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

.. only:: html

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

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

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

.. _sphx_glr_auto_examples_howto_conversions_plot_E_feflowlib_H_simulation.py:


Feflowlib: Hydraulic model - conversion and simulation
======================================================

.. sectionauthor:: Julian Heinze (Helmholtz Centre for Environmental Research GmbH - UFZ)

In this example we show how a simple flow/hydraulic FEFLOW model can be converted to a pyvista.UnstructuredGrid and then
be simulated in OGS.

.. GENERATED FROM PYTHON SOURCE LINES 12-13

0. Necessary imports

.. GENERATED FROM PYTHON SOURCE LINES 13-34

.. code-block:: Python

    import tempfile
    import xml.etree.ElementTree as ET
    from pathlib import Path

    import ifm_contrib as ifm
    import numpy as np
    import pyvista as pv

    import ogstools as ogs
    from ogstools.examples import feflow_model_box_Neumann
    from ogstools.feflowlib import (
        convert_properties_mesh,
        extract_cell_boundary_conditions,
        setup_prj_file,
        steady_state_diffusion,
    )
    from ogstools.feflowlib.tools import (
        extract_point_boundary_conditions,
        get_material_properties,
    )








.. GENERATED FROM PYTHON SOURCE LINES 35-37

1. Load a FEFLOW model (.fem) as a FEFLOW document, convert and save it. More details on
how the conversion function works can be found here: :py:mod:`ogstools.feflowlib.convert_properties_mesh`.

.. GENERATED FROM PYTHON SOURCE LINES 37-52

.. code-block:: Python

    feflow_model = ifm.loadDocument(str(feflow_model_box_Neumann))
    pyvista_mesh = convert_properties_mesh(feflow_model)

    pv.global_theme.colorbar_orientation = "vertical"
    pyvista_mesh.plot(
        show_edges=True,
        off_screen=True,
        scalars="P_HEAD",
        cpos=[0, 1, 0.5],
        scalar_bar_args={"position_x": 0.1, "position_y": 0.25},
    )
    print(pyvista_mesh)
    temp_dir = Path(tempfile.mkdtemp("feflow_test_simulation"))
    feflow_mesh_file = temp_dir / "boxNeumann.vtu"
    pyvista_mesh.save(feflow_mesh_file)







.. tab-set::



   .. tab-item:: Static Scene



            
     .. image-sg:: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_001.png
        :alt: plot E feflowlib H simulation
        :srcset: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_001.png
        :class: sphx-glr-single-img
     


   .. tab-item:: Interactive Scene



       .. offlineviewer:: /builds/ogs/tools/ogstools/docs/auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_001.vtksz



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

 .. code-block:: none

    UnstructuredGrid (0x7cd473c18220)
      N Cells:    11462
      N Points:   6768
      X Bounds:   0.000e+00, 1.000e+02
      Y Bounds:   0.000e+00, 1.000e+02
      Z Bounds:   -1.000e+02, 0.000e+00
      N Arrays:   23




.. GENERATED FROM PYTHON SOURCE LINES 53-54

2. Extract the point conditions (see: :py:mod:`ogstools.feflowlib.extract_point_boundary_conditions`).

.. GENERATED FROM PYTHON SOURCE LINES 54-69

.. code-block:: Python

    point_BC_dict = extract_point_boundary_conditions(temp_dir, pyvista_mesh)
    # Since there can be multiple point boundary conditions on the bulk mesh,
    # they are saved and plotted iteratively.
    plotter = pv.Plotter(shape=(len(point_BC_dict), 1))
    for i, (path, boundary_condition) in enumerate(point_BC_dict.items()):
        boundary_condition.save(path)
        plotter.subplot(i, 0)
        plotter.add_mesh(boundary_condition, scalars=Path(path).stem)
    plotter.show()
    path_topsurface, topsurface = extract_cell_boundary_conditions(
        feflow_mesh_file, pyvista_mesh
    )
    # On the topsurface can be cell based boundary condition.
    # The boundary conditions on the topsurface of the model are required for generalization.
    topsurface.save(path_topsurface)







.. tab-set::



   .. tab-item:: Static Scene



            
     .. image-sg:: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_002.png
        :alt: plot E feflowlib H simulation
        :srcset: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_002.png
        :class: sphx-glr-single-img
     


   .. tab-item:: Interactive Scene



       .. offlineviewer:: /builds/ogs/tools/ogstools/docs/auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_002.vtksz






.. GENERATED FROM PYTHON SOURCE LINES 70-71

3. Setup a prj-file (see: :py:mod:`ogstools.feflowlib.setup_prj_file`) to run a OGS-simulation.

.. GENERATED FROM PYTHON SOURCE LINES 71-88

.. code-block:: Python

    path_prjfile = feflow_mesh_file.with_suffix(".prj")
    prj = ogs.Project(output_file=path_prjfile)
    # Get the template prj-file configurations for a steady state diffusion process
    ssd_model = steady_state_diffusion(temp_dir / "sim_boxNeumann", prj)
    # Include the mesh specific configurations to the template.
    model = setup_prj_file(
        bulk_mesh_path=feflow_mesh_file,
        mesh=pyvista_mesh,
        material_properties=get_material_properties(pyvista_mesh, "P_CONDX"),
        process="steady state diffusion",
        model=ssd_model,
    )
    # The model must be written before it can be run.
    model.write_input(path_prjfile)
    # Simply print the prj-file as an example.
    model_prjfile = ET.parse(path_prjfile)
    ET.dump(model_prjfile)




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

 .. code-block:: none

    <OpenGeoSysProject>
        <meshes>
            <mesh>boxNeumann.vtu</mesh>
            <mesh>topsurface_boxNeumann.vtu</mesh>
            <mesh>P_BC_FLOW.vtu</mesh>
            <mesh>P_BCFLOW_2ND.vtu</mesh>
        </meshes>
        <processes>
            <process>
                <name>SteadyStateDiffusion</name>
                <type>STEADY_STATE_DIFFUSION</type>
                <integration_order>2</integration_order>
                <secondary_variables>
                    <secondary_variable internal_name="darcy_velocity" output_name="v" />
                </secondary_variables>
                <process_variables>
                    <process_variable>HEAD_OGS</process_variable>
                </process_variables>
            </process>
        </processes>
        <media>
            <medium id="0">
                <properties>
                    <property>
                        <name>diffusion</name>
                        <type>Constant</type>
                        <value>1.1574074074074073e-05</value>
                    </property>
                    <property>
                        <name>reference_temperature</name>
                        <type>Constant</type>
                        <value>293.15</value>
                    </property>
                </properties>
            </medium>
        </media>
        <time_loop>
            <processes>
                <process ref="SteadyStateDiffusion">
                    <nonlinear_solver>basic_picard</nonlinear_solver>
                    <convergence_criterion>
                        <type>DeltaX</type>
                        <norm_type>NORM2</norm_type>
                        <abstol>1e-15</abstol>
                    </convergence_criterion>
                    <time_discretization>
                        <type>BackwardEuler</type>
                    </time_discretization>
                    <time_stepping>
                        <type>SingleStep</type>
                    </time_stepping>
                </process>
            </processes>
            <output>
                <type>VTK</type>
                <prefix>/tmp/tmpskv4rql7feflow_test_simulation/sim_boxNeumann</prefix>
                <timesteps>
                    <pair>
                        <repeat>1</repeat>
                        <each_steps>1</each_steps>
                    </pair>
                </timesteps>
                <variables />
            </output>
        </time_loop>
        <parameters>
            <parameter>
                <name>p0</name>
                <type>Constant</type>
                <value>0</value>
            </parameter>
            <parameter>
                <name>P_BC_FLOW</name>
                <type>MeshNode</type>
                <mesh>P_BC_FLOW</mesh>
                <field_name>P_BC_FLOW</field_name>
            </parameter>
            <parameter>
                <name>P_BCFLOW_2ND</name>
                <type>MeshNode</type>
                <mesh>P_BCFLOW_2ND</mesh>
                <field_name>P_BCFLOW_2ND</field_name>
            </parameter>
        </parameters>
        <process_variables>
            <process_variable>
                <name>HEAD_OGS</name>
                <components>1</components>
                <order>1</order>
                <initial_condition>p0</initial_condition>
                <boundary_conditions>
                    <boundary_condition>
                        <type>Dirichlet</type>
                        <mesh>P_BC_FLOW</mesh>
                        <parameter>P_BC_FLOW</parameter>
                    </boundary_condition>
                    <boundary_condition>
                        <type>Neumann</type>
                        <mesh>P_BCFLOW_2ND</mesh>
                        <parameter>P_BCFLOW_2ND</parameter>
                    </boundary_condition>
                </boundary_conditions>
            </process_variable>
        </process_variables>
        <nonlinear_solvers>
            <nonlinear_solver>
                <name>basic_picard</name>
                <type>Picard</type>
                <max_iter>10</max_iter>
                <linear_solver>general_linear_solver</linear_solver>
            </nonlinear_solver>
        </nonlinear_solvers>
        <linear_solvers>
            <linear_solver>
                <name>general_linear_solver</name>
                <lis>-i cg -p jacobi -tol 1e-6 -maxiter 100000</lis>
                <eigen>
                    <solver_type>CG</solver_type>
                    <precon_type>DIAGONAL</precon_type>
                    <max_iteration_step>100000</max_iteration_step>
                    <error_tolerance>1e-6</error_tolerance>
                </eigen>
                <petsc>
                    <prefix>sd</prefix>
                    <parameters>-sd_ksp_type cg  -sd_pc_type bjacobi -sd_ksp_rtol 1e-16 -sd_ksp_max_it 10000</parameters>
                </petsc>
            </linear_solver>
        </linear_solvers>
    </OpenGeoSysProject>




.. GENERATED FROM PYTHON SOURCE LINES 89-90

4. Run the model

.. GENERATED FROM PYTHON SOURCE LINES 90-91

.. code-block:: Python

    model.run_model(logfile=temp_dir / "out.log")




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

 .. code-block:: none

    OGS finished with project file /tmp/tmpskv4rql7feflow_test_simulation/boxNeumann.prj.
    Execution took 0.3034629821777344 s
    Project file written to output.




.. GENERATED FROM PYTHON SOURCE LINES 92-93

5. Read the results and plot them.

.. GENERATED FROM PYTHON SOURCE LINES 93-107

.. code-block:: Python

    ms = ogs.MeshSeries(temp_dir / "sim_boxNeumann.pvd")
    # Read the last timestep:
    ogs_sim_res = ms.mesh(ms.timesteps[-1])
    """
    It is also possible to read the file directly with pyvista:
    ogs_sim_res = pv.read(temp_dir / "sim_boxNeumann_ts_1_t_1.000000.vtu")
    """
    ogs_sim_res.plot(
        show_edges=True,
        off_screen=True,
        scalars="HEAD_OGS",
        cpos=[0, 1, 0.5],
        scalar_bar_args={"position_x": 0.1, "position_y": 0.25},
    )







.. tab-set::



   .. tab-item:: Static Scene



            
     .. image-sg:: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_003.png
        :alt: plot E feflowlib H simulation
        :srcset: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_003.png
        :class: sphx-glr-single-img
     


   .. tab-item:: Interactive Scene



       .. offlineviewer:: /builds/ogs/tools/ogstools/docs/auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_003.vtksz






.. GENERATED FROM PYTHON SOURCE LINES 108-109

5.1 Plot the hydraulic head simulated in OGS with :py:mod:`ogstools.plot.contourf`.

.. GENERATED FROM PYTHON SOURCE LINES 109-115

.. code-block:: Python

    head = ogs.variables.Scalar(
        data_name="HEAD_OGS", data_unit="m", output_unit="m"
    )
    fig = ogs.plot.contourf(ogs_sim_res.slice(normal="z", origin=[50, 50, 0]), head)





.. image-sg:: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_004.png
   :alt: plot E feflowlib H simulation
   :srcset: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_004.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 116-117

6. Calculate the difference to the FEFLOW simulation and plot it.

.. GENERATED FROM PYTHON SOURCE LINES 117-126

.. code-block:: Python

    diff = pyvista_mesh["P_HEAD"] - ogs_sim_res["HEAD_OGS"]
    pyvista_mesh["diff_HEAD"] = diff
    pyvista_mesh.plot(
        show_edges=True,
        off_screen=True,
        scalars="diff_HEAD",
        cpos=[0, 1, 0.5],
        scalar_bar_args={"position_x": 0.1, "position_y": 0.25},
    )







.. tab-set::



   .. tab-item:: Static Scene



            
     .. image-sg:: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_005.png
        :alt: plot E feflowlib H simulation
        :srcset: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_005.png
        :class: sphx-glr-single-img
     


   .. tab-item:: Interactive Scene



       .. offlineviewer:: /builds/ogs/tools/ogstools/docs/auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_005.vtksz






.. GENERATED FROM PYTHON SOURCE LINES 127-129

6.1 Plot the differences in the hydraulic head with :py:mod:`ogstools.plot.contourf`.
Slices are taken along the z-axis.

.. GENERATED FROM PYTHON SOURCE LINES 129-137

.. code-block:: Python

    diff_head = ogs.variables.Scalar(
        data_name="diff_HEAD", data_unit="m", output_unit="m"
    )
    slices = np.reshape(list(pyvista_mesh.slice_along_axis(n=4, axis="z")), (2, 2))
    fig = ogs.plot.contourf(slices, diff_head)
    for ax, slice in zip(fig.axes, np.ravel(slices), strict=False):
        ax.set_title(f"z = {slice.center[2]:.1f} {ms.spatial_output_unit}")




.. image-sg:: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_006.png
   :alt: z = -99.0 m, z = -66.3 m, z = -33.7 m, z = -1.0 m
   :srcset: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_006.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 138-139

Slices are taken along the y-axis.

.. GENERATED FROM PYTHON SOURCE LINES 139-143

.. code-block:: Python

    slices = np.reshape(list(pyvista_mesh.slice_along_axis(n=4, axis="y")), (2, 2))
    fig = ogs.plot.contourf(slices, diff_head)
    for ax, slice in zip(fig.axes, np.ravel(slices), strict=False):
        ax.set_title(f"y = {slice.center[1]:.1f} {ms.spatial_output_unit}")



.. image-sg:: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_007.png
   :alt: y = 1.0 m, y = 33.7 m, y = 66.3 m, y = 99.0 m
   :srcset: /auto_examples/howto_conversions/images/sphx_glr_plot_E_feflowlib_H_simulation_007.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 3.755 seconds)


.. _sphx_glr_download_auto_examples_howto_conversions_plot_E_feflowlib_H_simulation.py:

.. only:: html

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

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

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

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

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

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

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