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"""Script to update symm_ops.json and symm_data.yaml in symmetry module due to issues #3845 and #3862.
symm_ops.json:
- adds Hermann_mauguin point group key and short Hermann Mauguin space group symbol
- converts screw axis notation to symm_data standard
symm_data.json
- removes mapping of rhombohedral space group types onto symbol + appended H
- replaces I/P2_12_121 key with I/P2_12_12_1
"""
from __future__ import annotations
import sys
from monty.serialization import dumpfn, loadfn
from pymatgen.symmetry.groups import PointGroup
__author__ = "Katharina Ueltzen @kaueltzen"
__date__ = "2024-06-06"
SYMM_OPS = loadfn("../src/pymatgen/symmetry/symm_ops.json")
SYMM_DATA = loadfn("../src/pymatgen/symmetry/symm_data.json")
def convert_symmops_to_sg_encoding(symbol: str) -> str:
"""
Utility function to convert SYMMOPS space group type symbol notation
into SYMM_DATA["space_group_encoding"] key notation with underscores before
translational part of screw axes.
Args:
symbol (str): "hermann_mauguin" or "universal_h_m" key of symmops.json
Returns:
str: symbol in the format of SYMM_DATA["space_group_encoding"] keys
"""
symbol_representation = symbol.split(":")
representation = ":" + "".join(symbol_representation[1].split(" ")) if len(symbol_representation) > 1 else ""
blickrichtungen = symbol_representation[0].split(" ")
blickrichtungen_new = []
for br in blickrichtungen:
if len(br) > 1 and br[0].isdigit() and br[1].isdigit():
blickrichtungen_new.append(br[0] + "_" + br[1:])
else:
blickrichtungen_new.append(br)
return "".join(blickrichtungen_new) + representation
def remove_identity_from_full_hermann_mauguin(symbol: str) -> str:
"""
Utility function to remove identity along blickrichtung (except in P1).
Args:
symbol (str): "hermann_mauguin" key of symmops.json
Returns:
str: short "hermann_mauguin" key
"""
if symbol in ("P 1", "C 1", "P 1 "):
return symbol
blickrichtungen = symbol.split(" ")
if blickrichtungen[1].startswith("3"):
return symbol
blickrichtungen_new = []
for br in blickrichtungen:
if br != "1":
blickrichtungen_new.append(br + " ")
return "".join(blickrichtungen_new)
new_symm_data = {}
for k, v in SYMM_DATA["space_group_encoding"].items():
if k.endswith("H"):
new_symm_data[k.removesuffix("H")] = v
elif k == "I2_12_121":
new_symm_data["I2_12_12_1"] = v
elif k == "P2_12_121":
new_symm_data["P2_12_12_1"] = v
else:
new_symm_data[k] = v
SYMM_DATA["space_group_encoding"] = new_symm_data
for sg_symbol in SYMM_DATA["space_group_encoding"]:
SYMM_DATA["space_group_encoding"][sg_symbol]["point_group"] = PointGroup.from_space_group(
sg_symbol=sg_symbol
).symbol
for spg in SYMM_OPS:
if "(" in spg["hermann_mauguin"]:
spg["hermann_mauguin"] = spg["hermann_mauguin"].split("(")[0]
short_h_m = remove_identity_from_full_hermann_mauguin(spg["hermann_mauguin"])
spg["short_h_m"] = convert_symmops_to_sg_encoding(short_h_m)
spg["hermann_mauguin_u"] = convert_symmops_to_sg_encoding(spg["hermann_mauguin"])
for spg_idx, spg in enumerate(SYMM_OPS):
try:
pg = PointGroup.from_space_group(spg["short_h_m"])
except AssertionError as e:
print(spg, str(e))
sys.exit(1)
SYMM_OPS[spg_idx]["point_group"] = pg.symbol
dumpfn(SYMM_DATA, "../src/pymatgen/symmetry/symm_data.json")
dumpfn(SYMM_OPS, "../src/pymatgen/symmetry/symm_ops.json")
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