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PAmrNS Class Reference

Class to manage non-subcycled advance for AMRINS with particles. More...

#include <PAmrNS.H>

Collaboration diagram for PAmrNS:

[legend]List of all members.

Public Methods
	PAmrNS ()
	default constructor
	PAmrNS (const ProblemDomain &a_vectDomain, const Vector< int > &a_vectRefRatio, const RealVect &a_domainLength, int a_maxLevel)
	full constructor -- calls matching define function
	~PAmrNS ()
	destructor.
void	define (const ProblemDomain &a_baseDomain, const Vector< int > &a_vectRefRatio, const RealVect &a_domainLength, int a_maxLevel)
	full define function
void	setupForFixedHierarchyRun (Vector< Vector< Box > > &a_vectBoxes)
	set up grids, etc for fixed-hiearchy run
void	setupForAmrRun ()
	set up grids, etc for AMR run
void	setupForRestart (const string &a_restartFile)
	set up for restart
void	setupForRestart (const HDF5Handle &a_restartFile)
	set up for restart
Real	doRun (Real a_maxTime, int a_maxStep)
	advance solution. returns time of final solution
void	conclude ()
	write final checkpoint and plot files, tells final stats, etc.
void	checkpointInterval (int a_checkpointInterval)
	related I/O stuff
void	plotInterval (int a_plotInterval)
void	checkpointPrefix (const string &a_prefix)
void	plotPrefix (const string &a_prefix)
void	maxGridSize (int a_maxGridSize)
void	maxBaseGridSize (int a_maxBaseGridSize)
void	fillRatio (Real a_fillRatio)
void	blockFactor (int a_blockFactor)
void	regridInterval (int a_regridInterval)
void	maxDtGrow (Real &a_maxDtGrow)
void	fixedDt (Real a_dt)
void	CFL (Real a_cfl)
	set CFL number
void	particleCFL (Real a_particle_cfl)
	set CFL number for computing timestep based on particles
void	refinementThreshold (Real a_refine_threshold)
	set refinement threshold
void	limitSolverCoarsening (bool a_limitSolverCoarsening)
	set solver parameter
void	verbosity (int a_verbosity)
	set verbosity level
int	finestLevel () const
	what is the finest defined level? (may be less than maxLevel)
int	maxLevel () const
	what is the finest allowable level?
bool	isEmpty (int a_level) const
	is a_level an empty level?
Real	Dx (int a_level) const
Real	Nu () const
	viscous coefficient
void	setPhysBC (const PhysBCUtil &a_BC)
	sets physical BC object
bool	isDefined () const
	has this object been defined?
Protected Methods
void	advance (Real a_dt)
	advance by one timestep (returns what, if anything?)
void	postTimeStep ()
	things to do after a timestep
void	tagCells (Vector< IntVectSet > &a_tags)
	create tags
void	tagCellsLevel (IntVectSet &a_tags, int a_level)
	create tags
void	tagCellsInit (Vector< IntVectSet > &a_tags)
	create tags at initialization
void	regrid ()
	regrid
void	postRegrid ()
	perform any post-regridding ops
void	initialGrid (const Vector< Vector< Box > > &a_new_grids, int a_baseLevel, bool a_clearStorage=false)
	initialize grids -- does load balancing as well
void	initialGrid (const Vector< DisjointBoxLayout > &a_new_grids, const Vector< DisjointBoxLayout > &a_new_particle_grids, int a_baseLevel, bool a_clearStorage=false)
	initialize grids -- no need to load-balance.
void	initialData ()
	initialize data
void	postInitialize ()
	things do do after initialization
Real	computeDt ()
	compute dt
Real	computeInitialDt ()
	compute dt with initial data
void	computeVorticity (LevelData< FArrayBox > &a_vorticity, int a_level) const
	compute vorticity on level a_level
void	computeKineticEnergy (LevelData< FArrayBox > &a_energy, int a_level) const
	compute kinetic energy on a_level (only on interior cells)
Real	particleKineticEnergy () const
	returns kinetic energy of all the particles in valid cells on all levels
void	dumpParticlesASCII (std::ostream &os) const
	dumps ASCII list of particles
void	dumpLoadBalanceInfo () const
	dumps load balance stats
LevelData< FArrayBox > &	newVel (int a_level)
const LevelData< FArrayBox > &	newVel (int a_level) const
LevelData< FArrayBox > &	oldVel (int a_level)
const LevelData< FArrayBox > &	oldVel (int a_level) const
void	velocity (LevelData< FArrayBox > &a_vel, Real a_time, int a_level) const
	returns velocity at time t
LevelData< BinFab< DragParticle > > &	particles (int a_level)
	returns particles
const LevelData< BinFab< DragParticle > > &	particles (int a_level) const
	returns particles (const version)
int	numParticles (int a_level) const
	number of particles on this AMR level
LevelData< FArrayBox > &	newScal (const int a_comp, int a_level)
const LevelData< FArrayBox > &	newScal (const int a_comp, int a_level) const
LevelData< FArrayBox > &	oldScal (const int a_comp, int a_level)
const LevelData< FArrayBox > &	oldScal (const int a_comp, int a_level) const
void	scalars (LevelData< FArrayBox > &a_scalars, const Real a_time, const int a_comp, int a_level) const
	returns scalars at time t
PhysBCUtil *	getPhysBCPtr () const
	gets physical BC object
void	loadBalance (Vector< DisjointBoxLayout > &a_vectGrids, Vector< DisjointBoxLayout > &a_vectParticleGrids, const Vector< Vector< Box > > &a_vectBoxes, int a_lbase)
void	setup ()
	set up the AMR hierarchy, etc for a_vectGrids.
void	regrid (const Vector< Vector< Box > > &a_new_grids)
	regrid once new boxes have been generated
void	defineParticles (List< DragParticle > &a_particles) const
	define particle list for entire domain
void	readParameters ()
	read parameters from parmParse database
void	finestLevel (int a_finest_level)
	set whether this is the finest level or not
void	swapOldAndNewStates ()
	move new-time state into old-time state -- also advances time by dt
void	resetStates (const Real a_time)
	exchange old and new states, resets time to a_time
void	computeAdvectionVelocities (Vector< LevelData< FluxBox > * > &a_adv_vel, Vector< LevelData< FArrayBox > * > &a_phi, Vector< LevelData< FArrayBox > * > &a_dragForce)
	compute advection velocities
void	predictVelocities (Vector< LevelData< FArrayBox > * > &a_uDelU, Vector< LevelData< FluxBox > * > &a_advVel, Vector< LevelData< FArrayBox > * > &a_phi, Vector< LevelData< FArrayBox > * > &a_dragForce)
void	computeUStar (Vector< LevelData< FArrayBox > * > &a_uStar, Vector< LevelData< FArrayBox > * > &a_dragForce, Vector< LevelData< FArrayBox > * > &a_Pi)
void	updateParticlePositions (Vector< LevelData< FArrayBox > * > &a_newDrag, Vector< LevelData< BinFab< DragParticle > > * > &a_particles, const Vector< LevelData< FArrayBox > * > &a_fluidVel, bool a_completeUpdate)
	move particles and compute new-time drag forcing
void	updateParticleForces (Vector< LevelData< BinFab< DragParticle > > * > &a_particles)
	update particle forces
void	interpVelToParticles (Vector< LevelData< BinFab< DragParticle > > * > &a_particles, const Vector< LevelData< FArrayBox > * > &a_velocity)
	update particle velocities by interpolating a_vel to particles
void	advectScalar (Vector< LevelData< FArrayBox > * > &a_new_scal, Vector< LevelData< FArrayBox > * > &a_old_scal, Vector< LevelData< FluxBox > * > &a_adv_vel, OldPhysIBC *a_scalIBC, Real a_dt)
	do scalar advection -- assumes all BC's already done
void	advectDiffuseScalar (Vector< LevelData< FArrayBox > * > &a_new_scal, Vector< LevelData< FArrayBox > * > &a_old_scal, Vector< LevelData< FluxBox > * > &a_adv_vel, const Real &a_diffusive_coeff, DomainGhostBC &a_scalPhysBC, OldPhysIBC *a_scalIBC, Real a_dt)
	advect/diffuse scalar -- assumes all BC's already done?
void	initializePressure ()
	manages pressure initialization after init or regrid
void	computeLapVel (Vector< LevelData< FArrayBox > * > &a_lapVel, Vector< LevelData< FArrayBox > * > &a_vel)
	compute Laplacian(velocity)
void	computeLapScal (Vector< LevelData< FArrayBox > * > &a_lapScal, Vector< LevelData< FArrayBox > * > &a_scal, DomainGhostBC &a_physBC)
	compute Laplacian(scalars)
void	fillVelocity (Vector< LevelData< FArrayBox > * > &a_vel, Real a_time)
	fill grown velocity field using piecewise-constant interp
void	fillVelocity (Vector< LevelData< FArrayBox > * > &a_vel, Real a_time, int vel_comp, int dest_comp, int num_comp)
	fill grown velocity field using piecewise-constant interp
void	fillScalars (Vector< LevelData< FArrayBox > * > &a_scal, Real a_time, const int a_comp) const
	fill interior and boundary cells (assume a_scal already sized)
int	numPlotComps () const
	number of components in plotfiles
void	getPlotDataNames (Vector< string > &a_vectNames)
	names of plot data components
void	getPlotData (Vector< LevelData< FArrayBox > * > &a_plot_data)
	stuff plotfile data -- not const because of ghost cell issues
void	fillCheckpointData (Vector< LevelData< FArrayBox > * > &a_vectData, Vector< string > &a_checkDataNames)
	allocate and stuff cell-centered checkpoint data.
void	setDefaultValues ()
	set default values for parameters at initialization
Protected Attributes
Vector< int >	m_vectRefRatio
	refinement ratios
Vector< ProblemDomain >	m_vectDomain
	problem domains
Vector< Real >	m_vectDx
	grid spacings
Vector< DisjointBoxLayout >	m_vectGrids
	grid hierarchy
Vector< DisjointBoxLayout >	m_vectParticleGrids
	grid hierarchy for particles
Vector< Vector< Box > >	m_vectBoxes
	need to save boxes?
int	m_maxLevel
	maximum allowable level
int	m_finestLevel
	finest extant level
int	m_regrid_interval
	how many timesteps between regridding
int	m_block_factor
	blocking factor
Real	m_fill_ratio
	grid effiency for meshrefine
int	m_nesting_radius
	proper nesting radius
int	m_max_box_size
	max box size
int	m_max_base_box_size
	max box size on level 0 (default is same as max_box_size)
Real	m_time
int	m_cur_step
Real	m_dt
Vector< LevelData< FArrayBox > * >	m_vectOldVel
	velocity vector at old time
Vector< LevelData< FArrayBox > * >	m_vectNewVel
	velocity vector at new time
Vector< LevelData< FArrayBox > * >	m_vectPi
	pressure from projection
Vector< LevelData< BinFab< DragParticle > > * >	m_vectParticles
	particles
Vector< Vector< LevelData< FArrayBox > * > >	m_vectOldScal
	scalars at old time
Vector< Vector< LevelData< FArrayBox > * > >	m_vectNewScal
	scalars at new time
int	m_num_vel_comps
	number of components of m_state (vel comps + lambda)
int	m_num_scal_comps
	number of scalars
int	m_max_scal_comps
	maximum possible number of scalar components
Vector< Real >	m_scal_coeffs
	diffusion coefficients for scalar advection-diffusion
RealVect	m_domLength
	size of physical domain
Real	m_init_shrink
	factor to shrink initial timestep
Real	m_max_dt
	maximum allowable timestep
Real	m_min_dt
	minimum allowable timestep
Real	m_prescribedDt
Real	m_max_dt_grow
int	m_verbosity
	how verbose to make output?
bool	m_project_initial_vel
	should we project initial velocity field (default is yes)
bool	m_update_velocity
	if this is false, velocity field is not updated... (useful for debugging)
bool	m_initialize_pressures
	should we initialize pressures after grid generation & regridding?
int	m_num_init_passes
	number of times to iterate when initializing pressures
bool	m_set_bogus_values
	debugging option -- initially set arrays to m_bogus_value
Real	m_bogus_value
	debugging option -- value to which arrays are initially set
bool	m_tag_vorticity
	tag on vorticity?
Real	m_vort_factor
	factor for tagging -- tag if vorticity greater than factor*max_vort
bool	m_tag_particles
	tag on particles?
int	m_tags_grow
	amount by which to grow tagged regions before calling meshrefine
int	m_viscous_solver_type
	viscous solver type: 0 = backwards euler, 1=Crank-Nicolson, 2=TGA
Real	m_viscous_solver_tol
	viscous solver tolerance (defaults to 1e-7)
int	m_viscous_num_smooth_up
	multigrid parameter for viscous solves
int	m_viscous_num_smooth_down
	multigrid parameter for viscous solves
bool	m_limitSolverCoarsening
Real	m_nu
	viscosity
bool	m_doRestart
	true if we're starting from a restart
bool	m_do_particles
	if true, do particle stuff, if false, don't
bool	m_read_particles_from_file
	read particle info from file?
string	m_particle_file
	file containing particle info
Real	m_particle_drag_coeff
	particle drag coefficient
RealVect	m_particle_body_force
	particle body force (gravity)
Real	m_particle_epsilon
	particle delta function parameter
Real	m_spreading_radius
	spreading radius for particle projector
Real	m_correction_radius
	safety radius for particle projector
int	m_particle_grids_buffer
	amount to grow auxiliary grids for particles
bool	m_use_image_particles
	if true, use image particles in particle projector near phys boundaries
int	m_order_vel_interp
	order of velocity interpolation for particles
bool	m_limit_vel_interp
	if order_vel_interp > 0, should we limit slopes?
int	m_particle_update_type
	method to update particle positions, velocities
bool	m_specifyInitialGrids
	do we specify initial grids in a gridFile?
string	m_initialGridFile
	gridfile where initial grids are spec'd, if relevant
bool	m_init_vel_from_vorticity
	initialize velocity field from vorticity field
Real	m_backgroundVel
	background velocity (in the z-direction)
bool	m_write_particles
	include particles in plotfile?
bool	m_write_divergence
	include divergence in plotfile?
bool	m_write_time_derivatives
	include du/dt in plotfile?
bool	m_write_vorticity
	include vorticity in plotfile?
bool	m_write_scalars
	include scalars in plotfile?
bool	m_write_dScalar_dt
	include d(scalars)/dt in plotfile?
bool	m_write_error
	include error (if there is an exact solution) in plotfile?
bool	m_write_proc_ids
	include processor distribution visualization in plotfile?
bool	m_compute_scal_err
	compute error and report norms after composite timesteps
bool	m_write_initial_solve_rhs
	dump out initial vorticity->stream function RHS's into plotfiles
bool	m_write_grids
	dump out grid info
Real	m_cfl
	cfl number
Real	m_particleCFL
	cfl number for particle updates
Vector< CoarseAverage * >	m_coarse_average
	averaging from fine to coarse level for velocity
Vector< CoarseAverage * >	m_coarse_average_scal
	averaging from fine to coarse level for scalar
AmrProjector	m_projection
	cell-centered projection object
AMRParticleProjector	m_particle_projector
	particle drag force projector object
int	m_particleProjCoarsening
	parameter for particleProjector
Vector< QuadCFInterp * >	m_velCFInterp_ptrs
	does quadratic coarse-fine interpolation for velocities
Vector< PoissonOp * >	m_scalarsPoissonOp_ptrs
	PoissonOp for advected scalars (for diffusion).
Vector< PatchAdvection * >	m_patchGod
Real	m_refine_threshold
	refinement threshold for regridding
PhysBCUtil *	m_physBCPtr
	physical BC object
int	m_plot_interval
	interval between plotfiles
int	m_check_interval
	interval between checkpoint files
int	m_lastcheck_step
	bookkeeping stuff last timestep we wrote a checkpoint file
int	m_restart_step
	if we're restarting, the timestep at restart
Vector< int >	m_cell_updates
	counts number of cells updated on each level
bool	m_ppInit
bool	m_isDefined
std::string	m_plotfile_prefix
std::string	m_checkpointfile_prefix
Static Protected Attributes
const char *	s_vel_names [CH_SPACEDIM]
	names of components
const char *	s_scal_names [NUM_SCAL_TYPES]
	names of scalars

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Detailed Description

Class to manage non-subcycled advance for AMRINS with particles.

This class manages the entire AMR hierarchy and non-subcycled advance for the AMR Incompressible Navier-Stokes with suspended drag particles problem

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Constructor & Destructor Documentation

PAmrNS::PAmrNS (    )

default constructor

PAmrNS::PAmrNS (  const ProblemDomain &    a_vectDomain, const Vector< int > &    a_vectRefRatio, const RealVect &    a_domainLength, int    a_maxLevel )

full constructor -- calls matching define function note that the PAmrNS class defines its own grid hierarchy

PAmrNS::~PAmrNS (    )

destructor.

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Member Function Documentation

void PAmrNS::advance (  Real    a_dt )  [protected]

advance by one timestep (returns what, if anything?)

void PAmrNS::advectDiffuseScalar (  Vector< LevelData< FArrayBox > * > &    a_new_scal, Vector< LevelData< FArrayBox > * > &    a_old_scal, Vector< LevelData< FluxBox > * > &    a_adv_vel, const Real &    a_diffusive_coeff, DomainGhostBC &    a_scalPhysBC, OldPhysIBC *    a_scalIBC, Real    a_dt )  [protected]

advect/diffuse scalar -- assumes all BC's already done?

void PAmrNS::advectScalar (  Vector< LevelData< FArrayBox > * > &    a_new_scal, Vector< LevelData< FArrayBox > * > &    a_old_scal, Vector< LevelData< FluxBox > * > &    a_adv_vel, OldPhysIBC *    a_scalIBC, Real    a_dt )  [protected]

do scalar advection -- assumes all BC's already done

void PAmrNS::blockFactor (  int    a_blockFactor )

void PAmrNS::CFL (  Real    a_cfl )

set CFL number

void PAmrNS::checkpointInterval (  int    a_checkpointInterval )

related I/O stuff

void PAmrNS::checkpointPrefix (  const string &    a_prefix )

void PAmrNS::computeAdvectionVelocities (  Vector< LevelData< FluxBox > * > &    a_adv_vel, Vector< LevelData< FArrayBox > * > &    a_phi, Vector< LevelData< FArrayBox > * > &    a_dragForce )  [protected]

compute advection velocities a_phi is the correction from the MAC projection.

Real PAmrNS::computeDt (    )  [protected]

compute dt

Real PAmrNS::computeInitialDt (    )  [protected]

compute dt with initial data

void PAmrNS::computeKineticEnergy (  LevelData< FArrayBox > &    a_energy, int    a_level )  const [protected]

compute kinetic energy on a_level (only on interior cells)

void PAmrNS::computeLapScal (  Vector< LevelData< FArrayBox > * > &    a_lapScal, Vector< LevelData< FArrayBox > * > &    a_scal, DomainGhostBC &    a_physBC )  [protected]

compute Laplacian(scalars)

void PAmrNS::computeLapVel (  Vector< LevelData< FArrayBox > * > &    a_lapVel, Vector< LevelData< FArrayBox > * > &    a_vel )  [protected]

compute Laplacian(velocity)

void PAmrNS::computeUStar (  Vector< LevelData< FArrayBox > * > &    a_uStar, Vector< LevelData< FArrayBox > * > &    a_dragForce, Vector< LevelData< FArrayBox > * > &    a_Pi )  [protected]

void PAmrNS::computeVorticity (  LevelData< FArrayBox > &    a_vorticity, int    a_level )  const [protected]

compute vorticity on level a_level

void PAmrNS::conclude (    )

write final checkpoint and plot files, tells final stats, etc.

void PAmrNS::define (  const ProblemDomain &    a_baseDomain, const Vector< int > &    a_vectRefRatio, const RealVect &    a_domainLength, int    a_maxLevel )

full define function

void PAmrNS::defineParticles (  List< DragParticle > &    a_particles )  const [protected]

define particle list for entire domain Defines all particles in domain; a_particles will then be distributed among the AMR levels

Real PAmrNS::doRun (  Real    a_maxTime, int    a_maxStep )

advance solution. returns time of final solution

void PAmrNS::dumpLoadBalanceInfo (    )  const [protected]

dumps load balance stats for each box, dumps box no, numPts, and numParticles, then sums for each proc -- for now, dump to std output

void PAmrNS::dumpParticlesASCII (  std::ostream &    os )  const [protected]

dumps ASCII list of particles

Real PAmrNS::Dx (  int    a_level )  const [inline]

void PAmrNS::fillCheckpointData (  Vector< LevelData< FArrayBox > * > &    a_vectData, Vector< string > &    a_checkDataNames )  [protected]

allocate and stuff cell-centered checkpoint data.

void PAmrNS::fillRatio (  Real    a_fillRatio )

void PAmrNS::fillScalars (  Vector< LevelData< FArrayBox > * > &    a_scal, Real    a_time, const int    a_comp )  const [protected]

fill interior and boundary cells (assume a_scal already sized)

void PAmrNS::fillVelocity (  Vector< LevelData< FArrayBox > * > &    a_vel, Real    a_time, int    vel_comp, int    dest_comp, int    num_comp )  [protected]

fill grown velocity field using piecewise-constant interp

void PAmrNS::fillVelocity (  Vector< LevelData< FArrayBox > * > &    a_vel, Real    a_time )  [protected]

fill grown velocity field using piecewise-constant interp

void PAmrNS::finestLevel (  int    a_finest_level )  [protected]

set whether this is the finest level or not

int PAmrNS::finestLevel (    )  const [inline]

what is the finest defined level? (may be less than maxLevel)

void PAmrNS::fixedDt (  Real    a_dt )

PhysBCUtil* PAmrNS::getPhysBCPtr (    )  const [protected]

gets physical BC object

void PAmrNS::getPlotData (  Vector< LevelData< FArrayBox > * > &    a_plot_data )  [protected]

stuff plotfile data -- not const because of ghost cell issues

void PAmrNS::getPlotDataNames (  Vector< string > &    a_vectNames )  [protected]

names of plot data components

void PAmrNS::initialData (    )  [protected]

initialize data

void PAmrNS::initialGrid (  const Vector< DisjointBoxLayout > &    a_new_grids, const Vector< DisjointBoxLayout > &    a_new_particle_grids, int    a_baseLevel, bool    a_clearStorage = false )  [protected]

initialize grids -- no need to load-balance. baseLevel is coarsest level to initialize if clearStorage = true, clear any existing storage

void PAmrNS::initialGrid (  const Vector< Vector< Box > > &    a_new_grids, int    a_baseLevel, bool    a_clearStorage = false )  [protected]

initialize grids -- does load balancing as well baseLevel is coarsest level to initialize if clearStorage = true, clear any existing storage

void PAmrNS::initializePressure (    )  [protected]

manages pressure initialization after init or regrid

void PAmrNS::interpVelToParticles (  Vector< LevelData< BinFab< DragParticle > > * > &    a_particles, const Vector< LevelData< FArrayBox > * > &    a_velocity )  [protected]

update particle velocities by interpolating a_vel to particles

bool PAmrNS::isDefined (    )  const

has this object been defined?

bool PAmrNS::isEmpty (  int    a_level )  const [inline]

is a_level an empty level?

void PAmrNS::limitSolverCoarsening (  bool    a_limitSolverCoarsening )

set solver parameter

void PAmrNS::loadBalance (  Vector< DisjointBoxLayout > &    a_vectGrids, Vector< DisjointBoxLayout > &    a_vectParticleGrids, const Vector< Vector< Box > > &    a_vectBoxes, int    a_lbase )  [protected]

void PAmrNS::maxBaseGridSize (  int    a_maxBaseGridSize )

void PAmrNS::maxDtGrow (  Real &    a_maxDtGrow )

void PAmrNS::maxGridSize (  int    a_maxGridSize )

int PAmrNS::maxLevel (    )  const [inline]

what is the finest allowable level?

const LevelData<FArrayBox>& PAmrNS::newScal (  const int    a_comp, int    a_level )  const [protected]

LevelData<FArrayBox>& PAmrNS::newScal (  const int    a_comp, int    a_level )  [protected]

const LevelData<FArrayBox>& PAmrNS::newVel (  int    a_level )  const [protected]

LevelData<FArrayBox>& PAmrNS::newVel (  int    a_level )  [protected]

Real PAmrNS::Nu (    )  const [inline]

viscous coefficient

int PAmrNS::numParticles (  int    a_level )  const [protected]

number of particles on this AMR level

int PAmrNS::numPlotComps (    )  const [protected]

number of components in plotfiles

const LevelData<FArrayBox>& PAmrNS::oldScal (  const int    a_comp, int    a_level )  const [protected]

LevelData<FArrayBox>& PAmrNS::oldScal (  const int    a_comp, int    a_level )  [protected]

const LevelData<FArrayBox>& PAmrNS::oldVel (  int    a_level )  const [protected]

LevelData<FArrayBox>& PAmrNS::oldVel (  int    a_level )  [protected]

void PAmrNS::particleCFL (  Real    a_particle_cfl )

set CFL number for computing timestep based on particles

Real PAmrNS::particleKineticEnergy (    )  const [protected]

returns kinetic energy of all the particles in valid cells on all levels

const LevelData<BinFab<DragParticle> >& PAmrNS::particles (  int    a_level )  const [protected]

returns particles (const version)

LevelData<BinFab<DragParticle> >& PAmrNS::particles (  int    a_level )  [protected]

returns particles

void PAmrNS::plotInterval (  int    a_plotInterval )

void PAmrNS::plotPrefix (  const string &    a_prefix )

void PAmrNS::postInitialize (    )  [protected]

things do do after initialization

void PAmrNS::postRegrid (    )  [protected]

perform any post-regridding ops

void PAmrNS::postTimeStep (    )  [protected]

things to do after a timestep

void PAmrNS::predictVelocities (  Vector< LevelData< FArrayBox > * > &    a_uDelU, Vector< LevelData< FluxBox > * > &    a_advVel, Vector< LevelData< FArrayBox > * > &    a_phi, Vector< LevelData< FArrayBox > * > &    a_dragForce )  [protected]

void PAmrNS::readParameters (    )  [protected]

read parameters from parmParse database

void PAmrNS::refinementThreshold (  Real    a_refine_threshold )

set refinement threshold

void PAmrNS::regrid (  const Vector< Vector< Box > > &    a_new_grids )  [protected]

regrid once new boxes have been generated

void PAmrNS::regrid (    )  [protected]

regrid

void PAmrNS::regridInterval (  int    a_regridInterval )

void PAmrNS::resetStates (  const Real    a_time )  [protected]

exchange old and new states, resets time to a_time

void PAmrNS::scalars (  LevelData< FArrayBox > &    a_scalars, const Real    a_time, const int    a_comp, int    a_level )  const [protected]

returns scalars at time t

void PAmrNS::setDefaultValues (    )  [protected]

set default values for parameters at initialization

void PAmrNS::setPhysBC (  const PhysBCUtil &    a_BC )

sets physical BC object

void PAmrNS::setup (    )  [protected]

set up the AMR hierarchy, etc for a_vectGrids.

void PAmrNS::setupForAmrRun (    )

set up grids, etc for AMR run

void PAmrNS::setupForFixedHierarchyRun (  Vector< Vector< Box > > &    a_vectBoxes )

set up grids, etc for fixed-hiearchy run

void PAmrNS::setupForRestart (  const HDF5Handle &    a_restartFile )

set up for restart

void PAmrNS::setupForRestart (  const string &    a_restartFile )

set up for restart

void PAmrNS::swapOldAndNewStates (    )  [protected]

move new-time state into old-time state -- also advances time by dt

void PAmrNS::tagCells (  Vector< IntVectSet > &    a_tags )  [protected]

create tags

void PAmrNS::tagCellsInit (  Vector< IntVectSet > &    a_tags )  [protected]

create tags at initialization

void PAmrNS::tagCellsLevel (  IntVectSet &    a_tags, int    a_level )  [protected]

create tags

void PAmrNS::updateParticleForces (  Vector< LevelData< BinFab< DragParticle > > * > &    a_particles )  [protected]

update particle forces

void PAmrNS::updateParticlePositions (  Vector< LevelData< FArrayBox > * > &    a_newDrag, Vector< LevelData< BinFab< DragParticle > > * > &    a_particles, const Vector< LevelData< FArrayBox > * > &    a_fluidVel, bool    a_completeUpdate )  [protected]

move particles and compute new-time drag forcing This is a little complicated, in order to avoid creating a second particle list. We first move particles to a predicted position P^* (where P refers to the particle state). Then, we compute an estimate of the particle forcing term at the new time and place it in a_newDrag. Then, if completeUpdate is true, we go back and correct the new particle state to be formally second-order accurate.

void PAmrNS::velocity (  LevelData< FArrayBox > &    a_vel, Real    a_time, int    a_level )  const [protected]

returns velocity at time t

void PAmrNS::verbosity (  int    a_verbosity )

set verbosity level

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Member Data Documentation

Real PAmrNS::m_backgroundVel [protected]

background velocity (in the z-direction)

int PAmrNS::m_block_factor [protected]

blocking factor

Real PAmrNS::m_bogus_value [protected]

debugging option -- value to which arrays are initially set

Vector<int> PAmrNS::m_cell_updates [protected]

counts number of cells updated on each level

Real PAmrNS::m_cfl [protected]

cfl number

int PAmrNS::m_check_interval [protected]

interval between checkpoint files

std::string PAmrNS::m_checkpointfile_prefix [protected]

Vector<CoarseAverage*> PAmrNS::m_coarse_average [protected]

averaging from fine to coarse level for velocity

Vector<CoarseAverage*> PAmrNS::m_coarse_average_scal [protected]

averaging from fine to coarse level for scalar

bool PAmrNS::m_compute_scal_err [protected]

compute error and report norms after composite timesteps

Real PAmrNS::m_correction_radius [protected]

safety radius for particle projector

int PAmrNS::m_cur_step [protected]

bool PAmrNS::m_do_particles [protected]

if true, do particle stuff, if false, don't

RealVect PAmrNS::m_domLength [protected]

size of physical domain

bool PAmrNS::m_doRestart [protected]

true if we're starting from a restart

Real PAmrNS::m_dt [protected]

Real PAmrNS::m_fill_ratio [protected]

grid effiency for meshrefine

int PAmrNS::m_finestLevel [protected]

finest extant level

Real PAmrNS::m_init_shrink [protected]

factor to shrink initial timestep

bool PAmrNS::m_init_vel_from_vorticity [protected]

initialize velocity field from vorticity field

string PAmrNS::m_initialGridFile [protected]

gridfile where initial grids are spec'd, if relevant

bool PAmrNS::m_initialize_pressures [protected]

should we initialize pressures after grid generation & regridding?

bool PAmrNS::m_isDefined [protected]

int PAmrNS::m_lastcheck_step [protected]

bookkeeping stuff last timestep we wrote a checkpoint file

bool PAmrNS::m_limit_vel_interp [protected]

if order_vel_interp > 0, should we limit slopes?

bool PAmrNS::m_limitSolverCoarsening [protected]

int PAmrNS::m_max_base_box_size [protected]

max box size on level 0 (default is same as max_box_size)

int PAmrNS::m_max_box_size [protected]

max box size

Real PAmrNS::m_max_dt [protected]

maximum allowable timestep

Real PAmrNS::m_max_dt_grow [protected]

int PAmrNS::m_max_scal_comps [protected]

maximum possible number of scalar components

int PAmrNS::m_maxLevel [protected]

maximum allowable level

Real PAmrNS::m_min_dt [protected]

minimum allowable timestep

int PAmrNS::m_nesting_radius [protected]

proper nesting radius

Real PAmrNS::m_nu [protected]

viscosity

int PAmrNS::m_num_init_passes [protected]

number of times to iterate when initializing pressures

int PAmrNS::m_num_scal_comps [protected]

number of scalars

int PAmrNS::m_num_vel_comps [protected]

number of components of m_state (vel comps + lambda)

int PAmrNS::m_order_vel_interp [protected]

order of velocity interpolation for particles

RealVect PAmrNS::m_particle_body_force [protected]

particle body force (gravity)

Real PAmrNS::m_particle_drag_coeff [protected]

particle drag coefficient

Real PAmrNS::m_particle_epsilon [protected]

particle delta function parameter

string PAmrNS::m_particle_file [protected]

file containing particle info

int PAmrNS::m_particle_grids_buffer [protected]

amount to grow auxiliary grids for particles this is a buffer to ensure that particles don't run off of the grown grids in the ParticleProjector. It should be something along the lines of particle_cfl*regridInteval

AMRParticleProjector PAmrNS::m_particle_projector [protected]

particle drag force projector object

int PAmrNS::m_particle_update_type [protected]

method to update particle positions, velocities

Real PAmrNS::m_particleCFL [protected]

cfl number for particle updates

int PAmrNS::m_particleProjCoarsening [protected]

parameter for particleProjector

Vector<PatchAdvection*> PAmrNS::m_patchGod [protected]

PhysBCUtil* PAmrNS::m_physBCPtr [protected]

physical BC object

int PAmrNS::m_plot_interval [protected]

interval between plotfiles

std::string PAmrNS::m_plotfile_prefix [protected]

bool PAmrNS::m_ppInit [protected]

Real PAmrNS::m_prescribedDt [protected]

bool PAmrNS::m_project_initial_vel [protected]

should we project initial velocity field (default is yes)

AmrProjector PAmrNS::m_projection [protected]

cell-centered projection object

bool PAmrNS::m_read_particles_from_file [protected]

read particle info from file?

Real PAmrNS::m_refine_threshold [protected]

refinement threshold for regridding

int PAmrNS::m_regrid_interval [protected]

how many timesteps between regridding

int PAmrNS::m_restart_step [protected]

if we're restarting, the timestep at restart this is to avoid clobbering the existing checkpoint file upon restart

Vector<Real> PAmrNS::m_scal_coeffs [protected]

diffusion coefficients for scalar advection-diffusion

Vector<PoissonOp*> PAmrNS::m_scalarsPoissonOp_ptrs [protected]

PoissonOp for advected scalars (for diffusion).

bool PAmrNS::m_set_bogus_values [protected]

debugging option -- initially set arrays to m_bogus_value

bool PAmrNS::m_specifyInitialGrids [protected]

do we specify initial grids in a gridFile?

Real PAmrNS::m_spreading_radius [protected]

spreading radius for particle projector

bool PAmrNS::m_tag_particles [protected]

tag on particles?

bool PAmrNS::m_tag_vorticity [protected]

tag on vorticity?

int PAmrNS::m_tags_grow [protected]

amount by which to grow tagged regions before calling meshrefine

Real PAmrNS::m_time [protected]

bool PAmrNS::m_update_velocity [protected]

if this is false, velocity field is not updated... (useful for debugging)

bool PAmrNS::m_use_image_particles [protected]

if true, use image particles in particle projector near phys boundaries

Vector<Vector<Box> > PAmrNS::m_vectBoxes [protected]

need to save boxes?

Vector<ProblemDomain> PAmrNS::m_vectDomain [protected]

problem domains

Vector<Real> PAmrNS::m_vectDx [protected]

grid spacings

Vector<DisjointBoxLayout> PAmrNS::m_vectGrids [protected]

grid hierarchy

Vector<Vector<LevelData<FArrayBox>* > > PAmrNS::m_vectNewScal [protected]

scalars at new time

Vector<LevelData<FArrayBox>* > PAmrNS::m_vectNewVel [protected]

velocity vector at new time

Vector<Vector<LevelData<FArrayBox>* > > PAmrNS::m_vectOldScal [protected]

scalars at old time

Vector<LevelData<FArrayBox>* > PAmrNS::m_vectOldVel [protected]

velocity vector at old time

Vector<DisjointBoxLayout> PAmrNS::m_vectParticleGrids [protected]

grid hierarchy for particles

Vector<LevelData<BinFab<DragParticle> >* > PAmrNS::m_vectParticles [protected]

particles

Vector<LevelData<FArrayBox>* > PAmrNS::m_vectPi [protected]

pressure from projection

Vector<int> PAmrNS::m_vectRefRatio [protected]

refinement ratios

Vector<QuadCFInterp*> PAmrNS::m_velCFInterp_ptrs [protected]

does quadratic coarse-fine interpolation for velocities

int PAmrNS::m_verbosity [protected]

how verbose to make output?

int PAmrNS::m_viscous_num_smooth_down [protected]

multigrid parameter for viscous solves

int PAmrNS::m_viscous_num_smooth_up [protected]

multigrid parameter for viscous solves

Real PAmrNS::m_viscous_solver_tol [protected]

viscous solver tolerance (defaults to 1e-7)

int PAmrNS::m_viscous_solver_type [protected]

viscous solver type: 0 = backwards euler, 1=Crank-Nicolson, 2=TGA

Real PAmrNS::m_vort_factor [protected]

factor for tagging -- tag if vorticity greater than factor*max_vort

bool PAmrNS::m_write_divergence [protected]

include divergence in plotfile?

bool PAmrNS::m_write_dScalar_dt [protected]

include d(scalars)/dt in plotfile?

bool PAmrNS::m_write_error [protected]

include error (if there is an exact solution) in plotfile?

bool PAmrNS::m_write_grids [protected]

dump out grid info

bool PAmrNS::m_write_initial_solve_rhs [protected]

dump out initial vorticity->stream function RHS's into plotfiles

bool PAmrNS::m_write_particles [protected]

include particles in plotfile?

bool PAmrNS::m_write_proc_ids [protected]

include processor distribution visualization in plotfile?

bool PAmrNS::m_write_scalars [protected]

include scalars in plotfile?

bool PAmrNS::m_write_time_derivatives [protected]

include du/dt in plotfile?

bool PAmrNS::m_write_vorticity [protected]

include vorticity in plotfile?

const char* PAmrNS::s_scal_names[NUM_SCAL_TYPES] [static, protected]

names of scalars

const char* PAmrNS::s_vel_names[CH_SPACEDIM] [static, protected]

names of components

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

• PAmrNS.H

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