This repo condensed_phase_properties contains the functions and exemplary input data for water that were used to compute thermodynamic properties. In the data folder, all published data is available (thermodynamic data and diffusion constants).
- Free software: MIT
- Documentation: https://github.com/AnnaPicha/condensed_phase_properties/.
The functions computing condensed phase properties use openff-toolkit, which has not been released for python 3.13 yet. So create an environment with python==3.12. Then, clone and install this package with
- pip install .
- conda install openff-toolkit -c conda-forge
All functions used to compute thermodynamic properties can be found in the analysis/cp_props.py script. In the data folder, there is some examplary data from a NPT water simulation using TIP3 water. In the data/all_property_data folder, all raw data (thermodynamic properties and diffusion constants) can be found.
The python script compute_properties.py uses the water report in the data folder and the property functions in the cp_props.py script to compute and print thermodynamic properties. The python cript compute_bootstrapping_samples.py computes the mean and standard deviation from NBoot = 100 bootstrapping samples from the water data using the property bootstrapping functions in the cp_props.py script. The python script get_available_properties.py collects and prints the raw data (stored in the data folder) for a given species. To execute those scripts (once installed this repository), run
python compute_properties.py
or
python compute_bootstrapping_samples.py
or
python get_available_properties.py water
water can be replaced by methanol, acetone, nma, benzene or hexane.
For the calculation of MSD and diffusion constants with respect to the center of mass, the NewAnalysis package was used (https://github.com/cbc-univie/mdy-newanalysis-package). Radial distribution functions were computed using MDAnalysis (https://github.com/MDAnalysis/mdanalysis).
This package was created with Cookiecutter and the mgancita/cookiecutter-pypackage project template.