Migration Guide from spglib

Based on spglib v2.6.0

Symmetry tolerance

symprec and mag_symprec

Same as in spglib.

angle_tolerance

angle_tolerance in moyopy is in radian unit, while in spglib it is in degree unit. That being said, moyopy is expected to work without specifying angle_tolerance in most cases.

Space group

Cell representation

Spglib’s cell = (lattice, positions, numbers) corresponds to moyopy.Cell(basis=lattice, positions=positions, numbers=numbers).

Space-group symmetry search

spglib.get_symmetry()

Replace with MoyoDataset.

Let symmetry be the returned dictionary of spglib.get_symmetry(), the fields correspond to MoyoDataset fields as follows:

• symmetry['rotations'] -> MoyoDataset.operations.rotations

• symmetry['translations'] -> MoyoDataset.operations.translations

• symmetry['equivalent_atoms'] is not directly available in MoyoDataset. However, MoyoDataset.orbits gives Spglib’s crystallographic_orbits.

spglib.get_symmetry_dataset()

Replace with MoyoDataset.

If you need to specify hall_number, use

MoyoDataset(..., setting=Setting.hall_number(hall_number))

spglib.SpglibDataset fields correspond to MoyoDataset fields as follows:

• Space-group type

  • number -> MoyoDataset.number

  • hall_number -> MoyoDataset.hall_number

• Symmetry operations in the input cell

  • rotations -> MoyoDataset.operations.rotations

  • translations -> MoyoDataset.operations.translations

• Site symmetry

  • crystallographic_orbits -> MoyoDataset.orbits

  • wyckoffs -> MoyoDataset.wyckoffs

  • site_symmetry_symbols -> MoyoDataset.site_symmetry_symbols

• Standardized cell

  • std_lattice -> MoyoDataset.std_cell.basis

  • std_positions -> MoyoDataset.std_cell.positions

  • std_types -> MoyoDataset.std_cell.numbers

  • transformation_matrix -> MoyoDataset.std_linear

  • origin_shift -> MoyoDataset.std_origin_shift

  • std_rotation_matrix -> MoyoDataset.std_rotation_matrix

• Primitive standardized cell

  • mapping_to_primitive -> MoyoDataset.mapping_std_prim

• Secondary information

  • hall -> Obtain hall_number from MoyoDataset.hall_number and Access HallSymbolEntry(hall_number).hm_short

  • choice -> Obtain hall_number from MoyoDataset.hall_number and Access HallSymbolEntry(hall_number).centering

  • international -> Obtain number from MoyoDataset.number and Access SpaceGroupType(number).hm_short

• Not supported in moyopy

  • equivalent_atoms: Use MoyoDataset.orbits to get crystallographic orbits instead

  • primitive_lattice: Use MoyoDataset.prim_std_cell if you need a primitive standardized cell

  • std_mapping_to_primitive: Recreate MoyoDataset again with MoyoDataset.prim_std_cell

  • pointgroup

Space-group type search

spglib.get_spacegroup()

Moyopy does not directly support this function. See spglib.get_symmetry_dataset().

Space-group dataset access

spglib.get_symmetry_from_database()

Replace spglib.get_symmetry_from_database(hall_number) with operations_from_number(number, setting). An ITA number, number, can be obtained from HallSymbolEntry(hall_number).number.

spglib.get_spacegroup_type()

Replace spglib.get_spacegroup_type(hall_number) with SpaceGroupType(number). An ITA number, number, can be obtained from HallSymbolEntry(hall_number).number.

spglib.SpaceGroupType fields correspond to SpaceGroupType fields as follows:

• Space-group type

  • number -> SpaceGroupType.number

  • international_short -> SpaceGroupType.hm_short

  • international_full -> SpaceGroupType.hm_full

  • international -> SpaceGroupType.hm_short

• Arithmetic crystal class

  • arithmetic_crystal_class_number -> SpaceGroupType.arithmetic_number

  • arithmetic_crystal_class_symbol -> SpaceGroupType.arithmetic_symbol

• Other classifications

  • pointgroup_international -> SpaceGroupType.geometric_crystal_class

• Not supported in moyopy

  • Hall symbol information (choice, hall_number, hall_symbol) -> Use HallSymbolEntry instead

  • pointgroup_schoenflies

  • schoenflies

spglib.get_spacegroup_type_from_symmetry()

Replace spglib.get_spacegroup_type_from_symmetry(rotations, translations, lattice) it with SpaceGroup(prim_rotations, prim_translations, basis=lattice). Be careful that SpaceGroup works only with symmetry operations in primitive.

Magnetic symmetry

Magnetic cell representation

Spglib’s magnetic cell cell = (lattice, positions, numbers, magmoms) with collinear (N, )-shape magmoms corresponds to MoyoCollinearMagneticCell(basis=lattice, positions=positions, numbers=numbers, magnetic_moments=magmoms). Spglib’s magnetic cell cell = (lattice, positions, numbers, magmoms) with noncollinear (N, 3)-shape magmoms corresponds to MoyoNonCollinearMagneticCell(basis=lattice, positions=positions, numbers=numbers, magnetic_moments=magmoms).

spglib.get_magnetic_symmetry()

Replace with MoyoCollinearMagneticDataset for collinear and MoyoNonCollinearMagneticDataset for noncollinear.

Let symmetry be the returned dictionary of spglib.get_magnetic_symmetry(), the fields correspond to MoyoNonCollinearMagneticDataset as follows:

• symmetry['rotations'] -> MoyoNonCollinearMagneticDataset.magnetic_operations.rotations

• symmetry['translations'] -> MoyoNonCollinearMagneticDataset.magnetic_operations.translations

• symmetry['time_reversals'] -> MoyoNonCollinearMagneticDataset.magnetic_operations.time_reversals

• symmetry['equivalent_atoms'] is not directly available in MoyoNonCollinearMagneticDataset. However, MoyoNonCollinearMagneticDataset.orbits gives Spglib’s crystallographic_orbits.

• symmetry['primitive_lattice'] -> MoyoNonCollinearMagneticDataset.prim_std_mag_cell.basis Reread MoyoNonCollinearMagneticDataset as MoyoCollinearMagneticDataset for collinear case.

spglib.get_magnetic_symmetry_dataset()

Replace with MoyoCollinearMagneticDataset for collinear and MoyoNonCollinearMagneticDataset for noncollinear.

spglib.SpglibMagneticDataset fields correspond to MoyoNonCollinearMagneticDataset fields as follows:

• Magnetic space-group type

  • uni_number -> MoyoNonCollinearMagneticDataset.uni_number

• Magnetic symmetry operations in the input cell

  • rotations -> MoyoNonCollinearMagneticDataset.magnetic_operations.rotations

  • translations -> MoyoNonCollinearMagneticDataset.magnetic_operations.translations

  • time_reversals -> MoyoNonCollinearMagneticDataset.magnetic_operations.time_reversals

  • n_operations -> MoyoNonCollinearMagneticDataset.magnetic_operations.num_operations

• Site symmetry

  • equivalent_atoms -> Use MoyoNonCollinearMagneticDataset.orbits to get crystallographic orbits instead

• Standardized magnetic cell

  • std_lattice -> MoyoNonCollinearMagneticDataset.std_mag_cell.basis

  • std_positions -> MoyoNonCollinearMagneticDataset.std_mag_cell.positions

  • std_types -> MoyoNonCollinearMagneticDataset.std_mag_cell.numbers

  • std_tensors -> MoyoNonCollinearMagneticDataset.std_mag_cell.magnetic_moments

  • n_std_atoms -> MoyoNonCollinearMagneticDataset.std_mag_cell.num_atoms

  • transformation_matrix -> MoyoNonCollinearMagneticDataset.std_linear

  • origin_shift -> MoyoNonCollinearMagneticDataset.std_origin_shift

  • std_rotation_matrix -> MoyoNonCollinearMagneticDataset.std_rotation_matrix

• Secondary information

  • msg_type -> Obtain uni_number from MoyoNonCollinearMagneticDataset.uni_number and Access MagneticSpaceGroupType(uni_number).construct_type

• Not supported in moyopy

  • primitive_lattice -> Use MoyoNonCollinearMagneticDataset.prim_std_mag_cell if you need a primitive standardized magnetic cell

  • hall_number -> Obtain uni_number from MoyoNonCollinearMagneticDataset.uni_number and Access MagneticSpaceGroupType(uni_number) instead

  • tensor_rank

  • n_atoms Reread MoyoNonCollinearMagneticDataset as MoyoCollinearMagneticDataset for collinear case.

spglib.get_magnetic_spacegroup_type()

Replace with MagneticSpaceGroupType(uni_number).

spglib.MagneticSpaceGroupType fields correspond to MagneticSpaceGroupType fields as follows:

• uni_number -> MagneticSpaceGroupType.uni_number

• litvin_number -> MagneticSpaceGroupType.litvin_number

• bns_number -> MagneticSpaceGroupType.bns_number

• og_number -> MagneticSpaceGroupType.og_number

• number -> MagneticSpaceGroupType.number

• type -> MagneticSpaceGroupType.construct_type

spglib.get_magnetic_spacegroup_type_from_symmetry()

Replace spglib.get_magnetic_spacegroup_type_from_symmetry(rotations, translations, time_reversals, lattice) with MagneticSpaceGroup(prim_rotations, prim_translations, prim_time_reversals, basis=lattice). Be careful that MagneticSpaceGroup works only with symmetry operations in primitive.

spglib.get_magnetic_symmetry_from_database()

Replace it with magnetic_operations_from_uni_number(uni_number).

Standardization and finding primitive cell

spglib.standardize_cell()

spglib.standardize_cell(..., to_primitive, no_idealize) is replaced with creating MoyoDataset with appropriate arguments:

• to_primitive=True -> MoyoDataset(..., rotate_basis=no_idealize).prim_std_cell

• to_primitive=False -> MoyoDataset(..., rotate_basis=no_idealize).std_cell

spglib.find_primitive()

Moyopy does not directly support this function. See spglib.standardize_cell().

spglib.refine_cell()

Moyopy does not directly support this function. See spglib.standardize_cell().

Lattice reduction

spglib.niggli_reduce()

TODO: not supported yet

spglib.delaunay_reduce()

TODO: not supported yet

Kpoints: spglib.get_ir_reciprocal_mesh()

moyopy does not plan to support it