#include <WarpXOpenPMD.H>

Public Types
using	ParticleContainer = typename WarpXParticleContainer::ContainerLike<amrex::PinnedArenaAllocator>

using	ParticleIter = typename amrex::ParConstIterSoA<PIdx::nattribs, 0, amrex::PinnedArenaAllocator>

Public Member Functions
	WarpXOpenPMDPlot (openPMD::IterationEncoding ie, const std::string &filetype, const std::string &operator_type, const std::map< std::string, std::string > &operator_parameters, const std::string &engine_type, const std::map< std::string, std::string > &engine_parameters, const std::vector< bool > &fieldPMLdirections, const std::string &authors)

	~WarpXOpenPMDPlot ()

	WarpXOpenPMDPlot (WarpXOpenPMDPlot const &)=delete

WarpXOpenPMDPlot &	operator= (WarpXOpenPMDPlot const &)=delete

	WarpXOpenPMDPlot (WarpXOpenPMDPlot &&)=default

WarpXOpenPMDPlot &	operator= (WarpXOpenPMDPlot &&)=default

void	SetStep (int ts, const std::string &dirPrefix, int file_min_digits, bool isBTD=false)

void	CloseStep (bool isBTD=false, bool isLastBTDFlush=false)

void	WriteOpenPMDParticles (const amrex::Vector< ParticleDiag > &particle_diags, amrex::Real time, bool use_pinned_pc=false, bool isBTD=false, bool isLastBTDFlush=false)

void	WriteOpenPMDFieldsAll (const std::vector< std::string > &varnames, const amrex::Vector< amrex::MultiFab > &mf, amrex::Vector< amrex::Geometry > &geom, int output_levels, int iteration, double time, bool isBTD=false, const amrex::Geometry &full_BTD_snapshot=amrex::Geometry()) const

std::string	OpenPMDFileType ()

void	FlushBTDToDisk ()

Private Member Functions
void	Init (openPMD::Access access, bool isBTD)

openPMD::Iteration	GetIteration (int const iteration, bool const isBTD) const

void	seriesFlush (bool isBTD) const

void	SetupFields (openPMD::Container< openPMD::Mesh > &meshes, amrex::Geometry &full_geom) const

void	SetupMeshComp (openPMD::Mesh &mesh, amrex::Geometry const &full_geom, std::string const &comp_name, std::string const &field_name, amrex::MultiFab const &mf, bool var_in_theta_mode) const

void	GetMeshCompNames (int meshLevel, const std::string &varname, std::string &field_name, std::string &comp_name, bool var_in_theta_mode) const

void	SetupPos (openPMD::ParticleSpecies &currSpecies, std::vector< std::string > const &positionComponents, const unsigned long long &np, bool isBTD=false)

void	SetConstParticleRecordsEDPIC (openPMD::ParticleSpecies &currSpecies, std::vector< std::string > const &positionComponents, const unsigned long long &np, amrex::ParticleReal charge, amrex::ParticleReal mass)

void	SetupRealProperties (ParticleContainer const *pc, openPMD::ParticleSpecies &currSpecies, const amrex::Vector< int > &write_real_comp, const amrex::Vector< std::string > &real_comp_names, const amrex::Vector< int > &write_int_comp, const amrex::Vector< std::string > &int_comp_names, unsigned long long np, bool isBTD=false) const

void	SaveRealProperty (ParticleIter &pti, openPMD::ParticleSpecies &currSpecies, unsigned long long offset, const amrex::Vector< int > &write_real_comp, const amrex::Vector< std::string > &real_comp_names, const amrex::Vector< int > &write_int_comp, const amrex::Vector< std::string > &int_comp_names) const

void	DumpToFile (ParticleContainer *pc, const std::string &name, int iteration, const amrex::Vector< int > &write_real_comp, const amrex::Vector< int > &write_int_comp, const amrex::Vector< std::string > &real_comp_names, const amrex::Vector< std::string > &int_comp_names, amrex::ParticleReal charge, amrex::ParticleReal mass, bool isBTD=false, bool isLastBTDFlush=false)

std::string	GetFileName (std::string &filepath)

Private Attributes
std::unique_ptr< openPMD::Series >	m_Series

std::string	m_dirPrefix

int	m_file_min_digits

int	m_MPIRank = 0

int	m_MPISize = 1

openPMD::IterationEncoding	m_Encoding = openPMD::IterationEncoding::fileBased

std::string	m_OpenPMDFileType = "bp5"

std::string	m_OpenPMDoptions = "{}"
	MPI-parallel openPMD backend: bp5, bp4 or h5.

int	m_CurrentStep = -1
	JSON option string for openPMD::Series constructor.

std::vector< bool >	m_fieldPMLdirections

std::string	m_authors

Detailed Description

Writer logic for openPMD particles and fields

Member Typedef Documentation

◆ ParticleContainer

using WarpXOpenPMDPlot::ParticleContainer = typename WarpXParticleContainer::ContainerLike<amrex::PinnedArenaAllocator>

◆ ParticleIter

using WarpXOpenPMDPlot::ParticleIter = typename amrex::ParConstIterSoA<PIdx::nattribs, 0, amrex::PinnedArenaAllocator>

Constructor & Destructor Documentation

◆ WarpXOpenPMDPlot() [1/3]

WarpXOpenPMDPlot::WarpXOpenPMDPlot	(	openPMD::IterationEncoding	ie,
		const std::string &	filetype,
		const std::string &	operator_type,
		const std::map< std::string, std::string > &	operator_parameters,
		const std::string &	engine_type,
		const std::map< std::string, std::string > &	engine_parameters,
		const std::vector< bool > &	fieldPMLdirections,
		const std::string &	authors )

Initialize openPMD I/O routines

Parameters

ie	iteration encoding from openPMD: "group, file, variable"
filetype	file backend, e.g. "bp5", "bp4", or "h5"
operator_type	openPMD-api backend operator (compressor) for ADIOS2
operator_parameters	openPMD-api backend operator parameters for ADIOS2
engine_type	ADIOS engine for output
engine_parameters	map of parameters for the engine
fieldPMLdirections	PML field solver,

See also: WarpX::getPMLdirections()

Parameters

authors a string specifying the authors of the simulation (can be empty)

◆ ~WarpXOpenPMDPlot()

WarpXOpenPMDPlot::~WarpXOpenPMDPlot ( )

◆ WarpXOpenPMDPlot() [2/3]

WarpXOpenPMDPlot::WarpXOpenPMDPlot ( WarpXOpenPMDPlot const & )

delete

◆ WarpXOpenPMDPlot() [3/3]

WarpXOpenPMDPlot::WarpXOpenPMDPlot ( WarpXOpenPMDPlot && )

default

Member Function Documentation

◆ CloseStep()

void WarpXOpenPMDPlot::CloseStep	(	bool	isBTD = false,
		bool	isLastBTDFlush = false )

Close the step

Signal that no further updates will be written for the step.

◆ DumpToFile()

void WarpXOpenPMDPlot::DumpToFile	(	ParticleContainer *	pc,
		const std::string &	name,
		int	iteration,
		const amrex::Vector< int > &	write_real_comp,
		const amrex::Vector< int > &	write_int_comp,
		const amrex::Vector< std::string > &	real_comp_names,
		const amrex::Vector< std::string > &	int_comp_names,
		amrex::ParticleReal	charge,
		amrex::ParticleReal	mass,
		bool	isBTD = false,
		bool	isLastBTDFlush = false )

private

This function saves the plot file

Parameters

[in]	pc	WarpX particle container
[in]	name	species name
[in]	iteration	timestep
[in]	write_real_comp	The real attribute ids, from WarpX
[in]	write_int_comp	The int attribute ids, from WarpX
[in]	real_comp_names	The real attribute names, from WarpX
[in]	int_comp_names	The int attribute names, from WarpX
[in]	charge	Charge of the particles (note: fix for ions)
[in]	mass	Mass of the particles
[in]	isBTD	is this a backtransformed diagnostics (BTD) write?
[in]	isLastBTDFlush	is this the last time we will flush this BTD station?

◆ FlushBTDToDisk()

void WarpXOpenPMDPlot::FlushBTDToDisk ( )

Ensure BTD buffers are written to disk

This function can be called to intermediately ensure ADIOS buffered "steps" are written to disk, and the valid metadata if checkpointing is required.

This is needed to read partial data while a simulation is running or to support restarting (the BTD diagnostics) in WarpX, so it can continue to append to a partially written labframe station after restart.

The frequency is controlled by FlushFormatOpenPMD::m_NumAggBTDBufferToFlush (default to 5). It can be adjusted in the input file: diag_name.buffer_flush_limit_btd

◆ GetFileName()

std::string WarpXOpenPMDPlot::GetFileName ( std::string & filepath )

private

Get the openPMD-api filename for openPMD::Series

No need for ts in the file name, openPMD handles steps (iterations).

Parameters

[in,out] filepath the path and filename for openPMD::Series passes a prefix path in and appends the filename

Returns: pure filename w/o path

◆ GetIteration()

openPMD::Iteration WarpXOpenPMDPlot::GetIteration	(	int const	iteration,
		bool const	isBTD ) const

inlinenodiscardprivate

Get the openPMD::Iteration object of the current Series

We use this helper function to differentiate between efficient, temporally sequentially increasing writes to iteration numbers and random-access writes to iterations, e.g., as needed for back-transformed diagnostics.

Parameters

[in]	iteration	iteration number (lab-frame for BTD)
[in]	isBTD	is this a backtransformed diagnostics write?

Returns: the iteration object

◆ GetMeshCompNames()

void WarpXOpenPMDPlot::GetMeshCompNames	(	int	meshLevel,
		const std::string &	varname,
		std::string &	field_name,
		std::string &	comp_name,
		bool	var_in_theta_mode ) const

private

Get Component Names from WarpX name

Get component names of a field for openPMD-api book-keeping Level is reflected as _lvl<meshLevel>

Parameters

[in]	meshLevel	level of mesh
[in]	varname	name from WarpX
[out]	field_name	field name for openPMD-api output
[in]	comp_name	comp name for openPMD-api output
[in]	var_in_theta_mode	indicate if this field will be output with theta modes (instead of a reconstructed 2D slice)

◆ Init()

void WarpXOpenPMDPlot::Init	(	openPMD::Access	access,
		bool	isBTD )

private

◆ OpenPMDFileType()

std::string WarpXOpenPMDPlot::OpenPMDFileType ( )

inline

Return OpenPMD File type ("bp5", "bp4", "h5" or "json")

◆ operator=() [1/2]

WarpXOpenPMDPlot & WarpXOpenPMDPlot::operator= ( WarpXOpenPMDPlot && )

default

◆ operator=() [2/2]

WarpXOpenPMDPlot & WarpXOpenPMDPlot::operator= ( WarpXOpenPMDPlot const & )

delete

◆ SaveRealProperty()

void WarpXOpenPMDPlot::SaveRealProperty	(	ParticleIter &	pti,
		openPMD::ParticleSpecies &	currSpecies,
		unsigned long long	offset,
		const amrex::Vector< int > &	write_real_comp,
		const amrex::Vector< std::string > &	real_comp_names,
		const amrex::Vector< int > &	write_int_comp,
		const amrex::Vector< std::string > &	int_comp_names ) const

private

This function saves the values of the entries for particle properties

Parameters

[in]	pti	WarpX particle iterator
[in]	currSpecies	The openPMD species to save to
[in]	offset	offset to start saving the particle iterator contents
[in]	write_real_comp	The real attribute ids, from WarpX
[in]	real_comp_names	The real attribute names, from WarpX
[in]	write_int_comp	The int attribute ids, from WarpX
[in]	int_comp_names	The int attribute names, from WarpX

◆ seriesFlush()

void WarpXOpenPMDPlot::seriesFlush ( bool isBTD ) const

private

Flushing out data of the current openPMD iteration

Parameters

[in] isBTD if the current diagnostic is BTD

if isBTD=false, apply the default flush behaviour in ADIOS, the action will be PerformDataWrite if isBTD=true, in ADIOS, the action will be PerformPut because no action is taken for the span tasks. This way we can aggregate buffers before calling FlushBTDToDisk() to write out.

iteration.seriesFlush() is used instead of series.flush() because the latter flushes only if data is dirty this causes trouble when the underlying writing function is collective (like PDW)

◆ SetConstParticleRecordsEDPIC()

void WarpXOpenPMDPlot::SetConstParticleRecordsEDPIC	(	openPMD::ParticleSpecies &	currSpecies,
		std::vector< std::string > const &	positionComponents,
		const unsigned long long &	np,
		amrex::ParticleReal	charge,
		amrex::ParticleReal	mass )

private

This function sets constant particle records and ED-PIC attributes.

Sets the entries for storing particle position offset, constant records (charge, mass) and ED-PIC attributes.

Parameters

[in]	currSpecies	Corresponding openPMD species
[in]	positionComponents	user-selected components of the particle position
[in]	np	Number of particles
[in]	charge	Charge of the particles (note: fix for ions)
[in]	mass	Mass of the particles

◆ SetStep()

void WarpXOpenPMDPlot::SetStep	(	int	ts,
		const std::string &	dirPrefix,
		int	file_min_digits,
		bool	isBTD = false )

Set Iteration Step for the series

Note: If an iteration has been written, then it will give a warning

◆ SetupFields()

void WarpXOpenPMDPlot::SetupFields	(	openPMD::Container< openPMD::Mesh > &	meshes,
		amrex::Geometry &	full_geom ) const

private

This function does initial setup for the fields when interation is newly created

Parameters

[in]	meshes	The meshes in a series
[in]	full_geom	The geometry

◆ SetupMeshComp()

void WarpXOpenPMDPlot::SetupMeshComp	(	openPMD::Mesh &	mesh,
		amrex::Geometry const &	full_geom,
		std::string const &	comp_name,
		std::string const &	field_name,
		amrex::MultiFab const &	mf,
		bool	var_in_theta_mode ) const

private

◆ SetupPos()

void WarpXOpenPMDPlot::SetupPos	(	openPMD::ParticleSpecies &	currSpecies,
		std::vector< std::string > const &	positionComponents,
		const unsigned long long &	np,
		bool	isBTD = false )

private

This function sets up the entries for storing the particle positions and global IDs

Parameters

[in]	currSpecies	Corresponding openPMD species
[in]	positionComponents	user-selected components of the particle position
[in]	np	Number of particles
[in]	isBTD	Is this a back-transformed diagnostics output?

◆ SetupRealProperties()

void WarpXOpenPMDPlot::SetupRealProperties	(	ParticleContainer const *	pc,
		openPMD::ParticleSpecies &	currSpecies,
		const amrex::Vector< int > &	write_real_comp,
		const amrex::Vector< std::string > &	real_comp_names,
		const amrex::Vector< int > &	write_int_comp,
		const amrex::Vector< std::string > &	int_comp_names,
		unsigned long long	np,
		bool	isBTD = false ) const

private

This function sets up the entries for particle properties

Parameters

[in]	pc	The particle container of the species
[in]	currSpecies	The openPMD species
[in]	write_real_comp	The real attribute ids, from WarpX
[in]	real_comp_names	The real attribute names, from WarpX
[in]	write_int_comp	The int attribute ids, from WarpX
[in]	int_comp_names	The int attribute names, from WarpX
[in]	np	Number of particles
[in]	isBTD	whether this is a back-transformed diagnostic

◆ WriteOpenPMDFieldsAll()

void WarpXOpenPMDPlot::WriteOpenPMDFieldsAll	(	const std::vector< std::string > &	varnames,
		const amrex::Vector< amrex::MultiFab > &	mf,
		amrex::Vector< amrex::Geometry > &	geom,
		int	output_levels,
		int	iteration,
		double	time,
		bool	isBTD = false,
		const amrex::Geometry &	full_BTD_snapshot = amrex::Geometry() ) const

Write out all openPMD fields for all active MR levels

Parameters

varnames	variable names in each multifab
mf	multifab for each level
geom	for each level
output_levels	the finest level to output, <= maxLevel
iteration	the current iteration or reconstructed labframe station number
time	the current simulation time in the lab frame
isBTD	true if this is part of a back-transformed diagnostics (BTD) station flush; in BTD, we write multiple times to the same iteration
full_BTD_snapshot	the geometry of the full lab frame for BTD

Write Field with all mesh levels

◆ WriteOpenPMDParticles()

void WarpXOpenPMDPlot::WriteOpenPMDParticles	(	const amrex::Vector< ParticleDiag > &	particle_diags,
		amrex::Real	time,
		bool	use_pinned_pc = false,
		bool	isBTD = false,
		bool	isLastBTDFlush = false )

Member Data Documentation

◆ m_authors

std::string WarpXOpenPMDPlot::m_authors

private

See also: WarpX::getPMLdirections()

◆ m_CurrentStep

int WarpXOpenPMDPlot::m_CurrentStep = -1

private

JSON option string for openPMD::Series constructor.

◆ m_dirPrefix

std::string WarpXOpenPMDPlot::m_dirPrefix

private

This is the output directory

This usually does not yet end in a /. It does not yet include the file prefix of the openPMD series, which will be appended by the GetFileName function.

◆ m_Encoding

openPMD::IterationEncoding WarpXOpenPMDPlot::m_Encoding = openPMD::IterationEncoding::fileBased

private

◆ m_fieldPMLdirections

std::vector< bool > WarpXOpenPMDPlot::m_fieldPMLdirections

private

◆ m_file_min_digits

int WarpXOpenPMDPlot::m_file_min_digits

private

This is the minimum number of digits in the step number that is used as the suffix for file names when doing file based encoding

◆ m_MPIRank

int WarpXOpenPMDPlot::m_MPIRank = 0

private

◆ m_MPISize

int WarpXOpenPMDPlot::m_MPISize = 1

private

◆ m_OpenPMDFileType

std::string WarpXOpenPMDPlot::m_OpenPMDFileType = "bp5"

private

◆ m_OpenPMDoptions

std::string WarpXOpenPMDPlot::m_OpenPMDoptions = "{}"

private

MPI-parallel openPMD backend: bp5, bp4 or h5.

◆ m_Series

std::unique_ptr<openPMD::Series> WarpXOpenPMDPlot::m_Series

private

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

/home/docs/checkouts/readthedocs.org/user_builds/warpx/checkouts/6270/Source/Diagnostics/WarpXOpenPMD.H
/home/docs/checkouts/readthedocs.org/user_builds/warpx/checkouts/6270/Source/Diagnostics/WarpXOpenPMD.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ ParticleContainer

◆ ParticleIter

Constructor & Destructor Documentation

◆ WarpXOpenPMDPlot() [1/3]

◆ ~WarpXOpenPMDPlot()

◆ WarpXOpenPMDPlot() [2/3]

◆ WarpXOpenPMDPlot() [3/3]

Member Function Documentation

◆ CloseStep()

◆ DumpToFile()

◆ FlushBTDToDisk()

◆ GetFileName()

◆ GetIteration()

◆ GetMeshCompNames()

◆ Init()

◆ OpenPMDFileType()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ SaveRealProperty()

◆ seriesFlush()

◆ SetConstParticleRecordsEDPIC()

◆ SetStep()

◆ SetupFields()

◆ SetupMeshComp()

◆ SetupPos()

◆ SetupRealProperties()

◆ WriteOpenPMDFieldsAll()

◆ WriteOpenPMDParticles()

Member Data Documentation

◆ m_authors

◆ m_CurrentStep

◆ m_dirPrefix

◆ m_Encoding

◆ m_fieldPMLdirections

◆ m_file_min_digits

◆ m_MPIRank

◆ m_MPISize

◆ m_OpenPMDFileType

◆ m_OpenPMDoptions

◆ m_Series