Pflotran output

.gitignore

@@ -146,3 +146,10 @@ examples/data/input_data/Claudius/Results_
 
 /docs/source/gen_modules/
 
+#examples folders
+examples/integrations/*.vs
+examples/integrations/*.ugi
+examples/integrations/*.h5
+examples/integrations/*.xmf
+examples/integrations/*.ss
+examples/integrations/*.out

examples/examples/real/Perth_basin.py

@@ -188,4 +188,4 @@
 # sim = np.load('sim.npy')
 # lith_block = np.load('lith.npy')
 
-gp.save_model(geo_model)
+gp.save_model(geo_model)

examples/integrations/gempy_export_perth_bassin_pflotran.py

@@ -0,0 +1,180 @@
+"""
+Simulation of the Perth Basin model with PFLOTRAN
+=================================================
+
+"""
+
+# %% 
+#
+# The purpose of this example is to introduce how to export GemPy geological 
+# model to the finite volume reactive transport simulator `PFLOTRAN <https://www.pflotran.org>`_.
+
+# %% 
+# The Perth Basin model
+# ^^^^^^^^^^^^^^^^^^^^^^^^^^
+# 
+# First, create the perf bassin model as in `examples/examples/real/Perth_bassin.py`.
+
+import gempy as gp
+data_path = 'https://raw.githubusercontent.com/cgre-aachen/gempy_data/master/'
+geo_model = gp.create_model('Perth_Basin')
+gp.init_data(geo_model,
+             extent=[337000, 400000, 6640000, 6710000, -18000, 1000],
+             resolution=[100, 100, 100],
+             path_i=data_path + "/data/input_data/Perth_basin/Paper_GU2F_sc_faults_topo_Points.csv",
+             path_o=data_path + "/data/input_data/Perth_basin/Paper_GU2F_sc_faults_topo_Foliations.csv")
+del_surfaces = ['Cadda', 'Woodada_Kockatea', 'Cattamarra']
+geo_model.delete_surfaces(del_surfaces, remove_data=True)
+ret = gp.map_stack_to_surfaces(geo_model,
+                          {"fault_Abrolhos_Transfer": ["Abrolhos_Transfer"],
+                           "fault_Coomallo": ["Coomallo"],
+                           "fault_Eneabba_South": ["Eneabba_South"],
+                           "fault_Hypo_fault_W": ["Hypo_fault_W"],
+                           "fault_Hypo_fault_E": ["Hypo_fault_E"],
+                           "fault_Urella_North": ["Urella_North"],
+                           "fault_Urella_South": ["Urella_South"],
+                           "fault_Darling": ["Darling"],
+                           "Sedimentary_Series": ['Cretaceous',
+                                                  'Yarragadee',
+                                                  'Eneabba',
+                                                  'Lesueur',
+                                                  'Permian']
+                           })
+order_series = ["fault_Abrolhos_Transfer",
+                "fault_Coomallo",
+                "fault_Eneabba_South",
+                "fault_Hypo_fault_W",
+                "fault_Hypo_fault_E",
+                "fault_Urella_North",
+                "fault_Darling",
+                "fault_Urella_South",
+                "Sedimentary_Series", 'Basement']
+geo_model.reorder_series(order_series)
+
+geo_model.surface_points.df.dropna(inplace=True)
+geo_model.orientations.df.dropna(inplace=True)
+geo_model.set_is_fault(["fault_Abrolhos_Transfer",
+                        "fault_Coomallo",
+                        "fault_Eneabba_South",
+                        "fault_Hypo_fault_W",
+                        "fault_Hypo_fault_E",
+                        "fault_Urella_North",
+                        "fault_Darling",
+                        "fault_Urella_South"])
+
+
+fr = geo_model.faults.faults_relations_df.values
+fr[:, :-2] = False
+ret = geo_model.set_fault_relation(fr)
+
+geo_model.set_topography(source='random')
+interp_data = gp.set_interpolator(geo_model,
+                                  compile_theano=True,
+                                  theano_optimizer='fast_run', gradient=False,
+                                  dtype='float32')
+gp.compute_model(geo_model)
+
+# %%
+# Here is the results:
+
+gp.plot_3d(geo_model, show_topography=True)
+
+
+# %% 
+#
+# Export the model in PFLOTRAN format
+# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+# Two format are available for PFLOTRAN and are automatically determined by the extension:
+# 
+# * `ascii`: every file are writed into human readable files (`ugi` extension).
+# * `hdf5`: all the mesh information are stored into one binary HDF5 file.
+# 
+# In this example, the `ascii` format is chosen, so the model is saved
+# under the name ``perth_bassin_mesh.ugi``:
+# 
+
+# sphinx_gallery_thumbnail_path = '_static/permeability_pflotran.png'
+import gempy.utils.export as export
+export.export_pflotran_input(geo_model, path='', filename="perth_basin_mesh.ugi")
+
+
+# %% 
+#
+#PFLOTRAN ASCII format description
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+# 
+#When using the `ascii` file format, several file are created. Mesh 
+#informations are stored into the main file ``perth_bassin_mesh.ugi``. Also, 
+#the stratigraphic information are stored in separed files, with the
+#name of the formation and the extension `.vs` 
+#(for Volume Submesh). For example, the Perth Basin model got several
+#formations which are saved in PFLOTRAN format under the following files:
+#
+#* basement -> basement.vs
+#* Cretaceous -> Cretaceous.vs
+#* Eneabba -> Eneabba.vs
+#* Lesueur -> Lesueur.vs
+#* and so on..
+#
+
+# %% 
+#Group based on stratigraphic information are loaded in PFLOTRAN with the
+#card ``REGION`` (see `here <https://www.pflotran.org/documentation/user_guide/cards/subsurface/region_card.html>`_).
+#For example for the `Cretaceous` formation:
+# .. code-block:: python
+#  
+#  REGION Cretaceous
+#    FILE ./Cretaceous.vs
+#  END
+#
+#
+#A sample PFLOTRAN input file is provided to correctly read the GemPy 
+#output ``pflotran_perth_bassin.in``.
+#It basically read the model and perform a saturated flow simulation 
+#using different hydraulic conductivity for each formation.
+#
+#  .. figure:: permeability_pflotran.png
+#    :width: 600
+#
+#Note: GemPy export a file named ``topography_surface.ss`` that represent
+#horizontal faces defining the topography. They can be used to apply a 
+#boundary condition such as specifying a rain. They are imported in PFLOTRAN by:
+# .. code-block:: python
+#  
+#  REGION topo
+#    FILE ./topography_surface.ss
+#  END
+
+# %% 
+# 
+#PFLOTRAN HDF5 format description
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+#At the contrary, if the `hdf5` format is used (extension ``.h5``), GemPy
+#only create one binary file. The stratigraphic information are stored
+#in the HDF5 file, and can also be assessed in PFLOTRAN using the ``REGION`` 
+#card. For example, for the `Cretaceous` formation and the topographic
+#surface:
+#
+# .. code-block:: python
+#   
+#  REGION Cretaceous
+#    FILE ./perth_bassin_mesh.h5
+#  END
+#  REGION Topography_surface
+#    FILE ./perth_bassin_mesh.h5
+#  END
+#
+#
+
+# %%
+#
+#Getting help with PFLOTRAN
+#^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+#For issue relating with PFLOTRAN, please see the discussion group `here <https://groups.google.com/g/pflotran-users>`_.
+#
+#
+#
+