Update dev docs

materialsproject · Aug 24, 2019 · bf9ac73 · bf9ac73
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Showing 130 changed files with 548 additions and 29,275 deletions.
diff --git a/custodian/__init__.py b/custodian/__init__.py
@@ -2,6 +2,6 @@
 
 __author__ = "Shyue Ping Ong, William Davidson Richards, Stephen Dacek, " \
              "Xiaohui Qu"
-__version__ = "2019.8.23"
+__version__ = "2019.8.24"
 
-from .custodian import Custodian
+from .custodian import Custodian
diff --git a/docs/_modules/custodian/ansible/actions.html b/docs/_modules/custodian/ansible/actions.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>custodian.ansible.actions &#8212; custodian 2019.8.23 documentation</title>
+    <title>custodian.ansible.actions &#8212; custodian 2019.8.24 documentation</title>
     <link rel="stylesheet" href="../../../_static/flasky.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></script>
@@ -37,7 +37,7 @@ <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 2019.8.23 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2019.8.24 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li> 
       </ul>
     </div>  
@@ -251,7 +251,7 @@ <h1>Source code for custodian.ansible.actions</h1><div class="highlight"><pre>
                 <span class="k">try</span><span class="p">:</span>
                     <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
                 <span class="k">except</span> <span class="ne">OSError</span><span class="p">:</span>
-                    <span class="c1">#Skip file not found error.</span>
+                    <span class="c1"># Skip file not found error.</span>
                     <span class="k">pass</span>
             <span class="k">elif</span> <span class="n">k</span> <span class="o">==</span> <span class="s2">&quot;mode&quot;</span> <span class="ow">and</span> <span class="n">v</span> <span class="o">==</span> <span class="s2">&quot;simulated&quot;</span><span class="p">:</span>
                 <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Simulated removal of </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="n">filename</span><span class="p">))</span></div>
@@ -280,9 +280,9 @@ <h1>Source code for custodian.ansible.actions</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">settings</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
             <span class="k">if</span> <span class="n">k</span> <span class="o">==</span> <span class="s2">&quot;mode&quot;</span><span class="p">:</span>
-                <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="n">v</span><span class="p">)</span>
+                <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span>
             <span class="k">if</span> <span class="n">k</span> <span class="o">==</span> <span class="s2">&quot;owners&quot;</span><span class="p">:</span>
-                <span class="n">os</span><span class="o">.</span><span class="n">chown</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="n">v</span><span class="p">)</span></div></div>
+                <span class="n">os</span><span class="o">.</span><span class="n">chown</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span></div></div>
 </pre></div>
 
           </div>

diff --git a/docs/_modules/custodian/ansible/interpreter.html b/docs/_modules/custodian/ansible/interpreter.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>custodian.ansible.interpreter &#8212; custodian 2019.8.23 documentation</title>
+    <title>custodian.ansible.interpreter &#8212; custodian 2019.8.24 documentation</title>
     <link rel="stylesheet" href="../../../_static/flasky.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></script>
@@ -37,7 +37,7 @@ <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 2019.8.23 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2019.8.24 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li> 
       </ul>
     </div>  
@@ -57,15 +57,13 @@ <h1>Source code for custodian.ansible.interpreter</h1><div class="highlight"><pr
 <span class="sd">using support actions.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
-
 <span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Shyue Ping Ong&quot;</span>
 <span class="n">__copyright__</span> <span class="o">=</span> <span class="s2">&quot;Copyright 2012, The Materials Project&quot;</span>
 <span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1&quot;</span>
 <span class="n">__maintainer__</span> <span class="o">=</span> <span class="s2">&quot;Shyue Ping Ong&quot;</span>
 <span class="n">__email__</span> <span class="o">=</span> <span class="s2">&quot;[email protected]&quot;</span>
 <span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;Jun 1, 2012&quot;</span>
 
-
 <span class="kn">import</span> <span class="nn">re</span>
 
 <span class="kn">from</span> <span class="nn">custodian.ansible.actions</span> <span class="k">import</span> <span class="n">DictActions</span>
@@ -92,6 +90,7 @@ <h1>Source code for custodian.ansible.interpreter</h1><div class="highlight"><pr
 <span class="sd">    &gt;&gt;&gt; d[&#39;Hello&#39;]</span>
 <span class="sd">    &#39;Universe&#39;</span>
 <span class="sd">    &quot;&quot;&quot;</span>
+
     <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">actions</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Initializes a Modder from a list of supported actions.</span>
@@ -150,6 +149,7 @@ <h1>Source code for custodian.ansible.interpreter</h1><div class="highlight"><pr
 
 <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
     <span class="kn">import</span> <span class="nn">doctest</span>
+
     <span class="n">doctest</span><span class="o">.</span><span class="n">testmod</span><span class="p">()</span>
 </pre></div>
 

diff --git a/docs/_modules/custodian/cli/converge_geometry.html b/docs/_modules/custodian/cli/converge_geometry.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>custodian.cli.converge_geometry &#8212; custodian 2019.8.23 documentation</title>
+    <title>custodian.cli.converge_geometry &#8212; custodian 2019.8.24 documentation</title>
     <link rel="stylesheet" href="../../../_static/flasky.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></script>
@@ -37,7 +37,7 @@ <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 2019.8.23 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2019.8.24 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li> 
       </ul>
     </div>  
@@ -71,13 +71,11 @@ <h1>Source code for custodian.cli.converge_geometry</h1><div class="highlight"><
 <span class="kn">from</span> <span class="nn">custodian.vasp.jobs</span> <span class="k">import</span> <span class="n">VaspJob</span>
 <span class="kn">from</span> <span class="nn">pymatgen.io.vasp.outputs</span> <span class="k">import</span> <span class="n">Vasprun</span>
 
-
 <span class="n">FORMAT</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%(asctime)s</span><span class="s1"> </span><span class="si">%(message)s</span><span class="s1">&#39;</span>
 <span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="nb">format</span><span class="o">=</span><span class="n">FORMAT</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="s2">&quot;run.log&quot;</span><span class="p">)</span>
 
 
 <div class="viewcode-block" id="get_runs"><a class="viewcode-back" href="../../../custodian.cli.html#custodian.cli.converge_geometry.get_runs">[docs]</a><span class="k">def</span> <span class="nf">get_runs</span><span class="p">(</span><span class="n">args</span><span class="p">):</span>
-
     <span class="n">vasp_command</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">command</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
     <span class="n">converged</span> <span class="o">=</span> <span class="kc">False</span>
     <span class="n">job_number</span> <span class="o">=</span> <span class="mi">0</span>
@@ -88,8 +86,8 @@ <h1>Source code for custodian.cli.converge_geometry</h1><div class="highlight"><
 
         <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>
-            <span class="c1">#assume the initial guess is poor,</span>
-            <span class="c1">#start with conjugate gradients</span>
+            <span class="c1"># assume the initial guess is poor,</span>
+            <span class="c1"># start with conjugate gradients</span>
             <span class="n">settings</span> <span class="o">=</span> <span class="p">[</span>
                 <span class="p">{</span><span class="s2">&quot;dict&quot;</span><span class="p">:</span> <span class="s2">&quot;INCAR&quot;</span><span class="p">,</span>
                  <span class="s2">&quot;action&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;_set&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;IBRION&quot;</span><span class="p">:</span> <span class="mi">2</span><span class="p">}}}</span>
@@ -110,8 +108,8 @@ <h1>Source code for custodian.cli.converge_geometry</h1><div class="highlight"><
                     <span class="p">{</span><span class="s2">&quot;file&quot;</span><span class="p">:</span> <span class="s2">&quot;CONTCAR&quot;</span><span class="p">,</span>
                      <span class="s2">&quot;action&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;_file_copy&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;dest&quot;</span><span class="p">:</span> <span class="s2">&quot;POSCAR&quot;</span><span class="p">}}}]</span>
 
-            <span class="c1">#switch to RMM-DIIS once we are near the</span>
-            <span class="c1">#local minimum (assumed after 2 runs of CG)</span>
+            <span class="c1"># switch to RMM-DIIS once we are near the</span>
+            <span class="c1"># local minimum (assumed after 2 runs of CG)</span>
             <span class="k">else</span><span class="p">:</span>
                 <span class="n">settings</span> <span class="o">=</span> <span class="p">[</span>
                     <span class="p">{</span><span class="s2">&quot;dict&quot;</span><span class="p">:</span> <span class="s2">&quot;INCAR&quot;</span><span class="p">,</span>

diff --git a/docs/_modules/custodian/cli/converge_kpoints.html b/docs/_modules/custodian/cli/converge_kpoints.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>custodian.cli.converge_kpoints &#8212; custodian 2019.8.23 documentation</title>
+    <title>custodian.cli.converge_kpoints &#8212; custodian 2019.8.24 documentation</title>
     <link rel="stylesheet" href="../../../_static/flasky.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></script>
@@ -37,7 +37,7 @@ <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 2019.8.23 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2019.8.24 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li> 
       </ul>
     </div>  
@@ -72,7 +72,6 @@ <h1>Source code for custodian.cli.converge_kpoints</h1><div class="highlight"><p
 <span class="kn">from</span> <span class="nn">custodian.vasp.jobs</span> <span class="k">import</span> <span class="n">VaspJob</span>
 <span class="kn">from</span> <span class="nn">pymatgen.io.vasp</span> <span class="k">import</span> <span class="n">VaspInput</span><span class="p">,</span> <span class="n">Vasprun</span>
 
-
 <span class="n">FORMAT</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%(asctime)s</span><span class="s1"> </span><span class="si">%(message)s</span><span class="s1">&#39;</span>
 <span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="nb">format</span><span class="o">=</span><span class="n">FORMAT</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="s2">&quot;run.log&quot;</span><span class="p">)</span>
 

diff --git a/docs/_modules/custodian/cli/cstdn.html b/docs/_modules/custodian/cli/cstdn.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>custodian.cli.cstdn &#8212; custodian 2019.8.23 documentation</title>
+    <title>custodian.cli.cstdn &#8212; custodian 2019.8.24 documentation</title>
     <link rel="stylesheet" href="../../../_static/flasky.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></script>
@@ -37,7 +37,7 @@ <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 2019.8.23 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2019.8.24 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li> 
       </ul>
     </div>  
@@ -62,7 +62,6 @@ <h1>Source code for custodian.cli.cstdn</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">custodian.custodian</span> <span class="k">import</span> <span class="n">Custodian</span>
 <span class="kn">import</span> <span class="nn">logging</span>
 
-
 <span class="n">example_yaml</span> <span class="o">=</span> <span class="s2">&quot;&quot;&quot;</span>
 <span class="s2"># This is an example of a Custodian yaml spec file. It shows how you can specify</span>
 <span class="s2"># a double relaxation followed by a static calculation. Minor modifications</span>

diff --git a/docs/_modules/custodian/cli/run_nwchem.html b/docs/_modules/custodian/cli/run_nwchem.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>custodian.cli.run_nwchem &#8212; custodian 2019.8.23 documentation</title>
+    <title>custodian.cli.run_nwchem &#8212; custodian 2019.8.24 documentation</title>
     <link rel="stylesheet" href="../../../_static/flasky.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></script>
@@ -37,7 +37,7 @@ <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 2019.8.23 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2019.8.24 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li> 
       </ul>
     </div>  
@@ -63,7 +63,6 @@ <h1>Source code for custodian.cli.run_nwchem</h1><div class="highlight"><pre>
 <span class="n">__status__</span> <span class="o">=</span> <span class="s2">&quot;Beta&quot;</span>
 <span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;6/18/13&quot;</span>
 
-
 <span class="kn">import</span> <span class="nn">logging</span>
 
 <span class="kn">from</span> <span class="nn">custodian.custodian</span> <span class="k">import</span> <span class="n">Custodian</span>