deploy: 37cf100

birdday · Jan 1, 2025 · 4466f3b · 4466f3b
1 parent 3cdf321
commit 4466f3b
Show file tree

Hide file tree

Showing 17 changed files with 923 additions and 36 deletions.
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/models.doctree b/.doctrees/models.doctree
diff --git a/.doctrees/visualize.doctree b/.doctrees/visualize.doctree
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
@@ -27,12 +27,15 @@ Contents
 .. toctree::
 
    usage
+   models
    lammps
    visualize
 
 Check out the :doc:`usage` section for further information, including how to
 :ref:`install <installation>` the project.
 
-Learn how to :ref:`view structures <visualization>` and generate movies!
+Learn about key :ref:`classes <models>`!
+
+:ref:`View structures <visualization>` and generate movies!
 
 Integrate with :ref:`LAMMPS <lammps>`!
diff --git a/_sources/models.rst.txt b/_sources/models.rst.txt
@@ -0,0 +1,12 @@
+Classes
+=======
+
+.. _models:
+
+Models: :mod:`atomaton.models` 
+--------------------------------------------
+
+.. automodule:: atomaton.models
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/_sources/visualize.rst.txt b/_sources/visualize.rst.txt
@@ -1,5 +1,5 @@
-View structures
-=====
+Visualize
+=========
 
 .. _visualization:
 

diff --git a/genindex.html b/genindex.html
@@ -128,6 +128,13 @@
 </li>
 
 
+<li class="nav-item ">
+  <a class="nav-link nav-internal" href="models.html">
+    Classes
+  </a>
+</li>
+
+
 <li class="nav-item ">
   <a class="nav-link nav-internal" href="lammps.html">
     LAMMPS
@@ -137,7 +144,7 @@
 
 <li class="nav-item ">
   <a class="nav-link nav-internal" href="visualize.html">
-    View structures
+    Visualize
   </a>
 </li>
 
@@ -219,6 +226,13 @@
 </li>
 
 
+<li class="nav-item ">
+  <a class="nav-link nav-internal" href="models.html">
+    Classes
+  </a>
+</li>
+
+
 <li class="nav-item ">
   <a class="nav-link nav-internal" href="lammps.html">
     LAMMPS
@@ -228,7 +242,7 @@
 
 <li class="nav-item ">
   <a class="nav-link nav-internal" href="visualize.html">
-    View structures
+    Visualize
   </a>
 </li>
 
@@ -291,16 +305,20 @@ <h1 id="index">Index</h1>
  | <a href="#C"><strong>C</strong></a>
  | <a href="#D"><strong>D</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="#R"><strong>R</strong></a>
  | <a href="#S"><strong>S</strong></a>
+ | <a href="#U"><strong>U</strong></a>
  | <a href="#V"><strong>V</strong></a>
  | <a href="#W"><strong>W</strong></a>
 
 </div>
 <h2 id="A">A</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="models.html#atomaton.models.Angle">Angle (class in atomaton.models)</a>
+</li>
       <li>
     atomaton.analyze
 
@@ -309,21 +327,30 @@ <h2 id="A">A</h2>
 </li>
       </ul></li>
       <li>
-    atomaton.visualize
+    atomaton.models
 
       <ul>
-        <li><a href="visualize.html#module-atomaton.visualize">module</a>
+        <li><a href="models.html#module-atomaton.models">module</a>
 </li>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li>
+    atomaton.visualize
+
+      <ul>
+        <li><a href="visualize.html#module-atomaton.visualize">module</a>
+</li>
+      </ul></li>
+      <li>
     atomaton.write_lammps_files
 
       <ul>
         <li><a href="lammps.html#module-atomaton.write_lammps_files">module</a>
 </li>
       </ul></li>
+      <li><a href="models.html#atomaton.models.Atoms">Atoms (class in atomaton.models)</a>
+</li>
   </ul></td>
 </tr></table>
 
@@ -334,6 +361,18 @@ <h2 id="B">B</h2>
 
       <ul>
         <li><a href="visualize.html#atomaton.visualize.bin_data">(in module atomaton.visualize)</a>
+</li>
+      </ul></li>
+      <li><a href="models.html#atomaton.models.Atoms.bind_from_ase">bind_from_ase() (atomaton.models.Atoms class method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="models.html#atomaton.models.Atoms.bind_from_file">bind_from_file() (atomaton.models.Atoms class method)</a>
+</li>
+      <li><a href="models.html#atomaton.models.Crystal.build_supercell">build_supercell() (atomaton.models.Crystal method)</a>
+
+      <ul>
+        <li><a href="models.html#atomaton.models.SimulationBox.build_supercell">(atomaton.models.SimulationBox method)</a>
 </li>
       </ul></li>
   </ul></td>
@@ -342,13 +381,29 @@ <h2 id="B">B</h2>
 <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="models.html#atomaton.models.Atoms.calculate_angles">calculate_angles() (atomaton.models.Atoms method)</a>
+</li>
+      <li><a href="models.html#atomaton.models.Atoms.calculate_bonds">calculate_bonds() (atomaton.models.Atoms method)</a>
+</li>
+      <li><a href="models.html#atomaton.models.Atoms.calculate_dihedrals_and_impropers">calculate_dihedrals_and_impropers() (atomaton.models.Atoms method)</a>
+</li>
+      <li><a href="models.html#atomaton.models.Atoms.center_atom_in_cell">center_atom_in_cell() (atomaton.models.Atoms method)</a>
+</li>
       <li><a href="visualize.html#atomaton.visualize.convert_images_to_gif">convert_images_to_gif() (in module atomaton.visualize)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="usage.html#atomaton.analyze.create_extended_cell">create_extended_cell() (in module atomaton.analyze)</a>
 </li>
-      <li><a href="usage.html#atomaton.analyze.create_extended_cell_minimal">create_extended_cell_minimal() (in module atomaton.analyze)</a>
+      <li><a href="models.html#atomaton.models.Atoms.create_extended_cell_minimal">create_extended_cell_minimal() (atomaton.models.Atoms method)</a>
+
+      <ul>
+        <li><a href="usage.html#atomaton.analyze.create_extended_cell_minimal">(in module atomaton.analyze)</a>
+</li>
+      </ul></li>
+      <li><a href="models.html#atomaton.models.SimulationBox.create_from_atoms">create_from_atoms() (atomaton.models.SimulationBox class method)</a>
+</li>
+      <li><a href="models.html#atomaton.models.Crystal">Crystal (class in atomaton.models)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -376,10 +431,18 @@ <h2 id="G">G</h2>
 </li>
       <li><a href="usage.html#atomaton.analyze.get_bonds_on_atom">get_bonds_on_atom() (in module atomaton.analyze)</a>
 </li>
-      <li><a href="lammps.html#atomaton.write_lammps_files.get_lammps_box_parameters">get_lammps_box_parameters() (in module atomaton.write_lammps_files)</a>
+      <li><a href="models.html#atomaton.models.UnitCell.get_center_of_cell">get_center_of_cell() (atomaton.models.UnitCell method)</a>
+</li>
+      <li><a href="models.html#atomaton.models.Atoms.get_center_of_positions">get_center_of_positions() (atomaton.models.Atoms method)</a>
+</li>
+      <li><a href="models.html#atomaton.models.UnitCell.get_corners">get_corners() (atomaton.models.UnitCell method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="models.html#atomaton.models.UnitCell.get_frac_to_cart_matrix">get_frac_to_cart_matrix() (atomaton.models.UnitCell method)</a>
+</li>
+      <li><a href="lammps.html#atomaton.write_lammps_files.get_lammps_box_parameters">get_lammps_box_parameters() (in module atomaton.write_lammps_files)</a>
+</li>
       <li><a href="lammps.html#atomaton.write_lammps_files.get_masses">get_masses() (in module atomaton.write_lammps_files)</a>
 </li>
       <li><a href="usage.html#atomaton.analyze.guess_angles">guess_angles() (in module atomaton.analyze)</a>
@@ -391,6 +454,18 @@ <h2 id="G">G</h2>
   </ul></td>
 </tr></table>
 
+<h2 id="I">I</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="models.html#atomaton.models.Improper">Improper (class in atomaton.models)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="models.html#atomaton.models.SimulationBox.insert_atoms">insert_atoms() (atomaton.models.SimulationBox method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="M">M</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
@@ -399,6 +474,8 @@ <h2 id="M">M</h2>
 
       <ul>
         <li><a href="usage.html#module-atomaton.analyze">atomaton.analyze</a>
+</li>
+        <li><a href="models.html#module-atomaton.models">atomaton.models</a>
 </li>
         <li><a href="visualize.html#module-atomaton.visualize">atomaton.visualize</a>
 </li>
@@ -423,13 +500,35 @@ <h2 id="R">R</h2>
 <h2 id="S">S</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="models.html#atomaton.models.Atoms.shift_atoms">shift_atoms() (atomaton.models.Atoms method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="models.html#atomaton.models.SimulationBox">SimulationBox (class in atomaton.models)</a>
+</li>
       <li><a href="usage.html#atomaton.analyze.split_by_property">split_by_property() (in module atomaton.analyze)</a>
 </li>
   </ul></td>
 </tr></table>
 
+<h2 id="U">U</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="models.html#atomaton.models.UnitCell">UnitCell (class in atomaton.models)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="V">V</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="models.html#atomaton.models.Atoms.view">view() (atomaton.models.Atoms method)</a>
+
+      <ul>
+        <li><a href="models.html#atomaton.models.SimulationBox.view">(atomaton.models.SimulationBox method)</a>
+</li>
+      </ul></li>
+  </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="visualize.html#atomaton.visualize.view_structure">view_structure() (in module atomaton.visualize)</a>
 </li>

diff --git a/index.html b/index.html
@@ -130,6 +130,13 @@
 </li>
 
 
+<li class="nav-item ">
+  <a class="nav-link nav-internal" href="models.html">
+    Classes
+  </a>
+</li>
+
+
 <li class="nav-item ">
   <a class="nav-link nav-internal" href="lammps.html">
     LAMMPS
@@ -139,7 +146,7 @@
 
 <li class="nav-item ">
   <a class="nav-link nav-internal" href="visualize.html">
-    View structures
+    Visualize
   </a>
 </li>
 
@@ -225,6 +232,13 @@
 </li>
 
 
+<li class="nav-item ">
+  <a class="nav-link nav-internal" href="models.html">
+    Classes
+  </a>
+</li>
+
+
 <li class="nav-item ">
   <a class="nav-link nav-internal" href="lammps.html">
     LAMMPS
@@ -234,7 +248,7 @@
 
 <li class="nav-item ">
   <a class="nav-link nav-internal" href="visualize.html">
-    View structures
+    Visualize
   </a>
 </li>
 
@@ -324,6 +338,44 @@ <h2>Contents<a class="headerlink" href="#contents" title="Link to this heading">
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="models.html">Classes</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="models.html#module-atomaton.models">Models: <code class="xref py py-mod docutils literal notranslate"><span class="pre">atomaton.models</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="models.html#atomaton.models.Angle"><code class="docutils literal notranslate"><span class="pre">Angle</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="models.html#atomaton.models.Atoms"><code class="docutils literal notranslate"><span class="pre">Atoms</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.Atoms.bind_from_ase"><code class="docutils literal notranslate"><span class="pre">Atoms.bind_from_ase()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.Atoms.bind_from_file"><code class="docutils literal notranslate"><span class="pre">Atoms.bind_from_file()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.Atoms.calculate_angles"><code class="docutils literal notranslate"><span class="pre">Atoms.calculate_angles()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.Atoms.calculate_bonds"><code class="docutils literal notranslate"><span class="pre">Atoms.calculate_bonds()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.Atoms.calculate_dihedrals_and_impropers"><code class="docutils literal notranslate"><span class="pre">Atoms.calculate_dihedrals_and_impropers()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.Atoms.center_atom_in_cell"><code class="docutils literal notranslate"><span class="pre">Atoms.center_atom_in_cell()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.Atoms.create_extended_cell_minimal"><code class="docutils literal notranslate"><span class="pre">Atoms.create_extended_cell_minimal()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.Atoms.get_center_of_positions"><code class="docutils literal notranslate"><span class="pre">Atoms.get_center_of_positions()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.Atoms.shift_atoms"><code class="docutils literal notranslate"><span class="pre">Atoms.shift_atoms()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.Atoms.view"><code class="docutils literal notranslate"><span class="pre">Atoms.view()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="models.html#atomaton.models.Crystal"><code class="docutils literal notranslate"><span class="pre">Crystal</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.Crystal.build_supercell"><code class="docutils literal notranslate"><span class="pre">Crystal.build_supercell()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="models.html#atomaton.models.Improper"><code class="docutils literal notranslate"><span class="pre">Improper</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="models.html#atomaton.models.SimulationBox"><code class="docutils literal notranslate"><span class="pre">SimulationBox</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.SimulationBox.build_supercell"><code class="docutils literal notranslate"><span class="pre">SimulationBox.build_supercell()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.SimulationBox.create_from_atoms"><code class="docutils literal notranslate"><span class="pre">SimulationBox.create_from_atoms()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.SimulationBox.insert_atoms"><code class="docutils literal notranslate"><span class="pre">SimulationBox.insert_atoms()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.SimulationBox.view"><code class="docutils literal notranslate"><span class="pre">SimulationBox.view()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="models.html#atomaton.models.UnitCell"><code class="docutils literal notranslate"><span class="pre">UnitCell</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.UnitCell.get_center_of_cell"><code class="docutils literal notranslate"><span class="pre">UnitCell.get_center_of_cell()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.UnitCell.get_corners"><code class="docutils literal notranslate"><span class="pre">UnitCell.get_corners()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="models.html#atomaton.models.UnitCell.get_frac_to_cart_matrix"><code class="docutils literal notranslate"><span class="pre">UnitCell.get_frac_to_cart_matrix()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="lammps.html">LAMMPS</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="lammps.html#module-atomaton.write_lammps_files">LAMMPS Input File Generation: <code class="xref py py-mod docutils literal notranslate"><span class="pre">atomaton.write_lammps_files</span></code></a><ul>
 <li class="toctree-l3"><a class="reference internal" href="lammps.html#atomaton.write_lammps_files.get_lammps_box_parameters"><code class="docutils literal notranslate"><span class="pre">get_lammps_box_parameters()</span></code></a></li>
@@ -333,7 +385,7 @@ <h2>Contents<a class="headerlink" href="#contents" title="Link to this heading">
 </li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="visualize.html">View structures</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="visualize.html">Visualize</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="visualize.html#module-atomaton.visualize">Visualizer: <code class="xref py py-mod docutils literal notranslate"><span class="pre">atomaton.visualize</span></code></a><ul>
 <li class="toctree-l3"><a class="reference internal" href="visualize.html#atomaton.visualize.bin_data"><code class="docutils literal notranslate"><span class="pre">bin_data()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="visualize.html#atomaton.visualize.convert_images_to_gif"><code class="docutils literal notranslate"><span class="pre">convert_images_to_gif()</span></code></a></li>
@@ -349,7 +401,8 @@ <h2>Contents<a class="headerlink" href="#contents" title="Link to this heading">
 </div>
 <p>Check out the <a class="reference internal" href="usage.html"><span class="doc">Usage</span></a> section for further information, including how to
 <a class="reference internal" href="usage.html#installation"><span class="std std-ref">install</span></a> the project.</p>
-<p>Learn how to <a class="reference internal" href="visualize.html#visualization"><span class="std std-ref">view structures</span></a> and generate movies!</p>
+<p>Learn about key <a class="reference internal" href="models.html#models"><span class="std std-ref">classes</span></a>!</p>
+<p><a class="reference internal" href="visualize.html#visualization"><span class="std std-ref">View structures</span></a> and generate movies!</p>
 <p>Integrate with <a class="reference internal" href="lammps.html#id1"><span class="std std-ref">LAMMPS</span></a>!</p>
 </section>
 </section>