Update DOI URLs

README.rst

@@ -134,7 +134,7 @@ work:
     Persson, Gerbrand Ceder. *Python Materials Genomics (pymatgen) : A Robust,
     Open-Source Python Library for Materials Analysis.* Computational
     Materials Science, 2013, 68, 314-319. `doi:10.1016/j.commatsci.2012.10.028
-    <http://dx.doi.org/10.1016/j.commatsci.2012.10.028>`_
+    <https://doi.org/10.1016/j.commatsci.2012.10.028>`_
 
 In addition, some of pymatgen's functionality is based on scientific advances
 / principles developed by the computational materials scientists in our team.

docs/_modules/pymatgen/analysis/aflow_prototypes.html

@@ -62,7 +62,7 @@ <h1>Source code for pymatgen.analysis.aflow_prototypes</h1><div class="highlight
 <span class="sd">Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).</span>
 <span class="sd">The AFLOW library of crystallographic prototypes: part 1.</span>
 <span class="sd">Computational Materials Science, 136, S1-S828.</span>
-<span class="sd">http://doi.org/10.1016/j.commatsci.2017.01.017</span>
+<span class="sd">https://doi.org/10.1016/j.commatsci.2017.01.017</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="n">module_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="vm">__file__</span><span class="p">))</span>
@@ -83,7 +83,7 @@ <h1>Source code for pymatgen.analysis.aflow_prototypes</h1><div class="highlight
 <span class="sd">    Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).</span>
 <span class="sd">    The AFLOW library of crystallographic prototypes: part 1.</span>
 <span class="sd">    Computational Materials Science, 136, S1-S828.</span>
-<span class="sd">    http://doi.org/10.1016/j.commatsci.2017.01.017</span>
+<span class="sd">    https://doi.org/10.1016/j.commatsci.2017.01.017</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">initial_ltol</span><span class="o">=</span><span class="mf">0.2</span><span class="p">,</span> <span class="n">initial_stol</span><span class="o">=</span><span class="mf">0.3</span><span class="p">,</span> <span class="n">initial_angle_tol</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
@@ -135,7 +135,7 @@ <h1>Source code for pymatgen.analysis.aflow_prototypes</h1><div class="highlight
 <span class="sd">        Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).</span>
 <span class="sd">        The AFLOW library of crystallographic prototypes: part 1.</span>
 <span class="sd">        Computational Materials Science, 136, S1-S828.</span>
-<span class="sd">        http://doi.org/10.1016/j.commatsci.2017.01.017</span>
+<span class="sd">        https://doi.org/10.1016/j.commatsci.2017.01.017</span>
 
 <span class="sd">        Args:</span>
 <span class="sd">            structure: structure to match</span>

docs/_modules/pymatgen/analysis/prototypes.html

@@ -59,7 +59,7 @@ <h1>Source code for pymatgen.analysis.prototypes</h1><div class="highlight"><pre
 <span class="sd">Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).</span>
 <span class="sd">The AFLOW library of crystallographic prototypes: part 1.</span>
 <span class="sd">Computational Materials Science, 136, S1-S828.</span>
-<span class="sd">http://doi.org/10.1016/j.commatsci.2017.01.017</span>
+<span class="sd">https://doi.org/10.1016/j.commatsci.2017.01.017</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">os</span>
@@ -85,7 +85,7 @@ <h1>Source code for pymatgen.analysis.prototypes</h1><div class="highlight"><pre
 <span class="sd">    Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).</span>
 <span class="sd">    The AFLOW library of crystallographic prototypes: part 1.</span>
 <span class="sd">    Computational Materials Science, 136, S1-S828.</span>
-<span class="sd">    http://doi.org/10.1016/j.commatsci.2017.01.017</span>
+<span class="sd">    https://doi.org/10.1016/j.commatsci.2017.01.017</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">initial_ltol</span><span class="o">=</span><span class="mf">0.2</span><span class="p">,</span> <span class="n">initial_stol</span><span class="o">=</span><span class="mf">0.3</span><span class="p">,</span> <span class="n">initial_angle_tol</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
@@ -137,7 +137,7 @@ <h1>Source code for pymatgen.analysis.prototypes</h1><div class="highlight"><pre
 <span class="sd">        Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).</span>
 <span class="sd">        The AFLOW library of crystallographic prototypes: part 1.</span>
 <span class="sd">        Computational Materials Science, 136, S1-S828.</span>
-<span class="sd">        http://doi.org/10.1016/j.commatsci.2017.01.017</span>
+<span class="sd">        https://doi.org/10.1016/j.commatsci.2017.01.017</span>
 
 <span class="sd">        Args:</span>
 <span class="sd">            structure: structure to match</span>

docs/_modules/pymatgen/analysis/quasiharmonic.html

@@ -56,8 +56,8 @@ <h1>Source code for pymatgen.analysis.quasiharmonic</h1><div class="highlight"><
 
 <span class="sd">See the following papers for more info:</span>
 
-<span class="sd">    http://doi.org/10.1016/j.comphy.2003.12.001 (2004)</span>
-<span class="sd">    http://doi.org/10.1103/PhysRevB.90.174107 (2014)</span>
+<span class="sd">    https://doi.org/10.1016/j.comphy.2003.12.001 (2004)</span>
+<span class="sd">    https://doi.org/10.1103/PhysRevB.90.174107 (2014)</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">defaultdict</span>

docs/_modules/pymatgen/command_line/critic2_caller.html

@@ -77,11 +77,11 @@ <h1>Source code for pymatgen.command_line.critic2_caller</h1><div class="highlig
 
 <span class="sd">A. Otero-de-la-Roza, E. R. Johnson and V. Luaña,</span>
 <span class="sd">Comput. Phys. Commun. 185, 1007-1018 (2014)</span>
-<span class="sd">(http://dx.doi.org/10.1016/j.cpc.2013.10.026)</span>
+<span class="sd">(https://doi.org/10.1016/j.cpc.2013.10.026)</span>
 
 <span class="sd">A. Otero-de-la-Roza, M. A. Blanco, A. Martín Pendás and</span>
 <span class="sd">V. Luaña, Comput. Phys. Commun. 180, 157–166 (2009)</span>
-<span class="sd">(http://dx.doi.org/10.1016/j.cpc.2008.07.018)</span>
+<span class="sd">(https://doi.org/10.1016/j.cpc.2008.07.018)</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">os</span>

docs/_modules/pymatgen/ext/crystalsai.html

@@ -71,7 +71,7 @@ <h1>Source code for pymatgen.ext.crystalsai</h1><div class="highlight"><pre>
 <span class="sd">    For the details of MEGNet and benchmarks, please refer to the following work:</span>
 <span class="sd">    Chen, C.; Ye, W.; Zuo, Y.; Zheng, C.; Ong, S. P. &lt;i&gt;Graph Networks as a Universal Machine Learning Framework</span>
 <span class="sd">        for Molecules and Crystals.&lt;/i&gt; Chemistry of Materials 2019, acs.chemmater.9b01294.</span>
-<span class="sd">     DOI: &lt;a href=&quot;http://dx.doi.org/10.1021/acs.chemmater.9b01294&quot;&gt;10.1021/acs.chemmater.9b01294&lt;/a&gt;.&lt;/p&gt;</span>
+<span class="sd">     DOI: &lt;a href=&quot;https://doi.org/10.1021/acs.chemmater.9b01294&quot;&gt;10.1021/acs.chemmater.9b01294&lt;/a&gt;.&lt;/p&gt;</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>

docs/_modules/pymatgen/ext/matproj.html

@@ -1230,7 +1230,7 @@ <h1>Source code for pymatgen.ext.matproj</h1><div class="highlight"><pre>
 <span class="sd">        Tran, R., Xu, Z., Radhakrishnan, B., Winston, D., Sun, W., Persson, K.</span>
 <span class="sd">        A., &amp; Ong, S. P. (2016). Data Descripter: Surface energies of elemental</span>
 <span class="sd">        crystals. Scientific Data, 3(160080), 1–13.</span>
-<span class="sd">        http://dx.doi.org/10.1038/sdata.2016.80</span>
+<span class="sd">        https://doi.org/10.1038/sdata.2016.80</span>
 
 <span class="sd">        Args:</span>
 <span class="sd">            material_id (str): Materials Project material_id, e.g. &#39;mp-123&#39;.</span>

docs/index.html

@@ -627,7 +627,7 @@ <h2>How to cite pymatgen<a class="headerlink" href="#how-to-cite-pymatgen" title
 Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent Chevrier, Kristin A.
 Persson, Gerbrand Ceder. <em>Python Materials Genomics (pymatgen) : A Robust,
 Open-Source Python Library for Materials Analysis.</em> Computational
-Materials Science, 2013, 68, 314–319. <a class="reference external" href="http://dx.doi.org/10.1016/j.commatsci.2012.10.028">doi:10.1016/j.commatsci.2012.10.028</a></p>
+Materials Science, 2013, 68, 314–319. <a class="reference external" href="https://doi.org/10.1016/j.commatsci.2012.10.028">doi:10.1016/j.commatsci.2012.10.028</a></p>
 </div></blockquote>
 <p>In addition, some of pymatgen’s functionality is based on scientific advances / principles developed by various
 scientists. Please refer to the <a class="reference internal" href="references.html"><span class="doc">references page</span></a> for citation info.</p>

docs/introduction.html

@@ -647,7 +647,7 @@ <h2>How to cite pymatgen<a class="headerlink" href="#how-to-cite-pymatgen" title
 Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent Chevrier, Kristin A.
 Persson, Gerbrand Ceder. <em>Python Materials Genomics (pymatgen) : A Robust,
 Open-Source Python Library for Materials Analysis.</em> Computational
-Materials Science, 2013, 68, 314–319. <a class="reference external" href="http://dx.doi.org/10.1016/j.commatsci.2012.10.028">doi:10.1016/j.commatsci.2012.10.028</a></p>
+Materials Science, 2013, 68, 314–319. <a class="reference external" href="https://doi.org/10.1016/j.commatsci.2012.10.028">doi:10.1016/j.commatsci.2012.10.028</a></p>
 </div></blockquote>
 <p>In addition, some of pymatgen’s functionality is based on scientific advances / principles developed by various
 scientists. Please refer to the <a class="reference internal" href="references.html"><span class="doc">references page</span></a> for citation info.</p>

docs/pymatgen.analysis.prototypes.html

@@ -211,7 +211,7 @@
 <p>Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).
 The AFLOW library of crystallographic prototypes: part 1.
 Computational Materials Science, 136, S1-S828.
-<a class="reference external" href="http://doi.org/10.1016/j.commatsci.2017.01.017">http://doi.org/10.1016/j.commatsci.2017.01.017</a></p>
+<a class="reference external" href="https://doi.org/10.1016/j.commatsci.2017.01.017">https://doi.org/10.1016/j.commatsci.2017.01.017</a></p>
 <dl class="py class">
 <dt id="pymatgen.analysis.prototypes.AflowPrototypeMatcher">
 <em class="property">class </em><code class="sig-name descname">AflowPrototypeMatcher</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">initial_ltol</span><span class="o">=</span><span class="default_value">0.2</span></em>, <em class="sig-param"><span class="n">initial_stol</span><span class="o">=</span><span class="default_value">0.3</span></em>, <em class="sig-param"><span class="n">initial_angle_tol</span><span class="o">=</span><span class="default_value">5</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2022.0.15/pymatgen/core/../analysis/prototypes.py#L28-L113"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.prototypes.AflowPrototypeMatcher" title="Permalink to this definition">¶</a></dt>
@@ -225,7 +225,7 @@
 <p>Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).
 The AFLOW library of crystallographic prototypes: part 1.
 Computational Materials Science, 136, S1-S828.
-<a class="reference external" href="http://doi.org/10.1016/j.commatsci.2017.01.017">http://doi.org/10.1016/j.commatsci.2017.01.017</a></p>
+<a class="reference external" href="https://doi.org/10.1016/j.commatsci.2017.01.017">https://doi.org/10.1016/j.commatsci.2017.01.017</a></p>
 <p>Tolerances as defined in StructureMatcher. Tolerances will be
 gradually decreased until only a single match is found (if possible).</p>
 <dl class="field-list simple">
@@ -248,7 +248,7 @@
 Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).
 The AFLOW library of crystallographic prototypes: part 1.
 Computational Materials Science, 136, S1-S828.
-<a class="reference external" href="http://doi.org/10.1016/j.commatsci.2017.01.017">http://doi.org/10.1016/j.commatsci.2017.01.017</a></p>
+<a class="reference external" href="https://doi.org/10.1016/j.commatsci.2017.01.017">https://doi.org/10.1016/j.commatsci.2017.01.017</a></p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><p><strong>structure</strong> – structure to match</p>

docs/pymatgen.analysis.quasiharmonic.html

@@ -208,8 +208,8 @@
 be used to compute thermal properties.</p>
 <p>See the following papers for more info:</p>
 <blockquote>
-<div><p><a class="reference external" href="http://doi.org/10.1016/j.comphy.2003.12.001">http://doi.org/10.1016/j.comphy.2003.12.001</a> (2004)
-<a class="reference external" href="http://doi.org/10.1103/PhysRevB.90.174107">http://doi.org/10.1103/PhysRevB.90.174107</a> (2014)</p>
+<div><p><a class="reference external" href="https://doi.org/10.1016/j.comphy.2003.12.001">https://doi.org/10.1016/j.comphy.2003.12.001</a> (2004)
+<a class="reference external" href="https://doi.org/10.1103/PhysRevB.90.174107">https://doi.org/10.1103/PhysRevB.90.174107</a> (2014)</p>
 </div></blockquote>
 <dl class="py class">
 <dt id="pymatgen.analysis.quasiharmonic.QuasiharmonicDebyeApprox">

docs/pymatgen.analysis.solar.slme.html

@@ -211,7 +211,7 @@
 <a class="reference external" href="https://github.com/usnistgov/jarvis">https://github.com/usnistgov/jarvis</a></p>
 <dl class="simple">
 <dt>References: 1) <a class="reference external" href="https://doi.org/10.1021/acs.chemmater.9b02166">https://doi.org/10.1021/acs.chemmater.9b02166</a>  &amp;</dt><dd><ol class="arabic simple" start="2">
-<li><p><a class="reference external" href="http://dx.doi.org/10.1103/PhysRevLett.108.068701">http://dx.doi.org/10.1103/PhysRevLett.108.068701</a></p></li>
+<li><p><a class="reference external" href="https://doi.org/10.1103/PhysRevLett.108.068701">https://doi.org/10.1103/PhysRevLett.108.068701</a></p></li>
 </ol>
 </dd>
 </dl>

docs/pymatgen.command_line.critic2_caller.html

@@ -233,10 +233,10 @@
 <p>If you use this module, please cite the following:</p>
 <p>A. Otero-de-la-Roza, E. R. Johnson and V. Luaña,
 Comput. Phys. Commun. 185, 1007-1018 (2014)
-(<a class="reference external" href="http://dx.doi.org/10.1016/j.cpc.2013.10.026">http://dx.doi.org/10.1016/j.cpc.2013.10.026</a>)</p>
+(<a class="reference external" href="https://doi.org/10.1016/j.cpc.2013.10.026">https://doi.org/10.1016/j.cpc.2013.10.026</a>)</p>
 <p>A. Otero-de-la-Roza, M. A. Blanco, A. Martín Pendás and
 V. Luaña, Comput. Phys. Commun. 180, 157–166 (2009)
-(<a class="reference external" href="http://dx.doi.org/10.1016/j.cpc.2008.07.018">http://dx.doi.org/10.1016/j.cpc.2008.07.018</a>)</p>
+(<a class="reference external" href="https://doi.org/10.1016/j.cpc.2008.07.018">https://doi.org/10.1016/j.cpc.2008.07.018</a>)</p>
 <dl class="py class">
 <dt id="pymatgen.command_line.critic2_caller.Critic2Analysis">
 <em class="property">class </em><code class="sig-name descname">Critic2Analysis</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">structure</span></em>, <em class="sig-param"><span class="n">stdout</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">stderr</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">cpreport</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">yt</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">zpsp</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2022.0.15/pymatgen/core/../command_line/critic2_caller.py#L400-L904"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.Critic2Analysis" title="Permalink to this definition">¶</a></dt>

docs/pymatgen.ext.crystalsai.html

@@ -223,7 +223,7 @@
 <div><blockquote>
 <div><p>for Molecules and Crystals.&lt;/i&gt; Chemistry of Materials 2019, acs.chemmater.9b01294.</p>
 </div></blockquote>
-<p>DOI: &lt;a href=”<a class="reference external" href="http://dx.doi.org/10.1021/acs.chemmater.9b01294">http://dx.doi.org/10.1021/acs.chemmater.9b01294</a>”&gt;10.1021/acs.chemmater.9b01294&lt;/a&gt;.&lt;/p&gt;</p>
+<p>DOI: &lt;a href=”<a class="reference external" href="https://doi.org/10.1021/acs.chemmater.9b01294">https://doi.org/10.1021/acs.chemmater.9b01294</a>”&gt;10.1021/acs.chemmater.9b01294&lt;/a&gt;.&lt;/p&gt;</p>
 </div></blockquote>
 <p>Init for Rester.</p>
 <dl class="py method">

docs/pymatgen.ext.matproj.html

@@ -859,7 +859,7 @@
 <p>Tran, R., Xu, Z., Radhakrishnan, B., Winston, D., Sun, W., Persson, K.
 A., &amp; Ong, S. P. (2016). Data Descripter: Surface energies of elemental
 crystals. Scientific Data, 3(160080), 1–13.
-<a class="reference external" href="http://dx.doi.org/10.1038/sdata.2016.80">http://dx.doi.org/10.1038/sdata.2016.80</a></p>
+<a class="reference external" href="https://doi.org/10.1038/sdata.2016.80">https://doi.org/10.1038/sdata.2016.80</a></p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">

docs/references.html

@@ -300,12 +300,12 @@ <h2>pymatgen.io.zeo<a class="headerlink" href="#pymatgen-io-zeo" title="Permalin
 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
-&lt;http://dx.doi.org/10.1016/j.micromeso.2011.08.020&gt;`_.
+&lt;https://doi.org/10.1016/j.micromeso.2011.08.020&gt;`_.
 
 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
-&lt;http://dx.doi.org/10.1021/ci200386x&gt;`_.
+&lt;https://doi.org/10.1021/ci200386x&gt;`_.
 </pre></div>
 </div>
 </div>

docs_rst/introduction.rst

@@ -500,7 +500,7 @@ If you use pymatgen in your research, please consider citing the following work:
     Persson, Gerbrand Ceder. *Python Materials Genomics (pymatgen) : A Robust,
     Open-Source Python Library for Materials Analysis.* Computational
     Materials Science, 2013, 68, 314–319. `doi:10.1016/j.commatsci.2012.10.028
-    <http://dx.doi.org/10.1016/j.commatsci.2012.10.028>`_
+    <https://doi.org/10.1016/j.commatsci.2012.10.028>`_
 
 In addition, some of pymatgen's functionality is based on scientific advances / principles developed by various
 scientists. Please refer to the :doc:`references page </references>` for citation info.

docs_rst/references.rst

@@ -122,9 +122,9 @@ consider citing the following publications::
     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>`_.
+    <https://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>`_.
+    <https://doi.org/10.1021/ci200386x>`_.