/usr/share/pyshared/ase/lattice/bulk.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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from ase.atoms import Atoms, string2symbols
from ase.data import reference_states, atomic_numbers, chemical_symbols
def bulk(name, crystalstructure=None, a=None, c=None, covera=None,
orthorhombic=False, cubic=False):
"""Creating bulk systems.
Crystal structure and lattice constant(s) will be guessed if not
provided.
name: str
Chemical symbol or symbols as in 'MgO' or 'NaCl'.
crystalstructure: str
Must be one of sc, fcc, bcc, hcp, diamond, zincblende or
rocksalt.
a: float
Lattice constant.
c: float
Lattice constant.
covera: float
c/a raitio used for hcp. Use sqrt(8/3.0) for ideal ratio.
orthorhombic: bool
Construct orthorhombic unit cell instead of primitive cell
which is the default.
cubic: bool
Construct cubic unit cell if possible.
"""
if a is not None:
a = float(a)
if c is not None:
c = float(c)
if covera is not None and c is not None:
raise ValueError("Don't specify both c and c/a!")
if name in chemical_symbols:
Z = atomic_numbers[name]
ref = reference_states[Z]
if ref is not None:
xref = ref['symmetry']
else:
xref = None
if crystalstructure is None:
crystalstructure = xref
if a is None:
assert xref == crystalstructure
a = ref['a']
if crystalstructure == 'hcp':
cubic = False
if c is not None:
covera = c / a
elif covera is None:
if xref == 'hcp':
covera = ref['c/a']
else:
covera = sqrt(8.0 / 3.0)
if orthorhombic and crystalstructure != 'sc':
return _orthorhombic_bulk(name, crystalstructure, a, covera)
if cubic and crystalstructure == 'bcc':
return _orthorhombic_bulk(name, crystalstructure, a, covera)
if cubic and crystalstructure != 'sc':
return _cubic_bulk(name, crystalstructure, a)
if crystalstructure == 'sc':
atoms = Atoms(name, cell=(a, a, a), pbc=True)
elif crystalstructure == 'fcc':
b = a / 2
atoms = Atoms(name, cell=[(0, b, b), (b, 0, b), (b, b, 0)], pbc=True)
elif crystalstructure == 'bcc':
b = a / 2
atoms = Atoms(name, cell=[(-b, b, b), (b, -b, b), (b, b, -b)],
pbc=True)
elif crystalstructure == 'hcp':
atoms = Atoms(2 * name,
scaled_positions=[(0, 0, 0),
(1.0 / 3.0, 2.0 / 3.0, 0.5)],
cell=[(a, 0, 0),
(-a / 2, a * sqrt(3) / 2, 0),
(0, 0, covera * a)],
pbc=True)
elif crystalstructure == 'diamond':
atoms = bulk(2 * name, 'zincblende', a)
elif crystalstructure == 'zincblende':
s1, s2 = string2symbols(name)
atoms = bulk(s1, 'fcc', a) + bulk(s2, 'fcc', a)
atoms.positions[1] += a / 4
elif crystalstructure == 'rocksalt':
s1, s2 = string2symbols(name)
atoms = bulk(s1, 'fcc', a) + bulk(s2, 'fcc', a)
atoms.positions[1, 0] += a / 2
else:
raise ValueError('Unknown crystal structure: ' + crystalstructure)
return atoms
def _orthorhombic_bulk(name, crystalstructure, a, covera=None):
if crystalstructure == 'fcc':
b = a / sqrt(2)
atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)])
elif crystalstructure == 'bcc':
atoms = Atoms(2 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)])
elif crystalstructure == 'hcp':
atoms = Atoms(4 * name,
cell=(a, a * sqrt(3), covera * a),
scaled_positions=[(0, 0, 0),
(0.5, 0.5, 0),
(0.5, 1.0 / 6.0, 0.5),
(0, 2.0 / 3.0, 0.5)],
pbc=True)
elif crystalstructure == 'diamond':
atoms = _orthorhombic_bulk(2 * name, 'zincblende', a)
elif crystalstructure == 'zincblende':
s1, s2 = string2symbols(name)
b = a / sqrt(2)
atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0, 0.25),
(0.5, 0.5, 0.5), (0, 0.5, 0.75)])
elif crystalstructure == 'rocksalt':
s1, s2 = string2symbols(name)
b = a / sqrt(2)
atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0),
(0.5, 0.5, 0.5), (0, 0, 0.5)])
else:
raise RuntimeError
return atoms
def _cubic_bulk(name, crystalstructure, a):
if crystalstructure == 'fcc':
atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0, 0.5, 0.5),
(0.5, 0, 0.5), (0.5, 0.5, 0)])
elif crystalstructure == 'diamond':
atoms = _cubic_bulk(2 * name, 'zincblende', a)
elif crystalstructure == 'zincblende':
atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.25, 0.25, 0.25),
(0, 0.5, 0.5), (0.25, 0.75, 0.75),
(0.5, 0, 0.5), (0.75, 0.25, 0.75),
(0.5, 0.5, 0), (0.75, 0.75, 0.25)])
elif crystalstructure == 'rocksalt':
atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0, 0),
(0, 0.5, 0.5), (0.5, 0.5, 0.5),
(0.5, 0, 0.5), (0, 0, 0.5),
(0.5, 0.5, 0), (0, 0.5, 0)])
else:
raise RuntimeError
return atoms
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