Welcome to pyLIon’s documentation!

pylion is a python3 wrapper for the popular molecular dynamics package LAMMPS. LAMMPS is a classical molecular dynamics code, the current version of which has been in active development since 2004. The project’s longevity and highly active use (the original 1995 paper was cited 1,127 times in 2013) has resulted in an optimised and feature-rich program.

pylion attempts to provide the ion trap community access to the features of LAMMPS via a more simplistic syntax and usage of familiar terms.

Contents:

• Getting started
  • Installation
  • Requirements
• Simulation
  • Simulation object
  • Attributes
• Examples
  • Simple example
  • Energy minimisation in a pseudopotential
  • Rigid bodies
  • Secular resonances of a single ion in a spherical Paul trap
  • Excess micromotion of a single ion in a spherical Paul trap
• Functions
  • efield()
  • placeions()
  • createioncloud()
  • evolve()
  • thermalvelocities()
  • minimise()
  • ionneutralheating()
  • langevinbath()
  • lasercool()
  • linearpaultrap()
  • endcappaultrap()
  • endcap_aq()
  • endcap_beta()
  • endcap_secular()
  • timeaverage()
  • squaresum()
  • dump()
  • trapaqtovoltage()
  • readdump()
• Extending pylion
  • Implementation
  • Customising a simulation
  • Testing
• FAQ

Indices and tables

• Index

• Module Index

• Search Page