Base time stepper class that advances the Ito-KMC-Poisson system of equations. If you want a different underlying solver, change the template arguments. More...

#include <CD_ItoKMCStepper.H>

Inheritance diagram for Physics::ItoKMC::ItoKMCStepper< I, C, R, F >:

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Collaboration diagram for Physics::ItoKMC::ItoKMCStepper< I, C, R, F >:

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Public Member Functions
	ItoKMCStepper () noexcept
	Default constructor. Sets default options.

	ItoKMCStepper (RefCountedPtr< ItoKMCPhysics > &a_physics) noexcept
	Full constructor. Calls the other constructor. More...

virtual	~ItoKMCStepper () noexcept
	Destructor.

virtual void	parseOptions () noexcept
	Parse options.

virtual void	parseRuntimeOptions () noexcept override
	Parse runtime configurable options.

virtual void	allocate () noexcept override
	Allocate storage for solvers.

virtual void	setupSolvers () noexcept override
	Set up solvers.

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

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

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

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

virtual Vector< std::string >	getPlotVariableNames () const noexcept override
	Get plot variable names.

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

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) override=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) noexcept override
	Synchronize solver times for all the solvers. More...

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

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

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

virtual void	prePlot () noexcept override
	Perform pre-plot operations.

virtual void	postPlot () noexcept override
	Perform post-plot operations.

virtual void	preRegrid (const int a_lmin, const int a_oldFinestLevel) noexcept override
	Perform pre-regrid operations - storing relevant data from the old grids. More...

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

virtual void	postRegrid () noexcept override
	Perform post-regrid operations.

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	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 { AdvectionIto , DiffusionIto , AdvectionDiffusionIto , AdvectionDiffusionCDR , RelaxationTime , Hardcap , Physics }
	An enum for encapsulating how time steps were restricted.

Protected Member Functions
virtual void	allocateInternals () noexcept
	Allocate "internal" storage.

virtual void	setupIto () noexcept
	Set up the Ito particle solvers.

virtual void	setupCdr () noexcept
	Set up the CDR solvers.

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

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

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

virtual void	intersectParticles (const SpeciesSubset a_speciesSubset, const bool a_delete, const std::function< void(ItoParticle &)> a_nonDeletionModifier=[](ItoParticle &) -> void { return;}) 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 bool a_delete, const std::function< void(ItoParticle &)> a_nonDeletionModifier=[](ItoParticle &) -> void { return;}) 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	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...

virtual void	writeNumberOfParticlesPerPatch (LevelData< EBCellFAB > &a_output, int &a_icomp, const std::string a_outputRealm, const int a_level) const noexcept
	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	getMaxMinCDRDensity (Real &a_maxDensity, Real &a_minDensity, std::string &a_maxSolver, std::string &a_minSolver) const noexcept
	Get maximum density of the CDr 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) const 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_itoDensities, const Vector< EBAMRCellData * > &a_cdrDensities) noexcept
	Compute the space charge density. 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	computeDensityGradients () noexcept
	Compute grad(phi) and phi for both CDR and Ito species and put the result on the fluid realm. 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	computeDriftVelocities () noexcept
	Compute ItoSolver velocities. More...

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

virtual void	setCdrVelocityFunctions () noexcept
	Set the Cdr velocities to be sgn(charge) * E. More...

virtual void	multiplyCdrVelocitiesByMobilities () noexcept
	Multiply CDR solver velocities by mobilities.

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

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

virtual void	computeMobilities (Vector< LevelData< EBCellFAB > * > &a_itoMobilities, Vector< LevelData< EBCellFAB > * > &a_cdrMobilities, 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	computeMobilities (Vector< EBCellFAB * > &a_itoMobilities, Vector< EBCellFAB * > &a_cdrMobilities, 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	computeDiffusionCoefficients () noexcept
	Compute mesh-based diffusion coefficients for LFA coupling. More...

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

virtual void	computeDiffusionCoefficients (Vector< LevelData< EBCellFAB > * > &a_itoDiffusionCoefficients, Vector< LevelData< EBCellFAB > * > &a_cdrDiffusionCoefficients, 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	computeDiffusionCoefficients (Vector< EBCellFAB * > &a_itoDiffusionCoefficients, Vector< EBCellFAB * > &a_cdrDiffusionCoefficients, 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	averageDiffusionCoefficientsCellToFace () noexcept
	Average cell-centered diffusion coefficient to faces.

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

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

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

virtual void	computeReactiveItoParticlesPerCell (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	computeReactiveCdrParticlesPerCell (EBAMRCellData &a_ppc) noexcept
	Compute the number of reactive particles per cell for the CDR solvers. More...

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

virtual void	computeReactiveCdrParticlesPerCell (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 for the CDR solvers. 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 Real a_dt) noexcept
	Chemistry advance over time a_dt. AMR version. More...

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

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

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

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

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

virtual void	reconcilePhotoionization () noexcept
	Reconcile the results from photoionization reactions. More...

virtual void	reconcileCdrDensities (const EBAMRCellData &a_newParticlesPerCell, const EBAMRCellData &a_oldParticlesPerCell, const Real a_dt) noexcept
	Reconcile the CDR densities after the reaction network. More...

virtual void	reconcileCdrDensities (const LevelData< EBCellFAB > &a_newParticlesPerCell, const LevelData< EBCellFAB > &a_oldParticlesPerCell, const int a_level, const Real a_dt) noexcept
	Reconcile the CDR densities after the reaction network. More...

virtual void	reconcileCdrDensities (const EBCellFAB &a_newParticlesPerCell, const EBCellFAB &a_oldParticlesPerCell, const int a_level, const DataIndex a_dit, const Box a_box, const Real a_dx, const Real a_dt) noexcept
	Reconcile the CDR densities after the reaction network. More...

virtual void	coarsenCDRSolvers () noexcept
	Coarsen data for CDR solvers.

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

virtual void	fillSecondaryEmissionEB (Vector< ParticleContainer< ItoParticle >> &a_secondaryParticles, Vector< EBAMRIVData > &a_cdrFluxes, Vector< ParticleContainer< Photon >> &a_secondaryPhotons, Vector< ParticleContainer< ItoParticle > * > &a_primaryParticles, Vector< EBAMRIVData > &a_cdrFluxesExtrap, Vector< ParticleContainer< Photon > * > &a_primaryPhotons, const EBAMRCellData &a_electricField, const Real a_dt) noexcept
	Compute secondary emission at the EB. More...

virtual void	resolveSecondaryEmissionEB (const Real a_dt) noexcept
	Resolve secondary emission at the EB. More...

virtual void	resolveSecondaryEmissionEB (Vector< ParticleContainer< ItoParticle > * > &a_secondaryParticles, Vector< ParticleContainer< ItoParticle > * > &a_primaryParticles, Vector< EBAMRIVData * > &a_cdrFluxes, EBAMRIVData &a_surfaceChargeDensity, const Real a_dt) noexcept
	Resolve secondary emission at the EB. More...

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 Real	computeTotalCharge () const noexcept
	Compute total charge.

virtual Real	computeQplus () const noexcept
	Compute positive charge.

virtual Real	computeQminu () const noexcept
	Compute negative charge.

virtual Real	computeQsurf () const noexcept
	Compute surface charge.

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

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

virtual void	initialSigma () noexcept
	Fill surface charge solver with initial data taken from the physics interface.

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

virtual void	parseExitOnFailure () noexcept
	Parse exit on failure.

virtual void	parseRedistributeCDR () noexcept
	Parse CDR mass redistribution when assigning reactive products.

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 parameters related to how we treat particle-EB interaction.

virtual void	parsePlotVariables () noexcept
	Parse plot variables.

virtual void	computePhysicsPlotVariables (EBAMRCellData &a_physicsPlotVars) noexcept
	Compute physics plot variables. More...

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< ItoKMCPhysics >	m_physics
	Implementation of ItoKMCPhysics. More...

RefCountedPtr< ItoLayout< ItoSolver > >	m_ito
	Ito solvers.

RefCountedPtr< CdrLayout< CdrSolver > >	m_cdr
	CDR solvers.

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

RefCountedPtr< FieldSolver >	m_fieldSolver
	Field solver.

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

Vector< ParticleContainer< ItoParticle > >	m_secondaryParticles
	List of secondary particles injected through the EB. More...

Vector< ParticleContainer< Photon > >	m_secondaryPhotons
	List of secondary photons injected through the EB. More...

Vector< EBAMRIVData >	m_cdrFluxes
	CDR fluxes for CDR BCs. More...

Vector< EBAMRIVData >	m_cdrFluxesExtrap
	Extrapolated CDR fluxes.

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_redistributeCDR
	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_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_prevDt
	Previous time step.

Real	m_maxGrowthDt
	Maximum permissible time step growth.

Real	m_maxShrinkDt
	Maximum permissible time step shrinkage.

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_minParticleAdvectionCFL
	Minimum CFL-like time step for particle advection.

Real	m_maxParticleAdvectionCFL
	Maximum CFL-like time step for particle advection.

Real	m_minParticleDiffusionCFL
	Minium CFL-like time step for particle diffusion.

Real	m_maxParticleDiffusionCFL
	Maximum CFL-like time step for particle diffusion.

Real	m_minParticleAdvectionDiffusionCFL
	Maximum CFL-like time step for particle advection-diffusion.

Real	m_maxParticleAdvectionDiffusionCFL
	Maximum CFL-like time step for particle advection-diffusion.

Real	m_fluidAdvectionDiffusionCFL
	CFL-like time step for fluid 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_particleAdvectionDt
	The particle advective time step.

Real	m_particleDiffusionDt
	The particle diffusive time step.

Real	m_particleAdvectionDiffusionDt
	The advection-diffusion time step.

Real	m_fluidAdvectionDiffusionDt
	The advection-diffusion time step for the CDR equations.

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< EBAMRCellData >	m_cdrMobilities
	For holding the mobilities for the CDR species. More...

Vector< EBAMRCellData >	m_fluidGradPhiCDR
	For holding the gradient of all CDR species densities. More...

Vector< EBAMRCellData >	m_fluidGradPhiIto
	For holding the gradient of all Ito species densities. More...

Vector< EBAMRCellData >	m_fluidPhiIto
	For holding the Ito species densities on the fluid realm.

Vector< ParticleContainer< PointParticle > >	m_cdrPhotoiProducts
	Photoionization products to be put in the CDR equations. More...

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

EBAMRCellData	m_currentDensity
	Storage for current density. More...

EBAMRCellData	m_physicsPlotVariables
	Storage for physics plot variables.

EBAMRCellData	m_conductivityCell
	Cell-centered conductivity. More...

EBAMRFluxData	m_conductivityFace
	Face-centered conductivity. More...

EBAMRIVData	m_conductivityEB
	EB-centered conductivity. More...

EBAMRCellData	m_particleItoPPC
	For holding the number of physical particles per cell for all Ito 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_particleOldItoPPC
	For holding the previous number of particles per cell for all species. More...

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

EBAMRCellData	m_fluidOldCdrPPC
	For holding the previous number of physical particles per cell for all CDR 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_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.

EBAMRIVData	m_fluidScratchEB
	Scratch storage for EB-only data on the fluid realm. One component.

EBAMRIVData	m_particleScratchEB
	Scratch storage for EB-only data on the particle realm. One component.

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

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>
class Physics::ItoKMC::ItoKMCStepper< I, C, R, F >

Base time stepper class that advances the Ito-KMC-Poisson system of equations. If you want a different underlying solver, change the template arguments.

Constructor & Destructor Documentation

◆ ItoKMCStepper()

template<typename I , typename C , typename R , typename F >

ItoKMCStepper::ItoKMCStepper ( RefCountedPtr< ItoKMCPhysics > & a_physics )

noexcept

Full constructor. Calls the other constructor.

Parameters

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

Member Function Documentation

◆ advance()

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

virtual Real Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::advance ( const Real a_dt )

overridepure 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::ItoKMC::ItoKMCGodunovStepper< I, C, R, F >.

◆ advancePhotons()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::advancePhotons ( const Real a_dt )

protectedvirtualnoexcept

Photon advancement routine.

Parameters

[in] a_dt Time step

◆ advanceReactionNetwork() [1/4]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::advanceReactionNetwork	(	const EBAMRCellData &	a_E,
		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_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]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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]

template<typename I , typename C , typename R , typename F >

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

inlineprotectednoexcept

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]	a_electricField	Electric field.
[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]

template<typename I , typename C , typename R , typename F >

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

inlineprotectednoexcept

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]	a_electricField	Electric field.
[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]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeConductivityCell ( EBAMRCellData & a_conductivity )

protectedvirtualnoexcept

Compute the cell-centered conductiivty.

Parameters

[out] a_conductivity Cell-centered conductivity

Note: User should have updated the mobilities before calling this routine.

◆ computeConductivityCell() [2/2]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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.

Note: User should have updated the mobilities before calling this routine.

◆ computeCurrentDensity()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeCurrentDensity ( EBAMRCellData & a_J )

protectedvirtualnoexcept

Compute the current density.

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

◆ computeDensityGradients()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeDensityGradients

protectedvirtualnoexcept

Compute grad(phi) and phi for both CDR and Ito species and put the result on the fluid realm.

This will compute the gradients using the results in the solvers. The user should make sure he/she deposits the Ito particles before calling this routine. The results are put in m_fluidGradPhiCDR and and m_fluidGradPhiito

◆ computeDiffusionCoefficients() [1/4]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeDiffusionCoefficients

protectedvirtualnoexcept

Compute mesh-based diffusion coefficients for LFA coupling.

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

◆ computeDiffusionCoefficients() [2/4]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeDiffusionCoefficients	(	Vector< EBAMRCellData * > &	a_itoDiffusionCoefficients,
		Vector< EBAMRCellData * > &	a_cdrDiffusionCoefficients,
		const EBAMRCellData &	a_electricField,
		const Real	a_time
	)

protectedvirtualnoexcept

Compute mesh-based diffusion coefficients for LFA coupling.

Parameters

[out]	a_itoDiffusionCoefficients	Mesh-based diffusion coefficients for Ito solvers. Must be defined on the particle realm.
[out]	a_cdrDiffusionCoefficients	Mesh-based diffusion coefficients for CDR solvers. Must be defined on the fluid realm.
[in]	a_electricField	Electric field. Must be defined on the fluid realm.
[in]	a_time	Time

◆ computeDiffusionCoefficients() [3/4]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeDiffusionCoefficients	(	Vector< EBCellFAB * > &	a_itoDiffusionCoefficients,
		Vector< EBCellFAB * > &	a_cdrDiffusionCoefficients,
		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_itoDiffusionCoefficients	Mesh-based diffusion coefficients for Ito solvers. Must be defined on the fluid realm.
[out]	a_cdrDiffusionCoefficients	Mesh-based diffusion coefficients for CDR solvers. 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

◆ computeDiffusionCoefficients() [4/4]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeDiffusionCoefficients	(	Vector< LevelData< EBCellFAB > * > &	a_itoDiffusionCoefficients,
		Vector< LevelData< EBCellFAB > * > &	a_cdrDiffusionCoefficients,
		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_itoDiffusionCoefficients	Mesh-based diffusion coefficients for Ito solvers. Must be defined on the fluid realm.
[out]	a_cdrDiffusionCoefficients	Mesh-based diffusion coefficients for CDR solvers. 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

◆ computeDriftVelocities()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeDriftVelocities

protectedvirtualnoexcept

Compute ItoSolver velocities.

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

◆ computeEdotJSource()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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.

◆ computeMaxElectricField()

template<typename I , typename C , typename R , typename F >

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

protectedvirtualnoexcept

Compute the maximum electric field (norm)

Parameters

[in] a_phase Phase where we compute the field.

◆ computeMobilities() [1/4]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeMobilities

protectedvirtualnoexcept

Compute mesh-based mobilities for LFA coupling.

This updates the mobilities in the Ito particle solvers AND m_cdrMobilities (not owned by solvers)

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

◆ computeMobilities() [2/4]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeMobilities	(	Vector< EBAMRCellData * > &	a_itoMobilities,
		Vector< EBAMRCellData > &	a_cdrMobilities,
		const EBAMRCellData &	a_electricField,
		const Real	a_time
	)

protectedvirtualnoexcept

Compute mesh-based mobilities for LFA coupling.

Parameters

[out]	a_itoMobilities	Mesh-based mobilities for Ito solvers. Must be defined on the particle realm.
[out]	a_cdrMobilities	Mesh-based mobilities for CDR solvers. Must be defined on the fluid realm.
[in]	a_electricField	Electric field. Must be defined on the fluid realm.
[in]	a_time	Time

◆ computeMobilities() [3/4]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeMobilities	(	Vector< EBCellFAB * > &	a_itoMobilities,
		Vector< EBCellFAB * > &	a_cdrMobilities,
		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_itoMobilities	Mesh-based mobilities for Ito solvers. Must be defined on the particle realm.
[out]	a_cdrMobilities	Mesh-based mobilities for CDR solvers. 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

◆ computeMobilities() [4/4]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeMobilities	(	Vector< LevelData< EBCellFAB > * > &	a_itoMobilities,
		Vector< LevelData< EBCellFAB > * > &	a_cdrMobilities,
		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_itoMobilities	Mesh-based mobilities for Ito solvers. Must be defined on the particle realm.
[out]	a_cdrMobilities	Mesh-based mobilities for CDR solvers. 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

◆ computePhysicsDt() [1/4]

template<typename I , typename C , typename R , typename F >

Real ItoKMCStepper::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]

template<typename I , typename C , typename R , typename F >

Real ItoKMCStepper::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]

template<typename I , typename C , typename R , typename F >

Real ItoKMCStepper::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]

template<typename I , typename C , typename R , typename F >

Real ItoKMCStepper::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.

◆ computePhysicsPlotVariables()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computePhysicsPlotVariables ( EBAMRCellData & a_physicsPlotVars )

protectedvirtualnoexcept

Compute physics plot variables.

Parameters

[out] a_physicsPlotVars Plot variables from physics implementation

◆ computeReactiveCdrParticlesPerCell() [1/3]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeReactiveCdrParticlesPerCell ( EBAMRCellData & a_ppc )

protectedvirtualnoexcept

Compute the number of reactive particles per cell for the CDR solvers.

This truncates the number of particles in the cell.

Parameters

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

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

◆ computeReactiveCdrParticlesPerCell() [2/3]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeReactiveCdrParticlesPerCell	(	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 for the CDR solvers.

Parameters

[out]	a_ppc	Number of physical particles per grid cell for all CDR 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 fluid realm and have the same number of components as the number of CDR species involved in the simulation.

◆ computeReactiveCdrParticlesPerCell() [3/3]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeReactiveCdrParticlesPerCell	(	LevelData< EBCellFAB > &	a_ppc,
		const int	a_level
	)

protectedvirtualnoexcept

Compute the number of reactive particles per cell for the CDR solvers.

Parameters

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

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

◆ computeReactiveItoParticlesPerCell() [1/3]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeReactiveItoParticlesPerCell ( 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.

◆ computeReactiveItoParticlesPerCell() [2/3]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeReactiveItoParticlesPerCell	(	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.

◆ computeReactiveItoParticlesPerCell() [3/3]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeReactiveItoParticlesPerCell	(	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.

◆ computeReactiveMeanEnergiesPerCell() [1/3]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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.

◆ computeSpaceChargeDensity() [1/2]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeSpaceChargeDensity

protectedvirtualnoexcept

Compute the space charge. Calls the other version.

Note: This runs through the ItoSolver and CdrSolver densities – user should remember to update these before calling this routine.

◆ computeSpaceChargeDensity() [2/2]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::computeSpaceChargeDensity	(	MFAMRCellData &	a_rho,
		const Vector< EBAMRCellData * > &	a_itoDensities,
		const Vector< EBAMRCellData * > &	a_cdrDensities
	)

protectedvirtualnoexcept

Compute the space charge density.

Parameters

[out]	a_rho	Space charge density
[in]	a_itoDensities	List of Ito solver species densities
[in]	a_cdrDensities	List of Cdr solver species densities

◆ depositParticles() [1/2]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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.

◆ fillSecondaryEmissionEB() [1/2]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::fillSecondaryEmissionEB ( const Real a_dt )

protectedvirtualnoexcept

Resolve particle injection at EBs.

Parameters

[in] a_dt Time step.

Note: Calls the other version.

◆ fillSecondaryEmissionEB() [2/2]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::fillSecondaryEmissionEB	(	Vector< ParticleContainer< ItoParticle >> &	a_secondaryParticles,
		Vector< EBAMRIVData > &	a_cdrFluxes,
		Vector< ParticleContainer< Photon >> &	a_secondaryPhotons,
		Vector< ParticleContainer< ItoParticle > * > &	a_primaryParticles,
		Vector< EBAMRIVData > &	a_cdrFluxesExtrap,
		Vector< ParticleContainer< Photon > * > &	a_primaryPhotons,
		const EBAMRCellData &	a_electricField,
		const Real	a_dt
	)

protectedvirtualnoexcept

Compute secondary emission at the EB.

This routine fills the input data holders using physics framework. It does NOT fill solvers.

Parameters

[out]	a_secondaryParticles	Secondary emitted (gained) particles at the EB
[out]	a_cdrFluxes	CDR fluxes for BCs.
[out]	a_secondaryPhotons	Secondary emitted photons at the EB
[in]	a_primaryParticles	Primary (lost) particles at the EB
[in]	a_cdrFluxesExtrap	Extrapolated CDR fluxes at the EB
[in]	a_primaryPhotons	Primary (lost) photons at the EB
[in]	a_electricField	Electric field at the EB.
[in]	a_dt	Time step.

◆ getCheckpointLoads()

template<typename I , typename C , typename R , typename F >

Vector< long int > ItoKMCStepper::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()

template<typename I , typename C , typename R , typename F >

Vector< RefCountedPtr< ItoSolver > > ItoKMCStepper::getLoadBalanceSolvers

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.

◆ getMaxMinCDRDensity()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::getMaxMinCDRDensity	(	Real &	a_maxDensity,
		Real &	a_minDensity,
		std::string &	a_maxSolver,
		std::string &	a_minSolver
	)		const

protectedvirtualnoexcept

Get maximum density of the CDr species.

Parameters

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

◆ getMaxMinItoDensity()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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

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

◆ getParticleStatistics()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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()

template<typename I , typename C , typename R , typename F >

Real ItoKMCStepper::getTime

virtualnoexcept

Get current simulation time.

Returns: m_time

◆ intersectParticles() [1/2]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::intersectParticles	(	const SpeciesSubset	a_speciesSubset,
		const bool	a_delete,
		const std::function< void(ItoParticle &)>	a_nonDeletionModifier = `[](ItoParticle&) -> void { return; }`
	)

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.
[in]	a_nonDeletionModifier	Optional input argument for letting the user manipulate particles that were intersected but not deleted

◆ intersectParticles() [2/2]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::intersectParticles	(	const SpeciesSubset	a_speciesSubset,
		const ItoSolver::WhichContainer	a_containerBulk,
		const ItoSolver::WhichContainer	a_containerEB,
		const ItoSolver::WhichContainer	a_containerDomain,
		const bool	a_delete,
		const std::function< void(ItoParticle &)>	a_nonDeletionModifier = `[](ItoParticle&) -> void { return; }`
	)

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.
[in]	a_nonDeletionModifier	Optional input argument for letting the user manipulate particles that were intersected but not deleted

◆ loadBalanceBoxes()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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 on each level. It is up to the user/programmer to decide if load balancing should be done independently on each level, or if loads per MPI rank are accumulated across levels.

Reimplemented from TimeStepper.

◆ loadBalanceFluidRealm()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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()

template<typename I , typename C , typename R , typename F >

bool ItoKMCStepper::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()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::parseDualGrid

protectedvirtualnoexcept

Parse dual or single realm calculations.

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

◆ parseSuperParticles()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::parseSuperParticles

protectedvirtualnoexcept

Parse the desired number of particles per cell.

Sets m_particlesPerCell from input script.

◆ parseVerbosity()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::parseVerbosity

protectedvirtualnoexcept

Parse chattiness.

Sets m_verbosity from input script.

◆ postCheckpointPoisson()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::postCheckpointPoisson

protectedvirtualnoexcept

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()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::postCheckpointSetup

overridevirtualnoexcept

Perform post-checkpoint operations.

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

Implements TimeStepper.

◆ preRegrid()

template<typename I , typename C , typename R , typename F >

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

overridevirtualnoexcept

Perform pre-regrid operations - storing relevant data from 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::ItoKMC::ItoKMCGodunovStepper< I, C, R, F >.

◆ reconcileCdrDensities() [1/3]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::reconcileCdrDensities	(	const EBAMRCellData &	a_newParticlesPerCell,
		const EBAMRCellData &	a_oldParticlesPerCell,
		const Real	a_dt
	)

protectedvirtualnoexcept

Reconcile the CDR densities after the reaction network.

This adds the a_newPPC - a_oldPPC to the densities and sets the source term to (a_newPPC - a_oldPPC)/(vol * dt)

Parameters

[in]	a_newParticlesPerCell	Particles per cell after the chemistry advance.
[in]	a_oldParticlesPerCell	Particles per cell before the chemistry advance.
[in]	a_dt	Time step

◆ reconcileCdrDensities() [2/3]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::reconcileCdrDensities	(	const EBCellFAB &	a_newParticlesPerCell,
		const EBCellFAB &	a_oldParticlesPerCell,
		const int	a_level,
		const DataIndex	a_dit,
		const Box	a_box,
		const Real	a_dx,
		const Real	a_dt
	)

protectedvirtualnoexcept

Reconcile the CDR densities after the reaction network.

This adds the a_newPPC - a_oldPPC to the densities and sets the source term to (a_newPPC - a_oldPPC)/(vol * dt)

Parameters

[in]	a_newParticlesPerCell	Particles per cell after the chemistry advance.
[in]	a_oldParticlesPerCell	Particles per cell before the chemistry advance.
[in]	a_level	Grid level
[in]	a_dit	Grid index
[in]	a_box	Grid box
[in]	a_dx	Grid resolution.
[in]	a_dt	Time step

◆ reconcileCdrDensities() [3/3]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::reconcileCdrDensities	(	const LevelData< EBCellFAB > &	a_newParticlesPerCell,
		const LevelData< EBCellFAB > &	a_oldParticlesPerCell,
		const int	a_level,
		const Real	a_dt
	)

protectedvirtualnoexcept

Reconcile the CDR densities after the reaction network.

This adds the a_newPPC - a_oldPPC to the densities and sets the source term to (a_newPPC - a_oldPPC)/(vol * dt)

Parameters

[in]	a_newParticlesPerCell	Particles per cell after the chemistry advance.
[in]	a_oldParticlesPerCell	Particles per cell before the chemistry advance.
[in]	a_level	Grid level
[in]	a_dt	Time step

◆ reconcileParticles() [1/3]

template<typename I , typename C , typename R , typename F >

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

inlineprotectednoexcept

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_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]

template<typename I , typename C , typename R , typename F >

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

inlineprotectednoexcept

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_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]

template<typename I , typename C , typename R , typename F >

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

inlineprotectednoexcept

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_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.

◆ reconcilePhotoionization()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::reconcilePhotoionization

protectedvirtualnoexcept

Reconcile the results from photoionization reactions.

Note: This adds particles directly into the ItoSolver particle data holders and into m_cdrPhotoiProducts.; This is not used (yet) – it does a per-patch call to m_physics, which means that its done outside of the cell-sorted requirement of advanceReactionNetwork.

◆ regrid()

template<typename I , typename C , typename R , typename F >

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

overridevirtualnoexcept

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::ItoKMC::ItoKMCGodunovStepper< I, C, R, F >.

◆ remapParticles() [1/2]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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

◆ resolveSecondaryEmissionEB() [1/2]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::resolveSecondaryEmissionEB ( const Real a_dt )

protectedvirtualnoexcept

Resolve secondary emission at the EB.

Parameters

[in] a_dt Time step.

Note: Calls the other version.

◆ resolveSecondaryEmissionEB() [2/2]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::resolveSecondaryEmissionEB	(	Vector< ParticleContainer< ItoParticle > * > &	a_secondaryParticles,
		Vector< ParticleContainer< ItoParticle > * > &	a_primaryParticles,
		Vector< EBAMRIVData * > &	a_cdrFluxes,
		EBAMRIVData &	a_surfaceChargeDensity,
		const Real	a_dt
	)

protectedvirtualnoexcept

Resolve secondary emission at the EB.

This does three things: 1) It deposits the primary and second particles on the mesh and update the surface charge density. 2) It removes the primary particles and adds the secondary particles to the Ito solvers. 3) It adds the CDR fluxes to the CDR solvers, and updates the surface charge density.

Parameters

[out]	a_secondaryParticles	Secondary emitted (gained) particles at the EB.
[out]	a_cdrFluxes	CDR fluxes for BCs.
[in]	a_primaryParticles	Primary (lost) particles at the EB.
[in]	a_surfaceChargeDensity	Surface charge density.
[in]	a_dt	Time step.

◆ setCdrVelocityFunctions()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::setCdrVelocityFunctions

protectedvirtualnoexcept

Set the Cdr velocities to be sgn(charge) * E.

To set the final drift velocity, mobilities should be computed and multiplied in with the drift velocities.

◆ setItoVelocityFunctions()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::setItoVelocityFunctions

protectedvirtualnoexcept

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

Note: This should be set before ItoSolver computes velocities.

◆ setVoltage()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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()

template<typename I , typename C , typename R , typename F >

bool ItoKMCStepper::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()

template<typename I , typename C , typename R , typename F >

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

protectedvirtualnoexcept

Sort photons by cells.

Parameters

[in] a_which Which container to sort by cell

◆ sortPhotonsByPatch()

template<typename I , typename C , typename R , typename F >

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

protectedvirtualnoexcept

Sort photons by patch.

Parameters

[in] a_which Which container to sort by patch

◆ synchronizeSolverTimes()

template<typename I , typename C , typename R , typename F >

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

overridevirtualnoexcept

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]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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]

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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

◆ writeData()

template<typename I , typename C , typename R , typename F >

void ItoKMCStepper::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 belogns
[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

◆ writeNumberOfParticlesPerPatch()

template<typename I , typename C , typename R , typename F >

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

protectedvirtualnoexcept

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.
[in]	a_outputRealm	Realm where a_output belogns
[in]	a_level	Grid level

◆ writePlotData()

template<typename I , typename C , typename R , typename F >

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

overridevirtualnoexcept

Write plot data to output holder.

Parameters

[in,out]	a_output	Output data holder.
[in,out]	a_icomp	Starting component in a_output to begin at.
[in]	a_outputRealm	Realm where a_output belongs
[in]	a_level	Grid level

Implements TimeStepper.

Member Data Documentation

◆ m_cdrFluxes

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

Vector<EBAMRIVData> Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_cdrFluxes

protected

CDR fluxes for CDR BCs.

There's a version of this inside the solvers, but we need this one because the EB coupling takes place on the particle realm.

◆ m_cdrMobilities

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

Vector<EBAMRCellData> Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_cdrMobilities

protected

For holding the mobilities for the CDR species.

Note: Defined on the fluid realm.

◆ m_cdrPhotoiProducts

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

Vector<ParticleContainer<PointParticle> > Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_cdrPhotoiProducts

mutableprotected

Photoionization products to be put in the CDR equations.

Note: This is agglomerated with Ito particle photoionization functionality, and is therefore defined on the particle realm.

◆ m_conductivityCell

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRCellData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_conductivityCell

protected

Cell-centered conductivity.

Note: Defined on the fluid realm with 1 component

◆ m_conductivityEB

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRIVData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_conductivityEB

protected

EB-centered conductivity.

Note: Defined on the fluid realm with 1 component

◆ m_conductivityFace

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRFluxData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_conductivityFace

protected

Face-centered conductivity.

Note: Defined on the fluid realm with 1 component

◆ m_currentDensity

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRCellData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_currentDensity

protected

Storage for current density.

Note: Defined over the fluid realm with SpaceDim components.

◆ m_energySources

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

Vector<EBAMRCellData> Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::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_fluidCdrPPC

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRCellData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_fluidCdrPPC

protected

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

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

◆ m_fluidGradPhiCDR

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

Vector<EBAMRCellData> Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_fluidGradPhiCDR

protected

For holding the gradient of all CDR species densities.

Note: Defined on the fluid realm

◆ m_fluidGradPhiIto

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

Vector<EBAMRCellData> Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_fluidGradPhiIto

protected

For holding the gradient of all Ito species densities.

Note: Defined on the fluid realm

◆ m_fluidOldCdrPPC

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRCellData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_fluidOldCdrPPC

protected

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

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

◆ m_fluidPPC

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRCellData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::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

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

std::string Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::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

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRCellData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::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

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

Real Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::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

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

int Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_mergeInterval

protected

How often to merge superparticles.

If <= 1 we merge every time step.

◆ m_particleEPS

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRCellData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_particleEPS

protected

For holding the mean particle energy.

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

◆ m_particleItoPPC

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRCellData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_particleItoPPC

protected

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

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

◆ m_particleOldItoPPC

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRCellData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_particleOldItoPPC

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_particleYPC

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

EBAMRCellData Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::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

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

RefCountedPtr<ItoKMCPhysics> Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_physics

protected

Implementation of ItoKMCPhysics.

All solver coupling occurs through the implementation of this class

◆ m_plasmaPhase

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

phase::which_phase Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_plasmaPhase

protected

Phase where we solve for the plasma.

Note: This is hardcoded to phase::gas

◆ m_relaxTimeFactor

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

Real Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_relaxTimeFactor

protected

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

Used for restricting dt < m_relaxTimeFactor * eps0/sigma

◆ m_secondaryParticles

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

Vector<ParticleContainer<ItoParticle> > Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_secondaryParticles

protected

List of secondary particles injected through the EB.

This is used when injecting secondary particles through the EB.

Note: Stored on the particle realm

◆ m_secondaryPhotons

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>

Vector<ParticleContainer<Photon> > Physics::ItoKMC::ItoKMCStepper< I, C, R, F >::m_secondaryPhotons

protected

List of secondary photons injected through the EB.

This is used when injecting secondary photons through the EB.

Note: Stored on the particle realm

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

Physics/ItoKMC/CD_ItoKMCStepper.H
Physics/ItoKMC/CD_ItoKMCStepperImplem.H

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid> class Physics::ItoKMC::ItoKMCStepper< I, C, R, F >

Constructor & Destructor Documentation

◆ ItoKMCStepper()

Member Function Documentation

◆ advance()

◆ advancePhotons()

◆ advanceReactionNetwork() [1/4]

◆ advanceReactionNetwork() [2/4]

◆ advanceReactionNetwork() [3/4]

◆ advanceReactionNetwork() [4/4]

◆ computeConductivityCell() [1/2]

◆ computeConductivityCell() [2/2]

◆ computeCurrentDensity()

◆ computeDensityGradients()

◆ computeDiffusionCoefficients() [1/4]

◆ computeDiffusionCoefficients() [2/4]

◆ computeDiffusionCoefficients() [3/4]

◆ computeDiffusionCoefficients() [4/4]

◆ computeDriftVelocities()

◆ computeEdotJSource()

◆ computeElectricField()

◆ computeMaxElectricField()

◆ computeMobilities() [1/4]

◆ computeMobilities() [2/4]

◆ computeMobilities() [3/4]

◆ computeMobilities() [4/4]

◆ computePhysicsDt() [1/4]

◆ computePhysicsDt() [2/4]

◆ computePhysicsDt() [3/4]

◆ computePhysicsDt() [4/4]

◆ computePhysicsPlotVariables()

◆ computeReactiveCdrParticlesPerCell() [1/3]

◆ computeReactiveCdrParticlesPerCell() [2/3]

◆ computeReactiveCdrParticlesPerCell() [3/3]

◆ computeReactiveItoParticlesPerCell() [1/3]

◆ computeReactiveItoParticlesPerCell() [2/3]

◆ computeReactiveItoParticlesPerCell() [3/3]

◆ computeReactiveMeanEnergiesPerCell() [1/3]

◆ computeReactiveMeanEnergiesPerCell() [2/3]

◆ computeReactiveMeanEnergiesPerCell() [3/3]

◆ computeSpaceChargeDensity() [1/2]

◆ computeSpaceChargeDensity() [2/2]

◆ depositParticles() [1/2]

◆ depositParticles() [2/2]

◆ fillSecondaryEmissionEB() [1/2]

◆ fillSecondaryEmissionEB() [2/2]

◆ getCheckpointLoads()

◆ getLoadBalanceSolvers()

◆ getMaxMinCDRDensity()

◆ getMaxMinItoDensity()

◆ getParticleStatistics()

◆ getPhysicalParticlesPerCell()

◆ getTime()

◆ intersectParticles() [1/2]

◆ intersectParticles() [2/2]

◆ loadBalanceBoxes()

◆ loadBalanceFluidRealm()

◆ loadBalanceParticleRealm()

◆ loadBalanceThisRealm()

◆ parseDualGrid()

◆ parseSuperParticles()

◆ parseVerbosity()

◆ postCheckpointPoisson()

◆ postCheckpointSetup()

◆ preRegrid()

◆ reconcileCdrDensities() [1/3]

◆ reconcileCdrDensities() [2/3]

◆ reconcileCdrDensities() [3/3]

◆ reconcileParticles() [1/3]

◆ reconcileParticles() [2/3]

◆ reconcileParticles() [3/3]

◆ reconcilePhotoionization()

◆ regrid()

◆ remapParticles() [1/2]

◆ remapParticles() [2/2]

template<typename I = ItoSolver, typename C = CdrCTU, typename R = McPhoto, typename F = FieldSolverMultigrid>
class Physics::ItoKMC::ItoKMCStepper< I, C, R, F >