pyrokinetics.gk_code.cgyro.GKInputCGYRO

class pyrokinetics.gk_code.cgyro.GKInputCGYRO(filename=None)

Bases: GKInput, FileReader

Class that can read CGYRO input files, and produce Numerics, LocalSpecies, and LocalGeometry objects

Parameters:

filename (PathLike | str | None)

__init__(filename=None)

Parameters:

filename (PathLike | str | None)

Methods

__init__([filename])
add_flags(flags)	Add extra flags to CGYRO input file
from_file(path[, file_type])	Read a file from disk, returning an instance of this class.
from_str(input_string)
get_local_geometry()	Returns local geometry.
get_local_geometry_fourier()	Load Fourier object from CGYRO file
get_local_geometry_miller()	Load Miller object from CGYRO file
get_local_geometry_mxh()	Load MXH object from CGYRO file
get_local_species()	Load LocalSpecies object from CGYRO file
get_ne_te_normalisation()
get_numerics()	Gather numerical info (grid spacing, time steps, etc)
get_pyro_cgyro_species([iSp])
get_reference_values(local_norm)	Reads in reference values from input file
is_linear()
is_nonlinear()	Return true if the GKCode is nonlinear, otherwise return False
parse_cgyro(lines)	Given lines of a cgyro file or a string split by '/n', return a dict of CGYRO input data
read_dict(input_dict[, detect_norm])	Reads GENE input file given as dict Uses default read_dict, which assumes input is a dict
read_from_file(filename[, detect_norm])	Reads CGYRO input file into a dictionary
read_str(input_string[, detect_norm])	Reads CGYRO input file given as string
set(local_geometry, local_species, numerics)	Set self.data using LocalGeometry, LocalSpecies, and Numerics.
set_legacy_cgyro(flag)	Set dictionay flags used to access namelist to legacy values or not
supported_file_types()	Returns a list of all registered file types.
verify_expected_keys(filename, keys)	Checks that the expected keys are present at the top level of self.data.
verify_file_type(filename)	Ensure this file is a valid cgyro input file, and that it contains sufficient info for Pyrokinetics to work with
write(filename[, float_format, local_norm, ...])	Writes self.data to an input file

Attributes

cgyro_eq_types
code_name
default_file_name
file_type
norm_convention	Convention used for normalising this code's quantities
pyro_cgyro_fourier
pyro_cgyro_fourier_defaults
pyro_cgyro_miller
pyro_cgyro_miller_defaults
pyro_cgyro_mxh
pyro_cgyro_mxh_defaults

add_flags(flags)

Add extra flags to CGYRO input file

Return type:

None

cgyro_eq_types = {1: 'SAlpha', 2: 'MXH', 3: 'Fourier'}

code_name = 'CGYRO'

default_file_name = 'input.cgyro'

file_type: ClassVar[str] = 'CGYRO'

get_local_geometry()

Returns local geometry. Delegates to more specific functions

Return type:

LocalGeometry

get_local_geometry_fourier()

Load Fourier object from CGYRO file

Return type:

LocalGeometryFourierCGYRO

get_local_geometry_miller()

Load Miller object from CGYRO file

Return type:

LocalGeometryMiller

get_local_geometry_mxh()

Load MXH object from CGYRO file

Return type:

LocalGeometryMXH

get_local_species()

Load LocalSpecies object from CGYRO file

get_ne_te_normalisation()

get_numerics()

Gather numerical info (grid spacing, time steps, etc)

Return type:

Numerics

static get_pyro_cgyro_species(iSp=1)

get_reference_values(local_norm)

Reads in reference values from input file

Return type:

Dict[str, Any]

Parameters:

local_norm (SimulationNormalisation)

is_nonlinear()

Return true if the GKCode is nonlinear, otherwise return False

Return type:

bool

norm_convention: str = 'cgyro'

Convention used for normalising this code’s quantities

static parse_cgyro(lines)

Given lines of a cgyro file or a string split by ‘/n’, return a dict of CGYRO input data

pyro_cgyro_fourier = {'Rmaj': 'RMAJ', 'Z0': 'ZMAG', 'bt_ccw': 'BTCCW', 'dZ0dr': 'DZMAG', 'delta': 'DELTA', 'ip_ccw': 'IPCCW', 'kappa': 'KAPPA', 'q': 'Q', 'rho': 'RMIN', 's_delta': 'S_DELTA', 's_kappa': 'S_KAPPA', 'shat': 'S', 'shift': 'SHIFT'}

pyro_cgyro_fourier_defaults = {'Rmaj': 3.0, 'Z0': 0.0, 'bt_ccw': -1.0, 'dZ0dr': 0.0, 'delta': 0.0, 'ip_ccw': -1.0, 'kappa': 1.0, 'q': 2.0, 'rho': 0.5, 's_delta': 0.0, 's_kappa': 0.0, 'shat': 1.0, 'shift': 0.0}

pyro_cgyro_miller = {'Rmaj': 'RMAJ', 'Z0': 'ZMAG', 'bt_ccw': 'BTCCW', 'dZ0dr': 'DZMAG', 'delta': 'DELTA', 'ip_ccw': 'IPCCW', 'kappa': 'KAPPA', 'q': 'Q', 'rho': 'RMIN', 's_delta': 'S_DELTA', 's_kappa': 'S_KAPPA', 'shat': 'S', 'shift': 'SHIFT'}

pyro_cgyro_miller_defaults = {'Rmaj': 3.0, 'Z0': 0.0, 'bt_ccw': -1.0, 'dZ0dr': 0.0, 'delta': 0.0, 'ip_ccw': -1.0, 'kappa': 1.0, 'q': 2.0, 'rho': 0.5, 's_delta': 0.0, 's_kappa': 0.0, 'shat': 1.0, 'shift': 0.0}

pyro_cgyro_mxh = {'Rmaj': 'RMAJ', 'Z0': 'ZMAG', 'bt_ccw': 'BTCCW', 'cn0': 'SHAPE_COS0', 'cn1': 'SHAPE_COS1', 'cn2': 'SHAPE_COS2', 'cn3': 'SHAPE_COS3', 'cn4': 'SHAPE_COS4', 'cn5': 'SHAPE_COS5', 'cn6': 'SHAPE_COS6', 'dZ0dr': 'DZMAG', 'dcndr0': 'SHAPE_S_COS0', 'dcndr1': 'SHAPE_S_COS1', 'dcndr2': 'SHAPE_S_COS2', 'dcndr3': 'SHAPE_S_COS3', 'dcndr4': 'SHAPE_S_COS4', 'dcndr5': 'SHAPE_S_COS5', 'dcndr6': 'SHAPE_S_COS6', 'delta': 'DELTA', 'dsndr3': 'SHAPE_S_SIN3', 'dsndr4': 'SHAPE_S_SIN4', 'dsndr5': 'SHAPE_S_SIN5', 'dsndr6': 'SHAPE_S_SIN6', 'ip_ccw': 'IPCCW', 'kappa': 'KAPPA', 'q': 'Q', 'rho': 'RMIN', 's_delta': 'S_DELTA', 's_kappa': 'S_KAPPA', 's_zeta': 'S_ZETA', 'shat': 'S', 'shift': 'SHIFT', 'sn3': 'SHAPE_SIN3', 'sn4': 'SHAPE_SIN4', 'sn5': 'SHAPE_SIN5', 'sn6': 'SHAPE_SIN6', 'zeta': 'ZETA'}

pyro_cgyro_mxh_defaults = {'Rmaj': 3.0, 'Z0': 0.0, 'bt_ccw': -1.0, 'cn0': 0.0, 'cn1': 0.0, 'cn2': 0.0, 'cn3': 0.0, 'cn4': 0.0, 'cn5': 0.0, 'cn6': 0.0, 'dZ0dr': 0.0, 'dcndr0': 0.0, 'dcndr1': 0.0, 'dcndr2': 0.0, 'dcndr3': 0.0, 'dcndr4': 0.0, 'dcndr5': 0.0, 'dcndr6': 0.0, 'delta': 0.0, 'dsndr3': 0.0, 'dsndr4': 0.0, 'dsndr5': 0.0, 'dsndr6': 0.0, 'ip_ccw': -1.0, 'kappa': 1.0, 'q': 2.0, 'rho': 0.5, 's_delta': 0.0, 's_kappa': 0.0, 's_zeta': 0.0, 'shat': 1.0, 'shift': 0.0, 'sn3': 0.0, 'sn4': 0.0, 'sn5': 0.0, 'sn6': 0.0, 'zeta': 0.0}

read_dict(input_dict, detect_norm=True)

Reads GENE input file given as dict Uses default read_dict, which assumes input is a dict

Return type:

Dict[str, Any]

Parameters:

• input_dict (dict)

• detect_norm (bool)

read_from_file(filename, detect_norm=True)

Reads CGYRO input file into a dictionary

Return type:

Dict[str, Any]

Parameters:

• filename (PathLike | str)

• detect_norm (bool)

read_str(input_string, detect_norm=True)

Reads CGYRO input file given as string

Return type:

Dict[str, Any]

Parameters:

• input_string (str)

• detect_norm (bool)

set(local_geometry, local_species, numerics, local_norm=None, template_file=None, code_normalisation=None, **kwargs)

Set self.data using LocalGeometry, LocalSpecies, and Numerics. These may be obtained via another GKInput file, or from Equilibrium/Kinetics objects.

Parameters:

• local_geometry (LocalGeometry)

• local_species (LocalSpecies)

• numerics (Numerics)

• local_norm (SimulationNormalisation | None)

• template_file (PathLike | str | None)

• code_normalisation (str | None)

set_legacy_cgyro(flag)

Set dictionay flags used to access namelist to legacy values or not

Parameters:

flag (bool)

verify_file_type(filename)

Ensure this file is a valid cgyro input file, and that it contains sufficient info for Pyrokinetics to work with

Parameters:

filename (PathLike | str)

write(filename, float_format='', local_norm=None, code_normalisation=None)

Writes self.data to an input file

Default version assumes a Fortran90 namelist

Parameters:

• filename (PathLike | str)

• float_format (str)

• local_norm (SimulationNormalisation | None)

• code_normalisation (str | None)