deploy: 389ba8e

phonopy · Nov 25, 2024 · be91cf4 · be91cf4
1 parent 1d130f6
commit be91cf4
Show file tree

Hide file tree

Showing 40 changed files with 181 additions and 126 deletions.
diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 514c4c7a11097615f83d1530b80b98dc
+config: b576cbdd806a5eae734b0e8a689e1622
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/changelog.doctree b/.doctrees/changelog.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/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.3.7.0</title>
+    <title>How to write phono3py documentation &#8212; Phono3py v.3.8.0</title>
 
 
 
@@ -39,7 +39,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
 
-    <script src="_static/documentation_options.js?v=f1d443ca"></script>
+    <script src="_static/documentation_options.js?v=e15476e9"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -48,7 +48,7 @@
     <link rel="search" title="Search" href="search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="3.7" />
+  <meta name="docsearch:version" content="3.8" />
   </head>
 
 
@@ -125,7 +125,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.7.0</p>
+    <p class="title logo__title">Phono3py v.3.8.0</p>
 
 </a></div>
         <div class="sidebar-primary-item">

diff --git a/_sources/changelog.md b/_sources/changelog.md
@@ -2,6 +2,12 @@
 
 # Change Log
 
+## Nov-25-2024: Version 3.8.0
+
+- Follow the change due to phonopy's refactoring of MLP interface.
+- Experimental option (`BUILD_WITHOUT_LAPACKE=ON`) to compile phono3py without
+  LAPACKE in C
+
 ## Nov-13-2024: Version 3.7.0
 
 - Update to follow the change of phonopy's internal functions

diff --git a/_sources/direct-solution.md b/_sources/direct-solution.md
@@ -307,7 +307,7 @@ is used through them. Multithreaded OpenBLAS is installed by conda and can be
 used via LAPACKE in phono3py. MKL LAPACK and BLAS are also able to be used via
 LAPACKE in phono3py with appropriate setting in `setup.py`.
 
-Using `--pinv-solver=[number]`, one of the following solver is chosen:
+Using `--pinv-solver NUMBER`, one of the following solver is chosen:
 
 1. Lapacke `dsyev`: Smaller memory consumption than `dsyevd`, but slower. This
    is the default solver when MKL LAPACKE is integrated or scipy is not
@@ -323,3 +323,8 @@ Using `--pinv-solver=[number]`, one of the following solver is chosen:
    LAPACKE is not integrated.
 5. Scipy's `dsyevd`: Similar to solver (2), this solver should be used
    carefully.
+
+```{note}
+`pinv-solver` =3, 4, and 5 are only available when phono3py is compiled
+without LAPACKE.
+```
diff --git a/_sources/install.md b/_sources/install.md
@@ -49,7 +49,7 @@ conda environment. Automatic search of required libraries and flags that are
 already on the system is performed by cmake.
 
 (install_with_cmake)=
-### Build with automatic search of library configurations by cmake
+### Building with automatic search of library configurations by cmake
 
 With installed cmake and required libraries on the system, cmake tries to find
 libraries to be linked and the compiler flags that are required during the build.
@@ -61,6 +61,21 @@ See an example at {ref}`install_an_example`. In the standard output, flags and
 libraries found by cmake are shown. Please carefully check if those
 configurations are expected ones or not.
 
+### Building without linking LAPACKE
+
+**Experimental**
+
+To compile phono3py without linking LAPACKE in C, use the following command:
+
+```
+% BUILD_WITHOUT_LAPACKE=ON pip install -e . -vvv
+```
+
+When this option is enabled, linking to BLAS and LAPACKE libraries is not
+required, so installing these libraries for C compilation may not be necessary.
+However, since numpy and scipy rely on BLAS and LAPACK libraries, their runtime
+versions are still required.
+
 (install_an_example)=
 
 ## Installation instruction of latest development version of phono3py

diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '3.7.0',
+    VERSION: '3.8.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

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.3.7.0</title>
+    <title>Auxiliary tools &#8212; Phono3py v.3.8.0</title>
 
 
 
@@ -39,7 +39,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
 
-    <script src="_static/documentation_options.js?v=f1d443ca"></script>
+    <script src="_static/documentation_options.js?v=e15476e9"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -52,7 +52,7 @@
     <link rel="prev" title="How to read the results stored in hdf5 files" href="hdf5_howto.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="3.7" />
+  <meta name="docsearch:version" content="3.8" />
   </head>
 
 
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.7.0</p>
+    <p class="title logo__title">Phono3py v.3.8.0</p>
 
 </a></div>
         <div class="sidebar-primary-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.3.7.0</title>
+    <title>Change Log &#8212; Phono3py v.3.8.0</title>
 
 
 
@@ -39,7 +39,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
 
-    <script src="_static/documentation_options.js?v=f1d443ca"></script>
+    <script src="_static/documentation_options.js?v=e15476e9"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -51,7 +51,7 @@
     <link rel="prev" title="References" href="reference.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="3.7" />
+  <meta name="docsearch:version" content="3.8" />
   </head>
 
 
@@ -126,7 +126,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.7.0</p>
+    <p class="title logo__title">Phono3py v.3.8.0</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -306,6 +306,7 @@ <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="#nov-25-2024-version-3-8-0">Nov-25-2024: Version 3.8.0</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#nov-13-2024-version-3-7-0">Nov-13-2024: Version 3.7.0</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#nov-3-2024-version-3-6-0">Nov-3-2024: Version 3.6.0</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#sep-24-2024-version-3-5-2">Sep-24-2024: Version 3.5.2</a></li>
@@ -401,6 +402,14 @@ <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="nov-25-2024-version-3-8-0">
+<h2>Nov-25-2024: Version 3.8.0<a class="headerlink" href="#nov-25-2024-version-3-8-0" title="Link to this heading">#</a></h2>
+<ul class="simple">
+<li><p>Follow the change due to phonopy’s refactoring of MLP interface.</p></li>
+<li><p>Experimental option (<code class="docutils literal notranslate"><span class="pre">BUILD_WITHOUT_LAPACKE=ON</span></code>) to compile phono3py without
+LAPACKE in C</p></li>
+</ul>
+</section>
 <section id="nov-13-2024-version-3-7-0">
 <h2>Nov-13-2024: Version 3.7.0<a class="headerlink" href="#nov-13-2024-version-3-7-0" title="Link to this heading">#</a></h2>
 <ul class="simple">
@@ -1177,6 +1186,7 @@ <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="#nov-25-2024-version-3-8-0">Nov-25-2024: Version 3.8.0</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#nov-13-2024-version-3-7-0">Nov-13-2024: Version 3.7.0</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#nov-3-2024-version-3-6-0">Nov-3-2024: Version 3.6.0</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#sep-24-2024-version-3-5-2">Sep-24-2024: Version 3.5.2</a></li>

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.3.7.0</title>
+    <title>How to cite phono3py &#8212; Phono3py v.3.8.0</title>
 
 
 
@@ -39,7 +39,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
 
-    <script src="_static/documentation_options.js?v=f1d443ca"></script>
+    <script src="_static/documentation_options.js?v=e15476e9"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -50,7 +50,7 @@
     <link rel="prev" title="Tips" href="tips.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="3.7" />
+  <meta name="docsearch:version" content="3.8" />
   </head>
 
 
@@ -125,7 +125,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.7.0</p>
+    <p class="title logo__title">Phono3py v.3.8.0</p>
 
 </a></div>
         <div class="sidebar-primary-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.3.7.0</title>
+    <title>Command options / Setting tags &#8212; Phono3py v.3.8.0</title>
 
 
 
@@ -39,7 +39,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
 
-    <script src="_static/documentation_options.js?v=f1d443ca"></script>
+    <script src="_static/documentation_options.js?v=e15476e9"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -52,7 +52,7 @@
     <link rel="prev" title="TURBOMOLE &amp; phono3py calculation" href="turbomole.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="3.7" />
+  <meta name="docsearch:version" content="3.8" />
   </head>
 
 
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.7.0</p>
+    <p class="title logo__title">Phono3py v.3.8.0</p>
 
 </a></div>
         <div class="sidebar-primary-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.3.7.0</title>
+    <title>CRYSTAL &amp; phono3py calculation &#8212; Phono3py v.3.8.0</title>
 
 
 
@@ -39,7 +39,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
 
-    <script src="_static/documentation_options.js?v=f1d443ca"></script>
+    <script src="_static/documentation_options.js?v=e15476e9"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -50,7 +50,7 @@
     <link rel="prev" title="Quantum ESPRESSO (pw) &amp; phono3py calculation" href="qe.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="3.7" />
+  <meta name="docsearch:version" content="3.8" />
   </head>
 
 
@@ -125,7 +125,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.7.0</p>
+    <p class="title logo__title">Phono3py v.3.8.0</p>
 
 </a></div>
         <div class="sidebar-primary-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.3.7.0</title>
+    <title>Force constants calculation with cutoff pair-distance &#8212; Phono3py v.3.8.0</title>
 
 
 
@@ -39,7 +39,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
 
-    <script src="_static/documentation_options.js?v=f1d443ca"></script>
+    <script src="_static/documentation_options.js?v=e15476e9"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -52,7 +52,7 @@
     <link rel="prev" title="Force constants calculation using pypolymlp (machine learning potential)" href="pypolymlp.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="3.7" />
+  <meta name="docsearch:version" content="3.8" />
   </head>
 
 
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.7.0</p>
+    <p class="title logo__title">Phono3py v.3.8.0</p>
 
 </a></div>
         <div class="sidebar-primary-item">