Implements an anomalous transport (advection-diffusion) model for the kinetic electrons in the plasma simulation. More...

#include <diffusion.hpp>

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Public Member Functions
bool	is_triggered_update (int step) const
	Determines whether the update of the diffusion coefficients should be executed on the given step. More...

int	trigger_count_update (int step) const
	Calculates how many times the update of the diffusion coefficient has been executed up to the given step. More...

	Diffusion ()
	Default constructor. Creates an uninitialized Diffusion object. More...

	Diffusion (NLReader::NamelistReader &nlr, const MagneticField< DeviceType > &magnetic_field, const Grid< DeviceType > &grid)

void	init (NLReader::NamelistReader &nlr, const MagneticField< DeviceType > &magnetic_field, const Grid< DeviceType > &grid)
	Constructs a Diffusion object by reading diffusion-related parameters from the namelist. More...

void	apply (const Simulation< DeviceType > &sml, const Grid< DeviceType > &grid, const MagneticField< DeviceType > &magnetic_field, ElectricField< DeviceType > &electric_field, const DomainDecomposition< DeviceType > &pol_decomp, const VelocityGrid &vgrid, Plasma &plasma, Smoothing &smoothing, DiagF0DF &diag_f0_df, const Moments &moments, const VGridDistribution< DeviceType > &f0_f, VGridDistribution< HostType > &f0_df0g, double dt)

void	update (const Plasma &plasma, const DomainDecomposition< DeviceType > &pol_decomp, const Grid< DeviceType > &grid)
	Updates the diffusion coefficients from an input BP file and passes the data to a Fortran routine. More...

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

Private Attributes
double	inner_psi_bound
	Inner boundary for diffusion in terms of normalized poloidal flux. More...

double	outer_psi_bound
	Outer boundary for diffusion in terms of normalized poloidal flux. More...

Boundary	bndry
	Boundary object for handling domain exclusion regions; now a member variable for later reuse. More...

bool	use_smoothing
	Whether to smooth the fluid moments before solving the transport equations. More...

bool	update_on
	Switch for periodic updates of the diffusion coefficients. More...

StepTrigger	step_trigger_update
	Triggers when it is time to update the diffusion coefficients. More...

XGC_IO_Stream	diffusion_update_stream
	Adios stream used for reading the updated diffusion coefficients. More...

Additional Inherited Members
Public Attributes inherited from Source
StepTrigger	step_trigger

Detailed Description

Implements an anomalous transport (advection-diffusion) model for the kinetic electrons in the plasma simulation.

This class extends the generic Source interface, providing functionality to apply an anomalous diffusion source term during the kinetic equation update. It sets diffusion boundaries based on poloidal flux surfaces and initializes a boundary mask for the domain.

Typical usage:

Construct a Diffusion object from a namelist and the necessary grid/magnetic-field data.
Call apply() at each time step (or when triggered) to modify the distribution function.

Example:

NLReader::NamelistReader nlr(...);
MagneticField<DeviceType> magField(...);
Grid<DeviceType> grid(...);
Diffusion diff(nlr, magField, grid);
...
diff.apply(...);

Constructor & Destructor Documentation

Diffusion::Diffusion ( )

inline

Default constructor. Creates an uninitialized Diffusion object.

This default constructor does not set any boundary conditions or read from the namelist. It is primarily intended for creating an object that will be assigned or initialized later.

Diffusion::Diffusion	(	NLReader::NamelistReader &	nlr,
		const MagneticField< DeviceType > &	magnetic_field,
		const Grid< DeviceType > &	grid
	)

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Member Function Documentation

void Diffusion::apply	(	const Simulation< DeviceType > &	sml,
		const Grid< DeviceType > &	grid,
		const MagneticField< DeviceType > &	magnetic_field,
		ElectricField< DeviceType > &	electric_field,
		const DomainDecomposition< DeviceType > &	pol_decomp,
		const VelocityGrid &	vgrid,
		Plasma &	plasma,
		Smoothing &	smoothing,
		DiagF0DF &	diag_f0_df,
		const Moments &	moments_h,
		const VGridDistribution< DeviceType > &	f0_f,
		VGridDistribution< HostType > &	f0_df0g_h,
		double	dt
	)

Calls the diffusion timestepper. The solve uses PETSc and the setup for that is still in Fortran.

Parameters

[in]	sml	Simulation parameters
[in]	grid	The grid object
[in]	magnetic_field	The magnetic field object
[in]	electric_field	Used for dpot to remove adiabatic response
[in]	pol_decomp	The domain decomposition
[in]	velocity_grid	Velocity grid
[in,out]	plasma	Plasma object. f0_delta_n/u/T are updated
[in]	moments_h	Moments
[in]	f0_f	The part of the distribution function represented on the velocity grid
[in,out]	f0_df0g_h	The change to the distribution function
[in]	dt	The time step return View marking whether each mesh node is in bounds

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void Diffusion::init	(	NLReader::NamelistReader &	nlr,
		const MagneticField< DeviceType > &	magnetic_field,
		const Grid< DeviceType > &	grid
	)

Constructs a Diffusion object by reading diffusion-related parameters from the namelist.

This constructor reads in electron settings (to verify that electrons are kinetic), boundary flux values for the diffusion model, and other solver-related parameters (e.g., start time) from the specified namelist reader. It then creates a Boundary object to handle domain exclusion regions and calls an external Fortran routine initialize_diffusion() to set up the diffusion mask.

Parameters

[in,out]	nlr	Namelist reader from which diffusion parameters and other simulation controls are retrieved.
[in]	magnetic_field	Provides poloidal-flux normalization factors (`psi_norm`) and in/out flux boundaries required for setting up the diffusion domain.
[in]	grid	The spatial grid defining the geometry of the problem; includes node information needed to map boundary settings to the correct domain regions.

Note

If sml_electron_on is false, the constructor will terminate the code via exit_XGC(), since anomalous diffusion requires kinetic electrons.
The constructor uses multiple namelists: first sml_param to verify that electrons are on, then diff_param to read specific diffusion boundaries and timing parameters.
The boundary settings constructed here are subsequently used within initialize_diffusion() to exclude regions (e.g., near-wall, private flux).

< Outer boundary (for Poisson solver), normalized poloidal flux

< Outer boundary (for Poisson solver, 2nd private region), normalized poloidal flux

< To move the outer boundary of the Poisson solver away from the inner wall (in m)

< Start time (in time steps) for anomalous diffusion

< Switch for periodic updates of the diffusion coefficients

< Period in time steps between subsequent updates of the diffusion coefficients

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bool Diffusion::is_triggered_update ( int step ) const

inline

Determines whether the update of the diffusion coefficients should be executed on the given step.

This function checks the trigger associated with updating the diffusion coefficients.

Parameters

step	The current step number.

Returns: True if the trigger condition is met for the given step, false otherwise.

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int Diffusion::trigger_count_update ( int step ) const

inline

Calculates how many times the update of the diffusion coefficient has been executed up to the given step.

This function calculates how many times the function updating the diffusion coefficients has been called up to the given time step, taking into account the start time and whether the update functionality is active.

Parameters

step	The current time step index.

Returns: The number of times the diffusivity update has been triggered.

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void Diffusion::update	(	const Plasma &	plasma,
		const DomainDecomposition< DeviceType > &	pol_decomp,
		const Grid< DeviceType > &	grid
	)

Updates the diffusion coefficients from an input BP file and passes the data to a Fortran routine.

This function uses the C++ routine ReadSpeciesData to read updated diffusion coefficient data from the specified BP file. The data consists of a common 1D array (x) and a 3D array (y) with dimensions [4, n_species, N] corresponding to four different diffusion coefficient types for each species. The routine then calls the Fortran routine update_diffusion_eq_ftn, passing pointers to the x and y data, as well as the number of species.

Parameters

input_filename	The name of the input BP file containing updated diffusion coefficients.
n_species	The number of particle species.

Exceptions

std::runtime_error if reading the diffusion coefficient data fails.

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Member Data Documentation

Boundary Diffusion::bndry

private

Boundary object for handling domain exclusion regions; now a member variable for later reuse.

XGC_IO_Stream Diffusion::diffusion_update_stream

private

Adios stream used for reading the updated diffusion coefficients.

double Diffusion::inner_psi_bound

private

Inner boundary for diffusion in terms of normalized poloidal flux.

double Diffusion::outer_psi_bound

private

Outer boundary for diffusion in terms of normalized poloidal flux.

StepTrigger Diffusion::step_trigger_update

private

Triggers when it is time to update the diffusion coefficients.

bool Diffusion::update_on

private

Switch for periodic updates of the diffusion coefficients.

bool Diffusion::use_smoothing

private

Whether to smooth the fluid moments before solving the transport equations.

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

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation