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phonopy · Jul 27, 2024 · 99bf6a4 · 99bf6a4
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diff --git a/.buildinfo b/.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: d67ae7397bd4b3f511ea1065ba67c286
+config: d51c0e48c433b18a043a7a88d09f6c47
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/changelog.doctree b/.doctrees/changelog.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/install.doctree b/.doctrees/install.doctree
diff --git a/README.html b/README.html
@@ -8,7 +8,7 @@
     <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" />
 
-    <title>How to write phono3py documentation &#8212; Phono3py v.3.3.0</title>
+    <title>How to write phono3py documentation &#8212; Phono3py v.3.3.2</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=b45e98f8"></script>
+    <script src="_static/documentation_options.js?v=18d69a83"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -132,7 +132,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.3.0</p>
+    <p class="title logo__title">Phono3py v.3.3.2</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -415,6 +415,10 @@ <h2>How to publish<a class="headerlink" href="#how-to-publish" title="Link to th
 
   <div class="footer-item">
 
+<p class="component-author">
+By Author name not set
+</p>
+
   </div>
 
   <div class="footer-item">

diff --git a/_sources/changelog.md b/_sources/changelog.md
@@ -2,6 +2,15 @@
 
 # Change Log
 
+## Jul-22-2024: Version 3.3.2
+
+- Minor fix of `phono3py.load` function for reading displacements from
+  `phono3py_disp.yaml` like file that doesn't contain forces.
+
+## Jul-8-2024: Version 3.3.1
+
+- Major refactoring to isolate reciprocal space grid code.
+
 ## Jul-8-2024: Version 3.3.0
 
 - Build system of phono3py was renewed. Now nanobind, cmake, and

diff --git a/_sources/install.md b/_sources/install.md
@@ -136,12 +136,13 @@ wrong python libraries can be imported.
    % cd phonopy
    % pip install -e . -vvv
    % cd ../phono3py
-   % pip install -e . -vvv
+   % pip install . -vvv
    ```
 
-   The conda packages dependency can often change and this recipe may not work
-   properly. So if you find this instruction doesn't work, it is very
-   appreciated if letting us know it in the phonopy mailing list.
+   The editable install (`pip install -e`) may not work depending on the
+   computer environment. The conda packages dependency can often change and this
+   recipe may not work properly. So if you find this instruction doesn't work,
+   it is very appreciated if letting us know it in the phonopy mailing list.
 
 (install_lapacke)=
 ## Installation of LAPACKE

diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '3.3.0',
+    VERSION: '3.3.2',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/_static/searchtools.js b/_static/searchtools.js
@@ -178,7 +178,7 @@ const Search = {
 
   htmlToText: (htmlString, anchor) => {
     const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
-    for (const removalQuery of [".headerlinks", "script", "style"]) {
+    for (const removalQuery of [".headerlink", "script", "style"]) {
       htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
     }
     if (anchor) {
@@ -328,13 +328,14 @@ const Search = {
     for (const [title, foundTitles] of Object.entries(allTitles)) {
       if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
         for (const [file, id] of foundTitles) {
-          let score = Math.round(100 * queryLower.length / title.length)
+          const score = Math.round(Scorer.title * queryLower.length / title.length);
+          const boost = titles[file] === title ? 1 : 0;  // add a boost for document titles
           normalResults.push([
             docNames[file],
             titles[file] !== title ? `${titles[file]} > ${title}` : title,
             id !== null ? "#" + id : "",
             null,
-            score,
+            score + boost,
             filenames[file],
           ]);
         }

diff --git a/auxiliary-tools.html b/auxiliary-tools.html
@@ -8,7 +8,7 @@
     <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" />
 
-    <title>Auxiliary tools &#8212; Phono3py v.3.3.0</title>
+    <title>Auxiliary tools &#8212; Phono3py v.3.3.2</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=b45e98f8"></script>
+    <script src="_static/documentation_options.js?v=18d69a83"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -134,7 +134,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.3.0</p>
+    <p class="title logo__title">Phono3py v.3.3.2</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -793,6 +793,10 @@ <h4><a class="toc-backref" href="#id28" role="doc-backlink"><code class="docutil
 
   <div class="footer-item">
 
+<p class="component-author">
+By Author name not set
+</p>
+
   </div>
 
   <div class="footer-item">

diff --git a/changelog.html b/changelog.html
@@ -8,7 +8,7 @@
     <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" />
 
-    <title>Change Log &#8212; Phono3py v.3.3.0</title>
+    <title>Change Log &#8212; Phono3py v.3.3.2</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=b45e98f8"></script>
+    <script src="_static/documentation_options.js?v=18d69a83"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -133,7 +133,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.3.0</p>
+    <p class="title logo__title">Phono3py v.3.3.2</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -323,6 +323,8 @@ <h2> Contents </h2>
             </div>
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#jul-22-2024-version-3-3-2">Jul-22-2024: Version 3.3.2</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#jul-8-2024-version-3-3-1">Jul-8-2024: Version 3.3.1</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#jul-8-2024-version-3-3-0">Jul-8-2024: Version 3.3.0</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#jun-29-2024-version-3-2-0">Jun-29-2024: Version 3.2.0</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#jun-19-2024-version-3-1-2">Jun-19-2024: Version 3.1.2</a></li>
@@ -408,6 +410,19 @@ <h2> Contents </h2>
 
   <section class="tex2jax_ignore mathjax_ignore" id="change-log">
 <span id="changelog"></span><h1>Change Log<a class="headerlink" href="#change-log" title="Link to this heading">#</a></h1>
+<section id="jul-22-2024-version-3-3-2">
+<h2>Jul-22-2024: Version 3.3.2<a class="headerlink" href="#jul-22-2024-version-3-3-2" title="Link to this heading">#</a></h2>
+<ul class="simple">
+<li><p>Minor fix of <code class="docutils literal notranslate"><span class="pre">phono3py.load</span></code> function for reading displacements from
+<code class="docutils literal notranslate"><span class="pre">phono3py_disp.yaml</span></code> like file that doesn’t contain forces.</p></li>
+</ul>
+</section>
+<section id="jul-8-2024-version-3-3-1">
+<h2>Jul-8-2024: Version 3.3.1<a class="headerlink" href="#jul-8-2024-version-3-3-1" title="Link to this heading">#</a></h2>
+<ul class="simple">
+<li><p>Major refactoring to isolate reciprocal space grid code.</p></li>
+</ul>
+</section>
 <section id="jul-8-2024-version-3-3-0">
 <h2>Jul-8-2024: Version 3.3.0<a class="headerlink" href="#jul-8-2024-version-3-3-0" title="Link to this heading">#</a></h2>
 <ul class="simple">
@@ -1117,6 +1132,8 @@ <h2>Changes in version 0.6.0<a class="headerlink" href="#changes-in-version-0-6-
   </div>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#jul-22-2024-version-3-3-2">Jul-22-2024: Version 3.3.2</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#jul-8-2024-version-3-3-1">Jul-8-2024: Version 3.3.1</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#jul-8-2024-version-3-3-0">Jul-8-2024: Version 3.3.0</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#jun-29-2024-version-3-2-0">Jun-29-2024: Version 3.2.0</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#jun-19-2024-version-3-1-2">Jun-19-2024: Version 3.1.2</a></li>
@@ -1202,6 +1219,10 @@ <h2>Changes in version 0.6.0<a class="headerlink" href="#changes-in-version-0-6-
 
   <div class="footer-item">
 
+<p class="component-author">
+By Author name not set
+</p>
+
   </div>
 
   <div class="footer-item">

diff --git a/citation.html b/citation.html
@@ -8,7 +8,7 @@
     <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" />
 
-    <title>How to cite phono3py &#8212; Phono3py v.3.3.0</title>
+    <title>How to cite phono3py &#8212; Phono3py v.3.3.2</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=b45e98f8"></script>
+    <script src="_static/documentation_options.js?v=18d69a83"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -132,7 +132,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.3.0</p>
+    <p class="title logo__title">Phono3py v.3.3.2</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -511,6 +511,10 @@ <h2>Citation of solution of the Wigner transport equation (<code class="docutils
 
   <div class="footer-item">
 
+<p class="component-author">
+By Author name not set
+</p>
+
   </div>
 
   <div class="footer-item">

diff --git a/command-options.html b/command-options.html
@@ -8,7 +8,7 @@
     <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" />
 
-    <title>Command options / Setting tags &#8212; Phono3py v.3.3.0</title>
+    <title>Command options / Setting tags &#8212; Phono3py v.3.3.2</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=b45e98f8"></script>
+    <script src="_static/documentation_options.js?v=18d69a83"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -134,7 +134,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.3.0</p>
+    <p class="title logo__title">Phono3py v.3.3.2</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -1878,6 +1878,10 @@ <h3><a class="toc-backref" href="#id83" role="doc-backlink"><code class="docutil
 
   <div class="footer-item">
 
+<p class="component-author">
+By Author name not set
+</p>
+
   </div>
 
   <div class="footer-item">

diff --git a/crystal.html b/crystal.html
@@ -8,7 +8,7 @@
     <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" />
 
-    <title>CRYSTAL &amp; phono3py calculation &#8212; Phono3py v.3.3.0</title>
+    <title>CRYSTAL &amp; phono3py calculation &#8212; Phono3py v.3.3.2</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=b45e98f8"></script>
+    <script src="_static/documentation_options.js?v=18d69a83"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -132,7 +132,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.3.0</p>
+    <p class="title logo__title">Phono3py v.3.3.2</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -473,6 +473,10 @@ <h2> Contents </h2>
 
   <div class="footer-item">
 
+<p class="component-author">
+By Author name not set
+</p>
+
   </div>
 
   <div class="footer-item">

diff --git a/cutoff-pair.html b/cutoff-pair.html
@@ -8,7 +8,7 @@
     <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" />
 
-    <title>Force constants calculation with cutoff pair-distance &#8212; Phono3py v.3.3.0</title>
+    <title>Force constants calculation with cutoff pair-distance &#8212; Phono3py v.3.3.2</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=b45e98f8"></script>
+    <script src="_static/documentation_options.js?v=18d69a83"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -134,7 +134,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.3.0</p>
+    <p class="title logo__title">Phono3py v.3.3.2</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -856,6 +856,10 @@ <h3><a class="toc-backref" href="#id11" role="doc-backlink">AlN-LDA</a><a class=
 
   <div class="footer-item">
 
+<p class="component-author">
+By Author name not set
+</p>
+
   </div>
 
   <div class="footer-item">