.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "gen_examples/plot_getting_started.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_gen_examples_plot_getting_started.py>`
        to download the full example code

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_gen_examples_plot_getting_started.py:


Getting Started
===============

This example showcases a simple, one-component plasma, and might be a good
starting point.

.. GENERATED FROM PYTHON SOURCE LINES 8-79



.. image-sg:: /gen_examples/images/sphx_glr_plot_getting_started_001.svg
   :alt: Be plasma at 2eV and 1g/cc with Z=2
   :srcset: /gen_examples/images/sphx_glr_plot_getting_started_001.svg
   :class: sphx-glr-single-img





.. code-block:: Python


    from functools import partial

    import matplotlib.pyplot as plt

    # jax provides a submodule which can be (mostly) used as a drop-in replacement
    # for numpy. We use jnp to avoid confusion.
    from jax import numpy as jnp

    import jaxrts

    # We use the jpu package (which is enabling the usage of pint with jax) to
    # handle units. See below for how to use this
    ureg = jaxrts.ureg

    # Initialize a Plasma State (We use a Berillium Plasma, here)
    state = jaxrts.PlasmaState(
        ions=[jaxrts.Element("Be")],  # Specify the elements as a list
        Z_free=jnp.array([2]),  # This is the ionization per species
        mass_density=jnp.array([1]) * ureg.gram / ureg.centimeter**3,
        T_e=2 * ureg.electron_volt / ureg.k_B,  # T_e is the electron temperature.
        # If no T_i (ion temperature) is given, we assume equilibrium of ion and
        # electron temperatures
    )

    # Now, we also have to define a Setup
    # jpu and pint also allow to convert string to quantities with units, as you
    # can see below.
    setup = jaxrts.Setup(
        scattering_angle=ureg("60°"),
        energy=ureg("4700 eV"),
        measured_energy=ureg("4700 eV")
        + jnp.linspace(-100, 40, 500) * ureg.electron_volt,
        instrument=partial(
            jaxrts.instrument_function.instrument_gaussian,
            sigma=ureg("5.0eV") / ureg.hbar / (2 * jnp.sqrt(2 * jnp.log(2))),
        ),
    )

    # Add Models. In the typical way, we use the Chihara decomposition in the code,
    # differentiating 4 contributions to the full XRTS signal, based on the
    # different processes causing them.
    #
    # These processes are
    #
    # free-free scattering
    # bound-free scattering
    # free-bound scattering
    # elastic scattering by electrons, which follow the motion of the ions, closely
    #
    # At a minimum, a user has to set models for these contributions. This is done
    # by adding keys to the plasma state.


    state["ionic scattering"] = jaxrts.models.OnePotentialHNCIonFeat()
    state["free-free scattering"] = jaxrts.models.RPA_DandreaFit()
    state["bound-free scattering"] = jaxrts.models.SchumacherImpulse()
    state["free-bound scattering"] = jaxrts.models.DetailedBalance()

    # Generate the spectrum
    See_tot = state.probe(setup)

    # Plot the result
    plt.plot(
        setup.measured_energy.m_as(ureg.electron_volt),
        See_tot.m_as(ureg.second),
    )
    plt.xlabel("Probed Energy [eV]")
    plt.ylabel("$S_{ee}^{tot}$ [s]")
    plt.title("Be plasma at 2eV and 1g/cc with Z=2")
    plt.show()


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 8.878 seconds)


.. _sphx_glr_download_gen_examples_plot_getting_started.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_getting_started.ipynb <plot_getting_started.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_getting_started.py <plot_getting_started.py>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_