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 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)
write(name + '.png', slab, show_unit_cell=2, radii=radii[name[:3]],
scale=10)
for name in surfaces:
f = getattr(surface, name)
for kwargs in [{}, {'orthogonal': False}, {'orthogonal': True}]:
print(name, kwargs)
try:
slab = f(symbols[name[:3]], size=(3, 4, 5), vacuum=4, **kwargs)
except (TypeError, NotImplementedError):
continue
try:
for site in slab.adsorbate_info['sites']:
if site.endswith('bridge'):
h = 1.5
else:
h = 1.2
surface.add_adsorbate(slab, adsorbates.get(site, 'F'), h, site)
except KeyError:
pass
if kwargs.get('orthogonal', None):
name += 'o'
save(name, slab)
for site, symbol in adsorbates.items():
write('%s-site.png' % site, Atoms(symbol), radii=1.08, scale=10)
fcc111_primitive = fcc111("Ag", (1, 1, 3))
fcc111_root = root_surface(fcc111_primitive, 27)
save("fcc111_root", fcc111_root)
# 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()
write(name + '.png', slab, show_unit_cell=2, radii=radii[name[:3]],
scale=10)
for name in surfaces:
f = getattr(surface, name)
for kwargs in [{}, {'orthogonal': False}, {'orthogonal': True}]:
print(name, kwargs)
try:
slab = f(symbols[name[:3]], size=(3, 4, 5), vacuum=4, **kwargs)
except (TypeError, NotImplementedError):
continue
try:
for site in slab.info['adsorbate_info']['sites']:
if site.endswith('bridge'):
h = 1.5
else:
h = 1.2
surface.add_adsorbate(slab, adsorbates.get(site, 'F'), h, site)
except KeyError:
pass
if kwargs.get('orthogonal', None):
name += 'o'
save(name, slab)
for site, symbol in adsorbates.items():
write('%s-site.png' % site, Atoms(symbol), radii=1.08, scale=10)
fcc111_primitive = fcc111("Ag", (1, 1, 3))
fcc111_root = root_surface(fcc111_primitive, 27)
save("fcc111_root", fcc111_root)
# 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()
