crystallography
type: Ontology
version IRI: crystallography
imports: cif core.ttl
imports: emmo-inferred-chemistry2.ttl
abstract: A toplevel crystallography ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language.
license: Creative Commons BY 4.0

cifLabel
type: AnnotationProperty
comment: Label of corresponding entity in the core CIF dictionary. See https://www.iucr.org/resources/cif/dictionaries/cif_core
sub property of: comment

cifMatch
type: AnnotationProperty
comment: URL to corresponding entity in the core CIF dictionary. See https://www.iucr.org/resources/cif/dictionaries/cif_core
sub property of: seeAlso

Constituent
type: Class
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The union of Atom and Molecule.
comment: The word "constituent" means part of a whole. Within the crystallography domain, constituents are defined as the real-world building blocks of a crystal (i.e. atoms or molecules).

FractionalPositionB
type: Class
subclass of: Restriction
cifLabel: _atom_site_fract_y
cifMatch: https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: Fractional position of a site along the b direction.
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L0 M0 I0 Θ0 N0 J0

LatticeParameterBeta
type: Class
subclass of: Restriction
cifLabel: _cell_angle_beta
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The angle between lattice vectors `a` and `c`, where lattice vectors `a`, `b` and `c` defines the unit cell,
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L0 M0 I0 Θ0 N0 J0

LatticeParameterA
type: Class
subclass of: Restriction
cifLabel: _cell_length_a
cifMatch: https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The length of lattice vectors `a`, where lattice vectors `a`, `b` and `c` defines the unit cell,
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L+1 M0 I0 Θ0 N0 J0

Hexagonal
type: Class
subclass of: Restriction
  has value: hexagonal
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A crystal system with 1 sixfold axes of rotation.

Occupancy
type: Class
subclass of: Restriction
cifLabel: _atom_site_occupancy
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The occupancy of a site. Must be a number between zero and one.
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L0 M0 I0 Θ0 N0 J0

LatticeParameterAlpha
type: Class
subclass of: Restriction
cifLabel: _cell_angle_alpha
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The angle between lattice vectors `b` and `c`, where lattice vectors `a`, `b` and `c` defines the unit cell,
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L0 M0 I0 Θ0 N0 J0

SymmetryMultiplicity
type: Class
subclass of: Restriction
cifLabel: _atom_site_site_symmetry_multiplicity
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The number of different sites that are generated by the application of the space-group symmetry to the coordinates given for this site.
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L0 M0 I0 Θ0 N0 J0

CrystallographicSymbol
type: Class
equivalent class: Class
subclass of: Restriction
  all values from: Class
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A symbol that stands for a crystallographical concept in the language of the crystallographical domain.

Crystal
type: Class
subclass of: Restriction
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A crystal is a solid whos constituents are ordered.

CrystalStructure
type: Class
subclass of: Restriction
subclass of: Restriction
  qualified cardinality: 1
subclass of: Restriction
  qualified cardinality: 1
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The crystal structure describes of the ordered arrangement of species in a crystal.

LatticeVector
type: Class
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A vector connecting two lattice sites, where the lattice sites defines the periodic structure of a crystal.
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L+1 M0 I0 Θ0 N0 J0

SpacegroupNumber
type: Class
subclass of: Restriction
cifLabel: _space_group_IT_number
cifMatch: https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_IT_number.html
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A number between 1 and 230 that uniquely identifies the space group.
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L0 M0 I0 Θ0 N0 J0
comment: Even though the spacegroups are unique, it is possible to choose the origin and basis differently resulting in different settings.

Trigonal
type: Class
subclass of: Restriction
  has value: trigonal
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A crystal system with 1 threefold axes of rotation.

Crystallographical
type: Class
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The symbolic object defining the basis for crystallography.

UnitCell
type: Class
subclass of: Restriction
subclass of: Restriction
  qualified cardinality: 3
subclass of: Restriction
  qualified cardinality: 6
cifLabel: _cell_[]
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A periodic unit in a crystal structure. It is spanned by three lattice vectors.
comment: A unit cell is ca be described by either specifying the three lattice vectors that it is spanned by, or by 6 the lattice parameters (the length of and angles between the 3 lattice vectors).

LatticeParameterB
type: Class
subclass of: Restriction
cifLabel: _cell_length_b
cifMatch: https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The length of lattice vectors `b`, where lattice vectors `a`, `b` and `c` defines the unit cell,
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L+1 M0 I0 Θ0 N0 J0

Shape3x3Matrix
type: Class
subclass of: Restriction
  qualified cardinality: 3

SymmetryOperationString
type: Class
subclass of: Restriction
cifLabel: _space_group_symop_operation_xyz
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A parsable string giving one of the symmetry operations of the space group in algebraic form.
EMMO b432d2d5 25f4 4165 99c5 5935a7763c1a: x,1/2-y,1/2+z
comment: If W is a matrix representation of the rotational part of the symmetry operation defined by the positions and signs of x, y and z, and w is a column of translations defined by fractions, an equivalent position X' is generated from a given position X by the equation X' = W X + w
comment: When a list of symmetry operations is given, it must contain a complete set of coordinate representatives which generates all the operations of the space group by the addition of all primitive translations of the space group. Such representatives are to be found as the coordinates of the general-equivalent position in International Tables for Crystallography Vol. A (2002), to which it is necessary to add any centring translations shown above the general-equivalent position. That is to say, it is necessary to list explicitly all the symmetry operations required to generate all the atoms in the unit cell defined by the setting used.

CellVolume
type: Class
cifLabel: _cell_volume
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: Volume of the unit cell.
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L+3 M0 I0 Θ0 N0 J0

Triclinic
type: Class
subclass of: Restriction
  has value: triclinic
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A crystal system with no symmetry axis.

LatticeParameterC
type: Class
subclass of: Restriction
cifLabel: _cell_length_c
cifMatch: https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The length of lattice vectors `c`, where lattice vectors `a`, `b` and `c` defines the unit cell,
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L+1 M0 I0 Θ0 N0 J0

SpacegroupSettingNumber
type: Class
subclass of: Restriction
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A number that stands for the space group setting, i.e. the choice of origin (and basis).
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L0 M0 I0 Θ0 N0 J0
comment: Typically the space group setting is represented as "1" for the standard setting and "2" for the alternative setting. The setting number does not appear in the CIF core dictionary, but is included in International Tables. The CIF core dictionary recommends usint the '_space_group_crystal_system' instead.

Species
type: Class
subclass of: Restriction
cifLabel: _atom_site_label
cifMatch: https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_label.html
EMMO 21ae69b4 235e 479d 8dd8 4f756f694c1b: ChemicalSpecies
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A symbol that stands for a constituent.
EMMO fe015383 afb3 44a6 ae86 043628697aa2: http://goldbook.iupac.org/terms/view/CT01038
comment: A chemical species is a well defined set of one or more atoms/ions. The chemical species can be atom, molecule, ion, radical, and it has a chemical name and chemical formula. The chemical species are associated to the crystalline site in a structure. Note that two otherwise identical molecules with differing orientation in the unit cell will be considered two different species.

SiteLabel
type: Class
cifLabel: _atom_site_label
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A unique identifier for a particular site in the crystal.

FractionalPositionA
type: Class
subclass of: Restriction
cifLabel: _atom_site_fract_x
cifMatch: https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: Fractional position of a site along the a direction.
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L0 M0 I0 Θ0 N0 J0

RotationMatrix
type: Class
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A rotation matrix.
comment: The determinant of a rotation matrix is one.

Cubic
type: Class
subclass of: Restriction
  has value: cubic
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A crystal system with 4 threefold axes of rotation.

Tetragonal
type: Class
subclass of: Restriction
  has value: tetragonal
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A crystal system with 1 fourfold axes of rotation.

TranslationVector
type: Class
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A translation vector.

SymmetryOperation
type: Class
subclass of: Restriction
  qualified cardinality: 1
subclass of: Restriction
  qualified cardinality: 1
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A symmetry operation is an action that leaves an object looking the same after it has been carried out. Mathematically it is described by a rotation followed by a translation.
EMMO b432d2d5 25f4 4165 99c5 5935a7763c1a: For example, if we take a molecule of water and rotate it by 180° about an axis passing through the central O atom (between the two H atoms) it will look the same as before.

FractionalPosition
type: Class
subclass of: Restriction
subclass of: Restriction
  qualified cardinality: 1
subclass of: Restriction
  qualified cardinality: 1
subclass of: Restriction
  qualified cardinality: 1
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A position expressed in fractional coordinates with respect to an origin and three spatial vectors.
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L0 M0 I0 Θ0 N0 J0

Orthorhombic
type: Class
subclass of: Restriction
  has value: orthorhombic
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A crystal system with 3 twofold axes of rotation or 1 twofold axis of rotation and 2 mirror planes.

LatticeParameterGamma
type: Class
subclass of: Restriction
cifLabel: _cell_angle_gamma
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The angle between lattice vectors `a` and `b`, where lattice vectors `a`, `b` and `c` defines the unit cell,
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L0 M0 I0 Θ0 N0 J0

FractionalPositionC
type: Class
subclass of: Restriction
cifLabel: _atom_site_fract_z
cifMatch: https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: Fractional position of a site along the c direction.
EMMO de178b12 5d35 4bca 8efa a4193162571d: T0 L0 M0 I0 Θ0 N0 J0

Monoclinic
type: Class
subclass of: Restriction
  has value: monoclinic
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A crystal system with 1 twofold axes of rotation or 1 mirror plane.

HallSymbol
type: Class
subclass of: Restriction
cifLabel: _space_group_name_Hall
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A symbol that uniquely defines the space group and its reference to a particular coordinate system. References: - Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981), A37, 921. - International Tables for Crystallography, Vol. B (2001), Chapter 1.4, Appendix 1.4.2

LatticeParameter
type: Class
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The 6 parameters defining the unit cell; a, b, c, alpha, beta, gamma, where a, b, c are the lengths of the 3 lattice vectors spanning the unit cell and alpha, beta, gamma are the angles between them.

Site
type: Class
subclass of: Restriction
  qualified cardinality: 1
subclass of: Restriction
  qualified cardinality: 1
subclass of: Restriction
  qualified cardinality: 1
subclass of: Restriction
  qualified cardinality: 1
subclass of: Restriction
  qualified cardinality: 1
subclass of: Restriction
  qualified cardinality: 1
cifLabel: _atom_site_[]
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A site within a unit cell related to the position of a species.

Spacegroup
type: Class
subclass of: Restriction
cifLabel: _space_group_[]
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The symmetry group that represents the symmetry of a crystal, in terms of the set of all its symmetry operations.
comment: A spacegroup is commonly identified by its number as given in International Tables for Crystallography Vol. A. Specific settings of the space groups can be identified either by their Hall symbol or by specifying their symmetry operations. Specific settings listed in International Tables for Crystallography Vol. A, may also be specified by specifying the setting number in combination with the space group number or Hermann-Mauguin symbol. The commonly used Hermann-Mauguin symbol determines the space-group type uniquely but several different Hermann-Mauguin symbols may refer to the same space-group type. A Hermann-Mauguin symbol contains information on the choice of the basis, but not on the choice of origin. Different formats for the Hermann-Mauguin symbol are found in the symmetry CIF dictionary.

WyckoffSymbol
type: Class
subclass of: Restriction
cifLabel: _atom_site_Wyckoff_symbol
cifMatch: https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_Wyckoff_symbol.html
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography Vol. A (2002).

HermannMauguinSymbol
type: Class
subclass of: Restriction
cifLabel: _space_group_name_H-M_alt
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A symbol that uniquely determines the space group.
comment: Note that a given spacegroup may be described by more than one Hermann Mauguin symbol. Spacegroups are therefore best described by spacegroup number.
comment: The Hermann-Mauguin symbol may contain information on the choice of basis, but not on the choice of origin. To define the setting uniquely, use _space_group_name_Hall or list the symmetry operations.

ConventionalUnitCell
type: Class
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The smallest unit cell that contains the same point group symmetries as the overall lattice.
comment: The conventional unit cell is the one that is referred to in International Tables for Crystallography vol. A.

CrystalSystem
type: Class
cifLabel: _space_group_crystal_system
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: The name of the system of geometric crystal classes of space groups (crystal system) to which the space group belongs.
comment: There are 7 crystal systems.

PrimitiveUnitCell
type: Class
EMMO 967080e5 2f42 4eb2 a3a9 c58143e835f9: A unit cell that contains exactly one lattice point. It is the smallest possible cell.
comment: There may be several choices of primitive unit cell, hence it is not unique.

qualified cardinality: 1

qualified cardinality: 1

qualified cardinality: 3

qualified cardinality: 1

qualified cardinality: 1

qualified cardinality: 1

qualified cardinality: 1

qualified cardinality: 1

qualified cardinality: 1

qualified cardinality: 1

qualified cardinality: 1

qualified cardinality: 1

qualified cardinality: 3

qualified cardinality: 1

qualified cardinality: 1