Manage hierarchy of levels for time-dependent AMR computations. More...

#include <AMReX_Amr.H>

Inheritance diagram for amrex::Amr:

Public Member Functions
	Amr (LevelBld *a_levelbld)
	Construct an AMR driver bound to a factory of AmrLevel implementations.

	Amr (const RealBox rb, int max_level_in, const Vector< int > &n_cell_in, int coord, LevelBld a_levelbld)
	Construct with explicit problem domain metadata and a level factory.

	Amr (const Amr &rhs)=delete
	Amr owns global driver state—disable copying to avoid duplicate hierarchies.

	Amr (Amr &&rhs)=delete
	Amr instances are not movable; they rely on pointers registered with static callbacks.

Amr &	operator= (const Amr &rhs)=delete
	Copy assignment is likewise disabled.

Amr &	operator= (Amr &&rhs)=delete
	Move assignment is disabled to keep ownership contracts simple.

void	InitAmr ()
	Initialize Amr-wide defaults and parse the amr.* ParmParse options.

	~Amr () override
	The destructor.

virtual void	init (Real strt_time, Real stop_time)
	Initialize hierarchy state (grid creation, initial conditions, etc.).

void	InitializeInit (Real strt_time, Real stop_time, const BoxArray lev0_grids=nullptr, const Vector< int > pmap=nullptr)
	First half of the two-phase initialization used by initialInit().

void	FinalizeInit (Real strt_time, Real stop_time)
	Second half of initial initialization; pairs with InitializeInit() using times `strt_time` and `stop_time`.

void	setDtLevel (const Vector< Real > &dt_lev) noexcept
	Set per-level time steps to the values in `dt_lev`.

void	setDtLevel (Real dt, int lev) noexcept
	Set the time step stored at AMR level `lev` to `dt`.

void	setDtMin (const Vector< Real > &dt_min_in) noexcept
	Override the maximum allowable dt (typically CFL-limited) for each level using `dt_min_in`.

void	setNCycle (const Vector< int > &ns) noexcept
	Provide the number of time subcycles per level via `ns`.

int	subCycle () const noexcept
	Subcycle in time?

const std::string &	subcyclingMode () const noexcept
	How are we subcycling?

int	level_being_advanced () const noexcept
	What is "level" in Amr::timeStep? This is only relevant if we are still in Amr::timeStep; it is set back to -1 on leaving Amr::timeStep.

Real	cumTime () const noexcept
	Physical time (time advanced so far).

void	setCumTime (Real t) noexcept
	Set the accumulated physical time to `t`.

Real	startTime () const noexcept
	Physical time this simulation started.

void	setStartTime (Real t) noexcept
	Set the recorded start time to `t`.

Real	dtLevel (int level) const noexcept
	Time step currently stored for level `level`.

Real	dtMin (int level) const noexcept
	Max time step (typically physics-limited) for level `level`.

const Vector< Real > &	dtLevel () const noexcept
	Vector of time steps (dt) for all levels.

int	nCycle (int level) const noexcept
	Number of subcycled time steps taken per coarse step on level `level`.

int	levelSteps (int lev) const noexcept
	Number of time steps completed so far on level `lev`.

void	setLevelSteps (int lev, int n) noexcept
	Override the recorded time-step count for level `lev`.

int	levelCount (int lev) const noexcept
	Which cycle number are we on for level `lev`?

void	setLevelCount (int lev, int n) noexcept
	Set the current cycle count for level `lev`.

int	regridInt (int lev) const noexcept
	Interval (in steps) between regrids on level `lev`.

int	checkInt () const noexcept
	Number of time steps between checkpoint files.

Real	checkPer () const noexcept
	Time between checkpoint files.

int	plotInt () const noexcept
	Number of time steps between plot files.

Real	plotPer () const noexcept
	Time between plot files.

Real	plotLogPer () const noexcept
	Spacing in log10(time) of logarithmically spaced plot files.

int	plotMaxLevel () const noexcept
	Maximum level index to include when writing plot files.

int	smallplotInt () const noexcept
	Number of time steps between small plot files.

Real	smallplotPer () const noexcept
	Time between plot files.

Real	smallplotLogPer () const noexcept
	Spacing in log10(time) of logarithmically spaced small plot files.

AmrLevel &	getLevel (int lev) noexcept
	Access the AmrLevel object stored at index `lev`.

Vector< std::unique_ptr< AmrLevel > > &	getAmrLevels () noexcept
	Return the container of level objects (index 0..finest).

Long	cellCount () noexcept

Long	cellCount (int lev) noexcept

int	numGrids () noexcept

int	numGrids (int lev) noexcept

int	okToContinue () noexcept

void	regrid (int lbase, Real time, bool initial=false) override
	Rebuild grid hierarchy finer than `lbase`.

void	RegridOnly (Real time, bool do_io=true)
	Regrid the hierarchy at physical time `time` without advancing any levels.

bool	okToRegrid (int level) noexcept
	Return true if level `level` is permitted to regrid on this step.

virtual void	coarseTimeStep (Real stop_time)
	Advance the hierarchy by one coarse step.

Real	coarseTimeStepDt (Real stop_time)
	Advance once and report the coarse level dt that was used.

std::unique_ptr< MultiFab >	derive (const std::string &name, Real time, int lev, int ngrow)
	Build a MultiFab containing the derived quantity named `name`.

void	derive (const std::string &name, Real time, const Vector< MultiFab * > &mf, int dcomp)
	Compute derived data on all levels and store it in the supplied MultiFabs.

Vector< std::unique_ptr< MultiFab > >	derive (const std::string &name, amrex::Real time, int ngrow)
	Compute derived data on all levels and return as owning MultiFabs.

const std::string &	theRestartFile () const noexcept
	Name of the most recent restart checkpoint file.

const std::string &	theRestartPlotFile () const noexcept
	Name of the restart plotfile.

std::ostream &	DataLog (int i)
	Return the `i` th datalog stream (opened lazily) for writing diagnostics.

std::string	DataLogName (int i) const noexcept
	The filename backing the `i` th datalog stream.

int	NumDataLogs () noexcept

virtual void	writePlotFile ()
	Write a full-resolution plot file to disk using the current hierarchy state.

int	stepOfLastPlotFile () const noexcept
	Return the AMR step index associated with the most recent plot file.

virtual void	writeSmallPlotFile ()
	Write the reduced “small plot” file (subset of variables/levels) to disk.

int	stepOfLastSmallPlotFile () const noexcept
	Return the AMR step index associated with the most recent small plot file.

virtual void	checkPoint ()
	Write current state into a chk* checkpoint directory.

int	stepOfLastCheckPoint () const noexcept
	Return the AMR step index associated with the most recent checkpoint.

void	setBoundaryGeometry (BoundaryPointList &IntersectLoX, BoundaryPointList &IntersectHiX, BoundaryPointList &IntersectLoY, BoundaryPointList &IntersectHiY) noexcept
	Specialized version: register intersection points for faces orthogonal to X/Y.

void	setBoundaryGeometry (BoundaryPointList &IntersectLoX, BoundaryPointList &IntersectHiX, BoundaryPointList &IntersectLoY, BoundaryPointList &IntersectHiY, BoundaryPointList &IntersectLoZ, BoundaryPointList &IntersectHiZ) noexcept
	General version: register intersections for all Cartesian faces.

BoundaryPointList &	getIntersectLoX () noexcept

BoundaryPointList &	getIntersectHiX () noexcept

BoundaryPointList &	getIntersectLoY () noexcept

BoundaryPointList &	getIntersectHiY () noexcept

BoundaryPointList &	getIntersectLoZ () noexcept

BoundaryPointList &	getIntersectHiZ () noexcept

void	RedistributeParticles ()
	Trigger a particle redistribution pass across all levels.

void	InstallNewDistributionMap (int lev, const DistributionMapping &newdm)
	Replace the distribution map on level `lev` with `newdm` and update metadata.

Public Member Functions inherited from amrex::AmrCore
	AmrCore ()
	Construct an empty AmrCore.

	AmrCore (const RealBox rb, int max_level_in, const Vector< int > &n_cell_in, int coord=-1, Vector< IntVect > ref_ratios=Vector< IntVect >(), const int is_per=nullptr)
	Construct using legacy inputs that mirror AmrMesh.

	AmrCore (const RealBox &rb, int max_level_in, const Vector< int > &n_cell_in, int coord, Vector< IntVect > const &ref_ratios, Array< int, 3 > const &is_per)
	Construct with an explicit domain and periodicity array.

	AmrCore (Geometry const &level_0_geom, AmrInfo const &amr_info)
	Construct from a ready-made Geometry and AmrInfo bundle.

	AmrCore (AmrCore &&rhs) noexcept

AmrCore &	operator= (AmrCore &&rhs) noexcept

	AmrCore (const AmrCore &rhs)=delete

AmrCore &	operator= (const AmrCore &rhs)=delete

	~AmrCore () override

AmrParGDB *	GetParGDB () const noexcept
	Return AmrParGDB pointer for particle containers.

void	InitFromScratch (Real time)
	Initialize BoxArray, DistributionMapping, and level data from scratch.

void	printGridSummary (std::ostream &os, int min_lev, int max_lev) const noexcept
	Print a human-readable summary of grid sizes between `min_lev` and `max_lev`.

Public Member Functions inherited from amrex::AmrMesh
	AmrMesh ()
	Construct an empty mesh.

	AmrMesh (const RealBox rb, int max_level_in, const Vector< int > &n_cell_in, int coord=-1, Vector< IntVect > refrat=Vector< IntVect >(), const int is_per=nullptr)
	Construct using legacy inputs (same signature as AmrCore).

	AmrMesh (const RealBox &rb, int max_level_in, const Vector< int > &n_cell_in, int coord, Vector< IntVect > const &a_refrat, Array< int, 3 > const &is_per)
	Construct with explicit domain and periodicity array.

	AmrMesh (Geometry const &level_0_geom, AmrInfo const &amr_info)
	Construct from a pre-built Geometry and AmrInfo bundle.

	AmrMesh (const AmrMesh &rhs)=delete

AmrMesh &	operator= (const AmrMesh &rhs)=delete

	AmrMesh (AmrMesh &&rhs)=default

AmrMesh &	operator= (AmrMesh &&rhs)=default

virtual	~AmrMesh ()=default

int	Verbose () const noexcept

int	maxLevel () const noexcept
	Return the max level.

int	finestLevel () const noexcept
	Return the finest level.

IntVect	refRatio (int lev) const noexcept
	Return the refinement ratio for level lev.

int	MaxRefRatio (int lev) const noexcept
	Return the maximum refinement ratio in any direction.

const Vector< IntVect > &	refRatio () const noexcept
	Return refinement ratios between all levels.

const Vector< Geometry > &	Geom () const noexcept

const Vector< DistributionMapping > &	DistributionMap () const noexcept

const Vector< BoxArray > &	boxArray () const noexcept

const Geometry &	Geom (int lev) const noexcept

const DistributionMapping &	DistributionMap (int lev) const noexcept

const BoxArray &	boxArray (int lev) const noexcept

Vector< Geometry >	Geom (int a_coarsest_lev, int a_finest_lev) const noexcept

Vector< BoxArray >	boxArray (int a_coarsest_lev, int a_finest_lev) const noexcept

Vector< DistributionMapping >	DistributionMap (int a_coarsest_lev, int a_finest_lev) const noexcept

Vector< Geometry > &	Geom () noexcept

Geometry &	Geom (int lev) noexcept

void	SetMaxGridSize (int new_mgs) noexcept
	Override the max grid size constraint for all levels (scalar version).

void	SetMaxGridSize (const IntVect &new_mgs) noexcept
	Override the max grid size constraint using explicit IntVect `new_mgs`.

void	SetMaxGridSize (const Vector< int > &new_mgs) noexcept
	Override per-level max grid sizes using scalar-per-level vector `new_mgs`.

void	SetMaxGridSize (const Vector< IntVect > &new_mgs) noexcept
	Override per-level max grid sizes using explicit IntVect-per-level vector `new_mgs`.

void	SetBlockingFactor (int new_bf) noexcept
	Override the blocking factor constraint for all levels (scalar version).

void	SetBlockingFactor (const IntVect &new_bf) noexcept
	Override blocking factor using explicit IntVect `new_bf`.

void	SetBlockingFactor (const Vector< int > &new_bf) noexcept
	Override per-level blocking factors using scalar-per-level vector `new_bf`.

void	SetBlockingFactor (const Vector< IntVect > &new_bf) noexcept
	Override per-level blocking factors using explicit IntVect vector `new_bf`.

void	SetGridEff (Real eff) noexcept
	Set the minimum acceptable grid efficiency to `eff`.

void	SetNProper (int n) noexcept
	Set the number of cell blocks required for proper nesting to `n`.

void	SetFinestLevel (int new_finest_level) noexcept
	Update the recorded finest level index to `new_finest_level` (without reallocating).

void	SetDistributionMap (int lev, const DistributionMapping &dmap_in) noexcept
	Install a DistributionMapping for level `lev`.

void	SetBoxArray (int lev, const BoxArray &ba_in) noexcept
	Install a BoxArray for level `lev`.

void	SetGeometry (int lev, const Geometry &geom_in) noexcept
	Install a Geometry object for level `lev`.

int	GetLevel (Box const &domain) const noexcept
	Given domain box, return AMR level. Return -1 if there is no match.

void	ClearDistributionMap (int lev) noexcept
	Clear the stored DistributionMapping for level `lev`.

void	ClearBoxArray (int lev) noexcept
	Clear the stored BoxArray for level `lev`.

int	nErrorBuf (int lev, int direction=0) const noexcept
	Return the number of buffer cells (as a single integer) in error estimator.

const IntVect &	nErrorBufVect (int lev) const noexcept
	Return the number of buffer cells (as an IntVect) in error estimator.

Real	gridEff () const noexcept
	Return the minimum allowable grid efficiency.

int	nProper () const noexcept
	Return the number of cell blocks to define proper nesting.

const IntVect &	blockingFactor (int lev) const noexcept
	Return the blocking factor at level lev.

const IntVect &	maxGridSize (int lev) const noexcept
	Return the largest allowable grid.

bool	LevelDefined (int lev) const noexcept
	Return true if valid grids/dmaps exist for level `lev`.

bool	useFixedCoarseGrids () const noexcept
	Should we keep the coarser grids fixed (and not regrid those levels) at all?

int	useFixedUpToLevel () const noexcept
	Up to what level should we keep the coarser grids fixed (and not regrid those levels)?

void	ChopGrids (int lev, BoxArray &ba, int target_size) const
	Try to chop grids on level `lev` until BoxArray `ba` has at least `target_size` boxes.

BoxArray	MakeBaseGrids () const
	Make a level-0 BoxArray covering the whole domain (without installing it).

void	MakeNewGrids (int lbase, Real time, int &new_finest, Vector< BoxArray > &new_grids)
	Make new grids based on error estimates. This function expects that valid BoxArrays exist in this->grids from level lbase to level this->finest_level (the current finest level). new_grids. On return, the new finest level is stored in new_finest, and the new grids are stored in new_grids from Array element lbase+1 to new_finest_level (unless fixed grids are used). Note that this function adds at most one more level to the existing levels, and it may remove all levels above the base level. This function does not change the value of this->finest_level, nor does it modifies any BoxArrays stored in this->grids. It also does not modify new_grids's elements outside the range [lbase+1,new_finest_level].

void	MakeNewGrids (Real time=0.0)
	Convenience overload that rebuilds every level (including level 0) at time `time`.

virtual void	PostProcessBaseGrids (BoxArray &box_array) const
	Allow derived classes to edit the base-level grids before installing them.

Long	CountCells (int lev) const noexcept
	Count the total number of cells at level `lev`.

virtual DistributionMapping	MakeDistributionMap (int lev, BoxArray const &ba)
	Build a distribution map for level `lev` grid layout `ba` (override to customize load balancing).

Static Public Member Functions
static bool	RegridOnRestart () noexcept
	Whether to regrid right after restart.

static const std::list< std::string > &	statePlotVars () noexcept
	The names of state variables to output in the plotfile. They can be set using the amr.plot_vars variable in a ParmParse inputs file.

static const std::list< std::string > &	stateSmallPlotVars () noexcept
	List of state variables written to the reduced “small” plot files.

static bool	isStatePlotVar (const std::string &name)
	Return true if `name` is already registered for full plotfiles.

static bool	isStateSmallPlotVar (const std::string &name)
	Return true if `name` is already registered for small plotfiles.

static void	addStatePlotVar (const std::string &name)
	Register `name` as a state variable to include in full plotfiles (no-op if already present).

static void	addStateSmallPlotVar (const std::string &name)
	Append `name` to the small-plot variable list if not already present.

static void	deleteStatePlotVar (const std::string &name)
	Remove `name` from the full-plot list if present.

static void	clearStatePlotVarList ()
	Clear the list of state_plot_vars.

static void	clearStateSmallPlotVarList ()
	Clear the list of variables written to small plot files.

static void	fillStatePlotVarList ()
	Fill the list of state_plot_vars with all of the state quantities.

static void	fillStateSmallPlotVarList ()
	Populate state_small_plot_vars with every state quantity registered on AmrLevel 0.

static bool	Plot_Files_Output ()
	Write out plotfiles (True/False)?

static const std::list< std::string > &	derivePlotVars () noexcept
	The names of derived variables to output in the plotfile. They can be set using the amr.derive_plot_vars variable in a ParmParse inputs file.

static const std::list< std::string > &	deriveSmallPlotVars () noexcept
	List of derived quantities included when writing small plot files.

static bool	isDerivePlotVar (const std::string &name) noexcept
	Return true if `name` is already registered for full derived-output.

static bool	isDeriveSmallPlotVar (const std::string &name) noexcept
	Return true if `name` is already registered for small derived-output.

static void	addDerivePlotVar (const std::string &name)
	Register `name` as a derived quantity to include in full plotfiles (no-op if already present).

static void	addDeriveSmallPlotVar (const std::string &name)
	Append `name` to the small-plot derived list if not already present.

static void	deleteDerivePlotVar (const std::string &name)
	Remove `name` from the full derived list.

static void	deleteDeriveSmallPlotVar (const std::string &name)
	Remove `name` from the small derived list.

static void	clearDerivePlotVarList ()
	Clear the list of derive_plot_vars.

static void	clearDeriveSmallPlotVarList ()
	Clear the list of derived quantities written to small plot files.

static void	fillDerivePlotVarList ()
	Fill the list of derive_plot_vars with all derived quantities.

static void	fillDeriveSmallPlotVarList ()
	Populate derive_small_plot_vars with every registered derived quantity.

static void	setComputeNewDtOnRegrid (bool flag)
	Toggle whether new time steps are recomputed immediately after each regrid (`flag=true` recomputes).

static void	Initialize ()
	Initialize global, Amr-wide static state (e.g., ParmParse defaults, logs).

static void	Finalize ()
	Release global Amr static resources allocated by Initialize().

static const BoxArray &	initialBa (int level) noexcept
	Return the user-specified BoxArray that initializes level `level` (1-based).

static int	initialBaLevels () noexcept

static Real	computeOptimalSubcycling (int n, int best, const Real dt_max, const Real est_work, const int cycle_max)
	Compute the optimal subcycling pattern. This assumes that anything less than cycle_max[i] is a valid number of subcycles at level[i]. For example if ref_ratio[i] = cycle_max[i] = 4, then 1,2,3,4 are all valid values for n_cycles[i].

static const Vector< BoxArray > &	getInitialBA () noexcept

static bool	UsingPrecreateDirectories () noexcept
	Whether plot/checkpoint writers pre-create directories (helps avoid races on some filesystems).

Public Attributes
BoundaryPointList	intersect_lox

BoundaryPointList	intersect_loy

BoundaryPointList	intersect_loz

BoundaryPointList	intersect_hix

BoundaryPointList	intersect_hiy

BoundaryPointList	intersect_hiz

Static Public Attributes
static bool	first_smallplotfile

Protected Member Functions
void	initialInit (Real strt_time, Real stop_time, const BoxArray lev0_grids=nullptr, const Vector< int > pmap=nullptr)
	Initialize the grid hierarchy (called by Amr::init()).

void	readProbinFile (int &init)
	Read the probin file, updating the flag `init` that tracks initialization iterations.

void	checkInput ()
	Check for valid input.

void	restart (const std::string &filename)
	Restart from a checkpoint file named `filename`.

void	defBaseLevel (Real strt_time, const BoxArray lev0_grids=nullptr, const Vector< int > pmap=nullptr)
	Define and initialize the coarsest level using optional level-0 grids `lev0_grids` and map `pmap`.

void	bldFineLevels (Real strt_time)
	Define and initialize refined levels at simulation time `strt_time`.

virtual void	regrid_level_0_on_restart ()
	Regrid level 0 on restart.

void	grid_places (int lbase, Real time, int &new_finest, Vector< BoxArray > &new_grids)
	Define new grid locations (called from regrid) and store them in `new_grids`.

DistributionMapping	makeLoadBalanceDistributionMap (int lev, Real time, const BoxArray &ba) const
	Build a DistributionMapping for level `lev` at time `time` using grid layout `ba`.

void	LoadBalanceLevel0 (Real time)
	Compute and install a new distribution map for level 0.

void	ErrorEst (int lev, TagBoxArray &tags, Real time, int ngrow) override
	Default error-estimation driver; forwards to the levelbld-defined callbacks.

BoxArray	GetAreaNotToTag (int lev) override
	Return cached regions that must not be tagged on level `lev`.

void	ManualTagsPlacement (int lev, TagBoxArray &tags, const Vector< IntVect > &bf_lev) override
	Allow derived classes to override tagging manually on level `lev`.

virtual void	timeStep (int level, Real time, int iteration, int niter, Real stop_time)
	Do a single time step on level `level`.

void	MakeNewLevelFromScratch (int, Real, const BoxArray &, const DistributionMapping &) override
	Create and fill a new level from scratch.

void	MakeNewLevelFromCoarse (int, Real, const BoxArray &, const DistributionMapping &) override
	Make a new level using provided metadata and populate it from the next coarser level.

void	RemakeLevel (int, Real, const BoxArray &, const DistributionMapping &) override
	Remake an existing level using provided metadata and refill from old data.

void	ClearLevel (int) override
	Delete level `lev` data structures owned by the derived class.

bool	checkPointNow () noexcept
	Whether checkpoint criteria are satisfied on this step.

bool	writePlotNow () noexcept
	Whether to write a plotfile now.

bool	writeSmallPlotNow () noexcept
	Whether to emit a small plot file on this step.

void	printGridInfo (std::ostream &os, int min_lev, int max_lev)
	Print per-level grid metadata to `os` for levels [`min_lev`, `max_lev`].

void	setRecordGridInfo (const std::string &filename)
	Record the log filename `filename` used when dumping grid info metadata.

void	setRecordRunInfo (const std::string &filename)
	Record the log filename `filename` used when writing detailed run information.

void	setRecordRunInfoTerse (const std::string &filename)
	Record the log filename `filename` used for terse run information.

void	setRecordDataInfo (int i, const std::string &filename)
	Configure the `i` th datalog stream to mirror file `filename`.

void	initSubcycle ()
	Parse ParmParse state and initialize subcycling-related arrays/flags.

void	initPltAndChk ()
	Initialize plot/checkpoint cadence, names, and counters from inputs.

int	updateInSitu ()
	Drive any per-step in-situ actions; returns 0 on success.

Protected Member Functions inherited from amrex::AmrMesh
void	checkInput ()
	Validate AmrInfo inputs (throws if inconsistent).

void	SetIterateToFalse () noexcept
	Disable the iterate-on-new-grids loop for the next MakeNewGrids call.

void	SetUseNewChop () noexcept
	Force MakeNewGrids to use the newer chopping algorithm.

Static Protected Member Functions
static int	initInSitu ()
	Set up in-situ analysis hooks; returns 0 on success.

static int	finalizeInSitu ()
	Tear down in-situ infrastructure; returns 0 on success.

Protected Attributes
std::string	regrid_grids_file
	Grids file that will bypass regridding.

std::string	initial_grids_file
	Grids file that will bypass regridding only at initialization.

Vector< std::unique_ptr< AmrLevel > >	amr_level
	Vector of levels.

Real	cumtime = std::numeric_limits<Real>::lowest()
	Physical time variable.

Real	start_time = std::numeric_limits<Real>::lowest()
	Physical time this simulation started.

Vector< Real >	dt_level
	Timestep at this level.

Vector< int >	level_steps
	Number of time steps at this level.

Vector< int >	level_count

Vector< int >	n_cycle

std::string	subcycling_mode
	Type of subcycling to use.

Vector< Real >	dt_min

Vector< int >	regrid_int
	Interval between regridding.

int	last_checkpoint
	Step number of previous checkpoint.

int	check_int
	How often checkpoint (# time steps).

Real	check_per
	How often checkpoint (units of time).

std::string	check_file_root
	Root name of checkpoint file.

int	last_plotfile
	Step number of previous plotfile.

int	last_smallplotfile
	Step number of previous small plotfile.

int	plot_int
	How often plotfile (# of time steps)

Real	plot_per
	How often plotfile (in units of time)

Real	plot_log_per
	How often plotfile (in units of log10(time))

int	plot_max_level
	Maximum AMR level to write to a plotfile.

int	small_plot_int
	How often small plotfile (# of time steps)

Real	small_plot_per
	How often small plotfile (in units of time)

Real	small_plot_log_per
	How often small plotfile (in units of log10(time))

bool	write_plotfile_with_checkpoint
	Write out a plotfile whenever we checkpoint.

int	file_name_digits
	How many digits to use in the plotfile and checkpoint names.

int	message_int
	How often checking messages touched by user, such as "stop_run".

std::string	plot_file_root
	Root name of plotfile.

std::string	small_plot_file_root
	Root name of small plotfile.

int	which_level_being_advanced = -1
	Only >=0 if we are in Amr::timeStep(level,...)

int	record_grid_info

int	record_run_info

int	record_run_info_terse

std::ofstream	gridlog

std::ofstream	runlog

std::ofstream	runlog_terse

Vector< std::unique_ptr< std::fstream > >	datalog

Vector< std::string >	datalogname

int	sub_cycle

std::string	restart_chkfile

std::string	restart_pltfile

std::string	probin_file

LevelBld *	levelbld

bool	abort_on_stream_retry_failure

int	stream_max_tries

int	loadbalance_with_workestimates

int	loadbalance_level0_int

Real	loadbalance_max_fac

bool	bUserStopRequest

Protected Attributes inherited from amrex::AmrCore
std::unique_ptr< AmrParGDB >	m_gdb
	Geometry, DistributionMapping and BoxArray for particle containers.

Protected Attributes inherited from amrex::AmrMesh
int	finest_level
	Current finest level.

Vector< Geometry >	geom

Vector< DistributionMapping >	dmap

Vector< BoxArray >	grids

unsigned int	num_setdm = 0

unsigned int	num_setba = 0

Protected Attributes inherited from amrex::AmrInfo
int	verbose = 0

int	max_level = 0
	Maximum allowed level.

Vector< IntVect >	ref_ratio {{IntVect(2)}}
	Refinement ratios.

Vector< IntVect >	blocking_factor {{IntVect(8)}}
	Blocking factor in grid generation (by level).

Vector< IntVect >	max_grid_size {{IntVect( 64 )}}
	Maximum allowable grid size (by level).

Vector< IntVect >	n_error_buf {{IntVect(1)}}
	Buffer cells around each tagged cell.

Real	grid_eff = static_cast<Real>(0.7)
	Grid efficiency.

int	n_proper = 1
	Cells required for proper nesting.

int	use_fixed_upto_level = 0

bool	use_fixed_coarse_grids = false

bool	refine_grid_layout = true

IntVect	refine_grid_layout_dims = IntVect(1)

bool	check_input = true

bool	use_new_chop = false

bool	iterate_on_new_grids = true

int	max_grid_iterations = 4

Static Protected Attributes
static std::list< std::string >	state_plot_vars
	State Vars to dump to plotfile.

static std::list< std::string >	state_small_plot_vars
	State Vars to dump to small plotfile.

static std::list< std::string >	derive_plot_vars
	Derived Vars to dump to plotfile.

static std::list< std::string >	derive_small_plot_vars
	Derived Vars to dump to small plotfile.

static bool	first_plotfile

static Vector< BoxArray >	initial_ba
	Array of BoxArrays read in to initially define grid hierarchy.

static Vector< BoxArray >	regrid_ba
	Array of BoxArrays read in to externally define grid hierarchy at each regrid.

static bool	compute_new_dt_on_regrid

Detailed Description

Manage hierarchy of levels for time-dependent AMR computations.

The Amr class is designed to manage parts of the computation which do not belong on a single level, like establishing and updating the hierarchy of levels, global timestepping, and managing the different AmrLevels

Constructor & Destructor Documentation

◆ Amr() [1/4]

amrex::Amr::Amr ( LevelBld * a_levelbld )

Construct an AMR driver bound to a factory of AmrLevel implementations.

Parameters

a_levelbld Factory responsible for creating level objects at runtime (must be non-null).

◆ Amr() [2/4]

amrex::Amr::Amr	(	const RealBox *	rb,
		int	max_level_in,
		const Vector< int > &	n_cell_in,
		int	coord,
		LevelBld *	a_levelbld
	)

Construct with explicit problem domain metadata and a level factory.

Parameters

rb	Optional physical domain for level 0.
max_level_in	Maximum AMR level allowed.
n_cell_in	Level-0 cell counts per direction.
coord	Coordinate system index.
a_levelbld	Factory responsible for creating AmrLevel instances.

◆ Amr() [3/4]

amrex::Amr::Amr ( const Amr & rhs )

delete

Amr owns global driver state—disable copying to avoid duplicate hierarchies.

◆ Amr() [4/4]

amrex::Amr::Amr ( Amr && rhs )

delete

Amr instances are not movable; they rely on pointers registered with static callbacks.

◆ ~Amr()

amrex::Amr::~Amr ( )

override

The destructor.

Member Function Documentation

◆ addDerivePlotVar()

void amrex::Amr::addDerivePlotVar ( const std::string & name )

static

Register name as a derived quantity to include in full plotfiles (no-op if already present).

Parameters

name	Derived quantity identifier.

◆ addDeriveSmallPlotVar()

void amrex::Amr::addDeriveSmallPlotVar ( const std::string & name )

static

Append name to the small-plot derived list if not already present.

Parameters

name	Derived quantity identifier.

◆ addStatePlotVar()

void amrex::Amr::addStatePlotVar ( const std::string & name )

static

Register name as a state variable to include in full plotfiles (no-op if already present).

Parameters

name	State variable identifier.

◆ addStateSmallPlotVar()

void amrex::Amr::addStateSmallPlotVar ( const std::string & name )

static

Append name to the small-plot variable list if not already present.

Parameters

name	State variable identifier.

◆ bldFineLevels()

void amrex::Amr::bldFineLevels ( Real strt_time )

protected

Define and initialize refined levels at simulation time strt_time.

◆ cellCount() [1/2]

Long amrex::Amr::cellCount ( )

noexcept

Returns: Total number of cells owned by all levels.

◆ cellCount() [2/2]

Long amrex::Amr::cellCount ( int lev )

noexcept

Returns: Number of cells at level lev.

◆ checkInput()

void amrex::Amr::checkInput ( )

protected

Check for valid input.

◆ checkInt()

int amrex::Amr::checkInt ( ) const

inlinenoexcept

Number of time steps between checkpoint files.

◆ checkPer()

Real amrex::Amr::checkPer ( ) const

inlinenoexcept

Time between checkpoint files.

◆ checkPointNow()

bool amrex::Amr::checkPointNow ( )

protectednoexcept

Whether checkpoint criteria are satisfied on this step.

◆ clearDerivePlotVarList()

void amrex::Amr::clearDerivePlotVarList ( )

static

Clear the list of derive_plot_vars.

◆ clearDeriveSmallPlotVarList()

void amrex::Amr::clearDeriveSmallPlotVarList ( )

static

Clear the list of derived quantities written to small plot files.

◆ ClearLevel()

void amrex::Amr::ClearLevel ( int lev )

inlineoverrideprotectedvirtual

Delete level lev data structures owned by the derived class.

Parameters

lev	Level index whose data should be released.

Implements amrex::AmrCore.

◆ clearStatePlotVarList()

void amrex::Amr::clearStatePlotVarList ( )

static

Clear the list of state_plot_vars.

◆ clearStateSmallPlotVarList()

void amrex::Amr::clearStateSmallPlotVarList ( )

static

Clear the list of variables written to small plot files.

◆ coarseTimeStep()

void amrex::Amr::coarseTimeStep ( Real stop_time )

virtual

Advance the hierarchy by one coarse step.

Parameters

stop_time Optional time limit; time stepping will stop once this value is reached.

◆ coarseTimeStepDt()

Real amrex::Amr::coarseTimeStepDt ( Real stop_time )

Advance once and report the coarse level dt that was used.

Parameters

stop_time Optional time limit (same semantics as coarseTimeStep()).

Returns: The dt associated with level 0 for that step.

◆ computeOptimalSubcycling()

Real amrex::Amr::computeOptimalSubcycling	(	int	n,
		int *	best,
		const Real *	dt_max,
		const Real *	est_work,
		const int *	cycle_max
	)

static

Compute the optimal subcycling pattern. This assumes that anything less than cycle_max[i] is a valid number of subcycles at level[i]. For example if ref_ratio[i] = cycle_max[i] = 4, then 1,2,3,4 are all valid values for n_cycles[i].

Parameters

n	Number of refinement levels under consideration.
best	Output array receiving cycle counts per level (size `n`).
dt_max	Maximum dt allowed at each level.
est_work	Estimated per-level work weights (same length as `dt_max`).
cycle_max	Maximum allowed subcycles per level (matches `n`).

Returns: The coarse-level dt associated with the best pattern.

◆ cumTime()

Real amrex::Amr::cumTime ( ) const

inlinenoexcept

Physical time (time advanced so far).

◆ DataLog()

std::ostream & amrex::Amr::DataLog ( int i )

Return the i th datalog stream (opened lazily) for writing diagnostics.

Parameters

i	Datalog index.

◆ DataLogName()

std::string amrex::Amr::DataLogName ( int i ) const

inlinenoexcept

The filename backing the i th datalog stream.

◆ defBaseLevel()

void amrex::Amr::defBaseLevel	(	Real	strt_time,
		const BoxArray *	lev0_grids = `nullptr`,
		const Vector< int > *	pmap = `nullptr`
	)

protected

Define and initialize the coarsest level using optional level-0 grids lev0_grids and map pmap.

◆ deleteDerivePlotVar()

void amrex::Amr::deleteDerivePlotVar ( const std::string & name )

static

Remove name from the full derived list.

Parameters

name	Derived quantity identifier.

◆ deleteDeriveSmallPlotVar()

void amrex::Amr::deleteDeriveSmallPlotVar ( const std::string & name )

static

Remove name from the small derived list.

Parameters

name	Derived quantity identifier.

◆ deleteStatePlotVar()

void amrex::Amr::deleteStatePlotVar ( const std::string & name )

static

Remove name from the full-plot list if present.

Parameters

name	State variable identifier.

◆ derive() [1/3]

Vector< std::unique_ptr< MultiFab > > amrex::Amr::derive	(	const std::string &	name,
		amrex::Real	time,
		int	ngrow
	)

Compute derived data on all levels and return as owning MultiFabs.

Parameters

name	Identifier registered with AmrLevel::derive().
time	Physical time at which the derived results should be evaluated.
ngrow	Number of ghost cells to fill (applied uniformly to all levels).

Returns: Vector of MultiFabs, slot lev containing the data for that level.

◆ derive() [2/3]

void amrex::Amr::derive	(	const std::string &	name,
		Real	time,
		const Vector< MultiFab * > &	mf,
		int	dcomp
	)

Compute derived data on all levels and store it in the supplied MultiFabs.

Parameters

name	Identifier registered with AmrLevel::derive().
time	Physical time at which to evaluate the derived quantity.
mf	Per-level buffers that will receive the results.
dcomp	Destination component inside each MultiFab `mf` entry.

◆ derive() [3/3]

std::unique_ptr< MultiFab > amrex::Amr::derive	(	const std::string &	name,
		Real	time,
		int	lev,
		int	ngrow
	)

Build a MultiFab containing the derived quantity named name.

Parameters

name	Identifier registered with AmrLevel::derive().
time	Physical time at which the quantity should be evaluated.
lev	AMR level on which to compute.
ngrow	Number of ghost cells to fill in the new MultiFab.

Returns: Owning pointer to a MultiFab populated with the requested data.

◆ derivePlotVars()

static const std::list< std::string > & amrex::Amr::derivePlotVars ( )

inlinestaticnoexcept

The names of derived variables to output in the plotfile. They can be set using the amr.derive_plot_vars variable in a ParmParse inputs file.

◆ deriveSmallPlotVars()

static const std::list< std::string > & amrex::Amr::deriveSmallPlotVars ( )

inlinestaticnoexcept

List of derived quantities included when writing small plot files.

◆ dtLevel() [1/2]

const Vector< Real > & amrex::Amr::dtLevel ( ) const

inlinenoexcept

Vector of time steps (dt) for all levels.

◆ dtLevel() [2/2]

Real amrex::Amr::dtLevel ( int level ) const

inlinenoexcept

Time step currently stored for level level.

◆ dtMin()

Real amrex::Amr::dtMin ( int level ) const

inlinenoexcept

Max time step (typically physics-limited) for level level.

◆ ErrorEst()

void amrex::Amr::ErrorEst	(	int	lev,
		TagBoxArray &	tags,
		Real	time,
		int	ngrow
	)

overrideprotectedvirtual

Default error-estimation driver; forwards to the levelbld-defined callbacks.

Parameters

lev	Level being tagged.
tags	Tag arrays populated by derived routines.
time	Physical time passed to tagging functors.
ngrow	Number of ghost cells available in `tags`.

Implements amrex::AmrCore.

◆ fillDerivePlotVarList()

void amrex::Amr::fillDerivePlotVarList ( )

static

Fill the list of derive_plot_vars with all derived quantities.

◆ fillDeriveSmallPlotVarList()

void amrex::Amr::fillDeriveSmallPlotVarList ( )

static

Populate derive_small_plot_vars with every registered derived quantity.

◆ fillStatePlotVarList()

void amrex::Amr::fillStatePlotVarList ( )

static

Fill the list of state_plot_vars with all of the state quantities.

◆ fillStateSmallPlotVarList()

void amrex::Amr::fillStateSmallPlotVarList ( )

static

Populate state_small_plot_vars with every state quantity registered on AmrLevel 0.

◆ Finalize()

void amrex::Amr::Finalize ( )

static

Release global Amr static resources allocated by Initialize().

◆ FinalizeInit()

void amrex::Amr::FinalizeInit	(	Real	strt_time,
		Real	stop_time
	)

Second half of initial initialization; pairs with InitializeInit() using times strt_time and stop_time.

◆ finalizeInSitu()

int amrex::Amr::finalizeInSitu ( )

staticprotected

Tear down in-situ infrastructure; returns 0 on success.

◆ getAmrLevels()

Vector< std::unique_ptr< AmrLevel > > & amrex::Amr::getAmrLevels ( )

noexcept

Return the container of level objects (index 0..finest).

◆ GetAreaNotToTag()

BoxArray amrex::Amr::GetAreaNotToTag ( int lev )

overrideprotectedvirtual

Return cached regions that must not be tagged on level lev.

Reimplemented from amrex::AmrMesh.

◆ getInitialBA()

const Vector< BoxArray > & amrex::Amr::getInitialBA ( )

staticnoexcept

Returns: Collection of BoxArrays that define the initial grid hierarchy.

◆ getIntersectHiX()

BoundaryPointList & amrex::Amr::getIntersectHiX ( )

inlinenoexcept

Returns: Intersection points between the boundary and the high-X plane.

◆ getIntersectHiY()

BoundaryPointList & amrex::Amr::getIntersectHiY ( )

inlinenoexcept

Returns: Intersection points between the boundary and the high-Y plane.

◆ getIntersectHiZ()

BoundaryPointList & amrex::Amr::getIntersectHiZ ( )

inlinenoexcept

Returns: Intersection points between the boundary and the high-Z plane.

◆ getIntersectLoX()

BoundaryPointList & amrex::Amr::getIntersectLoX ( )

inlinenoexcept

Returns: Intersection points between the domain boundary and the low-X plane.

◆ getIntersectLoY()

BoundaryPointList & amrex::Amr::getIntersectLoY ( )

inlinenoexcept

Returns: Intersection points between the boundary and the low-Y plane.

◆ getIntersectLoZ()

BoundaryPointList & amrex::Amr::getIntersectLoZ ( )

inlinenoexcept

Returns: Intersection points between the boundary and the low-Z plane.

◆ getLevel()

AmrLevel & amrex::Amr::getLevel ( int lev )

inlinenoexcept

Access the AmrLevel object stored at index lev.

Parameters

lev	Level index (0 = coarsest).

◆ grid_places()

void amrex::Amr::grid_places	(	int	lbase,
		Real	time,
		int &	new_finest,
		Vector< BoxArray > &	new_grids
	)

protected

Define new grid locations (called from regrid) and store them in new_grids.

Parameters

lbase	Coarsest level that may change.
time	Physical time used when tagging/refining.
new_finest	Output: index of the resulting finest level.
new_grids	Output: BoxArrays describing each new level.

◆ init()

void amrex::Amr::init	(	Real	strt_time,
		Real	stop_time
	)

virtual

Initialize hierarchy state (grid creation, initial conditions, etc.).

Parameters

strt_time	Simulation start time.
stop_time	Optional stop time for the initial solve (used by restart logic).

◆ InitAmr()

void amrex::Amr::InitAmr ( )

Initialize Amr-wide defaults and parse the amr.* ParmParse options.

This drives LevelBld::variableSetUp(), resets bookkeeping (plot/checkpoint cadence, logging, etc.), and seeds shared resources before grids are created.

◆ initialBa()

static const BoxArray & amrex::Amr::initialBa ( int level )

inlinestaticnoexcept

Return the user-specified BoxArray that initializes level level (1-based).

Parameters

level Logical level index (1-based).

◆ initialBaLevels()

static int amrex::Amr::initialBaLevels ( )

inlinestaticnoexcept

Returns: Number of levels for which grids were explicitly provided via inputs.

◆ initialInit()

void amrex::Amr::initialInit	(	Real	strt_time,
		Real	stop_time,
		const BoxArray *	lev0_grids = `nullptr`,
		const Vector< int > *	pmap = `nullptr`
	)

protected

Initialize the grid hierarchy (called by Amr::init()).

Parameters

strt_time	Simulation start time.
stop_time	Optional time limit for the initialization phase.
lev0_grids	Optional user-defined BoxArray for level 0.
pmap	Optional processor map that pairs with `lev0_grids`.

◆ Initialize()

void amrex::Amr::Initialize ( )

static

Initialize global, Amr-wide static state (e.g., ParmParse defaults, logs).

◆ InitializeInit()

void amrex::Amr::InitializeInit	(	Real	strt_time,
		Real	stop_time,
		const BoxArray *	lev0_grids = `nullptr`,
		const Vector< int > *	pmap = `nullptr`
	)

First half of the two-phase initialization used by initialInit().

Parameters

strt_time	Simulation start time.
stop_time	Optional stop time for the initial solve.
lev0_grids	Optional user-supplied level-0 grids.
pmap	Optional processor map matching `lev0_grids`.

◆ initInSitu()

int amrex::Amr::initInSitu ( )

staticprotected

Set up in-situ analysis hooks; returns 0 on success.

◆ initPltAndChk()

void amrex::Amr::initPltAndChk ( )

protected

Initialize plot/checkpoint cadence, names, and counters from inputs.

◆ initSubcycle()

void amrex::Amr::initSubcycle ( )

protected

Parse ParmParse state and initialize subcycling-related arrays/flags.

◆ InstallNewDistributionMap()

void amrex::Amr::InstallNewDistributionMap	(	int	lev,
		const DistributionMapping &	newdm
	)

Replace the distribution map on level lev with newdm and update metadata.

Parameters

lev	Level index whose data will be remapped.
newdm	DistributionMapping describing the new ownership of level `lev` grids.

◆ isDerivePlotVar()

bool amrex::Amr::isDerivePlotVar ( const std::string & name )

staticnoexcept

Return true if name is already registered for full derived-output.

Parameters

name	Derived quantity identifier.

◆ isDeriveSmallPlotVar()

bool amrex::Amr::isDeriveSmallPlotVar ( const std::string & name )

staticnoexcept

Return true if name is already registered for small derived-output.

Parameters

name	Derived quantity identifier.

◆ isStatePlotVar()

bool amrex::Amr::isStatePlotVar ( const std::string & name )

static

Return true if name is already registered for full plotfiles.

Parameters

name	State variable identifier.

◆ isStateSmallPlotVar()

bool amrex::Amr::isStateSmallPlotVar ( const std::string & name )

static

Return true if name is already registered for small plotfiles.

Parameters

name	State variable identifier.

◆ level_being_advanced()

int amrex::Amr::level_being_advanced ( ) const

inlinenoexcept

What is "level" in Amr::timeStep? This is only relevant if we are still in Amr::timeStep; it is set back to -1 on leaving Amr::timeStep.

◆ levelCount()

int amrex::Amr::levelCount ( int lev ) const

inlinenoexcept

Which cycle number are we on for level lev?

◆ levelSteps()

int amrex::Amr::levelSteps ( int lev ) const

inlinenoexcept

Number of time steps completed so far on level lev.

◆ LoadBalanceLevel0()

void amrex::Amr::LoadBalanceLevel0 ( Real time )

protected

Compute and install a new distribution map for level 0.

Parameters

time	Simulation time at which load-balancing decisions are made.

◆ makeLoadBalanceDistributionMap()

DistributionMapping amrex::Amr::makeLoadBalanceDistributionMap	(	int	lev,
		Real	time,
		const BoxArray &	ba
	)		const

protected

Build a DistributionMapping for level lev at time time using grid layout ba.

Returns: Load-balanced DistributionMapping suitable for the supplied BoxArray.

◆ MakeNewLevelFromCoarse()

void amrex::Amr::MakeNewLevelFromCoarse	(	int	lev,
		Real	time,
		const BoxArray &	ba,
		const DistributionMapping &	dm
	)

inlineoverrideprotectedvirtual

Make a new level using provided metadata and populate it from the next coarser level.

Parameters

lev	Level index being created.
time	Simulation time when the level is initialized.
ba	BoxArray describing the new grids.
dm	Distribution mapping describing ownership of those grids.

Implements amrex::AmrCore.

◆ MakeNewLevelFromScratch()

void amrex::Amr::MakeNewLevelFromScratch	(	int	lev,
		Real	time,
		const BoxArray &	ba,
		const DistributionMapping &	dm
	)

inlineoverrideprotectedvirtual

Create and fill a new level from scratch.

Only invoked during initialization; derived classes must allocate and populate all data for level lev using the supplied metadata.

Implements amrex::AmrCore.

◆ ManualTagsPlacement()

void amrex::Amr::ManualTagsPlacement	(	int	lev,
		TagBoxArray &	tags,
		const Vector< IntVect > &	bf_lev
	)

overrideprotectedvirtual

Allow derived classes to override tagging manually on level lev.

Parameters

lev	Level being tagged.
tags	Tag arrays that may be modified in-place.
bf_lev	Buffer sizes supplied by Amr::regrid().

Reimplemented from amrex::AmrMesh.

◆ nCycle()

int amrex::Amr::nCycle ( int level ) const

inlinenoexcept

Number of subcycled time steps taken per coarse step on level level.

◆ NumDataLogs()

int amrex::Amr::NumDataLogs ( )

noexcept

Returns: Number of datalog streams that have been opened so far.

◆ numGrids() [1/2]

int amrex::Amr::numGrids ( )

noexcept

Returns: Total number of grids currently allocated across all levels.

◆ numGrids() [2/2]

int amrex::Amr::numGrids ( int lev )

noexcept

Returns: Number of grids at level lev.

◆ okToContinue()

int amrex::Amr::okToContinue ( )

noexcept

Returns: Nonzero if the driver should continue advancing.

◆ okToRegrid()

bool amrex::Amr::okToRegrid ( int level )

noexcept

Return true if level level is permitted to regrid on this step.

Parameters

level Level index being queried.

◆ operator=() [1/2]

Amr & amrex::Amr::operator= ( Amr && rhs )

delete

Move assignment is disabled to keep ownership contracts simple.

◆ operator=() [2/2]

Amr & amrex::Amr::operator= ( const Amr & rhs )

delete

Copy assignment is likewise disabled.

◆ Plot_Files_Output()

bool amrex::Amr::Plot_Files_Output ( )

static

Write out plotfiles (True/False)?

◆ plotInt()

int amrex::Amr::plotInt ( ) const

inlinenoexcept

Number of time steps between plot files.

◆ plotLogPer()

Real amrex::Amr::plotLogPer ( ) const

inlinenoexcept

Spacing in log10(time) of logarithmically spaced plot files.

◆ plotMaxLevel()

int amrex::Amr::plotMaxLevel ( ) const

inlinenoexcept

Maximum level index to include when writing plot files.

◆ plotPer()

Real amrex::Amr::plotPer ( ) const

inlinenoexcept

Time between plot files.

◆ printGridInfo()

void amrex::Amr::printGridInfo	(	std::ostream &	os,
		int	min_lev,
		int	max_lev
	)

protected

Print per-level grid metadata to os for levels [min_lev, max_lev].

Parameters

os	Output stream receiving the report.
min_lev	Smallest AMR level to describe.
max_lev	Largest AMR level to describe.

◆ readProbinFile()

void amrex::Amr::readProbinFile ( int & init )

protected

Read the probin file, updating the flag init that tracks initialization iterations.

◆ RedistributeParticles()

void amrex::Amr::RedistributeParticles ( )

Trigger a particle redistribution pass across all levels.

Mirrors AmrLevel::particle_redistribute() but drives the full hierarchy.

◆ regrid()

void amrex::Amr::regrid	(	int	lbase,
		Real	time,
		bool	initial = `false`
	)

overridevirtual

Rebuild grid hierarchy finer than lbase.

Parameters

lbase	Base level (levels <= `lbase` are unchanged).
time	Physical time used when tagging/refining.
initial	Whether this call happens during initialization (affects logging and I/O).

Reimplemented from amrex::AmrCore.

◆ regrid_level_0_on_restart()

void amrex::Amr::regrid_level_0_on_restart ( )

protectedvirtual

Regrid level 0 on restart.

◆ regridInt()

int amrex::Amr::regridInt ( int lev ) const

inlinenoexcept

Interval (in steps) between regrids on level lev.

◆ RegridOnly()

void amrex::Amr::RegridOnly	(	Real	time,
		bool	do_io = `true`
	)

Regrid the hierarchy at physical time time without advancing any levels.

Parameters

time	Physical time used during tagging/refinement.
do_io	When true, emit log messages describing the regrid.

◆ RegridOnRestart()

bool amrex::Amr::RegridOnRestart ( )

staticnoexcept

Whether to regrid right after restart.

◆ RemakeLevel()

void amrex::Amr::RemakeLevel	(	int	lev,
		Real	time,
		const BoxArray &	ba,
		const DistributionMapping &	dm
	)

inlineoverrideprotectedvirtual

Remake an existing level using provided metadata and refill from old data.

Parameters

lev	Level index being regenerated.
time	Simulation time to stamp on the data.
ba	New BoxArray layout for that level.
dm	Distribution mapping describing ownership.

Implements amrex::AmrCore.

◆ restart()

void amrex::Amr::restart ( const std::string & filename )

protected

Restart from a checkpoint file named filename.

◆ setBoundaryGeometry() [1/2]

void amrex::Amr::setBoundaryGeometry	(	BoundaryPointList &	IntersectLoX,
		BoundaryPointList &	IntersectHiX,
		BoundaryPointList &	IntersectLoY,
		BoundaryPointList &	IntersectHiY
	)

inlinenoexcept

Specialized version: register intersection points for faces orthogonal to X/Y.

Define BoundaryPointLists that give the intersections of the external geometry with constant (i,k) and (j,k) planes on the coarsest level.

Parameters

IntersectLoX	Intersection list for the low-X face.
IntersectHiX	Intersection list for the high-X face.
IntersectLoY	Intersection list for the low-Y face.
IntersectHiY	Intersection list for the high-Y face.

◆ setBoundaryGeometry() [2/2]

void amrex::Amr::setBoundaryGeometry	(	BoundaryPointList &	IntersectLoX,
		BoundaryPointList &	IntersectHiX,
		BoundaryPointList &	IntersectLoY,
		BoundaryPointList &	IntersectHiY,
		BoundaryPointList &	IntersectLoZ,
		BoundaryPointList &	IntersectHiZ
	)

inlinenoexcept

General version: register intersections for all Cartesian faces.

Define BoundaryPointLists that give the intersections of the external geometry with constant (i,k), (j,k), and (i,j) planes on the coarsest level.

Parameters

IntersectLoX	Intersection list for the low-X face.
IntersectHiX	Intersection list for the high-X face.
IntersectLoY	Intersection list for the low-Y face.
IntersectHiY	Intersection list for the high-Y face.
IntersectLoZ	Intersection list for the low-Z face.
IntersectHiZ	Intersection list for the high-Z face.

◆ setComputeNewDtOnRegrid()

static void amrex::Amr::setComputeNewDtOnRegrid ( bool flag )

inlinestatic

Toggle whether new time steps are recomputed immediately after each regrid (flag=true recomputes).

◆ setCumTime()

void amrex::Amr::setCumTime ( Real t )

inlinenoexcept

Set the accumulated physical time to t.

◆ setDtLevel() [1/2]

void amrex::Amr::setDtLevel ( const Vector< Real > & dt_lev )

noexcept

Set per-level time steps to the values in dt_lev.

◆ setDtLevel() [2/2]

void amrex::Amr::setDtLevel	(	Real	dt,
		int	lev
	)

noexcept

Set the time step stored at AMR level lev to dt.

◆ setDtMin()

void amrex::Amr::setDtMin ( const Vector< Real > & dt_min_in )

noexcept

Override the maximum allowable dt (typically CFL-limited) for each level using dt_min_in.

◆ setLevelCount()

void amrex::Amr::setLevelCount	(	int	lev,
		int	n
	)

inlinenoexcept

Set the current cycle count for level lev.

Parameters

lev	Level index to update.
n	New cycle number.

◆ setLevelSteps()

void amrex::Amr::setLevelSteps	(	int	lev,
		int	n
	)

inlinenoexcept

Override the recorded time-step count for level lev.

Parameters

lev	Level index to update.
n	New time-step count.

◆ setNCycle()

void amrex::Amr::setNCycle ( const Vector< int > & ns )

noexcept

Provide the number of time subcycles per level via ns.

◆ setRecordDataInfo()

void amrex::Amr::setRecordDataInfo	(	int	i,
		const std::string &	filename
	)

protected

Configure the i th datalog stream to mirror file filename.

◆ setRecordGridInfo()

void amrex::Amr::setRecordGridInfo ( const std::string & filename )

protected

Record the log filename filename used when dumping grid info metadata.

◆ setRecordRunInfo()

void amrex::Amr::setRecordRunInfo ( const std::string & filename )

protected

Record the log filename filename used when writing detailed run information.

◆ setRecordRunInfoTerse()

void amrex::Amr::setRecordRunInfoTerse ( const std::string & filename )

protected

Record the log filename filename used for terse run information.

◆ setStartTime()

void amrex::Amr::setStartTime ( Real t )

inlinenoexcept

Set the recorded start time to t.

◆ smallplotInt()

int amrex::Amr::smallplotInt ( ) const

inlinenoexcept

Number of time steps between small plot files.

◆ smallplotLogPer()

Real amrex::Amr::smallplotLogPer ( ) const

inlinenoexcept

Spacing in log10(time) of logarithmically spaced small plot files.

◆ smallplotPer()

Real amrex::Amr::smallplotPer ( ) const

inlinenoexcept

Time between plot files.

◆ startTime()

Real amrex::Amr::startTime ( ) const

inlinenoexcept

Physical time this simulation started.

◆ statePlotVars()

static const std::list< std::string > & amrex::Amr::statePlotVars ( )

inlinestaticnoexcept

The names of state variables to output in the plotfile. They can be set using the amr.plot_vars variable in a ParmParse inputs file.

◆ stateSmallPlotVars()

static const std::list< std::string > & amrex::Amr::stateSmallPlotVars ( )

inlinestaticnoexcept

List of state variables written to the reduced “small” plot files.

◆ stepOfLastCheckPoint()

int amrex::Amr::stepOfLastCheckPoint ( ) const

inlinenoexcept

Return the AMR step index associated with the most recent checkpoint.

◆ stepOfLastPlotFile()

int amrex::Amr::stepOfLastPlotFile ( ) const

inlinenoexcept

Return the AMR step index associated with the most recent plot file.

◆ stepOfLastSmallPlotFile()

int amrex::Amr::stepOfLastSmallPlotFile ( ) const

inlinenoexcept

Return the AMR step index associated with the most recent small plot file.

◆ subCycle()

int amrex::Amr::subCycle ( ) const

inlinenoexcept

Subcycle in time?

◆ subcyclingMode()

const std::string & amrex::Amr::subcyclingMode ( ) const

inlinenoexcept

How are we subcycling?

◆ theRestartFile()

const std::string & amrex::Amr::theRestartFile ( ) const

inlinenoexcept

Name of the most recent restart checkpoint file.

◆ theRestartPlotFile()

const std::string & amrex::Amr::theRestartPlotFile ( ) const

inlinenoexcept

Name of the restart plotfile.

◆ timeStep()

void amrex::Amr::timeStep	(	int	level,
		Real	time,
		int	iteration,
		int	niter,
		Real	stop_time
	)

protectedvirtual

Do a single time step on level level.

Parameters

level	Level index to advance.
time	Physical time at the beginning of the step.
iteration	Which sub-iteration of this coarse step we are in.
niter	Total number of iterations that will run on this level.
stop_time	Optional physical time limit that halts advancement when reached.

◆ updateInSitu()

int amrex::Amr::updateInSitu ( )

protected

Drive any per-step in-situ actions; returns 0 on success.

◆ UsingPrecreateDirectories()

bool amrex::Amr::UsingPrecreateDirectories ( )

staticnoexcept

Whether plot/checkpoint writers pre-create directories (helps avoid races on some filesystems).

◆ writePlotNow()

bool amrex::Amr::writePlotNow ( )

protectednoexcept

Whether to write a plotfile now.

◆ writeSmallPlotFile()

void amrex::Amr::writeSmallPlotFile ( )

virtual

Write the reduced “small plot” file (subset of variables/levels) to disk.

◆ writeSmallPlotNow()

bool amrex::Amr::writeSmallPlotNow ( )

protectednoexcept

Whether to emit a small plot file on this step.

Member Data Documentation

◆ abort_on_stream_retry_failure

bool amrex::Amr::abort_on_stream_retry_failure

protected

◆ amr_level

Vector<std::unique_ptr<AmrLevel> > amrex::Amr::amr_level

protected

Vector of levels.

◆ bUserStopRequest

bool amrex::Amr::bUserStopRequest

protected

◆ check_file_root

std::string amrex::Amr::check_file_root

protected

Root name of checkpoint file.

◆ check_int

int amrex::Amr::check_int

protected

How often checkpoint (# time steps).

◆ check_per

Real amrex::Amr::check_per

protected

How often checkpoint (units of time).

◆ compute_new_dt_on_regrid

bool amrex::Amr::compute_new_dt_on_regrid

staticprotected

◆ cumtime

Real amrex::Amr::cumtime = std::numeric_limits<Real>::lowest()

protected

Physical time variable.

◆ datalog

Vector<std::unique_ptr<std::fstream> > amrex::Amr::datalog

protected

◆ datalogname

Vector<std::string> amrex::Amr::datalogname

protected

◆ derive_plot_vars

std::list< std::string > amrex::Amr::derive_plot_vars

staticprotected

Derived Vars to dump to plotfile.

◆ derive_small_plot_vars

std::list< std::string > amrex::Amr::derive_small_plot_vars

staticprotected

Derived Vars to dump to small plotfile.

◆ dt_level

Vector<Real> amrex::Amr::dt_level

protected

Timestep at this level.

◆ dt_min

Vector<Real> amrex::Amr::dt_min

protected

◆ file_name_digits

int amrex::Amr::file_name_digits

protected

How many digits to use in the plotfile and checkpoint names.

◆ first_plotfile

bool amrex::Amr::first_plotfile

staticprotected

◆ first_smallplotfile

bool amrex::Amr::first_smallplotfile

static

◆ gridlog

std::ofstream amrex::Amr::gridlog

protected

◆ initial_ba

Vector< BoxArray > amrex::Amr::initial_ba

staticprotected

Array of BoxArrays read in to initially define grid hierarchy.

◆ initial_grids_file

std::string amrex::Amr::initial_grids_file

protected

Grids file that will bypass regridding only at initialization.

◆ intersect_hix

BoundaryPointList amrex::Amr::intersect_hix

◆ intersect_hiy

BoundaryPointList amrex::Amr::intersect_hiy

◆ intersect_hiz

BoundaryPointList amrex::Amr::intersect_hiz

◆ intersect_lox

BoundaryPointList amrex::Amr::intersect_lox

◆ intersect_loy

BoundaryPointList amrex::Amr::intersect_loy

◆ intersect_loz

BoundaryPointList amrex::Amr::intersect_loz

◆ last_checkpoint

int amrex::Amr::last_checkpoint

protected

Step number of previous checkpoint.

◆ last_plotfile

int amrex::Amr::last_plotfile

protected

Step number of previous plotfile.

◆ last_smallplotfile

int amrex::Amr::last_smallplotfile

protected

Step number of previous small plotfile.

◆ level_count

Vector<int> amrex::Amr::level_count

protected

◆ level_steps

Vector<int> amrex::Amr::level_steps

protected

Number of time steps at this level.

◆ levelbld

LevelBld* amrex::Amr::levelbld

protected

◆ loadbalance_level0_int

int amrex::Amr::loadbalance_level0_int

protected

◆ loadbalance_max_fac

Real amrex::Amr::loadbalance_max_fac

protected

◆ loadbalance_with_workestimates

int amrex::Amr::loadbalance_with_workestimates

protected

◆ message_int

int amrex::Amr::message_int

protected

How often checking messages touched by user, such as "stop_run".

◆ n_cycle

Vector<int> amrex::Amr::n_cycle

protected

◆ plot_file_root

std::string amrex::Amr::plot_file_root

protected

Root name of plotfile.

◆ plot_int

int amrex::Amr::plot_int

protected

How often plotfile (# of time steps)

◆ plot_log_per

Real amrex::Amr::plot_log_per

protected

How often plotfile (in units of log10(time))

◆ plot_max_level

int amrex::Amr::plot_max_level

protected

Maximum AMR level to write to a plotfile.

◆ plot_per

Real amrex::Amr::plot_per

protected

How often plotfile (in units of time)

◆ probin_file

std::string amrex::Amr::probin_file

protected

◆ record_grid_info

int amrex::Amr::record_grid_info

protected

◆ record_run_info

int amrex::Amr::record_run_info

protected

◆ record_run_info_terse

int amrex::Amr::record_run_info_terse

protected

◆ regrid_ba

Vector< BoxArray > amrex::Amr::regrid_ba

staticprotected

Array of BoxArrays read in to externally define grid hierarchy at each regrid.

◆ regrid_grids_file

std::string amrex::Amr::regrid_grids_file

protected

Grids file that will bypass regridding.

◆ regrid_int

Vector<int> amrex::Amr::regrid_int

protected

Interval between regridding.

◆ restart_chkfile

std::string amrex::Amr::restart_chkfile

protected

◆ restart_pltfile

std::string amrex::Amr::restart_pltfile

protected

◆ runlog

std::ofstream amrex::Amr::runlog

protected

◆ runlog_terse

std::ofstream amrex::Amr::runlog_terse

protected

◆ small_plot_file_root

std::string amrex::Amr::small_plot_file_root

protected

Root name of small plotfile.

◆ small_plot_int

int amrex::Amr::small_plot_int

protected

How often small plotfile (# of time steps)

◆ small_plot_log_per

Real amrex::Amr::small_plot_log_per

protected

How often small plotfile (in units of log10(time))

◆ small_plot_per

Real amrex::Amr::small_plot_per

protected

How often small plotfile (in units of time)

◆ start_time

Real amrex::Amr::start_time = std::numeric_limits<Real>::lowest()

protected

Physical time this simulation started.

◆ state_plot_vars

std::list< std::string > amrex::Amr::state_plot_vars

staticprotected

State Vars to dump to plotfile.

◆ state_small_plot_vars

std::list< std::string > amrex::Amr::state_small_plot_vars

staticprotected

State Vars to dump to small plotfile.

◆ stream_max_tries

int amrex::Amr::stream_max_tries

protected

◆ sub_cycle

int amrex::Amr::sub_cycle

protected

◆ subcycling_mode

std::string amrex::Amr::subcycling_mode

protected

Type of subcycling to use.

◆ which_level_being_advanced

int amrex::Amr::which_level_being_advanced = -1

protected

Only >=0 if we are in Amr::timeStep(level,...)

◆ write_plotfile_with_checkpoint

bool amrex::Amr::write_plotfile_with_checkpoint

protected

Write out a plotfile whenever we checkpoint.

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

/home/runner/work/amrex/amrex/Src/Amr/AMReX_Amr.H
/home/runner/work/amrex/amrex/Src/Amr/AMReX_Amr.cpp

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Amr() [1/4]

◆ Amr() [2/4]

◆ Amr() [3/4]

◆ Amr() [4/4]

◆ ~Amr()

Member Function Documentation

◆ addDerivePlotVar()

◆ addDeriveSmallPlotVar()

◆ addStatePlotVar()

◆ addStateSmallPlotVar()

◆ bldFineLevels()

◆ cellCount() [1/2]

◆ cellCount() [2/2]

◆ checkInput()

◆ checkInt()

◆ checkPer()

◆ checkPointNow()

◆ clearDerivePlotVarList()

◆ clearDeriveSmallPlotVarList()

◆ ClearLevel()

◆ clearStatePlotVarList()

◆ clearStateSmallPlotVarList()

◆ coarseTimeStep()

◆ coarseTimeStepDt()

◆ computeOptimalSubcycling()

◆ cumTime()

◆ DataLog()

◆ DataLogName()

◆ defBaseLevel()

◆ deleteDerivePlotVar()

◆ deleteDeriveSmallPlotVar()

◆ deleteStatePlotVar()

◆ derive() [1/3]

◆ derive() [2/3]

◆ derive() [3/3]

◆ derivePlotVars()

◆ deriveSmallPlotVars()

◆ dtLevel() [1/2]

◆ dtLevel() [2/2]

◆ dtMin()

◆ ErrorEst()

◆ fillDerivePlotVarList()

◆ fillDeriveSmallPlotVarList()

◆ fillStatePlotVarList()

◆ fillStateSmallPlotVarList()

◆ Finalize()

◆ FinalizeInit()

◆ finalizeInSitu()

◆ getAmrLevels()

◆ GetAreaNotToTag()

◆ getInitialBA()

◆ getIntersectHiX()

◆ getIntersectHiY()

◆ getIntersectHiZ()

◆ getIntersectLoX()

◆ getIntersectLoY()

◆ getIntersectLoZ()

◆ getLevel()

◆ grid_places()

◆ init()

◆ InitAmr()

◆ initialBa()

◆ initialBaLevels()

◆ initialInit()

◆ Initialize()

◆ InitializeInit()

◆ initInSitu()

◆ initPltAndChk()

◆ initSubcycle()

◆ InstallNewDistributionMap()