Support for macOS

.gitignore

@@ -165,6 +165,10 @@ cython_debug/
 # Environment
 vpyopmspe11
 
+# OPM
+dune-*
+opm-*
+
 # Examples outputs
 tests/configs/test_compare
 tests/configs/output
@@ -173,4 +177,5 @@ tests/configs/spe11c
 examples/spe11a
 examples/spe11b
 examples/spe11c
-developing
+developing
+debugging

README.md

@@ -14,11 +14,7 @@ Here we use the [_OPM-Flow_](https://opm-project.org/?page_id=19) simulator.
 You will first need to install
 * Flow (https://opm-project.org, Release 2023.10 or current master branches)
 
-To build dune and the corresponding OPM master branches from source (e.g., you are a macOS user), you can run the script
-`./build_dune_and_opm-flow.bash`, which in turn should build flow in the folder 
-./build/opm-simulators/bin/flow (for macOS users the dependecies such as boost can be installed using brew or macports).
-
-You can install the requirements in a virtual environment with the following commands:
+You can install the Python requirements in a virtual environment with the following commands:
 
 ```bash
 # Clone the repo
@@ -37,8 +33,10 @@ pip install -e .
 pip install -r dev-requirements.txt
 ``` 
 
-See the [_CI.yml_](https://github.com/OPM/pyopmspe11/blob/main/.github/workflows/CI.yml) script
-for installation of OPM Flow and the pyopmspe11 package in Linux.
+See the [_CI.yml_](https://github.com/OPM/pyopmspe11/blob/main/.github/workflows/CI.yml) script 
+for installation of OPM Flow (binary packages) and the pyopmspe11 package. If you are a Linux user (including the windows subsystem for Linux), then you could try to build Flow from the master branches with mpi support, by running the script `./build_opm-flow_mpi.bash`, which in turn should build flow in the folder ./build/opm-simulators/bin/flow. 
+
+For macOS users with the latest chips (M1/M2, guessing also M3?), the resdata Python package is not available via pip install. Then before installation, remove resdata from the `requierements.txt`, then proceed with the Python requirements installation, install the OPM Flow dependencies (using macports or brew), and once inside the vpyopmspe11 Python environment, run the `./build_dune_and_opm-flow.bash`, and deactivate and activate the virtual environment (this script builds OPM Flow as well as the opm Python package, and it exports the required PYTHONPATH).
 
 ## Running pyopmspe11
 You can run _pyopmspe11_ as a single command line:
@@ -48,7 +46,7 @@ pyopmspe11 -i some_input.txt -o some_output_folder
 Run `pyopmspe11 --help` to see all possible command line 
 argument options. Inside the `some_input.txt` file you provide the path to the
 flow executable and simulation parameters. See the .txt files in the examples
-folders.
+folders. For macOS users, then always add the flag `-u opm` (resdata is the default one).
 
 ## Getting started
 See the [_documentation_](https://OPM.github.io/pyopmspe11/introduction.html).

build_dune_and_opm-flow.bash → build_opm-flow_macOS.bash

@@ -18,13 +18,15 @@ do
     git clone https://github.com/OPM/opm-$repo.git
 done
 
+source vpyopmspe11/bin/activate
+
 mkdir build
 
 for repo in common grid models
 do
     mkdir build/opm-$repo
     cd build/opm-$repo
-    cmake -DUSE_MPI=0 -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=$(which python) -DUSE_MPI=0 -DOPM_ENABLE_PYTHON=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$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
     cd ../..
 done    
@@ -33,4 +35,6 @@ mkdir build/opm-simulators
 cd build/opm-simulators
 cmake -DUSE_MPI=0 -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" $CURRENT_DIRECTORY/opm-simulators
 make -j5 flow
-cd ../..
+cd ../..
+
+echo "export PYTHONPATH=\$PYTHONPATH:$CURRENT_DIRECTORY/build/opm-common/build/python" >> $CURRENT_DIRECTORY/vpyopmspe11/bin/activate

docs/_sources/index.rst.txt

@@ -11,6 +11,7 @@ Welcome to pyopmspe11's documentation!
    examples
    api
    output_folder
+   related
    about
 
 Indices and tables

docs/_sources/introduction.rst.txt

@@ -30,6 +30,7 @@ where
 - \-g, \-\-generate: Write only the 'dense', 'sparse', 'performance', 'dense_performance', 'performance_sparse', 'dense_sparse', or 'all' ('performance_sparse' by default).
 - \-r, \-\-resolution: Number of x, y, and z elements to write the data ('100,10,50' by default).
 - \-t, \-\-time: Time interval for the spatial maps (spe11a [h]; spe11b/c [y]) ('5' by default).
+- \-u, \-\-use: Using the 'opm' or 'resdata' python package ('resdata' by default).
 - \-c, \-\-compare: Generate a common plot for the current folders for 'spe11a', 'spe11b', or 'spe11c' ('' by default).
 
 Installation

docs/_sources/related.rst.txt

@@ -0,0 +1,42 @@
+=======
+Related
+=======
+
+Below are some packages following the same configuration-file-to-postprocessing-folder approach; 
+check them out :).
+
+*************
+pyopmnearwell
+*************
+
+.. image:: ./figs/pyopmnearwell.gif
+    :scale: 50%
+
+`A framework to simulate near well dynamics using OPM Flow <https://github.com/daavid00/pyopmnearwell>`_.
+
+********
+expreccs
+********
+
+.. image:: ./figs/expreccs.gif
+    :scale: 50%
+
+`Expansion of ResourCes for CO2 Storage on the Horda Platform <https://github.com/daavid00/expreccs>`_.
+
+*******
+ad-micp
+*******
+
+.. image:: ./figs/ad-micp.gif
+    :scale: 40%
+
+`A module to study CO2 leakage remediation by microbially induced calcite precipitation (MICP) <https://github.com/daavid00/ad-micp>`_.
+
+****
+pymm
+****
+
+.. image:: ./figs/pymm.gif
+    :scale: 15%
+
+`An open-source image-based framework for CFD in microsystems <https://github.com/daavid00/pymm>`_.

docs/about.html

@@ -20,7 +20,7 @@
     <link rel="author" title="About these documents" href="#" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="prev" title="Output folder" href="output_folder.html" /> 
+    <link rel="prev" title="Related" href="related.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -49,6 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pyopmspe11 Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">About pyopmspe11</a></li>
 </ul>
 
@@ -89,7 +90,7 @@ <h1>About pyopmspe11<a class="headerlink" href="#about-pyopmspe11" title="Link t
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="output_folder.html" class="btn btn-neutral float-left" title="Output folder" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="related.html" class="btn btn-neutral float-left" title="Related" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
     </div>
 
   <hr/>

docs/api.html

@@ -56,6 +56,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>
 

docs/configuration_file.html

@@ -55,6 +55,7 @@
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pyopmspe11 Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>
 

docs/examples.html

@@ -54,6 +54,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pyopmspe11 Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>
 

docs/genindex.html

@@ -47,6 +47,7 @@
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pyopmspe11 Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>
 
@@ -82,6 +83,7 @@ <h1 id="index">Index</h1>
  | <a href="#D"><strong>D</strong></a>
  | <a href="#G"><strong>G</strong></a>
  | <a href="#I"><strong>I</strong></a>
+ | <a href="#L"><strong>L</strong></a>
  | <a href="#M"><strong>M</strong></a>
  | <a href="#O"><strong>O</strong></a>
  | <a href="#P"><strong>P</strong></a>
@@ -123,6 +125,8 @@ <h2 id="D">D</h2>
 <h2 id="G">G</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="pyopmspe11.utils.mapproperties.html#pyopmspe11.utils.mapproperties.get_cell_info">get_cell_info() (in module pyopmspe11.utils.mapproperties)</a>
+</li>
       <li><a href="pyopmspe11.utils.mapproperties.html#pyopmspe11.utils.mapproperties.get_lines">get_lines() (in module pyopmspe11.utils.mapproperties)</a>
 </li>
   </ul></td>
@@ -142,6 +146,14 @@ <h2 id="I">I</h2>
   </ul></td>
 </tr></table>
 
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="pyopmspe11.utils.mapproperties.html#pyopmspe11.utils.mapproperties.locate_wells">locate_wells() (in module pyopmspe11.utils.mapproperties)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="M">M</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>

docs/index.html

@@ -49,6 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pyopmspe11 Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>
 
@@ -109,6 +110,13 @@ <h1>Welcome to pyopmspe11’s documentation!<a class="headerlink" href="#welcome
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="related.html#pyopmnearwell">pyopmnearwell</a></li>
+<li class="toctree-l2"><a class="reference internal" href="related.html#expreccs">expreccs</a></li>
+<li class="toctree-l2"><a class="reference internal" href="related.html#ad-micp">ad-micp</a></li>
+<li class="toctree-l2"><a class="reference internal" href="related.html#pymm">pymm</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>
 </div>

docs/introduction.html

@@ -55,6 +55,7 @@
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pyopmspe11 Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>
 
@@ -107,6 +108,7 @@ <h2>Overview<a class="headerlink" href="#overview" title="Link to this heading">
 <li><p>-g, --generate: Write only the ‘dense’, ‘sparse’, ‘performance’, ‘dense_performance’, ‘performance_sparse’, ‘dense_sparse’, or ‘all’ (‘performance_sparse’ by default).</p></li>
 <li><p>-r, --resolution: Number of x, y, and z elements to write the data (‘100,10,50’ by default).</p></li>
 <li><p>-t, --time: Time interval for the spatial maps (spe11a [h]; spe11b/c [y]) (‘5’ by default).</p></li>
+<li><p>-u, --use: Using the ‘opm’ or ‘resdata’ python package (‘resdata’ by default).</p></li>
 <li><p>-c, --compare: Generate a common plot for the current folders for ‘spe11a’, ‘spe11b’, or ‘spe11c’ (’’ by default).</p></li>
 </ul>
 </section>

docs/modules.html

@@ -48,6 +48,7 @@
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pyopmspe11 Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>
 

docs/output_folder.html

@@ -20,7 +20,7 @@
     <link rel="author" title="About these documents" href="about.html" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="About pyopmspe11" href="about.html" />
+    <link rel="next" title="Related" href="related.html" />
     <link rel="prev" title="pyopmspe11.utils.writefile module" href="pyopmspe11.utils.writefile.html" /> 
 </head>
 
@@ -50,6 +50,7 @@
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pyopmspe11 Python API</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>
 
@@ -105,7 +106,7 @@ <h1>Output folder<a class="headerlink" href="#output-folder" title="Link to this
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="pyopmspe11.utils.writefile.html" class="btn btn-neutral float-left" title="pyopmspe11.utils.writefile module" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="about.html" class="btn btn-neutral float-right" title="About pyopmspe11" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="related.html" class="btn btn-neutral float-right" title="Related" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>

docs/py-modindex.html

@@ -50,6 +50,7 @@
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pyopmspe11 Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>
 

docs/pyopmspe11.core.html

@@ -50,6 +50,7 @@
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pyopmspe11 Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>
 

docs/pyopmspe11.core.pyopmspe11.html

@@ -50,6 +50,7 @@
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pyopmspe11 Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
+<li class="toctree-l1"><a class="reference internal" href="related.html">Related</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About pyopmspe11</a></li>
 </ul>