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elcorto · Jul 30, 2024 · 4de9a74 · 4de9a74
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diff --git a/_sources/written/background/index.rst.txt b/_sources/written/background/index.rst.txt
@@ -6,10 +6,11 @@ Background, details, special topics
 
 .. toctree::
 
-   ase
-   coord_trans
-   param_study
    parsing
    phonon_dos
+   qha
+   param_study
    pwscf
+   ase
    rbf
+   coord_trans
diff --git a/_sources/written/qha.md.txt → _sources/written/background/qha.md.txt b/_sources/written/qha.md.txt → _sources/written/background/qha.md.txt
@@ -2,7 +2,7 @@
 # Quasi-harmonic approximation
 
 See {class}`~pwtools.thermo.HarmonicThermo` +
-`test/test_qha.py`, {class}`~pwtools.thermo.Gibbs` + `tesst/test_gibbs.py`.
+`test/test_qha.py`, {class}`~pwtools.thermo.Gibbs` + `test/test_gibbs.py`.
 
 The distinctive feature of the pwtools implementation is that in
 {class}`~pwtools.thermo.Gibbs`, we treat unit cell axes instead of just the

diff --git a/index.html b/index.html
@@ -127,13 +127,14 @@ <h1>Welcome to the pwtools documentation<a class="headerlink" href="#welcome-to-
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="written/background/index.html">Background, details, special topics</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="written/background/ase.html">Relation to ASE</a></li>
-<li class="toctree-l2"><a class="reference internal" href="written/background/coord_trans.html">Coordinate transformation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="written/background/param_study.html">Parameter studies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="written/background/parsing.html">Parsing code output and using containers</a></li>
 <li class="toctree-l2"><a class="reference internal" href="written/background/phonon_dos.html">Velocity autocorrelation function and phonon DOS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="written/background/qha.html">Quasi-harmonic approximation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="written/background/param_study.html">Parameter studies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="written/background/pwscf.html">Pwscf</a></li>
+<li class="toctree-l2"><a class="reference internal" href="written/background/ase.html">Relation to ASE</a></li>
 <li class="toctree-l2"><a class="reference internal" href="written/background/rbf.html">Radial Basis Function interpolation an regression</a></li>
+<li class="toctree-l2"><a class="reference internal" href="written/background/coord_trans.html">Coordinate transformation</a></li>
 </ul>
 </li>
 </ul>

diff --git a/objects.inv b/objects.inv
diff --git a/searchindex.js b/searchindex.js
diff --git a/written/background/ase.html b/written/background/ase.html
@@ -13,8 +13,8 @@
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Coordinate transformation" href="coord_trans.html" />
-    <link rel="prev" title="Background, details, special topics" href="index.html" />
+    <link rel="next" title="Radial Basis Function interpolation an regression" href="rbf.html" />
+    <link rel="prev" title="Pwscf" href="pwscf.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
@@ -59,13 +59,14 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../tutorial.html">Tutorial</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html">Background, details, special topics</a><ul class="current">
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Relation to ASE</a></li>
-<li class="toctree-l2"><a class="reference internal" href="coord_trans.html">Coordinate transformation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="param_study.html">Parameter studies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="parsing.html">Parsing code output and using containers</a></li>
 <li class="toctree-l2"><a class="reference internal" href="phonon_dos.html">Velocity autocorrelation function and phonon DOS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="qha.html">Quasi-harmonic approximation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="param_study.html">Parameter studies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pwscf.html">Pwscf</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Relation to ASE</a></li>
 <li class="toctree-l2"><a class="reference internal" href="rbf.html">Radial Basis Function interpolation an regression</a></li>
+<li class="toctree-l2"><a class="reference internal" href="coord_trans.html">Coordinate transformation</a></li>
 </ul>
 </li>
 </ul>
@@ -76,8 +77,8 @@ <h3>Related Topics</h3>
   <li><a href="../../index.html">Documentation overview</a><ul>
   <li><a href="../index.html">&lt;no title&gt;</a><ul>
   <li><a href="index.html">Background, details, special topics</a><ul>
-      <li>Previous: <a href="index.html" title="previous chapter">Background, details, special topics</a></li>
-      <li>Next: <a href="coord_trans.html" title="next chapter">Coordinate transformation</a></li>
+      <li>Previous: <a href="pwscf.html" title="previous chapter">Pwscf</a></li>
+      <li>Next: <a href="rbf.html" title="next chapter">Radial Basis Function interpolation an regression</a></li>
   </ul></li>
   </ul></li>
   </ul></li>

diff --git a/written/background/coord_trans.html b/written/background/coord_trans.html
@@ -15,8 +15,7 @@
     <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Parameter studies" href="param_study.html" />
-    <link rel="prev" title="Relation to ASE" href="ase.html" />
+    <link rel="prev" title="Radial Basis Function interpolation an regression" href="rbf.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
@@ -61,13 +60,14 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../tutorial.html">Tutorial</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html">Background, details, special topics</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="ase.html">Relation to ASE</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Coordinate transformation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="param_study.html">Parameter studies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="parsing.html">Parsing code output and using containers</a></li>
 <li class="toctree-l2"><a class="reference internal" href="phonon_dos.html">Velocity autocorrelation function and phonon DOS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="qha.html">Quasi-harmonic approximation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="param_study.html">Parameter studies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pwscf.html">Pwscf</a></li>
+<li class="toctree-l2"><a class="reference internal" href="ase.html">Relation to ASE</a></li>
 <li class="toctree-l2"><a class="reference internal" href="rbf.html">Radial Basis Function interpolation an regression</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Coordinate transformation</a></li>
 </ul>
 </li>
 </ul>
@@ -78,8 +78,7 @@ <h3>Related Topics</h3>
   <li><a href="../../index.html">Documentation overview</a><ul>
   <li><a href="../index.html">&lt;no title&gt;</a><ul>
   <li><a href="index.html">Background, details, special topics</a><ul>
-      <li>Previous: <a href="ase.html" title="previous chapter">Relation to ASE</a></li>
-      <li>Next: <a href="param_study.html" title="next chapter">Parameter studies</a></li>
+      <li>Previous: <a href="rbf.html" title="previous chapter">Radial Basis Function interpolation an regression</a></li>
   </ul></li>
   </ul></li>
   </ul></li>

diff --git a/written/background/index.html b/written/background/index.html
@@ -15,7 +15,7 @@
     <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Relation to ASE" href="ase.html" />
+    <link rel="next" title="Parsing code output and using containers" href="parsing.html" />
     <link rel="prev" title="Tutorial" href="../tutorial.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
@@ -61,13 +61,14 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../tutorial.html">Tutorial</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Background, details, special topics</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="ase.html">Relation to ASE</a></li>
-<li class="toctree-l2"><a class="reference internal" href="coord_trans.html">Coordinate transformation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="param_study.html">Parameter studies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="parsing.html">Parsing code output and using containers</a></li>
 <li class="toctree-l2"><a class="reference internal" href="phonon_dos.html">Velocity autocorrelation function and phonon DOS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="qha.html">Quasi-harmonic approximation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="param_study.html">Parameter studies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pwscf.html">Pwscf</a></li>
+<li class="toctree-l2"><a class="reference internal" href="ase.html">Relation to ASE</a></li>
 <li class="toctree-l2"><a class="reference internal" href="rbf.html">Radial Basis Function interpolation an regression</a></li>
+<li class="toctree-l2"><a class="reference internal" href="coord_trans.html">Coordinate transformation</a></li>
 </ul>
 </li>
 </ul>
@@ -78,7 +79,7 @@ <h3>Related Topics</h3>
   <li><a href="../../index.html">Documentation overview</a><ul>
   <li><a href="../index.html">&lt;no title&gt;</a><ul>
       <li>Previous: <a href="../tutorial.html" title="previous chapter">Tutorial</a></li>
-      <li>Next: <a href="ase.html" title="next chapter">Relation to ASE</a></li>
+      <li>Next: <a href="parsing.html" title="next chapter">Parsing code output and using containers</a></li>
   </ul></li>
   </ul></li>
 </ul>
@@ -105,18 +106,6 @@ <h3 id="searchlabel">Quick search</h3>
 <h1>Background, details, special topics<a class="headerlink" href="#background-details-special-topics" title="Link to this heading">¶</a></h1>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="ase.html">Relation to ASE</a></li>
-<li class="toctree-l1"><a class="reference internal" href="coord_trans.html">Coordinate transformation</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="coord_trans.html#notation">Notation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="coord_trans.html#row-vs-column-form">Row vs. column form</a></li>
-<li class="toctree-l2"><a class="reference internal" href="coord_trans.html#theory">Theory</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="coord_trans.html#notes-for-the-special-case-fractional-cartesian">Notes for the special case fractional &lt;-&gt; cartesian</a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="coord_trans.html#implementation">Implementation</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="param_study.html">Parameter studies</a></li>
 <li class="toctree-l1"><a class="reference internal" href="parsing.html">Parsing code output and using containers</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="parsing.html#available-parsers">Available parsers</a></li>
 <li class="toctree-l2"><a class="reference internal" href="parsing.html#container-classes-structure-and-trajectory">Container classes <code class="xref py py-class docutils literal notranslate"><span class="pre">Structure</span></code> and <code class="xref py py-class docutils literal notranslate"><span class="pre">Trajectory</span></code></a></li>
@@ -130,12 +119,21 @@ <h1>Background, details, special topics<a class="headerlink" href="#background-d
 <li class="toctree-l2"><a class="reference internal" href="phonon_dos.html#calculation-of-the-phonon-dos-from-md-data">Calculation of the phonon DOS from MD data</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="qha.html">Quasi-harmonic approximation</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="qha.html#d">1d</a></li>
+<li class="toctree-l2"><a class="reference internal" href="qha.html#id1">2d</a></li>
+<li class="toctree-l2"><a class="reference internal" href="qha.html#fake-1d-a-k-a-usual-qha-with-varying-volume">“Fake” 1d a.k.a. usual QHA with varying volume</a></li>
+<li class="toctree-l2"><a class="reference internal" href="qha.html#other-tools">Other tools</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="param_study.html">Parameter studies</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pwscf.html">Pwscf</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="pwscf.html#units">Units</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pwscf.html#atomic-coordinates">Atomic coordinates</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pwscf.html#total-force-on-atoms">Total force on atoms</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="ase.html">Relation to ASE</a></li>
 <li class="toctree-l1"><a class="reference internal" href="rbf.html">Radial Basis Function interpolation an regression</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="rbf.html#theory">Theory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="rbf.html#rbf-parameter-p">RBF parameter <span class="math notranslate nohighlight">\(p\)</span></a></li>
@@ -145,6 +143,16 @@ <h1>Background, details, special topics<a class="headerlink" href="#background-d
 <li class="toctree-l2"><a class="reference internal" href="rbf.html#other-implementations">Other implementations</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="coord_trans.html">Coordinate transformation</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="coord_trans.html#notation">Notation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="coord_trans.html#row-vs-column-form">Row vs. column form</a></li>
+<li class="toctree-l2"><a class="reference internal" href="coord_trans.html#theory">Theory</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="coord_trans.html#notes-for-the-special-case-fractional-cartesian">Notes for the special case fractional &lt;-&gt; cartesian</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="coord_trans.html#implementation">Implementation</a></li>
+</ul>
+</li>
 </ul>
 </div>
 </section>

diff --git a/written/background/param_study.html b/written/background/param_study.html
@@ -13,8 +13,8 @@
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Parsing code output and using containers" href="parsing.html" />
-    <link rel="prev" title="Coordinate transformation" href="coord_trans.html" />
+    <link rel="next" title="Pwscf" href="pwscf.html" />
+    <link rel="prev" title="Quasi-harmonic approximation" href="qha.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
@@ -59,13 +59,14 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../tutorial.html">Tutorial</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html">Background, details, special topics</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="ase.html">Relation to ASE</a></li>
-<li class="toctree-l2"><a class="reference internal" href="coord_trans.html">Coordinate transformation</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Parameter studies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="parsing.html">Parsing code output and using containers</a></li>
 <li class="toctree-l2"><a class="reference internal" href="phonon_dos.html">Velocity autocorrelation function and phonon DOS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="qha.html">Quasi-harmonic approximation</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Parameter studies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pwscf.html">Pwscf</a></li>
+<li class="toctree-l2"><a class="reference internal" href="ase.html">Relation to ASE</a></li>
 <li class="toctree-l2"><a class="reference internal" href="rbf.html">Radial Basis Function interpolation an regression</a></li>
+<li class="toctree-l2"><a class="reference internal" href="coord_trans.html">Coordinate transformation</a></li>
 </ul>
 </li>
 </ul>
@@ -76,8 +77,8 @@ <h3>Related Topics</h3>
   <li><a href="../../index.html">Documentation overview</a><ul>
   <li><a href="../index.html">&lt;no title&gt;</a><ul>
   <li><a href="index.html">Background, details, special topics</a><ul>
-      <li>Previous: <a href="coord_trans.html" title="previous chapter">Coordinate transformation</a></li>
-      <li>Next: <a href="parsing.html" title="next chapter">Parsing code output and using containers</a></li>
+      <li>Previous: <a href="qha.html" title="previous chapter">Quasi-harmonic approximation</a></li>
+      <li>Next: <a href="pwscf.html" title="next chapter">Pwscf</a></li>
   </ul></li>
   </ul></li>
   </ul></li>