/usr/share/pyshared/ase/lattice/surface.py is in python-ase 3.6.0.2515-1.
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The helper functions can create the most common low-index surfaces,
add vacuum layers and add adsorbates.
"""
from math import sqrt
import numpy as np
from ase.atom import Atom
from ase.atoms import Atoms
from ase.data import reference_states, atomic_numbers
from ase.lattice.general_surface import surface
def fcc100(symbol, size, a=None, vacuum=None):
"""FCC(100) surface.
Supported special adsorption sites: 'ontop', 'bridge', 'hollow'."""
return _surface(symbol, 'fcc', '100', size, a, None, vacuum)
def fcc110(symbol, size, a=None, vacuum=None):
"""FCC(110) surface.
Supported special adsorption sites: 'ontop', 'longbridge',
'shortbridge','hollow'."""
return _surface(symbol, 'fcc', '110', size, a, None, vacuum)
def bcc100(symbol, size, a=None, vacuum=None):
"""BCC(100) surface.
Supported special adsorption sites: 'ontop', 'bridge', 'hollow'."""
return _surface(symbol, 'bcc', '100', size, a, None, vacuum)
def bcc110(symbol, size, a=None, vacuum=None, orthogonal=False):
"""BCC(110) surface.
Supported special adsorption sites: 'ontop', 'longbridge',
'shortbridge', 'hollow'.
Use *orthogonal=True* to get an orthogonal unit cell - works only
for size=(i,j,k) with j even."""
return _surface(symbol, 'bcc', '110', size, a, None, vacuum, orthogonal)
def bcc111(symbol, size, a=None, vacuum=None, orthogonal=False):
"""BCC(111) surface.
Supported special adsorption sites: 'ontop'.
Use *orthogonal=True* to get an orthogonal unit cell - works only
for size=(i,j,k) with j even."""
return _surface(symbol, 'bcc', '111', size, a, None, vacuum, orthogonal)
def fcc111(symbol, size, a=None, vacuum=None, orthogonal=False):
"""FCC(111) surface.
Supported special adsorption sites: 'ontop', 'bridge', 'fcc' and 'hcp'.
Use *orthogonal=True* to get an orthogonal unit cell - works only
for size=(i,j,k) with j even."""
return _surface(symbol, 'fcc', '111', size, a, None, vacuum, orthogonal)
def hcp0001(symbol, size, a=None, c=None, vacuum=None, orthogonal=False):
"""HCP(0001) surface.
Supported special adsorption sites: 'ontop', 'bridge', 'fcc' and 'hcp'.
Use *orthogonal=True* to get an orthogonal unit cell - works only
for size=(i,j,k) with j even."""
return _surface(symbol, 'hcp', '0001', size, a, c, vacuum, orthogonal)
def hcp10m10(symbol, size, a=None, c=None, vacuum=None):
"""HCP(10m10) surface.
Supported special adsorption sites: 'ontop'.
Works only for size=(i,j,k) with j even."""
return _surface(symbol, 'hcp', '10m10', size, a, c, vacuum)
def diamond100(symbol, size, a=None, vacuum=None):
"""DIAMOND(100) surface.
Supported special adsorption sites: 'ontop'."""
return _surface(symbol, 'diamond', '100', size, a, None, vacuum)
def diamond111(symbol, size, a=None, vacuum=None, orthogonal=False):
"""DIAMOND(111) surface.
Supported special adsorption sites: 'ontop'."""
if orthogonal:
raise NotImplementedError("Can't do orthogonal cell yet!")
return _surface(symbol, 'diamond', '111', size, a, None, vacuum, orthogonal)
def add_adsorbate(slab, adsorbate, height, position=(0, 0), offset=None,
mol_index=0):
"""Add an adsorbate to a surface.
This function adds an adsorbate to a slab. If the slab is
produced by one of the utility functions in ase.lattice.surface, it
is possible to specify the position of the adsorbate by a keyword
(the supported keywords depend on which function was used to
create the slab).
If the adsorbate is a molecule, the atom indexed by the mol_index
optional argument is positioned on top of the adsorption position
on the surface, and it is the responsibility of the user to orient
the adsorbate in a sensible way.
This function can be called multiple times to add more than one
adsorbate.
Parameters:
slab: The surface onto which the adsorbate should be added.
adsorbate: The adsorbate. Must be one of the following three types:
A string containing the chemical symbol for a single atom.
An atom object.
An atoms object (for a molecular adsorbate).
height: Height above the surface.
position: The x-y position of the adsorbate, either as a tuple of
two numbers or as a keyword (if the surface is produced by one
of the functions in ase.lattice.surfaces).
offset (default: None): Offsets the adsorbate by a number of unit
cells. Mostly useful when adding more than one adsorbate.
mol_index (default: 0): If the adsorbate is a molecule, index of
the atom to be positioned above the location specified by the
position argument.
Note *position* is given in absolute xy coordinates (or as
a keyword), whereas offset is specified in unit cells. This
can be used to give the positions in units of the unit cell by
using *offset* instead.
"""
info = slab.adsorbate_info
if 'cell' not in info:
info['cell'] = slab.get_cell()[:2, :2]
pos = np.array([0.0, 0.0]) # (x, y) part
spos = np.array([0.0, 0.0]) # part relative to unit cell
if offset is not None:
spos += np.asarray(offset, float)
if isinstance(position, str):
# A site-name:
if 'sites' not in info:
raise TypeError('If the atoms are not made by an ' +
'ase.lattice.surface function, ' +
'position cannot be a name.')
if position not in info['sites']:
raise TypeError('Adsorption site %s not supported.' % position)
spos += info['sites'][position]
else:
pos += position
pos += np.dot(spos, info['cell'])
# Convert the adsorbate to an Atoms object
if isinstance(adsorbate, Atoms):
ads = adsorbate
elif isinstance(adsorbate, Atom):
ads = Atoms([adsorbate])
else:
# Hope it is a useful string or something like that
ads = Atoms(adsorbate)
# Get the z-coordinate:
try:
a = info['top layer atom index']
except KeyError:
a = slab.positions[:, 2].argmax()
info['top layer atom index'] = a
z = slab.positions[a, 2] + height
# Move adsorbate into position
ads.translate([pos[0], pos[1], z] - ads.positions[mol_index])
# Attach the adsorbate
slab.extend(ads)
def _surface(symbol, structure, face, size, a, c, vacuum, orthogonal=True):
"""Function to build often used surfaces.
Don't call this function directly - use fcc100, fcc110, bcc111, ..."""
Z = atomic_numbers[symbol]
if a is None:
sym = reference_states[Z]['symmetry']
if sym != structure:
raise ValueError("Can't guess lattice constant for %s-%s!" %
(structure, symbol))
a = reference_states[Z]['a']
if structure == 'hcp' and c is None:
if reference_states[Z]['symmetry'] == 'hcp':
c = reference_states[Z]['c/a'] * a
else:
c = sqrt(8 / 3.0) * a
positions = np.empty((size[2], size[1], size[0], 3))
positions[..., 0] = np.arange(size[0]).reshape((1, 1, -1))
positions[..., 1] = np.arange(size[1]).reshape((1, -1, 1))
positions[..., 2] = np.arange(size[2]).reshape((-1, 1, 1))
numbers = np.ones(size[0] * size[1] * size[2], int) * Z
tags = np.empty((size[2], size[1], size[0]), int)
tags[:] = np.arange(size[2], 0, -1).reshape((-1, 1, 1))
slab = Atoms(numbers,
tags=tags.ravel(),
pbc=(True, True, False),
cell=size)
surface_cell = None
sites = {'ontop': (0, 0)}
surf = structure + face
if surf == 'fcc100':
cell = (sqrt(0.5), sqrt(0.5), 0.5)
positions[-2::-2, ..., :2] += 0.5
sites.update({'hollow': (0.5, 0.5), 'bridge': (0.5, 0)})
elif surf == 'diamond100':
cell = (sqrt(0.5), sqrt(0.5), 0.5 / 2)
positions[-4::-4, ..., :2] += (0.5, 0.5)
positions[-3::-4, ..., :2] += (0.0, 0.5)
positions[-2::-4, ..., :2] += (0.0, 0.0)
positions[-1::-4, ..., :2] += (0.5, 0.0)
elif surf == 'fcc110':
cell = (1.0, sqrt(0.5), sqrt(0.125))
positions[-2::-2, ..., :2] += 0.5
sites.update({'hollow': (0.5, 0.5), 'longbridge': (0.5, 0),
'shortbridge': (0, 0.5)})
elif surf == 'bcc100':
cell = (1.0, 1.0, 0.5)
positions[-2::-2, ..., :2] += 0.5
sites.update({'hollow': (0.5, 0.5), 'bridge': (0.5, 0)})
else:
if orthogonal and size[1] % 2 == 1:
raise ValueError(("Can't make orthorhombic cell with size=%r. " %
(tuple(size),)) +
'Second number in size must be even.')
if surf == 'fcc111':
cell = (sqrt(0.5), sqrt(0.375), 1 / sqrt(3))
if orthogonal:
positions[-1::-3, 1::2, :, 0] += 0.5
positions[-2::-3, 1::2, :, 0] += 0.5
positions[-3::-3, 1::2, :, 0] -= 0.5
positions[-2::-3, ..., :2] += (0.0, 2.0 / 3)
positions[-3::-3, ..., :2] += (0.5, 1.0 / 3)
else:
positions[-2::-3, ..., :2] += (-1.0 / 3, 2.0 / 3)
positions[-3::-3, ..., :2] += (1.0 / 3, 1.0 / 3)
sites.update({'bridge': (0.5, 0), 'fcc': (1.0 / 3, 1.0 / 3),
'hcp': (2.0 / 3, 2.0 / 3)})
elif surf == 'diamond111':
cell = (sqrt(0.5), sqrt(0.375), 1 / sqrt(3) / 2)
assert not orthogonal
positions[-1::-6, ..., :3] += (0.0, 0.0, 0.5)
positions[-2::-6, ..., :2] += (0.0, 0.0)
positions[-3::-6, ..., :3] += (-1.0 / 3, 2.0 / 3, 0.5)
positions[-4::-6, ..., :2] += (-1.0 / 3, 2.0 / 3)
positions[-5::-6, ..., :3] += (1.0 / 3, 1.0 / 3, 0.5)
positions[-6::-6, ..., :2] += (1.0 / 3, 1.0 / 3)
elif surf == 'hcp0001':
cell = (1.0, sqrt(0.75), 0.5 * c / a)
if orthogonal:
positions[:, 1::2, :, 0] += 0.5
positions[-2::-2, ..., :2] += (0.0, 2.0 / 3)
else:
positions[-2::-2, ..., :2] += (-1.0 / 3, 2.0 / 3)
sites.update({'bridge': (0.5, 0), 'fcc': (1.0 / 3, 1.0 / 3),
'hcp': (2.0 / 3, 2.0 / 3)})
elif surf == 'hcp10m10':
cell = (1.0, 0.5 * c / a, sqrt(0.75))
assert orthogonal
positions[-2::-2, ..., 0] += 0.5
positions[:, ::2, :, 2] += 2.0 / 3
elif surf == 'bcc110':
cell = (1.0, sqrt(0.5), sqrt(0.5))
if orthogonal:
positions[:, 1::2, :, 0] += 0.5
positions[-2::-2, ..., :2] += (0.0, 1.0)
else:
positions[-2::-2, ..., :2] += (-0.5, 1.0)
sites.update({'shortbridge': (0, 0.5),
'longbridge': (0.5, 0),
'hollow': (0.375, 0.25)})
elif surf == 'bcc111':
cell = (sqrt(2), sqrt(1.5), sqrt(3) / 6)
if orthogonal:
positions[-1::-3, 1::2, :, 0] += 0.5
positions[-2::-3, 1::2, :, 0] += 0.5
positions[-3::-3, 1::2, :, 0] -= 0.5
positions[-2::-3, ..., :2] += (0.0, 2.0 / 3)
positions[-3::-3, ..., :2] += (0.5, 1.0 / 3)
else:
positions[-2::-3, ..., :2] += (-1.0 / 3, 2.0 / 3)
positions[-3::-3, ..., :2] += (1.0 / 3, 1.0 / 3)
sites.update({'hollow': (1.0 / 3, 1.0 / 3)})
else:
2 / 0
surface_cell = a * np.array([(cell[0], 0),
(cell[0] / 2, cell[1])])
if not orthogonal:
cell = np.array([(cell[0], 0, 0),
(cell[0] / 2, cell[1], 0),
(0, 0, cell[2])])
if surface_cell is None:
surface_cell = a * np.diag(cell[:2])
if isinstance(cell, tuple):
cell = np.diag(cell)
slab.set_positions(positions.reshape((-1, 3)))
slab.set_cell([a * v * n for v, n in zip(cell, size)], scale_atoms=True)
if vacuum is not None:
slab.center(vacuum=vacuum, axis=2)
slab.adsorbate_info['cell'] = surface_cell
slab.adsorbate_info['sites'] = sites
return slab
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