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changelog/index.html

@@ -501,6 +501,84 @@
     </label>
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
 
+        <li class="md-nav__item">
+  <a href="#v030-2024-mm-dd-unreleased" class="md-nav__link">
+    <span class="md-ellipsis">
+      v0.3.0 / 2024-MM-DD (Unreleased)
+    </span>
+  </a>
+
+    <nav class="md-nav" aria-label="v0.3.0 / 2024-MM-DD (Unreleased)">
+      <ul class="md-nav__list">
+
+          <li class="md-nav__item">
+  <a href="#breaking-changes" class="md-nav__link">
+    <span class="md-ellipsis">
+      Breaking Changes
+    </span>
+  </a>
+
+</li>
+
+          <li class="md-nav__item">
+  <a href="#new-features" class="md-nav__link">
+    <span class="md-ellipsis">
+      New Features
+    </span>
+  </a>
+
+</li>
+
+          <li class="md-nav__item">
+  <a href="#enhancements" class="md-nav__link">
+    <span class="md-ellipsis">
+      Enhancements
+    </span>
+  </a>
+
+</li>
+
+          <li class="md-nav__item">
+  <a href="#bug-fixes" class="md-nav__link">
+    <span class="md-ellipsis">
+      Bug Fixes
+    </span>
+  </a>
+
+</li>
+
+          <li class="md-nav__item">
+  <a href="#misc" class="md-nav__link">
+    <span class="md-ellipsis">
+      Misc.
+    </span>
+  </a>
+
+</li>
+
+          <li class="md-nav__item">
+  <a href="#must-unmerged" class="md-nav__link">
+    <span class="md-ellipsis">
+      MUST (Unmerged)
+    </span>
+  </a>
+
+</li>
+
+          <li class="md-nav__item">
+  <a href="#wip-unmerged" class="md-nav__link">
+    <span class="md-ellipsis">
+      WIP (Unmerged)
+    </span>
+  </a>
+
+</li>
+
+      </ul>
+    </nav>
+
+</li>
+
         <li class="md-nav__item">
   <a href="#v021-2024-05-14" class="md-nav__link">
     <span class="md-ellipsis">
@@ -512,7 +590,7 @@
       <ul class="md-nav__list">
 
           <li class="md-nav__item">
-  <a href="#enhancements" class="md-nav__link">
+  <a href="#enhancements_1" class="md-nav__link">
     <span class="md-ellipsis">
       Enhancements
     </span>
@@ -536,7 +614,7 @@
       <ul class="md-nav__list">
 
           <li class="md-nav__item">
-  <a href="#new-features" class="md-nav__link">
+  <a href="#new-features_1" class="md-nav__link">
     <span class="md-ellipsis">
       New Features
     </span>
@@ -545,7 +623,7 @@
 </li>
 
           <li class="md-nav__item">
-  <a href="#enhancements_1" class="md-nav__link">
+  <a href="#enhancements_2" class="md-nav__link">
     <span class="md-ellipsis">
       Enhancements
     </span>
@@ -554,7 +632,7 @@
 </li>
 
           <li class="md-nav__item">
-  <a href="#bug-fixes" class="md-nav__link">
+  <a href="#bug-fixes_1" class="md-nav__link">
     <span class="md-ellipsis">
       Bug Fixes
     </span>
@@ -563,7 +641,7 @@
 </li>
 
           <li class="md-nav__item">
-  <a href="#misc" class="md-nav__link">
+  <a href="#misc_1" class="md-nav__link">
     <span class="md-ellipsis">
       Misc.
     </span>
@@ -587,7 +665,7 @@
       <ul class="md-nav__list">
 
           <li class="md-nav__item">
-  <a href="#new-features_1" class="md-nav__link">
+  <a href="#new-features_2" class="md-nav__link">
     <span class="md-ellipsis">
       New Features
     </span>
@@ -637,14 +715,30 @@ <h1 id="changelog">Changelog</h1>
 #### WIP (Unmerged)
 -->
 
-<h2 id="v021-2024-05-14">v0.2.1 / 2024-05-14</h2>
+<h2 id="v030-2024-mm-dd-unreleased">v0.3.0 / 2024-MM-DD (Unreleased)</h2>
+<h4 id="breaking-changes">Breaking Changes</h4>
+<ul>
+<li><a href="https://github.com/MolSSI/QCManyBody/pull/28">#28</a> Intf -- low-level "core" interface renamed from
+   <code>ManyBodyCalculator</code> to <code>ManyBodyCore</code>. The old name will continue to work for a few months. Also, its file changed
+   from <code>manybody.py</code> to <code>core.py</code> but it was already a top-level import.</li>
+</ul>
+<h4 id="new-features">New Features</h4>
 <h4 id="enhancements">Enhancements</h4>
 <ul>
+<li><a href="https://github.com/MolSSI/QCManyBody/pull/28">#28</a> Intf -- high-level interface is now importable from the top level module.</li>
+</ul>
+<h4 id="bug-fixes">Bug Fixes</h4>
+<h4 id="misc">Misc.</h4>
+<h4 id="must-unmerged">MUST (Unmerged)</h4>
+<h4 id="wip-unmerged">WIP (Unmerged)</h4>
+<h2 id="v021-2024-05-14">v0.2.1 / 2024-05-14</h2>
+<h4 id="enhancements_1">Enhancements</h4>
+<ul>
 <li><a href="https://github.com/MolSSI/QCManyBody/pull/27">#27</a> Intf -- move high-level interface from
   <code>qcmb.qcng_computer.ManyBodyComputerQCNG</code> to <code>qcmb.computer.ManyBodyComputer</code>. Suppressed remaining printing. @loriab</li>
 </ul>
 <h2 id="v020-2024-05-13">v0.2.0 / 2024-05-13</h2>
-<h4 id="new-features">New Features</h4>
+<h4 id="new-features_1">New Features</h4>
 <ul>
 <li><a href="https://github.com/MolSSI/QCManyBody/pull/25">#25</a> Schema -- added a new field <code>ManyBodyResults.component_results</code>
   to store subsystem <code>AtomicResult</code>s (or other Result if layered computation). By default this is not stored, but it can
@@ -654,28 +748,28 @@ <h4 id="new-features">New Features</h4>
   run <code>ManyBodyInput</code>s through QCEngine, not just <code>AtomicInput</code>s. Needs special QCElemental, QCEngine, and OptKing to
   work for now. @loriab</li>
 </ul>
-<h4 id="enhancements_1">Enhancements</h4>
+<h4 id="enhancements_2">Enhancements</h4>
 <ul>
 <li><a href="https://github.com/MolSSI/QCManyBody/pull/22">#22</a> Intf -- move high-level interface to main directory and remove
   unused functions. Most common route into interface is now: <code>qcmb.ManyBodyComputerQCNG.from_manybodyinput</code>. @loriab</li>
 <li><a href="https://github.com/MolSSI/QCManyBody/pull/25">#25</a> Schema -- <code>AtomicSpecification.protocols</code> set in
   <code>ManyBodySpecification.specification</code> will now be observed. @loriab</li>
 <li><a href="https://github.com/MolSSI/QCManyBody/pull/26">#26</a> Schema -- add <code>AtomicSpecification.extras</code>. @loriab</li>
 </ul>
-<h4 id="bug-fixes">Bug Fixes</h4>
+<h4 id="bug-fixes_1">Bug Fixes</h4>
 <ul>
 <li><a href="https://github.com/MolSSI/QCManyBody/pull/25">#25</a> Schema -- <code>ManyBodyKeywords.embedding_charges</code> now default to None
   rather than empty dict. @loriab</li>
 </ul>
-<h4 id="misc">Misc.</h4>
+<h4 id="misc_1">Misc.</h4>
 <ul>
 <li><a href="https://github.com/MolSSI/QCManyBody/pull/21">#21</a> Docs -- installation and molecule. @bennybp</li>
 <li><a href="https://github.com/MolSSI/QCManyBody/pull/24">#24</a> Intf -- release "frozen" pydantic on high-level
   ManyBodyComputerQCNG, so core-interface ManyBodyCalculator can live on the class. @loriab</li>
 <li><a href="https://github.com/MolSSI/QCManyBody/pull/26">#26</a> Cleanup -- remove most debug printing. @loriab</li>
 </ul>
 <h2 id="v010-2024-04-24">v0.1.0 / 2024-04-24</h2>
-<h4 id="new-features_1">New Features</h4>
+<h4 id="new-features_2">New Features</h4>
 <ul>
 <li>Runs CP, NoCP, VMFC energies, gradients, and Hessians. @bennybp @loriab</li>
 </ul>

core-interface/index.html

@@ -641,28 +641,31 @@ <h1 id="core-interface">Core Interface</h1>
 <p>Note that the user is expected to run the calculations themselves, and the core interface does not provide any tools for
 running the calculations.</p>
 <h2 id="using-the-core-interface">Using the core interface</h2>
-<p>The core interface is accessed through the <a class="autorefs autorefs-internal" href="../api/#qcmanybody.ManyBodyCalculator"><code>ManyBodyCalculator</code></a>
+<p>The core interface is accessed through the [<code>ManyBodyCore</code>][qcmanybody.manybody.ManyBodyCore]
 class.</p>
 <p>The first step is to create a molecule. This molecule is a
 <a href="https://molssi.github.io/QCElemental/model_molecule.html">QCElemental molecule object</a>, and must contain fragments.
 (see also: <a href="../keywords/#molecule">moleule input</a>)</p>
-<div class="highlight"><pre><span></span><code><span class="kn">import</span> <span class="nn">qcmanybody</span> <span class="k">as</span> <span class="nn">qcmb</span>
-<span class="kn">import</span> <span class="nn">qcelemental</span> <span class="k">as</span> <span class="nn">qcel</span>
+<div class="highlight"><pre><span></span><code><span class="kn">from</span> <span class="nn">qcelemental.models</span> <span class="kn">import</span> <span class="n">Molecule</span>
 
-<span class="c1"># Create a molecule with 3 hydrogen atoms, each as its own fragment</span>
-<span class="n">mol</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">Molecule</span><span class="p">(</span><span class="n">symbols</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;h&#39;</span><span class="p">,</span> <span class="s1">&#39;h&#39;</span><span class="p">,</span> <span class="s1">&#39;h&#39;</span><span class="p">],</span>
-                           <span class="n">geometry</span><span class="o">=</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="mi">0</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="mi">2</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="mi">4</span><span class="p">]],</span>
-                           <span class="n">fragments</span><span class="o">=</span><span class="p">[[</span><span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">2</span><span class="p">]])</span>
+<span class="c1"># Create a molecule with 3 neon atoms, each as its own fragment</span>
+
+<span class="n">mol</span> <span class="o">=</span> <span class="n">Molecule</span><span class="p">(</span><span class="n">symbols</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;ne&quot;</span><span class="p">,</span> <span class="s2">&quot;ne&quot;</span><span class="p">,</span> <span class="s2">&quot;ne&quot;</span><span class="p">],</span>
+               <span class="n">geometry</span><span class="o">=</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="mi">0</span><span class="p">],</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="mi">2</span><span class="p">],</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="mi">4</span><span class="p">]],</span>
+               <span class="n">fragments</span><span class="o">=</span><span class="p">[[</span><span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">2</span><span class="p">]])</span>
 </code></pre></div>
-<p>Next, create a <code>ManyBodyCalculator</code> object. This object is constructed using the molecule,
+<p>Next, create a <code>ManyBodyCore</code> object. This object is constructed using the molecule,
 the desired BSSE correction, levels of MBE, and other options of the MBE.</p>
-<div class="highlight"><pre><span></span><code><span class="n">mbc</span> <span class="o">=</span> <span class="n">qcmb</span><span class="o">.</span><span class="n">ManyBodyCalculator</span><span class="p">(</span>
-    <span class="n">molecule</span><span class="o">=</span><span class="n">mol</span><span class="p">,</span>
-    <span class="n">bsse_type</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;cp&#39;</span><span class="p">],</span>
-    <span class="n">levels</span><span class="o">=</span><span class="p">{</span><span class="mi">1</span><span class="p">:</span> <span class="s1">&#39;mp2/aug-cc-pvtz&#39;</span><span class="p">,</span> <span class="mi">2</span><span class="p">:</span> <span class="s1">&#39;b3lyp/def2-svp&#39;</span><span class="p">,</span> <span class="mi">3</span><span class="p">:</span> <span class="s1">&#39;hf/sto-3g&#39;</span><span class="p">},</span>
-    <span class="n">return_total_data</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
-    <span class="n">supersystem_ie_only</span><span class="o">=</span><span class="kc">False</span>
-<span class="p">)</span>
+<div class="highlight"><pre><span></span><code><span class="kn">from</span> <span class="nn">qcmanybody</span> <span class="kn">import</span> <span class="n">ManyBodyCore</span>
+
+<span class="n">mbc</span> <span class="o">=</span> <span class="n">ManyBodyCore</span><span class="p">(</span><span class="n">molecule</span><span class="o">=</span><span class="n">mol</span><span class="p">,</span>
+                   <span class="n">bsse_type</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;cp&quot;</span><span class="p">],</span>
+                   <span class="n">levels</span><span class="o">=</span><span class="p">{</span><span class="mi">1</span><span class="p">:</span> <span class="s2">&quot;ccsd/cc-pvtz&quot;</span><span class="p">,</span>
+                           <span class="mi">2</span><span class="p">:</span> <span class="s2">&quot;mp2/cc-pvdz&quot;</span><span class="p">,</span>
+                           <span class="mi">3</span><span class="p">:</span> <span class="s2">&quot;mp2/cc-pvdz&quot;</span><span class="p">},</span>
+                   <span class="n">return_total_data</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+                   <span class="n">supersystem_ie_only</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+                   <span class="n">embedding_charges</span><span class="p">:</span> <span class="kc">None</span><span class="p">)</span>
 </code></pre></div>
 <p>The <code>levels</code> option is a dictionary that specifies the n-body level as a key, then an arbitrary
 string as the description of the calculation to be performed at the n-body level. This string is
@@ -672,10 +675,10 @@ <h2 id="using-the-core-interface">Using the core interface</h2>
     In the core interface, all levels must be accounted for (that is, keys must go from 1 to the maximum
     nbody you would like to calculate). All levels must be present even if the model chemistry
     is the same for all levels.</p>
-<p>For a complete discussion of the other options available in the <code>ManyBodyCalculator</code> object, see the
+<p>For a complete discussion of the other options available in the <code>ManyBodyCore</code> object, see the
 <a href="../keywords/">keywords discussion</a>
-the <a class="autorefs autorefs-internal" href="../api/#qcmanybody.ManyBodyCalculator"><code>ManyBodyCalculator API documentation</code></a>.</p>
-<p>The next step is to obtain the calculations to be run from the <code>ManyBodyCalculator</code> object.
+the [<code>ManyBodyCore API documentation</code>][qcmanybody.manybody.ManyBodyCore].</p>
+<p>The next step is to obtain the calculations to be run from the <code>ManyBodyCore</code> object.
 This is done with a python generator function <code>iterate_molecules</code> that returns
 a tuple. This tuple contains</p>
 <ol>
@@ -691,7 +694,7 @@ <h2 id="using-the-core-interface">Using the core interface</h2>
 does not provide any tools for running the calculations.</p>
 <h3 id="results-dictionary">Results dictionary</h3>
 <p>The data returned from the calculations is expected to be stored in a nested dictionary.
-The level is the opaque label as given from the <code>QCManyBodyCalculator</code>.
+The level is the opaque label as given from the <code>QCManyBodyCore</code>.
 The second level is the name of the property.</p>
 <div class="highlight"><pre><span></span><code><span class="n">calculation_results</span> <span class="o">=</span> <span class="p">{</span>
     <span class="s1">&#39;label1&#39;</span><span class="p">:</span> <span class="p">{</span>

index.html

@@ -618,7 +618,7 @@
 
 
 <h1 id="qcmanybody-documentation">QCManyBody Documentation</h1>
-<p>QCManyBody is a python package for running quantum chemistry manybody expansions and interaction calculations in a
+<p>QCManyBody is a python package for running quantum chemistry many-body expansions and interaction calculations in a
 package-independent way.</p>
 <h2 id="installation">Installation</h2>
 <p>QCManyBody is available from <a href="https://pypi.org/project/qcmanybody">PyPI</a> and from