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@YHordijk @github-actions
YHordijk authored and github-actions[bot] committed Jun 4, 2024
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24 changes: 11 additions & 13 deletions docs/_build/html/_modules/tcutility/job/ams.html
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Expand Up @@ -467,19 +467,17 @@ <h1>Source code for tcutility.job.ams</h1><div class="highlight"><pre>
<span class="sd"> &#39;&#39;&#39;</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rundir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>

<span class="c1"># clean the workdir if it contains files</span>
<span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workdir</span><span class="p">):</span>
<span class="n">p</span> <span class="o">=</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="bp">self</span><span class="o">.</span><span class="n">workdir</span><span class="p">,</span> <span class="n">file</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.rkf&#39;</span><span class="p">):</span>
<span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="k">if</span> <span class="s1">&#39;ams.kid&#39;</span> <span class="ow">in</span> <span class="n">p</span><span class="p">:</span>
<span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;t21.&#39;</span><span class="p">):</span>
<span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;t12.&#39;</span><span class="p">):</span>
<span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>


<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workdir</span><span class="p">):</span>
<span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workdir</span><span class="p">):</span>
<span class="n">p</span> <span class="o">=</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="bp">self</span><span class="o">.</span><span class="n">workdir</span><span class="p">,</span> <span class="n">file</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.rkf&#39;</span><span class="p">):</span>
<span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="k">if</span> <span class="s1">&#39;ams.kid&#39;</span> <span class="ow">in</span> <span class="n">p</span><span class="p">:</span>
<span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;t21.&#39;</span><span class="p">):</span>
<span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;t12.&#39;</span><span class="p">):</span>
<span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">p</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">_molecule</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molecule_path</span> <span class="ow">and</span> <span class="s1">&#39;atoms&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">input</span><span class="o">.</span><span class="n">ams</span><span class="o">.</span><span class="n">system</span><span class="p">:</span>
<span class="n">log</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;You did not supply a molecule for this job. Call the </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1">.molecule method to add one.&#39;</span><span class="p">)</span>
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