{"id":138,"date":"2023-05-26T15:47:00","date_gmt":"2023-05-26T19:47:00","guid":{"rendered":"https:\/\/sciences.ucf.edu\/physics\/duyle\/?p=138"},"modified":"2025-09-13T23:57:39","modified_gmt":"2025-09-14T03:57:39","slug":"tpot-package","status":"publish","type":"post","link":"https:\/\/sciences.ucf.edu\/physics\/duyle\/tpot-package\/","title":{"rendered":"TPOT package"},"content":{"rendered":"\n<figure class=\"wp-block-video alignright\"><video height=\"600\" style=\"aspect-ratio: 600 \/ 600;\" width=\"600\" controls loop src=\"https:\/\/sciences.ucf.edu\/physics\/duyle\/wp-content\/uploads\/sites\/34\/2025\/07\/Movie_KCO2_TPOT_-1.0.mp4\"><\/video><\/figure>\n\n\n\n<p>We have developed an efficient computational method that enables<strong> grand-canonical (GC) <em>ab initio<\/em> molecular dynamics (AIMD) simulations<\/strong> of the electrochemical system that tracks the dynamics of explicit solvent molecules in the presence of constant electrode potential. In particular, we have developed an <strong>SOLHYBRID<\/strong> model,<sup>1<\/sup> an improvement of the implicit solvent model VASPSol,<sup>2, 3<\/sup>&nbsp; that explicitly simulate the solvent, ions, adsorbates near the electrode while treating the solvent elsewhere implicitly. More importantly, to make application of the self-consistent grand canonical DFT (GC-DFT)<sup>4, 5<\/sup> feasible for systems with few hundred atoms, we have recently developed the <strong>TPOT<\/strong> (<strong><u>T<\/u><\/strong>arget <strong><u>POT<\/u><\/strong>ential) routine<sup>1<\/sup> that was implemented locally to the popular Vienna Ab initio Simulation Package (VASP).<sup>6, 7<\/sup> It relies on an interactive optimization of the number of electrons for obtaining a predetermined target potential.<sup>1<\/sup> Figure below shows an example of constant electrode potential AIMD simulation of the CO<sub>2<\/sub> adsorption on Au(110) with the presence of K<sup>+<\/sup> cation. It shows that the number of electrons in the simulation cell varies to keep the potential of the electrode constant. The results of the simulations show that CO<sub>2<\/sub> forms a stable adsorption configuration with the presence of K<sup>+<\/sup> at an electrode potential of -1V vs RHE. It is worth mentioning that CO<sub>2<\/sub> is found to not adsorb on the Au(110) surface even with the presence of K<sup>+<\/sup> in traditional DFT simulations.<sup>8<\/sup><\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" width=\"1024\" height=\"683\" data-src=\"https:\/\/sciences.ucf.edu\/physics\/duyle\/wp-content\/uploads\/sites\/34\/2025\/07\/Figure7-1024x683.png\" alt=\"Line graphs of molecular dynamics data and a series of molecular simulation snapshots showing changes at a surface over time, with corresponding potential and charge measurements.\" class=\"wp-image-140 lazyload\" data-srcset=\"https:\/\/sciences.ucf.edu\/physics\/duyle\/wp-content\/uploads\/sites\/34\/2025\/07\/Figure7-1024x683.png 1024w, https:\/\/sciences.ucf.edu\/physics\/duyle\/wp-content\/uploads\/sites\/34\/2025\/07\/Figure7-300x200.png 300w, https:\/\/sciences.ucf.edu\/physics\/duyle\/wp-content\/uploads\/sites\/34\/2025\/07\/Figure7-768x512.png 768w, https:\/\/sciences.ucf.edu\/physics\/duyle\/wp-content\/uploads\/sites\/34\/2025\/07\/Figure7-1536x1024.png 1536w, https:\/\/sciences.ucf.edu\/physics\/duyle\/wp-content\/uploads\/sites\/34\/2025\/07\/Figure7-2048x1365.png 2048w\" data-sizes=\"(max-width: 1024px) 100vw, 1024px\" src=\"data:image\/svg+xml;base64,PHN2ZyB3aWR0aD0iMSIgaGVpZ2h0PSIxIiB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciPjwvc3ZnPg==\" style=\"--smush-placeholder-width: 1024px; --smush-placeholder-aspect-ratio: 1024\/683;\" \/><figcaption class=\"wp-element-caption\">GC-AIMD simulation of CO<sub>2<\/sub>-K<sup>+<\/sup>\/Au(111) at an electrode potential of 0 V vs RHE. Evolution of <strong>(a)<\/strong> distance&nbsp; from Au and C atom of CO<sub>2<\/sub> molecule (<em>d<sub>Au-C<\/sub><\/em>, distance from K<sup>+<\/sup> to two O atoms of CO<sub>2<\/sub> molecule (<em>d<sub>O1-K+<\/sub><\/em>&nbsp;and <em>d<sub>O2-K+<\/sub><\/em>), <strong>(b)<\/strong> bending angle of the CO<sub>2<\/sub> molecule (OCO), <strong>(c)<\/strong> potential of Au(110) electrode, and <strong>(d)<\/strong> charge in the supercell (q) during the GC-AIMD simulation of CO<sub>2<\/sub>-K<sup>+<\/sup>\/Au(111) with SOLHYBRID model at -1 V vs RHE. Snapshots of the simulations are shown in I-h).&nbsp; Yellow, black, red, and purple balls represent Au, C, O, and K atoms. The H<sub>2<\/sub>O molecules are shown by the pink-while ball-stick molecules.<\/figcaption><\/figure>\n\n\n\n<p>Details of this development can be found in the preprint.<sup>1<\/sup> The TPOT package is available for free of charge at our <a href=\"https:\/\/github.com\/comet-group\/tpot\">GitHub<\/a>.<\/p>\n\n\n\n<p><strong>Reference<\/strong>:<br>1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D. Le, &#8220;An Explicit-Implicit Hybrid Solvent Model for Grand Canonical Simulations of the Electrochemical Environment,&#8221; ChemRvix 10.26434\/chemrxiv-2023-z2n4n&nbsp; 10.26434\/chemrxiv-2023-z2n4n (2023). <a href=\"http:\/\/doi.org\/10.26434\/chemrxiv-2023-z2n4n\">http:\/\/doi.org\/10.26434\/chemrxiv-2023-z2n4n<\/a> <br>2.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; K. Mathew, V.S.C. Kolluru, S. Mula, S.N. Steinmann, and R.G. Hennig, &#8220;Implicit self-consistent electrolyte model in plane-wave density-functional theory,&#8221; The Journal of Chemical Physics <strong>151<\/strong>, 234101 (2019). <a href=\"http:\/\/doi.org\/10.1063\/1.5132354\">http:\/\/doi.org\/10.1063\/1.5132354<\/a> <br>3.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; K. Mathew, R. Sundararaman, K. Letchworth-Weaver, T.A. Arias, and R.G. Hennig, &#8220;Implicit solvation model for density-functional study of nanocrystal surfaces and reaction pathways,&#8221; The Journal of Chemical Physics <strong>140<\/strong>, 084106 (2014). <a href=\"http:\/\/doi.org\/10.1063\/1.4865107\">http:\/\/doi.org\/10.1063\/1.4865107<\/a> <br>4.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; R. Sundararaman, W.A. Goddard, and T.A. Arias, &#8220;Grand canonical electronic density-functional theory: Algorithms and applications to electrochemistry,&#8221; The Journal of Chemical Physics <strong>146<\/strong>, 114104 (2017). <a href=\"http:\/\/doi.org\/10.1063\/1.4978411\">http:\/\/doi.org\/10.1063\/1.4978411<\/a> <br>5.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; R. Sundararaman and T.A. Arias, &#8220;Joint and grand-canonical density-functional theory&#8221;&nbsp; in &#8220;Atomic\u2010Scale Modelling of Electrochemical Systems&#8221;. (eds. M.M. Melander, T.T. LaurilaandK. Laasonen) 139-172 (John Wiley &amp; Sons Ltd, 2021). <a href=\"http:\/\/doi.org\/10.1002\/9781119605652.ch4\">http:\/\/doi.org\/10.1002\/9781119605652.ch4<\/a> <br>6.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; J. Hafner, &#8220;Ab-initio simulations of materials using VASP: Density-functional theory and beyond,&#8221; Journal of Computational Chemistry <strong>29<\/strong>, 2044-78 (2008). <a href=\"http:\/\/doi.org\/10.1002\/jcc.21057\">http:\/\/doi.org\/10.1002\/jcc.21057<\/a> <br>7.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; G. Kresse and J. Furthm\u00fcller, &#8220;Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set,&#8221; Physical Review B <strong>54<\/strong>, 11169-11186 (1996). <a href=\"http:\/\/doi.org\/10.1103\/PhysRevB.54.11169\">http:\/\/doi.org\/10.1103\/PhysRevB.54.11169<\/a> 8.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; X. Qin, T. Vegge, and H.A. Hansen, &#8220;CO<sub>2<\/sub> activation at Au(110)\u2013water interfaces: An ab initio molecular dynamics study,&#8221; The Journal of Chemical Physics <strong>155<\/strong>, 134703 (2021). <a href=\"http:\/\/doi.org\/10.1063\/5.0066196\">http:\/\/doi.org\/10.1063\/5.0066196<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>We have developed an efficient computational method that enables grand-canonical (GC) ab initio molecular dynamics (AIMD) simulations of the electrochemical system that tracks the dynamics of explicit solvent molecules in the presence of constant electrode potential. In particular, we have developed an SOLHYBRID model,1 an improvement of the implicit solvent model VASPSol,2, 3&nbsp; that explicitly &#8230; <a title=\"TPOT package\" class=\"read-more\" href=\"https:\/\/sciences.ucf.edu\/physics\/duyle\/tpot-package\/\" aria-label=\"Read more about TPOT package\">Read more<\/a><\/p>\n","protected":false},"author":66,"featured_media":0,"comment_status":"off","ping_status":"off","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[10,12,9,11,8,7],"tags":[],"class_list":["post-138","post","type-post","status-publish","format-standard","hentry","category-electrocatalysis","category-gc-dft","category-github","category-molecular-dynamics-simulations","category-package","category-software"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.2 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>TPOT package - CoMET<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sciences.ucf.edu\/physics\/duyle\/tpot-package\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"TPOT package - CoMET\" \/>\n<meta property=\"og:description\" content=\"We have developed an efficient computational method that enables grand-canonical (GC) ab initio molecular dynamics (AIMD) simulations of the electrochemical system that tracks the dynamics of explicit solvent molecules in the presence of constant electrode potential. 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