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
More information on how to use ThermoLIB, including tutorials, can be found in its manual at https://molmod.github.io/ThermoLIB/.
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 properly configured your ssh to access GitHub.com using a key through the defined alias 'github', 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 [email protected] Center for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise stated.