Update dev docs

materialsproject · Jan 17, 2022 · 8909805 · 8909805
1 parent 2cee200
commit 8909805
Showing 46 changed files with 2,943 additions and 1,005 deletions.
diff --git a/custodian/__init__.py b/custodian/__init__.py
@@ -4,6 +4,6 @@
 """
 
 __author__ = "Shyue Ping Ong, William Davidson Richards, Stephen Dacek, Xiaohui Qu, Matthew Horton, Samuel M. Blau"
-__version__ = "2021.12.2"
+__version__ = "2022.1.17"
 
 from .custodian import Custodian
diff --git a/docs/_modules/custodian/ansible/actions.html b/docs/_modules/custodian/ansible/actions.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>custodian.ansible.actions &#8212; custodian 2021.12.2 documentation</title>
+    <title>custodian.ansible.actions &#8212; custodian 2022.1.17 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/flasky.css" />
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2021.12.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2022.1.17 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">custodian.ansible.actions</a></li> 
       </ul>

diff --git a/docs/_modules/custodian/ansible/interpreter.html b/docs/_modules/custodian/ansible/interpreter.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>custodian.ansible.interpreter &#8212; custodian 2021.12.2 documentation</title>
+    <title>custodian.ansible.interpreter &#8212; custodian 2022.1.17 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/flasky.css" />
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2021.12.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2022.1.17 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">custodian.ansible.interpreter</a></li> 
       </ul>

diff --git a/docs/_modules/custodian/cli/converge_geometry.html b/docs/_modules/custodian/cli/converge_geometry.html
@@ -5,14 +5,13 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>custodian.cli.converge_geometry &#8212; custodian 2021.1.8 documentation</title>
-    <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
-    <link rel="stylesheet" href="../../../_static/flasky.css" type="text/css" />
-    <script id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></script>
+    <title>custodian.cli.converge_geometry &#8212; custodian 2022.1.17 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/flasky.css" />
+    <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/doctools.js"></script>
-    <script src="../../../_static/language_data.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" />
 
@@ -37,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2021.1.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2022.1.17 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">custodian.cli.converge_geometry</a></li> 
       </ul>
@@ -61,11 +60,11 @@ <h1>Source code for custodian.cli.converge_geometry</h1><div class="highlight"><
 
 <span class="kn">from</span> <span class="nn">custodian.custodian</span> <span class="kn">import</span> <span class="n">Custodian</span>
 <span class="kn">from</span> <span class="nn">custodian.vasp.handlers</span> <span class="kn">import</span> <span class="p">(</span>
-    <span class="n">VaspErrorHandler</span><span class="p">,</span>
-    <span class="n">UnconvergedErrorHandler</span><span class="p">,</span>
     <span class="n">MeshSymmetryErrorHandler</span><span class="p">,</span>
     <span class="n">NonConvergingErrorHandler</span><span class="p">,</span>
     <span class="n">PotimErrorHandler</span><span class="p">,</span>
+    <span class="n">UnconvergedErrorHandler</span><span class="p">,</span>
+    <span class="n">VaspErrorHandler</span><span class="p">,</span>
 <span class="p">)</span>
 <span class="kn">from</span> <span class="nn">custodian.vasp.jobs</span> <span class="kn">import</span> <span class="n">VaspJob</span>
 
@@ -83,7 +82,7 @@ <h1>Source code for custodian.cli.converge_geometry</h1><div class="highlight"><
 
     <span class="k">while</span> <span class="p">(</span><span class="ow">not</span> <span class="n">converged</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="n">job_number</span> <span class="o">&lt;</span> <span class="n">args</span><span class="o">.</span><span class="n">max_relax</span><span class="p">):</span>
 
-        <span class="n">suffix</span> <span class="o">=</span> <span class="s2">&quot;.</span><span class="si">{}{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">&quot;relax&quot;</span><span class="p">,</span> <span class="n">job_number</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
+        <span class="n">suffix</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;.relax</span><span class="si">{</span><span class="n">job_number</span> <span class="o">+</span> <span class="mi">1</span><span class="si">}</span><span class="s2">&quot;</span>
 
         <span class="k">if</span> <span class="n">job_number</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="n">backup</span> <span class="o">=</span> <span class="kc">True</span>
@@ -160,8 +159,7 @@ <h1>Source code for custodian.cli.converge_geometry</h1><div class="highlight"><
         <span class="n">nargs</span><span class="o">=</span><span class="s2">&quot;?&quot;</span><span class="p">,</span>
         <span class="n">default</span><span class="o">=</span><span class="s2">&quot;pvasp&quot;</span><span class="p">,</span>
         <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
-        <span class="n">help</span><span class="o">=</span><span class="s2">&quot;VASP command. Defaults to pvasp. If you are using mpirun, &quot;</span>
-        <span class="s1">&#39;set this to something like &quot;mpirun pvasp&quot;.&#39;</span><span class="p">,</span>
+        <span class="n">help</span><span class="o">=</span><span class="s2">&quot;VASP command. Defaults to pvasp. If you are using mpirun, &quot;</span> <span class="s1">&#39;set this to something like &quot;mpirun pvasp&quot;.&#39;</span><span class="p">,</span>
     <span class="p">)</span>
 
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
@@ -202,7 +200,7 @@ <h1>Source code for custodian.cli.converge_geometry</h1><div class="highlight"><
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../../search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" />
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>

diff --git a/docs/_modules/custodian/cli/converge_kpoints.html b/docs/_modules/custodian/cli/converge_kpoints.html
@@ -5,14 +5,13 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>custodian.cli.converge_kpoints &#8212; custodian 2021.1.8 documentation</title>
-    <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
-    <link rel="stylesheet" href="../../../_static/flasky.css" type="text/css" />
-    <script id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></script>
+    <title>custodian.cli.converge_kpoints &#8212; custodian 2022.1.17 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/flasky.css" />
+    <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/doctools.js"></script>
-    <script src="../../../_static/language_data.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" />
 
@@ -37,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2021.1.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2022.1.17 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">custodian.cli.converge_kpoints</a></li> 
       </ul>
@@ -61,7 +60,7 @@ <h1>Source code for custodian.cli.converge_kpoints</h1><div class="highlight"><p
 <span class="kn">from</span> <span class="nn">pymatgen.io.vasp.outputs</span> <span class="kn">import</span> <span class="n">Vasprun</span>
 
 <span class="kn">from</span> <span class="nn">custodian.custodian</span> <span class="kn">import</span> <span class="n">Custodian</span>
-<span class="kn">from</span> <span class="nn">custodian.vasp.handlers</span> <span class="kn">import</span> <span class="n">VaspErrorHandler</span><span class="p">,</span> <span class="n">UnconvergedErrorHandler</span>
+<span class="kn">from</span> <span class="nn">custodian.vasp.handlers</span> <span class="kn">import</span> <span class="n">UnconvergedErrorHandler</span><span class="p">,</span> <span class="n">VaspErrorHandler</span>
 <span class="kn">from</span> <span class="nn">custodian.vasp.jobs</span> <span class="kn">import</span> <span class="n">VaspJob</span>
 
 <span class="n">FORMAT</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="si">%(asctime)s</span><span class="s2"> </span><span class="si">%(message)s</span><span class="s2">&quot;</span>
@@ -89,7 +88,7 @@ <h1>Source code for custodian.cli.converge_kpoints</h1><div class="highlight"><p
             <span class="n">e_per_atom</span> <span class="o">=</span> <span class="n">v</span><span class="o">.</span><span class="n">final_energy</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">v</span><span class="o">.</span><span class="n">final_structure</span><span class="p">)</span>
             <span class="n">ediff</span> <span class="o">=</span> <span class="nb">abs</span><span class="p">(</span><span class="n">e_per_atom</span> <span class="o">-</span> <span class="n">energy</span><span class="p">)</span>
             <span class="k">if</span> <span class="n">ediff</span> <span class="o">&lt;</span> <span class="n">target</span><span class="p">:</span>
-                <span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Converged to </span><span class="si">{}</span><span class="s2"> eV/atom!&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ediff</span><span class="p">))</span>
+                <span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Converged to </span><span class="si">{</span><span class="n">ediff</span><span class="si">}</span><span class="s2"> eV/atom!&quot;</span><span class="p">)</span>
                 <span class="k">break</span>
             <span class="n">energy</span> <span class="o">=</span> <span class="n">e_per_atom</span>
             <span class="n">settings</span> <span class="o">=</span> <span class="p">[</span>
@@ -104,7 +103,7 @@ <h1>Source code for custodian.cli.converge_kpoints</h1><div class="highlight"><p
             <span class="n">vasp_command</span><span class="p">,</span>
             <span class="n">final</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
             <span class="n">backup</span><span class="o">=</span><span class="n">backup</span><span class="p">,</span>
-            <span class="n">suffix</span><span class="o">=</span><span class="s2">&quot;.kpoints.</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">&quot;x&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">m</span><span class="p">))),</span>
+            <span class="n">suffix</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;.kpoints.</span><span class="si">{</span><span class="s1">&#39;x&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">m</span><span class="p">))</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
             <span class="n">settings_override</span><span class="o">=</span><span class="n">settings</span><span class="p">,</span>
         <span class="p">)</span></div>
 
@@ -144,7 +143,7 @@ <h1>Source code for custodian.cli.converge_kpoints</h1><div class="highlight"><p
 <span class="s2">    default convergence criteria is 1meV/atom, but this can be set using the</span>
 <span class="s2">    --target option.</span>
 <span class="s2">    &quot;&quot;&quot;</span><span class="p">,</span>
-        <span class="n">epilog</span><span class="o">=</span><span class="s2">&quot;&quot;&quot;Author: Shyue Ping Ong&quot;&quot;&quot;</span>
+        <span class="n">epilog</span><span class="o">=</span><span class="s2">&quot;&quot;&quot;Author: Shyue Ping Ong&quot;&quot;&quot;</span><span class="p">,</span>
     <span class="p">)</span>
 
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
@@ -154,8 +153,7 @@ <h1>Source code for custodian.cli.converge_kpoints</h1><div class="highlight"><p
         <span class="n">nargs</span><span class="o">=</span><span class="s2">&quot;?&quot;</span><span class="p">,</span>
         <span class="n">default</span><span class="o">=</span><span class="s2">&quot;pvasp&quot;</span><span class="p">,</span>
         <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
-        <span class="n">help</span><span class="o">=</span><span class="s2">&quot;VASP command. Defaults to pvasp. If you are using mpirun, &quot;</span>
-        <span class="s1">&#39;set this to something like &quot;mpirun pvasp&quot;.&#39;</span><span class="p">,</span>
+        <span class="n">help</span><span class="o">=</span><span class="s2">&quot;VASP command. Defaults to pvasp. If you are using mpirun, &quot;</span> <span class="s1">&#39;set this to something like &quot;mpirun pvasp&quot;.&#39;</span><span class="p">,</span>
     <span class="p">)</span>
 
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
@@ -221,7 +219,7 @@ <h1>Source code for custodian.cli.converge_kpoints</h1><div class="highlight"><p
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../../search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" />
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>

diff --git a/docs/_modules/custodian/cli/cstdn.html b/docs/_modules/custodian/cli/cstdn.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>custodian.cli.cstdn &#8212; custodian 2021.12.2 documentation</title>
+    <title>custodian.cli.cstdn &#8212; custodian 2022.1.17 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/flasky.css" />
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2021.12.2 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2022.1.17 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">custodian.cli.cstdn</a></li> 
       </ul>