wyckoff 0.2.5

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

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:

wyckoff_positions = WyckoffDatabase().wyckoff_positions
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 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