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ase
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<i class="fa fa-calendar"></i><time datetime="2014-12-20T23:26:00+01:00"> Sat 20 December 2014</time>
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<p><a href="https://wiki.fysik.dtu.dk/ase/index.html">ase</a> is a python library for atomic simulation. It can be used with a lot of code from first principle to classical md codes. It would be a good toy and test ground for atomic simulation. I plan to use it to test some algorithm with lj potential built in.</p>
<p>Here is the process for me to install it on killdevil.</p>
<div class="highlight"><pre><span></span><code><span class="n">module</span> <span class="n">load</span> <span class="n">anaconda</span>
<span class="n">source</span> <span class="n">activate</span> <span class="n">my_root</span>
<span class="n">export</span> <span class="n">ASE_TAGS</span><span class="o">=</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">svn</span><span class="o">.</span><span class="n">fysik</span><span class="o">.</span><span class="n">dtu</span><span class="o">.</span><span class="n">dk</span><span class="o">/</span><span class="n">projects</span><span class="o">/</span><span class="n">ase</span><span class="o">/</span><span class="n">tags</span><span class="o">/</span>
<span class="n">mkdir</span> <span class="o">~/</span><span class="n">software</span><span class="o">/</span><span class="n">ase</span>
<span class="n">cd</span> <span class="o">~/</span><span class="n">software</span><span class="o">/</span><span class="n">ase</span>
<span class="n">svn</span> <span class="n">co</span> <span class="o">-</span><span class="n">r</span> <span class="mi">3440</span> <span class="err">$</span><span class="n">ASE_TAGS</span><span class="o">/</span><span class="mf">3.8.1</span> <span class="n">ase</span><span class="o">-</span><span class="mf">3.8.1</span>
<span class="n">ln</span> <span class="o">-</span><span class="n">s</span> <span class="o">~/</span><span class="n">software</span><span class="o">/</span><span class="n">ase</span><span class="o">/</span><span class="n">ase</span><span class="o">-</span><span class="mf">3.8.1</span><span class="o">/</span> <span class="n">ase</span>
<span class="c1">#export PYTHONPATH=$HOME/ase:$PYTHONPATH</span>
<span class="c1">#export PATH=$HOME/ase/tools:$PATH</span>
<span class="n">cd</span> <span class="o">~/</span><span class="n">ase</span>
<span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span> <span class="o">--</span><span class="n">user</span>
<span class="n">mkdir</span> <span class="o">~/</span><span class="n">yiy</span><span class="o">/</span><span class="n">ase</span><span class="o">-</span><span class="n">test</span>
<span class="n">cd</span> <span class="o">~/</span><span class="n">yiy</span><span class="o">/</span><span class="n">ase</span><span class="o">-</span><span class="n">test</span>
<span class="n">python</span> <span class="o">-</span><span class="n">c</span> <span class="s2">"from ase.test import test; test(verbosity=2, display=False)"</span> <span class="mi">2</span><span class="o">>&</span><span class="mi">1</span> <span class="o">|</span> <span class="n">tee</span> <span class="n">testase</span><span class="o">.</span><span class="n">log</span>
</code></pre></div>
<p>And I got the result of </p>
<div class="highlight"><pre><span></span><code><span class="nb">----------------------------------------------------------------------</span><span class="c"></span>
<span class="c">Ran 96 tests in 64</span><span class="nt">.</span><span class="c">938s</span>
<span class="c">OK</span>
</code></pre></div>
<p>Now I can play around with it.</p>
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