#include <OutputVTKHDF.h>

Inherits Output.

Collaboration diagram for OutputVTKHDF:

Public Member Functions
	OutputVTKHDF (std::string casTest, std::string run, tinyxml2::XMLElement element, std::string fileName, Input entree)
	OutputVTKHDF (std::string nameRun, int fileNumberRestartMeshMapping, Input *input, const H5FD_mpio_xfer_t &transfer_mode)
	~OutputVTKHDF () override
virtual void	initializeSpecificOutput () override
virtual void	writeResults (Mesh mesh, std::vector< Cell > *cellsLvl) override
virtual void	readResults (Mesh mesh, std::vector< Cell > *cellsLvl, int cpu=-1) override
	Read results of a previous simulation to resume from it.
virtual const void *	getTransferMode () const override
	Get transfer_mode field (collective or independent hdf5 and MPI I/O mode for raw data transfer).
Public Member Functions inherited from Output
	Output ()
	Default constructor for specific output without specific needs.
	Output (std::string casTest, std::string nameRun, tinyxml2::XMLElement element, std::string fileName, Input entree)
	Main constructor for datasets used for OutputVTK and OutputGNU according to outputMode.
	Output (std::string nameRun, int fileNumberRestartMeshMapping, Input *input)
	Constructor for datasets used for OutputVTK when mesh mapping restart option is activated.
	Output (tinyxml2::XMLElement *element)
	Constructor for specific derived GNU outputs (boundary, probe, cut).
virtual	~Output ()
virtual void	probeDisplacement (const double &)
virtual void	locateProbeInMesh (const TypeMeshContainer< Cell * > &, const int &, bool=false)
virtual Cell *	locateProbeInAMRSubMesh (std::vector< Cell * > *, const int &)
void	copyInputFiles () const
void	initializeOutput (const Cell &cell)
void	initializeOutput (std::vector< CellInterface * > *cellInterfacesLvl)
	To initialize OutputBoundaryMassflowGNU.
void	initializeOutputMeshMapping (const Cell &cell)
	To initialize output for Mesh Mapping Restart.
virtual void	initializeOutputInfos ()
virtual void	writeResults (std::vector< CellInterface * > *)
virtual void	writeInfos ()
virtual void	writeProgress ()
virtual void	initializeSpecificOutput (std::vector< CellInterface * > *)
void	readInfos ()
	Currently only used for OutputBoundaryMassflowGNU.
int	readNbCpu ()
	Read and return the number of cpu from the infoCalcul file of a performed simulation.
void	readDomainDecompostion (Mesh *mesh)
void	readTree_common (Mesh mesh, TypeMeshContainer< Cell > cellsLvl, TypeMeshContainer< Cell > cellsLvlGhost, TypeMeshContainer< CellInterface > cellInterfacesLvl, const std::vector< AddPhys > &addPhys, int &lvl)
	Refine ghost cells, update of persistent communications of cells lvl + 1, reconstruct arrays of cells and cell interfaces of lvl + 1.
int	getNumFile () const
virtual double	getNextTime ()
virtual bool	possesses ()
const std::string &	getFolderOutput ()
const TypeOutput &	getType () const
bool	getReducedOutput () const
std::string	outputPhaseName (int phase, std::string phaseName, std::string &eosName) const

Protected Member Functions
void	initializeProperties (const H5FD_mpio_xfer_t &transfer_mode)
	Initialize fields needed by the two constructors that are provided (m_type and m_data_transfer) and assign hdf5 properties.
int	readScalarVTKHDF (hid_t group_id, const std::string &dataset_name, std::vector< size_t > &scalar_array) const
	Read a scalar array using parallel HDF5.
template<size_t N>
int	readArrayVTKHDF (hid_t group_id, std::string dataset_name, std::vector< double > &dataset, const hsize_t(&local_dims)[N], const hsize_t(&offsets)[N])
	Read an array of dimensions local_dims at offset offsets using parallel HDF5.
template<size_t N>
int	ReadPhysicalDataVTKHDF (Mesh mesh, std::vector< Cell > *cellsLvl, hid_t group_id, const hsize_t(&count_scalar)[N], const hsize_t(&start_scalar)[N])
	Read the list of ECOGEN physical data in a VTKHDF file with dimensions and offsets of area to read provided as input.
int	ReadPhysicalDataVTKHDF (Mesh mesh, std::vector< Cell > *cellsLvl, hid_t group_id, int cpu, const std::vector< size_t > &numberCells)
	Read the list of ECOGEN physical data in a VTKHDF file. Dimensions of area to parse are calculated automatically based on the mesh type (cartesian, AMR...).
std::string	createFilenameVTKHDF (const char *name, int numFile=-1, std::string nameVariable="defaut") const
int	openFileVTKHDF (hid_t &file_id, bool parallel_access, bool create) const
	Create or open a hdf5 file.
void	writeTimeseriesVTKHDF (int numFile)
	Write a Paraview .series file for time series visualization of VTKHDF outputs.
void	writeXDMF (Mesh *mesh, int numFile)
	Write a XDMF file to visualize cartesian VTKHDF outputs while VTKHDF file format is not yet specified.
void	writeResultsVTKHDF (Mesh mesh, std::vector< Cell > *cellsLvl)
	Write results at VTKHDF file format for current time step.
int	writePhysicalDataVTKHDF (hid_t &file, const Mesh mesh, std::vector< Cell > *cellsLvl, hid_t &vtkhdf_group_id, size_t numberCells) const
	Write physical data fields at VTKHDF file format in file hdf5 object.
template<size_t N, typename T>
int	writePhysicalDataVTKHDF (const Mesh mesh, std::vector< Cell > *cellsLvl, hid_t vtkhdf_group_id, size_t numberCells, const hsize_t(&dimsf_scalar)[N], const hsize_t(&count_scalar)[N], const hsize_t(&start_scalar)[N], const hsize_t(&chunk_scalar)[N]) const
	Helper to write physical data fields of rank N at VTKHDF file format in file hdf5 object.
int	writeScalarVTKHDF (const hid_t &group_id, const std::string &dataset_name, const size_t &scalar_val) const
	Write a distributed scalar array using parallel HDF5.
const void *	getOutputBuffer (const std::vector< double > &double_buffer, std::vector< float > &float_buffer) const
	Get buffer to write at suitable format for hdf5 (float or double).
template<typename T>
int	writeConnectivity (Mesh mesh, std::vector< Cell > *cellsLvl, hid_t &vtkhdf_group_id, size_t &numberCells, const size_t &numberNodes) const
template<typename T>
int	writeUnstructuredArrayVTKHDF (const hid_t &group_id, const std::string &dataset_name, hid_t hdf_file_dtype, hid_t hdf_mem_dtype, const std::vector< T > &dataset, const size_t &line_count, size_t column_count=1) const
	Write a 2-dimensional array of an unstructured mesh using parallel HDF5.
template<size_t N, typename T>
int	writeArrayVTKHDF (const hid_t &group_id, const std::string &dataset_name, hid_t hdf_mem_dtype, hid_t hdf_file_dtype, hid_t parallel_x_properties, const std::vector< T > &dataset, const hsize_t(&global_dims)[N], const hsize_t(&local_dims)[N], const hsize_t(&offsets)[N], const hsize_t(&chunk_dims)[N]) const
	Write a N-dimensional array of C++ type T and hdf5 type hdf_type using parallel HDF5.
int	writeArrayAttribute (const hid_t &group_id, const std::string &attribute_name, const hsize_t &nitem, const int *array) const
	Write array attribute in VTKHDF file.
int	writeHeaderVTKHDF (const hid_t &group_id, const std::string &mesh_type) const
	Write header of VTKHDF file.
int	writeMeshRectilinearVTKHDF (Mesh *mesh, hid_t &file, hid_t &vtkhdf_group_id, size_t &numberCells)
	Write cartesian mesh at VTKHDF file format.
int	writeMeshUnstructuredVTKHDF (Mesh mesh, std::vector< Cell > *cellsLvl, hid_t &file, hid_t &vtkhdf_group_id, size_t &numberCells) const
	Write unstructured mesh at VTKHDF file format.
void	writeDataset (std::vector< double >, std::ofstream &, TypeData) const
virtual void	prepareErrorFiles () const override
virtual void	writeErrorInFile (std::vector< Errors > &v, const int &ErrorType, const int &iteration, bool &warn) const override
virtual void	printTree (Mesh mesh, const std::vector< Cell > *cellsLvl, int m_resumeAMRsaveFreq) const override
	Write 'meshInfo' file that stores for each cell its subdivision status (1 if subdivided, 0 if not).
virtual void	readTree (Mesh mesh, TypeMeshContainer< Cell > cellsLvl, TypeMeshContainer< Cell > cellsLvlGhost, TypeMeshContainer< CellInterface > const cellInterfacesLvl, const std::vector< AddPhys > &addPhys, int &nbCellsTotalAMR) override
	Read 'meshInfo' file that stores for each cell its subdivision status (1 if subdivided, 0 if not).
Protected Member Functions inherited from Output
void	printWritingInfo () const
void	saveInfos () const
std::string	createFilename (const char *name, int lvl=-1, int proc=-1, int numFichier=-1) const
void	writeDataset (std::vector< double > dataset, std::ofstream &fileStream, TypeData typeData) const
void	getDataset (std::istringstream &data, std::vector< double > &dataset) const

Static Protected Member Functions
static void	writeDataXDMF (std::ofstream &fileStream, const std::string &dataFile, const std::string &dataName, const std::string &dataType, int numberCellsX, int numberCellsY, int numberCellsZ, int dimData)
	Write data array at XDMF format.
static void	unstructuredFirstRangeLayout (const size_t &line_count, hsize_t dimsf, hsize_t count, hsize_t *start)
	Compute size, position and offset of writing area from 'line_count' and 'column_count' data.
static void	getDataset (std::istringstream &, std::vector< double > &)

Private Attributes
hid_t	m_h5_file_floatType
	Hdf5 floating type to write in file depending on the precision asked by user.
hid_t	m_h5_file_intType
	Hdf5 integer type to write in file depending on the precision asked by user.
hid_t	m_h5_mem_floatType
	Hdf5 floating type in memory space: must match architecture (LE, BE) and the size of the data in memory (float, double...).
hid_t	m_h5_mem_intType
	Hdf5 integer type in memory space: must match architecture (LE, BE) and the size of the data in memory (int32_t, int64_t..).
hid_t	m_group_creation_properties
	Properties for hdf5 group creation.
hid_t	m_dataset_creation_properties
	Properties for hdf5 dataset creation.
hid_t	m_parallel_x_properties
	Properties for hdf5 raw data transfer.
H5FD_mpio_xfer_t	m_transfer_mode
	Perform collective (default or H5FD_MPIO_COLLECTIVE) or independent (H5FD_MPIO_INDEPENDENT) parallel I/Os.

Static Private Attributes
static constexpr size_t	DIM_OUTPUT {3}
	Always write 3D-coordinates in output files.
static constexpr int	VTKHDF_VERSION [2] = {2, 4}
	VTKHDF format version: set to version 2.4 in .cpp file.
static constexpr int	ERROR_VALUE = -1
	Error value.
static constexpr int	SUCCESS_VALUE = 0
	Success value.

Additional Inherited Members
Protected Attributes inherited from Output
Input *	m_input
	Pointer to input.
Run *	m_run
	Pointer to run.
TypeOutput	m_type
	Type of output.
std::string	m_simulationName
	Test case name (defined in "main.xml").
std::string	m_infoCalcul
	Filename to save useful info of computation.
std::string	m_treeStructure
	Filename for tree structure backup.
std::string	m_domainDecomposition
	Filename for domain decomposition backup.
std::string	m_fileNameResults
	Filename of result file.
std::string	m_filenameCollectionParaview
	Name of the collection containing the results files (for Paraview).
std::string	m_filenameCollectionVisIt
	Name of the collection containing the results files (for VisIt).
std::string	m_filenameVTKHDFTimeseries
	Name of the timeseries file containing the list of result files at vtkhdf format (for Paraview).
std::string	m_folderOutput
	Folder to store results.
std::string	m_folderSavesInput
	Folder to store a copy of input files.
std::string	m_folderDatasets
	Folder to save the datasets.
std::string	m_folderInfoMesh
	Folder to store mesh info.
std::string	m_folderCuts
	Cuts results folder location.
std::string	m_folderProbes
	Probes results folder location.
std::string	m_folderGlobalQuantities
	Global quantity (e.g. mass) results folder location.
std::string	m_folderBoundaries
	Boundaries flux results folder location.
std::string	m_fileCollectionParaview
	Chemin du file collection regroupant les fichiers resultats (for Paraview).
std::string	m_fileCollectionVisIt
	Chemin du file collection regroupant les fichiers resultats (for VisIt).
std::string	m_folderErrorsAndWarnings
	File path for errors and warnings.
bool	m_writeBinary
	Choice to write binary/ASCII (available for GNU and VTK outputs, GNU format only supports ASCII).
bool	m_splitData
	Choice print data in separate files.
int	m_precision
	Output files precision (number of digits) for GNU and VTK outputs //default: 6.
bool	m_reducedOutput
	Choice of reduced number of output variables when possible (depends on the model).
int	m_numFile
std::string	m_endianMode
int	m_nbCpusRestarted
	Number of CPUs of the simulation to be restarted.
Cell	m_cellRef
	Reference cell to extract variables name.

Constructor & Destructor Documentation

◆ OutputVTKHDF() [1/2]

OutputVTKHDF::OutputVTKHDF	(	std::string	casTest,
		std::string	run,
		tinyxml2::XMLElement *	element,
		std::string	fileName,
		Input *	entree )

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◆ OutputVTKHDF() [2/2]

OutputVTKHDF::OutputVTKHDF	(	std::string	nameRun,
		int	fileNumberRestartMeshMapping,
		Input *	input,
		const H5FD_mpio_xfer_t &	transfer_mode )

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◆ ~OutputVTKHDF()

OutputVTKHDF::~OutputVTKHDF ( )

override

Member Function Documentation

◆ createFilenameVTKHDF()

std::string OutputVTKHDF::createFilenameVTKHDF	(	const char *	name,
		int	numFile = -1,
		std::string	nameVariable = "defaut" ) const

protected

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◆ getDataset()

void OutputVTKHDF::getDataset	(	std::istringstream &	,
		std::vector< double > &	)

inlinestaticprotected

◆ getOutputBuffer()

const void * OutputVTKHDF::getOutputBuffer	(	const std::vector< double > &	double_buffer,
		std::vector< float > &	float_buffer ) const

protected

Get buffer to write at suitable format for hdf5 (float or double).

Parameters

double_buffer	buffer containing data at double precision.
float_buffer	buffer to store double data converted at float format if it is the output format asked by user

Returns: pointer to the buffer that has to be passed to hdf5.

◆ getTransferMode()

virtual const void * OutputVTKHDF::getTransferMode ( ) const

inlineoverridevirtual

Get transfer_mode field (collective or independent hdf5 and MPI I/O mode for raw data transfer).

Reimplemented from Output.

◆ initializeProperties()

void OutputVTKHDF::initializeProperties ( const H5FD_mpio_xfer_t & transfer_mode )

protected

Initialize fields needed by the two constructors that are provided (m_type and m_data_transfer) and assign hdf5 properties.

Two constructors are provided with 'OutputVTKHDF' class: a constructor to write output files and a constructor to read output files of a previous run when

Parameters

transfer_mode hdf5 parallel mode for raw data transfer (H5FD_MPIO_COLLECTIVE or H5FD_MPIO_INDEPENDENT)

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◆ initializeSpecificOutput()

void OutputVTKHDF::initializeSpecificOutput ( )

overridevirtual

Reimplemented from Output.

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◆ openFileVTKHDF()

int OutputVTKHDF::openFileVTKHDF	(	hid_t &	file_id,
		bool	parallel_access,
		bool	create ) const

protected

Create or open a hdf5 file.

Parameters

file_id	file identifier
parallel_access	true to open file with parallel access, false for serial access
create	true to create a new file, false to reopen an existing file in order to add data

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

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◆ prepareErrorFiles()

void OutputVTKHDF::prepareErrorFiles ( ) const

overrideprotectedvirtual

Reimplemented from Output.

◆ printTree()

void OutputVTKHDF::printTree	(	Mesh *	mesh,
		const std::vector< Cell * > *	cellsLvl,
		int	m_resumeAMRsaveFreq ) const

overrideprotectedvirtual

Write 'meshInfo' file that stores for each cell its subdivision status (1 if subdivided, 0 if not).

In case of VTKHDF outputs, 1 file per time step is saved at binary format. subdivision status is saved as a 'int8_t' so file can be inspected with 'od -v -t d4 <meshInfo.out>' command.

Parameters

mesh	Mesh object of the current simulation.
cellsLvl	Computationnal cells
m_resumeAMRsaveFreq	File output frequency

Remarks: Useful only in AMR case.

Reimplemented from Output.

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◆ readArrayVTKHDF()

template<size_t N>

int OutputVTKHDF::readArrayVTKHDF	(	hid_t	group_id,
		std::string	dataset_name,
		std::vector< double > &	dataset,
		const hsize_t(&)	local_dims[N],
		const hsize_t(&)	offsets[N] )

protected

Read an array of dimensions local_dims at offset offsets using parallel HDF5.

Template Parameters

N	Range of array to read

Parameters

group_id	Identifier of hdf5 object where data will be readed
dataset_name	String containing the name of the VTKHDF dataset to read
local_dims	Dimensions of area to read for current MPI process
offsets	Offsets along each direction where starts the area to read for current MPI process

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

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◆ ReadPhysicalDataVTKHDF() [1/2]

template<size_t N>

int OutputVTKHDF::ReadPhysicalDataVTKHDF	(	Mesh *	mesh,
		std::vector< Cell * > *	cellsLvl,
		hid_t	group_id,
		const hsize_t(&)	count_scalar[N],
		const hsize_t(&)	start_scalar[N] )

protected

Read the list of ECOGEN physical data in a VTKHDF file with dimensions and offsets of area to read provided as input.

Template Parameters

N	Range of array to read

Parameters

mesh	Mesh object of the current simulation
cellsLvl	Computationnal cells to be filled with results of previous simulation
group_id	Identifier o hdf5 object in which data will be readed
count_scalar	Dimensions of area to read for current MPI process and for a scalar data (dims for vectorial data are computed from dims of scalar datas)
start_scalar	Offsets along each direction where starts the area to read for current MPI process and for scalar data (offset for vectorial data are computed from scalar offsets)

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◆ ReadPhysicalDataVTKHDF() [2/2]

int OutputVTKHDF::ReadPhysicalDataVTKHDF	(	Mesh *	mesh,
		std::vector< Cell * > *	cellsLvl,
		hid_t	group_id,
		int	cpu,
		const std::vector< size_t > &	numberCells )

protected

Read the list of ECOGEN physical data in a VTKHDF file. Dimensions of area to parse are calculated automatically based on the mesh type (cartesian, AMR...).

Parameters

mesh	Mesh object of the current simulation
cellsLvl	Computationnal cells to be filled with results of previous simulation
group_id	Identifier o hdf5 object in which data will be readed
cpu	Rank of MPI process from which we want to read data from the file (not used for cartesian meshes)
numberCells	Vector of cell count per MPI process when file was saved. Readed from the 'NumberOfCells' file dataset (not used for cartesian meshes)

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◆ readResults()

void OutputVTKHDF::readResults	(	Mesh *	,
		std::vector< Cell * > *	,
		int	= -1 )

overridevirtual

Read results of a previous simulation to resume from it.

Available for all mesh types if the same number of cpus is used between both simulations

Parameters

mesh	Mesh object of the current simulation in case of resume. Mesh object of a single partition of the previous simulation (either the same one as current or older one in case of mapping).
cellsLvl	Computationnal cells to be filled with results of previous simulation
cpu	Index of cpu file to read if provided (meshMappingRestart case), otherwise, the file associated with current cpu rank is readed (simulation resume case)

Reimplemented from Output.

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◆ readScalarVTKHDF()

int OutputVTKHDF::readScalarVTKHDF	(	hid_t	group_id,
		const std::string &	dataset_name,
		std::vector< size_t > &	scalar_array ) const

protected

Read a scalar array using parallel HDF5.

Implements a collective read operation where each MPI rank reads the entire array

Parameters

group_id	Identifier of hdf5 object where data will be written
dataset_name	String containing the name of the VTKHDF dataset to write
scalar_array	Vector to store values that are readed

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

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◆ readTree()

void OutputVTKHDF::readTree	(	Mesh *	mesh,
		TypeMeshContainer< Cell * > *	cellsLvl,
		TypeMeshContainer< Cell * > *	cellsLvlGhost,
		TypeMeshContainer< CellInterface * > *const	cellInterfacesLvl,
		const std::vector< AddPhys * > &	addPhys,
		int &	nbCellsTotalAMR )

overrideprotectedvirtual

Read 'meshInfo' file that stores for each cell its subdivision status (1 if subdivided, 0 if not).

Parameters

mesh	Mesh object of the current simulation.
cellsLvl	Computationnal cells
cellsLvlGhost	Ghost cells
cellInterfacesLvl	Interface cells
addPhys	Vector of additional physics
nbCellsTotalAMR	Cell count

Remarks: Useful only in AMR case.

Reimplemented from Output.

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◆ unstructuredFirstRangeLayout()

void OutputVTKHDF::unstructuredFirstRangeLayout	(	const size_t &	line_count,
		hsize_t *	dimsf,
		hsize_t *	count,
		hsize_t *	start )

staticprotected

Compute size, position and offset of writing area from 'line_count' and 'column_count' data.

Compute size, position and offset of writing area from 'line_count' and 'column_count' argument using a collective call ('Allgather')

Parameters

line_count	number of line of array to write
dimsf	global dimension along range 0 of array to write (filled by this function)
count	local dimension along range 0 of array to write (filled by this function)
start	position from which local rank will start to write in global array along range 0 (filled by this function)

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◆ writeArrayAttribute()

int OutputVTKHDF::writeArrayAttribute	(	const hid_t &	group_id,
		const std::string &	attribute_name,
		const hsize_t &	nitem,
		const int *	array ) const

protected

Write array attribute in VTKHDF file.

Parameters

group_id	Identifier of hdf5 object where data will be written
attribute_name	name of attribute to save
nitem	number of item to write (array size)
array	pointer to the array to write

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

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◆ writeArrayVTKHDF()

template<size_t N, typename T>

int OutputVTKHDF::writeArrayVTKHDF	(	const hid_t &	group_id,
		const std::string &	dataset_name,
		hid_t	hdf_mem_dtype,
		hid_t	hdf_file_dtype,
		hid_t	parallel_x_properties,
		const std::vector< T > &	dataset,
		const hsize_t(&)	global_dims[N],
		const hsize_t(&)	local_dims[N],
		const hsize_t(&)	offsets[N],
		const hsize_t(&)	chunk_dims[N] ) const

protected

Write a N-dimensional array of C++ type T and hdf5 type hdf_type using parallel HDF5.

Implements a collective write operation where:

Each MPI rank writes the 'dataset' vector resized under the form of an array of rank N and dimensions 'local_dims'.
The resulting dataset spans all MPI ranks and is written in a region of rank N and size 'global_dims'
Size, position and offset of writing area are provided as argument Allow to write efficiently structured data and can be called by previous 'writeArrayVTKHDF' function.

Template Parameters

N	Range in hdf5 memory and file of array to write

Parameters

group_id	Identifier of hdf5 object where data will be written
dataset_name	String containing the name of the VTKHDF dataset to write
hdf5_mem_dtype	Hdf5 data type to use for storage and transfer: must match architecture (LE, BE) and the size of the data in memory (int32_t, int64_t..)
hdf5_file_dtype	Hdf5 data type saved in file: hdf5 will manage the conversion from the `hdf5_mem_dtype` to this type if needed
parallel_x_properties	Property for raw data transfer (collective or independent - collective writes are unavailable if file is not open in parallel)
dataset	Pointer to the array to write
global_dims	global dimensions of array to write in file
local_dims	local dimensions on the current MPI process of array to write in file
offsets	offsets at which write the array in file
chunk_dims	Wanted dimensions of file chunks (to optimize data access). If chunk_dims[0] is 0, chunking is disabled.

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

Note: - Exceptions are not used to avoid the creation of a corrupted file

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◆ writeConnectivity()

template<typename T>

int OutputVTKHDF::writeConnectivity	(	Mesh *	mesh,
		std::vector< Cell * > *	cellsLvl,
		hid_t &	vtkhdf_group_id,
		size_t &	numberCells,
		const size_t &	numberNodes ) const

protected

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◆ writeDataset()

void OutputVTKHDF::writeDataset	(	std::vector< double >	,
		std::ofstream &	,
		TypeData	) const

inlineprotected

◆ writeDataXDMF()

void OutputVTKHDF::writeDataXDMF	(	std::ofstream &	fileStream,
		const std::string &	dataFile,
		const std::string &	dataName,
		const std::string &	dataType,
		int	numberCellsX,
		int	numberCellsY,
		int	numberCellsZ,
		int	dimData )

staticprotected

Write data array at XDMF format.

Parameters

dataFile	Filename
dataNam	Name of data to write
dataType	Type ('Scalar' or 'Vector') of data to write
numberCellsX	Number of space steps in X direction
numberCellsY	Number of space steps in Y direction
numberCellsZ	Number of space steps in Z direction
dimData	Data dimension (1 for scalars, 3 for vectors)

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◆ writeErrorInFile()

void OutputVTKHDF::writeErrorInFile	(	std::vector< Errors > &	v,
		const int &	ErrorType,
		const int &	iteration,
		bool &	warn ) const

overrideprotectedvirtual

Reimplemented from Output.

◆ writeHeaderVTKHDF()

int OutputVTKHDF::writeHeaderVTKHDF	(	const hid_t &	group_id,
		const std::string &	mesh_type ) const

protected

Write header of VTKHDF file.

Parameters

group_id	Identifier of hdf5 object where data will be written
mesh_type	String containing the name of VTK mesh Type

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

Note: - file is saved at format 2.4 for now; - Exceptions are not used to avoid the creation of a corrupted file

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◆ writeMeshRectilinearVTKHDF()

int OutputVTKHDF::writeMeshRectilinearVTKHDF	(	Mesh *	mesh,
		hid_t &	file,
		hid_t &	vtkhdf_group_id,
		size_t &	numberCells )

protected

Write cartesian mesh at VTKHDF file format.

Parameters

mesh	Mesh object of the current simulation
file	Identifier of hdf5 object where data will be written
vtkhdf_group_id	Identifier of 'VTKHDF' group created by current function
numberCells	Number of cells in the mesh (filled by the current function)

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

Note: Temporary output while VTKHDF file format is not yet specified. For now, uses format specified on VTK discourse forum:

Warning: Rectilinear outputs are disabled for now because they are too inefficient

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◆ writeMeshUnstructuredVTKHDF()

int OutputVTKHDF::writeMeshUnstructuredVTKHDF	(	Mesh *	mesh,
		std::vector< Cell * > *	cellsLvl,
		hid_t &	file,
		hid_t &	vtkhdf_group_id,
		size_t &	numberCells ) const

protected

Write unstructured mesh at VTKHDF file format.

Parameters

mesh	Mesh object of the current simulation
cellsLvl	Computationnal cells to be filled with results of previous simulation
file	Identifier of hdf5 object where data will be written
vtkhdf_group_id	Identifier of 'VTKHDF' group created by current function
numberCells	Number of cells in the mesh (filled by the current function)

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

Note: Exceptions are not used to avoid the creation of a corrupted file

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◆ writePhysicalDataVTKHDF() [1/2]

template<size_t N, typename T>

int OutputVTKHDF::writePhysicalDataVTKHDF	(	const Mesh *	mesh,
		std::vector< Cell * > *	cellsLvl,
		hid_t	vtkhdf_group_id,
		size_t	numberCells,
		const hsize_t(&)	dimsf_scalar[N],
		const hsize_t(&)	count_scalar[N],
		const hsize_t(&)	start_scalar[N],
		const hsize_t(&)	chunk_scalar[N] ) const

protected

Helper to write physical data fields of rank N at VTKHDF file format in file hdf5 object.

Template Parameters

N	Range in hdf5 memory and file of scalar data to write
T	Precision at which to save data in file

Parameters

mesh	Mesh object of the current simulation
cellsLvl	Computationnal cells to be filled with results of previous simulation
vtkhdf_group_id	Identifier of hdf5 object where data will be written
numberCells	Number of Cells
dimsf_scalar	global dimensions of scalar data (global dimensions of vectorial data are computed from scalar ones)
count_scalar	local dimensions of scalar data (local dimensions of vectorial data are computed from scalar ones)
start_scalar	offset where to start to write scalar data for current MPI process (offsets of vectorial data are computed from scalar ones)
chunk_scalar	size of chunks to optimize data access efficiency (chunks of vectorial data are computed from scalar ones)

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

Note: Exceptions are not used to avoid the creation of a corrupted file

Warning: Rectilinear outputs are disabled for now because they are too inefficient

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◆ writePhysicalDataVTKHDF() [2/2]

int OutputVTKHDF::writePhysicalDataVTKHDF	(	hid_t &	file,
		const Mesh *	mesh,
		std::vector< Cell * > *	cellsLvl,
		hid_t &	vtkhdf_group_id,
		size_t	numberCells ) const

protected

Write physical data fields at VTKHDF file format in file hdf5 object.

For rectilinear meshes, data are saved using natural serial organization (data in files matches geometrical data representation). For unstructured meshes, data are saved by partitions in increasing order of MPI rank.

Parameters

mesh	Mesh object of the current simulation
cellsLvl	Computationnal cells to be filled with results of previous simulation
vtkhdf_group_id	Identifier of hdf5 object where data will be written
numberCells	Number of Cells

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

Note: Exceptions are not used to avoid the creation of a corrupted file

Warning: Rectilinear outputs are disabled for now because they are too inefficient

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◆ writeResults()

void OutputVTKHDF::writeResults	(	Mesh *	mesh,
		std::vector< Cell * > *	cellsLvl )

overridevirtual

Reimplemented from Output.

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◆ writeResultsVTKHDF()

void OutputVTKHDF::writeResultsVTKHDF	(	Mesh *	mesh,
		std::vector< Cell * > *	cellsLvl )

protected

Write results at VTKHDF file format for current time step.

Parameters

mesh	Mesh object of the current simulation
cellsLvl	Computationnal cells to be filled with results of previous simulation

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◆ writeScalarVTKHDF()

int OutputVTKHDF::writeScalarVTKHDF	(	const hid_t &	group_id,
		const std::string &	dataset_name,
		const size_t &	scalar_val ) const

protected

Write a distributed scalar array using parallel HDF5.

Implements a collective write operation where:

Each MPI rank writes exactly one scalar value
The resulting dataset spans all MPI ranks
Total size of the array equals the number of MPI processes

Parameters

group_id	Identifier of hdf5 object where data will be written
dataset_name	String containing the name of the VTKHDF dataset to write
scalar_val	Value to write for current MPI rank

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

Note: Exceptions are not used to avoid the creation of a corrupted file

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◆ writeTimeseriesVTKHDF()

void OutputVTKHDF::writeTimeseriesVTKHDF ( int numFile )

protected

Write a Paraview .series file for time series visualization of VTKHDF outputs.

Parameters

numFile Index of maximal timestep value to list (an empty list is saved if numFile is equal to -1).

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◆ writeUnstructuredArrayVTKHDF()

template<typename T>

int OutputVTKHDF::writeUnstructuredArrayVTKHDF	(	const hid_t &	group_id,
		const std::string &	dataset_name,
		hid_t	hdf_file_dtype,
		hid_t	hdf_mem_dtype,
		const std::vector< T > &	dataset,
		const size_t &	line_count,
		size_t	column_count = 1 ) const

protected

Write a 2-dimensional array of an unstructured mesh using parallel HDF5.

Implements a collective write operation to dump arrays of unstructured data (so for unstructured and AMR meshes) where:

array has C++ type T and hdf5 type hdf_type
Each MPI rank writes its line_count lines of the array and all its columns
The resulting dataset spans all MPI ranks
Size, position and offset of writing area is locally computed using a collective call ('Allgather')

Template Parameters

T	Type of dataset vector

Parameters

group_id	Identifier of hdf5 object where data will be written
dataset_name	String containing the name of the VTKHDF dataset to write
hdf5_mem_dtype	Hdf5 data type to use for storage and transfer: must match architecture (LE, BE) and the size of the data in memory (int32_t, int64_t..)
hdf5_file_dtype	Hdf5 data type saved in file: hdf5 will manage the conversion from the `hdf5_mem_dtype` to this type if needed
dataset	Reference to the local vector of type T to write
line_count	Size of the first dimension of the local array
column_count	Size of the second dimension of the local array (1 for a 1D array)

Returns: ERROR_VALUE if fail, SUCCESS_VALUE if success

Note: - Exceptions are not used to avoid the creation of a corrupted file

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◆ writeXDMF()

void OutputVTKHDF::writeXDMF	(	Mesh *	mesh,
		int	numFile )

protected

Write a XDMF file to visualize cartesian VTKHDF outputs while VTKHDF file format is not yet specified.

Parameters

numFile Index of maximal timestep value to list (an empty list is saved if numFile is equal to -1).

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Member Data Documentation

◆ DIM_OUTPUT

size_t OutputVTKHDF::DIM_OUTPUT {3}

staticconstexprprivate

Always write 3D-coordinates in output files.

◆ ERROR_VALUE

int OutputVTKHDF::ERROR_VALUE = -1

staticconstexprprivate

Error value.

◆ m_dataset_creation_properties

hid_t OutputVTKHDF::m_dataset_creation_properties

private

Properties for hdf5 dataset creation.

◆ m_group_creation_properties

hid_t OutputVTKHDF::m_group_creation_properties

private

Properties for hdf5 group creation.

◆ m_h5_file_floatType

hid_t OutputVTKHDF::m_h5_file_floatType

private

Hdf5 floating type to write in file depending on the precision asked by user.

◆ m_h5_file_intType

hid_t OutputVTKHDF::m_h5_file_intType

private

Hdf5 integer type to write in file depending on the precision asked by user.

◆ m_h5_mem_floatType

hid_t OutputVTKHDF::m_h5_mem_floatType

private

Hdf5 floating type in memory space: must match architecture (LE, BE) and the size of the data in memory (float, double...).

◆ m_h5_mem_intType

hid_t OutputVTKHDF::m_h5_mem_intType

private

Hdf5 integer type in memory space: must match architecture (LE, BE) and the size of the data in memory (int32_t, int64_t..).

◆ m_parallel_x_properties

hid_t OutputVTKHDF::m_parallel_x_properties

private

Properties for hdf5 raw data transfer.

◆ m_transfer_mode

H5FD_mpio_xfer_t OutputVTKHDF::m_transfer_mode

private

Perform collective (default or H5FD_MPIO_COLLECTIVE) or independent (H5FD_MPIO_INDEPENDENT) parallel I/Os.

◆ SUCCESS_VALUE

int OutputVTKHDF::SUCCESS_VALUE = 0

staticconstexprprivate

Success value.

◆ VTKHDF_VERSION

int OutputVTKHDF::VTKHDF_VERSION = {2, 4}

staticconstexprprivate

VTKHDF format version: set to version 2.4 in .cpp file.

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

/home/runner/work/ECOGEN/ECOGEN/doc_sources/src/InputOutput/OutputVTKHDF.h
/home/runner/work/ECOGEN/ECOGEN/doc_sources/src/InputOutput/OutputVTKHDF.cpp

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ OutputVTKHDF() [1/2]

◆ OutputVTKHDF() [2/2]

◆ ~OutputVTKHDF()

Member Function Documentation

◆ createFilenameVTKHDF()

◆ getDataset()

◆ getOutputBuffer()

◆ getTransferMode()

◆ initializeProperties()

◆ initializeSpecificOutput()

◆ openFileVTKHDF()

◆ prepareErrorFiles()

◆ printTree()

◆ readArrayVTKHDF()

◆ ReadPhysicalDataVTKHDF() [1/2]

◆ ReadPhysicalDataVTKHDF() [2/2]

◆ readResults()

◆ readScalarVTKHDF()

◆ readTree()

◆ unstructuredFirstRangeLayout()

◆ writeArrayAttribute()

◆ writeArrayVTKHDF()

◆ writeConnectivity()

◆ writeDataset()

◆ writeDataXDMF()

◆ writeErrorInFile()

◆ writeHeaderVTKHDF()

◆ writeMeshRectilinearVTKHDF()

◆ writeMeshUnstructuredVTKHDF()

◆ writePhysicalDataVTKHDF() [1/2]

◆ writePhysicalDataVTKHDF() [2/2]

◆ writeResults()

◆ writeResultsVTKHDF()

◆ writeScalarVTKHDF()

◆ writeTimeseriesVTKHDF()

◆ writeUnstructuredArrayVTKHDF()

◆ writeXDMF()

Member Data Documentation

◆ DIM_OUTPUT

◆ ERROR_VALUE

◆ m_dataset_creation_properties

◆ m_group_creation_properties

◆ m_h5_file_floatType

◆ m_h5_file_intType

◆ m_h5_mem_floatType

◆ m_h5_mem_intType

◆ m_parallel_x_properties

◆ m_transfer_mode

◆ SUCCESS_VALUE

◆ VTKHDF_VERSION