[skip ci] Updates

nanotheorygroup · Jul 7, 2024 · e139765 · e139765
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diff --git a/_modules/index.html b/_modules/index.html
@@ -217,168 +217,193 @@
   <ul class="md-nav__list">
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-      <span class="md-nav__link caption"><span class="caption-text">Documentation</span></span>
+      <span class="md-nav__link caption"><span class="caption-text">Introduction</span></span>
 
     </li>
     <li class="md-nav__item">
 
 
-      <a href="../docsource/introduction.html" class="md-nav__link">Introduction</a>
+      <a href="../docsource/introduction.html" class="md-nav__link">Overview</a>
 
 
     </li>
     <li class="md-nav__item">
 
 
-      <a href="../docsource/introduction.html#Quick-Install" class="md-nav__link">Quick Install</a>
+      <a href="../docsource/introduction.html#Features" class="md-nav__link">Features</a>
 
 
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     <li class="md-nav__item">
 
+      <span class="md-nav__link caption"><span class="caption-text">Getting Started</span></span>
 
-      <a href="../docsource/introduction.html#Interfacing-with-Other-Codes" class="md-nav__link">Interfacing with Other Codes</a>
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../docsource/getting_started.html" class="md-nav__link">Quick Install</a>
 
 
+    </li>
+    <li class="md-nav__item">
+
+      <span class="md-nav__link caption"><span class="caption-text">User Guide</span></span>
+
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     <li class="md-nav__item">
 
 
-      <a href="../docsource/introduction.html#Output-Storage" class="md-nav__link">Output Storage</a>
+      <a href="../docsource/theory.html" class="md-nav__link">Basic Concepts</a>
 
 
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     <li class="md-nav__item">
 
 
-      <a href="../docsource/introduction.html#Code-Architecture" class="md-nav__link">Code Architecture</a>
+      <a href="../docsource/theory.html#Workflow" class="md-nav__link">Workflow</a>
 
 
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     <li class="md-nav__item">
 
 
-      <a href="../docsource/introduction.html#Main-Features" class="md-nav__link">Main Features</a>
+      <a href="../docsource/user_guide.html" class="md-nav__link">Interfacing with Other Codes</a>
 
 
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     <li class="md-nav__item">
 
 
-      <a href="../docsource/introduction.html#Examples" class="md-nav__link">Examples</a>
+      <a href="../docsource/user_guide.html#Output-Storage" class="md-nav__link">Output Storage</a>
 
 
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+      <span class="md-nav__link caption"><span class="caption-text">Reference</span></span>
+
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+    <li class="md-nav__item">
 
-      <a href="../docsource/introduction.html#How-to-cite" class="md-nav__link">How to cite</a>
+
+      <a href="../docsource/api_forceconstants.html" class="md-nav__link">ForceConstants API Reference</a>
 
 
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     <li class="md-nav__item">
 
 
-      <a href="../docsource/introduction.html#Copyright" class="md-nav__link">Copyright</a>
+      <a href="../docsource/api_phonons.html" class="md-nav__link">Phonons API Reference</a>
 
 
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-      <a href="../docsource/introduction.html#Acknowledgements" class="md-nav__link">Acknowledgements</a>
+      <a href="../docsource/api_conductivity.html" class="md-nav__link">Conductivity API Reference</a>
 
 
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+      <span class="md-nav__link caption"><span class="caption-text">Tutorials and examples</span></span>
 
-      <a href="../docsource/introduction.html#Other-codes" class="md-nav__link">Other codes</a>
+    </li>
+    <li class="md-nav__item">
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+
+      <a href="../docsource/crystal_presentation.html" class="md-nav__link">Silicon diamond tutorial</a>
 
 
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-      <a href="../docsource/introduction.html#Project-template" class="md-nav__link">Project template</a>
+      <a href="../docsource/amorphous_presentation.html" class="md-nav__link">Amorphous silicon tutorial</a>
 
 
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     <li class="md-nav__item">
 
 
-      <a href="../docsource/introduction.html#How-to-contribute-changes" class="md-nav__link">How to contribute changes</a>
+      <a href="../docsource/examples.html" class="md-nav__link">Examples</a>
 
 
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     <li class="md-nav__item">
 
-      <span class="md-nav__link caption"><span class="caption-text">Theory</span></span>
+      <span class="md-nav__link caption"><span class="caption-text">Citations</span></span>
 
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     <li class="md-nav__item">
 
 
-      <a href="../docsource/theory.html" class="md-nav__link">Introduction</a>
+      <a href="../docsource/citations.html" class="md-nav__link">How to cite</a>
 
 
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     <li class="md-nav__item">
 
 
-      <a href="../docsource/theory.html#Theory" class="md-nav__link">Theory</a>
+      <a href="../publications/readme.html" class="md-nav__link">Publications using kALDo</a>
 
 
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     <li class="md-nav__item">
 
 
-      <a href="../docsource/theory.html#Benchmarks-applications" class="md-nav__link">Benchmarks applications</a>
+      <a href="../docsource/other_codes.html" class="md-nav__link">Other codes</a>
 
 
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     <li class="md-nav__item">
 
-      <span class="md-nav__link caption"><span class="caption-text">API</span></span>
+      <span class="md-nav__link caption"><span class="caption-text">Developer Guide</span></span>
 
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     <li class="md-nav__item">
 
 
-      <a href="../docsource/api_forceconstants.html" class="md-nav__link">ForceConstants</a>
+      <a href="../docsource/code_architecture.html" class="md-nav__link">Code Architecture</a>
 
 
     </li>
     <li class="md-nav__item">
 
 
-      <a href="../docsource/api_phonons.html" class="md-nav__link">Phonons API Reference</a>
+      <a href="../docsource/contributing.html" class="md-nav__link">How to contribute changes</a>
 
 
     </li>
     <li class="md-nav__item">
 
+      <span class="md-nav__link caption"><span class="caption-text">Acknowledgements</span></span>
 
-      <a href="../docsource/api_conductivity.html" class="md-nav__link">Conductivity API Reference</a>
+    </li>
+    <li class="md-nav__item">
+
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+      <a href="../docsource/credits.html" class="md-nav__link">Acknowledgements</a>
 
 
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-      <span class="md-nav__link caption"><span class="caption-text">Tutorials</span></span>
+      <span class="md-nav__link caption"><span class="caption-text">License</span></span>
 
     </li>
     <li class="md-nav__item">
 
 
-      <a href="../docsource/crystal_presentation.html" class="md-nav__link">Silicon diamond tutorial</a>
+      <a href="../docsource/license.html" class="md-nav__link">License Information</a>
 
 
     </li>
     <li class="md-nav__item">
 
 
-      <a href="../docsource/amorphous_presentation.html" class="md-nav__link">Amorphous silicon tutorial</a>
+      <a href="../docsource/license.html#copyright" class="md-nav__link">Copyright</a>
 
 
     </li>