AtomsBase

A Julian abstract interface for atomic structures.

AtomsBase is an abstract interface for representation of atomic geometries in Julia. It aims to be a lightweight means of facilitating interoperability between various tools including, e.g.,

Simulation engines, e.g. molecular dynamics, geometry optimization, etc
Computing chemical or mechanical properties, e.g., via DFT, or interatomic potentials,
Integration with third party-libraries
I/O with standard file formats (.cif, .xyz, ...)
automatic differentiation and machine learning systems
numerical tools: sampling, integration schemes, etc.
visualization (e.g. plot recipes)

While AtomsBase focusses on representation of atomic systems, the sister package AtomsCalculators provides a general interface to compute properties of such systems.

Currently, the design philosophy is to be as lightweight as possible with a small set of required function dispatches to make adopting the interface easy. We also provide prototype implementations that we envision to be broadly applicable. If features beyond these are required we encourage developers to open PRs or provide their own implementations. For more on how to use the package, see the documentation.

Packages using AtomsBase

The following (not all yet-registered) packages currently make use of AtomsBase:

ACEpotentials
ASEPotential
ASEconvert : integration with the Atomistic Simulation Environment
AtomIO: I/O for atomic structures, also wraps some ASE functionality
Atomistic: integrated workflow for MD simulations, part of CESMIX
AutoBZCore.jl: Brillouin-zone integration
BFPIS
ChemistryFeaturization: Interface for featurization of atomic structures for input into machine learning models, part of Chemellia
DFTK: density functional theory simulations
EmpiricalPotentials
ExtXYZ: Parser for extended XYZ files
InteratomicPotentials: implementations of a variety of interatomic potentials, also part of CESMIX
Molly: molecular dynamics simulations
Xtals: I/O and structure representation for crystals