def write_cif(
filename: str,
struct: Structure,
refine_cell=False,
resize_volume=False,
symprec=1e-2,
comment="",
):
"""
dump structure in CIF format after resizing to feasible volume and refing cell by symmetry.
Parameters
----------
filename: str
struct: pymatgen.core.Structure
refine_cell: bool, optional
if true, refine cell setting by spglib
resize_volume: bool, optional
if true, resize lattice by DLSVolumePredictor in pymatgen
symprec: float, optional
symprec in spglib
"""
struct = refine_and_resize_structure(struct, refine_cell, resize_volume)
cw = CifWriter(struct, symprec=symprec)
comment = f"# generated by {__version__}\n" + comment
with open(filename, "w") as f:
if comment:
f.write(comment + "\n" + cw.__str__())
else:
f.write(cw.__str__())
def pre_save_post_validation(cls, sender, document, **kwargs):
from mpcontribs.api.structures.views import StructuresResource
resource = StructuresResource()
d = resource.serialize(document, fields=["lattice", "sites", "charge"])
s = json.dumps(d, sort_keys=True).encode("utf-8")
document.md5 = md5(s).hexdigest()
structure = Structure.from_dict(d)
try:
writer = CifWriter(structure, symprec=1e-10)
except TypeError:
# save CIF string without symmetry information
writer = CifWriter(structure)
document.cif = writer.__str__()
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 get_string(self) -> str:
cw = CifWriter(self.structure)
return cw.__str__()
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 Gd1 1 0.317460 0.817460 0.000000 1.0
Gd Gd2 1 0.182540 0.317460 0.000000 1.0
Gd Gd3 1 0.817460 0.682540 0.000000 1.0
Gd Gd4 1 0.682540 0.182540 0.000000 1.0
B B5 1 0.000000 0.000000 0.202900 1.0
B B6 1 0.500000 0.500000 0.797100 1.0
B B7 1 0.000000 0.000000 0.797100 1.0
B B8 1 0.500000 0.500000 0.202900 1.0
B B9 1 0.175900 0.038000 0.500000 1.0
B B10 1 0.962000 0.175900 0.500000 1.0
B B11 1 0.038000 0.824100 0.500000 1.0
B B12 1 0.675900 0.462000 0.500000 1.0
B B13 1 0.324100 0.538000 0.500000 1.0
B B14 1 0.824100 0.962000 0.500000 1.0
B B15 1 0.538000 0.675900 0.500000 1.0
B B16 1 0.462000 0.324100 0.500000 1.0
B B17 1 0.086700 0.586700 0.500000 1.0
B B18 1 0.413300 0.086700 0.500000 1.0
B B19 1 0.586700 0.913300 0.500000 1.0
B B20 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
Gd1 5.05000 5.05000 0.00000
Gd2 -5.05000 5.05000 0.00000
Gd3 5.05000 -5.05000 0.00000
Gd4 -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 Gd1 1 0.317460 0.817460 0.000000 1.0
Gd Gd2 1 0.182540 0.317460 0.000000 1.0
Gd Gd3 1 0.817460 0.682540 0.000000 1.0
Gd Gd4 1 0.682540 0.182540 0.000000 1.0
B B5 1 0.000000 0.000000 0.202900 1.0
B B6 1 0.500000 0.500000 0.797100 1.0
B B7 1 0.000000 0.000000 0.797100 1.0
B B8 1 0.500000 0.500000 0.202900 1.0
B B9 1 0.175900 0.038000 0.500000 1.0
B B10 1 0.962000 0.175900 0.500000 1.0
B B11 1 0.038000 0.824100 0.500000 1.0
B B12 1 0.675900 0.462000 0.500000 1.0
B B13 1 0.324100 0.538000 0.500000 1.0
B B14 1 0.824100 0.962000 0.500000 1.0
B B15 1 0.538000 0.675900 0.500000 1.0
B B16 1 0.462000 0.324100 0.500000 1.0
B B17 1 0.086700 0.586700 0.500000 1.0
B B18 1 0.413300 0.086700 0.500000 1.0
B B19 1 0.586700 0.913300 0.500000 1.0
B B20 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
Gd1 0.00000 0.00000 7.14178
Gd2 0.00000 0.00000 7.14178
Gd3 0.00000 0.00000 -7.14178
Gd4 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)
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)
def test_symmetrized(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
writer = CifWriter(poscar.structure, symprec=0.1)
ans = """# generated using pymatgen
data_FePO4
_symmetry_space_group_name_H-M Pnma
_cell_length_a 10.41176687
_cell_length_b 6.06717188
_cell_length_c 4.75948954
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 62
_chemical_formula_structural FePO4
_chemical_formula_sum 'Fe4 P4 O16'
_cell_volume 300.65685512
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
2 '-x, -y, -z'
3 '-x+1/2, -y, z+1/2'
4 'x+1/2, y, -z+1/2'
5 'x+1/2, -y+1/2, -z+1/2'
6 '-x+1/2, y+1/2, z+1/2'
7 '-x, y+1/2, -z'
8 'x, -y+1/2, 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
Fe Fe1 4 0.218728 0.750000 0.474867 1
P P2 4 0.094613 0.250000 0.418243 1
O O3 8 0.165710 0.046072 0.285384 1
O O4 4 0.043372 0.750000 0.707138 1
O O5 4 0.096642 0.250000 0.741320 1"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
ans = """# generated using pymatgen
data_LiFePO4
_symmetry_space_group_name_H-M Pnma
_cell_length_a 4.74480000
_cell_length_b 6.06577000
_cell_length_c 10.41037000
_cell_angle_alpha 90.50179000
_cell_angle_beta 90.00019000
_cell_angle_gamma 90.00362000
_symmetry_Int_Tables_number 62
_chemical_formula_structural LiFePO4
_chemical_formula_sum 'Li4 Fe4 P4 O16'
_cell_volume 299.607967711
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
2 '-x, -y, -z'
3 'x+1/2, -y, -z+1/2'
4 '-x+1/2, y, z+1/2'
5 '-x+1/2, -y+1/2, z+1/2'
6 'x+1/2, y+1/2, -z+1/2'
7 '-x, y+1/2, -z'
8 'x, -y+1/2, 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
Li Li1 4 0.000010 0.500000 0.999990 1.0
Fe Fe2 4 0.025030 0.746540 0.281160 1.0
P P3 4 0.082060 0.248260 0.405570 1.0
O O4 8 0.213420 0.043980 0.334230 1.0
O O5 4 0.208430 0.251100 0.543180 1.0
O O6 4 0.241480 0.750450 0.596220 1.0
"""
s = Structure.from_file(os.path.join(test_dir, 'LiFePO4.cif'))
writer = CifWriter(s, symprec=0.1)
self.assertEqual(writer.__str__().strip(), ans.strip())
def test_write(self):
s_ncl = self.mcif_ncl.get_structures(primitive=False)[0]
cw = CifWriter(s_ncl, write_magmoms=True)
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 206.007290027
_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 Gd1 1 0.317460 0.817460 0.000000 1.0
Gd Gd2 1 0.182540 0.317460 0.000000 1.0
Gd Gd3 1 0.817460 0.682540 0.000000 1.0
Gd Gd4 1 0.682540 0.182540 0.000000 1.0
B B5 1 0.000000 0.000000 0.202900 1.0
B B6 1 0.500000 0.500000 0.797100 1.0
B B7 1 0.000000 0.000000 0.797100 1.0
B B8 1 0.500000 0.500000 0.202900 1.0
B B9 1 0.175900 0.038000 0.500000 1.0
B B10 1 0.962000 0.175900 0.500000 1.0
B B11 1 0.038000 0.824100 0.500000 1.0
B B12 1 0.675900 0.462000 0.500000 1.0
B B13 1 0.324100 0.538000 0.500000 1.0
B B14 1 0.824100 0.962000 0.500000 1.0
B B15 1 0.538000 0.675900 0.500000 1.0
B B16 1 0.462000 0.324100 0.500000 1.0
B B17 1 0.086700 0.586700 0.500000 1.0
B B18 1 0.413300 0.086700 0.500000 1.0
B B19 1 0.586700 0.913300 0.500000 1.0
B B20 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
Gd1 5.05 5.05 0.0
Gd2 -5.05 5.05 0.0
Gd3 5.05 -5.05 0.0
Gd4 -5.05 -5.05 0.0
"""
self.assertEqual(cw.__str__(), cw_ref_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 Gd1 1 0.317460 0.817460 0.000000 1.0
Gd Gd2 1 0.182540 0.317460 0.000000 1.0
Gd Gd3 1 0.817460 0.682540 0.000000 1.0
Gd Gd4 1 0.682540 0.182540 0.000000 1.0
B B5 1 0.000000 0.000000 0.202900 1.0
B B6 1 0.500000 0.500000 0.797100 1.0
B B7 1 0.000000 0.000000 0.797100 1.0
B B8 1 0.500000 0.500000 0.202900 1.0
B B9 1 0.175900 0.038000 0.500000 1.0
B B10 1 0.962000 0.175900 0.500000 1.0
B B11 1 0.038000 0.824100 0.500000 1.0
B B12 1 0.675900 0.462000 0.500000 1.0
B B13 1 0.324100 0.538000 0.500000 1.0
B B14 1 0.824100 0.962000 0.500000 1.0
B B15 1 0.538000 0.675900 0.500000 1.0
B B16 1 0.462000 0.324100 0.500000 1.0
B B17 1 0.086700 0.586700 0.500000 1.0
B B18 1 0.413300 0.086700 0.500000 1.0
B B19 1 0.586700 0.913300 0.500000 1.0
B B20 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
Gd1 5.05000 5.05000 0.00000
Gd2 -5.05000 5.05000 0.00000
Gd3 5.05000 -5.05000 0.00000
Gd4 -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 Gd1 1 0.317460 0.817460 0.000000 1.0
Gd Gd2 1 0.182540 0.317460 0.000000 1.0
Gd Gd3 1 0.817460 0.682540 0.000000 1.0
Gd Gd4 1 0.682540 0.182540 0.000000 1.0
B B5 1 0.000000 0.000000 0.202900 1.0
B B6 1 0.500000 0.500000 0.797100 1.0
B B7 1 0.000000 0.000000 0.797100 1.0
B B8 1 0.500000 0.500000 0.202900 1.0
B B9 1 0.175900 0.038000 0.500000 1.0
B B10 1 0.962000 0.175900 0.500000 1.0
B B11 1 0.038000 0.824100 0.500000 1.0
B B12 1 0.675900 0.462000 0.500000 1.0
B B13 1 0.324100 0.538000 0.500000 1.0
B B14 1 0.824100 0.962000 0.500000 1.0
B B15 1 0.538000 0.675900 0.500000 1.0
B B16 1 0.462000 0.324100 0.500000 1.0
B B17 1 0.086700 0.586700 0.500000 1.0
B B18 1 0.413300 0.086700 0.500000 1.0
B B19 1 0.586700 0.913300 0.500000 1.0
B B20 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
Gd1 0.00000 0.00000 7.14178
Gd2 0.00000 0.00000 7.14178
Gd3 0.00000 0.00000 -7.14178
Gd4 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)
def test_write(self):
s_ncl = self.mcif_ncl.get_structures(primitive=False)[0]
cw = CifWriter(s_ncl, write_magmoms=True)
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 206.007290027
_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 Gd1 1 0.317460 0.817460 0.000000 1.0
Gd Gd2 1 0.182540 0.317460 0.000000 1.0
Gd Gd3 1 0.817460 0.682540 0.000000 1.0
Gd Gd4 1 0.682540 0.182540 0.000000 1.0
B B5 1 0.000000 0.000000 0.202900 1.0
B B6 1 0.500000 0.500000 0.797100 1.0
B B7 1 0.000000 0.000000 0.797100 1.0
B B8 1 0.500000 0.500000 0.202900 1.0
B B9 1 0.175900 0.038000 0.500000 1.0
B B10 1 0.962000 0.175900 0.500000 1.0
B B11 1 0.038000 0.824100 0.500000 1.0
B B12 1 0.675900 0.462000 0.500000 1.0
B B13 1 0.324100 0.538000 0.500000 1.0
B B14 1 0.824100 0.962000 0.500000 1.0
B B15 1 0.538000 0.675900 0.500000 1.0
B B16 1 0.462000 0.324100 0.500000 1.0
B B17 1 0.086700 0.586700 0.500000 1.0
B B18 1 0.413300 0.086700 0.500000 1.0
B B19 1 0.586700 0.913300 0.500000 1.0
B B20 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
Gd1 5.05 5.05 0.0
Gd2 -5.05 5.05 0.0
Gd3 5.05 -5.05 0.0
Gd4 -5.05 -5.05 0.0
"""
self.assertEqual(cw.__str__(), cw_ref_string)
