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<title>References — pymatgen 2019.5.1 documentation</title>
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<div class="section" id="references">
<h1>References<a class="headerlink" href="#references" title="Permalink to this headline">¶</a></h1>
<p>Some of pymatgen’s functionality is based on scientific advances / principles
developed by various scientists. If you use some of these functionality in
your research, you may wish to consider citing the following works:</p>
<div class="section" id="pymatgen-analysis-path-finder">
<h2>pymatgen.analysis.path_finder<a class="headerlink" href="#pymatgen-analysis-path-finder" title="Permalink to this headline">¶</a></h2>
<p>The path finder code, which finds diffusion paths through a structure based on
a given potential field, is written by the Ceder group at UC Berkley:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Rong</span><span class="p">,</span> <span class="n">Z</span><span class="o">.</span><span class="p">,</span> <span class="n">Kitchaev</span><span class="p">,</span> <span class="n">D</span><span class="o">.</span><span class="p">,</span> <span class="n">Canepa</span><span class="p">,</span> <span class="n">P</span><span class="o">.</span><span class="p">,</span> <span class="n">Huang</span><span class="p">,</span> <span class="n">W</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">2016</span><span class="p">)</span><span class="o">.</span>
<span class="n">An</span> <span class="n">efficient</span> <span class="n">algorithm</span> <span class="k">for</span> <span class="n">finding</span> <span class="n">the</span> <span class="n">minimum</span> <span class="n">energy</span> <span class="n">path</span> <span class="k">for</span> <span class="n">cation</span>
<span class="n">migration</span> <span class="ow">in</span> <span class="n">ionic</span> <span class="n">materials</span><span class="o">.</span> <span class="n">The</span> <span class="n">Journal</span> <span class="n">of</span> <span class="n">Chemical</span> <span class="n">Physics</span><span class="p">,</span> <span class="mi">145</span><span class="p">(</span><span class="mi">7</span><span class="p">),</span>
<span class="mf">74112.</span> <span class="n">doi</span><span class="p">:</span><span class="mf">10.1063</span><span class="o">/</span><span class="mf">1.4960790</span>
</pre></div>
</div>
</div>
<div class="section" id="pymatgen-core-surface-and-pymatgen-analysis-wulff">
<h2>pymatgen.core.surface and pymatgen.analysis.wulff<a class="headerlink" href="#pymatgen-core-surface-and-pymatgen-analysis-wulff" title="Permalink to this headline">¶</a></h2>
<p>The surface generation code, which can automatically generate surfaces based
on any crystal, and the Wulff code, which plots the Wulff shape given a
crystal and surface energies, are written by the Materials Virtual Lab:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Tran</span><span class="p">,</span> <span class="n">R</span><span class="o">.</span><span class="p">;</span> <span class="n">Xu</span><span class="p">,</span> <span class="n">Z</span><span class="o">.</span><span class="p">;</span> <span class="n">Radhakrishnan</span><span class="p">,</span> <span class="n">B</span><span class="o">.</span><span class="p">;</span> <span class="n">Winston</span><span class="p">,</span> <span class="n">D</span><span class="o">.</span><span class="p">;</span> <span class="n">Sun</span><span class="p">,</span> <span class="n">W</span><span class="o">.</span><span class="p">;</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="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="n">Surface</span> <span class="n">energies</span> <span class="n">of</span> <span class="n">elemental</span> <span class="n">crystals</span><span class="p">,</span> <span class="n">Sci</span><span class="o">.</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="o">.</span><span class="mf">2016.80</span><span class="o">.</span>
</pre></div>
</div>
<p>and contains elements from the following publication:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>Sun, W.; Ceder, G. Efficient creation and convergence of surface slabs,
Surface Science, 2013, 617, 53–59, doi:10.1016/j.susc.2013.05.016.
</pre></div>
</div>
</div>
<div class="section" id="pymatgen-io-vasp-sets">
<h2>pymatgen.io.vasp.sets<a class="headerlink" href="#pymatgen-io-vasp-sets" title="Permalink to this headline">¶</a></h2>
<p>The MIT parameter sets, which are optimized for high-throughput computing, are
outlined the following work:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>Jain, A.; Hautier, G.; Moore, C. J.; Ong, S. P.; Fischer, C. C.;
Mueller, T.; Persson, K. A.; Ceder, G. A high-throughput infrastructure for
density functional theory calculations, Comput. Mater. Sci., 2011, 50,
2295–2310, doi:10.1016/j.commatsci.2011.02.023.
</pre></div>
</div>
</div>
<div class="section" id="pymatgen-phasediagram">
<h2>pymatgen.phasediagram<a class="headerlink" href="#pymatgen-phasediagram" title="Permalink to this headline">¶</a></h2>
<p>The phase diagram code, in particular the grand canonical phase diagram
analysis, is based on the work of Ong et al. and are used in following works:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>Ong, S. P.; Wang, L.; Kang, B.; Ceder, G. Li−Fe−P−O2 Phase Diagram from
First Principles Calculations, Chem. Mater., 2008, 20, 1798–1807,
doi:10.1021/cm702327g.
Ong, S. P.; Jain, A.; Hautier, G.; Kang, B.; Ceder, G. Thermal stabilities
of delithiated olivine MPO4 (M=Fe, Mn) cathodes investigated using first
principles calculations, Electrochem. commun., 2010, 12, 427–430,
doi:10.1016/j.elecom.2010.01.010.
</pre></div>
</div>
</div>
<div class="section" id="pymatgen-entries-compatibility">
<h2>pymatgen.entries.compatibility<a class="headerlink" href="#pymatgen-entries-compatibility" title="Permalink to this headline">¶</a></h2>
<p>The compatibility processing, which allows mixing of GGA and GGA+U runs that
have been calculated using the MaterialsProjectVaspInputSet or MITVaspInputSet,
is based on the following work:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Jain</span><span class="p">,</span> <span class="n">A</span><span class="o">.</span><span class="p">;</span> <span class="n">Hautier</span><span class="p">,</span> <span class="n">G</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="n">Moore</span><span class="p">,</span> <span class="n">C</span><span class="o">.</span> <span class="n">J</span><span class="o">.</span><span class="p">;</span> <span class="n">Fischer</span><span class="p">,</span> <span class="n">C</span><span class="o">.</span> <span class="n">C</span><span class="o">.</span><span class="p">;</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="n">Ceder</span><span class="p">,</span> <span class="n">G</span><span class="o">.</span> <span class="n">Formation</span> <span class="n">enthalpies</span> <span class="n">by</span> <span class="n">mixing</span> <span class="n">GGA</span> <span class="ow">and</span> <span class="n">GGA</span><span class="o">+</span><span class="n">U</span>
<span class="n">calculations</span><span class="p">,</span> <span class="n">Phys</span><span class="o">.</span> <span class="n">Rev</span><span class="o">.</span> <span class="n">B</span><span class="p">,</span> <span class="mi">2011</span><span class="p">,</span> <span class="mi">84</span><span class="p">,</span> <span class="mi">45115</span><span class="p">,</span> <span class="n">doi</span><span class="p">:</span><span class="mf">10.1103</span><span class="o">/</span><span class="n">PhysRevB</span><span class="o">.</span><span class="mf">84.045115</span><span class="o">.</span>
</pre></div>
</div>
</div>
<div class="section" id="pymatgen-matproj">
<h2>pymatgen.matproj<a class="headerlink" href="#pymatgen-matproj" title="Permalink to this headline">¶</a></h2>
<p>The matproj package contains an interface to the <a class="reference external" href="http://www.materialsproject.org/open">Materials Project REST API</a> (Materials API). If you use data
from the Materials Project, please cite the following works:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>Jain, A.; Ong, S. P.; Hautier, G.; Chen, W.; Richards, W. D.; Dacek,
S.; Cholia, S.; Gunter, D.; Skinner, D.; Ceder, G.; Persson, K. A.
Commentary: The Materials Project: A materials genome approach to
accelerating materials innovation, APL Mater., 2013, 1, 11002,
doi:10.1063/1.4812323.
Ong, S. P.; Cholia, S.; Jain, A.; Brafman, M.; Gunter, D.; Ceder, G.;
Persson, K. a. The Materials Application Programming Interface (API): A
simple, flexible and efficient API for materials data based on
REpresentational State Transfer (REST) principles, Comput. Mater. Sci.,
2015, 97, 209–215, doi:10.1016/j.commatsci.2014.10.037.
</pre></div>
</div>
</div>
<div class="section" id="pymatgen-symmetry">
<h2>pymatgen.symmetry<a class="headerlink" href="#pymatgen-symmetry" title="Permalink to this headline">¶</a></h2>
<p>The symmetry package is based on the excellent spglib developed by Atz Togo. For
more information, please refer to Atz Togo’s site at
<a class="reference external" href="http://spglib.sourceforge.net/">http://spglib.sourceforge.net/</a>.</p>
</div>
<div class="section" id="pymatgen-command-line-bader-caller">
<h2>pymatgen.command_line.bader_caller<a class="headerlink" href="#pymatgen-command-line-bader-caller" title="Permalink to this headline">¶</a></h2>
<p>This module implements an interface to the Henkelmann et al.’s excellent
Fortran code for calculating a Bader charge analysis. Please cite the
following:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>Henkelman, G., Arnaldsson, A., & Jónsson, H. (2006). A fast and robust
algorithm for Bader decomposition of charge density. Computational
Materials Science, 36(3), 354–360. doi:10.1016/j.commatsci.2005.04.010
</pre></div>
</div>
</div>
<div class="section" id="pymatgen-io-feff">
<h2>pymatgen.io.feff<a class="headerlink" href="#pymatgen-io-feff" title="Permalink to this headline">¶</a></h2>
<p>This module implements an io interface for FEFF calculations. Please
acknowledge the contribution of Alan Dozier, UKY.</p>
</div>
<div class="section" id="pymatgen-io-zeo">
<h2>pymatgen.io.zeo<a class="headerlink" href="#pymatgen-io-zeo" title="Permalink to this headline">¶</a></h2>
<p>This implements an interface to the excellent Zeo++ code base. Please
consider citing the following publications:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>T.F. Willems, C.H. Rycroft, M. Kazi, J.C. Meza, and M. Haranczyk,
Algorithms and tools for high-throughput geometry- based analysis of
crystalline porous materials, Microporous and Mesoporous Materials,
149 (2012) 134-141, `doi:10.1016/j.micromeso.2011.08.020
<http://dx.doi.org/10.1016/j.micromeso.2011.08.020>`_.
R.L. Martin, B. Smit, and M. Haranczyk, Addressing challenges of
identifying geometrically diverse sets of crystalline porous materials,
J. Chem. Information and Modelling, `doi:10.1021/ci200386x
<http://dx.doi.org/10.1021/ci200386x>`_.
</pre></div>
</div>
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<li><a class="reference internal" href="#">References</a><ul>
<li><a class="reference internal" href="#pymatgen-analysis-path-finder">pymatgen.analysis.path_finder</a></li>
<li><a class="reference internal" href="#pymatgen-core-surface-and-pymatgen-analysis-wulff">pymatgen.core.surface and pymatgen.analysis.wulff</a></li>
<li><a class="reference internal" href="#pymatgen-io-vasp-sets">pymatgen.io.vasp.sets</a></li>
<li><a class="reference internal" href="#pymatgen-phasediagram">pymatgen.phasediagram</a></li>
<li><a class="reference internal" href="#pymatgen-entries-compatibility">pymatgen.entries.compatibility</a></li>
<li><a class="reference internal" href="#pymatgen-matproj">pymatgen.matproj</a></li>
<li><a class="reference internal" href="#pymatgen-symmetry">pymatgen.symmetry</a></li>
<li><a class="reference internal" href="#pymatgen-command-line-bader-caller">pymatgen.command_line.bader_caller</a></li>
<li><a class="reference internal" href="#pymatgen-io-feff">pymatgen.io.feff</a></li>
<li><a class="reference internal" href="#pymatgen-io-zeo">pymatgen.io.zeo</a></li>
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