AMRLevel for mushy layer calculations. More...

#include <AMRLevelMushyLayer.H>

Inheritance diagram for AMRLevelMushyLayer:

Public Member Functions
	AMRLevelMushyLayer ()
	Default constructor.

	AMRLevelMushyLayer (MushyLayerOptions a_opt, MushyLayerParams a_params)
	Full constructor. Arguments are same as in define()

void	define (MushyLayerOptions a_opt, MushyLayerParams a_params)
	Defines this AMRLevelMushyLayer. More...

virtual	~AMRLevelMushyLayer ()
	Destructor.

virtual void	define (AMRLevel *a_coarserLevelPtr, const Box &a_problemDomain, int a_level, int a_refRatio)
	Never called: historical.

void	setDefaults ()
	Set default values. More...

virtual void	define (AMRLevel *a_coarserLevelPtr, const ProblemDomain &a_problemDomain, int a_level, int a_refRatio)
	Define new AMRLevelMushyLayer from coarser. More...

virtual Real	advance ()
	Advance by one timestep.

virtual void	postTimeStep ()
	Things to do after a timestep.

void	doExplicitReflux (int a_var)
	Explicitly reflux scalar field.

Real	doHCreflux ()
	Reflux enthalpy and bulk concentration.

void	doMomentumReflux (Vector< LevelData< FArrayBox > *> &compVel)
	Do reflux on momentum field.

virtual void	tagCells (IntVectSet &a_tags)
	Create tags for regridding.

void	tagMushLiquidBoundary (IntVectSet &localTags)
	Tags cells on the mush side of the mush-liquid boundary.

void	tagBoundaryLayerCells (IntVectSet &localTags)
	Tag cells on the domain boundary.

void	tagCenterCells (IntVectSet &localTags, Real radius=0)
	Tag cells inside grid.

void	tagMushyCells (IntVectSet &localTags)
	Tag cells with porosity < 1.

void	tagCellsVar (IntVectSet &localTags, Real refineThresh, int taggingVar, int vectorTaggingVar, TaggingMethod taggingMethod, int comp=-1)
	Add cells that specify criteria.

void	levelSetup ()
	Setup menagerie of data structures.

void	defineCFInterp ()
	Setup CF interp objects.

void	setEta (Real a_eta)
	Set eta on all projection operators. More...

Real	maxAllowedEta ()
	Maximum allowed eta.

void	setAdvVelCentering (Real a_fraction)
	Set adv_vel_centering on all levels.

virtual void	tagCellsInit (IntVectSet &a_tags)
	Create tags at initialization.

virtual void	regrid (const Vector< Box > &a_newGrids)
	Set up data on this level after regridding.

virtual void	initialGrid (const Vector< Box > &a_newGrids)
	Initialize grids.

virtual void	postInitialGrid (const bool a_restart)
	Operations to do after initial grids have been set up.

virtual void	postRegrid (int a_base_level)
	Operations to execute after we've done regridding.

void	createDataStructures ()
	Create structures to hold data.

void	initDataStructures ()
	Initialize data structures - resize arrays etc.

void	computeAllVelocities (bool doFRupdates)
	Compute cell-centred and face-centred velocities.

virtual void	initialData ()
	Initialize data.

void	initialDataCornerFlow ()
	Initial data for corner flow problem.

void	initialDataHRL ()
	Initial data for Horton-Rogers-Lapwood problem.

void	initialDataConvectionMixedPorous ()
	Initial data for convection in a hetrogeneous porous medium.

void	initialDataPoiseuille ()
	Initial data for poiseuille flow.

void	initialDataIceBlock ()
	Initial data for a solid ice block.

void	initialDataMushyLayer ()
	Initial data for mushy layer simulations.

void	initialDataPorousHole ()
	Mushy layer with a porous hole in the middle.

void	initialDataZeroPorosityTest ()
	Initial data for a test case with regions of zero porosity.

void	initialDataDiffusion ()
	Initial data for diffusion problem.

void	initialDataVortexPair ()
	Initial data for vortex pair problem.

void	addVortex (RealVect center, Real strength, Real radius)
	Add vortex to domain.

void	initialDataRayleighBenard ()
	Initial data for Rayleigh-Benard problem.

void	initialDataSoluteFlux ()
	Initial data for solute flux test problem.

void	initialDataSidewallHeating ()
	Initial data for sidewall heating problem.

void	initialDataDefault ()
	Default initial data.

void	initialDataBurgers ()
	Initial data for burgers problem.

void	initialDataRefluxTest ()
	Initial data for problem to test refluxing.

bool	loadAdvVel ()
	Whether or not we're loading advection velocities.

virtual bool	convergedToSteadyState ()
	Have we converged to steady state?

virtual void	postInitialize ()
	Things to do after initialization.

void	computeVorticityStreamfunction ()
	Calculate vorticity and streamfunction so we can plot them.

void	computeVorticity ()
	Compute vorticity.

void	getExtraPlotFields ()
	Get $\pi$ and $\phi$ from projection so we can plot them.

void	writeAMRHierarchy (string filename)
	Write AMR hierarchy to file.

void	setDimensionlessReferenceInitial ()
	Set reference point for nondimensionalisation to be the initial temperature/salinity.

void	setDimensionlessReferenceEutectic ()
	Set reference point for nondimensionalisation to be the eutectic temperature/salinity.

virtual Real	computeDt ()
	Returns the dt computed earlier for this level.

virtual Real	computeInitialDt ()
	Compute dt using initial data.

void	computeDiagnostics ()
	Compute nusselt number, salt fluxes etc.

void	defineSolvers (Real a_time)
	Define solvers.

void	computeChimneyDiagnostics ()
	Compute chimney diagnostics.

DisjointBoxLayout	grids ()
	Whether or not to compute diagnostics. More...

void	shiftData (int dir, int distance)
	Shift data in domain.

void	dx (Real newDx)
	Set $\Delta x$ on this level.

Real	dx ()
	Get $\Delta x$ on this level.

void	reshapeData (DisjointBoxLayout newGrids, ProblemDomain newDomain)
	Transfer data to new disjoint box layout. More...

void	refine (Real ref_ratio, DisjointBoxLayout a_grids, ProblemDomain a_domain)
	Refine data.

void	doPostRegridSmoothing (bool a_smoothVel=true, bool a_smoothScalar=true)
	Do smoothing after regridding.

void	setSmoothingCoeff (Real a_coeff)
	Set the coefficient for smoothing fields.

void	setSmoothingDone (bool a_smoothingDone)

void	addMeltPond (int depth, Real salinity, Real enthalpy, bool rescaleExistingSolution=false)
	Add a melt pond at the top of the domain. More...

void	setVelZero (LevelData< FArrayBox > &a_vel, Real a_limit=-1, int a_radius=0)
	Make sure zero porosity regions have no velocity (cell centred velocity)

void	setVelZero (LevelData< FluxBox > &a_vel, Real a_limit=-1)
	Make sure zero porosity regions have no velocity (face centred velocity)

void	setCCVelZero (Real a_limit)
	Set velocity to zero when porosity is below specified limit (cell centred)

void	updateEnthalpyVariables ()
	Update thermodynamic variables based on phase diagram.

void	computeLambdaPorosity ()
	Compute lambda/porosity.

void	set_compute_diagnostics (bool compute_diags)
	Set whether or not to compute diagnostics.

void	horizAverage ()
	Average enthalpy and bulk salinity then recalculate all other fields.

void	smoothScalarField (LevelData< FArrayBox > &a_phi, int a_var, Real a_smoothing)
	Smooth some scalar field. More...

void	smoothEnthalpyBulkConc (Real a_smoothing)

Public Member Functions inherited from AMRLevel
virtual void	preRegrid (int a_base_level, const Vector< Vector< Box > > &a_new_grids)

virtual void	conclude (int a_step) const

virtual void	writeCheckpointHeader (HDF5Handle &a_handle) const=0

virtual void	writeCheckpointLevel (HDF5Handle &a_handle) const=0

virtual void	readCheckpointHeader (HDF5Handle &a_handle)=0

virtual void	readCheckpointLevel (HDF5Handle &a_handle)=0

virtual void	writePlotHeader (HDF5Handle &a_handle) const=0

virtual void	writePlotLevel (HDF5Handle &a_handle) const=0

virtual void	writeCustomPlotFile (const std::string &a_prefix, int a_step) const

virtual void	finerLevelPtr (AMRLevel *a_finer_level_ptr)

virtual void	dt (Real a_dt)

virtual void	time (Real a_time)

virtual void	initialDtMultiplier (Real a_initial_dt_multiplier)

virtual Real	dt () const

virtual Real	time () const

virtual Real	initialDtMultiplier () const

virtual const ProblemDomain &	problemDomain () const

virtual Vector< Box >	boxes () const

bool	isDefined () const

bool	hasCoarserLevel () const

bool	hasFinerLevel () const

virtual int	level () const

virtual int	refRatio () const

Vector< AMRLevel *>	getAMRLevelHierarchy ()

Public Attributes
Diagnostics	m_diagnostics
	Diagnostics e.g. Nusselt number, solute flux.

Protected Types
enum	solverRestart { m_restartHalveDt, m_restartResetData }
	What to do when restarting after a failed timestep. More...

Protected Member Functions
Real	convergedToSteadyState (const int a_var, bool vector=false)
	Has a particular variable converged to steady state?

void	compute_d_dt (const int a_var, LevelData< FArrayBox > &diff, bool vector=false)
	Compute $\partial / \partial t$ of some field.

bool	solvingFullDarcyBrinkman ()
	Determine if we're solving the full time dependent equation, or just darcy's law.

void	updateEnthalpyVariablesOld ()
	Update thermodynamic variables based on phase diagram (old time)

bool	finestLevel ()
	Returns true if there is not a finer level with a grid defined on it.

int	getFinestLevel ()
	Return the finest level.

Real	computeDt (Real cfl)
	Returns $\Delta t$ .

Real	getMaxVelocity ()
	Get largest velocity in domain.

Real	getMaxVelocityForCFL ()
	get largest advection velocity, considering $\mathbf{U}/\chi$ if appropriate

Real	computeMaxUChi ()
	Compute max $\mathbf{U}/\chi$ .

Real	getMaxAdvVel ()
	Get max advection velocity.

Real	computeDt (bool growdt)
	Returns $\Delta t$ .

void	restartTimestepFromBackup (bool ignorePressure=false)
	Replace with data from before the last backup.

void	backupTimestep ()
	Save the current data.

void	getHierarchyAndGrids (Vector< AMRLevelMushyLayer *> &a_hierarchy, Vector< DisjointBoxLayout > &a_grids, Vector< int > &a_refRat, ProblemDomain &a_lev0Dom, Real &a_lev0Dx)
	Get information on the entire AMR hierarchy.

void	calculatePermeability ()
	Calculate permeability $\Pi$ .

void	calculateCoarseFineBoundaries (int a_var, bool vector=false)
	Fills coarse-fine boundaries on variable by quadratic interpolation.

int	multiCompAdvectDiffuse (LevelData< FArrayBox > &a_phi_old, LevelData< FArrayBox > &a_phi_new, LevelData< FArrayBox > &a_src, bool doFRupdates=false, bool computeAdvectiveSrc=true)
	Advection diffusion for multiple components.

void	computeScalarAdvectiveSrc (LevelData< FArrayBox > &a_src, int a_var, bool converged, int a_comp=0)
	Compute src term and add it to a_src.

void	computeScalarAdvectiveSrcHC (LevelData< FArrayBox > &a_src, LevelData< FluxBox > &edgeScalTotal, bool converged)
	Compute multi component source term: $(\mathbf{U} \cdot \nabla T, \mathbf{U} \cdot \nabla S_l)$ .

void	incrementHCFluxRegisters (LevelData< FluxBox > &flux, Real fluxMult)
	Increment Enthalpy-Bulk concentration flux registers with flux.

void	computeTotalAdvectiveFluxes (LevelData< FluxBox > &edgeScalTotal)
	Compute total fluxes that provide the source term for implicit enthalpy-salinity updates. More...

void	advectScalar (const int a_scalarVar, const int a_advectionVar, LevelData< FluxBox > &a_advVel, bool doFRupdates=true)
	Update a scalar field by advection. More...

void	advectScalar (const int a_scalarVar, const int a_advectionVar, LevelData< FluxBox > &a_advVel, bool doFRupdates, LevelData< FluxBox > &flux)
	Update a scalar field with advective terms.

void	updateScalarFluxRegister (int a_scalarVar, LevelData< FluxBox > &flux, Real scale)
	Update flux register for scalar field.

void	advectLambda (bool doFRupdates=true)
	Advect lambda field (for freestream preservation)

void	computeAdvectionVelSourceTerm (LevelData< FArrayBox > &advectionSourceTerm)
	Make source term for the advection velocity solve.

void	horizontallyAverage (LevelData< FArrayBox > &a_averaged, LevelData< FluxBox > &a_phi)
	Average vertical fluxes in the horizontal direction.

void	horizontallyAverage (Vector< Real > &averageVector, LevelData< FluxBox > &a_phi)
	Average vertical fluxes in the horizontal direction.

void	horizontallyAverage (LevelData< FArrayBox > &a_averaged, LevelData< FluxBox > &a_phi, Vector< Real > &averageVector)
	Average vertical fluxes in the horizontal direction.

void	horizontallyAverage (LevelData< FArrayBox > &a_averaged, LevelData< FArrayBox > &a_phi)
	Average cell centred fields in the horizontal direction.

void	horizontallyAverage (Vector< Real > &averageVector, LevelData< FArrayBox > &a_phi)
	Average cell centred fields in the horizontal direction.

void	horizontallyAverage (LevelData< FArrayBox > &a_averaged, LevelData< FArrayBox > &a_phi, Vector< Real > &globalAveraged)
	Average cell centred values in the horizontal direction.

Real	averageOverLiquidRegion (int a_var)
	Compute average value of some scalar field over the liquid region of the domain.

void	computeRadianceIntensity ()
	Compute the intensity of light from the surface at each point in the domain.

void	advectPassiveTracer ()
	Advect a passive tracer $\xi$ . More...

void	computeScalarDiffusiveSrc (int a_scalarBulkConc, LevelData< FArrayBox > &a_src)
	Compute diffusive src for some scalar with bulk concentration $\xi$ . More...

void	computeScalarConcInLiquid (LevelData< FArrayBox > &liquid_tracer_conc, int a_tracerVar)
	Compute concentration of scalar (with bulk concentration $\xi$ ) in the liquid phase. More...

void	advectTracer (int a_tracerVar, LevelData< FArrayBox > &a_src)
	Advect generic tracer.

void	advectActiveTracer ()
	Advect active tracer $\zeta$ . More...

void	computeActiveTracerSourceSink (LevelData< FArrayBox > &a_srcSink)
	Compute sources/sinks for active tracer.

Real	computeMushDepth (Real a_porosity_criteria=0.99)
	Compute mushy layer depth. More...

void	getTotalFlux (LevelData< FluxBox > &totalFlux)
	Calculate advective + diffusive flux.

void	computeLapVel (LevelData< FArrayBox > &a_lapVel, LevelData< FArrayBox > &a_vel, const LevelData< FArrayBox > *a_crseVelPtr)
	Compute $\nabla^2 \mathbf{U}$ .

void	computeScalDiffusion (const int a_var, LevelData< FArrayBox > &a_lapScal, Real a_time)
	Compute $\nabla^2 \phi$ .

void	computeScalDiffusion (LevelData< FArrayBox > &diffusiveSrc, Real a_time)
	Compute $\nabla^2 (H, S)$ .

void	computeScalDiffusion (LevelData< FArrayBox > &a_src, int a_var)
	Compute $\nabla^2 \psi$ for some scalar field $\psi$ .

void	computeCCvelocity (const LevelData< FArrayBox > &advectionSourceTerm, Real a_oldTime, Real a_dt, bool doFRupdates=false, bool a_doProjection=true, bool compute_uDelU=true, bool a_MACprojection=false)
	Compute new cell centred velocity. More...

bool	isVelocityTimeDependent ()
	Is velocity time dependent?

void	computeUstar (LevelData< FArrayBox > &a_uDelu, const LevelData< FArrayBox > &advectionSourceTerm, Real a_oldTime, Real a_dt, bool doFRupdates, bool a_MACprojection=false, bool compute_uDelU=true)
	Compute $\mathbf{U}^*$ , the velocity before we project it. More...

void	computeUstarSrc (LevelData< FArrayBox > &src, const LevelData< FArrayBox > &advectionSourceTerm, Real src_time, bool a_MACprojection=false, bool compute_uDelU=true)
	Compute the source term for the $\mathbf{U}^*$ solve.

void	computeUDelU (LevelData< FArrayBox > &U_adv_src, const LevelData< FArrayBox > &advectionSourceTerm, Real a_oldTime, Real a_dt)
	Compute $\mathbf{u} \cdot \nabla \left( \mathbf{U}/\chi \right)$ .

bool	isCurrentCFLSafe (bool printWarning=false)
	Check CFL based on latest velocity is safe to use for explicit updates.

void	addHeatSource (LevelData< FArrayBox > &src)
	Add a fixed heat source. More...

void	setVelZero (FArrayBox &a_vel, const FArrayBox &a_porosity, const Real a_limit, const int a_radius=0)
	Set velocity to zero where porosity is sufficiently small (FArrayBox version)

void	computeGradP (LevelData< FArrayBox > &gradP, Real a_time, bool a_macProjection=false)
	Returns $\nabla P$ at the specified time.

void	traceAdvectionVel (LevelData< FluxBox > &a_advVel, LevelData< FArrayBox > &a_old_vel, LevelData< FArrayBox > &U_chi, const LevelData< FArrayBox > &a_viscousSource, PatchGodunov &a_patchGodVelocity, Real a_old_time, Real a_dt)
	Trace the advection velocity forward in time.

void	computePredictedVelocities (LevelData< FluxBox > &U_chi_new, LevelData< FArrayBox > &a_traceVel, LevelData< FluxBox > &a_advVel, LevelData< FArrayBox > &U_chi, const LevelData< FArrayBox > &a_viscousSource, PatchGodunov &a_patchGodVelocity, LevelData< FluxBox > &a_grad_eLambda, LevelData< FluxBox > &a_gradPhi, LevelData< FluxBox > &porosityFace, Real a_old_time, Real a_dt)
	Compute advection velocities at the half time step.

void	computeScalarAdvectiveFlux (LevelData< FluxBox > &a_edgeScal, LevelData< FArrayBox > &a_old_scal, LevelData< FluxBox > &a_adv_vel, LevelData< FluxBox > &a_inflowOutflowVel, LevelData< FArrayBox > &a_old_vel, LevelData< FArrayBox > &a_diffusiveSrc, PatchGodunov &a_patchGod, Real a_old_time, Real a_dt)
	Compute the advective flux given the scalar field, advection velocity and source term specified. More...

void	upwind (LevelData< FluxBox > &a_edgeScal, LevelData< FArrayBox > &a_old_scal, LevelData< FluxBox > &a_adv_vel, LevelData< FluxBox > &a_inflowOutflowVel, LevelData< FArrayBox > &a_old_vel, LevelData< FArrayBox > &a_diffusiveSrc, PatchGodunov &a_patchGod, Real a_old_time, Real a_dt)
	Refactored this so we can also use for velocities if we want.

void	computeScalarAdvectiveFlux (LevelData< FluxBox > &a_edgeScal, LevelData< FArrayBox > &a_scalar_advection_old, LevelData< FArrayBox > &a_src, LevelData< FluxBox > &a_advVel, int a_advectionVar, Real a_old_time, Real a_dt)
	Compute advective flux.

void	computeScalarAdvectiveFlux (LevelData< FluxBox > &a_edgeScal, int a_advectionVar, int a_diffusionVar, LevelData< FluxBox > &a_advVel, Real a_old_time, Real a_dt)
	Compute the advective flux. More...

void	computeScalarAdvectiveFluxMultiComp (LevelData< FluxBox > &a_edgeScal, LevelData< FluxBox > &a_advVel, PatchGodunov &a_patchGod, LevelData< FArrayBox > &a_scalOld, Real a_old_time, Real a_dt)
	Compute the advective flux for the enthalpy and salinity equations,. More...

void	predictVelocities (LevelData< FArrayBox > &a_uDelU, LevelData< FluxBox > &a_advVel, const LevelData< FArrayBox > &a_src, Real old_time, Real a_dt, bool doFRupdates)
	Calculate $\mathbf{u} \cdot \nabla \left( \mathbf{u}/\chi \right)$ .

void	calculateTimeIndAdvectionVel (Real a_time, LevelData< FluxBox > &a_advVel)
	Calculate advection velocity for momentum equations which are time independent. More...

void	fillUnprojectedDarcyVelocity (LevelData< FluxBox > &a_advVel, Real time)
	Fill unprojected darcy velocity. More...

int	getMaxLevel ()
	Get maximum level allowed in AMR hierarchy.

void	computeViscosity ()
	Compute the viscosity given the current liquid concentration.

void	fillAdvVel (Real time, LevelData< FluxBox > &a_advVel)
	Fill advection velocity ghost cells.

void	fillAnalyticVel (LevelData< FluxBox > &a_advVel)
	Fill the velocity with some analytically determined function.

void	fillAnalyticVel (FArrayBox &velDir, int dir, int comp, bool project)
	Fill the velocity with some analytically determined function.

void	fillAnalyticVel (LevelData< FArrayBox > &velDir)
	Fill the velocity with some analytically determined function.

void	fillBuoyancy (LevelData< FArrayBox > &a_buoyancy, Real a_time)
	Compute the buoyancy force.

void	fillBuoyancy (LevelData< FArrayBox > &a_buoyancy, LevelData< FArrayBox > &a_temperature, LevelData< FArrayBox > &a_liquidConc, LevelData< FArrayBox > &a_porosity)
	Compute the buoyancy force.

void	fillBuoyancy (FArrayBox &buoyancy, FArrayBox &temperature, FArrayBox &liquidConc, FArrayBox &porosity, FArrayBox &bodyForce)
	Compute the buoyancy force. More...

void	fillPressureSrcTerm (LevelData< FArrayBox > &gradP, LevelData< FArrayBox > &pressureScale, Real a_time, bool a_MACprojection)
	Compute $\nabla P$ at time .

void	fillAMRVelPorosity (Vector< LevelData< FArrayBox > *> &amrVel, Vector< RefCountedPtr< LevelData< FluxBox > > > &amrPorosityFace, Vector< RefCountedPtr< LevelData< FArrayBox > > > &amrPorosity)
	Compile velocity and porosity across an AMR hierarchy.

void	fillHC (LevelData< FArrayBox > &a_phi, Real a_time, bool doInterior=true, bool quadInterp=true)
	Should include correct exchange calls.

void	fillFixedPorosity (LevelData< FArrayBox > &a_porosity)
	Fill porosity with some fixed value if appropriate.

void	fillTCl (LevelData< FArrayBox > &a_phi, Real a_time, bool doInterior=true, bool quadInterp=true)
	Should include correct exchange calls.

void	fillMultiComp (LevelData< FArrayBox > &a_phi, Real a_time, int scal1, int scal2, bool doInterior=true, bool quadInterp=true, bool apply_bcs=true)
	Should include correct exchange calls.

void	fillAMRLambda (Vector< LevelData< FArrayBox > *> &amrLambda)
	Compile $\lambda$ across the entire AMR hierarchy.

void	calculateAnalyticSolns (bool enforceSolutions=true)
	Calculate analytic solution to this problem (if possible)

void	setPorosity (FArrayBox &a_porosity)
	Set fixed porosity.

void	fillFrameVelocity ()
	Fill frame advection velocity.

void	addPerturbation (int a_var, Real alpha, int waveNumber=-1, Real phaseShift=0)
	Add a small perturbation to the solution.

void	addMeltPond ()
	Add a melt pond if we want.

void	defineUstarSolver (Vector< RefCountedPtr< LevelBackwardEuler > > &a_UstarBE, Vector< RefCountedPtr< LevelTGA > > &a_UstarTGA)
	Define implicit solver for $\mathbf{u}^*$ including timestepping.

void	defineUstarMultigrid ()
	Define multigrid solver for $\mathbf{u}^*$ .

void	initializeLevelPressure (Real a_currentTime, Real a_dtInit)
	Initialize pressure on this level.

void	initializeGlobalPressure (Real dtInit=-1, bool init=true)
	Initialize pressure across all levels.

void	computeInitAdvectionVel ()
	Compute initial advection velocities.

void	initTimeIndependentPressure (AMRLevelMushyLayer *lev, int a_max_num_iter=-1)
	Initialise phi (pressure for Darcy equation) More...

void	resetLambda ()
	Flag if a new level has been added. More...

void	AMRRefluxLambda ()
	Reflux $\lambda$ across AMR hierarchy. More...

void	defineRegridAMROp (AMRPoissonOpFactory &a_factory, const Vector< DisjointBoxLayout > &a_grids, const Vector< ProblemDomain > &a_domains, const Vector< Real > &a_amrDx, const Vector< int > &a_refRatios, const int &a_lBase)
	Define operator for post regrid smoothing.

void	getCoarseScalarDataPointers (const int a_scalarVar, LevelData< FArrayBox > a_coarserDataOldPtr, LevelData< FArrayBox > a_coarserDataNewPtr, LevelFluxRegister a_coarserFRPtr, LevelFluxRegister a_finerFRPtr, Real &a_tCoarserOld, Real &a_tCoarserNew)
	Smooth the velocity field. More...

void	fillVectorField (LevelData< FArrayBox > &a_vector, Real a_time, int a_var, bool doInterior=false, bool quadInterp=false)
	Doesn't do any time interpolation - just fills ghost cells if necessary.

void	fillScalars (LevelData< FArrayBox > &a_scal, Real a_time, const int a_var, bool doInterior=false, bool quadInterp=false, int a_comp=0, bool apply_bcs=true)
	Fill ghost cells of scalar field.

void	fillBuoyancy (LevelData< FArrayBox > &a_buoyancy, Real a_time, bool quadInterp)
	Helper function.

void	fillScalarFace (LevelData< FluxBox > &a_scal, Real a_time, const int a_var, bool doInterior=false, bool quadInterp=false)
	Fill ghost cells of scalar field (edge-centred)

void	fillScalarFace (LevelData< FluxBox > &a_scal, Real a_time, const int a_var, CellToEdgeAveragingMethod method, bool doInterior=false, bool quadInterp=false, Real smoothing=0.0)
	Fill ghost cells of scalar field (edge-centred)

void	getScalarBCs (BCHolder &thisBC, int a_var, bool a_homogeneous)
	Get boundary conditions for implicit problems.

void	computeInflowOutflowAdvVel ()
	Refactored this to be consistent.

PhysIBC *	getScalarIBCs (int a_var)
	Get initial and boundary conditions for advection.

void	convertBCType (const int a_implicitBC, const Real a_implicitVal, int &a_explicitBC, Real a_explicitVal)
	Need to convert implicit dirichlet/neuman/inflow outflow BCs to advection BCs.

int	convertBCType (const int a_implicitBC)
	Convert implicit BCs.

bool	crashed ()
	Check the simulation hasn't crashed.

void	doRegularisationOps (LevelData< FArrayBox > &a_scal, int a_var, int a_comp=0)
	Operations to keep variables bounded correctly. More...

void	doRegularisationOps (LevelData< FluxBox > &a_scal, int a_var, int a_comp=0)
	Operations to keep variables bounded correctly.

void	doRegularisationOps (int a_var, FArrayBox &a_state, int a_comp=0)
	Operations to keep variables bounded correctly.

void	doRegularisationOpsNew (int a_var, FArrayBox &a_state, int a_comp=0)
	New version of doRegularisationOps() which uses fortran routines.

void	setFluxRegistersZero ()
	Reset all flux registers.

void	copyNewToOldStates ()
	Copy new data to old data holders.

bool	doVelocityAdvection ()
	Do we need to do velocity advection? More...

void	computeAdvectionVelocities (LevelData< FArrayBox > &advectionSrc, Real advVelCentering=0.5)
	Compute advection velocity.

void	correctEdgeCentredVelocity (LevelData< FluxBox > &a_advVel, Real a_dt)
	Correct velocity (projection + volume discrepancy)

Real	computeDtInit (int finest_level)
	Compute initial $\Delta t$ .

AMRLevelMushyLayer *	getCoarserLevel () const
	Get the next coarser level.

AMRLevelMushyLayer *	getCoarsestLevel ()
	Get the coarsest level.

AMRLevelMushyLayer *	getFinerLevel () const
	Get the next finer level.

void	setAdvectionBCs ()
	Set BCs on advection physics classes.

void	defineIBCs ()
	Define initial and boundary conditions for advection problems.

Protected Attributes
LevelData< FluxBox >	m_advVel
	Advection velocity.

LevelData< FluxBox >	m_advVelOld
	Advection velocity at old time.

LevelData< FluxBox >	m_advVelNew
	Advection velocity at new time.

LevelData< FluxBox >	m_frameAdvVel
	Frame advection velocity.

LevelData< FluxBox >	m_totalAdvVel
	Frame advection velocity + fluid advection velocity.

Real	AMRSaltSum_new
	Total salt content in domain at new time.

Real	AMRSaltSum_old
	Total salt content in domain at old time.

Real	AMREnthalpySum_new
	Total heat content in domain at new time.

Real	AMREnthalpySum_old
	Total heat content in domain at new time.

LevelData< FArrayBox >	m_saltFluxTop
	Salt flux at the top of the domain.

LevelData< FArrayBox >	m_saltFluxBottom
	Salt flux at the bottom of the domain.

LevelData< FArrayBox >	m_frameVel
	Frame velocity (cell centred). Don't think we need this.

Vector< int >	m_outputScalarVars
	List of scalar vars to write out to HDF5 files.

Vector< int >	m_outputVectorVars
	List of vector vars to write out to HDF5 files.

Vector< int >	m_chkVectorVars
	List of vector vars to write to checkpoint files.

Vector< int >	m_chkScalarVars
	List of scalar vars to write to checkpoint files.

int	m_numOutputComps
	Number of component we write out to HDF5 files.

Real	m_maxLambda
	Store max value of $\lambda-1$ from previous timestep. More...

Vector< RefCountedPtr< LevelData< FArrayBox > > >	m_scalarNew
	Scalar fields at new time.

Vector< RefCountedPtr< LevelData< FArrayBox > > >	m_scalarOld
	Scalar fields at old time.

Vector< RefCountedPtr< LevelData< FArrayBox > > >	m_scalarRestart
	Backed up scalar fields to be used for restarting.

LevelData< FArrayBox >	m_dPorosity_dt
	Lagged $\partial \chi / \partial t$ .

Vector< RefCountedPtr< LevelData< FArrayBox > > >	m_vectorNew
	Vector fields at new time.

Vector< RefCountedPtr< LevelData< FArrayBox > > >	m_vectorOld
	Vector fields at old time.

Vector< RefCountedPtr< LevelData< FArrayBox > > >	m_vectorRestart
	Backed up vector fields to be used for restarting.

Vector< string >	m_scalarVarNames
	Names of scalar variables.

Vector< string >	m_vectorVarNames
	Names of vector variables.

Vector< int >	m_vectRestartVars
	Indexes of vector fields to save for restarting.

Vector< int >	m_scalRestartVars
	Indexes of scalar fields to save for restarting.

RefCountedPtr< LevelTGA >	m_enthalpySalinityTGA
	TGA integrators (2nd order in time)

RefCountedPtr< LevelBackwardEuler >	m_enthalpySalinityBE
	Backward Euler integrators (1st order in time)

RefCountedPtr< AMRMultiGrid< LevelData< FArrayBox > > >	m_diffuseAMRMG [m_numScalarVars]
	AMRMultigrid operators for each scalar.

RefCountedPtr< AMRFASMultiGrid< LevelData< FArrayBox > > >	m_diffuseAMRFASMG [m_numScalarVars]
	FASAMRMultigrid operators for each scalar.

RefCountedPtr< AMRFASMultiGrid< LevelData< FArrayBox > > >	m_multiCompFASMG
	Multicomponent FAS Multigrid solver (for enthalpy-bulk concentration solves)

RefCountedPtr< AMRLevelOpFactory< LevelData< FArrayBox > > >	m_HCOpFact
	Operator factories for scalar vars.

RefCountedPtr< AMRMultiGrid< LevelData< FArrayBox > > >	m_uStarAMRMG [SpaceDim]
	AMRMultigrid solver for unprojected velocity, $\mathbf{u}^*$ .

RefCountedPtr< AMRLevelOpFactory< LevelData< FArrayBox > > >	m_uStarOpFact [SpaceDim]
	Operator factory for unprojected velocity, $\mathbf{u}^*$ .

RefCountedPtr< AMRPoissonOp >	m_viscousOp [SpaceDim]
	Operator for computing components of $\nabla^2 \mathbf{u}$ .

bool	m_isDefined
	Is object defined.

MushyLayerOptions	m_opt
	Struct to contain all the options for this simulation. More...

Real	m_computedCFL
	The CFL number we're currently running at. More...

Real	m_domainWidth
	Domain width.

Real	m_domainHeight
	Domain height.

IntVect	m_numCells
	Number of cells in each direction of domain.

Real	m_max_dt_growth
	Maxmimum fractional growth in $\Delta t$ between timesteps.

bool	m_useLimiting
	Should we do slope limiting in advection solves?

Real	m_dx
	Cell spacing.

Real	m_scalarDiffusionCoeffs [m_numScalarVars]
	Diffusion coefficients for different scalar fields.

MushyLayerParams	m_parameters
	Physical parameters.

Real	m_prev_diag_output
	Time when we last produced diagnostics output.

bool	m_enforceGradP
	Should we enforce some analytic $\nabla P$ . More...

bool	m_usePrevPressureForUStar
	Should we use previous $\nabla P$ to calculate $\mathbf{u}^*$ . More...

int	m_pressureScaleVar
	Which field scales the pressure. More...

PhysBCUtil *	m_physBCPtr
	Pointer to physics boundary condition object.

FineInterp	m_fineInterpScalar
	For interpolating scalars from coarser grids.

FineInterp	m_fineInterpVector
	For interpolating vectors from coarser grids.

CoarseAverage	m_coarseAverageScalar
	For averaging scalars to coarse grids.

CoarseAverage	m_coarseAverageHC
	For 2 component enthalpy-salinity fields.

CoarseAverage	m_coarseAverageVector
	For averaging vectors to coarse grids.

bool	m_timestepReduced
	For reducing the timestep after a failed timestep.

int	m_dtReduction
	Factor reduce $\Delta t$ by after a failed timestep.

bool	m_timestepFailed
	Has this timestep failed?

Real	m_adv_vel_centering
	If this level has only just been added due to regridding. More...

Real	m_adv_vel_centering_growth
	Rate at which we grow m_adv_vel_centering each timestep.

QuadCFInterp	m_quadCFInterpScalar
	For doing quadratic interpolation at coarse fine boundaries (for scalars)

QuadCFInterp	m_quadCFInterpVector
	For doing quadratic interpolation at coarse fine boundaries (for vectors)

PiecewiseLinearFillPatch	m_piecewiseLinearFillPatchScalarOne
	For filling one ghost cell around the edge of a set of boxes on a level.

PiecewiseLinearFillPatch	m_piecewiseLinearFillPatchScalarTwo
	For filling two ghost cells around the edge of a set of boxes on a level.

PiecewiseLinearFillPatch	m_piecewiseLinearFillPatchScalarThree
	For filling three ghost cells around the edge of a set of boxes on a level.

PiecewiseLinearFillPatch	m_piecewiseLinearFillPatchScalarFour
	For filling four ghost cells around the edge of a set of boxes on a level.

int	m_numGhost
	Number of ghost cells for standard calculations.

int	m_numGhostAdvection
	Number of ghost cells for advection calculations. More...

PatchGodunov	m_patchGodVelocity
	Handles advection of velocity.

PatchGodunov	m_patchGodHC
	Operator For multi component H-C advection solve.

PatchGodunov	m_patchGodTSl
	Operator For multi component T-Sl advection solve.

PatchGodunov	m_patchGodH
	Operator For single component H advection solve.

PatchGodunov	m_patchGodC
	Operator For single component C advection solve.

PatchGodunov	m_patchGodT
	Operator For single component T advection solve.

PatchGodunov	m_patchGodSl
	Operator For single component Sl advection solve.

AdvectionPhysics	m_advectionPhysicsVelocity
	Physics for velocity advection.

AdvectionPhysics	m_advPhysHC
	Physics for coupled H-C advection solve.

AdvectionPhysics	m_advPhysTSl
	Physics for coupled T-Sl advection solve.

AdvectionPhysics	m_advPhysH
	Physics for H advection solve.

AdvectionPhysics	m_advPhysC
	Physics for C advection solve.

AdvectionPhysics	m_advPhysT
	Physics for T advection solve.

AdvectionPhysics	m_advPhysSl
	Physics for Sl advection solve.

RefCountedPtr< PatchGodunov >	m_patchGodScalars [m_numScalarVars]
	Handles advection of scalar vars.

PhysIBC *	m_scalarIBC [m_numScalarVars]
	Initial and Boundary Conditions for scalar vars.

Projector	m_projection
	Handles pressure projection.

Projector	m_projectionBackup
	Contains the old pressure, in case we need to restart.

RefCountedPtr< LevelFluxRegister >	m_fluxRegisters [m_numScalarVars]
	Flux registers for scalar variables.

RefCountedPtr< LevelFluxRegister >	m_fluxRegHC
	Flux Register for multi component HC solves.

RefCountedPtr< LevelFluxRegister >	m_vectorFluxRegisters [m_numVectorVars]
	Flux registers for vector variables.

LevelDomainFluxRegister	m_saltDomainFluxRegister
	Flux register for salt along the domain edge.

LevelDomainFluxRegister	m_heatDomainFluxRegister
	Flux register for heat (enthalpy) along the domain edge.

bool	m_makeFluxRegForScalarVar [m_numScalarVars]
	Which scalar vars should we bother making flux registers for?

bool	m_makeFluxRegForVectorVar [m_numVectorVars]
	Which vector vars should we bother making flux registers for?

bool	m_hasCoarser
	Does a coarser AMRLevelMushyLayer pointer exist?

bool	m_hasFiner
	Does a finer AMRLevelMushyLayer pointer exist?

DisjointBoxLayout	m_grids
	Grids on this level.

bool	m_newGrids_different
	Are the new grids different from current ones?

bool	m_regrid_smoothing_done
	Has post regrid smoothing been done?

Real	s_regrid_smoothing_coeff
	Coefficient for post regrid smoothing.

bool	s_implicit_reflux
	Do reflux implicitly?

Protected Attributes inherited from AMRLevel
ProblemDomain	m_problem_domain

Vector< Box >	m_level_grids

int	m_level

int	m_ref_ratio

Real	m_initial_dt_multiplier

Real	m_dt

Real	m_time

AMRLevel *	m_coarser_level_ptr

AMRLevel *	m_finer_level_ptr

bool	m_isDefined

Static Protected Attributes
static BiCGStabSolver< LevelData< FArrayBox > >	s_botSolverUStar
	bottom solver for velocity solve multigrid

static RelaxSolver< LevelData< FArrayBox > >	s_botSolverHC
	Bottom solve for enthalpy-bulk concentration multigrid.

Static Protected Attributes inherited from AMRLevel
static int	s_verbosity

Additional Inherited Members
Static Public Member Functions inherited from AMRLevel
static int	verbosity ()

static void	verbosity (int a_verbosity)

Detailed Description

AMRLevel for mushy layer calculations.

Big class to manage integration of nonlinear mushy layer equations on an AMR level

Member Enumeration Documentation

◆ solverRestart

enum AMRLevelMushyLayer::solverRestart

protected

What to do when restarting after a failed timestep.

Enumerator
m_restartHalveDt	Restart and set dt = dt/2.
m_restartResetData	Restart and return solution to it's state before this timestep.

Member Function Documentation

◆ addHeatSource()

void AMRLevelMushyLayer::addHeatSource ( LevelData< FArrayBox > & src )

protected

Add a fixed heat source.

$Q = \frac{Q_0}{\sigma \sqrt{2 \pi}} \exp\left[ - 0.5 \left( \frac{x-x_c}{\sigma} \right)^2 \right] 0.5 \left( 1 + \tanh\left[10 (z-(H-h)) \right]) \right)$

where the parameters are found from the inputs file as: Q_0 is given by heatSource.size sigma is heatSource.width x_c is heatSource.xpos h is heatSource.depth, and measures the depth that the heat source propagates down from the top of the domain

H is the domain height

◆ addMeltPond()

void AMRLevelMushyLayer::addMeltPond	(	int	depth,
		Real	salinity,
		Real	enthalpy,
		bool	rescaleExistingSolution = `false`
	)

Add a melt pond at the top of the domain.

We just do a very simple linear rescaling for now, so the old domain 0 < z < h becomes 0 < z < h-dh, and new variables are denoted by a , i.e. we need a mapping for H(0 < z < h) -> H(0 < z < h-dh), and S->S` We assume that the boundary conditions on the new domain are the same as the old domain at the new extent, i.e. H(h-dh) = H(h), H(h-dh) = S(h). then, H`(z) = H(z*(h-dh)/h) = H(z*(1-dh/h))

Stretching maps z->z, via z = z*stretching

◆ advectActiveTracer()

void AMRLevelMushyLayer::advectActiveTracer ( )

protected

Advect active tracer $\zeta$ .

$\frac{\partial \zeta}{\partial t} + \mathbf{U} \cdot \nabla (\zeta/\chi) = S(x,z)$ where $ S(x,z) $ is a source/sink of the tracer defined in computeActiveTracerSourceSink()

◆ advectPassiveTracer()

void AMRLevelMushyLayer::advectPassiveTracer ( )

protected

Advect a passive tracer $\xi$ .

$\frac{\partial \xi}{\partial t} + \mathbf{U} \cdot \nabla (\xi/\chi) = S(x,z)$

◆ advectScalar()

void AMRLevelMushyLayer::advectScalar	(	const int	a_scalarVar,
		const int	a_advectionVar,
		LevelData< FluxBox > &	a_advVel,
		bool	doFRupdates = `true`
	)

protected

Update a scalar field by advection.

a_scalarVar is the field which is updated, whilst a_advectionVar is the field that has been advected. These don't need to be the same, i.e. could do advectScalar(enthalpy, temperature, ...) in order to compute an update for the equation d(enthalpy)/dt + u.grad(temperature) = 0

◆ AMRRefluxLambda()

void AMRLevelMushyLayer::AMRRefluxLambda ( )

protected

Reflux $\lambda$ across AMR hierarchy.

Only call from base level

◆ calculateTimeIndAdvectionVel()

void AMRLevelMushyLayer::calculateTimeIndAdvectionVel	(	Real	time,
		LevelData< FluxBox > &	a_advVel
	)

protected

Calculate advection velocity for momentum equations which are time independent.

This source file contains methods relating to the velocity field

◆ computeCCvelocity()

void AMRLevelMushyLayer::computeCCvelocity	(	const LevelData< FArrayBox > &	advectionSourceTerm,
		Real	a_oldTime,
		Real	a_dt,
		bool	doFRupdates = `false`,
		bool	a_doProjection = `true`,
		bool	compute_uDelU = `true`,
		bool	a_MACprojection = `false`
	)

protected

Compute new cell centred velocity.

Generally done via an implicit update due to the viscous and darcy terms. Not required if just considering the Darcy equation.

◆ computeMushDepth()

Real AMRLevelMushyLayer::computeMushDepth ( Real a_porosity_criteria = 0.99 )

protected

Compute mushy layer depth.

Compute horizontally averaged porosity, then determine that the mushy layer starts at the minimum height where the porosity is < a_porosity_criteria.

◆ computeScalarAdvectiveFlux() [1/2]

void AMRLevelMushyLayer::computeScalarAdvectiveFlux	(	LevelData< FluxBox > &	a_edgeScal,
		LevelData< FArrayBox > &	a_old_scal,
		LevelData< FluxBox > &	a_adv_vel,
		LevelData< FluxBox > &	a_inflowOutflowVel,
		LevelData< FArrayBox > &	a_old_vel,
		LevelData< FArrayBox > &	a_diffusiveSrc,
		PatchGodunov &	a_patchGod,
		Real	a_old_time,
		Real	a_dt
	)

protected

Compute the advective flux given the scalar field, advection velocity and source term specified.

Should work for multiple components

◆ computeScalarAdvectiveFlux() [2/2]

void AMRLevelMushyLayer::computeScalarAdvectiveFlux	(	LevelData< FluxBox > &	a_edgeScal,
		int	a_advectionVar,
		int	a_diffusionVar,
		LevelData< FluxBox > &	a_advVel,
		Real	a_old_time,
		Real	a_dt
	)

protected

Compute the advective flux.

advection var is what we advect diffusion var determines the variable used to calculate the diffusive src. Set to -1 to use no source.

◆ computeScalarAdvectiveFluxMultiComp()

void AMRLevelMushyLayer::computeScalarAdvectiveFluxMultiComp	(	LevelData< FluxBox > &	a_edgeScal,
		LevelData< FluxBox > &	a_advVel,
		PatchGodunov &	a_patchGod,
		LevelData< FArrayBox > &	a_scalOld,
		Real	a_old_time,
		Real	a_dt
	)

protected

Compute the advective flux for the enthalpy and salinity equations,.

Compute temperature and salinity advective flux.

edgeScal contains two components: $(\mathbf{U} T, \mathbf{U} S_l)$ or $ (V H, V S) $ depending on the parameters given

◆ computeScalarConcInLiquid()

void AMRLevelMushyLayer::computeScalarConcInLiquid	(	LevelData< FArrayBox > &	liquid_tracer_conc,
		int	a_tracerVar
	)

protected

Compute concentration of scalar (with bulk concentration $\xi$ ) in the liquid phase.

$\xi/\chi$

◆ computeScalarDiffusiveSrc()

void AMRLevelMushyLayer::computeScalarDiffusiveSrc	(	int	a_scalarBulkConc,
		LevelData< FArrayBox > &	a_src
	)

protected

Compute diffusive src for some scalar with bulk concentration $\xi$ .

$S = \nabla \cdot \chi \nabla (\xi/\chi)$

◆ computeTotalAdvectiveFluxes()

void AMRLevelMushyLayer::computeTotalAdvectiveFluxes ( LevelData< FluxBox > & edgeScalTotal )

protected

Compute total fluxes that provide the source term for implicit enthalpy-salinity updates.

$(\mathbf{U} T + V H \mathbf{k}, \mathbf{U} S_l + V S \mathbf{k})$

◆ computeUstar()

void AMRLevelMushyLayer::computeUstar	(	LevelData< FArrayBox > &	a_uDelu,
		const LevelData< FArrayBox > &	advectionSourceTerm,
		Real	a_oldTime,
		Real	a_dt,
		bool	doFRupdates,
		bool	a_MACprojection = `false`,
		bool	compute_uDelU = `true`
	)

protected

Compute $\mathbf{U}^*$ , the velocity before we project it.

In particular, we explicitly solve for the velocity $\left[ 1 - \Delta t^\ell \, \left(Da \, \left(\nabla^\ell\right)^2 - \frac{\chi^{\ell, n+1}}{\Pi^{\ell, n+1}} \right) \right] \mathbf{U}^{\ell, n+1}_* = \mathbf{U}^{\ell, n} + \Delta t^\ell \left\{- \chi^{\ell, n+1/2} \, \nabla^\ell \pi^{\ell, n-1/2} + \chi^{\ell, n+1/2} \left[Pr \, Da^2 \left( Ra_T \theta^{\ell, n+1/2} - Ra_C \Theta^{\ell, n+1/2} \right) \right] - \mathbf{U}_{AD, CC}^{\ell, n+1/2} \cdot \nabla^\ell \left( \frac{\mathbf{U}}{\chi} \right)^{\ell, n+1/2} \right\}$

◆ define() [1/2]

void AMRLevelMushyLayer::define	(	MushyLayerOptions	a_opt,
		MushyLayerParams	a_params
	)

Defines this AMRLevelMushyLayer.

Porosity for Darcy-Brinkman, permeability for Darcy

◆ define() [2/2]

void AMRLevelMushyLayer::define	(	AMRLevel *	a_coarserLevelPtr,
		const ProblemDomain &	a_problemDomain,
		int	a_level,
		int	a_refRatio
	)

virtual

Define new AMRLevelMushyLayer from coarser.

Bio

Reimplemented from AMRLevel.

◆ doRegularisationOps()

void AMRLevelMushyLayer::doRegularisationOps	(	LevelData< FArrayBox > &	a_scal,
		int	a_var,
		int	a_comp = `0`
	)

protected

Operations to keep variables bounded correctly.

Porosity $\chi > 0$ Liquid concentration $-1 <= \Theta_l <= 0$

◆ doVelocityAdvection()

bool AMRLevelMushyLayer::doVelocityAdvection ( )

protected

Do we need to do velocity advection?

I.e. do we solve for $\mathbf{U} \cdot \nabla (\mathbf{U}/\chi)$ terms?

◆ fillBuoyancy()

void AMRLevelMushyLayer::fillBuoyancy	(	FArrayBox &	buoyancy,
		FArrayBox &	temperature,
		FArrayBox &	liquidConc,
		FArrayBox &	porosity,
		FArrayBox &	bodyForce
	)

protected

Compute the buoyancy force.

$\mathbf{B} = \chi ( Ra_T \theta - Ra_C \Theta_l + \mathbf{F} \cdot \mathbf{k} ) \mathbf{k}$

◆ fillUnprojectedDarcyVelocity()

void AMRLevelMushyLayer::fillUnprojectedDarcyVelocity	(	LevelData< FluxBox > &	a_advVel,
		Real	time
	)

protected

Fill unprojected darcy velocity.

$\mathbf{U}^* = (\Pi/\nu) * (Ra_T \theta - Ra_C \Theta_l + \mathbf{F}_B)$

where $\mathbf{F}_B$ is a body force (=0 by default)

◆ getCoarseScalarDataPointers()

void AMRLevelMushyLayer::getCoarseScalarDataPointers	(	const int	a_scalarVar,
		LevelData< FArrayBox > **	a_coarserDataOldPtr,
		LevelData< FArrayBox > **	a_coarserDataNewPtr,
		LevelFluxRegister **	a_coarserFRPtr,
		LevelFluxRegister **	a_finerFRPtr,
		Real &	a_tCoarserOld,
		Real &	a_tCoarserNew
	)

protected

Smooth the velocity field.

Utility function to get pointers to coarse level objects

◆ grids()

DisjointBoxLayout AMRLevelMushyLayer::grids ( )

Whether or not to compute diagnostics.

Get the grids on this level

◆ initTimeIndependentPressure()

void AMRLevelMushyLayer::initTimeIndependentPressure	(	AMRLevelMushyLayer *	lev,
		int	a_max_num_iter = `-1`
	)

protected

Initialise phi (pressure for Darcy equation)

By default a_max_num_iter = -1, meaning we use the globally defined value in m_opt.num_init_passes

◆ resetLambda()

void AMRLevelMushyLayer::resetLambda ( )

protected

Flag if a new level has been added.

Reset $\lambda = 1$

◆ reshapeData()

void AMRLevelMushyLayer::reshapeData	(	DisjointBoxLayout	newGrids,
		ProblemDomain	newDomain
	)

Transfer data to new disjoint box layout.

Changed to allow changes in either x or y directions.

◆ setDefaults()

void AMRLevelMushyLayer::setDefaults ( )

Set default values.

This source file contains methods for initialising and defining objects

◆ setEta()

void AMRLevelMushyLayer::setEta ( Real a_eta )

Set eta on all projection operators.

Only call from level 0

◆ smoothScalarField()

void AMRLevelMushyLayer::smoothScalarField	(	LevelData< FArrayBox > &	a_phi,
		int	a_var,
		Real	a_smoothing
	)

Smooth some scalar field.

smoothing done implicitly via an elliptic solve. Obtains smooth field $\phi_{smooth}$ by solving $(1-\alpha \nabla^2)\phi_{smooth} = \phi$ where $\alpha$ is the smoothing parameter a_smoothing

Member Data Documentation

◆ m_adv_vel_centering

Real AMRLevelMushyLayer::m_adv_vel_centering

protected

If this level has only just been added due to regridding.

The advection velocity is calculated at old_time + m_adv_vel_centering*dt Usually 0.5, but set to something smaller after regridding for stability

◆ m_computedCFL

Real AMRLevelMushyLayer::m_computedCFL

protected

The CFL number we're currently running at.

computed from the current max velocity and the grid spacing.

◆ m_enforceGradP

bool AMRLevelMushyLayer::m_enforceGradP

protected

Should we enforce some analytic $\nabla P$ .

Usually false, but can be useful to do this for benchmark problems

◆ m_maxLambda

Real AMRLevelMushyLayer::m_maxLambda

protected

Store max value of $\lambda-1$ from previous timestep.

We may decide to increase $\eta$ if we're not decreasing lambda quickly enough

◆ m_numGhostAdvection

int AMRLevelMushyLayer::m_numGhostAdvection

protected

Number of ghost cells for advection calculations.

Generally need extra ghost cells when doing advection problems

◆ m_opt

MushyLayerOptions AMRLevelMushyLayer::m_opt

protected

Struct to contain all the options for this simulation.

This is so we can easily pass all the options around, and don't have to keep going into parmparse

◆ m_pressureScaleVar

int AMRLevelMushyLayer::m_pressureScaleVar

protected

Which field scales the pressure.

We either have $\chi \nabla P$ or $\Pi \nabla P$

◆ m_usePrevPressureForUStar

bool AMRLevelMushyLayer::m_usePrevPressureForUStar

protected

Should we use previous $\nabla P$ to calculate $\mathbf{u}^*$ .

We then subtract off $\nabla P$ before actually doing the projection

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

/home/parkinsonjl/mushy-layer/srcSubcycle/AMRLevelMushyLayer.H
/home/parkinsonjl/mushy-layer/srcSubcycle/AMRLevelMushyLayer.cpp
/home/parkinsonjl/mushy-layer/srcSubcycle/AMRLevelMushyLayerBiogeochemistry.cpp
/home/parkinsonjl/mushy-layer/srcSubcycle/AMRLevelMushyLayerDiagnostics.cpp
/home/parkinsonjl/mushy-layer/srcSubcycle/AMRLevelMushyLayerFill.cpp
/home/parkinsonjl/mushy-layer/srcSubcycle/AMRLevelMushyLayerInit.cpp
/home/parkinsonjl/mushy-layer/srcSubcycle/AMRLevelMushyLayerIO.cpp
/home/parkinsonjl/mushy-layer/srcSubcycle/AMRLevelMushyLayerRegrid.cpp
/home/parkinsonjl/mushy-layer/srcSubcycle/AMRLevelMushyLayerSync.cpp
/home/parkinsonjl/mushy-layer/srcSubcycle/AMRLevelMushyLayerVel.cpp

Public Member Functions

Public Attributes

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ solverRestart

Member Function Documentation

◆ addHeatSource()

◆ addMeltPond()

◆ advectActiveTracer()

◆ advectPassiveTracer()

◆ advectScalar()

◆ AMRRefluxLambda()

◆ calculateTimeIndAdvectionVel()

◆ computeCCvelocity()

◆ computeMushDepth()

◆ computeScalarAdvectiveFlux() [1/2]

◆ computeScalarAdvectiveFlux() [2/2]

◆ computeScalarAdvectiveFluxMultiComp()

◆ computeScalarConcInLiquid()

◆ computeScalarDiffusiveSrc()

◆ computeTotalAdvectiveFluxes()

◆ computeUstar()

◆ define() [1/2]

◆ define() [2/2]

◆ doRegularisationOps()

◆ doVelocityAdvection()

◆ fillBuoyancy()

◆ fillUnprojectedDarcyVelocity()

◆ getCoarseScalarDataPointers()

◆ grids()

◆ initTimeIndependentPressure()

◆ resetLambda()

◆ reshapeData()

◆ setDefaults()

◆ setEta()

◆ smoothScalarField()

Member Data Documentation

◆ m_adv_vel_centering

◆ m_computedCFL

◆ m_enforceGradP

◆ m_maxLambda

◆ m_numGhostAdvection

◆ m_opt

◆ m_pressureScaleVar

◆ m_usePrevPressureForUStar