pyrokinetics.gk_code.gene.GKInputGENE

class pyrokinetics.gk_code.gene.GKInputGENE(filename=None)

Bases: GKInput, FileReader

Class that can read GENE 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 GENE input file Uses default, which assumes a Fortan90 namelist
from_file(path[, file_type])	Read a file from disk, returning an instance of this class.
from_str(input_string)
get_gene_geometry()
get_local_geometry()	Returns local geometry.
get_local_species()	Load LocalSpecies object from GENE file
get_local_species_names()	Returns a list of the local species names :returns: names -- List of local species names :rtype: Array
get_ne_te_normalisation()
get_numerics()	Gather numerical info (grid spacing, time steps, etc)
get_reference_values(local_norm)	Reads in reference values from input file
get_trpeps()
is_linear()
is_nonlinear()	Return true if the GKCode is nonlinear, otherwise return False
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 GENE input file into a dictionary Uses default read, which assumes input is a Fortran90 namelist
read_str(input_string[, detect_norm])	Reads GENE input file given as string Uses default read_str, which assumes input is a Fortran90 namelist
set(local_geometry, local_species, numerics)	Set self.data using LocalGeometry, LocalSpecies, and Numerics.
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 gene input file, and that it contains sufficient info for Pyrokinetics to work with
write(filename[, float_format, local_norm, ...])	Write self.data to a gyrokinetics input file.

Attributes

code_name
default_file_name
file_type
norm_convention	Convention used for normalising this code's quantities
pyro_gene_circular
pyro_gene_circular_default
pyro_gene_fourier
pyro_gene_fourier_default
pyro_gene_miller
pyro_gene_miller_default
pyro_gene_miller_turnbull
pyro_gene_miller_turnbull_default
pyro_gene_mxh
pyro_gene_mxh_default
pyro_gene_species

add_flags(flags)

Add extra flags to GENE input file Uses default, which assumes a Fortan90 namelist

Return type:

None

code_name = 'GENE'

default_file_name = 'input.gene'

file_type: ClassVar[str] = 'GENE'

get_gene_geometry()

Returns:

trpeps

Return type:

trpeps from the input file

get_local_geometry()

Returns local geometry. Delegates to more specific functions

Return type:

LocalGeometry

get_local_species()

Load LocalSpecies object from GENE file

get_local_species_names()

Returns a list of the local species names :returns: names – List of local species names :rtype: Array

get_ne_te_normalisation()

get_numerics()

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

Return type:

Numerics

get_reference_values(local_norm)

Reads in reference values from input file

Return type:

Dict[str, Any]

Parameters:

local_norm (SimulationNormalisation)

get_trpeps()

Returns:

trpeps

Return type:

trpeps from the input file

is_nonlinear()

Return true if the GKCode is nonlinear, otherwise return False

Return type:

bool

norm_convention: str = 'gene'

Convention used for normalising this code’s quantities

pyro_gene_circular = {'bt_ccw': ['geometry', 'sign_bt_cw'], 'ip_ccw': ['geometry', 'sign_ip_cw'], 'q': ['geometry', 'q0'], 'shat': ['geometry', 'shat']}

pyro_gene_circular_default = {'bt_ccw': -1, 'ip_ccw': -1, 'q': None, 'shat': 0.0}

pyro_gene_fourier = {'bt_ccw': ['geometry', 'sign_ip_cw'], 'cN': ['geometry', 'cn_m'], 'dcNdr': ['geometry', 'cndr_m'], 'dsNdr': ['geometry', 'sndr_m'], 'ip_ccw': ['geometry', 'sign_ip_cw'], 'q': ['geometry', 'q0'], 'sN': ['geometry', 'sn_m'], 'shat': ['geometry', 'shat']}

pyro_gene_fourier_default = {'bt_ccw': -1, 'cN': [0.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 'dcNdr': [0.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 'dsNdr': [0.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 'ip_ccw': -1, 'q': None, 'sN': [0.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 'shat': 0.0}

pyro_gene_miller = {'bt_ccw': ['geometry', 'sign_bt_cw'], 'dZ0dr': ['geometry', 'drz'], 'delta': ['geometry', 'delta'], 'ip_ccw': ['geometry', 'sign_ip_cw'], 'kappa': ['geometry', 'kappa'], 'q': ['geometry', 'q0'], 's_delta': ['geometry', 's_delta'], 's_kappa': ['geometry', 's_kappa'], 'shat': ['geometry', 'shat'], 'shift': ['geometry', 'drr']}

pyro_gene_miller_default = {'bt_ccw': -1, 'dZ0dr': 0.0, 'delta': 0.0, 'ip_ccw': -1, 'kappa': 1.0, 'q': None, 's_delta': 0.0, 's_kappa': 0.0, 'shat': 0.0, 'shift': 0.0}

pyro_gene_miller_turnbull = {'bt_ccw': ['geometry', 'sign_bt_cw'], 'dZ0dr': ['geometry', 'drz'], 'delta': ['geometry', 'delta'], 'ip_ccw': ['geometry', 'sign_ip_cw'], 'kappa': ['geometry', 'kappa'], 'q': ['geometry', 'q0'], 's_delta': ['geometry', 's_delta'], 's_kappa': ['geometry', 's_kappa'], 's_zeta': ['geometry', 's_zeta'], 'shat': ['geometry', 'shat'], 'shift': ['geometry', 'drr'], 'zeta': ['geometry', 'zeta']}

pyro_gene_miller_turnbull_default = {'bt_ccw': -1, 'dZ0dr': 0.0, 'delta': 0.0, 'ip_ccw': -1, 'kappa': 1.0, 'q': None, 's_delta': 0.0, 's_kappa': 0.0, 's_zeta': 0.0, 'shat': 0.0, 'shift': 0.0, 'zeta': 0.0}

pyro_gene_mxh = {'bt_ccw': ['geometry', 'sign_bt_cw'], 'cn': ['geometry', 'cN_m'], 'dZ0dr': ['geometry', 'drz'], 'dcndr': ['geometry', 'cNdr_m'], 'dsndr': ['geometry', 'sNdr_m'], 'ip_ccw': ['geometry', 'sign_ip_cw'], 'kappa': ['geometry', 'kappa'], 'q': ['geometry', 'q0'], 's_kappa': ['geometry', 's_kappa'], 'shat': ['geometry', 'shat'], 'shift': ['geometry', 'drr'], 'sn': ['geometry', 'sN_m']}

pyro_gene_mxh_default = {'bt_ccw': -1, 'cn': [0.0, 0.0, 0.0, 0.0], 'dZ0dr': 0.0, 'dcndr': [0.0, 0.0, 0.0, 0.0], 'dsndr': [0.0, 0.0, 0.0, 0.0], 'ip_ccw': -1, 'kappa': 1.0, 'q': None, 's_kappa': 0.0, 'shat': 0.0, 'shift': 0.0, 'sn': [0.0, 0.0, 0.0, 0.0]}

pyro_gene_species = {'dens': 'dens', 'inverse_ln': 'omn', 'inverse_lt': 'omt', 'mass': 'mass', 'temp': 'temp', 'z': 'charge'}

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 GENE input file into a dictionary Uses default read, which assumes input is a Fortran90 namelist

Return type:

Dict[str, Any]

Parameters:

• filename (PathLike | str)

• detect_norm (bool)

read_str(input_string, detect_norm=True)

Reads GENE input file given as string Uses default read_str, which assumes input is a Fortran90 namelist

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)

verify_file_type(filename)

Ensure this file is a valid gene 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)

Write self.data to a gyrokinetics input file. Uses default write, which writes to a Fortan90 namelist

Parameters:

• filename (PathLike | str)

• float_format (str)

• local_norm (SimulationNormalisation | None)

• code_normalisation (str | None)