Updated docs.

SINGROUP · May 28, 2024 · a1cf125 · a1cf125
1 parent fd56a5e
commit a1cf125
Show file tree

Hide file tree

Showing 68 changed files with 1,773 additions and 1,183 deletions.
diff --git a/docs/2.1.x/.buildinfo b/docs/2.1.x/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 979ed1add00f32f4bc116afafadc8e3c
+config: d2b1800fed63e4715a5ada69f6a537e2
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/2.1.x/_modules/dscribe/core/lattice.html b/docs/2.1.x/_modules/dscribe/core/lattice.html
@@ -1,22 +1,24 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../../">
 <head>
  <meta charset="utf-8" />
  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
  <title>dscribe.core.lattice &mdash; DScribe 2.1.x documentation</title>
- <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
- <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="../../../_static/css/style.css" type="text/css" />
+ <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
+ <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
+ <link rel="stylesheet" type="text/css" href="../../../_static/css/style.css?v=7d1ac55c" />
+
+
  <!--[if lt IE 9]>
  <script src="../../../_static/js/html5shiv.min.js"></script>
  <![endif]-->
 
- <script src="../../../_static/jquery.js"></script>
- <script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
- <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
- <script src="../../../_static/doctools.js"></script>
- <script src="../../../_static/sphinx_highlight.js"></script>
- <script defer="defer" src="../../../_static/js/versions.js"></script>
+ <script src="../../../_static/jquery.js?v=5d32c60e"></script>
+ <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+ <script src="../../../_static/documentation_options.js?v=c41997dc"></script>
+ <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+ <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
+ <script defer="defer" src="../../../_static/js/versions.js?v=413e22da"></script>
  <script src="../../../_static/js/theme.js"></script>
  <link rel="author" title="About these documents" href="../../../about.html" />
  <link rel="index" title="Index" href="../../../genindex.html" />
@@ -97,10 +99,13 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
 <span class="sd">See the License for the specific language governing permissions and</span>
 <span class="sd">limitations under the License.</span>
 <span class="sd">&quot;&quot;&quot;</span>
+
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 
 
-<div class="viewcode-block" id="Lattice"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice">[docs]</a><span class="k">class</span> <span class="nc">Lattice</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="Lattice">
+<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice">[docs]</a>
+<span class="k">class</span> <span class="nc">Lattice</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
 <span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd"> A lattice object. Essentially a matrix with conversion matrices. In</span>
 <span class="sd"> general, it is assumed that length units are in Angstroms and angles are in</span>
@@ -144,7 +149,9 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
  <span class="bp">self</span><span class="o">.</span><span class="n">_inv_matrix</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">inv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_matrix</span><span class="p">)</span>
  <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_inv_matrix</span>
 
-<div class="viewcode-block" id="Lattice.get_cartesian_coords"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_cartesian_coords">[docs]</a> <span class="k">def</span> <span class="nf">get_cartesian_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fractional_coords</span><span class="p">):</span>
+<div class="viewcode-block" id="Lattice.get_cartesian_coords">
+<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_cartesian_coords">[docs]</a>
+ <span class="k">def</span> <span class="nf">get_cartesian_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fractional_coords</span><span class="p">):</span>
 <span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd"> Returns the cartesian coordinates given fractional coordinates.</span>
 
@@ -156,7 +163,10 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
 <span class="sd"> &quot;&quot;&quot;</span>
  <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">fractional_coords</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_matrix</span><span class="p">)</span></div>
 
-<div class="viewcode-block" id="Lattice.get_fractional_coords"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_fractional_coords">[docs]</a> <span class="k">def</span> <span class="nf">get_fractional_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cart_coords</span><span class="p">):</span>
+
+<div class="viewcode-block" id="Lattice.get_fractional_coords">
+<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_fractional_coords">[docs]</a>
+ <span class="k">def</span> <span class="nf">get_fractional_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cart_coords</span><span class="p">):</span>
 <span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd"> Returns the fractional coordinates given cartesian coordinates.</span>
 
@@ -168,6 +178,7 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
 <span class="sd"> &quot;&quot;&quot;</span>
  <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">cart_coords</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">inv_matrix</span><span class="p">)</span></div>
 
+
  <span class="nd">@property</span>
  <span class="k">def</span> <span class="nf">lengths</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
  <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lengths</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
@@ -206,7 +217,9 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
 <span class="sd"> &quot;&quot;&quot;</span>
  <span class="k">return</span> <span class="n">Lattice</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">reciprocal_lattice</span><span class="o">.</span><span class="n">matrix</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">))</span>
 
-<div class="viewcode-block" id="Lattice.get_points_in_sphere"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_points_in_sphere">[docs]</a> <span class="k">def</span> <span class="nf">get_points_in_sphere</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">frac_points</span><span class="p">,</span> <span class="n">center</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">zip_results</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+<div class="viewcode-block" id="Lattice.get_points_in_sphere">
+<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_points_in_sphere">[docs]</a>
+ <span class="k">def</span> <span class="nf">get_points_in_sphere</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">frac_points</span><span class="p">,</span> <span class="n">center</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">zip_results</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"> Find all points within a sphere from the point taking into account</span>
 <span class="sd"> periodic boundary conditions. This includes sites in other periodic</span>
@@ -282,7 +295,9 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
  <span class="n">shifted_coords</span><span class="p">[</span><span class="n">within_r</span><span class="p">],</span>
  <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">d_2</span><span class="p">[</span><span class="n">within_r</span><span class="p">]),</span>
  <span class="n">indices</span><span class="p">[</span><span class="n">within_r</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span>
- <span class="p">)</span></div></div>
+ <span class="p">)</span></div>
+</div>
+
 </pre></div>
 
  </div>