.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "gen_examples/plot_multi_component.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_multi_component.py>`
        to download the full example code

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

.. _sphx_glr_gen_examples_plot_multi_component.py:


Multi-Species Plasmas
=====================

This example calculates a synthetic spectrum of a CHO plasma.

.. GENERATED FROM PYTHON SOURCE LINES 7-96



.. image-sg:: /gen_examples/images/sphx_glr_plot_multi_component_001.svg
   :alt: A Multicomponent Plasma
   :srcset: /gen_examples/images/sphx_glr_plot_multi_component_001.svg
   :class: sphx-glr-single-img





.. code-block:: Python


    from functools import partial

    import matplotlib.pyplot as plt
    from jax import numpy as jnp

    import jaxrts

    ureg = jaxrts.ureg

    # plt.style.use("science")

    ions = [jaxrts.Element("C"), jaxrts.Element("H"), jaxrts.Element("O")]
    rho = ureg("3g/cc")
    # This helper function can be used to calculate density fractions from number
    # fractions:
    number_fraction = jnp.array([1 / 4, 1 / 2, 1 / 4])
    mass_fraction = jaxrts.helpers.mass_from_number_fraction(number_fraction, ions)

    # Initialize a plasma state with has different temperatures for the electrons
    state = jaxrts.PlasmaState(
        ions=ions,
        Z_free=jnp.array([3.0, 1.0, 5.0]),  # This is the ionization per species
        mass_density=rho * mass_fraction,
        T_e=6 * ureg.electron_volt / ureg.k_B,
        T_i=jnp.array([5, 4, 4.5]) * ureg.electron_volt / ureg.k_B,
    )

    setup = jaxrts.Setup(
        scattering_angle=ureg("150°"),
        energy=ureg("8 keV"),
        measured_energy=jnp.linspace(7.4, 8.2, 500) * ureg.kiloelectron_volt,
        instrument=partial(
            jaxrts.instrument_function.instrument_gaussian,
            sigma=ureg("7.0eV") / ureg.hbar / (2 * jnp.sqrt(2 * jnp.log(2))),
        ),
    )

    # Add the required models

    state["ionic scattering"] = jaxrts.models.OnePotentialHNCIonFeat()
    state["free-free scattering"] = jaxrts.models.RPA_DandreaFit()
    # Models can have arguments:
    state["bound-free scattering"] = jaxrts.models.SchumacherImpulse(r_k=1)
    state["free-bound scattering"] = jaxrts.models.DetailedBalance()

    # Add additional models
    state["ipd"] = jaxrts.models.StewartPyattIPD()

    # Generate the spectrum
    # Here, we evaluate the contributions, individually, with the evaluate method
    See_el = state.evaluate("ionic scattering", setup)
    See_ff = state.evaluate("free-free scattering", setup)
    See_bf = state.evaluate("bound-free scattering", setup)
    See_fb = state.evaluate("free-bound scattering", setup)

    See_tot = See_el + See_bf + See_fb + See_ff

    # Plot the result
    plt.plot(
        setup.measured_energy.m_as(ureg.electron_volt),
        See_tot.m_as(ureg.second),
        lw=3,
        label="total",
    )
    plt.plot(
        setup.measured_energy.m_as(ureg.electron_volt),
        See_ff.m_as(ureg.second),
        ls="dotted",
        label="free-free",
    )
    plt.plot(
        setup.measured_energy.m_as(ureg.electron_volt),
        See_bf.m_as(ureg.second),
        ls="dashed",
        label="bound-free",
    )
    plt.plot(
        setup.measured_energy.m_as(ureg.electron_volt),
        See_fb.m_as(ureg.second),
        ls="dashdot",
        label="free-bound",
    )
    plt.legend()
    plt.xlabel("Probed Energy [eV]")
    plt.ylabel("$S_{ee}$ [s]")
    plt.title("A Multicomponent Plasma")
    plt.tight_layout()
    plt.show()


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

   **Total running time of the script:** (0 minutes 21.442 seconds)


.. _sphx_glr_download_gen_examples_plot_multi_component.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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