update index page in documentation

docs/build/html/_sources/index.rst

@@ -9,13 +9,6 @@ Welcome to fuNEGF's documentation!
 
 The `fuNEGF project <https://github.com/liborsold/fuNEGF/>`_ is a Python package for the calculation of the electronic transport properties of nanostructures using the Non-Equilibrium Green's Function (NEGF) formalism for educational purposes. Limited to a 1D linear chain for now.
 
-.. fuNEGF example image
-.. image::
-   ./_images/example_fuNEGF.png
-   :width: 650px
-   :align: center
-
-
 Quickstart
 ================
 
@@ -32,6 +25,22 @@ then
 and execute the ``./examples/one-dimensional_channel.ipynb`` Jupyter notebook to see an example of calculating the NEGF transmission and chemical potential in the presence of impurities.
 
 
+.. fuNEGF example image
+.. image::
+   ./_images/multiple_imp_wire.png
+   :width: 310px
+   :align: right
+
+.. fuNEGF example image
+.. image::
+   ./_images/example_fuNEGF.png
+   :width: 650px
+   :align: center
+
+From the occupation it is clear that each impurity acts as a quantum resistor, causing a drop in the chemical potential. Without phase relaxation, however, it might be difficult to see. Momentum relaxation distributes the potential drop also into the clean wire region, causing a linear drop. 
+
+The transmission function is reduced due to strong localized impurities from the clean limit :math:`T(E) = 1.0 = \mathrm{const.}` to half of its value. With many weak and randomly distributed impurities, the transmission starts to resemble the clean limit again.
+
 Navigation
 ==========
 

docs/build/html/index.html

@@ -45,6 +45,7 @@
     <script src="_static/clipboard.min.js"></script>
     <script src="_static/copybutton.js"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
+    <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'index';</script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -311,7 +312,6 @@ <h2> Contents </h2>
   <div class="section" id="welcome-to-funegf-s-documentation">
 <h1>Welcome to fuNEGF’s documentation!<a class="headerlink" href="#welcome-to-funegf-s-documentation" title="Permalink to this heading">#</a></h1>
 <p>The <a class="reference external" href="https://github.com/liborsold/fuNEGF/">fuNEGF project</a> is a Python package for the calculation of the electronic transport properties of nanostructures using the Non-Equilibrium Green’s Function (NEGF) formalism for educational purposes. Limited to a 1D linear chain for now.</p>
-<a class="reference internal image-reference" href="_images/example_fuNEGF.png"><img alt="_images/example_fuNEGF.png" class="align-center" src="_images/example_fuNEGF.png" style="width: 650px;" /></a>
 <div class="section" id="quickstart">
 <h2>Quickstart<a class="headerlink" href="#quickstart" title="Permalink to this heading">#</a></h2>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">fuNEGF</span>
@@ -322,6 +322,10 @@ <h2>Quickstart<a class="headerlink" href="#quickstart" title="Permalink to this
 </pre></div>
 </div>
 <p>and execute the <code class="docutils literal notranslate"><span class="pre">./examples/one-dimensional_channel.ipynb</span></code> Jupyter notebook to see an example of calculating the NEGF transmission and chemical potential in the presence of impurities.</p>
+<a class="reference internal image-reference" href="_images/multiple_imp_wire.png"><img alt="_images/multiple_imp_wire.png" class="align-right" src="_images/multiple_imp_wire.png" style="width: 310px;" /></a>
+<a class="reference internal image-reference" href="_images/example_fuNEGF.png"><img alt="_images/example_fuNEGF.png" class="align-center" src="_images/example_fuNEGF.png" style="width: 650px;" /></a>
+<p>From the occupation it is clear that each impurity acts as a quantum resistor, causing a drop in the chemical potential. Without phase relaxation, however, it might be difficult to see. Momentum relaxation distributes the potential drop also into the clean wire region, causing a linear drop.</p>
+<p>The transmission function is reduced due to strong localized impurities from the clean limit <span class="math notranslate nohighlight">\(T(E) = 1.0 = \mathrm{const.}\)</span> to half of its value. With many weak and randomly distributed impurities, the transmission starts to resemble the clean limit again.</p>
 </div>
 <div class="section" id="navigation">
 <h2>Navigation<a class="headerlink" href="#navigation" title="Permalink to this heading">#</a></h2>

docs/source/index.rst

@@ -9,13 +9,6 @@ Welcome to fuNEGF's documentation!
 
 The `fuNEGF project <https://github.com/liborsold/fuNEGF/>`_ is a Python package for the calculation of the electronic transport properties of nanostructures using the Non-Equilibrium Green's Function (NEGF) formalism for educational purposes. Limited to a 1D linear chain for now.
 
-.. fuNEGF example image
-.. image::
-   ./_images/example_fuNEGF.png
-   :width: 650px
-   :align: center
-
-
 Quickstart
 ================
 
@@ -32,6 +25,22 @@ then
 and execute the ``./examples/one-dimensional_channel.ipynb`` Jupyter notebook to see an example of calculating the NEGF transmission and chemical potential in the presence of impurities.
 
 
+.. fuNEGF example image
+.. image::
+   ./_images/multiple_imp_wire.png
+   :width: 310px
+   :align: right
+
+.. fuNEGF example image
+.. image::
+   ./_images/example_fuNEGF.png
+   :width: 650px
+   :align: center
+
+From the occupation it is clear that each impurity acts as a quantum resistor, causing a drop in the chemical potential. Without phase relaxation, however, it might be difficult to see. Momentum relaxation distributes the potential drop also into the clean wire region, causing a linear drop. 
+
+The transmission function is reduced due to strong localized impurities from the clean limit :math:`T(E) = 1.0 = \mathrm{const.}` to half of its value. With many weak and randomly distributed impurities, the transmission starts to resemble the clean limit again.
+
 Navigation
 ==========
 

examples/one-dimensional_channel.ipynb

@@ -61,6 +61,17 @@
       "\u001b[1;32mc:\\ProgramData\\Anaconda3\\lib\\site-packages\\ovito\\_extensions\\scripts\\modifiers\\__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m      5\u001b[0m \u001b[1;31m# Note: Using importlib.import_module() here to load them, because human-readable Python filenames contain whitespace.\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      6\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 7\u001b[1;33m \u001b[0movito\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mmodifiers\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mIdentifyFCCPlanarFaultsModifier\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mimportlib\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mimport_module\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\".Identify fcc planar faults\"\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0m__name__\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mIdentifyFCCPlanarFaultsModifier\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      8\u001b[0m \u001b[0movito\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mmodifiers\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m__all__\u001b[0m \u001b[1;33m+=\u001b[0m \u001b[1;33m[\u001b[0m\u001b[1;34m'IdentifyFCCPlanarFaultsModifier'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      9\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
       "\u001b[1;31mAttributeError\u001b[0m: module 'ovito' has no attribute 'modifiers'"
      ]
+    },
+    {
+     "ename": "",
+     "evalue": "",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31mThe Kernel crashed while executing code in the current cell or a previous cell. \n",
+      "\u001b[1;31mPlease review the code in the cell(s) to identify a possible cause of the failure. \n",
+      "\u001b[1;31mClick <a href='https://aka.ms/vscodeJupyterKernelCrash'>here</a> for more info. \n",
+      "\u001b[1;31mView Jupyter <a href='command:jupyter.viewOutput'>log</a> for further details."
+     ]
     }
    ],
    "source": [