{"id":20172651,"url":"https://github.com/usarmyresearchlab/arl_transire","last_synced_at":"2025-04-10T02:56:33.068Z","repository":{"id":88549751,"uuid":"164665839","full_name":"USArmyResearchLab/ARL_Transire","owner":"USArmyResearchLab","description":null,"archived":false,"fork":false,"pushed_at":"2019-10-18T13:32:28.000Z","size":268,"stargazers_count":3,"open_issues_count":0,"forks_count":3,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-03-24T04:23:59.060Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/USArmyResearchLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-01-08T14:26:22.000Z","updated_at":"2021-01-25T14:05:22.000Z","dependencies_parsed_at":null,"dependency_job_id":"7f4d8590-2b0a-47c5-a3a0-2c0a5e593f24","html_url":"https://github.com/USArmyResearchLab/ARL_Transire","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/USArmyResearchLab%2FARL_Transire","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/USArmyResearchLab%2FARL_Transire/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/USArmyResearchLab%2FARL_Transire/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/USArmyResearchLab%2FARL_Transire/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/USArmyResearchLab","download_url":"https://codeload.github.com/USArmyResearchLab/ARL_Transire/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248147700,"owners_count":21055545,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-14T01:31:44.863Z","updated_at":"2025-04-10T02:56:33.060Z","avatar_url":"https://github.com/USArmyResearchLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Transire generates and manipulates crystalline interface structures built \non the Atomic Simulation Environment (ASE).   A number of search methods \nare available to minimize the interface energy, including a random walk \nMarkov Chain search and rotations of one slab relative to the other.  \nEnergy calculations are performed using CP2K or LAMMPS, and any method \navailable in either can be used for calculating the interface energy.\nThe electron transport properties across the interface can be calculated\nusing the non-equilibrium Green's function (NEGF) method implemented in ASE\n(requires CP2K calculation).\n\nTransire is Latin for \"to cross over\" in reference to transport\nacross the interface.\n\nRequirements\n==============\n\nPython 2.7\n\nASE 3.12 or newer\n\npycp2k (if using cp2k)\n        \n        available from project page: https://github.com/SINGROUP/pycp2k\n\ncp2k 4.1 or newer (optional)\n        \n        If not using cp2k, make sure all energy related flags are set to\n        False in the input file \n\nLAMMPS (26 Jan 2017) or newer (optional)\n        \n        install serial version with mode=shlib and install-python options\n\nlammpslib\n        \n        https://svn.fysik.dtu.dk/projects/ase-extra/trunk/ase/calculators\n        \n        copy the file into your local library folder, usually\n        ~/.local/lib/python2.7/site-packages which is where python installs\n        the other libraries\n\nInstallation\n==============\n\nInstallation performed using setup.py in the main directory:\n\n```\n\u003e\u003e\u003e  python setup.py install\n```\n\nTo install into the local user space:\n\n```\n\u003e\u003e\u003e  python setup.py install --user\n```\n\nIf transire is installed in local space, ensure that the path environmental variables are set.\nThe $PYTHONPATH variable needs to include ~/.local/lib/pythonX/site-packages where pythonX is\nthe version of python on your system.  The $PATH variable needs to include ~/.local/bin.\nExample commands to set environment variables (cshell):\n\n```\n\u003e\u003e\u003e  setenv PYTHONPATH $(PYTHONPATH):~/.local/lib/pythonX/site-packages\n\u003e\u003e\u003e  setenv PATH $(PATH):~/.local/bin\n```\n\nTo test for successful installation use:\n\n```\n\u003e\u003e\u003e  transire.py -h\n```  \n\nor\n\n```\n\u003e\u003e\u003e  python -m transire.py -h\n```\n\nIf installed correctly, the help description of input options for transire will be printed.\n\n\nDocumentation\n=============\n\nDocumentation is designed for sphinx v1.7.0 and can be compiled by running:\n\n\u003e\u003e\u003e make html\n\nin the 'doc' directory.  Documentation output defaults to 'doc/html/'.\n\n\nCitations\n=========\n\nIf you find ARL Transire useful, please cite its [![DOI](https://zenodo.org/badge/164665839.svg)](https://zenodo.org/badge/latestdoi/164665839)\n\nLegal\n=====\n\nTransire is available under the GNU Lesser General Public License (LGPL).\nA copy of the LGPL is provided in the LICENSE file.\n\nCopyright (2018) Caleb Carlin.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fusarmyresearchlab%2Farl_transire","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fusarmyresearchlab%2Farl_transire","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fusarmyresearchlab%2Farl_transire/lists"}