update docs accordingly and imports

WMD-group · Aug 17, 2023 · d9ad61a · d9ad61a
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diff --git a/.gitignore b/.gitignore
@@ -144,15 +144,14 @@ dmypy.json
 Affinity/
 .vscode/settings.json
 
-# Miscellaneous
-shakenbreak/.vscode/settings.json
-snb_test.ipynb
-
 # Sourcery
 .sourcery.yaml
 
 # Conda Packaging Notes
 conda_packaging.md
 
+# Miscellaneous
 docs/_build/*
-docs/_build/html
+docs/_build/doctrees/*
+docs/_build/html/
+docs/_build/_sources/
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/macrodensity.alpha.doctree b/docs/_build/doctrees/macrodensity.alpha.doctree
diff --git a/docs/_build/doctrees/macrodensity.density.doctree b/docs/_build/doctrees/macrodensity.density.doctree
diff --git a/docs/_build/doctrees/macrodensity.doctree b/docs/_build/doctrees/macrodensity.doctree
diff --git a/docs/_build/doctrees/macrodensity.plotting.doctree b/docs/_build/doctrees/macrodensity.plotting.doctree
diff --git a/docs/_build/html/_sources/index.rst b/docs/_build/html/_sources/index.rst
@@ -6,9 +6,7 @@
 Welcome to MacroDensity
 =======================
 
-Summary
-=======
-``MacroDensity`` is a Python package to read and process electrostatic potential and 
+``MacroDensity`` is a Python package to post-process electrostatic potential and 
 electron density files from electronic structure calculations and plot in a number of ways, including:
 
 1. Planar average

diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html
@@ -271,43 +271,20 @@ <h1></h1>
 <h1 id="index">Index</h1>
 
 <div class="genindex-jumpbox">
- <a href="#B"><strong>B</strong></a>
- | <a href="#C"><strong>C</strong></a>
- | <a href="#D"><strong>D</strong></a>
+ <a href="#D"><strong>D</strong></a>
  | <a href="#E"><strong>E</strong></a>
  | <a href="#G"><strong>G</strong></a>
  | <a href="#I"><strong>I</strong></a>
  | <a href="#M"><strong>M</strong></a>
  | <a href="#N"><strong>N</strong></a>
  | <a href="#O"><strong>O</strong></a>
  | <a href="#P"><strong>P</strong></a>
- | <a href="#R"><strong>R</strong></a>
  | <a href="#S"><strong>S</strong></a>
  | <a href="#T"><strong>T</strong></a>
  | <a href="#U"><strong>U</strong></a>
  | <a href="#V"><strong>V</strong></a>
 
 </div>
-<h2 id="B">B</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.bulk_interstitial_alignment">bulk_interstitial_alignment() (in module macrodensity.alpha)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.bulk_vac">bulk_vac() (in module macrodensity.alpha)</a>
-</li>
-  </ul></td>
-</tr></table>
-
-<h2 id="C">C</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.create_plotting_mesh">create_plotting_mesh() (in module macrodensity.alpha)</a>
-</li>
-  </ul></td>
-</tr></table>
-
 <h2 id="D">D</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
@@ -316,8 +293,6 @@ <h2 id="D">D</h2>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="macrodensity.density.html#macrodensity.density.density_2_grid_gulp">density_2_grid_gulp() (in module macrodensity.density)</a>
-</li>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.diff_potentials">diff_potentials() (in module macrodensity.alpha)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -326,12 +301,6 @@ <h2 id="E">E</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="macrodensity.density.html#macrodensity.density.element_vol">element_vol() (in module macrodensity.density)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.plotting.html#macrodensity.plotting.energy_band_alignment_diagram">energy_band_alignment_diagram() (in module macrodensity.plotting)</a>
-</li>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.extend_potential">extend_potential() (in module macrodensity.alpha)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -342,12 +311,10 @@ <h2 id="G">G</h2>
       <li><a href="macrodensity.density.html#macrodensity.density.GCD">GCD() (in module macrodensity.density)</a>
 </li>
       <li><a href="macrodensity.density.html#macrodensity.density.GCD_List">GCD_List() (in module macrodensity.density)</a>
-</li>
-      <li><a href="macrodensity.vasp.html#macrodensity.vasp.get_band_extrema">get_band_extrema() (in module macrodensity.vasp)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.get_third_coordinate">get_third_coordinate() (in module macrodensity.alpha)</a>
+      <li><a href="macrodensity.vasp.html#macrodensity.vasp.get_band_extrema">get_band_extrema() (in module macrodensity.vasp)</a>
 </li>
       <li><a href="macrodensity.density.html#macrodensity.density.get_volume">get_volume() (in module macrodensity.density)</a>
 </li>
@@ -368,31 +335,10 @@ <h2 id="M">M</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li>
-    macrodensity
-
-      <ul>
-        <li><a href="macrodensity.html#module-macrodensity">module</a>
-</li>
-      </ul></li>
-      <li>
-    macrodensity.alpha
-
-      <ul>
-        <li><a href="macrodensity.alpha.html#module-macrodensity.alpha">module</a>
-</li>
-      </ul></li>
-      <li>
     macrodensity.density
 
       <ul>
         <li><a href="macrodensity.density.html#module-macrodensity.density">module</a>
-</li>
-      </ul></li>
-      <li>
-    macrodensity.plotting
-
-      <ul>
-        <li><a href="macrodensity.plotting.html#module-macrodensity.plotting">module</a>
 </li>
       </ul></li>
       <li>
@@ -406,31 +352,19 @@ <h2 id="M">M</h2>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.match_resolution">match_resolution() (in module macrodensity.alpha)</a>
-</li>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.matched_spline_generate">matched_spline_generate() (in module macrodensity.alpha)</a>
-</li>
       <li><a href="macrodensity.density.html#macrodensity.density.matrix_2_abc">matrix_2_abc() (in module macrodensity.density)</a>
 </li>
       <li>
     module
 
       <ul>
-        <li><a href="macrodensity.html#module-macrodensity">macrodensity</a>
-</li>
-        <li><a href="macrodensity.alpha.html#module-macrodensity.alpha">macrodensity.alpha</a>
-</li>
         <li><a href="macrodensity.density.html#module-macrodensity.density">macrodensity.density</a>
-</li>
-        <li><a href="macrodensity.plotting.html#module-macrodensity.plotting">macrodensity.plotting</a>
 </li>
         <li><a href="macrodensity.vasp.html#module-macrodensity.vasp">macrodensity.vasp</a>
 </li>
         <li><a href="setup.html#module-setup">setup</a>
 </li>
       </ul></li>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.moving_cube">moving_cube() (in module macrodensity.alpha)</a>
-</li>
   </ul></td>
 </tr></table>
 
@@ -458,55 +392,17 @@ <h2 id="P">P</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="macrodensity.density.html#macrodensity.density.planar_average">planar_average() (in module macrodensity.density)</a>
-</li>
-      <li><a href="macrodensity.density.html#macrodensity.density.planar_average_charge">planar_average_charge() (in module macrodensity.density)</a>
-</li>
-      <li><a href="macrodensity.plotting.html#macrodensity.plotting.plot_active_plane">plot_active_plane() (in module macrodensity.plotting)</a>
-</li>
-      <li><a href="macrodensity.plotting.html#macrodensity.plotting.plot_active_space">plot_active_space() (in module macrodensity.plotting)</a>
-</li>
-      <li><a href="macrodensity.plotting.html#macrodensity.plotting.plot_field_at_point">plot_field_at_point() (in module macrodensity.plotting)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.plotting.html#macrodensity.plotting.plot_gulp_potential">plot_gulp_potential() (in module macrodensity.plotting)</a>
-</li>
-      <li><a href="macrodensity.plotting.html#macrodensity.plotting.plot_on_site_potential">plot_on_site_potential() (in module macrodensity.plotting)</a>
-</li>
-      <li><a href="macrodensity.plotting.html#macrodensity.plotting.plot_planar_average">plot_planar_average() (in module macrodensity.plotting)</a>
-</li>
-      <li><a href="macrodensity.plotting.html#macrodensity.plotting.plot_planar_cube">plot_planar_cube() (in module macrodensity.plotting)</a>
-</li>
-      <li><a href="macrodensity.plotting.html#macrodensity.plotting.plot_plane_field">plot_plane_field() (in module macrodensity.plotting)</a>
-</li>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.points_2_plane">points_2_plane() (in module macrodensity.alpha)</a>
-</li>
-  </ul></td>
-</tr></table>
-
-<h2 id="R">R</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.read_cube_density">read_cube_density() (in module macrodensity.alpha)</a>
-</li>
-      <li><a href="macrodensity.density.html#macrodensity.density.read_gulp_potential">read_gulp_potential() (in module macrodensity.density)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.density.html#macrodensity.density.read_vasp_density">read_vasp_density() (in module macrodensity.density)</a>
-</li>
-      <li><a href="macrodensity.density.html#macrodensity.density.read_vasp_density_classic">read_vasp_density_classic() (in module macrodensity.density)</a>
-</li>
-      <li><a href="macrodensity.density.html#macrodensity.density.read_vasp_parchg">read_vasp_parchg() (in module macrodensity.density)</a>
+      <li><a href="macrodensity.density.html#macrodensity.density.planar_average_charge">planar_average_charge() (in module macrodensity.density)</a>
 </li>
   </ul></td>
 </tr></table>
 
 <h2 id="S">S</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.scissors_shift">scissors_shift() (in module macrodensity.alpha)</a>
-</li>
       <li>
     setup
 
@@ -515,24 +411,10 @@ <h2 id="S">S</h2>
 </li>
       </ul></li>
   </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.sort_potential">sort_potential() (in module macrodensity.alpha)</a>
-</li>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.spherical_average">spherical_average() (in module macrodensity.alpha)</a>
-</li>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.spline_generate">spline_generate() (in module macrodensity.alpha)</a>
-</li>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.subs_potentials">subs_potentials() (in module macrodensity.alpha)</a>
-</li>
-  </ul></td>
 </tr></table>
 
 <h2 id="T">T</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="macrodensity.alpha.html#macrodensity.alpha.translate_grid">translate_grid() (in module macrodensity.alpha)</a>
-</li>
-  </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="macrodensity.density.html#macrodensity.density.travelling_volume_average">travelling_volume_average() (in module macrodensity.density)</a>
 </li>

diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
@@ -315,8 +315,7 @@ <h2> Contents </h2>
             </div>
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">Welcome to MacroDensity</a></li>
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#summary">Summary</a><ul class="visible nav section-nav flex-column">
+<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">Welcome to MacroDensity</a><ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#statement-of-need">Statement of Need</a></li>
 </ul>
 </li>
@@ -347,10 +346,7 @@ <h2> Contents </h2>
 
   <section id="welcome-to-macrodensity">
 <h1>Welcome to MacroDensity<a class="headerlink" href="#welcome-to-macrodensity" title="Permalink to this heading">#</a></h1>
-</section>
-<section id="summary">
-<h1>Summary<a class="headerlink" href="#summary" title="Permalink to this heading">#</a></h1>
-<p><code class="docutils literal notranslate"><span class="pre">MacroDensity</span></code> is a Python package to read and process electrostatic potential and
+<p><code class="docutils literal notranslate"><span class="pre">MacroDensity</span></code> is a Python package to post-process electrostatic potential and
 electron density files from electronic structure calculations and plot in a number of ways, including:</p>
 <ol class="arabic simple">
 <li><p>Planar average</p></li>
@@ -471,8 +467,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Pe
   </div>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">Welcome to MacroDensity</a></li>
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#summary">Summary</a><ul class="visible nav section-nav flex-column">
+<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">Welcome to MacroDensity</a><ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#statement-of-need">Statement of Need</a></li>
 </ul>
 </li>