class KpointTest(unittest.TestCase):
def setUp(self):
self.lattice = Lattice.cubic(10.0)
self.kpoint = Kpoint([0.1, 0.4, -0.5], self.lattice, label="X")
def test_properties(self):
self.assertEqual(self.kpoint.frac_coords[0], 0.1)
self.assertEqual(self.kpoint.frac_coords[1], 0.4)
self.assertEqual(self.kpoint.frac_coords[2], -0.5)
self.assertEqual(self.kpoint.a, 0.1)
self.assertEqual(self.kpoint.b, 0.4)
self.assertEqual(self.kpoint.c, -0.5)
self.assertEqual(self.lattice, Lattice.cubic(10.0))
self.assertEqual(self.kpoint.cart_coords[0], 1.0)
self.assertEqual(self.kpoint.cart_coords[1], 4.0)
self.assertEqual(self.kpoint.cart_coords[2], -5.0)
self.assertEqual(self.kpoint.label, "X")
def test_as_dict(self):
self.assertIsInstance(self.kpoint.as_dict()["fcoords"], list)
self.assertIsInstance(self.kpoint.as_dict()["ccoords"], list)
self.assertNotIsInstance(self.kpoint.as_dict()["fcoords"][0],
numpy.float64)
self.assertNotIsInstance(self.kpoint.as_dict()["ccoords"][0],
numpy.float64)
self.assertListEqual(self.kpoint.as_dict()["fcoords"],
[0.1, 0.4, -0.5])
self.assertListEqual(self.kpoint.as_dict()["ccoords"],
[1.0, 4.0, -5.0])
def get_band_structure(self):
"""Return a BandStructureSymmLine object interpolating bands along a
High symmetry path calculated from the structure using HighSymmKpath function"""
kpath = HighSymmKpath(self.data.structure)
kpt_line = [
Kpoint(k, self.data.structure.lattice)
for k in kpath.get_kpoints(coords_are_cartesian=False)[0]
]
kpoints = np.array([kp.frac_coords for kp in kpt_line])
labels_dict = {
l: k
for k, l in zip(*kpath.get_kpoints(coords_are_cartesian=False))
if l
}
lattvec = self.data.get_lattvec()
egrid, vgrid = fite.getBands(kpoints, self.equivalences, lattvec,
self.coeffs)
bands_dict = {Spin.up: (egrid / units.eV)}
sbs = BandStructureSymmLine(
kpoints,
bands_dict,
self.data.structure.lattice.reciprocal_lattice,
self.efermi / units.eV,
labels_dict=labels_dict)
return sbs
def test_from_dict(self):
d = self.kpoint.as_dict()
kpoint = Kpoint.from_dict(d)
self.assertEqual(kpoint.frac_coords[0], 0.1)
self.assertEqual(kpoint.frac_coords[1], 0.4)
self.assertEqual(kpoint.frac_coords[2], -0.5)
self.assertEqual(kpoint.a, 0.1)
self.assertEqual(kpoint.b, 0.4)
self.assertEqual(kpoint.c, -0.5)
self.assertEqual(kpoint.lattice, Lattice.cubic(10.0))
self.assertEqual(kpoint.cart_coords[0], 1.0)
self.assertEqual(kpoint.cart_coords[1], 4.0)
self.assertEqual(kpoint.cart_coords[2], -5.0)
self.assertEqual(kpoint.label, "X")
def __init__(self,
qpoints,
frequencies,
lattice,
nac_frequencies=None,
eigendisplacements=None,
nac_eigendisplacements=None,
labels_dict=None,
coords_are_cartesian=False,
structure=None):
"""
Args:
qpoints: list of qpoint as numpy arrays, in frac_coords of the
given lattice by default
frequencies: list of phonon frequencies in THz as a numpy array with shape
(3*len(structure), len(qpoints)). The First index of the array
refers to the band and the second to the index of the qpoint.
lattice: The reciprocal lattice as a pymatgen Lattice object.
Pymatgen uses the physics convention of reciprocal lattice vectors
WITH a 2*pi coefficient.
nac_frequencies: Frequencies with non-analytical contributions at Gamma in THz.
A list of tuples. The first element of each tuple should be a list
defining the direction (not necessarily a versor, will be normalized
internally). The second element containing the 3*len(structure)
phonon frequencies with non-analytical correction for that direction.
eigendisplacements: the phonon eigendisplacements associated to the
frequencies in cartesian coordinates. A numpy array of complex
numbers with shape (3*len(structure), len(qpoints), len(structure), 3).
he First index of the array refers to the band, the second to the index
of the qpoint, the third to the atom in the structure and the fourth
to the cartesian coordinates.
nac_eigendisplacements: the phonon eigendisplacements associated to the
non-analytical frequencies in nac_frequencies in cartesian coordinates.
A list of tuples. The first element of each tuple should be a list
defining the direction. The second element containing a numpy array of
complex numbers with shape (3*len(structure), len(structure), 3).
labels_dict: (dict) of {} this links a qpoint (in frac coords or
cartesian coordinates depending on the coords) to a label.
coords_are_cartesian: Whether the qpoint coordinates are cartesian.
structure: The crystal structure (as a pymatgen Structure object)
associated with the band structure. This is needed if we
provide projections to the band structure
"""
self.lattice_rec = lattice
self.qpoints = []
self.labels_dict = {}
self.structure = structure
if eigendisplacements is None:
eigendisplacements = np.array([])
self.eigendisplacements = eigendisplacements
if labels_dict is None:
labels_dict = {}
for q in qpoints:
# let see if this qpoint has been assigned a label
label = None
for c in labels_dict:
if np.linalg.norm(q - np.array(labels_dict[c])) < 0.0001:
label = c
self.labels_dict[label] = Kpoint(
q,
lattice,
label=label,
coords_are_cartesian=coords_are_cartesian)
self.qpoints.append(
Kpoint(q,
lattice,
label=label,
coords_are_cartesian=coords_are_cartesian))
self.bands = frequencies
self.nb_bands = len(self.bands)
self.nb_qpoints = len(self.qpoints)
# normalize directions for nac_frequencies and nac_eigendisplacements
self.nac_frequencies = []
self.nac_eigendisplacements = []
if nac_frequencies is not None:
for t in nac_frequencies:
self.nac_frequencies.append(
([i / np.linalg.norm(t[0]) for i in t[0]], t[1]))
if nac_eigendisplacements is not None:
for t in nac_eigendisplacements:
self.nac_eigendisplacements.append(
([i / np.linalg.norm(t[0]) for i in t[0]], t[1]))
def setUp(self):
self.lattice = Lattice.cubic(10.0)
self.kpoint = Kpoint([0.1, 0.4, -0.5], self.lattice, label="X")