def test_structure_2_lmpdata(self):
matrix = np.diag(np.random.randint(5, 14, size=(3,))) \
+ np.random.rand(3, 3) * 0.2 - 0.1
latt = Lattice(matrix)
frac_coords = np.random.rand(10, 3)
random_structure = Structure(latt, ["H"] * 10, frac_coords)
oxi_states = np.random.rand(10) - 0.5
random_structure.add_oxidation_state_by_site(oxi_states)
ld = structure_2_lmpdata(random_structure)
box_tilt = [0.0, 0.0, 0.0] if not ld.box_tilt else ld.box_tilt
box_bounds = np.array(ld.box_bounds)
np.testing.assert_array_equal(box_bounds[:, 0], np.zeros(3))
new_matrix = np.diag(box_bounds[:, 1])
new_matrix[1, 0] = box_tilt[0]
new_matrix[2, 0] = box_tilt[1]
new_matrix[2, 1] = box_tilt[2]
new_latt = Lattice(new_matrix)
np.testing.assert_array_almost_equal(new_latt.abc, latt.abc)
np.testing.assert_array_almost_equal(new_latt.angles, latt.angles)
coords = ld.atoms[["x", "y", "z"]].values
new_structure = Structure(new_latt, ['H'] * 10,
coords,
coords_are_cartesian=True)
np.testing.assert_array_almost_equal(new_structure.frac_coords,
frac_coords)
self.assertEqual(len(ld.masses), 1)
def test_write(self):
cw_ref_string = """# generated using pymatgen
data_GdB4
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 7.13160000
_cell_length_b 7.13160000
_cell_length_c 4.05050000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural GdB4
_chemical_formula_sum 'Gd4 B16'
_cell_volume 206.00729003
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Gd Gd0 1 0.31746000 0.81746000 0.00000000 1.0
Gd Gd1 1 0.18254000 0.31746000 0.00000000 1.0
Gd Gd2 1 0.81746000 0.68254000 0.00000000 1.0
Gd Gd3 1 0.68254000 0.18254000 0.00000000 1.0
B B4 1 0.00000000 0.00000000 0.20290000 1.0
B B5 1 0.50000000 0.50000000 0.79710000 1.0
B B6 1 0.00000000 0.00000000 0.79710000 1.0
B B7 1 0.50000000 0.50000000 0.20290000 1.0
B B8 1 0.17590000 0.03800000 0.50000000 1.0
B B9 1 0.96200000 0.17590000 0.50000000 1.0
B B10 1 0.03800000 0.82410000 0.50000000 1.0
B B11 1 0.67590000 0.46200000 0.50000000 1.0
B B12 1 0.32410000 0.53800000 0.50000000 1.0
B B13 1 0.82410000 0.96200000 0.50000000 1.0
B B14 1 0.53800000 0.67590000 0.50000000 1.0
B B15 1 0.46200000 0.32410000 0.50000000 1.0
B B16 1 0.08670000 0.58670000 0.50000000 1.0
B B17 1 0.41330000 0.08670000 0.50000000 1.0
B B18 1 0.58670000 0.91330000 0.50000000 1.0
B B19 1 0.91330000 0.41330000 0.50000000 1.0
loop_
_atom_site_moment_label
_atom_site_moment_crystalaxis_x
_atom_site_moment_crystalaxis_y
_atom_site_moment_crystalaxis_z
Gd0 5.05000000 5.05000000 0.00000000
Gd1 -5.05000000 5.05000000 0.00000000
Gd2 5.05000000 -5.05000000 0.00000000
Gd3 -5.05000000 -5.05000000 0.00000000
"""
s_ncl = self.mcif_ncl.get_structures(primitive=False)[0]
cw = CifWriter(s_ncl, write_magmoms=True)
self.assertEqual(cw.__str__(), cw_ref_string)
# from list-type magmoms
list_magmoms = [list(m) for m in s_ncl.site_properties['magmom']]
# float magmoms (magnitude only)
float_magmoms = [float(m) for m in s_ncl.site_properties['magmom']]
s_ncl.add_site_property('magmom', list_magmoms)
cw = CifWriter(s_ncl, write_magmoms=True)
self.assertEqual(cw.__str__(), cw_ref_string)
s_ncl.add_site_property('magmom', float_magmoms)
cw = CifWriter(s_ncl, write_magmoms=True)
cw_ref_string_magnitudes = """# generated using pymatgen
data_GdB4
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 7.13160000
_cell_length_b 7.13160000
_cell_length_c 4.05050000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural GdB4
_chemical_formula_sum 'Gd4 B16'
_cell_volume 206.00729003
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Gd Gd0 1 0.31746000 0.81746000 0.00000000 1.0
Gd Gd1 1 0.18254000 0.31746000 0.00000000 1.0
Gd Gd2 1 0.81746000 0.68254000 0.00000000 1.0
Gd Gd3 1 0.68254000 0.18254000 0.00000000 1.0
B B4 1 0.00000000 0.00000000 0.20290000 1.0
B B5 1 0.50000000 0.50000000 0.79710000 1.0
B B6 1 0.00000000 0.00000000 0.79710000 1.0
B B7 1 0.50000000 0.50000000 0.20290000 1.0
B B8 1 0.17590000 0.03800000 0.50000000 1.0
B B9 1 0.96200000 0.17590000 0.50000000 1.0
B B10 1 0.03800000 0.82410000 0.50000000 1.0
B B11 1 0.67590000 0.46200000 0.50000000 1.0
B B12 1 0.32410000 0.53800000 0.50000000 1.0
B B13 1 0.82410000 0.96200000 0.50000000 1.0
B B14 1 0.53800000 0.67590000 0.50000000 1.0
B B15 1 0.46200000 0.32410000 0.50000000 1.0
B B16 1 0.08670000 0.58670000 0.50000000 1.0
B B17 1 0.41330000 0.08670000 0.50000000 1.0
B B18 1 0.58670000 0.91330000 0.50000000 1.0
B B19 1 0.91330000 0.41330000 0.50000000 1.0
loop_
_atom_site_moment_label
_atom_site_moment_crystalaxis_x
_atom_site_moment_crystalaxis_y
_atom_site_moment_crystalaxis_z
Gd0 0.00000000 0.00000000 7.14177849
Gd1 0.00000000 0.00000000 7.14177849
Gd2 0.00000000 0.00000000 -7.14177849
Gd3 0.00000000 0.00000000 -7.14177849
"""
self.assertEqual(cw.__str__().strip(),
cw_ref_string_magnitudes.strip())
# test we're getting correct magmoms in ncl case
s_ncl2 = self.mcif_ncl2.get_structures()[0]
list_magmoms = [list(m) for m in s_ncl2.site_properties['magmom']]
self.assertEqual(list_magmoms[0][0], 0.0)
self.assertAlmostEqual(list_magmoms[0][1], 5.9160793408726366)
self.assertAlmostEqual(list_magmoms[1][0], -5.1234749999999991)
self.assertAlmostEqual(list_magmoms[1][1], 2.9580396704363183)
# test creating an structure without oxidation state doesn't raise errors
s_manual = Structure(Lattice.cubic(4.2), ["Cs", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
s_manual.add_spin_by_site([1, -1])
cw = CifWriter(s_manual, write_magmoms=True)
# check oxidation state
cw_manual_oxi_string = """# generated using pymatgen
data_CsCl
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 4.20000000
_cell_length_b 4.20000000
_cell_length_c 4.20000000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural CsCl
_chemical_formula_sum 'Cs1 Cl1'
_cell_volume 74.08800000
_cell_formula_units_Z 1
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Cs+ 1.0
Cl+ 1.0
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Cs+ Cs0 1 0.00000000 0.00000000 0.00000000 1
Cl+ Cl1 1 0.50000000 0.50000000 0.50000000 1
loop_
_atom_site_moment_label
_atom_site_moment_crystalaxis_x
_atom_site_moment_crystalaxis_y
_atom_site_moment_crystalaxis_z
"""
s_manual.add_oxidation_state_by_site([1, 1])
cw = CifWriter(s_manual, write_magmoms=True)
self.assertEqual(cw.__str__(), cw_manual_oxi_string)
def test_write(self):
cw_ref_string = """# generated using pymatgen
data_GdB4
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 7.13160000
_cell_length_b 7.13160000
_cell_length_c 4.05050000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural GdB4
_chemical_formula_sum 'Gd4 B16'
_cell_volume 206.00729003
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Gd Gd0 1 0.317460 0.817460 0.000000 1.0
Gd Gd1 1 0.182540 0.317460 0.000000 1.0
Gd Gd2 1 0.817460 0.682540 0.000000 1.0
Gd Gd3 1 0.682540 0.182540 0.000000 1.0
B B4 1 0.000000 0.000000 0.202900 1.0
B B5 1 0.500000 0.500000 0.797100 1.0
B B6 1 0.000000 0.000000 0.797100 1.0
B B7 1 0.500000 0.500000 0.202900 1.0
B B8 1 0.175900 0.038000 0.500000 1.0
B B9 1 0.962000 0.175900 0.500000 1.0
B B10 1 0.038000 0.824100 0.500000 1.0
B B11 1 0.675900 0.462000 0.500000 1.0
B B12 1 0.324100 0.538000 0.500000 1.0
B B13 1 0.824100 0.962000 0.500000 1.0
B B14 1 0.538000 0.675900 0.500000 1.0
B B15 1 0.462000 0.324100 0.500000 1.0
B B16 1 0.086700 0.586700 0.500000 1.0
B B17 1 0.413300 0.086700 0.500000 1.0
B B18 1 0.586700 0.913300 0.500000 1.0
B B19 1 0.913300 0.413300 0.500000 1.0
loop_
_atom_site_moment_label
_atom_site_moment_crystalaxis_x
_atom_site_moment_crystalaxis_y
_atom_site_moment_crystalaxis_z
Gd0 5.05000 5.05000 0.00000
Gd1 -5.05000 5.05000 0.00000
Gd2 5.05000 -5.05000 0.00000
Gd3 -5.05000 -5.05000 0.00000
"""
s_ncl = self.mcif_ncl.get_structures(primitive=False)[0]
cw = CifWriter(s_ncl, write_magmoms=True)
self.assertEqual(cw.__str__(), cw_ref_string)
# from list-type magmoms
list_magmoms = [list(m) for m in s_ncl.site_properties['magmom']]
# float magmoms (magnitude only)
float_magmoms = [float(m) for m in s_ncl.site_properties['magmom']]
s_ncl.add_site_property('magmom', list_magmoms)
cw = CifWriter(s_ncl, write_magmoms=True)
self.assertEqual(cw.__str__(), cw_ref_string)
s_ncl.add_site_property('magmom', float_magmoms)
cw = CifWriter(s_ncl, write_magmoms=True)
cw_ref_string_magnitudes = """# generated using pymatgen
data_GdB4
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 7.13160000
_cell_length_b 7.13160000
_cell_length_c 4.05050000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural GdB4
_chemical_formula_sum 'Gd4 B16'
_cell_volume 206.00729003
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Gd Gd0 1 0.317460 0.817460 0.000000 1.0
Gd Gd1 1 0.182540 0.317460 0.000000 1.0
Gd Gd2 1 0.817460 0.682540 0.000000 1.0
Gd Gd3 1 0.682540 0.182540 0.000000 1.0
B B4 1 0.000000 0.000000 0.202900 1.0
B B5 1 0.500000 0.500000 0.797100 1.0
B B6 1 0.000000 0.000000 0.797100 1.0
B B7 1 0.500000 0.500000 0.202900 1.0
B B8 1 0.175900 0.038000 0.500000 1.0
B B9 1 0.962000 0.175900 0.500000 1.0
B B10 1 0.038000 0.824100 0.500000 1.0
B B11 1 0.675900 0.462000 0.500000 1.0
B B12 1 0.324100 0.538000 0.500000 1.0
B B13 1 0.824100 0.962000 0.500000 1.0
B B14 1 0.538000 0.675900 0.500000 1.0
B B15 1 0.462000 0.324100 0.500000 1.0
B B16 1 0.086700 0.586700 0.500000 1.0
B B17 1 0.413300 0.086700 0.500000 1.0
B B18 1 0.586700 0.913300 0.500000 1.0
B B19 1 0.913300 0.413300 0.500000 1.0
loop_
_atom_site_moment_label
_atom_site_moment_crystalaxis_x
_atom_site_moment_crystalaxis_y
_atom_site_moment_crystalaxis_z
Gd0 0.00000 0.00000 7.14178
Gd1 0.00000 0.00000 7.14178
Gd2 0.00000 0.00000 -7.14178
Gd3 0.00000 0.00000 -7.14178
"""
self.assertEqual(cw.__str__(), cw_ref_string_magnitudes)
# test we're getting correct magmoms in ncl case
s_ncl2 = self.mcif_ncl2.get_structures()[0]
list_magmoms = [list(m) for m in s_ncl2.site_properties['magmom']]
self.assertEqual(list_magmoms[0][0], 0.0)
self.assertAlmostEqual(list_magmoms[0][1], 5.9160793408726366)
self.assertAlmostEqual(list_magmoms[1][0], -5.1234749999999991)
self.assertAlmostEqual(list_magmoms[1][1], 2.9580396704363183)
# test creating an structure without oxidation state doesn't raise errors
s_manual = Structure(Lattice.cubic(4.2), ["Cs", "Cl"],[[0, 0, 0], [0.5, 0.5, 0.5]])
s_manual.add_spin_by_site([1, -1])
cw = CifWriter(s_manual, write_magmoms=True)
# check oxidation state
cw_manual_oxi_string = """# generated using pymatgen
data_CsCl
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 4.20000000
_cell_length_b 4.20000000
_cell_length_c 4.20000000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural CsCl
_chemical_formula_sum 'Cs1 Cl1'
_cell_volume 74.08800000
_cell_formula_units_Z 1
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Cs+ 1.0
Cl+ 1.0
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Cs+ Cs0 1 0.000000 0.000000 0.000000 1
Cl+ Cl1 1 0.500000 0.500000 0.500000 1
loop_
_atom_site_moment_label
_atom_site_moment_crystalaxis_x
_atom_site_moment_crystalaxis_y
_atom_site_moment_crystalaxis_z
"""
s_manual.add_oxidation_state_by_site([1,1])
cw = CifWriter(s_manual, write_magmoms=True)
self.assertEqual(cw.__str__(), cw_manual_oxi_string)
