.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "api/gallery/photochem/jablonski/plot_01_jablonski_kinetics.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_api_gallery_photochem_jablonski_plot_01_jablonski_kinetics.py>`
        to download the full example code.

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

.. _sphx_glr_api_gallery_photochem_jablonski_plot_01_jablonski_kinetics.py:


Jablonski-diagram excited-state kinetics
===========================================

:func:`~chemistrykit.photochem.systems.jablonski.jablonski_network`
builds the 3-state (S1, T1, S0) Jablonski excited-state decay network as
a :class:`~chemistrykit.kinetics.systems.networks.StoichiometricNetwork`
-- reusing the kinetics domain's general mass-action reaction-network
engine rather than reimplementing rate-equation integration. The
numerical integration is checked here against
:func:`~chemistrykit.photochem.systems.jablonski.jablonski_populations_analytic`'s
closed-form solution.

.. GENERATED FROM PYTHON SOURCE LINES 16-36

.. code-block:: Python

    import matplotlib.pyplot as plt
    import numpy as np

    from chemistrykit.photochem.systems.jablonski import jablonski_network, jablonski_populations_analytic
    from chemistrykit.photochem.visualizers.photochem_plots import plot_state_populations

    kf, kic, kisc, kp, kic_T = 2.0, 1.0, 0.5, 0.3, 0.2
    S1_0 = 1.0

    net = jablonski_network(kf, kic, kisc, kp, kic_T, S1_0=S1_0)
    result = net.integrate((0.0, 15.0), dt=1e-3, method="rk4")

    S1_analytic, T1_analytic, S0_analytic = jablonski_populations_analytic(kf, kic, kisc, kp, kic_T, S1_0, result.t)
    max_error = max(
        np.max(np.abs(result.concentration("S1") - S1_analytic)),
        np.max(np.abs(result.concentration("T1") - T1_analytic)),
        np.max(np.abs(result.concentration("S0") - S0_analytic)),
    )
    print(f"Max deviation between numerical and closed-form populations: {max_error:.2e}")





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Max deviation between numerical and closed-form populations: 4.61e-13




.. GENERATED FROM PYTHON SOURCE LINES 37-43

.. code-block:: Python

    ax = plot_state_populations(result)
    ax.plot(result.t, S1_analytic, "k--", linewidth=1, label="S1 analytic")
    ax.plot(result.t, T1_analytic, "k:", linewidth=1, label="T1 analytic")
    ax.legend()
    plt.tight_layout()




.. image-sg:: /api/gallery/photochem/jablonski/images/sphx_glr_plot_01_jablonski_kinetics_001.png
   :alt: Excited-state population vs. time
   :srcset: /api/gallery/photochem/jablonski/images/sphx_glr_plot_01_jablonski_kinetics_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 44-46

Quantum-yield-relevant quantities: the S1 total decay rate, and the
fraction of excited molecules that ever populate the triplet state.

.. GENERATED FROM PYTHON SOURCE LINES 46-52

.. code-block:: Python

    k_S1_total = kf + kic + kisc
    isc_fraction = kisc / k_S1_total
    print(f"\nTotal S1 decay rate: {k_S1_total:.3f}")
    print(f"Fraction of excited S1 crossing to T1: {isc_fraction:.3f}")

    plt.show()




.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    Total S1 decay rate: 3.500
    Fraction of excited S1 crossing to T1: 0.143





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

   **Total running time of the script:** (0 minutes 0.356 seconds)


.. _sphx_glr_download_api_gallery_photochem_jablonski_plot_01_jablonski_kinetics.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: plot_01_jablonski_kinetics.ipynb <plot_01_jablonski_kinetics.ipynb>`

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

      :download:`Download Python source code: plot_01_jablonski_kinetics.py <plot_01_jablonski_kinetics.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_01_jablonski_kinetics.zip <plot_01_jablonski_kinetics.zip>`


.. only:: html

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

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