{"id":43547699,"url":"https://github.com/molmod/thermolib","last_synced_at":"2026-02-05T21:00:46.429Z","repository":{"id":335497078,"uuid":"1145991863","full_name":"molmod/ThermoLIB","owner":"molmod","description":"ThermoLIB is a library for the construction, manipulation and post-processing of free energy surfaces from output of molecular simulations","archived":false,"fork":false,"pushed_at":"2026-02-02T16:42:28.000Z","size":104378,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2026-02-05T04:53:24.262Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://molmod.github.io/ThermoLIB/","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/molmod.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-01-30T13:34:33.000Z","updated_at":"2026-02-02T16:48:10.000Z","dependencies_parsed_at":null,"dependency_job_id":"94ff48ae-d4ee-4a87-ab35-8b7d34aff22f","html_url":"https://github.com/molmod/ThermoLIB","commit_stats":null,"previous_names":["molmod/thermolib"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/molmod/ThermoLIB","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/molmod%2FThermoLIB","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/molmod%2FThermoLIB/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/molmod%2FThermoLIB/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/molmod%2FThermoLIB/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/molmod","download_url":"https://codeload.github.com/molmod/ThermoLIB/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/molmod%2FThermoLIB/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29134200,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-05T20:50:26.975Z","status":"ssl_error","status_checked_at":"2026-02-05T20:49:26.082Z","response_time":65,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2026-02-03T19:07:41.623Z","updated_at":"2026-02-05T21:00:46.386Z","avatar_url":"https://github.com/molmod.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src='https://github.com/molmod/ThermoLIB/blob/master/logo_thermolib_light.png#gh-light-mode-only' width='200'\u003e\n\u003cimg src='https://github.com/molmod/ThermoLIB/blob/master/logo_thermolib_dark.png#gh-dark-mode-only' width='200'\u003e\n\n[![License](https://flat.badgen.net/static/LICENSE/GNU%20GPL%20(v3)/red)](https://github.com/molmod/ThermoLIB/blob/master/LICENSE)\n![Python](https://flat.badgen.net/static/Python/3.14/blue)\n[![Documentation](https://flat.badgen.net/static/Documentation/GitHUB%20Pages/green)](https://molmod.github.io/ThermoLIB/)\n# What is ThermoLIB?\n\nThermoLIB is a library developed at the [Center for Molecular Modeling (CMM)](https://molmod.ugent.be/) for the application of Statistical Physics and/or Thermodynamics to molecular simulations. The library consists of:\n\n*  ***Thermodynamics*** - Module for constructing, manipulating and post-processing of 1D free energy profiles (FEP) and 2D free energy surfaces (FES). Functions include \n\n    - construction of FEPs using WHAM including error estimatoin\n    - definition of (meta)stable micro- and macrostates\n    - transformation of FEPs from one collective variable to another\n    - (de)projection of a FES to a lower/higher dimensional FES.\n\n*  ***Kinetics*** - Module for computing the rate constant of a process/reaction using transition state theory (TST). Functions include:\n\n    - compute rate constant (which is theoretically indepedent of used CV)\n    - compute associated phenomenological free energy barrier\n    - error propagation from FEP to rate constant/phenomenological barrier\n\n# Documentation\n\nA full illustration on the use of ThermoLIB can be find in [the preprint on Arxiv](https://doi.org/10.48550/arXiv.2601.23071). More information on how to use ThermoLIB, including tutorials, can be found in its manual at [https://molmod.github.io/ThermoLIB/](https://molmod.github.io/ThermoLIB/).\n\n# How to cite ThermoLIB\n\nIf you use ThermoLIB in your research, please cite it as follows:\n\n    M. Bocus, L. Vanduyfhuys, 2026, 10.48550/arXiv.2601.23071\n\n# How to install?\n\nThermoLIB has the following dependencies:\n\n* [Cython](http://cython.org/)\n* [numpy](http://numpy.org/)\n* [scipy](http://www.scipy.org/)\n* [scikit-learn](https://scikit-learn.org/)\n* [matplotlib](http://matplotlib.sourceforge.net)\n* [h5py](https://www.h5py.org/)\n* [ase](https://wiki.fysik.dtu.dk/ase/) (Version 3.23.0 or newer)\n\nTo **install ThermoLIB** using pip either download the master branch as zip, go to your desired pip environment and run \n\n    pip install ThermoLIB-master.zip\n\nor if you have set up your ssh config file to access github.com using key authentication through an alias defined as 'github', you can install ThermoLIB as follows:, you can simply run:\n\n    pip install git+ssh://github/molmod/ThermoLIB.git\n\n# Terms of use\n\nThermoLIB is mainly developed by prof. Louis Vanduyfhuys at the Center for Molecular Modeling. Usage of ThermoLIB should be requested with prof. Vanduyfhuys.\n\nCopyright (C) 2019 - 2026 Louis Vanduyfhuys \u003cLouis.Vanduyfhuys@UGent.be\u003e\nCenter for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise stated.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmolmod%2Fthermolib","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmolmod%2Fthermolib","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmolmod%2Fthermolib/lists"}