mdtools

This is a (growing) collection of tools I use when working with LAMMPs.

See also lammps-binary-dump-reader.

logplotter.py

This serves two purposes:

• A command line interface for quickly inspecting the results of a simulation (the simulation does not have to be finished!). Basic usage: logplotter.py -i log.part1 log.part2 -x Time -y Temp. Use logplotter.py -h to see more options.
• A module containing the find_data function, which reads a log file and returns the contained data as a dictionary. Basic usage: data = find_data("log.lammps"); plt.plot(data["Step"], data["Temp"]).

Installation

pip install .

sync.sh

A janky bash script for continuous downloading of a remote data file until no further changes are detected.

Arguments:

1. The remote file, e.g. cluster:/work/username/dump.simulation
2. The local destination (optional, default .), e.g. dump.18_12_24