AMR Class Reference

#include <AMR.H>

Detailed Description

Framework for Berger-Oliger timestepping for AMR.

This class is a framework for Berger-Oliger timestepping for adaptive mesh refinement of time-dependent problems. It is applicable to both hyperbolic and parabolic problems. It represents a hierarchy of levels of refinement as a collection of AMRLevel objects.

The usage pattern is this:

Call define() to define the stuff that does not change throughout the run (maxlevel, refinement ratios, domain, and operator).
Modify any parameters you like (blocking factor, max grid size, etc.) using parameter-setting functions.
Call any one of the three setup functions (setupForRestart(), setupForNewAMRRun(), or setupForFixedHierarchyRun()) so AMR can set up all its internal data structures.
Call run() to run the calculation.
Call conclude() to output (to stdout) how many cells were updated and so forth.


Public Member Functions
	AMR ()
virtual	~AMR ()
void	define (int a_max_level, const Vector< int > &a_ref_ratios, const Box &a_prob_domain, const AMRLevelFactory *const a_amrLevelFact)
void	define (int a_max_level, const Vector< int > &a_ref_ratios, const ProblemDomain &a_prob_domain, const AMRLevelFactory *const a_amrLevelFact)
void	setupForRestart (HDF5Handle &a_handle)
void	setupForNewAMRRun ()
void	setupForFixedHierarchyRun (const Vector< Vector< Box > > &a_amr_grids, int a_proper_nest=1)
void	run (Real a_max_time, int a_max_step)
void	conclude () const
Parameter-setting functions
void	checkpointPrefix (const std::string &a_checkpointfile_prefix)
void	plotInterval (int a_plot_interval)
	Tells AMR to write plot files after every a_plot_interval steps.
void	checkForSteadyState (bool a_steadyState)
	Tells AMR to check each level for steady state and stop if we get there.
void	plotPeriod (Real a_plot_period)
	Tells AMR to write plot files after every a_plot_period time units.
void	schedule (RefCountedPtr< Scheduler > a_scheduler)
	Sets up a schedule for periodically-called functions.
void	checkpointInterval (int a_checkpoint_interval)
void	maxGridSize (int a_max_grid_size)
void	maxBaseGridSize (int a_max_base_grid_size)
void	dtToleranceFactor (Real a_dt_tolerance_factor)
void	setMeshRefine (RefCountedPtr< MeshRefine > a_mesh_refine_ptr)
void	fillRatio (Real a_fillRat)
void	blockFactor (int a_blockFactor)
void	gridBufferSize (int a_grid_buffer_size)
void	verbosity (int a_verbosity)
void	regridIntervals (const Vector< int > &a_regridIntervals)
void	maxDtGrow (Real a_dtGrowFactor)
void	timeEps (Real a_timeEps)
void	fixedDt (Real a_dt)
void	initialTime (Real a_initialTime)
void	useSubcyclingInTime (bool a_useSubcycling)
void	plotPrefix (const std::string &a_plotfile_prefix)
Access functions
bool	isDefined () const
bool	isSetUp () const
int	maxGridSize () const
int	maxBaseGridSize () const
int	verbosity () const
Real	maxDtGrow () const
Real	timeEps () const
Real	fixedDt () const
Vector< AMRLevel * >	getAMRLevels ()
Real	getCurrentTime () const
Static Public Attributes
static int	s_step
Protected Member Functions
int	timeStep (int a_level, int a_stepsLeft, bool a_coarseTimeBoundary)
void	clearMemory ()
void	regrid (int a_base_level)
void	initialGrid ()
void	writePlotFile () const
void	writeCheckpointFile () const
void	assignDt ()
bool	needToRegrid (int a_level, int a_numStepsLeft) const
virtual void	makeBaseLevelMesh (Vector< Box > &a_grids) const
void	setDefaultValues ()
Protected Attributes
bool	m_useSubcycling
int	m_blockFactor
Real	m_fillRatio
int	m_max_level
int	m_finest_level_old
int	m_finest_level
int	m_checkpoint_interval
int	m_plot_interval
Real	m_plot_period
Real	m_next_plot_time
int	m_max_grid_size
int	m_max_base_grid_size
Real	m_dt_tolerance_factor
Real	m_fixedDt
bool	m_checkForSteadyState
bool	m_isDefined
bool	m_isSetUp
Vector< AMRLevel * >	m_amrlevels
Vector< int >	m_ref_ratios
Vector< int >	m_reduction_factor
Vector< int >	m_regrid_intervals
Real	m_dt_base
Vector< Real >	m_dt_new
Vector< Real >	m_dt_cur
Real	m_maxDtGrow
Real	m_time_eps
RefCountedPtr< MeshRefine >	m_mesh_refine_ptr
bool	m_use_meshrefine
Vector< Vector< Box > >	m_amr_grids
int	m_cur_step
int	m_restart_step
int	m_lastcheck_step
Real	m_cur_time
Vector< int >	m_steps_since_regrid
Vector< long long >	m_cell_updates
std::string	m_plotfile_prefix
std::string	m_checkpointfile_prefix
int	m_verbosity
RefCountedPtr< Scheduler >	m_scheduler

Constructor & Destructor Documentation

AMR::AMR ( )

Default constructor. Use must subsequently call a define() function and a setup function.

virtual AMR::~AMR ( ) [virtual]

Destructor.

Member Function Documentation

void AMR::define	(	int	a_max_level,
		const Vector< int > &	a_ref_ratios,
		const Box &	a_prob_domain,
		const AMRLevelFactory *const	a_amrLevelFact
	)

Defines this object. User must call a setup function before running.

Arguments:

a_max_level (not modified): the maximum level allowed, where the base level is zero. There will be a total of a_max_level+1 levels, since level zero and level a_max_level will both exist.
a_ref_ratios (not modified): refinement ratios. There must be at least a_max_level+1 elements, or an error will result. Element zero is the base level.
a_prob_domain (not modified): problem domain on the base level.
a_amrlevelFact (not modified): pointer to a physics class factory object. The object it points to is used to construct the collection of AMRLevel objects in this AMR as objects of the physics class type. It can be destructed after this define() returns.

void AMR::define	(	int	a_max_level,
		const Vector< int > &	a_ref_ratios,
		const ProblemDomain &	a_prob_domain,
		const AMRLevelFactory *const	a_amrLevelFact
	)

Defines this object. User must call a setup function before running.

Arguments:

a_max_level (not modified): the maximum level allowed, where the base level is zero. There will be a total of a_max_level+1 levels, since level zero and level a_max_level will both exist.
a_ref_ratios (not modified): refinement ratios. There must be at least a_max_level+1 elements, or an error will result. Element zero is the base level.
a_prob_domain (not modified): problem domain on the base level.
a_amrlevelFact (not modified): pointer to a physics class factory object. The object it points to is used to construct the collection of AMRLevel objects in this AMR as objects of the physics class type. It can be destructed after this define() returns.

void AMR::setupForRestart ( HDF5Handle & a_handle )

Sets up this object from checkpointed data. User must have previously called define().

Need to call this function or setupForNewAMRRun() or setupforFixedHierarchyRun() before you run.

void AMR::setupForNewAMRRun ( )

Sets up this object for cold start. User must have previously called define().

Need to call this function or setupForRestart() or setupforFixedHierarchyRun() before you run.

void AMR::setupForFixedHierarchyRun	(	const Vector< Vector< Box > > &	a_amr_grids,
		int	a_proper_nest = `1`
	)

This function sets the hierarchy and sets m_regrid_intervals to -1 (turns off regridding). If you want to keep regridding on, call regridIntervals() after this call.

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

Runs the calculation. User must have previously called both the define() function and a setup function.

void AMR::conclude ( ) const

You should call this last. It writes the last checkpoint file and tells you how many cells you updated and all that.

void AMR::checkpointPrefix ( const std::string & a_checkpointfile_prefix )

Sets the checkpoint file prefix.

Should be called after define() and before setup.

void AMR::plotInterval ( int a_plot_interval )

Tells AMR to write plot files after every a_plot_interval steps.

void AMR::checkForSteadyState ( bool a_steadyState )

Tells AMR to check each level for steady state and stop if we get there.

void AMR::plotPeriod ( Real a_plot_period )

Tells AMR to write plot files after every a_plot_period time units.

void AMR::schedule ( RefCountedPtr< Scheduler > a_scheduler )

Sets up a schedule for periodically-called functions.

void AMR::checkpointInterval ( int a_checkpoint_interval )

Sets the interval to write checkpoint files, in terms of the base level time step.

void AMR::maxGridSize ( int a_max_grid_size )

Set the maximum grid size. Should be called after define() and before setup.

void AMR::maxBaseGridSize ( int a_max_base_grid_size )

Set the maximum grid size for level 0 grids.

Defaults to m_max_grid_size, so should be called after maxGridSize() and before setup.

void AMR::dtToleranceFactor ( Real a_dt_tolerance_factor )

Set the factor by which the current dt must exceed the new (max) dt for time subcycling to occur (i.e., reduction of the current dt by powers of 2).

void AMR::setMeshRefine ( RefCountedPtr< MeshRefine > a_mesh_refine_ptr )

Set the MeshRefine instance. Should be called before define() if you want a_mesh_refine_ptr defined.

void AMR::fillRatio ( Real a_fillRat )

Set the fill ratio for MeshRefine. Should be called after define() and before setup.

void AMR::blockFactor ( int a_blockFactor )

Set the blocking factor for MeshRefine. Should be called after define() and before setup.

void AMR::gridBufferSize ( int a_grid_buffer_size )

Set the buffering for MeshRefine. Should be called after define() and before setup.

void AMR::verbosity ( int a_verbosity )

Sets verbosity level to a_verbosity.

-inf to 0: print nothing.
1: prints a message every coarse time step.
2: also prints a message when regridding and writing files.
3: also prints function trace, and some more inf during file I/O.
4 to inf: also prints list of boxes and processor maps during regrid.

This should be OK to call any time after define and before run.

void AMR::regridIntervals ( const Vector< int > & a_regridIntervals )

Sets the regridding intervals. This should be OK to call any time after define() and before run.

void AMR::maxDtGrow ( Real a_dtGrowFactor )

Set maximum factor by which a timestep can grow.

void AMR::timeEps ( Real a_timeEps )

Set amount by which two times may differ and still be considered equal (used to determine whether we've reached stop time yet) In practice, this is multiplied by the current base-level timestep, so we consider ourselves finished if (stopTime - time) < timeEps*dt0

void AMR::fixedDt ( Real a_dt )

Set a fixed timestep. This must be called before calling setupForFixedHierarchyRun(), setupForNewAMRRun(), or setupForRestart(). Note also that fixedDt is not currently saved in checkpoint files

void AMR::initialTime ( Real a_initialTime )

Sets the initial time before starting compututation; this must be called before calling setupForFixedHierarchyRun() or setupForNewAMRRun(). Note that this will be over-ridden by m_checkpointfile if restarting using setupForRestart().

void AMR::useSubcyclingInTime ( bool a_useSubcycling )

Turn subcycling in time off or on. Default is true (use cycling).

void AMR::plotPrefix ( const std::string & a_plotfile_prefix )

Sets the plot file prefix.

Should be called after define() and before setup.

bool AMR::isDefined ( ) const

Has a define() function been called? Lots of these functions will assert fail if not.

bool AMR::isSetUp ( ) const

Has a setup function been called? If not, you can't call run().

int AMR::maxGridSize ( ) const

Returns the maximum grid size.

int AMR::maxBaseGridSize ( ) const

Returns the maximum grid size for level 0 grids.

int AMR::verbosity ( ) const

Returns current verbosity level.

-inf to 0: print nothing.
1: prints a message every coarse time step.
2: also prints a message when regridding and writing files.
3: also prints function trace, and some more inf during file I/O.
4 to inf: also prints list of boxes and processor maps during regrid.

Real AMR::maxDtGrow ( ) const

Returns current maximum factor by which a timestep can grow.

Real AMR::timeEps ( ) const

Returns amount by which two times may differ and still be considered equal (used to determine whether we've reached stop time yet)

Real AMR::fixedDt ( ) const

Returns the fixed timestep.

Vector<AMRLevel*> AMR::getAMRLevels ( )

Returns a vector of all the AMR levels

Real AMR::getCurrentTime ( ) const

Returns the current time

int AMR::timeStep	(	int	a_level,
		int	a_stepsLeft,
		bool	a_coarseTimeBoundary
	)			`[protected]`

void AMR::clearMemory ( ) [protected]

void AMR::regrid ( int a_base_level ) [protected]

void AMR::initialGrid ( ) [protected]

void AMR::writePlotFile ( ) const [protected]

void AMR::writeCheckpointFile ( ) const [protected]

void AMR::assignDt ( ) [protected]

bool AMR::needToRegrid	(	int	a_level,
		int	a_numStepsLeft
	)			const `[protected]`

virtual void AMR::makeBaseLevelMesh ( Vector< Box > & a_grids ) const [protected, virtual]

void AMR::setDefaultValues ( ) [protected]

Member Data Documentation

int AMR::s_step [static]

bool AMR::m_useSubcycling [protected]

int AMR::m_blockFactor [protected]

Real AMR::m_fillRatio [protected]

int AMR::m_max_level [protected]

int AMR::m_finest_level_old [protected]

int AMR::m_finest_level [protected]

int AMR::m_checkpoint_interval [protected]

int AMR::m_plot_interval [protected]

Real AMR::m_plot_period [protected]

Real AMR::m_next_plot_time [protected]

int AMR::m_max_grid_size [protected]

int AMR::m_max_base_grid_size [protected]

Real AMR::m_dt_tolerance_factor [protected]

Real AMR::m_fixedDt [protected]

bool AMR::m_checkForSteadyState [protected]

bool AMR::m_isDefined [protected]

bool AMR::m_isSetUp [protected]

Vector<AMRLevel*> AMR::m_amrlevels [protected]

Vector<int> AMR::m_ref_ratios [protected]

Vector<int> AMR::m_reduction_factor [protected]

Vector<int> AMR::m_regrid_intervals [protected]

Real AMR::m_dt_base [protected]

Vector<Real> AMR::m_dt_new [protected]

Vector<Real> AMR::m_dt_cur [protected]

Real AMR::m_maxDtGrow [protected]

Real AMR::m_time_eps [protected]

RefCountedPtr<MeshRefine> AMR::m_mesh_refine_ptr [protected]

bool AMR::m_use_meshrefine [protected]

Vector<Vector<Box> > AMR::m_amr_grids [protected]

int AMR::m_cur_step [protected]

int AMR::m_restart_step [protected]

int AMR::m_lastcheck_step [protected]

Real AMR::m_cur_time [protected]

Vector<int> AMR::m_steps_since_regrid [protected]

Vector<long long> AMR::m_cell_updates [protected]

std::string AMR::m_plotfile_prefix [protected]

std::string AMR::m_checkpointfile_prefix [protected]

int AMR::m_verbosity [protected]

RefCountedPtr<Scheduler> AMR::m_scheduler [protected]

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

AMR.H

AMR Class Reference

Detailed Description

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation