atomlib 0.3

A collection of utilities to manipulate atomic structures

atomlib: A modern, extensible library for creating atomic structures

atomlib is a package for creating, modifying, and controlling atomic structures. It draws heavy inspiration from previous tools like Atomsk and ASE, but attempts to provide a cleaner, more consistent interface that can be used from Python or a command line.

atomlib has minimal dependencies: numpy, scipy, and polars are required for core atom structure manipulation, and click is required for command line functionality.

Atomic representation & supported properties

Atomic structures are stored as polars DataFrames, providing a clean, immutable interface that maximizes expressiveness and minimizes errors. For formats that allow arbitrary properties, these properties can be passed through transparently. atomlib has first-class support for fractional occupancy, Debye-Waller factors, atomic forces, and labels.

Translational symmetry is stored in Cell objects, which represent a fully generic cell. Atoms can be modified in any coordinate system that makes sense (global, local real-space, cell fraction, box fraction, etc.). Support for non-translational symmetry operations is limited at this point.

For more information, check out the example notebooks and the API documentation.

Currently supported file formats

File format support is still a work in progress. Where possible, parsers are implemented from scratch in-repo. Most formats are implemented in two steps: Parsing to an intermediate representation which preserves all format-specific information, and then conversion to the generic Atoms & AtomCell types for manipulation & display. This means you can write your own code to utilize advanced format features even if they're not supported out of the box.

Format	Ext.	Read	Write	Notes
CIF	.cif	:white_check_mark:	:x:	CIF1 & CIF2. Isotropic B-factor only
XCrysDen	.xsf	:white_check_mark:	:white_check_mark:
AtomEye CFG	.cfg	:white_check_mark:	:white_check_mark:	Currently basic format only
Basic XYZ	.xyz	:white_check_mark:	:white_check_mark:
Ext. XYZ	.exyz	:white_check_mark:	:white_check_mark:	Arbitrary properties not implemented
Special XYZ	.sxyz	:x:	:x:	To be implemented
LAMMPS Data	.lmp	:x:	:white_check_mark:
Quantum Espresso	.qe	:x:	:white_check_mark:	pw.x format
pyMultislicer	.mslice	:x:	:white_check_mark: