle container by cell.

Parameters

[in] a_container Container to be sorted.

◆ organizeParticlesByPatch()

void ItoSolver::organizeParticlesByPatch ( const WhichContainer a_container )

virtual

Sort the input particle container by patch.

Parameters

[in] a_container Container to be sorted.

◆ preRegrid()

void ItoSolver::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 caches the bulk particles.

◆ randomDirection()

RealVect ItoSolver::randomDirection ( ) const

inline

Draw a random direction in N-dimensional space.

We use the algorithm by Marsaglia (1972).

◆ randomGaussian()

RealVect ItoSolver::randomGaussian ( ) const

inline

Draw a random N-dimensional Gaussian number from a normal distribution with zero with and unit standard deviation.

Note: The distribution is truncated at m_normalDistributionTruncation – values above that threshold will be replaced by m_normalDistributionTruncation.

◆ redistributeAMR()

void ItoSolver::redistributeAMR ( EBAMRCellData & a_phi ) const

protectedvirtual

Redistribute mass in an AMR context.

We will have deposited particles into each cell, i.e. phi_i = m_i/dx^3. To obtain the true density in an EB context we need to divide by kappa such that phi_i = m_i/(kappa_i*dx^3). Unfortunately, this is numerically unstable because kappa_i can be arbitrarily small. We can set the density as phi_i = m_i/dx^3 but we will be missing a mass m_i*(1-kappa_i) from the cell. This mass can be smooshed into neighboring cells such as to make the total scheme conservative. As an option, we can also use a "non-conservative" divergence but the scheme is not guaranteed to be non-negative. All of this is just to say that we take the mass that fell inside the EB and put it back into the domain.

Parameters

[in,out] a_phi Quantity to be redistributed.

◆ registerOperators()

void ItoSolver::registerOperators ( ) const

virtual

Register operators.

This will register the required operators for running this class.

◆ regrid()

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

virtual

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.

◆ reinitializeParticles()

void ItoSolver::reinitializeParticles	(	List< ItoParticle > &	a_particles,
		const CellInfo &	a_cellInfo,
		const int	a_particlesPerCell
	)		const

virtualnoexcept

Particle re-initialization algorithm.

Parameters

[in,out]	a_particles	Particles to be merged/split
[in]	a_cellInfo	Arithmetic information about the current grid cell.
[in]	a_particlesPerCell	Target number of particles per cell

◆ remap()

void ItoSolver::remap ( const WhichContainer a_container )

virtual

Remap all particles in the input container.

Parameters

[in] a_container Particle container

◆ removeCoveredParticles() [1/3]

void ItoSolver::removeCoveredParticles	(	const EBRepresentation	a_representation,
		const Real	a_tol
	)

virtual

Remove particles that are inside the EB.

Parameters

[in]	a_ebRepresentation	EB representation (e.g. implicit function, discrete, voxel)
[in]	a_tol	Tolerance – removes particles if they are less than a_tol*dx away from the boundary.

Calls the other version with m_particles.

◆ removeCoveredParticles() [2/3]

void ItoSolver::removeCoveredParticles	(	const WhichContainer	a_container,
		const EBRepresentation	a_representation,
		const Real	a_tol
	)

virtual

Remove particles that are inside the EB.

Parameters

[in]	a_container	Which particle container to remove particles from
[in]	a_ebRepresentation	EB representation (e.g. implicit function, discrete, voxel)
[in]	a_tol	Tolerance – removes particles if they are less than a_tol*dx away from the boundary.

Note: Calls the other version with ParticleContainer = m_particles.at(a_container)

◆ removeCoveredParticles() [3/3]

void ItoSolver::removeCoveredParticles	(	ParticleContainer< ItoParticle > &	a_particles,
		const EBRepresentation	a_representation,
		const Real	a_tol
	)		const

virtual

Remove particles that are inside the EB.

Parameters

[in]	a_particles	Particles to remove.
[in]	a_ebRepresentation	EB representation (e.g. implicit function, discrete, voxel)
[in]	a_tol	Tolerance – removes particles if they are less than a_tol*dx away from the boundary.

◆ setAmr()

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

virtual

Set the AmrMesh object.

Parameters

[in] a_amr AmrMesh object.

◆ setComputationalGeometry()

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

virtual

Set computational geometry.

Parameters

[in] a_computationalGeometry Computational geometry.

◆ setDiffusionFunction()

void ItoSolver::setDiffusionFunction ( const Real a_diffusionCoefficient )

virtual

Utility function – set a constant diffusion coefficient.

Parameters

[in] a_diffusionCoefficient Diffusion coefficient

◆ setParticleDiffusion()

void ItoSolver::setParticleDiffusion ( const Real a_diffusion )

virtual

Sets diffusion coefficient for all particles.

Parameters

[in] a_diffusion Particle diffusion value.

◆ setParticleMerger()

void ItoSolver::setParticleMerger ( const ParticleManagement::ParticleMerger< ItoParticle > & a_particleMerger )

virtualnoexcept

Set the particle merger. This will get called when merging particles using makeSuperparticles.

Parameters

[in] a_particleMerger Particle merger

◆ setParticleMobility()

void ItoSolver::setParticleMobility ( const Real a_mobility )

virtual

Sets mobility coefficient for all particles.

Parameters

[in] a_mobility Particle mobility.

◆ setPhase()

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

virtual

Set phase where the particles will live.

Parameters

[in] a_phase Phase

◆ setRealm()

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

virtual

Set the realm where this solver will live.

Parameters

[in] a_realm Realm name.

◆ setSpecies()

void ItoSolver::setSpecies ( const RefCountedPtr< ItoSpecies > & a_species )

virtual

Set the species.

Parameters

[in] a_species Species to be solved for.

◆ setTime()

void ItoSolver::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

◆ setVelocityFunction()

void ItoSolver::setVelocityFunction ( const RealVect a_velocity )

virtual

Utility function – set a constant velocity.

Parameters

[in] a_velocity Velocity

◆ setVerbosity()

void ItoSolver::setVerbosity ( const int a_verbosity )

virtual

Set verbosity level for this solver.

Parameters

[in] a_verbosity Verbosity level.

◆ transferCoveredParticles() [1/3]

void ItoSolver::transferCoveredParticles	(	const EBRepresentation	a_representation,
		const Real	a_tol
	)

virtual

Transfer particles that are covered (within a_tol distance from EB) to another container.

Calls the other version with m_particles and m_coveredParticles

Parameters

[in]	a_ebRepresentation	EB representation (e.g. implicit function, discrete, voxel)
[in]	a_tol	Tolerance – removes particles if they are less than a_tol*dx away from the boundary.

◆ transferCoveredParticles() [2/3]

void ItoSolver::transferCoveredParticles	(	const WhichContainer	a_containerFrom,
		const WhichContainer	a_containerTo,
		const EBRepresentation	a_representation,
		const Real	a_tol
	)

virtual

Transfer particles that are covered (within a_tol distance from EB) to another container.

Parameters

[in]	a_containerFrom	Which particle container to transfer particles from
[in]	a_containerFrom	Which particle container to move particles into
[in]	a_ebRepresentation	EB representation (e.g. implicit function, discrete, voxel)
[in]	a_tol	Tolerance – removes particles if they are less than a_tol*dx away from the boundary.

◆ transferCoveredParticles() [3/3]

void ItoSolver::transferCoveredParticles	(	ParticleContainer< ItoParticle > &	a_particlesFrom,
		ParticleContainer< ItoParticle > &	a_particlesTo,
		const EBRepresentation	a_representation,
		const Real	a_tol
	)		const

virtual

Transfer particles that are inside the EB to another container.

Parameters

[in]	a_particlesFrom	Which particle container to transfer particles from
[in]	a_particlesTo	Which particle container to move particles into
[in]	a_ebRepresentation	EB representation (e.g. implicit function, discrete, voxel)
[in]	a_tol	Tolerance – removes particles if they are less than a_tol*dx away from the boundary.

◆ updateDiffusion() [1/2]

void ItoSolver::updateDiffusion ( )

virtual

Update mobilities parametrically from the particle energy.

This calls the diffusion function implemented by ItoSpecies. The particle diffusion is set D = f(p.energy()) where f is the diffusion function in ItoSpecies

◆ updateDiffusion() [2/2]

void ItoSolver::updateDiffusion	(	const int	a_level,
		const DataIndex	a_dit
	)

protectedvirtual

Update mobilities parametrically from the particle energy.

This calls the diffusion function implemented by ItoSpecies. The particle diffusion is set D = f(p.energy()) where f is the diffusion function in ItoSpecies

Parameters

[in]	a_level	Grid level
[in]	a_dit	Grid index

◆ updateMobilities() [1/2]

void ItoSolver::updateMobilities ( )

virtual

Update mobilities parametrically from the particle energy.

This calls the mobility function implemented by ItoSpecies. The particle mobility is set mu = f(p.energy()) where f is the mobility function in ItoSpecies

◆ updateMobilities() [2/2]

void ItoSolver::updateMobilities	(	const int	a_level,
		const DataIndex	a_dit
	)

protectedvirtual

Update mobilities parametrically from the particle energy.

This calls the mobility function implemented by ItoSpecies. The particle mobility is set mu = f(p.energy()) where f is the mobility function in ItoSpecies

Parameters

[in]	a_level	Grid level
[in]	a_dit	Grid index

◆ writeData()

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

virtualnoexcept

Write plot data.

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

Member Data Documentation

◆ m_className

std::string ItoSolver::m_className

protected

Class name.

ItoSolver for parent class – derived classes might be named something else.

◆ m_normalDistributionTruncation

Real ItoSolver::m_normalDistributionTruncation

protected

Truncation value for normal distribution.

This is used when drawing numbers from the Gaussian distribution, replacing all values above m_normalDistributionTruncation by m_normalDistributionTruncation.

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

Source/ItoDiffusion/CD_ItoSolver.H
Source/ItoDiffusion/CD_ItoSolver.cpp
Source/ItoDiffusion/CD_ItoSolverImplem.H

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ WhichCheckpoint

◆ WhichContainer

◆ WhichMobilityInterpolation

Member Function Documentation

◆ addParticles()

◆ allocate()

◆ clear() [1/3]

◆ clear() [2/3]

◆ clear() [3/3]

◆ computeAdvectiveDt() [1/2]

◆ computeAdvectiveDt() [2/2]

◆ computeAverageDiffusion()

◆ computeAverageEnergy()

◆ computeAverageMobility()

◆ computeDiffusiveDt() [1/2]

◆ computeDiffusiveDt() [2/2]

◆ computeDt() [1/3]

◆ computeDt() [2/3]

◆ computeDt() [3/3]

◆ computeHopDt() [1/3]

◆ computeHopDt() [2/3]

◆ computeHopDt() [3/3]

◆ computeLoads()

◆ depositConductivity() [1/2]

◆ depositConductivity() [2/2]

◆ depositDiffusivity() [1/2]

◆ depositDiffusivity() [2/2]

◆ depositEnergyDensity() [1/2]

◆ depositEnergyDensity() [2/2]

◆ depositHybrid()

◆ depositKappaConservative() [1/2]

◆ depositKappaConservative() [2/2]

◆ depositNonConservative()

◆ depositParticles() [1/5]

◆ depositParticles() [2/5]

◆ depositParticles() [3/5]

◆ depositParticles() [4/5]

◆ depositParticles() [5/5]

◆ depositParticlesNGP() [1/2]

◆ depositParticlesNGP() [2/2]

◆ drawNewParticles()

◆ getDeposition()

◆ getDiffusionFunction() [1/2]

◆ getDiffusionFunction() [2/2]

◆ getMobilityFunction() [1/2]

◆ getMobilityFunction() [2/2]

◆ getName()

◆ getNumberOfPlotVariables()

◆ getNumParticles()

◆ getParticles() [1/2]

◆ getParticles() [2/2]

◆ getPhase()

◆ getPhi()

◆ getPlotVariableNames()

◆ getRealm()

◆ getSpecies()

◆ getVelocityFunction() [1/2]

◆ getVelocityFunction() [2/2]

◆ initialData()

◆ interpolateDiffusion() [1/2]

◆ interpolateDiffusion() [2/2]

◆ interpolateMobilities() [1/2]

◆ interpolateMobilities() [2/2]

◆ interpolateMobilitiesDirect()

◆ interpolateMobilitiesVelocity()

◆ interpolateVelocities() [1/2]

◆ interpolateVelocities() [2/2]

◆ intersectParticles() [1/3]

◆ intersectParticles() [2/3]

◆ intersectParticles() [3/3]

◆ isDiffusive()

◆ isMobile()