Major improvements in the framework and documentation

cssr-tools · Sep 29, 2023 · 7dcc578 · 7dcc578
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -1,4 +1,4 @@
-name: Run expreccs executable
+name: Run the expreccs executable
 
 on:
  push:
@@ -34,13 +34,38 @@ jobs:
         sudo apt-get install -y build-essential gfortran pkg-config cmake
         sudo apt-get install -y mpi-default-dev
         sudo apt-get install -y libblas-dev libboost-all-dev libsuitesparse-dev libtrilinos-zoltan-dev
-        chmod u+x build_dune_and_opm-flow.bash
-        ./build_dune_and_opm-flow.bash
+        sudo apt-get install libdune-common-dev libdune-geometry-dev libdune-istl-dev libdune-grid-dev
+
+        CURRENT_DIRECTORY="$PWD"
+
+        # OPM modules
+        for repo in common grid models simulators
+        do
+            git clone https://github.com/OPM/opm-$repo.git
+        done
+
+        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="$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid" $CURRENT_DIRECTORY/opm-$repo
+            make -j
+            cd ../..
+        done    
+
+        mkdir build/opm-simulators
+        cd build/opm-simulators
+        cmake -DUSE_MPI=0 -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
+        make -j flow_gasoil
+        cd ../..
         
     - name: Install test dependecies
       run: |
         pip install --upgrade pip setuptools wheel
         pip install -r dev-requirements.txt
+        pip install opm
         
     - name: Install expreccs
       run: |

diff --git a/.gitignore b/.gitignore
@@ -131,9 +131,26 @@ dmypy.json
 # MacOS
 .DS_Store
 
+# DUNE
+dune-common/
+dune-geometry/
+dune-grid/
+dune-istl/
+
+# The OPM
+opm-common/
+opm-grid/
+opm-models/
+opm-simulators/
+
 # Extra folders
+tests/configs/output
+tests/configs/compare
 gift
 vexpreccs
 examples/output
 developing
-workshop
+workshop
+debugging
+cssr
+results
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,6 +1,7 @@
 include README.md
 include LICENSE
 include src/expreccs/core/*
-include src/expreccs/templates/co2/*
 include src/expreccs/templates/common/*
-include src/expreccs/utils/*
+include src/expreccs/templates/decks/*
+include src/expreccs/utils/*
+include src/expreccs/visualization/*
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
-# Expansion of ResourCes for CO2 Storage on the Horda Platform (ExpReCCS)
+# A Python framework for the project: Expansion of ResourCes for CO2 Storage on the Horda Platform (ExpReCCS)
 
 <img src="docs/text/figs/expreccs.gif" width="830" height="500">
 
@@ -14,12 +14,6 @@ for CO2 storage using the [_OPM-Flow_](https://opm-project.org/?page_id=19) simu
 You will first need to install
 * Flow (https://opm-project.org)
 
-For now you need to build OPM from source using the master branch (this since there have been updates for
-the boundary conditions (BC) keywords, which will be available in the next OPM stable release 2023.10). 
-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 (this builds OPM without mpi support [for macOS users]; changue
-the mpi cmake flags accordingly for mpi support).
-
 You can install the Python requirements in a virtual environment with the following commands:
 
 ```bash
@@ -39,6 +33,21 @@ pip install -e .
 pip install -r dev-requirements.txt
 ``` 
 
+For now you need to build OPM from source using the master branch (this since there have been updates for
+the boundary conditions (BC) keywords, which will be available in the next OPM stable release 2023.10). 
+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 macports).
+If you are a Linux user (including the windows subsystem for Linux), then you could try to build Flow with mpi support,
+by running the script `./build_dune_and_opm-flow_mpi.bash` instead of `./build_dune_and_opm-flow.bash`.
+
+For macOS users with the latest chips (M1/M2), the ecl package is not available via pip install. Then
+before installation, remove ecl from the requierements.txt, then proceed with the Python requirements installation, and 
+once inside the vexpreccs Python environment, add the flag `-DPYTHON_EXECUTABLE=/Users/dmar/expreccs/vexpreccs/bin/python`
+(by typing `which  python` in the terminal you get your path) to the cmake (lines 24 in the bash scripts), build flow by
+running the bash script, and finally, add to the python path the folder where you have built it, e.g., by running in the terminal
+`export PYTHONPATH=$PYTHONPATH:/Users/dmar/expreccs/build/opm-common/build/python`.
+
 ## Running expreccs
 You can run _expreccs_ as a single command line:
 ```
@@ -53,6 +62,6 @@ folders.
 See the [_documentation_](https://daavid00.github.io/expreccs/introduction.html). 
 
 ## About expreccs
-The expreccs package was funded by Wintershall Dea, Equinor, Shell, and the Research Council of Norway [project number 104908].
+The expreccs package is funded by Wintershall Dea, Equinor, Shell, and the Research Council of Norway [project number 104908].
 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.
 Contributions are more than welcome using the fork and pull request approach.
diff --git a/build_dune_and_opm-flow.bash b/build_dune_and_opm-flow.bash
@@ -21,13 +21,13 @@ 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 -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    
 
 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" $CURRENT_DIRECTORY/opm-simulators
-make -j5 flow_gasoil
+make -j5 flow
 cd ../..
diff --git a/build_dune_and_opm-flow_mpi.bash b/build_dune_and_opm-flow_mpi.bash
@@ -0,0 +1,33 @@
+CURRENT_DIRECTORY="$PWD"
+
+# Dune modules
+for module in common geometry grid istl
+do   git clone https://gitlab.dune-project.org/core/dune-$module.git --branch v2.9.0
+done
+for module in common geometry grid istl
+do   ./dune-common/bin/dunecontrol --only=dune-$module cmake
+     ./dune-common/bin/dunecontrol --only=dune-$module make -j5
+done
+
+# OPM modules
+for repo in common grid models simulators
+do
+    git clone https://github.com/OPM/opm-$repo.git
+done
+
+mkdir build
+
+for repo in common grid models
+do
+    mkdir build/opm-$repo
+    cd build/opm-$repo
+    cmake -DUSE_MPI=1 -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    
+
+mkdir build/opm-simulators
+cd build/opm-simulators
+cmake -DUSE_MPI=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
+make -j5 flow
+cd ../..
diff --git a/docs/_images/ad-micp.gif b/docs/_images/ad-micp.gif
diff --git a/docs/_images/confile.png b/docs/_images/confile.png
diff --git a/docs/_images/contents.png b/docs/_images/contents.png
diff --git a/docs/_images/distance_from_border.png b/docs/_images/distance_from_border.png
diff --git a/docs/_images/gridding.png b/docs/_images/gridding.png
diff --git a/docs/_images/grids.png b/docs/_images/grids.png
diff --git a/docs/_images/introduction.gif b/docs/_images/introduction.gif
diff --git a/docs/_images/maximum_pressure_difference_over_time.png b/docs/_images/maximum_pressure_difference_over_time.png
diff --git a/docs/_images/maximum_saturation_difference_over_time.png b/docs/_images/maximum_saturation_difference_over_time.png
diff --git a/docs/_images/output.png b/docs/_images/output.png
diff --git a/docs/_images/pymm.gif b/docs/_images/pymm.gif
diff --git a/docs/_images/pyopmcsp11.gif b/docs/_images/pyopmcsp11.gif
diff --git a/docs/_images/pyopmnearwell.gif b/docs/_images/pyopmnearwell.gif
diff --git a/docs/_images/reference_saturation.png b/docs/_images/reference_saturation.png
diff --git a/docs/_images/reference_watfluxi+.png b/docs/_images/reference_watfluxi+.png
diff --git a/docs/_images/regional_watfluxi+.png b/docs/_images/regional_watfluxi+.png
diff --git a/docs/_images/sands.png b/docs/_images/sands.png
diff --git a/docs/_images/site_flux_watfluxi+.png b/docs/_images/site_flux_watfluxi+.png
diff --git a/docs/_images/site_saturation.png b/docs/_images/site_saturation.png
diff --git a/docs/_images/test_distance_from_border.png b/docs/_images/test_distance_from_border.png
diff --git a/docs/_images/test_saturation.png b/docs/_images/test_saturation.png
diff --git a/docs/_images/tranxy.png b/docs/_images/tranxy.png
diff --git a/docs/_images/wells.png b/docs/_images/wells.png
diff --git a/docs/_images/wells_pressure_site_reference.png b/docs/_images/wells_pressure_site_reference.png
diff --git a/docs/_sources/about.rst.txt b/docs/_sources/about.rst.txt
@@ -5,7 +5,7 @@ About expreccs
 .. image:: ./figs/about.png
     :scale: 50%
 
-The **expreccs** package was funded by 
+The **expreccs** package is funded by 
 Wintershall Dea, Equinor, Shell, and the Research Council of Norway [project number 104908]. 
 
 This is work in progress. 

diff --git a/docs/_sources/api.rst.txt b/docs/_sources/api.rst.txt
@@ -5,8 +5,7 @@ expreccs Python API
 The main script for the **expreccs** executable is located in the core folder.
 The expreccss folder contains mako files to generate the corresponding opm
 input decks. The scripts in the utils folder process the input configuration
-file, runs the reference, regional, and site (including a site simulation 
-considering open boundaries) simulations, and generate images (.png) to show
+file, runs the reference, regional, and site simulations, and generate images (.png) to show
 comparisons between the different runs.
 
 .. figure:: figs/contents.png