Merge branch 'main' into 177-add-cli-command-to-read-a-calculation

TheoChem-VU · Mar 21, 2024 · 5c352c9 · 5c352c9
2 parents 3ae4623 + 3c743ff
commit 5c352c9
Show file tree

Hide file tree

Showing 103 changed files with 1,519,205 additions and 258 deletions.
diff --git a/docs/_build/doctrees/analysis/analysis.doctree b/docs/_build/doctrees/analysis/analysis.doctree
diff --git a/docs/_build/doctrees/analysis/transition_state_analysis.doctree b/docs/_build/doctrees/analysis/transition_state_analysis.doctree
diff --git a/docs/_build/doctrees/analysis/vdd_charge_analysis.doctree b/docs/_build/doctrees/analysis/vdd_charge_analysis.doctree
diff --git a/docs/_build/doctrees/api/modules.doctree b/docs/_build/doctrees/api/modules.doctree
diff --git a/docs/_build/doctrees/api/tcutility.analysis.doctree b/docs/_build/doctrees/api/tcutility.analysis.doctree
diff --git a/docs/_build/doctrees/api/tcutility.analysis.vdd.doctree b/docs/_build/doctrees/api/tcutility.analysis.vdd.doctree
diff --git a/docs/_build/doctrees/api/tcutility.analysis.vibration.doctree b/docs/_build/doctrees/api/tcutility.analysis.vibration.doctree
diff --git a/docs/_build/doctrees/api/tcutility.data.doctree b/docs/_build/doctrees/api/tcutility.data.doctree
diff --git a/docs/_build/doctrees/api/tcutility.doctree b/docs/_build/doctrees/api/tcutility.doctree
diff --git a/docs/_build/doctrees/api/tcutility.job.doctree b/docs/_build/doctrees/api/tcutility.job.doctree
diff --git a/docs/_build/doctrees/api/tcutility.job.postscripts.doctree b/docs/_build/doctrees/api/tcutility.job.postscripts.doctree
diff --git a/docs/_build/doctrees/api/tcutility.results.doctree b/docs/_build/doctrees/api/tcutility.results.doctree
diff --git a/docs/_build/doctrees/api/tcutility.typing.doctree b/docs/_build/doctrees/api/tcutility.typing.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/results/results.doctree b/docs/_build/doctrees/results/results.doctree
diff --git a/docs/_build/doctrees/tcutility.job.doctree b/docs/_build/doctrees/tcutility.job.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.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: 8499a731569d6f31f0531b2423d0f7b6
+config: 3482944cb2e97d2b743759ec6237a459
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_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; TCutility v0.10.4 documentation</title>
+    <title>Overview: module code &#8212; TCutility v0.10.5 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
   <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
-    <script src="../_static/documentation_options.js?v=d53db652"></script>
+    <script src="../_static/documentation_options.js?v=7145324b"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -255,6 +255,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="tcutility/analysis/vibration/ts_vibration.html">tcutility.analysis.vibration.ts_vibration</a></li>
 <li><a href="tcutility/cache.html">tcutility.cache</a></li>
 <li><a href="tcutility/data/atom.html">tcutility.data.atom</a></li>
+<li><a href="tcutility/data/basis_sets.html">tcutility.data.basis_sets</a></li>
 <li><a href="tcutility/data/functionals.html">tcutility.data.functionals</a></li>
 <li><a href="tcutility/data/molecules.html">tcutility.data.molecules</a></li>
 <li><a href="tcutility/formula.html">tcutility.formula</a></li>

diff --git a/docs/_build/html/_modules/tcutility.html b/docs/_build/html/_modules/tcutility.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>tcutility &#8212; TCutility v0.10.4 documentation</title>
+    <title>tcutility &#8212; TCutility v0.10.5 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
   <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
-    <script src="../_static/documentation_options.js?v=d53db652"></script>
+    <script src="../_static/documentation_options.js?v=7145324b"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>

diff --git a/docs/_build/html/_modules/tcutility/analysis/vdd/charge.html b/docs/_build/html/_modules/tcutility/analysis/vdd/charge.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>tcutility.analysis.vdd.charge &#8212; TCutility v0.10.4 documentation</title>
+    <title>tcutility.analysis.vdd.charge &#8212; TCutility v0.10.5 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="../../../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
   <script src="../../../../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
-    <script src="../../../../_static/documentation_options.js?v=d53db652"></script>
+    <script src="../../../../_static/documentation_options.js?v=7145324b"></script>
     <script src="../../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>

diff --git a/docs/_build/html/_modules/tcutility/analysis/vdd/manager.html b/docs/_build/html/_modules/tcutility/analysis/vdd/manager.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>tcutility.analysis.vdd.manager &#8212; TCutility v0.10.4 documentation</title>
+    <title>tcutility.analysis.vdd.manager &#8212; TCutility v0.10.5 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="../../../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
   <script src="../../../../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
-    <script src="../../../../_static/documentation_options.js?v=d53db652"></script>
+    <script src="../../../../_static/documentation_options.js?v=7145324b"></script>
     <script src="../../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>

diff --git a/docs/_build/html/_modules/tcutility/analysis/vibration/ts_vibration.html b/docs/_build/html/_modules/tcutility/analysis/vibration/ts_vibration.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>tcutility.analysis.vibration.ts_vibration &#8212; TCutility v0.10.4 documentation</title>
+    <title>tcutility.analysis.vibration.ts_vibration &#8212; TCutility v0.10.5 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="../../../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
   <script src="../../../../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
-    <script src="../../../../_static/documentation_options.js?v=d53db652"></script>
+    <script src="../../../../_static/documentation_options.js?v=7145324b"></script>
     <script src="../../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>

diff --git a/docs/_build/html/_modules/tcutility/cache.html b/docs/_build/html/_modules/tcutility/cache.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>tcutility.cache &#8212; TCutility v0.10.4 documentation</title>
+    <title>tcutility.cache &#8212; TCutility v0.10.5 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
   <script src="../../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
-    <script src="../../_static/documentation_options.js?v=d53db652"></script>
+    <script src="../../_static/documentation_options.js?v=7145324b"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>

diff --git a/docs/_build/html/_modules/tcutility/data/atom.html b/docs/_build/html/_modules/tcutility/data/atom.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>tcutility.data.atom &#8212; TCutility v0.10.4 documentation</title>
+    <title>tcutility.data.atom &#8212; TCutility v0.10.5 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="../../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
   <script src="../../../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
-    <script src="../../../_static/documentation_options.js?v=d53db652"></script>
+    <script src="../../../_static/documentation_options.js?v=7145324b"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -341,8 +341,31 @@ <h1>Source code for tcutility.data.atom</h1><div class="highlight"><pre>
 
 
 
+<div class="viewcode-block" id="atom_number">
+<a class="viewcode-back" href="../../../api/tcutility.data.html#tcutility.data.atom.atom_number">[docs]</a>
+<span class="k">def</span> <span class="nf">atom_number</span><span class="p">(</span><span class="n">element</span><span class="p">):</span>
+    <span class="k">return</span> <span class="n">parse_element</span><span class="p">(</span><span class="n">element</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="symbol">
+<a class="viewcode-back" href="../../../api/tcutility.data.html#tcutility.data.atom.symbol">[docs]</a>
+<span class="k">def</span> <span class="nf">symbol</span><span class="p">(</span><span class="n">element</span><span class="p">):</span>
+    <span class="n">num</span> <span class="o">=</span> <span class="n">parse_element</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">_symbol_order</span><span class="p">[</span><span class="n">num</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="element">
+<a class="viewcode-back" href="../../../api/tcutility.data.html#tcutility.data.atom.element">[docs]</a>
+<span class="k">def</span> <span class="nf">element</span><span class="p">(</span><span class="n">element</span><span class="p">):</span>
+    <span class="n">num</span> <span class="o">=</span> <span class="n">parse_element</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">_element_order</span><span class="p">[</span><span class="n">num</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span></div>
+
+
+
 <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="nb">print</span><span class="p">(</span><span class="n">color</span><span class="p">(</span><span class="s2">&quot;carbon&quot;</span><span class="p">))</span>
+    <span class="nb">print</span><span class="p">(</span><span class="n">symbol</span><span class="p">(</span><span class="mi">2</span><span class="p">))</span>
 </pre></div>
 
                 </article>