Container for N-dimensional, homogeneous Records. More...

#include <Mesh.hpp>

Inheritance diagram for openPMD::Mesh:

Collaboration diagram for openPMD::Mesh:

Public Types
enum class	Geometry { cartesian , thetaMode , cylindrical , spherical , other }
	Enumerated datatype for the geometry of the mesh. More...

enum class	DataOrder : char { C = 'C' , F = 'F' }
	Enumerated datatype for the memory layout of N-dimensional data.

Public Types inherited from openPMD::BaseRecord< MeshRecordComponent >
using	T_RecordComponent = MeshRecordComponent

using	T_Container = Container< MeshRecordComponent >

using	key_type = typename Container< MeshRecordComponent >::key_type

using	mapped_type = typename Container< MeshRecordComponent >::mapped_type

using	value_type = typename Container< MeshRecordComponent >::value_type

using	size_type = typename Container< MeshRecordComponent >::size_type

using	difference_type = typename Container< MeshRecordComponent >::difference_type

using	allocator_type = typename Container< MeshRecordComponent >::allocator_type

using	reference = typename Container< MeshRecordComponent >::reference

using	const_reference = typename Container< MeshRecordComponent >::const_reference

using	pointer = typename Container< MeshRecordComponent >::pointer

using	const_pointer = typename Container< MeshRecordComponent >::const_pointer

using	iterator = internal::ScalarIterator< T_Self, Data_t, typename T_Container::InternalContainer::iterator >

using	const_iterator = internal::ScalarIterator< T_Self const, Data_t const, typename T_Container::InternalContainer::const_iterator >

using	reverse_iterator = internal::ScalarIterator< T_Self, Data_t, typename T_Container::InternalContainer::reverse_iterator >

using	const_reverse_iterator = internal::ScalarIterator< T_Self const, Data_t const, typename T_Container::InternalContainer::const_reverse_iterator >

Public Types inherited from openPMD::Container< T, T_key, T_container >
using	key_type = typename InternalContainer::key_type

using	mapped_type = typename InternalContainer::mapped_type

using	value_type = typename InternalContainer::value_type

using	size_type = typename InternalContainer::size_type

using	difference_type = typename InternalContainer::difference_type

using	allocator_type = typename InternalContainer::allocator_type

using	reference = typename InternalContainer::reference

using	const_reference = typename InternalContainer::const_reference

using	pointer = typename InternalContainer::pointer

using	const_pointer = typename InternalContainer::const_pointer

using	iterator = typename InternalContainer::iterator

using	const_iterator = typename InternalContainer::const_iterator

using	reverse_iterator = typename InternalContainer::reverse_iterator

using	const_reverse_iterator = typename InternalContainer::const_reverse_iterator

Public Types inherited from openPMD::Attributable
enum	ReadMode { IgnoreExisting , OverrideExisting , FullyReread }

Public Types inherited from openPMD::RecordComponent
enum class	Allocation { USER , API , AUTO }

using	shared_ptr_dataset_types = auxiliary::detail::map_variant< auxiliary::detail::as_shared_pointer, dataset_types >::type

Public Member Functions
	Mesh (Mesh const &)=default

Mesh &	operator= (Mesh const &)=default

Geometry	geometry () const

std::string	geometryString () const

Mesh &	setGeometry (Geometry g)
	Set the geometry of the mesh of the mesh record. More...

Mesh &	setGeometry (std::string geometry)
	Set the geometry of the mesh of the mesh record. More...

std::string	geometryParameters () const

Mesh &	setGeometryParameters (std::string const &geometryParameters)
	Set additional parameters for the geometry, separated by a. More...

DataOrder	dataOrder () const

Mesh &	setDataOrder (DataOrder dor)
	Set the memory layout of N-dimensional data. More...

std::vector< std::string >	axisLabels () const

Mesh &	setAxisLabels (std::vector< std::string > const &axisLabels)
	Set the ordering of the labels for the Mesh::geometry of the mesh. More...

template<typename T >
std::vector< T >	gridSpacing () const

template<typename T , typename = std::enable_if_t<std::is_floating_point<T>::value>>
Mesh &	setGridSpacing (std::vector< T > const &gridSpacing)
	Set the spacing of the grid points along each dimension (in the units of the simulation). More...

std::vector< double >	gridGlobalOffset () const

Mesh &	setGridGlobalOffset (std::vector< double > const &gridGlobalOffset)
	Set the start of the current domain of the simulation (position of the beginning of the first cell) in simulation units. More...

double	gridUnitSI () const

Mesh &	setGridUnitSI (double gridUnitSI)
	Set the unit-conversion factor to multiply each value in Mesh::gridSpacing and Mesh::gridGlobalOffset, in order to convert from simulation units to SI units. More...

Mesh &	setUnitDimension (std::map< UnitDimension, double > const &unitDimension)
	Set the powers of the 7 base measures characterizing the record's unit in SI. More...

template<typename T >
T	timeOffset () const

template<typename T , typename = std::enable_if_t<std::is_floating_point<T>::value>>
Mesh &	setTimeOffset (T timeOffset)
	Set the offset between the time at which this record is defined and the Iteration::time attribute of the Series::basePath level. More...

Public Member Functions inherited from openPMD::BaseRecord< MeshRecordComponent >
iterator	begin ()

const_iterator	begin () const

const_iterator	cbegin () const

iterator	end ()

const_iterator	end () const

const_iterator	cend () const

reverse_iterator	rbegin ()

const_reverse_iterator	rbegin () const

const_reverse_iterator	crbegin () const

reverse_iterator	rend ()

const_reverse_iterator	rend () const

const_reverse_iterator	crend () const

mapped_type &	operator[] (key_type const &key)

mapped_type &	operator[] (key_type &&key)

mapped_type &	at (key_type const &key)

mapped_type const &	at (key_type const &key) const

size_type	erase (key_type const &key)

iterator	erase (iterator res)

bool	empty () const noexcept

iterator	find (key_type const &key)

const_iterator	find (key_type const &key) const

size_type	count (key_type const &key) const

size_type	size () const

void	clear ()

std::pair< iterator, bool >	insert (value_type const &value)

std::pair< iterator, bool >	insert (value_type &&value)

iterator	insert (const_iterator hint, value_type const &value)

iterator	insert (const_iterator hint, value_type &&value)

void	insert (InputIt first, InputIt last)

void	insert (std::initializer_list< value_type > ilist)

auto	insert (InputIt first, InputIt last) -> void

void	swap (BaseRecord &other)

bool	contains (key_type const &key) const

auto	emplace (Args &&...args) -> std::pair< iterator, bool >

std::array< double, 7 >	unitDimension () const
	Return the physical dimension (quantity) of a record. More...

void	setDatasetDefined (BaseRecordComponent::Data_t &data) override

bool	scalar () const
	Returns true if this record only contains a single component. More...

Public Member Functions inherited from openPMD::Container< T, T_key, T_container >
iterator	begin () noexcept

const_iterator	begin () const noexcept

const_iterator	cbegin () const noexcept

iterator	end () noexcept

const_iterator	end () const noexcept

const_iterator	cend () const noexcept

reverse_iterator	rbegin () noexcept

const_reverse_iterator	rbegin () const noexcept

const_reverse_iterator	crbegin () const noexcept

reverse_iterator	rend () noexcept

const_reverse_iterator	rend () const noexcept

const_reverse_iterator	crend () const noexcept

bool	empty () const noexcept

size_type	size () const noexcept

void	clear ()
	Remove all objects from the container and (if written) from disk. More...

std::pair< iterator, bool >	insert (value_type const &value)

std::pair< iterator, bool >	insert (value_type &&value)

iterator	insert (const_iterator hint, value_type const &value)

iterator	insert (const_iterator hint, value_type &&value)

template<class InputIt >
void	insert (InputIt first, InputIt last)

void	insert (std::initializer_list< value_type > ilist)

void	swap (Container &other)

mapped_type &	at (key_type const &key)

mapped_type const &	at (key_type const &key) const

mapped_type &	operator[] (key_type const &key)
	Access the value that is mapped to a key equivalent to key, creating it if such key does not exist already. More...

mapped_type &	operator[] (key_type &&key)
	Access the value that is mapped to a key equivalent to key, creating it if such key does not exist already. More...

iterator	find (key_type const &key)

const_iterator	find (key_type const &key) const

size_type	count (key_type const &key) const
	This returns either 1 if the key is found in the container of 0 if not. More...

bool	contains (key_type const &key) const
	Checks if there is an element with a key equivalent to an exiting key in the container. More...

size_type	erase (key_type const &key)
	Remove a single element from the container and (if written) from disk. More...

iterator	erase (iterator res)

template<class... Args>
auto	emplace (Args &&...args) -> decltype(InternalContainer().emplace(std::forward< Args >(args)...))

protected void	clear_unchecked ()

	Container (NoInit)

	Container (Container const &other)

	Container (Container &&other)

Container &	operator= (Container const &other)

Container &	operator= (Container &&other)

Public Member Functions inherited from openPMD::Attributable
	Attributable (NoInit)

Attribute	getAttribute (std::string const &key) const
	Retrieve value of Attribute stored with provided key. More...

bool	deleteAttribute (std::string const &key)
	Remove Attribute of provided value both logically and physically. More...

std::vector< std::string >	attributes () const
	List all currently stored Attributes' keys. More...

size_t	numAttributes () const
	Count all currently stored Attributes. More...

bool	containsAttribute (std::string const &key) const
	Check whether am Attribute with a given key exists. More...

std::string	comment () const
	Retrieve a user-supplied comment associated with the object. More...

Attributable &	setComment (std::string const &comment)
	Populate Attribute corresponding to a comment with the user-supplied comment. More...

void	seriesFlush (std::string backendConfig="{}")
	Flush the corresponding Series object. More...

MyPath	myPath () const
	The path to this object within its containing Series. More...

protected Series	retrieveSeries () const

void	seriesFlush (internal::FlushParams const &)

void	flushAttributes (internal::FlushParams const &)

void	readAttributes (ReadMode)

template<typename T >
T	readFloatingpoint (std::string const &key) const
	Retrieve the value of a floating point Attribute of user-defined precision with ensured type-safety. More...

template<typename T >
std::vector< T >	readVectorFloatingpoint (std::string const &key) const
	Retrieve a vector of values of a floating point Attributes of user-defined precision with ensured type-safety. More...

AbstractIOHandler *	IOHandler ()

AbstractIOHandler const *	IOHandler () const

Writable *&	parent ()

Writable const *	parent () const

Writable &	writable ()

Writable const &	writable () const

void	setData (std::shared_ptr< internal::AttributableData > attri)

internal::AttributableData &	get ()

internal::AttributableData const &	get () const

bool	dirty () const

bool	dirtyRecursive () const
	O(1).

void	setDirty (bool dirty_in)

void	setDirtyRecursive (bool dirty_in)

bool	written () const

bool &	written ()

template<typename T >
bool	setAttribute (std::string const &key, T value)
	Populate Attribute of provided name with provided value. More...

bool	setAttribute (std::string const &key, char const value[])

Iteration const &	containingIteration () const
	Returns the corresponding Iteration. More...

Iteration &	containingIteration ()

Public Member Functions inherited from openPMD::MeshRecordComponent
	MeshRecordComponent (BaseRecord< MeshRecordComponent > const &)
	Avoid object slicing when using a Record as a scalar Record Component. More...

template<typename T >
std::vector< T >	position () const
	Position on an element. More...

template<typename T >
MeshRecordComponent &	setPosition (std::vector< T > pos)
	Position on an element. More...

template<typename T >
MeshRecordComponent &	makeConstant (T)
	Create a dataset with regular extent and constant value. More...

Public Member Functions inherited from openPMD::RecordComponent
	RecordComponent (BaseRecord< RecordComponent > const &)
	Avoid object slicing when using a Record as a scalar Record Component. More...

RecordComponent &	setUnitSI (double)

virtual RecordComponent &	resetDataset (Dataset)
	Declare the dataset's type and extent. More...

uint8_t	getDimensionality () const

Extent	getExtent () const

template<typename T >
RecordComponent &	makeConstant (T)
	Create a dataset with regular extent and constant value. More...

template<typename T >
RecordComponent &	makeEmpty (uint8_t dimensions)
	Create a dataset with zero extent in each dimension. More...

RecordComponent &	makeEmpty (Datatype dt, uint8_t dimensions)
	Non-template overload of RecordComponent::makeEmpty(). More...

bool	empty () const
	Returns true if this is an empty record component. More...

template<typename T >
std::shared_ptr< T >	loadChunk (Offset={0u}, Extent={-1u})
	Load and allocate a chunk of data. More...

shared_ptr_dataset_types	loadChunkVariant (Offset={0u}, Extent={-1u})
	std::variant-based version of allocating loadChunk<T>(Offset, Extent) More...

template<typename T >
void	loadChunk (std::shared_ptr< T > data, Offset offset, Extent extent)
	Load a chunk of data into pre-allocated memory. More...

template<typename T >
void	loadChunk (std::shared_ptr< T[]> data, Offset offset, Extent extent)
	Load a chunk of data into pre-allocated memory, array version. More...

template<typename T >
void	loadChunkRaw (T *data, Offset offset, Extent extent)
	Load a chunk of data into pre-allocated memory, raw pointer version. More...

template<typename T >
void	storeChunk (std::shared_ptr< T > data, Offset offset, Extent extent)
	Store a chunk of data from a chunk of memory. More...

template<typename T >
void	storeChunk (std::shared_ptr< T[]> data, Offset offset, Extent extent)
	Store a chunk of data from a chunk of memory, array version. More...

template<typename T >
void	storeChunk (UniquePtrWithLambda< T > data, Offset offset, Extent extent)
	Store a chunk of data from a chunk of memory, unique pointer version. More...

template<typename T , typename Del >
void	storeChunk (std::unique_ptr< T, Del > data, Offset offset, Extent extent)
	Store a chunk of data from a chunk of memory, unique pointer version. More...

template<typename T >
void	storeChunkRaw (T *data, Offset offset, Extent extent)
	Store a chunk of data from a chunk of memory, raw pointer version. More...

template<typename T_ContiguousContainer >
std::enable_if_t< auxiliary::IsContiguousContainer_v< T_ContiguousContainer > >	storeChunk (T_ContiguousContainer &data, Offset offset={0u}, Extent extent={-1u})
	Store a chunk of data from a contiguous container. More...

template<typename T , typename F >
DynamicMemoryView< T >	storeChunk (Offset offset, Extent extent, F &&createBuffer)
	Overload of storeChunk() that lets the openPMD API allocate a buffer. More...

template<typename T >
DynamicMemoryView< T >	storeChunk (Offset, Extent)
	Overload of span-based storeChunk() that uses operator new() to create a buffer.

template<typename Visitor , typename... Args>
auto	visit (Args &&...args) -> decltype(Visitor::template call< char >(std::declval< RecordComponent & >(), std::forward< Args >(args)...))
	Run a template functor on the type of the record component, similar to std::visit(). More...

Public Member Functions inherited from openPMD::BaseRecordComponent
	BaseRecordComponent (BaseRecordComponent const &other)

	BaseRecordComponent (BaseRecordComponent &&other)

BaseRecordComponent &	operator= (BaseRecordComponent const &other)

BaseRecordComponent &	operator= (BaseRecordComponent &&other)

double	unitSI () const

BaseRecordComponent &	resetDatatype (Datatype)

Datatype	getDatatype () const

bool	constant () const
	Returns true if this is a constant record component. More...

std::optional< size_t >	joinedDimension () const

ChunkTable	availableChunks ()
	Get data chunks that are available to be loaded from the backend. More...

Friends
class	Container< Mesh >

class	Iteration

Additional Inherited Members
Static Public Attributes inherited from openPMD::RecordComponent
static constexpr char const *const	SCALAR = "\vScalar"

Protected Types inherited from openPMD::Container< T, T_key, T_container >
using	ContainerData = internal::ContainerData< T, T_key, T_container >

using	InternalContainer = T_container

Protected Types inherited from openPMD::Attributable
using	Data_t = internal::AttributableData

Protected Types inherited from openPMD::BaseRecordComponent
using	Data_t = internal::BaseRecordComponentData

Protected Member Functions inherited from openPMD::BaseRecord< MeshRecordComponent >
void	setData (std::shared_ptr< Data_t > data)

void	readBase ()

Protected Member Functions inherited from openPMD::Container< T, T_key, T_container >
void	setData (std::shared_ptr< ContainerData > containerData)

InternalContainer const &	container () const

InternalContainer &	container ()

Protected Member Functions inherited from openPMD::RecordComponent
void	flush (std::string const &, internal::FlushParams const &)

void	read (bool require_unit_si)

Protected Member Functions inherited from openPMD::BaseRecordComponent
Data_t const &	get () const

Data_t &	get ()

void	setData (std::shared_ptr< Data_t > data)

virtual void	setDatasetDefined (Data_t &)

bool	datasetDefined () const

	BaseRecordComponent (NoInit)

Protected Attributes inherited from openPMD::Container< T, T_key, T_container >
std::shared_ptr< ContainerData >	m_containerData

Protected Attributes inherited from openPMD::Attributable
std::shared_ptr< Data_t >	m_attri

Protected Attributes inherited from openPMD::BaseRecordComponent
std::shared_ptr< Data_t >	m_baseRecordComponentData

Detailed Description

Container for N-dimensional, homogeneous Records.

See also: https://github.com/openPMD/openPMD-standard/blob/latest/STANDARD.md#mesh-based-records

Member Enumeration Documentation

◆ Geometry

enum openPMD::Mesh::Geometry

strong

Enumerated datatype for the geometry of the mesh.

Note: If the default values do not suit your application, you can set arbitrary Geometry with MeshRecordComponent::setAttribute("geometry", VALUE). Note that this might break openPMD compliance and tool support.

Member Function Documentation

◆ axisLabels()

std::vector< std::string > openPMD::Mesh::axisLabels ( ) const

Returns: Ordering of the labels for the Mesh::geometry of the mesh.

◆ dataOrder()

Mesh::DataOrder openPMD::Mesh::dataOrder ( ) const

Returns: Memory layout of N-dimensional data.

◆ geometry()

Mesh::Geometry openPMD::Mesh::geometry ( ) const

Returns: Enum representing the geometry of the mesh of the mesh record.

◆ geometryParameters()

std::string openPMD::Mesh::geometryParameters ( ) const

Exceptions

no_such_attribute_error If Mesh::geometry is not Mesh::Geometry::thetaMode.

Returns: String representing additional parameters for the geometry, separated by a
;

.

◆ geometryString()

std::string openPMD::Mesh::geometryString ( ) const

Returns: String representing the geometry of the mesh of the mesh record.

◆ gridGlobalOffset()

std::vector< double > openPMD::Mesh::gridGlobalOffset ( ) const

Returns: Vector of (double) representing the start of the current domain of the simulation (position of the beginning of the first cell) in simulation units.

◆ gridSpacing()

template<typename T >

std::vector< T > openPMD::Mesh::gridSpacing

inline

Template Parameters

T	Floating point type of user-selected precision (e.g. float, double).

Returns: vector of T representing the spacing of the grid points along each dimension (in the units of the simulation).

◆ gridUnitSI()

double openPMD::Mesh::gridUnitSI ( ) const

Returns: Unit-conversion factor to multiply each value in Mesh::gridSpacing and Mesh::gridGlobalOffset, in order to convert from simulation units to SI units.

◆ setAxisLabels()

Mesh & openPMD::Mesh::setAxisLabels ( std::vector< std::string > const & axisLabels )

Set the ordering of the labels for the Mesh::geometry of the mesh.

Note: Dimensionality constraint is not verified by API.

Parameters

axisLabels vector containing N (string) elements, where N is the number of dimensions in the simulation.

Returns: Reference to modified mesh.

◆ setDataOrder()

Mesh & openPMD::Mesh::setDataOrder ( Mesh::DataOrder dor )

Set the memory layout of N-dimensional data.

Parameters

dor	memory layout of N-dimensional data.

Returns: Reference to modified mesh.

◆ setGeometry() [1/2]

Mesh & openPMD::Mesh::setGeometry ( Mesh::Geometry g )

Set the geometry of the mesh of the mesh record.

Parameters

g	geometry of the mesh of the mesh record.

Returns: Reference to modified mesh.

◆ setGeometry() [2/2]

Mesh & openPMD::Mesh::setGeometry ( std::string geometry )

Set the geometry of the mesh of the mesh record.

If the geometry is unknown to the openPMD-api, the string is prefixed with "other:" automatically unless the prefix is already present.

Parameters

geometry geometry of the mesh of the mesh record, as string

Returns: Reference to modified mesh.

◆ setGeometryParameters()

Mesh & openPMD::Mesh::setGeometryParameters ( std::string const & geometryParameters )

Set additional parameters for the geometry, separated by a.

;

.

Note: Separation constraint is not verified by API.

Parameters

geometryParameters

additional parameters for the geometry, separated by a

;

.

Returns: Reference to modified mesh.

◆ setGridGlobalOffset()

Mesh & openPMD::Mesh::setGridGlobalOffset ( std::vector< double > const & gridGlobalOffset )

Set the start of the current domain of the simulation (position of the beginning of the first cell) in simulation units.

Note: Dimensionality constraint is not verified by API.

Parameters

gridGlobalOffset vector containing N (double) elements, where N is the number of dimensions in the simulation.

Returns: Reference to modified mesh.

◆ setGridSpacing()

template<typename T , typename >

template Mesh & openPMD::Mesh::setGridSpacing ( std::vector< T > const & gridSpacing )

Set the spacing of the grid points along each dimension (in the units of the simulation).

Note: Dimensionality constraint is not verified by API.

Template Parameters

T	Floating point type of user-selected precision (e.g. float, double).

Parameters

gridSpacing vector containing N (T) elements, where N is the number of dimensions in the simulation.

Returns: Reference to modified mesh.

◆ setGridUnitSI()

Mesh & openPMD::Mesh::setGridUnitSI ( double gridUnitSI )

Set the unit-conversion factor to multiply each value in Mesh::gridSpacing and Mesh::gridGlobalOffset, in order to convert from simulation units to SI units.

Parameters

gridUnitSI unit-conversion factor to multiply each value in Mesh::gridSpacing and Mesh::gridGlobalOffset, in order to convert from simulation units to SI units.

Returns: Reference to modified mesh.

◆ setTimeOffset()

template<typename T , typename >

template Mesh & openPMD::Mesh::setTimeOffset ( T timeOffset )

Set the offset between the time at which this record is defined and the Iteration::time attribute of the Series::basePath level.

Note: This should be written in the same unit system as Iteration::time.

Template Parameters

T	Floating point type of user-selected precision (e.g. float, double).

Parameters

timeOffset Offset between the time at which this record is defined and the Iteration::time attribute of the Series::basePath level.

Returns: Reference to modified mesh.

◆ setUnitDimension()

Mesh & openPMD::Mesh::setUnitDimension ( std::map< UnitDimension, double > const & unitDimension )

Set the powers of the 7 base measures characterizing the record's unit in SI.

Parameters

unitDimension map containing pairs of (UnitDimension, double) that represent the power of the particular base.

Returns: Reference to modified mesh.

◆ timeOffset()

template<typename T >

T openPMD::Mesh::timeOffset

inline

Template Parameters

T	Floating point type of user-selected precision (e.g. float, double).

Returns: Offset between the time at which this record is defined and the Iteration::time attribute of the Series::basePath level.

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

/home/docs/checkouts/readthedocs.org/user_builds/openpmd-api/checkouts/latest/include/openPMD/Mesh.hpp
/home/docs/checkouts/readthedocs.org/user_builds/openpmd-api/checkouts/latest/src/Mesh.cpp

Public Types

Public Member Functions

Friends

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ Geometry

Member Function Documentation

◆ axisLabels()

◆ dataOrder()

◆ geometry()

◆ geometryParameters()

◆ geometryString()

◆ gridGlobalOffset()

◆ gridSpacing()

◆ gridUnitSI()

◆ setAxisLabels()

◆ setDataOrder()

◆ setGeometry() [1/2]

◆ setGeometry() [2/2]

◆ setGeometryParameters()

◆ setGridGlobalOffset()

◆ setGridSpacing()

◆ setGridUnitSI()

◆ setTimeOffset()

◆ setUnitDimension()

◆ timeOffset()