A class used to abstract away reading/writing files for visualization. More...

#include <HDF5writer.h>

Inheritance diagram for AMP::IO::HDF5writer:

Public Types
enum class	DecompositionType : uint8_t { SINGLE , MULTIPLE }

enum class	VectorType : uint8_t { DOUBLE , SINGLE , INT }

Public Member Functions
std::string	getExtension () const
	Function to return the file extension.

WriterProperties	getProperties () const override
	Function to get the writer properties.

	HDF5writer ()
	Default constructor.

	HDF5writer (const HDF5writer &)=delete
	Delete copy constructor.

void	readFile (const std::string &fname) override
	Function to read a file.

void	registerData (std::function< void(hid_t, std::string, Xdmf &)> fun)
	Register arbitrary data.

void	registerMatrix (std::shared_ptr< AMP::LinearAlgebra::Matrix > mat, const std::string &name="")
	Function to register a matrix.

void	registerMesh (std::shared_ptr< AMP::Mesh::Mesh > mesh, int level=1, const std::string &path=std::string())
	Function to register a mesh.

void	registerVector (std::shared_ptr< AMP::LinearAlgebra::Vector > vec, const std::string &name="")
	Function to register a vector.

virtual void	registerVector (std::shared_ptr< AMP::LinearAlgebra::Vector > vec, std::shared_ptr< AMP::Mesh::Mesh > mesh, AMP::Mesh::GeomType type, const std::string &name="", VectorType precision=VectorType::DOUBLE, bool isStatic=false)
	Function to register a vector.

virtual void	setDecomposition (int decomposition)
	Function to set the file decomposition.

void	writeFile (const std::string &fname, size_t iteration, double time=0) override
	Function to write a file.

virtual	~HDF5writer ()
	Default destructor.

Static Public Member Functions
static std::shared_ptr< AMP::IO::Writer >	buildWriter (std::shared_ptr< AMP::Database > db)
	Function to build a writer.

static std::shared_ptr< AMP::IO::Writer >	buildWriter (std::string type, AMP_MPI comm=AMP_COMM_WORLD)
	Function to build a writer.

Protected Types
using	GeomType = AMP::Mesh::GeomType

Protected Member Functions
void	createDirectories (const std::string &filename)

GlobalID	getID (const AMP_MPI &comm) const

void	registerMesh2 (std::shared_ptr< AMP::Mesh::Mesh > mesh, int level, const std::string &path, std::set< GlobalID > &base_ids)

template<class TYPE >
void	syncData (std::vector< TYPE > &data, int root) const

std::tuple< std::vector< multiMeshData >, std::map< GlobalID, baseMeshData > >	syncMultiMeshData (int root=-1) const

void	syncVectors ()

Static Protected Member Functions
static std::vector< AMP::Mesh::MeshID >	getMeshIDs (std::shared_ptr< AMP::Mesh::Mesh > mesh)

static void	getNodeElemList (std::shared_ptr< const AMP::Mesh::Mesh > mesh, const AMP::Mesh::MeshIterator &elements, AMP::Array< double > *x, AMP::Array< int > &nodelist, std::vector< AMP::Mesh::MeshElementID > &nodelist_ids)

Protected Attributes
std::map< GlobalID, baseMeshData >	d_baseMeshes

AMP_MPI	d_comm = AMP_COMM_WORLD

DecompositionType	d_decomposition = DecompositionType::MULTIPLE

std::map< GlobalID, MatrixData >	d_matrices

std::map< GlobalID, multiMeshData >	d_multiMeshes

std::map< GlobalID, VectorData >	d_vectors

std::vector< std::shared_ptr< AMP::LinearAlgebra::Vector > >	d_vectorsMesh

Private Member Functions
Xdmf::MeshData	writeBoxMesh (hid_t fid, const std::string &filename, const baseMeshData &mesh) const

Xdmf::MeshData	writeDefaultMesh (hid_t fid, const std::string &filename, const baseMeshData &mesh) const

Xdmf::MeshData	writeMesh (hid_t fid, const std::string &filename, const baseMeshData &mesh) const

Private Attributes
std::vector< std::function< void(hid_t, std::string, Xdmf &)> >	d_fun

Detailed Description

A class used to abstract away reading/writing files for visualization.

This class provides routines for reading, accessing and writing meshes and vectors using HDF5. Note: for visualization an Xdmf file will also be written

Definition at line 29 of file HDF5writer.h.

Member Typedef Documentation

◆ GeomType

using AMP::IO::Writer::GeomType = AMP::Mesh::GeomType

protectedinherited

Definition at line 219 of file Writer.h.

Member Enumeration Documentation

◆ DecompositionType

enum class AMP::IO::Writer::DecompositionType : uint8_t

stronginherited

Enumerator
SINGLE
MULTIPLE

Definition at line 51 of file Writer.h.

◆ VectorType

enum class AMP::IO::Writer::VectorType : uint8_t

stronginherited

Enumerator
DOUBLE
SINGLE
INT

Definition at line 50 of file Writer.h.

Constructor & Destructor Documentation

◆ HDF5writer() [1/2]

AMP::IO::HDF5writer::HDF5writer ( )

Default constructor.

◆ ~HDF5writer()

virtual AMP::IO::HDF5writer::~HDF5writer ( )

virtual

Default destructor.

◆ HDF5writer() [2/2]

AMP::IO::HDF5writer::HDF5writer ( const HDF5writer & )

delete

Delete copy constructor.

Member Function Documentation

◆ buildWriter() [1/2]

static std::shared_ptr< AMP::IO::Writer > AMP::IO::Writer::buildWriter ( std::shared_ptr< AMP::Database > db )

staticinherited

Function to build a writer.

This function will build a default writer for use.

Parameters

[in] db Input database for the writer

◆ buildWriter() [2/2]

static std::shared_ptr< AMP::IO::Writer > AMP::IO::Writer::buildWriter	(	std::string	type,
		AMP_MPI	comm = `AMP_COMM_WORLD`
	)

staticinherited

Function to build a writer.

This function will build a default writer for use.

Parameters

[in]	type	Writer type: "None" - An empty writer will be created "Silo" - A silo writer will be created if silo is configured, otherwise an empty writer will be created. "Ascii" - A simple ascii writer "HDF5" - A simple HDF5 writer "auto" - Choose the writer based on the comm size and compiled packages
[in]	comm	Communicator to use

◆ createDirectories()

void AMP::IO::Writer::createDirectories ( const std::string & filename )

protectedinherited

◆ getExtension()

std::string AMP::IO::Writer::getExtension ( ) const

inherited

Function to return the file extension.

◆ getID()

GlobalID AMP::IO::Writer::getID ( const AMP_MPI & comm ) const

protectedinherited

◆ getMeshIDs()

static std::vector< AMP::Mesh::MeshID > AMP::IO::Writer::getMeshIDs ( std::shared_ptr< AMP::Mesh::Mesh > mesh )

staticprotectedinherited

◆ getNodeElemList()

static void AMP::IO::Writer::getNodeElemList	(	std::shared_ptr< const AMP::Mesh::Mesh >	mesh,
		const AMP::Mesh::MeshIterator &	elements,
		AMP::Array< double > *	x,
		AMP::Array< int > &	nodelist,
		std::vector< AMP::Mesh::MeshElementID > &	nodelist_ids
	)

staticprotectedinherited

◆ getProperties()

WriterProperties AMP::IO::HDF5writer::getProperties ( ) const

overridevirtual

Function to get the writer properties.

Implements AMP::IO::Writer.

◆ readFile()

void AMP::IO::HDF5writer::readFile ( const std::string & fname )

overridevirtual

Function to read a file.

Implements AMP::IO::Writer.

◆ registerData()

void AMP::IO::HDF5writer::registerData ( std::function< void(hid_t, std::string, Xdmf &)> fun )

Register arbitrary data.

◆ registerMatrix()

void AMP::IO::Writer::registerMatrix	(	std::shared_ptr< AMP::LinearAlgebra::Matrix >	mat,
		const std::string &	name = `""`
	)

inherited

Function to register a matrix.

This function will register a matrix with the writer. This version of registerMatrix only stores the raw data.. It is not associated with a mesh.

Parameters

[in]	mat	The matrix we want to write
[in]	name	Optional name for the vector.

◆ registerMesh()

void AMP::IO::Writer::registerMesh	(	std::shared_ptr< AMP::Mesh::Mesh >	mesh,
		int	level = `1`,
		const std::string &	path = `std::string()`
	)

inherited

Function to register a mesh.

This function will register a mesh with the writer. Note: if mesh is a MultiMesh, it will register all sub meshes.

Parameters

[in]	mesh	The mesh to register
[in]	level	How many sub meshes do we want? 0: Only register the local base meshes (advanced users only) 1: Register current mesh only (default) 2: Register all meshes (do not separate for the ranks) 3: Register all mesh pieces including the individual ranks
[in]	path	The directory path for the mesh. Default is an empty string.

◆ registerMesh2()

void AMP::IO::Writer::registerMesh2	(	std::shared_ptr< AMP::Mesh::Mesh >	mesh,
		int	level,
		const std::string &	path,
		std::set< GlobalID > &	base_ids
	)

protectedinherited

◆ registerVector() [1/2]

void AMP::IO::Writer::registerVector	(	std::shared_ptr< AMP::LinearAlgebra::Vector >	vec,
		const std::string &	name = `""`
	)

inherited

Function to register a vector.

This function will register a vector with the writer. This version of registerVector only stores the raw data. It is not associated with a mesh.

Parameters

[in]	vec	The vector we want to write
[in]	name	Optional name for the vector.

◆ registerVector() [2/2]

virtual void AMP::IO::Writer::registerVector	(	std::shared_ptr< AMP::LinearAlgebra::Vector >	vec,
		std::shared_ptr< AMP::Mesh::Mesh >	mesh,
		AMP::Mesh::GeomType	type,
		const std::string &	name = `""`,
		VectorType	precision = `VectorType::DOUBLE`,
		bool	isStatic = `false`
	)

virtualinherited

Function to register a vector.

This function will register a vector with the writer and register it with the given mesh. This version of registerVector allows the data to be "stored" on the mesh for visualization or mesh-based operations.

Parameters

[in]	vec	The vector we want to write
[in]	mesh	The mesh we want to write the vector over. Note: any writers require the vector to completely cover the mesh. Note: mesh does not have to be previously registered with registerMesh.
[in]	type	The entity type we want to save (vertex, face, cell, etc.) Note: some writers only supports writing one entity type. If the vector spans multiple entity type (eg cell+vertex) the user should register the vector multiple times (one for each entity type).
[in]	name	Optional name for the vector.
[in]	precision	Desired precision in output file. Note: not all types are supported by all writers.
[in]	isStatic	Is the vectors static (constant vs time)

◆ setDecomposition()

virtual void AMP::IO::Writer::setDecomposition ( int decomposition )

virtualinherited

Function to set the file decomposition.

This function will set the method used for file IO. When writing files, there are different decompositions that affect the performance and usability of the output files. By default, this writer will generate a single file.

Parameters

[in] decomposition Decomposition method to use: 1: This will write all of the data to a single file. Note that this requires a serial write and will have the worst performance 2: Each processor will write a separate file and a separate summary file will be written. Note that this will have better performance at large scale, but will write many files simultaneously.

◆ syncData()

template<class TYPE >

void AMP::IO::Writer::syncData	(	std::vector< TYPE > &	data,
		int	root
	)		const

protectedinherited

◆ syncMultiMeshData()

std::tuple< std::vector< multiMeshData >, std::map< GlobalID, baseMeshData > > AMP::IO::Writer::syncMultiMeshData ( int root = -1 ) const

protectedinherited

◆ syncVectors()

void AMP::IO::Writer::syncVectors ( )

protectedinherited

◆ writeBoxMesh()

Xdmf::MeshData AMP::IO::HDF5writer::writeBoxMesh	(	hid_t	fid,
		const std::string &	filename,
		const baseMeshData &	mesh
	)		const

private

◆ writeDefaultMesh()

Xdmf::MeshData AMP::IO::HDF5writer::writeDefaultMesh	(	hid_t	fid,
		const std::string &	filename,
		const baseMeshData &	mesh
	)		const

private

◆ writeFile()

void AMP::IO::HDF5writer::writeFile	(	const std::string &	fname,
		size_t	iteration,
		double	time = `0`
	)

overridevirtual

Function to write a file.

This function will write a file with all mesh/vector data that was registered. If the filename included a relative or absolute path, the directory structure will be created.

Parameters

fname	The filename to use
iteration	The iteration number
time	The current simulation time

Implements AMP::IO::Writer.

◆ writeMesh()

Xdmf::MeshData AMP::IO::HDF5writer::writeMesh	(	hid_t	fid,
		const std::string &	filename,
		const baseMeshData &	mesh
	)		const

private

Member Data Documentation

◆ d_baseMeshes

std::map<GlobalID, baseMeshData> AMP::IO::Writer::d_baseMeshes

protectedinherited

Definition at line 323 of file Writer.h.

◆ d_comm

AMP_MPI AMP::IO::Writer::d_comm = AMP_COMM_WORLD

protectedinherited

Definition at line 317 of file Writer.h.

◆ d_decomposition

DecompositionType AMP::IO::Writer::d_decomposition = DecompositionType::MULTIPLE

protectedinherited

Definition at line 320 of file Writer.h.

◆ d_fun

std::vector<std::function<void( hid_t, std::string, Xdmf & )> > AMP::IO::HDF5writer::d_fun

private

Definition at line 71 of file HDF5writer.h.

◆ d_matrices

std::map<GlobalID, MatrixData> AMP::IO::Writer::d_matrices

protectedinherited

Definition at line 330 of file Writer.h.

◆ d_multiMeshes

std::map<GlobalID, multiMeshData> AMP::IO::Writer::d_multiMeshes

protectedinherited

Definition at line 324 of file Writer.h.

◆ d_vectors

std::map<GlobalID, VectorData> AMP::IO::Writer::d_vectors

protectedinherited

Definition at line 327 of file Writer.h.

◆ d_vectorsMesh

std::vector<std::shared_ptr<AMP::LinearAlgebra::Vector> > AMP::IO::Writer::d_vectorsMesh

protectedinherited

Definition at line 333 of file Writer.h.

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

src/IO/HDF5writer.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ GeomType

Member Enumeration Documentation

◆ DecompositionType

◆ VectorType

Constructor & Destructor Documentation

◆ HDF5writer() [1/2]

◆ ~HDF5writer()

◆ HDF5writer() [2/2]

Member Function Documentation

◆ buildWriter() [1/2]

◆ buildWriter() [2/2]

◆ createDirectories()

◆ getExtension()

◆ getID()

◆ getMeshIDs()

◆ getNodeElemList()

◆ getProperties()

◆ readFile()

◆ registerData()

◆ registerMatrix()

◆ registerMesh()

◆ registerMesh2()

◆ registerVector() [1/2]

◆ registerVector() [2/2]

◆ setDecomposition()

◆ syncData()

◆ syncMultiMeshData()

◆ syncVectors()

◆ writeBoxMesh()

◆ writeDefaultMesh()

◆ writeFile()

◆ writeMesh()

Member Data Documentation

◆ d_baseMeshes

◆ d_comm

◆ d_decomposition

◆ d_fun

◆ d_matrices

◆ d_multiMeshes

◆ d_vectors

◆ d_vectorsMesh