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 band_structure(self):
self.calculate()
perm = self.parameters.get('perm', self.label)
if self.calc.get_spin_polarized():
alpha = np.loadtxt(os.path.join(perm, self.label + '.alpha_band'))
beta = np.loadtxt(os.path.join(perm, self.label + '.beta_band'))
energies = np.array([alpha[:, 1:], beta[:, 1:]]) * Hartree
else:
data = np.loadtxt(
os.path.join(perm, self.label + '.restricted_band'))
energies = data[np.newaxis, :, 1:] * Hartree
eref = self.calc.get_fermi_level()
if eref is None:
eref = 0.
return BandStructure(self.parameters.bandpath, energies, eref)
def resolve_band_structure(path, kpts, energies, efermi):
"""Convert input BandPath along with Siesta outputs into BS object."""
# Right now this function doesn't do much.
#
# Not sure how the output kpoints in the siesta.bands file are derived.
# They appear to be related to the lattice parameter.
#
# We should verify that they are consistent with our input path,
# but since their meaning is unclear, we can't quite do so.
#
# Also we should perhaps verify the cell. If we had the cell, we
# could construct the bandpath from scratch (i.e., pure outputs).
from ase.spectrum.band_structure import BandStructure
ksn2e = energies
skn2e = np.swapaxes(ksn2e, 0, 1)
bs = BandStructure(path, skn2e, reference=efermi)
return bs
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 read_bandstructure(self):
if not os.path.isfile(f'{self.label}_band.dat'):
return
# Construct the higher-resolution bandpath from the *_band.labelinfo.dat file
with open(f'{self.label}_band.labelinfo.dat') as fd:
flines = fd.readlines()
kpts = []
self.atoms.cell.pbc = True
for start, end in zip(flines[:-1], flines[1:]):
start_label, i_start = start.split()[:2]
end_label, i_end = end.split()[:2]
kpts += self.atoms.cell.bandpath(start_label + end_label,
int(i_end) - int(i_start) +
1).kpts[:-1].tolist()
kpts.append([float(x) for x in flines[-1].split()[-3:]])
path = self.parameters.kpoint_path.path
special_points = self.parameters.kpoint_path.special_points
kpath = BandPath(self.atoms.cell,
kpts,
path=path,
special_points=special_points)
# Read in the eigenvalues from the *_band.dat file
with open(f'{self.label}_band.dat') as fd:
flines = fd.readlines()
eigs = [[]]
for line in flines[:-1]:
splitline = line.strip().split()
if len(splitline) == 0:
eigs.append([])
else:
eigs[-1].append(line.strip().split()[-1])
eigs = np.array(eigs, dtype=float).T
# Construct the bandstructure
bs = BandStructure(kpath, eigs[np.newaxis, :, :])
self.results['band structure'] = bs
def create_ase_object(objtype, dct):
# We just try each object type one after another and instantiate
# them manually, depending on which kind it is.
# We can formalize this later if it ever becomes necessary.
if objtype == 'cell':
from ase.cell import Cell
dct.pop('pbc', None) # compatibility; we once had pbc
obj = Cell(**dct)
elif objtype == 'bandstructure':
from ase.spectrum.band_structure import BandStructure
obj = BandStructure(**dct)
elif objtype == 'bandpath':
from ase.dft.kpoints import BandPath
obj = BandPath(path=dct.pop('labelseq'), **dct)
elif objtype == 'atoms':
from ase import Atoms
obj = Atoms.fromdict(dct)
else:
raise ValueError('Do not know how to decode object type {} '
'into an actual object'.format(objtype))
assert obj.ase_objtype == objtype
return obj
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
28.6214, 29.1794, 29.1794, 29.6229, 30.5584, 32.8451
],
[
-3.0876, -0.8863, 3.0037, 3.0037, 6.2623, 6.7765,
14.7728, 14.7728, 17.1201, 17.4077, 17.8504, 17.8504,
19.3349, 19.8627, 22.8644, 23.6249, 23.6249, 24.7429,
27.5978, 27.9651, 27.9651, 29.0422, 30.4427, 32.3347
],
[
-2.5785, -1.4744, 2.9437, 2.9437, 6.3021, 6.5565,
15.41, 15.41, 17.2036, 17.2036, 17.7555, 18.0538,
19.0775, 19.1146, 23.7456, 24.5645, 24.5645, 24.9649,
26.8166, 26.8167, 26.9285, 27.9975, 30.8961, 31.8679
],
[
-2.0397, -2.0397, 2.9235, 2.9235, 6.399, 6.3991,
15.775, 15.775, 16.8298, 16.8298, 18.4119, 18.4119,
18.6257, 18.6257, 24.5738, 24.5739, 25.3583, 25.3583,
25.9521, 25.9521, 27.1466, 27.1466, 31.3822, 31.3825
]]])
# Update to new band structure stuff
lattice = atoms.cell.get_bravais_lattice()
bandpath = lattice.bandpath('WGX', npoints=30)
maxerr = np.abs(bandpath.kpts - kpts).max()
assert maxerr < 1e-5
bs = BandStructure(bandpath, energies=energies, reference=ref)
bs.plot(emin=-13, filename='vasp_si_bandstructure.png')
