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ReactionMechanismGenerator · Nov 21, 2024 · bc6be3e · bc6be3e
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diff --git a/_sources/advanced.rst.txt b/_sources/advanced.rst.txt
@@ -18,7 +18,7 @@ __ xyz_format_
 Specify a specific job type to execute
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 To run ARC with a particular job type **only**, set ``specific_job_type`` to the job type you want.
-Currently, ARC supports the following job types: ``conformers``, ``opt``, ``fine``, ``freq``,
+Currently, ARC supports the following job types: ``conf_opt``, ``conf_sp``, ``opt``, ``fine``, ``freq``,
 ``sp``, ``rotors``, ``onedmin``, ``orbitals``, ``bde``, ``irc``.
 
 Note: ``specific_job_type`` takes higher precedence than ``job_types``. If you specify both attributes, ARC will
@@ -53,7 +53,8 @@ a level of theory. ARC allows users to specify a level of theory per job type, w
 as described below. Job types for which levels of theory may be specified (otherwise ARC will assume
 defaults values) are:
 
-    - ``conformer_level``
+    - ``conformer_opt_level``
+    - ``conformer_sp_level``
     - ``ts_guess_level``
     - ``opt_level``
     - ``freq_level``
@@ -72,9 +73,9 @@ arguments to be defined: ``method``, ``basis``, ``auxiliary_basis``, ``dispersio
 
 For example::
 
-    conformer_level: {'method': 'b3lyp',
-                      'basis': '6-31g(d,p)',
-                      'dispersion': 'empiricaldispersion=gd3bj',
+    conformer_opt_level: {'method': 'b3lyp',
+                          'basis': '6-31g(d,p)',
+                          'dispersion': 'empiricaldispersion=gd3bj',
                       }
 
 specifies ``b3lyp/6-31g(d,p)`` model chemistry along with the
@@ -101,8 +102,8 @@ THe following are examples for **equivalent** definitions::
     opt_level = 'apfd/def2tzvp'
     opt_level = {'method': 'apfd', 'basis': 'def2tzvp'}
 
-    conformer_level = 'PM6'
-    conformer_level = {'method': 'PM6'}
+    conformer_opt_level = 'PM6'
+    conformer_opt_level = {'method': 'PM6'}
 
 
 Note that the ``cabs`` and ``solvation_scheme_level`` arguments currently have no effect
@@ -499,7 +500,7 @@ but just be an arbitrary conformer with the required chiralities to be preserved
 
 Don't generate conformers for specific species
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-The ``conformers`` entry in the ``job_types`` dictionary is a global flag,
+The ``conf_opt`` entry in the ``job_types`` dictionary is a global flag,
 affecting conformer generation of all species in the project.
 
 If you'd like to avoid generating conformers just for selected species,
@@ -616,7 +617,7 @@ The above code generated the following input file::
 
     job_types:
       rotors: true
-      conformers: true
+      conf_opt: true
       fine: true
       freq: true
       lennard_jones: false
@@ -715,7 +716,7 @@ Below is an example requesting all hydrogen BDEs in ethanol including the ``C--O
 
     job_types:
       rotors: true
-      conformers: true
+      conf_opt: true
       fine: true
       freq: true
       opt: true

diff --git a/_sources/examples.rst.txt b/_sources/examples.rst.txt
@@ -28,7 +28,7 @@ Multiple species are defined using SMILES / an XYZ list / InChI::
 
     job_types:
       rotors: true
-      conformers: true
+      conf_opt: true
       fine: true
       freq: true
       opt: true
@@ -130,7 +130,7 @@ The same example as above ran via the API (e.g., in `Jupyter notebooks`__) would
               max_job_time=24,
               level_of_theory='CCSD(T)-F12/cc-pVTZ-F12//wb97xd/def2tzvp',
               scan_level='wb97xd/def2tzvp',
-              conformer_level='b3lyp/6-311+g(d,p)',
+              conformer_opt_level='b3lyp/6-311+g(d,p)',
               species=[spc1, spc2, spc3],
               )
 

diff --git a/advanced.html b/advanced.html
@@ -204,7 +204,7 @@
 <section id="specify-a-specific-job-type-to-execute">
 <h2>Specify a specific job type to execute<a class="headerlink" href="#specify-a-specific-job-type-to-execute" title="Permalink to this heading">¶</a></h2>
 <p>To run ARC with a particular job type <strong>only</strong>, set <code class="docutils literal notranslate"><span class="pre">specific_job_type</span></code> to the job type you want.
-Currently, ARC supports the following job types: <code class="docutils literal notranslate"><span class="pre">conformers</span></code>, <code class="docutils literal notranslate"><span class="pre">opt</span></code>, <code class="docutils literal notranslate"><span class="pre">fine</span></code>, <code class="docutils literal notranslate"><span class="pre">freq</span></code>,
+Currently, ARC supports the following job types: <code class="docutils literal notranslate"><span class="pre">conf_opt</span></code>, <code class="docutils literal notranslate"><span class="pre">conf_sp</span></code>, <code class="docutils literal notranslate"><span class="pre">opt</span></code>, <code class="docutils literal notranslate"><span class="pre">fine</span></code>, <code class="docutils literal notranslate"><span class="pre">freq</span></code>,
 <code class="docutils literal notranslate"><span class="pre">sp</span></code>, <code class="docutils literal notranslate"><span class="pre">rotors</span></code>, <code class="docutils literal notranslate"><span class="pre">onedmin</span></code>, <code class="docutils literal notranslate"><span class="pre">orbitals</span></code>, <code class="docutils literal notranslate"><span class="pre">bde</span></code>, <code class="docutils literal notranslate"><span class="pre">irc</span></code>.</p>
 <p>Note: <code class="docutils literal notranslate"><span class="pre">specific_job_type</span></code> takes higher precedence than <code class="docutils literal notranslate"><span class="pre">job_types</span></code>. If you specify both attributes, ARC will
 dismiss the given <code class="docutils literal notranslate"><span class="pre">job_types</span></code> and will only populate the <code class="docutils literal notranslate"><span class="pre">job_types</span></code> dictionary using the given
@@ -234,7 +234,8 @@ <h2>Specify a specific job type to execute<a class="headerlink" href="#specify-a
 defaults values) are:</p>
 <blockquote>
 <div><ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">conformer_level</span></code></p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">conformer_opt_level</span></code></p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">conformer_sp_level</span></code></p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">ts_guess_level</span></code></p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">opt_level</span></code></p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">freq_level</span></code></p></li>
@@ -252,9 +253,9 @@ <h2>Specify a specific job type to execute<a class="headerlink" href="#specify-a
 <code class="docutils literal notranslate"><span class="pre">cabs</span></code> (complementary auxiliary basis set for F12 calculations), <code class="docutils literal notranslate"><span class="pre">software</span></code>,
 <code class="docutils literal notranslate"><span class="pre">software_version</span></code> (not used), <code class="docutils literal notranslate"><span class="pre">solvation_method</span></code>, <code class="docutils literal notranslate"><span class="pre">solvent</span></code>, <code class="docutils literal notranslate"><span class="pre">solvation_scheme_level</span></code>, <code class="docutils literal notranslate"><span class="pre">args</span></code>.</p>
 <p>For example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conformer_level</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;method&#39;</span><span class="p">:</span> <span class="s1">&#39;b3lyp&#39;</span><span class="p">,</span>
-                  <span class="s1">&#39;basis&#39;</span><span class="p">:</span> <span class="s1">&#39;6-31g(d,p)&#39;</span><span class="p">,</span>
-                  <span class="s1">&#39;dispersion&#39;</span><span class="p">:</span> <span class="s1">&#39;empiricaldispersion=gd3bj&#39;</span><span class="p">,</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conformer_opt_level</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;method&#39;</span><span class="p">:</span> <span class="s1">&#39;b3lyp&#39;</span><span class="p">,</span>
+                      <span class="s1">&#39;basis&#39;</span><span class="p">:</span> <span class="s1">&#39;6-31g(d,p)&#39;</span><span class="p">,</span>
+                      <span class="s1">&#39;dispersion&#39;</span><span class="p">:</span> <span class="s1">&#39;empiricaldispersion=gd3bj&#39;</span><span class="p">,</span>
                   <span class="p">}</span>
 </pre></div>
 </div>
@@ -278,8 +279,8 @@ <h2>Specify a specific job type to execute<a class="headerlink" href="#specify-a
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">opt_level</span> <span class="o">=</span> <span class="s1">&#39;apfd/def2tzvp&#39;</span>
 <span class="n">opt_level</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;method&#39;</span><span class="p">:</span> <span class="s1">&#39;apfd&#39;</span><span class="p">,</span> <span class="s1">&#39;basis&#39;</span><span class="p">:</span> <span class="s1">&#39;def2tzvp&#39;</span><span class="p">}</span>
 
-<span class="n">conformer_level</span> <span class="o">=</span> <span class="s1">&#39;PM6&#39;</span>
-<span class="n">conformer_level</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;method&#39;</span><span class="p">:</span> <span class="s1">&#39;PM6&#39;</span><span class="p">}</span>
+<span class="n">conformer_opt_level</span> <span class="o">=</span> <span class="s1">&#39;PM6&#39;</span>
+<span class="n">conformer_opt_level</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;method&#39;</span><span class="p">:</span> <span class="s1">&#39;PM6&#39;</span><span class="p">}</span>
 </pre></div>
 </div>
 <p>Note that the <code class="docutils literal notranslate"><span class="pre">cabs</span></code> and <code class="docutils literal notranslate"><span class="pre">solvation_scheme_level</span></code> arguments currently have no effect
@@ -639,7 +640,7 @@ <h2>Consider a specific diastereomer<a class="headerlink" href="#consider-a-spec
 </section>
 <section id="don-t-generate-conformers-for-specific-species">
 <h2>Don’t generate conformers for specific species<a class="headerlink" href="#don-t-generate-conformers-for-specific-species" title="Permalink to this heading">¶</a></h2>
-<p>The <code class="docutils literal notranslate"><span class="pre">conformers</span></code> entry in the <code class="docutils literal notranslate"><span class="pre">job_types</span></code> dictionary is a global flag,
+<p>The <code class="docutils literal notranslate"><span class="pre">conf_opt</span></code> entry in the <code class="docutils literal notranslate"><span class="pre">job_types</span></code> dictionary is a global flag,
 affecting conformer generation of all species in the project.</p>
 <p>If you’d like to avoid generating conformers just for selected species,
 pass their labels to ARC in the <code class="docutils literal notranslate"><span class="pre">dont_gen_confs</span></code> list, e.g.:</p>
@@ -751,7 +752,7 @@ <h2>Writing an ARC input file using the API<a class="headerlink" href="#writing-
 
 <span class="n">job_types</span><span class="p">:</span>
   <span class="n">rotors</span><span class="p">:</span> <span class="n">true</span>
-  <span class="n">conformers</span><span class="p">:</span> <span class="n">true</span>
+  <span class="n">conf_opt</span><span class="p">:</span> <span class="n">true</span>
   <span class="n">fine</span><span class="p">:</span> <span class="n">true</span>
   <span class="n">freq</span><span class="p">:</span> <span class="n">true</span>
   <span class="n">lennard_jones</span><span class="p">:</span> <span class="n">false</span>
@@ -850,7 +851,7 @@ <h2>Calculating BDEs (bond dissociation energies)<a class="headerlink" href="#ca
 
 <span class="n">job_types</span><span class="p">:</span>
   <span class="n">rotors</span><span class="p">:</span> <span class="n">true</span>
-  <span class="n">conformers</span><span class="p">:</span> <span class="n">true</span>
+  <span class="n">conf_opt</span><span class="p">:</span> <span class="n">true</span>
   <span class="n">fine</span><span class="p">:</span> <span class="n">true</span>
   <span class="n">freq</span><span class="p">:</span> <span class="n">true</span>
   <span class="n">opt</span><span class="p">:</span> <span class="n">true</span>

diff --git a/examples.html b/examples.html
@@ -191,7 +191,7 @@ <h2>Calculating thermodynamic properties<a class="headerlink" href="#calculating
 
 <span class="n">job_types</span><span class="p">:</span>
   <span class="n">rotors</span><span class="p">:</span> <span class="n">true</span>
-  <span class="n">conformers</span><span class="p">:</span> <span class="n">true</span>
+  <span class="n">conf_opt</span><span class="p">:</span> <span class="n">true</span>
   <span class="n">fine</span><span class="p">:</span> <span class="n">true</span>
   <span class="n">freq</span><span class="p">:</span> <span class="n">true</span>
   <span class="n">opt</span><span class="p">:</span> <span class="n">true</span>
@@ -290,7 +290,7 @@ <h2>Calculating thermodynamic properties<a class="headerlink" href="#calculating
           <span class="n">max_job_time</span><span class="o">=</span><span class="mi">24</span><span class="p">,</span>
           <span class="n">level_of_theory</span><span class="o">=</span><span class="s1">&#39;CCSD(T)-F12/cc-pVTZ-F12//wb97xd/def2tzvp&#39;</span><span class="p">,</span>
           <span class="n">scan_level</span><span class="o">=</span><span class="s1">&#39;wb97xd/def2tzvp&#39;</span><span class="p">,</span>
-          <span class="n">conformer_level</span><span class="o">=</span><span class="s1">&#39;b3lyp/6-311+g(d,p)&#39;</span><span class="p">,</span>
+          <span class="n">conformer_opt_level</span><span class="o">=</span><span class="s1">&#39;b3lyp/6-311+g(d,p)&#39;</span><span class="p">,</span>
           <span class="n">species</span><span class="o">=</span><span class="p">[</span><span class="n">spc1</span><span class="p">,</span> <span class="n">spc2</span><span class="p">,</span> <span class="n">spc3</span><span class="p">],</span>
           <span class="p">)</span>
 

diff --git a/searchindex.js b/searchindex.js