Merge pull request #18 from daavid00/developing

Improving the generic functionality

Author: daavid00

README.md

@@ -46,7 +46,7 @@ See the [_installation_](https://cssr-tools.github.io/exprecss/installation.html
 ## Running expreccs
 You can run _expreccs_ as a single command line:
 ```
-expreccs -i configuration_file.txt
+expreccs -i name_of_input_file
 ```
 Run `expreccs --help` to see all possible command line 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/expreccs/tree/main/examples) and [_tests_](https://github.com/cssr-tools/expreccs/tree/main/tests/configs) folders.
@@ -57,13 +57,13 @@ See the [_examples_](https://cssr-tools.github.io/expreccs/examples.html) in the
 ## Citing
 If you would like to cite this repository:
 
-* Landa-Marbán, D. 2024. expreccs: A Python framework using OPM Flow to simulate regional and site reservoirs for CO2 storage. V2024.04. https://doi.org/10.5281/zenodo.12100600.
+* Landa-Marbán, D. 2024. expreccs: A Python framework using OPM Flow to simulate regional and site reservoirs for CO2 storage. https://doi.org/10.5281/zenodo.12100600.
 
 ## Publications
 The following is a list of manuscripts in which _expreccs_ is used:
 
 1. Tveit, S., Gasda, S.E., Landa-Marbán, D., Sandve, T.H., submitted. A hierarchical approach for modeling regional pressure interference in multi-site CO2 operations. http://dx.doi.org/10.2139/ssrn.5005237.
-1. Gasda, S.E., et al., submitted. Quantifying the impact of regional-scale pressure interference on commercial CO2 storage targets for multiple licenses. 
+1. Gasda, S.E., et al., 2024. Quantifying the impact of regional-scale pressure interference on commercial CO2 storage targets for multiple licenses. http://dx.doi.org/10.2139/ssrn.5053633.
 
 ## About expreccs
 The _expreccs_ package is funded by Wintershall Dea, Equinor, Shell, and the Research Council of Norway [project number 336294].

docs/_images/generic.png

@@ -5,8 +5,8 @@ About expreccs
 .. image:: ./figs/about.png
     :scale: 50%
 
-The **expreccs** package is funded by 
-Wintershall Dea, Equinor, Shell, and the Research Council of Norway [project number 336294]. 
+The **expreccs** tool is funded by 
+Harbour Energy, Equinor, Shell, and the Research Council of Norway [project number 336294]. 
 
 This is work in progress. 
 `Here <https://www.norceresearch.no/en/projects/expansion-of-resources-for-co2-storage-on-the-horda-platform-expreccs>`_ is the link to the project details.

docs/_images/reference_sgas.png

@@ -1,6 +1,13 @@
 ==================
 Configuration file
 ==================
+.. Note::
+    The configuration files allow to set the integrated studies (generation of regional and site models,
+    in addition to set the different boundary projection approaches). To use **expreccs** in any given two OPM Flow geological models
+    to dynamically project pressures, this can be achieve without a configuration file, but setting
+    the parameters via command lines (see the :ref:`overview` or run `pycopm -h` for the definition 
+    of the argument options, as well as the example in :ref:`generic`).
+
 We consider the configuration file (`input.txt <https://github.com/cssr-tools/expreccs/blob/main/examples/input.txt>`_) available in the 
 examples folder. The parameters are chosen to show the functionality and capabilities of the **expreccs** framework regarding generation
 of corner-point grids (cpg), heterogeinities (e.g., different rock properties, faults), adding wells, and defining schedules for the
@@ -13,7 +20,7 @@ The first input parameter in the configuration file is:
     :linenos:
 
     """Set the full path to the flow executable and flags"""
-    flow --enable-opm-rst-file=true  --linear-solver=cprw --enable-tuning=true  
+    flow --enable-opm-rst-file=true --enable-tuning=true  
 
 If **flow** is not in your path, then write the full path to the executable
 (e.g., /Users/dmar/expreccs/build/opm-simulators/bin/flow). We also add in the same 

docs/_sources/about.rst.txt

@@ -2,8 +2,12 @@
 Examples
 ********
 
-Example 1
----------
+=======================
+Via configuration files
+=======================
+
+Hello world
+-----------
 
 We consider the configuration file `example1.txt <https://github.com/cssr-tools/expreccs/blob/main/examples/example1.txt>`_ in the 
 examples folder (the animation in the `GitHub home page <https://github.com/cssr-tools/expreccs>`_ was based on this configuration file). 
@@ -57,8 +61,8 @@ Below are some of the figures generated inside the postprocessing folder:
     hello_world_distance_from_border.png respectively
 
 
-Example 2
----------
+Layered model 
+-------------
 
 The configuration file example2.txt set a more complex geological model with more grid cells (1 417 500). This was used
 to generate the animation (using ResInsight) in the :doc:`introduction section <./introduction>` by running
@@ -67,17 +71,12 @@ to generate the animation (using ResInsight) in the :doc:`introduction section <
 
     expreccs -i example2.txt -m reference
 
-Generic (under development)
----------------------------
-
-See/run the `test_generic_deck.py <https://github.com/cssr-tools/expreccs/blob/main/tests/test_generic_deck.py>`_ 
-for an example where **expreccs** is used in two given models (regional and site, in this case they are created using
-the **expreccs** package, but in general can be any given geological models), generating a new input deck where
-the pressures are projected.
-
-.. code-block:: bash
+.. tip::
 
-    expreccs -e name_of_folder_for_the_regional_model,name_of_folder_for_the_site_model
+    This example shows how **expreccs** can be used to generate the requiered input files to run OPM Flow for heterogenous
+    layered models at different grid sizes, which can be used for further studies such as optimization. Regarding the configuration 
+    files in `examples/newcases <https://github.com/cssr-tools/expreccs/tree/main/examples/newcases>`_, these are explained in 
+    `this manuscript <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5005237>`_.
 
 .. _back_coupling:
 
@@ -97,13 +96,10 @@ This is one of the generated figures in the back-coupling/postprocessing folder
 .. image:: ./figs/back-coupling_summary_BPR_regional_reference.png
 
 The figures in the postprocessing includes the results for the first two iterations and the last one (in this case 9 since the number of 
-iteration is set to 10 in line 22 of the `configuration_file <https://github.com/cssr-tools/expreccs/blob/main/examples/example1_back.txt>`_). To visualize/compare results
-between any of the iterations, we can use our friend `plopm <https://github.com/cssr-tools/plopm>`_. 
+iteration is set to 10 in line 22 of the `configuration_file <https://github.com/cssr-tools/expreccs/blob/main/examples/example1_back.txt>`_).
 
-.. tip::
-    You can install `plopm <https://github.com/cssr-tools/plopm>`_ by executing in the terminal: **pip install git+https://github.com/cssr-tools/plopm.git**.
-
-For example, to show the difference in the spatial maps for pressure between iteration 4 and 7 at the third restart, this is achieved by executing:
+For example, to show the difference in the spatial maps for pressure between iteration 4 and 7 at the third restart, this can be achieved using 
+`plopm <https://github.com/cssr-tools/plopm>`_ by executing:
 
 .. code-block:: bash
 
@@ -117,4 +113,40 @@ and to show the comparison for the summary vector FPR for iterations 1, 5, 7, an
 
     plopm -i 'back-coupling/output/regional_1/regional_1 back-coupling/output/regional_5/regional_5 back-coupling/output/regional_7/regional_7 back-coupling/output/regional_9/regional_9' -v fpr -d 5,5 -f 10
 
-.. image:: ./figs/fpr_plopm.png
+.. image:: ./figs/fpr_plopm.png
+
+.. tip::
+    You can install `plopm <https://github.com/cssr-tools/plopm>`_ by executing in the terminal: **pip install git+https://github.com/cssr-tools/plopm.git**.
+
+.. _generic:
+
+==================
+Via OPM Flow decks 
+==================
+
+See/run the `test_generic_deck.py <https://github.com/cssr-tools/expreccs/blob/main/tests/test_generic_deck.py>`_ 
+for an example where **expreccs** is used in two given models (regional and site, in this case they are created using
+the **expreccs** package, but in general can be any given geological models), generating a new input deck where
+the pressures are projected.
+
+.. code-block:: bash
+
+    expreccs -e name_of_folder_for_the_regional_model,name_of_folder_for_the_site_model
+
+In the current implementation, the name of the decks need to match the name of the given folder (e.g., regional/REGIONAL.DATA).
+For example, to run the test, this can be achieved by executing:
+
+.. code-block:: bash
+
+    pytest --cov=expreccs --cov-report term-missing tests/test_generic_deck.py
+
+To visualize/compare results between the model with static (input) and dynamic (generated by expreccs) boundary conditions, 
+we can use our friend `plopm <https://github.com/cssr-tools/plopm>`_: 
+
+.. code-block:: bash
+
+    plopm -i 'tests/configs/rotate/output/site_closed/SITE_CLOSED tests/configs/rotate/output/expreccs/EXPRECCS tests/configs/rotate/output/reference/REFERENCE' -v sgas -s ',,1 ,,1 ,,1' -subfigs 1,3 -suptitle 0 -cbsfax 0.2,0.95,0.6,0.02 -d 24,8 -cformat .1f -f 20 -xunits km -yunits km -xformat .0f -yformat .0f -x '[0,15000]' -y '[0,15000]' -delax 1
+
+.. figure:: figs/reference_sgas.png
+    
+    Comparison of the gas saturation on the top cells at the end of the simulations.

docs/_sources/configuration_file.rst.txt

@@ -41,6 +41,7 @@ where
 -u  Using 'gasoil' or 'gaswater' co2store implementation ('gaswater' by default).
 -t  Grades to rotate the site geological model ('0' by default).
 -e  Name of the regional and site folders to project pressures ('' by default).
+-b  Set the number of entries to skip the bc projections on the site, where 'j=0,i=nx,j=ny,i=0', e.g., '0,2,0,0' would skip all cells with i=nx and i=nx-1; this becomes handly for models where all cells in a given site are inactive along a side ('0,0,0,0' by default).
 -w  Set to 1 to print warnings ('0' by default).
 -l  Set to 0 to not use LaTeX formatting ('1' by default).
 

docs/_sources/examples.rst.txt

@@ -1,6 +1,10 @@
-=============
+*************
 Output folder
-=============
+*************
+
+=======================
+Via configuration files
+=======================
 
 The following screenshot shows the generated files in the selected output folder after 
 executing **expreccs**.
@@ -15,4 +19,23 @@ Then after running **expreccs**, one could modify the generated OPM related file
 the preprocessing folder and  run directly the simulations calling the Flow solvers, e.g., to add tracers 
 (see the OPM Flow documentation `here <https://opm-project.org/?page_id=955>`_).
 In addition, some plots comparing the site simulations to the reference 
-and the site are generated in the postprocessing folder.
+and the site are generated in the postprocessing folder.
+
+==================
+Via OPM Flow decks
+==================
+
+The following screenshot shows the generated files in the selected output folder after 
+executing **expreccs**, this corresponds to the `test_generic_deck.py <https://github.com/cssr-tools/expreccs/blob/main/tests/test_generic_deck.py>`_:
+
+.. code-block:: bash
+
+    expreccs -o expreccs -e regional,site_closed
+
+.. figure:: figs/generic.png
+
+    Generated files after executing **expreccs**.
+
+The dynamic boundary conditions are saved in the expreccs/bc folder, and the definition of the boundary connections in 
+expreccs/BCCON.INC. In addition, OPERNUM is used to label de boundary cells in the site, and also to label the overlapping cells and
+cells to use for the pressure interpolator in the regional model (regional/OPERNUM_EXPRECCS.INC).

docs/_sources/introduction.rst.txt

@@ -1,17 +1,21 @@
 const themeFlyoutDisplay = "hidden";
-const themeVersionSelector = "True";
-const themeLanguageSelector = "True";
+const themeVersionSelector = true;
+const themeLanguageSelector = true;
 
 if (themeFlyoutDisplay === "attached") {
   function renderLanguages(config) {
     if (!config.projects.translations.length) {
       return "";
     }
 
+    // Insert the current language to the options on the selector
+    let languages = config.projects.translations.concat(config.projects.current);
+    languages = languages.sort((a, b) => a.language.name.localeCompare(b.language.name));
+
     const languagesHTML = `
       <dl>
         <dt>Languages</dt>
-        ${config.projects.translations
+        ${languages
           .map(
             (translation) => `
         <dd ${translation.slug == config.projects.current.slug ? 'class="rtd-current-item"' : ""}>

docs/_sources/output_folder.rst.txt

@@ -6,9 +6,9 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
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 .highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */
 .highlight .cp { color: #9C6500 } /* Comment.Preproc */
@@ -25,34 +25,34 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */
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@@ -67,9 +67,9 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
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docs/_static/js/versions.js

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>About expreccs &mdash; expreccs  documentation</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b86133f3" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
 
 
@@ -83,8 +83,8 @@
 <h1>About expreccs<a class="headerlink" href="#about-expreccs" title="Link to this heading"></a></h1>
 <a class="reference internal image-reference" href="_images/about.png"><img alt="_images/about.png" src="_images/about.png" style="width: 369.0px; height: 308.5px;" />
 </a>
-<p>The <strong>expreccs</strong> package is funded by
-Wintershall Dea, Equinor, Shell, and the Research Council of Norway [project number 336294].</p>
+<p>The <strong>expreccs</strong> tool is funded by
+Harbour Energy, Equinor, Shell, and the Research Council of Norway [project number 336294].</p>
 <p>This is work in progress.
 <a class="reference external" href="https://www.norceresearch.no/en/projects/expansion-of-resources-for-co2-storage-on-the-horda-platform-expreccs">Here</a> is the link to the project details.</p>
 <p>Contributions are more than welcome using the fork and pull request approach.</p>
@@ -101,7 +101,7 @@ <h1>About expreccs<a class="headerlink" href="#about-expreccs" title="Link to th
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2025, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/_static/pygments.css

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>expreccs Python API &mdash; expreccs  documentation</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b86133f3" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
 
 
@@ -142,7 +142,7 @@ <h2>expreccs<a class="headerlink" href="#expreccs" title="Link to this heading">
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2025, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a