.. auto-generated by dev_tools.docs.nxdl from the NXDL source contributed_definitions/NXcrystal_structure.nxdl.xml -- DO NOT EDIT .. index:: ! NXcrystal_structure (base class) ! crystal_structure (base class) see: crystal_structure (base class); NXcrystal_structure .. _NXcrystal_structure: =================== NXcrystal_structure =================== **Status**: base class, extends :ref:`NXobject` **Description**: .. collapse:: Base class to describe the atomic crystal structure of a phase. ... Base class to describe the atomic crystal structure of a phase. This base class contains key metadata that are relevant parameter to every physics-based model to simulate radiation matter interaction. Examples where such base class is useful are kinematic or dynamic diffraction simulations of e.g. (Kikuchi or other type of) patterns. **Symbols**: **n_hkl**: Number of reflectors (Miller crystallographic plane triplets). **n_pos**: Number of atom positions. **d**: Dimensionality of the lattice. **Groups cited**: :ref:`NXidentifier`, :ref:`NXms_ipf`, :ref:`NXms_odf`, :ref:`NXms_pf` .. index:: NXidentifier (base class); used in base class, NXms_ipf (base class); used in base class, NXms_pf (base class); used in base class, NXms_odf (base class); used in base class **Structure**: .. _/NXcrystal_structure@depends_on-attribute: .. index:: depends_on (file attribute) **@depends_on**: (optional) :ref:`NX_CHAR ` Detail in which reference frame the unit cell is defined. .. _/NXcrystal_structure/dimensionality-field: .. index:: dimensionality (field) **dimensionality**: (optional) :ref:`NX_POSINT ` .. collapse:: Dimensionality of the lattice. ... Dimensionality of the lattice. Any of these values: ``1`` | ``2`` | ``3`` .. _/NXcrystal_structure/a_b_c-field: .. index:: a_b_c (field) **a_b_c**: (optional) :ref:`NX_NUMBER ` (Rank: 1, Dimensions: [d]) {units=\ :ref:`NX_LENGTH `} Crystallography unit cell parameters a, b, and c. .. _/NXcrystal_structure/alpha_beta_gamma-field: .. index:: alpha_beta_gamma (field) **alpha_beta_gamma**: (optional) :ref:`NX_NUMBER ` (Rank: 1, Dimensions: [d]) {units=\ :ref:`NX_ANGLE `} Crystallography unit cell parameters alpha, beta, and gamma. .. _/NXcrystal_structure/area-field: .. index:: area (field) **area**: (optional) :ref:`NX_NUMBER ` {units=\ :ref:`NX_AREA `} Area of the unit cell considering that d = 2. .. _/NXcrystal_structure/volume-field: .. index:: volume (field) **volume**: (optional) :ref:`NX_NUMBER ` {units=\ :ref:`NX_VOLUME `} Volume of the unit cell considering that d = 3. .. _/NXcrystal_structure/crystal_system-field: .. index:: crystal_system (field) **crystal_system**: (optional) :ref:`NX_CHAR ` .. collapse:: Crystal system ... Crystal system Any of these values: * ``triclinic`` * ``monoclinic`` * ``orthorhombic`` * ``tetragonal`` * ``rhombohedral`` * ``hexagonal`` * ``cubic`` .. _/NXcrystal_structure/laue_group-field: .. index:: laue_group (field) **laue_group**: (optional) :ref:`NX_CHAR ` Laue group using International Table of Crystallography Notation. .. _/NXcrystal_structure/point_group-field: .. index:: point_group (field) **point_group**: (optional) :ref:`NX_CHAR ` Point group using International Table of Crystallography Notation. .. _/NXcrystal_structure/space_group-field: .. index:: space_group (field) **space_group**: (optional) :ref:`NX_CHAR ` Space group from the International Table of Crystallography Notation. .. _/NXcrystal_structure/is_centrosymmetric-field: .. index:: is_centrosymmetric (field) **is_centrosymmetric**: (optional) :ref:`NX_BOOLEAN ` .. collapse:: True if space group is considered a centrosymmetric one. ... True if space group is considered a centrosymmetric one. False if space group is considered a non-centrosymmetric one. Centrosymmetric has all types and combinations of symmetry elements (translation, rotational axis, mirror planes, center of inversion) Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). Chiral compared to non-centrosymmetric is constrained (no mirror planes). .. _/NXcrystal_structure/is_chiral-field: .. index:: is_chiral (field) **is_chiral**: (optional) :ref:`NX_BOOLEAN ` .. collapse:: True if space group is considered a chiral one. ... True if space group is considered a chiral one. False if space group is consider a non-chiral one. .. _/NXcrystal_structure/phase_identifier-field: .. index:: phase_identifier (field) **phase_identifier**: (optional) :ref:`NX_INT ` {units=\ :ref:`NX_UNITLESS `} .. collapse:: Identifier for each phase. ... Identifier for each phase. The value 0 is reserved for the unknown phase that represents the null-model no sufficiently significant confirmation. In other words, the phase_name is n/a, notIndexed. The phase identifier value has to match with the integer postfix of the group name which represents that instance in a NeXus/HDF5 file, i.e. if two phases were used e.g. 0 and 1, two instances of an :ref:`NXcrystal_structure` named phase0 and phase1 should be stored in the HDF5 file. .. _/NXcrystal_structure/phase_name-field: .. index:: phase_name (field) **phase_name**: (optional) :ref:`NX_CHAR ` .. collapse:: Name of the phase/alias. ... Name of the phase/alias. If the phase_identifier is 0 and one would like to use the field phase_name the value should be n/a. .. _/NXcrystal_structure/atom_identifier-field: .. index:: atom_identifier (field) **atom_identifier**: (optional) :ref:`NX_CHAR ` (Rank: 1, Dimensions: [n_pos]) Label for each atom position. .. _/NXcrystal_structure/atom_type-field: .. index:: atom_type (field) **atom_type**: (optional) :ref:`NX_UINT ` (Rank: 1, Dimensions: [n_pos]) {units=\ :ref:`NX_UNITLESS `} .. collapse:: The hash value :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` ... The hash value :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` the number of protons and :math:`N` the number of neutrons of each isotope respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. For the rationale behind this `M. Kühbach et al. (2021) `_ .. _/NXcrystal_structure/atom_position-field: .. index:: atom_position (field) **atom_position**: (optional) :ref:`NX_NUMBER ` (Rank: 2, Dimensions: [n_pos, d]) {units=\ :ref:`NX_ANY `} Atom positions. .. _/NXcrystal_structure/atom_position@depends_on-attribute: .. index:: depends_on (field attribute) **@depends_on**: (optional) :ref:`NX_CHAR ` .. collapse:: Reference to an instance of :ref:`NXcoordinate_system` ... Reference to an instance of :ref:`NXcoordinate_system` whereby the positions can be resolved. .. _/NXcrystal_structure/atom_occupancy-field: .. index:: atom_occupancy (field) **atom_occupancy**: (optional) :ref:`NX_NUMBER ` (Rank: 1, Dimensions: [n_pos]) {units=\ :ref:`NX_DIMENSIONLESS `} Relative occupancy of the atom position. .. _/NXcrystal_structure/number_of_planes-field: .. index:: number_of_planes (field) **number_of_planes**: (optional) :ref:`NX_UINT ` {units=\ :ref:`NX_UNITLESS `} .. collapse:: How many reflectors are distinguished. ... How many reflectors are distinguished. Value has to match value for symbol n_hkl. .. _/NXcrystal_structure/miller-field: .. index:: miller (field) **miller**: (optional) :ref:`NX_NUMBER ` (Rank: 2, Dimensions: [n_hkl, 6]) {units=\ :ref:`NX_UNITLESS `} .. collapse:: Miller indices :math:`(hkl)[uvw]` of the planes. ... Miller indices :math:`(hkl)[uvw]` of the planes. The first triplet specify :math:`(hkl)` the second triplet :math:`[uvw]`. Miller indices refer to the Cartesian right-handed coordinate system of the unit cell. .. _/NXcrystal_structure/dspacing-field: .. index:: dspacing (field) **dspacing**: (optional) :ref:`NX_NUMBER ` (Rank: 1, Dimensions: [n_hkl]) {units=\ :ref:`NX_LENGTH `} Spacing between crystallographic planes as defined by field miller. .. _/NXcrystal_structure/relative_intensity-field: .. index:: relative_intensity (field) **relative_intensity**: (optional) :ref:`NX_NUMBER ` (Rank: 1, Dimensions: [n_hkl]) {units=\ :ref:`NX_DIMENSIONLESS `} Relative intensity of the signal for the plane. .. _/NXcrystal_structure/number_of_scan_points-field: .. index:: number_of_scan_points (field) **number_of_scan_points**: (optional) :ref:`NX_UINT ` {units=\ :ref:`NX_UNITLESS `} .. collapse:: In case the :ref:`NXcrystal_structure` base class is used ... In case the :ref:`NXcrystal_structure` base class is used with analyzed orientation maps this field stores how many scan points of the map were identified as that phase. .. _/NXcrystal_structure/reference-group: **reference**: (optional) :ref:`NXidentifier` .. collapse:: Reference to another resource that was used for ... Reference to another resource that was used for instantiating this structure model. .. _/NXcrystal_structure/ipfID-group: **ipfID**: (optional) :ref:`NXms_ipf` .. _/NXcrystal_structure/pfID-group: **pfID**: (optional) :ref:`NXms_pf` .. _/NXcrystal_structure/odfID-group: **odfID**: (optional) :ref:`NXms_odf` Hypertext Anchors ----------------- List of hypertext anchors for all groups, fields, attributes, and links defined in this class. * :ref:`/NXcrystal_structure/a_b_c-field ` * :ref:`/NXcrystal_structure/alpha_beta_gamma-field ` * :ref:`/NXcrystal_structure/area-field ` * :ref:`/NXcrystal_structure/atom_identifier-field ` * :ref:`/NXcrystal_structure/atom_occupancy-field ` * :ref:`/NXcrystal_structure/atom_position-field ` * :ref:`/NXcrystal_structure/atom_position@depends_on-attribute ` * :ref:`/NXcrystal_structure/atom_type-field ` * :ref:`/NXcrystal_structure/crystal_system-field ` * :ref:`/NXcrystal_structure/dimensionality-field ` * :ref:`/NXcrystal_structure/dspacing-field ` * :ref:`/NXcrystal_structure/ipfID-group ` * :ref:`/NXcrystal_structure/is_centrosymmetric-field ` * :ref:`/NXcrystal_structure/is_chiral-field ` * :ref:`/NXcrystal_structure/laue_group-field ` * :ref:`/NXcrystal_structure/miller-field ` * :ref:`/NXcrystal_structure/number_of_planes-field ` * :ref:`/NXcrystal_structure/number_of_scan_points-field ` * :ref:`/NXcrystal_structure/odfID-group ` * :ref:`/NXcrystal_structure/pfID-group ` * :ref:`/NXcrystal_structure/phase_identifier-field ` * :ref:`/NXcrystal_structure/phase_name-field ` * :ref:`/NXcrystal_structure/point_group-field ` * :ref:`/NXcrystal_structure/reference-group ` * :ref:`/NXcrystal_structure/relative_intensity-field ` * :ref:`/NXcrystal_structure/space_group-field ` * :ref:`/NXcrystal_structure/volume-field ` * :ref:`/NXcrystal_structure@depends_on-attribute ` **NXDL Source**: https://github.com/FAIRmat-NFDI/nexus_definitions/tree/fairmat/contributed_definitions/NXcrystal_structure.nxdl.xml