Utilities

This page documents some utilities that AtomsBase provides in addition to the interface. This documentation is preliminary. PRs to improve it are welcome.

Cell Types

As of AtomsBase 0.4 we recommend that implementations of the interface specify a computational cell type. To simplify this, AtomsBase provides two prototype implementations:

• PeriodicCell : implements the standard parallepiped shaped cell defined through three cell vectors and periodicity (true or false) along each cell vector.
• IsolatedCell : implements a computational cell that is open (infinite) in all directions, i.e. the entire space.

Chemical Species

The function AtomsBase.species(sys, i) return the particle species of a particle (or multiple particles). AtomsBase does not enforce any specific type to be returned. However, it is recommended that systems describing atomic structures use - whenever possible - the ChemicalSpecies type that is implemented as part of AtomsBase.

• ChemicalSpecies : a prototype implementation and recommended default for the species of an atom.

Convenience functions

AtomsBase provides a number of convenience utilities that should work for any system that implements the AtomsBase interface. If they not work as expected this is likely a bug and should be reported as an issue.

• atomic_mass = mass : deprecated
• n_dimensions
• atomic_symbol
• atomic_number
• element_symbol
• chemical_formula
• element
• visualize_ascii

Testing Utilities

The AtomsBaseTesting package provides a few utility functions to test downstream packages for having properly implemented the AtomsBase interface. The tests are probably not complete, but they should be a good start ... and as always PRs are welcome.

Two functions are provided, namely make_test_system to generate standard FlexibleSystem test systems and test_approx_eq for testing approximate equality between AtomsBase systems (of not necessarily the same type). The basic idea of the functions is to use make_test_system to obtain a test system, construct an identical system in a downstream library and then use test_approx_eq to check they are actually equal.

For usage examples see the tests of ExtXYZ, AtomsIO, Chemfiles and ASEconnect.