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pyiron virtual workshop 2020: Workflows for atomistic simulations
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<div class="section" id="pyiron-virtual-workshop-2020-workflows-for-atomistic-simulations">
<h1>pyiron virtual workshop 2020: Workflows for atomistic simulations<a class="headerlink" href="#pyiron-virtual-workshop-2020-workflows-for-atomistic-simulations" title="Permalink to this headline">¶</a></h1>
<p>Tutorials, exercises, and solutions for the pyiron workshop 2020.</p>
<div class="section" id="things-to-do-before-the-workshop">
<h2>Things to do before the workshop<a class="headerlink" href="#things-to-do-before-the-workshop" title="Permalink to this headline">¶</a></h2>
<p>For this workshop, you will need to have pyiron installed on your workstation. While
pyiron is platform independent, Linux is required to run certain external
simulation codes like LAMMPS and Sphinx. For windows users, it is recommended that you install the linux
subsystem for windows. More details <a class="reference external" href="https://docs.microsoft.com/en-us/windows/wsl/install-win10">here</a>. THe Debian distribution of Linux is recommended although Ubuntu works fine as well. If you are a Mac user, you will only be able to run LAMMPS examples (which is still fine!)</p>
<div class="section" id="installing-conda">
<h3>Installing conda<a class="headerlink" href="#installing-conda" title="Permalink to this headline">¶</a></h3>
<p>While pyiron can be installed in several ways, installation via conda is recommended for this workshop since this
ensures that you are working with the latest and stable version of pyiron. As a
first step, follow <a class="reference external" href="https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html">this guide</a>
to install miniconda (recommended) or anaconda. Using the Linux/Mac or linux subsystem terminal on windows, conda can be installed as follows.
Choose the appropriate 64 bit or 32 bit installer available <a class="reference external" href="https://docs.conda.io/en/latest/miniconda.html#linux-installers">here</a>.
For example, the 64 bit executable for linux can be installed as follows:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">apt</span><span class="o">-</span><span class="n">get</span> <span class="n">install</span> <span class="n">wget</span>
<span class="n">wget</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">repo</span><span class="o">.</span><span class="n">anaconda</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">miniconda</span><span class="o">/</span><span class="n">Miniconda3</span><span class="o">-</span><span class="n">latest</span><span class="o">-</span><span class="n">Linux</span><span class="o">-</span><span class="n">x86_64</span><span class="o">.</span><span class="n">sh</span>
<span class="n">chmod</span> <span class="o">+</span><span class="n">x</span> <span class="n">Miniconda3</span><span class="o">-</span><span class="n">latest</span><span class="o">-</span><span class="n">Linux</span><span class="o">-</span><span class="n">x86_64</span><span class="o">.</span><span class="n">sh</span>
<span class="o">./</span><span class="n">Miniconda3</span><span class="o">-</span><span class="n">latest</span><span class="o">-</span><span class="n">Linux</span><span class="o">-</span><span class="n">x86_64</span><span class="o">.</span><span class="n">sh</span>
<span class="n">source</span> <span class="o">~/.</span><span class="n">bashrc</span>
</pre></div>
</div>
<div class="section" id="creating-a-new-conda-environment">
<h4>Creating a new conda environment<a class="headerlink" href="#creating-a-new-conda-environment" title="Permalink to this headline">¶</a></h4>
<p>After installing conda, it is recommended to create a new conda environment to install the required packages for the workshop</p>
<p><code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">create</span> <span class="pre">--name</span> <span class="pre">pyiron_workshop</span> <span class="pre">python=3.7</span> <span class="pre">-y</span></code></p>
<p>To activate this conda environment, type</p>
<p><code class="docutils literal notranslate"><span class="pre">source</span> <span class="pre">activate</span> <span class="pre">pyiron_workshop</span></code></p>
<p>or for MacOS</p>
<p><code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">activate</span> <span class="pre">pyiron_workshop</span></code></p>
<p>Please install all packages and run the notebooks only after you have activated this environment.
After the workshop is over, this environment can be deactivated <code class="docutils literal notranslate"><span class="pre">source</span> <span class="pre">deactivate</span></code> or <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">deactivate</span></code>.
If you want to run the notebooks later, just reactivate the environment.</p>
</div>
</div>
<div class="section" id="installing-pyiron-and-other-packages-using-conda-forge">
<h3>Installing pyiron and other packages using conda-forge<a class="headerlink" href="#installing-pyiron-and-other-packages-using-conda-forge" title="Permalink to this headline">¶</a></h3>
<p>Once you’ve activated the <code class="docutils literal notranslate"><span class="pre">pyiron_workshop</span></code> environment, install the necessary packages using</p>
<p><code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">install</span> <span class="pre">-y</span> <span class="pre">-c</span> <span class="pre">conda-forge</span> <span class="pre">git</span> <span class="pre">pyiron</span> <span class="pre">nglview</span> <span class="pre">lammps</span> <span class="pre">nodejs=13.13.0</span> <span class="pre">jupyterlab</span></code></p>
<p>If you are using Linux (or Linux subsystem for windows), you can also use SPHINX</p>
<p><code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">install</span> <span class="pre">-y</span> <span class="pre">-c</span> <span class="pre">conda-forge</span> <span class="pre">sphinxdft=2.6.1=h6ced99e_5</span></code></p>
<p>Further, to get nglview working smoothly on jupyter notebooks, the following commands need to be typed</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">jupyter</span> <span class="n">nbextension</span> <span class="n">install</span> <span class="n">nglview</span> <span class="o">--</span><span class="n">py</span> <span class="o">--</span><span class="n">sys</span><span class="o">-</span><span class="n">prefix</span>
<span class="n">jupyter</span> <span class="n">nbextension</span> <span class="n">enable</span> <span class="n">nglview</span> <span class="o">--</span><span class="n">py</span> <span class="o">--</span><span class="n">sys</span><span class="o">-</span><span class="n">prefix</span>
<span class="n">jupyter</span> <span class="n">labextension</span> <span class="n">install</span> <span class="nd">@jupyter</span><span class="o">-</span><span class="n">widgets</span><span class="o">/</span><span class="n">jupyterlab</span><span class="o">-</span><span class="n">manager</span> <span class="o">--</span><span class="n">no</span><span class="o">-</span><span class="n">build</span>
<span class="n">jupyter</span> <span class="n">labextension</span> <span class="n">install</span> <span class="n">nglview</span><span class="o">-</span><span class="n">js</span><span class="o">-</span><span class="n">widgets</span>
<span class="n">jupyter</span> <span class="n">labextension</span> <span class="n">install</span> <span class="nd">@jupyterlab</span><span class="o">/</span><span class="n">toc</span>
</pre></div>
</div>
</div>
<div class="section" id="configuring-pyiron">
<h3>Configuring pyiron<a class="headerlink" href="#configuring-pyiron" title="Permalink to this headline">¶</a></h3>
<p>Type the following lines to configure pyiron and dowload the necessary resources (binaries and potentials)</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>cd
printf "[DEFAULT]\nTOP_LEVEL_DIRS = ${HOME}\nRESOURCE_PATHS = ${HOME}/resources" > ${HOME}/.pyiron
git clone https://github.com/pyiron/pyiron-resources.git ${HOME}/resources
</pre></div>
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