.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_user-guide/plot_msh2vtu.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_auto_user-guide_plot_msh2vtu.py>`
        to download the full example code.

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

.. _sphx_glr_auto_user-guide_plot_msh2vtu.py:


Meshes from gmsh (msh2vtu)
==========================

.. sectionauthor:: Florian Zill (Helmholtz Centre for Environmental Research GmbH - UFZ)

Here you find, how you can generate OGS-compatible meshes from a .msh file.
This is accomplished by extracting domain-, boundary- and physical groups
from the gmsh mesh. This requires the mesh entities to be assigned to a physical
group in the gmsh mesh.

.. GENERATED FROM PYTHON SOURCE LINES 14-25

.. code-block:: Python

    from pathlib import Path
    from tempfile import mkdtemp

    import pyvista as pv

    import ogstools as ot
    from ogstools import examples

    model_dir = Path(mkdtemp())
    msh = examples.msh_geolayers_2d








.. GENERATED FROM PYTHON SOURCE LINES 26-36

Conversion
----------

Using :func:`~ogstools.meshlib.gmsh_converter.meshes_from_gmsh` we can
generate unstructured grids from a given .msh file. As OGS wants to have the
MaterialIDs numbered beginning from zero, you usually want to set reindex to
True. The return value is a dict with the mesh names pointing to the
corresponding meshes. Here we print the filenames and the number of cells. For
a purely file based approach, OGSTools also provides `msh2vtu` as a command
line application. Please, call it with `--help` for info about the usage.

.. GENERATED FROM PYTHON SOURCE LINES 38-41

.. code-block:: Python

    meshes = ot.meshes_from_gmsh(filename=msh, reindex=True, log=False)
    print(*[f"{name}: {mesh.n_cells=}" for name, mesh in meshes.items()], sep="\n")





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

 .. code-block:: none


    domain: mesh.n_cells=2520
    physical_group_Left: mesh.n_cells=8
    physical_group_Bottom: mesh.n_cells=120
    physical_group_Right: mesh.n_cells=8
    physical_group_Top: mesh.n_cells=120
    physical_group_SedimentLayer1: mesh.n_cells=69
    physical_group_SedimentLayer2: mesh.n_cells=146
    physical_group_SedimentLayer3: mesh.n_cells=230
    physical_group_RockBed: mesh.n_cells=2075




.. GENERATED FROM PYTHON SOURCE LINES 42-43

Let's plot the domain mesh and mark the subdomains.

.. GENERATED FROM PYTHON SOURCE LINES 45-53

.. code-block:: Python

    domain = meshes["domain"]
    fig = ot.plot.contourf(domain, ot.variables.material_id, show_edges=False)

    style = {"size": 32, "backgroundcolor": "lightgrey", "ha": "center"}
    for name, mesh in meshes.items():
        text_xy = [mesh.center[0], 0.5 * (mesh.center[1] + mesh.bounds[2])]
        fig.axes[0].annotate(name.split("_")[-1], text_xy, **style)




.. image-sg:: /auto_user-guide/images/sphx_glr_plot_msh2vtu_001.png
   :alt: plot msh2vtu
   :srcset: /auto_user-guide/images/sphx_glr_plot_msh2vtu_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 54-60

Note regarding saving
---------------------

If you want to save the meshes to be used in a OGS simulation, make sure
to save the meshes in the following way, so that they are conforming to OGS
standards:

.. GENERATED FROM PYTHON SOURCE LINES 62-64

.. code-block:: Python

    for name, mesh in meshes.items():
        pv.save_meshio(Path(model_dir, name + ".vtu"), mesh)








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

   **Total running time of the script:** (0 minutes 0.585 seconds)


.. _sphx_glr_download_auto_user-guide_plot_msh2vtu.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: plot_msh2vtu.ipynb <plot_msh2vtu.ipynb>`

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

      :download:`Download Python source code: plot_msh2vtu.py <plot_msh2vtu.py>`

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

      :download:`Download zipped: plot_msh2vtu.zip <plot_msh2vtu.zip>`