Implementation of ItoKMCStepper that uses a semi-implicit split-step formalism for advancing the Ito-Poisson-KMC system. More...

#include <CD_ItoKMCGodunovStepper.H>

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

[legend]

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

[legend]

Public Member Functions
	ItoKMCGodunovStepper ()=delete
	Disallowed default constructor. Use the full constructor.

	ItoKMCGodunovStepper (RefCountedPtr< ItoKMCPhysics > &a_physics)
	Full constructor. More...

virtual	~ItoKMCGodunovStepper ()
	Destructor. Does nothing.

virtual Real	advance (const Real a_dt) override
	Advance the Ito-Poisson-KMC system over a_dt. More...

virtual void	allocate () noexcept override
	Allocate storage required for advancing the equations.

virtual void	parseOptions () noexcept override
	Parse options.

virtual void	parseRuntimeOptions () noexcept override
	Parse run-time options.

virtual void	preRegrid (const int a_lmin, const int a_oldFinestLevel) noexcept override
	Perform pre-regrid operations. 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	postPlot () noexcept override
	Perform post-plot operations.

Public Member Functions inherited from Physics::ItoKMC::ItoKMCStepper< ItoSolver, CdrCTU, McPhoto, FieldSolverMultigrid >
	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	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	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	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	WhichAlgorithm { EulerMaruyama }
	Simple enum for distinguishing between algorithms.

Protected Types inherited from Physics::ItoKMC::ItoKMCStepper< ItoSolver, CdrCTU, McPhoto, FieldSolverMultigrid >
enum class	TimeCode
	An enum for encapsulating how time steps were restricted.

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

virtual void	parseAlgorithm () noexcept
	Parse advancement algorithm.

virtual void	parseCheckpointParticles () noexcept
	Parse checkpoint-restart functionality.

virtual void	setOldPositions () noexcept
	Set the starting positions for the ItoSolver particles.

virtual void	barrier () const noexcept
	Set an MPI barrier if using debug mode. More...

virtual void	remapPointParticles (Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &a_particles, const SpeciesSubset a_subset) noexcept
	Remap the input point particles. More...

virtual void	depositPointParticles (const Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &a_particles, const SpeciesSubset a_subset) noexcept
	Deposit the input point particles on the mesh. More...

virtual void	clearPointParticles (const Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &a_particles, const SpeciesSubset a_subset) noexcept
	Clear the input particle data holders. More...

virtual void	computeConductivities (const Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &a_particles) noexcept
	Compute all conductivities (cell, face, and EB) from the input point particles. More...

virtual void	computeCellConductivity (EBAMRCellData &a_conductivityCell, const Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &a_particles) noexcept
	Compute the cell-centered conductivity. More...

virtual void	computeFaceConductivity () noexcept
	Compute the cell-centered conductivity. More...

virtual void	computeSemiImplicitRho () noexcept
	Set up the space charge density for the regrid operation.

virtual void	setupSemiImplicitPoisson (const Real a_dt) noexcept
	Set up the semi-implicit Poisson solver.

virtual void	removeCoveredPointParticles (Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &a_particles, const EBRepresentation a_representation, const Real a_tolerance) const noexcept
	Remove covered particles. More...

virtual void	copyConductivityParticles (Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &a_conductivityParticles) noexcept
	Copy particles from the ItoSolver into PointParticles whose weight are ItoParticle::m_weight * ItoParticle::m_mobility. More...

virtual void	advanceEulerMaruyama (const Real a_dt) noexcept
	Advance the particles using the Euler-Maruyama scheme. More...

virtual void	diffuseParticlesEulerMaruyama (Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &a_rhoDaggerParticles, const Real a_dt) noexcept
	Perform the diffusive Ito advance in the Euler-Maruyama step. More...

virtual void	computeDiffusionTermCDR (EBAMRCellData &m_semiImplicitRhoCDR, const Real a_dt) noexcept
	Compute the diffusion term for the CDR equations as well as the resulting CDR-contributions to the space charge density. More...

virtual void	stepEulerMaruyamaParticles (const Real a_dt) noexcept
	Step the particles according to the regular Euler-Maruyama scheme. More...

virtual void	stepEulerMaruyamaCDR (const Real a_dt) noexcept
	Step the CDR equations according to the regular Euler-Maruyama scheme. More...

virtual void	plotParticles () const noexcept
	Utility function for plotting the ItoSolver particles. These are written in a particles folder.

Protected Member Functions inherited from Physics::ItoKMC::ItoKMCStepper< ItoSolver, CdrCTU, McPhoto, FieldSolverMultigrid >
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
bool	m_writeCheckpointParticles
	If true, then the particles are checkpointed so we can regrid on checkpoint-restart.

bool	m_readCheckpointParticles
	If true, then the HDF5 checkpoint file contained particles that we can read.

bool	m_canRegridOnRestart
	If true, then the class supports regrid-on-restart. More...

bool	m_extendConductivityEB
	For achieving a slightly smoother gradient in the conductivity near the EB.

bool	m_smoothConductivity
	Smooth the conductivity or not.

WhichAlgorithm	m_algorithm
	Which advancement algorithm to use.

Timer	m_timer
	Timer used for run-time logging of routines.

Vector< RefCountedPtr< ParticleContainer< PointParticle > > >	m_conductivityParticles
	Storage for simplified particles that gave us sigma^k. More...

Vector< RefCountedPtr< ParticleContainer< PointParticle > > >	m_irregularParticles
	Storage for particles that fell inside the EB but should still contribute to the conductivity.

Vector< RefCountedPtr< ParticleContainer< PointParticle > > >	m_rhoDaggerParticles
	Storage for particles that gave rho^dagger. More...

EBAMRCellData	m_semiImplicitRhoCDR
	Storage for CDR densities used during the semi-implicit solve. More...

EBAMRCellData	m_semiImplicitConductivityCDR
	Storage for conductivity term due to mobile CDR species. More...

EBAMRCellData	m_scratchSemiImplicitRhoCDR
	Scratch storage for CDR contribution to space charge density. More...

EBAMRCellData	m_scratchSemiImplicitConductivityCDR
	Scratch storage for CDR contribution to conductivity. More...

Vector< EBAMRCellData >	m_cdrDivD
	Storage for the finite-volume approximation of div(D*grad(phi)) for the CDR equations.

Protected Attributes inherited from Physics::ItoKMC::ItoKMCStepper< ItoSolver, CdrCTU, McPhoto, FieldSolverMultigrid >
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::ItoKMCGodunovStepper< I, C, R, F >

Implementation of ItoKMCStepper that uses a semi-implicit split-step formalism for advancing the Ito-Poisson-KMC system.

Constructor & Destructor Documentation

◆ ItoKMCGodunovStepper()

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

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

Full constructor.

Parameters

[in] a_phyics Physics implementation.

Member Function Documentation

◆ advance()

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

Real ItoKMCGodunovStepper::advance ( const Real a_dt )

overridevirtual

Advance the Ito-Poisson-KMC system over a_dt.

Parameters

[in] a_dt Time step

Implements Physics::ItoKMC::ItoKMCStepper< ItoSolver, CdrCTU, McPhoto, FieldSolverMultigrid >.

◆ advanceEulerMaruyama()

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

void ItoKMCGodunovStepper::advanceEulerMaruyama ( const Real a_dt )

protectedvirtualnoexcept

Advance the particles using the Euler-Maruyama scheme.

Parameters

[in] a_dt Time step

◆ barrier()

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

void ItoKMCGodunovStepper::barrier

protectedvirtualnoexcept

Set an MPI barrier if using debug mode.

This defaults to ParallelOps::barrier() if m_debug=true

◆ clearPointParticles()

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

void ItoKMCGodunovStepper::clearPointParticles	(	const Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &	a_particles,
		const SpeciesSubset	a_subset
	)

protectedvirtualnoexcept

Clear the input particle data holders.

Parameters

[in,out]	a_particles	List of particle containers to remap. Indices must correspond to indices in the ItoSolvers
[in]	a_subset	Particle subset to remap.

◆ computeCellConductivity()

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

void ItoKMCGodunovStepper::computeCellConductivity	(	EBAMRCellData &	a_conductivityCell,
		const Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &	a_particles
	)

protectedvirtualnoexcept

Compute the cell-centered conductivity.

Parameters

[out]	a_conductivityCell	Cell-centered conductivity
[in]	a_particles	Particles to deposit. Particle weights must hold the mobility*weight

Note: Also adds in the conductive contribution from the CDR solvers.

◆ computeConductivities()

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

void ItoKMCGodunovStepper::computeConductivities ( const Vector< RefCountedPtr< ParticleContainer< PointParticle >>> & a_particles )

protectedvirtualnoexcept

Compute all conductivities (cell, face, and EB) from the input point particles.

Parameters

[in] a_particles Particles to deposit. Particle weights must hold the mobility*weight

Note: This deposits the input particle weights onto m_conductivityCell, m_conductivityFace.; Also adds in the conductive contribution from the CDR solvers.

◆ computeDiffusionTermCDR()

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

void ItoKMCGodunovStepper::computeDiffusionTermCDR	(	EBAMRCellData &	m_semiImplicitRhoCDR,
		const Real	a_dt
	)

protectedvirtualnoexcept

Compute the diffusion term for the CDR equations as well as the resulting CDR-contributions to the space charge density.

This does an explicit diffusion advance over a_dt for the diffusive CDR species. This also stores the resultant space charge on m_semiImplicitRhoCDR.

◆ computeFaceConductivity()

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

void ItoKMCGodunovStepper::computeFaceConductivity

protectedvirtualnoexcept

Compute the cell-centered conductivity.

Note: Interpolates m_conductivityCell to m_conductivityFace

◆ copyConductivityParticles()

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

void ItoKMCGodunovStepper::copyConductivityParticles ( Vector< RefCountedPtr< ParticleContainer< PointParticle >>> & a_conductivityParticles )

protectedvirtualnoexcept

Copy particles from the ItoSolver into PointParticles whose weight are ItoParticle::m_weight * ItoParticle::m_mobility.

Parameters

[out] a_conductivityParticles Point-particles holding the mobility * weight

◆ depositPointParticles()

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

void ItoKMCGodunovStepper::depositPointParticles	(	const Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &	a_particles,
		const SpeciesSubset	a_subset
	)

protectedvirtualnoexcept

Deposit the input point particles on the mesh.

Parameters

[in,out]	a_particles	List of particle containers to remap. Indices must correspond to indices in the ItoSolvers
[in]	a_subset	Particle subset to remap.

Note: This deposits into the ItoSolver m_phi data.

◆ diffuseParticlesEulerMaruyama()

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

void ItoKMCGodunovStepper::diffuseParticlesEulerMaruyama	(	Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &	a_rhoDaggerParticles,
		const Real	a_dt
	)

protectedvirtualnoexcept

Perform the diffusive Ito advance in the Euler-Maruyama step.

This computes the diffusion hop onto run-time enabled storage on the ItoParticles. We also store the "rho dagger" particles which correspond to the position of the charged particles after the diffusionhop.

◆ preRegrid()

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

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

overridevirtualnoexcept

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.

Note: This will store the "conductivity" and "rho dagger" particles.

Reimplemented from Physics::ItoKMC::ItoKMCStepper< ItoSolver, CdrCTU, McPhoto, FieldSolverMultigrid >.

◆ regrid()

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

void ItoKMCGodunovStepper::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.

Reimplemented from Physics::ItoKMC::ItoKMCStepper< ItoSolver, CdrCTU, McPhoto, FieldSolverMultigrid >.

◆ remapPointParticles()

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

void ItoKMCGodunovStepper::remapPointParticles	(	Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &	a_particles,
		const SpeciesSubset	a_subset
	)

protectedvirtualnoexcept

Remap the input point particles.

Parameters

[in,out]	a_particles	List of particle containers to remap. Indices must correspond to indices in the ItoSolvers
[in]	a_subset	Particle subset to remap.

◆ removeCoveredPointParticles()

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

void ItoKMCGodunovStepper::removeCoveredPointParticles	(	Vector< RefCountedPtr< ParticleContainer< PointParticle >>> &	a_particles,
		const EBRepresentation	a_representation,
		const Real	a_tolerance
	)		const

protectedvirtualnoexcept

Remove covered particles.

Parameters

[in,out]	a_particles	Particles to remove
[in]	a_representation	Representation of the EB
[in]	a_tolerance	EB tolerance

◆ stepEulerMaruyamaCDR()

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

void ItoKMCGodunovStepper::stepEulerMaruyamaCDR ( const Real a_dt )

protectedvirtualnoexcept

Step the CDR equations according to the regular Euler-Maruyama scheme.

Parameters

[in] a_dt Time step.

This sets phi^(k+1) = phi^k - a_dt * div(v * phi) + a_dt * div(D*grad(phi))

◆ stepEulerMaruyamaParticles()

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

void ItoKMCGodunovStepper::stepEulerMaruyamaParticles ( const Real a_dt )

protectedvirtualnoexcept

Step the particles according to the regular Euler-Maruyama scheme.

Parameters

[in] a_dt Time step.

This sets X^(k+1) = X^k + a_dt * V + sqrt(2*D*a_dt) * W

Note: The hop MUST have been stored on the particle run-time storage

Member Data Documentation

◆ m_canRegridOnRestart

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

bool Physics::ItoKMC::ItoKMCGodunovStepper< I, C, R, F >::m_canRegridOnRestart

protected

If true, then the class supports regrid-on-restart.

This is populated in the constructor or when reading the checkpoint file.

◆ m_conductivityParticles

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

Vector<RefCountedPtr<ParticleContainer<PointParticle> > > Physics::ItoKMC::ItoKMCGodunovStepper< I, C, R, F >::m_conductivityParticles

protected

Storage for simplified particles that gave us sigma^k.

Note: Needed for regrids

◆ m_rhoDaggerParticles

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

Vector<RefCountedPtr<ParticleContainer<PointParticle> > > Physics::ItoKMC::ItoKMCGodunovStepper< I, C, R, F >::m_rhoDaggerParticles

protected

Storage for particles that gave rho^dagger.

Note: Needed for regrids

◆ m_scratchSemiImplicitConductivityCDR

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

EBAMRCellData Physics::ItoKMC::ItoKMCGodunovStepper< I, C, R, F >::m_scratchSemiImplicitConductivityCDR

protected

Scratch storage for CDR contribution to conductivity.

Note: Only used during regrids.

◆ m_scratchSemiImplicitRhoCDR

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

EBAMRCellData Physics::ItoKMC::ItoKMCGodunovStepper< I, C, R, F >::m_scratchSemiImplicitRhoCDR

protected

Scratch storage for CDR contribution to space charge density.

Note: Only used during regrids.

◆ m_semiImplicitConductivityCDR

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

EBAMRCellData Physics::ItoKMC::ItoKMCGodunovStepper< I, C, R, F >::m_semiImplicitConductivityCDR

protected

Storage for conductivity term due to mobile CDR species.

Note: This is needed because the semi-implicit requires the conductivity when solving the Poisson equation.

◆ m_semiImplicitRhoCDR

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

EBAMRCellData Physics::ItoKMC::ItoKMCGodunovStepper< I, C, R, F >::m_semiImplicitRhoCDR

protected

Storage for CDR densities used during the semi-implicit solve.

Note: This is needed because the semi-implicit requires the space charge from before the reaction step.

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

Physics/ItoKMC/TimeSteppers/ItoKMCGodunovStepper/CD_ItoKMCGodunovStepper.H
Physics/ItoKMC/TimeSteppers/ItoKMCGodunovStepper/CD_ItoKMCGodunovStepperImplem.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::ItoKMCGodunovStepper< I, C, R, F >

Constructor & Destructor Documentation

◆ ItoKMCGodunovStepper()

Member Function Documentation

◆ advance()

◆ advanceEulerMaruyama()

◆ barrier()

◆ clearPointParticles()

◆ computeCellConductivity()

◆ computeConductivities()

◆ computeDiffusionTermCDR()

◆ computeFaceConductivity()

◆ copyConductivityParticles()

◆ depositPointParticles()

◆ diffuseParticlesEulerMaruyama()

◆ preRegrid()

◆ regrid()

◆ remapPointParticles()

◆ removeCoveredPointParticles()

◆ stepEulerMaruyamaCDR()

◆ stepEulerMaruyamaParticles()

Member Data Documentation

◆ m_canRegridOnRestart

◆ m_conductivityParticles

◆ m_rhoDaggerParticles

◆ m_scratchSemiImplicitConductivityCDR

◆ m_scratchSemiImplicitRhoCDR

◆ m_semiImplicitConductivityCDR

◆ m_semiImplicitRhoCDR

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