Class IBStandardInitializer is a concrete LInitStrategy that initializes the configuration of one or more Lagrangian structures from input files. More...

#include </home/runner/work/IBAMR/IBAMR/include/ibamr/IBStandardInitializer.h>

Inheritance diagram for IBAMR::IBStandardInitializer:

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Public Member Functions
	IBStandardInitializer (std::string object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db)
	Constructor.

	~IBStandardInitializer ()
	Destructor.

void	init () override
	Initialize structure specific configurations.

Public Member Functions inherited from IBAMR::IBRedundantInitializer
	IBRedundantInitializer (std::string object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db)
	Constructor.

virtual	~IBRedundantInitializer ()
	Destructor.

void	registerLSiloDataWriter (SAMRAI::tbox::Pointer< IBTK::LSiloDataWriter > silo_writer)
	Register a Silo data writer with the IB initializer object.

bool	getLevelHasLagrangianData (int level_number, bool can_be_refined) const override
	Determine whether there are any Lagrangian nodes on the specified patch level.

bool	getIsAllLagrangianDataInDomain (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy) const override

unsigned int	computeGlobalNodeCountOnPatchLevel (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, int level_number, double init_data_time, bool can_be_refined, bool initial_time) override
	Determine the number of global nodes on the specified patch level.

unsigned int	computeLocalNodeCountOnPatchLevel (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, int level_number, double init_data_time, bool can_be_refined, bool initial_time) override
	Determine the number of local nodes on the specified patch level.

void	registerInitStructureFunction (InitStructureOnLevel fcn, void *ctx=nullptr)

void	registerInitSpringDataFunction (InitSpringDataOnLevel fcn, void *ctx=nullptr)
	Register a function to initialize spring data structures on a given level.

void	registerInitXSpringDataFunction (InitXSpringDataOnLevel fcn, void *ctx=nullptr)
	Register a function to initialize xspring data structures on a given level.

void	registerInitBeamDataFunction (InitBeamDataOnLevel fcn, void *ctx=nullptr)
	Register a function to initialize beam data structures on a given level.

void	registerInitDirectorAndRodFunction (InitDirectorAndRodOnLevel fcn, void *ctx=nullptr)
	Register a funcion to initialize director and rod data structures on a given level.

void	registerInitBoundaryMassFunction (InitBoundaryMassOnLevel fcn, void *ctx=nullptr)
	Register a function to initialize massive points on a given level.

void	registerInitTargetPtFunction (InitTargetPtOnLevel fcn, void *ctx=nullptr)
	Register a function to initialize target points on a given level.

void	registerInitAnchorPtFunction (InitAnchorPtOnLevel fcn, void *ctx=nullptr)
	Register a function to initialize anchor points on a given level.

void	registerInitInstrumentationFunction (InitInstrumentationOnLevel fcn, void *ctx=nullptr)
	Register a function to initialize instrumentation data on a given level.

void	registerInitSourceFunction (InitSourceOnLevel fcn, void *ctx=nullptr)
	Register a funciton to initialize source/sink data on a given level.

void	initializeStructureIndexingOnPatchLevel (std::map< int, std::string > &strct_id_to_strct_name_map, std::map< int, std::pair< int, int > > &strct_id_to_lag_idx_range_map, int level_number, double init_data_time, bool can_be_refined, bool initial_time, IBTK::LDataManager *l_data_manager) override
	Initialize the structure indexing information on the patch level.

unsigned int	initializeDataOnPatchLevel (int lag_node_index_idx, unsigned int global_index_offset, unsigned int local_index_offset, SAMRAI::tbox::Pointer< IBTK::LData > X_data, SAMRAI::tbox::Pointer< IBTK::LData > U_data, SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, int level_number, double init_data_time, bool can_be_refined, bool initial_time, IBTK::LDataManager *l_data_manager) override
	Initialize the LNode and LData data needed to specify the configuration of the curvilinear mesh on the patch level.

unsigned int	initializeMassDataOnPatchLevel (unsigned int global_index_offset, unsigned int local_index_offset, SAMRAI::tbox::Pointer< IBTK::LData > M_data, SAMRAI::tbox::Pointer< IBTK::LData > K_data, SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, int level_number, double init_data_time, bool can_be_refined, bool initial_time, IBTK::LDataManager *l_data_manager) override
	Initialize the LData needed to specify the mass and spring constant data required by the penalty IB method.

unsigned int	initializeDirectorDataOnPatchLevel (unsigned int global_index_offset, unsigned int local_index_offset, SAMRAI::tbox::Pointer< IBTK::LData > D_data, SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, int level_number, double init_data_time, bool can_be_refined, bool initial_time, IBTK::LDataManager *l_data_manager) override
	Initialize the LNode data needed to specify director vectors required by some material models.

void	tagCellsForInitialRefinement (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, int level_number, double error_data_time, int tag_index) override
	Tag cells for initial refinement.

void	setStructureNamesOnLevel (const int &level_num, const std::vector< std::string > &strct_names)
	Set the names of the structures on a given level.

Public Member Functions inherited from IBTK::LInitStrategy
	LInitStrategy ()=default
	Default constructor.

virtual	~LInitStrategy ()=default
	Destructor.

Additional Inherited Members
Public Types inherited from IBAMR::IBRedundantInitializer
using	InitStructureOnLevel = void()(const unsigned int &strct_num, const int &level_num, int &num_vertices, std::vector< IBTK::Point > &vertex_posn, void ctx)

using	Edge = std::pair< int, int >

using	InitSpringDataOnLevel = void()(const unsigned int &strct_num, const int &level_num, std::multimap< int, Edge > &spring_map, std::map< Edge, SpringSpec, EdgeComp > &spring_spec, void ctx)

using	InitXSpringDataOnLevel = void()(const unsigned int &strct_num, const int &level_num, std::multimap< int, Edge > &xspring_map, std::map< Edge, XSpringSpec, EdgeComp > xspring_spec, void ctx)

using	InitBeamDataOnLevel = void()(const unsigned int &strct_num, const int &level_num, std::multimap< int, BeamSpec > &beam_spec, void ctx)

using	InitDirectorAndRodOnLevel = void()(const unsigned int &strct_num, const int &level_num, std::vector< std::vector< double > > &director_spec, std::multimap< int, Edge > &rod_edge_map, std::map< Edge, RodSpec, EdgeComp > &rod_spec, void ctx)

using	InitBoundaryMassOnLevel = void()(const unsigned int &strct_num, const int &level_num, std::multimap< int, BdryMassSpec > &bdry_mass_spec, void ctx)

using	InitTargetPtOnLevel = void()(const unsigned int &strct_num, const int &level_num, std::multimap< int, TargetSpec > &tg_pt_spec, void ctx)

using	InitAnchorPtOnLevel = void()(const unsigned int &strct_num, const int &level_num, std::multimap< int, AnchorSpec > &anchor_pt_spec, void ctx)

using	InitInstrumentationOnLevel = void()(const unsigned int &strct_num, const int &level_num, std::vector< std::string > &instrument_name, std::map< int, std::pair< int, int > > &instrument_spec, void ctx)

using	InitSourceOnLevel = void()(const unsigned int &strct_num, const int &level_num, std::map< int, int > &source_spec, std::vector< std::string > &source_names, std::vector< double > &source_radii, void ctx)

Protected Member Functions inherited from IBAMR::IBRedundantInitializer
	IBRedundantInitializer ()
	Default constructor.

	IBRedundantInitializer (const IBRedundantInitializer &from)=delete
	Copy constructor.

IBRedundantInitializer &	operator= (const IBRedundantInitializer &that)=delete
	Assignment operator.

void	initializeLSiloDataWriter (int level_number)
	Configure the Lagrangian Silo data writer to plot the data associated with the specified level of the locally refined Cartesian grid.

void	initializeStructurePosition ()
	Initialize vertex data programmatically.

void	initializeSprings ()
	Initialize spring data programmatically.

void	initializeXSprings ()
	Initialize xspring data programmatically.

void	initializeBeams ()
	Initialize beam data programmatically.

void	initializeDirectorAndRods ()
	Initialize director and rod data programmatically.

void	initializeBoundaryMass ()
	Initialize massive point data programmatically.

void	initializeTargetPts ()
	Initialize target point data programmatically.

void	initializeAnchorPts ()
	Initialize anchor points programmatically.

void	initializeInstrumentationData ()
	Initialize instrumentation data.

void	initializeSourceData ()
	Initialize source/sink data.

void	getPatchVertices (std::vector< std::pair< int, int > > &point_indices, SAMRAI::tbox::Pointer< SAMRAI::hier::Patch< NDIM > > patch, SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy) const
	Determine the indices of any vertices initially owned by the specified patch.

void	getPatchVerticesAtLevel (std::vector< std::pair< int, int > > &point_indices, SAMRAI::tbox::Pointer< SAMRAI::hier::Patch< NDIM > > patch, SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, int level_number) const
	Determine the indices of any vertices associated with a given level number initially located within the specified patch.

int	getCanonicalLagrangianIndex (const std::pair< int, int > &point_index, int level_number) const

IBTK::Point	getVertexPosn (const std::pair< int, int > &point_index, int level_number) const

IBTK::Point	getShiftedVertexPosn (const std::pair< int, int > &point_index, int level_number, const double domain_x_lower, const double domain_x_upper, const SAMRAI::hier::IntVector< NDIM > &periodic_shift) const

const TargetSpec &	getVertexTargetSpec (const std::pair< int, int > &point_index, int level_number) const

const AnchorSpec &	getVertexAnchorSpec (const std::pair< int, int > &point_index, int level_number) const

const BdryMassSpec &	getVertexBdryMassSpec (const std::pair< int, int > &point_index, int level_number) const

const std::vector< double > &	getVertexDirectors (const std::pair< int, int > &point_index, int level_number) const

std::pair< int, int >	getVertexInstrumentationIndices (const std::pair< int, int > &point_index, int level_number) const

int	getVertexSourceIndices (const std::pair< int, int > &point_index, int level_number) const

void	getFromInput (SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > db)

Protected Attributes inherited from IBAMR::IBRedundantInitializer
std::string	d_object_name

int	d_max_levels = -1

std::vector< bool >	d_level_is_initialized

SAMRAI::tbox::Pointer< IBTK::LSiloDataWriter >	d_silo_writer

std::vector< std::vector< std::string > >	d_base_filename

double	d_length_scale_factor = 1.0

IBTK::Vector	d_posn_shift

std::vector< std::vector< int > >	d_num_vertex

std::vector< std::vector< int > >	d_vertex_offset

std::vector< std::vector< std::vector< IBTK::Point > > >	d_vertex_posn

std::vector< std::vector< std::multimap< int, Edge > > >	d_spring_edge_map

std::vector< std::vector< std::map< Edge, SpringSpec, EdgeComp > > >	d_spring_spec_data

std::vector< std::vector< std::multimap< int, Edge > > >	d_xspring_edge_map

std::vector< std::vector< std::map< Edge, XSpringSpec, EdgeComp > > >	d_xspring_spec_data

std::vector< std::vector< std::multimap< int, BeamSpec > > >	d_beam_spec_data

std::vector< std::vector< std::multimap< int, Edge > > >	d_rod_edge_map

std::vector< std::vector< std::map< Edge, RodSpec, EdgeComp > > >	d_rod_spec_data

std::vector< std::vector< std::vector< TargetSpec > > >	d_target_spec_data

std::vector< std::vector< std::vector< AnchorSpec > > >	d_anchor_spec_data

std::vector< std::vector< std::vector< BdryMassSpec > > >	d_bdry_mass_spec_data

std::vector< std::vector< std::vector< std::vector< double > > > >	d_directors

std::vector< std::vector< std::map< int, std::pair< int, int > > > >	d_instrument_idx

std::vector< std::vector< std::map< int, int > > >	d_source_idx

std::vector< unsigned int >	d_global_index_offset

bool	d_data_processed = false

Detailed Description

Class IBStandardInitializer is a concrete LInitStrategy that initializes the configuration of one or more Lagrangian structures from input files.

Todo:: Document input database entries.

Note: "C-style" indices are used for all input files.

Vertex file format

Vertex input files end with the extension ".vertex" and have the following format for two-dimensional models:

N           # number of vertices in the file
x_0   y_0   # (x,y)-coordinates of vertex 0
x_1   y_1   # (x,y)-coordinates of vertex 1
x_2   y_2   # (x,y)-coordinates of vertex 2
...

Vertex input files end with the extension ".vertex" and have the following format for three-dimensional models:

N                 # number of vertices in the file
x_0   y_0   z_0   # (x,y,z)-coordinates of vertex 0
x_1   y_1   z_1   # (x,y,z)-coordinates of vertex 1
x_2   y_2   z_2   # (x,y,z)-coordinates of vertex 2
...

Spring file format

Spring input files end with the extension ".spring" and have the following format:

M                                            # number of links in the file
i_0   j_0   kappa_0   length_0   fcn_idx_0   # first vertex index, second vertex index, spring
constant, rest length, spring function index
i_1   j_1   kappa_1   length_1   fcn_idx_1
i_2   j_2   kappa_2   length_2   fcn_idx_2
...

Note: There is no restriction on the number of springs that may be associated with any particular node of the Lagrangian mesh.; The rest length and force function index are optional values. If they are not provided, by default the rest length will be set to the value 0.0 and the force function index will be set to 0. This corresponds to a linear spring with zero rest length.; Spring specifications are used by class LSiloDataWriter to construct unstructured mesh representations of the Lagrangian structures. Consequently, even if your structure does not have any springs, it may be worthwhile to generate a spring input file with all spring constants set to 0.0.; min(i,j) is always used as the "master" node index when constructing the corresponding IBSpringForceSpec object.

See also: IBSpringForceGen; IBSpringForceSpec

Crosslink spring file format

Crosslink spring ("x-spring") input files end with the extension ".xspring" and have the following format:

M                                            # number of links in the file
i_0   j_0   kappa_0   length_0   fcn_idx_0   # first vertex index, second vertex index, spring
constant, rest length, spring function index
i_1   j_1   kappa_1   length_1   fcn_idx_1
i_2   j_2   kappa_2   length_2   fcn_idx_2
...

Note: Unlike standard spring files, in which all indices are required to refer to points within a particular structure, x-spring files may connect points from different structures. Consequently, the node indices in an x-spring file must be global indices. Notice that global indices are determined by the order in which the structures are specified in the input file. Changes in the order in which structures are specified necessarily change the global indexing scheme.; Crosslink springs may connect only structures assigned to the same level of the locally refined grid.; There is no restriction on the number of x-springs that may be associated with any particular node of the Lagrangian mesh.; The rest length and force function index are optional values. If they are not provided, then by default the rest length will be set to the value 0.0 and the force function index will be set to 0. This corresponds to a linear spring with zero rest length.; Crosslink spring specifications are used by class LSiloDataWriter to construct unstructured mesh representations of the Lagrangian structures. Consequently, even if your structure does not have any springs, it may be worthwhile to generate a spring input file with all spring constants set to 0.0.; min(i,j) is always used as the "master" node index when constructing the corresponding IBSpringForceSpec object.

See also: IBSpringForceGen; IBSpringForceSpec

Beam file format

Beam input files end with the extension ".beam" and have the following format:

M                           # number of beams in the file
i_0   j_0   k_0   kappa_0   # first vertex index, second vertex index, third vertex index,
bending
rigidity
i_1   j_1   k_1   kappa_1
i_2   j_2   k_2   kappa_2
...

Note: There is no restriction on the number of beams that may be associated with any particular node of the Lagrangian mesh.; For each bending-resistant triple (i,j,k), it is necessary that vertex j correspond to an "interior" node, i.e., a node that is not the first or last node in the beam.; The second vertex index is always used as the "master" node index when constructing the corresponding IBBeamForceSpec object.

See also: IBBeamForceGen; IBBeamForceSpec

Rod file format

Rod input files end with the extension ".rod" and have the following format:

M                                                                                          #
number
of rods in the file
i_0   j_0   ds_0   a1_0   a2_0   a3_0   b1_0   b2_0   b3_0   kappa1_0   kappa2_0   tau_0   #
first
vertex index, second vertex index, material parameters
i_1   j_1   ds_1   a1_1   a2_1   a3_1   b1_1   b2_1   b3_1   kappa1_1   kappa2_1   tau_1
i_2   j_2   ds_2   a1_2   a2_2   a3_2   b1_2   b2_2   b3_2   kappa1_2   kappa2_2   tau_2
...

Note: There is no restriction on the number of rods that may be associated with any particular node of the Lagrangian mesh.; The first vertex index is always used as the "master" node index when constructing the corresponding IBRodForceSpec object.; The parameters kappa1, kappa2, and tau (the intrinsic curvatures and twist of the rod) are optional. If not provided in the input file, they are assumed to be zero.

See also: IBKirchhoffRodForceGen; IBRodForceSpec

Target point file format

Target point input files end with the extension ".target" and have the following format:

M                       # number of target points in the file
i_0   kappa_0   eta_0   # vertex index, penalty spring constant, penalty damping coefficient
i_1   kappa_1   eta_1
i_2   kappa_2   eta_2
...

Note: Target points are anchored to their initial positions by linear springs with the specified spring constants and with zero resting lengths. Consequently, target points approximately enforce internal Dirichlet boundary conditions. The penalty parameter provides control over the energetic penalty imposed when the position of the Lagrangian immersed boundary point deviates from that of its specified fixed location.; Damping coefficients $\eta$ are optional and are set to 0.0 if not supplied. Target points are "anchored" in place using Kelvin-Voigt viscoelastic elements.

See also: IBTargetPointForceGen; IBTargetPointForceSpec

Anchor point file format

Anchor point input files end with the extension ".anchor" and have the following format:

M                           # number of anchor points in the file
i_0                         # vertex index
i_1
i_2
...

Note: Anchor points are immersed boundary nodes that are "anchored" in place. Such points neither spread force nor interpolate velocity.

Mass point file format

Mass point input files end with the extension ".mass" and have the following format:

M                           # number of mass points in the file
i_0   mass_0   kappa_0      # vertex index, point mass, penalty spring constant
i_1   mass_1   kappa_1
i_2   mass_2   kappa_2
...

Note: Mass points are anchored to "ghost" massive particles by linear springs with the specified spring constants and with zero resting lengths. The massive particles are "isolated" and simply move according to Newton's laws. The penalty parameter provides control over the energetic penalty imposed when the position of the Lagrangian immersed boundary point deviates from that of its massive copy.

Instrumentation file format

Instrumentation input files (specifying the nodes employed to determine the time-dependent positions of flow meters and pressure gauges) end with the extension ".inst" and have the following format:

M                                      # number of instruments in the file
meter_name_0                           # meter names
meter_name_1
meter_name_2
...
N                                      # number of instrumentation points in the file
i_0   meter_idx_0   meter_node_idx_0   # vertex index, meter index, node index within meter
i_1   meter_idx_1   meter_node_idx_1
i_2   meter_idx_2   meter_node_idx_2
...

Note: Flow meters and pressure gauges are constructed out of "rings" of immersed boundary points. The flow is computed by computing the total velocity flux through a web spanning the perimeter of the flow meter. The pressure is measured at the centroid of each flow meter.

Note that each meter may have a different number of nodes specifying its perimeter; however, the values of meter_node_idx associated with a particular meter must be a continuous range of integers, starting with index 0. E.g., the following is a valid input file:

2           # number of instruments in the file
meter0      # meter names
meter1
6           # number of instrumentation points in the file
0   0   0   # perimeter of meter 0 consists of vertices 0, 1, and 2
1   0   1
2   0   2
9   1   0   # perimeter of meter 1 consists of vertices 9, 10, and 11
10  1   1
11  1   2

See also: IBInstrumentPanel; IBInstrumentationSpec

Source/sink file format

Source/sink input files (specifying the nodes employed to determine the time-dependent positions of internal sources and sinks) end with the extension ".source" and have the following format:

M                    # number of sources/sinks in the file
source_name_0        # source/sink names
source_name_1
source_name_2
...
source_radius_0      # source/sink radii
source_radius_1
source_radius_2
...
N                    # number of source/sink points in the file
i_0   source_idx_0   # vertex index, source/sink index
i_1   source_idx_1
i_2   source_idx_2
...

Note: The position of each internal source/sink is the arithmetic mean of the positions of the nodes that are associated with that source/sink.

2         # number of sources/sinks in the file
source0   # source/sink names
source1
1.0       # source/sink radii
0.5
6         # number of source/sink points in the file
0   0     # position of source0 is determined from vertices 0, 1, and 2
1   0
2   0
9   1     # position of source1 is determined from vertices 9, 10, and 11
10  1
11  1

See also: IBStandardSourceGenerator; IBSourceSpec

Director file format

Orthonormal director vector input files end with the extension ".director" and have the following format, independent of spatial dimension:

N                         # number of triads in the file
D0_x_0   D0_y_0   D0_z_0  # coordinates of director D0 associated with vertex 0
D1_x_0   D1_y_0   D1_z_0  # coordinates of director D1 associated with vertex 0
D2_x_0   D2_y_0   D2_z_0  # coordinates of director D2 associated with vertex 0
D0_x_1   D0_y_1   D0_z_1  # coordinates of director D0 associated with vertex 1
D1_x_1   D1_y_1   D1_z_1  # coordinates of director D1 associated with vertex 1
D2_x_1   D2_y_1   D2_z_1  # coordinates of director D2 associated with vertex 1
D0_x_2   D0_y_2   D0_z_2  # coordinates of director D0 associated with vertex 2
D1_x_2   D1_y_2   D1_z_2  # coordinates of director D1 associated with vertex 2
D2_x_2   D2_y_2   D2_z_2  # coordinates of director D2 associated with vertex 2
...

Member Function Documentation

◆ init()

void IBAMR::IBStandardInitializer::init ( )

overridevirtual

Initialize structure specific configurations.

This function will attempt to load, in sequence, the vertex, spring, xspring, beam, rod, target point, anchor point, boundary mass, director, instrumentation, and source files. Of these, only the vertex files are required. The instrumentation and source files will only be loaded if both enable_instrumentation or enable_sources are enabled on the input database and the input files exist. The rest will only be loaded if files with matching suffixes (e.g., .beam) are in the current working directory.

Reimplemented from IBAMR::IBRedundantInitializer.

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

/home/runner/work/IBAMR/IBAMR/include/ibamr/IBStandardInitializer.h
/home/runner/work/IBAMR/IBAMR/src/IB/IBStandardInitializer.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ init()