pyrokinetics.gk_code.neo.GKInputNEO

pyrokinetics.gk_code.neo.GKInputNEO#

class pyrokinetics.gk_code.neo.GKInputNEO(filename=None)[source]#

Bases: GKInput, FileReader

Class that can read NEO 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 NEO 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 NEO file
`get_local_geometry_miller`()	Load Miller object from NEO file
`get_local_geometry_mxh`()	Load MXH object from NEO file
`get_local_species`()	Load LocalSpecies object from NEO file
`get_ne_te_normalisation`()
`get_numerics`()	Gather numerical info (grid spacing, time steps, etc)
`get_pyro_neo_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_neo`(lines)	Given lines of a neo file or a string split by '/n', return a dict of NEO 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 NEO input file into a dictionary
`read_str`(input_string[, detect_norm])	Reads NEO input file given as string
`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 neo 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

`code_name`
`default_file_name`
`file_type`
`neo_eq_types`
`norm_convention`	`Convention` used for normalising this code's quantities
`pyro_neo_fourier`
`pyro_neo_fourier_defaults`
`pyro_neo_miller`
`pyro_neo_miller_defaults`
`pyro_neo_mxh`
`pyro_neo_mxh_defaults`

add_flags(flags)[source]#

Add extra flags to NEO input file

Return type:: None

code_name = 'NEO'#

default_file_name = 'input.neo'#

file_type: ClassVar[str] = 'NEO'#

get_local_geometry()[source]#

Returns local geometry. Delegates to more specific functions

Return type:: LocalGeometry

get_local_geometry_fourier()[source]#

Load Fourier object from NEO file

Return type:: LocalGeometryFourierCGYRO

get_local_geometry_miller()[source]#

Load Miller object from NEO file

Return type:: LocalGeometryMiller

get_local_geometry_mxh()[source]#

Load MXH object from NEO file

Return type:: LocalGeometryMXH

get_local_species()[source]#: Load LocalSpecies object from NEO file

get_ne_te_normalisation()[source]#

get_numerics()[source]#

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

Return type:: Numerics

static get_pyro_neo_species(iSp=1)[source]#

get_reference_values(local_norm)[source]#

Reads in reference values from input file

Return type:: Dict[str, Any]
Parameters:: local_norm (SimulationNormalisation)

is_nonlinear()[source]#

Return true if the GKCode is nonlinear, otherwise return False

Return type:: bool

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

norm_convention: str = 'neo'#: Convention used for normalising this code’s quantities

static parse_neo(lines)[source]#: Given lines of a neo file or a string split by ‘/n’, return a dict of NEO input data

pyro_neo_fourier = {'Rmaj': 'RMAJ_OVER_A', 'Z0': 'ZMAG_OVER_A', 'beta_prime': 'BETA_STAR', 'bt_ccw': 'BTCCW', 'dZ0dr': 'S_ZMAG', 'delta': 'DELTA', 'ip_ccw': 'IPCCW', 'kappa': 'KAPPA', 'q': 'Q', 'rho': 'RMIN_OVER_A', 's_delta': 'S_DELTA', 's_kappa': 'S_KAPPA', 'shat': 'SHEAR', 'shift': 'SHIFT'}#

pyro_neo_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_neo_miller = {'Rmaj': 'RMAJ_OVER_A', 'Z0': 'ZMAG_OVER_A', 'beta_prime': 'BETA_STAR', 'bt_ccw': 'BTCCW', 'dZ0dr': 'S_ZMAG', 'delta': 'DELTA', 'ip_ccw': 'IPCCW', 'kappa': 'KAPPA', 'q': 'Q', 'rho': 'RMIN_OVER_A', 's_delta': 'S_DELTA', 's_kappa': 'S_KAPPA', 'shat': 'SHEAR', 'shift': 'SHIFT'}#

pyro_neo_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_neo_mxh = {'Rmaj': 'RMAJ_OVER_A', 'Z0': 'ZMAG_OVER_A', 'beta_prime': 'BETA_STAR', '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': 'S_ZMAG', '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_OVER_A', 's_delta': 'S_DELTA', 's_kappa': 'S_KAPPA', 's_zeta': 'S_ZETA', 'shat': 'SHEAR', 'shift': 'SHIFT', 'sn3': 'SHAPE_SIN3', 'sn4': 'SHAPE_SIN4', 'sn5': 'SHAPE_SIN5', 'sn6': 'SHAPE_SIN6', 'zeta': 'ZETA'}#

pyro_neo_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)[source]#

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)[source]#

Reads NEO input file into a dictionary

Return type:

Dict[str, Any]

Parameters:

filename (PathLike | str)
detect_norm (bool)

read_str(input_string, detect_norm=True)[source]#

Reads NEO 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)[source]#

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)[source]#

Ensure this file is a valid neo 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)[source]#

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)

pyrokinetics.gk_code.neo.GKInputNEO

Contents

pyrokinetics.gk_code.neo.GKInputNEO#