toolbox::particles::FileReaderHDF5 Class Reference

An HDF5 file reader This class works if and only if you have compiled Peano using –with-hdf5. More...

#include <FileReaderHDF5.h>

Collaboration diagram for toolbox::particles::FileReaderHDF5:

Public Member Functions
void	readHDF5File (const std::string &filename)
	Read HDF5 file in SWIFT format.
std::list< tarch::la::Vector< Dimensions, double > >	getParticlesWithinVoxel (const tarch::la::Vector< Dimensions, double > &x, const tarch::la::Vector< Dimensions, double > &h, bool remove)
	Take particles from database which fall into given voxel.
void	clear ()
bool	empty () const
bool	getNumberOfCoordinates () const
void	clearVoxel ()
	Clear data of a voxel carried by this instance of FileReaderHDF5.
bool	isVoxelEmpty () const
	Check whether voxel data carried by this instance of FileReaderHDF5 is empty.
std::vector< tarch::la::Vector< Dimensions, double > >	getVelocityWithinVoxel () const
std::vector< double >	getMassWithinVoxel () const
std::vector< double >	getSmoothingLengthWithinVoxel () const
std::vector< double >	getInternalEnergyWithinVoxel () const
std::vector< int >	getParticleIDsWithinVoxel () const

Private Attributes
std::list< tarch::la::Vector< Dimensions, double > >	_Coordinates
std::vector< tarch::la::Vector< Dimensions, double > >	_Velocity
std::vector< double >	_Mass
std::vector< double >	_SmoothingLength
std::vector< double >	_InternalEnergy
std::vector< int >	_ParticleIDs
std::list< int >	_ParticleIndex
std::vector< tarch::la::Vector< Dimensions, double > >	_VelocityWithinVoxel
std::vector< double >	_MassWithinVoxel
std::vector< double >	_SmoothingLengthWithinVoxel
std::vector< double >	_InternalEnergyWithinVoxel
std::vector< int >	_ParticleIDsWithinVoxel

Static Private Attributes
static tarch::logging::Log	_log

Detailed Description

An HDF5 file reader This class works if and only if you have compiled Peano using –with-hdf5.

Particle coordinates are stored in list containers. Importantly, this will be used by the getParticlesWithinVoxel method to retrieve particles from each cell (and then remove them if desired). Other HDF5 groups are stored in vector containers so we can use subscripts to access them. @TODO use templates to unify the readers for the different return types.

Definition at line 35 of file FileReaderHDF5.h.

Member Function Documentation

clear()

void toolbox::particles::FileReaderHDF5::clear

(

)

Definition at line 578 of file FileReaderHDF5.cpp.

Referenced by peano4.output.Makefile.Makefile::__init__().

Here is the caller graph for this function:

clearVoxel()

void toolbox::particles::FileReaderHDF5::clearVoxel

(

)

Clear data of a voxel carried by this instance of FileReaderHDF5.

Definition at line 507 of file FileReaderHDF5.cpp.

empty()

bool toolbox::particles::FileReaderHDF5::empty

(

)

const

Definition at line 588 of file FileReaderHDF5.cpp.

getInternalEnergyWithinVoxel()

std::vector< double > toolbox::particles::FileReaderHDF5::getInternalEnergyWithinVoxel

(

)

const

Definition at line 613 of file FileReaderHDF5.cpp.

getMassWithinVoxel()

std::vector< double > toolbox::particles::FileReaderHDF5::getMassWithinVoxel

(

)

const

Definition at line 603 of file FileReaderHDF5.cpp.

getNumberOfCoordinates()

bool toolbox::particles::FileReaderHDF5::getNumberOfCoordinates

(

)

const

Definition at line 593 of file FileReaderHDF5.cpp.

getParticleIDsWithinVoxel()

std::vector< int > toolbox::particles::FileReaderHDF5::getParticleIDsWithinVoxel

(

)

const

Definition at line 618 of file FileReaderHDF5.cpp.

getParticlesWithinVoxel()

std::list< tarch::la::Vector< Dimensions, double > > toolbox::particles::FileReaderHDF5::getParticlesWithinVoxel	(	const tarch::la::Vector< Dimensions, double > &	x,
		const tarch::la::Vector< Dimensions, double > &	h,
		bool	remove )

Take particles from database which fall into given voxel.

Overlapping vs. non-overlapping domain decomposition

In an SPMD environment, it is convenient to make each rank maintain its own input database. As a consequence, ranks have redundant particles and we will have to clean up eventually. To mirror this behaviour in the multithreaded context, we can remove particles whenever we assign them to an inner vertex, but we should also hand them out redundantly for boundary vertices.

Parameters

x	Center of voxel. If you use this within touchVertexFirstTime(), you can use the vertex position, i.e. the x() operation of the marker. If you use this function within a cell event, you can use x() as well, as it returns the centre.
h	Size of voxel. If you use this function within a cell event, just pass in h(). If you use it within a vertex event, you should scale h with 0.5.
remove	Remove a particle form the internal database if it is a match. In most cases, removing the particles immediately speeds up things, even though we then have a lot of (uneccessary) locks.

See also

peano4::datamanagement::CellMarker::x()

peano4::datamanagement::VertexMarker::x()

Definition at line 523 of file FileReaderHDF5.cpp.

References tarch::la::greaterEquals(), and tarch::la::smallerEquals().

Here is the call graph for this function:

getSmoothingLengthWithinVoxel()

std::vector< double > toolbox::particles::FileReaderHDF5::getSmoothingLengthWithinVoxel

(

)

const

Definition at line 608 of file FileReaderHDF5.cpp.

getVelocityWithinVoxel()

std::vector< tarch::la::Vector< Dimensions, double > > toolbox::particles::FileReaderHDF5::getVelocityWithinVoxel

(

)

const

Definition at line 598 of file FileReaderHDF5.cpp.

isVoxelEmpty()

bool toolbox::particles::FileReaderHDF5::isVoxelEmpty

(

)

const

Check whether voxel data carried by this instance of FileReaderHDF5 is empty.

Definition at line 515 of file FileReaderHDF5.cpp.

readHDF5File()

void toolbox::particles::FileReaderHDF5::readHDF5File

(

const std::string &

filename

)

Read HDF5 file in SWIFT format.

The coordinates are stored into lists, which allow efficient manipulation for inserting/removing entries later on, see getParticlesWithinVoxel below.

Parameters

filename

string with file name of the HDF5 file.

Definition at line 12 of file FileReaderHDF5.cpp.

References _Coordinates, _InternalEnergy, _Mass, _ParticleIDs, _ParticleIndex, _SmoothingLength, _Velocity, logError, and logInfo.

Field Documentation

_Coordinates

std::list< tarch::la::Vector<Dimensions,double> > toolbox::particles::FileReaderHDF5::_Coordinates

private

Definition at line 40 of file FileReaderHDF5.h.

Referenced by readHDF5File().

_InternalEnergy

std::vector<double> toolbox::particles::FileReaderHDF5::_InternalEnergy

private

Definition at line 46 of file FileReaderHDF5.h.

Referenced by readHDF5File().

_InternalEnergyWithinVoxel

std::vector<double> toolbox::particles::FileReaderHDF5::_InternalEnergyWithinVoxel

private

Definition at line 61 of file FileReaderHDF5.h.

_log

tarch::logging::Log toolbox::particles::FileReaderHDF5::_log

staticprivate

Definition at line 37 of file FileReaderHDF5.h.

_Mass

std::vector<double> toolbox::particles::FileReaderHDF5::_Mass

private

Definition at line 44 of file FileReaderHDF5.h.

Referenced by readHDF5File().

_MassWithinVoxel

std::vector<double> toolbox::particles::FileReaderHDF5::_MassWithinVoxel

private

Definition at line 59 of file FileReaderHDF5.h.

_ParticleIDs

std::vector<int> toolbox::particles::FileReaderHDF5::_ParticleIDs

private

Definition at line 47 of file FileReaderHDF5.h.

Referenced by readHDF5File().

_ParticleIDsWithinVoxel

std::vector<int> toolbox::particles::FileReaderHDF5::_ParticleIDsWithinVoxel

private

Definition at line 62 of file FileReaderHDF5.h.

_ParticleIndex

std::list<int> toolbox::particles::FileReaderHDF5::_ParticleIndex

private

Definition at line 52 of file FileReaderHDF5.h.

Referenced by readHDF5File().

_SmoothingLength

std::vector<double> toolbox::particles::FileReaderHDF5::_SmoothingLength

private

Definition at line 45 of file FileReaderHDF5.h.

Referenced by readHDF5File().

_SmoothingLengthWithinVoxel

std::vector<double> toolbox::particles::FileReaderHDF5::_SmoothingLengthWithinVoxel

private

Definition at line 60 of file FileReaderHDF5.h.

_Velocity

std::vector< tarch::la::Vector<Dimensions,double> > toolbox::particles::FileReaderHDF5::_Velocity

private

Definition at line 43 of file FileReaderHDF5.h.

Referenced by readHDF5File().

_VelocityWithinVoxel

std::vector< tarch::la::Vector<Dimensions,double> > toolbox::particles::FileReaderHDF5::_VelocityWithinVoxel

private

Definition at line 58 of file FileReaderHDF5.h.

---

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

• src/toolbox/particles/FileReaderHDF5.h
• src/toolbox/particles/FileReaderHDF5.cpp