#include <FullDiagnostics.H>

Inheritance diagram for FullDiagnostics:

Public Types
enum struct	TimeAverageType { None , Static , Dynamic }

Public Member Functions
	FullDiagnostics (int i, const std::string &name, DiagTypes diag_type)

Public Member Functions inherited from Diagnostics
	Diagnostics (int i, std::string name, DiagTypes diag_type)

virtual	~Diagnostics ()

	Diagnostics (Diagnostics const &)=delete

Diagnostics &	operator= (Diagnostics const &)=delete

	Diagnostics (Diagnostics &&)=default

Diagnostics &	operator= (Diagnostics &&)=default

void	ComputeAndPack ()

void	InitData (const MultiParticleContainer &mpc)

void	InitDataBeforeRestart ()

void	InitDataAfterRestart (const MultiParticleContainer &mpc)

virtual void	InitializeParticleFunctors ()

void	NewIteration ()

void	FilterComputePackFlush (int step, bool force_flush=false)

bool	DoDumpLastTimestep () const

int	getnumbuffers () const

virtual amrex::Real	gettlab (int i_buffer)

virtual void	settlab (int i_buffer, amrex::Real tlab)

virtual int	get_buffer_k_index_hi (int i_buffer)

virtual void	set_buffer_k_index_hi (int i_buffer, int kindex)

virtual amrex::Real	get_snapshot_domain_lo (int i_buffer, int idim)

virtual amrex::Real	get_snapshot_domain_hi (int i_buffer, int idim)

void	setSnapshotDomainLo (int i_buffer, int idim, amrex::Real domain_lab_lo)

void	setSnapshotDomainHi (int i_buffer, int idim, amrex::Real domain_lab_hi)

virtual int	get_flush_counter (int i_buffer)

virtual void	set_flush_counter (int i_buffer, int flush_counter)

virtual int	get_last_valid_Zslice (int i_buffer)

virtual void	set_last_valid_Zslice (int i_buffer, int last_valid_Zslice)

virtual int	get_snapshot_full_flag (int i_buffer)

virtual void	set_snapshot_full (int i_buffer, int snapshot_full)

Private Member Functions
void	ReadParameters ()

void	Flush (int i_buffer, bool) override

void	FlushRaw ()

void	DerivedInitData () override

bool	DoComputeAndPack (int step, bool force_flush=false) override

bool	DoDump (int step, int i_buffer, bool force_flush=false) override

void	AddRZModesToOutputNames (const std::string &field, int ncomp)

void	InitializeBufferData (int i_buffer, int lev, bool restart=false) override

void	InitializeFieldFunctorsRZopenPMD (int lev) override

void	AddRZModesToDiags (int lev)

void	InitializeFieldFunctors (int lev) override

void	InitializeParticleBuffer (const MultiParticleContainer &mpc) override

void	PrepareFieldDataForOutput () override

void	PrepareParticleDataForOutput () override

void	MovingWindowAndGalileanDomainShift (int step) override

void	BackwardCompatibility ()

Private Attributes
utils::parser::IntervalsParser	m_intervals

bool	m_plot_raw_fields = false

bool	m_plot_raw_fields_guards = false

bool	m_dump_rz_modes = false

bool	m_solver_deposits_current = true

TimeAverageType	m_time_average_mode = TimeAverageType::None

int	m_average_period_steps = -1

amrex::Real	m_average_period_time = -1.0

int	m_average_start_step = -1

Additional Inherited Members
Public Attributes inherited from Diagnostics
DiagTypes	m_diag_type

Protected Member Functions inherited from Diagnostics
bool	BaseReadParameters ()

void	InitBaseData ()

virtual void	PrepareBufferData ()

virtual void	UpdateBufferData ()

Protected Attributes inherited from Diagnostics
int	m_verbose = 2

std::string	m_diag_name

std::string	m_file_prefix

int	m_file_min_digits = 6

int	m_diag_index

amrex::Vector< std::string >	m_varnames

amrex::Vector< std::string >	m_varnames_fields

amrex::Vector< std::string >	m_pfield_varnames

std::vector< std::string >	m_pfield_species

std::vector< bool >	m_pfield_do_average

std::vector< int >	m_pfield_species_index

std::vector< std::string >	m_pfield_strings

std::vector< bool >	m_pfield_dofilter

std::vector< std::string >	m_pfield_filter_strings

bool	m_dump_last_timestep = true

std::string	m_format = "plotfile"

int	m_already_done = false

std::unique_ptr< FlushFormat >	m_flush_format

amrex::Vector< amrex::Vector< amrex::MultiFab > >	m_mf_output

amrex::Vector< amrex::Vector< amrex::MultiFab > >	m_sum_mf_output

amrex::Vector< amrex::Vector< amrex::Geometry > >	m_geom_output

int	nlev

int	nmax_lev

int	nlev_output

std::vector< std::string >	m_output_species_names

std::vector< std::string >	m_all_species_names

amrex::Vector< amrex::Vector< ParticleDiag > >	m_output_species

amrex::Vector< amrex::Vector< std::unique_ptr< ComputeDiagFunctor > > >	m_all_field_functors

amrex::IntVect	m_crse_ratio = amrex::IntVect(1)

amrex::Vector< amrex::Real >	m_lo

amrex::Vector< amrex::Real >	m_hi

int	m_num_buffers

amrex::Vector< int >	m_rho_per_species_index

amrex::Vector< int >	m_T_per_species_index

amrex::Vector< amrex::Vector< std::unique_ptr< PinnedMemoryParticleContainer > > >	m_particles_buffer

amrex::Vector< std::unique_ptr< ComputeParticleDiagFunctor > >	m_all_particle_functors

amrex::Vector< amrex::Vector< int > >	m_totalParticles_in_buffer

amrex::Vector< amrex::RealBox >	m_snapshot_domain_lab

Member Enumeration Documentation

◆ TimeAverageType

enum struct FullDiagnostics::TimeAverageType

strong

Type of time averaging for diagnostics (fields only) None corresponds to instantaneous diags Static corresponds to a fixed starting step for averaging, will average until the end, and dump out intermediate average results Dynamic corresponds to a moving period for averaging where the start step is as many steps before the output interval as the averaging period is long.

Enumerator
None
Static
Dynamic

Constructor & Destructor Documentation

◆ FullDiagnostics()

FullDiagnostics::FullDiagnostics	(	int	i,
		const std::string &	name,
		DiagTypes	diag_type )

Member Function Documentation

◆ AddRZModesToDiags()

void FullDiagnostics::AddRZModesToDiags ( int lev )

private

Append m_all_field_functors[lev] with all modes of all components of E B and j and add name to varnames.

Parameters

[in] lev level on which source multifabs are defined.

◆ AddRZModesToOutputNames()

void FullDiagnostics::AddRZModesToOutputNames	(	const std::string &	field,
		int	ncomp )

private

Append varnames with names for all modes of a field

Parameters

[in]	field	field name (includes component, e.g., Er)
[in]	ncomp	number of components (modes, real and imag)

◆ BackwardCompatibility()

void FullDiagnostics::BackwardCompatibility ( )

private

This function queries deprecated input parameters and abort the run if one of them is specified.

◆ DerivedInitData()

void FullDiagnostics::DerivedInitData ( )

overrideprivatevirtual

Initialize Data required to compute TimeAveraged diagnostics

Reimplemented from Diagnostics.

◆ DoComputeAndPack()

bool FullDiagnostics::DoComputeAndPack	(	int	step,
		bool	force_flush = false )

overrideprivatevirtual

whether to compute and pack cell-centered data in m_mf_output

Parameters

[in]	step	current time step
[in]	force_flush	if true, return true for any step since output must be computed in this case

Returns: bool, whether to flush

Implements Diagnostics.

◆ DoDump()

bool FullDiagnostics::DoDump	(	int	step,
		int	i_buffer,
		bool	force_flush = false )

overrideprivatevirtual

whether to flush at this time step

Parameters

[in]	step	current time step
[in]	i_buffer	index of a back-transformed snapshot
[in]	force_flush	if true, return true for any step

Returns: bool, whether to flush

Implements Diagnostics.

◆ Flush()

void FullDiagnostics::Flush	(	int	i_buffer,
		bool	)

overrideprivatevirtual

Flush m_mf_output or m_sum_mf_output and particles to file for the i^th buffer

Implements Diagnostics.

◆ FlushRaw()

void FullDiagnostics::FlushRaw ( )

private

Flush raw data

◆ InitializeBufferData()

void FullDiagnostics::InitializeBufferData	(	int	i_buffer,
		int	lev,
		bool	restart = false )

overrideprivatevirtual

Define the cell-centered multifab m_mf_output depending on user-defined lo and hi and coarsening ratio. This MultiFab may have a different BoxArray and DistributionMap than field MultiFabs in the simulation.

Parameters

[in]	i_buffer	index of a back-transformed snapshot
[in]	lev	level on which source multifabs are defined
[in]	restart	whether this is called upon restarting a previous simulation

Implements Diagnostics.

◆ InitializeFieldFunctors()

void FullDiagnostics::InitializeFieldFunctors ( int lev )

overrideprivatevirtual

Initialize functors that store pointers to the fields requested by the user.

Parameters

[in] lev level on which the vector of unique_ptrs to field functors is initialized.

Implements Diagnostics.

◆ InitializeFieldFunctorsRZopenPMD()

void FullDiagnostics::InitializeFieldFunctorsRZopenPMD ( int lev )

overrideprivatevirtual

Initialize functors that store pointers to the RZ fields requested by the user.

Parameters

[in] lev level on which the vector of unique_ptrs to field functors is initialized.

Reimplemented from Diagnostics.

◆ InitializeParticleBuffer()

void FullDiagnostics::InitializeParticleBuffer ( const MultiParticleContainer & mpc )

overrideprivatevirtual

This function initialized particle buffers (not implemented in diagnostics, yet)

Parameters

[in] mpc a constant reference to the multi-particle container.

Implements Diagnostics.

◆ MovingWindowAndGalileanDomainShift()

void FullDiagnostics::MovingWindowAndGalileanDomainShift ( int step )

overrideprivatevirtual

Update the physical extent of the diagnostic domain for moving window and galilean shift simulations

Parameters

[in] step current time step

Reimplemented from Diagnostics.

◆ PrepareFieldDataForOutput()

void FullDiagnostics::PrepareFieldDataForOutput ( )

overrideprivatevirtual

Prepare field data to be used for diagnostics

Reimplemented from Diagnostics.

◆ PrepareParticleDataForOutput()

void FullDiagnostics::PrepareParticleDataForOutput ( )

inlineoverrideprivatevirtual

Prepare particle data to be used for diagnostics.

Reimplemented from Diagnostics.

◆ ReadParameters()

void FullDiagnostics::ReadParameters ( )

private

Read user-requested parameters for full diagnostics

Whether the diagnostics are averaging data over time or not Valid options are "fixed_start" and "dynamic_start".

Member Data Documentation

◆ m_average_period_steps

int FullDiagnostics::m_average_period_steps = -1

private

Period to average fields over: in steps

◆ m_average_period_time

amrex::Real FullDiagnostics::m_average_period_time = -1.0

private

Period to average fields over: in seconds

◆ m_average_start_step

int FullDiagnostics::m_average_start_step = -1

private

Time step to start averaging

◆ m_dump_rz_modes

bool FullDiagnostics::m_dump_rz_modes = false

private

Whether to dump the RZ modes

◆ m_intervals

utils::parser::IntervalsParser FullDiagnostics::m_intervals

private

Determines timesteps at which full diagnostics are written to file

◆ m_plot_raw_fields

bool FullDiagnostics::m_plot_raw_fields = false

private

Whether to plot raw (i.e., NOT cell-centered) fields

◆ m_plot_raw_fields_guards

bool FullDiagnostics::m_plot_raw_fields_guards = false

private

Whether to plot guard cells of raw fields

◆ m_solver_deposits_current

bool FullDiagnostics::m_solver_deposits_current = true

private

Whether the field solver deposits current density, if not it will be done before writing the diagnostic.

◆ m_time_average_mode

TimeAverageType FullDiagnostics::m_time_average_mode = TimeAverageType::None

private

Whether the diagnostics are averaging data over time or not

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

/home/docs/checkouts/readthedocs.org/user_builds/warpx/checkouts/6102/Source/Diagnostics/FullDiagnostics.H
/home/docs/checkouts/readthedocs.org/user_builds/warpx/checkouts/6102/Source/Diagnostics/FullDiagnostics.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Enumeration Documentation

◆ TimeAverageType

Constructor & Destructor Documentation

◆ FullDiagnostics()

Member Function Documentation

◆ AddRZModesToDiags()

◆ AddRZModesToOutputNames()

◆ BackwardCompatibility()

◆ DerivedInitData()

◆ DoComputeAndPack()

◆ DoDump()

◆ Flush()

◆ FlushRaw()

◆ InitializeBufferData()

◆ InitializeFieldFunctors()

◆ InitializeFieldFunctorsRZopenPMD()

◆ InitializeParticleBuffer()

◆ MovingWindowAndGalileanDomainShift()

◆ PrepareFieldDataForOutput()

◆ PrepareParticleDataForOutput()

◆ ReadParameters()

Member Data Documentation

◆ m_average_period_steps

◆ m_average_period_time

◆ m_average_start_step

◆ m_dump_rz_modes

◆ m_intervals

◆ m_plot_raw_fields

◆ m_plot_raw_fields_guards

◆ m_solver_deposits_current

◆ m_time_average_mode