Class LSiloDataWriter provides functionality to output Lagrangian data for visualization via the VisIt visualization tool in the Silo data format. More...

#include <ibtk/LSiloDataWriter.h>

Inheritance diagram for IBTK::LSiloDataWriter:

[legend]

Public Member Functions
	LSiloDataWriter (std::string object_name, std::string dump_directory_name, bool register_for_restart=true)
	Constructor. More...

	~LSiloDataWriter ()
	Destructor. More...

Methods to set the hierarchy and range of levels.
std::string	d_object_name

bool	d_registered_for_restart

std::string	d_dump_directory_name

int	d_time_step_number = -1

SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > >	d_hierarchy

int	d_coarsest_ln = 0

int	d_finest_ln = 0

std::vector< int >	d_nclouds

std::vector< std::vector< std::string > >	d_cloud_names

std::vector< std::vector< int > >	d_cloud_nmarks

std::vector< std::vector< int > >	d_cloud_first_lag_idx

std::vector< int >	d_nblocks

std::vector< std::vector< std::string > >	d_block_names

std::vector< std::vector< SAMRAI::hier::IntVector< NDIM > > >	d_block_nelems

std::vector< std::vector< SAMRAI::hier::IntVector< NDIM > > >	d_block_periodic

std::vector< std::vector< int > >	d_block_first_lag_idx

std::vector< int >	d_nmbs

std::vector< std::vector< std::string > >	d_mb_names

std::vector< std::vector< int > >	d_mb_nblocks

std::vector< std::vector< std::vector< SAMRAI::hier::IntVector< NDIM > > > >	d_mb_nelems

std::vector< std::vector< std::vector< SAMRAI::hier::IntVector< NDIM > > > >	d_mb_periodic

std::vector< std::vector< std::vector< int > > >	d_mb_first_lag_idx

std::vector< int >	d_nucd_meshes

std::vector< std::vector< std::string > >	d_ucd_mesh_names

std::vector< std::vector< std::set< int > > >	d_ucd_mesh_vertices

std::vector< std::vector< std::multimap< int, std::pair< int, int > > > >	d_ucd_mesh_edge_maps

std::vector< SAMRAI::tbox::Pointer< LData > >	d_coords_data

std::vector< int >	d_nvars

std::vector< std::vector< std::string > >	d_var_names

std::vector< std::vector< int > >	d_var_start_depths

std::vector< std::vector< int > >	d_var_plot_depths

std::vector< std::vector< int > >	d_var_depths

std::vector< std::vector< SAMRAI::tbox::Pointer< LData > > >	d_var_data

std::vector< AO >	d_ao

std::vector< bool >	d_build_vec_scatters

std::vector< std::map< int, Vec > >	d_src_vec

std::vector< std::map< int, Vec > >	d_dst_vec

std::vector< std::map< int, VecScatter > >	d_vec_scatter

bool	d_summary_file_opened = false

void	setPatchHierarchy (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy)
	Reset the patch hierarchy over which operations occur. More...

void	resetLevels (int coarsest_ln, int finest_ln)
	Reset range of patch levels over which operations occur. More...

void	registerMarkerCloud (const std::string &name, int nmarks, int first_lag_idx, int level_number)
	Register or update a range of Lagrangian indices that are to be visualized as a cloud of marker particles. More...

void	registerLogicallyCartesianBlock (const std::string &name, const SAMRAI::hier::IntVector< NDIM > &nelem, const SAMRAI::hier::IntVector< NDIM > &periodic, int first_lag_idx, int level_number)
	Register or update a range of Lagrangian indices that are to be treated as a logically Cartesian block. More...

void	registerLogicallyCartesianMultiblock (const std::string &name, const std::vector< SAMRAI::hier::IntVector< NDIM > > &nelem, const std::vector< SAMRAI::hier::IntVector< NDIM > > &periodic, const std::vector< int > &first_lag_idx, int level_number)
	Register or update several ranges of Lagrangian indices that are to be treated as logically Cartesian blocks. More...

void	registerUnstructuredMesh (const std::string &name, const std::multimap< int, std::pair< int, int > > &edge_map, int level_number)
	Register or update an unstructured mesh. More...

void	registerCoordsData (SAMRAI::tbox::Pointer< LData > coords_data, int level_number)
	Register the coordinates of the curvilinear mesh with the Silo data writer. More...

void	registerVariableData (const std::string &var_name, SAMRAI::tbox::Pointer< LData > var_data, int level_number)
	Register a variable for plotting with the Silo data writer. More...

void	registerVariableData (const std::string &var_name, SAMRAI::tbox::Pointer< LData > var_data, int start_depth, int var_depth, int level_number)
	Register a variable for plotting with the Silo data writer with a specified starting depth and data depth. More...

void	registerLagrangianAO (AO &ao, int level_number)
	Register or update a single Lagrangian AO (application ordering) objects with the Silo data writer. More...

void	registerLagrangianAO (std::vector< AO > &ao, int coarsest_ln, int finest_ln)
	Register or update a collection of Lagrangian AO (application ordering) objects with the Silo data writer. More...

void	writePlotData (int time_step_number, double simulation_time)
	Write the plot data to disk. More...

void	putToDatabase (SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > db) override

	LSiloDataWriter ()=delete
	Default constructor. More...

	LSiloDataWriter (const LSiloDataWriter &from)=delete
	Copy constructor. More...

LSiloDataWriter &	operator= (const LSiloDataWriter &that)=delete
	Assignment operator. More...

void	buildVecScatters (AO &ao, int level_number)
	Build the VecScatter objects required to communicate data for plotting. More...

void	getFromRestart ()

Detailed Description

For more information about Silo, see the Silo manual here.

Constructor & Destructor Documentation

◆ LSiloDataWriter() [1/3]

IBTK::LSiloDataWriter::LSiloDataWriter	(	std::string	object_name,
		std::string	dump_directory_name,
		bool	register_for_restart = `true`
	)

Parameters

object_name	String used for error reporting.
dump_directory_name	String indicating the directory where visualization data is to be written.
register_for_restart	Boolean indicating whether to register this object with the restart manager.

◆ ~LSiloDataWriter()

IBTK::LSiloDataWriter::~LSiloDataWriter ( )

◆ LSiloDataWriter() [2/3]

IBTK::LSiloDataWriter::LSiloDataWriter ( )

privatedelete

Note: This constructor is not implemented and should not be used.

◆ LSiloDataWriter() [3/3]

IBTK::LSiloDataWriter::LSiloDataWriter ( const LSiloDataWriter & from )

privatedelete

Note: This constructor is not implemented and should not be used.

Parameters

from	The value to copy to this object.

Member Function Documentation

◆ setPatchHierarchy()

void IBTK::LSiloDataWriter::setPatchHierarchy ( SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy )

◆ resetLevels()

void IBTK::LSiloDataWriter::resetLevels	(	int	coarsest_ln,
		int	finest_ln
	)

◆ registerMarkerCloud()

void IBTK::LSiloDataWriter::registerMarkerCloud	(	const std::string &	name,
		int	nmarks,
		int	first_lag_idx,
		int	level_number
	)

Note: This method is not collective over all MPI processes. A particular cloud of markers must be registered on only one MPI process.

◆ registerLogicallyCartesianBlock()

void IBTK::LSiloDataWriter::registerLogicallyCartesianBlock	(	const std::string &	name,
		const SAMRAI::hier::IntVector< NDIM > &	nelem,
		const SAMRAI::hier::IntVector< NDIM > &	periodic,
		int	first_lag_idx,
		int	level_number
	)

Note: This method is not collective over all MPI processes. A particular block of indices must be registered on only one MPI process.

◆ registerLogicallyCartesianMultiblock()

void IBTK::LSiloDataWriter::registerLogicallyCartesianMultiblock	(	const std::string &	name,
		const std::vector< SAMRAI::hier::IntVector< NDIM > > &	nelem,
		const std::vector< SAMRAI::hier::IntVector< NDIM > > &	periodic,
		const std::vector< int > &	first_lag_idx,
		int	level_number
	)

Note: This method is not collective over all MPI processes. A particular block of indices must be registered on only one MPI process.

◆ registerUnstructuredMesh()

void IBTK::LSiloDataWriter::registerUnstructuredMesh	(	const std::string &	name,
		const std::multimap< int, std::pair< int, int > > &	edge_map,
		int	level_number
	)

Note: This method is not collective over all MPI processes. A particular collection of indices must be registered on only one MPI process.

◆ registerCoordsData()

void IBTK::LSiloDataWriter::registerCoordsData	(	SAMRAI::tbox::Pointer< LData >	coords_data,
		int	level_number
	)

◆ registerVariableData() [1/2]

void IBTK::LSiloDataWriter::registerVariableData	(	const std::string &	var_name,
		SAMRAI::tbox::Pointer< LData >	var_data,
		int	level_number
	)

◆ registerVariableData() [2/2]

void IBTK::LSiloDataWriter::registerVariableData	(	const std::string &	var_name,
		SAMRAI::tbox::Pointer< LData >	var_data,
		int	start_depth,
		int	var_depth,
		int	level_number
	)

◆ registerLagrangianAO() [1/2]

void IBTK::LSiloDataWriter::registerLagrangianAO	(	AO &	ao,
		int	level_number
	)

These AO objects are used to map between (fixed) Lagrangian indices and (time-dependent) PETSc indices. Each time that the AO objects are reset (e.g., during adaptive regridding), the new AO objects must be supplied to the Silo data writer.

◆ registerLagrangianAO() [2/2]

void IBTK::LSiloDataWriter::registerLagrangianAO	(	std::vector< AO > &	ao,
		int	coarsest_ln,
		int	finest_ln
	)

These AO objects are used to map between (fixed) Lagrangian indices and (time-dependent) PETSc indices. Each time that the AO objects are reset (e.g., during adaptive regridding), the new AO objects must be supplied to the Silo data writer.

◆ writePlotData()

void IBTK::LSiloDataWriter::writePlotData	(	int	time_step_number,
		double	simulation_time
	)

◆ putToDatabase()

void IBTK::LSiloDataWriter::putToDatabase ( SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > db )

overridevirtual

Write out object state to the given database.

When assertion checking is active, database pointer must be non-null.

Implements SAMRAI::tbox::Serializable.

◆ operator=()

LSiloDataWriter& IBTK::LSiloDataWriter::operator= ( const LSiloDataWriter & that )

privatedelete

Note: This operator is not implemented and should not be used.

Parameters

that	The value to assign to this object.

Returns: A reference to this object.

◆ buildVecScatters()

void IBTK::LSiloDataWriter::buildVecScatters	(	AO &	ao,
		int	level_number
	)

private

◆ getFromRestart()

void IBTK::LSiloDataWriter::getFromRestart ( )

private

Read object state from the restart file and initialize class data members. The database from which the restart data is read is determined by the object_name specified in the constructor.

Unrecoverable Errors:

The database corresponding to object_name is not found in the restart file.
The class version number and restart version number do not match.

Member Data Documentation

◆ d_object_name

std::string IBTK::LSiloDataWriter::d_object_name

private

◆ d_registered_for_restart

bool IBTK::LSiloDataWriter::d_registered_for_restart

private

◆ d_dump_directory_name

std::string IBTK::LSiloDataWriter::d_dump_directory_name

private

◆ d_time_step_number

int IBTK::LSiloDataWriter::d_time_step_number = -1

private

◆ d_hierarchy

SAMRAI::tbox::Pointer<SAMRAI::hier::PatchHierarchy<NDIM> > IBTK::LSiloDataWriter::d_hierarchy

private

◆ d_coarsest_ln

int IBTK::LSiloDataWriter::d_coarsest_ln = 0

private

◆ d_finest_ln

int IBTK::LSiloDataWriter::d_finest_ln = 0

private

◆ d_nclouds

std::vector<int> IBTK::LSiloDataWriter::d_nclouds

private

◆ d_cloud_names

std::vector<std::vector<std::string> > IBTK::LSiloDataWriter::d_cloud_names

private

◆ d_cloud_nmarks

std::vector<std::vector<int> > IBTK::LSiloDataWriter::d_cloud_nmarks

private

◆ d_cloud_first_lag_idx

std::vector<std::vector<int> > IBTK::LSiloDataWriter::d_cloud_first_lag_idx

private

◆ d_nblocks

std::vector<int> IBTK::LSiloDataWriter::d_nblocks

private

◆ d_block_names

std::vector<std::vector<std::string> > IBTK::LSiloDataWriter::d_block_names

private

◆ d_block_nelems

std::vector<std::vector<SAMRAI::hier::IntVector<NDIM> > > IBTK::LSiloDataWriter::d_block_nelems

private

◆ d_block_periodic

std::vector<std::vector<SAMRAI::hier::IntVector<NDIM> > > IBTK::LSiloDataWriter::d_block_periodic

private

◆ d_block_first_lag_idx

std::vector<std::vector<int> > IBTK::LSiloDataWriter::d_block_first_lag_idx

private

◆ d_nmbs

std::vector<int> IBTK::LSiloDataWriter::d_nmbs

private

◆ d_mb_names

std::vector<std::vector<std::string> > IBTK::LSiloDataWriter::d_mb_names

private

◆ d_mb_nblocks

std::vector<std::vector<int> > IBTK::LSiloDataWriter::d_mb_nblocks

private

◆ d_mb_nelems

std::vector<std::vector<std::vector<SAMRAI::hier::IntVector<NDIM> > > > IBTK::LSiloDataWriter::d_mb_nelems

private

◆ d_mb_periodic

std::vector<std::vector<std::vector<SAMRAI::hier::IntVector<NDIM> > > > IBTK::LSiloDataWriter::d_mb_periodic

private

◆ d_mb_first_lag_idx

std::vector<std::vector<std::vector<int> > > IBTK::LSiloDataWriter::d_mb_first_lag_idx

private

◆ d_nucd_meshes

std::vector<int> IBTK::LSiloDataWriter::d_nucd_meshes

private

◆ d_ucd_mesh_names

std::vector<std::vector<std::string> > IBTK::LSiloDataWriter::d_ucd_mesh_names

private

◆ d_ucd_mesh_vertices

std::vector<std::vector<std::set<int> > > IBTK::LSiloDataWriter::d_ucd_mesh_vertices

private

◆ d_ucd_mesh_edge_maps

std::vector<std::vector<std::multimap<int, std::pair<int, int> > > > IBTK::LSiloDataWriter::d_ucd_mesh_edge_maps

private

◆ d_coords_data

std::vector<SAMRAI::tbox::Pointer<LData> > IBTK::LSiloDataWriter::d_coords_data

private

◆ d_nvars

std::vector<int> IBTK::LSiloDataWriter::d_nvars

private

◆ d_var_names

std::vector<std::vector<std::string> > IBTK::LSiloDataWriter::d_var_names

private

◆ d_var_start_depths

std::vector<std::vector<int> > IBTK::LSiloDataWriter::d_var_start_depths

private

◆ d_var_plot_depths

std::vector<std::vector<int> > IBTK::LSiloDataWriter::d_var_plot_depths

private

◆ d_var_depths

std::vector<std::vector<int> > IBTK::LSiloDataWriter::d_var_depths

private

◆ d_var_data

std::vector<std::vector<SAMRAI::tbox::Pointer<LData> > > IBTK::LSiloDataWriter::d_var_data

private

◆ d_ao

std::vector<AO> IBTK::LSiloDataWriter::d_ao

private

◆ d_build_vec_scatters

std::vector<bool> IBTK::LSiloDataWriter::d_build_vec_scatters

private

◆ d_src_vec

std::vector<std::map<int, Vec> > IBTK::LSiloDataWriter::d_src_vec

private

◆ d_dst_vec

std::vector<std::map<int, Vec> > IBTK::LSiloDataWriter::d_dst_vec

private

◆ d_vec_scatter

std::vector<std::map<int, VecScatter> > IBTK::LSiloDataWriter::d_vec_scatter

private

◆ d_summary_file_opened

bool IBTK::LSiloDataWriter::d_summary_file_opened = false

private

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

ibtk/include/ibtk/LSiloDataWriter.h

Public Member Functions

Methods to set the hierarchy and range of levels.

Detailed Description

Constructor & Destructor Documentation

◆ LSiloDataWriter() [1/3]

◆ ~LSiloDataWriter()

◆ LSiloDataWriter() [2/3]

◆ LSiloDataWriter() [3/3]

Member Function Documentation

◆ setPatchHierarchy()

◆ resetLevels()

◆ registerMarkerCloud()

◆ registerLogicallyCartesianBlock()

◆ registerLogicallyCartesianMultiblock()

◆ registerUnstructuredMesh()

◆ registerCoordsData()

◆ registerVariableData() [1/2]

◆ registerVariableData() [2/2]

◆ registerLagrangianAO() [1/2]

◆ registerLagrangianAO() [2/2]

◆ writePlotData()

◆ putToDatabase()

◆ operator=()

◆ buildVecScatters()

◆ getFromRestart()

Member Data Documentation

◆ d_object_name

◆ d_registered_for_restart

◆ d_dump_directory_name

◆ d_time_step_number

◆ d_hierarchy

◆ d_coarsest_ln

◆ d_finest_ln

◆ d_nclouds

◆ d_cloud_names

◆ d_cloud_nmarks

◆ d_cloud_first_lag_idx

◆ d_nblocks

◆ d_block_names

◆ d_block_nelems

◆ d_block_periodic

◆ d_block_first_lag_idx

◆ d_nmbs

◆ d_mb_names

◆ d_mb_nblocks

◆ d_mb_nelems

◆ d_mb_periodic

◆ d_mb_first_lag_idx

◆ d_nucd_meshes

◆ d_ucd_mesh_names

◆ d_ucd_mesh_vertices

◆ d_ucd_mesh_edge_maps

◆ d_coords_data

◆ d_nvars

◆ d_var_names

◆ d_var_start_depths

◆ d_var_plot_depths

◆ d_var_depths

◆ d_var_data

◆ d_ao

◆ d_build_vec_scatters

◆ d_src_vec

◆ d_dst_vec

◆ d_vec_scatter

◆ d_summary_file_opened