pyrokinetics.local_species.LocalSpecies

class pyrokinetics.local_species.LocalSpecies(*args, **kwargs)

Bases: CleverDict

Dictionary of local species parameters where the key is different species

For example LocalSpecies[‘electron’] contains all the local info for that species in a dictionary

Local parameters are normalised to reference values

name : Name mass : Mass z : Charge dens : Density temp : Temperature omega0 : Angular velocity nu : Collision Frequency

inverse_lt : 1/Lt inverse_ln : 1/Ln domega_drho : Gradient in angular velocity

zeff : Zeff \(\sum_{ions} n_i Z_i^2 / n_e\)

__init__(*args, **kwargs)

Methods

__init__(*args, **kwargs)
add_alias(name, alias)	Adds an alias to a given key/name.
add_species(name, species_data[, norms])	Adds a new species to LocalSpecies
autosave([fullcopy, silent])	Toggles autosave to a config file.
check_if_unallowed_key([mapping, _aliases])
check_quasineutrality([tol])	Checks quasi-neutrality is satisfied and raises a warning if it is not
clear()
convert_physical_units(norms)	Convert each species' physical-unit quantities to generic simulation units.
copy()
create_save_file()	Creates a skeleton file to store autosave data if one doesn't already exist.
delete([name])	Called every time a CleverDict key/attribute is deleted.
delete_alias(alias)	deletes an alias
enforce_quasineutrality(modify_species)	Enforces quasineutrality by adjusting the density and gradient of one species
from_dict(species_dict, **kwargs)	Reads local species parameters from a dictionary
from_global_kinetics(kinetics, psi_n, local_norm)
from_json([json_data, file_path, ignore, ...])	Creates a new CleverDict object and loads data from a JSON object or file.
from_kinetics(kinetics, psi_n, norm)	Loads local species data from kinetics object
from_lines([lines, file_path, ...])	Creates a new CleverDict object and loads data from a line ('
fromkeys(iterable, value[, ignore, exclude, ...])	Instantiates an object using supplied keys/aliases and values e.g.
get(key[, default])	Return the value for key if key is in the dictionary, else default.
get_aliases([name])	Returns all alliases or aliases for a given name.
get_key(name)	Returns the primary key for a given name.
get_new_save_path()	Get Operating System specific default for settings folder; Return a (hopefully) unique filename comprising time and variable name
info([as_str, ignore, exclude, only])	Prints or returns a string showing variable name equivalence and object attribute/dictionary key equivalence.
items()
keys()
merge_species(base_species, merge_species[, ...])	Merge multiple species into one.
normalise([norms, context])	Normalise to pyrokinetics normalisations and calculate total pressure gradient
original_delete([name])	Called every time a CleverDict key/attribute is deleted.
original_save([name, value])	Called every time a CleverDict value is created or change.
pop(k[,d])	If the key is not found, return the default if given; otherwise, raise a KeyError.
popitem()	Remove and return a (key, value) pair as a 2-tuple.
remove_species(*names)	Removes a species from the LocalSpecies
save([name, value])	Called every time a CleverDict value is created or change.
set_autodelete([deletefunc])	Overwrites the default (inactive) delete method of an instance with a new custom function.
set_autosave([savefunc])	Overwrites the default (dummy) save method of an instance with a new custom function.
set_zeff()	Calculates Z_eff from the kinetics object
setattr_direct(name, value)	Sets an attribute directly, i.e. without making it into an item.
setdefault(key[, default])	Insert key with a value of default if key is not in the dictionary.
to(norms[, context])	Thin wrapper for normalise
to_dict([ignore, exclude, only])	Returns a regular dict of the core data dictionary
to_json([file_path, fullcopy, ignore, ...])	Generates a JSON formatted string representing the CleverDict data and optionally saves to file.
to_lines([file_path, start_from_key, ...])	Creates a line ("
to_list([ignore, exclude, only])	Creates a list of k,v pairs as a list of tuples.
update([mapping])
update_pressure([norms])	Calculate inverse_lp and pressure for species
values()

Attributes

domega_drho
expand
ignore_internals
nspec

class SingleLocalSpecies(localspecies, species_dict, norms=None)

Bases: object

Dictionary of local species parameters for one species

For example SingleLocalSpecies[‘electron’] contains all the local info for that species in a dictionary

Local parameters are normalised to reference values

name : Name mass : Mass z : Charge dens : Density temp : Temperature omega0 : Angular Velocity nu : Collision Frequency

inverse_lt : 1/Lt [units] [1 / lref_minor_radius] inverse_ln : 1/Ln [units] [1 / lref_minor_radius] domega_drho : domega/drho [units] [vref / lref_minor_radius**2]

Parameters:

• species_dict (Dict[str, float])

• norms (SimulationNormalisation | None)

property dens

property domega_drho

property inverse_ln

property inverse_lt

property temp

add_species(name, species_data, norms=None)

Adds a new species to LocalSpecies

Parameters:

• name (str) – Name of species

• species_data (Dict[str, Any]) – Dictionary like object of Species Data

• norms (SimulationNormalisation | None)

Return type:

None

check_quasineutrality(tol=0.01)

Checks quasi-neutrality is satisfied and raises a warning if it is not

Return type:

bool

Parameters:

tol (float)

convert_physical_units(norms)

Convert each species’ physical-unit quantities to generic simulation units.

property domega_drho

enforce_quasineutrality(modify_species)

Enforces quasineutrality by adjusting the density and gradient of one species

Parameters:

modify_species (str) – Name of species to modify

Raises:

ValueError – If there is no species with given name or the quasineutrality can’t be set with that species for some reason

Return type:

None

from_dict(species_dict, **kwargs)

Reads local species parameters from a dictionary

classmethod from_global_kinetics(kinetics, psi_n, local_norm)

Parameters:

• kinetics (Kinetics)

• psi_n (float)

• local_norm (SimulationNormalisation)

from_kinetics(kinetics, psi_n, norm)

Loads local species data from kinetics object

merge_species(base_species, merge_species, keep_base_species_z=False, keep_base_species_mass=False)

Merge multiple species into one. Performs a weighted average depending on the densities of each species to preserve quasineutrality.

Parameters:

• base_species (str) – Names of species that will absorb other species

• merge_species (Iterable[str]) – List of species names to be merged into the base_species

• keep_base_species_z (bool) –

  Charge of new species

  True preserves base_species charge and adjusts ion density False/None preserves ion density (before/after merge) and adjusts z

• keep_base_species_mass (bool) –

  Mass of new species

  True keeps base_species mass False/None results in a density-weighted average

Raises:

ValueError – If there is no species with a given name.

Return type:

None

normalise(norms=None, context=None)

Normalise to pyrokinetics normalisations and calculate total pressure gradient

property nspec

remove_species(*names)

Removes a species from the LocalSpecies

Parameters:

names (str) – Names of species to remove

Raises:

ValueError – If there is no species with a given name.

Return type:

None

set_zeff()

Calculates Z_eff from the kinetics object

Return type:

None

to(norms, context=None)

Thin wrapper for normalise

update_pressure(norms=None)

Calculate inverse_lp and pressure for species

Return type:

None