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 bcc111_root
from ase.build import hcp0001_root
from ase.build import root_surface
from ase.build import root_surface_analysis
# Manually checked set of roots for FCC111
fcc111_21_set = set([1, 3, 4, 7, 9, 12, 13, 16, 19, 21])
# Keep pairs for testing
bulk_root = ((fcc111, fcc111_root), (bcc111, bcc111_root), (hcp0001,
hcp0001_root))
for bulk, root_surf in bulk_root:
prim = bulk("H", (1, 1, 2), a=1)
# Check valid roots up to root 21 (the 10th root cell)
assert fcc111_21_set == root_surface_analysis(prim, 21)
# Use internal function
internal_func_atoms = root_surface(prim, 7)
# Remake using surface function
helper_func_atoms = root_surf("H", 7, (1, 1, 2), a=1)
# Right number of atoms
assert len(internal_func_atoms) == 14
assert len(helper_func_atoms) == 14
assert (internal_func_atoms.cell == helper_func_atoms.cell).all()
# Try bad root
with pytest.raises(ValueError):
fcc111_root("H", 5, (1, 1, 2), a=1)
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 slabgen(termination, size, adsorbate, position):
if termination == '100':
prim = fcc100('Cu',
a=3.6302862146117354,
size=(1, 1, 5),
vacuum=15,
orthogonal=True,
periodic=True)
elif termination == '111':
prim = fcc111_root('Cu',
root=3,
a=3.6302862146117354,
size=(1, 1, 5),
vacuum=15)
super = make_supercell(prim, size)
add_adsorbate(slab=super,
adsorbate=adsorbate,
height=ads_height,
position=position)
constr = FixAtoms(
indices=[atom.index for atom in super if atom.position[2] < 19])
super.set_constraint(constr)
return super
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()
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()