Added functionality, updated docs, and new drogon generic example

.gitignore

@@ -164,8 +164,17 @@ cython_debug/
 
 # Tests
 tests/configs/ert/
-tests/configs/output/
 tests/generic_deck
+tests/configs/ert
+tests/configs/jobs
+tests/configs/logs
+tests/configs/observations
+tests/configs/parameters
+tests/configs/output
+tests/configs/postprocessing
+tests/configs/preprocessing
+tests/configs/.ert_runpath_list
+tests/configs/ert.ert
 
 # Python environment
 vpycopm/

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # Contributing
 
-Hola hola :).
+Hola hola 🙂.
 The following is a set of guidelines for contributing to pycopm.
 
 ## Ground Rules

README.md

@@ -45,7 +45,7 @@ See the [_installation_](https://cssr-tools.github.io/pycopm/installation.html)
 ## Running pycopm
 You can run _pycopm_ as a single command line:
 ```
-pycopm -i some_input -o some_output_folder
+pycopm -i name_of_input_file
 ```
 Run `pycopm --help` to see all possible command line argument options.
 

docs/_sources/examples.rst.txt

@@ -48,11 +48,10 @@ then:
 
 .. code-block:: bash
 
-    pycopm -i Statoil_Feasibility_sim_model_with_depletion_KROSS_INJ_SECTOR_20.DATA -o . -c 5,4,3 -a mode -j 1000
+    pycopm -i Statoil_Feasibility_sim_model_with_depletion_KROSS_INJ_SECTOR_20.DATA -o . -c 5,4,3 -a mode
 
 will generate a coarser model 5 times in the x direction, 4 in the y direction, and 3 in the z direction, where the mode is 
-used to decide if a coarser cell should be active or inactive. The jump (-j) is set to a higher value (1000) to avoid removal
-of grid connections (this is a tunning value to remove generated connections between neighbours in the coarse model).
+used to decide if a coarser cell should be active or inactive.
 
 We can execute a dry run of OPM Flow to generate the grid and static variables of the coarser model:
 
@@ -76,4 +75,28 @@ We use our `plopm <https://github.com/cssr-tools/plopm>`_ friend to generate PNG
 .. note::
     In the current implementation of the **pycopm** tool, the handling of properties that require definitions of i,j,k indices 
     (e.g., FAULTS, WELLSPECS) are assumed to be define in the main .DATA deck. Then, in order to use **pycopm** for simulation models 
-    where these properties are define via include files, replace those includes in the .DATA deck with the actual content of the include files.
+    where these properties are define via include files, replace those includes in the .DATA deck with the actual content of the include files.
+
+Generic Drogon
+--------------
+Following the note above, then by downloading the `DROGON model <https://github.com/OPM/opm-tests/tree/master/drogon>`_, replacing the lines in
+`DROGON_HIST.DATA <https://github.com/OPM/opm-tests/blob/master/drogon/model/DROGON_HIST.DATA>`_ for the FAULTS (L127-128) and SCHEDULE (L242-243) with
+the actual content of those include files, then by executing:
+
+.. code-block:: bash
+
+    pycopm -i DROGON_HIST.DATA -o . -c 1,1,3 -a min -n max -p 1
+    pycopm -i DROGON_HIST_PYCOPM.DATA -o . -c 1,3,1 -a mode -n mode -p 1 -j 1.9
+
+this would generate the following coarse model:
+
+.. figure:: figs/drogon_generic.png
+
+    Note that the total pore volume is conserved for the coarse model.
+
+Here, we first coarse in the z direction, which reduces the number of cells from 31 to 11, and after we coarse in the y direction.
+After trial and error, the jump (-j) is set to 1.9 to avoid generated connections across the faults.
+
+.. note::
+    After genereting the first coarser deck (DROGON_HIST_PYCOPM.DATA), change the path '../include/props/drogon.swatinit' to 'SWATINIT.INC',
+    which contains the right number of values for the coarse model.

docs/_sources/installation.rst.txt

@@ -51,25 +51,25 @@ in the terminal the following lines (which in turn should build flow in the fold
 
     CURRENT_DIRECTORY="$PWD"
 
-    for repo in common grid models simulators
+    for repo in common grid simulators
     do
         git clone https://github.com/OPM/opm-$repo.git
     done
 
     mkdir build
 
-    for repo in common grid models
+    for repo in common grid
     do
         mkdir build/opm-$repo
         cd build/opm-$repo
-        cmake -DUSE_MPI=1 -DWITH_NDEBUG=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid" $CURRENT_DIRECTORY/opm-$repo
+        cmake -DUSE_MPI=1 -DWITH_NDEBUG=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/build/opm-common" $CURRENT_DIRECTORY/opm-$repo
         make -j5 opm$repo
         cd ../..
     done    
 
     mkdir build/opm-simulators
     cd build/opm-simulators
-    cmake -DUSE_MPI=1 -DWITH_NDEBUG=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid;$CURRENT_DIRECTORY/build/opm-models" $CURRENT_DIRECTORY/opm-simulators
+    cmake -DUSE_MPI=1 -DWITH_NDEBUG=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid" $CURRENT_DIRECTORY/opm-simulators
     make -j5 flow
     cd ../..
 
@@ -95,25 +95,25 @@ For macOS, there are no available binary packages, so OPM Flow needs to be built
          ./dune-common/bin/dunecontrol --only=dune-$module make -j5
     done
 
-    for repo in common grid models simulators
+    for repo in common grid simulators
     do
         git clone https://github.com/OPM/opm-$repo.git
     done
 
     mkdir build
 
-    for repo in common grid models
+    for repo in common grid
     do
         mkdir build/opm-$repo
         cd build/opm-$repo
-        cmake -DUSE_MPI=0 -DWITH_NDEBUG=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/dune-common/build-cmake;$CURRENT_DIRECTORY/dune-grid/build-cmake;$CURRENT_DIRECTORY/dune-geometry/build-cmake;$CURRENT_DIRECTORY/dune-istl/build-cmake;$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid" $CURRENT_DIRECTORY/opm-$repo
+        cmake -DPYTHON_EXECUTABLE=$(which python) -DWITH_NDEBUG=1 -DUSE_MPI=0 -DOPM_ENABLE_PYTHON=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/dune-common/build-cmake;$CURRENT_DIRECTORY/dune-grid/build-cmake;$CURRENT_DIRECTORY/dune-geometry/build-cmake;$CURRENT_DIRECTORY/dune-istl/build-cmake;$CURRENT_DIRECTORY/build/opm-common" $CURRENT_DIRECTORY/opm-$repo
         make -j5 opm$repo
         cd ../..
     done    
 
     mkdir build/opm-simulators
     cd build/opm-simulators
-    cmake -DUSE_MPI=0 -DWITH_NDEBUG=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/dune-common/build-cmake;$CURRENT_DIRECTORY/dune-grid/build-cmake;$CURRENT_DIRECTORY/dune-geometry/build-cmake;$CURRENT_DIRECTORY/dune-istl/build-cmake;$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid;$CURRENT_DIRECTORY/build/opm-models" $CURRENT_DIRECTORY/opm-simulators
+    cmake -DUSE_MPI=0 -DWITH_NDEBUG=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/dune-common/build-cmake;$CURRENT_DIRECTORY/dune-grid/build-cmake;$CURRENT_DIRECTORY/dune-geometry/build-cmake;$CURRENT_DIRECTORY/dune-istl/build-cmake;$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid" $CURRENT_DIRECTORY/opm-simulators
     make -j5 flow
     cd ../..
 

docs/_sources/introduction.rst.txt

@@ -4,7 +4,7 @@ Introduction
 
 .. image:: ./figs/pycopm.gif
 
-This documentation describes the content of the **pycopm** package.
+This documentation describes the **pycopm** tool hosted in `https://github.com/cssr-tools/pycopm <https://github.com/cssr-tools/pycopm>`_.
 
 Concept
 -------
@@ -28,17 +28,20 @@ The current implementation supports the following executable with the argument o
 
 .. code-block:: bash
 
-    pycopm -i some_input -o some_output_folder
+    pycopm -i name_of_input_file
 
 where 
 
-- \-i: The base name of the :doc:`configuration file <./configuration_file>` or the name of the deck (`input.txt` by default).
-- \-o: The base name of the :doc:`output folder <./output_folder>` (`output` by default).
-- \-f: OPM Flow full path to executable or just `flow` (`flow` by default).
-- \-c: Level of coarsening in the x, y, and z dir (`2,2,2` by default).
-- \-a: Use min, max, or mode to scale the actnum (`min` by default).
-- \-j: Tunning parameter to avoid creation of nnc on the structural faults (`2.` by default).
-- \-x: Vector of x-coarsening (`` by default).
-- \-y: Vector of y-coarsening (`` by default).
-- \-z: Vector of z-coarsening (`` by default).
-- \-e: Use `utf8` or `ISO-8859-1` encoding to read the deck (`ISO-8859-1` by default).
+-i  The base name of the :doc:`configuration file <./configuration_file>` or the name of the deck, e.g., `DROGON.DATA`, (`input.txt` by default).
+-o  The base name of the :doc:`output folder <./output_folder>` ('.'' by default, i.e., the folder where pycopm is executed).
+-f  OPM Flow full path to executable or just `flow` (`flow` by default).
+-c  Level of coarsening in the x, y, and z dir (`2,2,2` by default).
+-a  Use `min`, `max`, or `mode` to scale the actnum, e.g., min makes the new coarser cell inactive it at least one cell is inactive, while max makes it active it at least one cell is active (`max` by default).
+-j  Tuning parameter to avoid creation of neighbouring connections in the coarser model where there are discontinuities between cells along the z direction, e.g., around faults ('' by default, i.e., nothing corrected; if need it, try with values of the order of 1).
+-x  Vector of x-coarsening, e.g., if the grid has 6 cells in the x direction, then `0,2,0,2,0,2,0` would generate a coarser model with 3 cells, while `0,2,2,2,2,2,0` would generate a coarser model with 1 cell, i.e., 0 keeps the pilars while 2 removes them ('' by default),
+-y  Vector of y-coarsening, see the description for -x ('' by default).
+-z  Vector of z-coarsening, see the description for -x ('' by default).
+-e  Use `utf8` or `ISO-8859-1` encoding to read the deck (`ISO-8859-1` by default).
+-p  Add the removed pore volume to the closest coarser cells (`0` by default, `1` to enable).
+-n  Use `min`, `max`, or `mode` to scale satnum, fipnum, pvtnum, eqlnum, imbnum, and multnum (`mode` by default).
+-s  Use `min`, `max`, or `mean` to scale permx, permy, permz, and poro ('' by default, i.e., using the arithmetic average for permx/permy, harmonic average for permz, and the mean for the porosity).

docs/_sources/related.rst.txt

@@ -28,7 +28,7 @@ plopm
 
 .. image:: ./figs/plopm.png
 
-`Quick generation of PNG figures from a simulation model given any 2D slide <https://github.com/cssr-tools/plopm>`_.
+`Quick generation of PNGs, GIFs, and VTKs from a OPM Flow type model <https://github.com/cssr-tools/plopm>`_.
 
 ********
 expreccs

docs/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

docs/_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

docs/_static/language_data.js

@@ -5,15 +5,15 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, if available */
+/* Non-minified version is copied as a separate JS file, is available */
 
 /**
  * Porter Stemmer