Installation

Install python3.

Installation via pip from local directory, editable:

git clone https://github.com/paulboone/lammps_tools.git
cd lammps_tools
pip install -e ./

# run with:
# npytraj_diffusivity.py ...

Running locally:

git clone https://github.com/paulboone/lammps_tools.git
cd lammps_tools
pip install -r requirements.txt

# run with:
# ./bin/npytraj_diffusivity.py ...

Calculating diffusivity from a LAMMPS trajectory file

These assume you installed with pip install -e as above; if not, you'll need to call the scripts directly.

1. Convert the trajectory file to a numy array:

lammpstrj_to_npy.py --atoms-per-molecule 3 ./gas.lammpstrj

The flag atoms-per-molecule is obviously 3 for CO2, but will be 2 for N2

2. Do block averaging and output plots and diffusivity:

npytraj_diffusivity.py ./lammpstrj.npy --output-molecule-plots --fs-per-row 10 --average-rows 4000

The --average-rows flag should be set to something that will leave you a reasonable number of points. For a 4M row trajectory, averaging every 4000 rows, leaves you 1000 points. For a 500K row trajectory, averaging every 500 rows will leave you with 1000 points. So this needs to be picked appropriately for the trajectory length.