Getting started

Installation

To use pyLIon a lammps executable must be installed in the system. In macOS this can be simply done via homebrew which will install all the necessary dependencies:

brew tap homebrew/science
brew install lammps

The executable is automatically added to the path with the alias lammps. Compiling from source is similarly easy but make sure to include the misc and rigid packages:

make yes-rigid
make yes-misc
make serial

You should get an executable named lmp_serial if you used the above. Trying running it and you should see the lammps input prompt. With lammps installed, install pylion with:

python3 setup.py

pylion is python3 only and has been tested with python 3.8 and the lammps 3Mar20 build.

Hint

Use the Anaconda python distribution that comes batteries included.

To check if the installation has worked try import pylion on a python3 prompt.

Requirements

pylion depends on a few packages that will be installed via pip when running the included setup file. If you are using Anaconda you probably have some of them installed already.

• h5py for dealing with h5 files.

• pexpect for real-time tty output.

• termcolor for pretty-printing of function documentation.

• jinja2 for generating the lammps templates.

• numpy for less than you might think.