deploy: 2fced3a

phonopy · Oct 19, 2023 · 71394b7 · 71394b7
1 parent 4faf7c1
commit 71394b7
Show file tree

Hide file tree

Showing 74 changed files with 1,139 additions and 14,083 deletions.
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: 10547dcae032bf068a7be3db635d5521
+config: 941b29f326e01963e1df49c743ed4f5d
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/README.doctree b/.doctrees/README.doctree
diff --git a/.doctrees/auxiliary-tools.doctree b/.doctrees/auxiliary-tools.doctree
diff --git a/.doctrees/changelog.doctree b/.doctrees/changelog.doctree
diff --git a/.doctrees/citation.doctree b/.doctrees/citation.doctree
diff --git a/.doctrees/command-options.doctree b/.doctrees/command-options.doctree
diff --git a/.doctrees/crystal.doctree b/.doctrees/crystal.doctree
diff --git a/.doctrees/cutoff-pair.doctree b/.doctrees/cutoff-pair.doctree
diff --git a/.doctrees/direct-solution.doctree b/.doctrees/direct-solution.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/examples.doctree b/.doctrees/examples.doctree
diff --git a/.doctrees/external-tools.doctree b/.doctrees/external-tools.doctree
diff --git a/.doctrees/hdf5_howto.doctree b/.doctrees/hdf5_howto.doctree
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/input-output-files.doctree b/.doctrees/input-output-files.doctree
diff --git a/.doctrees/install.doctree b/.doctrees/install.doctree
diff --git a/.doctrees/interfaces.doctree b/.doctrees/interfaces.doctree
diff --git a/.doctrees/phono3py-api.doctree b/.doctrees/phono3py-api.doctree
diff --git a/.doctrees/phono3py-load.doctree b/.doctrees/phono3py-load.doctree
diff --git a/.doctrees/qe.doctree b/.doctrees/qe.doctree
diff --git a/.doctrees/reference.doctree b/.doctrees/reference.doctree
diff --git a/.doctrees/tips.doctree b/.doctrees/tips.doctree
diff --git a/.doctrees/turbomole.doctree b/.doctrees/turbomole.doctree
diff --git a/.doctrees/vasp.doctree b/.doctrees/vasp.doctree
diff --git a/.doctrees/wigner-solution.doctree b/.doctrees/wigner-solution.doctree
diff --git a/.doctrees/workflow.doctree b/.doctrees/workflow.doctree
diff --git a/.doctrees/workload-distribution.doctree b/.doctrees/workload-distribution.doctree
diff --git a/README.html b/README.html
@@ -7,7 +7,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
     <title>How to write phono3py documentation &#8212; Phono3py v.2.7.0</title>
 
@@ -19,12 +19,12 @@
   </script>
 
   <!-- Loaded before other Sphinx assets -->
-  <link href="_static/styles/theme.css?digest=e353d410970836974a52" rel="stylesheet" />
-<link href="_static/styles/bootstrap.css?digest=e353d410970836974a52" rel="stylesheet" />
-<link href="_static/styles/pydata-sphinx-theme.css?digest=e353d410970836974a52" rel="stylesheet" />
+  <link href="_static/styles/theme.css?digest=ac02cc09edc035673794" rel="stylesheet" />
+<link href="_static/styles/bootstrap.css?digest=ac02cc09edc035673794" rel="stylesheet" />
+<link href="_static/styles/pydata-sphinx-theme.css?digest=ac02cc09edc035673794" rel="stylesheet" />
 
 
-  <link href="_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=e353d410970836974a52" rel="stylesheet" />
+  <link href="_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=ac02cc09edc035673794" rel="stylesheet" />
   <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-solid-900.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" />
@@ -33,13 +33,11 @@
     <link rel="stylesheet" href="_static/styles/sphinx-book-theme.css?digest=14f4ca6b54d191a8c7657f6c759bf11a5fb86285" type="text/css" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=e353d410970836974a52" />
-<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52" />
+  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=ac02cc09edc035673794" />
+<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=ac02cc09edc035673794" />
+  <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=ac02cc09edc035673794"></script>
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
-    <script src="_static/jquery.js"></script>
-    <script src="_static/underscore.js"></script>
-    <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="_static/doctools.js"></script>
     <script src="_static/sphinx_highlight.js"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -57,6 +55,15 @@
 
   <a class="skip-link" href="#main-content">Skip to main content</a>
 
+  <div id="pst-scroll-pixel-helper"></div>
+
+
+  <button type="button" class="btn rounded-pill" id="pst-back-to-top">
+    <i class="fa-solid fa-arrow-up"></i>
+    Back to top
+  </button>
+
+
   <input type="checkbox"
           class="sidebar-toggle"
           name="__primary"
@@ -255,18 +262,18 @@
 
 <script>
 document.write(`
-  <button class="theme-switch-button btn btn-sm btn-outline-primary navbar-btn rounded-circle" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
-    <span class="theme-switch" data-mode="light"><i class="fa-solid fa-sun"></i></span>
-    <span class="theme-switch" data-mode="dark"><i class="fa-solid fa-moon"></i></span>
-    <span class="theme-switch" data-mode="auto"><i class="fa-solid fa-circle-half-stroke"></i></span>
+  <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
   </button>
 `);
 </script>
 
 <script>
 document.write(`
   <button class="btn btn-sm navbar-btn search-button search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
-    <i class="fa-solid fa-magnifying-glass"></i>
+    <i class="fa-solid fa-magnifying-glass fa-lg"></i>
   </button>
 `);
 </script>
@@ -349,16 +356,12 @@ <h2>How to publish<a class="headerlink" href="#how-to-publish" title="Permalink
 
 
 
-                <footer class="bd-footer-article">
-
-<div class="footer-article-items footer-article__inner">
-
-    <div class="footer-article-item"><!-- Previous / next buttons -->
+
+
+                <footer class="prev-next-footer">
+                  <!-- Previous / next buttons -->
 <div class="prev-next-area">
-</div></div>
-
 </div>
-
                 </footer>
 
             </div>
@@ -419,8 +422,8 @@ <h2>How to publish<a class="headerlink" href="#how-to-publish" title="Permalink
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script src="_static/scripts/bootstrap.js?digest=e353d410970836974a52"></script>
-<script src="_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52"></script>
+  <script src="_static/scripts/bootstrap.js?digest=ac02cc09edc035673794"></script>
+<script src="_static/scripts/pydata-sphinx-theme.js?digest=ac02cc09edc035673794"></script>
 
   <footer class="bd-footer">
   </footer>

diff --git a/_sources/command-options.md b/_sources/command-options.md
@@ -174,7 +174,7 @@ created from `FORCES_FC2` and `phono3py_disp.yaml` instead of `FORCES_FC3` and
 % phono3py --cfs --dim-fc2="x x x"
 ```
 
-## Supercell and primitive cell
+## Supercell, primitive cell, masses, magnetic moments
 
 (dim_option)=
 
@@ -237,6 +237,16 @@ http://phonopy.github.io/phonopy/setting-tags.html#primitive-axis. When a proper
 `phono3py_disp.yaml` exists in the current directory, this is unnecessary to be
 specified.
 
+### `--mass` (`MASS`)
+
+Atomic masses of **primitive cell** are overwritten. See more details in
+[phonopy web page](https://phonopy.github.io/phonopy/setting-tags.html#mass).
+
+### `--magmom` (`MAGMOM`)
+
+Magnetic moments of **unit cell** are specified. This information is used to find crystal symmetry. See more details in [phonopy
+web page](https://phonopy.github.io/phonopy/setting-tags.html#magmom).
+
 ## Displacement creation
 
 (create_displacements_option)=
@@ -627,7 +637,6 @@ option works only when `--br` options are activated. Therefore third-order force
 constants are not necessary to input. The physical unit of the value is
 $\text{eV}^2$. See also references {cite}`Togo-PRB-2015,Mizokami-PRB-2018`.
 
-
 ```bash
 % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --const-ave-pp=1e-10
 ```
@@ -908,12 +917,10 @@ file, where $A_{\mathrm{q}j}$ is normalied as given above, i.e., numerical
 sum of stored value for each band should become roughly 1.
 ```
 
-
 (jdos_option)=
 
 ## Joint density of states (JDOS) and weighted-JDOS
 
-
 ### `--jdos` (`JOINT_DOS = .TRUE.`)
 
 Two classes of joint density of states (JDOS) are calculated. The result is
@@ -1240,8 +1247,8 @@ This modifies default input and output file names.
 
 This is equivalent to setting `-i` and `-o` simultaneously.
 
-
 ## References
+
 ```{bibliography}
 :filter: docname in docnames
 ```
diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js