Merge pull request #10 from daavid00/dev

Docs, fixing co2eor, and option to not output cell values

README.md

@@ -47,16 +47,30 @@ in Linux, Windows, and macOS.
 ## Running pyopmnearwell
 You can run _pyopmnearwell_ as a single command line:
 ```
-pyopmnearwell -i some_input.txt -o some_output_folder
+pyopmnearwell -i configuration_file.txt
 ```
 Run `pyopmnearwell --help` to see all possible command line 
-argument options. Inside the `some_input.txt` file you provide the path to the
+argument options. Inside the `configuration_file.txt` file you provide the path to the
 flow executable and simulation parameters. See the .txt files in the [_examples_](https://github.com/cssr-tools/pyopmnearwell/tree/main/examples),
 [_tests/geometries/_](https://github.com/cssr-tools/pyopmnearwell/tree/main/tests/geometries), and [_tests/models/_](https://github.com/cssr-tools/pyopmnearwell/tree/main/tests/models) folders. 
 
 ## Getting started
 See the [_examples_](https://cssr-tools.github.io/pyopmnearwell/examples.html) in the [_documentation_](https://cssr-tools.github.io/pyopmnearwell/introduction.html).
 
+## Citing
+If you would like to cite this repository:
+
+* Landa-Marbán, D. and von Schultzendorff, P.M. 2023. Pyopmnearwell: A framework to simulate near well dynamics using OPM Flow. V2023.10. https://doi.org/10.5281/zenodo.10266791.
+
+## Publications
+The following is a list of manuscripts in which _pyopmnearwell_ is used:
+
+1. Landa-Marbán, D., Zamani, N., Sandve, T.H., Gasda, S.E., 2024. Impact of Intermittency on Salt Precipitation During CO2 Injection, presented at SPE
+Norway Subsurface Conference, Bergen, Norway, April 2024. doi: 10.2118/218477-MS.   
+1. von Schultzendorff, P., Sandve, T.H., Kane, B., Landa-Marbán, D., Both, J.W., Nordbotten, J.M., 2024. A Machine-Learned Near-Well Model in OPM Flow, presented at ECMOR 2024, European Association of Geoscientists & Engineers, Sep. 2024, pp. 1–23. doi: 10.3997/2214-4609.202437033.
+1. Lliguizaca, J.R., Landa-Marbán, D., Gasda, S.E., Sandve, T.H., Alcorn, Z.P., 2024. Data-Driven Predictions of CO2 EOR Numerical Studies Using Machine Learning in an Open-Source Framework, presented at SPE Norway Subsurface Conference, Bergen, Norway, April 2024. doi: 10.2118/218441-MS.
+1. Mushabe, R., Minougou, J.D., Landa-Marbán, D., Kane, B., Sandve, T.H., Submitted. Predicting Ultimate Hydrogen Production and Residual Volume during Cyclic Underground Hydrogen Storage in Porous Media using Machine Learning.
+
 ## About pyopmnearwell
 The pyopmnearwell package is being funded by the [_HPC Simulation Software for the Gigatonne Storage Challenge project_](https://www.norceresearch.no/en/projects/hpc-simulation-software-for-the-gigatonne-storage-challenge) [project number 622059] and [_Center for Sustainable Subsurface Resources (CSSR)_](https://cssr.no) 
 [project no. 331841].

docs/_sources/examples.rst.txt

@@ -74,7 +74,13 @@ The following are some of the plots created by the **pyopmnearwell** executable:
 .. figure:: figs/nearwell_saturation.png
 
     Permeability (top), CO2 injection schedule (middle), and saturation values over time on the cells along the well location
-    at three different locations (bottom). 
+    at three different locations (bottom).
+
+CCUS (machine learning)
+-----------------------
+See `this folder <https://github.com/cssr-tools/pyopmnearwell/tree/main/examples/cemracs2023/ml_example_co2eor>`_ for an example of
+how to use **pyopmnearwell** to generate data for different input parameters (e.g., injection rates) and read the data (e.g., 
+production volumes). This example could be used as a starting point for the ones interested in ML. 
 
 Publications
 ------------

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 ../..
 
@@ -98,7 +98,7 @@ package (see the `prerequisites <https://opm-project.org/?page_id=239>`_, which
          ./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
@@ -107,18 +107,18 @@ package (see the `prerequisites <https://opm-project.org/?page_id=239>`_, which
 
     mkdir build
 
-    for repo in common grid models
+    for repo in common grid
     do
         mkdir build/opm-$repo
         cd build/opm-$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/build/opm-grid" $CURRENT_DIRECTORY/opm-$repo
-        make -j5
+        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

@@ -5,14 +5,12 @@ Introduction
 .. image:: ./figs/introduction.gif
     :scale: 50%
 
-This documentation describes the content of the **pyopmnearwell** package.
-The numerical studies are performed using the 
-`OPM Flow <https://opm-project.org/?page_id=19>`_ simulator.
+This documentation describes the **pyopmnearwell** package hosted in `https://github.com/cssr-tools/pyopmnearwell <https://github.com/cssr-tools/pyopmnearwell>`_.
 
 Concept
 -------
 Simplified and flexible testing framework for near-well simulations via a
-:doc:`configuration file <./configuration_file>`:
+:doc:`configuration file <./configuration_file>` using the `OPM Flow simulator <https://opm-project.org/?page_id=19>`_:
 
 - Set the physical model (current ones are co2store, co2eor, h2store, and saltprec).
 - Choose a `specific template <https://github.com/cssr-tools/pyopmnearwell/blob/main/src/pyopmnearwell/templates>`_ inside the folder for the chosen physical model.
@@ -31,18 +29,19 @@ The current implementation supports the following executable with the argument o
 
 .. code-block:: bash
 
-    pyopmnearwell -i input.txt -o output -p resdata -g all -z 10 -s log -m co2store
+    pyopmnearwell -i input.txt -o output -p resdata -c '' -g all -w yes -z 10 -s log -m co2store
 
 where 
 
-- \-i: The base name of the :doc:`configuration file <./configuration_file>` ('input.txt' by default).
-- \-o: The base name of the :doc:`output folder <./output_folder>` ('output' by default).
-- \-p: Using the 'resdata' or 'opm' Python package to generate the figures ('resdata' by default, 'off' to skip the plotting).
-- \-c: Compare the results from different output folders (write any name to actiate, '' by default).
-- \-g: Run the whole framework ('all'), only run flow ('flow'), or only create plots ('plot') ('all' by default).
-- \-z: xlim in meters for the zoomed in plots (20 by default).
-- \-s: Scale for the x axis in the figures: 'normal' or 'log' ('normal' by default).
-- \-m: Simulated model (5th row in the configuration file). This is used for the plotting compare method (it gets overwritten by the configuration file) ('co2store' by default).
+-i  The base name of the :doc:`configuration file <./configuration_file>` ('input.txt' by default).
+-o  The base name of the :doc:`output folder <./output_folder>` ('output' by default).
+-p  Using the 'resdata' or 'opm' Python package to generate the figures ('resdata' by default, 'off' to skip the plotting).
+-c  Compare the results from different output folders (write any name to actiate, '' by default).
+-g  Run the whole framework ('all'), only run flow ('flow'), only write the deck and run flow together in the output folder ('single'), or only create plots ('plot') ('all' by default).
+-w  Write cell values, i.e., EGRID, INIT, UNRST ('yes' by default).
+-z  xlim in meters for the zoomed in plots (20 by default).
+-s  Scale for the x axis in the figures: 'normal' or 'log' ('normal' by default).
+-m  Simulated model (5th row in the configuration file). This is used for the plotting compare method (it gets overwritten by the configuration file) ('co2store' by default).
 
 .. warning::
     The H2CH4 template in the h2store model folder is under development and it is based on an input deck available in 

docs/_sources/related.rst.txt

@@ -29,7 +29,7 @@ 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

@@ -1,12 +1,5 @@
 /*
- * basic.css
- * ~~~~~~~~~
- *
  * Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 /* -- main layout ----------------------------------------------------------- */
@@ -115,15 +108,11 @@ img {
 /* -- search page ----------------------------------------------------------- */
 
 ul.search {
-    margin: 10px 0 0 20px;
-    padding: 0;
+    margin-top: 10px;
 }
 
 ul.search li {
-    padding: 5px 0 5px 20px;
-    background-image: url(file.png);
-    background-repeat: no-repeat;
-    background-position: 0 7px;
+    padding: 5px 0;
 }
 
 ul.search li a {