#include <WarpXOpenPMD.H>

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

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

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

	~WarpXOpenPMDPlot ()

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, const bool use_pinned_pc=false, const bool isBTD=false, const bool isLastBTDFlush=false, const amrex::Vector< int > &totalParticlesFlushedAlready=amrex::Vector< int >())

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

std::string	OpenPMDFileType ()

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

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

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

void	SetupMeshComp (openPMD::Mesh &mesh, amrex::Geometry &full_geom, std::string comp_name, std::string 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 is_theta_mode) const

void	SetupPos (openPMD::ParticleSpecies &currSpecies, const unsigned long long &np, bool const isBTD=false)

void	SetConstParticleRecordsEDPIC (openPMD::ParticleSpecies &currSpecies, const unsigned long long &np, amrex::ParticleReal const charge, amrex::ParticleReal const 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, const unsigned long long np, bool const 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 const charge, amrex::ParticleReal const mass, const bool isBTD=false, const bool isLastBTDFlush=false, int ParticleFlushOffset=0)

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 = "bp"

std::string	m_OpenPMDoptions = "{}"
	MPI-parallel openPMD backend: bp or h5. More...

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

std::vector< bool >	m_fieldPMLdirections

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::ParConstIter<0, 0, PIdx::nattribs, 0, amrex::PinnedArenaAllocator>

Constructor & Destructor Documentation

◆ WarpXOpenPMDPlot()

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

Initialize openPMD I/O routines

Parameters

ie	iteration encoding from openPMD: "group, file, variable"
filetype	file backend, e.g. "bp" 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()

◆ ~WarpXOpenPMDPlot()

WarpXOpenPMDPlot::~WarpXOpenPMDPlot ( )

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 const	charge,
		amrex::ParticleReal const	mass,
		const bool	isBTD = `false`,
		const bool	isLastBTDFlush = `false`,
		int	ParticleFlushOffset = `0`
	)

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]	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]	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?
[in]	ParticleFlushOffset	previously flushed number of particles in 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

inlineprivate

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	is_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]	is_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 ("bp" or "h5" or "json")

◆ 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

◆ SetConstParticleRecordsEDPIC()

void WarpXOpenPMDPlot::SetConstParticleRecordsEDPIC	(	openPMD::ParticleSpecies &	currSpecies,
		const unsigned long long &	np,
		amrex::ParticleReal const	charge,
		amrex::ParticleReal const	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]	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 &	full_geom,
		std::string	comp_name,
		std::string	field_name,
		amrex::MultiFab const &	mf,
		bool	var_in_theta_mode
	)		const

private

◆ SetupPos()

void WarpXOpenPMDPlot::SetupPos	(	openPMD::ParticleSpecies &	currSpecies,
		const unsigned long long &	np,
		bool const	isBTD = `false`
	)

private

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

Parameters

[in]	currSpecies	Corresponding openPMD species
[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,
		const unsigned long long	np,
		bool const	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,
		const int	iteration,
		const 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,
		const bool	use_pinned_pc = `false`,
		const bool	isBTD = `false`,
		const bool	isLastBTDFlush = `false`,
		const amrex::Vector< int > &	totalParticlesFlushedAlready = `amrex::Vector<int>()`
	)

Member Data Documentation

◆ 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 = "bp"

private

◆ m_OpenPMDoptions

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

private

MPI-parallel openPMD backend: bp 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/artemis-em/checkouts/latest/Source/Diagnostics/WarpXOpenPMD.H
/home/docs/checkouts/readthedocs.org/user_builds/artemis-em/checkouts/latest/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()

◆ ~WarpXOpenPMDPlot()

Member Function Documentation

◆ CloseStep()

◆ DumpToFile()

◆ GetFileName()

◆ GetIteration()

◆ GetMeshCompNames()

◆ Init()

◆ OpenPMDFileType()

◆ SaveRealProperty()

◆ SetConstParticleRecordsEDPIC()

◆ SetStep()

◆ SetupFields()

◆ SetupMeshComp()

◆ SetupPos()

◆ SetupRealProperties()

◆ WriteOpenPMDFieldsAll()

◆ WriteOpenPMDParticles()

Member Data Documentation

◆ m_CurrentStep

◆ m_dirPrefix

◆ m_Encoding

◆ m_fieldPMLdirections

◆ m_file_min_digits

◆ m_MPIRank

◆ m_MPISize

◆ m_OpenPMDFileType

◆ m_OpenPMDoptions

◆ m_Series