def test_magmom(self):
symprec = 1e-5
cell = read_cell_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_get_supercell_convcell_sio2(convcell_sio2: PhonopyAtoms,
helper_methods,
is_old_style=True):
smat = np.diag([1, 2, 3])
fname = "SiO2-123.yaml"
scell = get_supercell(convcell_sio2, smat, is_old_style=is_old_style)
cell_ref = read_cell_yaml(os.path.join(data_dir, fname))
if is_old_style is True:
helper_methods.compare_cells_with_order(scell, cell_ref)
else:
helper_methods.compare_cells(scell, cell_ref)
def test_read_pwscf():
"""Test of read_pwscf."""
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 = read_cell_yaml(filename)
assert (np.abs(cell.cell - cell_ref.cell) < 1e-5).all()
diff_pos = cell.scaled_positions - cell_ref.scaled_positions
diff_pos -= np.rint(diff_pos)
assert (np.abs(diff_pos) < 1e-5).all()
for s, s_r in zip(cell.symbols, cell_ref.symbols):
assert s == s_r
def test_read_vasp():
"""Test read_vasp."""
cell = read_vasp(os.path.join(data_dir, "..", "POSCAR_NaCl"))
filename = os.path.join(data_dir, "NaCl-vasp.yaml")
cell_ref = read_cell_yaml(filename)
assert (np.abs(cell.cell - cell_ref.cell) < 1e-5).all()
diff_pos = cell.scaled_positions - cell_ref.scaled_positions
diff_pos -= np.rint(diff_pos)
assert (np.abs(diff_pos) < 1e-5).all()
for s, s_r in zip(cell.symbols, cell_ref.symbols):
assert s == s_r
def test_read_turbomole():
"""Test read_turbomole."""
cell = read_turbomole(os.path.join(data_dir, "Si-TURBOMOLE-control"))
filename = os.path.join(data_dir, "Si-TURBOMOLE.yaml")
cell_ref = read_cell_yaml(filename)
assert (np.abs(cell.cell - cell_ref.cell) < 1e-5).all()
diff_pos = cell.scaled_positions - cell_ref.scaled_positions
diff_pos -= np.rint(diff_pos)
assert (np.abs(diff_pos) < 1e-5).all()
for s, s_r in zip(cell.symbols, cell_ref.symbols):
assert s == s_r
def _test_get_supercell_primcell_si(primcell_si: PhonopyAtoms,
helper_methods,
is_old_style=True):
smat = [[-1, 1, 1], [1, -1, 1], [1, 1, -1]]
fname = "Si-conv.yaml"
scell = get_supercell(primcell_si, smat, is_old_style=is_old_style)
cell_ref = read_cell_yaml(os.path.join(data_dir, fname))
if is_old_style is True:
helper_methods.compare_cells_with_order(scell, cell_ref)
else:
helper_methods.compare_cells(scell, cell_ref)
def test_read_crystal():
"""Test of read_crystal."""
cell, pp_filenames = read_crystal(os.path.join(data_dir, "Si-CRYSTAL.o"))
filename = os.path.join(data_dir, "Si-CRYSTAL.yaml")
cell_ref = read_cell_yaml(filename)
assert (np.abs(cell.cell - cell_ref.cell) < 1e-5).all()
diff_pos = cell.scaled_positions - cell_ref.scaled_positions
diff_pos -= np.rint(diff_pos)
assert (np.abs(diff_pos) < 1e-5).all()
for s, s_r in zip(cell.symbols, cell_ref.symbols):
assert s == s_r
def test_read_cp2k(self):
cell, _ = read_cp2k(os.path.join(data_dir, "Si-CP2K.inp"))
cell_ref = read_cell_yaml(os.path.join(data_dir, "Si-CP2K.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_parse_wien2k_struct():
"""Test structure parsing."""
filename_BaGa2 = os.path.join(data_dir, "BaGa2.struct")
cell, _, _, _ = parse_wien2k_struct(filename_BaGa2)
filename = os.path.join(data_dir, "BaGa2-wien2k.yaml")
cell_ref = read_cell_yaml(filename)
assert (np.abs(cell.cell - cell_ref.cell) < 1e-5).all()
diff_pos = cell.scaled_positions - cell_ref.scaled_positions
diff_pos -= np.rint(diff_pos)
assert (np.abs(diff_pos) < 1e-5).all()
for s, s_r in zip(cell.symbols, cell_ref.symbols):
assert s == s_r
def test_read_castep(self):
cell = read_castep(os.path.join(data_dir, "NaCl-castep.cell"))
filename = os.path.join(data_dir, "NaCl-castep.yaml")
cell_ref = read_cell_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_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 = read_cell_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 = read_cell_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 = read_cell_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 = read_cell_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_turbomole(self):
cell = read_turbomole(os.path.join(data_dir,
"Si-TURBOMOLE-control"))
filename = os.path.join(data_dir, "Si-TURBOMOLE.yaml")
cell_ref = read_cell_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_watch_GeneralizedRegularGridPoints(ph_tio2: Phonopy, helper_methods):
"""Test for q-points positions obtained from GeneralizedRegularGridPoints."""
grgp = GeneralizedRegularGridPoints(ph_tio2.unitcell, 10, x_fastest=False)
tmat = grgp.transformation_matrix
# direct basis vectors in row vectors
plat = np.dot(tmat.T, ph_tio2.unitcell.cell)
# reciprocal basis vectors in row vectors (10 times magnified)
rec_plat = np.linalg.inv(plat).T * 10
nums = [
1,
] * len(grgp.qpoints)
cell = PhonopyAtoms(cell=rec_plat,
scaled_positions=grgp.qpoints,
numbers=nums)
yaml_filename = os.path.join(current_dir, "tio2_qpoints.yaml")
cell_ref = read_cell_yaml(yaml_filename)
helper_methods.compare_cells(cell, cell_ref)
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 = read_cell_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 = read_cell_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):
pmat = [[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]]
smat2 = np.eye(3, dtype='intc') * 2
pmat2 = np.dot(np.linalg.inv(smat2), pmat)
smat3 = np.eye(3, dtype='intc') * 3
pmat3 = np.dot(np.linalg.inv(smat3), pmat)
cell = read_cell_yaml(os.path.join(data_dir, "..", "NaCl.yaml"))
scell2 = get_supercell(cell, smat2)
scell3 = get_supercell(cell, smat3)
n = len(scell3) // 2
# swap first and last half of atomic order
indices = [i + n for i in range(n)] + list(range(n))
scell3_swap = PhonopyAtoms(
cell=scell3.cell,
scaled_positions=scell3.scaled_positions[indices],
numbers=scell3.numbers[indices])
self._tcell2 = TrimmedCell(pmat2, scell2)
self._tcell3 = TrimmedCell(
pmat3,
scell3_swap,
positions_to_reorder=self._tcell2.scaled_positions)
def setUp(self):
self.pmat = [[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]]
self.smat = np.eye(3, dtype='int') * 2
self.cell = read_cell_yaml(os.path.join(data_dir, "..", "NaCl.yaml"))
self.scell, self.pcell = _get_supercell_and_primitive(
self.cell,
primitive_matrix=self.pmat,
supercell_matrix=self.smat)
self.idx = [self.scell.u2u_map[i]
for i in self.scell.s2u_map[self.pcell.p2s_map]]
self.epsilon = np.array([[2.43533967, 0, 0],
[0, 2.43533967, 0],
[0, 0, 2.43533967]])
self.borns = np.array([[[1.08875538, 0, 0],
[0, 1.08875538, 0],
[0, 0, 1.08875538]],
[[1.08875538, 0, 0],
[0, 1.08875538, 0],
[0, 0, 1.08875538]],
[[1.08875538, 0, 0],
[0, 1.08875538, 0],
[0, 0, 1.08875538]],
[[1.08875538, 0, 0],
[0, 1.08875538, 0],
[0, 0, 1.08875538]],
[[-1.08875538, 0, 0],
[0, -1.08875538, 0],
[0, 0, -1.08875538]],
[[-1.08875538, 0, 0],
[0, -1.08875538, 0],
[0, 0, -1.08875538]],
[[-1.08875538, 0, 0],
[0, -1.08875538, 0],
[0, 0, -1.08875538]],
[[-1.08875538, 0, 0],
[0, -1.08875538, 0],
[0, 0, -1.08875538]]])
def setUp(self):
self._cell = read_cell_yaml(os.path.join(data_dir, "POSCAR.yaml"))
def setUp(self):
cell = read_cell_yaml(os.path.join(data_dir, "..", "NaCl.yaml"))
self._pcell = get_primitive(cell, [[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]])
def setUp(self):
filename = os.path.join("..", "NaCl.yaml")
self._cell = read_cell_yaml(os.path.join(data_dir, filename))
def agno2_cell():
"""Return AgNO2 cell (Imm2)."""
cell = read_cell_yaml(os.path.join(current_dir, "AgNO2_cell.yaml"))
return cell
