asaf 0.0.1

Library to facilitate the processing and analysis of data from the grand canonical transition matrix Monte Carlo adsorption simulations.

Quick and easy analysis of the data from the flat histogram simulations

ASAF (Adsorption Simulation Analysis Facilitator) is a python library created to facilitate the processing and analysis of data from grand canonical transition matrix Monte Carlo adsorption simulations.

[!WARNING] ASAF is under active development. Backward compatibility with older versions is not currently guaranteed.

Features:

• calculation of the macrostate probability distribution (MPC) from the transition probabilities
• interpolation of the transition probabilities
• calculation of the adsorption isotherm from the MPD
• calculation of the free energy from the MPD
• temperature extrapolation of the macrostate probability distribution
• saving the isotherms to an AIF file

Installation

For the latest PyPI release:

pip install asaf

For the development version:

pip install "asaf @ git+https://github.com/bartoszmazurwro/asaf.git"

Development

ASAF uses uv for local development. To set up the repository:

git clone https://github.com/bartoszmazurwro/asaf.git
cd asaf
uv sync --locked --all-extras --dev
uv run pytest

See CONTRIBUTING.md for the full development, testing, and release workflow.

Citing

If you use ASAF in your work, please consider citing the following paper:

Efficient Modeling of Water Adsorption in MOFs Using Interpolated Transition Matrix Monte Carlo, B. Mazur, L. Firlej, and B. Kuchta, 2024, ACS Appl. Mater. Interfaces, DOI: 10.1021/acsami.4c02616.

FAQ

In my prob files I see current_cycle column instead of macrostate.

That's because you're looking at a prob file for a simulation in a particular macrostate. To calculate the macrostate probability distribution you need at least several simulations in different macrostates. The diagram below explains the scheme for creating the prob file used by ASAF from prob files generated by RASPA.

I don't have .metadata.json file.

Currently, the only options are to create this file manually (for example, by copying one of the example files and modifying it) or to add a function to your workflow that generates such a file based on RASPA input files. In the future, ASAF will be able to do this.

Prob files are not generated.

Make sure that you are using modified version of RASPA.

My prob files are huge

In general, you can play with PrintGhostProbabilitesEvery parameter. A more frequent print will be useful when you want to use energy fluctuations to extrapolate MPD, otherwise a value similar to that used in PrintEvery will be sufficient to monitor the simulation.