Hdf5 data exporter, implementation of Exporter. More...

#include <ExporterHDF5.hpp>

Inheritance diagram for ExporterHDF5< MeshType >:

Collaboration diagram for ExporterHDF5< MeshType >:

Public typedefs
typedef MeshType	mesh_Type

typedef Exporter< MeshType >	super

typedef super::meshPtr_Type	meshPtr_Type

typedef super::vector_Type	vector_Type

typedef super::vectorPtr_Type	vectorPtr_Type

typedef super::exporterData_Type	exporterData_Type

typedef EpetraExt::HDF5	hdf5_Type

typedef std::shared_ptr< hdf5_Type >	hdf5Ptr_Type

typedef std::vector< std::vector< Int > >	graph_Type

typedef std::shared_ptr< graph_Type >	graphPtr_Type

typedef std::shared_ptr< std::vector< meshPtr_Type > >	serial_meshPtr_Type

Static members
static MapEpetraType const	MapType
	returns the type of the map to use for the VectorEpetra More...

Constructor & Destructor
	ExporterHDF5 ()
	Empty Constructor for ExporterHDF5. More...

	ExporterHDF5 (const GetPot &dfile, meshPtr_Type mesh, const std::string &prefix, const Int &procId)
	Constructor for ExporterHDF5. More...

	ExporterHDF5 (const GetPot &dfile, const std::string &prefix)
	Constructor for ExporterHDF5 without prefix and procID. More...

virtual	~ExporterHDF5 ()
	Destructor for ExporterHDF5. More...

Public Methods
virtual void	postProcess (const Real &time)
	Post-process the variables added to the list. More...

UInt	importFromTime (const Real &Time)
	Import data from previous simulations at a certain time. More...

Real	importFromIter (const UInt &)
	Import data from previous simulations at a certain time. More...

void	import (const Real &startTime, const Real &dt)
	Import data from previous simulations. More...

void	import (const Real &time)
	Import data from previous simulations. More...

void	closeFile ()
	Close the Hdf5 file. More...

void	readVariable (exporterData_Type &dvar)
	Read variable. More...

Set Methods
void	setDataFromGetPot (const GetPot &dataFile, const std::string &section="exporter")
	Set data from file. More...

Get Methods
MapEpetraType	mapType () const
	returns the type of the map to use for the VectorEpetra More...

Protected Methods
void	defineShape ()
	Define the shape of the elements. More...

void	writeInitXdmf ()
	write empty xdmf file More...

void	writeXdmf (const Real &time)
	append to xdmf file More...

void	writeCloseLinesXdmf ()
	save position and write closing lines More...

void	removeCloseLinesXdmf ()
	remove closing lines More...

void	writeTopology (std::ofstream &xdmf)

void	writeGeometry (std::ofstream &xdmf)

void	writeAttributes (std::ofstream &xdmf)

void	writeScalarDatastructure (std::ofstream &xdmf, const exporterData_Type &dvar)

void	writeVectorDatastructure (std::ofstream &xdmf, const exporterData_Type &dvar)

void	writeVariable (const exporterData_Type &dvar)

void	writeScalar (const exporterData_Type &dvar)

void	writeVector (const exporterData_Type &dvar)

void	writeGeometry ()

void	readScalar (exporterData_Type &dvar)
	A method to read a scalar field (to be implemented in derived classes) More...

void	readVector (exporterData_Type &dvar)
	A method to read a vector field (to be implemented in derived classes) More...

Protected data members
hdf5Ptr_Type	M_HDF5

std::ofstream	M_xdmf

const std::string	M_closingLines

std::streampos	M_closingLinesPosition

std::string	M_outputFileName

bool	M_printConnectivity
	do we want to write on file the connectivity? More...

Additional Inherited Members
Public Types inherited from Exporter< MeshType >
typedef MeshType	mesh_Type

typedef std::shared_ptr< MeshType >	meshPtr_Type

typedef Epetra_Comm	comm_Type

typedef std::shared_ptr< comm_Type >	commPtr_Type

typedef ExporterData< mesh_Type >	exporterData_Type

typedef exporterData_Type::vector_Type	vector_Type

typedef exporterData_Type::vectorPtr_Type	vectorPtr_Type

typedef exporterData_Type::feSpace_Type	feSpace_Type

typedef exporterData_Type::feSpacePtr_Type	feSpacePtr_Type

typedef exporterData_Type::WhereEnum	WhereEnum

typedef exporterData_Type::FieldTypeEnum	FieldTypeEnum

typedef exporterData_Type::FieldRegimeEnum	FieldRegimeEnum

typedef std::vector< exporterData_Type >	dataVector_Type

typedef dataVector_Type::iterator	dataVectorIterator_Type

typedef std::multimap< WhereEnum, UInt >	whereToDataIdMap_Type

typedef std::multimap< FE_TYPE, UInt >	feTypeToDataIdMap_Type

Public Member Functions inherited from Exporter< MeshType >
	Exporter ()
	Empty constructor for Exporter. More...

	Exporter (const GetPot &dfile, const std::string &prefix)
	Constructor for Exporter without prefix and procID. More...

virtual	~Exporter ()
	Destructor. More...

void	addVariable (const FieldTypeEnum &type, const std::string &variableName, const feSpacePtr_Type &feSpacePtr, const vectorPtr_Type &vectorPtr, const UInt &start, const FieldRegimeEnum &regime=exporterData_Type::UnsteadyRegime, const WhereEnum &where=exporterData_Type::Node)
	Adds a new variable to be post-processed. More...

virtual void	exportPID (meshPtr_Type &mesh, commPtr_Type &comm, const bool binaryFormat=false)
	Export the Processor ID as P0 variable. More...

void	exportRegionMarkerID (std::shared_ptr< MeshType > mesh, std::shared_ptr< Epetra_Comm > comm)
	Export the region marker ID as P0 variable. More...

virtual void	exportFlags (std::shared_ptr< MeshType > mesh, std::shared_ptr< Epetra_Comm > comm, flag_Type const &flag=EntityFlags::ALL)
	Export entity flags. More...

void	setPrefix (const std::string &prefix)
	Set prefix. More...

void	setPostDir (const std::string &Directory)
	Set the folder for pre/postprocessing. More...

void	setTimeIndex (const UInt &timeIndex)
	Set the current time index. More...

void	setTimeIndexStart (const UInt &timeIndexStart)
	Set the time index of the first file. More...

void	setSave (const UInt &save)
	Set how many time step between two snapshots. More...

void	setMultimesh (const bool &multimesh)
	Set if to save the mesh at each time step. More...

virtual void	setMeshProcId (const meshPtr_Type mesh, const int &procId)

const UInt &	save () const
	returns how many time steps between two snapshots More...

const UInt &	timeIndexStart () const
	returns the time index of the first snapshot More...

const UInt &	timeIndex () const
	returns the time index of the current snapshot More...

Protected Member Functions inherited from Exporter< MeshType >
void	computePostfix ()
	compute postfix More...

Protected Attributes inherited from Exporter< MeshType >
std::string	M_prefix
	the file prefix More...

std::string	M_postDir
	the name of the folder where to read or write files More...

UInt	M_timeIndexStart
	the time index of the first snapshot More...

UInt	M_timeIndex
	the time index of the current snapshot More...

UInt	M_save
	how many time steps between subsequent snapshots More...

bool	M_multimesh
	do we want to save the mesh with each snapshot? More...

UInt	M_timeIndexWidth
	how many digits (in the file suffix) for the time index More...

meshPtr_Type	M_mesh
	a pointer to the mesh More...

Int	M_procId
	the ID of the process More...

std::string	M_postfix
	the file suffix More...

UInt	M_numImportProc
	how many processes produced the data that we want to import More...

whereToDataIdMap_Type	M_whereToDataIdMap
	a map to retrieve all data located in the same geo entities (node or element) More...

feTypeToDataIdMap_Type	M_feTypeToDataIdMap
	a map to retrieve all data defined in the same FE space More...

dataVector_Type	M_dataVector
	the vector of ExporterData objects More...

std::list< Real >	M_timeSteps
	the list of time steps (for use in import procedures) More...

Detailed Description

template<typename MeshType>
class LifeV::ExporterHDF5< MeshType >

Hdf5 data exporter, implementation of Exporter.

Author: Simone Deparis simon.nosp@m.e.de.nosp@m.paris.nosp@m.@epf.nosp@m.l.ch; Radu Popescu radu..nosp@m.pope.nosp@m.scu@e.nosp@m.pfl..nosp@m.ch

Usage: two steps

first: add the variables using addVariable
second: call postProcess( time );

Definition at line 83 of file ExporterHDF5.hpp.

Member Typedef Documentation

◆ mesh_Type

typedef MeshType mesh_Type

Definition at line 89 of file ExporterHDF5.hpp.

◆ super

typedef Exporter<MeshType> super

Definition at line 90 of file ExporterHDF5.hpp.

◆ meshPtr_Type

typedef super::meshPtr_Type meshPtr_Type

Definition at line 91 of file ExporterHDF5.hpp.

◆ vector_Type

typedef super::vector_Type vector_Type

Definition at line 92 of file ExporterHDF5.hpp.

◆ vectorPtr_Type

typedef super::vectorPtr_Type vectorPtr_Type

Definition at line 93 of file ExporterHDF5.hpp.

◆ exporterData_Type

typedef super::exporterData_Type exporterData_Type

Definition at line 94 of file ExporterHDF5.hpp.

◆ hdf5_Type

typedef EpetraExt::HDF5 hdf5_Type

Definition at line 96 of file ExporterHDF5.hpp.

◆ hdf5Ptr_Type

typedef std::shared_ptr<hdf5_Type> hdf5Ptr_Type

Definition at line 97 of file ExporterHDF5.hpp.

◆ graph_Type

typedef std::vector<std::vector<Int> > graph_Type

Definition at line 98 of file ExporterHDF5.hpp.

◆ graphPtr_Type

typedef std::shared_ptr<graph_Type> graphPtr_Type

Definition at line 99 of file ExporterHDF5.hpp.

◆ serial_meshPtr_Type

typedef std::shared_ptr<std::vector<meshPtr_Type> > serial_meshPtr_Type

Definition at line 100 of file ExporterHDF5.hpp.

Constructor & Destructor Documentation

◆ ExporterHDF5() [1/3]

ExporterHDF5 ( )

Empty Constructor for ExporterHDF5.

Definition at line 261 of file ExporterHDF5.hpp.

◆ ExporterHDF5() [2/3]

ExporterHDF5	(	const GetPot &	dfile,
		meshPtr_Type	mesh,
		const std::string &	prefix,
		const Int &	procId
	)

Constructor for ExporterHDF5.

Parameters

dfile	the GetPot data file where you must provide an [exporter] section with: "start" (start index for sections in the hdf5 data structure 0 for 000, 1 for 001 etc.), "save" (how many time steps per postprocessing) "multimesh" ( = true if the mesh has to be saved at each post-processing step)
mesh	the mesh
the	prefix for the case file (ex. "test" for test.case)
the	procId determines de CPU id. if negative, it ussemes there is only one processor

Definition at line 271 of file ExporterHDF5.hpp.

◆ ExporterHDF5() [3/3]

ExporterHDF5	(	const GetPot &	dfile,
		const std::string &	prefix
	)

Constructor for ExporterHDF5 without prefix and procID.

Parameters

dfile	the GetPot data file where you must provide an [exporter] section with: "start" (start index for sections in the hdf5 data structure 0 for 000, 1 for 001 etc.), "save" (how many time steps per postprocessing) "multimesh" ( = true if the mesh has to be saved at each post-processing step)
mesh	the mesh

Definition at line 283 of file ExporterHDF5.hpp.

◆ ~ExporterHDF5()

virtual ~ExporterHDF5 ( )

inlinevirtual

Destructor for ExporterHDF5.

Definition at line 139 of file ExporterHDF5.hpp.

Member Function Documentation

◆ postProcess()

void postProcess ( const Real & time )

virtual

Post-process the variables added to the list.

Parameters

time	the solver time

Implements Exporter< MeshType >.

Reimplemented in ExporterHDF5Mesh3D< MeshType >.

Definition at line 297 of file ExporterHDF5.hpp.

◆ importFromTime()

UInt importFromTime ( const Real & Time )

virtual

Import data from previous simulations at a certain time.

Parameters

Time	the time of the data to be imported

Returns: number of iteration corresponding at the time step

Implements Exporter< MeshType >.

Definition at line 355 of file ExporterHDF5.hpp.

◆ importFromIter()

Real importFromIter ( const UInt & iter )

Import data from previous simulations at a certain time.

Parameters

Time	the time of the data to be imported

Returns: the simulation time corresponding to the iteration

Definition at line 424 of file ExporterHDF5.hpp.

◆ import() [1/2]

void import	(	const Real &	startTime,
		const Real &	dt
	)

virtual

Import data from previous simulations.

Parameters

time	the solver time

Implements Exporter< MeshType >.

Definition at line 512 of file ExporterHDF5.hpp.

◆ import() [2/2]

void import ( const Real & time )

virtual

Import data from previous simulations.

Parameters

time	the solver time

! Simone

!!! Simone

Implements Exporter< MeshType >.

Definition at line 529 of file ExporterHDF5.hpp.

◆ closeFile()

void closeFile ( )

inlinevirtual

Close the Hdf5 file.

Close the HDF5 file.

Reimplemented from Exporter< MeshType >.

Definition at line 177 of file ExporterHDF5.hpp.

◆ readVariable()

void readVariable ( exporterData_Type & dvar )

virtual

Read variable.

! Simone

Reimplemented from Exporter< MeshType >.

Definition at line 562 of file ExporterHDF5.hpp.

◆ setDataFromGetPot()

void setDataFromGetPot	(	const GetPot &	dataFile,
		const std::string &	section = `"exporter"`
	)

virtual

Set data from file.

Parameters

dataFile	data file.
section	section in the data file.

Reimplemented from Exporter< MeshType >.

Definition at line 576 of file ExporterHDF5.hpp.

◆ mapType()

MapEpetraType mapType ( ) const

virtual

returns the type of the map to use for the VectorEpetra

Implements Exporter< MeshType >.

Definition at line 586 of file ExporterHDF5.hpp.

◆ defineShape()

void defineShape ( )

protected

Define the shape of the elements.

Definition at line 595 of file ExporterHDF5.hpp.

◆ writeInitXdmf()

void writeInitXdmf ( )

protected

write empty xdmf file

Definition at line 601 of file ExporterHDF5.hpp.

◆ writeXdmf()

void writeXdmf ( const Real & time )

protected

append to xdmf file

Definition at line 632 of file ExporterHDF5.hpp.

◆ writeCloseLinesXdmf()

void writeCloseLinesXdmf ( )

protected

save position and write closing lines

Definition at line 704 of file ExporterHDF5.hpp.

◆ removeCloseLinesXdmf()

void removeCloseLinesXdmf ( )

protected

remove closing lines

Definition at line 717 of file ExporterHDF5.hpp.

◆ writeTopology()

void writeTopology ( std::ofstream & xdmf )

protected

Definition at line 723 of file ExporterHDF5.hpp.

◆ writeGeometry() [1/2]

void writeGeometry ( std::ofstream & xdmf )

protected

Definition at line 770 of file ExporterHDF5.hpp.

◆ writeAttributes()

void writeAttributes ( std::ofstream & xdmf )

protected

Definition at line 811 of file ExporterHDF5.hpp.

◆ writeScalarDatastructure()

void writeScalarDatastructure	(	std::ofstream &	xdmf,
		const exporterData_Type &	dvar
	)

protected

Definition at line 840 of file ExporterHDF5.hpp.

◆ writeVectorDatastructure()

void writeVectorDatastructure	(	std::ofstream &	xdmf,
		const exporterData_Type &	dvar
	)

protected

Definition at line 882 of file ExporterHDF5.hpp.

◆ writeVariable()

void writeVariable ( const exporterData_Type & dvar )

protected

Definition at line 918 of file ExporterHDF5.hpp.

◆ writeScalar()

void writeScalar ( const exporterData_Type & dvar )

protected

Definition at line 933 of file ExporterHDF5.hpp.

◆ writeVector()

void writeVector ( const exporterData_Type & dvar )

protected

Definition at line 967 of file ExporterHDF5.hpp.

◆ writeGeometry() [2/2]

void writeGeometry ( )

protected

Definition at line 1030 of file ExporterHDF5.hpp.

◆ readScalar()

void readScalar ( exporterData_Type & dvar )

protectedvirtual

A method to read a scalar field (to be implemented in derived classes)

Parameters

dvar	the ExporterData object

Implements Exporter< MeshType >.

Definition at line 1216 of file ExporterHDF5.hpp.

◆ readVector()

void readVector ( exporterData_Type & dvar )

protectedvirtual

A method to read a vector field (to be implemented in derived classes)

Parameters

dvar	the ExporterData object

Implements Exporter< MeshType >.

Definition at line 1240 of file ExporterHDF5.hpp.

Field Documentation

◆ MapType

MapEpetraType const MapType

static

returns the type of the map to use for the VectorEpetra

Definition at line 105 of file ExporterHDF5.hpp.

◆ M_HDF5

hdf5Ptr_Type M_HDF5

protected

Definition at line 240 of file ExporterHDF5.hpp.

◆ M_xdmf

std::ofstream M_xdmf

protected

Definition at line 241 of file ExporterHDF5.hpp.

◆ M_closingLines

const std::string M_closingLines

protected

Definition at line 243 of file ExporterHDF5.hpp.

◆ M_closingLinesPosition

std::streampos M_closingLinesPosition

protected

Definition at line 244 of file ExporterHDF5.hpp.

◆ M_outputFileName

std::string M_outputFileName

protected

Definition at line 245 of file ExporterHDF5.hpp.

◆ M_printConnectivity

bool M_printConnectivity

protected

do we want to write on file the connectivity?

Definition at line 248 of file ExporterHDF5.hpp.

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

ExporterHDF5.hpp

Public typedefs

Static members

Constructor & Destructor

Public Methods

Set Methods

Get Methods

Protected Methods

Protected data members

Additional Inherited Members

Detailed Description

template<typename MeshType> class LifeV::ExporterHDF5< MeshType >

Member Typedef Documentation

◆ mesh_Type

◆ super

◆ meshPtr_Type

◆ vector_Type

◆ vectorPtr_Type

◆ exporterData_Type

◆ hdf5_Type

◆ hdf5Ptr_Type

◆ graph_Type

◆ graphPtr_Type

◆ serial_meshPtr_Type

Constructor & Destructor Documentation

◆ ExporterHDF5() [1/3]

◆ ExporterHDF5() [2/3]

◆ ExporterHDF5() [3/3]

◆ ~ExporterHDF5()

Member Function Documentation

◆ postProcess()

◆ importFromTime()

◆ importFromIter()

◆ import() [1/2]

◆ import() [2/2]

◆ closeFile()

◆ readVariable()

◆ setDataFromGetPot()

◆ mapType()

◆ defineShape()

◆ writeInitXdmf()

◆ writeXdmf()

◆ writeCloseLinesXdmf()

◆ removeCloseLinesXdmf()

◆ writeTopology()

◆ writeGeometry() [1/2]

◆ writeAttributes()

◆ writeScalarDatastructure()

◆ writeVectorDatastructure()

◆ writeVariable()

◆ writeScalar()

◆ writeVector()

◆ writeGeometry() [2/2]

◆ readScalar()

◆ readVector()

Field Documentation

◆ MapType

◆ M_HDF5

◆ M_xdmf

◆ M_closingLines

◆ M_closingLinesPosition

◆ M_outputFileName

◆ M_printConnectivity

template<typename MeshType>
class LifeV::ExporterHDF5< MeshType >