{"id":1663,"date":"2021-07-16T08:25:42","date_gmt":"2021-07-16T08:25:42","guid":{"rendered":"http:\/\/tribchem.it\/?page_id=1663"},"modified":"2025-01-20T11:39:24","modified_gmt":"2025-01-20T11:39:24","slug":"tribchem-2","status":"publish","type":"page","link":"https:\/\/tribchem.it\/?page_id=1663","title":{"rendered":"TribChem"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"1663\" class=\"elementor elementor-1663\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-52b988b elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"52b988b\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-f1094a9\" data-id=\"f1094a9\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-4a9cb62 elementor-widget elementor-widget-text-editor\" data-id=\"4a9cb62\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p><span style=\"font-size: 18pt;\"><strong><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">The Tribchem package<\/span><\/strong><\/span><\/p><p><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">Tribchem is a Python based package, containing several workflows, designed to perform the high-throughput screening of fundamental tribological, mechanical and electronic properties of materials and their solid-solid interfaces. Tribchem is designed for non-expert users, it requires a limited number of input parameters and automatically creates input files and geometries, submits and runs simulations, collects data in external databases and analyzes them.<\/span><\/p><p><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">TribChem is based on the <a href=\"https:\/\/materialsproject.github.io\/fireworks\/\"><span style=\"text-decoration: underline;\">FireWorks platform<\/span><\/a> for running high throughput DFT calculations, and general tools for calculating tribological properties and analyzing results. At present Tribchem is connected to VASP. Work is in progress to enable its use in connection with Quantum Espresso and LAMMPS. <\/span><\/p><p><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">Tribchem v1<\/span><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">.0.0 is available for download at <a id=\"LPlnk744394\" href=\"https:\/\/triboteam.gitlab.io\/tribchem\/\" target=\"_blank\" rel=\"noopener noreferrer\" data-auth=\"NotApplicable\" data-linkindex=\"1\"><span style=\"text-decoration: underline;\">https:\/\/triboteam.gitlab.io\/tribchem\/<\/span><\/a>.<br \/><\/span><\/p><p><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">\u00a0<\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-5184daf elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"5184daf\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-ccdd06d\" data-id=\"ccdd06d\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-8c71fa1 elementor-widget elementor-widget-text-editor\" data-id=\"8c71fa1\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p><strong><span style=\"font-family: verdana, geneva, sans-serif; color: #000000; font-size: 14pt;\">Workflows<\/span><\/strong><\/p><p><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">The ab initio determination of the properties of solid-solid interfaces is a complex multistep procedure: starting from the determination of optimal computational parameters to describe the selected materials, the bulk structure is characterized, two surfaces are built and optimized, and only then the interface can be created and studied.<\/span><\/p><p><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">Within this simple logical scheme important sub-procedures are nested. Tribchem can automatically carry out these tasks through\u00a0<strong>workflows<\/strong>, which are organized hierarchically and modularly so that users can decide to carry out the whole simulation from bulks to interfaces, or only part of it. Thanks to the modularity, creating new custom workflows to perform the high-throughput screening of specific properties of bulks\/surface\/interfaces is greatly simplified.<br \/><\/span><\/p><p><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">The workflows currently available in TribChem are organized in four main units, as follows: <\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-1d3f7b5 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"1d3f7b5\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-8892821\" data-id=\"8892821\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-732b55e elementor-widget elementor-widget-text-editor\" data-id=\"732b55e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">BULK<\/span><\/span><\/p><ul><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Query online databases to save data to an internal database<\/span><\/span><\/p><\/li><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Calculation of the optimal kinetic energy cutoff for the the electronic wavefunction<\/span><\/span><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\"><span lang=\"en-US\"> expansion in plane-wave basis set<\/span><\/span><\/span><\/p><\/li><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Calculation of the optimal density of K-points to perform Brillouin zone summations<\/span><\/span><\/p><\/li><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">C<\/span><\/span><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\"><span lang=\"en-US\">alculation of the lattice parameter, bulk modulus and c<\/span><\/span><\/span><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">ohesion energy <\/span><\/span><\/p><\/li><\/ul><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">SURFACE<\/span><\/span><\/p><ul><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Calculation of the optimal <\/span><\/span><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\"><span lang=\"en-US\">slab <\/span><\/span><\/span><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">thickness for accurate modeling <\/span><\/span><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\"><span lang=\"en-US\">of the <\/span><\/span><\/span><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">solid surface<\/span><\/span><\/p><\/li><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Surface energy calculation<\/span><\/span><\/p><\/li><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Adsorption of atoms on surfaces: most favorable adsorption site and coverage<\/span><\/span><\/p><\/li><\/ul><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">INTERFACE<\/span><\/span><\/p><ul><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Matching two surfaces <\/span><\/span><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\"><span lang=\"en-US\">by means of the <a href=\"https:\/\/aip.scitation.org\/doi\/abs\/10.1063\/1.333084\"><span style=\"text-decoration: underline;\">Zur algorithm<\/span> <\/a><\/span><\/span><\/span><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">and generation of a solid interface<\/span><\/span><\/p><\/li><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Calculation of the redistribution of the electronic charge that takes place when <\/span><\/span><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\"><span lang=\"en-US\">the <\/span><\/span><\/span><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">two surfaces are put in contact<\/span><\/span><\/p><\/li><\/ul><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">TRIBOLOGY (ADHESION AND SHEAR STRENGTH)<\/span><\/span><\/p><ul><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Calculation of the potenial energy surface (PES) experienced by the sliding interface<\/span><\/span><\/p><\/li><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Calculation of the adhesion energy as a function of the interfacial separation <\/span><\/span><\/p><\/li><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Extraction of the minimum energy path (MEP) by means of the\u00a0<\/span><\/span><a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/jp0455430\"><span style=\"color: #03a9f4;\"><span style=\"font-family: Verdana, serif;\"><u>Zero temperature sting method<\/u><\/span><\/span><\/a><\/p><\/li><li><p><span style=\"color: #000000;\"><span style=\"font-family: Verdana, serif;\">Calculation of the interfacial shear strength<\/span><\/span><\/p><\/li><\/ul>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-b8cb731\" data-id=\"b8cb731\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-e975287 elementor-widget elementor-widget-image\" data-id=\"e975287\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img fetchpriority=\"high\" decoding=\"async\" width=\"619\" height=\"722\" src=\"https:\/\/tribchem.it\/wp-content\/uploads\/2022\/10\/workflow_chart.png\" class=\"attachment-large size-large wp-image-2629\" alt=\"\" srcset=\"https:\/\/tribchem.it\/wp-content\/uploads\/2022\/10\/workflow_chart.png 619w, https:\/\/tribchem.it\/wp-content\/uploads\/2022\/10\/workflow_chart-257x300.png 257w\" sizes=\"(max-width: 619px) 100vw, 619px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-9483aee elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"9483aee\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-f3ed3f2\" data-id=\"f3ed3f2\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-3d66b2f elementor-widget elementor-widget-text-editor\" data-id=\"3d66b2f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p><strong><span style=\"font-family: verdana, geneva, sans-serif; color: #000000; font-size: 14pt;\">Technical features<\/span><\/strong><\/p><p><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">Tribchem is a Python based package containing two main modules, the physics and the highthroughput modules. On top of that, Tribchem relies on the Material Project and on two main internal databases to efficiently retrieve and store data and results.<\/span><\/p><p><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">The physics module relies on the Pyt<\/span><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">hon Materials Genomics (<a href=\"https:\/\/pymatgen.org\/\"><span style=\"text-decoration: underline;\">Pymatgen<\/span><\/a>) and <a href=\"https:\/\/github.com\/henniggroup\/MPInterfaces\"><span style=\"text-decoration: underline;\">MPInterfaces<\/span><\/a> packages. It implements several functions to perform basic solid-state physics, math, geometry, file manipulation, plotting, post-processing operations and more advanced operations on electronic, mechanical, and tribological properties. Thanks to the modular design, it is possible to use these functions outside TribChem as external modules.<\/span><\/p><p><img decoding=\"async\" class=\"alignright wp-image-2620\" src=\"https:\/\/tribchem.it\/wp-content\/uploads\/2022\/10\/software_scheme.png-300x240.png\" alt=\"Pictorial representation of the workflow structure\" width=\"449\" height=\"360\" srcset=\"https:\/\/tribchem.it\/wp-content\/uploads\/2022\/10\/software_scheme.png-300x240.png 300w, https:\/\/tribchem.it\/wp-content\/uploads\/2022\/10\/software_scheme.png-768x615.png 768w, https:\/\/tribchem.it\/wp-content\/uploads\/2022\/10\/software_scheme.png.png 976w\" sizes=\"(max-width: 449px) 100vw, 449px\" \/><\/p><p><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">The high throughput module extensively employs <a href=\"https:\/\/materialsproject.github.io\/fireworks\/\"><span style=\"text-decoration: underline;\">Fireworks<\/span><\/a> and <a href=\"https:\/\/atomate.org\/\"><span style=\"text-decoration: underline;\">Atomate<\/span><\/a> as workflow managers. Thanks to the FireWorks library structure it is possible to create complex workflows by combining FireTasks and FireWorks. To maintain the highest level of modularity, with few exceptions, within Tribchem, each FireWorks employs just one FireTask at a time.<\/span><\/p><p><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">The database used by the FireWorks library is <a href=\"https:\/\/www.mongodb.com\/\"><span style=\"text-decoration: underline;\">MongoDB<\/span><\/a>, a NoSQL database which uses JSON like-documents to store and manipulate data. The most important and relevant databases that are created when Tribchem is installed are the FireWorks and the tribchem databases. The FireWorks database contains all data for workflow execution, simulation results, and some relevant metadata such as the location of the VASP output files. The tribchem database includes several collections divided into different structures and functionals used for performing the DFT calculations. In our case, we have three main collections classes about bulks, slabs, and interfaces. For connecting to the Materials Project database a high-level interface <\/span><span style=\"font-family: verdana, geneva, sans-serif; color: #000000;\">class named NavigatorMP is available.<\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>The Tribchem package Tribchem is a Python based package, containing several workflows, designed to perform the high-throughput screening of fundamental tribological, mechanical and electronic properties of materials and their solid-solid interfaces. Tribchem is designed for non-expert users, it requires a limited number of input parameters and automatically creates input files and geometries, submits and runs&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/tribchem.it\/?page_id=1663\">Read more<\/a><\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":""},"class_list":["post-1663","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/tribchem.it\/index.php?rest_route=\/wp\/v2\/pages\/1663","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/tribchem.it\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/tribchem.it\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/tribchem.it\/index.php?rest_route=\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/tribchem.it\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1663"}],"version-history":[{"count":67,"href":"https:\/\/tribchem.it\/index.php?rest_route=\/wp\/v2\/pages\/1663\/revisions"}],"predecessor-version":[{"id":3534,"href":"https:\/\/tribchem.it\/index.php?rest_route=\/wp\/v2\/pages\/1663\/revisions\/3534"}],"wp:attachment":[{"href":"https:\/\/tribchem.it\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1663"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}