https://github.com/romerogroup/pyprocar
Revision e5149c529e11d44cd206d323df17f7759cf21f8a authored by Uthpala Herath on 24 February 2020, 16:59:40 UTC, committed by Uthpala Herath on 24 February 2020, 16:59:40 UTC
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Tip revision: e5149c529e11d44cd206d323df17f7759cf21f8a authored by Uthpala Herath on 24 February 2020, 16:59:40 UTC
Fixed band unfolding bug
Fixed band unfolding bug
Tip revision: e5149c5
filter.html
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<li class="toctree-l2 current"><a class="current reference internal" href="#">Filtering data</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#to-filter-selected-orbitals">To filter selected orbitals</a></li>
<li class="toctree-l3"><a class="reference internal" href="#to-filter-selected-k-points">To filter selected <span class="math notranslate nohighlight">\(k\)</span>-points</a></li>
<li class="toctree-l3"><a class="reference internal" href="#to-filter-selected-spins">To filter selected spins</a></li>
<li class="toctree-l3"><a class="reference internal" href="#to-filter-selected-atoms">To filter selected atoms</a></li>
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<div class="section" id="filtering-data">
<h1>Filtering data<a class="headerlink" href="#filtering-data" title="Permalink to this headline">¶</a></h1>
<p>A simpler version of PROCAR file containing only a subset of information from the original dataset can be generated with this utility. This feature is very useful when there are many bands in the PROCAR file (e.g. in heterostructures or supercells calculations) making the file size enormously large for post-processing while only bands near the Fermi-level are needed for analysis. In this case, one can filter data of selected bands near the Fermi-level. This considerably reduces the file size and makes the post-processing of data faster. In the same way, one could use the <code class="docutils literal notranslate"><span class="pre">filter</span></code> utility to filter the <strong>PROCAR</strong> file to extract information regarding particular spins, atoms, or orbitals in a relatively smaller <strong>PROCAR-new</strong> file.</p>
<p>The following example extracts information of bands ranging from index 50 to 70 from a <strong>PROCAR</strong> file (Fermi-level is near band #60) while ignoring all other bands located far from the Fermi-level, and stores resulting dataset in a new file named <strong>PROCAR-band50-70</strong>. Now the new <strong>PROCAR-band50-70</strong> file can be used for further post-processing of data at relatively low memory requirements:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pyprocar</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="s1">'PROCAR'</span><span class="p">,</span><span class="s1">'PROCAR-band50-70'</span><span class="p">,</span><span class="n">bands</span><span class="o">=</span><span class="p">[</span><span class="mi">50</span><span class="p">,</span><span class="mi">70</span><span class="p">])</span>
</pre></div>
</div>
<div class="section" id="to-filter-selected-orbitals">
<h2>To filter selected orbitals<a class="headerlink" href="#to-filter-selected-orbitals" title="Permalink to this headline">¶</a></h2>
<p>To make a new PROCAR file containing only three columns, one for <span class="math notranslate nohighlight">\(s\)</span> orbitals, one for <span class="math notranslate nohighlight">\(p\)</span>, and one for total (real total, not total of <span class="math notranslate nohighlight">\(s+p\)</span>):</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>pyprocar.filter('PROCAR’,'PROCAR-filtered_sp’, orbitals=[[0],[1,2,3]])
</pre></div>
</div>
<p>If you want to select only <span class="math notranslate nohighlight">\(p_x\)</span> orbitals, just use <code class="docutils literal notranslate"><span class="pre">orbitals=[[3]]</span></code>.</p>
<p>In the same way to plot the projection of total <span class="math notranslate nohighlight">\(p\)</span>-orbitals use <code class="docutils literal notranslate"><span class="pre">orbitals=[[1,2,3]]</span></code> (i.e. <span class="math notranslate nohighlight">\(px+py+pz\)</span>). Same goes for other orbitals.</p>
</div>
<div class="section" id="to-filter-selected-k-points">
<h2>To filter selected <span class="math notranslate nohighlight">\(k\)</span>-points<a class="headerlink" href="#to-filter-selected-k-points" title="Permalink to this headline">¶</a></h2>
<p>This is helpful especially for hybrid calculations where the weighted <span class="math notranslate nohighlight">\(k\)</span>-points should be filtered to perform band structure plotting.
To filter <span class="math notranslate nohighlight">\(k\)</span>-points within a minimum and maximum range:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>pyprocar.filter('PROCAR’,'PROCAR-filtered_kpoints’, kpoints=[10,13])
</pre></div>
</div>
<p>This creates a new PROCAR file containing only the selected <span class="math notranslate nohighlight">\(k\)</span>-points.</p>
</div>
<div class="section" id="to-filter-selected-spins">
<h2>To filter selected spins<a class="headerlink" href="#to-filter-selected-spins" title="Permalink to this headline">¶</a></h2>
<p>This can be used to generate a PROCAR that contains a selected spin component.
For example, to filter the spin in the <span class="math notranslate nohighlight">\(S_x\)</span> direction:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>pyprocar.filter('PROCAR’,'PROCAR-filtered_spin’, spin=[1])
</pre></div>
</div>
<p>This creates a new PROCAR file containing only the selected spin component(s).</p>
</div>
<div class="section" id="to-filter-selected-atoms">
<h2>To filter selected atoms<a class="headerlink" href="#to-filter-selected-atoms" title="Permalink to this headline">¶</a></h2>
<p>Usage:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>pyprocar.filter(‘PROCAR’,’PROCAR-filter_ATOMS’, atoms=[[0]])
</pre></div>
</div>
<p>PyProcar counts each row of ions in PROCAR file starting from 0. Keep in mind: <code class="docutils literal notranslate"><span class="pre">atoms=0</span></code> does not define the atom_type, rather it defines only the first ion in the POSCAR. So if you have more than one ion of the same element, use <code class="docutils literal notranslate"><span class="pre">atoms</span> <span class="pre">=</span> <span class="pre">[[0,1,2,3,...]]</span></code>.</p>
<span class="target" id="module-pyprocar.scriptFilter"></span><dl class="function">
<dt id="pyprocar.scriptFilter.filter">
<code class="sig-prename descclassname">pyprocar.scriptFilter.</code><code class="sig-name descname">filter</code><span class="sig-paren">(</span><em class="sig-param">inFile</em>, <em class="sig-param">outFile</em>, <em class="sig-param">atoms=None</em>, <em class="sig-param">orbitals=None</em>, <em class="sig-param">orbital_names=None</em>, <em class="sig-param">bands=None</em>, <em class="sig-param">spin=None</em>, <em class="sig-param">kpoints=None</em>, <em class="sig-param">human_atoms=False</em><span class="sig-paren">)</span><a class="headerlink" href="#pyprocar.scriptFilter.filter" title="Permalink to this definition">¶</a></dt>
<dd><p>This module filters the PROCAR file and re-write a new one.</p>
</dd></dl>
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