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dehe1011 · Nov 25, 2024 · 87a04e7 · 87a04e7
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diff --git a/docs/_build/doctrees/apidoc/classes.doctree b/docs/_build/doctrees/apidoc/classes.doctree
diff --git a/docs/_build/doctrees/apidoc/functions.doctree b/docs/_build/doctrees/apidoc/functions.doctree
diff --git a/docs/_build/doctrees/apidoc/plotting.doctree b/docs/_build/doctrees/apidoc/plotting.doctree
diff --git a/docs/_build/doctrees/apidoc/utils.doctree b/docs/_build/doctrees/apidoc/utils.doctree
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/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 75f74a8ba4eca8b78817fec4238c3b28
+config: 0ddaa2a6a2c02a5cffaf66f59ffdd527
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/.buildinfo.bak b/docs/_build/html/.buildinfo.bak
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 75f74a8ba4eca8b78817fec4238c3b28
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_sources/apidoc/functions.rst.txt b/docs/_build/html/_sources/apidoc/functions.rst.txt
@@ -1,8 +1,15 @@
 Functions
 =========
 
+Linear Combination of Atomic Orbitals (LCAO)
+--------------------------------------------
 
-Tight-binding basis
+.. automodule:: qDNA.lcao
+   :members: calc_orbital_energy, calc_orbital_overlap, load_xyz, convert_json_to_xyz, convert_pdb_to_xyz, calc_tb_energies_monomers, calc_tb_params_dimer, calc_tb_params
+   :show-inheritance: False
+
+
+Tight-binding Basis
 -------------------
 
 There are three relevant bases:
@@ -17,7 +24,7 @@ The first two are refered to as `local` bases, the third as the `global` basis.
    :members: get_tb_basis, get_eh_basis, get_eh_distance, get_particle_eh_states, basis_change, local_to_global, global_to_local
    :show-inheritance: False
 
-Tight-binding configuration
+Tight-binding Configuration
 ---------------------------
 
 .. automodule:: qDNA.model

diff --git a/docs/_build/html/_sources/apidoc/plotting.rst.txt b/docs/_build/html/_sources/apidoc/plotting.rst.txt
@@ -4,22 +4,22 @@ Plotting
 Plot DNA base frequency
 -----------------------
 
-.. automodule:: qDNA.plotting
+.. automodule:: qDNA.visualization
    :members: plot_dna_base_frequency
    :show-inheritance: False
 
 Plot eigenspectrum
 ------------------
 
-.. automodule:: qDNA.plotting
+.. automodule:: qDNA.visualization
    :members: plot_eigv, plot_eigs
    :show-inheritance: False
    :noindex:
 
 Plot Fourier analysis
 ---------------------
 
-.. automodule:: qDNA.plotting
+.. automodule:: qDNA.visualization
    :members: plot_fourier, plot_average_pop
    :show-inheritance: False
    :noindex:
@@ -28,7 +28,7 @@ Plot Fourier analysis
 Plot poulations and coherences
 ------------------------------
 
-.. automodule:: qDNA.plotting
+.. automodule:: qDNA.visualization
    :members: plot_pop_fourier, plot_pop, plot_pops, plot_coh, plot_test_fourier
    :show-inheritance: False
    :noindex:
diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt
@@ -21,7 +21,7 @@ This documentation includes:
 - **API Reference**: Description on QuantumDNA's functions and classes.
 - **User Guide**: Tutorials and instructions for getting started and using QuantumDNA effectively.
 
-For additional resources and development information, visit the `QuantumDNA GitHub repository <https://github.com/dehe1011/QuantumDNA>`_. For hands-on learning, check out the `Tutorial Notebooks <https://github.com/dehe1011/QuantumDNA-notebooks>`_ repository, which contains examples and guided exercises.
+For additional resources and development information, visit the `QuantumDNA GitHub repository <https://github.com/dehe1011/QuantumDNA>`_. For hands-on learning, check out the `Tutorial Notebook GitHub repository <https://github.com/dehe1011/QuantumDNA-notebooks>`_, which contains examples and guided exercises.
 
 .. toctree::
    :maxdepth: 3

diff --git a/docs/_build/html/_static/documentation_options.js b/docs/_build/html/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.1.5',
+    VERSION: '0.1.8',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/_build/html/apidoc/apidoc.html b/docs/_build/html/apidoc/apidoc.html
@@ -6,14 +6,14 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>API documentation &mdash; QuantumDNA 0.1.5 documentation</title>
+  <title>API documentation &mdash; QuantumDNA 0.1.8 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
 
 
       <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=59fadc99"></script>
+      <script src="../_static/documentation_options.js?v=22607128"></script>
       <script src="../_static/doctools.js?v=9bcbadda"></script>
       <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
       <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
@@ -98,7 +98,18 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="functions.html">Functions</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="functions.html#tight-binding-basis">Tight-binding basis</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="functions.html#module-qDNA.lcao">Linear Combination of Atomic Orbitals (LCAO)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.lcao.calc_orbital_energy"><code class="docutils literal notranslate"><span class="pre">calc_orbital_energy()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.lcao.calc_orbital_overlap"><code class="docutils literal notranslate"><span class="pre">calc_orbital_overlap()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.lcao.calc_tb_energies_monomers"><code class="docutils literal notranslate"><span class="pre">calc_tb_energies_monomers()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.lcao.calc_tb_params"><code class="docutils literal notranslate"><span class="pre">calc_tb_params()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.lcao.calc_tb_params_dimer"><code class="docutils literal notranslate"><span class="pre">calc_tb_params_dimer()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.lcao.convert_json_to_xyz"><code class="docutils literal notranslate"><span class="pre">convert_json_to_xyz()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.lcao.convert_pdb_to_xyz"><code class="docutils literal notranslate"><span class="pre">convert_pdb_to_xyz()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.lcao.load_xyz"><code class="docutils literal notranslate"><span class="pre">load_xyz()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="functions.html#tight-binding-basis">Tight-binding Basis</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.model.basis_change"><code class="docutils literal notranslate"><span class="pre">basis_change()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.model.get_eh_basis"><code class="docutils literal notranslate"><span class="pre">get_eh_basis()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.model.get_eh_distance"><code class="docutils literal notranslate"><span class="pre">get_eh_distance()</span></code></a></li>
@@ -108,7 +119,7 @@
 <li class="toctree-l3"><a class="reference internal" href="functions.html#qDNA.model.local_to_global"><code class="docutils literal notranslate"><span class="pre">local_to_global()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="functions.html#tight-binding-configuration">Tight-binding configuration</a></li>
+<li class="toctree-l2"><a class="reference internal" href="functions.html#tight-binding-configuration">Tight-binding Configuration</a></li>
 <li class="toctree-l2"><a class="reference internal" href="functions.html#tight-binding-hamiltonian">Tight-binding Hamiltonian</a></li>
 <li class="toctree-l2"><a class="reference internal" href="functions.html#save-and-load-tight-binding-parameters">Save and load tight-binding parameters</a></li>
 <li class="toctree-l2"><a class="reference internal" href="functions.html#module-qDNA.dynamics">Reduced density matrix</a><ul>
@@ -151,8 +162,8 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="plotting.html">Plotting</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="plotting.html#module-qDNA.plotting">Plot DNA base frequency</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="plotting.html#qDNA.plotting.plot_dna_base_frequency"><code class="docutils literal notranslate"><span class="pre">plot_dna_base_frequency()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="plotting.html#module-qDNA.visualization">Plot DNA base frequency</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="plotting.html#qDNA.visualization.plot_dna_base_frequency"><code class="docutils literal notranslate"><span class="pre">plot_dna_base_frequency()</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="plotting.html#plot-eigenspectrum">Plot eigenspectrum</a></li>