def test_Unfolding_NaCl(ph_nacl):
"""Test to reproduce proper band structure of primitive cell
Results are written to "bin-unfolding-test.dat".
This data can be plotted by
% plot_band.py bin-unfolding-test.dat
Increase nd to get better plot.
The test is done with nd=10.
"""
# ph = _get_phonon(ph_nacl)
ph = ph_nacl
nd = 10
qpoints = np.array([[
x,
] * 3 for x in range(nd)]) / float(nd) - 0.5
unfolding_supercell_matrix = [[-2, 2, 2], [2, -2, 2], [2, 2, -2]]
mapping = np.arange(len(ph.supercell), dtype=int)
unfolding = Unfolding(ph, unfolding_supercell_matrix,
ph.supercell.scaled_positions, mapping, qpoints)
unfolding.run()
weights = _get_weights(unfolding, qpoints)
# _write_weights(weights, "unfolding.dat")
filename_out = os.path.join(data_dir, "bin-unfolding-test.dat")
_compare(weights,
os.path.join(data_dir, "bin-unfolding.dat"),
filename_out=None)
def test_Unfolding_SC(ph_nacl):
"""Test to reproduce unfoled band structure
Atomic positions are considered as the lattice ponts.
Results are written to "bin-unfolding_to_atoms-test.dat".
This data can be plotted by
% plot_band.py bin-unfolding_to_atoms-test.dat
Increase nd to get better plot.
The test is done with nd=10.
"""
# ph = _get_phonon(ph_nacl)
ph = ph_nacl
nd = 10
qpoints = np.array([[
x,
] * 3 for x in range(nd)]) / float(nd) - 0.5
unfolding_supercell_matrix = np.diag([4, 4, 4])
mapping = np.arange(len(ph.supercell), dtype=int)
unfolding = Unfolding(ph, unfolding_supercell_matrix,
ph.supercell.scaled_positions, mapping, qpoints)
unfolding.run()
weights = _get_weights(unfolding, qpoints)
# _write_weights(weights, "unfolding_to_atoms.dat")
filename_out = os.path.join(data_dir, "bin-unfolding_to_atoms-test.dat")
_compare(weights,
os.path.join(data_dir, "bin-unfolding_to_atoms.dat"),
filename_out=None)
def _prepare_unfolding(self, qpoints, unfolding_supercell_matrix):
supercell = get_supercell(self._cell, np.diag([2, 2, 2]))
phonon = self._get_phonon(supercell)
mapping = range(supercell.get_number_of_atoms())
self._unfolding = Unfolding(phonon, unfolding_supercell_matrix,
supercell.get_scaled_positions(), mapping,
qpoints)
def _prepare_unfolding(self, qpoints, unfolding_supercell_matrix):
supercell = get_supercell(self._cell, np.diag([2, 2, 2]))
phonon = self._get_phonon(supercell)
self._set_nac_params(phonon)
mapping = range(supercell.get_number_of_atoms())
self._unfolding = Unfolding(
phonon, unfolding_supercell_matrix, supercell.get_scaled_positions(), mapping, qpoints
)
class TestUnfolding(unittest.TestCase):
def setUp(self):
self._cell = read_vasp("POSCAR")
print(PhonopyAtoms(atoms=self._cell))
self._unfolding = None
def tearDown(self):
pass
def test_Unfolding_NaCl(self):
## mesh
# nd = 10
# qpoints = np.array(list(np.ndindex(nd, nd, nd))) / float(nd)
## band
nd = 100
qpoints = np.array([[
x,
] * 3 for x in range(nd)]) / float(nd)
unfolding_supercell_matrix = [[-2, 2, 2], [2, -2, 2], [2, 2, -2]]
self._prepare_unfolding(qpoints, unfolding_supercell_matrix)
self._run_unfolding()
self._write_wieghts(qpoints, unfolding_supercell_matrix,
"unfolding.dat")
def test_Unfolding_SC(self):
## mesh
# nd = 10
# qpoints = np.array(list(np.ndindex(nd, nd, nd))) / float(nd)
## band
nd = 100
qpoints = np.array([[
x,
] * 3 for x in range(nd)]) / float(nd)
unfolding_supercell_matrix = np.diag([4, 4, 4])
self._prepare_unfolding(qpoints, unfolding_supercell_matrix)
self._run_unfolding()
self._write_wieghts(qpoints, unfolding_supercell_matrix,
"unfolding_to_atoms.dat")
def _prepare_unfolding(self, qpoints, unfolding_supercell_matrix):
supercell = get_supercell(self._cell, np.diag([2, 2, 2]))
phonon = self._get_phonon(supercell)
self._set_nac_params(phonon)
mapping = range(supercell.get_number_of_atoms())
self._unfolding = Unfolding(phonon, unfolding_supercell_matrix,
supercell.get_scaled_positions(), mapping,
qpoints)
def _run_unfolding(self):
self._unfolding.run(verbose=True)
print(self._unfolding.get_unfolding_weights().shape)
def _write_wieghts(self, qpoints, unfolding_supercell_matrix, filename):
P = np.linalg.inv(unfolding_supercell_matrix)
comm_points = self._unfolding.get_commensurate_points()
# (nd + 1, num_atom_super / num_atom_prim, num_atom_super * 3)
weights = self._unfolding.get_unfolding_weights()
freqs = self._unfolding.get_frequencies()
with open(filename, 'w') as w:
lines = []
for i, q in enumerate(qpoints):
q_prim = np.dot(P.T, q)
for j, G in enumerate(comm_points):
q_k = q_prim + G
q_k -= np.rint(q_k)
if (np.abs(q_k[0] - q_k[1:]) > 1e-5).any():
continue
for k, f in enumerate(freqs[i]):
uw = weights[i, k, j]
lines.append("%10.7f %10.7f %10.7f %12.7f %10.7f" %
(q_k[0], q_k[1], q_k[2], f, uw))
w.write("\n".join(lines))
def _get_phonon(self, cell):
phonon = Phonopy(cell, np.diag([1, 1, 1]), is_auto_displacements=False)
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
def _set_nac_params(self, phonon):
supercell = phonon.get_supercell()
born_elems = {
'Na': [[1.08703, 0, 0], [0, 1.08703, 0], [0, 0, 1.08703]],
'Cl': [[-1.08672, 0, 0], [0, -1.08672, 0], [0, 0, -1.08672]]
}
born = [born_elems[s] for s in supercell.get_chemical_symbols()]
epsilon = [[2.43533967, 0, 0], [0, 2.43533967, 0], [0, 0, 2.43533967]]
factors = 14.400
phonon.set_nac_params({
'born': born,
'factor': factors,
'dielectric': epsilon
})
class TestUnfolding(unittest.TestCase):
def setUp(self):
self._cell = read_vasp("../POSCAR_NaCl")
# print(self._cell)
self._unfolding = None
def tearDown(self):
pass
def test_Unfolding_NaCl(self):
## mesh
# nd = 10
# qpoints = np.array(list(np.ndindex(nd, nd, nd))) / float(nd)
## band
nd = 50
qpoints = np.array([[
x,
] * 3 for x in range(nd)]) / float(nd)
unfolding_supercell_matrix = [[-2, 2, 2], [2, -2, 2], [2, 2, -2]]
self._prepare_unfolding(qpoints, unfolding_supercell_matrix)
self._run_unfolding()
weights = self._get_weights(qpoints, unfolding_supercell_matrix)
# self._write_weights(weights, "unfolding.dat")
self._compare(weights, "bin-unfolding.dat")
def test_Unfolding_SC(self):
## mesh
# nd = 10
# qpoints = np.array(list(np.ndindex(nd, nd, nd))) / float(nd)
## band
nd = 100
qpoints = np.array([[
x,
] * 3 for x in range(nd)]) / float(nd)
unfolding_supercell_matrix = np.diag([4, 4, 4])
self._prepare_unfolding(qpoints, unfolding_supercell_matrix)
self._run_unfolding()
weights = self._get_weights(qpoints, unfolding_supercell_matrix)
# self._write_weights(weights, "unfolding_to_atoms.dat")
self._compare(weights, "bin-unfolding_to_atoms.dat")
def _compare(self, weights, filename):
bin_data = self._binning(weights)
# self._write_bin_data(bin_data, filename)
with open(filename) as f:
bin_data_in_file = np.loadtxt(f)
self.assertTrue((np.abs(bin_data - bin_data_in_file) < 1e-4).all())
def _prepare_unfolding(self, qpoints, unfolding_supercell_matrix):
supercell = get_supercell(self._cell, np.diag([2, 2, 2]))
phonon = self._get_phonon(supercell)
self._set_nac_params(phonon)
mapping = range(supercell.get_number_of_atoms())
self._unfolding = Unfolding(phonon, unfolding_supercell_matrix,
supercell.get_scaled_positions(), mapping,
qpoints)
def _run_unfolding(self):
self._unfolding.run(verbose=False)
# print(self._unfolding.get_unfolding_weights().shape)
def _get_weights(self, qpoints, unfolding_supercell_matrix):
P = np.linalg.inv(unfolding_supercell_matrix)
comm_points = self._unfolding.get_commensurate_points()
# (nd + 1, num_atom_super / num_atom_prim, num_atom_super * 3)
weights = self._unfolding.get_unfolding_weights()
freqs = self._unfolding.get_frequencies()
out_vals = []
for i, q in enumerate(qpoints):
q_prim = np.dot(P.T, q)
for j, G in enumerate(comm_points):
q_k = q_prim + G
q_k -= np.rint(q_k)
if (np.abs(q_k[0] - q_k[1:]) > 1e-5).any():
continue
for k, f in enumerate(freqs[i]):
uw = weights[i, k, j]
out_vals.append([q_k[0], q_k[1], q_k[2], f, uw])
return out_vals
def _write_weights(self, weights, filename):
with open(filename, 'w') as w:
lines = [
"%10.7f %10.7f %10.7f %12.7f %10.7f" % tuple(x)
for x in weights
]
w.write("\n".join(lines))
def _write_bin_data(self, bin_data, filename):
with open(filename, 'w') as w:
lines = ["%8.5f %8.5f %8.5f" % tuple(v) for v in bin_data]
w.write("\n".join(lines))
def _get_phonon(self, cell):
phonon = Phonopy(cell, np.diag([1, 1, 1]))
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
def _set_nac_params(self, phonon):
supercell = phonon.get_supercell()
born_elems = {
'Na': [[1.08703, 0, 0], [0, 1.08703, 0], [0, 0, 1.08703]],
'Cl': [[-1.08672, 0, 0], [0, -1.08672, 0], [0, 0, -1.08672]]
}
born = [born_elems[s] for s in supercell.get_chemical_symbols()]
epsilon = [[2.43533967, 0, 0], [0, 2.43533967, 0], [0, 0, 2.43533967]]
factors = 14.400
phonon.set_nac_params({
'born': born,
'factor': factors,
'dielectric': epsilon
})
def _binning(self, data):
x = []
y = []
w = []
for vals in data:
if vals[4] > 1e-3:
x.append(vals[0])
y.append(vals[3])
w.append(vals[4])
x = np.around(x, decimals=5)
y = np.around(y, decimals=5)
w = np.array(w)
points = {}
for e_x, e_y, e_z in zip(x, y, w):
if (e_x, e_y) in points:
points[(e_x, e_y)] += e_z
else:
points[(e_x, e_y)] = e_z
x = []
y = []
w = []
for key in points:
x.append(key[0])
y.append(key[1])
w.append(points[key])
data = np.transpose([x, y, w])
data = sorted(data, key=lambda data: data[1])
data = sorted(data, key=lambda data: data[0])
return np.array(data)
class TestUnfolding(unittest.TestCase):
def setUp(self):
self._cell = read_vasp("POSCAR")
print(PhonopyAtoms(atoms=self._cell))
self._unfolding = None
def tearDown(self):
pass
def test_Unfolding_NaCl(self):
## mesh
# nd = 10
# qpoints = np.array(list(np.ndindex(nd, nd, nd))) / float(nd)
## band
nd = 100
qpoints = np.array([[x,] * 3 for x in range(nd)]) / float(nd)
unfolding_supercell_matrix=[[-2, 2, 2],
[2, -2, 2],
[2, 2, -2]]
self._prepare_unfolding(qpoints, unfolding_supercell_matrix)
self._run_unfolding()
self._write_wieghts(qpoints,
unfolding_supercell_matrix,
"unfolding.dat")
def test_Unfolding_SC(self):
## mesh
# nd = 10
# qpoints = np.array(list(np.ndindex(nd, nd, nd))) / float(nd)
## band
nd = 100
qpoints = np.array([[x,] * 3 for x in range(nd)]) / float(nd)
unfolding_supercell_matrix = np.diag([4, 4, 4])
self._prepare_unfolding(qpoints, unfolding_supercell_matrix)
self._run_unfolding()
self._write_wieghts(qpoints,
unfolding_supercell_matrix,
"unfolding_to_atoms.dat")
def _prepare_unfolding(self, qpoints, unfolding_supercell_matrix):
supercell = get_supercell(self._cell, np.diag([2, 2, 2]))
phonon = self._get_phonon(supercell)
self._set_nac_params(phonon)
mapping = range(supercell.get_number_of_atoms())
self._unfolding = Unfolding(phonon,
unfolding_supercell_matrix,
supercell.get_scaled_positions(),
mapping,
qpoints)
def _run_unfolding(self):
self._unfolding.run(verbose=True)
print(self._unfolding.get_unfolding_weights().shape)
def _write_wieghts(self, qpoints, unfolding_supercell_matrix, filename):
P = np.linalg.inv(unfolding_supercell_matrix)
comm_points = self._unfolding.get_commensurate_points()
# (nd + 1, num_atom_super / num_atom_prim, num_atom_super * 3)
weights = self._unfolding.get_unfolding_weights()
freqs = self._unfolding.get_frequencies()
with open(filename, 'w') as w:
lines = []
for i, q in enumerate(qpoints):
q_prim = np.dot(P.T, q)
for j, G in enumerate(comm_points):
q_k = q_prim + G
q_k -= np.rint(q_k)
if (np.abs(q_k[0] - q_k[1:]) > 1e-5).any():
continue
for k, f in enumerate(freqs[i]):
uw = weights[i, k, j]
lines.append("%10.7f %10.7f %10.7f %12.7f %10.7f" %
(q_k[0], q_k[1], q_k[2], f, uw))
w.write("\n".join(lines))
def _get_phonon(self, cell):
phonon = Phonopy(cell,
np.diag([1, 1, 1]),
is_auto_displacements=False)
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
def _set_nac_params(self, phonon):
supercell = phonon.get_supercell()
born_elems = {'Na': [[1.08703, 0, 0],
[0, 1.08703, 0],
[0, 0, 1.08703]],
'Cl': [[-1.08672, 0, 0],
[0, -1.08672, 0],
[0, 0, -1.08672]]}
born = [born_elems[s]
for s in supercell.get_chemical_symbols()]
epsilon = [[2.43533967, 0, 0],
[0, 2.43533967, 0],
[0, 0, 2.43533967]]
factors = 14.400
phonon.set_nac_params({'born': born,
'factor': factors,
'dielectric': epsilon})
class TestUnfolding(unittest.TestCase):
def setUp(self):
self._cell = read_vasp(os.path.join(data_dir, "..", "POSCAR_NaCl"))
# print(self._cell)
self._unfolding = None
def tearDown(self):
pass
def test_Unfolding_NaCl(self):
# mesh
# nd = 10
# qpoints = np.array(list(np.ndindex(nd, nd, nd))) / float(nd)
# band
nd = 50
qpoints = np.array([[x, ] * 3 for x in range(nd)]) / float(nd)
unfolding_supercell_matrix = [[-2, 2, 2],
[2, -2, 2],
[2, 2, -2]]
self._prepare_unfolding(qpoints, unfolding_supercell_matrix)
self._run_unfolding()
weights = self._get_weights(qpoints, unfolding_supercell_matrix)
# self._write_weights(weights, "unfolding.dat")
self._compare(weights, os.path.join(data_dir, "bin-unfolding.dat"))
def test_Unfolding_SC(self):
# mesh
# nd = 10
# qpoints = np.array(list(np.ndindex(nd, nd, nd))) / float(nd)
# band
nd = 100
qpoints = np.array([[x, ] * 3 for x in range(nd)]) / float(nd)
unfolding_supercell_matrix = np.diag([4, 4, 4])
self._prepare_unfolding(qpoints, unfolding_supercell_matrix)
self._run_unfolding()
weights = self._get_weights(qpoints, unfolding_supercell_matrix)
# self._write_weights(weights, "unfolding_to_atoms.dat")
self._compare(weights, os.path.join(data_dir,
"bin-unfolding_to_atoms.dat"))
def _compare(self, weights, filename):
bin_data = self._binning(weights)
# self._write_bin_data(bin_data, filename)
with open(filename) as f:
bin_data_in_file = np.loadtxt(f)
np.testing.assert_allclose(bin_data, bin_data_in_file, atol=1e-2)
def _prepare_unfolding(self, qpoints, unfolding_supercell_matrix):
supercell = get_supercell(self._cell, np.diag([2, 2, 2]))
phonon = self._get_phonon(supercell)
mapping = range(supercell.get_number_of_atoms())
self._unfolding = Unfolding(phonon,
unfolding_supercell_matrix,
supercell.get_scaled_positions(),
mapping,
qpoints)
def _run_unfolding(self):
self._unfolding.run(verbose=False)
# print(self._unfolding.get_unfolding_weights().shape)
def _get_weights(self, qpoints, unfolding_supercell_matrix):
P = np.linalg.inv(unfolding_supercell_matrix)
comm_points = self._unfolding.get_commensurate_points()
# (nd + 1, num_atom_super / num_atom_prim, num_atom_super * 3)
weights = self._unfolding.get_unfolding_weights()
freqs = self._unfolding.get_frequencies()
out_vals = []
for i, q in enumerate(qpoints):
q_prim = np.dot(P.T, q)
for j, G in enumerate(comm_points):
q_k = q_prim + G
q_k -= np.rint(q_k)
if (np.abs(q_k[0] - q_k[1:]) > 1e-5).any():
continue
for k, f in enumerate(freqs[i]):
uw = weights[i, k, j]
out_vals.append([q_k[0], q_k[1], q_k[2], f, uw])
return out_vals
def _write_weights(self, weights, filename):
with open(filename, 'w') as w:
lines = ["%10.7f %10.7f %10.7f %12.7f %10.7f" % tuple(x)
for x in weights]
w.write("\n".join(lines))
def _write_bin_data(self, bin_data, filename):
with open(filename, 'w') as w:
lines = ["%8.5f %8.5f %8.5f" % tuple(v) for v in bin_data]
w.write("\n".join(lines))
def _get_phonon(self, cell):
phonon = Phonopy(cell, np.diag([1, 1, 1]))
force_sets = parse_FORCE_SETS(
filename=os.path.join(data_dir, "FORCE_SETS"))
phonon.dataset = force_sets
phonon.produce_force_constants()
supercell = phonon.get_supercell()
born_elems = {'Na': [[1.08703, 0, 0],
[0, 1.08703, 0],
[0, 0, 1.08703]],
'Cl': [[-1.08672, 0, 0],
[0, -1.08672, 0],
[0, 0, -1.08672]]}
born = [born_elems[s]
for s in supercell.get_chemical_symbols()]
epsilon = [[2.43533967, 0, 0],
[0, 2.43533967, 0],
[0, 0, 2.43533967]]
factors = 14.400
phonon.set_nac_params({'born': born,
'factor': factors,
'dielectric': epsilon})
return phonon
def _binning(self, data):
x = []
y = []
w = []
for vals in data:
if vals[4] > 1e-3:
x.append(vals[0])
y.append(vals[3])
w.append(vals[4])
x = np.around(x, decimals=5)
y = np.around(y, decimals=5)
w = np.array(w)
points = {}
for e_x, e_y, e_z in zip(x, y, w):
if (e_x, e_y) in points:
points[(e_x, e_y)] += e_z
else:
points[(e_x, e_y)] = e_z
x = []
y = []
w = []
for key in points:
x.append(key[0])
y.append(key[1])
w.append(points[key])
data = np.transpose([x, y, w])
data = sorted(data, key=lambda data: data[1])
data = sorted(data, key=lambda data: data[0])
return np.array(data)