def MakeAtoms(elem1, elem2=None):
if elem2 is None:
elem2 = elem1
a1 = reference_states[elem1]['a']
a2 = reference_states[elem2]['a']
a0 = (0.5 * a1**3 + 0.5 * a2**3)**(1.0/3.0) * 1.03
if ismaster:
# 50*50*50 would be big enough, but some vacancies are nice.
print "Z1 = %i, Z2 = %i, a0 = %.5f" % (elem1, elem2, a0)
atoms = FaceCenteredCubic(symbol='Cu', size=(51,51,51))
nremove = len(atoms) - 500000
assert nremove > 0
remove = np.random.choice(len(atoms), nremove, replace=False)
del atoms[remove]
if isparallel:
atoms = atoms.repeat(cpuLayout)
if elem1 != elem2:
z = atoms.get_atomic_numbers()
z[np.random.choice(len(atoms), len(atoms)/2, replace=False)] = elem2
atoms.set_atomic_numbers(z)
else:
atoms = None
if isparallel:
atoms = MakeParallelAtoms(atoms, cpuLayout)
MaxwellBoltzmannDistribution(atoms, T * units.kB)
return atoms
def fcc211(symbol, size, a=None, vacuum=None, orthogonal=True):
"""FCC(211) surface.
Does not currently support special adsorption sites.
Currently only implemented for *orthogonal=True* with size specified
as (i, j, k), where i, j, and k are number of atoms in each direction.
i must be divisible by 3 to accommodate the step width.
"""
if not orthogonal:
raise NotImplementedError('Only implemented for orthogonal '
'unit cells.')
if size[0] % 3 != 0:
raise NotImplementedError('First dimension of size must be '
'divisible by 3.')
atoms = FaceCenteredCubic(symbol,
directions=[[1, -1, -1],
[0, 2, -2],
[2, 1, 1]],
miller=(None, None, (2, 1, 1)),
latticeconstant=a,
size=(1, 1, 1),
pbc=True)
z = (size[2] + 1) // 2
atoms = atoms.repeat((size[0] // 3, size[1], z))
if size[2] % 2: # Odd: remove bottom layer and shrink cell.
remove_list = [atom.index for atom in atoms
if atom.z < atoms[1].z]
del atoms[remove_list]
dz = atoms[0].z
atoms.translate((0., 0., -dz))
atoms.cell[2][2] -= dz
atoms.cell[2] = 0.0
atoms.pbc[2] = False
if vacuum:
atoms.center(vacuum, axis=2)
# Renumber systematically from top down.
orders = [(atom.index, round(atom.x, 3), round(atom.y, 3),
-round(atom.z, 3), atom.index) for atom in atoms]
orders.sort(key=itemgetter(3, 1, 2))
newatoms = atoms.copy()
for index, order in enumerate(orders):
newatoms[index].position = atoms[order[0]].position.copy()
# Add empty 'sites' dictionary for consistency with other functions
newatoms.info['adsorbate_info'] = {'sites': {}}
return newatoms
def fcc211(symbol, size, a=None, vacuum=None, orthogonal=True):
"""FCC(211) surface.
Does not currently support special adsorption sites.
Currently only implemented for *orthogonal=True* with size specified
as (i, j, k), where i, j, and k are number of atoms in each direction.
i must be divisible by 3 to accommodate the step width.
"""
if not orthogonal:
raise NotImplementedError('Only implemented for orthogonal '
'unit cells.')
if size[0] % 3 != 0:
raise NotImplementedError('First dimension of size must be '
'divisible by 3.')
atoms = FaceCenteredCubic(symbol,
directions=[[1, -1, -1],
[0, 2, -2],
[2, 1, 1]],
miller=(None, None, (2, 1, 1)),
latticeconstant=a,
size=(1, 1, 1),
pbc=True)
z = (size[2] + 1) // 2
atoms = atoms.repeat((size[0] // 3, size[1], z))
if size[2] % 2: # Odd: remove bottom layer and shrink cell.
remove_list = [atom.index for atom in atoms
if atom.z < atoms[1].z]
del atoms[remove_list]
dz = atoms[0].z
atoms.translate((0., 0., -dz))
atoms.cell[2][2] -= dz
atoms.cell[2] = 0.0
atoms.pbc[1] = False
if vacuum:
atoms.center(vacuum, axis=2)
# Renumber systematically from top down.
orders = [(atom.index, round(atom.x, 3), round(atom.y, 3),
-round(atom.z, 3), atom.index) for atom in atoms]
orders.sort(key=itemgetter(3, 1, 2))
newatoms = atoms.copy()
for index, order in enumerate(orders):
newatoms[index].position = atoms[order[0]].position.copy()
return newatoms
if __name__ == '__main__':
from ase.lattice.cubic import FaceCenteredCubic
from ase.lattice.bravais import cross
a = np.array([0.5, 0, 0])
c = np.array([0, 1, 0], dtype=np.float)
b1 = c - a
a = np.array([0, 1, 0], np.float)
c = np.array([0, 0.5, 0.5])
b2 = c - a
a3 = np.array([2, 1, 1], np.float)
a1 = cross(b1, a3)
a2 = cross(b2, a3)
v211 = FaceCenteredCubic(directions=[a1, a2, a3],
miller=(None, None, [2, 1, 1]),
symbol='Pd',
size=(1, 1, 2),
debug=0)
uc = v211.get_cell()
uc[2][2] += 10.0
v211.set_cell(uc)
plot_atoms(v211.repeat((2, 2, 1)))
