def test_bravais_2d_cell_pbc():
"""Verify 2D Bravais lattice and band path versus pbc information."""
from ase.cell import Cell
cell = Cell([[1.,0.,0.],
[.1,1.,0.],
[0.,0.,0.]])
lat = cell.get_bravais_lattice()
print(cell.cellpar())
print(lat)
assert lat.name == 'OBL'
cell[2, 2] = 7
lat3d = cell.get_bravais_lattice()
print(lat3d)
assert lat3d.name == 'MCL'
lat2d_pbc = cell.get_bravais_lattice(pbc=[1, 1, 0])
print(lat2d_pbc)
assert lat2d_pbc.name == 'OBL'
path = cell.bandpath()
print(path)
path2d = cell.bandpath(pbc=[1, 1, 0])
print(path2d)
assert path2d.cell.rank == 2
assert path2d.cell.get_bravais_lattice().name == 'OBL'
def find_niggli_ops(latcls, length_grid, angle_grid):
niggli_ops = {}
for lat in lattice_loop(latcls, length_grid, angle_grid):
cell = lat.tocell()
try:
rcell, op = cell.niggli_reduce()
except RuntimeError:
print('Niggli reduce did not converge')
continue
assert op.dtype == int
op_key = tuple(op.ravel())
if op_key in niggli_ops:
niggli_ops[op_key] += 1
else:
niggli_ops[op_key] = 1
rcell_test = Cell(op.T @ cell)
rcellpar_test = rcell_test.cellpar()
rcellpar = rcell.cellpar()
err = np.abs(rcellpar_test - rcellpar).max()
assert err < 1e-7, err
return niggli_ops
def test_monoclinic():
"""Test band structure from different variations of hexagonal cells."""
mc1 = Cell([[1, 0, 0], [0, 1, 0], [0, 0.2, 1]])
par = mc1.cellpar()
mc2 = Cell.new(par)
mc3 = Cell([[1, 0, 0], [0, 1, 0], [-0.2, 0, 1]])
mc4 = Cell([[1, 0, 0], [-0.2, 1, 0], [0, 0, 1]])
path = 'GYHCEM1AXH1'
firsttime = True
for cell in [mc1, mc2, mc3, mc4]:
a = Atoms(cell=cell, pbc=True)
a.cell *= 3
a.calc = FreeElectrons(nvalence=1, kpts={'path': path})
lat = a.cell.get_bravais_lattice()
assert lat.name == 'MCL'
a.get_potential_energy()
bs = a.calc.band_structure()
coords, labelcoords, labels = bs.get_labels()
assert ''.join(labels) == path
e_skn = bs.energies
if firsttime:
coords1 = coords
labelcoords1 = labelcoords
e_skn1 = e_skn
firsttime = False
else:
for d in [coords - coords1,
labelcoords - labelcoords1,
e_skn - e_skn1]:
print(abs(d).max())
assert abs(d).max() < 1e-13, d
def format_cell(cell: Cell) -> str:
assert cell.rank == 3
lines = []
for name, value in zip(CIFBlock.cell_tags, cell.cellpar()):
line = '{:20} {:g}\n'.format(name, value)
lines.append(line)
assert len(lines) == 6
return ''.join(lines)
def test_niggli_op():
import numpy as np
from ase.cell import Cell
rng = np.random.RandomState(3)
for i in range(5):
cell = Cell(rng.rand(3, 3))
print(cell.cellpar())
rcell, op = cell.niggli_reduce()
print(op)
rcell1 = Cell(op.T @ cell)
rcellpar = rcell.cellpar()
rcellpar1 = rcell1.cellpar()
err = np.abs(rcellpar - rcellpar1).max()
print(err)
assert err < 1e-10, err
def check_single(name, cell, pbc=None):
c = Cell(cell, pbc=pbc)
try:
lattice = c.get_bravais_lattice()
except RuntimeError:
print('error checking {}'.format(name))
raise
name1 = lattice.name.lower()
latname = name.split('@')[0]
ok = latname == name1
print(name, '-->', name1, 'OK' if ok else 'ERR', c.cellpar())
assert ok, 'Expected {latname} but found {name1}'.format(latname, name1)
def check_single(name, cell, pbc=None):
c = Cell(cell)
try:
print('TEST', c, pbc)
if pbc[:2].all() or sum(pbc) == 1:
lattice = c.get_bravais_lattice(pbc=pbc)
else:
with must_raise(UnsupportedLattice):
lattice = c.get_bravais_lattice(pbc=pbc)
return
except RuntimeError:
print('error checking {}'.format(name))
raise
name1 = lattice.name.lower()
latname = name.split('@')[0]
ok = latname == name1
print(name, '-->', name1, 'OK' if ok else 'ERR', c.cellpar())
assert ok, 'Expected {} but found {}'.format(latname, name1)
"""Verify 2D Bravais lattice and band path versus pbc information.""" from ase.cell import Cell cell = Cell([[1., 0., 0.], [.1, 1., 0.], [0., 0., 0.]]) lat = cell.get_bravais_lattice() print(cell.cellpar()) print(lat) assert lat.name == 'OBL' cell[2, 2] = 7 lat3d = cell.get_bravais_lattice() print(lat3d) assert lat3d.name == 'MCL' lat2d_pbc = cell.get_bravais_lattice(pbc=[1, 1, 0]) print(lat2d_pbc) assert lat2d_pbc.name == 'OBL' path = cell.bandpath() print(path) path2d = cell.bandpath(pbc=[1, 1, 0]) print(path2d) assert path2d.cell.rank == 2 assert path2d.cell.get_bravais_lattice().name == 'OBL'
def get_2d_bravais_lattice(origcell, eps=2e-4, *, pbc=True):
pbc = origcell.any(1) & pbc2pbc(pbc)
if list(pbc) != [1, 1, 0]:
raise UnsupportedLattice(
'Can only get 2D Bravais lattice of cell with '
'pbc==[1, 1, 0]; but we have {}'.format(pbc))
nonperiodic = pbc.argmin()
# Start with op = I
ops = [np.eye(3)]
for i in range(-1, 1):
for j in range(-1, 1):
op = [[1, j], [i, 1]]
if np.abs(np.linalg.det(op)) > 1e-5:
# Only touch periodic dirs:
op = np.insert(op, nonperiodic, [0, 0], 0)
op = np.insert(op, nonperiodic, ~pbc, 1)
ops.append(np.array(op))
def allclose(a, b):
return np.allclose(a, b, atol=eps)
symrank = 0
for op in ops:
cell = Cell(op.dot(origcell))
cellpar = cell.cellpar()
angles = cellpar[3:]
# Find a, b and gamma
gamma = angles[~pbc][0]
a, b = cellpar[:3][pbc]
anglesm90 = np.abs(angles - 90)
# Maximum one angle different from 90 deg in 2d please
if np.sum(anglesm90 > eps) > 1:
continue
all_lengths_equal = abs(a - b) < eps
if all_lengths_equal:
if allclose(gamma, 90):
lat = SQR(a)
rank = 5
elif allclose(gamma, 120):
lat = HEX2D(a)
rank = 4
else:
lat = CRECT(a, gamma)
rank = 3
else:
if allclose(gamma, 90):
lat = RECT(a, b)
rank = 2
else:
lat = OBL(a, b, gamma)
rank = 1
op = lat.get_transformation(origcell, eps=eps)
if not allclose(
np.dot(op, lat.tocell())[pbc][:, pbc],
origcell.array[pbc][:, pbc]):
msg = ('Cannot recognize cell at all somehow! {}, {}, {}'.format(
a, b, gamma))
raise RuntimeError(msg)
if rank > symrank:
finalop = op
symrank = rank
finallat = lat
return finallat, finalop.T
import numpy as np
from ase.cell import Cell
rng = np.random.RandomState(3)
for i in range(5):
cell = Cell(rng.rand(3, 3))
print(cell.cellpar())
rcell, op = cell.niggli_reduce()
print(op)
rcell1 = Cell(op.T @ cell)
rcellpar = rcell.cellpar()
rcellpar1 = rcell1.cellpar()
err = np.abs(rcellpar - rcellpar1).max()
print(err)
assert err < 1e-10, err
