cssr-tools · daavid00 · Sep 8, 2024 · Sep 8, 2024
diff --git a/.gitignore b/.gitignore
@@ -163,22 +163,27 @@ cython_debug/
 .DS_Store
 
 # Tests
-examples/fipnum_*,1,*.png
-examples/permx_*,1,*.png
-examples/permz_*,1,*.png
-examples/poro_*,1,*.png
-examples/porv_*,1,*.png
-examples/satnum_*,1,*.png
-examples/sgas_*,1,*.png
-examples/rsw_*,1,*.png
+examples/spe11b_fipnum_*,1,*_t5.png
+examples/spe11b_permx_*,1,*_t5.png
+examples/spe11b_permz_*,1,*_t5.png
+examples/spe11b_poro_*,1,*_t5.png
+examples/spe11b_porv_*,1,*_t5.png
+examples/spe11b_satnum_*,1,*_t5.png
+examples/spe11b_sgas_*,1,*_t4.png
+examples/spe11b_rsw_*,1,*_t5.png
+examples/spe11b_sgas_*,1,*_t5.png
+examples/subfigs_summary.png
+examples/spe11b_xco2l.gif
 examples/fgip.png
 examples/SPE11B-*.vtu
+examples/SPE11B.pvd
 tests/generic_deck
 
 # Python environment
 vplopm/
 
 # Developing
+debugging/
 developing/
 studies/
 prototyping/

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 # plopm: Simplified and flexible tool to visualize OPM Flow geological models
 
 ## Main feature
-Quick generation of PNG figures and VTKs from a OPM Flow type model.
+Quick generation of PNG figures, GIFs, and VTKs from a OPM Flow type model.
 
 ## Installation
 To install the _plopm_ executable in an existing Python environment: 

diff --git a/docs/_images/comparison.png b/docs/_images/comparison.png
diff --git a/docs/_images/fgip.png b/docs/_images/fgip.png
diff --git a/docs/_images/fgip_spe11b.png b/docs/_images/fgip_spe11b.png
diff --git a/docs/_images/fgipm.png b/docs/_images/fgipm.png
diff --git a/docs/_images/norne.png b/docs/_images/norne.png
diff --git a/docs/_images/norne_transformed.png b/docs/_images/norne_transformed.png
diff --git a/docs/_images/satnum_spe11b.png b/docs/_images/satnum_spe11b.png
diff --git a/docs/_images/sgas_diff.png b/docs/_images/sgas_diff.png
diff --git a/docs/_images/sgas_diff_edit.png b/docs/_images/sgas_diff_edit.png
diff --git a/docs/_images/sgas_spe11b.png b/docs/_images/sgas_spe11b.png
diff --git a/docs/_images/spe10.png b/docs/_images/spe10.png
diff --git a/docs/_images/spe10_model2_permz_*,4,*_t0.png b/docs/_images/spe10_model2_permz_*,4,*_t0.png
diff --git a/docs/_images/spe11b_satnum_*,1,*_t5.png b/docs/_images/spe11b_satnum_*,1,*_t5.png
diff --git a/docs/_images/spe11b_sgas_*,1,*_t4.png b/docs/_images/spe11b_sgas_*,1,*_t4.png
diff --git a/docs/_images/wells.png b/docs/_images/wells.png
diff --git a/docs/_images/xco2l.gif b/docs/_images/xco2l.gif
diff --git a/docs/_sources/examples.rst.txt b/docs/_sources/examples.rst.txt
@@ -16,32 +16,27 @@ Then, if you succeed in installing **plopm**, inside the `examples folder <https
 
 the following figure should be generated (this example is used in the `tests <https://github.com/cssr-tools/plopm/blob/main/tests>`_, then it runs with the default terminal argument options).
 
-.. figure:: figs/satnum_spe11b.png
+.. figure:: figs/spe11b_satnum_*,1,*_t5.png
 
-The default argument options are:
-
-.. code-block:: bash
-
-    plopm -i SPE11B -o . -v '' -m png -s ,1, -p flow -z yes -f 14 -x '' -y '' -u resdata  -c ''  -e '' -n '' -b '' -d 8,16 -l '' -t '' -r -1 -w 0 -g 0 -a 1 -time s -ylabel '' -xlabel '' -ylnum 4 -xlnum 4 -cnum '' -clabel '' -labels '' -axgrid 1 -dpi 300 -xformat '' -yformat '' -xunits m -yunits m -remove 0,0,0,0 -facecolor w -save '' -log 0 -rotate 0 -translate '[0,0]' -global 0 -ncolor w
-
-See the :ref:`overview` or run `plopm -h` for the definition of the argument options.
+See the :ref:`overview` or run `plopm -h` for the definition of the argument options, as well as using `-printv` flag to output the available
+summary, init, and restart available variables given an input deck.
 
 For example, for the gas saturation at the report step number 4 using a given colormap (-c):
 
 .. code-block:: bash
 
     plopm -i SPE11B -v sgas -r 4 -c cubehelix
 
-.. figure:: figs/sgas_spe11b.png
+.. figure:: figs/spe11b_sgas_*,1,*_t4.png
 
-and for the gas in place summary vector given a color, line style, font size, dimension of the figure, and using dates for the times:
+and for the gas in place summary vector given a color, line style, font size, dimension of the figure, line width, and using dates for the times:
 
 .. code-block:: bash
 
-    plopm -i SPE11B -v fgip -c b -e ':' -f 12 -d 5,5 -time dates
+    plopm -i SPE11B -v fgip -c b -e dotted -f 12 -d 5,5 -lw 4 -tunits dates
 
-.. figure:: figs/fgip_spe11b.png
-    :scale: 30%
+.. figure:: figs/fgip.png
+    :scale: 7%
 
 ============
 Generic deck 
@@ -52,23 +47,26 @@ for an example where **plopm** is used to generate figures from the
 `SPE10_MODEL2 model <https://github.com/OPM/opm-data/tree/master/spe10model2>`_ by downloading the files and using the
 `OPM Flow <https://opm-project.org/?page_id=19>`_ simulator.
 
-.. image:: ./figs/spe10.png
+.. image:: ./figs/spe10_model2_permz_*,4,*_t0.png
 
 .. code-block:: bash
 
     plopm -i SPE10_MODEL2 -v permz -s ,4, -log 1 -xunits km -yunits km -xlnum 6 -yformat .2f -t 'K$_z$ at the forth slide in the xz plane' -b '[1e-7,1e3]'
 
 Here, we look at the forth slide in the xz plane and use log scale for the permeability in the z direction, as well as changing the axis units to km, 
-setting the format to the numbers to two floats in the y axis, and setting manualli the upper and lower bound for the color map.
+setting the format to the numbers to two floats in the y axis, and setting manually the upper and lower bound for the color map.
 
 To plot information for the grid, and also the location of the wells from the top view, this is achieved by:
 
 .. code-block:: bash
 
-    plopm -i SPE10_MODEL2 -s 1,, -d 3,4 -f 8 -g 1 && plopm -i SPE10_MODEL2 -s 1,, -d 3,4 -f 8 -w 1
+    plopm -i SPE10_MODEL2 -s ,,1 -d 3,4 -f 8 -v grid -remove 0,0,1,0 && plopm -i SPE10_MODEL2 -s ,,1 -d 3,4 -f 8 -v wells -remove 0,0,0,1
 
 .. image:: ./figs/wells.png
 
+Here, we use the remove flag to delete the colorbar axis in the maps for the grid and to delete the generated title in the wells plot (the first entry
+in remove would delete the left axis, e.g., the y label and y ticks in this example, while the second entry if set to 1 would remove the x axis).
+
 ===============================
 Rotation, translation, and zoom
 ===============================
@@ -88,10 +86,31 @@ In order to reduce the white space outside the active cells, as well as to rotat
 
 .. code-block:: bash
 
-    plopm -i NORNE_ATW2013 -s ,,1 -rotate 65 -translate '[6456335.5,-3476500]' -x '[0,5600]' -y '[0,7600]' -f 20
+    plopm -i NORNE_ATW2013 -s ,,1 -rotate 65 -translate '[6456335.5,-3476500]' -x '[0,5600]' -y '[0,7600]' -f 30
 
 .. image:: ./figs/norne_transformed.png
 
+==============
+Convert to VTK 
+==============
+Inside the `examples folder <https://github.com/cssr-tools/plopm/blob/main/examples>`_, then we can create VTKs from the
+OPM Flow simulation results (i.e., .EGRID, .INIT, .UNRST). For example, to create VTKS for the temperature, fipnum, the co2 mass, and the co2 mass fraction in the liquid phase  
+from the restart files from the initial (0) to the number 5 restart, using a OPM Flow build from source in a given path, this can be achieved by:
+
+.. code-block:: bash
+
+    plopm -i SPE11B -v temp,fipnum,co2m,xco2l -vtkformat Float32,UInt16,Float64,Float32 -r 0,5 -m vtk
+
+.. figure:: ./figs/vtk_temp.png
+
+    Visualization using paraview of the grid and temperature after 25 years of CO2 injection.
+
+.. note::
+
+    It is possible to write directly VTKs from OPM Flow simulations by adding the flag **--enable-vtk-output=true**.
+    However, there are quantities that are not written (e.g., fipnum, flores), in addition to quantities not supported
+    such as component mass (e.g., co2, h2o). This is when **plopm** can be helpful.
+
 =====================
 Different input files 
 =====================
@@ -101,49 +120,39 @@ called spe11b_larger_inj. Then, to plot the summary vector for both runs we can
 
 .. code-block:: bash
 
-    plopm -i spe11b/SPE11B,/home/user/spe11b_larger_inj/SPE11B -v fgipm -a 1e-6 -time w -d 5,5 -c r,b -e 'solid;:' -t 'Comparing the total mass' -f 10
+    plopm -i 'spe11b/SPE11B spe11b_larger_inj/SPE11B' -v 'fgip,fgipm,RGIP:3 / 2' -a 1,1e-6 -tunits w -d 10,5 -c r,b -e 'solid,dashed' -t 'Field gas in place  Comparing the total mass  Half gas in place in fipnum 3' -f 14 -subfigs 2,2 -delax 1 -loc empty,empty,empty,center -save comparison
 
-.. image:: ./figs/fgipm.png
-    :scale: 30%
+.. image:: ./figs/comparison.png
+    :scale: 6%
 
-Here, we plot the injected mass and scaled to kilo tons, and the time is shown in weeks.
+Here, using subplots, we plot the gas in place, injected mass and scaled to kilo tons, the regional gas in place in fipnum 3 divided by 2, and the time is shown in weeks.
 
 .. tip::
-    For any summary variable, one can give the path to more than two different simulation cases, just by separating the folder paths by commas in the -i.
+    For any summary variable, one can give the path to more than two different simulation cases, just by separating the folder paths by spaces in the -i.
 
 To look at the difference between these two simulations for the dynamic variable sgas at the restar step 3, this can be achieved by executing:
 
 .. code-block:: bash
 
-    plopm -i spe11b/SPE11B,spe11b_larger_inj/SPE11B -v sgas -r 3
+    plopm -i spe11b_larger_inj/SPE11B -v sgas -r 3 -diff spe11b/SPE11B -remove 0,0,0,1
 
 .. image:: ./figs/sgas_diff.png
 
-To changue the colormap and setting the clorbar limits manually, this can be achieved by:
+To changue the colormap and setting the colorbar limits manually, this can be achieved by:
 
 .. code-block:: bash
 
-    plopm -i spe11b/SPE11B,spe11b_larger_inj/SPE11B -v sgas -r 3 -c tab20c -b '[-0.8,0]' -n "lambda x, _: f'{x:.3f}'"
+    plopm -i spe11b_larger_inj/SPE11B -v sgas -r 3 -diff spe11b/SPE11B -remove 0,0,0,1 -c tab20c_r -b '[0,0.8]' -cformat .3 -cnum 9
 
 .. image:: ./figs/sgas_diff_edit.png
 
-==============
-Convert to VTK 
-==============
-Inside the `examples folder <https://github.com/cssr-tools/plopm/blob/main/examples>`_, then we can create VTKs from the
-OPM Flow simulation results (i.e., .EGRID, .INIT, .UNRST). For example, to create VTKS for the temperature, fipnum, and the co2 mass 
-from the restart files from the initial (0) to the number 5 restart, using a OPM Flow build from source in a given path, this can be achieved by:
+============
+GIF and mask 
+============
+To create a gif and mask the results using the satnum numbers (any variable should be supported) for the different rock properties, this can be achieved by:
 
 .. code-block:: bash
-
-    plopm -i SPE11B -v temp,fipnum,co2m -r 0,5 -m vtk -p /Users/dmar/build/opm-simulators/bin/flow
 
-.. figure:: ./figs/vtk_temp.png
-
-    Visualization using paraview of the grid and temperature after 25 years of CO2 injection.
+    plopm -v xco2l -subfigs 1,2 -i 'spe11b/SPE11B spe11b_larger_inj/SPE11B' -d 16,2.5 -mask satnum -r 0,5 -m gif -dpi 1000 -t "spe11b  spe11b larger injection" -f 16 -interval 1000 -loop 1 -cformat .2f -cbsfax 0.30,0.01,0.4,0.02
 
-.. note::
-
-    It is possible to write directly VTKs from OPM Flow simulations by adding the flag **--enable-vtk-output=true**.
-    However, there are quantities that are not written (e.g., fipnum, flores), in addition to quantities not supported
-    such as component mass (e.g., co2, h2o). This is when **plopm** can be helpful.
+.. image:: ./figs/xco2l.gif
diff --git a/docs/_sources/installation.rst.txt b/docs/_sources/installation.rst.txt
@@ -57,25 +57,25 @@ 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 ../..
 
@@ -106,7 +106,7 @@ 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
@@ -115,18 +115,18 @@ 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 ../..