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test_cif.py extract long CIF reference strings into test/files/*.mcif
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@janosh
janosh committed Oct 23, 2023
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38 changes: 38 additions & 0 deletions tests/files/CsCl-manual-oxi-ref.mcif
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# 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
55 changes: 55 additions & 0 deletions tests/files/GdB4-str-magnitudes-ref.mcif
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# 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
55 changes: 55 additions & 0 deletions tests/files/GdB4-writer-ref.mcif
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# 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
160 changes: 8 additions & 152 deletions tests/io/test_cif.py
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Expand Up @@ -942,62 +942,8 @@ def test_get_structures(self):
assert s_ncl.matches(s_ncl_from_msg)

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
"""
with open(f"{TEST_FILES_DIR}/GdB4-writer-ref.mcif") as file:
cw_ref_string = file.read()
s_ncl = self.mcif_ncl.get_structures(primitive=False)[0]

cw = CifWriter(s_ncl, write_magmoms=True)
Expand All @@ -1016,62 +962,9 @@ def test_write(self):
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
"""
with open(f"{TEST_FILES_DIR}/GdB4-str-magnitudes-ref.mcif") as file:
cw_ref_string_magnitudes = file.read()

assert str(cw).strip() == cw_ref_string_magnitudes.strip()
# test we're getting correct magmoms in ncl case
s_ncl2 = self.mcif_ncl2.get_structures()[0]
Expand All @@ -1081,51 +974,14 @@ def test_write(self):
assert list_magmoms[1][0] == approx(-5.1234749999999991)
assert list_magmoms[1][1] == approx(2.9580396704363183)

# test creating an structure without oxidation state doesn't raise errors
# test creating a 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
"""
with open(f"{TEST_FILES_DIR}/CsCl-manual-oxi-ref.mcif") as file:
cw_manual_oxi_string = file.read()
s_manual.add_oxidation_state_by_site([1, 1])
cw = CifWriter(s_manual, write_magmoms=True)
assert str(cw) == cw_manual_oxi_string
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