[skip ci] Updates

_sources/publications/readme.md.txt

@@ -15,7 +15,11 @@
 [Openbte: a solver for ab-initio phonon transport in multidimensional structures](https://arxiv.org/abs/2106.02764)
 
 
-## 2024 (5)
+## 2024 (7)
+
+* Fredrik Eriksson, [Beyond Perturbation: Modeling Anharmonicity in Materials](https://research.chalmers.se/publication/540860/file/540860_Fulltext.pdf)
+
+* Haoyu Dong,  Zhiqiang Li,  Baole Sun,  Yanguang Zhou,  Linhua Liu, Jia-Yue Yang, [Thermal transport in disordered wurtzite ScAlN alloys using machine learning interatomic potentials](https://www.sciencedirect.com/science/article/pii/S2352492824011942?casa_token=c7LgMcZwdLsAAAAA:0d5iitbkKJ-Y0v90-K6ZjyiXrmk4yqyYMHmGhNuWzhChNFEPWyYODKaUbxkWKReY5dc6lss) 
 
 * Philip Yox, Frank T Cerasoli, Arka Sarkar, Genevieve Amobi, Gayatri Viswanathan, Jackson Voyles, Oleg l Lebedev, Davide Donadio, Kirill Kovnir[Organizing Chaos: Boosting Thermoelectric Properties by Ordering the Clathrate Framework of Ba8Cu16As30](https://pubs.acs.org/doi/abs/10.1021/acs.chemmater.4c00419)
 

docsource/api_forceconstants.html

@@ -647,40 +647,42 @@ <h2 id="api-reference">API Reference<a class="headerlink" href="#api-reference"
 <dl class="py class">
 <dt class="sig sig-object py" id="kaldo.forceconstants.ForceConstants">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">kaldo.forceconstants.</span></span><span class="sig-name descname"><span class="pre">ForceConstants</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">supercell</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(1,</span> <span class="pre">1,</span> <span class="pre">1)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">third_supercell</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">folder</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'displacement'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">distance_threshold</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 internal" href="../_modules/kaldo/forceconstants.html#ForceConstants"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#kaldo.forceconstants.ForceConstants" title="Permalink to this definition">¶</a></dt>
-<dd><p>The ForceConstants class creates objects that store the system information and load (or calculate) force constant
-matrices (IFCs) to be used by an instance of the Phonon class.</p>
+<dd><p>Class for constructing the finite difference object to calculate
+the second/third order force constant matrices after providing the
+unit cell geometry and calculator information.</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>atoms</strong> (<em>ase.Atoms</em>) – The atoms to study. This is required to be an ASE Atoms object, and if you would like to calculate the IFCs in
-kALDo, it should have a calculator object set.</p></li>
-<li><p><strong>supercell</strong> (<em>(</em><em>int</em><em>, </em><em>int</em><em>, </em><em>int</em><em>)</em>) – Size of supercell given by the number of repetitions (l, m, n) of the unit cell in each direction. You should be
-able to calculate this by dividing the size of the supercell by the size of the unit cell in orthorhombic cells,
-but may be more complicated for other cell types.
-Default: (1, 1, 1)</p></li>
-<li><p><strong>third_supercell</strong> (<em>(</em><em>int</em><em>, </em><em>int</em><em>, </em><em>int</em><em>)</em><em>, </em><em>optional</em>) – This argument should be used if you are loading force constants from an external source in the event that the
-second and third order forces were calculated on different supercells. If not provided, we assume those
-supercells were equivalent. This argument is most likely to be used for those with ab initio calculations, where
-third order force constants are regularly calculated on smaller supercells to save computational cost.
-Default: self.supercell</p></li>
-<li><p><strong>folder</strong> (<em>str</em><em>, </em><em>optional</em>) – Name to be used for the displacement information folder, in the event you would like to save to a custom
-location. You can adjust the default value on line 13 of this file.
-Default: “displacement”</p></li>
-<li><p><strong>distance_threshold</strong> (<em>float</em><em>, </em><em>optional</em>) – If the distance between two atoms exceeds threshold, the forces will be ignored when calculating both harmonic
-(e.g. frequency, velocity) and anharmonic (e.g. lifetimes) phonon properties. This is useful for systems with
-coulomb forces or other long range interactions.
-Default: None</p></li>
+<li><p><strong>atoms</strong> (<em>Tabulated xyz files</em><em> or </em><em>ASE Atoms object</em>) – The atoms to work on.</p></li>
+<li><p><strong>supercell</strong> – Size of supercell given by the number of repetitions (l, m, n) of
+the small unit cell in each direction.
+Defaults to (1, 1, 1)</p></li>
+<li><p><strong>third_supercell</strong> (<em>tuple</em><em>, </em><em>optional</em>) – Same as supercell, but for the third order force constant matrix.
+If not provided, it’s copied from supercell.
+Defaults to <img alt="self.supercell" class="math" src="../_images/math/11c0006d15164d9da615ed3ccfd97139860f7f16.png"/></p></li>
+<li><p><strong>folder</strong> (<em>str</em><em>, </em><em>optional</em>) – Name to be used for the displacement information folder.
+Defaults to ‘displacement’</p></li>
+<li><p><strong>distance_threshold</strong> (<em>float</em><em>, </em><em>optional</em>) – If the distance between two atoms exceeds threshold, the interatomic
+force is ignored.
+Defaults to <img alt="None" class="math" src="../_images/math/66f3449a3b20a6309557813edf86759218d71d30.png"/></p></li>
 </ul>
 </dd>
 </dl>
 <p class="rubric">Methods</p>
 <table class="autosummary longtable docutils align-default">
 <tbody>
 <tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_folder</span></code>(folder[, supercell, format, ...])</p></td>
-<td><p>Initializes a ForceConstants object from data in the folder provided.</p></td>
+<td><p>Create a finite difference object from a folder</p></td>
 </tr>
 <tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">unfold_third_order</span></code>([reduced_third, ...])</p></td>
-<td><p>This method extrapolates a third order force constant matrix from a unit cell into a matrix for the full supercell.</p></td>
+<td><p>This method extrapolates a third order force constant matrix from a unit cell into a matrix for a larger supercell.</p></td>
+</tr>
+</tbody>
+</table>
+<table>
+<tbody>
+<tr class="row-odd"><td><p><strong>elastic_prop</strong></p></td>
+<td></td>
 </tr>
 </tbody>
 </table>

docsource/introduction.html

@@ -682,12 +682,12 @@ <h2 id="Alternative-Storage">Alternative Storage<a class="headerlink" href="#Alt
 </section>
 <section id="Code-Architecture">
 <h1 id="Code-Architecture">Code Architecture<a class="headerlink" href="#Code-Architecture" title="Permalink to this heading">¶</a></h1>
-<p><img alt="1f34a03d95d8472d80ef172e69ee8108" class="no-scaled-link" src="../_images/class_diagram.png" style="width: 650px;"/></p>
+<p><img alt="1d16f24dbc464e1d96cd41f6d157aa0a" class="no-scaled-link" src="../_images/class_diagram.png" style="width: 650px;"/></p>
 </section>
 <section id="Main-Features">
 <h1 id="Main-Features">Main Features<a class="headerlink" href="#Main-Features" title="Permalink to this heading">¶</a></h1>
 <p>Below we illustrate the main features of the code</p>
-<p><img alt="e101770b53ba4218b1bdff68e2a933dc" class="no-scaled-link" src="../_images/features.png" style="width: 650px;"/></p>
+<p><img alt="abeef008cc284c0ab3676f8865b73e26" class="no-scaled-link" src="../_images/features.png" style="width: 650px;"/></p>
 </section>
 <section id="Examples">
 <h1 id="Examples">Examples<a class="headerlink" href="#Examples" title="Permalink to this heading">¶</a></h1>
@@ -716,7 +716,7 @@ <h1 id="Copyright">Copyright<a class="headerlink" href="#Copyright" title="Perma
 </section>
 <section id="Acknowledgements">
 <h1 id="Acknowledgements">Acknowledgements<a class="headerlink" href="#Acknowledgements" title="Permalink to this heading">¶</a></h1>
-<p><img alt="47084542a8354efbae68d83c73f3704f" class="no-scaled-link" src="../_images/funding.png" style="width: 650px;"/></p>
+<p><img alt="2aea465f0a07422ab9016cf6c7a064e5" class="no-scaled-link" src="../_images/funding.png" style="width: 650px;"/></p>
 <p>We gratefully acknowledge support by the Investment Software Fellowships (grant No. ACI-1547580-479590) of the NSF Molecular Sciences Software Institute (grant No. ACI-1547580) at Virginia Tech.</p>
 <p>MolSSI builds open source software and data which serves the computational molecular science community. <a class="reference external" href="https://molssi.org/software-projects/">Explore MolSSI’s software infrastructure projects.</a></p>
 </section>

docsource/theory.html

@@ -643,7 +643,7 @@ <h2 id="Quasi-Harmonic-Green-Kubo">Quasi-Harmonic Green Kubo<a class="headerlink
 <section id="Benchmarks-applications">
 <h1 id="Benchmarks-applications">Benchmarks applications<a class="headerlink" href="#Benchmarks-applications" title="Permalink to this heading">¶</a></h1>
 <p>The workflow for ALD calculations is illustrated below</p>
-<p><img alt="96bd8a93769c4f10a633459b5535f345" class="no-scaled-link" src="../_images/timeline.png" style="width: 650px;"/></p>
+<p><img alt="99760efb70a0407f9d6aede15e885cb8" class="no-scaled-link" src="../_images/timeline.png" style="width: 650px;"/></p>
 <p>Here, we present two example simulations of both a periodic and an amorphous structure.</p>
 <section id="Ab-initio-silicon-diamond">
 <h2 id="Ab-initio-silicon-diamond"><em>Ab initio</em> silicon diamond<a class="headerlink" href="#Ab-initio-silicon-diamond" title="Permalink to this heading">¶</a></h2>
@@ -672,7 +672,7 @@ <h2 id="Ab-initio-silicon-diamond"><em>Ab initio</em> silicon diamond<a class="h
 </div>
 <p>We performed the simulation using the local density approximation for the exchange and correlation functional and a Bachelet-Hamann-Schluter norm-conserving pseudoptential. Kohn-Sham orbitals are represented on a plane-waves basis set with a cutoff of 20 Ry and (8, 8, 8) k-points mesh. The minimized lattice parameter is 5.398A. The third-order IFC is calculated using finite difference displacement on (5, 5, 5) replicas of the irreducible fcc-unit cell, including up to the 5th nearest neighbor.
 We obtained the following thermal properties</p>
-<p><img alt="6b14f27d66a040b08524b6506deb4b58" class="no-scaled-link" src="../_images/si-diamond-observables.png" style="width: 650px;"/></p>
+<p><img alt="b5de9d568e864948b9bc9ca60e391fb3" class="no-scaled-link" src="../_images/si-diamond-observables.png" style="width: 650px;"/></p>
 <p>The silicon diamond modes analysis is shown above. Quantum (red) and classical (blue) results are compared. a) Normalized density of states, b) Normalized phase-space per mode <img alt="g" class="math" src="../_images/math/86b44067536d63fd1271ac76c4a35eb79a6aa5dd.png"/>, c) lifetime per mode <img alt="\tau" class="math" src="../_images/math/303b8f73dd9a98bea8df8d22419bc3436abe91a9.png"/>, d) mean free path <img alt="\lambda" class="math" src="../_images/math/b67363a3f3c2ddf224f82975c53b7004abc08d20.png"/>, and e) cumulative conductivity <img alt="\kappa_{cum}" class="math" src="../_images/math/b1c775a79651621157c3335eeba4f6b733d71b1d.png"/>.</p>
 </section>
 <section id="Amorphous-silicon">
@@ -694,7 +694,7 @@ <h2 id="Amorphous-silicon">Amorphous silicon<a class="headerlink" href="#Amorpho
 </pre></div>
 </div>
 <p>In a simliar treatment to the silicon crystal, a full battery of modal analysis can be calculated with both quantum and classical statistics on the amorphous systems re- turning the phonon DoS as well as the associated lifetimes, generalized diffusivities, normalized phase space and cumulative conductivity</p>
-<p><img alt="24ad5be78ecb426aa6dcb9871f93b696" class="no-scaled-link" src="../_images/amorphous.png" style="width: 650px;"/></p>
+<p><img alt="9eff53e9b5e64b36b3cf6ea1019217fb" class="no-scaled-link" src="../_images/amorphous.png" style="width: 650px;"/></p>
 <p>Classical and quantum properties for 4096 atom amorphous silicon system are shown above. a) density of states, b) lifetimes, c) diffusivities, and e) cumulative thermal conductivity. In spite of the increased quantum lifetimes, a decrease of 0.17W/m/K is seen in the quantum conductivity. The difference in conductivity is primarily a result of the overestimation of classical high frequency heat capacities.</p>
 </section>
 <section id="References">

publications/readme.html

@@ -401,7 +401,7 @@
               <ul class="md-nav__list">
         <li class="md-nav__item"><a href="#preprints-4" class="md-nav__link">Preprints (4)</a>
         </li>
-        <li class="md-nav__item"><a href="#id1" class="md-nav__link">2024 (5)</a>
+        <li class="md-nav__item"><a href="#id1" class="md-nav__link">2024 (7)</a>
         </li>
         <li class="md-nav__item"><a href="#id2" class="md-nav__link">2023 (7)</a>
         </li>
@@ -443,8 +443,10 @@ <h2 id="preprints-4">Preprints (4)<a class="headerlink" href="#preprints-4" titl
 </ul>
 </section>
 <section id="id1">
-<h2 id="id1">2024 (5)<a class="headerlink" href="#id1" title="Permalink to this heading">¶</a></h2>
+<h2 id="id1">2024 (7)<a class="headerlink" href="#id1" title="Permalink to this heading">¶</a></h2>
 <ul class="simple">
+<li><p>Fredrik Eriksson, <a class="reference external" href="https://research.chalmers.se/publication/540860/file/540860_Fulltext.pdf">Beyond Perturbation: Modeling Anharmonicity in Materials</a></p></li>
+<li><p>Haoyu Dong,  Zhiqiang Li,  Baole Sun,  Yanguang Zhou,  Linhua Liu, Jia-Yue Yang, <a class="reference external" href="https://www.sciencedirect.com/science/article/pii/S2352492824011942?casa_token=c7LgMcZwdLsAAAAA:0d5iitbkKJ-Y0v90-K6ZjyiXrmk4yqyYMHmGhNuWzhChNFEPWyYODKaUbxkWKReY5dc6lss">Thermal transport in disordered wurtzite ScAlN alloys using machine learning interatomic potentials</a></p></li>
 <li><p>Philip Yox, Frank T Cerasoli, Arka Sarkar, Genevieve Amobi, Gayatri Viswanathan, Jackson Voyles, Oleg l Lebedev, Davide Donadio, Kirill Kovnir<a class="reference external" href="https://pubs.acs.org/doi/abs/10.1021/acs.chemmater.4c00419">Organizing Chaos: Boosting Thermoelectric Properties by Ordering the Clathrate Framework of Ba8Cu16As30</a></p></li>
 <li><p>Angela F. Harper,  Kamil Iwanowski,  William C. Witt,  Mike C. Payne, Michele Simoncelli,
 <a class="reference external" href="https://journals.aps.org/prmaterials/references/10.1103/PhysRevMaterials.8.043601">Vibrational and thermal properties of amorphous alumina from first principles</a></p></li>