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 test_hex():
"""Test band structure from different variations of hexagonal cells."""
firsttime = True
for cell in [[[1, 0, 0], [0.5, 3**0.5 / 2, 0], [0, 0, 1]],
[[1, 0, 0], [-0.5, 3**0.5 / 2, 0], [0, 0, 1]],
[[0.5, -3**0.5 / 2, 0], [0.5, 3**0.5 / 2, 0], [0, 0, 1]]]:
a = Atoms(cell=cell, pbc=True)
a.cell *= 3
a.calc = FreeElectrons(nvalence=1, kpts={'path': 'GMKG'})
lat = a.cell.get_bravais_lattice()
assert lat.name == 'HEX'
print(repr(a.cell.get_bravais_lattice()))
r = a.cell.reciprocal()
k = get_special_points(a.cell)['K']
print(np.dot(k, r))
a.get_potential_energy()
bs = a.calc.band_structure()
coords, labelcoords, labels = bs.get_labels()
assert ''.join(labels) == 'GMKG'
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
]:
assert abs(d).max() < 1e-13
def test_lattice_bandstructure(testdir, i, lat, figure):
xid = '{:02d}.{}'.format(i, lat.variant)
path = lat.bandpath(density=10)
path.write('path.{}.json'.format(xid))
atoms = Atoms(cell=lat.tocell(), pbc=True)
atoms.calc = FreeElectrons(nvalence=0, kpts=path.kpts)
bs = calculate_band_structure(atoms, path)
bs.write('bs.{}.json'.format(xid))
ax = figure.gca()
bs.plot(ax=ax, emin=0, emax=20, filename='fig.{}.png'.format(xid))
def free_electron_band_structure(self, **kwargs):
"""Return band structure of free electrons for this bandpath.
This is for mostly testing."""
from ase import Atoms
from ase.calculators.test import FreeElectrons
from ase.dft.band_structure import calculate_band_structure
atoms = Atoms(cell=self.cell, pbc=True)
atoms.calc = FreeElectrons(**kwargs)
bs = calculate_band_structure(atoms, path=self)
return bs
def test_bandstructure(testdir, plt):
atoms = bulk('Cu')
path = special_paths['fcc']
atoms.calc = FreeElectrons(nvalence=1, kpts={'path': path, 'npoints': 200})
atoms.get_potential_energy()
bs = atoms.calc.band_structure()
coords, labelcoords, labels = bs.get_labels()
print(labels)
bs.write('hmm.json')
bs = BandStructure.read('hmm.json')
coords, labelcoords, labels = bs.get_labels()
print(labels)
assert ''.join(labels) == 'GXWKGLUWLKUX'
bs.plot(emax=10, filename='bs.png')
def free_electron_band_structure(
self, **kwargs) -> 'ase.spectrum.band_structure.BandStructure':
"""Return band structure of free electrons for this bandpath.
Keyword arguments are passed to
:class:`~ase.calculators.test.FreeElectrons`.
This is for mostly testing and visualization."""
from ase import Atoms
from ase.calculators.test import FreeElectrons
from ase.spectrum.band_structure import calculate_band_structure
atoms = Atoms(cell=self.cell, pbc=True)
atoms.calc = FreeElectrons(**kwargs)
bs = calculate_band_structure(atoms, path=self)
return bs
def test():
ax = plt.gca()
for i, lat in enumerate(all_variants()):
if lat.ndim == 2:
break
xid = '{:02d}.{}'.format(i, lat.variant)
path = lat.bandpath(density=10)
path.write('path.{}.json'.format(xid))
atoms = Atoms(cell=lat.tocell(), pbc=True)
atoms.calc = FreeElectrons(nvalence=0, kpts=path.kpts)
bs = calculate_band_structure(atoms, path)
bs.write('bs.{}.json'.format(xid))
bs.plot(ax=ax, emin=0, emax=20, filename='fig.{}.png'.format(xid))
ax.clear()
def test_bandstructure_json(testdir):
atoms = bulk('Au')
lat = atoms.cell.get_bravais_lattice()
path = lat.bandpath(npoints=100)
atoms.calc = FreeElectrons()
bs = calculate_band_structure(atoms, path)
bs.write('bs.json')
bs.path.write('path.json')
bs1 = read_json('bs.json')
bs2 = BandStructure.read('bs.json')
path1 = read_json('path.json')
assert type(bs1) == type(bs) # noqa
assert type(bs2) == type(bs) # noqa
assert type(path1) == type(bs.path) # noqa
def test_monoclinic():
"""Test band structure from different variations of hexagonal cells."""
import numpy as np
from ase import Atoms
from ase.calculators.test import FreeElectrons
from ase.geometry import (crystal_structure_from_cell, cell_to_cellpar,
cellpar_to_cell)
from ase.dft.kpoints import get_special_points
mc1 = [[1, 0, 0], [0, 1, 0], [0, 0.2, 1]]
par = cell_to_cellpar(mc1)
mc2 = cellpar_to_cell(par)
mc3 = [[1, 0, 0], [0, 1, 0], [-0.2, 0, 1]]
mc4 = [[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})
cs = crystal_structure_from_cell(a.cell)
assert cs == 'monoclinic'
r = a.cell.reciprocal()
k = get_special_points(a.cell)['H']
print(np.dot(k, r))
a.get_potential_energy()
bs = a.calc.band_structure()
coords, labelcoords, labels = bs.get_labels()
assert ''.join(labels) == path
e_skn = bs.energies
# bs.plot()
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 test_bandstructure(plt):
from ase.build import bulk
from ase.calculators.test import FreeElectrons
from ase.dft.kpoints import special_paths
from ase.dft.band_structure import BandStructure
a = bulk('Cu')
path = special_paths['fcc']
a.calc = FreeElectrons(nvalence=1,
kpts={'path': path, 'npoints': 200})
a.get_potential_energy()
bs = a.calc.band_structure()
coords, labelcoords, labels = bs.get_labels()
print(labels)
bs.write('hmm.json')
bs = BandStructure.read('hmm.json')
coords, labelcoords, labels = bs.get_labels()
print(labels)
assert ''.join(labels) == 'GXWKGLUWLKUX'
bs.plot(emax=10, filename='bs.png')
def test_bandstructure_json():
from ase.build import bulk
from ase.spectrum.band_structure import calculate_band_structure, BandStructure
from ase.io.jsonio import read_json
from ase.calculators.test import FreeElectrons
atoms = bulk('Au')
lat = atoms.cell.get_bravais_lattice()
path = lat.bandpath(npoints=100)
atoms.calc = FreeElectrons()
bs = calculate_band_structure(atoms, path)
bs.write('bs.json')
bs.path.write('path.json')
bs1 = read_json('bs.json')
bs2 = BandStructure.read('bs.json')
path1 = read_json('path.json')
assert type(bs1) == type(bs) # noqa
assert type(bs2) == type(bs) # noqa
assert type(path1) == type(bs.path) # noqa
import matplotlib
from ase.build import bulk
from ase.calculators.test import FreeElectrons
from ase.dft.kpoints import special_paths
from ase.dft.band_structure import BandStructure
a = bulk('Cu')
path = special_paths['fcc']
a.calc = FreeElectrons(nvalence=1, kpts={'path': path, 'npoints': 200})
a.get_potential_energy()
bs = a.calc.band_structure()
coords, labelcoords, labels = bs.get_labels()
print(labels)
bs.write('hmm.json')
bs = BandStructure.read('hmm.json')
coords, labelcoords, labels = bs.get_labels()
print(labels)
assert ''.join(labels) == 'GXWKGLUWLKUX'
matplotlib.use('Agg', warn=False)
bs.plot(emax=10, filename='bs.png')
def _atoms(cell):
atoms = Atoms(cell=cell, pbc=True)
atoms.calc = FreeElectrons()
return atoms
"""Test band structure from different variations of hexagonal cells."""
import numpy as np
from ase import Atoms
from ase.calculators.test import FreeElectrons
from ase.dft.kpoints import get_special_points
firsttime = True
for cell in [[[1, 0, 0], [0.5, 3**0.5 / 2, 0], [0, 0, 1]],
[[1, 0, 0], [-0.5, 3**0.5 / 2, 0], [0, 0, 1]],
[[0.5, -3**0.5 / 2, 0], [0.5, 3**0.5 / 2, 0], [0, 0, 1]]]:
a = Atoms(cell=cell, pbc=True)
a.cell *= 3
a.calc = FreeElectrons(nvalence=1, kpts={'path': 'GMKG'})
lat = a.cell.get_bravais_lattice()
assert lat.name == 'HEX'
print(repr(a.cell.get_bravais_lattice()))
#print(crystal_structure_from_cell(a.cell))
r = a.get_reciprocal_cell()
k = get_special_points(a.cell)['K']
print(np.dot(k, r))
a.get_potential_energy()
bs = a.calc.band_structure()
coords, labelcoords, labels = bs.get_labels()
assert ''.join(labels) == 'GMKG'
e_skn = bs.energies
if firsttime:
coords1 = coords
labelcoords1 = labelcoords
e_skn1 = e_skn
firsttime = False
else:
from ase import Atoms
from ase.calculators.test import FreeElectrons
from ase.geometry import crystal_structure_from_cell, cell_to_cellpar, cellpar_to_cell
from ase.dft.kpoints import get_special_points
mc1 = [[1, 0, 0], [0, 1, 0], [0, 0.2, 1]]
par = cell_to_cellpar(mc1)
mc2 = cellpar_to_cell(par)
mc3 = [[1, 0, 0], [0, 1, 0], [-0.2, 0, 1]]
path = 'GYHCEM1AXH1'
firsttime = True
for cell in [mc1, mc2, mc3]:
a = Atoms(cell=cell, pbc=True)
a.cell *= 3
a.calc = FreeElectrons(nvalence=1, kpts={'path': path})
print(crystal_structure_from_cell(a.cell))
r = a.get_reciprocal_cell()
k = get_special_points(a.cell)['H']
print(np.dot(k, r))
a.get_potential_energy()
bs = a.calc.band_structure()
coords, labelcoords, labels = bs.get_labels()
assert ''.join(labels) == path
e_skn = bs.energies
# bs.plot()
if firsttime:
coords1 = coords
labelcoords1 = labelcoords
e_skn1 = e_skn
firsttime = False
from ase.build import bulk
from ase.dft.band_structure import calculate_band_structure
from ase.io.jsonio import read_json
from ase.calculators.test import FreeElectrons
atoms = bulk('Au')
lat, _ = atoms.cell.bravais()
path = lat.bandpath(npoints=100)
atoms.calc = FreeElectrons()
bs = calculate_band_structure(atoms, path)
bs.write('bs.json')
bs.path.write('path.json')
bs1 = read_json('bs.json')
path1 = read_json('path.json')
print(bs1)
print(path1)
assert type(bs1) == type(bs)
assert type(path1) == type(bs.path)