wyckoff 0.3.0

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

Simple Example:

from wyckoff import WyckoffDatabase

wyckoff = WyckoffDatabase()
data = wyckoff.data

for items in data["2"]:
    print(items)

print("Spacegroup 3 (which is 3-b varient):")
print(data["3"][0])

for more complex example checkout the example file

Info

IMPORTANT: If variations are available for a spacegroup, and functions/dictionary are called/indexed without specifying the variation then first available 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.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.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.wyckoff_positions("148-hexagonal")  # Space group 148 with hexagonal cell
print(positions)

Data Source

This implementation is inspierd by a utility fuction in doped project. That version used a non-standard datafile for parsing the Wyckoff positions from bilbao crystallographic server. This implementation uses a standard JSON file for parsing the Wyckoff positions, add additional checks and validations to ensure data integrity, remove a bug that produces duplicate Wyckoff positions and custom wyckoff dataclass, etc,.

License

MIT