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315 lines
12 KiB
315 lines
12 KiB
2 years ago
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from math import sqrt
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from cmmde_atoms import Atoms
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from cmmde_symbols import string2symbols
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from cmmde_data import reference_states, atomic_numbers, chemical_symbols
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from cmmde_utils import plural
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def incompatible_cell(*, want, have):
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return RuntimeError('Cannot create {} cell for {} structure'
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.format(want, have))
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def bulk(name, crystalstructure=None, a=None, b=None, c=None, *, alpha=None,
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covera=None, u=None, orthorhombic=False, cubic=False,
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basis=None):
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"""Creating bulk systems.
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Crystal structure and lattice constant(s) will be guessed if not
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provided.
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name: str
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Chemical symbol or symbols as in 'MgO' or 'NaCl'.
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crystalstructure: str
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Must be one of sc, fcc, bcc, tetragonal, bct, hcp, rhombohedral,
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orthorhombic, mlc, diamond, zincblende, rocksalt, cesiumchloride,
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fluorite or wurtzite.
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a: float
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Lattice constant.
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b: float
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Lattice constant. If only a and b is given, b will be interpreted
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as c instead.
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c: float
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Lattice constant.
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alpha: float
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Angle in degrees for rhombohedral lattice.
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covera: float
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c/a ratio used for hcp. Default is ideal ratio: sqrt(8/3).
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u: float
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Internal coordinate for Wurtzite structure.
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orthorhombic: bool
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Construct orthorhombic unit cell instead of primitive cell
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which is the default.
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cubic: bool
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Construct cubic unit cell if possible.
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"""
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if c is None and b is not None:
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# If user passes (a, b) positionally, we want it as (a, c) instead:
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c, b = b, c
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if covera is not None and c is not None:
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raise ValueError("Don't specify both c and c/a!")
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xref = None
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ref = {}
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if name in chemical_symbols:
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Z = atomic_numbers[name]
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ref = reference_states[Z]
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if ref is not None:
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xref = ref['symmetry']
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# If user did not specify crystal structure, and no basis
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# is given, and the reference state says we need one, but
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# does not have one, then we can't proceed.
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if (crystalstructure is None and basis is None
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and 'basis' in ref and ref['basis'] is None):
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# XXX This is getting much too complicated, we need to split
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# this function up. A lot.
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raise RuntimeError('This structure requires an atomic basis')
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if ref is None:
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ref = {} # easier to 'get' things from empty dictionary than None
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if xref == 'cubic':
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# P and Mn are listed as 'cubic' but the lattice constants
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# are 7 and 9. They must be something other than simple cubic
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# then. We used to just return the cubic one but that must
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# have been wrong somehow. --askhl
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raise RuntimeError('Only simple cubic ("sc") supported')
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# Mapping of name to number of atoms in primitive cell.
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structures = {'sc': 1, 'fcc': 1, 'bcc': 1,
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'tetragonal': 1,
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'bct': 1,
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'hcp': 1,
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'rhombohedral': 1,
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'orthorhombic': 1,
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'mcl': 1,
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'diamond': 1,
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'zincblende': 2, 'rocksalt': 2, 'cesiumchloride': 2,
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'fluorite': 3, 'wurtzite': 2}
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if crystalstructure is None:
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crystalstructure = xref
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if crystalstructure not in structures:
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raise ValueError('No suitable reference data for bulk {}.'
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' Reference data: {}'
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.format(name, ref))
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if crystalstructure not in structures:
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raise ValueError('Unknown structure: {}.'
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.format(crystalstructure))
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# Check name:
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natoms = len(string2symbols(name))
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natoms0 = structures[crystalstructure]
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if natoms != natoms0:
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raise ValueError('Please specify {} for {} and not {}'
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.format(plural(natoms0, 'atom'),
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crystalstructure, natoms))
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if alpha is None:
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alpha = ref.get('alpha')
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if a is None:
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if xref != crystalstructure:
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raise ValueError('You need to specify the lattice constant.')
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try:
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a = ref['a']
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except KeyError:
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raise KeyError('No reference lattice parameter "a" for "{}"'
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.format(name))
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if b is None:
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bovera = ref.get('b/a')
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if bovera is not None and a is not None:
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b = bovera * a
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if crystalstructure in ['hcp', 'wurtzite']:
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if cubic:
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raise incompatible_cell(want='cubic', have=crystalstructure)
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if c is not None:
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covera = c / a
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elif covera is None:
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if xref == crystalstructure:
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covera = ref['c/a']
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else:
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covera = sqrt(8 / 3)
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if covera is None:
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covera = ref.get('c/a')
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if c is None and covera is not None:
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c = covera * a
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if orthorhombic and crystalstructure not in ['sc', 'tetragonal',
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'orthorhombic']:
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return _orthorhombic_bulk(name, crystalstructure, a, covera, u)
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if cubic and crystalstructure in ['bcc', 'cesiumchloride']:
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return _orthorhombic_bulk(name, crystalstructure, a, covera)
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if cubic and crystalstructure != 'sc':
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return _cubic_bulk(name, crystalstructure, a)
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if crystalstructure == 'sc':
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atoms = Atoms(name, cell=(a, a, a), pbc=True)
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elif crystalstructure == 'fcc':
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b = a / 2
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atoms = Atoms(name, cell=[(0, b, b), (b, 0, b), (b, b, 0)], pbc=True)
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elif crystalstructure == 'bcc':
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b = a / 2
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atoms = Atoms(name, cell=[(-b, b, b), (b, -b, b), (b, b, -b)],
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pbc=True)
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elif crystalstructure == 'hcp':
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atoms = Atoms(2 * name,
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scaled_positions=[(0, 0, 0),
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(1 / 3, 2 / 3, 0.5)],
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cell=[(a, 0, 0),
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(-a / 2, a * sqrt(3) / 2, 0),
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(0, 0, covera * a)],
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pbc=True)
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elif crystalstructure == 'diamond':
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atoms = bulk(2 * name, 'zincblende', a)
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elif crystalstructure == 'zincblende':
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s1, s2 = string2symbols(name)
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atoms = bulk(s1, 'fcc', a) + bulk(s2, 'fcc', a)
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atoms.positions[1] += a / 4
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elif crystalstructure == 'rocksalt':
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s1, s2 = string2symbols(name)
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atoms = bulk(s1, 'fcc', a) + bulk(s2, 'fcc', a)
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atoms.positions[1, 0] += a / 2
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elif crystalstructure == 'cesiumchloride':
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s1, s2 = string2symbols(name)
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atoms = bulk(s1, 'sc', a) + bulk(s2, 'sc', a)
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atoms.positions[1, :] += a / 2
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elif crystalstructure == 'fluorite':
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s1, s2, s3 = string2symbols(name)
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atoms = bulk(s1, 'fcc', a) + bulk(s2, 'fcc', a) + bulk(s3, 'fcc', a)
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atoms.positions[1, :] += a / 4
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atoms.positions[2, :] += a * 3 / 4
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elif crystalstructure == 'wurtzite':
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u = u or 0.25 + 1 / 3 / covera**2
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atoms = Atoms(2 * name,
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scaled_positions=[(0, 0, 0),
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(1 / 3, 2 / 3, 0.5 - u),
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(1 / 3, 2 / 3, 0.5),
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(0, 0, 1 - u)],
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cell=[(a, 0, 0),
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(-a / 2, a * sqrt(3) / 2, 0),
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(0, 0, a * covera)],
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pbc=True)
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elif crystalstructure == 'bct':
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from ase.lattice import BCT
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if basis is None:
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basis = ref.get('basis')
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if basis is not None:
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natoms = len(basis)
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lat = BCT(a=a, c=c)
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atoms = Atoms([name] * natoms, cell=lat.tocell(), pbc=True,
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scaled_positions=basis)
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elif crystalstructure == 'rhombohedral':
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atoms = _build_rhl(name, a, alpha, basis)
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elif crystalstructure == 'orthorhombic':
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atoms = Atoms(name, cell=[a, b, c], pbc=True)
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else:
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raise ValueError('Unknown crystal structure: ' + crystalstructure)
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if orthorhombic:
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assert atoms.cell.orthorhombic
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if cubic:
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assert abs(atoms.cell.angles() - 90).all() < 1e-10
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return atoms
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def _build_rhl(name, a, alpha, basis):
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from ase.lattice import RHL
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lat = RHL(a, alpha)
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cell = lat.tocell()
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if basis is None:
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# RHL: Given by A&M as scaled coordinates "x" of cell.sum(0):
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basis_x = reference_states[atomic_numbers[name]]['basis_x']
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basis = basis_x[:, None].repeat(3, axis=1)
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natoms = len(basis)
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return Atoms([name] * natoms, cell=cell, scaled_positions=basis, pbc=True)
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def _orthorhombic_bulk(name, crystalstructure, a, covera=None, u=None):
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if crystalstructure == 'fcc':
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b = a / sqrt(2)
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atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
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scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)])
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elif crystalstructure == 'bcc':
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atoms = Atoms(2 * name, cell=(a, a, a), pbc=True,
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scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)])
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elif crystalstructure == 'hcp':
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atoms = Atoms(4 * name,
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cell=(a, a * sqrt(3), covera * a),
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scaled_positions=[(0, 0, 0),
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(0.5, 0.5, 0),
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(0.5, 1 / 6, 0.5),
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(0, 2 / 3, 0.5)],
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pbc=True)
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elif crystalstructure == 'diamond':
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atoms = _orthorhombic_bulk(2 * name, 'zincblende', a)
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elif crystalstructure == 'zincblende':
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s1, s2 = string2symbols(name)
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b = a / sqrt(2)
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atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
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scaled_positions=[(0, 0, 0), (0.5, 0, 0.25),
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(0.5, 0.5, 0.5), (0, 0.5, 0.75)])
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elif crystalstructure == 'rocksalt':
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s1, s2 = string2symbols(name)
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b = a / sqrt(2)
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atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
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scaled_positions=[(0, 0, 0), (0.5, 0.5, 0),
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(0.5, 0.5, 0.5), (0, 0, 0.5)])
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elif crystalstructure == 'cesiumchloride':
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atoms = Atoms(name, cell=(a, a, a), pbc=True,
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scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)])
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elif crystalstructure == 'wurtzite':
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u = u or 0.25 + 1 / 3 / covera**2
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atoms = Atoms(4 * name,
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cell=(a, a * 3**0.5, covera * a),
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scaled_positions=[(0, 0, 0),
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(0, 1 / 3, 0.5 - u),
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(0, 1 / 3, 0.5),
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(0, 0, 1 - u),
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(0.5, 0.5, 0),
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(0.5, 5 / 6, 0.5 - u),
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(0.5, 5 / 6, 0.5),
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(0.5, 0.5, 1 - u)],
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pbc=True)
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else:
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raise incompatible_cell(want='orthorhombic', have=crystalstructure)
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return atoms
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def _cubic_bulk(name, crystalstructure, a):
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if crystalstructure == 'fcc':
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atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
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scaled_positions=[(0, 0, 0), (0, 0.5, 0.5),
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(0.5, 0, 0.5), (0.5, 0.5, 0)])
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elif crystalstructure == 'diamond':
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atoms = _cubic_bulk(2 * name, 'zincblende', a)
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elif crystalstructure == 'zincblende':
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atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
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scaled_positions=[(0, 0, 0), (0.25, 0.25, 0.25),
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(0, 0.5, 0.5), (0.25, 0.75, 0.75),
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(0.5, 0, 0.5), (0.75, 0.25, 0.75),
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(0.5, 0.5, 0), (0.75, 0.75, 0.25)])
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elif crystalstructure == 'rocksalt':
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atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
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scaled_positions=[(0, 0, 0), (0.5, 0, 0),
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(0, 0.5, 0.5), (0.5, 0.5, 0.5),
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(0.5, 0, 0.5), (0, 0, 0.5),
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(0.5, 0.5, 0), (0, 0.5, 0)])
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else:
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raise incompatible_cell(want='cubic', have=crystalstructure)
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return atoms
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