class to manage non-subcycled AMR ice-sheet model More...

#include <AmrIce.H>

Inheritance diagram for AmrIce:

Collaboration diagram for AmrIce:

[legend]

Classes
class	Observer
	part of Observer-Observee implementation More...

Public Types
enum	velSolverTypes { Picard = 0, JFNK = 1, KnownVelocity = 2, PetscNLSolver = 3, FASMGAMR = 4, Python = 5, InverseVerticallyIntegrated = 6, NUM_SOLVER_TYPES }
	compute area of ice with grounded/floating status given by a_maskval More...

Public Types inherited from AmrIceBase
enum	viscousTensorComponent { xx, xy, yx, yy, max }

Public Member Functions
	AmrIce ()
	Default constructor. More...

virtual	~AmrIce ()
	destructor More...

void	setDefaults ()
	set default values before initialization More...

void	initialize ()
	initializes object based on inputs data passed in through parmParse More...

void	setDomainSize (const RealVect &a_domainSize)
	set domain size (in meters) More...

void	setConstitutiveRelation (ConstitutiveRelation *a_constRelPtr)
	set constitutive relation More...

void	setRateFactor (RateFactor *a_rateFactorPtr)
	set rate factor More...

void	setBasalRateFactor (RateFactor *a_rateFactorPtr)
	set rate factor at base More...

void	setBasalFrictionRelation (BasalFrictionRelation *a_basalFrictionRelPtr)
	set basal Friction relation More...

void	setThicknessBC (IceThicknessIBC *a_thicknessIBC)
	set BC for thickness advection More...

void	setInternalEnergyBC (IceInternalEnergyIBC *a_internalEnergyIBC)
	set BC for internalEnergy advection More...

void	setSurfaceFlux (SurfaceFlux *a_surfaceFluxPtr)
	set surfact flux for ice sheet More...

void	setBasalFlux (SurfaceFlux *a_basalFluxPtr)
	set basal flux for ice sheet More...

void	setSurfaceHeatBoundaryData (SurfaceFlux *a_surfaceHeatBoundaryDataPtr, bool a_dirichlett, bool a_temperature)
	set surface Heat flux for ice sheet More...

void	setBasalHeatBoundaryData (SurfaceFlux *a_basalHeatBoundaryDataPtr)
	set basal Heat flux for ice sheet. Does not include the heat flux due to sliding friction More...

void	setTopographyFlux (SurfaceFlux *a_topographyFluxPtr)
	set bedrock flux for ice sheet More...

void	setBasalFriction (const BasalFriction *a_basalFrictionPtr)
	set basal friction More...

void	setMuCoefficient (const MuCoefficient *a_muCoefficientPtr)

void	setCalvingModel (CalvingModel *a_calvingModelPtr)

void	run (Real a_max_time, int a_max_step)
	advance solution until either max_time or max_step are reached More...

void	timeStep (Real a_dt)
	compute one timestep More...

void	computeH_half (Vector< LevelData< FluxBox > * > &a_H_half, Real a_dt)

void	computeThicknessFluxes (Vector< LevelData< FluxBox > * > &a_vectFluxes, const Vector< LevelData< FluxBox > * > &a_H_half, const Vector< LevelData< FluxBox > * > &a_faceVelAdvection)

void	updateGeometry (Vector< RefCountedPtr< LevelSigmaCS > > &a_vect_coordSys_new, Vector< RefCountedPtr< LevelSigmaCS > > &a_vectCoords_old, const Vector< LevelData< FluxBox > * > &a_vectFluxes, Real a_dt)

void	regrid ()
	do regridding More...

Real	computeTotalIce () const
	diagnostic function – integrates thickness over domain More...

void	getIceThickness (Real a_data_ptr, int a_dim_info, Real a_dew, Real a_dns) const
	fill flattened Fortran array of data with ice thickness More...

bool	isDefined () const
	is this object defined and initialized? More...

void	setHeader (const std::string &a_key, const std::string &a_val)

void	getHeader (const std::string &a_key, std::string &a_val)

void	setHeader (const std::string &a_key, const int &a_val)

void	getHeader (const std::string &a_key, int &a_val)

void	setHeader (const std::string &a_key, const Real &a_val)

void	getHeader (const std::string &a_key, Real &a_val)

void	writeAMRHierarchyHDF5 (HDF5Handle &a_handle, const Vector< DisjointBoxLayout > &a_grids, const Vector< LevelData< FArrayBox > * > &a_data, const Vector< string > &a_name, const Box &a_domain, const Real &a_dx, const Real &a_dt, const Real &a_time, const Vector< int > &a_ratio, const int &a_numLevels) const

void	writeAMRHierarchyHDF5 (const string &filename, const Vector< DisjointBoxLayout > &a_grids, const Vector< LevelData< FArrayBox > * > &a_data, const Vector< string > &a_name, const Box &a_domain, const Real &a_dx, const Real &a_dt, const Real &a_time, const Vector< int > &a_ratio, const int &a_numLevels) const
	Write an AMR hierarchy to an hdf5 file. More...

void	writePlotFile ()
	write hdf5 plotfile to the standard location More...

void	writeAMRPlotFile ()
	write hdf5 plotfile to the standard location More...

void	writeCheckpointFile ()
	write checkpoint file out for later restarting More...

void	writeCheckpointFile (const string &a_file)
	write checkpoint file out for later restarting More...

void	readCheckpointFile (HDF5Handle &a_handle)
	read checkpoint file for restart More...

void	restart (const string &a_restart_file)
	set up for restart More...

void	computeAreaFraction (LevelData< FArrayBox > &a_area, int a_maskVal, int a_level) const
	compute total ice and total grounded ice (volume, at this point) More...

void	setTime (Real a_time)

Real	time () const
	read only access members implementing AMRIceBase More...

Real	dt () const

int	finestLevel () const

const RealVect	dx (int a_level) const

const RefCountedPtr< LevelSigmaCS >	geometry (int a_level) const

const DisjointBoxLayout &	grids (int a_level) const

const Vector< DisjointBoxLayout > &	grids () const

const Vector< RefCountedPtr< LevelSigmaCS > > &	amrGeometry () const

void	incrementIceThickness (Vector< LevelData< FArrayBox > *> a_thk)
	nearly direct access to the ice thickness More...

const Vector< int > &	refRatios () const

const Vector< Real > &	amrDx () const

const LevelData< FArrayBox > *	velocity (int a_level) const

const Vector< LevelData< FArrayBox > *> &	amrVelocity ()

SurfaceFlux &	surfaceHeatBoundaryData () const

bool	surfaceHeatBoundaryDirichlett () const

LevelData< FArrayBox > *	iceFrac (int a_level)
	return pointer to real-valued ice fraction on level a_level More...

bool	surfaceHeatBoundaryTemperature () const

SurfaceFlux &	basalHeatBoundaryData () const

const LevelData< FArrayBox > *	iceFrac (int a_level) const
	return pointer to real-valued ice fraction on level a_level More...

const LevelData< FArrayBox > &	muCoef (int a_level) const
	return const ref to real-valued 'mu coefficient' on level a_level More...

Vector< LevelData< FArrayBox > *> &	amrIceFrac ()
	return reference to full AMR ice fraction More...

const Vector< LevelData< FArrayBox > *> &	amrIceFrac () const
	return const reference to full AMR ice fraction More...

const LevelData< FArrayBox > *	groundingLineProximity (int a_level) const

Real	groundingLineProximityScale () const

const LevelData< FArrayBox > *	surfaceThicknessSource (int a_level) const

const LevelData< FArrayBox > *	basalThicknessSource (int a_level) const

const LevelData< FArrayBox > *	viscousTensor (int a_level) const

const LevelData< FArrayBox > *	dragCoefficient (int a_level) const

const LevelData< FArrayBox > *	viscosityCoefficient (int a_level) const

const Vector< LevelData< FluxBox > *> &	faceVelocities ()
	access function for face-centered velocities More...

const Vector< LevelData< FluxBox > *> &	faceVelocitiesLayered () const
	access function for layered face-centered velocities More...

const Vector< LevelData< FArrayBox > *> &	calvedIceThickness () const
	access function for calved ice data More...

const Vector< LevelData< FArrayBox > *> &	removedIceThickness () const

const Vector< LevelData< FArrayBox > *> &	addedIceThickness () const

const Vector< LevelData< FArrayBox > *> &	surfaceInternalEnergy () const
	access function for surface temperature More...

const Vector< LevelData< FArrayBox > *> &	surfaceHeatFlux () const
	access function for surface heat flux More...

const Vector< Real > &	getFaceSigma () const

void	addObserver (Observer *a_observer)

void	removeObserver (Observer *a_observer)

Public Member Functions inherited from AmrIceBase
virtual	~AmrIceBase ()

Protected Types
enum	initialGuessTypes { SlidingLaw =0, ConstMu =1, Function =2, NUM_INITIAL_GUESS_TYPES }

enum	DiffusionTreatment { NONE, IMPLICIT, EXPLICIT }

Protected Member Functions
void	tagCells (Vector< IntVectSet > &a_tags)
	compute tags for regridding More...

void	tagCellsLevel (IntVectSet &a_tags, int a_level)
	compute tags for the level a_level More...

void	tagCellsInit (Vector< IntVectSet > &a_tags)
	compute tags at initial time More...

void	initGrids (int a_finest_level)
	initialize grids at initial time More...

void	setupFixedGrids (const std::string &a_gridFile)
	set up grids from grids file More...

void	levelSetup (int a_level, const DisjointBoxLayout &a_grids)
	set up storage, etc on an AMR level More...

void	initData (Vector< RefCountedPtr< LevelSigmaCS > > &a_vectCoordSys, Vector< LevelData< FArrayBox > * > &a_initialVelocity)
	initialize data on hierarchy More...

virtual void	defineSolver ()
	initialize diagnostics More...

virtual void	solveVelocityField (bool a_forceSolve=false, Real a_convergenceMetric=-1.0)
	solve for velocity field (or just set up some auxilliary quantities) More...

virtual void	defineVelRHS (Vector< LevelData< FArrayBox > * > &a_vectRhs)
	compute RHS for velocity field solve More...

virtual void	setBasalFriction (Vector< LevelData< FArrayBox > * > &a_C, Vector< LevelData< FArrayBox > * > &a_C0)
	set basal friction coefficients C,C0 prior to velocity solve More...

virtual void	setMuCoefficient (Vector< LevelData< FArrayBox > * > &a_cellMuCoef)
	set mu coefficient (phi) prior to velocity solve More...

void	computeFaceVelocity (Vector< LevelData< FluxBox > * > &a_faceVelAdvection, Vector< LevelData< FluxBox > * > &a_faceVelTotal, Vector< LevelData< FluxBox > * > &a_diffusivity, Vector< LevelData< FluxBox > * > &a_layerXYFaceXYVel, Vector< LevelData< FArrayBox > * > &a_layerSFaceXYVel)
	given the current cell centred velocity field, compute a face centred velocity field More...

void	incrementWithDivFlux (Vector< LevelData< FArrayBox > * > &a_phi, const Vector< LevelData< FArrayBox > * > &a_dphi, Real a_dt)

void	updateCoordSysWithNewThickness (const Vector< LevelData< FArrayBox > * > &a_thickness)

void	setIceFrac (const LevelData< FArrayBox > &a_thickness, int a_level)
	initialize real-valued ice fraction More...

void	updateIceFrac (LevelData< FArrayBox > &a_thickness, int a_level)
	update real-valued ice fraction after thickness update More...

void	setIceFracBC (LevelData< FArrayBox > &a_iceFrac, const ProblemDomain &a_domain)

void	advectIceFrac (Vector< LevelData< FArrayBox > * > &a_iceFrac, const Vector< LevelData< FluxBox > * > &a_faceVelAdvection, Real a_dt)
	update real-valued ice fraction through advection from neighboring cells More...

void	updateInvalidIceFrac (Vector< LevelData< FArrayBox > *> a_iceFrac)
	update covered cells, ghost cells etc, of a_iceFrac More...

Real	computeDt ()
	compute timestep More...

Real	computeInitialDt ()
	compute timestep at initial time More...

void	setToZero (Vector< LevelData< FArrayBox > *> &a_data)

void	implicitThicknessCorrection (Real a_dt, const Vector< LevelData< FArrayBox > * > &a_sts, const Vector< LevelData< FArrayBox > * > &a_bts, const Vector< LevelData< FArrayBox > * > &a_vts)
	implicit solve for diffusive fluxes More...

void	applyCalvingCriterion (CalvingModel::Stage a_stage)

void	eliminateRemoteIce ()

void	helmholtzSolve (Vector< LevelData< FArrayBox > * > &a_phi, const Vector< LevelData< FArrayBox > * > &a_rhs, Real a_alpha, Real a_beta) const

void	helmholtzSolve (Vector< LevelData< FArrayBox > * > &a_phi, Real a_alpha, Real a_beta) const

void	computeA (Vector< LevelData< FArrayBox > * > &a_A, Vector< LevelData< FArrayBox > * > &a_sA, Vector< LevelData< FArrayBox > * > &a_bA, const Vector< LevelData< FArrayBox > * > &a_internalEnergy, const Vector< LevelData< FArrayBox > * > &a_sInternalEnergy, const Vector< LevelData< FArrayBox > * > &a_bInternalEnergy, const Vector< RefCountedPtr< LevelSigmaCS > > &a_coordSys) const
	compute the flow rate coefficient A given bulk internal energy & geometry More...

void	computeInternalEnergyHalf (Vector< LevelData< FluxBox > * > &a_layerEH_half, Vector< LevelData< FluxBox > * > &a_layerH_half, const Vector< LevelData< FluxBox > * > &a_layerXYFaceXYVel, const Real a_dt, const Real a_time)

void	updateInternalEnergy (Vector< LevelData< FluxBox > * > &a_layerTH_half, Vector< LevelData< FluxBox > * > &a_layerH_half, const Vector< LevelData< FluxBox > * > &a_layerXYFaceXYVel, const Vector< LevelData< FArrayBox > * > &a_layerSFaceXYVel, const Real a_dt, const Real a_time, Vector< RefCountedPtr< LevelSigmaCS > > &a_coordSysNew, Vector< RefCountedPtr< LevelSigmaCS > > &a_coordSysOld, const Vector< LevelData< FArrayBox > > &a_surfaceThicknessSource, const Vector< LevelData< FArrayBox > > &a_basalThicknessSource, const Vector< LevelData< FArrayBox > *> &a_volumeThicknessSource)
	Update the internalEnergy and tillWaterDepth fields. More...

void	updateTemperature ()
	update the temperature (a derived field) More...

void	computeDischarge (const Vector< LevelData< FluxBox > * > &a_vectFluxes)

int	finestTimestepLevel () const

void	setStableSources (FArrayBox &a_sts, FArrayBox &a_bts, FArrayBox &a_vts, const FArrayBox &a_divuh, const BaseFab< int > &a_mask, const Box &a_box) const
	modify the source terms (surface,basal,volume) to keep all or part of the ice sheet/shelf steady More...

void	updateViscousTensor () const

void	updateGroundingLineProximity () const

void	setLayers (const Vector< Real > &a_sigma)

Static Protected Member Functions
static void	postInterpolationReFloat (LevelData< FArrayBox > &a_H, const LevelData< FArrayBox > &a_coarseH, const LevelData< FArrayBox > &a_coarseBed, const DisjointBoxLayout a_newDBL, const ProblemDomain &a_domain, int a_refRatio, Real a_seaLevel, Real a_waterDensity, Real a_iceDensity)

Protected Attributes
int	m_temporalAccuracy
	temporal accuracy More...

int	m_num_thickness_ghost
	number of ghost cells we need for m_old_thickness More...

int	m_solverType
	what type of nonlinear solver to use for velocity field More...

int	m_maxSolverIterations
	max number of iterations for velocity solver More...

Real	m_velocity_solver_tolerance
	solver tolerance for velSolver. More...

int	m_velocity_solve_interval
	solve the velocity problem every m_velocitySolveInterval timesteps More...

Real	m_velocitySolveInitialResidualNorm
	Residual norms at the start and end of the last velocity solve. More...

Real	m_velocitySolveFinalResidualNorm

IceVelocitySolver *	m_velSolver
	nonlinear elliptic solver for velocity field More...

ConstitutiveRelation *	m_constitutiveRelation
	constitutive relation More...

RateFactor *	m_rateFactor
	rate factor More...

BasalFrictionRelation *	m_basalFrictionRelation
	basal Friction relation More...

RateFactor *	m_basalRateFactor
	rate factor at base More...

bool	m_reset_floating_friction_to_zero
	if false, don't reset basal friction for floating ice to zero (default is true) More...

GodunovPhysics *	m_thicknessPhysPtr
	pointer to a GodunovPhysics for thickness advection More...

Vector< PatchGodunov * >	m_thicknessPatchGodVect
	PatchGodunov used for thickness advection – one for each level. More...

IceThicknessIBC *	m_thicknessIBCPtr
	IBC for thickness advection. More...

IceInternalEnergyIBC *	m_internalEnergyIBCPtr
	IBC for internalEnergy advection. More...

CalvingModel *	m_calvingModelPtr
	Calving model. More...

SurfaceFlux *	m_surfaceFluxPtr
	sets surface flux for ice sheet More...

SurfaceFlux *	m_basalFluxPtr
	sets basal flux for ice sheet More...

SurfaceFlux *	m_surfaceHeatBoundaryDataPtr
	sets surface heat flux or internalEnergy for ice sheet More...

SurfaceFlux *	m_basalHeatBoundaryDataPtr
	sets basal heat flux or temperature for ice sheet More...

SurfaceFlux *	m_topographyFluxPtr
	sets topography flux (which raises/lowers bedrock) More...

Vector< LevelData< FArrayBox > * >	m_deltaTopography

BasalFriction *	m_basalFrictionPtr
	sets basal friction coefficient (beta^2) More...

MuCoefficient *	m_muCoefficientPtr
	sets mu coefficient (phi) More...

int	m_max_level
	max number ofSflux levels More...

int	m_finest_level
	current finest level More...

int	m_finest_timestep_level

int	m_tag_cap
	maximum level at which refinement tags are computed More...

int	m_block_factor
	blocking factor More...

IntVectSet	m_tag_subset
	only allow tagging within a subset of the coarse domain More...

Vector< IntVectSet >	m_vectTagSubset

Real	m_fill_ratio
	grid efficiency More...

int	m_nesting_radius
	proper nesting radius More...

int	m_max_box_size
	max box size More...

int	m_max_base_grid_size
	max box size for level 0 (defaults to max_box_size) More...

int	m_regrid_interval
	regrid interval More...

int	m_n_regrids

bool	m_doInitialVelSolve

bool	m_doInitialVelGuess
	if true, use nonzero initial guess for velocity field (default is false) More...

int	m_initialGuessType

Real	m_initialGuessConstMu

int	m_initialGuessSolverType

RealVect	m_initialGuessConstVel

bool	m_interpolate_zb
	if true, interpolate things like base topography at regrid time More...

int	m_regrid_thickness_interpolation_method
	thickness interpolation method to use on regrid, see LevelSigmaCS::ThicknessInterpolationMethod More...

Real	m_basalLengthScale

Vector< IntVectSet >	m_vectTags
	stores tags from previous regrids More...

bool	m_tagOnGradVel
	tag on grad(velocity)? More...

Real	m_tagging_val
	tagging value (undivided gradient(vel) threshold for regridding) More...

bool	m_tagOnLapVel
	tag on laplacian(velocity) More...

bool	m_tagOnGroundedLapVel
	tag on laplacian(velocity) in grounded regions only More...

Real	m_laplacian_tagging_val
	tagging threshold value for undivided lap(vel) More...

Real	m_laplacian_tagging_max_basal_friction_coef
	when tagging on undivided lap(vel), ignore cells where the basal friction coeffcient exceeds More...

bool	m_tagOnEpsSqr
	tag on strain rate invariant? More...

Real	m_epsSqr_tagVal
	tagging value for strain rate invariant More...

bool	m_tagOnVelRHS
	tag on velocity solve RHS More...

Real	m_velRHS_tagVal
	tagging value for velocity RHS More...

bool	m_tagOndivHgradVel
	tag on div(H grad (vel)) More...

Real	m_divHGradVel_tagVal
	tagging threshold value for undivided div(H grad(vel)) More...

bool	m_tagGroundingLine
	tag the grounding line More...

Real	m_groundingLineTaggingMinVel
	threshold velocity at the grounding line : tag if \|u\| > value More...

Real	m_groundingLineTaggingMaxBasalFrictionCoef
	threshold Basal friction coefficient at the grounding line : tag if C < value More...

bool	m_tagVelDx
	tag where \|vel\| * dx > m_maxVelDxVal More...

Real	m_velDx_tagVal

int	m_velDx_tagVal_finestLevelGrounded

int	m_velDx_tagVal_finestLevelFloating

bool	m_tag_thin_cavity

Real	m_tag_thin_cavity_thickness

bool	m_tagMargin
	tag at the ice margin More...

int	m_margin_tagVal_finestLevel

bool	m_tagAllIce
	tag any cell with ice in it More...

bool	m_tagAllIceOnLevel0
	tag any cell with ice in it on level 0 More...

bool	m_tagEntireDomain
	tag all cells for refinement (refine entire domain) More...

bool	m_eliminate_remote_ice

int	m_eliminate_remote_ice_max_iter

Real	m_eliminate_remote_ice_tol

bool	m_eliminate_remote_ice_after_regrid

bool	m_tagPython
	tag cells according to a python function More...

PyObject *	m_tagPythonModule

PyObject *	m_tagPythonFunction

int	m_tags_grow
	amount to buffer tags used in regridding More...

IntVect	m_tags_grow_dir

Vector< int >	m_refinement_ratios
	refinement ratios More...

Vector< Real >	m_amrDx
	cell spacing at each level More...

Vector< ProblemDomain >	m_amrDomains
	problem domains at each level More...

RealVect	m_domainSize

Vector< DisjointBoxLayout >	m_amrGrids
	current grids More...

Vector< int >	m_covered_level
	keeps track of which levels are completely covered More...

Vector< int >	m_num_cells
	book-keeping; keeps track of number of cells per level More...

Real	m_time
	current time More...

Real	m_offsetTime

Real	m_dt
	most recent timestep More...

Real	m_stable_dt
	most recent stable timestep (> m_dt if we took a step just to hit a plot interval) More...

Real	m_cfl
	timestep scaling More...

Real	m_initial_cfl
	cfl number for initial timestep (useful if initial data needs small cfl) More...

Real	m_max_dt_grow
	maximum amount cfl number may grow in one timestep More...

Real	m_velocity_exit
	maximum acceptable velocity: if max(u) > m_vel_exit , then dump a plot file and exit More...

int	m_cur_step

bool	m_isothermal

Real	m_waterDepth

bool	m_surfaceBoundaryHeatDataDirichlett
	should a Dirichlett internal energy condition be imposed at the upper surface? More...

bool	m_surfaceBoundaryHeatDataTemperature
	is the Dirichlett data a temperature (rather than an internal energy)? More...

Real	m_iceDensity

Real	m_seaWaterDensity

Real	m_gravity

Real	m_seconds_per_unit_time

Vector< LevelData< FArrayBox > * >	m_old_thickness
	current old-time data More...

Vector< LevelData< FArrayBox > * >	m_velocity
	horizontal velocity field (found by an IceVelocitySolver) More...

Vector< LevelData< FArrayBox > *>	m_velRHS
	velocity solve RHS (in case we want to save it) More...

Vector< LevelData< FArrayBox > *>	m_velBasalC

Vector< LevelData< FArrayBox > *>	m_cellMuCoef

Vector< LevelData< FluxBox > *>	m_diffusivity

Real	m_additionalDiffusivity

Vector< LevelData< FluxBox > *>	m_faceVelAdvection

Vector< LevelData< FluxBox > *>	m_faceVelTotal

Vector< LevelData< FArrayBox > *>	m_layerSFaceXYVel

Vector< LevelData< FArrayBox > *>	m_layerSFaceSVel

Vector< LevelData< FluxBox > *>	m_layerXYFaceXYVel

Vector< RefCountedPtr< LevelSigmaCS > >	m_vect_coordSys

Vector< LevelData< FArrayBox > *>	m_iceFrac

Vector< LevelData< FArrayBox > *>	m_internalEnergy

Vector< LevelData< FArrayBox > *>	m_temperature

Vector< LevelData< FArrayBox > *>	m_tillWaterDepth

Vector< LevelData< FArrayBox > *>	m_A

bool	m_A_valid

Vector< LevelData< FArrayBox > *>	m_sInternalEnergy

Vector< LevelData< FArrayBox > *>	m_sTemperature

Vector< LevelData< FArrayBox > *>	m_bInternalEnergy

Vector< LevelData< FArrayBox > *>	m_bTemperature

Vector< LevelData< FArrayBox > *>	m_sHeatFlux

Vector< LevelData< FArrayBox > *>	m_bHeatFlux

Vector< LevelData< FArrayBox > *>	m_sA

Vector< LevelData< FArrayBox > *>	m_bA

Vector< LevelData< FArrayBox > *>	m_surfaceThicknessSource

Vector< LevelData< FArrayBox > *>	m_basalThicknessSource

Vector< LevelData< FArrayBox > *>	m_volumeThicknessSource

Vector< LevelData< FArrayBox > *>	m_divThicknessFlux

Vector< LevelData< FArrayBox > *>	m_calvedIceThickness

Vector< LevelData< FArrayBox > *>	m_removedIceThickness

Vector< LevelData< FArrayBox > *>	m_addedIceThickness

Vector< LevelData< FArrayBox > *>	m_calvedThicknessSource

Vector< LevelData< FArrayBox > *>	m_dragCoef

Vector< LevelData< FArrayBox > *>	m_viscosityCoefCell

Vector< LevelData< FArrayBox > *>	m_viscousTensorCell

Vector< LevelData< FluxBox > *>	m_viscousTensorFace

bool	m_viscousTensor_valid

Vector< LevelData< FArrayBox > *>	m_groundingLineProximity

bool	m_groundingLineProximity_valid

Real	m_groundingLineProximityScale

int	m_groundingLineProximityCalcType

bool	m_report_discharge
	if true, report discharge of solid ice from the ice edge More...

Real	m_report_time_interval
	report diagnostic every m_report_time_interval years (rather than every time step) More...

Real	m_next_report_time

int	m_beta_type
	type of basal friction distribution More...

Real	m_betaVal
	background value for beta More...

Real	m_betaEps
	small parameter for use in computing beta, if needed More...

RealVect	m_basalSlope
	background slope of bottom topography More...

bool	m_is_defined
	is this object initialized? More...

bool	m_do_restart

int	m_restart_step
	if starting from a restart, timestep of restart More...

string	m_plot_prefix

string	m_check_prefix

bool	m_check_overwrite

bool	m_check_exit

int	m_plot_interval

Real	m_plot_time_interval
	write a plot file every m_plot_time_interval years (rather than steps) More...

bool	m_reduced_plot
	if true, reduce the number of fields written to plot files More...

bool	m_write_muCoeff
	if true, include viscosity multiplier (muCoefficient) in plotfiles More...

bool	m_write_mask
	if true, include mask in plotfiles More...

bool	m_write_dHDt
	if true, include dH/dt in plotfiles More...

bool	m_write_fluxVel

bool	m_write_viscousTensor

bool	m_write_baseVel

bool	m_write_solver_rhs
	if true, include velocity solver RHS in plotfiles More...

bool	m_write_internal_energy

bool	m_write_thickness_sources

bool	m_write_ismip6

bool	m_write_map_file
	if true, write out .map.hdf5 file More...

bool	m_write_presolve_plotfiles
	if true, write out plotfile before doing velocity solves More...

int	m_check_interval

bool	m_evolve_thickness

bool	m_evolve_ice_frac

bool	m_evolve_velocity

bool	m_evolve_topography_fix_surface

bool	m_grounded_ice_stable

bool	m_floating_ice_stable

bool	m_floating_ice_basal_flux_is_dhdt

bool	m_floating_ice_basal_flux_is_min_dhdt

bool	m_grounded_ice_basal_flux_is_dhdt

bool	m_frac_sources

DiffusionTreatment	m_diffusionTreatment

bool	m_timeStepTicks

Real	m_fixed_dt

bool	m_reportGroundedIce

bool	m_sigmaSet

unsigned int	m_nLayers

Vector< Real >	m_faceSigma

bool	m_write_layer_velocities

bool	m_additionalVelocity

Static Protected Attributes
static int	s_verbosity = 1
	how verbose should we be? More...

Friends
class	DomainDiagnosticData

Detailed Description

class to manage non-subcycled AMR ice-sheet model

Member Enumeration Documentation

◆ DiffusionTreatment

enum AmrIce::DiffusionTreatment

protected

Enumerator
NONE
IMPLICIT
EXPLICIT

◆ initialGuessTypes

enum AmrIce::initialGuessTypes

protected

Enumerator
SlidingLaw
ConstMu
Function
NUM_INITIAL_GUESS_TYPES

◆ velSolverTypes

enum AmrIce::velSolverTypes

compute area of ice with grounded/floating status given by a_maskval

compute area of grounded ice. compute area of floating ice. compute flux over ice compute change in volume over ice compute flux domain

Enumerator
Picard
JFNK
KnownVelocity
PetscNLSolver
FASMGAMR
Python
InverseVerticallyIntegrated
NUM_SOLVER_TYPES

Constructor & Destructor Documentation

◆ AmrIce()

AmrIce::AmrIce ( )

Default constructor.

At the moment, there is only one constructor, which defines itself based on an inputs file. (This may change, of course)

References setDefaults().

◆ ~AmrIce()

AmrIce::~AmrIce ( )

virtual

destructor

References m_A, m_addedIceThickness, m_bA, m_basalFluxPtr, m_basalFrictionPtr, m_basalFrictionRelation, m_basalHeatBoundaryDataPtr, m_basalRateFactor, m_basalThicknessSource, m_bHeatFlux, m_bInternalEnergy, m_bTemperature, m_calvedIceThickness, m_calvingModelPtr, m_cellMuCoef, m_constitutiveRelation, m_deltaTopography, m_diffusivity, m_divThicknessFlux, m_dragCoef, m_faceVelAdvection, m_faceVelTotal, m_groundingLineProximity, m_iceFrac, m_internalEnergy, m_internalEnergyIBCPtr, m_layerSFaceSVel, m_layerSFaceXYVel, m_layerXYFaceXYVel, m_muCoefficientPtr, m_old_thickness, m_rateFactor, m_removedIceThickness, m_sA, m_sHeatFlux, m_sInternalEnergy, m_sTemperature, m_surfaceFluxPtr, m_surfaceHeatBoundaryDataPtr, m_surfaceThicknessSource, m_tagPythonFunction, m_tagPythonModule, m_temperature, m_thicknessIBCPtr, m_thicknessPatchGodVect, m_thicknessPhysPtr, m_tillWaterDepth, m_velBasalC, m_velocity, m_velRHS, m_velSolver, m_viscosityCoefCell, m_viscousTensorCell, m_viscousTensorFace, m_volumeThicknessSource, and s_verbosity.

Member Function Documentation

◆ addedIceThickness()

const Vector<LevelData<FArrayBox>* >& AmrIce::addedIceThickness ( ) const

inline

References m_addedIceThickness.

◆ addObserver()

void AmrIce::addObserver ( Observer * a_observer )

inline

Referenced by init_bisicles_instance(), and main().

◆ advectIceFrac()

void AmrIce::advectIceFrac	(	Vector< LevelData< FArrayBox > * > &	a_iceFrac,
		const Vector< LevelData< FluxBox > * > &	a_faceVelAdvection,
		Real	a_dt
	)

protected

update real-valued ice fraction through advection from neighboring cells

References dx(), LevelSigmaCS::getFloatingMask(), LevelSigmaCS::getH(), LevelSigmaCS::getTopography(), m_amrDomains, m_amrDx, m_amrGrids, m_cfl, m_cur_step, m_dt, m_finest_level, m_max_box_size, m_refinement_ratios, m_thicknessIBCPtr, m_time, m_vect_coordSys, m_velocity, IceThicknessIBC::setIceFractionBCs(), time(), and IceThicknessIBC::velocityGhostBC().

Referenced by surfaceHeatFlux(), and timeStep().

◆ amrDx()

const Vector<Real>& AmrIce::amrDx ( ) const

inline

References m_amrDx.

Referenced by MaximumExtentCalvingModel::applyCriterion(), and CliffCollapseCalvingModel::applyCriterion().

◆ amrGeometry()

const Vector<RefCountedPtr<LevelSigmaCS> >& AmrIce::amrGeometry ( ) const

inline

References incrementIceThickness(), and m_vect_coordSys.

Referenced by AMRDamage::timestep(), and AMRMelange::timestep().

◆ amrIceFrac() [1/2]

Vector<LevelData<FArrayBox>* >& AmrIce::amrIceFrac ( )

inline

return reference to full AMR ice fraction

References m_iceFrac.

◆ amrIceFrac() [2/2]

const Vector<LevelData<FArrayBox>* >& AmrIce::amrIceFrac ( ) const

inline

return const reference to full AMR ice fraction

References groundingLineProximity(), and m_iceFrac.

◆ amrVelocity()

const Vector<LevelData<FArrayBox>* >& AmrIce::amrVelocity ( )

inline

References m_velocity.

Referenced by AMRDamage::timestep().

◆ applyCalvingCriterion()

void AmrIce::applyCalvingCriterion ( CalvingModel::Stage a_stage )

protected

References CalvingModel::applyCriterion(), eliminateRemoteIce(), CalvingModel::Initialization, m_addedIceThickness, m_calvedIceThickness, m_calvingModelPtr, m_eliminate_remote_ice, m_finest_level, m_iceFrac, m_removedIceThickness, m_vect_coordSys, AmrIce::Observer::PostCalving, and AmrIce::Observer::PreCalving.

Referenced by initData(), solveVelocityField(), surfaceHeatFlux(), and updateGeometry().

◆ basalHeatBoundaryData()

SurfaceFlux& AmrIce::basalHeatBoundaryData ( ) const

inlinevirtual

Implements AmrIceBase.

References m_basalHeatBoundaryDataPtr.

Referenced by updateInternalEnergy().

◆ basalThicknessSource()

const LevelData< FArrayBox > * AmrIce::basalThicknessSource ( int a_level ) const

References m_basalThicknessSource.

Referenced by groundingLineProximityScale(), and AMRDamage::timestep().

◆ calvedIceThickness()

const Vector<LevelData<FArrayBox>* >& AmrIce::calvedIceThickness ( ) const

inline

access function for calved ice data

References m_calvedIceThickness.

◆ computeA()

void AmrIce::computeA	(	Vector< LevelData< FArrayBox > * > &	a_A,
		Vector< LevelData< FArrayBox > * > &	a_sA,
		Vector< LevelData< FArrayBox > * > &	a_bA,
		const Vector< LevelData< FArrayBox > * > &	a_internalEnergy,
		const Vector< LevelData< FArrayBox > * > &	a_sInternalEnergy,
		const Vector< LevelData< FArrayBox > * > &	a_bInternalEnergy,
		const Vector< RefCountedPtr< LevelSigmaCS > > &	a_coordSys
	)		const

protected

compute the flow rate coefficient A given bulk internal energy & geometry

update the flow law coefficient A

References IceUtility::computeA(), LevelSigmaCS::getSigma(), m_amrGrids, m_finest_level, m_nLayers, m_rateFactor, m_refinement_ratios, and s_verbosity.

Referenced by solveVelocityField(), and surfaceHeatFlux().

◆ computeAreaFraction()

void AmrIce::computeAreaFraction	(	LevelData< FArrayBox > &	a_area,
		int	a_maskVal,
		int	a_level
	)		const

compute total ice and total grounded ice (volume, at this point)

compute volume over flotation fill a_area with per-cell area fraction given by a_maskval e.g when a_maskVal == GROUNDEDMASKVAL, a_area will be filled with values from 0 (not grounded ice) to 1 (entirely grounded ice)

References m_finest_level, and m_vect_coordSys.

Referenced by restart().

◆ computeDischarge()

void AmrIce::computeDischarge ( const Vector< LevelData< FluxBox > * > & a_vectFluxes )

protected

Referenced by surfaceHeatFlux().

◆ computeDt()

Real AmrIce::computeDt ( )

protected

compute timestep

References dt(), EXPLICIT, finestTimestepLevel(), m_amrDx, m_amrGrids, m_cfl, m_cur_step, m_diffusionTreatment, m_faceVelAdvection, m_fixed_dt, m_initial_cfl, m_max_dt_grow, m_plot_prefix, m_stable_dt, m_timeStepTicks, m_velocity_exit, s_verbosity, and writePlotFile().

Referenced by computeInitialDt(), run(), and surfaceHeatFlux().

◆ computeFaceVelocity()

void AmrIce::computeFaceVelocity	(	Vector< LevelData< FluxBox > * > &	a_faceVelAdvection,
		Vector< LevelData< FluxBox > * > &	a_faceVelTotal,
		Vector< LevelData< FluxBox > * > &	a_diffusivity,
		Vector< LevelData< FluxBox > * > &	a_layerXYFaceXYVel,
		Vector< LevelData< FArrayBox > * > &	a_layerSFaceXYVel
	)

protected

given the current cell centred velocity field, compute a face centred velocity field

References IceUtility::computeFaceVelocity(), IMPLICIT, m_A, m_additionalVelocity, m_amrGrids, m_bA, m_constitutiveRelation, m_diffusionTreatment, m_finest_level, m_refinement_ratios, m_sA, m_thicknessIBCPtr, m_vect_coordSys, and m_velocity.

Referenced by solveVelocityField(), and surfaceHeatFlux().

◆ computeH_half()

void AmrIce::computeH_half	(	Vector< LevelData< FluxBox > * > &	a_H_half,
		Real	a_dt
	)

◆ computeInitialDt()

Real AmrIce::computeInitialDt ( )

protected

compute timestep at initial time

References computeDt(), dt(), and s_verbosity.

Referenced by run(), and surfaceHeatFlux().

◆ computeInternalEnergyHalf()

void AmrIce::computeInternalEnergyHalf	(	Vector< LevelData< FluxBox > * > &	a_layerEH_half,
		Vector< LevelData< FluxBox > * > &	a_layerH_half,
		const Vector< LevelData< FluxBox > * > &	a_layerXYFaceXYVel,
		const Real	a_dt,
		const Real	a_time
	)

protected

References m_amrDomains, m_amrDx, m_amrGrids, m_finest_level, m_internalEnergy, m_internalEnergyIBCPtr, m_nLayers, m_old_thickness, m_refinement_ratios, and m_time.

Referenced by surfaceHeatFlux(), and timeStep().

◆ computeThicknessFluxes()

void AmrIce::computeThicknessFluxes	(	Vector< LevelData< FluxBox > * > &	a_vectFluxes,
		const Vector< LevelData< FluxBox > * > &	a_H_half,
		const Vector< LevelData< FluxBox > * > &	a_faceVelAdvection
	)

References finestTimestepLevel(), m_amrGrids, and m_refinement_ratios.

Referenced by setCalvingModel(), and timeStep().

◆ computeTotalIce()

Real AmrIce::computeTotalIce ( ) const

diagnostic function – integrates thickness over domain

References LevelSigmaCS::getH(), m_amrDx, m_finest_level, m_refinement_ratios, and m_vect_coordSys.

Referenced by regrid(), and setCalvingModel().

◆ defineSolver()

void AmrIce::defineSolver ( )

protectedvirtual

initialize diagnostics

define nonlinear ellipic solver for computing velocity field

References IceVelocitySolver::define(), FASIceSolver::define(), InverseVerticallyIntegratedVelocitySolver::define(), FASMGAMR, InverseVerticallyIntegrated, JFNK, KnownVelocity, m_amrDomains, m_amrDx, m_amrGrids, m_basalFrictionRelation, m_constitutiveRelation, m_finest_level, m_maxSolverIterations, m_refinement_ratios, m_solverType, m_thicknessIBCPtr, m_vect_coordSys, m_velocity_solver_tolerance, m_velSolver, PetscNLSolver, Picard, Python, s_verbosity, IceThicknessIBC::setGridHierarchy(), IceVelocitySolver::setMaxIterations(), FASIceSolver::setMaxIterations(), IceVelocitySolver::setTolerance(), FASIceSolver::setTolerance(), and IceVelocitySolver::setVerbosity().

Referenced by initGrids(), readCheckpointFile(), regrid(), setupFixedGrids(), solveVelocityField(), and surfaceHeatFlux().

◆ defineVelRHS()

void AmrIce::defineVelRHS ( Vector< LevelData< FArrayBox > * > & a_vectRhs )

protectedvirtual

compute RHS for velocity field solve

References IceUtility::defineRHS(), dx(), m_amrDomains, m_amrGrids, m_dt, m_finest_level, m_thicknessIBCPtr, m_time, m_vect_coordSys, and IceThicknessIBC::modifyVelocityRHS().

Referenced by solveVelocityField(), surfaceHeatFlux(), and writeAMRPlotFile().

◆ dragCoefficient()

const LevelData< FArrayBox > * AmrIce::dragCoefficient ( int a_level ) const

References m_dragCoef, and m_viscousTensor_valid.

Referenced by groundingLineProximityScale(), restart(), and writeAMRPlotFile().

◆ dt()

Real AmrIce::dt ( ) const

inline

References m_dt.

Referenced by CliffCollapseCalvingModel::applyCriterion(), computeDt(), computeInitialDt(), MelangeIceObserver::notify(), DamageIceObserver::notify(), run(), and updateGroundingLineProximity().

◆ dx()

const RealVect AmrIce::dx ( int a_level ) const

inlinevirtual

◆ eliminateRemoteIce()

void AmrIce::eliminateRemoteIce ( )

protected

Identify regions of floating ice that are remote from grounded ice and eliminate them.

References IceUtility::eliminateRemoteIce(), m_addedIceThickness, m_amrDomains, m_amrDx, m_amrGrids, m_calvedIceThickness, m_eliminate_remote_ice_max_iter, m_eliminate_remote_ice_tol, m_finest_level, m_refinement_ratios, m_removedIceThickness, m_vect_coordSys, m_velocity, AmrIce::Observer::PostCalving, AmrIce::Observer::PreCalving, and s_verbosity.

Referenced by applyCalvingCriterion(), initData(), regrid(), solveVelocityField(), and surfaceHeatFlux().

◆ faceVelocities()

const Vector<LevelData<FluxBox>* >& AmrIce::faceVelocities ( )

inline

access function for face-centered velocities

References m_faceVelTotal.

Referenced by AMRDamage::timestep().

◆ faceVelocitiesLayered()

const Vector<LevelData<FluxBox>* >& AmrIce::faceVelocitiesLayered ( ) const

inline

access function for layered face-centered velocities

References m_layerXYFaceXYVel.

◆ finestLevel()

int AmrIce::finestLevel ( ) const

inlinevirtual

Implements AmrIceBase.

References m_finest_level.

Referenced by bisicles_push_pop_thin_ice(), MelangeIceObserver::notify(), DamageIceObserver::notify(), setToZero(), and AMRDamage::timestep().

◆ finestTimestepLevel()

int AmrIce::finestTimestepLevel ( ) const

inlineprotected

References m_finest_level.

Referenced by computeDt(), computeH_half(), computeThicknessFluxes(), implicitThicknessCorrection(), incrementIceThickness(), timeStep(), updateGeometry(), and updateGroundingLineProximity().

◆ geometry()

const RefCountedPtr<LevelSigmaCS> AmrIce::geometry ( int a_level ) const

inlinevirtual

Implements AmrIceBase.

References m_vect_coordSys.

◆ getFaceSigma()

const Vector<Real>& AmrIce::getFaceSigma ( ) const

inline

References m_faceSigma, and setLayers().

Referenced by levelSetup(), readCheckpointFile(), and writeCheckpointFile().

◆ getHeader() [1/3]

void AmrIce::getHeader	(	const std::string &	a_key,
		std::string &	a_val
	)

inline

Referenced by bisicles_get_header().

◆ getHeader() [2/3]

void AmrIce::getHeader	(	const std::string &	a_key,
		int &	a_val
	)

inline

◆ getHeader() [3/3]

void AmrIce::getHeader	(	const std::string &	a_key,
		Real &	a_val
	)

inline

References readCheckpointFile(), restart(), writeAMRHierarchyHDF5(), writeAMRPlotFile(), writeCheckpointFile(), and writePlotFile().

◆ getIceThickness()

void AmrIce::getIceThickness	(	Real *	a_data_ptr,
		int *	a_dim_info,
		Real *	a_dew,
		Real *	a_dns
	)		const

fill flattened Fortran array of data with ice thickness

References LevelSigmaCS::getH(), m_amrDomains, m_amrDx, m_amrGrids, m_finest_level, and m_vect_coordSys.

Referenced by setCalvingModel().

◆ grids() [1/2]

const DisjointBoxLayout& AmrIce::grids ( int a_level ) const

inlinevirtual

Implements AmrIceBase.

References m_amrGrids.

Referenced by bisicles_push_pop_thin_ice(), MelangeIceObserver::notify(), and DamageIceObserver::notify().

◆ grids() [2/2]

const Vector<DisjointBoxLayout>& AmrIce::grids ( ) const

inline

References m_amrGrids.

Referenced by helmholtzSolve(), implicitThicknessCorrection(), readCheckpointFile(), restart(), and updateGroundingLineProximity().

◆ groundingLineProximity()

const LevelData< FArrayBox > * AmrIce::groundingLineProximity ( int a_level ) const

virtual

Implements AmrIceBase.

References m_groundingLineProximity, and updateGroundingLineProximity().

Referenced by amrIceFrac(), and ProximityCalvingModel::applyCriterion().

◆ groundingLineProximityScale()

Real AmrIce::groundingLineProximityScale ( ) const

inlinevirtual

Implements AmrIceBase.

References basalThicknessSource(), dragCoefficient(), m_groundingLineProximityScale, surfaceThicknessSource(), viscosityCoefficient(), and viscousTensor().

◆ helmholtzSolve() [1/2]

void AmrIce::helmholtzSolve	(	Vector< LevelData< FArrayBox > * > &	a_phi,
		const Vector< LevelData< FArrayBox > * > &	a_rhs,
		Real	a_alpha,
		Real	a_beta
	)		const

protected

solve a_alpha * phi - a_beta * laplacian(phi) = a_rhs and grad(phi).n = 0 on the domain boundaries

References grids(), m_amrDomains, m_amrDx, m_amrGrids, m_finest_level, m_refinement_ratios, and s_verbosity.

Referenced by helmholtzSolve(), implicitThicknessCorrection(), surfaceHeatFlux(), and updateInternalEnergy().

◆ helmholtzSolve() [2/2]

void AmrIce::helmholtzSolve	(	Vector< LevelData< FArrayBox > * > &	a_phi,
		Real	a_alpha,
		Real	a_beta
	)		const

protected

solve a_alpha* phi - a_beta * laplacian(phi) = phi' and grad(phi).n = 0 on the domain boundaries

References helmholtzSolve(), m_amrGrids, and m_finest_level.

◆ iceFrac() [1/2]

LevelData<FArrayBox>* AmrIce::iceFrac ( int a_level )

inline

return pointer to real-valued ice fraction on level a_level

(0 = no ice, 1 = full of ice, 0<phi<1 – partially filled (useful for calving model and for communication with POP

References m_iceFrac.

◆ iceFrac() [2/2]

const LevelData<FArrayBox>* AmrIce::iceFrac ( int a_level ) const

inline

return pointer to real-valued ice fraction on level a_level

(0 = no ice, 1 = full of ice, 0<phi<1 – partially filled (useful for calving model and for communication with POP

References m_iceFrac.

◆ implicitThicknessCorrection()

void AmrIce::implicitThicknessCorrection	(	Real	a_dt,
		const Vector< LevelData< FArrayBox > * > &	a_sts,
		const Vector< LevelData< FArrayBox > * > &	a_bts,
		const Vector< LevelData< FArrayBox > * > &	a_vts
	)

protected

implicit solve for diffusive fluxes

References finestTimestepLevel(), LevelSigmaCS::getH(), grids(), helmholtzSolve(), m_additionalDiffusivity, m_amrDomains, m_amrDx, m_amrGrids, m_diffusivity, m_refinement_ratios, m_temporalAccuracy, m_vect_coordSys, and s_verbosity.

Referenced by surfaceHeatFlux(), and updateGeometry().

◆ incrementIceThickness()

void AmrIce::incrementIceThickness ( Vector< LevelData< FArrayBox > *> a_thk )

nearly direct access to the ice thickness

References finestTimestepLevel(), LevelSigmaCS::getH(), m_amrDomains, m_amrDx, m_amrGrids, m_dt, m_finest_level, m_refinement_ratios, m_thicknessIBCPtr, m_time, m_vect_coordSys, LevelSigmaCS::recomputeGeometry(), and IceThicknessIBC::setGeometryBCs().

Referenced by amrGeometry(), and setLayers().

◆ incrementWithDivFlux()

void AmrIce::incrementWithDivFlux	(	Vector< LevelData< FArrayBox > * > &	a_phi,
		const Vector< LevelData< FArrayBox > * > &	a_dphi,
		Real	a_dt
	)

protected

Referenced by surfaceHeatFlux().

◆ initData()

void AmrIce::initData	(	Vector< RefCountedPtr< LevelSigmaCS > > &	a_vectCoordSys,
		Vector< LevelData< FArrayBox > * > &	a_initialVelocity
	)

protected

◆ initGrids()

void AmrIce::initGrids ( int a_finest_level )

protected

initialize grids at initial time

References defineSolver(), initData(), levelSetup(), m_A_valid, m_amrDomains, m_amrGrids, m_block_factor, m_fill_ratio, m_finest_level, m_groundingLineProximity_valid, m_max_base_grid_size, m_max_box_size, m_max_level, m_nesting_radius, m_refinement_ratios, m_tag_cap, m_vect_coordSys, m_velocity, m_viscousTensor_valid, s_verbosity, and tagCellsInit().

Referenced by initialize(), and surfaceHeatFlux().

◆ initialize()

void AmrIce::initialize ( )

initializes object based on inputs data passed in through parmParse

initializes new object based on data in ParmParse database. This may change to a more explicit initialization if it's thought to be a good idea.

PatchGodunov used for thickness advection

References EXPLICIT, IMPLICIT, DomainDiagnosticData::initDiagnostics(), initGrids(), PythonInterface::InitializePythonFunction(), PythonInterface::InitializePythonModule(), m_addedIceThickness, m_additionalDiffusivity, m_additionalVelocity, m_amrDomains, m_amrDx, m_amrGrids, m_basalLengthScale, m_basalSlope, m_basalThicknessSource, m_bHeatFlux, m_bInternalEnergy, m_block_factor, m_calvedIceThickness, m_cellMuCoef, m_cfl, m_covered_level, m_cur_step, m_deltaTopography, m_diffusionTreatment, m_diffusivity, m_divHGradVel_tagVal, m_divThicknessFlux, m_do_restart, m_doInitialVelGuess, m_doInitialVelSolve, m_domainSize, m_eliminate_remote_ice, m_eliminate_remote_ice_after_regrid, m_eliminate_remote_ice_max_iter, m_eliminate_remote_ice_tol, m_epsSqr_tagVal, m_evolve_ice_frac, m_evolve_thickness, m_evolve_topography_fix_surface, m_evolve_velocity, m_faceVelAdvection, m_faceVelTotal, m_fill_ratio, m_finest_level, m_finest_timestep_level, m_fixed_dt, m_floating_ice_basal_flux_is_dhdt, m_floating_ice_basal_flux_is_min_dhdt, m_floating_ice_stable, m_frac_sources, m_gravity, m_grounded_ice_basal_flux_is_dhdt, m_grounded_ice_stable, m_groundingLineProximityCalcType, m_groundingLineProximityScale, m_groundingLineTaggingMaxBasalFrictionCoef, m_groundingLineTaggingMinVel, m_iceDensity, m_iceFrac, m_initial_cfl, m_initialGuessConstMu, m_initialGuessConstVel, m_initialGuessSolverType, m_initialGuessType, m_internalEnergy, m_interpolate_zb, m_isothermal, m_laplacian_tagging_max_basal_friction_coef, m_laplacian_tagging_val, m_layerSFaceSVel, m_layerSFaceXYVel, m_layerXYFaceXYVel, m_margin_tagVal_finestLevel, m_max_base_grid_size, m_max_box_size, m_max_dt_grow, m_max_level, m_maxSolverIterations, m_n_regrids, m_nesting_radius, m_num_cells, m_num_thickness_ghost, m_offsetTime, m_old_thickness, m_refinement_ratios, m_regrid_interval, m_regrid_thickness_interpolation_method, m_removedIceThickness, m_report_discharge, m_report_time_interval, m_reset_floating_friction_to_zero, m_seaWaterDensity, m_seconds_per_unit_time, m_sHeatFlux, m_sInternalEnergy, m_solverType, m_surfaceThicknessSource, m_tag_cap, m_tag_thin_cavity, m_tag_thin_cavity_thickness, m_tagAllIce, m_tagAllIceOnLevel0, m_tagEntireDomain, m_tagging_val, m_tagGroundingLine, m_tagMargin, m_tagOndivHgradVel, m_tagOnEpsSqr, m_tagOnGradVel, m_tagOnGroundedLapVel, m_tagOnLapVel, m_tagOnVelRHS, m_tagPython, m_tagPythonFunction, m_tagPythonModule, m_tags_grow, m_tags_grow_dir, m_tagVelDx, m_temporalAccuracy, m_thicknessIBCPtr, m_thicknessPatchGodVect, m_thicknessPhysPtr, m_tillWaterDepth, m_time, m_timeStepTicks, m_vect_coordSys, m_vectTagSubset, m_velBasalC, m_velDx_tagVal, m_velDx_tagVal_finestLevelFloating, m_velDx_tagVal_finestLevelGrounded, m_velocity, m_velocity_exit, m_velocity_solve_interval, m_velocity_solver_tolerance, m_velRHS, m_velRHS_tagVal, m_volumeThicknessSource, m_write_dHDt, m_write_mask, m_write_muCoeff, m_write_solver_rhs, restart(), s_verbosity, IceThermodynamics::setConstants(), setLayers(), setupFixedGrids(), and time().

Referenced by init_bisicles_instance(), and main().

◆ isDefined()

bool AmrIce::isDefined ( ) const

is this object defined and initialized?

References m_is_defined.

Referenced by levelSetup(), and setCalvingModel().

◆ levelSetup()

void AmrIce::levelSetup	(	int	a_level,
		const DisjointBoxLayout &	a_grids
	)

protected

◆ muCoef()

const LevelData<FArrayBox>& AmrIce::muCoef ( int a_level ) const

inline

return const ref to real-valued 'mu coefficient' on level a_level

References m_cellMuCoef.

Referenced by ThicknessCalvingModel::applyCriterion().

◆ postInterpolationReFloat()

static void AmrIce::postInterpolationReFloat	(	LevelData< FArrayBox > &	a_H,
		const LevelData< FArrayBox > &	a_coarseH,
		const LevelData< FArrayBox > &	a_coarseBed,
		const DisjointBoxLayout	a_newDBL,
		const ProblemDomain &	a_domain,
		int	a_refRatio,
		Real	a_seaLevel,
		Real	a_waterDensity,
		Real	a_iceDensity
	)

staticprotected

Referenced by surfaceHeatFlux().

◆ readCheckpointFile()

void AmrIce::readCheckpointFile ( HDF5Handle & a_handle )

read checkpoint file for restart

read checkpoint data from file pointed to by a_handle

note that although this check appears to work, it makes a mess of a_handle and the next lot of data are not read...

References InverseIceVelocitySolver::basalFriction(), IceThermodynamics::composeInternalEnergy(), defineSolver(), dx(), getFaceSigma(), LevelSigmaCS::getH(), grids(), m_addedIceThickness, m_amrDomains, m_amrDx, m_amrGrids, m_basalFrictionPtr, m_basalThicknessSource, m_bHeatFlux, m_bInternalEnergy, m_calvedIceThickness, m_cellMuCoef, m_cfl, m_cur_step, m_deltaTopography, m_diffusivity, m_divThicknessFlux, m_doInitialVelGuess, m_doInitialVelSolve, m_dt, m_faceSigma, m_faceVelAdvection, m_faceVelTotal, m_finest_level, m_gravity, m_iceDensity, m_iceFrac, m_internalEnergy, m_layerSFaceSVel, m_layerSFaceXYVel, m_layerXYFaceXYVel, m_max_level, m_muCoefficientPtr, m_nLayers, m_num_thickness_ghost, m_old_thickness, m_refinement_ratios, m_removedIceThickness, m_restart_step, m_seaWaterDensity, m_seconds_per_unit_time, m_sHeatFlux, m_sInternalEnergy, m_surfaceThicknessSource, m_tillWaterDepth, m_time, m_vect_coordSys, m_velBasalC, m_velocity, m_velocitySolveInitialResidualNorm, m_velRHS, m_velSolver, m_volumeThicknessSource, InverseIceVelocitySolver::muCoefficient(), LevelSigmaCS::recomputeGeometry(), refRatios(), s_verbosity, setIceFrac(), LevelSigmaCS::setTopography(), solveVelocityField(), time(), and updateTemperature().

Referenced by getHeader(), and restart().

◆ refRatios()

const Vector<int>& AmrIce::refRatios ( ) const

inlinevirtual

Implements AmrIceBase.

References m_refinement_ratios.

Referenced by MelangeIceObserver::notify(), DamageIceObserver::notify(), and readCheckpointFile().

◆ regrid()

void AmrIce::regrid ( )

do regridding

References computeTotalIce(), defineSolver(), destructiveRegrid(), dx(), eliminateRemoteIce(), m_A_valid, m_addedIceThickness, m_amrDomains, m_amrDx, m_amrGrids, m_basalThicknessSource, m_bHeatFlux, m_bInternalEnergy, m_block_factor, m_calvedIceThickness, m_cellMuCoef, m_covered_level, m_deltaTopography, m_diffusivity, m_divThicknessFlux, m_domainSize, m_dt, m_eliminate_remote_ice, m_eliminate_remote_ice_after_regrid, m_evolve_velocity, m_faceVelAdvection, m_faceVelTotal, m_fill_ratio, m_finest_level, m_groundingLineProximity_valid, m_iceFrac, m_internalEnergy, m_internalEnergyIBCPtr, m_interpolate_zb, m_layerSFaceSVel, m_layerSFaceXYVel, m_layerXYFaceXYVel, m_max_box_size, m_max_level, m_n_regrids, m_nesting_radius, m_nLayers, m_num_cells, m_old_thickness, m_refinement_ratios, m_regrid_thickness_interpolation_method, m_removedIceThickness, m_sHeatFlux, m_sInternalEnergy, m_surfaceThicknessSource, m_thicknessIBCPtr, m_tillWaterDepth, m_time, m_vect_coordSys, m_velBasalC, m_velocity, m_velocitySolveInitialResidualNorm, m_velRHS, m_volumeThicknessSource, IceThicknessIBC::regridIceGeometry(), s_verbosity, IceThicknessIBC::setGeometryBCs(), IceInternalEnergyIBC::setIceInternalEnergyBC(), solveVelocityField(), tagCells(), updateTemperature(), and IceThicknessIBC::velocityGhostBC().

Referenced by run(), and setCalvingModel().

◆ removedIceThickness()

const Vector<LevelData<FArrayBox>* >& AmrIce::removedIceThickness ( ) const

inline

References m_removedIceThickness.

◆ removeObserver()

void AmrIce::removeObserver ( Observer * a_observer )

inline

References AmrIce::Observer::notify().

Referenced by AmrIce::Observer::~Observer().

◆ restart()

void AmrIce::restart ( const string & a_restart_file )

◆ run()

void AmrIce::run	(	Real	a_max_time,
		int	a_max_step
	)

advance solution until either max_time or max_step are reached

References computeDt(), computeInitialDt(), dt(), m_addedIceThickness, m_calvedIceThickness, m_check_exit, m_check_interval, m_cur_step, m_do_restart, m_next_report_time, m_plot_interval, m_plot_time_interval, m_regrid_interval, m_removedIceThickness, m_report_time_interval, m_restart_step, m_time, regrid(), s_verbosity, setToZero(), timeStep(), writeCheckpointFile(), and writePlotFile().

Referenced by main(), and setCalvingModel().

◆ setBasalFlux()

void AmrIce::setBasalFlux ( SurfaceFlux * a_basalFluxPtr )

inline

set basal flux for ice sheet

References m_basalFluxPtr, and SurfaceFlux::new_surfaceFlux().

Referenced by init_bisicles_instance(), and main().

◆ setBasalFriction() [1/2]

void AmrIce::setBasalFriction ( const BasalFriction * a_basalFrictionPtr )

inline

set basal friction

References m_basalFrictionPtr, and BasalFriction::new_basalFriction().

Referenced by init_bisicles_instance(), main(), solveVelocityField(), surfaceHeatFlux(), and writeAMRPlotFile().

◆ setBasalFriction() [2/2]

void AmrIce::setBasalFriction	(	Vector< LevelData< FArrayBox > * > &	a_C,
		Vector< LevelData< FArrayBox > * > &	a_C0
	)

protectedvirtual

set basal friction coefficients C,C0 prior to velocity solve

References IceUtility::computeA(), IceUtility::computeC0(), m_amrDx, m_amrGrids, m_basalFrictionPtr, m_basalRateFactor, m_bInternalEnergy, m_dt, m_finest_level, m_reset_floating_friction_to_zero, m_vect_coordSys, BasalFriction::setBasalFriction(), IceUtility::setFloatingBasalFriction(), and time().

◆ setBasalFrictionRelation()

void AmrIce::setBasalFrictionRelation ( BasalFrictionRelation * a_basalFrictionRelPtr )

inline

set basal Friction relation

needs to be done before calling initialize

References BasalFrictionRelation::getNewBasalFrictionRelation(), m_basalFrictionRelation, setInternalEnergyBC(), and setThicknessBC().

Referenced by init_bisicles_instance(), and main().

◆ setBasalHeatBoundaryData()

void AmrIce::setBasalHeatBoundaryData ( SurfaceFlux * a_basalHeatBoundaryDataPtr )

inline

set basal Heat flux for ice sheet. Does not include the heat flux due to sliding friction

References m_basalHeatBoundaryDataPtr, and SurfaceFlux::new_surfaceFlux().

Referenced by init_bisicles_instance(), and main().

◆ setBasalRateFactor()

void AmrIce::setBasalRateFactor ( RateFactor * a_rateFactorPtr )

inline

set rate factor at base

needs to be done before calling initialize

References RateFactor::getNewRateFactor(), and m_basalRateFactor.

Referenced by init_bisicles_instance(), and main().

◆ setCalvingModel()

void AmrIce::setCalvingModel ( CalvingModel * a_calvingModelPtr )

inline

References computeH_half(), computeThicknessFluxes(), computeTotalIce(), getIceThickness(), isDefined(), m_calvingModelPtr, CalvingModel::new_CalvingModel(), regrid(), run(), timeStep(), and updateGeometry().

Referenced by init_bisicles_instance(), and main().

◆ setConstitutiveRelation()

void AmrIce::setConstitutiveRelation ( ConstitutiveRelation * a_constRelPtr )

inline

set constitutive relation

needs to be done before calling initialize

References ConstitutiveRelation::getNewConstitutiveRelation(), and m_constitutiveRelation.

Referenced by init_bisicles_instance(), and main().

◆ setDefaults()

void AmrIce::setDefaults ( )

set default values before initialization

References JFNK, m_A_valid, m_additionalDiffusivity, m_additionalVelocity, m_basalFluxPtr, m_basalLengthScale, m_basalSlope, m_betaEps, m_betaVal, m_block_factor, m_cfl, m_diffusionTreatment, m_divHGradVel_tagVal, m_do_restart, m_doInitialVelGuess, m_doInitialVelSolve, m_domainSize, m_dt, m_eliminate_remote_ice, m_eliminate_remote_ice_after_regrid, m_eliminate_remote_ice_max_iter, m_eliminate_remote_ice_tol, m_epsSqr_tagVal, m_evolve_ice_frac, m_evolve_thickness, m_evolve_topography_fix_surface, m_evolve_velocity, m_fill_ratio, m_finest_level, m_finest_timestep_level, m_fixed_dt, m_floating_ice_basal_flux_is_dhdt, m_floating_ice_basal_flux_is_min_dhdt, m_floating_ice_stable, m_frac_sources, m_gravity, m_grounded_ice_basal_flux_is_dhdt, m_grounded_ice_stable, m_groundingLineProximity_valid, m_groundingLineProximityCalcType, m_groundingLineProximityScale, m_groundingLineTaggingMaxBasalFrictionCoef, m_groundingLineTaggingMinVel, m_iceDensity, m_initialGuessConstMu, m_initialGuessConstVel, m_initialGuessSolverType, m_initialGuessType, m_interpolate_zb, m_is_defined, m_isothermal, m_laplacian_tagging_max_basal_friction_coef, m_laplacian_tagging_val, m_margin_tagVal_finestLevel, m_max_base_grid_size, m_max_box_size, m_max_dt_grow, m_max_level, m_maxSolverIterations, m_nesting_radius, m_num_thickness_ghost, m_offsetTime, m_regrid_thickness_interpolation_method, m_report_discharge, m_report_time_interval, m_reset_floating_friction_to_zero, m_restart_step, m_seaWaterDensity, m_seconds_per_unit_time, m_sigmaSet, m_solverType, m_stable_dt, m_surfaceBoundaryHeatDataDirichlett, m_surfaceBoundaryHeatDataTemperature, m_tag_cap, m_tag_thin_cavity, m_tag_thin_cavity_thickness, m_tagAllIce, m_tagAllIceOnLevel0, m_tagEntireDomain, m_tagging_val, m_tagGroundingLine, m_tagMargin, m_tagOndivHgradVel, m_tagOnEpsSqr, m_tagOnGradVel, m_tagOnGroundedLapVel, m_tagOnLapVel, m_tagOnVelRHS, m_tagPython, m_tagPythonFunction, m_tagPythonModule, m_tags_grow, m_tags_grow_dir, m_tagVelDx, m_temporalAccuracy, m_timeStepTicks, m_velDx_tagVal, m_velDx_tagVal_finestLevelFloating, m_velDx_tagVal_finestLevelGrounded, m_velocity_exit, m_velocity_solve_interval, m_velocity_solver_tolerance, m_velocitySolveInitialResidualNorm, m_velRHS_tagVal, m_viscousTensor_valid, m_waterDepth, NONE, and SlidingLaw.

Referenced by AmrIce().

◆ setDomainSize()

void AmrIce::setDomainSize ( const RealVect & a_domainSize )

inline

set domain size (in meters)

References m_domainSize.

Referenced by init_bisicles_instance(), and main().

◆ setHeader() [1/3]

void AmrIce::setHeader	(	const std::string &	a_key,
		const std::string &	a_val
	)

inline

Referenced by bisicles_set_header().

◆ setHeader() [2/3]

void AmrIce::setHeader	(	const std::string &	a_key,
		const int &	a_val
	)

inline

◆ setHeader() [3/3]

void AmrIce::setHeader	(	const std::string &	a_key,
		const Real &	a_val
	)

inline

◆ setIceFrac()

void AmrIce::setIceFrac	(	const LevelData< FArrayBox > &	a_thickness,
		int	a_level
	)

protected

initialize real-valued ice fraction

this is entirely based on ice thickness h, as opposed to the advective update

References m_iceFrac.

Referenced by initData(), readCheckpointFile(), surfaceHeatFlux(), and updateGeometry().

◆ setIceFracBC()

void AmrIce::setIceFracBC	(	LevelData< FArrayBox > &	a_iceFrac,
		const ProblemDomain &	a_domain
	)

protected

Referenced by surfaceHeatFlux().

◆ setInternalEnergyBC()

void AmrIce::setInternalEnergyBC ( IceInternalEnergyIBC * a_internalEnergyIBC )

set BC for internalEnergy advection

References m_internalEnergyIBCPtr, and IceInternalEnergyIBC::new_internalEnergyIBC().

Referenced by init_bisicles_instance(), main(), and setBasalFrictionRelation().

◆ setLayers()

void AmrIce::setLayers ( const Vector< Real > & a_sigma )

protected

References incrementIceThickness(), m_faceSigma, m_nLayers, and m_sigmaSet.

Referenced by getFaceSigma(), and initialize().

◆ setMuCoefficient() [1/2]

void AmrIce::setMuCoefficient ( const MuCoefficient * a_muCoefficientPtr )

inline

References m_muCoefficientPtr, and MuCoefficient::new_muCoefficient().

Referenced by init_bisicles_instance(), main(), solveVelocityField(), and surfaceHeatFlux().

◆ setMuCoefficient() [2/2]

void AmrIce::setMuCoefficient ( Vector< LevelData< FArrayBox > * > & a_cellMuCoef )

protectedvirtual

set mu coefficient (phi) prior to velocity solve

References m_amrDomains, m_amrGrids, m_dt, m_finest_level, m_muCoefficientPtr, m_refinement_ratios, m_vect_coordSys, MuCoefficient::setMuCoefficient(), and time().

◆ setRateFactor()

void AmrIce::setRateFactor ( RateFactor * a_rateFactorPtr )

inline

set rate factor

needs to be done before calling initialize

References RateFactor::getNewRateFactor(), and m_rateFactor.

Referenced by init_bisicles_instance(), and main().

◆ setStableSources()

void AmrIce::setStableSources	(	FArrayBox &	a_sts,
		FArrayBox &	a_bts,
		FArrayBox &	a_vts,
		const FArrayBox &	a_divuh,
		const BaseFab< int > &	a_mask,
		const Box &	a_box
	)		const

protected

modify the source terms (surface,basal,volume) to keep all or part of the ice sheet/shelf steady

References m_evolve_thickness, m_floating_ice_basal_flux_is_dhdt, m_floating_ice_basal_flux_is_min_dhdt, m_floating_ice_stable, m_grounded_ice_basal_flux_is_dhdt, and m_grounded_ice_stable.

Referenced by updateGeometry().

◆ setSurfaceFlux()

void AmrIce::setSurfaceFlux ( SurfaceFlux * a_surfaceFluxPtr )

inline

set surfact flux for ice sheet

References m_surfaceFluxPtr, and SurfaceFlux::new_surfaceFlux().

Referenced by init_bisicles_instance(), and main().

◆ setSurfaceHeatBoundaryData()

void AmrIce::setSurfaceHeatBoundaryData	(	SurfaceFlux *	a_surfaceHeatBoundaryDataPtr,
		bool	a_dirichlett,
		bool	a_temperature
	)

inline

set surface Heat flux for ice sheet

References m_surfaceBoundaryHeatDataDirichlett, m_surfaceBoundaryHeatDataTemperature, m_surfaceHeatBoundaryDataPtr, and SurfaceFlux::new_surfaceFlux().

Referenced by init_bisicles_instance(), and main().

◆ setThicknessBC()

void AmrIce::setThicknessBC ( IceThicknessIBC * a_thicknessIBC )

set BC for thickness advection

References m_thicknessIBCPtr, and IceThicknessIBC::new_thicknessIBC().

Referenced by init_bisicles_instance(), main(), and setBasalFrictionRelation().

◆ setTime()

void AmrIce::setTime ( Real a_time )

inline

References m_offsetTime, and m_time.

◆ setTopographyFlux()

void AmrIce::setTopographyFlux ( SurfaceFlux * a_topographyFluxPtr )

inline

set bedrock flux for ice sheet

References m_topographyFluxPtr, and SurfaceFlux::new_surfaceFlux().

Referenced by init_bisicles_instance(), and main().

◆ setToZero()

void AmrIce::setToZero ( Vector< LevelData< FArrayBox > *> & a_data )

protected

References finestLevel().

Referenced by computeH_half(), initData(), run(), and surfaceHeatFlux().

◆ setupFixedGrids()

void AmrIce::setupFixedGrids ( const std::string & a_gridFile )

protected

set up grids from grids file

References defineSolver(), dx(), initData(), levelSetup(), m_amrDomains, m_amrDx, m_amrGrids, m_block_factor, m_finest_level, m_max_base_grid_size, m_max_box_size, m_max_level, m_num_thickness_ghost, m_refinement_ratios, m_vect_coordSys, m_velocity, and s_verbosity.

Referenced by initialize(), and surfaceHeatFlux().

◆ solveVelocityField()

void AmrIce::solveVelocityField	(	bool	a_forceSolve = `false`,
		Real	a_convergenceMetric = `-1.0`
	)

protectedvirtual

solve for velocity field (or just set up some auxilliary quantities)

solve for velocity field

This is probably the most useful notification, as a velocity solve is carried out at the end of every major stage

References applyCalvingCriterion(), InverseIceVelocitySolver::basalFriction(), computeA(), computeFaceVelocity(), ConstMu, IceVelocitySolver::define(), defineSolver(), defineVelRHS(), dx(), eliminateRemoteIce(), Function, LevelSigmaCS::getFloatingMask(), JFNK, m_A, m_A_valid, m_addedIceThickness, m_amrDomains, m_amrDx, m_amrGrids, m_bA, m_basalFrictionPtr, m_basalFrictionRelation, m_bInternalEnergy, m_calvedIceThickness, m_cellMuCoef, m_constitutiveRelation, m_cur_step, m_diffusivity, m_doInitialVelGuess, m_doInitialVelSolve, m_eliminate_remote_ice, m_faceVelAdvection, m_faceVelTotal, m_finest_level, m_initialGuessConstMu, m_initialGuessConstVel, m_initialGuessSolverType, m_initialGuessType, m_internalEnergy, m_layerSFaceXYVel, m_layerXYFaceXYVel, m_muCoefficientPtr, m_plot_interval, m_plot_prefix, m_refinement_ratios, m_removedIceThickness, m_sA, m_sInternalEnergy, m_solverType, m_thicknessIBCPtr, m_tillWaterDepth, m_time, m_vect_coordSys, m_velBasalC, m_velocity, m_velocity_solve_interval, m_velocitySolveFinalResidualNorm, m_velocitySolveInitialResidualNorm, m_velRHS, m_velSolver, m_viscousTensor_valid, m_write_fluxVel, m_write_presolve_plotfiles, InverseIceVelocitySolver::muCoefficient(), Picard, AmrIce::Observer::PostCalving, CalvingModel::PostVelocitySolve, AmrIce::Observer::PostVelocitySolve, AmrIce::Observer::PreCalving, AmrIce::Observer::PreVelocitySolve, s_verbosity, setBasalFriction(), IceVelocitySolver::setMaxIterations(), setMuCoefficient(), IceVelocitySolver::setTolerance(), SlidingLaw, IceVelocitySolver::solve(), JFNKSolver::solve(), BasalFrictionRelation::updateThermodynamics(), updateViscousTensor(), IceThicknessIBC::velocityGhostBC(), and writePlotFile().

Referenced by initData(), readCheckpointFile(), regrid(), surfaceHeatFlux(), and timeStep().

◆ surfaceHeatBoundaryData()

SurfaceFlux& AmrIce::surfaceHeatBoundaryData ( ) const

inlinevirtual

Implements AmrIceBase.

References m_surfaceHeatBoundaryDataPtr.

Referenced by updateInternalEnergy().

◆ surfaceHeatBoundaryDirichlett()

bool AmrIce::surfaceHeatBoundaryDirichlett ( ) const

inlinevirtual

Implements AmrIceBase.

References m_surfaceBoundaryHeatDataDirichlett.

Referenced by updateInternalEnergy().

◆ surfaceHeatBoundaryTemperature()

bool AmrIce::surfaceHeatBoundaryTemperature ( ) const

inlinevirtual

Implements AmrIceBase.

References m_surfaceBoundaryHeatDataTemperature.

Referenced by updateInternalEnergy().

◆ surfaceHeatFlux()

const Vector<LevelData<FArrayBox>* >& AmrIce::surfaceHeatFlux ( ) const

inline

◆ surfaceInternalEnergy()

const Vector<LevelData<FArrayBox>* >& AmrIce::surfaceInternalEnergy ( ) const

inline

access function for surface temperature

References m_sInternalEnergy.

◆ surfaceThicknessSource()

const LevelData< FArrayBox > * AmrIce::surfaceThicknessSource ( int a_level ) const

References m_surfaceThicknessSource.

Referenced by groundingLineProximityScale(), and AMRDamage::timestep().

◆ tagCells()

void AmrIce::tagCells ( Vector< IntVectSet > & a_tags )

protected

compute tags for regridding

References m_finest_level, m_tag_cap, m_vectTagSubset, s_verbosity, and tagCellsLevel().

Referenced by regrid(), surfaceHeatFlux(), and tagCellsInit().

◆ tagCellsInit()

void AmrIce::tagCellsInit ( Vector< IntVectSet > & a_tags )

protected

compute tags at initial time

References m_vectTags, s_verbosity, and tagCells().

Referenced by initGrids(), and surfaceHeatFlux().

◆ tagCellsLevel()

void AmrIce::tagCellsLevel	(	IntVectSet &	a_tags,
		int	a_level
	)

protected

compute tags for the level a_level

References ConstitutiveRelation::computeStrainRateInvariant(), dx(), LevelSigmaCS::getFaceH(), LevelSigmaCS::getFloatingMask(), LevelSigmaCS::getH(), LevelSigmaCS::getTopography(), m_amrDomains, m_amrDx, m_amrGrids, m_constitutiveRelation, m_divHGradVel_tagVal, m_epsSqr_tagVal, m_groundingLineTaggingMaxBasalFrictionCoef, m_groundingLineTaggingMinVel, m_laplacian_tagging_max_basal_friction_coef, m_laplacian_tagging_val, m_margin_tagVal_finestLevel, m_refinement_ratios, m_tag_thin_cavity, m_tag_thin_cavity_thickness, m_tagAllIce, m_tagAllIceOnLevel0, m_tagEntireDomain, m_tagging_val, m_tagGroundingLine, m_tagMargin, m_tagOndivHgradVel, m_tagOnEpsSqr, m_tagOnGradVel, m_tagOnGroundedLapVel, m_tagOnLapVel, m_tagOnVelRHS, m_tagPython, m_tagPythonFunction, m_tags_grow, m_tags_grow_dir, m_tagVelDx, m_vect_coordSys, m_velBasalC, m_velDx_tagVal, m_velDx_tagVal_finestLevelFloating, m_velDx_tagVal_finestLevelGrounded, m_velocity, m_velRHS, m_velRHS_tagVal, PythonInterface::PythonEval(), and s_verbosity.

Referenced by surfaceHeatFlux(), and tagCells().

◆ time()

Real AmrIce::time ( ) const

inlinevirtual

read only access members implementing AMRIceBase

Implements AmrIceBase.

References m_offsetTime, and m_time.

Referenced by advectIceFrac(), ProximityCalvingModel::applyCriterion(), initialize(), readCheckpointFile(), DomainDiagnosticData::record(), restart(), setBasalFriction(), setMuCoefficient(), timeStep(), updateGroundingLineProximity(), updateInternalEnergy(), updateInvalidIceFrac(), and writeAMRPlotFile().

◆ timeStep()

void AmrIce::timeStep ( Real a_dt )

compute one timestep

References advectIceFrac(), DomainDiagnosticData::computeDischarge(), computeH_half(), computeInternalEnergyHalf(), computeThicknessFluxes(), dx(), DomainDiagnosticData::endTimestepDiagnostics(), finestTimestepLevel(), LevelSigmaCS::getFaceSigma(), LevelSigmaCS::getH(), LevelSigmaCS::getTopography(), LevelSigmaCS::gravity(), LevelSigmaCS::iceDensity(), m_addedIceThickness, m_amrDomains, m_amrDx, m_amrGrids, m_basalThicknessSource, m_calvedIceThickness, m_cur_step, m_divThicknessFlux, m_dt, m_evolve_ice_frac, m_evolve_velocity, m_faceVelAdvection, m_finest_level, m_iceFrac, m_isothermal, m_layerSFaceXYVel, m_layerXYFaceXYVel, m_next_report_time, m_num_cells, m_old_thickness, m_refinement_ratios, m_removedIceThickness, m_report_discharge, m_surfaceThicknessSource, m_temporalAccuracy, m_time, m_vect_coordSys, m_volumeThicknessSource, AmrIce::Observer::PostGeometryUpdate, s_verbosity, solveVelocityField(), time(), updateGeometry(), updateInternalEnergy(), and LevelSigmaCS::waterDensity().

Referenced by run(), and setCalvingModel().

◆ updateCoordSysWithNewThickness()

void AmrIce::updateCoordSysWithNewThickness ( const Vector< LevelData< FArrayBox > * > & a_thickness )

protected

References LevelSigmaCS::getH(), m_finest_level, m_refinement_ratios, m_vect_coordSys, and LevelSigmaCS::recomputeGeometry().

Referenced by surfaceHeatFlux().

◆ updateGeometry()

void AmrIce::updateGeometry	(	Vector< RefCountedPtr< LevelSigmaCS > > &	a_vect_coordSys_new,
		Vector< RefCountedPtr< LevelSigmaCS > > &	a_vectCoords_old,
		const Vector< LevelData< FluxBox > * > &	a_vectFluxes,
		Real	a_dt
	)

References applyCalvingCriterion(), LevelSigmaCS::dx(), dx(), finestTimestepLevel(), LevelSigmaCS::getFloatingMask(), LevelSigmaCS::getH(), LevelSigmaCS::getTopography(), IMPLICIT, implicitThicknessCorrection(), m_amrDomains, m_amrDx, m_amrGrids, m_basalThicknessSource, m_deltaTopography, m_diffusionTreatment, m_divThicknessFlux, m_dt, m_evolve_ice_frac, m_evolve_thickness, m_evolve_topography_fix_surface, m_finest_level, m_floating_ice_stable, m_frac_sources, m_grounded_ice_stable, m_groundingLineProximity_valid, m_iceFrac, m_refinement_ratios, m_surfaceThicknessSource, m_thicknessIBCPtr, m_time, m_topographyFluxPtr, m_vect_coordSys, m_volumeThicknessSource, CalvingModel::PostThicknessAdvection, LevelSigmaCS::recomputeGeometry(), IceThicknessIBC::setGeometryBCs(), setIceFrac(), setStableSources(), SurfaceFlux::surfaceThicknessFlux(), and updateIceFrac().

Referenced by setCalvingModel(), and timeStep().

◆ updateGroundingLineProximity()

void AmrIce::updateGroundingLineProximity ( ) const

protected

Solves the elliptic problem a * phi - b* grad^2 phi = 0; with natural boundary conditions.

for grounded ice, a = 10^5 and b = 1 for floating ice, s = 0 and b = 1

References dt(), dx(), finestTimestepLevel(), LevelSigmaCS::getFloatingMask(), grids(), m_amrDomains, m_amrDx, m_amrGrids, m_finest_level, m_groundingLineProximity, m_groundingLineProximity_valid, m_groundingLineProximityCalcType, m_groundingLineProximityScale, m_refinement_ratios, m_time, m_vect_coordSys, s_verbosity, and time().

Referenced by groundingLineProximity().

◆ updateIceFrac()

void AmrIce::updateIceFrac	(	LevelData< FArrayBox > &	a_thickness,
		int	a_level
	)

protected

update real-valued ice fraction after thickness update

this is different from setIceFrac in that it preserves fractional values, but still sets values to zero in cells with no ice. Thickness is non-const because it may set very small values of H (less than epsilon) to zero

References m_iceFrac.

Referenced by surfaceHeatFlux(), and updateGeometry().

◆ updateInternalEnergy()

void AmrIce::updateInternalEnergy	(	Vector< LevelData< FluxBox > * > &	a_layerTH_half,
		Vector< LevelData< FluxBox > * > &	a_layerH_half,
		const Vector< LevelData< FluxBox > * > &	a_layerXYFaceXYVel,
		const Vector< LevelData< FArrayBox > * > &	a_layerSFaceXYVel,
		const Real	a_dt,
		const Real	a_time,
		Vector< RefCountedPtr< LevelSigmaCS > > &	a_coordSysNew,
		Vector< RefCountedPtr< LevelSigmaCS > > &	a_coordSysOld,
		const Vector< LevelData< FArrayBox > *> &	a_surfaceThicknessSource,
		const Vector< LevelData< FArrayBox > *> &	a_basalThicknessSource,
		const Vector< LevelData< FArrayBox > *> &	a_volumeThicknessSource
	)

protected

Update the internalEnergy and tillWaterDepth fields.

compute (spatially variable) till water drainage rate

References basalHeatBoundaryData(), IceThermodynamics::composeInternalEnergy(), BasalFrictionRelation::computeDissipation(), ConstitutiveRelation::computeDissipation(), IceUtility::computeSigmaVelocity(), LevelSigmaCS::dx(), dx(), SurfaceFlux::evaluate(), LevelSigmaCS::getDSigma(), LevelSigmaCS::getFaceSigma(), LevelSigmaCS::getFloatingMask(), LevelSigmaCS::getH(), LevelSigmaCS::gravity(), helmholtzSolve(), IceThermodynamics::IceConductivity(), LevelSigmaCS::iceDensity(), IceThermodynamics::IceHeatCapacity(), m_A, m_A_valid, m_amrDomains, m_amrGrids, m_basalFrictionRelation, m_bHeatFlux, m_bInternalEnergy, m_constitutiveRelation, m_finest_level, m_internalEnergy, m_layerSFaceSVel, m_nLayers, m_refinement_ratios, m_sHeatFlux, m_sInternalEnergy, m_surfaceHeatBoundaryDataPtr, IceThermodynamics::m_till_water_drain_factor, m_tillWaterDepth, m_time, m_velBasalC, m_velocity, SurfaceFlux::parse(), column_thermodynamics::rhoi, column_thermodynamics::rhoo, surfaceHeatBoundaryData(), surfaceHeatBoundaryDirichlett(), surfaceHeatBoundaryTemperature(), surfaceHeatFlux(), time(), IceThermodynamics::timestep(), updateTemperature(), and LevelSigmaCS::waterDensity().

Referenced by surfaceHeatFlux(), and timeStep().

◆ updateInvalidIceFrac()

void AmrIce::updateInvalidIceFrac ( Vector< LevelData< FArrayBox > *> a_iceFrac )

protected

update covered cells, ghost cells etc, of a_iceFrac

Also increment a_thicknessSource based on the calving rate Also increment a_thicknessSource based on the calving rate

References dx(), m_amrDomains, m_amrDx, m_amrGrids, m_dt, m_finest_level, m_iceFrac, m_refinement_ratios, m_thicknessIBCPtr, IceThicknessIBC::setIceFractionBCs(), and time().

Referenced by surfaceHeatFlux().

◆ updateTemperature()

void AmrIce::updateTemperature ( )

protected

update the temperature (a derived field)

References IceThermodynamics::decomposeInternalEnergy(), m_amrGrids, m_bInternalEnergy, m_bTemperature, m_finest_level, m_internalEnergy, m_sInternalEnergy, m_sTemperature, m_temperature, and m_vect_coordSys.

Referenced by initData(), readCheckpointFile(), regrid(), surfaceHeatFlux(), and updateInternalEnergy().

◆ updateViscousTensor()

void AmrIce::updateViscousTensor ( ) const

protected

◆ velocity()

const LevelData<FArrayBox>* AmrIce::velocity ( int a_level ) const

inlinevirtual

Implements AmrIceBase.

References m_velocity.

Referenced by ProximityCalvingModel::applyCriterion(), CrevasseCalvingModel::computeStressMeasure(), and RateProportionalToSpeedCalvingModel::getCalvingRate().

◆ viscosityCoefficient()

const LevelData< FArrayBox > * AmrIce::viscosityCoefficient ( int a_level ) const

References m_viscosityCoefCell, and m_viscousTensor_valid.

Referenced by groundingLineProximityScale(), and writeAMRPlotFile().

◆ viscousTensor()

const LevelData< FArrayBox > * AmrIce::viscousTensor ( int a_level ) const

References m_viscousTensor_valid, and m_viscousTensorCell.

Referenced by CrevasseCalvingModel::computeStressMeasure(), groundingLineProximityScale(), AMRDamage::timestep(), and writeAMRPlotFile().

◆ writeAMRHierarchyHDF5() [1/2]

void AmrIce::writeAMRHierarchyHDF5	(	HDF5Handle &	a_handle,
		const Vector< DisjointBoxLayout > &	a_grids,
		const Vector< LevelData< FArrayBox > * > &	a_data,
		const Vector< string > &	a_name,
		const Box &	a_domain,
		const Real &	a_dx,
		const Real &	a_dt,
		const Real &	a_time,
		const Vector< int > &	a_ratio,
		const int &	a_numLevels
	)		const

Referenced by getHeader(), restart(), writeAMRHierarchyHDF5(), and writeAMRPlotFile().

◆ writeAMRHierarchyHDF5() [2/2]

void AmrIce::writeAMRHierarchyHDF5	(	const string &	filename,
		const Vector< DisjointBoxLayout > &	a_grids,
		const Vector< LevelData< FArrayBox > * > &	a_data,
		const Vector< string > &	a_name,
		const Box &	a_domain,
		const Real &	a_dx,
		const Real &	a_dt,
		const Real &	a_time,
		const Vector< int > &	a_ratio,
		const int &	a_numLevels
	)		const

virtual

Write an AMR hierarchy to an hdf5 file.

Specifying this as part of the interface permits AmrIceBase aware functions to have e.g AmrIce modify their writes to include standard metadata

Parameters

filename	name of hdf5 file
a_grids	mesh hierarchy
a_data	data hierarchy, defined on a_grids
a_name	component names
a_domain	domain limits on coarse level
a_dx	mesh spacing on coarse level
a_dt	time step on coarsest level
a_time	time
a_ratio	refinement ratio : $\Delta x_{i} = r_i \Delta x_{i+1}$
a_numLevels	number of levels to write

Implements AmrIceBase.

References writeAMRHierarchyHDF5().

◆ writeAMRPlotFile()

void AmrIce::writeAMRPlotFile ( )

write hdf5 plotfile to the standard location

References defineVelRHS(), dragCoefficient(), LevelSigmaCS::getBackgroundSlope(), LevelSigmaCS::getFloatingMask(), LevelSigmaCS::getH(), LevelSigmaCS::getSurfaceHeight(), LevelSigmaCS::getTopography(), m_amrDomains, m_amrDx, m_amrGrids, m_basalFluxPtr, m_basalThicknessSource, m_bHeatFlux, m_bInternalEnergy, m_bTemperature, m_calvedIceThickness, m_cellMuCoef, m_divThicknessFlux, m_dt, m_faceVelTotal, m_finest_level, m_frac_sources, m_iceFrac, m_internalEnergy, m_layerSFaceSVel, m_layerSFaceXYVel, m_nLayers, m_old_thickness, m_plot_prefix, m_reduced_plot, m_refinement_ratios, m_sHeatFlux, m_sInternalEnergy, m_sTemperature, m_surfaceFluxPtr, m_surfaceThicknessSource, m_tillWaterDepth, m_time, m_vect_coordSys, m_velBasalC, m_velocity, m_velRHS, m_write_baseVel, m_write_dHDt, m_write_fluxVel, m_write_internal_energy, m_write_ismip6, m_write_layer_velocities, m_write_map_file, m_write_mask, m_write_muCoeff, m_write_solver_rhs, m_write_thickness_sources, m_write_viscousTensor, s_verbosity, setBasalFriction(), SurfaceFlux::surfaceThicknessFlux(), time(), viscosityCoefficient(), viscousTensor(), writeAMRHierarchyHDF5(), and WriteSigmaMappedAMRHierarchyHDF5().

Referenced by getHeader(), and writePlotFile().

◆ writeCheckpointFile() [1/2]

void AmrIce::writeCheckpointFile ( )

write checkpoint file out for later restarting

writes checkpoint data to the standard location; filename is <check_root>.<step>.<DIM>d.hdf5

References m_check_overwrite, m_check_prefix, and s_verbosity.

Referenced by bisicles_write_checkpoint(), getHeader(), and run().

◆ writeCheckpointFile() [2/2]

void AmrIce::writeCheckpointFile ( const string & a_file )

write checkpoint file out for later restarting

writes checkpoint data to the location specified by a_file

References getFaceSigma(), LevelSigmaCS::getH(), LevelSigmaCS::getTopography(), m_amrDomains, m_amrDx, m_amrGrids, m_bInternalEnergy, m_cellMuCoef, m_cfl, m_cur_step, m_deltaTopography, m_dt, m_finest_level, m_iceFrac, m_internalEnergy, m_max_level, m_refinement_ratios, m_sInternalEnergy, m_tillWaterDepth, m_time, m_vect_coordSys, m_velBasalC, m_velocity, and s_verbosity.

◆ writePlotFile()

void AmrIce::writePlotFile ( )

write hdf5 plotfile to the standard location

writes plotfile to the standard location; filename is <plot_root>.<step>.<DIM>d.hdf5

References m_cur_step, and writeAMRPlotFile().

Referenced by bisicles_write_plot(), computeDt(), getHeader(), initData(), run(), and solveVelocityField().

Friends And Related Function Documentation

◆ DomainDiagnosticData

friend class DomainDiagnosticData

friend

Member Data Documentation

◆ m_A

Vector<LevelData<FArrayBox>* > AmrIce::m_A

protected

Referenced by computeFaceVelocity(), solveVelocityField(), updateInternalEnergy(), updateViscousTensor(), and ~AmrIce().

◆ m_A_valid

bool AmrIce::m_A_valid

mutableprotected

Referenced by initData(), initGrids(), regrid(), setDefaults(), solveVelocityField(), and updateInternalEnergy().

◆ m_addedIceThickness

Vector<LevelData<FArrayBox>* > AmrIce::m_addedIceThickness

protected

Referenced by addedIceThickness(), applyCalvingCriterion(), eliminateRemoteIce(), initialize(), levelSetup(), readCheckpointFile(), regrid(), run(), solveVelocityField(), timeStep(), and ~AmrIce().

◆ m_additionalDiffusivity

Real AmrIce::m_additionalDiffusivity

protected

Referenced by implicitThicknessCorrection(), initialize(), and setDefaults().

◆ m_additionalVelocity

bool AmrIce::m_additionalVelocity

protected

Referenced by computeFaceVelocity(), initialize(), and setDefaults().

◆ m_amrDomains

Vector<ProblemDomain> AmrIce::m_amrDomains

protected

◆ m_amrDx

Vector<Real> AmrIce::m_amrDx

protected

◆ m_amrGrids

Vector<DisjointBoxLayout> AmrIce::m_amrGrids

protected

◆ m_bA

Vector<LevelData<FArrayBox>* > AmrIce::m_bA

protected

Referenced by computeFaceVelocity(), solveVelocityField(), and ~AmrIce().

◆ m_basalFluxPtr

SurfaceFlux* AmrIce::m_basalFluxPtr

protected

sets basal flux for ice sheet

Referenced by computeH_half(), setBasalFlux(), setDefaults(), writeAMRPlotFile(), and ~AmrIce().

◆ m_basalFrictionPtr

BasalFriction* AmrIce::m_basalFrictionPtr

protected

sets basal friction coefficient (beta^2)

Referenced by readCheckpointFile(), setBasalFriction(), solveVelocityField(), and ~AmrIce().

◆ m_basalFrictionRelation

BasalFrictionRelation* AmrIce::m_basalFrictionRelation

protected

basal Friction relation

Referenced by defineSolver(), setBasalFrictionRelation(), solveVelocityField(), updateInternalEnergy(), updateViscousTensor(), and ~AmrIce().

◆ m_basalHeatBoundaryDataPtr

SurfaceFlux* AmrIce::m_basalHeatBoundaryDataPtr

protected

sets basal heat flux or temperature for ice sheet

Referenced by basalHeatBoundaryData(), setBasalHeatBoundaryData(), and ~AmrIce().

◆ m_basalLengthScale

Real AmrIce::m_basalLengthScale

protected

Referenced by initialize(), and setDefaults().

◆ m_basalRateFactor

RateFactor* AmrIce::m_basalRateFactor

protected

rate factor at base

Referenced by setBasalFriction(), setBasalRateFactor(), and ~AmrIce().

◆ m_basalSlope

RealVect AmrIce::m_basalSlope

protected

background slope of bottom topography

for various reasons (mostly having to do with periodicity) it's simpler to just keep this as a parameter here in AmrIce, where it's added to the grad(z_surf) when it comes time to compute the RHS for the velocity solve, rather than include it in the sigmaCS definition.

The way this is implemented, the basal height at a realVect location X is defined as

z_b = sigmaCS.getTopography() +basalSlope[0]*X[0] +basalSlope[1]*X[1]

Referenced by initialize(), and setDefaults().

◆ m_basalThicknessSource

Vector<LevelData<FArrayBox>* > AmrIce::m_basalThicknessSource

mutableprotected

Referenced by basalThicknessSource(), computeH_half(), initialize(), levelSetup(), readCheckpointFile(), regrid(), restart(), timeStep(), updateGeometry(), writeAMRPlotFile(), and ~AmrIce().

◆ m_beta_type

int AmrIce::m_beta_type

protected

type of basal friction distribution

◆ m_betaEps

Real AmrIce::m_betaEps

protected

small parameter for use in computing beta, if needed

Referenced by setDefaults().

◆ m_betaVal

Real AmrIce::m_betaVal

protected

background value for beta

Referenced by setDefaults().

◆ m_bHeatFlux

Vector<LevelData<FArrayBox>* > AmrIce::m_bHeatFlux

protected

Referenced by initialize(), levelSetup(), readCheckpointFile(), regrid(), updateInternalEnergy(), writeAMRPlotFile(), and ~AmrIce().

◆ m_bInternalEnergy

Vector<LevelData<FArrayBox>* > AmrIce::m_bInternalEnergy

protected

Referenced by initData(), initialize(), levelSetup(), readCheckpointFile(), regrid(), setBasalFriction(), solveVelocityField(), updateInternalEnergy(), updateTemperature(), writeAMRPlotFile(), writeCheckpointFile(), and ~AmrIce().

◆ m_block_factor

int AmrIce::m_block_factor

protected

blocking factor

Referenced by initGrids(), initialize(), regrid(), setDefaults(), and setupFixedGrids().

◆ m_bTemperature

Vector<LevelData<FArrayBox>* > AmrIce::m_bTemperature

protected

Referenced by restart(), updateTemperature(), writeAMRPlotFile(), and ~AmrIce().

◆ m_calvedIceThickness

Vector<LevelData<FArrayBox>* > AmrIce::m_calvedIceThickness

protected

Referenced by applyCalvingCriterion(), calvedIceThickness(), eliminateRemoteIce(), initialize(), levelSetup(), readCheckpointFile(), regrid(), restart(), run(), solveVelocityField(), timeStep(), writeAMRPlotFile(), and ~AmrIce().

◆ m_calvedThicknessSource

Vector<LevelData<FArrayBox>* > AmrIce::m_calvedThicknessSource

protected

◆ m_calvingModelPtr

CalvingModel* AmrIce::m_calvingModelPtr

protected

Calving model.

Referenced by applyCalvingCriterion(), setCalvingModel(), and ~AmrIce().

◆ m_cellMuCoef

Vector<LevelData<FArrayBox>* > AmrIce::m_cellMuCoef

protected

Referenced by initialize(), levelSetup(), muCoef(), readCheckpointFile(), regrid(), solveVelocityField(), writeAMRPlotFile(), writeCheckpointFile(), and ~AmrIce().

◆ m_cfl

Real AmrIce::m_cfl

protected

timestep scaling

Referenced by advectIceFrac(), computeDt(), initialize(), readCheckpointFile(), setDefaults(), and writeCheckpointFile().

◆ m_check_exit

bool AmrIce::m_check_exit

protected

Referenced by run().

◆ m_check_interval

int AmrIce::m_check_interval

protected

Referenced by run().

◆ m_check_overwrite

bool AmrIce::m_check_overwrite

protected

Referenced by writeCheckpointFile().

◆ m_check_prefix

string AmrIce::m_check_prefix

protected

Referenced by writeCheckpointFile().

◆ m_constitutiveRelation

ConstitutiveRelation* AmrIce::m_constitutiveRelation

protected

constitutive relation

Referenced by computeFaceVelocity(), defineSolver(), setConstitutiveRelation(), solveVelocityField(), tagCellsLevel(), updateInternalEnergy(), updateViscousTensor(), and ~AmrIce().

◆ m_covered_level

Vector<int> AmrIce::m_covered_level

protected

keeps track of which levels are completely covered

Referenced by initialize(), and regrid().

◆ m_cur_step

int AmrIce::m_cur_step

protected

Referenced by advectIceFrac(), computeDt(), initialize(), readCheckpointFile(), run(), solveVelocityField(), timeStep(), writeCheckpointFile(), and writePlotFile().

◆ m_deltaTopography

Vector<LevelData<FArrayBox>*> AmrIce::m_deltaTopography

protected

stores the accumulated bedrock difference. This is needed because when m_interpolate_zb == false, the regrid() function re-reads the bedrock, which in many cases is a DEM (e.g, bedmap2), so that the evolution of topography would be obliterated

Referenced by initData(), initialize(), levelSetup(), readCheckpointFile(), regrid(), updateGeometry(), writeCheckpointFile(), and ~AmrIce().

◆ m_diffusionTreatment

DiffusionTreatment AmrIce::m_diffusionTreatment

protected

Referenced by computeDt(), computeFaceVelocity(), computeH_half(), initialize(), setDefaults(), and updateGeometry().

◆ m_diffusivity

Vector<LevelData<FluxBox>* > AmrIce::m_diffusivity

protected

Referenced by computeH_half(), implicitThicknessCorrection(), initialize(), levelSetup(), readCheckpointFile(), regrid(), solveVelocityField(), and ~AmrIce().

◆ m_divHGradVel_tagVal

Real AmrIce::m_divHGradVel_tagVal

protected

tagging threshold value for undivided div(H grad(vel))

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_divThicknessFlux

Vector<LevelData<FArrayBox>* > AmrIce::m_divThicknessFlux

protected

Referenced by initialize(), levelSetup(), readCheckpointFile(), regrid(), timeStep(), updateGeometry(), writeAMRPlotFile(), and ~AmrIce().

◆ m_do_restart

bool AmrIce::m_do_restart

protected

Referenced by initialize(), run(), and setDefaults().

◆ m_doInitialVelGuess

bool AmrIce::m_doInitialVelGuess

protected

if true, use nonzero initial guess for velocity field (default is false)

if true, make semi-informed initial guess for first pass through ice velocity solver

Referenced by initialize(), readCheckpointFile(), setDefaults(), and solveVelocityField().

◆ m_doInitialVelSolve

bool AmrIce::m_doInitialVelSolve

protected

if false, don't do initial velocity solve during problem setup. (default is true)

Referenced by initialize(), readCheckpointFile(), setDefaults(), and solveVelocityField().

◆ m_domainSize

RealVect AmrIce::m_domainSize

protected

Referenced by initData(), initialize(), regrid(), setDefaults(), and setDomainSize().

◆ m_dragCoef

Vector<LevelData<FArrayBox>* > AmrIce::m_dragCoef

mutableprotected

Referenced by dragCoefficient(), updateViscousTensor(), and ~AmrIce().

◆ m_dt

Real AmrIce::m_dt

protected

most recent timestep

Referenced by advectIceFrac(), defineVelRHS(), dt(), incrementIceThickness(), readCheckpointFile(), regrid(), restart(), setBasalFriction(), setDefaults(), setMuCoefficient(), timeStep(), updateGeometry(), updateInvalidIceFrac(), writeAMRPlotFile(), and writeCheckpointFile().

◆ m_eliminate_remote_ice

bool AmrIce::m_eliminate_remote_ice

protected

Referenced by applyCalvingCriterion(), initData(), initialize(), regrid(), setDefaults(), and solveVelocityField().

◆ m_eliminate_remote_ice_after_regrid

bool AmrIce::m_eliminate_remote_ice_after_regrid

protected

Referenced by initData(), initialize(), regrid(), and setDefaults().

◆ m_eliminate_remote_ice_max_iter

int AmrIce::m_eliminate_remote_ice_max_iter

protected

Referenced by eliminateRemoteIce(), initialize(), and setDefaults().

◆ m_eliminate_remote_ice_tol

Real AmrIce::m_eliminate_remote_ice_tol

protected

Referenced by eliminateRemoteIce(), initialize(), and setDefaults().

◆ m_epsSqr_tagVal

Real AmrIce::m_epsSqr_tagVal

protected

tagging value for strain rate invariant

tag if epsSqr*dx > than this value

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_evolve_ice_frac

bool AmrIce::m_evolve_ice_frac

protected

Referenced by initialize(), setDefaults(), timeStep(), and updateGeometry().

◆ m_evolve_thickness

bool AmrIce::m_evolve_thickness

protected

Referenced by initialize(), setDefaults(), setStableSources(), and updateGeometry().

◆ m_evolve_topography_fix_surface

bool AmrIce::m_evolve_topography_fix_surface

protected

Referenced by initialize(), setDefaults(), and updateGeometry().

◆ m_evolve_velocity

bool AmrIce::m_evolve_velocity

protected

Referenced by initialize(), regrid(), setDefaults(), and timeStep().

◆ m_faceSigma

Vector<Real> AmrIce::m_faceSigma

protected

Referenced by getFaceSigma(), readCheckpointFile(), and setLayers().

◆ m_faceVelAdvection

Vector<LevelData<FluxBox>* > AmrIce::m_faceVelAdvection

protected

Referenced by computeDt(), computeH_half(), initialize(), levelSetup(), readCheckpointFile(), regrid(), solveVelocityField(), timeStep(), and ~AmrIce().

◆ m_faceVelTotal

Vector<LevelData<FluxBox>* > AmrIce::m_faceVelTotal

protected

Referenced by faceVelocities(), initialize(), levelSetup(), readCheckpointFile(), regrid(), solveVelocityField(), writeAMRPlotFile(), and ~AmrIce().

◆ m_fill_ratio

Real AmrIce::m_fill_ratio

protected

grid efficiency

Referenced by initGrids(), initialize(), regrid(), and setDefaults().

◆ m_finest_level

int AmrIce::m_finest_level

protected

◆ m_finest_timestep_level

int AmrIce::m_finest_timestep_level

protected

if 0 < m_finest_timestep_level < m_finest_level and >= 0, timestep only levels 0 to m_finest_timestep_level, and interpolate any levels above that. The idea is to avoid being hammered too hard by diminishing stability limits on dt

Referenced by initialize(), and setDefaults().

◆ m_fixed_dt

Real AmrIce::m_fixed_dt

protected

Referenced by computeDt(), initialize(), and setDefaults().

◆ m_floating_ice_basal_flux_is_dhdt

bool AmrIce::m_floating_ice_basal_flux_is_dhdt

protected

Referenced by initialize(), setDefaults(), and setStableSources().

◆ m_floating_ice_basal_flux_is_min_dhdt

bool AmrIce::m_floating_ice_basal_flux_is_min_dhdt

protected

Referenced by initialize(), setDefaults(), and setStableSources().

◆ m_floating_ice_stable

bool AmrIce::m_floating_ice_stable

protected

Referenced by initialize(), setDefaults(), setStableSources(), and updateGeometry().

◆ m_frac_sources

bool AmrIce::m_frac_sources

protected

if true, scale thickness sources (surface flux and basal flux) by iceFrac values (allows for effective partial cells)

Referenced by initialize(), setDefaults(), updateGeometry(), and writeAMRPlotFile().

◆ m_gravity

Real AmrIce::m_gravity

protected

Referenced by initialize(), levelSetup(), readCheckpointFile(), and setDefaults().

◆ m_grounded_ice_basal_flux_is_dhdt

bool AmrIce::m_grounded_ice_basal_flux_is_dhdt

protected

Referenced by initialize(), setDefaults(), and setStableSources().

◆ m_grounded_ice_stable

bool AmrIce::m_grounded_ice_stable

protected

Referenced by initialize(), setDefaults(), setStableSources(), and updateGeometry().

◆ m_groundingLineProximity

Vector<LevelData<FArrayBox>* > AmrIce::m_groundingLineProximity

mutableprotected

Referenced by groundingLineProximity(), updateGroundingLineProximity(), and ~AmrIce().

◆ m_groundingLineProximity_valid

bool AmrIce::m_groundingLineProximity_valid

mutableprotected

Referenced by initData(), initGrids(), regrid(), setDefaults(), updateGeometry(), and updateGroundingLineProximity().

◆ m_groundingLineProximityCalcType

int AmrIce::m_groundingLineProximityCalcType

protected

Referenced by initialize(), setDefaults(), and updateGroundingLineProximity().

◆ m_groundingLineProximityScale

Real AmrIce::m_groundingLineProximityScale

protected

Referenced by groundingLineProximityScale(), initialize(), setDefaults(), and updateGroundingLineProximity().

◆ m_groundingLineTaggingMaxBasalFrictionCoef

Real AmrIce::m_groundingLineTaggingMaxBasalFrictionCoef

protected

threshold Basal friction coefficient at the grounding line : tag if C < value

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_groundingLineTaggingMinVel

Real AmrIce::m_groundingLineTaggingMinVel

protected

threshold velocity at the grounding line : tag if |u| > value

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_iceDensity

Real AmrIce::m_iceDensity

protected

Referenced by initialize(), levelSetup(), readCheckpointFile(), DomainDiagnosticData::record(), and setDefaults().

◆ m_iceFrac

Vector<LevelData<FArrayBox>* > AmrIce::m_iceFrac

protected

real-valued ice fraction real-valued ice fraction on level a_level (0 = no ice, 1 = full of ice, 0<phi<1 – partially filled (useful for calving model and for communication with POP

Referenced by amrIceFrac(), applyCalvingCriterion(), computeH_half(), iceFrac(), initialize(), levelSetup(), readCheckpointFile(), regrid(), setIceFrac(), timeStep(), updateGeometry(), updateIceFrac(), updateInvalidIceFrac(), writeAMRPlotFile(), writeCheckpointFile(), and ~AmrIce().

◆ m_initial_cfl

Real AmrIce::m_initial_cfl

protected

cfl number for initial timestep (useful if initial data needs small cfl)

Referenced by computeDt(), and initialize().

◆ m_initialGuessConstMu

Real AmrIce::m_initialGuessConstMu

protected

Referenced by initialize(), setDefaults(), and solveVelocityField().

◆ m_initialGuessConstVel

RealVect AmrIce::m_initialGuessConstVel

protected

Referenced by initialize(), setDefaults(), and solveVelocityField().

◆ m_initialGuessSolverType

int AmrIce::m_initialGuessSolverType

protected

Referenced by initialize(), setDefaults(), and solveVelocityField().

◆ m_initialGuessType

int AmrIce::m_initialGuessType

protected

Referenced by initialize(), setDefaults(), and solveVelocityField().

◆ m_internalEnergy

Vector<LevelData<FArrayBox>* > AmrIce::m_internalEnergy

protected

Referenced by computeInternalEnergyHalf(), initData(), initialize(), levelSetup(), readCheckpointFile(), regrid(), solveVelocityField(), updateInternalEnergy(), updateTemperature(), writeAMRPlotFile(), writeCheckpointFile(), and ~AmrIce().

◆ m_internalEnergyIBCPtr

IceInternalEnergyIBC* AmrIce::m_internalEnergyIBCPtr

protected

IBC for internalEnergy advection.

Referenced by computeInternalEnergyHalf(), initData(), regrid(), setInternalEnergyBC(), and ~AmrIce().

◆ m_interpolate_zb

bool AmrIce::m_interpolate_zb

protected

if true, interpolate things like base topography at regrid time

if false, use IceThicknesIBC::regridIceGeometry function to set values

Referenced by initialize(), regrid(), and setDefaults().

◆ m_is_defined

bool AmrIce::m_is_defined

protected

is this object initialized?

Referenced by isDefined(), and setDefaults().

◆ m_isothermal

bool AmrIce::m_isothermal

protected

Referenced by initialize(), setDefaults(), and timeStep().

◆ m_laplacian_tagging_max_basal_friction_coef

Real AmrIce::m_laplacian_tagging_max_basal_friction_coef

protected

when tagging on undivided lap(vel), ignore cells where the basal friction coeffcient exceeds

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_laplacian_tagging_val

Real AmrIce::m_laplacian_tagging_val

protected

tagging threshold value for undivided lap(vel)

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_layerSFaceSVel

Vector<LevelData<FArrayBox>* > AmrIce::m_layerSFaceSVel

protected

Referenced by initialize(), levelSetup(), readCheckpointFile(), regrid(), updateInternalEnergy(), writeAMRPlotFile(), and ~AmrIce().

◆ m_layerSFaceXYVel

Vector<LevelData<FArrayBox>* > AmrIce::m_layerSFaceXYVel

protected

Referenced by initialize(), levelSetup(), readCheckpointFile(), regrid(), restart(), solveVelocityField(), timeStep(), writeAMRPlotFile(), and ~AmrIce().

◆ m_layerXYFaceXYVel

Vector<LevelData<FluxBox>* > AmrIce::m_layerXYFaceXYVel

protected

Referenced by faceVelocitiesLayered(), initialize(), levelSetup(), readCheckpointFile(), regrid(), solveVelocityField(), timeStep(), and ~AmrIce().

◆ m_margin_tagVal_finestLevel

int AmrIce::m_margin_tagVal_finestLevel

protected

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_max_base_grid_size

int AmrIce::m_max_base_grid_size

protected

max box size for level 0 (defaults to max_box_size)

this allows a different max box size for the level 0 domain, which can be useful since the number of boxes on level 0 is often driven by load balancing concerns, while max_box_size on other levels is generally driven by issues of cache size, etc)

Referenced by initGrids(), initialize(), setDefaults(), and setupFixedGrids().

◆ m_max_box_size

int AmrIce::m_max_box_size

protected

max box size

Referenced by advectIceFrac(), initGrids(), initialize(), regrid(), setDefaults(), and setupFixedGrids().

◆ m_max_dt_grow

Real AmrIce::m_max_dt_grow

protected

maximum amount cfl number may grow in one timestep

Referenced by computeDt(), initialize(), and setDefaults().

◆ m_max_level

int AmrIce::m_max_level

protected

max number ofSflux levels

Referenced by initGrids(), initialize(), levelSetup(), readCheckpointFile(), regrid(), setDefaults(), setupFixedGrids(), and writeCheckpointFile().

◆ m_maxSolverIterations

int AmrIce::m_maxSolverIterations

protected

max number of iterations for velocity solver

Referenced by defineSolver(), initialize(), and setDefaults().

◆ m_muCoefficientPtr

MuCoefficient* AmrIce::m_muCoefficientPtr

protected

sets mu coefficient (phi)

Referenced by readCheckpointFile(), setMuCoefficient(), solveVelocityField(), and ~AmrIce().

◆ m_n_regrids

int AmrIce::m_n_regrids

protected

Referenced by initialize(), and regrid().

◆ m_nesting_radius

int AmrIce::m_nesting_radius

protected

proper nesting radius

Referenced by initGrids(), initialize(), regrid(), and setDefaults().

◆ m_next_report_time

Real AmrIce::m_next_report_time

protected

Referenced by run(), and timeStep().

◆ m_nLayers

unsigned int AmrIce::m_nLayers

protected

Referenced by computeA(), computeInternalEnergyHalf(), levelSetup(), readCheckpointFile(), regrid(), restart(), setLayers(), updateInternalEnergy(), and writeAMRPlotFile().

◆ m_num_cells

Vector<int> AmrIce::m_num_cells

protected

book-keeping; keeps track of number of cells per level

Referenced by initialize(), regrid(), and timeStep().

◆ m_num_thickness_ghost

int AmrIce::m_num_thickness_ghost

protected

number of ghost cells we need for m_old_thickness

this is dependent on the advection scheme we're using AMRGodunov-based – 4 RK4 – 1

Referenced by initialize(), levelSetup(), readCheckpointFile(), setDefaults(), and setupFixedGrids().

◆ m_offsetTime

Real AmrIce::m_offsetTime

protected

Referenced by initialize(), setDefaults(), setTime(), and time().

◆ m_old_thickness

Vector<LevelData<FArrayBox>*> AmrIce::m_old_thickness

protected

current old-time data

Referenced by computeH_half(), computeInternalEnergyHalf(), initData(), initialize(), levelSetup(), readCheckpointFile(), regrid(), restart(), timeStep(), writeAMRPlotFile(), and ~AmrIce().

◆ m_plot_interval

int AmrIce::m_plot_interval

protected

Referenced by initData(), run(), and solveVelocityField().

◆ m_plot_prefix

string AmrIce::m_plot_prefix

protected

Referenced by computeDt(), restart(), solveVelocityField(), and writeAMRPlotFile().

◆ m_plot_time_interval

Real AmrIce::m_plot_time_interval

protected

write a plot file every m_plot_time_interval years (rather than steps)

Referenced by run().

◆ m_rateFactor

RateFactor* AmrIce::m_rateFactor

protected

rate factor

Referenced by computeA(), setRateFactor(), and ~AmrIce().

◆ m_reduced_plot

bool AmrIce::m_reduced_plot

protected

if true, reduce the number of fields written to plot files

Referenced by writeAMRPlotFile().

◆ m_refinement_ratios

Vector<int> AmrIce::m_refinement_ratios

protected

◆ m_regrid_interval

int AmrIce::m_regrid_interval

protected

regrid interval

Referenced by initialize(), and run().

◆ m_regrid_thickness_interpolation_method

int AmrIce::m_regrid_thickness_interpolation_method

protected

thickness interpolation method to use on regrid, see LevelSigmaCS::ThicknessInterpolationMethod

Referenced by initialize(), regrid(), and setDefaults().

◆ m_removedIceThickness

Vector<LevelData<FArrayBox>* > AmrIce::m_removedIceThickness

protected

Referenced by applyCalvingCriterion(), eliminateRemoteIce(), initialize(), levelSetup(), readCheckpointFile(), regrid(), removedIceThickness(), run(), solveVelocityField(), timeStep(), and ~AmrIce().

◆ m_report_discharge

bool AmrIce::m_report_discharge

protected

if true, report discharge of solid ice from the ice edge

Referenced by initialize(), setDefaults(), and timeStep().

◆ m_report_time_interval

Real AmrIce::m_report_time_interval

protected

report diagnostic every m_report_time_interval years (rather than every time step)

Referenced by initialize(), run(), and setDefaults().

◆ m_reportGroundedIce

bool AmrIce::m_reportGroundedIce

protected

◆ m_reset_floating_friction_to_zero

bool AmrIce::m_reset_floating_friction_to_zero

protected

if false, don't reset basal friction for floating ice to zero (default is true)

This option exists primarly so that we can run the CISM circular shelf test problem

Referenced by initialize(), setBasalFriction(), and setDefaults().

◆ m_restart_step

int AmrIce::m_restart_step

protected

if starting from a restart, timestep of restart

Referenced by readCheckpointFile(), run(), and setDefaults().

◆ m_sA

Vector<LevelData<FArrayBox>* > AmrIce::m_sA

protected

Referenced by computeFaceVelocity(), solveVelocityField(), and ~AmrIce().

◆ m_seaWaterDensity

Real AmrIce::m_seaWaterDensity

protected

Referenced by initialize(), levelSetup(), readCheckpointFile(), and setDefaults().

◆ m_seconds_per_unit_time

Real AmrIce::m_seconds_per_unit_time

protected

Referenced by initialize(), readCheckpointFile(), and setDefaults().

◆ m_sHeatFlux

Vector<LevelData<FArrayBox>* > AmrIce::m_sHeatFlux

protected

Referenced by initialize(), levelSetup(), readCheckpointFile(), regrid(), surfaceHeatFlux(), updateInternalEnergy(), writeAMRPlotFile(), and ~AmrIce().

◆ m_sigmaSet

bool AmrIce::m_sigmaSet

protected

Referenced by setDefaults(), and setLayers().

◆ m_sInternalEnergy

Vector<LevelData<FArrayBox>* > AmrIce::m_sInternalEnergy

protected

Referenced by initData(), initialize(), levelSetup(), readCheckpointFile(), regrid(), solveVelocityField(), surfaceInternalEnergy(), updateInternalEnergy(), updateTemperature(), writeAMRPlotFile(), writeCheckpointFile(), and ~AmrIce().

◆ m_solverType

int AmrIce::m_solverType

protected

what type of nonlinear solver to use for velocity field

Referenced by defineSolver(), initialize(), setDefaults(), and solveVelocityField().

◆ m_stable_dt

Real AmrIce::m_stable_dt

protected

most recent stable timestep (> m_dt if we took a step just to hit a plot interval)

Referenced by computeDt(), and setDefaults().

◆ m_sTemperature

Vector<LevelData<FArrayBox>* > AmrIce::m_sTemperature

protected

Referenced by restart(), updateTemperature(), writeAMRPlotFile(), and ~AmrIce().

◆ m_surfaceBoundaryHeatDataDirichlett

bool AmrIce::m_surfaceBoundaryHeatDataDirichlett

protected

should a Dirichlett internal energy condition be imposed at the upper surface?

Referenced by setDefaults(), setSurfaceHeatBoundaryData(), and surfaceHeatBoundaryDirichlett().

◆ m_surfaceBoundaryHeatDataTemperature

bool AmrIce::m_surfaceBoundaryHeatDataTemperature

protected

is the Dirichlett data a temperature (rather than an internal energy)?

Referenced by setDefaults(), setSurfaceHeatBoundaryData(), and surfaceHeatBoundaryTemperature().

◆ m_surfaceFluxPtr

SurfaceFlux* AmrIce::m_surfaceFluxPtr

protected

sets surface flux for ice sheet

Referenced by computeH_half(), setSurfaceFlux(), writeAMRPlotFile(), and ~AmrIce().

◆ m_surfaceHeatBoundaryDataPtr

SurfaceFlux* AmrIce::m_surfaceHeatBoundaryDataPtr

protected

sets surface heat flux or internalEnergy for ice sheet

Referenced by setSurfaceHeatBoundaryData(), surfaceHeatBoundaryData(), updateInternalEnergy(), and ~AmrIce().

◆ m_surfaceThicknessSource

Vector<LevelData<FArrayBox>* > AmrIce::m_surfaceThicknessSource

mutableprotected

Referenced by computeH_half(), initialize(), levelSetup(), readCheckpointFile(), regrid(), restart(), surfaceThicknessSource(), timeStep(), updateGeometry(), writeAMRPlotFile(), and ~AmrIce().

◆ m_tag_cap

int AmrIce::m_tag_cap

protected

maximum level at which refinement tags are computed

Referenced by initGrids(), initialize(), setDefaults(), and tagCells().

◆ m_tag_subset

IntVectSet AmrIce::m_tag_subset

protected

only allow tagging within a subset of the coarse domain

◆ m_tag_thin_cavity

bool AmrIce::m_tag_thin_cavity

protected

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tag_thin_cavity_thickness

Real AmrIce::m_tag_thin_cavity_thickness

protected

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagAllIce

bool AmrIce::m_tagAllIce

protected

tag any cell with ice in it

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagAllIceOnLevel0

bool AmrIce::m_tagAllIceOnLevel0

protected

tag any cell with ice in it on level 0

(useful when running a case like Antarctica or Greenland where the useful domain is subset of the computational domain)

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagEntireDomain

bool AmrIce::m_tagEntireDomain

protected

tag all cells for refinement (refine entire domain)

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagging_val

Real AmrIce::m_tagging_val

protected

tagging value (undivided gradient(vel) threshold for regridding)

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagGroundingLine

bool AmrIce::m_tagGroundingLine

protected

tag the grounding line

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagMargin

bool AmrIce::m_tagMargin

protected

tag at the ice margin

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagOndivHgradVel

bool AmrIce::m_tagOndivHgradVel

protected

tag on div(H grad (vel))

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagOnEpsSqr

bool AmrIce::m_tagOnEpsSqr

protected

tag on strain rate invariant?

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagOnGradVel

bool AmrIce::m_tagOnGradVel

protected

tag on grad(velocity)?

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagOnGroundedLapVel

bool AmrIce::m_tagOnGroundedLapVel

protected

tag on laplacian(velocity) in grounded regions only

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagOnLapVel

bool AmrIce::m_tagOnLapVel

protected

tag on laplacian(velocity)

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagOnVelRHS

bool AmrIce::m_tagOnVelRHS

protected

tag on velocity solve RHS

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagPython

bool AmrIce::m_tagPython

protected

tag cells according to a python function

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagPythonFunction

PyObject* AmrIce::m_tagPythonFunction

protected

Referenced by initialize(), setDefaults(), tagCellsLevel(), and ~AmrIce().

◆ m_tagPythonModule

PyObject* AmrIce::m_tagPythonModule

protected

Referenced by initialize(), setDefaults(), and ~AmrIce().

◆ m_tags_grow

int AmrIce::m_tags_grow

protected

amount to buffer tags used in regridding

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tags_grow_dir

IntVect AmrIce::m_tags_grow_dir

protected

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_tagVelDx

bool AmrIce::m_tagVelDx

protected

tag where |vel| * dx > m_maxVelDxVal

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_temperature

Vector<LevelData<FArrayBox>* > AmrIce::m_temperature

protected

Referenced by initData(), updateTemperature(), and ~AmrIce().

◆ m_temporalAccuracy

int AmrIce::m_temporalAccuracy

protected

temporal accuracy

1 = 1st-order (use old-time velocity for flux computation) 2 = 2nd-order (recompute velocity at half-time for flux computation) 3 = 3rd-order Runge-Kutta update (if eventually implemented) 4 = 4th-order Runge-Kutta update

Referenced by implicitThicknessCorrection(), initialize(), setDefaults(), and timeStep().

◆ m_thicknessIBCPtr

IceThicknessIBC* AmrIce::m_thicknessIBCPtr

protected

IBC for thickness advection.

Referenced by advectIceFrac(), computeFaceVelocity(), defineSolver(), defineVelRHS(), incrementIceThickness(), initData(), initialize(), regrid(), setThicknessBC(), solveVelocityField(), updateGeometry(), updateInvalidIceFrac(), updateViscousTensor(), and ~AmrIce().

◆ m_thicknessPatchGodVect

Vector<PatchGodunov*> AmrIce::m_thicknessPatchGodVect

protected

PatchGodunov used for thickness advection – one for each level.

Referenced by computeH_half(), initialize(), and ~AmrIce().

◆ m_thicknessPhysPtr

GodunovPhysics* AmrIce::m_thicknessPhysPtr

protected

pointer to a GodunovPhysics for thickness advection

Referenced by initialize(), and ~AmrIce().

◆ m_tillWaterDepth

Vector<LevelData<FArrayBox>* > AmrIce::m_tillWaterDepth

protected

Referenced by initData(), initialize(), levelSetup(), readCheckpointFile(), regrid(), solveVelocityField(), updateInternalEnergy(), writeAMRPlotFile(), writeCheckpointFile(), and ~AmrIce().

◆ m_time

Real AmrIce::m_time

protected

◆ m_timeStepTicks

bool AmrIce::m_timeStepTicks

protected

Referenced by computeDt(), initialize(), and setDefaults().

◆ m_topographyFluxPtr

SurfaceFlux* AmrIce::m_topographyFluxPtr

protected

sets topography flux (which raises/lowers bedrock)

Referenced by setTopographyFlux(), and updateGeometry().

◆ m_vect_coordSys

◆ m_vectTags

Vector<IntVectSet> AmrIce::m_vectTags

protected

stores tags from previous regrids

Referenced by tagCellsInit().

◆ m_vectTagSubset

Vector<IntVectSet> AmrIce::m_vectTagSubset

protected

Referenced by initialize(), and tagCells().

◆ m_velBasalC

Vector<LevelData<FArrayBox>* > AmrIce::m_velBasalC

protected

Referenced by initialize(), levelSetup(), readCheckpointFile(), regrid(), solveVelocityField(), tagCellsLevel(), updateInternalEnergy(), updateViscousTensor(), writeAMRPlotFile(), writeCheckpointFile(), and ~AmrIce().

◆ m_velDx_tagVal

Real AmrIce::m_velDx_tagVal

protected

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_velDx_tagVal_finestLevelFloating

int AmrIce::m_velDx_tagVal_finestLevelFloating

protected

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_velDx_tagVal_finestLevelGrounded

int AmrIce::m_velDx_tagVal_finestLevelGrounded

protected

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_velocity

Vector<LevelData<FArrayBox>*> AmrIce::m_velocity

protected

horizontal velocity field (found by an IceVelocitySolver)

Referenced by advectIceFrac(), amrVelocity(), computeFaceVelocity(), eliminateRemoteIce(), initData(), initGrids(), initialize(), levelSetup(), readCheckpointFile(), regrid(), restart(), setupFixedGrids(), solveVelocityField(), tagCellsLevel(), updateInternalEnergy(), updateViscousTensor(), velocity(), writeAMRPlotFile(), writeCheckpointFile(), and ~AmrIce().

◆ m_velocity_exit

Real AmrIce::m_velocity_exit

protected

maximum acceptable velocity: if max(u) > m_vel_exit , then dump a plot file and exit

Referenced by computeDt(), initialize(), and setDefaults().

◆ m_velocity_solve_interval

int AmrIce::m_velocity_solve_interval

protected

solve the velocity problem every m_velocitySolveInterval timesteps

Referenced by initialize(), setDefaults(), and solveVelocityField().

◆ m_velocity_solver_tolerance

Real AmrIce::m_velocity_solver_tolerance

protected

solver tolerance for velSolver.

Referenced by defineSolver(), initialize(), and setDefaults().

◆ m_velocitySolveFinalResidualNorm

Real AmrIce::m_velocitySolveFinalResidualNorm

protected

Referenced by solveVelocityField().

◆ m_velocitySolveInitialResidualNorm

Real AmrIce::m_velocitySolveInitialResidualNorm

protected

Residual norms at the start and end of the last velocity solve.

Referenced by readCheckpointFile(), regrid(), setDefaults(), and solveVelocityField().

◆ m_velRHS

Vector<LevelData<FArrayBox>* > AmrIce::m_velRHS

protected

velocity solve RHS (in case we want to save it)

Referenced by initialize(), levelSetup(), readCheckpointFile(), regrid(), solveVelocityField(), tagCellsLevel(), writeAMRPlotFile(), and ~AmrIce().

◆ m_velRHS_tagVal

Real AmrIce::m_velRHS_tagVal

protected

tagging value for velocity RHS

Referenced by initialize(), setDefaults(), and tagCellsLevel().

◆ m_velSolver

IceVelocitySolver* AmrIce::m_velSolver

protected

nonlinear elliptic solver for velocity field

Referenced by defineSolver(), readCheckpointFile(), restart(), solveVelocityField(), and ~AmrIce().

◆ m_viscosityCoefCell

Vector<LevelData<FArrayBox>* > AmrIce::m_viscosityCoefCell

mutableprotected

Referenced by updateViscousTensor(), viscosityCoefficient(), and ~AmrIce().

◆ m_viscousTensor_valid

bool AmrIce::m_viscousTensor_valid

mutableprotected

Referenced by dragCoefficient(), initGrids(), setDefaults(), solveVelocityField(), updateViscousTensor(), viscosityCoefficient(), and viscousTensor().

◆ m_viscousTensorCell

Vector<LevelData<FArrayBox>* > AmrIce::m_viscousTensorCell

mutableprotected

Referenced by updateViscousTensor(), viscousTensor(), and ~AmrIce().

◆ m_viscousTensorFace

Vector<LevelData<FluxBox>* > AmrIce::m_viscousTensorFace

mutableprotected

Referenced by updateViscousTensor(), and ~AmrIce().

◆ m_volumeThicknessSource

Vector<LevelData<FArrayBox>* > AmrIce::m_volumeThicknessSource

mutableprotected

Referenced by computeH_half(), initialize(), levelSetup(), readCheckpointFile(), regrid(), restart(), timeStep(), updateGeometry(), and ~AmrIce().

◆ m_waterDepth

Real AmrIce::m_waterDepth

protected

Referenced by setDefaults().

◆ m_write_baseVel

bool AmrIce::m_write_baseVel

protected

Referenced by writeAMRPlotFile().

◆ m_write_dHDt

bool AmrIce::m_write_dHDt

protected

if true, include dH/dt in plotfiles

Referenced by initialize(), and writeAMRPlotFile().

◆ m_write_fluxVel

bool AmrIce::m_write_fluxVel

protected

Referenced by solveVelocityField(), and writeAMRPlotFile().

◆ m_write_internal_energy

bool AmrIce::m_write_internal_energy

protected

Referenced by writeAMRPlotFile().

◆ m_write_ismip6

bool AmrIce::m_write_ismip6

protected

Referenced by restart(), and writeAMRPlotFile().

◆ m_write_layer_velocities

bool AmrIce::m_write_layer_velocities

protected

Referenced by writeAMRPlotFile().

◆ m_write_map_file

bool AmrIce::m_write_map_file

protected

if true, write out .map.hdf5 file

Referenced by writeAMRPlotFile().

◆ m_write_mask

bool AmrIce::m_write_mask

protected

if true, include mask in plotfiles

Referenced by initialize(), and writeAMRPlotFile().

◆ m_write_muCoeff

bool AmrIce::m_write_muCoeff

protected

if true, include viscosity multiplier (muCoefficient) in plotfiles

Referenced by initialize(), and writeAMRPlotFile().

◆ m_write_presolve_plotfiles

bool AmrIce::m_write_presolve_plotfiles

protected

if true, write out plotfile before doing velocity solves

this can be convenient when working with the solverBenchmark

Referenced by solveVelocityField().

◆ m_write_solver_rhs

bool AmrIce::m_write_solver_rhs

protected

if true, include velocity solver RHS in plotfiles

Referenced by initialize(), and writeAMRPlotFile().

◆ m_write_thickness_sources

bool AmrIce::m_write_thickness_sources

protected

Referenced by writeAMRPlotFile().

◆ m_write_viscousTensor

bool AmrIce::m_write_viscousTensor

protected

Referenced by writeAMRPlotFile().

◆ s_verbosity

int AmrIce::s_verbosity = 1

staticprotected

how verbose should we be?

Referenced by computeA(), computeDt(), computeInitialDt(), defineSolver(), eliminateRemoteIce(), helmholtzSolve(), implicitThicknessCorrection(), initData(), initGrids(), initialize(), readCheckpointFile(), regrid(), restart(), run(), setupFixedGrids(), solveVelocityField(), tagCells(), tagCellsInit(), tagCellsLevel(), timeStep(), updateGroundingLineProximity(), writeAMRPlotFile(), writeCheckpointFile(), and ~AmrIce().

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

Classes

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Friends

Detailed Description

Member Enumeration Documentation

◆ DiffusionTreatment

◆ initialGuessTypes

◆ velSolverTypes

Constructor & Destructor Documentation

◆ AmrIce()

◆ ~AmrIce()

Member Function Documentation

◆ addedIceThickness()

◆ addObserver()

◆ advectIceFrac()

◆ amrDx()

◆ amrGeometry()

◆ amrIceFrac() [1/2]

◆ amrIceFrac() [2/2]

◆ amrVelocity()

◆ applyCalvingCriterion()

◆ basalHeatBoundaryData()

◆ basalThicknessSource()

◆ calvedIceThickness()

◆ computeA()

◆ computeAreaFraction()

◆ computeDischarge()

◆ computeDt()

◆ computeFaceVelocity()

◆ computeH_half()

◆ computeInitialDt()

◆ computeInternalEnergyHalf()

◆ computeThicknessFluxes()

◆ computeTotalIce()

◆ defineSolver()

◆ defineVelRHS()

◆ dragCoefficient()

◆ dt()

◆ dx()

◆ eliminateRemoteIce()

◆ faceVelocities()

◆ faceVelocitiesLayered()

◆ finestLevel()

◆ finestTimestepLevel()

◆ geometry()

◆ getFaceSigma()

◆ getHeader() [1/3]

◆ getHeader() [2/3]

◆ getHeader() [3/3]

◆ getIceThickness()

◆ grids() [1/2]

◆ grids() [2/2]

◆ groundingLineProximity()

◆ groundingLineProximityScale()

◆ helmholtzSolve() [1/2]

◆ helmholtzSolve() [2/2]

◆ iceFrac() [1/2]

◆ iceFrac() [2/2]

◆ implicitThicknessCorrection()

◆ incrementIceThickness()

◆ incrementWithDivFlux()

◆ initData()

◆ initGrids()

◆ initialize()

◆ isDefined()

◆ levelSetup()

◆ muCoef()

◆ postInterpolationReFloat()

◆ readCheckpointFile()

◆ refRatios()

◆ regrid()

◆ removedIceThickness()

◆ removeObserver()

◆ restart()