def asesurf2xxyz(symb, lattice, index, size=(1,1,3), vac=15.0, orthogonal=0):
"""
An interface function for ase.lattice.surface
Usage:
>>> atoms = asesurf2xxyz(symb, lattice, index, size,
vac=15.0, orthogonal=0))
Parameters:
symb: atomic symbol
lattice: 'fcc', 'bcc', or 'hcp0001'
index: '100', '111' or '110' (if lattice is 'hcp0001', this will not work.)
size: the number of atoms per each vector
Optional Parameters:
vac (default: 15.0 angstron): the thickness of space normal to the surface
orthogonal (default: False) : if True, two lateral cell vectors will be
orthogonal.
Example:
>>> Fe_100_1x1 = asesurf2xxyz('Fe', 'bcc', '100', (1,1,2))
>>> Au_111_2x2 = asesurf2xxyz('Au', 'fcc', '111', (1,1,3))
"""
if lattice == 'fcc':
if index == '100': at_ase = AS.fcc100(symb, size, vacuum=vac)
elif index == '111': at_ase = AS.fcc111(symb, size,
orthogonal=orthogonal,
vacuum=vac)
elif index == '110': at_ase = AS.fcc110(symb, size, vacuum=vac)
else: raise ValueError, "100, 111, or 110 surface is supported."
elif lattice == 'bcc':
if index == '100': at_ase = AS.bcc100(symb, size, vacuum=vac)
elif index == '111': at_ase = AS.bcc111(symb, size,
orthogonal=orthogonal,
vacuum=vac)
elif index == '110': at_ase = AS.bcc110(symb, size,
orthogonal=orthogonal,
vacuum=vac)
else: raise ValueError, "100, 111, or 110 surface is supported."
elif lattice == 'hcp0001':
at_ase = AS.hcp0001(symb, size, orthogonal=orthogonal, vacuum=vac)
else: raise ValueError, "fcc, bcc, or hcp0001 surface is supported."
symbols = at_ase.get_chemical_symbols()
posits = at_ase.get_positions()
cell = at_ase.get_cell()
pbc = at_ase.get_pbc()
atoms = []; i=0
for sym in symbols:
temp_at = Atom(sym, list(posits[i]))
atoms.append(temp_at.copy()); i+=1
at_xxyz = AtomsSystem(atoms, cell=cell, pbc=pbc)
return at_xxyz
def asesurf2xxyz(symb, lattice, index, size=(1,1,3), vac=15.0, orthogonal=0):
"""
An interface function for ase.lattice.surface
Usage:
>>> atoms = asesurf2xxyz(symb, lattice, index, size,
vac=15.0, orthogonal=0))
Parameters:
symb: atomic symbol
lattice: 'fcc', 'bcc', or 'hcp0001'
index: '100', '111' or '110' (if lattice is 'hcp0001', this will not work.)
size: the number of atoms per each vector
Optional Parameters:
vac (default: 15.0 angstron): the thickness of space normal to the surface
orthogonal (default: False) : if True, two lateral cell vectors will be
orthogonal.
Example:
>>> Fe_100_1x1 = asesurf2xxyz('Fe', 'bcc', '100', (1,1,2))
>>> Au_111_2x2 = asesurf2xxyz('Au', 'fcc', '111', (1,1,3))
"""
if lattice == 'fcc':
if index == '100': at_ase = AS.fcc100(symb, size, vacuum=vac)
elif index == '111': at_ase = AS.fcc111(symb, size,
orthogonal=orthogonal,
vacuum=vac)
elif index == '110': at_ase = AS.fcc110(symb, size, vacuum=vac)
else: raise ValueError("100, 111, or 110 surface is supported.")
elif lattice == 'bcc':
if index == '100': at_ase = AS.bcc100(symb, size, vacuum=vac)
elif index == '111': at_ase = AS.bcc111(symb, size,
orthogonal=orthogonal,
vacuum=vac)
elif index == '110': at_ase = AS.bcc110(symb, size,
orthogonal=orthogonal,
vacuum=vac)
else: raise ValueError("100, 111, or 110 surface is supported.")
elif lattice == 'hcp0001':
at_ase = AS.hcp0001(symb, size, orthogonal=orthogonal, vacuum=vac)
else: raise ValueError("fcc, bcc, or hcp0001 surface is supported.")
symbols = at_ase.get_chemical_symbols()
posits = at_ase.get_positions()
cell = at_ase.get_cell()
pbc = at_ase.get_pbc()
atoms = []; i=0
for sym in symbols:
temp_at = Atom(sym, list(posits[i]))
atoms.append(temp_at.copy()); i+=1
at_xxyz = AtomsSystem(atoms, cell=cell, pbc=pbc)
return at_xxyz
def build():
p = OptionParser(usage='%prog [options] [ads@]surf [output file]',
version='%prog 0.1',
description='Example ads/surf: fcc-CO@2x2Ru0001')
p.add_option('-l',
'--layers',
type='int',
default=4,
help='Number of layers.')
p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.')
p.add_option('-x',
'--crystal-structure',
help='Crystal structure.',
choices=['sc', 'fcc', 'bcc', 'hcp'])
p.add_option('-a',
'--lattice-constant',
type='float',
help='Lattice constant in Angstrom.')
p.add_option('--c-over-a', type='float', help='c/a ratio.')
p.add_option('--height',
type='float',
help='Height of adsorbate over surface.')
p.add_option('--distance',
type='float',
help='Distance between adsorbate and nearest surface atoms.')
p.add_option('-M',
'--magnetic-moment',
type='float',
default=0.0,
help='Magnetic moment.')
p.add_option('-G', '--gui', action='store_true', help="Pop up ASE's GUI.")
p.add_option('-P',
'--python',
action='store_true',
help="Write Python script.")
opt, args = p.parse_args()
if not 1 <= len(args) <= 2:
p.error("incorrect number of arguments")
if '@' in args[0]:
ads, surf = args[0].split('@')
else:
ads = None
surf = args[0]
if surf[0].isdigit():
i1 = surf.index('x')
n = int(surf[:i1])
i2 = i1 + 1
while surf[i2].isdigit():
i2 += 1
m = int(surf[i1 + 1:i2])
surf = surf[i2:]
else:
n = 1
m = 1
if surf[-1].isdigit():
if surf[1].isdigit():
face = surf[1:]
surf = surf[0]
else:
face = surf[2:]
surf = surf[:2]
else:
face = None
Z = atomic_numbers[surf]
state = reference_states[Z]
if opt.crystal_structure:
x = opt.crystal_structure
else:
x = state['symmetry']
if opt.lattice_constant:
a = opt.lattice_constant
else:
a = estimate_lattice_constant(surf, x, opt.c_over_a)
script = [
'from ase.lattice.surface import ',
'vac = %r' % opt.vacuum,
'a = %r' % a
]
if x == 'fcc':
if face is None:
face = '111'
slab = fcc111(surf, (n, m, opt.layers), a, opt.vacuum)
script[0] += 'fcc111'
script += [
'slab = fcc111(%r, (%d, %d, %d), a, vac)' %
(surf, n, m, opt.layers)
]
r = a / np.sqrt(2) / 2
elif x == 'bcc':
if face is None:
face = '110'
if face == '110':
slab = bcc110(surf, (n, m, opt.layers), a, opt.vacuum)
elif face == '100':
slab = bcc100(surf, (n, m, opt.layers), a, opt.vacuum)
script[0] += 'bcc' + face
script += [
'slab = bcc%s(%r, (%d, %d, %d), a, vac)' %
(face, surf, n, m, opt.layers)
]
r = a * np.sqrt(3) / 4
elif x == 'hcp':
if face is None:
face = '0001'
if opt.c_over_a is None:
c = np.sqrt(8 / 3.0) * a
else:
c = opt.c_over_a * a
slab = hcp0001(surf, (n, m, opt.layers), a, c, opt.vacuum)
script[0] += 'hcp0001'
script += [
'c = %r * a' % (c / a),
'slab = hcp0001(%r, (%d, %d, %d), a, c, vac)' %
(surf, n, m, opt.layers)
]
r = a / 2
elif x == 'diamond':
if face is None:
face = '111'
slab = diamond111(surf, (n, m, opt.layers), a, opt.vacuum)
script[0] += 'diamond111'
script += [
'slab = diamond111(%r, (%d, %d, %d), a, vac)' %
(surf, n, m, opt.layers)
]
r = a * np.sqrt(3) / 8
else:
raise NotImplementedError
magmom = opt.magnetic_moment
if magmom is None:
magmom = {'Ni': 0.6, 'Co': 1.2, 'Fe': 2.3}.get(surf, 0.0)
slab.set_initial_magnetic_moments([magmom] * len(slab))
if magmom != 0:
script += [
'slab.set_initial_magnetic_moments([%r] * len(slab))' % magmom
]
slab.pbc = 1
script += ['slab.pbc = True']
name = '%dx%d%s%s' % (n, m, surf, face)
if ads:
site = 'ontop'
if '-' in ads:
site, ads = ads.split('-')
name = site + '-' + ads + '@' + name
symbols = string2symbols(ads)
nads = len(symbols)
if nads == 1:
script[:0] = ['from ase import Atoms']
script += ['ads = Atoms(%r)' % ads]
ads = Atoms(ads)
else:
script[:0] = ['from ase.data.molecules import molecule']
script += ['ads = molecule(%r)' % ads]
ads = molecule(ads)
add_adsorbate(slab, ads, 0.0, site)
d = opt.distance
if d is None:
d = r + covalent_radii[ads[0].number] / 2
h = opt.height
if h is None:
R = slab.positions
y = ((R[:-nads] - R[-nads])**2).sum(1).min()**0.5
h = (d**2 - y**2)**0.5
else:
assert opt.distance is None
slab.positions[-nads:, 2] += h
script[1] += ', add_adsorbate'
script += ['add_adsorbate(slab, ads, %r, %r)' % (h, site)]
if len(args) == 2:
write(args[1], slab)
script[1:1] = ['from ase.io import write']
script += ['write(%r, slab)' % args[1]]
elif not opt.gui:
write(name + '.traj', slab)
script[1:1] = ['from ase.io import write']
script += ['write(%r, slab)' % (name + '.traj')]
if opt.gui:
view(slab)
script[1:1] = ['from ase.visualize import view']
script += ['view(slab)']
if opt.python:
print('\n'.join(script))
def build():
p = OptionParser(usage='%prog [options] [ads@]surf [output file]',
version='%prog 0.1',
description='Example ads/surf: fcc-CO@2x2Ru0001')
p.add_option('-l', '--layers', type='int',
default=4,
help='Number of layers.')
p.add_option('-v', '--vacuum', type='float',
default=5.0,
help='Vacuum.')
p.add_option('-x', '--crystal-structure',
help='Crystal structure.',
choices=['sc', 'fcc', 'bcc', 'hcp'])
p.add_option('-a', '--lattice-constant', type='float',
help='Lattice constant in Angstrom.')
p.add_option('--c-over-a', type='float',
help='c/a ratio.')
p.add_option('--height', type='float',
help='Height of adsorbate over surface.')
p.add_option('--distance', type='float',
help='Distance between adsorbate and nearest surface atoms.')
p.add_option('-M', '--magnetic-moment', type='float', default=0.0,
help='Magnetic moment.')
p.add_option('-G', '--gui', action='store_true',
help="Pop up ASE's GUI.")
p.add_option('-P', '--python', action='store_true',
help="Write Python script.")
opt, args = p.parse_args()
if not 1 <= len(args) <= 2:
p.error("incorrect number of arguments")
if '@' in args[0]:
ads, surf = args[0].split('@')
else:
ads = None
surf = args[0]
if surf[0].isdigit():
i1 = surf.index('x')
n = int(surf[:i1])
i2 = i1 + 1
while surf[i2].isdigit():
i2 += 1
m = int(surf[i1 + 1:i2])
surf = surf[i2:]
else:
n = 1
m = 1
if surf[-1].isdigit():
if surf[1].isdigit():
face = surf[1:]
surf = surf[0]
else:
face = surf[2:]
surf = surf[:2]
else:
face = None
Z = atomic_numbers[surf]
state = reference_states[Z]
if opt.crystal_structure:
x = opt.crystal_structure
else:
x = state['symmetry']
if opt.lattice_constant:
a = opt.lattice_constant
else:
a = estimate_lattice_constant(surf, x, opt.c_over_a)
script = ['from ase.lattice.surface import ',
'vac = %r' % opt.vacuum,
'a = %r' % a]
if x == 'fcc':
if face is None:
face = '111'
slab = fcc111(surf, (n, m, opt.layers), a, opt.vacuum)
script[0] += 'fcc111'
script += ['slab = fcc111(%r, (%d, %d, %d), a, vac)' %
(surf, n, m, opt.layers)]
r = a / np.sqrt(2) / 2
elif x == 'bcc':
if face is None:
face = '110'
if face == '110':
slab = bcc110(surf, (n, m, opt.layers), a, opt.vacuum)
elif face == '100':
slab = bcc100(surf, (n, m, opt.layers), a, opt.vacuum)
script[0] += 'bcc' + face
script += ['slab = bcc%s(%r, (%d, %d, %d), a, vac)' %
(face, surf, n, m, opt.layers)]
r = a * np.sqrt(3) / 4
elif x == 'hcp':
if face is None:
face = '0001'
if opt.c_over_a is None:
c = np.sqrt(8 / 3.0) * a
else:
c = opt.c_over_a * a
slab = hcp0001(surf, (n, m, opt.layers), a, c, opt.vacuum)
script[0] += 'hcp0001'
script += ['c = %r * a' % (c / a),
'slab = hcp0001(%r, (%d, %d, %d), a, c, vac)' %
(surf, n, m, opt.layers)]
r = a / 2
elif x == 'diamond':
if face is None:
face = '111'
slab = diamond111(surf, (n, m, opt.layers), a, opt.vacuum)
script[0] += 'diamond111'
script += ['slab = diamond111(%r, (%d, %d, %d), a, vac)' %
(surf, n, m, opt.layers)]
r = a * np.sqrt(3) / 8
else:
raise NotImplementedError
magmom = opt.magnetic_moment
if magmom is None:
magmom = {'Ni': 0.6, 'Co': 1.2, 'Fe': 2.3}.get(surf, 0.0)
slab.set_initial_magnetic_moments([magmom] * len(slab))
if magmom != 0:
script += ['slab.set_initial_magnetic_moments([%r] * len(slab))' %
magmom]
slab.pbc = 1
script += ['slab.pbc = True']
name = '%dx%d%s%s' % (n, m, surf, face)
if ads:
site = 'ontop'
if '-' in ads:
site, ads = ads.split('-')
name = site + '-' + ads + '@' + name
symbols = string2symbols(ads)
nads = len(symbols)
if nads == 1:
script[:0] = ['from ase import Atoms']
script += ['ads = Atoms(%r)' % ads]
ads = Atoms(ads)
else:
script[:0] = ['from ase.structure import molecule']
script += ['ads = molecule(%r)' % ads]
ads = molecule(ads)
add_adsorbate(slab, ads, 0.0, site)
d = opt.distance
if d is None:
d = r + covalent_radii[ads[0].number] / 2
h = opt.height
if h is None:
R = slab.positions
y = ((R[:-nads] - R[-nads])**2).sum(1).min()**0.5
h = (d**2 - y**2)**0.5
else:
assert opt.distance is None
slab.positions[-nads:, 2] += h
script[1] += ', add_adsorbate'
script += ['add_adsorbate(slab, ads, %r, %r)' % (h, site)]
if len(args) == 2:
write(args[1], slab)
script[1:1] = ['from ase.io import write']
script += ['write(%r, slab)' % args[1]]
elif not opt.gui:
write(name + '.traj', slab)
script[1:1] = ['from ase.io import write']
script += ['write(%r, slab)' % (name + '.traj')]
if opt.gui:
view(slab)
script[1:1] = ['from ase.visualize import view']
script += ['view(slab)']
if opt.python:
print('\n'.join(script))
def initlatticepositions(params, nlayers):
"""
Return nlayers of positions according to lattice type/plane and
shift positions so that no atoms are on the edges of the box.
"""
lxsurf = params['lxsurf']
lysurf = params['lysurf']
alat = params['alat']
if params['surftype'] == 'fcc':
if params['plane'] == '111':
surf = ase.fcc111('O',
a=alat,
size=(lxsurf, lysurf, nlayers),
orthogonal=True)
positions = surf.positions
positions[:, 0] = positions[:, 0] + (alat / 2.0**0.5) / 4.0
positions[:, 1] = (positions[:, 1] + (1.0 / 2.0) * (3.0**0.5) *
(alat / 2.0**0.5) / 4.0)
elif params['plane'] == '100':
surf = ase.fcc100('O', a=alat, size=(lxsurf, lysurf, nlayers))
positions = surf.positions
positions[:, 0] = positions[:, 0] + (alat / 2.0**0.5) / 4.0
positions[:, 1] = positions[:, 1] + (alat / 2.0**0.5) / 4.0
elif params['plane'] == '110':
surf = ase.fcc110('O', a=alat, size=(lxsurf, lysurf, nlayers))
positions = surf.positions
positions[:, 0] = positions[:, 0] + alat / 4.0
positions[:, 1] = positions[:, 1] + (alat / 2.0**0.5) / 4.0
elif params['surftype'] == 'bcc':
if params['plane'] == '100':
surf = ase.bcc100('O', a=alat, size=(lxsurf, lysurf, nlayers))
positions = surf.positions
positions[:, 0] = positions[:, 0] + alat / 2.0
positions[:, 1] = positions[:, 1] + alat / 2.0
elif params['surftype'] == 'hcp':
clat = params['clat']
if params['plane'] == '0001':
surf = ase.hcp0001('O',
a=alat,
c=clat,
size=(lxsurf, lysurf, nlayers),
orthogonal=True)
positions = surf.positions
positions[:, 0] = positions[:, 0] + alat / 4.0
positions[:,
1] = positions[:,
1] + (1.0 / 2.0) * (3.0**0.5) * alat / 4.0
elif params['plane'] == '1010':
surf = ase.hcp10m10('O',
a=alat,
c=clat,
size=(lxsurf, lysurf, nlayers))
positions = surf.positions
positions[:, 0] = positions[:, 0] + alat / 4.0
positions[:, 1] = positions[:, 1] + clat / 4.0
return positions