Struphy model base class

class struphy.models.base.StruphyModel

Bases: object

Base class for all Struphy models.

Note

All Struphy models are subclasses of StruphyModel and should be added to struphy/models/ in one of the modules fluid.py, kinetic.py, hybrid.py or toy.py.

class Propagators

Bases: object

abstract property bulk_species: Species

Bulk species of the plasma. Must be an attribute of species_static().

abstract property velocity_scale: str

Velocity unit scale of the model. Must be one of “alfvén”, “cyclotron”, “light” or “thermal”.

abstract allocate_helpers()

Allocate helper arrays that are needed during simulation.

abstract update_scalar_quantities()

Specify an update rule for each item in scalar_quantities using update_scalar().

setup_equation_params(units: Units, verbose=False)

Set euqation parameters for each fluid and kinetic species.

setup_domain_and_equil(domain: Domain, equil: FluidEquilibrium)

If a numerical equilibirum is used, the domain is taken from this equilibirum.

property field_species: dict

property fluid_species: dict

property particle_species: dict

property diagnostic_species: dict

property species

allocate_feec(grid: TensorProductGrid, derham_opts: DerhamOptions)

allocate_propagators()

static diagnostics_dct()

Diagnostics dictionary. Model specific variables (FemField) which is going to be saved during the simulation.

property params

Model parameters from parameters.yml.

property pparams

Plasma parameters for each species.

property equation_params

Parameters appearing in model equation due to Struphy normalization.

property clone_config

Config in case domain clones are used.

property domain

Domain object, see Geometry.

property equil

Fluid equilibrium object, see Fluid equilibria.

property derham

3d Derham sequence, see derham.

property projected_equil

Fluid equilibrium projected on 3d Derham sequence with commuting projectors.

property units: Units

All Struphy units.

property mass_ops

WeighteMassOperators object, see mass_ops.

property basis_ops

Basis projection operators.

property prop_list

List of Propagator objects.

property prop_fields

Module struphy.propagators.propagators_fields.

property prop_coupling

Module struphy.propagators.propagators_coupling.

property prop_markers

Module struphy.propagators.propagators_markers.

property kwargs

Dictionary holding the keyword arguments for each propagator specified in propagators_cls. Keys must be the same as in propagators_cls, values are dictionaries holding the keyword arguments.

property scalar_quantities

A dictionary of scalar quantities to be saved during the simulation.

property time_state

A pointer to the time variable of the dynamics (‘t’).

property verbose

show model info on screen.

Type:

Bool

classmethod options()

Dictionary for available species options of the form {‘em_fields’: {}, ‘fluid’: {}, ‘kinetic’: {}}.

classmethod add_option(species: str | list, option, dct: dict, *, key=None)

Add an option to the dictionary of parameters under [species][options].

Test with “struphy params MODEL”.

Parameters:

• species (str or list) – path in the dict before the ‘options’ key

• option (any) – value which should be added in the dict

• dct (dict) – dictionary to which the value should be added at the corresponding position

• key (str or list) – path in the dict after the ‘options’ key

add_scalar(name: str, variable: PICVariable | SPHVariable | None = None, compute=None, summands=None)

Add a scalar to be saved during the simulation.

Parameters:

• name (str) – Dictionary key for the scalar.

• variable (PICVariable | SPHVariable, optional) – The variable associated with the scalar. Required if compute is ‘from_particles’.

• compute (str, optional) – Type of scalar, determines the compute operations. Options: ‘from_particles’ or ‘from_field’. Default is None.

• summands (list, optional) – List of other scalar names whose values should be summed to compute the value of this scalar. Default is None.

update_scalar(name, value=None)

Add a scalar that should be saved during the simulation.

Parameters:

• name (str) – Dictionary key of the scalar.

• value (float, optional) – Value to be saved. Required if there are no summands.

add_time_state(time_state)

Add a pointer to the time variable of the dynamics (‘t’) to the model and to all propagators of the model.

Parameters:

time_state (ndarray) – Of size 1, holds the current physical time ‘t’.

allocate_variables(verbose: bool = False)

Allocate memory for model variables and set initial conditions.

integrate(dt, split_algo='LieTrotter')

Advance the model by a time step dt by sequentially calling its Propagators.

Parameters:

• dt (float) – Time step of time integration.

• split_algo (str) – Splitting algorithm. Currently available: “LieTrotter” and “Strang”.

update_markers_to_be_saved()

Writes markers with IDs that are supposed to be saved into corresponding array.

update_distr_functions()

Writes distribution functions slices that are supposed to be saved into corresponding array.

print_scalar_quantities()

Check if scalar_quantities are not “nan” and print to screen.

initialize_from_restart(data)

Set initial conditions for FE coefficients (electromagnetic and fluid) and markers from restart group in hdf5 files.

Parameters:

data (struphy.io.output_handling.DataContainer) – The data object that links to the hdf5 files.

initialize_data_output(data: DataContainer, size)

Create datasets in hdf5 files according to model unknowns and diagnostics data.

Parameters:

• data (struphy.io.output_handling.DataContainer) – The data object that links to the hdf5 files.

• size (int) – Number of MPI processes of the model run.

Returns:

• save_keys_all (list) – Keys of datasets which are saved during the simulation.

• save_keys_end (list) – Keys of datasets which are saved at the end of a simulation to enable restarts.

classmethod show_options()

Print available model options to screen.

classmethod write_parameters_to_file(parameters=None, file=None, save=True, prompt=True)

generate_default_parameter_file(path: str | None = None, prompt: bool = True)

Generate a parameter file with default options for each species, and save it to the current input path.

The default name is params_<model_name>.yml.

Parameters:

• path (str) – Alternative path to getcwd()/params_MODEL.py.

• prompt (bool) – Whether to prompt for overwriting the specified .yml file.

Returns:

params_path – The path of the parameter file.

Return type:

str

compute_plasma_params(verbose=True)

Compute and print volume averaged plasma parameters for each species of the model.

Global parameters: - plasma volume - transit length - magnetic field

Species dependent parameters: - mass - charge - density - pressure - thermal energy kBT - Alfvén speed v_A - thermal speed v_th - thermal frequency Omega_th - cyclotron frequency Omega_c - plasma frequency Omega_p - Alfvèn frequency Omega_A - thermal Larmor radius rho_th - MHD length scale v_a/Omega_c - rho/L - alpha = Omega_p/Omega_c - epsilon = 1/(t*Omega_c)