cssr-tools · daavid00 · Jan 7, 2025 · Jan 7, 2025
diff --git a/README.md b/README.md
@@ -53,7 +53,7 @@ See the [_examples_](https://cssr-tools.github.io/plopm/examples.html) in the [_
 ## Citing
 If you would like to cite this repository:
 
-* Landa-Marbán, D. 2024. plopm: Quick generation of PNGs, GIFs, and VTKs from a OPM Flow type model. v2024.04. https://doi.org/10.5281/zenodo.13332415.
+* Landa-Marbán, D. 2024. plopm: Quick generation of PNGs, GIFs, and VTKs from a OPM Flow type model. https://doi.org/10.5281/zenodo.13332415.
 
 ## About plopm
 The _plopm_ 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) 

diff --git a/docs/_sources/examples.rst.txt b/docs/_sources/examples.rst.txt
@@ -86,7 +86,7 @@ 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 30
+    plopm -i NORNE_ATW2013 -s ,,1 -ro
8000
tate 65 -translate '[6456335.5,-3476500]' -x '[0,5600]' -y '[0,7600]' -f 8
 
 .. image:: ./figs/norne_transformed.png
 
@@ -95,7 +95,7 @@ To show all faults in the model and to only show the ones connected all along th
 .. code-block:: bash
 
     plopm -i NORNE_ATW2013 -v faults -s ,,1 -rotate 65 -translate '[6456335.5,-3476500]' -x '[0,5600]' -y '[0,8800]' -f 8 -global 1
-    plopm -i NORNE_ATW2013 -v faults -s ,,1:22 -rotate 65 -translate '[6456335.5,-3476500]' -x '[0,5600]' -y '[0,8800]' -f 8
+    plopm -i NORNE_ATW2013 -v faults -s ,,1:22 -rotate 65 -translate '[6456335.5,-3476500]' -x '[0,5600]' -y '[0,8800]' -f 8 -how max
 
 .. image:: ./figs/norne_faults.png
 
@@ -164,7 +164,7 @@ To changue the colormap and setting the colorbar limits manually, this can be ac
 
 .. code-block:: bash
 
-    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
+    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]' -cnum 9
 
 .. image:: ./figs/sgas_diff_edit.png
 

diff --git a/docs/_sources/introduction.rst.txt b/docs/_sources/introduction.rst.txt
@@ -44,7 +44,7 @@ where
 -c    Specify the colormap, e.g., 'jet', or color(s) for the summary, e.g., 'b,r' ('' by default, i.e., set by plopm).
 -e    Specify the linestyles, e.g., 'solid,dotted' ('' by default, i.e., set by plopm).
 -b    Specify the upper and lower bounds for the color map, e.g., '[-0.1,11]' ('' by default, i.e., set by plopm).
--d    Specify the dimensions in inches generated png, e.g., '8,16' ('5,5' by default).
+-d    Specify the dimensions in inches generated png, e.g., '8,16' ('7,5' by default).
 -t    Specify the figure title, e.g., 'Final saturation map' ('' by default, i.e., set by plopm).
 -r    Restart number to plot the dynamic variable, where 0 corresponds to the initial one ('-1' by default, i.e., the last restart file).
 -a    Scale the mass variable, e.g., 1e-9 for the color bar for the CO2 mass to be in Mt ('1' by default).
@@ -69,6 +69,7 @@ where
 -facecolor  Color outside the spatial map ('w' by default, i.e., white).
 -save       Name of the output files ('' by default, i.e., set by plopm).
 -log        Log scale for the color map ('0' by default).
+-clogthks   Set the thicks for the color maps with log scale, e.g., '[1,2,3]' ('' by default).
 -rotate     Grades to rotate the grid in the 2D maps ('0' by default).
 -translate  Translate the grid in the 2D maps x,y directions ('[0,0]' by default).
 -global     Min and max in the colorbars from the current 2D slide values (0) or whole 3D model '1' ('0' by default).

diff --git a/docs/_sources/related.rst.txt b/docs/_sources/related.rst.txt
@@ -29,7 +29,7 @@ expreccs
 .. image:: ./figs/expreccs.gif
     :scale: 50%
 
-`Expansion of ResourCes for CO2 Storage on the Horda Platform <https://github.com/cssr-tools/expreccs>`_.
+`A Python framework using OPM Flow to simulate regional and site reservoirs for CO2 storage <https://github.com/cssr-tools/expreccs>`_.
 
 ******
 pycopm

diff --git a/docs/_static/pygments.css b/docs/_static/pygments.css
@@ -6,9 +6,9 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
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@@ -67,9 +67,9 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
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diff --git a/docs/about.html b/docs/about.html
@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>About plopm &mdash; plopm  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" />
 
 

diff --git a/docs/api.html b/docs/api.html
@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>plopm Python API &mdash; plopm  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" />
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diff --git a/docs/contributing.html b/docs/contributing.html
@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Contributing &mdash; plopm  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" />
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diff --git a/docs/examples.html b/docs/examples.html
@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Examples &mdash; plopm  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" />
 
 
@@ -148,13 +148,13 @@ <h2>Rotation, translation, and zoom<a class="headerlink" href="#rotation-transla
 <p>these are some of the generated figures:</p>
 <img alt="_images/norne.png" src="_images/norne.png" />
 <p>In order to reduce the white space outside the active cells, as well as to rotate the grid and translate it, this can be ahieved by:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>plopm<span class="w"> </span>-i<span class="w"> </span>NORNE_ATW2013<span class="w"> </span>-s<span class="w"> </span>,,1<span class="w"> </span>-rotate<span class="w"> </span><span class="m">65</span><span class="w"> </span>-translate<span class="w"> </span><span class="s1">&#39;[6456335.5,-3476500]&#39;</span><span class="w"> </span>-x<span class="w"> </span><span class="s1">&#39;[0,5600]&#39;</span><span class="w"> </span>-y<span class="w"> </span><span class="s1">&#39;[0,7600]&#39;</span><span class="w"> </span>-f<span class="w"> </span><span class="m">30</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>plopm<span class="w"> </span>-i<span class="w"> </span>NORNE_ATW2013<span class="w"> </span>-s<span class="w"> </span>,,1<span class="w"> </span>-rotate<span class="w"> </span><span class="m">65</span><span class="w"> </span>-translate<span class="w"> </span><span class="s1">&#39;[6456335.5,-3476500]&#39;</span><span class="w"> </span>-x<span class="w"> </span><span class="s1">&#39;[0,5600]&#39;</span><span class="w"> </span>-y<span class="w"> </span><span class="s1">&#39;[0,7600]&#39;</span><span class="w"> </span>-f<span class="w"> </span><span class="m">8</span>
 </pre></div>
 </div>
 <img alt="_images/norne_transformed.png" src="_images/norne_transformed.png" />
 <p>To show all faults in the model and to only show the ones connected all along the z direction, this can be achieved by:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>plopm<span class="w"> </span>-i<span class="w"> </span>NORNE_ATW2013<span class="w"> </span>-v<span class="w"> </span>faults<span class="w"> </span>-s<span class="w"> </span>,,1<span class="w"> </span>-rotate<span class="w"> </span><span class="m">65</span><span class="w"> </span>-translate<span class="w"> </span><span class="s1">&#39;[6456335.5,-3476500]&#39;</span><span class="w"> </span>-x<span class="w"> </span><span class="s1">&#39;[0,5600]&#39;</span><span class="w"> </span>-y<span class="w"> </span><span class="s1">&#39;[0,8800]&#39;</span><span class="w"> </span>-f<span class="w"> </span><span class="m">8</span><span class="w"> </span>-global<span class="w"> </span><span class="m">1</span>
-plopm<span class="w"> </span>-i<span class="w"> </span>NORNE_ATW2013<span class="w"> </span>-v<span class="w"> </span>faults<span class="w"> </span>-s<span class="w"> </span>,,1:22<span class="w"> </span>-rotate<span class="w"> </span><span class="m">65</span><span class="w"> </span>-translate<span class="w"> </span><span class="s1">&#39;[6456335.5,-3476500]&#39;</span><span class="w"> </span>-x<span class="w"> </span><span class="s1">&#39;[0,5600]&#39;</span><span class="w"> </span>-y<span class="w"> </span><span class="s1">&#39;[0,8800]&#39;</span><span class="w"> </span>-f<span class="w"> </span><span class="m">8</span>
+plopm<span class="w"> </span>-i<span class="w"> </span>NORNE_ATW2013<span class="w"> </span>-v<span class="w"> </span>faults<span class="w"> </span>-s<span class="w"> </span>,,1:22<span class="w"> </span>-rotate<span class="w"> </span><span class="m">65</span><span class="w"> </span>-translate<span class="w"> </span><span class="s1">&#39;[6456335.5,-3476500]&#39;</span><span class="w"> </span>-x<span class="w"> </span><span class="s1">&#39;[0,5600]&#39;</span><span class="w"> </span>-y<span class="w"> </span><span class="s1">&#39;[0,8800]&#39;</span><span class="w"> </span>-f<span class="w"> </span><span class="m">8</span><span class="w"> </span>-how<span class="w"> </span>max
 </pre></div>
 </div>
 <img alt="_images/norne_faults.png" src="_images/norne_faults.png" />
@@ -211,7 +211,7 @@ <h2>Different input files<a class="headerlink" href="#different-input-files" tit
 </div>
 <img alt="_images/sgas_diff.png" src="_images/sgas_diff.png" />
 <p>To changue the colormap and setting the colorbar limits manually, this can be achieved by:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>plopm<span class="w"> </span>-i<span class="w"> </span>spe11b_larger_inj/SPE11B<span class="w"> </span>-v<span class="w"> </span>sgas<span class="w"> </span>-r<span class="w"> </span><span class="m">3</span><span class="w"> </span>-diff<span class="w"> </span>spe11b/SPE11B<span class="w"> </span>-remove<span class="w"> </span><span class="m">0</span>,0,0,1<span class="w"> </span>-c<span class="w"> </span>tab20c_r<span class="w"> </span>-b<span class="w"> </span><span class="s1">&#39;[0,0.8]&#39;</span><span class="w"> </span>-cformat<span class="w"> </span>.3<span class="w"> </span>-cnum<span class="w"> </span><span class="m">9</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>plopm<span class="w"> </span>-i<span class="w"> </span>spe11b_larger_inj/SPE11B<span class="w"> </span>-v<span class="w"> </span>sgas<span class="w"> </span>-r<span class="w"> </span><span class="m">3</span><span class="w"> </span>-diff<span class="w"> </span>spe11b/SPE11B<span class="w"> </span>-remove<span class="w"> </span><span class="m">0</span>,0,0,1<span class="w"> </span>-c<span class="w"> </span>tab20c_r<span class="w"> </span>-b<span class="w"> </span><span class="s1">&#39;[0,0.8]&#39;</span><span class="w"> </span>-cnum<span class="w"> </span><span class="m">9</span>
 </pre></div>
 </div>
 <img alt="_images/sgas_diff_edit.png" src="_images/sgas_diff_edit.png" />

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -6,7 +6,7 @@
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Index &mdash; plopm  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" />
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diff --git a/docs/index.html b/docs/index.html
@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Welcome to plopm’s documentation! &mdash; plopm  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" />
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diff --git a/docs/installation.html b/docs/installation.html
@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Installation &mdash; plopm  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" />
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diff --git a/docs/introduction.html b/docs/introduction.html
@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Introduction &mdash; plopm  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" />
 
 
@@ -148,7 +148,7 @@ <h2>Concept<a class="headerlink" href="#concept" title="Link to this heading">
 <dd><p>Specify the upper and lower bounds for the color map, e.g., ‘[-0.1,11]’ (’’ by default, i.e., set by plopm).</p>
 </dd>
 <dt><kbd><span class="option">-d</span></kbd></dt>
-<dd><p>Specify the dimensions in inches generated png, e.g., ‘8,16’ (‘5,5’ by default).</p>
+<dd><p>Specify the dimensions in inches generated png, e.g., ‘8,16’ (‘7,5’ by default).</p>
 </dd>
 <dt><kbd><span class="option">-t</span></kbd></dt>
 <dd><p>Specify the figure title, e.g., ‘Final saturation map’ (’’ by default, i.e., set by plopm).</p>
@@ -222,6 +222,9 @@ <h2>Concept<a class="headerlink" href="#concept" title="Link to this heading">
 <dt><kbd><span class="option">-l<var>og</var></span></kbd></dt>
 <dd><p>Log scale for the color map (‘0’ by default).</p>
 </dd>
+<dt><kbd><span class="option">-c<var>logthks</var></span></kbd></dt>
+<dd><p>Set the thicks for the color maps with log scale, e.g., ‘[1,2,3]’ (’’ by default).</p>
+</dd>
 <dt><kbd><span class="option">-r<var>otate</var></span></kbd></dt>
 <dd><p>Grades to rotate the grid in the 2D maps (‘0’ by default).</p>
 </dd>

diff --git a/docs/modules.html b/docs/modules.html
@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>plopm &mdash; plopm  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" />
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diff --git a/docs/plopm.core.html b/docs/plopm.core.html
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>plopm.core package &mdash; plopm  documentation</title>
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diff --git a/docs/plopm.core.plopm.html b/docs/plopm.core.plopm.html
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