Diagnostic for writing diffusion profile data using ADIOS2. More...

#include <diag_diffusion_profiles.hpp>

Inheritance diagram for DiffusionProfilesDiag:

Collaboration diagram for DiffusionProfilesDiag:

Public Member Functions
	DiffusionProfilesDiag ()

void	init (NLReader::NamelistReader &nlr, const Simulation< DeviceType > &sml, const Grid< DeviceType > &grid, const Plasma &plasma, int f_source_period)
	Initialize the DiffusionProfilesDiag diagnostic. More...

int	get_n_species () const
	Return whether the diffusion diagnostic is on. More...

int	get_n_surf () const
	Get the number of flux-surfaces sampled. More...

int	get_n_samples () const
	Get the number of samples taken. More...

bool	is_triggered_output (int step)
	Returns whether the buffer should be written out on this step. More...

void	collect_sample (const Simulation< DeviceType > &sml, const Grid< DeviceType > &grid, Plasma &plasma, const Moments &f0_moments, const DomainDecomposition< DeviceType > &pol_decomp)
	Collect a sample of diffusion profile data. More...

void	write ()
	Write the buffered diffusion profile data to disk. More...

void	reset_buffer ()
	Reset the profile data buffer. More...

Public Member Functions inherited from Diagnostic
bool	is_triggered (int step)

bool	has_been_triggered (int step)

int	get_period () const

	Diagnostic ()

void	init (const std::string &name, int period, int first_step=-1)

void	open_stream (const std::string &filename, const XGC_IO_Mode &mode)

void	close_stream ()

void	write (const XGC_IO &xgc_io)

void	start_write_step ()

bool	is_first_step ()

void	end_write_step ()

Public Attributes
bool	is_on
	Flag to indicate if this diagnostic is active. More...

View< double ***, CLayout, HostType >	profiles_buffer_n

View< double ***, CLayout, HostType >	profiles_buffer_u

View< double ***, CLayout, HostType >	profiles_buffer_T

View< double *, CLayout, HostType >	psi_grid
	Poloidal flux grid of the sampled profile data. More...

View< double *, CLayout, HostType >	time_buffer
	Time (in s) of each sample. More...

View< int *, CLayout, HostType >	step_buffer
	Time step index of each sample. More...

Public Attributes inherited from Diagnostic
bool	is_on

Private Attributes
int	output_rate
	Rate (time steps) at which the collected data is written out. More...

int	sampling_rate
	Rate (multiples of sml_f_source_period) at which the profile data is sampled. More...

StepTrigger	step_trigger_output
	Trigger for writing the diagnostic output. (The default trigger is used for the data sampling step.) More...

int	n_species

int	n_surf

int	n_samples

int	sample_count

Additional Inherited Members
Protected Attributes inherited from Diagnostic
StepTrigger	step_trigger

Detailed Description

Diagnostic for writing diffusion profile data using ADIOS2.

This diagnostic is controlled by a boolean switch (is_on) and an output interval. It collects and buffers the evolution of the flux-surface averaged plasma profiles—specifically density, parallel mean flow, and temperature profiles—along with the corresponding poloidal flux grid, time stamps, and simulation step indices. The diagnostic is defined in diagnostics.hpp and utilizes the diagnostic template interface.

Constructor & Destructor Documentation

DiffusionProfilesDiag::DiffusionProfilesDiag ( )

inline

Member Function Documentation

void DiffusionProfilesDiag::collect_sample	(	const Simulation< DeviceType > &	sml,
		const Grid< DeviceType > &	grid,
		Plasma &	plasma,
		const Moments &	f0_moments,
		const DomainDecomposition< DeviceType > &	pol_decomp
	)

Collect a sample of diffusion profile data.

This function gathers global moment data (density, parallel flow, and temperature) from the simulation. It first copies the host-resident moment data to temporary device views, then performs a toroidal average. The data is further averaged over flux-surfaces by mapping the simulation data from the 2D planar mesh representation to the required number of surfaces. Finally, the averaged data is copied into the host buffers.

Parameters

sml	Reference to the Simulation object.
grid	Reference to the Grid object.
plasma	Reference to the Plasma object.
f0_moments	Reference to the Moments object containing the f0 moment data.
pol_decomp	Reference to the DomainDecomposition object for the poloidal plane.

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int DiffusionProfilesDiag::get_n_samples ( ) const

inline

Get the number of samples taken.

Returns: Number of samples.

int DiffusionProfilesDiag::get_n_species ( ) const

inline

Return whether the diffusion diagnostic is on.

Returns: Whether the diffusion diagnostic is on Get the number of species being buffered.; Number of species.

int DiffusionProfilesDiag::get_n_surf ( ) const

inline

Get the number of flux-surfaces sampled.

Returns: Number of flux-surfaces.

void DiffusionProfilesDiag::init	(	NLReader::NamelistReader &	nlr,
		const Simulation< DeviceType > &	sml,
		const Grid< DeviceType > &	grid,
		const Plasma &	plasma,
		int	f_source_period
	)

Initialize the DiffusionProfilesDiag diagnostic.

This function reads the necessary configuration options from the input namelists. The on/off switch and output rate are taken from the "diff_param" namelist, while the sampling rate is read from the "diag_param" namelist. It also performs a consistency check to ensure that the output rate is divisible by both the sampling rate and the base source period. In addition, the function allocates the buffers for the profile data and initializes the output trigger.

Parameters

nlr	Reference to the NamelistReader holding configuration options.
sml	Reference to the Simulation object.
grid	Reference to the Grid object.
plasma	Reference to the Plasma object.
f_source_period	The base period for sampling.

< Rate (multiples of sml_f_source_period) at which the profile data is sampled. (Must be compatible with diff_update_period!)

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bool DiffusionProfilesDiag::is_triggered_output ( int step )

inline

Returns whether the buffer should be written out on this step.

Returns: TRUE if buffer should be written, FALSE otherwise

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void DiffusionProfilesDiag::reset_buffer ( )

inline

Reset the profile data buffer.

Resets the internal buffer for the profile data and the sample counter to zero.

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void DiffusionProfilesDiag::write ( )

Write the buffered diffusion profile data to disk.

This function is executed on the rank-zero process. It creates an XGC_IO object, adds the various buffered arrays (including the number of species, number of samples, flux-surface grid, time and step data, and the profile arrays for density, flow, and temperature) to the IO object, and then invokes the base diagnostic write routines. The output is wrapped between a start and end write step.

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Member Data Documentation

bool DiffusionProfilesDiag::is_on

Flag to indicate if this diagnostic is active.

int DiffusionProfilesDiag::n_samples

private

int DiffusionProfilesDiag::n_species

private

int DiffusionProfilesDiag::n_surf

private

int DiffusionProfilesDiag::output_rate

private

Rate (time steps) at which the collected data is written out.

View<double***,CLayout,HostType> DiffusionProfilesDiag::profiles_buffer_n

View<double***,CLayout,HostType> DiffusionProfilesDiag::profiles_buffer_T

View<double***,CLayout,HostType> DiffusionProfilesDiag::profiles_buffer_u

View<double*,CLayout,HostType> DiffusionProfilesDiag::psi_grid

Poloidal flux grid of the sampled profile data.

int DiffusionProfilesDiag::sample_count

private

int DiffusionProfilesDiag::sampling_rate

private

Rate (multiples of sml_f_source_period) at which the profile data is sampled.

View<int*,CLayout,HostType> DiffusionProfilesDiag::step_buffer

Time step index of each sample.

StepTrigger DiffusionProfilesDiag::step_trigger_output

private

Trigger for writing the diagnostic output. (The default trigger is used for the data sampling step.)

View<double*,CLayout,HostType> DiffusionProfilesDiag::time_buffer

Time (in s) of each sample.

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

/u/gitlab-xgc/builds/YGMz2TJ8/0/xgc/XGC-Devel/XGC_core/cpp/diag_diffusion_profiles.hpp
/u/gitlab-xgc/builds/YGMz2TJ8/0/xgc/XGC-Devel/XGC_core/cpp/diag_diffusion_profiles.cpp

Public Member Functions

Public Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation