def bcc111_root(symbol, root, size, a=None,
vacuum=None, orthogonal=False):
"""BCC(111) surface maniupulated to have a x unit side length
of *root* before repeating. This also results in *root* number
of repetitions of the cell.
The first 20 valid roots for nonorthogonal are...
1, 3, 4, 7, 9, 12, 13, 16, 19, 21, 25,
27, 28, 31, 36, 37, 39, 43, 48, 49"""
atoms = bcc111(symbol=symbol, size=(1, 1, size[2]),
a=a, vacuum=vacuum, orthogonal=orthogonal)
atoms = root_surface(atoms, root)
atoms *= (size[0], size[1], 1)
return atoms
def bcc111_root(symbol, root, size, a=None, vacuum=None, orthogonal=False):
"""BCC(111) surface maniupulated to have a x unit side length
of *root* before repeating. This also results in *root* number
of repetitions of the cell.
The first 20 valid roots for nonorthogonal are...
1, 3, 4, 7, 9, 12, 13, 16, 19, 21, 25,
27, 28, 31, 36, 37, 39, 43, 48, 49"""
atoms = bcc111(symbol=symbol,
size=(1, 1, size[2]),
a=a,
vacuum=vacuum,
orthogonal=orthogonal)
atoms = root_surface(atoms, root)
atoms *= (size[0], size[1], 1)
return atoms
def test_root_surf():
from ase.build import fcc111
from ase.build import bcc111
from ase.build import hcp0001
from ase.build import fcc111_root
from ase.build import root_surface
from ase.build import root_surface_analysis
# Make samples of primitive cell
prim_fcc111 = fcc111("H", (1, 1, 2), a=1)
prim_bcc111 = bcc111("H", (1, 1, 2), a=1)
prim_hcp0001 = hcp0001("H", (1, 1, 2), a=1)
# Check valid roots up to root 21 (the 10th root cell)
valid_fcc111 = root_surface_analysis(prim_fcc111, 21)
valid_bcc111 = root_surface_analysis(prim_bcc111, 21)
valid_hcp0001 = root_surface_analysis(prim_hcp0001, 21)
# These should have different positions, but the same
# cell geometry.
assert valid_fcc111 == valid_bcc111 == valid_hcp0001
# Make an easy sample to check code errors
atoms1 = root_surface(prim_fcc111, 7)
# Ensure the valid roots are the roots are valid against
# a set of manually checked roots for this system
assert valid_fcc111 == [1.0, 3.0, 4.0, 7.0, 9.0,
12.0, 13.0, 16.0, 19.0, 21.0]
# Remake easy sample using surface function
atoms2 = fcc111_root("H", 7, (1, 1, 2), a=1)
# Right number of atoms
assert len(atoms1) == len(atoms2) == 14
# Same positions
assert (atoms1.positions == atoms2.positions).all()
# Same cell
assert (atoms1.cell == atoms2.cell).all()
def opt_bcc111(self) -> None:
''' Optimize bcc111 slab '''
slab = bcc111(self.symbol, self.repeats_surface, self.a, self.vacuum)
self.prepare_slab_opt(slab)
from ase.build import fcc111
from ase.build import bcc111
from ase.build import hcp0001
from ase.build import fcc111_root
from ase.build import root_surface
from ase.build import root_surface_analysis
# Make samples of primitive cell
prim_fcc111 = fcc111("H", (1, 1, 2), a=1)
prim_bcc111 = bcc111("H", (1, 1, 2), a=1)
prim_hcp0001 = hcp0001("H", (1, 1, 2), a=1)
# Check valid roots up to root 21 (the 10th root cell)
valid_fcc111 = root_surface_analysis(prim_fcc111, 21)
valid_bcc111 = root_surface_analysis(prim_bcc111, 21)
valid_hcp0001 = root_surface_analysis(prim_hcp0001, 21)
# These should have different positions, but the same
# cell geometry.
assert valid_fcc111 == valid_bcc111 == valid_hcp0001
# Make an easy sample to check code errors
atoms1 = root_surface(prim_fcc111, 7)
# Ensure the valid roots are the roots are valid against
# a set of manually checked roots for this system
assert valid_fcc111 == [1.0, 3.0, 4.0, 7.0, 9.0,
12.0, 13.0, 16.0, 19.0, 21.0]
# Remake easy sample using surface function
atoms2 = fcc111_root("H", 7, (1, 1, 2), a=1)
from ase.build import fcc111
from ase.build import bcc111
from ase.build import hcp0001
from ase.build import fcc111_root
from ase.build import root_surface
from ase.build import root_surface_analysis
# Make samples of primitive cell
prim_fcc111 = fcc111("H", (1, 1, 2), a=1)
prim_bcc111 = bcc111("H", (1, 1, 2), a=1)
prim_hcp0001 = hcp0001("H", (1, 1, 2), a=1)
# Check valid roots up to root 21 (the 10th root cell)
valid_fcc111 = root_surface_analysis(prim_fcc111, 21)
valid_bcc111 = root_surface_analysis(prim_bcc111, 21)
valid_hcp0001 = root_surface_analysis(prim_hcp0001, 21)
# These should have different positions, but the same
# cell geometry.
assert valid_fcc111 == valid_bcc111 == valid_hcp0001
# Make an easy sample to check code errors
atoms1 = root_surface(prim_fcc111, 7)
# Ensure the valid roots are the roots are valid against
# a set of manually checked roots for this system
assert valid_fcc111 == [1.0, 3.0, 4.0, 7.0, 9.0,
12.0, 13.0, 16.0, 19.0, 21.0]
# Remake easy sample using surface function
atoms2 = fcc111_root("H", 7, (1, 1, 2), a=1)