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# Source code for ase.build.bulk

    from math import sqrt

    from ase.atoms import Atoms
    from ase.symbols import string2symbols
    from ase.data import reference_states, atomic_numbers, chemical_symbols
    from ase.utils import plural

    def incompatible_cell(*, want, have):
        return RuntimeError('Cannot create {} cell for {} structure'
                            .format(want, have))

    def bulk(name, crystalstructure=None, a=None, b=None, c=None, *, alpha=None,
             covera=None, u=None, orthorhombic=False, cubic=False,
             basis=None):
        """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,
            rocksalt, cesiumchloride, fluorite or wurtzite.
        a: float
            Lattice constant.
        b: float
            Lattice constant.  If only a and b is given, b will be interpreted
            as c instead.
        c: float
            Lattice constant.
        alpha: float
            Angle in degrees for rhombohedral lattice.
        covera: float
            c/a ratio used for hcp.  Default is ideal ratio: sqrt(8/3).
        u: float
            Internal coordinate for Wurtzite structure.
        orthorhombic: bool
            Construct orthorhombic unit cell instead of primitive cell
            which is the default.
        cubic: bool
            Construct cubic unit cell if possible.
        """

        if c is None and b is not None:
            # If user passes (a, b) positionally, we want it as (a, c) instead:
            c, b = b, c

        if covera is not None and c is not None:
            raise ValueError("Don't specify both c and c/a!")

        xref = None
        ref = {}

        if name in chemical_symbols:
            Z = atomic_numbers[name]
            ref = reference_states[Z]
            if ref is not None:
                xref = ref['symmetry']

                # If user did not specify crystal structure, and no basis
                # is given, and the reference state says we need one, but
                # does not have one, then we can't proceed.
                if (crystalstructure is None and basis is None
                    and 'basis' in ref and ref['basis'] is None):
                    # XXX This is getting much too complicated, we need to split
                    # this function up.  A lot.
                    raise RuntimeError('This structure requires an atomic basis')

            if ref is None:
                ref = {}  # easier to 'get' things from empty dictionary than None

            if xref == 'cubic':
                # P and Mn are listed as 'cubic' but the lattice constants
                # are 7 and 9.  They must be something other than simple cubic
                # then. We used to just return the cubic one but that must
                # have been wrong somehow.  --askhl
                raise RuntimeError('Only simple cubic ("sc") supported')

        # Mapping of name to number of atoms in primitive cell.
        structures = {'sc': 1, 'fcc': 1, 'bcc': 1,
                      'tetragonal': 1,
                      'bct': 1,
                      'hcp': 1,
                      'rhombohedral': 1,
                      'orthorhombic': 1,
                      'mcl': 1,
                      'diamond': 1,
                      'zincblende': 2, 'rocksalt': 2, 'cesiumchloride': 2,
                      'fluorite': 3, 'wurtzite': 2}

        if crystalstructure is None:
            crystalstructure = xref
            if crystalstructure not in structures:
                raise ValueError('No suitable reference data for bulk {}.'
                                 '  Reference data: {}'
                                 .format(name, ref))

        if crystalstructure not in structures:
            raise ValueError('Unknown structure: {}.'
                             .format(crystalstructure))

        # Check name:
        natoms = len(string2symbols(name))
        natoms0 = structures[crystalstructure]
        if natoms != natoms0:
            raise ValueError('Please specify {} for {} and not {}'
                             .format(plural(natoms0, 'atom'),
                                     crystalstructure, natoms))

        if alpha is None:
            alpha = ref.get('alpha')

        if a is None:
            if xref != crystalstructure:
                raise ValueError('You need to specify the lattice constant.')
            try:
                a = ref['a']
            except KeyError:
                raise KeyError('No reference lattice parameter "a" for "{}"'
                               .format(name))

        if b is None:
            bovera = ref.get('b/a')
            if bovera is not None and a is not None:
                b = bovera * a

        if crystalstructure in ['hcp', 'wurtzite']:
            if cubic:
                raise incompatible_cell(want='cubic', have=crystalstructure)

            if c is not None:
                covera = c / a
            elif covera is None:
                if xref == crystalstructure:
                    covera = ref['c/a']
                else:
                    covera = sqrt(8 / 3)

        if covera is None:
            covera = ref.get('c/a')
            if c is None and covera is not None:
                c = covera * a

        if orthorhombic and crystalstructure not in ['sc', 'tetragonal',
                                                     'orthorhombic']:
            return _orthorhombic_bulk(name, crystalstructure, a, covera, u)

        if cubic and crystalstructure in ['bcc', 'cesiumchloride']:
            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 / 3, 2 / 3, 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
        elif crystalstructure == 'cesiumchloride':
            s1, s2 = string2symbols(name)
            atoms = bulk(s1, 'sc', a) + bulk(s2, 'sc', a)
            atoms.positions[1, :] += a / 2
        elif crystalstructure == 'fluorite':
            s1, s2, s3 = string2symbols(name)
            atoms = bulk(s1, 'fcc', a) + bulk(s2, 'fcc', a) + bulk(s3, 'fcc', a)
            atoms.positions[1, :] += a / 4
            atoms.positions[2, :] += a * 3 / 4
        elif crystalstructure == 'wurtzite':
            u = u or 0.25 + 1 / 3 / covera**2
            atoms = Atoms(2 * name,
                          scaled_positions=[(0, 0, 0),
                                            (1 / 3, 2 / 3, 0.5 - u),
                                            (1 / 3, 2 / 3, 0.5),
                                            (0, 0, 1 - u)],
                          cell=[(a, 0, 0),
                                (-a / 2, a * sqrt(3) / 2, 0),
                                (0, 0, a * covera)],
                          pbc=True)
        elif crystalstructure == 'bct':
            from ase.lattice import BCT
            if basis is None:
                basis = ref.get('basis')
            if basis is not None:
                natoms = len(basis)
            lat = BCT(a=a, c=c)
            atoms = Atoms([name] * natoms, cell=lat.tocell(), pbc=True,
                          scaled_positions=basis)
        elif crystalstructure == 'rhombohedral':
            atoms = _build_rhl(name, a, alpha, basis)
        elif crystalstructure == 'orthorhombic':
            atoms = Atoms(name, cell=[a, b, c], pbc=True)
        else:
            raise ValueError('Unknown crystal structure: ' + crystalstructure)

        if orthorhombic:
            assert atoms.cell.orthorhombic
        if cubic:
            assert abs(atoms.cell.angles() - 90).all() < 1e-10
        return atoms

    def _build_rhl(name, a, alpha, basis):
        from ase.lattice import RHL
        lat = RHL(a, alpha)
        cell = lat.tocell()
        if basis is None:
            # RHL: Given by A&M as scaled coordinates "x" of cell.sum(0):
            basis_x = reference_states[atomic_numbers[name]]['basis_x']
            basis = basis_x[:, None].repeat(3, axis=1)
        natoms = len(basis)
        return Atoms([name] * natoms, cell=cell, scaled_positions=basis, pbc=True)

    def _orthorhombic_bulk(name, crystalstructure, a, covera=None, u=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 / 6, 0.5),
                                            (0, 2 / 3, 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)])
        elif crystalstructure == 'cesiumchloride':
            atoms = Atoms(name, cell=(a, a, a), pbc=True,
                          scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)])
        elif crystalstructure == 'wurtzite':
            u = u or 0.25 + 1 / 3 / covera**2
            atoms = Atoms(4 * name,
                          cell=(a, a * 3**0.5, covera * a),
                          scaled_positions=[(0, 0, 0),
                                            (0, 1 / 3, 0.5 - u),
                                            (0, 1 / 3, 0.5),
                                            (0, 0, 1 - u),
                                            (0.5, 0.5, 0),
                                            (0.5, 5 / 6, 0.5 - u),
                                            (0.5, 5 / 6, 0.5),
                                            (0.5, 0.5, 1 - u)],
                          pbc=True)
        else:
            raise incompatible_cell(want='orthorhombic', have=crystalstructure)

        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 incompatible_cell(want='cubic', have=crystalstructure)

        return atoms

Documentation v: 3.19.0

Versions
  3.20.0b1 (development)
  3.19.0 (latest stable)