diffusion.cpp File Reference

#include "timer_macro.hpp"
#include "update_ptl_weights.hpp"
#include "toroidal_average.hpp"
#include "poly_basis.hpp"
#include "moments.hpp"
#include "loadable_buffer.hpp"
#include "basic_physics.hpp"
#include "grid_node_tr_mapping.hpp"
#include "diffusion.hpp"
#include "read_diffusion_coeffs.hpp"
#include "checkpoint.hpp"

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Functions
void	smooth_pol_wrap (double *input_array, double *output_array)
void	diffusion_solve (int n, double *buffer, double dt)
void	df0g_nan_check (double *f0_df0g)
void	update_diffusion_eq_ftn (const int n_species, const int npsi, const double *psi, const double *diff_coeff)
void	transpose_moments (Plasma &plasma, const Moments &moments_h, View< double **, CLayout, DeviceType > &den, View< double **, CLayout, DeviceType > &u_para, View< double **, CLayout, DeviceType > &T_para, View< double **, CLayout, DeviceType > &T_perp)
void	smooth_and_filter (const Grid< DeviceType > &grid, const MagneticField< DeviceType > &magnetic_field, const DomainDecomposition< DeviceType > &pol_decomp, Smoothing &smoothing, const View< double *, CLayout, DeviceType > &view)
void	smooth_moments (const Grid< DeviceType > &grid, const MagneticField< DeviceType > &magnetic_field, const DomainDecomposition< DeviceType > &pol_decomp, Smoothing &smoothing, const View< double *, CLayout, DeviceType > &den, View< double **, CLayout, DeviceType > &u_para, View< double **, CLayout, DeviceType > &T_para, View< double **, CLayout, DeviceType > &T_perp, bool is_XGCa)
void	pack_solve_unpack (const View< double *, CLayout, DeviceType > &den, View< double **, CLayout, DeviceType > &u_para, View< double **, CLayout, DeviceType > &T_para, View< double **, CLayout, DeviceType > &T_perp, double dt)
void	calculate_df_one_sp (const DomainDecomposition< DeviceType > &pol_decomp, const Species< DeviceType > &species, const PolynomialBasis< DeviceType > &polynomial_basis, const VGridDistribution< DeviceType > &f0_f, const View< double **, CLayout, DeviceType > &den, const View< double **, CLayout, DeviceType > &den_old, const View< double **, CLayout, DeviceType > &u_para, const View< double **, CLayout, DeviceType > &T_para, const View< double **, CLayout, DeviceType > &T_perp, const View< bool *, CLayout, DeviceType > &is_in_bounds, VGridDistribution< DeviceType > &delta_f)
VGridDistribution< DeviceType >	calculate_df (Plasma &plasma, const DomainDecomposition< DeviceType > &pol_decomp, const VelocityGrid &vgrid, const VGridDistribution< DeviceType > &f0_f, const View< double **, CLayout, DeviceType > &den, const View< double **, CLayout, DeviceType > &den_old, const View< double **, CLayout, DeviceType > &u_para, const View< double **, CLayout, DeviceType > &T_para, const View< double **, CLayout, DeviceType > &T_perp, const View< bool *, CLayout, DeviceType > &is_in_bounds)
void	calculate_flux_surface_averaged_diffs (const Grid< DeviceType > &grid, const View< double **, CLayout, DeviceType > &den_old, const View< double **, CLayout, DeviceType > &den, const View< double **, CLayout, DeviceType > &u_para_old, const View< double **, CLayout, DeviceType > &u_para, const View< double **, CLayout, DeviceType > &T_old, const View< double **, CLayout, DeviceType > &T, View< double **, CLayout, DeviceType > &delta_den00, View< double **, CLayout, DeviceType > &delta_u_para00, View< double **, CLayout, DeviceType > &delta_T00)
void	calculate_dfM (const DomainDecomposition< DeviceType > &pol_decomp, Plasma &plasma, const View< bool *, CLayout, DeviceType > &is_in_bounds, const View< double **, CLayout, DeviceType > &delta_den00, const View< double **, CLayout, DeviceType > &delta_u_para00, const View< double **, CLayout, DeviceType > &delta_T00, VGridDistribution< DeviceType > &dfM)
void	update_analytic (const DomainDecomposition< DeviceType > &pol_decomp, Plasma &plasma, const ElectricField< DeviceType > &electric_field, const View< bool *, CLayout, DeviceType > &is_in_bounds, const View< double **, CLayout, DeviceType > &delta_den00, const View< double **, CLayout, DeviceType > &delta_u_para00, const View< double **, CLayout, DeviceType > &delta_T00, bool is_XGCa, double dpot_te_limit)
void	add_delta_f_to_f0_df0g (VGridDistribution< DeviceType > &f0_df0g, VGridDistribution< DeviceType > &delta_f)
void	remove_dfM_from_f0_df0g (VGridDistribution< DeviceType > &f0_df0g, VGridDistribution< DeviceType > &dfM)
View< bool *, CLayout, DeviceType >	check_is_in_bounds (const Grid< DeviceType > &grid, const DomainDecomposition< DeviceType > &pol_decomp, double inner_psi_bound, double outer_psi_bound)
void	calculate_full_T (const View< double **, CLayout, DeviceType > &T_perp, const View< double **, CLayout, DeviceType > &T_para, const View< double **, CLayout, DeviceType > &T)
void	calculate_moment_increments (const View< double *, CLayout, DeviceType > &den, const View< double *, CLayout, DeviceType > &den_old, const View< double **, CLayout, DeviceType > &u_para, const View< double **, CLayout, DeviceType > &u_para_old, const View< double **, CLayout, DeviceType > &T_para, const View< double **, CLayout, DeviceType > &T_para_old, const View< double **, CLayout, DeviceType > &T_perp, const View< double **, CLayout, DeviceType > &T_perp_old)
void	calculate_nonsmoothed_moments (const View< double **, CLayout, DeviceType > &den_delta, const View< double **, CLayout, DeviceType > &den_old, const View< double **, CLayout, DeviceType > &u_para_delta, const View< double **, CLayout, DeviceType > &u_para_old, const View< double **, CLayout, DeviceType > &T_para_delta, const View< double **, CLayout, DeviceType > &T_para_old, const View< double **, CLayout, DeviceType > &T_perp_delta, const View< double **, CLayout, DeviceType > &T_perp_old)

Function Documentation

void add_delta_f_to_f0_df0g	(	VGridDistribution< DeviceType > &	f0_df0g,
		VGridDistribution< DeviceType > &	delta_f
	)

Adds delta_f to f0_df0g

Parameters

[in,out]	f0_df0g	Overall change to distribution function
[in]	delta_f	The change in distribution function inferred from evolution of the moments

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VGridDistribution<DeviceType> calculate_df	(	Plasma &	plasma,
		const DomainDecomposition< DeviceType > &	pol_decomp,
		const VelocityGrid &	vgrid,
		const VGridDistribution< DeviceType > &	f0_f,
		const View< double **, CLayout, DeviceType > &	den,
		const View< double **, CLayout, DeviceType > &	den_old,
		const View< double **, CLayout, DeviceType > &	u_para,
		const View< double **, CLayout, DeviceType > &	T_para,
		const View< double **, CLayout, DeviceType > &	T_perp,
		const View< bool *, CLayout, DeviceType > &	is_in_bounds
	)

Calculates delta_f of each species inferred from evolution of the moments

Parameters

[in]	plasma	Plasma object used to loop over species
[in]	pol_decomp	Domain decomposition object
[in]	vgrid	Velocity grid information
[in]	f0_f	Initial distribution function
[out]	den	Density moment
[out]	den_old	Density moment before diffusion
[out]	u_para	Parallel velocity moment
[out]	T_para	Parallel temperature moment
[out]	T_perp	Perpendicular temperature moment
[in]	is_in_bounds	Whether each mesh node is in bounds return The change in distribution function inferred from evolution of the moments

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void calculate_df_one_sp	(	const DomainDecomposition< DeviceType > &	pol_decomp,
		const Species< DeviceType > &	species,
		const PolynomialBasis< DeviceType > &	polynomial_basis,
		const VGridDistribution< DeviceType > &	f0_f,
		const View< double **, CLayout, DeviceType > &	den,
		const View< double **, CLayout, DeviceType > &	den_old,
		const View< double **, CLayout, DeviceType > &	u_para,
		const View< double **, CLayout, DeviceType > &	T_para,
		const View< double **, CLayout, DeviceType > &	T_perp,
		const View< bool *, CLayout, DeviceType > &	is_in_bounds,
		VGridDistribution< DeviceType > &	delta_f
	)

Calculates delta_f of one species inferred from evolution of the moments

Parameters

[in]	pol_decomp	Domain decomposition object
[in]	species	Species object
[in]	polynomial_basis	Basis functions to represent distribution with polynomials
[in]	f0_f	Initial distribution function
[out]	den	Density moment
[out]	den_old	Density moment before diffusion
[out]	u_para	Parallel velocity moment
[out]	T_para	Parallel temperature moment
[out]	T_perp	Perpendicular temperature moment
[in]	is_in_bounds	Whether each mesh node is in bounds
[in,out]	delta_f	The change in distribution function inferred from evolution of the moments

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void calculate_dfM	(	const DomainDecomposition< DeviceType > &	pol_decomp,
		Plasma &	plasma,
		const View< bool *, CLayout, DeviceType > &	is_in_bounds,
		const View< double **, CLayout, DeviceType > &	delta_den00,
		const View< double **, CLayout, DeviceType > &	delta_u_para00,
		const View< double **, CLayout, DeviceType > &	delta_T00,
		VGridDistribution< DeviceType > &	dfM
	)

Calculates the change to the distribution function that was transferred to f0_delta_n etc

Parameters

[in]	pol_decomp	Domain decomposition object
[in]	plasma	Plasma object used to loop over species and for analytic moments
[in]	is_in_bounds	Whether each mesh node is in bounds
[in]	delta_den00	Flux surface averaged change in density moment
[in]	delta_u_para00	Flux surface averaged change in parallel velocity moment
[in]	delta_T00	Flux surface averaged change in temperature moment
[out]	dfM	The change to the distribution function that was transferred to f0_delta_n etc

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void calculate_flux_surface_averaged_diffs	(	const Grid< DeviceType > &	grid,
		const View< double **, CLayout, DeviceType > &	den_old,
		const View< double **, CLayout, DeviceType > &	den,
		const View< double **, CLayout, DeviceType > &	u_para_old,
		const View< double **, CLayout, DeviceType > &	u_para,
		const View< double **, CLayout, DeviceType > &	T_old,
		const View< double **, CLayout, DeviceType > &	T,
		View< double **, CLayout, DeviceType > &	delta_den00,
		View< double **, CLayout, DeviceType > &	delta_u_para00,
		View< double **, CLayout, DeviceType > &	delta_T00
	)

Returns the flux surface average of the difference between the old moments and the updated moments. Most of the code is to copy the moments to CPU and the results back to GPU. This can be streamlined when the flux surface average function is moved to C++.

Parameters

[in]	den_old	Density moment before diffusion
[in]	den	Density moment
[in]	u_para_old	Parallel velocity moment before diffusion
[in]	u_para	Parallel velocity moment
[in]	T_old	Temperature moments before diffusion
[in]	T	Temperature moment
[out]	delta_den00	Flux surface averaged change in density moment
[out]	delta_u_para00	Flux surface averaged change in parallel velocity moment
[out]	delta_T00	Flux surface averaged change in temperature moment

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void calculate_full_T	(	const View< double **, CLayout, DeviceType > &	T_perp,
		const View< double **, CLayout, DeviceType > &	T_para,
		const View< double **, CLayout, DeviceType > &	T
	)

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void calculate_moment_increments	(	const View< double *, CLayout, DeviceType > &	den,
		const View< double *, CLayout, DeviceType > &	den_old,
		const View< double **, CLayout, DeviceType > &	u_para,
		const View< double **, CLayout, DeviceType > &	u_para_old,
		const View< double **, CLayout, DeviceType > &	T_para,
		const View< double **, CLayout, DeviceType > &	T_para_old,
		const View< double **, CLayout, DeviceType > &	T_perp,
		const View< double **, CLayout, DeviceType > &	T_perp_old
	)

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void calculate_nonsmoothed_moments	(	const View< double **, CLayout, DeviceType > &	den_delta,
		const View< double **, CLayout, DeviceType > &	den_old,
		const View< double **, CLayout, DeviceType > &	u_para_delta,
		const View< double **, CLayout, DeviceType > &	u_para_old,
		const View< double **, CLayout, DeviceType > &	T_para_delta,
		const View< double **, CLayout, DeviceType > &	T_para_old,
		const View< double **, CLayout, DeviceType > &	T_perp_delta,
		const View< double **, CLayout, DeviceType > &	T_perp_old
	)

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View<bool*, CLayout, DeviceType> check_is_in_bounds	(	const Grid< DeviceType > &	grid,
		const DomainDecomposition< DeviceType > &	pol_decomp,
		double	inner_psi_bound,
		double	outer_psi_bound
	)

Returns a view marking whether each mesh node is in bounds

Parameters

[in]	grid	The grid object
[in]	pol_decomp	The domain decomposition
[in]	inner_psi_bound	The minimum psi value to be in bounds
[in]	outer_psi_bound	The maximum psi value to be in bounds return View marking whether each mesh node is in bounds

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void df0g_nan_check

(

double *

f0_df0g

)

void diffusion_solve	(	int	n,
		double *	buffer,
		double	dt
	)

void pack_solve_unpack	(	const View< double *, CLayout, DeviceType > &	den,
		View< double **, CLayout, DeviceType > &	u_para,
		View< double **, CLayout, DeviceType > &	T_para,
		View< double **, CLayout, DeviceType > &	T_perp,
		double	dt
	)

Packs the moments into a buffer formatted for the diffusion solve, calls the solve and unpacks back into the original format. This also transfers the moments from device to host and back

Parameters

[in,out]	den	Density moment
[in,out]	u_para	Parallel velocity moment
[in,out]	T_para	Parallel temperature moment
[in,out]	T_perp	Perpendicular temperature moment
[in]	dt	Time step

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void remove_dfM_from_f0_df0g	(	VGridDistribution< DeviceType > &	f0_df0g,
		VGridDistribution< DeviceType > &	dfM
	)

Subtracts dfM to f0_df0g since this part of the distribution function has been transferred to the analytic f0 representation (f0_delta_n etc)

Parameters

[in,out]	f0_df0g	Overall change to distribution function
[in]	dfM	The change to the distribution function that was transferred to f0_delta_n etc

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void smooth_and_filter	(	const Grid< DeviceType > &	grid,
		const MagneticField< DeviceType > &	magnetic_field,
		const DomainDecomposition< DeviceType > &	pol_decomp,
		Smoothing &	smoothing,
		const View< double *, CLayout, DeviceType > &	view
	)

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void smooth_moments	(	const Grid< DeviceType > &	grid,
		const MagneticField< DeviceType > &	magnetic_field,
		const DomainDecomposition< DeviceType > &	pol_decomp,
		Smoothing &	smoothing,
		const View< double *, CLayout, DeviceType > &	den,
		View< double **, CLayout, DeviceType > &	u_para,
		View< double **, CLayout, DeviceType > &	T_para,
		View< double **, CLayout, DeviceType > &	T_perp,
		bool	is_XGCa
	)

Toroidally average, smooth and filter the input moments

Parameters

[in]	pol_decomp	Domain decomposition object for toroidal averaging
[in,out]	den	Density moment
[in,out]	u_para	Parallel velocity moment
[in,out]	T_para	Parallel temperature moment
[in,out]	T_perp	Perpendicular temperature moment

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void smooth_pol_wrap	(	double *	input_array,
		double *	output_array
	)

void transpose_moments	(	Plasma &	plasma,
		const Moments &	moments_h,
		View< double **, CLayout, DeviceType > &	den,
		View< double **, CLayout, DeviceType > &	u_para,
		View< double **, CLayout, DeviceType > &	T_para,
		View< double **, CLayout, DeviceType > &	T_perp
	)

Transposes the moments and sends to device. The moments in the Moments class have species as the contiguous index, while the functions in diffusion expect those reversed. The moments class is also only for nonadiabatic species, so adiabatic electrons are handled separately here.

Parameters

[in]	plasma	Plasma object used to loop over species
[in]	moments_h	Moments
[out]	den	Density moment
[out]	u_para	Parallel velocity moment
[out]	T_para	Parallel temperature moment
[out]	T_perp	Perpendicular temperature moment

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void update_analytic	(	const DomainDecomposition< DeviceType > &	pol_decomp,
		Plasma &	plasma,
		const ElectricField< DeviceType > &	electric_field,
		const View< bool *, CLayout, DeviceType > &	is_in_bounds,
		const View< double **, CLayout, DeviceType > &	delta_den00,
		const View< double **, CLayout, DeviceType > &	delta_u_para00,
		const View< double **, CLayout, DeviceType > &	delta_T00,
		bool	is_XGCa,
		double	dpot_te_limit
	)

Updates delta_n, delta_u, and delta_T for each species, based on the flux surface averaged moment changes

Parameters

[in]	pol_decomp	Domain decomposition object
[in,out]	plasma	Plasma object to be updated
[in]	electric_field	Used for dpot to remove adiabatic response
[in]	is_in_bounds	Whether each mesh node is in bounds
[in]	delta_den00	Flux surface averaged change in density moment
[in]	delta_u_para00	Flux surface averaged change in parallel velocity moment
[in]	delta_T00	Flux surface averaged change in temperature moment
[in]	is_XGCa	Whether simulation is XGCa. dpot is toroidally averaged but this is not needed for XGCa due to axisymmetry
[in]	dpot_te_limit	Limit for dpot. This should be removed eventually (it should be a member variable of a dpot class)

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void update_diffusion_eq_ftn	(	const int	n_species,
		const int	npsi,
		const double *	psi,
		const double *	diff_coeff
	)