Base time stepper class that advances the Ito-Poisson system of equations. More...

#include <CD_ItoPlasmaStepper.H>

Inheritance diagram for Physics::ItoPlasma::ItoPlasmaStepper:

Collaboration diagram for Physics::ItoPlasma::ItoPlasmaStepper:

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Public Member Functions
	ItoPlasmaStepper ()
	Default constructor. Sets default options.

	ItoPlasmaStepper (RefCountedPtr< ItoPlasmaPhysics > &a_physics)
	Full constructor. Calls the other constructor. More...

virtual	~ItoPlasmaStepper ()
	Destructor.

virtual void	parseOptions ()
	Parse options.

virtual void	parseRuntimeOptions () override
	Parse runtime configurable options.

virtual void	allocate () override
	Allocate storage for solvers.

virtual void	allocateInternals ()
	Allocate "internal" storage.

virtual void	setupSolvers () override
	Set up solvers.

virtual void	initialData () override
	Fill solvers with initial data.

virtual void	postCheckpointSetup () override
	Perform post-checkpoint operations. More...

virtual void	postCheckpointPoisson ()
	Do some post-checkpoint operations for the electrostatic part. More...

virtual void	postInitialize () override
	Post-initialization operations. Default does nothing.

virtual void	writePlotData (EBAMRCellData &a_output, Vector< std::string > &a_plotVariableNames, int &a_icomp) const override
	Write plot data to output holder. More...

virtual int	getNumberOfPlotVariables () const override
	Get number of plot variables for the output file.

virtual Vector< long int >	getCheckpointLoads (const std::string a_realm, const int a_level) const override
	Get computational loads to be checkpointed. More...

virtual Real	advance (const Real a_dt)=0
	Advancement method. Needs to be implemented by subclasses. More...

virtual Real	computeDt () override
	Compute a time step used for the advance method.

virtual void	synchronizeSolverTimes (const int a_step, const Real a_time, const Real a_dt) override
	Synchronize solver times for all the solvers. More...

virtual void	printStepReport () override
	Print a step report. Used by Driver for user monitoring of simulation.

virtual void	registerRealms () override
	Register realms used for the simulation.

virtual void	registerOperators () override
	Register operators used for the simulation.

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

virtual void	regrid (const int a_lmin, const int a_oldFinestLevel, const int a_newFinestLevel) override
	Regrid methods – puts all data on the new mesh. More...

virtual void	postRegrid () override
	Perform post-regrid operations – default implementation does nothing.

virtual bool	loadBalanceThisRealm (const std::string a_realm) const override
	Load balancing query for a specified realm. If this returns true for a_realm, load balancing routines will be called during regrids for the input realm. More...

virtual void	loadBalanceBoxes (Vector< Vector< int >> &a_procs, Vector< Vector< Box >> &a_boxes, const std::string a_realm, const Vector< DisjointBoxLayout > &a_grids, const int a_lmin, const int a_finestLevel) override
	Load balance grid boxes for a specified realm. More...

virtual void	setIto (RefCountedPtr< ItoLayout< ItoSolver >> &a_itoLayout) noexcept
	Set the Ito layout. More...

virtual void	setFieldSolver (RefCountedPtr< FieldSolver > &a_fieldSolver) noexcept
	Set the field solver. More...

virtual void	setRadiativeTransferSolvers (RefCountedPtr< RtLayout< McPhoto >> &a_rteLayout) noexcept
	Set the radiative transfer solvers. More...

virtual void	setVoltage (const std::function< Real(const Real a_time)> &a_voltage) noexcept
	Set voltage used for the simulation. More...

virtual Real	getTime () const noexcept
	Get current simulation time. More...

virtual void	computeElectricField (EBAMRCellData &a_electricField, const phase::which_phase a_phase) const noexcept
	Recompute the electric field onto the specified data holder. More...

Public Member Functions inherited from TimeStepper
	TimeStepper ()
	Default constructor (does nothing)

virtual	~TimeStepper ()
	Default destructor (does nothing)

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

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

virtual bool	needToRegrid ()
	Fuction which can have Driver do regrids at arbitrary points in the simulation. More...

Protected Types
enum class	TimeCode { Advection , Diffusion , AdvectionDiffusion , RelaxationTime , Hardcap , Physics }
	An enum for encapsulating how time steps were restricted.

Protected Member Functions
virtual void	setupIto ()
	Set up the Ito particle solvers.

virtual void	setupPoisson ()
	Set up the electrostatic field solver.

virtual void	setupRadiativeTransfer ()
	Set up the radiative transfer solver.

virtual void	setupSigma ()
	Set up the surface charge solver.

virtual void	intersectParticles (const SpeciesSubset a_speciesSubset, const EBIntersection a_interactionAlg, const bool a_delete) noexcept
	Intersect a subset of the particles with the domain and embedded boundary. More...

virtual void	intersectParticles (const SpeciesSubset a_speciesSubset, const ItoSolver::WhichContainer a_containerBulk, const ItoSolver::WhichContainer a_containerEB, const ItoSolver::WhichContainer a_containerDomain, const EBIntersection a_intersectionAlg, const bool a_delete) noexcept
	Intersect a subset of the particles with the domain and embedded boundary. More...

virtual void	removeCoveredParticles (const SpeciesSubset a_which, const EBRepresentation a_representation, const Real a_tolerance) noexcept
	Remove covered particles (i.e., particles inside the EB) More...

virtual void	removeCoveredParticles (const SpeciesSubset a_which, const ItoSolver::WhichContainer a_container, const EBRepresentation a_representation, const Real a_tolerance) noexcept
	Remove covered particles (i.e., particles inside the EB) More...

virtual void	transferCoveredParticles (const SpeciesSubset a_speciesSubset, const EBRepresentation a_representation, const Real a_tolerance) noexcept
	Transfer covered particles (i.e., particles inside the EB) from the ItoSolver bulk container to EB container. More...

virtual void	transferCoveredParticles (const SpeciesSubset a_speciesSubset, const ItoSolver::WhichContainer a_containerFrom, const ItoSolver::WhichContainer a_containerTo, const EBRepresentation a_representation, const Real a_tolerance) noexcept
	Transfer covered particles (i.e., particles inside the EB) from the ItoSolver bulk container to EB container. More...

virtual void	writeNumParticlesPerPatch (EBAMRCellData &a_output, int &a_icomp) const
	Write number of particles per patch to output holder. More...

virtual void	getMaxMinItoDensity (Real &a_maxDensity, Real &a_minDensity, std::string &a_maxSolver, std::string &a_minSolver) const noexcept
	Get maximum density of the Ito species. More...

virtual void	getParticleStatistics (Real &a_avgParticles, Real &a_sigma, Real &a_minParticles, Real &a_maxParticles, int &a_minRank, int &a_maxRank)
	Compute some particle statistics. More...

virtual void	loadBalanceParticleRealm (Vector< Vector< int >> &a_procs, Vector< Vector< Box >> &a_boxes, const std::string a_realm, const Vector< DisjointBoxLayout > &a_grids, const int a_lmin, const int a_finestLevel) noexcept
	Routine called by loadBalanceBoxes and used for particle-based load balancing. More...

virtual void	loadBalanceFluidRealm (Vector< Vector< int >> &a_procs, Vector< Vector< Box >> &a_boxes, const std::string a_realm, const Vector< DisjointBoxLayout > &a_grids, const int a_lmin, const int a_finestLevel) noexcept
	Routine called by loadBalanceBoxes and used for particle-based load balancing. More...

virtual Vector< RefCountedPtr< ItoSolver > >	getLoadBalanceSolvers () const noexcept
	Get the solvers used for load balancing. More...

virtual Real	computeMaxElectricField (const phase::which_phase a_phase) noexcept
	Compute the maximum electric field (norm) More...

virtual void	computeSpaceChargeDensity () noexcept
	Compute the space charge. Calls the other version. More...

virtual void	computeSpaceChargeDensity (MFAMRCellData &a_rho, const Vector< EBAMRCellData * > &a_densities) noexcept
	Compute the space charge density (both phases) More...

virtual void	computeConductivityCell (EBAMRCellData &a_conductivity) noexcept
	Compute the cell-centered conductiivty. More...

virtual void	computeConductivityCell (EBAMRCellData &a_conductivity, const Vector< ParticleContainer< ItoParticle > * > &a_particles) noexcept
	Compute the cell-centered conductiivty. More...

virtual void	computeCurrentDensity (EBAMRCellData &a_J) noexcept
	Compute the current density. More...

virtual Real	computeRelaxationTime () noexcept
	Compute the dielectric relaxation time.

virtual bool	solvePoisson () noexcept
	Solve the electrostatic problem. More...

virtual void	depositParticles (const SpeciesSubset a_speciesSubset) noexcept
	Deposit a subset of the ItoSolver particles on the mesh. More...

virtual void	depositParticles (const SpeciesSubset a_speciesSubset, const ItoSolver::WhichContainer a_container) noexcept
	Deposit a subset of the ItoSolver particles on the mesh. More...

virtual void	remapParticles (const SpeciesSubset a_speciesSubset) noexcept
	Remap a subset of ItoSolver particles. More...

virtual void	remapParticles (const SpeciesSubset a_speciesSubset, const ItoSolver::WhichContainer a_container) noexcept
	Remap a subset of ItoSolver particles. More...

virtual void	setItoVelocityFunctions () noexcept
	Set the Ito velocity functions. This is sgn(charge) * E. More...

virtual void	computeItoVelocities () noexcept
	Compute ItoSolver velocities. More...

virtual void	computeItoDiffusion () noexcept
	Compute ItoSolver velocities. More...

virtual void	computeItoMobilitiesLFA () noexcept
	Compute mesh-based mobilities for LFA coupling. More...

virtual void	computeItoMobilitiesLFA (Vector< EBAMRCellData * > &a_meshMobilities, const EBAMRCellData &a_electricField, const Real a_time) noexcept
	Compute mesh-based mobilities for LFA coupling. More...

virtual void	computeItoMobilitiesLFA (Vector< LevelData< EBCellFAB > * > &a_meshMobilities, const LevelData< EBCellFAB > &a_E, const int a_level, const Real a_time) noexcept
	Level-routine when computing mesh-based mobilities for LFA coupling. More...

virtual void	computeItoMobilitiesLFA (Vector< EBCellFAB * > &a_meshMobilities, const EBCellFAB &a_electricField, const int a_level, const DataIndex a_dit, const Box a_cellBox, const Real a_time) noexcept
	Patch-routine when computing mesh-based mobilities for LFA coupling. More...

virtual void	computeItoMobilitiesLEA () noexcept
	Compute the IonSolver particle mobilities in the LEA coupling regime. More...

virtual void	computeItoDiffusionLFA () noexcept
	Compute mesh-based diffusion coefficients for LFA coupling. More...

virtual void	computeItoDiffusionLFA (Vector< EBAMRCellData * > &a_diffusionCoefficient, const EBAMRCellData &a_electricField, const Real a_time) noexcept
	Compute mesh-based diffusion coefficients for LFA coupling. More...

virtual void	computeItoDiffusionLFA (Vector< LevelData< EBCellFAB > * > &a_diffusionCoefficient, const LevelData< EBCellFAB > &a_electricField, const int a_level, const Real a_time) noexcept
	Level-routine when computing mesh-based mobilities for LFA coupling. More...

virtual void	computeItoDiffusionLFA (Vector< EBCellFAB * > &a_diffusionCoefficient, const EBCellFAB &a_E, const int a_level, const DataIndex a_dit, const Box a_box, const Real a_time) noexcept
	Patch-routine when computing mesh-based diffusion coefficients in the LFA coupling. More...

virtual void	computeItoDiffusionLEA () noexcept
	Compute the IonSolver particle diffusion coefficients in the LEA coupling regime. More...

virtual void	getPhysicalParticlesPerCell (EBAMRCellData &a_ppc) const noexcept
	Get the physical number of particles per cell. More...

virtual void	computeReactiveParticlesPerCell (EBAMRCellData &a_ppc) noexcept
	Compute the number of reactive particles per cell. More...

virtual void	computeReactiveParticlesPerCell (LevelData< EBCellFAB > &a_ppc, const int a_level) noexcept
	Compute the number of reactive particles per cell. More...

virtual void	computeReactiveParticlesPerCell (EBCellFAB &a_ppc, const int a_level, const DataIndex a_dit, const Box a_box, const EBISBox &a_ebisbox) noexcept
	Compute the number of reactive particles per cell. More...

virtual void	computeReactiveMeanEnergiesPerCell (EBAMRCellData &a_meanEnergies) noexcept
	Compute the mean particle energy in all grid cells. More...

virtual void	computeReactiveMeanEnergiesPerCell (LevelData< EBCellFAB > &a_meanEnergies, const int a_level) noexcept
	Compute the mean particle energy in all grid cells. Level version. More...

virtual void	computeReactiveMeanEnergiesPerCell (EBCellFAB &a_meanEnergies, const int a_level, const DataIndex a_dit, const Box a_box, const EBISBox &a_ebisbox) noexcept
	Compute the mean particle energy in all grid cells. Patch version. More...

virtual void	advanceReactionNetwork (const Real a_dt) noexcept
	Chemistry advance over time a_dt. More...

virtual void	advanceReactionNetwork (const EBAMRCellData &a_E, const EBAMRCellData &a_EdotJ, const Real a_dt) noexcept
	Chemistry advance over time a_dt. AMR version. More...

virtual void	advanceReactionNetwork (LevelData< EBCellFAB > &a_particlesPerCell, LevelData< EBCellFAB > &a_newPhotonsPerCell, LevelData< EBCellFAB > &a_meanParticleEnergies, const LevelData< EBCellFAB > &a_electricField, const LevelData< EBCellFAB > &a_EdotJ, const int a_level, const Real a_dt) noexcept
	Chemistry advance over time a_dt. Level version. More...

virtual void	advanceReactionNetwork (EBCellFAB &a_particlesPerCell, EBCellFAB &a_newPhotonsPerCell, EBCellFAB &a_meanParticleEnergies, const EBCellFAB &a_electricField, const EBCellFAB &a_EdotJ, const int a_level, const DataIndex a_dit, const Box a_box, const Real a_dx, const Real a_dt) noexcept
	Chemistry advance over time a_dt. Patch version. More...

virtual void	reconcileParticles (const EBAMRCellData &a_newParticlesPerCell, const EBAMRCellData &a_oldParticlesPerCell, const EBAMRCellData &a_meanParticleEnergies, const EBAMRCellData &a_newPhotonsPerCell) noexcept
	Reconcile particles. At the bottom, this will call the physics interface for particle reconciliation. More...

virtual void	reconcileParticles (const LevelData< EBCellFAB > &a_newParticlesPerCell, const LevelData< EBCellFAB > &a_oldParticlesPerCell, const LevelData< EBCellFAB > &a_meanParticleEnergies, const LevelData< EBCellFAB > &a_newPhotonsPerCell, const int a_level) noexcept
	Reconcile particles. At the bottom, this will call the physics interface for particle reconciliation. More...

virtual void	reconcileParticles (const EBCellFAB &a_newParticlesPerCell, const EBCellFAB &a_oldParticlesPerCell, const EBCellFAB &a_meanParticleEnergies, const EBCellFAB &a_newPhotonsPerCell, const int a_level, const DataIndex a_dit, const Box a_box, const Real a_dx) noexcept
	Reconcile particles. At the bottom, this will call the physics interface for particle reconciliation. More...

virtual void	resolveParticlesEB (const Real a_dt) noexcept
	Resolve particle injection at EBs. More...

virtual void	resolveParticlesEB (Vector< ParticleContainer< ItoParticle > * > &a_inOutParticles, Vector< ParticleContainer< Photon > * > &a_inOutPhotons, const EBAMRCellData &a_electricField, const Real a_dt) noexcept
	Resolve particle injection at EBs. More...

virtual void	injectParticlesEB () noexcept
	Inject particles through the EB. More...

virtual void	injectParticlesEB (Vector< ParticleContainer< ItoParticle > * > a_bulkParticles, Vector< ParticleContainer< ItoParticle > * > a_injectedParticles) noexcept
	Inject particles through the EB.

virtual Real	computePhysicsDt () noexcept
	Compute a maximum time step from the physics interface. More...

virtual Real	computePhysicsDt (const EBAMRCellData &a_electricField) noexcept
	Compute a maximum time step from the physics interface. More...

virtual Real	computePhysicsDt (const LevelData< EBCellFAB > &a_electricField, const LevelData< EBCellFAB > &a_particlesPerCell, const int a_level) noexcept
	Compute a maximum time step from the physics interface. More...

virtual Real	computePhysicsDt (const EBCellFAB &a_electricField, const EBCellFAB &a_particlesPercCell, const int a_level, const DataIndex a_dit, const Box a_box) noexcept
	Compute a maximum time step from the physics interface. More...

virtual void	advancePhotons (const Real a_dt) noexcept
	Photon advancement routine. More...

virtual void	sortPhotonsByCell (const McPhoto::WhichContainer a_which) noexcept
	Sort photons by cells. More...

virtual void	sortPhotonsByPatch (const McPhoto::WhichContainer a_which) noexcept
	Sort photons by patch. More...

virtual void	computeEdotJSource (const Real a_dt) noexcept
	Compute the energy source term for the various plasma species. More...

virtual void	initialSigma ()
	Fill surface charge solver with initial data.

virtual void	parseVerbosity () noexcept
	Parse chattiness. More...

virtual void	parseAbort () noexcept
	Parse abort on failure.

virtual void	parseSuperParticles () noexcept
	Parse the desired number of particles per cell. More...

virtual void	parseDualGrid () noexcept
	Parse dual or single realm calculations. More...

virtual void	parseLoadBalance () noexcept
	Parse load balancing.

virtual void	parseTimeStepRestrictions () noexcept
	Parse time step restrictions.

virtual void	parseParametersEB () noexcept
	Parse things related to the EB.

virtual void	parsePlotVariables () noexcept
	Parse plot variables.

Protected Attributes
BoxSorting	m_boxSort
	Box sorting method when using dual-grid with particle load balancing.

TimeCode	m_timeCode
	Time code for understanding how the time step was restricted.

std::string	m_fluidRealm
	Realm used for the fluid part (i.e., electrostatic) part of the simulation. More...

std::string	m_particleRealm
	Realm used for the particle part of the simulation.

std::string	m_name
	Time stepper name.

phase::which_phase	m_plasmaPhase
	Phase where we solve for the plasma. More...

RefCountedPtr< ItoPlasmaPhysics >	m_physics
	Implementation of ItoPlasmaPhysics. More...

RefCountedPtr< ItoLayout< ItoSolver > >	m_ito
	Ito solvers.

RefCountedPtr< RtLayout< McPhoto > >	m_rte
	Radiative transfer solvers.

RefCountedPtr< FieldSolver >	m_fieldSolver
	Field solver.

RefCountedPtr< SurfaceODESolver< 1 > >	m_sigmaSolver
	Surface charge solver.

std::function< Real(const Real a_time)>	m_voltage
	Voltage curve on the electrodes used in the simulation.

bool	m_abortOnFailure
	Flag for abandoning simulation of Poisson solver fails.

bool	m_dualGrid
	Using dual grid or not.

bool	m_profile
	Profile kernels or not.

bool	m_regridSuperparticles
	Do or do not superparticle merging/splitting on regrids.

bool	m_loadBalanceParticles
	Load balance particle realm or not.

bool	m_loadBalanceFluid
	Load balance fluid realm or not.

bool	m_useNewReactionAlgorithm
	For switching between the old and new reaction algorithms.

bool	m_plotConductivity
	Plot conductivity or not.

bool	m_plotCurrentDensity
	Plot conductivity or not.

bool	m_plotParticlesPerPatch
	Plot number of particles per patch or not.

Vector< int >	m_particlesPerCell
	Target number of particles per cell when squishing ItoParticle's into superparticles.

int	m_mergeInterval
	How often to merge superparticles. More...

Real	m_loadPerCell
	The "background" load per cell when using particle load balancing. More...

Real	m_toleranceEB
	Accepted tolerance (relative to dx) for EB intersection.

Real	m_advectionCFL
	CFL-like time step for advection.

Real	m_diffusionCFL
	CFL-like time step for diffusion.

Real	m_advectionDiffusionCFL
	CFL-like time step for advection-diffusion.

Real	m_relaxTimeFactor
	Factor proportional to the dielectric relaxation time dtRelax = eps0/sigma. More...

Real	m_minDt
	Minimum permitted time step.

Real	m_maxDt
	Maximum permitted time step.

Real	m_advectionDt
	The advective time step (not multiplied by m_advectionCFL)

Real	m_diffusionDt
	The diffusive time step (not multiplied by m_diffusionCFL)

Real	m_advectionDiffusionDt
	The advection-diffusion time step (not multiplied by m_advectionDiffusionCFL)

Real	m_relaxationTime
	The relaxation time eps0/sigma.

Real	m_physicsDt
	The physics-based time step.

Vector< EBAMRCellData >	m_loadBalancePPC
	For holding the number of computational particles per cell when load balancing.

Vector< int >	m_loadBalanceIndices
	Solver indices used when load-balancing the particle solvers.

EBAMRCellData	m_currentDensity
	Storage for current density. More...

EBAMRCellData	m_conductivityCell
	Cell-centered conductivity. More...

EBAMRFluxData	m_conductivityFace
	Face-centered conductivity. More...

EBAMRIVData	m_conductivityEB
	EB-centered conductivity. More...

EBAMRCellData	m_oldPPC
	For holding the number of physical particles per cell. More...

EBAMRCellData	m_newPPC
	For holding the number of physical particles per cell. More...

EBAMRCellData	m_particlePPC
	For holding the number of physical particles per cell for all species. More...

EBAMRCellData	m_particleYPC
	For holding the number of generated photons per cell. More...

EBAMRCellData	m_particleEPS
	For holding the mean particle energy. More...

EBAMRCellData	m_particleOldPPC
	For holding the previous number of particles per cell for all species. More...

EBAMRCellData	m_fluidPPC
	For holding the number of particles per cell for all species. More...

EBAMRCellData	m_fluidYPC
	For holding the number of generated photons per cell. More...

EBAMRCellData	m_fluidEPS
	For holding the mean particle energy. More...

EBAMRCellData	m_electricFieldFluid
	Storage for holding the plasma phase electric field on the fluid realm.

EBAMRCellData	m_electricFieldParticle
	Storage for holding the plasma phase electric field on the particle realm.

Vector< EBAMRCellData >	m_energySources
	Storage for holding the energy sources for each species. More...

EBAMRCellData	m_EdotJ
	Storage for holdnig E*J on the fluid realm. 1 component.

EBAMRCellData	m_fluidScratch1
	Scratch storage on the fluid realm having 1 component.

EBAMRCellData	m_fluidScratchD
	Scratch storage on the fluid realm with SpaceDim components.

EBAMRCellData	m_particleScratch1
	Scratch storage on the particle realm with 1 component.

EBAMRCellData	m_particleScratchD
	Scratch storage on the particle realm with SpaceDim components.

Protected Attributes inherited from TimeStepper
int	m_verbosity
	Class verbosity.

int	m_timeStep
	Time step.

Real	m_time
	TIme.

Real	m_dt
	Previous time step size.

RefCountedPtr< AmrMesh >	m_amr
	AmrMesh.

RefCountedPtr< ComputationalGeometry >	m_computationalGeometry
	Computational geometry.

Detailed Description

Base time stepper class that advances the Ito-Poisson system of equations.

Constructor & Destructor Documentation

◆ ItoPlasmaStepper()

ItoPlasmaStepper::ItoPlasmaStepper ( RefCountedPtr< ItoPlasmaPhysics > & a_physics )

Full constructor. Calls the other constructor.

Parameters

[in] a_physics Implementation of the Ito plasma physics model.

Member Function Documentation

◆ advance()

virtual Real Physics::ItoPlasma::ItoPlasmaStepper::advance ( const Real a_dt )

pure virtual

Advancement method. Needs to be implemented by subclasses.

Parameters

[in] a_dt Time step to be used for advancement

Returns: Returns the time step that was used.

Implements TimeStepper.

Implemented in Physics::ItoPlasma::ItoPlasmaGodunovStepper.

◆ advancePhotons()

void ItoPlasmaStepper::advancePhotons ( const Real a_dt )

protectedvirtualnoexcept

Photon advancement routine.

Parameters

[in] a_dt Time step

◆ advanceReactionNetwork() [1/4]

void ItoPlasmaStepper::advanceReactionNetwork	(	const EBAMRCellData &	a_E,
		const EBAMRCellData &	a_EdotJ,
		const Real	a_dt
	)

protectedvirtualnoexcept

Chemistry advance over time a_dt. AMR version.

Parameters

[in]	a_electricField	Electric field. Must be defined on the fluid realm.
[in]	a_EdotJ	Source term EdotJ for each species. Must have same number of components as Ito layout and be defined on the fluid realm.
[in]	a_dt	Time step

Note: This will call the level versions AND reconcileParticles. The kernel will only run over valid grid cells (not covered by a finer grid.

◆ advanceReactionNetwork() [2/4]

void ItoPlasmaStepper::advanceReactionNetwork ( const Real a_dt )

protectedvirtualnoexcept

Chemistry advance over time a_dt.

Parameters

[in] a_dt Time step

Note: This will call the other version. The kernel will only run over valid grid cells (not covered by a finer grid.

◆ advanceReactionNetwork() [3/4]

void ItoPlasmaStepper::advanceReactionNetwork	(	EBCellFAB &	a_particlesPerCell,
		EBCellFAB &	a_newPhotonsPerCell,
		EBCellFAB &	a_meanParticleEnergies,
		const EBCellFAB &	a_electricField,
		const EBCellFAB &	a_EdotJ,
		const int	a_level,
		const DataIndex	a_dit,
		const Box	a_box,
		const Real	a_dx,
		const Real	a_dt
	)

protectedvirtualnoexcept

Chemistry advance over time a_dt. Patch version.

Parameters

[in,out]	a_particlesPerCell	Number of particles per cell for each plasma species
[in,out]	a_newPhotonsPerCell	Number of physical photons to be generated for each photon species
[in,out]	a_meanParticleEnergies	Mean particle energies for each plasma species
[in]	a_electricField	Electric field.
[in]	a_EdotJ	EdotJ for each plasma species.
[in]	a_level	Grid level
[in]	a_dit	Grid index.
[in]	a_box	Grid box
[in]	a_dx	Grid resolution.
[in]	a_dt	Time increment

Note: This should be called through the AMR signature. All data should be defined on the fluid realm. The kernel will only run over valid grid cells (not covered by a finer grid.

◆ advanceReactionNetwork() [4/4]

void ItoPlasmaStepper::advanceReactionNetwork	(	LevelData< EBCellFAB > &	a_particlesPerCell,
		LevelData< EBCellFAB > &	a_newPhotonsPerCell,
		LevelData< EBCellFAB > &	a_meanParticleEnergies,
		const LevelData< EBCellFAB > &	a_electricField,
		const LevelData< EBCellFAB > &	a_EdotJ,
		const int	a_level,
		const Real	a_dt
	)

protectedvirtualnoexcept

Chemistry advance over time a_dt. Level version.

Parameters

[in,out]	a_particlesPerCell	Number of particles per cell for each plasma species
[in,out]	a_newPhotonsPerCell	Number of physical photons to be generated for each photon species
[in,out]	a_meanParticleEnergies	Mean particle energies for each plasma species
[in]	a_electricField	Electric field.
[in]	a_EdotJ	EdotJ for each plasma species.
[in]	a_level	Grid level
[in]	a_dt	Time increment

Note: This should be called through the AMR signature. All data should be defined on the fluid realm. The kernel will only run over valid grid cells (not covered by a finer grid.

◆ computeConductivityCell() [1/2]

void ItoPlasmaStepper::computeConductivityCell ( EBAMRCellData & a_conductivity )

protectedvirtualnoexcept

Compute the cell-centered conductiivty.

Parameters

[out] a_conductivity Cell-centered conductivity

Note: Calls the other version.

◆ computeConductivityCell() [2/2]

void ItoPlasmaStepper::computeConductivityCell	(	EBAMRCellData &	a_conductivity,
		const Vector< ParticleContainer< ItoParticle > * > &	a_particles
	)

protectedvirtualnoexcept

Compute the cell-centered conductiivty.

Parameters

[out]	a_conductivity	Cell-centered conductivity
[in]	a_particles	Ito particles.

◆ computeCurrentDensity()

void ItoPlasmaStepper::computeCurrentDensity ( EBAMRCellData & a_J )

protectedvirtualnoexcept

Compute the current density.

Note: This calls computeConductivityCell and uses m_electricFieldFluid. Make sure they're updated.

◆ computeEdotJSource()

void ItoPlasmaStepper::computeEdotJSource ( const Real a_dt )

protectedvirtualnoexcept

Compute the energy source term for the various plasma species.

Parameters

[in] a_dt Time step during which the particles move.

Note: This fills m_EdotJ

◆ computeElectricField()

void ItoPlasmaStepper::computeElectricField	(	EBAMRCellData &	a_electricField,
		const phase::which_phase	a_phase
	)		const

virtualnoexcept

Recompute the electric field onto the specified data holder.

Parameters

[out]	a_electricField	Electric field on cell centroid (defined on the fluid realm).
[in]	a_phase	Phase where we compute the electric field.

◆ computeItoDiffusion()

void ItoPlasmaStepper::computeItoDiffusion ( )

protectedvirtualnoexcept

Compute ItoSolver velocities.

This will compute the diffusion coefficients (in the specified coupling regime)

◆ computeItoDiffusionLEA()

void ItoPlasmaStepper::computeItoDiffusionLEA ( )

protectedvirtualnoexcept

Compute the IonSolver particle diffusion coefficients in the LEA coupling regime.

Note: This one is very simple because the solvers just update the diffusion coefficients from appropriate coupling functions.

◆ computeItoDiffusionLFA() [1/4]

void ItoPlasmaStepper::computeItoDiffusionLFA ( )

protectedvirtualnoexcept

Compute mesh-based diffusion coefficients for LFA coupling.

Note: Calls the other version with diffusion coefficients taken from ItoSolver solvers.

◆ computeItoDiffusionLFA() [2/4]

void ItoPlasmaStepper::computeItoDiffusionLFA	(	Vector< EBAMRCellData * > &	a_diffusionCoefficient,
		const EBAMRCellData &	a_electricField,
		const Real	a_time
	)

protectedvirtualnoexcept

Compute mesh-based diffusion coefficients for LFA coupling.

Parameters

[out]	a_diffusionCoefficients	Mesh-based diffusion coefficients. Must be defined on the particle realm.
[in]	a_electricField	Electric field. Must be defined on the fluid realm.
[in]	a_time	Time

◆ computeItoDiffusionLFA() [3/4]

void ItoPlasmaStepper::computeItoDiffusionLFA	(	Vector< EBCellFAB * > &	a_diffusionCoefficient,
		const EBCellFAB &	a_E,
		const int	a_level,
		const DataIndex	a_dit,
		const Box	a_box,
		const Real	a_time
	)

protectedvirtualnoexcept

Patch-routine when computing mesh-based diffusion coefficients in the LFA coupling.

Parameters

[out]	a_diffusionCoefficients	Diffusion coefficients. Must be defined on the fluid realm.
[in]	a_electricField	Electric field. Must be defined on the fluid realm.
[in]	a_level	Grid level
[in]	a_time	Time
[in]	a_level	Grid level
[in]	a_dit	Grid index
[in]	a_cellBox	Computation box
[in]	a_time	Time

◆ computeItoDiffusionLFA() [4/4]

void ItoPlasmaStepper::computeItoDiffusionLFA	(	Vector< LevelData< EBCellFAB > * > &	a_diffusionCoefficient,
		const LevelData< EBCellFAB > &	a_electricField,
		const int	a_level,
		const Real	a_time
	)

protectedvirtualnoexcept

Level-routine when computing mesh-based mobilities for LFA coupling.

Parameters

[out]	a_diffusionCoefficients	Diffusion coefficients. Must be defined on the fluid realm.
[in]	a_electricField	Electric field. Must be defined on the fluid realm.
[in]	a_level	Grid level
[in]	a_time	Time

◆ computeItoMobilitiesLEA()

void ItoPlasmaStepper::computeItoMobilitiesLEA ( )

protectedvirtualnoexcept

Compute the IonSolver particle mobilities in the LEA coupling regime.

Note: This one is very simple because the solvers just update the mobilities from appropriate coupling functions.

◆ computeItoMobilitiesLFA() [1/4]

void ItoPlasmaStepper::computeItoMobilitiesLFA ( )

protectedvirtualnoexcept

Compute mesh-based mobilities for LFA coupling.

Note: Calls the other version with mesh mobilities taken from ItoSolver solvers.

◆ computeItoMobilitiesLFA() [2/4]

void ItoPlasmaStepper::computeItoMobilitiesLFA	(	Vector< EBAMRCellData * > &	a_meshMobilities,
		const EBAMRCellData &	a_electricField,
		const Real	a_time
	)

protectedvirtualnoexcept

Compute mesh-based mobilities for LFA coupling.

Parameters

[out]	a_meshMobilities	Mesh-based mobilities. Must be defined on the particle realm.
[in]	a_electricField	Electric field. Must be defined on the fluid realm.
[in]	a_time	Time

◆ computeItoMobilitiesLFA() [3/4]

void ItoPlasmaStepper::computeItoMobilitiesLFA	(	Vector< EBCellFAB * > &	a_meshMobilities,
		const EBCellFAB &	a_electricField,
		const int	a_level,
		const DataIndex	a_dit,
		const Box	a_cellBox,
		const Real	a_time
	)

protectedvirtualnoexcept

Patch-routine when computing mesh-based mobilities for LFA coupling.

Parameters

[out]	a_meshMobilities	Mesh-based mobilities. Must be defined on the fluid realm.
[in]	a_electricField	Electric field. Must be defined on the fluid realm.
[in]	a_level	Grid level
[in]	a_dit	Grid index
[in]	a_cellBox	Computation box
[in]	a_time	Time

◆ computeItoMobilitiesLFA() [4/4]

void ItoPlasmaStepper::computeItoMobilitiesLFA	(	Vector< LevelData< EBCellFAB > * > &	a_meshMobilities,
		const LevelData< EBCellFAB > &	a_E,
		const int	a_level,
		const Real	a_time
	)

protectedvirtualnoexcept

Level-routine when computing mesh-based mobilities for LFA coupling.

Parameters

[out]	a_meshMobilities	Mesh-based mobilities. Must be defined on the fluid realm.
[in]	a_electricField	Electric field. Must be defined on the fluid realm.
[in]	a_level	Grid level
[in]	a_time	Time

◆ computeItoVelocities()

void ItoPlasmaStepper::computeItoVelocities ( )

protectedvirtualnoexcept

Compute ItoSolver velocities.

This will compute the mobilities and then interpolate mu*E to particle positions.

◆ computeMaxElectricField()

Real ItoPlasmaStepper::computeMaxElectricField ( const phase::which_phase a_phase )

protectedvirtualnoexcept

Compute the maximum electric field (norm)

Parameters

[in] a_phase Phase where we compute the field.

◆ computePhysicsDt() [1/4]

Real ItoPlasmaStepper::computePhysicsDt ( )

protectedvirtualnoexcept

Compute a maximum time step from the physics interface.

Note: Calls the other version with m_electricFieldParticle and the ItoSolver densities. The kernels are only called on the valid region.

◆ computePhysicsDt() [2/4]

Real ItoPlasmaStepper::computePhysicsDt ( const EBAMRCellData & a_electricField )

protectedvirtualnoexcept

Compute a maximum time step from the physics interface.

Parameters

[in]	a_electricField	Electric field.
[in]	a_densities	ItoSolver mesh densities.

Note: Input data must be defined on the fluid realms. Kernels are only called on the valid region.

◆ computePhysicsDt() [3/4]

Real ItoPlasmaStepper::computePhysicsDt	(	const EBCellFAB &	a_electricField,
		const EBCellFAB &	a_particlesPercCell,
		const int	a_level,
		const DataIndex	a_dit,
		const Box	a_box
	)

protectedvirtualnoexcept

Compute a maximum time step from the physics interface.

Parameters

[in]	a_electricField	Electric field.
[in]	a_particlesPerCell	Number of particles per grid cell
[in]	a_level	Grid level
[in]	a_dit	Grid index
[in]	a_box	Grid box

Note: Input data must be defined on the fluid realms. Kernels are only called on the valid region.

◆ computePhysicsDt() [4/4]

Real ItoPlasmaStepper::computePhysicsDt	(	const LevelData< EBCellFAB > &	a_electricField,
		const LevelData< EBCellFAB > &	a_particlesPerCell,
		const int	a_level
	)

protectedvirtualnoexcept

Compute a maximum time step from the physics interface.

Parameters

[in]	a_electricField	Electric field.
[in]	a_particlesPerCell	Number of particles per grid cell
[in]	a_level	Grid level

Note: Input data must be defined on the fluid realms. Kernels are only called on the valid region.

◆ computeReactiveMeanEnergiesPerCell() [1/3]

void ItoPlasmaStepper::computeReactiveMeanEnergiesPerCell ( EBAMRCellData & a_meanEnergies )

protectedvirtualnoexcept

Compute the mean particle energy in all grid cells.

Parameters

[out] a_meanEnergies Mean particle energies = sum(w * E)/sum(w) for all species.

Note: a_meanEnergies must be defined over the particle realm and have the same number of components as the number of palsma species involved in the simulation.

◆ computeReactiveMeanEnergiesPerCell() [2/3]

void ItoPlasmaStepper::computeReactiveMeanEnergiesPerCell	(	EBCellFAB &	a_meanEnergies,
		const int	a_level,
		const DataIndex	a_dit,
		const Box	a_box,
		const EBISBox &	a_ebisbox
	)

protectedvirtualnoexcept

Compute the mean particle energy in all grid cells. Patch version.

Parameters

[out]	a_meanEnergies	Number of physical particles per grid cell for all species
[in]	a_level	Grid level
[in]	a_dit	Grid index
[in]	a_box	Grid box
[in]	a_ebisbox	EB grid box

Note: a_meanEnergies must be defined over the particle realm and have the same number of components as the number of palsma species involved in the simulation.

◆ computeReactiveMeanEnergiesPerCell() [3/3]

void ItoPlasmaStepper::computeReactiveMeanEnergiesPerCell	(	LevelData< EBCellFAB > &	a_meanEnergies,
		const int	a_level
	)

protectedvirtualnoexcept

Compute the mean particle energy in all grid cells. Level version.

Parameters

[out]	a_meanEnergies	Mean particle energies = sum(w * E)/sum(w) for all species.
[in]	a_level	Grid level

Note: a_meanEnergies must be defined over the particle realm and have the same number of components as the number of palsma species involved in the simulation.

◆ computeReactiveParticlesPerCell() [1/3]

void ItoPlasmaStepper::computeReactiveParticlesPerCell ( EBAMRCellData & a_ppc )

protectedvirtualnoexcept

Compute the number of reactive particles per cell.

Parameters

[out] a_ppc Number of physical particles per grid cell for all species

Note: a_ppc Must be defined over the particle realm and have the same number of components as the number of plasma species involved in the simulation.

◆ computeReactiveParticlesPerCell() [2/3]

void ItoPlasmaStepper::computeReactiveParticlesPerCell	(	EBCellFAB &	a_ppc,
		const int	a_level,
		const DataIndex	a_dit,
		const Box	a_box,
		const EBISBox &	a_ebisbox
	)

protectedvirtualnoexcept

Compute the number of reactive particles per cell.

Parameters

[out]	a_ppc	Number of physical particles per grid cell for all species
[in]	a_level	Grid level
[in]	a_dit	Grid index
[in]	a_box	Grid box
[in]	a_ebisbox	EB grid box

Note: a_ppc Must be defined over the particle realm and have the same number of components as the number of plasma species involved in the simulation.

◆ computeReactiveParticlesPerCell() [3/3]

void ItoPlasmaStepper::computeReactiveParticlesPerCell	(	LevelData< EBCellFAB > &	a_ppc,
		const int	a_level
	)

protectedvirtualnoexcept

Compute the number of reactive particles per cell.

Parameters

[out]	a_ppc	Number of physical particles per grid cell for all species
[in]	a_level	Grid level

Note: a_ppc Must be defined over the particle realm and have the same number of components as the number of plasma species involved in the simulation.

◆ computeSpaceChargeDensity() [1/2]

void ItoPlasmaStepper::computeSpaceChargeDensity ( )

protectedvirtualnoexcept

Compute the space charge. Calls the other version.

Note: This runs through the ItoSolver densities – user should remember to deposit before calling this routine.

◆ computeSpaceChargeDensity() [2/2]

void ItoPlasmaStepper::computeSpaceChargeDensity	(	MFAMRCellData &	a_rho,
		const Vector< EBAMRCellData * > &	a_densities
	)

protectedvirtualnoexcept

Compute the space charge density (both phases)

Parameters

[out]	a_rho	Space cahrge density
[in]	a_phase	Phase where we compute the space charge density

◆ depositParticles() [1/2]

void ItoPlasmaStepper::depositParticles ( const SpeciesSubset a_speciesSubset )

protectedvirtualnoexcept

Deposit a subset of the ItoSolver particles on the mesh.

Note: Calls the other version with ItoSolver::WhichContainer::Bulk

◆ depositParticles() [2/2]

void ItoPlasmaStepper::depositParticles	(	const SpeciesSubset	a_speciesSubset,
		const ItoSolver::WhichContainer	a_container
	)

protectedvirtualnoexcept

Deposit a subset of the ItoSolver particles on the mesh.

Parameters

[in]	a_speciesSubset	Subset of species to deposit
[in]	a_container	Which container in ItoSolver to deposit.

◆ getCheckpointLoads()

Vector< long int > ItoPlasmaStepper::getCheckpointLoads	(	const std::string	a_realm,
		const int	a_level
	)		const

overridevirtual

Get computational loads to be checkpointed.

This is used by Driver both for setting up load-balanced restarts AND for plotting the computational loads to a file. This routine is disjoint from loadBalanceBoxes because this routine is not part of a regrid. This means that we are not operating with temporarily load balanced grids, and all operators etc. are already in place.

Parameters

[in]	a_realm	Realm
[in]	a_level	Grid level

Returns: Returns computational loads for each box on grid level a_level.

Reimplemented from TimeStepper.

◆ getLoadBalanceSolvers()

Vector< RefCountedPtr< ItoSolver > > ItoPlasmaStepper::getLoadBalanceSolvers ( ) const

protectedvirtualnoexcept

Get the solvers used for load balancing.

This depends on m_loadBalanceIndex – if it's < 0 we use ALL plasma species for load balancing.

◆ getMaxMinItoDensity()

void ItoPlasmaStepper::getMaxMinItoDensity	(	Real &	a_maxDensity,
		Real &	a_minDensity,
		std::string &	a_maxSolver,
		std::string &	a_minSolver
	)		const

protectedvirtualnoexcept

Get maximum density of the Ito species.

Parameters

[out]	a_maxDensity	Maximum mesh density
[out]	a_minDensity	Minium mesh density
[out]	a_maxSolver	Solver with highest density
[out]	a_minSolver	Solver with lowest density

◆ getParticleStatistics()

void ItoPlasmaStepper::getParticleStatistics	(	Real &	a_avgParticles,
		Real &	a_sigma,
		Real &	a_minParticles,
		Real &	a_maxParticles,
		int &	a_minRank,
		int &	a_maxRank
	)

protectedvirtual

Compute some particle statistics.

Parameters

[out]	a_avgParticles	Average numer of particles
[out]	a_sigma	Particle standard deviation (across MPI ranks)
[out]	a_minParticles	Minimum number of particles
[out]	a_maxParticles	Maximum number of particles
[out]	a_minRank	MPI rank with lowest number of particles
[out]	a_maxRank	MPI rank with highest number of particles

◆ getPhysicalParticlesPerCell()

void ItoPlasmaStepper::getPhysicalParticlesPerCell ( EBAMRCellData & a_ppc ) const

protectedvirtualnoexcept

Get the physical number of particles per cell.

Parameters

[out] a_ppc Number of physical particles per cell. Must be defined over the fluid realm.

◆ getTime()

Real ItoPlasmaStepper::getTime ( ) const

virtualnoexcept

Get current simulation time.

Returns: m_time

◆ injectParticlesEB()

void ItoPlasmaStepper::injectParticlesEB ( )

protectedvirtualnoexcept

Inject particles through the EB.

Note: Calls the other version with solver containers.

◆ intersectParticles() [1/2]

void ItoPlasmaStepper::intersectParticles	(	const SpeciesSubset	a_speciesSubset,
		const EBIntersection	a_interactionAlg,
		const bool	a_delete
	)

protectedvirtualnoexcept

Intersect a subset of the particles with the domain and embedded boundary.

This calls the other version, intersecting the Ito bulk particles with the EB and placing the collided particles in the appropriate particle containers (ItoSolver::WhichContainer::EB, for example).

Parameters

[in]	a_speciesSubset	Subset of particles to intersect. Can be charged, mobile, diffusive, etc.
[in]	a_intersectionAlg	Representation of the EB – basically an algorithmic selection.
[in]	a_delete	Delete original particles. If this is left to false, the particles are copied into the other containers.

◆ intersectParticles() [2/2]

void ItoPlasmaStepper::intersectParticles	(	const SpeciesSubset	a_speciesSubset,
		const ItoSolver::WhichContainer	a_containerBulk,
		const ItoSolver::WhichContainer	a_containerEB,
		const ItoSolver::WhichContainer	a_containerDomain,
		const EBIntersection	a_intersectionAlg,
		const bool	a_delete
	)

protectedvirtualnoexcept

Intersect a subset of the particles with the domain and embedded boundary.

Parameters

[in]	a_speciesSubset	Subset of particles to intersect. Can be charged, mobile, diffusive, etc.
[in]	a_containerBulk	ItoSolver container for "bulk" particles, i.e. particles that will be intersected.
[in]	a_containerEB	ItoSolver container for EB particles.
[in]	a_containerDomain	ItoSolver container for domain particles.
[in]	a_intersectionAlg	EB intersection algorithm
[in]	a_delete	Delete original particles. If this is left to false, the particles are copied into the other containers.

◆ loadBalanceBoxes()

void ItoPlasmaStepper::loadBalanceBoxes	(	Vector< Vector< int >> &	a_procs,
		Vector< Vector< Box >> &	a_boxes,
		const std::string	a_realm,
		const Vector< DisjointBoxLayout > &	a_grids,
		const int	a_lmin,
		const int	a_finestLevel
	)

overridevirtual

Load balance grid boxes for a specified realm.

Parameters

[out]	a_procs	MPI ranks owning the various grid boxes.
[out]	a_boxes	Grid boxes on every level (obtain them with a_grids[lvl].boxArray())
[in]	a_realm	Realm identifier
[in]	a_grids	Original grids
[in]	a_lmin	Coarsest grid level that changed
[in]	a_finestLevel	New finest grid level

This is only called by Driver if TimeStepper::loadBalanceThisRealm(a_realm) returned true. The default implementation uses volume-based loads for the grid patches. If the user wants to load balance boxes on a realm, this routine must be overwritten and he should compute loads for the various patches in a_grids and call LoadBalancing::makeBalance(Vector<int>, Vector<T>, Vector<Box>).

Reimplemented from TimeStepper.

◆ loadBalanceFluidRealm()

void ItoPlasmaStepper::loadBalanceFluidRealm	(	Vector< Vector< int >> &	a_procs,
		Vector< Vector< Box >> &	a_boxes,
		const std::string	a_realm,
		const Vector< DisjointBoxLayout > &	a_grids,
		const int	a_lmin,
		const int	a_finestLevel
	)

protectedvirtualnoexcept

Routine called by loadBalanceBoxes and used for particle-based load balancing.

Parameters

[out]	a_procs	MPI ranks owning the various grid boxes.
[out]	a_boxes	Grid boxes on every level (obtain them with a_grids[lvl].boxArray())
[in]	a_realm	Realm identifier
[in]	a_grids	Original grids
[in]	a_lmin	Coarsest grid level to load balance.
[in]	a_finestLevel	Finest grid level

◆ loadBalanceParticleRealm()

void ItoPlasmaStepper::loadBalanceParticleRealm	(	Vector< Vector< int >> &	a_procs,
		Vector< Vector< Box >> &	a_boxes,
		const std::string	a_realm,
		const Vector< DisjointBoxLayout > &	a_grids,
		const int	a_lmin,
		const int	a_finestLevel
	)

protectedvirtualnoexcept

Routine called by loadBalanceBoxes and used for particle-based load balancing.

Parameters

[out]	a_procs	MPI ranks owning the various grid boxes.
[out]	a_boxes	Grid boxes on every level (obtain them with a_grids[lvl].boxArray())
[in]	a_realm	Realm identifier
[in]	a_grids	Original grids
[in]	a_lmin	Coarsest grid level to load balance.
[in]	a_finestLevel	Finest grid level

◆ loadBalanceThisRealm()

bool ItoPlasmaStepper::loadBalanceThisRealm ( const std::string a_realm ) const

overridevirtual

Load balancing query for a specified realm. If this returns true for a_realm, load balancing routines will be called during regrids for the input realm.

Parameters

[in] a_realm Realm name

Reimplemented from TimeStepper.

◆ parseDualGrid()

void ItoPlasmaStepper::parseDualGrid ( )

protectedvirtualnoexcept

Parse dual or single realm calculations.

Sets m_particleRealm = "ParticleRealm" if 'dual_grid' is true.

◆ parseSuperParticles()

void ItoPlasmaStepper::parseSuperParticles ( )

protectedvirtualnoexcept

Parse the desired number of particles per cell.

Sets m_particlesPerCell from input script.

◆ parseVerbosity()

void ItoPlasmaStepper::parseVerbosity ( )

protectedvirtualnoexcept

Parse chattiness.

Sets m_verbosity from input script.

◆ postCheckpointPoisson()

void ItoPlasmaStepper::postCheckpointPoisson ( )

virtual

Do some post-checkpoint operations for the electrostatic part.

This computes the electric field from the checkpointed potential and populates m_electricFieldFluid and m_electricFieldParticle.

◆ postCheckpointSetup()

void ItoPlasmaStepper::postCheckpointSetup ( )

overridevirtual

Perform post-checkpoint operations.

This allocates the internal storage, recomputes the electric field and recomputes the velocity and diffusion coefficients.

Implements TimeStepper.

◆ preRegrid()

void ItoPlasmaStepper::preRegrid	(	const int	a_lmin,
		const int	a_oldFinestLevel
	)

overridevirtual

Perform pre-regrid operations.

This stores the particles and mesh data on the old grids.

Parameters

[in]	a_lmin	The coarsest level that changes
[in]	a_oldFinestLevel	The finest level before the regrid.

Implements TimeStepper.

Reimplemented in Physics::ItoPlasma::ItoPlasmaGodunovStepper.

◆ reconcileParticles() [1/3]

void ItoPlasmaStepper::reconcileParticles	(	const EBAMRCellData &	a_newParticlesPerCell,
		const EBAMRCellData &	a_oldParticlesPerCell,
		const EBAMRCellData &	a_meanParticleEnergies,
		const EBAMRCellData &	a_newPhotonsPerCell
	)

protectedvirtualnoexcept

Reconcile particles. At the bottom, this will call the physics interface for particle reconciliation.

Parameters

[in]	a_newParticlesPerCell	Particles per cell after the chemistry advance.
[in]	a_oldParticlesPerCell	Particles per cell before the chemistry advance.
[in]	a_meanParticleEnergies	Mean particle energies after the chemistry advance.
[in]	a_newPhotonsPerCell	Newly generated photons per cell after the chemistry avance.

Note: All data should be defined on the particle realm since this is where the particle reconciliation takes place.

◆ reconcileParticles() [2/3]

void ItoPlasmaStepper::reconcileParticles	(	const EBCellFAB &	a_newParticlesPerCell,
		const EBCellFAB &	a_oldParticlesPerCell,
		const EBCellFAB &	a_meanParticleEnergies,
		const EBCellFAB &	a_newPhotonsPerCell,
		const int	a_level,
		const DataIndex	a_dit,
		const Box	a_box,
		const Real	a_dx
	)

protectedvirtualnoexcept

Reconcile particles. At the bottom, this will call the physics interface for particle reconciliation.

Parameters

[in]	a_newParticlesPerCell	Particles per cell after the chemistry advance.
[in]	a_oldParticlesPerCell	Particles per cell before the chemistry advance.
[in]	a_meanParticleEnergies	Mean particle energies after the chemistry advance.
[in]	a_newPhotonsPerCell	Newly generated photons per cell after the chemistry avance.
[in]	a_level	Grid level
[in]	a_dit	Grid index
[in]	a_box	Grid box
[in]	a_dx	Grid resolution.

Note: All data should be defined on the particle realm since this is where the particle reconciliation takes place.

◆ reconcileParticles() [3/3]

void ItoPlasmaStepper::reconcileParticles	(	const LevelData< EBCellFAB > &	a_newParticlesPerCell,
		const LevelData< EBCellFAB > &	a_oldParticlesPerCell,
		const LevelData< EBCellFAB > &	a_meanParticleEnergies,
		const LevelData< EBCellFAB > &	a_newPhotonsPerCell,
		const int	a_level
	)

protectedvirtualnoexcept

Reconcile particles. At the bottom, this will call the physics interface for particle reconciliation.

Parameters

[in]	a_newParticlesPerCell	Particles per cell after the chemistry advance.
[in]	a_oldParticlesPerCell	Particles per cell before the chemistry advance.
[in]	a_meanParticleEnergies	Mean particle energies after the chemistry advance.
[in]	a_newPhotonsPerCell	Newly generated photons per cell after the chemistry avance.
[in]	a_level	Grid level

Note: All data should be defined on the particle realm since this is where the particle reconciliation takes place.

◆ regrid()

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

overridevirtual

Regrid methods – puts all data on the new mesh.

Parameters

[in]	a_lmin	The coarsest level that changed.
[in]	a_oldFinestLevel	The finest level before the regrid.
[in]	a_newFinestLevel	The finest level after the regrid.

Implements TimeStepper.

Reimplemented in Physics::ItoPlasma::ItoPlasmaGodunovStepper.

◆ remapParticles() [1/2]

void ItoPlasmaStepper::remapParticles ( const SpeciesSubset a_speciesSubset )

protectedvirtualnoexcept

Remap a subset of ItoSolver particles.

Parameters

[in] a_speciesSubset Subset of species to remap

Note: Calls the other version with ItoSolver::WhichContainer::Bulk

◆ remapParticles() [2/2]

void ItoPlasmaStepper::remapParticles	(	const SpeciesSubset	a_speciesSubset,
		const ItoSolver::WhichContainer	a_container
	)

protectedvirtualnoexcept

Remap a subset of ItoSolver particles.

Parameters

[in]	a_speciesSubset	Subset of species to remap
[in]	a_container	Which container in ItoSolver to remap.

◆ removeCoveredParticles() [1/2]

void ItoPlasmaStepper::removeCoveredParticles	(	const SpeciesSubset	a_which,
		const EBRepresentation	a_representation,
		const Real	a_tolerance
	)

protectedvirtualnoexcept

Remove covered particles (i.e., particles inside the EB)

Parameters

[in]	a_speciesSubset	Subset of particles to intersect. Can be charged, mobile, diffusive, etc.
[in]	a_representation	Representation of the EB.
[in]	a_tolerance	Tolerance for removal. Removes up to distance a_tolerance from the EB.

Note: a_representation is basically an algorithmic selection that propagates into ItoSolver

◆ removeCoveredParticles() [2/2]

void ItoPlasmaStepper::removeCoveredParticles	(	const SpeciesSubset	a_which,
		const ItoSolver::WhichContainer	a_container,
		const EBRepresentation	a_representation,
		const Real	a_tolerance
	)

protectedvirtualnoexcept

Remove covered particles (i.e., particles inside the EB)

Parameters

[in]	a_speciesSubset	Subset of particles to intersect. Can be charged, mobile, diffusive, etc.
[in]	a_container	Which of the containers in ItoSolver to remove from.
[in]	a_representation	Representation of the EB.
[in]	a_tolerance	Tolerance for removal. Removes up to distance a_tolerance from the EB.

Note: a_representation is basically an algorithmic selection that propagates into ItoSolver

◆ resolveParticlesEB() [1/2]

void ItoPlasmaStepper::resolveParticlesEB ( const Real a_dt )

protectedvirtualnoexcept

Resolve particle injection at EBs.

Parameters

[in] a_dt Time step.

Note: Calls the other version.

◆ resolveParticlesEB() [2/2]

void ItoPlasmaStepper::resolveParticlesEB	(	Vector< ParticleContainer< ItoParticle > * > &	a_inOutParticles,
		Vector< ParticleContainer< Photon > * > &	a_inOutPhotons,
		const EBAMRCellData &	a_electricField,
		const Real	a_dt
	)

protectedvirtualnoexcept

Resolve particle injection at EBs.

Parameters

[in] a_dt Time step

◆ setFieldSolver()

void ItoPlasmaStepper::setFieldSolver ( RefCountedPtr< FieldSolver > & a_fieldSolver )

virtualnoexcept

Set the field solver.

Parameters

[in] a_fieldSolver Field solver

◆ setIto()

void ItoPlasmaStepper::setIto ( RefCountedPtr< ItoLayout< ItoSolver >> & a_itoLayout )

virtualnoexcept

Set the Ito layout.

Parameters

[in] a_itoLayout Set of ItoSolver solvers.

◆ setItoVelocityFunctions()

void ItoPlasmaStepper::setItoVelocityFunctions ( )

protectedvirtualnoexcept

Set the Ito velocity functions. This is sgn(charge) * E.

Note: This should be set before ItoSolver computes velocities.

◆ setRadiativeTransferSolvers()

void ItoPlasmaStepper::setRadiativeTransferSolvers ( RefCountedPtr< RtLayout< McPhoto >> & a_rteLayout )

virtualnoexcept

Set the radiative transfer solvers.

Parameters

[in] a_rteLayout Radiative transfer solvers

◆ setVoltage()

void ItoPlasmaStepper::setVoltage ( const std::function< Real(const Real a_time)> & a_voltage )

virtualnoexcept

Set voltage used for the simulation.

Parameters

[in] a_voltage Voltage

Note: This should be done BEFORE calling setupSolvers.

◆ solvePoisson()

bool ItoPlasmaStepper::solvePoisson ( )

protectedvirtualnoexcept

Solve the electrostatic problem.

This calls the other version with all lhs/rhs taken from the field solver. Space charge density is computed in this routine.

Returns: Returns true if the solver converged.

◆ sortPhotonsByCell()

void ItoPlasmaStepper::sortPhotonsByCell ( const McPhoto::WhichContainer a_which )

protectedvirtualnoexcept

Sort photons by cells.

Parameters

[in] a_which Which container to sort by cell

◆ sortPhotonsByPatch()

void ItoPlasmaStepper::sortPhotonsByPatch ( const McPhoto::WhichContainer a_which )

protectedvirtualnoexcept

Sort photons by patch.

Parameters

[in] a_which Which container to sort by patch

◆ synchronizeSolverTimes()

void ItoPlasmaStepper::synchronizeSolverTimes	(	const int	a_step,
		const Real	a_time,
		const Real	a_dt
	)

overridevirtual

Synchronize solver times for all the solvers.

Parameters

[in]	a_step	Time step
[in]	a_time	Simulation time
[in]	a_dt	Last time step used.

Implements TimeStepper.

◆ transferCoveredParticles() [1/2]

void ItoPlasmaStepper::transferCoveredParticles	(	const SpeciesSubset	a_speciesSubset,
		const EBRepresentation	a_representation,
		const Real	a_tolerance
	)

protectedvirtualnoexcept

Transfer covered particles (i.e., particles inside the EB) from the ItoSolver bulk container to EB container.

Parameters

[in]	a_speciesSubset	Subset of particles to intersect. Can be charged, mobile, diffusive, etc.
[in]	a_representation	Representation of the EB.
[in]	a_tolerance	Tolerance for transfer. Transfers up to distance a_tolerance from the EB.

Note: a_representation is basically an algorithmic selection that propagates into ItoSolver

◆ transferCoveredParticles() [2/2]

void ItoPlasmaStepper::transferCoveredParticles	(	const SpeciesSubset	a_speciesSubset,
		const ItoSolver::WhichContainer	a_containerFrom,
		const ItoSolver::WhichContainer	a_containerTo,
		const EBRepresentation	a_representation,
		const Real	a_tolerance
	)

protectedvirtualnoexcept

Transfer covered particles (i.e., particles inside the EB) from the ItoSolver bulk container to EB container.

Parameters

[in]	a_speciesSubset	Subset of particles to intersect. Can be charged, mobile, diffusive, etc.
[in]	a_containerFrom	Particle container (in ItoSolver) to transfer from
[in]	a_containerTo	Particle container (in ItoSolver) to transfer to
[in]	a_representation	Representation of the EB.
[in]	a_tolerance	Tolerance for transfer. Transfers up to distance a_tolerance from the EB.

Note: a_representation is basically an algorithmic selection that propagates into ItoSolver

◆ writeNumParticlesPerPatch()

void ItoPlasmaStepper::writeNumParticlesPerPatch	(	EBAMRCellData &	a_output,
		int &	a_icomp
	)		const

protectedvirtual

Write number of particles per patch to output holder.

Parameters

[in,out]	a_output	Output data holder.
[in,out]	a_icomp	Starting component in a_output to begin at.

◆ writePlotData()

void ItoPlasmaStepper::writePlotData	(	EBAMRCellData &	a_output,
		Vector< std::string > &	a_plotVariableNames,
		int &	a_icomp
	)		const

overridevirtual

Write plot data to output holder.

Parameters

[in,out]	a_output	Output data holder.
[in]	a_plotVariableNames	Plot variable names.
[in,out]	a_icomp	Starting component in a_output to begin at.

Implements TimeStepper.

Member Data Documentation

◆ m_conductivityCell

EBAMRCellData Physics::ItoPlasma::ItoPlasmaStepper::m_conductivityCell

protected

Cell-centered conductivity.

Note: Defined on the fluid realm with 1 component

◆ m_conductivityEB

EBAMRIVData Physics::ItoPlasma::ItoPlasmaStepper::m_conductivityEB

protected

EB-centered conductivity.

Note: Defined on the fluid realm with 1 component

◆ m_conductivityFace

EBAMRFluxData Physics::ItoPlasma::ItoPlasmaStepper::m_conductivityFace

protected

Face-centered conductivity.

Note: Defined on the fluid realm with 1 component

◆ m_currentDensity

EBAMRCellData Physics::ItoPlasma::ItoPlasmaStepper::m_currentDensity

protected

Storage for current density.

Note: Defined over the fluid realm with SpaceDim components.

◆ m_energySources

Vector<EBAMRCellData> Physics::ItoPlasma::ItoPlasmaStepper::m_energySources

protected

Storage for holding the energy sources for each species.

Note: Defined on the particle realm but about to get deprecated when we switch to the new reaction algorithm.

◆ m_fluidEPS

EBAMRCellData Physics::ItoPlasma::ItoPlasmaStepper::m_fluidEPS

protected

For holding the mean particle energy.

Note: Defined on the fluid realm with components = number of plasma species

◆ m_fluidPPC

EBAMRCellData Physics::ItoPlasma::ItoPlasmaStepper::m_fluidPPC

protected

For holding the number of particles per cell for all species.

Note: Defined on the fluid realm with components = number of plasma species

◆ m_fluidRealm

std::string Physics::ItoPlasma::ItoPlasmaStepper::m_fluidRealm

protected

Realm used for the fluid part (i.e., electrostatic) part of the simulation.

Note: This is hardcoded to Realm::Primal

◆ m_fluidYPC

EBAMRCellData Physics::ItoPlasma::ItoPlasmaStepper::m_fluidYPC

protected

For holding the number of generated photons per cell.

Note: Defined on the fluid realm with components = number of photon species

◆ m_loadPerCell

Real Physics::ItoPlasma::ItoPlasmaStepper::m_loadPerCell

protected

The "background" load per cell when using particle load balancing.

Note: This is used when computing the loads per patch on the particle realm such that the total load is m_loadPerCell * numGridPoints + numParticles.

◆ m_mergeInterval

int Physics::ItoPlasma::ItoPlasmaStepper::m_mergeInterval

protected

How often to merge superparticles.

If <= 1 we merge every time step.

◆ m_newPPC

EBAMRCellData Physics::ItoPlasma::ItoPlasmaStepper::m_newPPC

protected

For holding the number of physical particles per cell.

Note: Defined over the particle realm.

◆ m_oldPPC

EBAMRCellData Physics::ItoPlasma::ItoPlasmaStepper::m_oldPPC

protected

For holding the number of physical particles per cell.

Note: Defined over the particle realm.

◆ m_particleEPS

EBAMRCellData Physics::ItoPlasma::ItoPlasmaStepper::m_particleEPS

protected

For holding the mean particle energy.

Note: Defined on the particle realm with components = number of plasma species

◆ m_particleOldPPC

EBAMRCellData Physics::ItoPlasma::ItoPlasmaStepper::m_particleOldPPC

protected

For holding the previous number of particles per cell for all species.

Note: Defined on the particle realm with components = number of plasma species

◆ m_particlePPC

EBAMRCellData Physics::ItoPlasma::ItoPlasmaStepper::m_particlePPC

protected

For holding the number of physical particles per cell for all species.

Note: Defined on the particle realm with components = number of plasma species

◆ m_particleYPC

EBAMRCellData Physics::ItoPlasma::ItoPlasmaStepper::m_particleYPC

protected

For holding the number of generated photons per cell.

Note: Defined on the particle realm with components = number of photon species

◆ m_physics

RefCountedPtr<ItoPlasmaPhysics> Physics::ItoPlasma::ItoPlasmaStepper::m_physics

protected

Implementation of ItoPlasmaPhysics.

All solver coupling occurs through the implementation of this class

◆ m_plasmaPhase

phase::which_phase Physics::ItoPlasma::ItoPlasmaStepper::m_plasmaPhase

protected

Phase where we solve for the plasma.

Note: This is hardcoded to phase::gas

◆ m_relaxTimeFactor

Real Physics::ItoPlasma::ItoPlasmaStepper::m_relaxTimeFactor

protected

Factor proportional to the dielectric relaxation time dtRelax = eps0/sigma.

Used for restricting dt < m_relaxTimeFactor * eps0/sigma

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

Physics/ItoPlasma/CD_ItoPlasmaStepper.H
Physics/ItoPlasma/CD_ItoPlasmaStepper.cpp

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ItoPlasmaStepper()

Member Function Documentation

◆ advance()

◆ advancePhotons()

◆ advanceReactionNetwork() [1/4]

◆ advanceReactionNetwork() [2/4]

◆ advanceReactionNetwork() [3/4]

◆ advanceReactionNetwork() [4/4]

◆ computeConductivityCell() [1/2]

◆ computeConductivityCell() [2/2]

◆ computeCurrentDensity()

◆ computeEdotJSource()

◆ computeElectricField()

◆ computeItoDiffusion()

◆ computeItoDiffusionLEA()

◆ computeItoDiffusionLFA() [1/4]

◆ computeItoDiffusionLFA() [2/4]

◆ computeItoDiffusionLFA() [3/4]

◆ computeItoDiffusionLFA() [4/4]

◆ computeItoMobilitiesLEA()

◆ computeItoMobilitiesLFA() [1/4]

◆ computeItoMobilitiesLFA() [2/4]

◆ computeItoMobilitiesLFA() [3/4]

◆ computeItoMobilitiesLFA() [4/4]

◆ computeItoVelocities()

◆ computeMaxElectricField()

◆ computePhysicsDt() [1/4]

◆ computePhysicsDt() [2/4]

◆ computePhysicsDt() [3/4]

◆ computePhysicsDt() [4/4]

◆ computeReactiveMeanEnergiesPerCell() [1/3]

◆ computeReactiveMeanEnergiesPerCell() [2/3]

◆ computeReactiveMeanEnergiesPerCell() [3/3]

◆ computeReactiveParticlesPerCell() [1/3]

◆ computeReactiveParticlesPerCell() [2/3]

◆ computeReactiveParticlesPerCell() [3/3]

◆ computeSpaceChargeDensity() [1/2]

◆ computeSpaceChargeDensity() [2/2]

◆ depositParticles() [1/2]

◆ depositParticles() [2/2]

◆ getCheckpointLoads()

◆ getLoadBalanceSolvers()

◆ getMaxMinItoDensity()

◆ getParticleStatistics()

◆ getPhysicalParticlesPerCell()

◆ getTime()

◆ injectParticlesEB()

◆ intersectParticles() [1/2]

◆ intersectParticles() [2/2]

◆ loadBalanceBoxes()

◆ loadBalanceFluidRealm()

◆ loadBalanceParticleRealm()

◆ loadBalanceThisRealm()

◆ parseDualGrid()

◆ parseSuperParticles()

◆ parseVerbosity()

◆ postCheckpointPoisson()

◆ postCheckpointSetup()

◆ preRegrid()

◆ reconcileParticles() [1/3]

◆ reconcileParticles() [2/3]

◆ reconcileParticles() [3/3]

◆ regrid()

◆ remapParticles() [1/2]

◆ remapParticles() [2/2]

◆ removeCoveredParticles() [1/2]

◆ removeCoveredParticles() [2/2]

◆ resolveParticlesEB() [1/2]

◆ resolveParticlesEB() [2/2]

◆ setFieldSolver()

◆ setIto()

◆ setItoVelocityFunctions()

◆ setRadiativeTransferSolvers()

◆ setVoltage()