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peterspackman · Jan 6, 2025 · 9164f38 · 9164f38
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diff --git a/classocc_1_1core_1_1Molecule-members.html b/classocc_1_1core_1_1Molecule-members.html
@@ -146,7 +146,7 @@
   <tr><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html#a15770d2a798f3999b4051904c0715178">set_asymmetric_unit_symop</a>(const IVec &amp;symop)</td><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html">occ::core::Molecule</a></td><td class="entry"></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html#afeb07fa6ed184313cca484c07f1965cc">set_asymmetric_unit_transformation</a>(const Mat3 &amp;rot, const Vec3 &amp;trans)</td><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html">occ::core::Molecule</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html#af3c830e1874223f520a2d4dd6856767c">set_bonds</a>(const std::vector&lt; std::pair&lt; size_t, size_t &gt;&gt; &amp;bonds)</td><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html">occ::core::Molecule</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html#a39048da6bf383e723e58dc8dd6d0b27e">set_cell_shift</a>(const IVec3 &amp;shift)</td><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html">occ::core::Molecule</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html#ab38fd08ea1bd76b798d20f616da608a2">set_cell_shift</a>(const IVec3 &amp;shift, bool update_atoms=true)</td><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html">occ::core::Molecule</a></td><td class="entry"></td></tr>
   <tr><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html#a6db76f2ee69b21df4389dbf572e7ae64">set_charge</a>(int c)</td><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html">occ::core::Molecule</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html#a20ccb2353b97c739c4099c11e0238a1b">set_multiplicity</a>(int m)</td><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html">occ::core::Molecule</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html#af30a3010257f85cb70a3858901ef155c">set_name</a>(const std::string &amp;name)</td><td class="entry"><a class="el" href="classocc_1_1core_1_1Molecule.html">occ::core::Molecule</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>

diff --git a/classocc_1_1core_1_1Molecule.html b/classocc_1_1core_1_1Molecule.html
@@ -165,9 +165,9 @@
 <tr class="memitem:a93f7a741a4de2781cb26095165559a9f"><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="structocc_1_1core_1_1Atom.html">core::Atom</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classocc_1_1core_1_1Molecule.html#a93f7a741a4de2781cb26095165559a9f">atoms</a> () const</td></tr>
 <tr class="memdesc:a93f7a741a4de2781cb26095165559a9f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Convert the atoms represented by this molecule to a std:vector&lt;Atom&gt;  <a href="classocc_1_1core_1_1Molecule.html#a93f7a741a4de2781cb26095165559a9f">More...</a><br /></td></tr>
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-<tr class="memitem:a39048da6bf383e723e58dc8dd6d0b27e"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classocc_1_1core_1_1Molecule.html#a39048da6bf383e723e58dc8dd6d0b27e">set_cell_shift</a> (const <a class="el" href="namespaceocc.html#a22e6fea5025901b5dee48e48a69dcce3">IVec3</a> &amp;shift)</td></tr>
-<tr class="memdesc:a39048da6bf383e723e58dc8dd6d0b27e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Set the unit cell offset for this <a class="el" href="classocc_1_1core_1_1Molecule.html" title="Storage class for relevant information of a Molecule.">Molecule</a> (default 000)  <a href="classocc_1_1core_1_1Molecule.html#a39048da6bf383e723e58dc8dd6d0b27e">More...</a><br /></td></tr>
-<tr class="separator:a39048da6bf383e723e58dc8dd6d0b27e"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ab38fd08ea1bd76b798d20f616da608a2"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classocc_1_1core_1_1Molecule.html#ab38fd08ea1bd76b798d20f616da608a2">set_cell_shift</a> (const <a class="el" href="namespaceocc.html#a22e6fea5025901b5dee48e48a69dcce3">IVec3</a> &amp;shift, bool update_atoms=true)</td></tr>
+<tr class="memdesc:ab38fd08ea1bd76b798d20f616da608a2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Set the unit cell offset for this <a class="el" href="classocc_1_1core_1_1Molecule.html" title="Storage class for relevant information of a Molecule.">Molecule</a> (default 000)  <a href="classocc_1_1core_1_1Molecule.html#ab38fd08ea1bd76b798d20f616da608a2">More...</a><br /></td></tr>
+<tr class="separator:ab38fd08ea1bd76b798d20f616da608a2"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a58efc833193cdeb25e25cf4c83d8960e"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="namespaceocc.html#a22e6fea5025901b5dee48e48a69dcce3">IVec3</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classocc_1_1core_1_1Molecule.html#a58efc833193cdeb25e25cf4c83d8960e">cell_shift</a> () const</td></tr>
 <tr class="memdesc:a58efc833193cdeb25e25cf4c83d8960e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the unit cell offset for this <a class="el" href="classocc_1_1core_1_1Molecule.html" title="Storage class for relevant information of a Molecule.">Molecule</a> (default 000)  <a href="classocc_1_1core_1_1Molecule.html#a58efc833193cdeb25e25cf4c83d8960e">More...</a><br /></td></tr>
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@@ -796,7 +796,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#a58efc833193cdeb25e25cf4c
 
 <p>Get the unit cell offset for this <a class="el" href="classocc_1_1core_1_1Molecule.html" title="Storage class for relevant information of a Molecule.">Molecule</a> (default 000) </p>
 <dl class="section return"><dt>Returns</dt><dd>the CellShift stored in this <a class="el" href="classocc_1_1core_1_1Molecule.html" title="Storage class for relevant information of a Molecule.">Molecule</a></dd></dl>
-<p>See <a class="el" href="classocc_1_1core_1_1Molecule.html#a39048da6bf383e723e58dc8dd6d0b27e" title="Set the unit cell offset for this Molecule (default 000)">Molecule::set_cell_shift</a> </p>
+<p>See <a class="el" href="classocc_1_1core_1_1Molecule.html#ab38fd08ea1bd76b798d20f616da608a2" title="Set the unit cell offset for this Molecule (default 000)">Molecule::set_cell_shift</a> </p>
 
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@@ -1708,8 +1708,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#af3c830e1874223f520a2d4dd
 
 </div>
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-<a id="a39048da6bf383e723e58dc8dd6d0b27e"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a39048da6bf383e723e58dc8dd6d0b27e">&#9670;&nbsp;</a></span>set_cell_shift()</h2>
+<a id="ab38fd08ea1bd76b798d20f616da608a2"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ab38fd08ea1bd76b798d20f616da608a2">&#9670;&nbsp;</a></span>set_cell_shift()</h2>
 
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@@ -1718,8 +1718,18 @@ <h2 class="memtitle"><span class="permalink"><a href="#a39048da6bf383e723e58dc8d
           <td class="memname">void occ::core::Molecule::set_cell_shift </td>
           <td>(</td>
           <td class="paramtype">const <a class="el" href="namespaceocc.html#a22e6fea5025901b5dee48e48a69dcce3">IVec3</a> &amp;&#160;</td>
-          <td class="paramname"><em>shift</em></td><td>)</td>
+          <td class="paramname"><em>shift</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool&#160;</td>
+          <td class="paramname"><em>update_atoms</em> = <code>true</code>&#160;</td>
+        </tr>
+        <tr>
           <td></td>
+          <td>)</td>
+          <td></td><td></td>
         </tr>
       </table>
 </div><div class="memdoc">
@@ -1967,7 +1977,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#a0dfd9ecf6ce4303e4e879abc
   </table>
   </dd>
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-<p>See also <a class="el" href="classocc_1_1core_1_1Molecule.html#a39048da6bf383e723e58dc8dd6d0b27e" title="Set the unit cell offset for this Molecule (default 000)">Molecule::set_cell_shift</a> if you wish to set the unit cell molecule shift rather than atom indices. </p>
+<p>See also <a class="el" href="classocc_1_1core_1_1Molecule.html#ab38fd08ea1bd76b798d20f616da608a2" title="Set the unit cell offset for this Molecule (default 000)">Molecule::set_cell_shift</a> if you wish to set the unit cell molecule shift rather than atom indices. </p>
 
 </div>
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diff --git a/classocc_1_1core_1_1Molecule.js b/classocc_1_1core_1_1Molecule.js
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diff --git a/functions_func_s.html b/functions_func_s.html
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+: <a class="el" href="classocc_1_1core_1_1Molecule.html#ab38fd08ea1bd76b798d20f616da608a2">occ::core::Molecule</a>
 </li>
 <li>set_charge()
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diff --git a/functions_s.html b/functions_s.html
@@ -222,7 +222,7 @@ <h3><a id="index_s"></a>- s -</h3><ul>
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+: <a class="el" href="classocc_1_1core_1_1Molecule.html#ab38fd08ea1bd76b798d20f616da608a2">occ::core::Molecule</a>
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 <li>set_charge()
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