new v2.8 docs

lanl · Feb 1, 2024 · f5b82dd · f5b82dd
1 parent 8a71a63
commit f5b82dd
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Showing 48 changed files with 1,494 additions and 14,229 deletions.
diff --git a/docs/_config.yml b/docs/_config.yml
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -28,7 +28,7 @@
 
 
 
-          <a href="../index.html" class="icon icon-home">
+          <a href="../index_docs.html" class="icon icon-home">
             dfnWorks
               <img src="../_static/dfnworks_logo.png" class="logo" alt="Logo"/>
           </a>
@@ -68,14 +68,14 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="../index.html">dfnWorks</a>
+          <a href="../index_docs.html">dfnWorks</a>
       </nav>
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li><a href="../index_docs.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">Overview: module code</li>
       <li class="wy-breadcrumbs-aside">
       </li>
@@ -97,8 +97,9 @@ <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/mesh_dfn.html">pydfnworks.dfnGen.meshing.mesh_dfn</a></li>
-<li><a href="pydfnworks/dfnGen/meshing/mesh_dfn_helper.html">pydfnworks.dfnGen.meshing.mesh_dfn_helper</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>
 <li><a href="pydfnworks/dfnGen/meshing/udfm/false_connections.html">pydfnworks.dfnGen.meshing.udfm.false_connections</a></li>
 <li><a href="pydfnworks/dfnGen/meshing/udfm/map2continuum.html">pydfnworks.dfnGen.meshing.udfm.map2continuum</a></li>
 <li><a href="pydfnworks/dfnGen/meshing/udfm/upscale.html">pydfnworks.dfnGen.meshing.udfm.upscale</a></li>

diff --git a/docs/_modules/pydfnworks/dfnFlow/fehm.html b/docs/_modules/pydfnworks/dfnFlow/fehm.html
@@ -119,18 +119,19 @@ <h1>Source code for pydfnworks.dfnFlow.fehm</h1><div class="highlight"><pre>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="c1"># Make input file for C Stor converter</span>
     <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">flow_solver</span> <span class="o">!=</span> <span class="s2">&quot;FEHM&quot;</span><span class="p">:</span>
-        <span class="n">error</span> <span class="o">=</span> <span class="s2">&quot;ERROR! Wrong flow solver requested</span><span class="se">\n</span><span class="s2">&quot;</span>
+        <span class="n">error</span> <span class="o">=</span> <span class="s2">&quot;Error. Incorrect flow solver requested</span><span class="se">\n</span><span class="s2">&quot;</span>
         <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">error</span><span class="p">)</span>
         <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
 
+    <span class="bp">self</span><span class="o">.</span><span class="n">dump_hydraulic_values</span><span class="p">(</span><span class="nb">format</span> <span class="o">=</span> <span class="s2">&quot;FEHM&quot;</span><span class="p">)</span>
+
     <span class="bp">self</span><span class="o">.</span><span class="n">stor_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">inp_file</span><span class="p">[:</span><span class="o">-</span><span class="mi">4</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;.stor&#39;</span>
     <span class="bp">self</span><span class="o">.</span><span class="n">mat_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">inp_file</span><span class="p">[:</span><span class="o">-</span><span class="mi">4</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;_material.zone&#39;</span>
-    <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;convert_stor_params.txt&quot;</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span>
-    <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="se">\n</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">mat_file</span><span class="p">)</span>
-    <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="se">\n</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">stor_file</span><span class="p">)</span>
-    <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stor_file</span><span class="p">[:</span><span class="o">-</span><span class="mi">5</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;_vol_area.stor</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">))</span>
-    <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="se">\n</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">aper_file</span><span class="p">)</span>
-    <span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;convert_stor_params.txt&quot;</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="se">\n</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">mat_file</span><span class="p">)</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="se">\n</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">stor_file</span><span class="p">)</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stor_file</span><span class="p">[:</span><span class="o">-</span><span class="mi">5</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;_vol_area.stor</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">))</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="se">\n</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">aper_file</span><span class="p">)</span>
 
     <span class="n">t</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span>
     <span class="n">cmd</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;CORRECT_STOR_EXE&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39; convert_stor_params.txt&#39;</span>
@@ -194,15 +195,15 @@ <h1>Source code for pydfnworks.dfnFlow.fehm</h1><div class="highlight"><pre>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;--&gt; Running FEHM&quot;</span><span class="p">)</span>
     <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">flow_solver</span> <span class="o">!=</span> <span class="s2">&quot;FEHM&quot;</span><span class="p">:</span>
-        <span class="n">error</span> <span class="o">=</span> <span class="s2">&quot;ERROR! Wrong flow solver requested</span><span class="se">\n</span><span class="s2">&quot;</span>
+        <span class="n">error</span> <span class="o">=</span> <span class="s2">&quot;Error. Incorrect flow solver requested</span><span class="se">\n</span><span class="s2">&quot;</span>
         <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">error</span><span class="p">)</span>
         <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
 
     <span class="k">try</span><span class="p">:</span>
-        <span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dfnFlow_file</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">())</span>
+        <span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dfnFlow_file</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobname</span><span class="p">)</span>
     <span class="k">except</span><span class="p">:</span>
-        <span class="n">error</span> <span class="o">=</span> <span class="s2">&quot;--&gt;ERROR copying FEHM run file: </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">dfnFlow_file</span>
-        <span class="n">std</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">error</span><span class="p">)</span>
+        <span class="n">error</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;--&gt; Error copying FEHM run file: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">dfnFlow_file</span><span class="si">}</span><span class="s2">&quot;</span>
+        <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">error</span><span class="p">)</span>
         <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
 
     <span class="n">path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">dfnFlow_file</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">local_dfnFlow_file</span><span class="p">)</span>

diff --git a/docs/_modules/pydfnworks/dfnFlow/flow.html b/docs/_modules/pydfnworks/dfnFlow/flow.html
@@ -217,10 +217,10 @@ <h1>Source code for pydfnworks.dfnFlow.flow</h1><div class="highlight"><pre>
     <span class="n">files</span> <span class="o">=</span> <span class="p">[</span>
         <span class="s1">&#39;full_mesh.uge&#39;</span><span class="p">,</span> <span class="s1">&#39;full_mesh.inp&#39;</span><span class="p">,</span> <span class="s1">&#39;full_mesh_vol_area.uge&#39;</span><span class="p">,</span>
         <span class="s1">&#39;materialid.dat&#39;</span><span class="p">,</span> <span class="s1">&#39;full_mesh.stor&#39;</span><span class="p">,</span> <span class="s1">&#39;full_mesh_material.zone&#39;</span><span class="p">,</span>
-        <span class="s1">&#39;full_mesh.fehmn&#39;</span><span class="p">,</span> <span class="s1">&#39;allboundaries.zone&#39;</span><span class="p">,</span> <span class="s1">&#39;pboundary_bottom.zone&#39;</span><span class="p">,</span>
-        <span class="s1">&#39;pboundary_top.zone&#39;</span><span class="p">,</span> <span class="s1">&#39;pboundary_back_s.zone&#39;</span><span class="p">,</span>
-        <span class="s1">&#39;pboundary_front_n.zone&#39;</span><span class="p">,</span> <span class="s1">&#39;pboundary_left_w.zone&#39;</span><span class="p">,</span>
-        <span class="s1">&#39;pboundary_right_e.zone&#39;</span><span class="p">,</span> <span class="s1">&#39;perm.dat&#39;</span><span class="p">,</span> <span class="s1">&#39;aperture.dat&#39;</span><span class="p">,</span> <span class="s1">&#39;params.txt&#39;</span>
+        <span class="s1">&#39;full_mesh.fehmn&#39;</span><span class="p">,</span> <span class="s1">&#39;allboundaries.zone&#39;</span><span class="p">,</span> <span class="s1">&#39;boundary_bottom.zone&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;boundary_top.zone&#39;</span><span class="p">,</span> <span class="s1">&#39;boundary_back_s.zone&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;boundary_front_n.zone&#39;</span><span class="p">,</span> <span class="s1">&#39;boundary_left_w.zone&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;boundary_right_e.zone&#39;</span><span class="p">,</span> <span class="s1">&#39;perm.dat&#39;</span><span class="p">,</span> <span class="s1">&#39;aperture.dat&#39;</span><span class="p">,</span> <span class="s1">&#39;params.txt&#39;</span>
     <span class="p">]</span>
     <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
         <span class="k">try</span><span class="p">:</span>