https://github.com/romerogroup/pyprocar
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
bands.html
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<li class="toctree-l2 current"><a class="current reference internal" href="#">Band structure</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#plain-band-structure">1. Plain band structure</a></li>
<li class="toctree-l3"><a class="reference internal" href="#spin-projection">2. Spin projection</a></li>
<li class="toctree-l3"><a class="reference internal" href="#atom-projection">3. Atom projection</a></li>
<li class="toctree-l3"><a class="reference internal" href="#orbital-projection">4. Orbital projection</a></li>
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<li class="toctree-l2"><a class="reference internal" href="filter.html">Filtering data</a></li>
<li class="toctree-l2"><a class="reference internal" href="comparebands.html">Compare bands</a></li>
<li class="toctree-l2"><a class="reference internal" href="cat.html">Concatenating multiple calculations</a></li>
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<div class="section" id="band-structure">
<h1>Band structure<a class="headerlink" href="#band-structure" title="Permalink to this headline">¶</a></h1>
<p>PyProcar goes beyond the conventional plain band structure to plot the projected bands that carry even more information. The projected bands are color coded in an informative manner to portray fine details.</p>
<div class="section" id="plain-band-structure">
<h2>1. Plain band structure<a class="headerlink" href="#plain-band-structure" title="Permalink to this headline">¶</a></h2>
<p>This is the most basic type of band structure. No projection information is contained here. In order to use the plain mode one sets <code class="docutils literal notranslate"><span class="pre">mode=`plain'</span></code>. <code class="docutils literal notranslate"><span class="pre">elimit</span></code> sets the energy window limits. <code class="docutils literal notranslate"><span class="pre">outcar</span></code> specifies the <strong>OUTCAR</strong> file. For Abinit calculations, <code class="docutils literal notranslate"><span class="pre">abinit_output</span></code> is used instead. <code class="docutils literal notranslate"><span class="pre">color</span></code> lets the user use any color available in the matplotlib package. If an output file is not present one can set <code class="docutils literal notranslate"><span class="pre">fermi</span></code> manually. One may save the plot using the <code class="docutils literal notranslate"><span class="pre">savefig</span></code> tag, for example, <code class="docutils literal notranslate"><span class="pre">savefig='figure.png'</span></code> with a desired image file format. This applies to all other band structure plotting functions in PyProcar as well.</p>
<p>Usage:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pyprocar</span><span class="o">.</span><span class="n">bandsplot</span><span class="p">(</span><span class="s1">'PROCAR'</span><span class="p">,</span><span class="n">outcar</span><span class="o">=</span><span class="s1">'OUTCAR'</span><span class="p">,</span><span class="n">elimit</span><span class="o">=</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span><span class="mi">2</span><span class="p">],</span><span class="n">mode</span><span class="o">=</span><span class="s1">'plain'</span><span class="p">,</span><span class="n">color</span><span class="o">=</span><span class="s1">'blue'</span><span class="p">)</span>
</pre></div>
</div>
<p>PyProcar is capable of labeling the <span class="math notranslate nohighlight">\(k\)</span>-path names automatically, however, the user can manually input them as desired.</p>
<p>If a <strong>KPOINTS</strong> file is present automatic labeling can be enabled as follows:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pyprocar</span><span class="o">.</span><span class="n">bandsplot</span><span class="p">(</span><span class="s1">'PROCAR'</span><span class="p">,</span><span class="n">outcar</span><span class="o">=</span><span class="s1">'OUTCAR'</span><span class="p">,</span><span class="n">elimit</span><span class="o">=</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span><span class="mi">2</span><span class="p">],</span><span class="n">mode</span><span class="o">=</span><span class="s1">'plain'</span><span class="p">,</span><span class="n">color</span><span class="o">=</span><span class="s1">'blue'</span><span class="p">,</span><span class="n">kpointsfile</span><span class="o">=</span><span class="s1">'KPOINTS'</span><span class="p">)</span>
</pre></div>
</div>
<p>One may manually label the <span class="math notranslate nohighlight">\(k\)</span>-path as well. <code class="docutils literal notranslate"><span class="pre">knames</span></code> and <code class="docutils literal notranslate"><span class="pre">kticks</span></code> corresponds to the labels and the number of grid points between the high symmetry points in the <span class="math notranslate nohighlight">\(k\)</span>-path used for the band structure calculation. Usage:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pyprocar</span><span class="o">.</span><span class="n">bandsplot</span><span class="p">(</span><span class="s1">'PROCAR'</span><span class="p">,</span><span class="n">outcar</span><span class="o">=</span><span class="s1">'OUTCAR'</span><span class="p">,</span><span class="n">elimit</span><span class="o">=</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span><span class="mi">2</span><span class="p">],</span><span class="n">mode</span><span class="o">=</span><span class="s1">'plain'</span><span class="p">,</span><span class="n">color</span><span class="o">=</span><span class="s1">'blue'</span><span class="p">,</span><span class="n">kticks</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">39</span><span class="p">,</span><span class="mi">79</span><span class="p">,</span><span class="mi">119</span><span class="p">,</span><span class="mi">159</span><span class="p">],</span><span class="n">knames</span><span class="o">=</span><span class="p">[</span><span class="s1">'G'</span><span class="p">,</span><span class="s1">'X'</span><span class="p">,</span><span class="s1">'M'</span><span class="p">,</span><span class="s1">'G'</span><span class="p">,</span><span class="s1">'R'</span><span class="p">])</span>
</pre></div>
</div>
<p>This is valid for the rest of the band plotting projections and also for the <code class="docutils literal notranslate"><span class="pre">bandscompare()</span></code> function.</p>
</div>
<div class="section" id="spin-projection">
<h2>2. Spin projection<a class="headerlink" href="#spin-projection" title="Permalink to this headline">¶</a></h2>
<p>For collinear spin polarized and non-collinear spin calculations of DFT codes, PyProcar is able to plot the bands of each spin channel or direction separately. For the former case setting <code class="docutils literal notranslate"><span class="pre">spin=0</span></code> plots the unpolarized bands and <code class="docutils literal notranslate"><span class="pre">spin=1</span></code> plots the spin channels separately.</p>
<p>For non-collinear spin calculations, spin=1,2,3 corresponds to spins oriented in <span class="math notranslate nohighlight">\(S_x\)</span>, <span class="math notranslate nohighlight">\(S_y\)</span> and <span class="math notranslate nohighlight">\(S_z\)</span> directions respectively. Setting <code class="docutils literal notranslate"><span class="pre">spin='st'</span></code> plots the spin texture perpendicular in the plane (<span class="math notranslate nohighlight">\(k_x\)</span>,:math:<cite>k_y</cite>) to each (<span class="math notranslate nohighlight">\(k_x\)</span>,:math:<cite>k_y</cite>) vector. This is useful for Rashba-like states in surfaces. For parametric plots such as spin, atom and orbitals, the user should set <code class="docutils literal notranslate"><span class="pre">mode=`parametric'</span></code>. <code class="docutils literal notranslate"><span class="pre">cmap</span></code> refers to the matplotlib color map used for the parametric plotting and can be modified by using the same color maps used in matplotlib.</p>
<p>Usage:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pyprocar</span><span class="o">.</span><span class="n">bandsplot</span><span class="p">(</span><span class="s1">'PROCAR'</span><span class="p">,</span><span class="n">outcar</span><span class="o">=</span><span class="s1">'OUTCAR'</span><span class="p">,</span><span class="n">elimit</span><span class="o">=</span><span class="p">[</span><span class="o">-</span><span class="mi">5</span><span class="p">,</span><span class="mi">5</span><span class="p">],</span><span class="n">kticks</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">39</span><span class="p">,</span><span class="mi">79</span><span class="p">,</span><span class="mi">119</span><span class="p">,</span><span class="mi">159</span><span class="p">],</span><span class="n">knames</span><span class="o">=</span><span class="p">[</span><span class="s1">'G'</span><span class="p">,</span><span class="s1">'X'</span><span class="p">,</span><span class="s1">'M'</span><span class="p">,</span><span class="s1">'G'</span><span class="p">,</span><span class="s1">'R'</span><span class="p">],</span><span class="n">cmap</span><span class="o">=</span><span class="s1">'jet'</span><span class="p">,</span><span class="n">mode</span><span class="o">=</span><span class="s1">'parametric'</span><span class="p">,</span><span class="n">spin</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
</pre></div>
</div>
<p>If spin-up and spin-down bands are to be plot separately, one may use the <code class="docutils literal notranslate"><span class="pre">filter()</span></code> function to create two PROCARs for each case and plot them individually. An example is given below:</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-up'</span><span class="p">,</span><span class="n">spin</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">])</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-down'</span><span class="p">,</span><span class="n">spin</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">pyprocar</span><span class="o">.</span><span class="n">bandsplot</span><span class="p">(</span><span class="s1">'PROCAR-up'</span><span class="p">,</span><span class="o">...</span><span class="p">)</span>
<span class="n">pyprocar</span><span class="o">.</span><span class="n">bandsplot</span><span class="p">(</span><span class="s1">'PROCAR-down'</span><span class="p">,</span><span class="o">...</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="section" id="atom-projection">
<h2>3. Atom projection<a class="headerlink" href="#atom-projection" title="Permalink to this headline">¶</a></h2>
<p>The projection of atoms onto bands can provide information such as which atoms contribute to the electronic states near the Fermi level. PyProcar counts each row of ions in the PROCAR file, starting from zero. In an example of a five atom SrVO_3, the indexes of <code class="docutils literal notranslate"><span class="pre">atoms</span></code> for Sr, V and the three O atoms would be 1,2 and 3,4,5 respectively. It is also possible to include more than one type of atom by using an array such as <code class="docutils literal notranslate"><span class="pre">atoms</span> <span class="pre">=</span> <span class="pre">[1,2,3]</span></code>.</p>
<p>Usage:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pyprocar</span><span class="o">.</span><span class="n">bandsplot</span><span class="p">(</span><span class="s1">'PROCAR'</span><span class="p">,</span><span class="n">outcar</span><span class="o">=</span><span class="s1">'OUTCAR'</span><span class="p">,</span><span class="n">elimit</span><span class="o">=</span><span class="p">[</span><span class="o">-</span><span class="mi">5</span><span class="p">,</span><span class="mi">5</span><span class="p">],</span><span class="n">kticks</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">39</span><span class="p">,</span><span class="mi">79</span><span class="p">,</span><span class="mi">119</span><span class="p">,</span><span class="mi">159</span><span class="p">],</span><span class="n">knames</span><span class="o">=</span><span class="p">[</span><span class="s1">'G'</span><span class="p">,</span><span class="s1">'X'</span><span class="p">,</span><span class="s1">'M'</span><span class="p">,</span><span class="s1">'G'</span><span class="p">,</span><span class="s1">'R'</span><span class="p">],</span><span class="n">cmap</span><span class="o">=</span><span class="s1">'jet'</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s1">'parametric'</span><span class="p">,</span><span class="n">atoms</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
</pre></div>
</div>
</div>
<div class="section" id="orbital-projection">
<h2>4. Orbital projection<a class="headerlink" href="#orbital-projection" title="Permalink to this headline">¶</a></h2>
<p>The projection of atomic orbitals onto bands is also useful to identify the contribution of orbitals to bands. For instance, to identify correlated <span class="math notranslate nohighlight">\(d\)</span> or <span class="math notranslate nohighlight">\(f\)</span> orbitals in a strongly correlated material near the Fermi level. It is possible to include more than one type of orbital projection. The mapping of the index of orbitals to be used in <code class="docutils literal notranslate"><span class="pre">orbitals</span></code> is as follows (this is the same order from the PROCAR file).</p>
<img alt="_images/orbitals.png" src="_images/orbitals.png" />
<p>Usage: To project all five <span class="math notranslate nohighlight">\(d\)</span>-orbitals:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pyprocar</span><span class="o">.</span><span class="n">bandsplot</span><span class="p">(</span><span class="s1">'PROCAR'</span><span class="p">,</span><span class="n">outcar</span><span class="o">=</span><span class="s1">'OUTCAR'</span><span class="p">,</span><span class="n">elimit</span><span class="o">=</span><span class="p">[</span><span class="o">-</span><span class="mi">5</span><span class="p">,</span><span class="mi">5</span><span class="p">],</span><span class="n">kticks</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">39</span><span class="p">,</span><span class="mi">79</span><span class="p">,</span><span class="mi">119</span><span class="p">,</span><span class="mi">159</span><span class="p">],</span><span class="n">knames</span><span class="o">=</span><span class="p">[</span><span class="s1">'G'</span><span class="p">,</span><span class="s1">'X'</span><span class="p">,</span><span class="s1">'M'</span><span class="p">,</span><span class="s1">'G'</span><span class="p">,</span><span class="s1">'R'</span><span class="p">],</span><span class="n">cmap</span><span class="o">=</span><span class="s1">'jet'</span><span class="p">,</span><span class="n">mode</span><span class="o">=</span><span class="s1">'parametric'</span><span class="p">,</span><span class="n">orbitals</span><span class="o">=</span><span class="p">[</span><span class="mi">4</span><span class="p">,</span><span class="mi">5</span><span class="p">,</span><span class="mi">6</span><span class="p">,</span><span class="mi">7</span><span class="p">,</span><span class="mi">8</span><span class="p">])</span>
</pre></div>
</div>
<p>One or many of the above can be combined together to allow the user to probe into more specific queries such as a collinear spin projection of a certain orbital of a certain atom.</p>
<p>Different modes of band structures are useful for obtaining information for different cases. The four modes available within PyProcar are <code class="docutils literal notranslate"><span class="pre">plain,</span> <span class="pre">scatter,</span> <span class="pre">parametric</span></code> and <code class="docutils literal notranslate"><span class="pre">atomic</span></code>. The <code class="docutils literal notranslate"><span class="pre">plain</span></code> bands contain no projection information. The <code class="docutils literal notranslate"><span class="pre">scatter</span></code> mode creates a scatter plot of points. The <code class="docutils literal notranslate"><span class="pre">parametric</span></code> mode interpolates between points to create bands which are also projectable. Finally, the <code class="docutils literal notranslate"><span class="pre">atomic</span></code> mode is useful to plot energy levels for atoms. To set maximum and minimum projections for color map, one could use <code class="docutils literal notranslate"><span class="pre">vmin</span></code> and <code class="docutils literal notranslate"><span class="pre">vmax</span></code> tags.</p>
</div>
<div class="section" id="export-plot-as-a-matplotlib-pyplot-object">
<h2>Export plot as a matplotlib.pyplot object<a class="headerlink" href="#export-plot-as-a-matplotlib-pyplot-object" title="Permalink to this headline">¶</a></h2>
<p>PyProcar allows the plot to be exported as a matplotlib.pyplot object. This allows for further processing of the plot through options available in matplotlib.
This can be enabled by setting <code class="docutils literal notranslate"><span class="pre">exportplt</span> <span class="pre">=</span> <span class="pre">True</span></code>.
Usage:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="kn">import</span> <span class="nn">pyprocar</span>
<span class="n">plt</span> <span class="o">=</span> <span class="n">pyprocar</span><span class="o">.</span><span class="n">bandsplot</span><span class="p">(</span><span class="s1">'PROCAR'</span><span class="p">,</span> <span class="n">outcar</span><span class="o">=</span><span class="s1">'OUTCAR'</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s1">'plain'</span><span class="p">,</span> <span class="n">exportplt</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s1">'Using matplotlib options'</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>
</div>
<span class="target" id="module-pyprocar.scriptBandsplot"></span><dl class="function">
<dt id="pyprocar.scriptBandsplot.bandsplot">
<code class="sig-prename descclassname">pyprocar.scriptBandsplot.</code><code class="sig-name descname">bandsplot</code><span class="sig-paren">(</span><em class="sig-param">file</em>, <em class="sig-param">mode='scatter'</em>, <em class="sig-param">color='blue'</em>, <em class="sig-param">abinit_output=None</em>, <em class="sig-param">spin=0</em>, <em class="sig-param">atoms=None</em>, <em class="sig-param">orbitals=None</em>, <em class="sig-param">fermi=None</em>, <em class="sig-param">elimit=None</em>, <em class="sig-param">mask=None</em>, <em class="sig-param">markersize=0.02</em>, <em class="sig-param">cmap='jet'</em>, <em class="sig-param">vmax=None</em>, <em class="sig-param">vmin=None</em>, <em class="sig-param">grid=True</em>, <em class="sig-param">marker='o'</em>, <em class="sig-param">permissive=False</em>, <em class="sig-param">human=False</em>, <em class="sig-param">savefig=None</em>, <em class="sig-param">kticks=None</em>, <em class="sig-param">knames=None</em>, <em class="sig-param">title=None</em>, <em class="sig-param">outcar=None</em>, <em class="sig-param">kpointsfile=None</em>, <em class="sig-param">exportplt=False</em><span class="sig-paren">)</span><a class="headerlink" href="#pyprocar.scriptBandsplot.bandsplot" title="Permalink to this definition">¶</a></dt>
<dd><p>This function plots band structures</p>
</dd></dl>
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