Variables#

Variables frequently used in C-API are explained. In interfaces of other languages, the definition may be different, e.g., lattice for Python interface is transposed.

lattice#

Attention: In Python interface, lattice is transposed (Crystal structure (cell)).

Basis vectors (in Cartesian)

[ [ a_x, b_x, c_x ],
  [ a_y, b_y, c_y ],
  [ a_z, b_z, c_z ] ]

Cartesian position \(\mathbf{x}_\mathrm{Cart}\) is obtained by

\[ \mathbf{x}_\mathrm{Cart} = \mathrm{L}\cdot\mathbf{x}_\mathrm{frac}\]

where \(\mathrm{L}\) is the basis vectors defined above and is \(\mathrm{L}=(\mathbf{a},\mathbf{b},\mathbf{c})\), and \(\mathbf{x}_\mathrm{frac}\) is the atomic position in fractional coordinates given below.

position#

Atomic points (in fractional coordinates with respect to basis vectors)

[ [ x1_a, x1_b, x1_c ],
  [ x2_a, x2_b, x2_c ],
  [ x3_a, x3_b, x3_c ],
  ...                   ]

types#

Atomic species are differentiated by integers. The numbers are just used to distinguishes atoms, and is not related to atomic numbers.

[ type_1, type_2, type_3, ... ]

The number of elements is same as the number of atoms.

rotation#

Rotation matrices (integer) of symmetry operations.

[ [ r_aa, r_ab, r_ac ],
  [ r_ba, r_bb, r_bc ],
  [ r_ca, r_cb, r_cc ] ]

translation#

Translation vectors corresponding to symmetry operations in fractional coordinates.

[ t_a, t_b, t_c ]

symprec#

Distance tolerance in Cartesian coordinates to find crystal symmetry.

For atomic positions, roughly speaking, two position vectors x and x' in Cartesian coordinates are considered to be the same if |x' - x| < symprec. For more details, see the spglib paper, Sec. II-A.

The angle distortion between basis vectors is converted to a length and compared with this distance tolerance. For more details, see the spglib paper, Sec. IV-A. It is possible to specify angle tolerance explicitly, see angle_tolerance.

angle_tolerance#

Tolerance of angle between basis vectors in degrees to be tolerated in the symmetry finding. To use angle tolerance, another set of functions are prepared for C-API as follows

spgat_get_dataset
spgat_get_symmetry
spgat_get_symmetry_with_collinear_spin
spgat_get_multiplicity
spgat_find_primitive
spgat_get_international
spgat_get_schoenflies
spgat_refine_cell

mag_symprec#

Tolerance for magnetic symmetry search in the unit of spins or magmoms. By specifying a negative value, the same value as symprec is used to compare magnetic moments.

The following functions are called by the same way with an additional argument of const double angle_tolerance in degrees. By specifying a negative value, the behavior becomes the same as usual functions (e.g. spg_get_magnetic_dataset). For python-API, the magnetic tolerance is given with a keyword argument of mag_symprec, where the default value of mag_symprec is a negative value.

spgms_get_magnetic_dataset
spgms_get_symmetry_with_collinear_spin
spgms_get_symmetry_with_site_tensors