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<p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
<p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t"> <span class="key">with</span> <span class="nam">warnings</span><span class="op">.</span><span class="nam">catch_warnings</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
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<p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t"> <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'Reading: {top_file} to extract charges'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
<p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t"> <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="fst">Reading: </span><span class="op">{</span><span class="nam">top_file</span><span class="op">}</span><span class="fst"> to extract charges</span><span class="fst">'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
<p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t"> <span class="nam">charges_list</span> <span class="op">=</span> <span class="nam">get_topology_charges</span><span class="op">(</span><span class="nam">top_file</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
<p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t"> <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'Reading: {top_file} to extract elements'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
<p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t"> <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="fst">Reading: </span><span class="op">{</span><span class="nam">top_file</span><span class="op">}</span><span class="fst"> to extract elements</span><span class="fst">'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
<p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t"> <span class="nam">elements_list</span> <span class="op">=</span> <span class="nam">get_topology_cmip_elements_canonical</span><span class="op">(</span><span class="nam">top_file</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
<p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t"> <span class="nam">two_letter_elements</span> <span class="op">=</span> <span class="op">{</span><span class="str">"CL"</span><span class="op">:</span> <span class="str">"Cl"</span><span class="op">,</span> <span class="str">"NA"</span><span class="op">:</span> <span class="str">"Na"</span><span class="op">,</span> <span class="str">"ZN"</span><span class="op">:</span> <span class="str">"Zn"</span><span class="op">,</span> <span class="str">"MG"</span><span class="op">:</span> <span class="str">"Mg"</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
<p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t"> <span class="nam">elements_list</span> <span class="op">=</span> <span class="op">[</span><span class="nam">two_letter_elements</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="nam">element</span><span class="op">,</span> <span class="nam">element</span><span class="op">)</span> <span class="key">for</span> <span class="nam">element</span> <span class="key">in</span> <span class="nam">elements_list</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
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