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

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

.. _sphx_glr_auto_examples_howto_conversions_plot_C_feflowlib_prj.py:


Feflowlib: How to modify the project-file after converting a FEFLOW model.
==========================================================================

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

This example shows how to convert a FEFLOW model and how to modify the corresponding OGS project file and boundary meshes after conversion.

.. GENERATED FROM PYTHON SOURCE LINES 11-12

0. Necessary imports

.. GENERATED FROM PYTHON SOURCE LINES 12-19

.. code-block:: Python

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

    import ogstools as ot
    from ogstools.examples import feflow_model_2D_CT_t_560








.. GENERATED FROM PYTHON SOURCE LINES 20-22

1. Load a FEFLOW model (.fem) as a FeflowModel object to further work it.
During the initialisation, the FEFLOW file is converted.

.. GENERATED FROM PYTHON SOURCE LINES 22-24

.. code-block:: Python

    temp_dir = Path(tempfile.mkdtemp("converted_models"))
    feflow_model = ot.FeflowModel(feflow_model_2D_CT_t_560, temp_dir / "CT_model")







.. GENERATED FROM PYTHON SOURCE LINES 25-26

2. Get the mesh and run the FEFLOW model in OGS.

.. GENERATED FROM PYTHON SOURCE LINES 26-31

.. code-block:: Python

    mesh = feflow_model.mesh
    feflow_model.setup_prj(
        end_time=1e11, time_stepping=[(1, 1e6), (1, 1e8), (1, 1e10)]
    )
    feflow_model.run()




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

 .. code-block:: none

    OGS finished with project file /tmp/tmpxkx0_ojuconverted_models/CT_model.prj.
    Execution took 0.6365079879760742 s
    Project file written to output.




.. GENERATED FROM PYTHON SOURCE LINES 32-33

3. Plot the results.

.. GENERATED FROM PYTHON SOURCE LINES 33-36

.. code-block:: Python

    ms = ot.MeshSeries(temp_dir / "CT_model.pvd")
    ogs_sim_res = ms.mesh(ms.timesteps[-1])
    ot.plot.contourf(ogs_sim_res, "single_species")



.. image-sg:: /auto_examples/howto_conversions/images/sphx_glr_plot_C_feflowlib_prj_001.png
   :alt: plot C feflowlib prj
   :srcset: /auto_examples/howto_conversions/images/sphx_glr_plot_C_feflowlib_prj_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none


    <Figure size 2520x1080 with 2 Axes>



.. GENERATED FROM PYTHON SOURCE LINES 37-39

4. Replace the scalar pore diffusion constant by a tensor to introducec anisotropy.
How to manipulate a prj file also is explained in this example: :ref:`sphx_glr_auto_examples_howto_prjfile_plot_manipulation.py`.

.. GENERATED FROM PYTHON SOURCE LINES 39-48

.. code-block:: Python

    tensor = """
            1e-9 1e-12
            """
    feflow_model.project.replace_phase_property_value(
        mediumid=0, component="single_species", name="pore_diffusion", value=tensor
    )
    feflow_model.save()
    model_prjfile = ET.parse(temp_dir / "CT_model.prj")
    ET.dump(model_prjfile)




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

 .. code-block:: none

    <OpenGeoSysProject>
        <meshes>
            <mesh>CT_model.vtu</mesh>
            <mesh>single_species_P_BC_MASS.vtu</mesh>
        </meshes>
        <processes>
            <process>
                <name>CT</name>
                <type>ComponentTransport</type>
                <coupling_scheme>staggered</coupling_scheme>
                <integration_order>2</integration_order>
                <specific_body_force>0 0</specific_body_force>
                <secondary_variables>
                    <secondary_variable internal_name="darcy_velocity" output_name="v" />
                </secondary_variables>
                <process_variables>
                    <pressure>HEAD_OGS</pressure>
                    <concentration>single_species</concentration>
                </process_variables>
            </process>
        </processes>
        <media>
            <medium id="0">
                <phases>
                    <phase>
                        <type>AqueousLiquid</type>
                        <properties>
                            <property>
                                <name>viscosity</name>
                                <type>Constant</type>
                                <value>1</value>
                            </property>
                            <property>
                                <name>density</name>
                                <type>Constant</type>
                                <value>1</value>
                            </property>
                        </properties>
                        <components>
                            <component>
                                <name>single_species</name>
                                <properties>
                                    <property>
                                        <name>decay_rate</name>
                                        <type>Constant</type>
                                        <value>0.0</value>
                                    </property>
                                    <property>
                                        <name>pore_diffusion</name>
                                        <type>Constant</type>
                                        <value>
            1e-9 1e-12
            </value>
                                    </property>
                                    <property>
                                        <name>retardation_factor</name>
                                        <type>Constant</type>
                                        <value>16441.72737282367</value>
                                    </property>
                                </properties>
                            </component>
                        </components>
                    </phase>
                </phases>
                <properties>
                    <property>
                        <name>porosity</name>
                        <type>Constant</type>
                        <value>0.10999999940395355</value>
                    </property>
                    <property>
                        <name>longitudinal_dispersivity</name>
                        <type>Constant</type>
                        <value>0.0</value>
                    </property>
                    <property>
                        <name>transversal_dispersivity</name>
                        <type>Constant</type>
                        <value>0.0</value>
                    </property>
                    <property>
                        <name>permeability</name>
                        <type>Constant</type>
                        <value>1.1574074074074073e-05</value>
                    </property>
                </properties>
            </medium>
        </media>
        <time_loop>
            <processes>
                <process ref="CT">
                    <nonlinear_solver>basic_picard</nonlinear_solver>
                    <convergence_criterion>
                        <type>DeltaX</type>
                        <norm_type>NORM2</norm_type>
                        <reltol>1e-6</reltol>
                    </convergence_criterion>
                    <time_discretization>
                        <type>BackwardEuler</type>
                    </time_discretization>
                    <time_stepping>
                        <type>FixedTimeStepping</type>
                        <t_initial>0</t_initial>
                        <t_end>100000000000.0</t_end>
                        <timesteps>
                            <pair>
                                <repeat>1</repeat>
                                <delta_t>1000000.0</delta_t>
                            </pair>
                            <pair>
                                <repeat>1</repeat>
                                <delta_t>100000000.0</delta_t>
                            </pair>
                            <pair>
                                <repeat>1</repeat>
                                <delta_t>10000000000.0</delta_t>
                            </pair>
                        </timesteps>
                    </time_stepping>
                </process>
                <process ref="CT">
                    <nonlinear_solver>basic_picard</nonlinear_solver>
                    <convergence_criterion>
                        <type>DeltaX</type>
                        <norm_type>NORM2</norm_type>
                        <reltol>1e-6</reltol>
                    </convergence_criterion>
                    <time_discretization>
                        <type>BackwardEuler</type>
                    </time_discretization>
                    <time_stepping>
                        <type>FixedTimeStepping</type>
                        <t_initial>0</t_initial>
                        <t_end>100000000000.0</t_end>
                        <timesteps>
                            <pair>
                                <repeat>1</repeat>
                                <delta_t>1000000.0</delta_t>
                            </pair>
                            <pair>
                                <repeat>1</repeat>
                                <delta_t>100000000.0</delta_t>
                            </pair>
                            <pair>
                                <repeat>1</repeat>
                                <delta_t>10000000000.0</delta_t>
                            </pair>
                        </timesteps>
                    </time_stepping>
                </process>
            </processes>
            <output>
                <type>VTK</type>
                <prefix>/tmp/tmpxkx0_ojuconverted_models/CT_model</prefix>
                <timesteps>
                    <pair>
                        <repeat>1</repeat>
                        <each_steps>1</each_steps>
                    </pair>
                </timesteps>
                <variables>
                    <variable>single_species</variable>
                    <variable>HEAD_OGS</variable>
                </variables>
                <fixed_output_times>100000000000.0</fixed_output_times>
            </output>
            <global_process_coupling>
                <max_iter>1</max_iter>
                <convergence_criteria>
                    <convergence_criterion>
                        <type>DeltaX</type>
                        <norm_type>NORM2</norm_type>
                        <reltol>1e-10</reltol>
                    </convergence_criterion>
                    <convergence_criterion>
                        <type>DeltaX</type>
                        <norm_type>NORM2</norm_type>
                        <reltol>1e-10</reltol>
                    </convergence_criterion>
                </convergence_criteria>
            </global_process_coupling>
        </time_loop>
        <parameters>
            <parameter>
                <name>C0</name>
                <type>Constant</type>
                <value>0</value>
            </parameter>
            <parameter>
                <name>p0</name>
                <type>Constant</type>
                <value>0</value>
            </parameter>
            <parameter>
                <name>single_species_P_BC_MASS</name>
                <type>MeshNode</type>
                <mesh>single_species_P_BC_MASS</mesh>
                <field_name>single_species_P_BC_MASS</field_name>
            </parameter>
        </parameters>
        <process_variables>
            <process_variable>
                <name>single_species</name>
                <components>1</components>
                <order>1</order>
                <initial_condition>C0</initial_condition>
                <boundary_conditions>
                    <boundary_condition>
                        <type>Dirichlet</type>
                        <mesh>single_species_P_BC_MASS</mesh>
                        <parameter>single_species_P_BC_MASS</parameter>
                    </boundary_condition>
                </boundary_conditions>
            </process_variable>
            <process_variable>
                <name>HEAD_OGS</name>
                <components>1</components>
                <order>1</order>
                <initial_condition>p0</initial_condition>
            </process_variable>
        </process_variables>
        <nonlinear_solvers>
            <nonlinear_solver>
                <name>basic_picard</name>
                <type>Picard</type>
                <max_iter>100</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-10 -maxiter 100000</lis>
                <eigen>
                    <solver_type>CG</solver_type>
                    <precon_type>DIAGONAL</precon_type>
                    <max_iteration_step>100000</max_iteration_step>
                    <error_tolerance>1e-10</error_tolerance>
                </eigen>
            </linear_solver>
        </linear_solvers>
    </OpenGeoSysProject>




.. GENERATED FROM PYTHON SOURCE LINES 49-50

5. Remove some points of the boundary mesh, which is part of the subdomains.

.. GENERATED FROM PYTHON SOURCE LINES 50-55

.. code-block:: Python

    bounds = [0.037, 0.039, 0.003, 0.006, 0, 0]
    new_bc_mesh = feflow_model.subdomains["single_species_P_BC_MASS"].clip_box(
        bounds, invert=False
    )
    feflow_model.subdomains["single_species_P_BC_MASS"] = new_bc_mesh







.. GENERATED FROM PYTHON SOURCE LINES 56-57

6. Run the model.

.. GENERATED FROM PYTHON SOURCE LINES 57-61

.. code-block:: Python

    feflow_model.run(overwrite=True)
    ms = ot.MeshSeries(temp_dir / "CT_model.pvd")
    ogs_sim_res = ms.mesh(ms.timesteps[-1])
    ot.plot.contourf(ogs_sim_res, "single_species")



.. image-sg:: /auto_examples/howto_conversions/images/sphx_glr_plot_C_feflowlib_prj_002.png
   :alt: plot C feflowlib prj
   :srcset: /auto_examples/howto_conversions/images/sphx_glr_plot_C_feflowlib_prj_002.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    OGS finished with project file /tmp/tmpxkx0_ojuconverted_models/CT_model.prj.
    Execution took 0.7029359340667725 s
    Project file written to output.

    <Figure size 2520x1080 with 2 Axes>




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

   **Total running time of the script:** (0 minutes 1.920 seconds)


.. _sphx_glr_download_auto_examples_howto_conversions_plot_C_feflowlib_prj.py:

.. only:: html

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

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

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

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

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

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

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