.. _userguide:

Userguide
=========

This guide takes you through the classes used in Struphy launch files generated by::

    struphy params MODEL

for a valid ``MODEL`` from the list of :ref:`models`.
All information for running simulations are contained and can be altered in such launch (parameter) files.
It is recommended to generate such a file and inspect it with an editor like VScode (using a type checker like "mypy").

:ref:`pproc` is discussed at the end of this section.


Basic options 
-------------

.. autoclass:: struphy.io.options.EnvironmentOptions

.. autoclass:: struphy.io.options.BaseUnits

.. autoclass:: struphy.io.options.Time


Simulation domains 
------------------

See :ref:`avail_mappings`.


Fluid backgrounds 
-----------------

See :ref:`equils_avail`.


Grids 
-----

.. autoclass:: struphy.topology.grids.TensorProductGrid
    :show-inheritance:


Derham complex
--------------

.. autoclass:: struphy.io.options.DerhamOptions


Models 
------

See :ref:`models`.


Species types
^^^^^^^^^^^^^

Each Struphy model is a collection of species of one of the following types:

.. autoclass:: struphy.models.species.FieldSpecies

.. autoclass:: struphy.models.species.FluidSpecies

.. autoclass:: struphy.models.species.ParticleSpecies

.. automethod:: struphy.models.species.Species.set_phys_params


Variable types
^^^^^^^^^^^^^^

Each species can contain multiple variables.

.. autoclass:: struphy.models.variables.PICVariable

.. autoclass:: struphy.models.variables.FEECVariable

.. autoclass:: struphy.models.variables.SPHVariable


Setting particle parameters
---------------------------

.. automethod:: struphy.models.species.ParticlesSpecies.set_markers

.. automethod:: struphy.models.species.ParticlesSpecies.set_sorting_boxes

.. automethod:: struphy.models.species.ParticlesSpecies.set_save_data

.. autoclass:: struphy.pic.utilities.LoadingParameters

.. autoclass:: struphy.pic.utilities.WeightsParameters

.. autoclass:: struphy.pic.utilities.BoundaryParameters

.. autoclass:: struphy.pic.utilities.BinningPlot

.. autoclass:: struphy.pic.utilities.KernelDensityPlot


Setting backgrounds
-------------------

.. automethod:: struphy.models.variables.FEECVariable.add_background

.. automethod:: struphy.models.variables.PICVariable.add_background

.. automethod:: struphy.models.variables.SPHVariable.add_background

.. autoclass:: struphy.io.options.FieldsBackground


Adding perturbations
--------------------

.. automethod:: struphy.models.variables.FEECVariable.add_perturbation

.. automethod:: struphy.models.variables.SPHVariable.add_perturbation


.. autoclass:: struphy.initial.base.Perturbation

See available :ref:`perturbations`.


Setting initial conditions
--------------------------

.. automethod:: struphy.models.variables.PICVariable.add_initial_condition


For :class:`~struphy.models.variables.FEECVariable` and :class:`~struphy.models.variables.SPHVariable` the initial condition is automatically
created as the sum of background + perturbation.


.. _pproc:

Post-processing
---------------

.. automodule:: struphy.main
    :members:
    :exclude-members: run