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

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

.. _sphx_glr_auto_examples_howto_feflowlib_plot_simulation.py:


How to convert a FEFLOW model and simulate it in OGS.
=====================================================

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

In this example we show how a simple 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 13-33

.. code-block:: default

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

    import ifm_contrib as ifm
    from ogs6py import ogs
    from pyvista import read

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








.. GENERATED FROM PYTHON SOURCE LINES 34-35

1. Load a FEFLOW model (.fem) as a FEFLOW document and convert it.

.. GENERATED FROM PYTHON SOURCE LINES 35-44

.. code-block:: default

    feflow_model = ifm.loadDocument(path_box_Neumann)
    pyvista_mesh = convert_properties_mesh(feflow_model)
    pyvista_mesh.plot(
        show_edges=True, off_screen=True, scalars="P_HEAD", cpos=[0, 1, 0.5]
    )
    print(pyvista_mesh)
    path_writing = Path(tempfile.mkdtemp("feflow_test_simulation"))
    path_mesh = path_writing / "boxNeumann.vtu"
    pyvista_mesh.save(str(path_mesh))



.. image-sg:: /auto_examples/howto_feflowlib/images/sphx_glr_plot_simulation_001.png
   :alt: plot simulation
   :srcset: /auto_examples/howto_feflowlib/images/sphx_glr_plot_simulation_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    UnstructuredGrid (0x7f59355e1880)
      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 45-46

2. Extract the point and cell boundary conditions and write them to a temporary directory.

.. GENERATED FROM PYTHON SOURCE LINES 46-58

.. code-block:: default

    point_BC_dict = extract_point_boundary_conditions(path_writing, pyvista_mesh)
    # Since there can be multiple point boundary conditions on the bulk mesh,
    # they are saved and plotted iteratively.
    for path, boundary_condition in point_BC_dict.items():
        boundary_condition.save(path)
        boundary_condition.plot()
    path_topsurface, topsurface = extract_cell_boundary_conditions(
        path_mesh, 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)



.. rst-class:: sphx-glr-horizontal


    *

      .. image-sg:: /auto_examples/howto_feflowlib/images/sphx_glr_plot_simulation_002.png
          :alt: plot simulation
          :srcset: /auto_examples/howto_feflowlib/images/sphx_glr_plot_simulation_002.png
          :class: sphx-glr-multi-img

    *

      .. image-sg:: /auto_examples/howto_feflowlib/images/sphx_glr_plot_simulation_003.png
          :alt: plot simulation
          :srcset: /auto_examples/howto_feflowlib/images/sphx_glr_plot_simulation_003.png
          :class: sphx-glr-multi-img





.. GENERATED FROM PYTHON SOURCE LINES 59-60

3. Setup a prj-file to run a OGS-simulation

.. GENERATED FROM PYTHON SOURCE LINES 60-81

.. code-block:: default

    path_prjfile = str(path_mesh.with_suffix(".prj"))
    prjfile = ogs.OGS(PROJECT_FILE=str(path_prjfile))
    # Get the template prj-file configurations for a steady state diffusion process
    model = steady_state_diffusion(
        path_writing / "sim_boxNeumann",
        prjfile,
    )
    # Include the mesh specific configurations to the template.
    model = setup_prj_file(
        path_mesh,
        pyvista_mesh,
        get_material_properties(pyvista_mesh, "P_CONDX"),
        "steady state diffusion",
        model,
    )
    # The model must be written before it can be run.
    model.write_input(str(path_prjfile))
    # Simply print the prj-file as an example.
    read_model = ET.parse(str(path_prjfile))
    root = read_model.getroot()
    ET.dump(root)




.. 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/tmpiepoz_brfeflow_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>
            <parameter>
                <name>P_IOFLOW</name>
                <type>MeshElement</type>
                <mesh>topsurface_boxNeumann</mesh>
                <field_name>P_IOFLOW</field_name>
            </parameter>
            <parameter>
                <name>P_SOUF</name>
                <type>MeshElement</type>
                <mesh>topsurface_boxNeumann</mesh>
                <field_name>P_SOUF</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_condition>
                        <type>Neumann</type>
                        <mesh>topsurface_boxNeumann</mesh>
                        <parameter>P_IOFLOW</parameter>
                    </boundary_condition>
                </boundary_conditions>
                <source_terms>
                    <source_term>
                        <type>Volumetric</type>
                        <mesh>topsurface_boxNeumann</mesh>
                        <parameter>P_SOUF</parameter>
                    </source_term>
                </source_terms>
            </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 82-83

4. Run the model

.. GENERATED FROM PYTHON SOURCE LINES 83-84

.. code-block:: default

    model.run_model(logfile=str(path_writing / "out.log"))




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

 .. code-block:: none

    OGS finished with project file /tmp/tmpiepoz_brfeflow_test_simulation/boxNeumann.prj.
    Execution took 0.29024648666381836 s




.. GENERATED FROM PYTHON SOURCE LINES 85-86

5. Read the results and plot them.

.. GENERATED FROM PYTHON SOURCE LINES 86-91

.. code-block:: default

    ogs_sim_res = read(str(path_writing / "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]
    )




.. image-sg:: /auto_examples/howto_feflowlib/images/sphx_glr_plot_simulation_004.png
   :alt: plot simulation
   :srcset: /auto_examples/howto_feflowlib/images/sphx_glr_plot_simulation_004.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 92-93

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

.. GENERATED FROM PYTHON SOURCE LINES 93-98

.. code-block:: default

    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]
    )



.. image-sg:: /auto_examples/howto_feflowlib/images/sphx_glr_plot_simulation_005.png
   :alt: plot simulation
   :srcset: /auto_examples/howto_feflowlib/images/sphx_glr_plot_simulation_005.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 1.269 seconds)


.. _sphx_glr_download_auto_examples_howto_feflowlib_plot_simulation.py:

.. only:: html

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




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

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

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

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