deploy: 564210e

_sources/content/formation-energy.ipynb

@@ -112,9 +112,9 @@
     "\n",
     "$$\n",
     "\\begin{aligned}\n",
-    "\\mu_{\\rm Ga} + \\mu_{\\rm N} &= \\Delta H_{\\rm GaN} \\\\\n",
-    "5\\mu_{\\rm Mg} + 2\\mu_{\\rm Ga} + \\mu_{\\rm N} &\\leq \\Delta H_{\\rm Mg_5Ga_2} \\\\\n",
-    "3\\mu_{\\rm Mg} + 2\\mu_{\\rm N} &\\leq \\Delta H_{\\rm Mg_3N_2} \\\\\n",
+    "\\Delta\\mu_{\\rm Ga} + \\Delta\\mu_{\\rm N} &= \\Delta H_{\\rm GaN} \\\\\n",
+    "5\\Delta\\mu_{\\rm Mg} + 2\\Delta\\mu_{\\rm Ga} + \\Delta\\mu_{\\rm N} &\\leq \\Delta H_{\\rm Mg_5Ga_2} \\\\\n",
+    "3\\Delta\\mu_{\\rm Mg} + 2\\Delta\\mu_{\\rm N} &\\leq \\Delta H_{\\rm Mg_3N_2} \\\\\n",
     "\\end{aligned}\n",
     "$$\n",
     "\n",
@@ -130,9 +130,9 @@
    "outputs": [],
    "source": [
     "for i, p in enumerate(fed.chempot_limits):\n",
-    "    print(f\"Chemical potential limits for point {i}\")\n",
+    "    print(f\"Limits for the chemical potential changes for point {i}\")\n",
     "    for k,v in p.items():\n",
-    "        print(f\"μ_{k} = {v:.2f} eV\")"
+    "        print(f\"Δμ_{k} = {v:.2f} eV\")"
    ]
   },
   {

_sources/content/freysoldt-correction.ipynb

@@ -146,7 +146,11 @@
     "        )\n",
     "        plot_plnr_avg(\n",
     "            freysoldt_results[q].metadata[\"plot_data\"][direction], ax=axs[direction, 0]\n",
-    "        )"
+    "        )\n",
+    "        axs[direction, 0].set_title(f\"q={q} direction={direction} (Python)\")\n",
+    "        axs[direction, 1].set_title(f\"q={q} direction={direction} (SXDefectAlign)\")\n",
+    "        axs[direction, 0].set_xlabel(\"\")\n",
+    "        axs[direction, 1].set_xlabel(\"\")"
    ]
   },
   {

_sources/content/nonradiative.ipynb

@@ -95,7 +95,9 @@
     "\n",
     "The potential energy surface of the defect in a particular charge state is given by:\n",
     "\n",
-    "$$\\frac{1}{2} \\omega^2 Q^2$$\n"
+    "$$\\frac{1}{2} \\omega^2 Q^2$$\n",
+    "\n",
+    "where $\\omega$ is the harmonic frequency and $Q$ is the mass-weighted displacement (configuration coordinate) of the defect as it changes between different charge states."
    ]
   },
   {

api_ref/pymatgen.analysis.defects.core.html

@@ -410,7 +410,7 @@ <h1>pymatgen.analysis.defects.core</h1>
 <td><p>Get a vacancy defect from a structure and site index.</p></td>
 </tr>
 <tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">perturb_sites</span></code>(structure, distance[, ...])</p></td>
-<td><p>Performs a random perturbation of the sites in a structure to break symmetries.</p></td>
+<td><p>Performs a random perturbation.</p></td>
 </tr>
 <tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_structure</span></code>(structure, site, defect_type)</p></td>
 <td><p>Update the structure with the defect site.</p></td>

api_ref/pymatgen.analysis.defects.utils.html

@@ -436,7 +436,7 @@ <h1>pymatgen.analysis.defects.utils</h1>
 <td><p>Find the (band, kpt, spin) index of the most localized state.</p></td>
 </tr>
 <tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_plane_spacing</span></code>(lattice)</p></td>
-<td><p>Get the cartesian spacing between periodic planes of a unit cell.</p></td>
+<td><p>Compute the plane spacing of a lattice.</p></td>
 </tr>
 <tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_zfile</span></code>(directory, base_name[, allow_missing])</p></td>
 <td><p>Find gzipped or non-gzipped versions of a file in a directory listing.</p></td>

content/formation-energy.html

@@ -496,9 +496,9 @@ <h2>Getting the Elemental Chemical Potentials<a class="headerlink" href="#gettin
 <div class="math notranslate nohighlight">
 \[\begin{split}
 \begin{aligned}
-\mu_{\rm Ga} + \mu_{\rm N} &amp;= \Delta H_{\rm GaN} \\
-5\mu_{\rm Mg} + 2\mu_{\rm Ga} + \mu_{\rm N} &amp;\leq \Delta H_{\rm Mg_5Ga_2} \\
-3\mu_{\rm Mg} + 2\mu_{\rm N} &amp;\leq \Delta H_{\rm Mg_3N_2} \\
+\Delta\mu_{\rm Ga} + \Delta\mu_{\rm N} &amp;= \Delta H_{\rm GaN} \\
+5\Delta\mu_{\rm Mg} + 2\Delta\mu_{\rm Ga} + \Delta\mu_{\rm N} &amp;\leq \Delta H_{\rm Mg_5Ga_2} \\
+3\Delta\mu_{\rm Mg} + 2\Delta\mu_{\rm N} &amp;\leq \Delta H_{\rm Mg_3N_2} \\
 \end{aligned}
 \end{split}\]</div>
 <p>Here since the defect must form in GaN the chemical potentials are pinned by the plane defined by the enthalpy of formation of GaN.
@@ -507,25 +507,25 @@ <h2>Getting the Elemental Chemical Potentials<a class="headerlink" href="#gettin
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">p</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">fed</span><span class="o">.</span><span class="n">chempot_limits</span><span class="p">):</span>
-    <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Chemical potential limits for point </span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+    <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Limits for the chemical potential changes for point </span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="n">p</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
-        <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;μ_</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s2"> = </span><span class="si">{</span><span class="n">v</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2"> eV&quot;</span><span class="p">)</span>
+        <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Δμ_</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s2"> = </span><span class="si">{</span><span class="n">v</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2"> eV&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Chemical potential limits for point 0
-μ_Mg = -1.49 eV
-μ_Ga = -1.75 eV
-μ_N = 0.00 eV
-Chemical potential limits for point 1
-μ_Mg = -0.35 eV
-μ_Ga = -0.03 eV
-μ_N = -1.71 eV
-Chemical potential limits for point 2
-μ_Mg = -0.44 eV
-μ_Ga = 0.00 eV
-μ_N = -1.75 eV
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Limits for the chemical potential changes for point 0
+Δμ_Mg = -1.49 eV
+Δμ_Ga = -1.75 eV
+Δμ_N = 0.00 eV
+Limits for the chemical potential changes for point 1
+Δμ_Mg = -0.35 eV
+Δμ_Ga = -0.03 eV
+Δμ_N = -1.71 eV
+Limits for the chemical potential changes for point 2
+Δμ_Mg = -0.44 eV
+Δμ_Ga = 0.00 eV
+Δμ_N = -1.75 eV
 </pre></div>
 </div>
 </div>

content/freysoldt-correction.html

@@ -530,6 +530,10 @@ <h1>Freysoldt Correction<a class="headerlink" href="#freysoldt-correction" title
         <span class="n">plot_plnr_avg</span><span class="p">(</span>
             <span class="n">freysoldt_results</span><span class="p">[</span><span class="n">q</span><span class="p">]</span><span class="o">.</span><span class="n">metadata</span><span class="p">[</span><span class="s2">&quot;plot_data&quot;</span><span class="p">][</span><span class="n">direction</span><span class="p">],</span> <span class="n">ax</span><span class="o">=</span><span class="n">axs</span><span class="p">[</span><span class="n">direction</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
         <span class="p">)</span>
+        <span class="n">axs</span><span class="p">[</span><span class="n">direction</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;q=</span><span class="si">{</span><span class="n">q</span><span class="si">}</span><span class="s2"> direction=</span><span class="si">{</span><span class="n">direction</span><span class="si">}</span><span class="s2"> (Python)&quot;</span><span class="p">)</span>
+        <span class="n">axs</span><span class="p">[</span><span class="n">direction</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;q=</span><span class="si">{</span><span class="n">q</span><span class="si">}</span><span class="s2"> direction=</span><span class="si">{</span><span class="n">direction</span><span class="si">}</span><span class="s2"> (SXDefectAlign)&quot;</span><span class="p">)</span>
+        <span class="n">axs</span><span class="p">[</span><span class="n">direction</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
+        <span class="n">axs</span><span class="p">[</span><span class="n">direction</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
@@ -553,7 +557,7 @@ <h1>Freysoldt Correction<a class="headerlink" href="#freysoldt-correction" title
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/12b94744957638a952621f3eba27496aaf5264deab480ae537894bb965ab24fb.png" src="../_images/12b94744957638a952621f3eba27496aaf5264deab480ae537894bb965ab24fb.png" />
+<img alt="../_images/6cc905e40d855818af0f907a2b95f8422e6ac9cab34515ab2e5fd6d532fc4c4c.png" src="../_images/6cc905e40d855818af0f907a2b95f8422e6ac9cab34515ab2e5fd6d532fc4c4c.png" />
 </div>
 </div>
 <p><em>Result from larger simulation cell</em> The LOCPOT data is too large to be included in the repository.

content/nonradiative.html

@@ -477,6 +477,7 @@ <h3>Potential energy surface<a class="headerlink" href="#potential-energy-surfac
 <p>The potential energy surface of the defect in a particular charge state is given by:</p>
 <div class="math notranslate nohighlight">
 \[\frac{1}{2} \omega^2 Q^2\]</div>
+<p>where <span class="math notranslate nohighlight">\(\omega\)</span> is the harmonic frequency and <span class="math notranslate nohighlight">\(Q\)</span> is the mass-weighted displacement (configuration coordinate) of the defect as it changes between different charge states.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span>
@@ -547,7 +548,7 @@ <h2>Evaluating the Electron-Phonon Matrix Element with PAWs<a class="headerlink"
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>The parsed WSWQ files are: [&#39;WSWQ.0&#39;, &#39;WSWQ.1&#39;, &#39;WSWQ.2&#39;]
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>The parsed WSWQ files are: [&#39;WSWQ.2&#39;, &#39;WSWQ.1&#39;, &#39;WSWQ.0&#39;]
 </pre></div>
 </div>
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Parsed 3 WSWQ files.