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

.. only:: html

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

        Click :ref:`here <sphx_glr_download_Tutorials_Export_MOOSE.py>`
        to download the full example code

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

.. _sphx_glr_Tutorials_Export_MOOSE.py:


Export a GemPy Model to MOOSE
=============================

This section briefly describes how to export a GemPy model to get a working input file for MOOSE. 
This example is mainly taken from the tutorial `gempy export MOOSE <https://github.com/cgre-aachen/gempy/blob/master/examples/integrations/gempy_export_MOOSE.py>`_ from the official GemPy repository.
It will guide you through the process of exporting a geological model generated in `GemPy <https://www.gempy.org/>`_ (Tutorial Chapter 1-1 therein) so it is usable as a Mesh
# in the `MOOSE <https://mooseframework.org/>`_ framework.

.. GENERATED FROM PYTHON SOURCE LINES 12-17

Creating a geological model  
---------------------------

The procedure of generating a geological model is presented in detail in `Chapter 1-1 <https://nbviewer.jupyter.org/github/cgre-aachen/gempy/blob/master/notebooks/tutorials/ch1-1_Basics.ipynb>`_ 
of the GemPy tutorials, so it will only be briefly presented here:

.. GENERATED FROM PYTHON SOURCE LINES 19-29

.. code-block:: default

    import gempy as gp
    import matplotlib.pyplot as plt

    geo_model = gp.create_model('tutorial_moose_exp')

    gp.init_data(geo_model, [0,2000., 0,2000., 0,2000.], [50, 50, 80],
                path_o = "../../data/GemPy/simple_fault_model_orientations.csv",
                path_i = "../../data/GemPy/simple_fault_model_points.csv",
                default_values = True)





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

 Out:

 .. code-block:: none

    Active grids: ['regular']

    tutorial_moose_exp  2021-10-27 16:58



.. GENERATED FROM PYTHON SOURCE LINES 30-31

present the units and series

.. GENERATED FROM PYTHON SOURCE LINES 33-36

.. code-block:: default

    geo_model.surfaces







.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <style  type="text/css" >
        #T_511b27e3_3736_11ec_b94d_00e04c6800carow0_col3 {
                background-color:  #015482;
            }    #T_511b27e3_3736_11ec_b94d_00e04c6800carow1_col3 {
                background-color:  #9f0052;
            }    #T_511b27e3_3736_11ec_b94d_00e04c6800carow2_col3 {
                background-color:  #ffbe00;
            }    #T_511b27e3_3736_11ec_b94d_00e04c6800carow3_col3 {
                background-color:  #728f02;
            }    #T_511b27e3_3736_11ec_b94d_00e04c6800carow4_col3 {
                background-color:  #443988;
            }    #T_511b27e3_3736_11ec_b94d_00e04c6800carow5_col3 {
                background-color:  #ff3f20;
            }</style><table id="T_511b27e3_3736_11ec_b94d_00e04c6800ca" ><thead>    <tr>        <th class="blank level0" ></th>        <th class="col_heading level0 col0" >surface</th>        <th class="col_heading level0 col1" >series</th>        <th class="col_heading level0 col2" >order_surfaces</th>        <th class="col_heading level0 col3" >color</th>        <th class="col_heading level0 col4" >id</th>    </tr></thead><tbody>
                    <tr>
                            <th id="T_511b27e3_3736_11ec_b94d_00e04c6800calevel0_row0" class="row_heading level0 row0" >0</th>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow0_col0" class="data row0 col0" >Shale</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow0_col1" class="data row0 col1" >Default series</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow0_col2" class="data row0 col2" >1</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow0_col3" class="data row0 col3" >#015482</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow0_col4" class="data row0 col4" >1</td>
                </tr>
                <tr>
                            <th id="T_511b27e3_3736_11ec_b94d_00e04c6800calevel0_row1" class="row_heading level0 row1" >1</th>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow1_col0" class="data row1 col0" >Sandstone_1</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow1_col1" class="data row1 col1" >Default series</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow1_col2" class="data row1 col2" >2</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow1_col3" class="data row1 col3" >#9f0052</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow1_col4" class="data row1 col4" >2</td>
                </tr>
                <tr>
                            <th id="T_511b27e3_3736_11ec_b94d_00e04c6800calevel0_row2" class="row_heading level0 row2" >2</th>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow2_col0" class="data row2 col0" >Siltstone</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow2_col1" class="data row2 col1" >Default series</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow2_col2" class="data row2 col2" >3</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow2_col3" class="data row2 col3" >#ffbe00</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow2_col4" class="data row2 col4" >3</td>
                </tr>
                <tr>
                            <th id="T_511b27e3_3736_11ec_b94d_00e04c6800calevel0_row3" class="row_heading level0 row3" >3</th>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow3_col0" class="data row3 col0" >Sandstone_2</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow3_col1" class="data row3 col1" >Default series</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow3_col2" class="data row3 col2" >4</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow3_col3" class="data row3 col3" >#728f02</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow3_col4" class="data row3 col4" >4</td>
                </tr>
                <tr>
                            <th id="T_511b27e3_3736_11ec_b94d_00e04c6800calevel0_row4" class="row_heading level0 row4" >4</th>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow4_col0" class="data row4 col0" >Main_Fault</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow4_col1" class="data row4 col1" >Default series</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow4_col2" class="data row4 col2" >5</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow4_col3" class="data row4 col3" >#443988</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow4_col4" class="data row4 col4" >5</td>
                </tr>
                <tr>
                            <th id="T_511b27e3_3736_11ec_b94d_00e04c6800calevel0_row5" class="row_heading level0 row5" >5</th>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow5_col0" class="data row5 col0" >basement</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow5_col1" class="data row5 col1" >Basement</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow5_col2" class="data row5 col2" >1</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow5_col3" class="data row5 col3" >#ff3f20</td>
                            <td id="T_511b27e3_3736_11ec_b94d_00e04c6800carow5_col4" class="data row5 col4" >6</td>
                </tr>
        </tbody></table>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 37-38

combine units in series and make two series, as the fault needs its own

.. GENERATED FROM PYTHON SOURCE LINES 38-46

.. code-block:: default

    gp.map_series_to_surfaces(geo_model,
                             {"Fault_Series" : 'Main_Fault',
                              "Strat_Series" : ('Sandstone_2', 'Siltstone', 'Shale', 'Sandstone_1', 'basement')},
                             remove_unused_series=True)

    # set the fault series to be fault object
    geo_model.set_is_fault(['Fault_Series'], change_color=False)






.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <table border="1" class="dataframe">
      <thead>
        <tr style="text-align: right;">
          <th></th>
          <th>order_series</th>
          <th>BottomRelation</th>
          <th>isActive</th>
          <th>isFault</th>
          <th>isFinite</th>
        </tr>
      </thead>
      <tbody>
        <tr>
          <th>Fault_Series</th>
          <td>1</td>
          <td>Fault</td>
          <td>True</td>
          <td>True</td>
          <td>False</td>
        </tr>
        <tr>
          <th>Strat_Series</th>
          <td>2</td>
          <td>Erosion</td>
          <td>True</td>
          <td>False</td>
          <td>False</td>
        </tr>
      </tbody>
    </table>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 47-48

check whether series were assigned correctly

.. GENERATED FROM PYTHON SOURCE LINES 48-51

.. code-block:: default


    geo_model.surfaces






.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <style  type="text/css" >
        #T_513a655c_3736_11ec_b53f_00e04c6800carow0_col3 {
                background-color:  #443988;
            }    #T_513a655c_3736_11ec_b53f_00e04c6800carow1_col3 {
                background-color:  #015482;
            }    #T_513a655c_3736_11ec_b53f_00e04c6800carow2_col3 {
                background-color:  #9f0052;
            }    #T_513a655c_3736_11ec_b53f_00e04c6800carow3_col3 {
                background-color:  #ffbe00;
            }    #T_513a655c_3736_11ec_b53f_00e04c6800carow4_col3 {
                background-color:  #728f02;
            }    #T_513a655c_3736_11ec_b53f_00e04c6800carow5_col3 {
                background-color:  #ff3f20;
            }</style><table id="T_513a655c_3736_11ec_b53f_00e04c6800ca" ><thead>    <tr>        <th class="blank level0" ></th>        <th class="col_heading level0 col0" >surface</th>        <th class="col_heading level0 col1" >series</th>        <th class="col_heading level0 col2" >order_surfaces</th>        <th class="col_heading level0 col3" >color</th>        <th class="col_heading level0 col4" >id</th>    </tr></thead><tbody>
                    <tr>
                            <th id="T_513a655c_3736_11ec_b53f_00e04c6800calevel0_row0" class="row_heading level0 row0" >4</th>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow0_col0" class="data row0 col0" >Main_Fault</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow0_col1" class="data row0 col1" >Fault_Series</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow0_col2" class="data row0 col2" >1</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow0_col3" class="data row0 col3" >#443988</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow0_col4" class="data row0 col4" >1</td>
                </tr>
                <tr>
                            <th id="T_513a655c_3736_11ec_b53f_00e04c6800calevel0_row1" class="row_heading level0 row1" >0</th>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow1_col0" class="data row1 col0" >Shale</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow1_col1" class="data row1 col1" >Strat_Series</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow1_col2" class="data row1 col2" >1</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow1_col3" class="data row1 col3" >#015482</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow1_col4" class="data row1 col4" >2</td>
                </tr>
                <tr>
                            <th id="T_513a655c_3736_11ec_b53f_00e04c6800calevel0_row2" class="row_heading level0 row2" >1</th>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow2_col0" class="data row2 col0" >Sandstone_1</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow2_col1" class="data row2 col1" >Strat_Series</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow2_col2" class="data row2 col2" >2</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow2_col3" class="data row2 col3" >#9f0052</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow2_col4" class="data row2 col4" >3</td>
                </tr>
                <tr>
                            <th id="T_513a655c_3736_11ec_b53f_00e04c6800calevel0_row3" class="row_heading level0 row3" >2</th>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow3_col0" class="data row3 col0" >Siltstone</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow3_col1" class="data row3 col1" >Strat_Series</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow3_col2" class="data row3 col2" >3</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow3_col3" class="data row3 col3" >#ffbe00</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow3_col4" class="data row3 col4" >4</td>
                </tr>
                <tr>
                            <th id="T_513a655c_3736_11ec_b53f_00e04c6800calevel0_row4" class="row_heading level0 row4" >3</th>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow4_col0" class="data row4 col0" >Sandstone_2</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow4_col1" class="data row4 col1" >Strat_Series</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow4_col2" class="data row4 col2" >4</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow4_col3" class="data row4 col3" >#728f02</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow4_col4" class="data row4 col4" >5</td>
                </tr>
                <tr>
                            <th id="T_513a655c_3736_11ec_b53f_00e04c6800calevel0_row5" class="row_heading level0 row5" >5</th>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow5_col0" class="data row5 col0" >basement</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow5_col1" class="data row5 col1" >Strat_Series</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow5_col2" class="data row5 col2" >5</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow5_col3" class="data row5 col3" >#ff3f20</td>
                            <td id="T_513a655c_3736_11ec_b53f_00e04c6800carow5_col4" class="data row5 col4" >6</td>
                </tr>
        </tbody></table>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 52-55

Model generation
----------------
After loading in the data, we set it up for interpolation and compute the model.

.. GENERATED FROM PYTHON SOURCE LINES 55-66

.. code-block:: default


    gp.set_interpolator(geo_model,
                             compile_theano=True,
                             theano_optimizer='fast_compile',
                             verbose=[])

    gp.compute_model(geo_model, compute_mesh=False)

    # sphinx_gallery_thumbnail_number = 1
    gp.plot_2d(geo_model, direction='y', cell_number=45,show_data=False, show_boundaries=False, show_topography=False)




.. image:: /Tutorials/images/sphx_glr_Export_MOOSE_001.png
    :alt: Cell Number: 45 Direction: y
    :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    Setting kriging parameters to their default values.
    Compiling theano function...
    Level of Optimization:  fast_compile
    Device:  cpu
    Precision:  float64
    Number of faults:  1
    Compilation Done!
    Kriging values: 
                      values
    range            3464.1
    $C_o$            285714
    drift equations  [3, 3]

    <gempy.plot.visualization_2d.Plot2D object at 0x00000218013CCAC0>



.. GENERATED FROM PYTHON SOURCE LINES 67-72

Exporting the Model to MOOSE
----------------------------

The voxel-model above already is the same as a model discretized in a hexahedral grid, so my immediately be used as input in a simulation tool, e.g. `MOOSE <https://mooseframework.org/>`_. 
For this, we need to access to the unit IDs assigned to each voxel in GemPy. The array containing these IDs is called `lith_block`. 

.. GENERATED FROM PYTHON SOURCE LINES 72-76

.. code-block:: default


    ids = geo_model.solutions.lith_block
    print(ids)





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

 Out:

 .. code-block:: none

    [6. 6. 6. ... 2. 2. 2.]




.. GENERATED FROM PYTHON SOURCE LINES 77-81

This array has the shape of `(x,)` and would be immediately useful, if GemPy and the chosen simulation code would _populate_ a grid in the same way. Of course, however, that is not the case. 
This is why we have to restructure the `lith_block` array, so it can be read correctly by MOOSE.

The model resolution is extracted, so is the model extent:

.. GENERATED FROM PYTHON SOURCE LINES 81-87

.. code-block:: default


    nx, ny, nz = geo_model.grid.regular_grid.resolution

    # model extent
    xmin, xmax, ymin, ymax, zmin, zmax = geo_model.grid.regular_grid.extent








.. GENERATED FROM PYTHON SOURCE LINES 88-90

These two parameters are important to, a) restructure `lith_block`, and b) write the input file for MOOSE correctly. 
For a), we need to reshape `lith_block` again to its three dimensions and _re-flatten_ it in a _MOOSE-conform_ way, i.e. reshape to 3D array and then flattened:

.. GENERATED FROM PYTHON SOURCE LINES 90-95

.. code-block:: default


    units = ids.reshape((nx, ny, nz))
    # flatten MOOSE conform
    units = units.flatten('F')








.. GENERATED FROM PYTHON SOURCE LINES 96-133

The importance of `nx, ny, nz` is apparent from the cell above. But what about `xmin`, ..., `zmax`?  
A MOOSE input-file for mesh generation has the following syntax:  

.. code-block:: python  

   [MeshGenerators] 
     [./gmg] 
       type = GeneratedMeshGenerator 
       dim = 3 
       nx = 50 
       ny = 50 
       nz = 80 
       xmin = 0.0 
       xmax = 2000.0 
       yim = 0.0 
       ymax = 2000.0 
       zmin = 0.0 
       zmax = 2000.0 
       block_id = '1 2 3 4 5 6' 
       block_name = 'Main_Fault Sandstone_2 Siltstone Shale Sandstone_1 basement' 
     [../]

     [./subdomains]
       type = ElementSubdomainIDGenerator 
       input = gmg 
       subdomain_ids = ' ' # here you paste the transformed lith_block vector 
     [../]
   []

   [Mesh]
     type = MeshGeneratorMesh 
   []


So these parameters are required inputs in the `[MeshGenerators]` object in the MOOSE input file. `GemPy` has a method to directly create such an input file, stored in `gempy.utils.export.py`.  

The following cell shows how to call the method:

.. GENERATED FROM PYTHON SOURCE LINES 133-137

.. code-block:: default


    import gempy.utils.export as export
    export.export_moose_input(geo_model, path='')





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

 Out:

 .. code-block:: none

    Successfully exported geological model as moose input to ./




.. GENERATED FROM PYTHON SOURCE LINES 138-163

This method automatically stores a file `geo_model_units_moose_input.i` at the specified path. Either this input file could be extended with parameters to directly run a simulation, or it is used just for creating a mesh. In the latter case, the next step would be, to run the compiled MOOSE executable witch the optional flag `--mesh-only`.  

E.g. with using the `PorousFlow module <https://mooseframework.inl.gov/modules/porous_flow/>`_:

```bash
$path_to_moose/moose/modules/porous_flow/porous_flow-opt -i pct_voxel_mesh.i --mesh-only
```

How to compile MOOSE is described in their `documentation <https://mooseframework.inl.gov/getting_started/index.html>`_. 

The now generated mesh with the name `geo_model_units_moose_input_in.e` can be used as input for another MOOSE input file, which contains the main simulation parameters. 
To call the file with the grid, the following part has to be added in the MOOSE simulation input file:  

.. code-block:: python  

   [Mesh]  
     file = geo_model_units_moose_input_in.e  
   []  


The final output of the simulation may also be such an `.e`, which can, for instance, be opened with `paraview <https://www.paraview.org/>`_. 
A simulated temperature field (purely conductive) of the created model would look like this: 

.. image:: ../../_static/GemPy_model_combined.png
  :width: 800
  :alt: Side by side example of gempy model and MOOSE HT-simulation


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

   **Total running time of the script:** ( 0 minutes  10.081 seconds)


.. _sphx_glr_download_Tutorials_Export_MOOSE.py:


.. only :: html

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



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

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



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

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


.. only:: html

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

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