def test_magmom(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml(os.path.join(data_dir,"Cr.yaml"))
symmetry_nonspin = Symmetry(cell, symprec=symprec)
atom_map_nonspin = symmetry_nonspin.get_map_atoms()
len_sym_nonspin = len(
symmetry_nonspin.get_symmetry_operations()['rotations'])
spin = [1, -1]
cell_withspin = cell.copy()
cell_withspin.set_magnetic_moments(spin)
symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
atom_map_withspin = symmetry_withspin.get_map_atoms()
len_sym_withspin = len(
symmetry_withspin.get_symmetry_operations()['rotations'])
broken_spin = [1, -2]
cell_brokenspin = cell.copy()
cell_brokenspin = cell.copy()
cell_brokenspin.set_magnetic_moments(broken_spin)
symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
len_sym_brokenspin = len(
symmetry_brokenspin.get_symmetry_operations()['rotations'])
self.assertTrue((atom_map_nonspin == atom_map_withspin).all())
self.assertFalse((atom_map_nonspin == atom_map_brokenspin).all())
self.assertTrue(len_sym_nonspin == len_sym_withspin)
self.assertFalse(len_sym_nonspin == len_sym_brokenspin)
def test_magmom(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml(
os.path.join(data_dir, "Cr.yaml"))
symmetry_nonspin = Symmetry(cell, symprec=symprec)
atom_map_nonspin = symmetry_nonspin.get_map_atoms()
len_sym_nonspin = len(
symmetry_nonspin.get_symmetry_operations()['rotations'])
spin = [1, -1]
cell_withspin = cell.copy()
cell_withspin.set_magnetic_moments(spin)
symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
atom_map_withspin = symmetry_withspin.get_map_atoms()
len_sym_withspin = len(
symmetry_withspin.get_symmetry_operations()['rotations'])
broken_spin = [1, -2]
cell_brokenspin = cell.copy()
cell_brokenspin = cell.copy()
cell_brokenspin.set_magnetic_moments(broken_spin)
symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
len_sym_brokenspin = len(
symmetry_brokenspin.get_symmetry_operations()['rotations'])
self.assertTrue((atom_map_nonspin == atom_map_withspin).all())
self.assertFalse((atom_map_nonspin == atom_map_brokenspin).all())
self.assertTrue(len_sym_nonspin == len_sym_withspin)
self.assertFalse(len_sym_nonspin == len_sym_brokenspin)
def test_read_pwscf(self):
cell, pp_filenames = read_pwscf("NaCl-pwscf.in")
cell_ref = get_unitcell_from_phonopy_yaml("NaCl-pwscf.yaml")
self.assertTrue(
(np.abs(cell.get_cell() - cell_ref.get_cell()) < 1e-5).all())
diff_pos = cell.get_scaled_positions() - cell_ref.get_scaled_positions()
diff_pos -= np.rint(diff_pos)
self.assertTrue((np.abs(diff_pos) < 1e-5).all())
for s, s_r in zip(cell.get_chemical_symbols(),
cell_ref.get_chemical_symbols()):
self.assertTrue(s == s_r)
def test_read_abinit(self):
cell = read_abinit(os.path.join(data_dir, "NaCl-abinit.in"))
filename = os.path.join(data_dir, "NaCl-abinit-pwscf.yaml")
cell_ref = get_unitcell_from_phonopy_yaml(filename)
self.assertTrue(
(np.abs(cell.get_cell() - cell_ref.get_cell()) < 1e-5).all())
diff_pos = cell.get_scaled_positions() - cell_ref.get_scaled_positions()
diff_pos -= np.rint(diff_pos)
self.assertTrue((np.abs(diff_pos) < 1e-5).all())
for s, s_r in zip(cell.get_chemical_symbols(),
cell_ref.get_chemical_symbols()):
self.assertTrue(s == s_r)
def test_read_crystal(self):
cell, pp_filenames = read_crystal(os.path.join(data_dir,"Si-CRYSTAL.o"))
filename = os.path.join(data_dir,"Si-CRYSTAL.yaml")
cell_ref = get_unitcell_from_phonopy_yaml(filename)
self.assertTrue(
(np.abs(cell.get_cell() - cell_ref.get_cell()) < 1e-5).all())
diff_pos = cell.get_scaled_positions() - cell_ref.get_scaled_positions()
diff_pos -= np.rint(diff_pos)
self.assertTrue((np.abs(diff_pos) < 1e-5).all())
for s, s_r in zip(cell.get_chemical_symbols(),
cell_ref.get_chemical_symbols()):
self.assertTrue(s == s_r)
def test_read_pwscf(self):
cell, pp_filenames = read_pwscf(os.path.join(data_dir,"NaCl-pwscf.in"))
filename = os.path.join(data_dir,"NaCl-abinit-pwscf.yaml")
cell_ref = get_unitcell_from_phonopy_yaml(filename)
self.assertTrue(
(np.abs(cell.get_cell() - cell_ref.get_cell()) < 1e-5).all())
diff_pos = cell.get_scaled_positions() - cell_ref.get_scaled_positions()
diff_pos -= np.rint(diff_pos)
self.assertTrue((np.abs(diff_pos) < 1e-5).all())
for s, s_r in zip(cell.get_chemical_symbols(),
cell_ref.get_chemical_symbols()):
self.assertTrue(s == s_r)
def test_parse_wien2k_struct(self):
filename_BaGa2 = os.path.join(data_dir,"BaGa2.struct")
cell, npts, r0s, rmts = parse_wien2k_struct(filename_BaGa2)
filename = os.path.join(data_dir,"BaGa2-wien2k.yaml")
cell_ref = get_unitcell_from_phonopy_yaml(filename)
self.assertTrue(
(np.abs(cell.get_cell() - cell_ref.get_cell()) < 1e-5).all())
diff_pos = cell.get_scaled_positions() - cell_ref.get_scaled_positions()
diff_pos -= np.rint(diff_pos)
self.assertTrue((np.abs(diff_pos) < 1e-5).all())
for s, s_r in zip(cell.get_chemical_symbols(),
cell_ref.get_chemical_symbols()):
self.assertTrue(s == s_r)
def test_parse_wien2k_struct(self):
filename_BaGa2 = os.path.join(data_dir, "BaGa2.struct")
cell, npts, r0s, rmts = parse_wien2k_struct(filename_BaGa2)
filename = os.path.join(data_dir, "BaGa2-wien2k.yaml")
cell_ref = get_unitcell_from_phonopy_yaml(filename)
self.assertTrue(
(np.abs(cell.get_cell() - cell_ref.get_cell()) < 1e-5).all())
diff_pos = (cell.get_scaled_positions() -
cell_ref.get_scaled_positions())
diff_pos -= np.rint(diff_pos)
self.assertTrue((np.abs(diff_pos) < 1e-5).all())
for s, s_r in zip(cell.get_chemical_symbols(),
cell_ref.get_chemical_symbols()):
self.assertTrue(s == s_r)
def test_get_map_operations(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml("../NaCl.yaml")
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
map_ops_cmp = [
0, 2, 51, 53, 8, 1, 65, 98, 3, 14, 34, 24, 76, 69, 54, 110, 576,
198, 229, 208, 201, 192, 210, 294, 5, 67, 36, 57, 18, 90, 23, 114,
0, 9, 1, 96, 6, 323, 98, 326, 3, 42, 17, 293, 16, 130, 99, 337,
192, 194, 202, 199, 205, 196, 200, 193, 12, 5, 30, 108, 37, 128,
291, 302
]
start = time.time()
symmetry._set_map_operations()
end = time.time()
# print(end - start)
map_ops = symmetry.get_map_operations()
self.assertTrue((map_ops_cmp == map_ops).all())
def test_get_supercell(self):
for i, (cell, smat, fname) in enumerate(zip(self._cells,
self._smats,
self._fnames)):
scell = get_supercell(cell, smat)
scell_yaml = get_unitcell_from_phonopy_yaml(os.path.join(data_dir,
fname))
np.testing.assert_allclose(scell.get_cell(), scell_yaml.get_cell(),
atol=1e-5)
pos = scell.get_scaled_positions()
pos -= np.rint(pos)
pos_yaml = scell_yaml.get_scaled_positions()
pos_yaml -= np.rint(pos_yaml)
np.testing.assert_allclose(pos, pos_yaml, atol=1e-5)
np.testing.assert_array_equal(scell.get_atomic_numbers(),
scell_yaml.get_atomic_numbers())
np.testing.assert_allclose(scell.get_masses(),
scell_yaml.get_masses(),
atol=1e-5)
def test_get_map_operations(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml(
os.path.join(data_dir, "..", "NaCl.yaml"))
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
# start = time.time()
symmetry._set_map_operations()
# end = time.time()
# print(end - start)
map_ops = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
positions = scell.get_scaled_positions()
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
for i, (op_i, atom_i) in enumerate(zip(map_ops, map_atoms)):
r_pos = np.dot(rotations[op_i], positions[i]) + translations[op_i]
diff = positions[atom_i] - r_pos
diff -= np.rint(diff)
self.assertTrue((diff < symprec).all())
def test_get_supercell(self):
for i, (cell, smat,
fname) in enumerate(zip(self._cells, self._smats,
self._fnames)):
scell = get_supercell(cell, smat)
scell_yaml = get_unitcell_from_phonopy_yaml(
os.path.join(data_dir, fname))
np.testing.assert_allclose(scell.get_cell(),
scell_yaml.get_cell(),
atol=1e-5)
pos = scell.get_scaled_positions()
pos -= np.rint(pos)
pos_yaml = scell_yaml.get_scaled_positions()
pos_yaml -= np.rint(pos_yaml)
np.testing.assert_allclose(pos, pos_yaml, atol=1e-5)
np.testing.assert_array_equal(scell.get_atomic_numbers(),
scell_yaml.get_atomic_numbers())
np.testing.assert_allclose(scell.get_masses(),
scell_yaml.get_masses(),
atol=1e-5)
def test_get_map_operations(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml(
os.path.join(data_dir,"../NaCl.yaml"))
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
start = time.time()
symmetry._set_map_operations()
end = time.time()
# print(end - start)
map_ops = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
positions = scell.get_scaled_positions()
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
for i, (op_i, atom_i) in enumerate(zip(map_ops, map_atoms)):
r_pos = np.dot(rotations[op_i], positions[i]) + translations[op_i]
diff = positions[atom_i] - r_pos
diff -= np.rint(diff)
self.assertTrue((diff < symprec).all())
def setUp(self):
filename = "POSCAR.yaml"
self._cell = get_unitcell_from_phonopy_yaml(filename)
def setUp(self):
filename = os.path.join("..", "NaCl.yaml")
self._cell = get_unitcell_from_phonopy_yaml(
os.path.join(data_dir, filename))
def setUp(self):
filename = "../NaCl.yaml"
self._cell = get_unitcell_from_phonopy_yaml(os.path.join(data_dir,filename))
def setUp(self):
filename = "../NaCl.yaml"
self._cell = get_unitcell_from_phonopy_yaml(filename)
