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loriab committed Oct 24, 2023
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2 changes: 1 addition & 1 deletion .buildinfo
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# 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.
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6 changes: 3 additions & 3 deletions _modules/index.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &mdash; QCEngine 0+untagged.1.g1b27a14 documentation</title>
<title>Overview: module code &mdash; QCEngine 0+untagged.1.gc7ba717 documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
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<script src="../_static/jquery.js?v=5d32c60e"></script>
<script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=b0704a97"></script>
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<script src="../_static/sphinx_highlight.js?v=4825356b"></script>
<script src="../_static/js/theme.js"></script>
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QCEngine
</a>
<div class="version">
0+untagged.1.g1b27a14
0+untagged.1.gc7ba717
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<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
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9 changes: 6 additions & 3 deletions _modules/qcelemental/models/results.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>qcelemental.models.results &mdash; QCEngine 0+untagged.1.g1b27a14 documentation</title>
<title>qcelemental.models.results &mdash; QCEngine 0+untagged.1.gc7ba717 documentation</title>
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<script src="../../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js?v=b0704a97"></script>
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js?v=f6e35c0c"></script>
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<script src="../../../_static/js/theme.js"></script>
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QCEngine
</a>
<div class="version">
0+untagged.1.g1b27a14
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</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
Expand Down Expand Up @@ -616,6 +616,7 @@ <h1>Source code for qcelemental.models.results</h1><div class="highlight"><pre>

<span class="nb">all</span> <span class="o">=</span> <span class="s2">&quot;all&quot;</span>
<span class="n">orbitals_and_eigenvalues</span> <span class="o">=</span> <span class="s2">&quot;orbitals_and_eigenvalues&quot;</span>
<span class="n">occupations_and_eigenvalues</span> <span class="o">=</span> <span class="s2">&quot;occupations_and_eigenvalues&quot;</span>
<span class="n">return_results</span> <span class="o">=</span> <span class="s2">&quot;return_results&quot;</span>
<span class="n">none</span> <span class="o">=</span> <span class="s2">&quot;none&quot;</span>

Expand Down Expand Up @@ -811,6 +812,8 @@ <h1>Source code for qcelemental.models.results</h1><div class="highlight"><pre>
<span class="p">]</span>
<span class="k">elif</span> <span class="n">wfnp</span> <span class="o">==</span> <span class="s2">&quot;orbitals_and_eigenvalues&quot;</span><span class="p">:</span>
<span class="n">return_keep</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;orbitals_a&quot;</span><span class="p">,</span> <span class="s2">&quot;orbitals_b&quot;</span><span class="p">,</span> <span class="s2">&quot;eigenvalues_a&quot;</span><span class="p">,</span> <span class="s2">&quot;eigenvalues_b&quot;</span><span class="p">]</span>
<span class="k">elif</span> <span class="n">wfnp</span> <span class="o">==</span> <span class="s2">&quot;occupations_and_eigenvalues&quot;</span><span class="p">:</span>
<span class="n">return_keep</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;occupations_a&quot;</span><span class="p">,</span> <span class="s2">&quot;occupations_b&quot;</span><span class="p">,</span> <span class="s2">&quot;eigenvalues_a&quot;</span><span class="p">,</span> <span class="s2">&quot;eigenvalues_b&quot;</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Protocol `wavefunction:</span><span class="si">{</span><span class="n">wfnp</span><span class="si">}</span><span class="s2">` is not understood.&quot;</span><span class="p">)</span>

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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>qcengine.compute &mdash; QCEngine 0+untagged.1.g1b27a14 documentation</title>
<title>qcengine.compute &mdash; QCEngine 0+untagged.1.gc7ba717 documentation</title>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
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<script src="../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=b0704a97"></script>
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<script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
<script src="../../_static/js/theme.js"></script>
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QCEngine
</a>
<div class="version">
0+untagged.1.g1b27a14
0+untagged.1.gc7ba717
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
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6 changes: 3 additions & 3 deletions _modules/qcengine/config.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>qcengine.config &mdash; QCEngine 0+untagged.1.g1b27a14 documentation</title>
<title>qcengine.config &mdash; QCEngine 0+untagged.1.gc7ba717 documentation</title>
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<script src="../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=b0704a97"></script>
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=f6e35c0c"></script>
<script src="../../_static/doctools.js?v=888ff710"></script>
<script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
<script src="../../_static/js/theme.js"></script>
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QCEngine
</a>
<div class="version">
0+untagged.1.g1b27a14
0+untagged.1.gc7ba717
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
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16 changes: 12 additions & 4 deletions _modules/qcengine/mdi_server.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>qcengine.mdi_server &mdash; QCEngine 0+untagged.1.g1b27a14 documentation</title>
<title>qcengine.mdi_server &mdash; QCEngine 0+untagged.1.gc7ba717 documentation</title>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../_static/graphviz.css" type="text/css" />
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<script src="../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=b0704a97"></script>
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=f6e35c0c"></script>
<script src="../../_static/doctools.js?v=888ff710"></script>
<script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
<script src="../../_static/js/theme.js"></script>
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QCEngine
</a>
<div class="version">
0+untagged.1.g1b27a14
0+untagged.1.gc7ba717
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
Expand Down Expand Up @@ -379,6 +379,11 @@ <h1>Source code for qcengine.mdi_server</h1><div class="highlight"><pre>
<span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecule_validated</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;MDI attempting to compute energy on an unvalidated molecule&quot;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">run_energy</span><span class="p">()</span>

<span class="c1"># Confirm that the calculation completed successfully</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">compute_return</span><span class="p">,</span> <span class="s2">&quot;properties&quot;</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;MDI Calculation failed: </span><span class="se">\n\n</span><span class="s2">&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">compute_return</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">error_message</span><span class="p">))</span>

<span class="n">properties</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">compute_return</span><span class="o">.</span><span class="n">properties</span><span class="o">.</span><span class="n">dict</span><span class="p">()</span>
<span class="n">energy</span> <span class="o">=</span> <span class="n">properties</span><span class="p">[</span><span class="s2">&quot;return_energy&quot;</span><span class="p">]</span>
<span class="n">MDI_Send</span><span class="p">(</span><span class="n">energy</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">MDI_DOUBLE</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">comm</span><span class="p">)</span>
Expand Down Expand Up @@ -414,8 +419,11 @@ <h1>Source code for qcengine.mdi_server</h1><div class="highlight"><pre>

<span class="c1"># Respond to the SCF command</span>
<div class="viewcode-block" id="MDIServer.run_energy"><a class="viewcode-back" href="../../api/qcengine.MDIServer.html#qcengine.MDIServer.run_energy">[docs]</a> <span class="k">def</span> <span class="nf">run_energy</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>

<span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">energy_is_current</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Ensure that the orientation of the molecule remains fixed&quot;&quot;&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">update_molecule</span><span class="p">(</span><span class="s2">&quot;fix_com&quot;</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">update_molecule</span><span class="p">(</span><span class="s2">&quot;fix_orientation&quot;</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>

<span class="w"> </span><span class="sd">&quot;&quot;&quot;Run an energy calculation&quot;&quot;&quot;</span>
<span class="nb">input</span> <span class="o">=</span> <span class="n">qcel</span><span class="o">.</span><span class="n">models</span><span class="o">.</span><span class="n">AtomicInput</span><span class="p">(</span>
<span class="n">molecule</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">molecule</span><span class="p">,</span> <span class="n">driver</span><span class="o">=</span><span class="s2">&quot;gradient&quot;</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keywords</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">keywords</span>
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6 changes: 3 additions & 3 deletions _modules/qcengine/procedures/base.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>qcengine.procedures.base &mdash; QCEngine 0+untagged.1.g1b27a14 documentation</title>
<title>qcengine.procedures.base &mdash; QCEngine 0+untagged.1.gc7ba717 documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
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<script src="../../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js?v=b0704a97"></script>
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<script src="../../../_static/sphinx_highlight.js?v=4825356b"></script>
<script src="../../../_static/js/theme.js"></script>
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QCEngine
</a>
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6 changes: 3 additions & 3 deletions _modules/qcengine/programs/base.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>qcengine.programs.base &mdash; QCEngine 0+untagged.1.g1b27a14 documentation</title>
<title>qcengine.programs.base &mdash; QCEngine 0+untagged.1.gc7ba717 documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
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Expand All @@ -14,7 +14,7 @@

<script src="../../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js?v=b0704a97"></script>
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<script src="../../../_static/sphinx_highlight.js?v=4825356b"></script>
<script src="../../../_static/js/theme.js"></script>
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QCEngine
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6 changes: 3 additions & 3 deletions _modules/qcengine/programs/model.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>qcengine.programs.model &mdash; QCEngine 0+untagged.1.g1b27a14 documentation</title>
<title>qcengine.programs.model &mdash; QCEngine 0+untagged.1.gc7ba717 documentation</title>
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Expand All @@ -14,7 +14,7 @@

<script src="../../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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QCEngine
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