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<section id="module-pymatgen.analysis.surface_analysis">
<span id="pymatgen-analysis-surface-analysis-module"></span><h1>pymatgen.analysis.surface_analysis module<a class="headerlink" href="#module-pymatgen.analysis.surface_analysis" title="Permalink to this heading"></a></h1>
<p>This module defines tools to analyze surface and adsorption related
quantities as well as related plots. If you use this module, please
consider citing the following works:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">R</span><span class="o">.</span> <span class="n">Tran</span><span class="p">,</span> <span class="n">Z</span><span class="o">.</span> <span class="n">Xu</span><span class="p">,</span> <span class="n">B</span><span class="o">.</span> <span class="n">Radhakrishnan</span><span class="p">,</span> <span class="n">D</span><span class="o">.</span> <span class="n">Winston</span><span class="p">,</span> <span class="n">W</span><span class="o">.</span> <span class="n">Sun</span><span class="p">,</span> <span class="n">K</span><span class="o">.</span> <span class="n">A</span><span class="o">.</span> <span class="n">Persson</span><span class="p">,</span>
<span class="n">S</span><span class="o">.</span> <span class="n">P</span><span class="o">.</span> <span class="n">Ong</span><span class="p">,</span> <span class="s2">"Surface Energies of Elemental Crystals"</span><span class="p">,</span> <span class="n">Scientific</span>
<span class="n">Data</span><span class="p">,</span> <span class="mi">2016</span><span class="p">,</span> <span class="mi">3</span><span class="p">:</span><span class="mi">160080</span><span class="p">,</span> <span class="n">doi</span><span class="p">:</span> <span class="mf">10.1038</span><span class="o">/</span><span class="n">sdata</span><span class="mf">.2016.80</span><span class="o">.</span>
<span class="ow">and</span>
<span class="n">Kang</span><span class="p">,</span> <span class="n">S</span><span class="o">.</span><span class="p">,</span> <span class="n">Mo</span><span class="p">,</span> <span class="n">Y</span><span class="o">.</span><span class="p">,</span> <span class="n">Ong</span><span class="p">,</span> <span class="n">S</span><span class="o">.</span> <span class="n">P</span><span class="o">.</span><span class="p">,</span> <span class="o">&</span> <span class="n">Ceder</span><span class="p">,</span> <span class="n">G</span><span class="o">.</span> <span class="p">(</span><span class="mi">2014</span><span class="p">)</span><span class="o">.</span> <span class="n">Nanoscale</span>
<span class="n">stabilization</span> <span class="n">of</span> <span class="n">sodium</span> <span class="n">oxides</span><span class="p">:</span> <span class="n">Implications</span> <span class="k">for</span> <span class="n">Na</span><span class="o">-</span><span class="n">O2</span> <span class="n">batteries</span><span class="o">.</span>
<span class="n">Nano</span> <span class="n">Letters</span><span class="p">,</span> <span class="mi">14</span><span class="p">(</span><span class="mi">2</span><span class="p">),</span> <span class="mi">1016</span><span class="o">-</span><span class="mf">1020.</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">doi</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="mf">10.1021</span><span class="o">/</span><span class="n">nl404557w</span>
<span class="ow">and</span>
<span class="n">Montoya</span><span class="p">,</span> <span class="n">J</span><span class="o">.</span> <span class="n">H</span><span class="o">.</span><span class="p">,</span> <span class="o">&</span> <span class="n">Persson</span><span class="p">,</span> <span class="n">K</span><span class="o">.</span> <span class="n">A</span><span class="o">.</span> <span class="p">(</span><span class="mi">2017</span><span class="p">)</span><span class="o">.</span> <span class="n">A</span> <span class="n">high</span><span class="o">-</span><span class="n">throughput</span> <span class="n">framework</span>
<span class="k">for</span> <span class="n">determining</span> <span class="n">adsorption</span> <span class="n">energies</span> <span class="n">on</span> <span class="n">solid</span> <span class="n">surfaces</span><span class="o">.</span> <span class="n">Npj</span>
<span class="n">Computational</span> <span class="n">Materials</span><span class="p">,</span> <span class="mi">3</span><span class="p">(</span><span class="mi">1</span><span class="p">),</span> <span class="mf">14.</span>
<span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">doi</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="mf">10.1038</span><span class="o">/</span><span class="n">s41524</span><span class="o">-</span><span class="mi">017</span><span class="o">-</span><span class="mi">0017</span><span class="o">-</span><span class="n">z</span>
</pre></div>
</div>
<p>Todo:
- Still assumes individual elements have their own chempots</p>
<blockquote>
<div><p>in a molecular adsorbate instead of considering a single
chempot for a single molecular adsorbate. E.g. for an OH
adsorbate, the surface energy is a function of delu_O and
delu_H instead of delu_OH</p>
</div></blockquote>
<ul class="simple">
<li><dl class="simple">
<dt>Need a method to automatically get chempot range when</dt><dd><p>dealing with non-stoichiometric slabs</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>Simplify the input for SurfaceEnergyPlotter such that the</dt><dd><p>user does not need to generate a dict</p>
</dd>
</dl>
</li>
</ul>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">NanoscaleStability</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">se_analyzers</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symprec</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1687-L1980"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<dl>
<dt>A class for analyzing the stability of nanoparticles of different</dt><dd><p>polymorphs with respect to size. The Wulff shape will be the
model for the nanoparticle. Stability will be determined by
an energetic competition between the weighted surface energy
(surface energy of the Wulff shape) and the bulk energy. A
future release will include a 2D phase diagram (e.g. wrt size
vs chempot for adsorbed or non-stoichiometric surfaces). Based
on the following work:</p>
<dl class="simple">
<dt>Kang, S., Mo, Y., Ong, S. P., & Ceder, G. (2014). Nanoscale</dt><dd><p>stabilization of sodium oxides: Implications for Na-O2
batteries. Nano Letters, 14(2), 1016-1020.
<a class="reference external" href="https://doi.org/10.1021/nl404557w">https://doi.org/10.1021/nl404557w</a></p>
</dd>
</dl>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.se_analyzers">
<span class="sig-name descname"><span class="pre">se_analyzers</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.se_analyzers" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>List of SurfaceEnergyPlotter objects. Each item corresponds to a</dt><dd><p>different polymorph.</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.symprec">
<span class="sig-name descname"><span class="pre">symprec</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.symprec" title="Permalink to this definition"></a></dt>
<dd><p>See WulffShape.</p>
</dd></dl>
<p>Analyzes the nanoscale stability of different polymorphs.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.bulk_gform">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">bulk_gform</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bulk_entry</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1820-L1827"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.bulk_gform" title="Permalink to this definition"></a></dt>
<dd><p>Returns the formation energy of the bulk
:param bulk_entry: Entry of the corresponding bulk.
:type bulk_entry: ComputedStructureEntry</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.plot_all_stability_map">
<span class="sig-name descname"><span class="pre">plot_all_stability_map</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">max_r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">increments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">from_sphere_area</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'keV'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'nanometers'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_per_atom</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1920-L1980"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.plot_all_stability_map" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Returns the plot of the formation energy of a particles</dt><dd><p>of different polymorphs against its effect radius</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>max_r</strong> (<em>float</em>) – The maximum radius of the particle to plot up to.</p></li>
<li><p><strong>increments</strong> (<em>int</em>) – Number of plot points</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>plt</strong> (<em>pyplot</em>) – Plot</p></li>
<li><p><strong>labels</strong> (<em>list</em>) – List of labels for each plot, corresponds to the
list of se_analyzers</p></li>
<li><p><strong>from_sphere_area</strong> (<em>bool</em>) – There are two ways to calculate the bulk
formation energy. Either by treating the volume and thus surface
area of the particle as a perfect sphere, or as a Wulff shape.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.plot_one_stability_map">
<span class="sig-name descname"><span class="pre">plot_one_stability_map</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">analyzer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">increments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">from_sphere_area</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'keV'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'nanometers'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_per_atom</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1855-L1918"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.plot_one_stability_map" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Returns the plot of the formation energy of a particle against its</dt><dd><p>effect radius</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>analyzer</strong> (<a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter" title="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter"><em>SurfaceEnergyPlotter</em></a>) – Analyzer associated with the
first polymorph</p></li>
<li><p><strong>max_r</strong> (<em>float</em>) – The maximum radius of the particle to plot up to.</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>label</strong> (<em>str</em>) – Label of the plot for legend</p></li>
<li><p><strong>increments</strong> (<em>int</em>) – Number of plot points</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>plt</strong> (<em>pyplot</em>) – Plot</p></li>
<li><p><strong>from_sphere_area</strong> (<em>bool</em>) – There are two ways to calculate the bulk
formation energy. Either by treating the volume and thus surface
area of the particle as a perfect sphere, or as a Wulff shape.</p></li>
<li><p><strong>r_units</strong> (<em>str</em>) – Can be nanometers or Angstrom</p></li>
<li><p><strong>e_units</strong> (<em>str</em>) – Can be keV or eV</p></li>
<li><p><strong>normalize</strong> (<em>str</em>) – Whether or not to normalize energy by volume</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.scaled_wulff">
<span class="sig-name descname"><span class="pre">scaled_wulff</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">wulffshape</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1829-L1853"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.scaled_wulff" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Scales the Wulff shape with an effective radius r. Note that the resulting</dt><dd><p>Wulff does not necessarily have the same effective radius as the one
provided. The Wulff shape is scaled by its surface energies where first
the surface energies are scale by the minimum surface energy and then
multiplied by the given effective radius.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>wulffshape</strong> (<a class="reference internal" href="pymatgen.analysis.wulff.html#pymatgen.analysis.wulff.WulffShape" title="pymatgen.analysis.wulff.WulffShape"><em>WulffShape</em></a>) – Initial, unscaled WulffShape</p></li>
<li><p><strong>r</strong> (<em>float</em>) – Arbitrary effective radius of the WulffShape</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>WulffShape (scaled by r)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.solve_equilibrium_point">
<span class="sig-name descname"><span class="pre">solve_equilibrium_point</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">analyzer1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">analyzer2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'nanometers'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1720-L1755"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.solve_equilibrium_point" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Gives the radial size of two particles where equilibrium is reached</dt><dd><p>between both particles. NOTE: the solution here is not the same
as the solution visualized in the plot because solving for r
requires that both the total surface area and volume of the
particles are functions of r.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>analyzer1</strong> (<a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter" title="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter"><em>SurfaceEnergyPlotter</em></a>) – Analyzer associated with the
first polymorph</p></li>
<li><p><strong>analyzer2</strong> (<a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter" title="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter"><em>SurfaceEnergyPlotter</em></a>) – Analyzer associated with the
second polymorph</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>units</strong> (<em>str</em>) – Can be nanometers or Angstrom</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Particle radius in nm</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.wulff_gform_and_r">
<span class="sig-name descname"><span class="pre">wulff_gform_and_r</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">wulffshape</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bulk_entry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">from_sphere_area</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'nanometers'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'keV'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_per_atom</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1757-L1818"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.wulff_gform_and_r" title="Permalink to this definition"></a></dt>
<dd><p>Calculates the formation energy of the particle with arbitrary radius r.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>wulffshape</strong> (<a class="reference internal" href="pymatgen.analysis.wulff.html#pymatgen.analysis.wulff.WulffShape" title="pymatgen.analysis.wulff.WulffShape"><em>WulffShape</em></a>) – Initial, unscaled WulffShape</p></li>
<li><p><strong>bulk_entry</strong> (<a class="reference internal" href="pymatgen.entries.computed_entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><em>ComputedStructureEntry</em></a>) – Entry of the corresponding bulk.</p></li>
<li><p><strong>r</strong> (<em>float</em><em> (</em><em>Ang</em><em>)</em>) – Arbitrary effective radius of the WulffShape</p></li>
<li><p><strong>from_sphere_area</strong> (<em>bool</em>) – There are two ways to calculate the bulk
formation energy. Either by treating the volume and thus surface
area of the particle as a perfect sphere, or as a Wulff shape.</p></li>
<li><p><strong>r_units</strong> (<em>str</em>) – Can be nanometers or Angstrom</p></li>
<li><p><strong>e_units</strong> (<em>str</em>) – Can be keV or eV</p></li>
<li><p><strong>normalize</strong> (<em>bool</em>) – Whether or not to normalize energy by volume</p></li>
<li><p><strong>scale_per_atom</strong> (<em>True</em>) – Whether or not to normalize by number of
atoms in the particle</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>particle formation energy (float in keV), effective radius</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SlabEntry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">correction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parameters</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entry_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adsorbates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clean_entry</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">marker</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L64-L367"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.entries.computed_entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">ComputedStructureEntry</span></code></a></p>
<dl class="simple">
<dt>A ComputedStructureEntry object encompassing all data relevant to a</dt><dd><p>slab for analyzing surface thermodynamics.</p>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.miller_index">
<span class="sig-name descname"><span class="pre">miller_index</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.miller_index" title="Permalink to this definition"></a></dt>
<dd><p>Miller index of plane parallel to surface.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.label">
<span class="sig-name descname"><span class="pre">label</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.label" title="Permalink to this definition"></a></dt>
<dd><p>Brief description for this slab.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.adsorbates">
<span class="sig-name descname"><span class="pre">adsorbates</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.adsorbates" title="Permalink to this definition"></a></dt>
<dd><p>List of ComputedStructureEntry for the types of adsorbates</p>
</dd></dl>
<p>..attribute:: clean_entry</p>
<blockquote>
<div><p>SlabEntry for the corresponding clean slab for an adsorbed slab</p>
</div></blockquote>
<p>..attribute:: ads_entries_dict</p>
<blockquote>
<div><dl class="simple">
<dt>Dictionary where the key is the reduced composition of the</dt><dd><p>adsorbate entry and value is the entry itself</p>
</dd>
</dl>
</div></blockquote>
<p>Make a SlabEntry containing all relevant surface thermodynamics data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.surface.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><em>Slab</em></a>) – The primary slab associated with this entry.</p></li>
<li><p><strong>energy</strong> (<em>float</em>) – Energy from total energy calculation</p></li>
<li><p><strong>miller_index</strong> (<em>tuple</em><em>(</em><em>h</em><em>, </em><em>k</em><em>, </em><em>l</em><em>)</em>) – Miller index of plane parallel
to surface</p></li>
<li><p><strong>correction</strong> (<em>float</em>) – See ComputedSlabEntry</p></li>
<li><p><strong>parameters</strong> (<em>dict</em>) – See ComputedSlabEntry</p></li>
<li><p><strong>data</strong> (<em>dict</em>) – See ComputedSlabEntry</p></li>
<li><p><strong>entry_id</strong> (<em>str</em>) – See ComputedSlabEntry</p></li>
<li><p><strong>data</strong> – See ComputedSlabEntry</p></li>
<li><p><strong>entry_id</strong> – See ComputedSlabEntry</p></li>
<li><p><strong>label</strong> (<em>str</em>) – Any particular label for this slab, e.g. “Tasker 2”,
“non-stoichiometric”, “reconstructed”</p></li>
<li><p><strong>adsorbates</strong> (<em>[</em><a class="reference internal" href="pymatgen.entries.computed_entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><em>ComputedStructureEntry</em></a><em>]</em>) – List of reference entries
for the adsorbates on the slab, can be an isolated molecule
(e.g. O2 for O or O2 adsorption), a bulk structure (eg. fcc
Cu for Cu adsorption) or anything.</p></li>
<li><p><strong>clean_entry</strong> (<a class="reference internal" href="pymatgen.entries.computed_entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><em>ComputedStructureEntry</em></a>) – If the SlabEntry is for an
adsorbed slab, this is the corresponding SlabEntry for the
clean slab</p></li>
<li><p><strong>marker</strong> (<em>str</em>) – Custom marker for gamma plots (”–” and “-” are typical)</p></li>
<li><p><strong>color</strong> (<em>str</em><em> or </em><em>rgba</em>) – Custom color for gamma plots</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.Nads_in_slab">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Nads_in_slab</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.Nads_in_slab" title="Permalink to this definition"></a></dt>
<dd><p>Returns the TOTAL number of adsorbates in the slab on BOTH sides</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.Nsurfs_ads_in_slab">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Nsurfs_ads_in_slab</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.Nsurfs_ads_in_slab" title="Permalink to this definition"></a></dt>
<dd><p>Returns the TOTAL number of adsorbed surfaces in the slab</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L149-L161"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.as_dict" title="Permalink to this definition"></a></dt>
<dd><p>Returns dict which contains Slab Entry data.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.cleaned_up_slab">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">cleaned_up_slab</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.cleaned_up_slab" title="Permalink to this definition"></a></dt>
<dd><p>Returns a slab with the adsorbates removed</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.create_slab_label">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">create_slab_label</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.create_slab_label" title="Permalink to this definition"></a></dt>
<dd><p>Returns a label (str) for this particular slab based on composition, coverage and Miller index.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.from_computed_structure_entry">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_computed_structure_entry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adsorbates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clean_entry</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L354-L367"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.from_computed_structure_entry" title="Permalink to this definition"></a></dt>
<dd><p>Returns SlabEntry from a ComputedStructureEntry</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L295-L314"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.from_dict" title="Permalink to this definition"></a></dt>
<dd><p>Returns a SlabEntry by reading in an dictionary</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.get_monolayer">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_monolayer</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.get_monolayer" title="Permalink to this definition"></a></dt>
<dd><p>Returns the primitive unit surface area density of the
adsorbate.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.get_unit_primitive_area">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_unit_primitive_area</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.get_unit_primitive_area" title="Permalink to this definition"></a></dt>
<dd><p>Returns the surface area of the adsorbed system per
unit area of the primitive slab system.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.gibbs_binding_energy">
<span class="sig-name descname"><span class="pre">gibbs_binding_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">eads</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L163-L176"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.gibbs_binding_energy" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Returns the adsorption energy or Gibbs binding energy</dt><dd><p>of an adsorbate on a surface</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>eads</strong> (<em>bool</em>) – Whether to calculate the adsorption energy
(True) or the binding energy (False) which is just
adsorption energy normalized by number of adsorbates.</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.surface_area">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">surface_area</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.surface_area" title="Permalink to this definition"></a></dt>
<dd><p>Calculates the surface area of the slab</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.surface_energy">
<span class="sig-name descname"><span class="pre">surface_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ucell_entry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_entries</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L178-L241"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.surface_energy" title="Permalink to this definition"></a></dt>
<dd><p>Calculates the surface energy of this SlabEntry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ucell_entry</strong> (<em>entry</em>) – An entry object for the bulk</p></li>
<li><p><strong>(</strong><strong>list</strong> (<em>ref_entries</em>) – [entry]): A list of entries for each type
of element to be used as a reservoir for non-stoichiometric
systems. The length of this list MUST be n-1 where n is the
number of different elements in the bulk entry. The chempot
of the element ref_entry that is not in the list will be
treated as a variable.</p></li>
</ul>
</dd>
</dl>
<p>Returns (Add (Sympy class)): Surface energy</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SurfaceEnergyPlotter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">all_slab_entries</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ucell_entry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_entries</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L370-L1364"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<dl class="simple">
<dt>A class used for generating plots to analyze the thermodynamics of surfaces</dt><dd><p>of a material. Produces stability maps of different slab configurations,
phases diagrams of two parameters to determine stability of configurations
(future release), and Wulff shapes.</p>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.all_slab_entries">
<span class="sig-name descname"><span class="pre">all_slab_entries</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.all_slab_entries" title="Permalink to this definition"></a></dt>
<dd><dl>
<dt>Either a list of SlabEntry objects (note for a list, the SlabEntry must</dt><dd><p>have the adsorbates and clean_entry parameter pulgged in) or a Nested
dictionary containing a list of entries for slab calculations as
items and the corresponding Miller index of the slab as the key.
To account for adsorption, each value is a sub-dictionary with the
entry of a clean slab calculation as the sub-key and a list of
entries for adsorption calculations as the sub-value. The sub-value
can contain different adsorption configurations such as a different
site or a different coverage, however, ordinarily only the most stable
configuration for a particular coverage will be considered as the
function of the adsorbed surface energy has an intercept dependent on
the adsorption energy (ie an adsorption site with a higher adsorption
energy will always provide a higher surface energy than a site with a
lower adsorption energy). An example parameter is provided:
{(h1,k1,l1): {clean_entry1: [ads_entry1, ads_entry2, …],</p>
<blockquote>
<div><p>clean_entry2: […], …}, (h2,k2,l2): {…}}</p>
</div></blockquote>
<p>where clean_entry1 can be a pristine surface and clean_entry2 can be a
reconstructed surface while ads_entry1 can be adsorption at site 1 with
a 2x2 coverage while ads_entry2 can have a 3x3 coverage. If adsorption
entries are present (i.e. if all_slab_entries[(h,k,l)][clean_entry1]), we
consider adsorption in all plots and analysis for this particular facet.</p>
</dd>
</dl>
</dd></dl>
<p>..attribute:: color_dict</p>
<blockquote>
<div><dl class="simple">
<dt>Dictionary of colors (r,g,b,a) when plotting surface energy stability. The</dt><dd><p>keys are individual surface entries where clean surfaces have a solid
color while the corresponding adsorbed surface will be transparent.</p>
</dd>
</dl>
</div></blockquote>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.ucell_entry">
<span class="sig-name descname"><span class="pre">ucell_entry</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.ucell_entry" title="Permalink to this definition"></a></dt>
<dd><p>ComputedStructureEntry of the bulk reference for this particular material.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.ref_entries">
<span class="sig-name descname"><span class="pre">ref_entries</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.ref_entries" title="Permalink to this definition"></a></dt>
<dd><p>List of ComputedStructureEntries to be used for calculating chemical potential.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.color_dict">
<span class="sig-name descname"><span class="pre">color_dict</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.color_dict" title="Permalink to this definition"></a></dt>
<dd><p>Randomly generated dictionary of colors associated with each facet.</p>
</dd></dl>
<dl class="simple">
<dt>Object for plotting surface energy in different ways for clean and</dt><dd><p>adsorbed surfaces.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>all_slab_entries</strong> (<em>dict</em><em> or </em><em>list</em>) – Dictionary or list containing
all entries for slab calculations. See attributes.</p></li>
<li><p><strong>ucell_entry</strong> (<a class="reference internal" href="pymatgen.entries.computed_entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><em>ComputedStructureEntry</em></a>) – ComputedStructureEntry
of the bulk reference for this particular material.</p></li>
<li><p><strong>ref_entries</strong> (<em>[</em><em>ComputedStructureEntries</em><em>]</em>) – A list of entries for
each type of element to be used as a reservoir for
non-stoichiometric systems. The length of this list MUST be
n-1 where n is the number of different elements in the bulk
entry. The bulk energy term in the grand surface potential can
be defined by a summation of the chemical potentials for each
element in the system. As the bulk energy is already provided,
one can solve for one of the chemical potentials as a function
of the other chemical potetinals and bulk energy. i.e. there
are n-1 variables (chempots). e.g. if your ucell_entry is for
LiFePO4 than your ref_entries should have an entry for Li, Fe,
and P if you want to use the chempot of O as the variable.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.BE_vs_clean_SE">
<span class="sig-name descname"><span class="pre">BE_vs_clean_SE</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot_eads</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annotate_monolayer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">JPERM2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1130-L1179"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.BE_vs_clean_SE" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>For each facet, plot the clean surface energy against the most</dt><dd><p>stable binding energy.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>plot_eads</strong> (<em>bool</em>) – Option to plot the adsorption energy (binding
energy multiplied by number of adsorbates) instead.</p></li>
<li><p><strong>annotate_monolayer</strong> (<em>bool</em>) – Whether or not to label each data point
with its monolayer (adsorbate density per unit primiitve area)</p></li>
<li><p><strong>JPERM2</strong> (<em>bool</em>) – Whether to plot surface energy in /m^2 (True) or
eV/A^2 (False)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Plot of clean surface energy vs binding energy for</dt><dd><p>all facets.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>(Plot)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.area_frac_vs_chempot_plot">
<span class="sig-name descname"><span class="pre">area_frac_vs_chempot_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ref_delu</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chempot_range</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">increments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L576-L657"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.area_frac_vs_chempot_plot" title="Permalink to this definition"></a></dt>
<dd><p>1D plot. Plots the change in the area contribution
of each facet as a function of chemical potential.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ref_delu</strong> (<em>sympy Symbol</em>) – The free variable chempot with the format:
Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>chempot_range</strong> (<em>list</em>) – Min/max range of chemical potential to plot along</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>increments</strong> (<em>int</em>) – Number of data points between min/max or point
of intersection. Defaults to 10 points.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Plot of area frac on the Wulff shape</dt><dd><p>for each facet vs chemical potential.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>(pyplot)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_plot_addons">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">chempot_plot_addons</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">plt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xrange</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_el</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pad</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2.4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ylim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1094-L1128"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_plot_addons" title="Permalink to this definition"></a></dt>
<dd><p>Helper function to a chempot plot look nicer.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>plt</strong> (<em>Plot</em>) – </p></li>
<li><p><strong>xrange</strong> (<em>list</em>) – xlim parameter</p></li>
<li><p><strong>ref_el</strong> (<em>str</em>) – Element of the referenced chempot.</p></li>
<li><p><strong>axes</strong> (<em>axes</em>) – </p></li>
<li><p><strong>pad</strong> (<em>float</em>) – </p></li>
<li><p><strong>rect</strong> (<em>list</em>) – For tight layout</p></li>
<li><p><strong>ylim</strong> (<em>ylim parameter</em>) – </p></li>
</ul>
</dd>
</dl>
<p>return (Plot): Modified plot with addons.
return (Plot): Modified plot with addons.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_vs_gamma">
<span class="sig-name descname"><span class="pre">chempot_vs_gamma</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ref_delu</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chempot_range</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_index</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">JPERM2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_unstable</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ylim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_entry_labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L937-L1054"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_vs_gamma" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Plots the surface energy as a function of chemical potential.</dt><dd><p>Each facet will be associated with its own distinct colors.
Dashed lines will represent stoichiometries different from that
of the mpid’s compound. Transparent lines indicates adsorption.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ref_delu</strong> (<em>sympy Symbol</em>) – The range stability of each slab is based
on the chempot range of this chempot. Should be a sympy Symbol
object of the format: Symbol(“delu_el”) where el is the name of
the element</p></li>
<li><p><strong>chempot_range</strong> (<em>[</em><em>max_chempot</em><em>, </em><em>min_chempot</em><em>]</em>) – Range to consider the
stability of the slabs.</p></li>
<li><p><strong>miller_index</strong> (<em>list</em>) – Miller index for a specific facet to get a
dictionary for.</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>JPERM2</strong> (<em>bool</em>) – Whether to plot surface energy in /m^2 (True) or
eV/A^2 (False)</p></li>
<li><p><strong>show_unstable</strong> (<em>bool</em>) – Whether or not to show parts of the surface
energy plot outside the region of stability.</p></li>
<li><p><strong>ylim</strong> (<em>[</em><em>ymax</em><em>, </em><em>ymin</em><em>]</em>) – Range of y axis</p></li>
<li><p><strong>no_doped</strong> (<em>bool</em>) – Whether to plot for the clean slabs only.</p></li>
<li><p><strong>no_clean</strong> (<em>bool</em>) – Whether to plot for the doped slabs only.</p></li>
<li><p><strong>use_entry_labels</strong> (<em>bool</em>) – If True, will label each slab configuration
according to their given label in the SlabEntry object.</p></li>
<li><p><strong>no_label</strong> (<em>bool</em>) – Option to turn off labels.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Plot of surface energy vs chempot for all entries.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>(Plot)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_vs_gamma_plot_one">
<span class="sig-name descname"><span class="pre">chempot_vs_gamma_plot_one</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">plt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_delu</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chempot_range</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">JPERM2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L869-L935"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_vs_gamma_plot_one" title="Permalink to this definition"></a></dt>
<dd><p>Helper function to help plot the surface energy of a
single SlabEntry as a function of chemical potential.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>plt</strong> (<em>Plot</em>) – A plot.</p></li>
<li><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry" title="pymatgen.analysis.surface_analysis.SlabEntry"><em>SlabEntry</em></a>) – Entry of the slab whose surface energy we want
to plot</p></li>
<li><p><strong>ref_delu</strong> (<em>sympy Symbol</em>) – The range stability of each slab is based
on the chempot range of this chempot. Should be a sympy Symbol
object of the format: Symbol(“delu_el”) where el is the name of
the element</p></li>
<li><p><strong>chempot_range</strong> (<em>[</em><em>max_chempot</em><em>, </em><em>min_chempot</em><em>]</em>) – Range to consider the
stability of the slabs.</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>label</strong> (<em>str</em>) – Label of the slab for the legend.</p></li>
<li><p><strong>JPERM2</strong> (<em>bool</em>) – Whether to plot surface energy in /m^2 (True) or
eV/A^2 (False)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Plot of surface energy vs chemical potential for one entry.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>(Plot)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.color_palette_dict">
<span class="sig-name descname"><span class="pre">color_palette_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.35</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L832-L867"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.color_palette_dict" title="Permalink to this definition"></a></dt>
<dd><p>Helper function to assign each facet a unique color using a dictionary.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>alpha</strong> (<em>float</em>) – Degree of transparency</p>
</dd>
</dl>
<dl class="simple">
<dt>return (dict): Dictionary of colors (r,g,b,a) when plotting surface</dt><dd><p>energy stability. The keys are individual surface entries where
clean surfaces have a solid color while the corresponding adsorbed
surface will be transparent.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.get_stable_entry_at_u">
<span class="sig-name descname"><span class="pre">get_stable_entry_at_u</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">miller_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L480-L532"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.get_stable_entry_at_u" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Returns the entry corresponding to the most stable slab for a particular</dt><dd><p>facet at a specific chempot. We assume that surface energy is constant
so all free variables must be set with delu_dict, otherwise they are
assumed to be equal to delu_default.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>miller_index</strong> (<em>(</em><em>h</em><em>,</em><em>k</em><em>,</em><em>l</em><em>)</em>) – The facet to find the most stable slab in</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>no_doped</strong> (<em>bool</em>) – Consider stability of clean slabs only.</p></li>
<li><p><strong>no_clean</strong> (<em>bool</em>) – Consider stability of doped slabs only.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>SlabEntry, surface_energy (float)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.get_surface_equilibrium">
<span class="sig-name descname"><span class="pre">get_surface_equilibrium</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slab_entries</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L659-L700"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.get_surface_equilibrium" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Takes in a list of SlabEntries and calculates the chemical potentials</dt><dd><p>at which all slabs in the list coexists simultaneously. Useful for
building surface phase diagrams. Note that to solve for x equations
(x slab_entries), there must be x free variables (chemical potentials).
Adjust delu_dict as need be to get the correct number of free variables.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slab_entries</strong> (<em>array</em>) – The coefficients of the first equation</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Array containing a solution to x equations with x</dt><dd><p>variables (x-1 chemical potential and 1 surface energy)</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>(array)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.monolayer_vs_BE">
<span class="sig-name descname"><span class="pre">monolayer_vs_BE</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">plot_eads</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1056-L1092"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.monolayer_vs_BE" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Plots the binding energy as a function of monolayers (ML), i.e.</dt><dd><p>the fractional area adsorbate density for all facets. For each
facet at a specific monlayer, only plot the lowest binding energy.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>plot_eads</strong> (<em>bool</em>) – Option to plot the adsorption energy (binding
energy multiplied by number of adsorbates) instead.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Plot of binding energy vs monolayer for all facets.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>(Plot)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.set_all_variables">
<span class="sig-name descname"><span class="pre">set_all_variables</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1321-L1364"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.set_all_variables" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Sets all chemical potential values and returns a dictionary where</dt><dd><p>the key is a sympy Symbol and the value is a float (chempot).</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry" title="pymatgen.analysis.surface_analysis.SlabEntry"><em>SlabEntry</em></a>) – Computed structure entry of the slab</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dictionary of set chemical potential values</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.stable_u_range_dict">
<span class="sig-name descname"><span class="pre">stable_u_range_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chempot_range</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_delu</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_index</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dmu_at_0</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_se_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L702-L830"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.stable_u_range_dict" title="Permalink to this definition"></a></dt>
<dd><p>Creates a dictionary where each entry is a key pointing to a
chemical potential range where the surface of that entry is stable.
Does so by enumerating through all possible solutions (intersect)
for surface energies of a specific facet.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>chempot_range</strong> (<em>[</em><em>max_chempot</em><em>, </em><em>min_chempot</em><em>]</em>) – Range to consider the
stability of the slabs.</p></li>
<li><p><strong>ref_delu</strong> (<em>sympy Symbol</em>) – The range stability of each slab is based
on the chempot range of this chempot. Should be a sympy Symbol
object of the format: Symbol(“delu_el”) where el is the name of
the element</p></li>
<li><p><strong>no_doped</strong> (<em>bool</em>) – Consider stability of clean slabs only.</p></li>
<li><p><strong>no_clean</strong> (<em>bool</em>) – Consider stability of doped slabs only.</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>miller_index</strong> (<em>list</em>) – Miller index for a specific facet to get a
dictionary for.</p></li>
<li><p><strong>dmu_at_0</strong> (<em>bool</em>) – If True, if the surface energies corresponding to
the chemical potential range is between a negative and positive
value, the value is a list of three chemical potentials with the
one in the center corresponding a surface energy of 0. Uselful
in identifying unphysical ranges of surface energies and their
chemical potential range.</p></li>
<li><p><strong>return_se_dict</strong> (<em>bool</em>) – Whether or not to return the corresponding
dictionary of surface energies</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.surface_chempot_range_map">
<span class="sig-name descname"><span class="pre">surface_chempot_range_map</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">elements</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ranges</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">incr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annotate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_unphyiscal_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fontsize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1181-L1319"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.surface_chempot_range_map" title="Permalink to this definition"></a></dt>
<dd><dl class="simple">
<dt>Adapted from the get_chempot_range_map() method in the PhaseDiagram</dt><dd><p>class. Plot the chemical potential range map based on surface
energy stability. Currently works only for 2-component PDs. At
the moment uses a brute force method by enumerating through the
range of the first element chempot with a specified increment
and determines the chempot rangeo fht e second element for each
SlabEntry. Future implementation will determine the chempot range
map first by solving systems of equations up to 3 instead of 2.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>elements</strong> (<em>list</em>) – Sequence of elements to be considered as independent
variables. E.g., if you want to show the stability ranges of
all Li-Co-O phases wrt to duLi and duO, you will supply
[Element(“Li”), Element(“O”)]</p></li>
<li><p><strong>miller_index</strong> (<em>[</em><em>h</em><em>, </em><em>k</em><em>, </em><em>l</em><em>]</em>) – Miller index of the surface we are interested in</p></li>
<li><p><strong>ranges</strong> (<em>[</em><em>[</em><em>range1</em><em>]</em><em>, </em><em>[</em><em>range2</em><em>]</em><em>]</em>) – List of chempot ranges (max and min values)
for the first and second element.</p></li>
<li><p><strong>incr</strong> (<em>int</em>) – Number of points to sample along the range of the first chempot</p></li>
<li><p><strong>no_doped</strong> (<em>bool</em>) – Whether or not to include doped systems.</p></li>
<li><p><strong>no_clean</strong> (<em>bool</em>) – Whether or not to include clean systems.</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>plt</strong> (<em>Plot</em>) – Plot object to plot on. If None, will create a new plot.</p></li>
<li><p><strong>annotate</strong> (<em>bool</em>) – Whether to annotate each “phase” with the label of
the entry. If no label, uses the reduced formula</p></li>
<li><p><strong>show_unphyiscal_only</strong> (<em>bool</em>) – Whether to only show the shaded region where
surface energy is negative. Useful for drawing other chempot range maps.</p></li>
<li><p><strong>fontsize</strong> (<em>int</em>) – Font size of the annotation</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.wulff_from_chempot">
<span class="sig-name descname"><span class="pre">wulff_from_chempot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symprec</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L534-L574"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.wulff_from_chempot" title="Permalink to this definition"></a></dt>
<dd><p>Method to get the Wulff shape at a specific chemical potential.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>symprec</strong> (<em>float</em>) – See WulffShape.</p></li>
<li><p><strong>no_doped</strong> (<em>bool</em>) – Consider stability of clean slabs only.</p></li>
<li><p><strong>no_clean</strong> (<em>bool</em>) – Consider stability of doped slabs only.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The WulffShape at u_ref and u_ads.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>(<a class="reference internal" href="pymatgen.analysis.wulff.html#pymatgen.analysis.wulff.WulffShape" title="pymatgen.analysis.wulff.WulffShape">WulffShape</a>)</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">WorkFunctionAnalyzer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">locpot_along_c</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">efermi</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shift</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">blength</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3.5</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/surface_analysis.py#L1396-L1684"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<dl class="simple">
<dt>A class used for calculating the work function</dt><dd><p>from a slab model and visualizing the behavior