update example page in documentation

liborsold · Oct 11, 2024 · 0e45e7a · 0e45e7a
1 parent fc991f8
commit 0e45e7a
Show file tree

Hide file tree

Showing 21 changed files with 111 additions and 100 deletions.
diff --git a/docs/build/doctrees/classes.doctree b/docs/build/doctrees/classes.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/example.doctree b/docs/build/doctrees/example.doctree
diff --git a/docs/build/doctrees/generated/fuNEGF.doctree b/docs/build/doctrees/generated/fuNEGF.doctree
diff --git a/docs/build/doctrees/generated/fuNEGF.models.doctree b/docs/build/doctrees/generated/fuNEGF.models.doctree
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/modules.doctree b/docs/build/doctrees/modules.doctree
diff --git a/docs/build/doctrees/theory.doctree b/docs/build/doctrees/theory.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.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: 582d0f8e2f1710734c73a1e8e7af2ead
+config: d17a8cebba502e1f432dfa0ae56f4b9f
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_sources/example.rst b/docs/build/html/_sources/example.rst
@@ -18,7 +18,7 @@ There is also a time-complexity study in ``./examples/time_complexity.ipynb``.
 
 .. image::
    ./_images/clean_wire.png
-   :width: 370px
+   :width: 330px
    :align: center
 
 .. image::
@@ -181,6 +181,11 @@ Let us now compare the transmission for several cases.
       )
    ...
 
+.. fuNEGF example image
+.. image::
+   ./_images/multiple_imp_wire.png
+   :width: 200px
+   :align: right
 
 .. image::
    ./_images/example_fuNEGF.png

diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css
@@ -236,16 +236,6 @@ div.body p, div.body dd, div.body li, div.body blockquote {
 a.headerlink {
     visibility: hidden;
 }
-a.brackets:before,
-span.brackets > a:before{
-    content: "[";
-}
-
-a.brackets:after,
-span.brackets > a:after {
-    content: "]";
-}
-
 
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
@@ -334,11 +324,15 @@ aside.sidebar {
 p.sidebar-title {
     font-weight: bold;
 }
+nav.contents,
+aside.topic,
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
+nav.contents,
+aside.topic,
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -377,13 +371,17 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -608,19 +606,26 @@ ol.simple p,
 ul.simple p {
     margin-bottom: 0;
 }
-dl.footnote > dt,
-dl.citation > dt {
+aside.footnote > span,
+div.citation > span {
     float: left;
-    margin-right: 0.5em;
 }
-
-dl.footnote > dd,
-dl.citation > dd {
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+  padding-right: 0.5em;
+}
+aside.footnote > p {
+  margin-left: 2em;
+}
+div.citation > p {
+  margin-left: 4em;
+}
+aside.footnote > p:last-of-type,
+div.citation > p:last-of-type {
     margin-bottom: 0em;
 }
-
-dl.footnote > dd:after,
-dl.citation > dd:after {
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
     content: "";
     clear: both;
 }
@@ -636,10 +641,6 @@ dl.field-list > dt {
     padding-left: 0.5em;
     padding-right: 5px;
 }
-dl.field-list > dt:after {
-    content: ":";
-}
-
 
 dl.field-list > dd {
     padding-left: 0.5em;

diff --git a/docs/build/html/classes.html b/docs/build/html/classes.html
@@ -7,7 +7,8 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+
     <title>Classes &#8212; fuNEGF 0.1.11 documentation</title>
 
 
@@ -316,7 +317,7 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article" role="main">
 
-  <div class="section" id="classes">
+  <section id="classes">
 <h1>Classes<a class="headerlink" href="#classes" title="Permalink to this heading">#</a></h1>
 <p>For now, there is the LinearChain class including both the model and NEGF solver routines. This will be in future separated into a generic System class, with child classes of different specific systems (like LinearChain).</p>
 <dl class="py class">
@@ -329,17 +330,17 @@ <h1>Classes<a class="headerlink" href="#classes" title="Permalink to this headin
 <span class="sig-name descname"><span class="pre">G_R_fun</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">k</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">E</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Sigma_0</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#fuNEGF.models.LinearChain.G_R_fun" title="Permalink to this definition">#</a></dt>
 <dd><p>The retarded Green’s function for a given k and energy E.</p>
 <dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>k</strong> (<em>float</em>) – the Bloch wave vector.</p></li>
 <li><p><strong>E</strong> (<em>float</em>) – Energy in eV.</p></li>
 <li><p><strong>Sigma_0</strong> (<em>N-by-N numpy array</em><em>, </em><em>optional</em>) – The internal self-energy. Defaults to None.</p></li>
 </ul>
 </dd>
-<dt class="field-even">Returns</dt>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p>the retarded Green’s function in matrix form.</p>
 </dd>
-<dt class="field-odd">Return type</dt>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
 <dd class="field-odd"><p>N-by-N numpy array</p>
 </dd>
 </dl>
@@ -353,7 +354,7 @@ <h1>Classes<a class="headerlink" href="#classes" title="Permalink to this headin
 </dd>
 </dl>
 <dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>k</strong> (<em>float</em>) – the Bloch wave vector.</p></li>
 <li><p><strong>E</strong> (<em>float</em>) – Energy in eV.</p></li>
@@ -362,14 +363,14 @@ <h1>Classes<a class="headerlink" href="#classes" title="Permalink to this headin
 <li><p><strong>N_sc</strong> (<em>int</em><em>, </em><em>optional</em>) – Number of self-consistent iteration steps: typically a value around 50 should be enough. Defaults to 70.</p></li>
 </ul>
 </dd>
-<dt class="field-even">Returns</dt>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p><dl class="simple">
 <dt>the self-consistently solved Green’s functions (retarded, advanced, electron occupation), the internal self-energy Sigma_0,</dt><dd><p>and the in-scattering self-energy Sigma_in_0.</p>
 </dd>
 </dl>
 </p>
 </dd>
-<dt class="field-odd">Return type</dt>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
 <dd class="field-odd"><p>N-by-N numpy arrays</p>
 </dd>
 </dl>
@@ -380,7 +381,7 @@ <h1>Classes<a class="headerlink" href="#classes" title="Permalink to this headin
 <span class="sig-name descname"><span class="pre">add_H_impurity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">H_impurity</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot_dispersion</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#fuNEGF.models.LinearChain.add_H_impurity" title="Permalink to this definition">#</a></dt>
 <dd><p>Add an impurity Hamiltonian.</p>
 <dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>H_impurity</strong> (<em>N-by-N numpy array</em>) – The impurity Hamiltonian (typically an Anderson disorder).</p></li>
 <li><p><strong>plot_dispersion</strong> (<em>bool</em><em>, </em><em>optional</em>) – Plot the numerical and analytical dispersion. Defaults to False.</p></li>
@@ -400,7 +401,7 @@ <h1>Classes<a class="headerlink" href="#classes" title="Permalink to this headin
 <span class="sig-name descname"><span class="pre">construct_H</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">make_H_periodic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">print_H_matrix</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#fuNEGF.models.LinearChain.construct_H" title="Permalink to this definition">#</a></dt>
 <dd><p>Construct the linear chain tight-binding Hamiltonian.</p>
 <dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>make_H_periodic</strong> (<em>bool</em><em>, </em><em>optional</em>) – If True, the Hamiltonian will be made periodic by adding t hopping to the [N-1, 0] and [0, N-1] sites. Defaults to False.</p></li>
 <li><p><strong>print_H_matrix</strong> (<em>bool</em><em>, </em><em>optional</em>) – If True, prints the Hamiltonian matrix. Defaults to False.</p></li>
@@ -418,7 +419,7 @@ <h1>Classes<a class="headerlink" href="#classes" title="Permalink to this headin
 </dd>
 </dl>
 <dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>D0_phase</strong> (<em>float</em>) – The phase relaxation parameter.</p></li>
 <li><p><strong>D0_phase_momentum</strong> (<em>float</em>) – The phase+momentum relaxation parameter.</p></li>
@@ -437,7 +438,7 @@ <h1>Classes<a class="headerlink" href="#classes" title="Permalink to this headin
 <span class="sig-name descname"><span class="pre">plot_onsite_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#fuNEGF.models.LinearChain.plot_onsite_energy" title="Permalink to this definition">#</a></dt>
 <dd><p>Plot the on-site energy as horizontal lines.</p>
 <dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><p><strong>ax</strong> (<em>matplotlib.pyplot axis object</em><em>, </em><em>optional</em>) – If provided, the figure will be plotted to ax. Defaults to None.</p>
 </dd>
 </dl>
@@ -448,15 +449,15 @@ <h1>Classes<a class="headerlink" href="#classes" title="Permalink to this headin
 <span class="sig-name descname"><span class="pre">plot_transmission</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#fuNEGF.models.LinearChain.plot_transmission" title="Permalink to this definition">#</a></dt>
 <dd><p>Plots the transmission function T(E) given by T = Tr[Gamma_1 G_R Gamma_2 G_A].</p>
 <dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><p><strong>ax</strong> (<em>matplotlib.pyplot axis object</em><em>, </em><em>optional</em>) – If provided, the figure will be plotted to ax. Defaults to None.</p>
 </dd>
 </dl>
 </dd></dl>
 
 </dd></dl>
 
-</div>
+</section>
 
 
                 </article>