Atooms

atooms is a Python framework for simulations of interacting particles. It makes it easy to develop simulation and analysis tools using an expressive language, without sacrificing efficiency. To achieve this, atooms relies on backends written in C, CUDA or Fortran.

This tutorial guides you through some of the features of atooms. You can run this tutorial live on Binder or by downloading the jupyter notebooks from the Framagit repository.

Core library

• Basics
  • Particles’ properties
  • Dealing with velocities
  • Boundary conditions
  • The System object
  • Interaction and backends
  • Trajectory files
  • Particles on a lattice
• Simulations
  • A minimal simulation backend
  • Simple random walk
  • Adding callbacks
  • Fine-tuning the scheduler
  • Compute statistical averages
  • Faster backends
  • Molecular dynamics with LAMMPS
  • Molecular dynamics with RUMD
• Trajectories
  • Trajectory formats
  • Custom trajectory formats
  • Custom trajectory output
  • Conversion between trajectory formats
  • Add and modify trajectory properties on the fly with callbacks
  • Extend trajectory classes