About

mlyzed is a small library for post-processing molecular dynamics (MD) simulations. The main features of the code are trajectory unwrapping, FFT calculation of the MSD, and ease of use.

Note: The library is not guaranteed to be bug free. If you observe unexpected results, errors, please report an issue at the github.

For more details, see the documentation.

Installation

git clone https://github.com/dembart/mlyzed
cd mlyzed
pip install .

Minimum usage example

from mlyzed import Lyze
calc = Lyze()
traj = calc.read_file('traj.lammpstrj') # can be XDATCAR, OUTCAR, extxyz
dt, msd = calc.classical_msd(
                            specie = 'Li', # specie of interest
                            timestep = 2,  # in fs
                            skip = 1000,   # skip first 1000 steps
                            )

Alternatives:

Here are some alternatives and inspirations for this library (see below). You may find them better in some ways.

• pymatgen-diffusion-analysis
• kinisi
• MDAnalysis
• LLC_Membranes