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is-small is-grey tooltip is-tooltip-top" data-tooltip="Materials Science">cond-mat.mtrl-sci</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Machine Learning">cs.LG</span> </div> <div class="is-inline-block" style="margin-left: 0.5rem"> <div class="tags has-addons"> <span class="tag is-dark is-size-7">doi</span> <span class="tag is-light is-size-7"><a class="" href="https://doi.org/10.1038/s41524-021-00510-y">10.1038/s41524-021-00510-y <i class="fa fa-external-link" aria-hidden="true"></i></a></span> </div> </div> </div> <p class="title is-5 mathjax"> Bayesian Force Fields from Active Learning for Simulation of Inter-Dimensional Transformation of Stanene </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/cs?searchtype=author&query=Xie%2C+Y">Yu Xie</a>, <a href="/search/cs?searchtype=author&query=Vandermause%2C+J">Jonathan Vandermause</a>, <a href="/search/cs?searchtype=author&query=Sun%2C+L">Lixin Sun</a>, <a href="/search/cs?searchtype=author&query=Cepellotti%2C+A">Andrea Cepellotti</a>, <a href="/search/cs?searchtype=author&query=Kozinsky%2C+B">Boris Kozinsky</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2008.11796v2-abstract-short" style="display: inline;"> We present a way to dramatically accelerate Gaussian process models for interatomic force fields based on many-body kernels by mapping both forces and uncertainties onto functions of low-dimensional features. This allows for automated active learning of models combining near-quantum accuracy, built-in uncertainty, and constant cost of evaluation that is comparable to classical analytical models, c… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2008.11796v2-abstract-full').style.display = 'inline'; document.getElementById('2008.11796v2-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2008.11796v2-abstract-full" style="display: none;"> We present a way to dramatically accelerate Gaussian process models for interatomic force fields based on many-body kernels by mapping both forces and uncertainties onto functions of low-dimensional features. This allows for automated active learning of models combining near-quantum accuracy, built-in uncertainty, and constant cost of evaluation that is comparable to classical analytical models, capable of simulating millions of atoms. Using this approach, we perform large scale molecular dynamics simulations of the stability of the stanene monolayer. We discover an unusual phase transformation mechanism of 2D stanene, where ripples lead to nucleation of bilayer defects, densification into a disordered multilayer structure, followed by formation of bulk liquid at high temperature or nucleation and growth of the 3D bcc crystal at low temperature. The presented method opens possibilities for rapid development of fast accurate uncertainty-aware models for simulating long-time large-scale dynamics of complex materials. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2008.11796v2-abstract-full').style.display = 'none'; document.getElementById('2008.11796v2-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 18 February, 2021; <span class="has-text-black-bis has-text-weight-semibold">v1</span> submitted 26 August, 2020; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> August 2020. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">30 pages of main text, 14 pages of supplementary materials, 9 figures in total</span> </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Journal ref:</span> npj Comput Mater 7, 40 (2021) </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2003.12476">arXiv:2003.12476</a> <span> [<a href="https://arxiv.org/pdf/2003.12476">pdf</a>, <a href="https://arxiv.org/format/2003.12476">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Distributed, Parallel, and Cluster Computing">cs.DC</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Materials Science">cond-mat.mtrl-sci</span> </div> <div class="is-inline-block" style="margin-left: 0.5rem"> <div class="tags has-addons"> <span class="tag is-dark is-size-7">doi</span> <span class="tag is-light is-size-7"><a class="" href="https://doi.org/10.1038/s41597-020-00638-4">10.1038/s41597-020-00638-4 <i class="fa fa-external-link" aria-hidden="true"></i></a></span> </div> </div> </div> <p class="title is-5 mathjax"> AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/cs?searchtype=author&query=Huber%2C+S+P">Sebastiaan. P. Huber</a>, <a href="/search/cs?searchtype=author&query=Zoupanos%2C+S">Spyros Zoupanos</a>, <a href="/search/cs?searchtype=author&query=Uhrin%2C+M">Martin Uhrin</a>, <a href="/search/cs?searchtype=author&query=Talirz%2C+L">Leopold Talirz</a>, <a href="/search/cs?searchtype=author&query=Kahle%2C+L">Leonid Kahle</a>, <a href="/search/cs?searchtype=author&query=H%C3%A4uselmann%2C+R">Rico H盲uselmann</a>, <a href="/search/cs?searchtype=author&query=Gresch%2C+D">Dominik Gresch</a>, <a href="/search/cs?searchtype=author&query=M%C3%BCller%2C+T">Tiziano M眉ller</a>, <a href="/search/cs?searchtype=author&query=Yakutovich%2C+A+V">Aliaksandr V. Yakutovich</a>, <a href="/search/cs?searchtype=author&query=Andersen%2C+C+W">Casper W. Andersen</a>, <a href="/search/cs?searchtype=author&query=Ramirez%2C+F+F">Francisco F. Ramirez</a>, <a href="/search/cs?searchtype=author&query=Adorf%2C+C+S">Carl S. Adorf</a>, <a href="/search/cs?searchtype=author&query=Gargiulo%2C+F">Fernando Gargiulo</a>, <a href="/search/cs?searchtype=author&query=Kumbhar%2C+S">Snehal Kumbhar</a>, <a href="/search/cs?searchtype=author&query=Passaro%2C+E">Elsa Passaro</a>, <a href="/search/cs?searchtype=author&query=Johnston%2C+C">Conrad Johnston</a>, <a href="/search/cs?searchtype=author&query=Merkys%2C+A">Andrius Merkys</a>, <a href="/search/cs?searchtype=author&query=Cepellotti%2C+A">Andrea Cepellotti</a>, <a href="/search/cs?searchtype=author&query=Mounet%2C+N">Nicolas Mounet</a>, <a href="/search/cs?searchtype=author&query=Marzari%2C+N">Nicola Marzari</a>, <a href="/search/cs?searchtype=author&query=Kozinsky%2C+B">Boris Kozinsky</a>, <a href="/search/cs?searchtype=author&query=Pizzi%2C+G">Giovanni Pizzi</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2003.12476v1-abstract-short" style="display: inline;"> The ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of calculations and data to manage. Next-generation exascale supercomputers will harden these challenges, such that automated and scalable solutions become crucial.… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2003.12476v1-abstract-full').style.display = 'inline'; document.getElementById('2003.12476v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2003.12476v1-abstract-full" style="display: none;"> The ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of calculations and data to manage. Next-generation exascale supercomputers will harden these challenges, such that automated and scalable solutions become crucial. In recent years, we have been developing AiiDA (http://www.aiida.net), a robust open-source high-throughput infrastructure addressing the challenges arising from the needs of automated workflow management and data provenance recording. Here, we introduce developments and capabilities required to reach sustained performance, with AiiDA supporting throughputs of tens of thousands processes/hour, while automatically preserving and storing the full data provenance in a relational database making it queryable and traversable, thus enabling high-performance data analytics. AiiDA's workflow language provides advanced automation, error handling features and a flexible plugin model to allow interfacing with any simulation software. The associated plugin registry enables seamless sharing of extensions, empowering a vibrant user community dedicated to making simulations more robust, user-friendly and reproducible. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2003.12476v1-abstract-full').style.display = 'none'; document.getElementById('2003.12476v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 24 March, 2020; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> March 2020. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Journal ref:</span> Scientific Data 7, 300 (2020) </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/1504.01163">arXiv:1504.01163</a> <span> [<a href="https://arxiv.org/pdf/1504.01163">pdf</a>, <a href="https://arxiv.org/format/1504.01163">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Computational Physics">physics.comp-ph</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Materials Science">cond-mat.mtrl-sci</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Software Engineering">cs.SE</span> </div> <div class="is-inline-block" style="margin-left: 0.5rem"> <div class="tags has-addons"> <span class="tag is-dark is-size-7">doi</span> <span class="tag is-light is-size-7"><a class="" href="https://doi.org/10.1016/j.commatsci.2015.09.013">10.1016/j.commatsci.2015.09.013 <i class="fa fa-external-link" aria-hidden="true"></i></a></span> </div> </div> </div> <p class="title is-5 mathjax"> AiiDA: Automated Interactive Infrastructure and Database for Computational Science </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/cs?searchtype=author&query=Pizzi%2C+G">Giovanni Pizzi</a>, <a href="/search/cs?searchtype=author&query=Cepellotti%2C+A">Andrea Cepellotti</a>, <a href="/search/cs?searchtype=author&query=Sabatini%2C+R">Riccardo Sabatini</a>, <a href="/search/cs?searchtype=author&query=Marzari%2C+N">Nicola Marzari</a>, <a href="/search/cs?searchtype=author&query=Kozinsky%2C+B">Boris Kozinsky</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="1504.01163v2-abstract-short" style="display: inline;"> Computational science has seen in the last decades a spectacular rise in the scope, breadth, and depth of its efforts. Notwithstanding this prevalence and impact, it is often still performed using the renaissance model of individual artisans gathered in a workshop, under the guidance of an established practitioner. Great benefits could follow instead from adopting concepts and tools coming from co… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1504.01163v2-abstract-full').style.display = 'inline'; document.getElementById('1504.01163v2-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="1504.01163v2-abstract-full" style="display: none;"> Computational science has seen in the last decades a spectacular rise in the scope, breadth, and depth of its efforts. Notwithstanding this prevalence and impact, it is often still performed using the renaissance model of individual artisans gathered in a workshop, under the guidance of an established practitioner. Great benefits could follow instead from adopting concepts and tools coming from computer science to manage, preserve, and share these computational efforts. We illustrate here our paradigm sustaining such vision, based around the four pillars of Automation, Data, Environment, and Sharing. We then discuss its implementation in the open-source AiiDA platform (http://www.aiida.net), that has been tuned first to the demands of computational materials science. AiiDA's design is based on directed acyclic graphs to track the provenance of data and calculations, and ensure preservation and searchability. Remote computational resources are managed transparently, and automation is coupled with data storage to ensure reproducibility. Last, complex sequences of calculations can be encoded into scientific workflows. We believe that AiiDA's design and its sharing capabilities will encourage the creation of social ecosystems to disseminate codes, data, and scientific workflows. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1504.01163v2-abstract-full').style.display = 'none'; document.getElementById('1504.01163v2-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 8 September, 2015; <span class="has-text-black-bis has-text-weight-semibold">v1</span> submitted 5 April, 2015; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> April 2015. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">30 pages, 7 figures</span> </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Journal ref:</span> G. Pizzi, A. Cepellotti, R. Sabatini, N. Marzari, and B. Kozinsky, Comp. Mat. Sci 111, 218-230 (2016) </p> </li> </ol> <div class="is-hidden-tablet"> <!-- feedback for mobile only --> <span class="help" style="display: inline-block;"><a href="https://github.com/arXiv/arxiv-search/releases">Search v0.5.6 released 2020-02-24</a> </span> </div> </div> </main> <footer> <div class="columns is-desktop" role="navigation" aria-label="Secondary"> <!-- MetaColumn 1 --> <div class="column"> <div class="columns"> <div class="column"> <ul class="nav-spaced"> <li><a href="https://info.arxiv.org/about">About</a></li> <li><a href="https://info.arxiv.org/help">Help</a></li> </ul> </div> <div class="column"> <ul class="nav-spaced"> <li> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512" class="icon filter-black" role="presentation"><title>contact arXiv</title><desc>Click here to contact arXiv</desc><path d="M502.3 190.8c3.9-3.1 9.7-.2 9.7 4.7V400c0 26.5-21.5 48-48 48H48c-26.5 0-48-21.5-48-48V195.6c0-5 5.7-7.8 9.7-4.7 22.4 17.4 52.1 39.5 154.1 113.6 21.1 15.4 56.7 47.8 92.2 47.6 35.7.3 72-32.8 92.3-47.6 102-74.1 131.6-96.3 154-113.7zM256 320c23.2.4 56.6-29.2 73.4-41.4 132.7-96.3 142.8-104.7 173.4-128.7 5.8-4.5 9.2-11.5 9.2-18.9v-19c0-26.5-21.5-48-48-48H48C21.5 64 0 85.5 0 112v19c0 7.4 3.4 14.3 9.2 18.9 30.6 23.9 40.7 32.4 173.4 128.7 16.8 12.2 50.2 41.8 73.4 41.4z"/></svg> <a href="https://info.arxiv.org/help/contact.html"> Contact</a> </li> <li> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512" class="icon filter-black" role="presentation"><title>subscribe to arXiv mailings</title><desc>Click here to subscribe</desc><path d="M476 3.2L12.5 270.6c-18.1 10.4-15.8 35.6 2.2 43.2L121 358.4l287.3-253.2c5.5-4.9 13.3 2.6 8.6 8.3L176 407v80.5c0 23.6 28.5 32.9 42.5 15.8L282 426l124.6 52.2c14.2 6 30.4-2.9 33-18.2l72-432C515 7.8 493.3-6.8 476 3.2z"/></svg> <a href="https://info.arxiv.org/help/subscribe"> Subscribe</a> </li> </ul> </div> </div> </div> <!-- end MetaColumn 1 --> <!-- MetaColumn 2 --> <div class="column"> <div class="columns"> <div class="column"> <ul class="nav-spaced"> <li><a href="https://info.arxiv.org/help/license/index.html">Copyright</a></li> <li><a href="https://info.arxiv.org/help/policies/privacy_policy.html">Privacy Policy</a></li> </ul> </div> <div class="column sorry-app-links"> <ul class="nav-spaced"> <li><a href="https://info.arxiv.org/help/web_accessibility.html">Web Accessibility Assistance</a></li> <li> <p class="help"> <a class="a11y-main-link" href="https://status.arxiv.org" target="_blank">arXiv Operational Status <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 256 512" class="icon filter-dark_grey" role="presentation"><path d="M224.3 273l-136 136c-9.4 9.4-24.6 9.4-33.9 0l-22.6-22.6c-9.4-9.4-9.4-24.6 0-33.9l96.4-96.4-96.4-96.4c-9.4-9.4-9.4-24.6 0-33.9L54.3 103c9.4-9.4 24.6-9.4 33.9 0l136 136c9.5 9.4 9.5 24.6.1 34z"/></svg></a><br> Get status notifications via <a class="is-link" href="https://subscribe.sorryapp.com/24846f03/email/new" target="_blank"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512" class="icon filter-black" role="presentation"><path d="M502.3 190.8c3.9-3.1 9.7-.2 9.7 4.7V400c0 26.5-21.5 48-48 48H48c-26.5 0-48-21.5-48-48V195.6c0-5 5.7-7.8 9.7-4.7 22.4 17.4 52.1 39.5 154.1 113.6 21.1 15.4 56.7 47.8 92.2 47.6 35.7.3 72-32.8 92.3-47.6 102-74.1 131.6-96.3 154-113.7zM256 320c23.2.4 56.6-29.2 73.4-41.4 132.7-96.3 142.8-104.7 173.4-128.7 5.8-4.5 9.2-11.5 9.2-18.9v-19c0-26.5-21.5-48-48-48H48C21.5 64 0 85.5 0 112v19c0 7.4 3.4 14.3 9.2 18.9 30.6 23.9 40.7 32.4 173.4 128.7 16.8 12.2 50.2 41.8 73.4 41.4z"/></svg>email</a> or <a class="is-link" href="https://subscribe.sorryapp.com/24846f03/slack/new" target="_blank"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512" class="icon filter-black" role="presentation"><path d="M94.12 315.1c0 25.9-21.16 47.06-47.06 47.06S0 341 0 315.1c0-25.9 21.16-47.06 47.06-47.06h47.06v47.06zm23.72 0c0-25.9 21.16-47.06 47.06-47.06s47.06 21.16 47.06 47.06v117.84c0 25.9-21.16 47.06-47.06 47.06s-47.06-21.16-47.06-47.06V315.1zm47.06-188.98c-25.9 0-47.06-21.16-47.06-47.06S139 32 164.9 32s47.06 21.16 47.06 47.06v47.06H164.9zm0 23.72c25.9 0 47.06 21.16 47.06 47.06s-21.16 47.06-47.06 47.06H47.06C21.16 243.96 0 222.8 0 196.9s21.16-47.06 47.06-47.06H164.9zm188.98 47.06c0-25.9 21.16-47.06 47.06-47.06 25.9 0 47.06 21.16 47.06 47.06s-21.16 47.06-47.06 47.06h-47.06V196.9zm-23.72 0c0 25.9-21.16 47.06-47.06 47.06-25.9 0-47.06-21.16-47.06-47.06V79.06c0-25.9 21.16-47.06 47.06-47.06 25.9 0 47.06 21.16 47.06 47.06V196.9zM283.1 385.88c25.9 0 47.06 21.16 47.06 47.06 0 25.9-21.16 47.06-47.06 47.06-25.9 0-47.06-21.16-47.06-47.06v-47.06h47.06zm0-23.72c-25.9 0-47.06-21.16-47.06-47.06 0-25.9 21.16-47.06 47.06-47.06h117.84c25.9 0 47.06 21.16 47.06 47.06 0 25.9-21.16 47.06-47.06 47.06H283.1z"/></svg>slack</a> </p> </li> </ul> </div> </div> </div> <!-- end MetaColumn 2 --> </div> </footer> <script src="https://static.arxiv.org/static/base/1.0.0a5/js/member_acknowledgement.js"></script> </body> </html>