pylion

A LAMMPS wrapper for molecular dynamics simulations of trapped ions.

Documentation on readthedocs pyLIon

Bentine2019 https://arxiv.org/abs/1907.10514
Trypogeorgos2013 https://arxiv.org/abs/1310.6294
Foot2018 https://arxiv.org/abs/1801.00424

Installation

First install lammps using your preferred method. If installing from source make sure the rigid and misc packages are installed as well. Something like the following should do it:

make yes-rigid
make yes-misc
make serial

# other useful commands
make package # list available packages and help
make ps # list package status

This will make the lmp-serial executable. On macOS you can also try make mac or installing the precompiled package from homebrew.

With lammps installed, install pylion with:

python3 setup.py

pylion is python 3 only and has been tested with python 3.8 and the lammps 3Mar20 build, but might work with other configurations just as well. We suggest using the Anaconda python distribution that comes batteries included. To make the documentation use make html in the documentation folder.

Getting started

Once you're done with the installation you can start simulating clouds of ions within a few lines of code. The following simulates the trajectories of 100 ions, trapped in a linear Paul trap.

import pylion as pl

s = pl.Simulation('simple')

ions = {'mass': 40, 'charge': 1}
s.append(pl.createioncloud(ions, 1e-3, 100))

trap = {'radius': 3.75e-3, 'length': 2.75e-3, 'kappa': 0.244,
        'frequency': 3.85e6, 'voltage': 500, 'endcapvoltage': 15}
s.append(pl.linearpaultrap(trap))

s.append(pl.langevinbath(0, 1e-5))

s.append(pl.dump('positions.txt', variables=['x', 'y', 'z'], steps=10))

s.append(pl.evolve(1e4))
s.execute()

Look into the examples and tests folders for more ideas.

Tests

Run all autodiscovered tests with pytest will take a few minutes. If you don't want to wait that much use pytest -m 'not slow'. The tests/test_pylion.py is for implementation details. You can run this only while developing which will be much faster. The other tests are slower because they test for correct physics and have to run a bunch of simulations.

Documentation

You will need sphinx and the sphix_rtd_theme to build the documentation. Both can be installed with:

pip install sphinx # or conda install sphinx
pip install sphinx_rtd_theme

If you're using Anaconda you probably have sphinx already. Go to the docs folder folder and run make html or whatever format you prefer.

Features

Simulate multiple ion species in the same trap.
Use multiple trap driving frequencies. See Phys. Rev. A 94, 023609 for details.
Define rigid bodies from groups of ions to simulate mesoscopic charged objects.

If you find this software useful in your research please cite:

E. Bentine et al., Computer Physics Communications, 253, 107187, (2020)

D. Trypogeorgos et al., Phys. Rev. A 94, 023609, (2016)

C. Foot et al., IJMS Volume 430, July 2018, Pages 117-125

File structure

pylion: contains all the main classes for managing the simulation.
examples: example simulations showing different features of (py)lion.
tests: a collection of scripts used to test the correct implementation of (py)lion.
docs: documentation folder including user and developer manuals.

Free software: MIT license