mlyzed 0.2.3

Molecular dynamics post-processing toolbox

About

mlyzed is the python library for post-processing molecular dynamics (MD) simulations. The main features of the code are trajectory unwrapping, FFT calculation of the MSD, analysis of the hop events, 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. (Not ready yet)

Installation

pip install mlyzed

or

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

Minimum usage example

import mlyzed as md

traj = md.Trajectory.from_file('traj.lammpstrj') # any ASE readable format
msd = md.classical_msd(traj[100:], specie = 'Li', timestep = 2)
msd.plot()

Alternatives:

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

• mdtraj - a huge inspiration to this library
• pymatgen-diffusion-analysis
• kinisi
• MDAnalysis
• LLC_Membranes