Definitions and conventions

Information in this page is valid for spglib 1.8.1 or later. The definitions of transformation matrix and origin shift were different in the previous versions.

References

Some references about crystallographic definitions and conventions are shown below. Though spglib may not follow them fully, it doesn’t mean spglib doesn’t respect them, rather it is due to the lack of understanding by the author of spglib.

  • International Tables for Crystallography.
  • Bilbao Crystallographic Server. The references of many useful papers are found at http://www.cryst.ehu.es/wiki/index.php/Articles.
  • Ulrich Müller, “Symmetry Relationships between Crystal Structures”
  • E. Parthé, K. Cenzual, and R. E. Gladyshevskii, “Standardization of crystal structure data as an aid to the classification of crystal structure types”, Journal of Alloys and Compounds, 197, 291-301 (1993). [doi2]
  • E. Parthé and L. M. Gelato, “The ’best’ unit cell for monoclinic structures consistent with b axis unique and cell choice 1 of international tables for crystallography (1983)”, Acta Cryst. A 41, 142-151 (1985) [doi3]
  • E. Parthé and L. M. Gelato, “The standardization of inorganic crystal-structure data”, Acta Cryst. A 40, 169-183 (1984) [doi4]
  • S. Hall, “Space-group notation with an explicit origin”, Acta Cryst. A 37, 517-525 (1981) [doi1]

Basis vectors (\mathbf{a}, \mathbf{b}, \mathbf{c}) or (\mathbf{a}_1, \mathbf{a}_2, \mathbf{a}_3)

In spglib, basis vectors are represented by three column vectors:

\mathbf{a}= \begin{pmatrix}
a_x \\
a_y \\
a_z \\
\end{pmatrix},
\mathbf{b}= \begin{pmatrix}
b_x \\
b_y \\
b_z \\
\end{pmatrix},
\mathbf{c}= \begin{pmatrix}
c_x \\
c_y \\
c_z \\
\end{pmatrix},

in Cartesian coordinates. Depending on the situation, (\mathbf{a}_1, \mathbf{a}_2, \mathbf{a}_3) is used instead of (\mathbf{a}, \mathbf{b}, \mathbf{c}).

Atomic point coordinates \boldsymbol{x}

Coordinates of an atomic point \boldsymbol{x} are represented as three fractional values relative to basis vectors as follows,

\boldsymbol{x}= \begin{pmatrix}
x_1 \\
x_2 \\
x_3 \\
\end{pmatrix},

where 0 \le x_i < 1. A position vector \mathbf{x} in Cartesian coordinates is obtained by

\mathbf{x} = (\mathbf{a}, \mathbf{b}, \mathbf{c}) \boldsymbol{x}.

or

\mathbf{x} = \sum_i x_i \mathbf{a}_i.

Symmetry operation (\boldsymbol{W}, \boldsymbol{w})

A symmetry operation consists of a pair of the rotation part \boldsymbol{W} and translation part \boldsymbol{w}, and is represented as (\boldsymbol{W}, \boldsymbol{w}) in the spglib document. The symmetry operation transfers \boldsymbol{x} to \tilde{\boldsymbol{x}} as follows:

\tilde{\boldsymbol{x}} = \boldsymbol{W}\boldsymbol{x} + \boldsymbol{w}.

Transformation matrix \boldsymbol{P} and origin shift \boldsymbol{p}

The transformation matrix \boldsymbol{P} changes choice of basis vectors as follows

( \mathbf{a} \; \mathbf{b} \; \mathbf{c} )
= ( \mathbf{a}_\mathrm{s} \; \mathbf{b}_\mathrm{s} \;
\mathbf{c}_\mathrm{s} )  \boldsymbol{P},

where ( \mathbf{a} \; \mathbf{b} \; \mathbf{c} ) and (
\mathbf{a}_\mathrm{s} \; \mathbf{b}_\mathrm{s} \;
\mathbf{c}_\mathrm{s} ) are the basis vectors of an arbitrary system and of a starndardized system, respectively. Transformation matrix doesn’t rotate a crystal in Cartesian coordinates, but just changes the choices of basis vectors.

The origin shift \boldsymbol{p} gives the vector from the origin of the standardized system \boldsymbol{O}_\mathrm{s} to the origin of the arbitrary system \boldsymbol{O},

\boldsymbol{p} = \boldsymbol{O} - \boldsymbol{O}_\mathrm{s}.

Origin shift doesn’t move a crystal in Cartesian coordinates, but just changes the origin to measure the coordinates of atomic points.

A change of basis is described by the combination of the transformation matrix and the origin shift denoted by (\boldsymbol{P}, \boldsymbol{p}) where first the transformation matrix is applied and then origin shift. The points in the standardized system \boldsymbol{x}_\mathrm{s} and arbitrary system \boldsymbol{x} are related by

\boldsymbol{x}_\mathrm{s} = \boldsymbol{P}\boldsymbol{x} +
\boldsymbol{p},

or equivalently,

\boldsymbol{x} = \boldsymbol{P}^{-1}\boldsymbol{x}_\mathrm{s} -
\boldsymbol{P}^{-1}\boldsymbol{p}.

A graphical example is shown below.

cob

(click the figure to enlarge)

In this example,

\renewcommand*{\arraystretch}{1.4}
\boldsymbol{P} = \begin{pmatrix}
\frac{1}{2} & \frac{1}{2} & 0 \\
\frac{\bar{1}}{2} & \frac{1}{2} & 0 \\
0 & 0 & 1
\end{pmatrix}.

Conventions of standardized unit cell

Choice of basis vectors

Using the APIs spg_get_dataset, spg_get_dataset_with_hall_number, or spg_standardize_cell, the starndardized unit cell is obtained. The “starndardized unit cell” in this document means that the (conventional) unit cell structure is standardized by the crystal symmetry and lengths of basis vectors. Crystals are categorized by Hall symbols in 530 different types in terms of 230 space group types, unique axes, settings, and cell choices. Moreover in spglib, lengths of basis vectors are used to choose the order of (\mathbf{a}, \mathbf{b}, \mathbf{c}) if the order can not be determined only by the symmetrical conventions.

Transformation to the primitive cell

In the standardized unit cells, there are five different centring types available, base centrings of A and C, rhombohedral (R), body centred (I), and face centred (F). The transformation is applied to the standardized unit cell by

( \mathbf{a}_\mathrm{p} \; \mathbf{b}_\mathrm{p} \; \mathbf{c}_\mathrm{p} )
= ( \mathbf{a}_\mathrm{s} \; \mathbf{b}_\mathrm{s} \;
\mathbf{c}_\mathrm{s} )  \boldsymbol{P}_\mathrm{c},

where \mathbf{a}_\mathrm{p}, \mathbf{b}_\mathrm{p}, and \mathbf{c}_\mathrm{p} are the basis vectors of the primitive cell and \boldsymbol{P}_\mathrm{c} is the transformation matrix from the standardized unit cell to the primitive cell. \boldsymbol{P}_\mathrm{c} for centring types are given as follows:

\renewcommand*{\arraystretch}{1.4}
\boldsymbol{P}_\mathrm{A} =
\begin{pmatrix}
1 & 0 & 0 \\
0 & \frac{1}{2} & \frac{\bar{1}}{2} \\
0 & \frac{1}{2} & \frac{{1}}{2}
\end{pmatrix},
\renewcommand*{\arraystretch}{1.4}
\boldsymbol{P}_\mathrm{C} =
\begin{pmatrix}
\frac{1}{2} & \frac{{1}}{2} & 0 \\
\frac{\bar{1}}{2} & \frac{1}{2} & 0\\
0 & 0 & 1
\end{pmatrix},
\boldsymbol{P}_\mathrm{R} =
\begin{pmatrix}
\frac{2}{3} & \frac{\bar{1}}{3} & \frac{\bar{1}}{3} \\
\frac{1}{3} & \frac{{1}}{3} & \frac{\bar{2}}{3} \\
\frac{1}{3} & \frac{{1}}{3} & \frac{{1}}{3}
\end{pmatrix},
\boldsymbol{P}_\mathrm{I} =
\begin{pmatrix}
\frac{\bar{1}}{2} & \frac{{1}}{2} & \frac{{1}}{2} \\
\frac{{1}}{2} & \frac{\bar{1}}{2} & \frac{{1}}{2} \\
\frac{{1}}{2} & \frac{{1}}{2} & \frac{\bar{1}}{2}
\end{pmatrix},
\boldsymbol{P}_\mathrm{F} =
\begin{pmatrix}
0 & \frac{{1}}{2} & \frac{{1}}{2} \\
\frac{{1}}{2} & 0 & \frac{{1}}{2} \\
\frac{{1}}{2} & \frac{{1}}{2} & 0
\end{pmatrix}.

For rhombohedral lattice systems with the choice of hexagonal axes, \boldsymbol{P}_\mathrm{R} is applied.

Idealization of unit cell structure

Spglib allows tolerance parameters to match a slightly distorted unit cell structure to a space group type with some higher symmetry. Using obtained symmetry operations, the distortion is removed to idealize the unit cell structure. The coordinates of atomic points are idealized using respective site-symmetries (Grosse-Kunstleve et al. (2002)). The basis vectors are idealized by forceing them into respective lattice shapes as follows. In this treatment, except for triclinic crystals, crystals can be rotated in Cartesian coordinates, which is the different type of transformation from that of the change-of-basis transformation explained above.

Triclinic lattice

  • Niggli reduced cell is used for choosing \mathbf{a}, \mathbf{b}, \mathbf{c}.
  • \mathbf{a} is set along +x direction of Cartesian coordinates.
  • \mathbf{b} is set in x\text{-}y plane of Cartesian coordinates so that \mathbf{a}\times\mathbf{b} is along +z direction of Cartesian coordinates.

Monoclinic lattice

  • b axis is taken as the unique axis.
  • \alpha = 90^\circ and \gamma = 90^\circ
  • 90^\circ < \beta < 120^\circ.
  • \mathbf{a} is set along +x direction of Cartesian coordinates.
  • \mathbf{b} is set along +y direction of Cartesian coordinates.
  • \mathbf{c} is set in x\text{-}z plane of Cartesian coordinates.

Orthorhombic lattice

  • \alpha = \beta = \gamma = 90^\circ.
  • \mathbf{a} is set along +x direction of Cartesian coordinates.
  • \mathbf{b} is set along +y direction of Cartesian coordinates.
  • \mathbf{c} is set along +z direction of Cartesian coordinates.

Tetragonal lattice

  • \alpha = \beta = \gamma = 90^\circ.
  • a=b.
  • \mathbf{a} is set along +x direction of Cartesian coordinates.
  • \mathbf{b} is set along +y direction of Cartesian coordinates.
  • \mathbf{c} is set along +z direction of Cartesian coordinates.

Rhombohedral lattice

  • \alpha = \beta = \gamma.
  • a=b=c.
  • Let \mathbf{a}, \mathbf{b}, and \mathbf{c} projected on x\text{-}y plane in Cartesian coordinates be \mathbf{a}_{xy}, \mathbf{b}_{xy}, and \mathbf{c}_{xy}, respectively, and their angles be \alpha_{xy}, \beta_{xy}, \gamma_{xy}, respectively.
  • Let \mathbf{a}, \mathbf{b}, and \mathbf{c} projected along z-axis in Cartesian coordinates be \mathbf{a}_{z}, \mathbf{b}_{z}, and \mathbf{c}_{z}, respectively.
  • \mathbf{a}_{xy} is set along +x direction of Cartesian coordinates, and \mathbf{b}_{xy} and \mathbf{c}_{xy} are placed by angles 120^\circ and 240^\circ from \mathbf{a}_{xy} counter-clockwise, respectively.
  • \alpha_{xy} = \beta_{xy} = \gamma_{xy} = 120^\circ.
  • a_{xy} = b_{xy} = c_{xy}.
  • a_{z} = b_{z} = c_{z}.

Hexagonal lattice

  • \alpha = \beta = 90^\circ.
  • \gamma = 120^\circ.
  • a=b.
  • \mathbf{a} is set along +x direction of Cartesian coordinates.
  • \mathbf{b} is set in x\text{-}y plane of Cartesian coordinates.
  • \mathbf{c} is set along +z direction of Cartesian coordinates.

Cubic lattice

  • \alpha = \beta = \gamma = 90^\circ.
  • a=b=c.
  • \mathbf{a} is set along +x direction of Cartesian coordinates.
  • \mathbf{b} is set along +y direction of Cartesian coordinates.
  • \mathbf{c} is set along +z direction of Cartesian coordinates.