Merge branch 'docs'

lanl · Feb 1, 2024 · 62e88f7 · 62e88f7
2 parents 3ec9951 + 90cdfcb
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diff --git a/Documentation/sphinx-docs/source/conf.py b/Documentation/sphinx-docs/source/conf.py
@@ -80,7 +80,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en' 
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:

diff --git a/Documentation/sphinx-docs/source/pydfnGen.rst b/Documentation/sphinx-docs/source/pydfnGen.rst
@@ -193,12 +193,8 @@ DFM
 
 Creating a conforming DFM mesh DFN
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: pydfnworks.dfnGen.meshing.dfm
+.. automodule:: pydfnworks.dfnGen.meshing.dfm.mesh_dfm
     :members:  mesh_dfm
 
 
 
-
-
-
-
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -97,6 +97,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="pydfnworks/dfnGen/generation/output_report/gen_output.html">pydfnworks.dfnGen.generation.output_report.gen_output</a></li>
 <li><a href="pydfnworks/dfnGen/generation/stress.html">pydfnworks.dfnGen.generation.stress</a></li>
 <li><a href="pydfnworks/dfnGen/meshing/add_attribute_to_mesh.html">pydfnworks.dfnGen.meshing.add_attribute_to_mesh</a></li>
+<li><a href="pydfnworks/dfnGen/meshing/dfm/mesh_dfm.html">pydfnworks.dfnGen.meshing.dfm.mesh_dfm</a></li>
 <li><a href="pydfnworks/dfnGen/meshing/mapdfn_ecpm/mapdfn_ecpm.html">pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm</a></li>
 <li><a href="pydfnworks/dfnGen/meshing/mesh_dfn/mesh_dfn.html">pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn</a></li>
 <li><a href="pydfnworks/dfnGen/meshing/mesh_dfn/mesh_dfn_helper.html">pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper</a></li>

diff --git a/docs/_modules/pydfnworks/dfnGen/meshing/mesh_dfn/mesh_dfn.html b/docs/_modules/pydfnworks/dfnGen/meshing/mesh_dfn/mesh_dfn.html
@@ -93,6 +93,7 @@ <h1>Source code for pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn</h1><div class="
 <span class="sd">.. moduleauthor:: Jeffrey Hyman &lt;[email protected]&gt;</span>
 
 <span class="sd">&quot;&quot;&quot;</span>
+
 <span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">import</span> <span class="nn">sys</span>
 <span class="kn">import</span> <span class="nn">shutil</span>
@@ -119,21 +120,20 @@ <h1>Source code for pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn</h1><div class="
                  <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
                  <span class="n">quiet</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    </span>
-<span class="sd">    Mesh fracture network using LaGriT</span>
+<span class="sd">      Mesh fracture network using LaGriT</span>
 
 <span class="sd">    Parameters</span>
-<span class="sd">    ------------</span>
+<span class="sd">    ----------</span>
 <span class="sd">        self : object </span>
 <span class="sd">            DFN Class</span>
 <span class="sd">        uniform_mesh : bool</span>
 <span class="sd">            toggle for uniform or variable mesh. Default : False </span>
 <span class="sd">        min_dist : float</span>
-<span class="sd">            Defines the minimum distance from the intersections with resolution h/2. This value is the factor of h, distance = min_dist x h</span>
+<span class="sd">            Defines the minimum distance from the intersections with resolution h/2. This value is the factor of h, distance = min_dist * h</span>
 <span class="sd">        max_dist : float</span>
-<span class="sd">            Defines the minimum distance from the intersections with resolution max_resolution x h. This value is the factor of h, distance = max_dist x h</span>
+<span class="sd">            Defines the minimum distance from the intersections with resolution max_resolution * h. This value is the factor of h, distance = max_dist * h</span>
 <span class="sd">        max_resolution_factor : float</span>
-<span class="sd">            Maximum factor of the mesh resolultion (max_resolution x h). Depending on the slope of the linear function and size of the fracture, this may not be realized in the mesh. </span>
+<span class="sd">            Maximum factor of the mesh resolultion (max_resolution *h). Depending on the slope of the linear function and size of the fracture, this may not be realized in the mesh. </span>
 <span class="sd">        cleanup : bool</span>
 <span class="sd">            toggle to clean up directory (remove meshing files after a run). Default : True</span>
 <span class="sd">        strict : bool</span>
@@ -142,11 +142,11 @@ <h1>Source code for pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn</h1><div class="
 <span class="sd">            Toggle to turn on/off verbose information to screen about meshing. Default is true, does not print to screen</span>
 
 <span class="sd">    Returns</span>
-<span class="sd">    ------------</span>
+<span class="sd">    -------</span>
 <span class="sd">        None</span>
 
 <span class="sd">    Notes</span>
-<span class="sd">    ------------</span>
+<span class="sd">    ------</span>
 <span class="sd">        1. All fractures in self.prune_file must intersect at least 1 other fracture</span>
 
 <span class="sd">    &quot;&quot;&quot;</span>

diff --git a/docs/_sources/pydfnGen.rst.txt b/docs/_sources/pydfnGen.rst.txt
@@ -193,12 +193,8 @@ DFM
 
 Creating a conforming DFM mesh DFN
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: pydfnworks.dfnGen.meshing.dfm
+.. automodule:: pydfnworks.dfnGen.meshing.dfm.mesh_dfm
     :members:  mesh_dfm
 
 
 
-
-
-
-
diff --git a/docs/genindex.html b/docs/genindex.html
@@ -264,8 +264,17 @@ <h2 id="M">M</h2>
       <li><a href="pydfnGen.html#pydfnworks.dfnGen.meshing.udfm.map2continuum.map_to_continuum">map_to_continuum() (in module pydfnworks.dfnGen.meshing.udfm.map2continuum)</a>
 </li>
       <li><a href="pydfnGen.html#pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm.mapdfn_ecpm">mapdfn_ecpm() (in module pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm)</a>
+</li>
+      <li><a href="pydfnGen.html#pydfnworks.dfnGen.meshing.dfm.mesh_dfm.mesh_dfm">mesh_dfm() (in module pydfnworks.dfnGen.meshing.dfm.mesh_dfm)</a>
 </li>
       <li>
+    mesh_dfm.py
+
+      <ul>
+        <li><a href="pydfnGen.html#module-mesh_dfm.py">module</a>
+</li>
+      </ul></li>
+      <li>
     mesh_dfn.py
 
       <ul>
@@ -290,6 +299,8 @@ <h2 id="M">M</h2>
         <li><a href="pydfnGraph.html#module-graph_transport.py">graph_transport.py</a>
 </li>
         <li><a href="pydfnGen.html#module-map2continuum.py">map2continuum.py</a>
+</li>
+        <li><a href="pydfnGen.html#module-mesh_dfm.py">mesh_dfm.py</a>
 </li>
         <li><a href="pydfnGen.html#module-mesh_dfn.py">mesh_dfn.py</a>
 </li>
@@ -315,7 +326,7 @@ <h2 id="M">M</h2>
 </li>
         <li><a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.add_attribute_to_mesh">pydfnworks.dfnGen.meshing.add_attribute_to_mesh</a>
 </li>
-        <li><a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.dfm">pydfnworks.dfnGen.meshing.dfm</a>
+        <li><a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.dfm.mesh_dfm">pydfnworks.dfnGen.meshing.dfm.mesh_dfm</a>
 </li>
         <li><a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm">pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm</a>
 </li>
@@ -445,10 +456,10 @@ <h2 id="P">P</h2>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li>
-    pydfnworks.dfnGen.meshing.dfm
+    pydfnworks.dfnGen.meshing.dfm.mesh_dfm
 
       <ul>
-        <li><a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.dfm">module</a>
+        <li><a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.dfm.mesh_dfm">module</a>
 </li>
       </ul></li>
       <li>

diff --git a/docs/index.html b/docs/index.html
@@ -190,7 +190,7 @@ <h1>Welcome to dfnWorks 2.8 documentation!<a class="headerlink" href="#welcome-t
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="pydfnGen.html#dfm">DFM</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.dfm">Creating a conforming DFM mesh DFN</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.dfm.mesh_dfm">Creating a conforming DFM mesh DFN</a></li>
 </ul>
 </li>
 </ul>

diff --git a/docs/index_docs.html b/docs/index_docs.html
@@ -191,7 +191,7 @@ <h1>Welcome to dfnWorks 2.8 documentation!<a class="headerlink" href="#welcome-t
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="pydfnGen.html#dfm">DFM</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.dfm">Creating a conforming DFM mesh DFN</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.dfm.mesh_dfm">Creating a conforming DFM mesh DFN</a></li>
 </ul>
 </li>
 </ul>

diff --git a/docs/objects.inv b/docs/objects.inv
diff --git a/docs/py-modindex.html b/docs/py-modindex.html
@@ -146,20 +146,31 @@ <h1>Python Module Index</h1>
        <td><img src="_static/minus.png" class="toggler"
               id="toggle-4" style="display: none" alt="-" /></td>
        <td>
-       <code class="xref">mesh_dfn</code></td><td>
+       <code class="xref">mesh_dfm</code></td><td>
        <em></em></td></tr>
      <tr class="cg-4">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="pydfnGen.html#module-mesh_dfm.py"><code class="xref">mesh_dfm.py</code></a></td><td>
+       <em>meshing driver for conforming DFM</em></td></tr>
+     <tr>
+       <td><img src="_static/minus.png" class="toggler"
+              id="toggle-5" style="display: none" alt="-" /></td>
+       <td>
+       <code class="xref">mesh_dfn</code></td><td>
+       <em></em></td></tr>
+     <tr class="cg-5">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-mesh_dfn.py"><code class="xref">mesh_dfn.py</code></a></td><td>
        <em>meshing driver for DFN</em></td></tr>
      <tr>
        <td><img src="_static/minus.png" class="toggler"
-              id="toggle-5" style="display: none" alt="-" /></td>
+              id="toggle-6" style="display: none" alt="-" /></td>
        <td>
        <code class="xref">mesh_dfn_helper</code></td><td>
        <em></em></td></tr>
-     <tr class="cg-5">
+     <tr class="cg-6">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-mesh_dfn_helper.py"><code class="xref">mesh_dfn_helper.py</code></a></td><td>
@@ -169,121 +180,121 @@ <h1>Python Module Index</h1>
        <strong>p</strong></td><td></td></tr>
      <tr>
        <td><img src="_static/minus.png" class="toggler"
-              id="toggle-6" style="display: none" alt="-" /></td>
+              id="toggle-7" style="display: none" alt="-" /></td>
        <td>
        <code class="xref">pydfnworks</code></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnFlow.html#module-pydfnworks.dfnFlow.fehm"><code class="xref">pydfnworks.dfnFlow.fehm</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnFlow.html#module-pydfnworks.dfnFlow.flow"><code class="xref">pydfnworks.dfnFlow.flow</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnFlow.html#module-pydfnworks.dfnFlow.mass_balance"><code class="xref">pydfnworks.dfnFlow.mass_balance</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnFlow.html#module-pydfnworks.dfnFlow.pflotran"><code class="xref">pydfnworks.dfnFlow.pflotran</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.generation.generator"><code class="xref">pydfnworks.dfnGen.generation.generator</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.generation.input_checking"><code class="xref">pydfnworks.dfnGen.generation.input_checking</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions"><code class="xref">pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.generation.output_report.gen_output"><code class="xref">pydfnworks.dfnGen.generation.output_report.gen_output</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.generation.stress"><code class="xref">pydfnworks.dfnGen.generation.stress</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.add_attribute_to_mesh"><code class="xref">pydfnworks.dfnGen.meshing.add_attribute_to_mesh</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.dfm"><code class="xref">pydfnworks.dfnGen.meshing.dfm</code></a></td><td>
+       <a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.dfm.mesh_dfm"><code class="xref">pydfnworks.dfnGen.meshing.dfm.mesh_dfm</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm"><code class="xref">pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn"><code class="xref">pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper"><code class="xref">pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.udfm.false_connections"><code class="xref">pydfnworks.dfnGen.meshing.udfm.false_connections</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.udfm.map2continuum"><code class="xref">pydfnworks.dfnGen.meshing.udfm.map2continuum</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.udfm.upscale"><code class="xref">pydfnworks.dfnGen.meshing.udfm.upscale</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnWorks-well.html#module-pydfnworks.dfnGen.well_package.wells"><code class="xref">pydfnworks.dfnGen.well_package.wells</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGraph.html#module-pydfnworks.dfnGraph.dfn2graph"><code class="xref">pydfnworks.dfnGraph.dfn2graph</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGraph.html#module-pydfnworks.dfnGraph.graph_flow"><code class="xref">pydfnworks.dfnGraph.graph_flow</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGraph.html#module-pydfnworks.dfnGraph.graph_transport"><code class="xref">pydfnworks.dfnGraph.graph_transport</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGraph.html#module-pydfnworks.dfnGraph.pruning"><code class="xref">pydfnworks.dfnGraph.pruning</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-6">
+     <tr class="cg-7">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnTrans.html#module-pydfnworks.dfnTrans.transport"><code class="xref">pydfnworks.dfnTrans.transport</code></a></td><td>
@@ -293,11 +304,11 @@ <h1>Python Module Index</h1>
        <strong>u</strong></td><td></td></tr>
      <tr>
        <td><img src="_static/minus.png" class="toggler"
-              id="toggle-7" style="display: none" alt="-" /></td>
+              id="toggle-8" style="display: none" alt="-" /></td>
        <td>
        <code class="xref">upscale</code></td><td>
        <em></em></td></tr>
-     <tr class="cg-7">
+     <tr class="cg-8">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="pydfnGen.html#module-upscale.py"><code class="xref">upscale.py</code></a></td><td>