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.

Warning

The documentation is under construction.

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Documentation

Getting started

• Overview
  • Design principles
  • Quick start
• Installation

Core packages

• System
  • Particles’ properties
  • Dealing with velocities
  • Boundary conditions
  • The System object
  • Interaction and backends
  • Trajectory files
  • Particles on a lattice
• Trajectory
  • 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
• Simulation
  • A minimal simulation backend
  • Simple random walk
  • Adding callbacks
  • Fine-tuning the scheduler
  • Compute statistical averages
  • Faster backends

Backends

• Native backends
  • Interactions
  • Dynamics
  • Active
• Third-party backends
  • LAMMPS
  • RUMD

Frontends

• Database
  • Interaction models
  • Trajectory samples
• Lennard-Jones equation of state
  • Setup
  • Production
  • Analysis
  • Library
• Correlation
  • Setup
  • Analysis of the trajectory
  • Writing your own correlation functions
  • Storing results and analysis
• Landscape

Extras

• Tips and tricks
  • First trick
  • Second trick