wyckoff 0.2.3

A package for working with Wyckoff positions in crystallography

Wyckoff

A Python package for working with Wyckoff positions in crystallography.

Installation

pip install wyckoff

OR

uv add wyckoff

Usage

from wyckoff import WyckoffDatabase
# OR
# from wyckoff import wyckoff_positions, wyckoff_database

wycoff = WyckoffDatabase()
data = wycoff.data # or wyckoff_database()
wyckoff_positions = wycoff.wyckoff_positions # or wyckoff_positions

# Get Wyckoff positions for a specific space group
positions = wyckoff_positions(1)  # Space group 1
print(positions)

# Get the entire database
data = wyckoff_database()
# Print first label and positions of space group 2
for item in data["2"]:
    print(f"{item.label}: {item.positions}")

Info

If spacegroup variations are available, and functions are called without specifying the variabtion then first variation will be returned.

Following variation types are included in the database:

1. Unique axis settings: Suffixes like "-b" and "-c" typically indicate which crystallographic axis is chosen as the unique axis, especially in monoclinic and orthorhombic systems. For example:
   • "3-b" means space group 3 with b-axis as the unique axis
   • "3-c" means space group 3 with c-axis as the unique axis

Example:

positions = wyckoff_positions("3-b")  # Space group 3 with b-axis as the unique axis
print(positions)

2. Origin choice: Suffixes like "-1" and "-2" usually indicate different origin choices for the same space group:
   • "48-1" is space group 48 with origin choice 1
   • "48-2" is space group 48 with origin choice 2

Example:

positions = wyckoff_positions("48-1")  # Space group 48 with origin choice 1
print(positions)

3. Cell choices: Some suffixes may represent different conventional cell choices (hexagonal vs. rhombohedral settings in trigonal groups, for example).

Example:

positions = wyckoff_positions("148-hexagonal")  # Space group 148 with hexagonal cell
print(positions)

Data Source

This package is based on crystallographic data from bilbao crystallographic server. The inspiration for this package was drawn from the doped project: S. R. Kavanagh et al. doped: Python toolkit for robust and repeatable charged defect supercell calculations. Journal of Open Source Software 9 (96), 6433, 2024. Where they implemented a similar approach for handling wyckoff positions but they have custom data format.

License

MIT