ThermoLIB is a library developed at the Center for Molecular Modeling (CMM) 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
A full illustration on the use of ThermoLIB can be find in the preprint on Arxiv. More information on how to use ThermoLIB, including tutorials, can be found in its manual at https://molmod.github.io/ThermoLIB/.
If you use ThermoLIB in your research, please cite it as follows:
M. Bocus, L. Vanduyfhuys, 2026, 10.48550/arXiv.2601.23071
ThermoLIB has the following dependencies:
- Cython
- numpy
- scipy
- scikit-learn
- matplotlib
- h5py
- 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
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 Louis.Vanduyfhuys@UGent.be Center for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise stated.