Grain-boundary generator with Atomman
from pathlib import Path
import numpy as np
from atomman import Atoms, Box, System
from atomman_gb import CubicGBGenerator, CubicGBInfo
def get_system_fcc() -> System:
vects = 4.05 * np.eye(3)
box = Box(vects=vects)
atype = 1
pos = [
[0, 0, 0],
[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0],
]
atoms = Atoms(atype=atype, pos=pos)
symbols = ("Al",)
system = System(atoms=atoms, box=box, symbols=symbols, scale=True) # set "scale=True" for fractional coordinates!
return system
if __name__ == "__main__":
system = get_system_fcc()
# STGB <001>/(100)
uvw = (0, 0, 1)
hkl = (1, 0, 0)
uvw_str = "".join(map(str, uvw))
hkl_str = "".join(map(str, hkl))
root_dir = Path(__file__).resolve().parent / f"Al_stgb_{uvw_str}_{hkl_str}"
root_dir.mkdir(exist_ok=True)
gbinfo = CubicGBInfo(uvw=uvw, max_sigma=32)
for data in gbinfo.datum:
for planes in data["symmetric_tilt"]:
plane_mid = planes["plane_mid"]
if not np.allclose(plane_mid, hkl):
continue
gbgen = CubicGBGenerator.make_tilt(
system, data["rotation"], uvw, data["csl"], planes["plane_1"]
)
gb = gbgen.generate(dmin=0.0)[0] # Fix microscopic DoF for simplicity
with open(
root_dir / f"gb_{data['sigma']}_{int(np.degrees(data['theta']))}.atom_dump", "w"
) as f:
atom_dump = gb.dump("atom_dump")
f.write(atom_dump)git clone [email protected]:lan496/atomman-gb.git
cd atomman-gb
conda create -n atomman-gb python=3.10 pip
conda activate atomman-gb
pip install .atomman-gb is released under a MIT license.
Installation
pip install -e ".[dev,docs]" Document
sphinx-autobuild --host=0.0.0.0 --port=8000 docs docs_build -v