deploy: 17b9439

molssi-seamm · May 23, 2024 · 2f15b0f · 2f15b0f
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diff --git a/.buildinfo b/.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: 00d735607d2f0027c0b8ec9c25c84daa
+config: 5a200e8542c42515f6cc6aad9f6c888a
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_modules/index.html b/_modules/index.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Overview: module code &#8212; SEAMM Psi4 Plug-in 2024.3.17 documentation</title>
+    <title>Overview: module code &#8212; SEAMM Psi4 Plug-in 2024.5.23 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../_static/documentation_options.js?v=f2da1504"></script>
-    <script src="../_static/doctools.js?v=888ff710"></script>
+    <script src="../_static/documentation_options.js?v=cd6ff733"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=f281be69"></script>
@@ -495,6 +495,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="psi4_step/initialization.html">psi4_step.initialization</a></li>
 <li><a href="psi4_step/initialization_parameters.html">psi4_step.initialization_parameters</a></li>
 <li><a href="psi4_step/initialization_step.html">psi4_step.initialization_step</a></li>
+<li><a href="psi4_step/installer.html">psi4_step.installer</a></li>
 <li><a href="psi4_step/optimization.html">psi4_step.optimization</a></li>
 <li><a href="psi4_step/optimization_parameters.html">psi4_step.optimization_parameters</a></li>
 <li><a href="psi4_step/optimization_step.html">psi4_step.optimization_step</a></li>

diff --git a/_modules/psi4_step/accelerated_optimization.html b/_modules/psi4_step/accelerated_optimization.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>psi4_step.accelerated_optimization &#8212; SEAMM Psi4 Plug-in 2024.3.17 documentation</title>
+    <title>psi4_step.accelerated_optimization &#8212; SEAMM Psi4 Plug-in 2024.5.23 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=f2da1504"></script>
-    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/documentation_options.js?v=cd6ff733"></script>
+    <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>

diff --git a/_modules/psi4_step/accelerated_optimization_parameters.html b/_modules/psi4_step/accelerated_optimization_parameters.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>psi4_step.accelerated_optimization_parameters &#8212; SEAMM Psi4 Plug-in 2024.3.17 documentation</title>
+    <title>psi4_step.accelerated_optimization_parameters &#8212; SEAMM Psi4 Plug-in 2024.5.23 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=f2da1504"></script>
-    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/documentation_options.js?v=cd6ff733"></script>
+    <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>

diff --git a/_modules/psi4_step/accelerated_optimization_step.html b/_modules/psi4_step/accelerated_optimization_step.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>psi4_step.accelerated_optimization_step &#8212; SEAMM Psi4 Plug-in 2024.3.17 documentation</title>
+    <title>psi4_step.accelerated_optimization_step &#8212; SEAMM Psi4 Plug-in 2024.5.23 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=f2da1504"></script>
-    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/documentation_options.js?v=cd6ff733"></script>
+    <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>

diff --git a/_modules/psi4_step/energy.html b/_modules/psi4_step/energy.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>psi4_step.energy &#8212; SEAMM Psi4 Plug-in 2024.3.17 documentation</title>
+    <title>psi4_step.energy &#8212; SEAMM Psi4 Plug-in 2024.5.23 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=f2da1504"></script>
-    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/documentation_options.js?v=cd6ff733"></script>
+    <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>
@@ -555,7 +555,7 @@ <h1>Source code for psi4_step.energy</h1><div class="highlight"><pre>
     <span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Prepare information about what this node will do&quot;&quot;&quot;</span>
 
-        <span class="k">if</span> <span class="n">P</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="k">if</span> <span class="n">P</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="n">P</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="o">.</span><span class="n">values_to_dict</span><span class="p">()</span>
 
         <span class="k">if</span> <span class="n">P</span><span class="p">[</span><span class="s2">&quot;level&quot;</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;recommended&quot;</span><span class="p">:</span>
@@ -771,6 +771,7 @@ <h1>Source code for psi4_step.energy</h1><div class="highlight"><pre>
                 <span class="n">lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
                     <span class="sa">f</span><span class="s2">&quot;Eelec, wfn = </span><span class="si">{</span><span class="n">calculation_type</span><span class="si">}</span><span class="s2">(&#39;</span><span class="si">{</span><span class="n">functional</span><span class="si">}</span><span class="s2">&#39;, return_wfn=True)&quot;</span>
                 <span class="p">)</span>
+                <span class="n">lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;G = gradient(&#39;</span><span class="si">{</span><span class="n">functional</span><span class="si">}</span><span class="s2">&#39;, ref_wfn=wfn)&quot;</span><span class="p">)</span>
             <span class="k">else</span><span class="p">:</span>
                 <span class="k">if</span> <span class="n">calculation_type</span> <span class="o">==</span> <span class="s2">&quot;gradient&quot;</span><span class="p">:</span>
                     <span class="n">lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
@@ -788,6 +789,7 @@ <h1>Source code for psi4_step.energy</h1><div class="highlight"><pre>
                 <span class="n">lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
                     <span class="sa">f</span><span class="s2">&quot;Eelec, wfn = </span><span class="si">{</span><span class="n">calculation_type</span><span class="si">}</span><span class="s2">(&#39;</span><span class="si">{</span><span class="n">method</span><span class="si">}</span><span class="s2">&#39;, return_wfn=True)&quot;</span>
                 <span class="p">)</span>
+                <span class="n">lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;G = gradient(&#39;</span><span class="si">{</span><span class="n">method</span><span class="si">}</span><span class="s2">&#39;, ref_wfn=wfn)&quot;</span><span class="p">)</span>
             <span class="k">else</span><span class="p">:</span>
                 <span class="k">if</span> <span class="n">calculation_type</span> <span class="o">==</span> <span class="s2">&quot;gradient&quot;</span><span class="p">:</span>
                     <span class="n">lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
@@ -830,6 +832,11 @@ <h1>Source code for psi4_step.energy</h1><div class="highlight"><pre>
 <span class="s2">for item in arrays:</span>
 <span class="s2">    variables[item] = wfn.array_variable(item).np.tolist()</span>
 <span class="s2">variables[&quot;Eelec&quot;] = Eelec</span>
+<span class="s2">variables[&quot;energy&quot;] = Eelec</span>
+<span class="s2">try:</span>
+<span class="s2">    variables[&quot;gradient&quot;] = np.array(G).tolist()</span>
+<span class="s2">except Exception:</span>
+<span class="s2">    pass</span>
 <span class="s2">variables[&quot;_method&quot;] = &quot;</span><span class="si">{</span><span class="n">method</span><span class="si">}</span><span class="s2">&quot;</span>
 <span class="s2">variables[&quot;_method_string&quot;] = &quot;</span><span class="si">{</span><span class="n">method_string</span><span class="si">}</span><span class="s2">&quot;</span>
 

diff --git a/_modules/psi4_step/energy_parameters.html b/_modules/psi4_step/energy_parameters.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>psi4_step.energy_parameters &#8212; SEAMM Psi4 Plug-in 2024.3.17 documentation</title>
+    <title>psi4_step.energy_parameters &#8212; SEAMM Psi4 Plug-in 2024.5.23 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=f2da1504"></script>
-    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/documentation_options.js?v=cd6ff733"></script>
+    <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>

diff --git a/_modules/psi4_step/energy_step.html b/_modules/psi4_step/energy_step.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>psi4_step.energy_step &#8212; SEAMM Psi4 Plug-in 2024.3.17 documentation</title>
+    <title>psi4_step.energy_step &#8212; SEAMM Psi4 Plug-in 2024.5.23 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=f2da1504"></script>
-    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/documentation_options.js?v=cd6ff733"></script>
+    <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>

diff --git a/_modules/psi4_step/initialization.html b/_modules/psi4_step/initialization.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>psi4_step.initialization &#8212; SEAMM Psi4 Plug-in 2024.3.17 documentation</title>
+    <title>psi4_step.initialization &#8212; SEAMM Psi4 Plug-in 2024.5.23 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=f2da1504"></script>
-    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/documentation_options.js?v=cd6ff733"></script>
+    <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>

diff --git a/_modules/psi4_step/initialization_parameters.html b/_modules/psi4_step/initialization_parameters.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>psi4_step.initialization_parameters &#8212; SEAMM Psi4 Plug-in 2024.3.17 documentation</title>
+    <title>psi4_step.initialization_parameters &#8212; SEAMM Psi4 Plug-in 2024.5.23 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=f2da1504"></script>
-    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/documentation_options.js?v=cd6ff733"></script>
+    <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>

diff --git a/_modules/psi4_step/initialization_step.html b/_modules/psi4_step/initialization_step.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>psi4_step.initialization_step &#8212; SEAMM Psi4 Plug-in 2024.3.17 documentation</title>
+    <title>psi4_step.initialization_step &#8212; SEAMM Psi4 Plug-in 2024.5.23 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=f2da1504"></script>
-    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/documentation_options.js?v=cd6ff733"></script>
+    <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>