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127 lines
4.1 KiB
127 lines
4.1 KiB
2 years ago
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"""Function-like object creating hexagonal lattices.
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The following lattice creators are defined:
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* Hexagonal
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* HexagonalClosedPacked
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* Graphite
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* Graphene
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Example for using Graphene to create atoms object gra::
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from ase.lattice.hexagonal import *
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import ase.io as io
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from ase import Atoms, Atom
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index1=6
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index2=7
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mya = 2.45
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myc = 20.0
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gra = Graphene(symbol = 'C',latticeconstant={'a':mya,'c':myc},
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size=(index1,index2,1))
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io.write('test.xyz', gra, format='xyz')
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"""
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from ase.lattice.triclinic import TriclinicFactory
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class HexagonalFactory(TriclinicFactory):
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"A factory for creating simple hexagonal lattices."
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# The name of the crystal structure in ChemicalElements
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xtal_name = "hexagonal"
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def make_crystal_basis(self):
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"""Make the basis matrix for the crystal and system unit cells."""
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# First convert the basis specification to a triclinic one
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if isinstance(self.latticeconstant, type({})):
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self.latticeconstant['alpha'] = 90
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self.latticeconstant['beta'] = 90
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self.latticeconstant['gamma'] = 120
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self.latticeconstant['b/a'] = 1.0
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else:
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if len(self.latticeconstant) == 2:
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a, c = self.latticeconstant
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self.latticeconstant = (a, a, c, 90, 90, 120)
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else:
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raise ValueError(
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"Improper lattice constants for hexagonal crystal.")
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TriclinicFactory.make_crystal_basis(self)
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def find_directions(self, directions, miller):
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"""Find missing directions and miller indices from the specified ones.
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Also handles the conversion of hexagonal-style 4-index notation to
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the normal 3-index notation.
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"""
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directions = list(directions)
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miller = list(miller)
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if miller != [None, None, None]:
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raise NotImplementedError(
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'Specifying Miller indices of surfaces currently '
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'broken for hexagonal crystals.')
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for obj in (directions, miller):
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for i in range(3):
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if obj[i] is not None:
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(a, b, c, d) = obj[i]
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if a + b + c != 0:
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raise ValueError(
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("(%d,%d,%d,%d) is not a valid hexagonal Miller " +
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"index, as the sum of the first three numbers " +
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"should be zero.") % (a, b, c, d))
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x = 4 * a + 2 * b
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y = 2 * a + 4 * b
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z = 3 * d
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obj[i] = (x, y, z)
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TriclinicFactory.find_directions(self, directions, miller)
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def print_directions_and_miller(self, txt=""):
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"Print direction vectors and Miller indices."
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print("Direction vectors of unit cell%s:" % (txt,))
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for i in (0, 1, 2):
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self.print_four_vector("[]", self.directions[i])
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print("Miller indices of surfaces%s:" % (txt,))
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for i in (0, 1, 2):
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self.print_four_vector("()", self.miller[i])
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def print_four_vector(self, bracket, numbers):
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bra, ket = bracket
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(x, y, z) = numbers
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a = 2 * x - y
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b = -x + 2 * y
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c = -x - y
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d = 2 * z
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print(" %s%d, %d, %d%s ~ %s%d, %d, %d, %d%s" %
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(bra, x, y, z, ket, bra, a, b, c, d, ket))
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Hexagonal = HexagonalFactory()
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class HexagonalClosedPackedFactory(HexagonalFactory):
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"A factory for creating HCP lattices."
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xtal_name = "hcp"
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bravais_basis = [[0, 0, 0], [1.0 / 3.0, 2.0 / 3.0, 0.5]]
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HexagonalClosedPacked = HexagonalClosedPackedFactory()
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class GraphiteFactory(HexagonalFactory):
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"A factory for creating graphite lattices."
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xtal_name = "graphite"
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bravais_basis = [[0, 0, 0], [1.0 / 3.0, 2.0 / 3.0, 0],
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[1.0 / 3.0, 2.0 / 3.0, 0.5], [2.0 / 3.0, 1.0 / 3.0, 0.5]]
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Graphite = GraphiteFactory()
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class GrapheneFactory(HexagonalFactory):
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"A factory for creating graphene lattices."
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xtal_name = "graphene"
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bravais_basis = [[0, 0, 0], [1.0 / 3.0, 2.0 / 3.0, 0]]
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Graphene = GrapheneFactory()
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