Merge pull request #122 from OMalenfantThuot/schnetupdates

Schnetupdates
OMalenfantThuot · Jul 31, 2020 · 4cca27e · 4cca27e
2 parents ed840d8 + 4ee28a2
commit 4cca27e
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diff --git a/docs/.buildinfo b/docs/.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: 69a96a50c6ea83abf4c7ce2fa6daa413
+config: 32a1edb12b6ec666742c74190f1d60ac
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -1,8 +1,7 @@
 
 
 <!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
-<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<html class="writer-html5" lang="en" >
 <head>
   <meta charset="utf-8">
 
@@ -12,28 +11,30 @@
 
 
 
+  <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+
+
 
 
 
 
 
-  <script type="text/javascript" src="../_static/js/modernizr.min.js"></script>
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
 
 
       <script type="text/javascript" id="documentation_options" data-url_root="../" 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>
-        <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
+        <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
     <script type="text/javascript" src="../_static/js/theme.js"></script>
 
 
-
-
-  <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
-  <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
 </head>
@@ -49,7 +50,7 @@
 
 
 
-            <a href="../index.html" class="icon icon-home"> ML_Calc_Driver
+            <a href="../index.html" class="icon icon-home" alt="Documentation Home"> ML_Calc_Driver
 
 
 
@@ -72,6 +73,7 @@
 
         </div>
 
+
         <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
 
 
@@ -91,6 +93,7 @@
 
 
         </div>
+
       </div>
     </nav>
 
@@ -129,7 +132,7 @@
 
   <ul class="wy-breadcrumbs">
 
-      <li><a href="../index.html">Docs</a> &raquo;</li>
+      <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
 
       <li>Overview: module code</li>
 
@@ -167,11 +170,19 @@ <h1>All modules for which code is available</h1>
 
   <div role="contentinfo">
     <p>
+
         &copy; Copyright 2020, Olivier Malenfant-Thuot
 
     </p>
   </div>
-  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
+
+
+
+    Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
+
+    <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
+
+    provided by <a href="https://readthedocs.org">Read the Docs</a>. 
 
 </footer>
 
@@ -183,7 +194,6 @@ <h1>All modules for which code is available</h1>
   </div>
 
 
-
   <script type="text/javascript">
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);

diff --git a/docs/_modules/mlcalcdriver/base/job.html b/docs/_modules/mlcalcdriver/base/job.html
@@ -1,8 +1,7 @@
 
 
 <!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
-<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<html class="writer-html5" lang="en" >
 <head>
   <meta charset="utf-8">
 
@@ -12,28 +11,30 @@
 
 
 
+  <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+
+
 
 
 
 
 
-  <script type="text/javascript" src="../../../_static/js/modernizr.min.js"></script>
+  <!--[if lt IE 9]>
+    <script src="../../../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
 
 
       <script type="text/javascript" id="documentation_options" data-url_root="../../../" 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>
-        <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
+        <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
     <script type="text/javascript" src="../../../_static/js/theme.js"></script>
 
 
-
-
-  <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
-  <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
 </head>
@@ -49,7 +50,7 @@
 
 
 
-            <a href="../../../index.html" class="icon icon-home"> ML_Calc_Driver
+            <a href="../../../index.html" class="icon icon-home" alt="Documentation Home"> ML_Calc_Driver
 
 
 
@@ -72,6 +73,7 @@
 
         </div>
 
+
         <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
 
 
@@ -91,6 +93,7 @@
 
 
         </div>
+
       </div>
     </nav>
 
@@ -129,7 +132,7 @@
 
   <ul class="wy-breadcrumbs">
 
-      <li><a href="../../../index.html">Docs</a> &raquo;</li>
+      <li><a href="../../../index.html" class="icon icon-home"></a> &raquo;</li>
 
           <li><a href="../../index.html">Module code</a> &raquo;</li>
 
@@ -284,7 +287,7 @@ <h1>Source code for mlcalcdriver.base.job</h1><div class="highlight"><pre>
 <span class="sd">                &quot;&quot;&quot;</span>
             <span class="p">)</span>
 
-<div class="viewcode-block" id="Job.run"><a class="viewcode-back" href="../../../job.html#mlcalcdriver.base.job.Job.run">[docs]</a>    <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">property</span><span class="p">,</span> <span class="n">device</span><span class="o">=</span><span class="s2">&quot;cpu&quot;</span><span class="p">,</span> <span class="n">batch_size</span><span class="o">=</span><span class="mi">128</span><span class="p">,</span> <span class="n">finite_difference</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<div class="viewcode-block" id="Job.run"><a class="viewcode-back" href="../../../job.html#mlcalcdriver.base.job.Job.run">[docs]</a>    <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">property</span><span class="p">,</span> <span class="n">batch_size</span><span class="o">=</span><span class="mi">128</span><span class="p">,</span> <span class="n">finite_difference</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
         <span class="sa">r</span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Main method to call to obtain results for a Job</span>
 
@@ -295,20 +298,10 @@ <h1>Source code for mlcalcdriver.base.job</h1><div class="highlight"><pre>
 <span class="sd">            available_properties of the Calculator except the</span>
 <span class="sd">            forces which can be derived from an energy</span>
 <span class="sd">            Calculator.</span>
-<span class="sd">        device : str</span>
-<span class="sd">            Device on which to run the calculation.</span>
-<span class="sd">            Either `&quot;cpu&quot;` or `&quot;cuda&quot;` to run on cpu or gpu.</span>
-<span class="sd">            Default is `&quot;cpu&quot;` and should not be changed, except</span>
-<span class="sd">            for very large systems.</span>
 <span class="sd">        batch_size : int</span>
 <span class="sd">            Size of the mini-batches used in predictions.</span>
 <span class="sd">            Default is 128.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">device</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">device</span><span class="p">)</span>
-        <span class="k">if</span> <span class="n">device</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;cuda&quot;</span><span class="p">):</span>
-            <span class="k">if</span> <span class="ow">not</span> <span class="n">torch</span><span class="o">.</span><span class="n">cuda</span><span class="o">.</span><span class="n">is_available</span><span class="p">():</span>
-                <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;CUDA was asked for, but is not available.&quot;</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">)</span>
-
         <span class="k">if</span> <span class="ow">not</span> <span class="n">finite_difference</span><span class="p">:</span>
             <span class="n">predictions</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">calculator</span><span class="o">.</span><span class="n">run</span><span class="p">(</span>
                 <span class="nb">property</span><span class="o">=</span><span class="nb">property</span><span class="p">,</span> <span class="n">posinp</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">posinp</span><span class="p">,</span> <span class="n">batch_size</span><span class="o">=</span><span class="n">batch_size</span>
@@ -477,11 +470,19 @@ <h1>Source code for mlcalcdriver.base.job</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>
+
         &copy; Copyright 2020, Olivier Malenfant-Thuot
 
     </p>
   </div>
-  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
+
+
+
+    Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
+
+    <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
+
+    provided by <a href="https://readthedocs.org">Read the Docs</a>. 
 
 </footer>
 
@@ -493,7 +494,6 @@ <h1>Source code for mlcalcdriver.base.job</h1><div class="highlight"><pre>
   </div>
 
 
-
   <script type="text/javascript">
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);

diff --git a/docs/_modules/mlcalcdriver/base/posinp.html b/docs/_modules/mlcalcdriver/base/posinp.html
@@ -1,8 +1,7 @@
 
 
 <!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
-<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<html class="writer-html5" lang="en" >
 <head>
   <meta charset="utf-8">
 
@@ -12,28 +11,30 @@
 
 
 
+  <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+
+
 
 
 
 
 
-  <script type="text/javascript" src="../../../_static/js/modernizr.min.js"></script>
+  <!--[if lt IE 9]>
+    <script src="../../../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
 
 
       <script type="text/javascript" id="documentation_options" data-url_root="../../../" 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>
-        <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
+        <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
     <script type="text/javascript" src="../../../_static/js/theme.js"></script>
 
 
-
-
-  <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
-  <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
 </head>
@@ -49,7 +50,7 @@
 
 
 
-            <a href="../../../index.html" class="icon icon-home"> ML_Calc_Driver
+            <a href="../../../index.html" class="icon icon-home" alt="Documentation Home"> ML_Calc_Driver
 
 
 
@@ -72,6 +73,7 @@
 
         </div>
 
+
         <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
 
 
@@ -91,6 +93,7 @@
 
 
         </div>
+
       </div>
     </nav>
 
@@ -129,7 +132,7 @@
 
   <ul class="wy-breadcrumbs">
 
-      <li><a href="../../../index.html">Docs</a> &raquo;</li>
+      <li><a href="../../../index.html" class="icon icon-home"></a> &raquo;</li>
 
           <li><a href="../../index.html">Module code</a> &raquo;</li>
 
@@ -329,12 +332,10 @@ <h1>Source code for mlcalcdriver.base.posinp</h1><div class="highlight"><pre>
         <span class="c1"># Decode the second line</span>
         <span class="n">line2</span> <span class="o">=</span> <span class="n">lines</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
         <span class="n">boundary_conditions</span> <span class="o">=</span> <span class="n">line2</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
-        <span class="k">if</span> <span class="n">boundary_conditions</span> <span class="o">==</span> <span class="s2">&quot;periodic&quot;</span><span class="p">:</span>
-            <span class="n">cell</span> <span class="o">=</span> <span class="n">line2</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="mi">4</span><span class="p">]</span>
-        <span class="k">elif</span> <span class="n">boundary_conditions</span> <span class="o">==</span> <span class="s2">&quot;surface&quot;</span><span class="p">:</span>
-            <span class="n">cell</span> <span class="o">=</span> <span class="p">[</span><span class="n">line2</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="mf">0.0</span><span class="p">,</span> <span class="n">line2</span><span class="p">[</span><span class="mi">3</span><span class="p">]]</span>
-        <span class="k">else</span><span class="p">:</span>
+        <span class="k">if</span> <span class="n">boundary_conditions</span> <span class="o">==</span> <span class="s2">&quot;free&quot;</span><span class="p">:</span>
             <span class="n">cell</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">cell</span> <span class="o">=</span> <span class="n">line2</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="mi">4</span><span class="p">]</span>
         <span class="c1"># Angles if present</span>
         <span class="k">if</span> <span class="n">lines</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;angles&quot;</span><span class="p">:</span>
             <span class="n">angles</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="nb">float</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">lines</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)[</span><span class="mi">1</span><span class="p">:]])</span>
@@ -1031,11 +1032,19 @@ <h1>Source code for mlcalcdriver.base.posinp</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>
+
         &copy; Copyright 2020, Olivier Malenfant-Thuot
 
     </p>
   </div>
-  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
+
+
+
+    Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
+
+    <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
+
+    provided by <a href="https://readthedocs.org">Read the Docs</a>. 
 
 </footer>
 
@@ -1047,7 +1056,6 @@ <h1>Source code for mlcalcdriver.base.posinp</h1><div class="highlight"><pre>
   </div>
 
 
-
   <script type="text/javascript">
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);