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deploy: df19d8f
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@alongd
alongd committed Jul 27, 2024
1 parent 5a7b7ca commit 9a417bb
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Showing 8 changed files with 62 additions and 38 deletions.
3 changes: 2 additions & 1 deletion _modules/arc/common.html
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Original file line number Diff line number Diff line change
Expand Up @@ -1867,9 +1867,10 @@ <h1>Source code for arc.common</h1><div class="highlight"><pre>

<span class="k">for</span> <span class="n">element</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="n">element_dict_mol</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">if</span> <span class="n">element</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">element_dict_xyz</span> <span class="ow">or</span> <span class="n">element_dict_xyz</span><span class="p">[</span><span class="n">element</span><span class="p">]</span> <span class="o">!=</span> <span class="n">count</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">False</span>
<span class="k">return</span> <span class="kc">False</span>
<span class="k">return</span> <span class="kc">True</span></div>


<div class="viewcode-block" id="convert_to_hours"><a class="viewcode-back" href="../../api/common.html#arc.common.convert_to_hours">[docs]</a><span class="k">def</span> <span class="nf">convert_to_hours</span><span class="p">(</span><span class="n">time_str</span><span class="p">:</span><span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;Convert walltime string in format HH:MM:SS to hours.</span>

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33 changes: 23 additions & 10 deletions _modules/arc/level.html
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Expand Up @@ -173,7 +173,6 @@ <h1>Source code for arc.level</h1><div class="highlight"><pre>

<span class="kn">import</span> <span class="nn">arkane.encorr.data</span> <span class="k">as</span> <span class="nn">arkane_data</span>
<span class="kn">from</span> <span class="nn">arkane.encorr.bac</span> <span class="kn">import</span> <span class="n">BAC</span>
<span class="kn">from</span> <span class="nn">arkane.encorr.corr</span> <span class="kn">import</span> <span class="n">assign_frequency_scale_factor</span>
<span class="kn">from</span> <span class="nn">arkane.modelchem</span> <span class="kn">import</span> <span class="n">METHODS_THAT_REQUIRE_SOFTWARE</span><span class="p">,</span> <span class="n">LevelOfTheory</span><span class="p">,</span> <span class="n">standardize_name</span>

<span class="kn">from</span> <span class="nn">arc.common</span> <span class="kn">import</span> <span class="n">ARC_PATH</span><span class="p">,</span> <span class="n">get_logger</span><span class="p">,</span> <span class="n">get_ordered_intersection_of_two_lists</span><span class="p">,</span> <span class="n">read_yaml_file</span>
Expand Down Expand Up @@ -223,7 +222,7 @@ <h1>Source code for arc.level</h1><div class="highlight"><pre>
<span class="n">method_type</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">software</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">software_version</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="nb">str</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">compatible_ess</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="o">...</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">compatible_ess</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">solvation_method</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">solvent</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">solvation_scheme_level</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Level</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
Expand Down Expand Up @@ -318,8 +317,6 @@ <h1>Source code for arc.level</h1><div class="highlight"><pre>
<span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">arg</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">if</span> <span class="n">key</span> <span class="o">==</span> <span class="s1">&#39;keyword&#39;</span><span class="p">:</span>
<span class="n">str_</span> <span class="o">+=</span> <span class="sa">f</span><span class="s1">&#39; </span><span class="si">{</span><span class="n">arg</span><span class="si">}</span><span class="s1">&#39;</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">method_type</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">str_</span> <span class="o">+=</span> <span class="sa">f</span><span class="s1">&#39; (</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">method_type</span><span class="si">}</span><span class="s1">)&#39;</span>
<span class="k">return</span> <span class="n">str_</span>

<div class="viewcode-block" id="Level.copy"><a class="viewcode-back" href="../../api/level.html#arc.level.Level.copy">[docs]</a> <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
Expand Down Expand Up @@ -562,12 +559,7 @@ <h1>Source code for arc.level</h1><div class="highlight"><pre>
<span class="n">var_1</span> <span class="o">=</span> <span class="kc">None</span>

<span class="k">if</span> <span class="n">variant</span> <span class="o">==</span> <span class="s1">&#39;freq&#39;</span><span class="p">:</span>
<span class="c1"># if not found, the factor is set to exactly 1</span>
<span class="k">if</span> <span class="n">assign_frequency_scale_factor</span><span class="p">(</span><span class="n">level_of_theory</span><span class="o">=</span><span class="n">var_1</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">return</span> <span class="n">var_1</span>
<span class="k">if</span> <span class="n">assign_frequency_scale_factor</span><span class="p">(</span><span class="n">level_of_theory</span><span class="o">=</span><span class="n">var_2</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">return</span> <span class="n">var_2</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="k">return</span> <span class="n">var_2</span>

<span class="k">if</span> <span class="n">variant</span> <span class="o">==</span> <span class="s1">&#39;AEC&#39;</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
Expand Down Expand Up @@ -737,6 +729,27 @@ <h1>Source code for arc.level</h1><div class="highlight"><pre>
<span class="n">splits</span> <span class="o">=</span> <span class="n">arkane_level</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">key</span><span class="si">}</span><span class="s2">=&#39;&quot;</span><span class="p">)</span>
<span class="n">level_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">splits</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;&#39;&quot;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">return</span> <span class="n">level_dict</span></div>


<div class="viewcode-block" id="assign_frequency_scale_factor"><a class="viewcode-back" href="../../api/level.html#arc.level.assign_frequency_scale_factor">[docs]</a><span class="k">def</span> <span class="nf">assign_frequency_scale_factor</span><span class="p">(</span><span class="n">level</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Level</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">int</span><span class="p">]:</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Assign a frequency scaling factor to a level of theory.</span>

<span class="sd"> Args:</span>
<span class="sd"> level (Union[str, Level]): The level of theory.</span>

<span class="sd"> Returns:</span>
<span class="sd"> Optional[int]: The frequency scaling factor.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">freq_scale_factors</span> <span class="o">=</span> <span class="n">read_yaml_file</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">ARC_PATH</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">,</span> <span class="s1">&#39;freq_scale_factors.yml&#39;</span><span class="p">))[</span><span class="s1">&#39;freq_scale_factors&#39;</span><span class="p">]</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">level</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
<span class="k">if</span> <span class="n">level</span> <span class="ow">in</span> <span class="n">freq_scale_factors</span><span class="p">:</span>
<span class="k">return</span> <span class="n">freq_scale_factors</span><span class="p">[</span><span class="n">level</span><span class="p">]</span>
<span class="n">level</span> <span class="o">=</span> <span class="n">Level</span><span class="p">(</span><span class="nb">repr</span><span class="o">=</span><span class="n">level</span><span class="p">)</span>
<span class="n">level_str</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">level</span><span class="p">)</span>
<span class="k">if</span> <span class="n">level_str</span> <span class="ow">in</span> <span class="n">freq_scale_factors</span><span class="p">:</span>
<span class="k">return</span> <span class="n">freq_scale_factors</span><span class="p">[</span><span class="n">level_str</span><span class="p">]</span>
<span class="k">return</span> <span class="kc">None</span></div>
</pre></div>

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