https://github.com/molmod/thermolib

ThermoLIB is a library for the construction, manipulation and post-processing of free energy surfaces from output of molecular simulations
https://github.com/molmod/thermolib

Last synced: 4 months ago
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ThermoLIB is a library for the construction, manipulation and post-processing of free energy surfaces from output of molecular simulations

• Host: GitHub
• URL: https://github.com/molmod/thermolib
• Owner: molmod
• License: gpl-3.0
• Created: 2026-01-30T13:34:33.000Z (5 months ago)
• Default Branch: master
• Last Pushed: 2026-02-02T16:42:28.000Z (4 months ago)
• Last Synced: 2026-02-05T04:53:24.262Z (4 months ago)
• Language: Jupyter Notebook
• Homepage: https://molmod.github.io/ThermoLIB/
• Size: 99.5 MB
• Stars: 3
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# What is ThermoLIB?

ThermoLIB 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:

*  ***Thermodynamics*** - Module for constructing, manipulating and post-processing of 1D free energy profiles (FEP) and 2D free energy surfaces (FES). Functions include 

    - construction of FEPs using WHAM including error estimatoin

    - definition of (meta)stable micro- and macrostates

    - transformation of FEPs from one collective variable to another

    - (de)projection of a FES to a lower/higher dimensional FES.

*  ***Kinetics*** - Module for computing the rate constant of a process/reaction using transition state theory (TST). Functions include:

    - compute rate constant (which is theoretically indepedent of used CV)

    - compute associated phenomenological free energy barrier

    - error propagation from FEP to rate constant/phenomenological barrier

# Documentation

A 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/).

# How to cite ThermoLIB

If you use ThermoLIB in your research, please cite it as follows:

    M. Bocus, L. Vanduyfhuys, 2026, 10.48550/arXiv.2601.23071

# How to install?

ThermoLIB has the following dependencies:

* [Cython](http://cython.org/)

* [numpy](http://numpy.org/)

* [scipy](http://www.scipy.org/)

* [scikit-learn](https://scikit-learn.org/)

* [matplotlib](http://matplotlib.sourceforge.net)

* [h5py](https://www.h5py.org/)

* [ase](https://wiki.fysik.dtu.dk/ase/) (Version 3.23.0 or newer)

To **install ThermoLIB** using pip either download the master branch as zip, go to your desired pip environment and run 

    pip install ThermoLIB-master.zip

or 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:

    pip install git+ssh://github/molmod/ThermoLIB.git

# Terms of use

ThermoLIB is mainly developed by prof. Louis Vanduyfhuys at the Center for Molecular Modeling. Usage of ThermoLIB should be requested with prof. Vanduyfhuys.

Copyright (C) 2019 - 2026 Louis Vanduyfhuys 

Center for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise stated.