pyrokinetics.pyroscan.PyroScan

class pyrokinetics.pyroscan.PyroScan(pyro=None, parameter_dict=None, p_prime_type=0, value_fmt='.2f', value_separator='_', parameter_separator='/', file_name=None, base_directory='.', load_default_parameter_keys=True, pyroscan_json=None, runfile_dict=None, load_base_pyro=False)

Bases: object

Creates a dictionary of pyro objects in pyro_dict

Need a templates pyro object

Dict of parameters to scan through { param : [values], }

__init__(pyro=None, parameter_dict=None, p_prime_type=0, value_fmt='.2f', value_separator='_', parameter_separator='/', file_name=None, base_directory='.', load_default_parameter_keys=True, pyroscan_json=None, runfile_dict=None, load_base_pyro=False)

Methods

__init__([pyro, parameter_dict, ...])
add_parameter_func([parameter_key, ...])	Applies function parameter_func(pyro, **kwargs) on pyro object each time after parameter_key is set in a scan
add_parameter_key([parameter_key, ...])	parameter_key: string to access variable parameter_attr: string of attribute storing value in pyro parameter_location: list of strings showing path to value in pyro
convert_gk_code(gk_code)	Converts all gyrokinetics codes to the code type 'gk_code'.
create_single_run(parameters)	Create a new Pyro instance from the PyroScan base with new run parameters
format_single_run_name(parameters)	Concatenate parameter names/values with separator.
load_default_parameter_keys()	Loads default parameters name into parameter_map
load_gk_output([output_convention, ...])	Loads PyroScanGKOutput into self.gk_output
outer_product()	Creates generator of outer product for all parameter permutations
update_self_parameters()	Updates all pyro object parameters based on pyro_dict values
write([file_name, base_directory, ...])	Creates and writes GK input files for parameters in scan

Attributes

JSON_ATTRS
base_directory
file_name
gk_code

JSON_ATTRS = ['value_fmt', 'value_separator', 'parameter_separator', 'parameter_dict', 'file_name', 'base_directory', 'runfile_dict', 'p_prime_type', 'parameter_map']

add_parameter_func(parameter_key=None, parameter_func=None, parameter_kwargs=None)

Applies function parameter_func(pyro, **kwargs) on pyro object each time after parameter_key is set in a scan

parameter_key: string to access variable parameter_func: function that take in a pyro object applies modification parameter_kwargs: Dictionary of kwargs to apply to function

add_parameter_key(parameter_key=None, parameter_attr=None, parameter_location=None)

parameter_key: string to access variable parameter_attr: string of attribute storing value in pyro parameter_location: list of strings showing path to value in pyro

property base_directory

convert_gk_code(gk_code)

Converts all gyrokinetics codes to the code type ‘gk_code’. This can be any viable GKInput type (GS2, CGYRO, GENE,…)

Return type:

None

Parameters:

gk_code (str)

create_single_run(parameters)

Create a new Pyro instance from the PyroScan base with new run parameters

Parameters:

parameters (dict)

property file_name

format_single_run_name(parameters)

Concatenate parameter names/values with separator. Handles both tuple-style and string-style runfile_dict keys for backward compatibility.

property gk_code

load_default_parameter_keys()

Loads default parameters name into parameter_map

{param : [“attribute”, [“key_to_location_1”, “key_to_location_2” ]] }

for example

{‘electron_temp_gradient’: [

“local_species”, [‘electron’,’inverse_lt’]] }

load_gk_output(output_convention='pyrokinetics', tolerance_time_range=0.8, netcdf_file=None, load_fields=True, load_fluxes=True, load_moments=False, sum_ky=True, drop_nan=False, **kwargs)

Loads PyroScanGKOutput into self.gk_output

Parameters:

• output_convention (str default 'pyrokinetics') – ConventionNormalisation to convert output to

• tolerance_time_range (float default 0.8) – Time window over which to calculate growth rate tolerance

• netcdf_file (PathLike default None) – If supplied then load PyroScanGKOutput from existing netCDF

• (bool (drop_nan)

• not (default False) – Flag to load moments or)

• (bool

• not

• (bool

• not

• (bool

• default (default False) – If NaNs are found in the output then that data is dropped. Off by)

• GKOutputReader. (**kwargs – Arguments to pass to the)

Return type:

None

outer_product()

Creates generator of outer product for all parameter permutations

update_self_parameters()

Updates all pyro object parameters based on pyro_dict values

write(file_name=None, base_directory=None, template_file=None, relative_path=True)

Creates and writes GK input files for parameters in scan