Merge pull request #300 from OMalenfantThuot/docs

docs updated
OMalenfantThuot · May 12, 2022 · b65cd0f · b65cd0f
2 parents be23a63 + ac23510
commit b65cd0f
Show file tree

Hide file tree

Showing 121 changed files with 1,507 additions and 15,265 deletions.
diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@ ML\_Calc\_Driver is a driver to emulate DFT calculations using machine learned p
 To use this package, one needs an already trained model, that can predict energy or forces from an input atomic geometry.
 Supported systems depends on the model, this package should not be a limitation.
 
-This package has been tested with python 3.7, but should work with older python 3 versions.
+This package is tested with python 3.8 and 3.9.
 
 Credit to [mmoriniere](https://gitlab.com/mmoriniere) for the [MyBigDFT package](https://gitlab.com/mmoriniere/MyBigDFT)
 which served as a foundation for this work. Some classes have been directly adapted from MyBigDFT.

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: dad214e7207eecf6d105a355df37c5af
+config: af6cd381fb97079085fd269f818d8dd5
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; ML_Calc_Driver 1.1.0 documentation</title>
+  <title>Overview: module code &mdash; ML_Calc_Driver 1.1.3 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -73,7 +73,9 @@ <h1>All modules for which code is available</h1>
 <li><a href="mlcalcdriver/calculators/calculator.html">mlcalcdriver.calculators.calculator</a></li>
 <li><a href="mlcalcdriver/calculators/ensemble.html">mlcalcdriver.calculators.ensemble</a></li>
 <li><a href="mlcalcdriver/calculators/schnetpack.html">mlcalcdriver.calculators.schnetpack</a></li>
+<li><a href="mlcalcdriver/calculators/schnetpack_patch.html">mlcalcdriver.calculators.schnetpack_patch</a></li>
 <li><a href="mlcalcdriver/interfaces/ase_interface.html">mlcalcdriver.interfaces.ase_interface</a></li>
+<li><a href="mlcalcdriver/interfaces/atoms_to_patches.html">mlcalcdriver.interfaces.atoms_to_patches</a></li>
 <li><a href="mlcalcdriver/interfaces/schnetpack_interface.html">mlcalcdriver.interfaces.schnetpack_interface</a></li>
 <li><a href="mlcalcdriver/workflows/geopt.html">mlcalcdriver.workflows.geopt</a></li>
 <li><a href="mlcalcdriver/workflows/phonon.html">mlcalcdriver.workflows.phonon</a></li>
@@ -86,7 +88,7 @@ <h1>All modules for which code is available</h1>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2020, Olivier Malenfant-Thuot.</p>
+    <p>&#169; Copyright 2022, Olivier Malenfant-Thuot.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/_modules/mlcalcdriver/base/job.html b/docs/_modules/mlcalcdriver/base/job.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mlcalcdriver.base.job &mdash; ML_Calc_Driver 1.1.0 documentation</title>
+  <title>mlcalcdriver.base.job &mdash; ML_Calc_Driver 1.1.3 documentation</title>
       <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -76,8 +76,6 @@ <h1>Source code for mlcalcdriver.base.job</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">torch</span>
 <span class="kn">from</span> <span class="nn">copy</span> <span class="kn">import</span> <span class="n">deepcopy</span>
-<span class="kn">from</span> <span class="nn">mlcalcdriver.calculators</span> <span class="kn">import</span> <span class="n">Calculator</span>
-<span class="kn">from</span> <span class="nn">mlcalcdriver.base</span> <span class="kn">import</span> <span class="n">Posinp</span>
 <span class="kn">from</span> <span class="nn">mlcalcdriver.globals</span> <span class="kn">import</span> <span class="n">HA_TO_EV</span><span class="p">,</span> <span class="n">B_TO_ANG</span><span class="p">,</span> <span class="n">ANG_TO_B</span>
 <span class="kn">import</span> <span class="nn">warnings</span>
 
@@ -125,6 +123,8 @@ <h1>Source code for mlcalcdriver.base.job</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;A Job instance has no initial positions.&quot;</span><span class="p">)</span>
         <span class="k">elif</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">posinp</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
             <span class="n">posinp</span> <span class="o">=</span> <span class="p">[</span><span class="n">posinp</span><span class="p">]</span>
+        <span class="kn">from</span> <span class="nn">mlcalcdriver.base.posinp</span> <span class="kn">import</span> <span class="n">Posinp</span>
+
         <span class="k">for</span> <span class="n">pos</span> <span class="ow">in</span> <span class="n">posinp</span><span class="p">:</span>
             <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">pos</span><span class="p">,</span> <span class="n">Posinp</span><span class="p">):</span>
                 <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span>
@@ -193,6 +193,8 @@ <h1>Source code for mlcalcdriver.base.job</h1><div class="highlight"><pre>
 
     <span class="nd">@calculator</span><span class="o">.</span><span class="n">setter</span>
     <span class="k">def</span> <span class="nf">calculator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">calculator</span><span class="p">):</span>
+        <span class="kn">from</span> <span class="nn">mlcalcdriver.calculators.calculator</span> <span class="kn">import</span> <span class="n">Calculator</span>
+
         <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">calculator</span><span class="p">,</span> <span class="n">Calculator</span><span class="p">):</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_calculator</span> <span class="o">=</span> <span class="n">calculator</span>
         <span class="k">else</span><span class="p">:</span>
@@ -383,7 +385,7 @@ <h1>Source code for mlcalcdriver.base.job</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2020, Olivier Malenfant-Thuot.</p>
+    <p>&#169; Copyright 2022, Olivier Malenfant-Thuot.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a