.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/co2_leakage_along_a_fault/4_import_and_visualize_simulation_outputs_in_pyvista.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_co2_leakage_along_a_fault_4_import_and_visualize_simulation_outputs_in_pyvista.py>`
        to download the full example code

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

.. _sphx_glr_examples_co2_leakage_along_a_fault_4_import_and_visualize_simulation_outputs_in_pyvista.py:


Import and visualize simulation outputs in PyVista
==================================================

Once the TOUGH simulation has ended, there is not much things left to do with :mod:`toughio`. We can either:

-   Run the command :code:`toughio-export OUTPUT_ELEME.csv -m mesh.pickle` and drag-and-drop the generated VTK file in a compatible visualization software (e.g., ParaView),

.. image:: ../../figures/co2_leakage_along_a_fault_paraview.png

-   Import the output file *OUTPUT_ELEME.csv* in Python using :mod:`toughio` (two-liners) and do whatever post-processing we want and need.

This example briefly shows how to import TOUGH output file using :mod:`toughio` and how to visualize it with :mod:`pyvista` (adapted from :mod:`pyvista`'s `documentation <https://docs.pyvista.org/>`__).

.. GENERATED FROM PYTHON SOURCE LINES 18-19

First, we unpickle the mesh file and import the last time step of the output file (`OUTPUT_ELEME.csv` in TOUGH3, `OUTPUT` in TOUGH2).

.. GENERATED FROM PYTHON SOURCE LINES 19-25

.. code-block:: Python


    import toughio

    mesh = toughio.read_mesh("mesh.pickle")
    mesh.read_output("OUTPUT_ELEME.csv", time_step=-1)








.. GENERATED FROM PYTHON SOURCE LINES 28-29

Once output data have been imported, we can simply call the method :meth:`toughio.Mesh.to_pyvista` to convert the mesh to a :class:`pyvista.UnstructuredGrid` object that can be processed by :mod:`pyvista`.

.. GENERATED FROM PYTHON SOURCE LINES 29-65

.. code-block:: Python


    import pyvista
    pyvista.set_plot_theme("document")

    p = pyvista.Plotter(window_size=(1000, 1000))
    p.add_mesh(
        mesh.to_pyvista(),
        scalars="SAT_G",
        cmap="viridis_r",
        clim=(0.0, 1.0),
        n_colors=20,
        show_edges=False,
        edge_color=(0.5, 0.5, 0.5),
        scalar_bar_args={
            "title": "Gas saturation",
            "position_y": 0.01,
            "vertical": False,
            "n_labels": 6,
            "fmt": "%.1f",
            "title_font_size": 20,
            "font_family": "arial",
            "shadow": True,
        },
    )
    p.show_grid(
        show_xaxis=True,
        show_yaxis=False,
        show_zaxis=True,
        xlabel="Distance (m)",
        zlabel="Elevation (m)",
        ticks="outside",
        font_family="arial",
    )
    p.view_xz()
    p.show()




.. image-sg:: /examples/co2_leakage_along_a_fault/images/sphx_glr_4_import_and_visualize_simulation_outputs_in_pyvista_001.png
   :alt: 4 import and visualize simulation outputs in pyvista
   :srcset: /examples/co2_leakage_along_a_fault/images/sphx_glr_4_import_and_visualize_simulation_outputs_in_pyvista_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pyvista/plotting/renderer.py:1456: PyVistaDeprecationWarning: `xlabel` is deprecated. Use `xtitle` instead.
      warnings.warn(
    /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pyvista/plotting/renderer.py:1468: PyVistaDeprecationWarning: `zlabel` is deprecated. Use `ztitle` instead.
      warnings.warn(





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

   **Total running time of the script:** (0 minutes 1.951 seconds)


.. _sphx_glr_download_examples_co2_leakage_along_a_fault_4_import_and_visualize_simulation_outputs_in_pyvista.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: 4_import_and_visualize_simulation_outputs_in_pyvista.ipynb <4_import_and_visualize_simulation_outputs_in_pyvista.ipynb>`

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

      :download:`Download Python source code: 4_import_and_visualize_simulation_outputs_in_pyvista.py <4_import_and_visualize_simulation_outputs_in_pyvista.py>`


.. only:: html

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

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