2.3.3.3.85. NXcrystal_structure

Status:

base class, extends NXobject

Description:

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:

NXidentifier, NXmicrostructure_ipf, NXmicrostructure_odf, NXmicrostructure_pf

Structure:

depends_on: (optional) NX_CHAR

Details in which reference frame the unit cell is defined.

dimensionality: (optional) NX_POSINT

Dimensionality of the lattice. ...

Dimensionality of the lattice.

Any of these values: 1 | 2 | 3

a_b_c: (optional) NX_NUMBER (Rank: 1, Dimensions: [d]) {units=NX_LENGTH}

Crystallography unit cell parameters a, b, and c.

alpha_beta_gamma: (optional) NX_NUMBER (Rank: 1, Dimensions: [d]) {units=NX_ANGLE}

Crystallography unit cell parameters alpha, beta, and gamma.

area: (optional) NX_NUMBER {units=NX_AREA}

Area of the unit cell considering that d = 2.

volume: (optional) NX_NUMBER {units=NX_VOLUME}

Volume of the unit cell considering that d = 3.

crystal_system: (optional) NX_CHAR

Crystal system ...

Crystal system

Any of these values:

  • triclinic

  • monoclinic

  • orthorhombic

  • tetragonal

  • rhombohedral

  • hexagonal

  • cubic

laue_group: (optional) NX_CHAR

Laue group using International Table of Crystallography Notation.

point_group: (optional) NX_CHAR

Point group using International Table of Crystallography Notation.

space_group: (optional) NX_CHAR

Space group from the International Table of Crystallography Notation.

is_centrosymmetric: (optional) NX_BOOLEAN

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).

is_chiral: (optional) NX_BOOLEAN

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.

phase_identifier: (optional) NX_INT {units=NX_UNITLESS}

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 NXcrystal_structure named phase0 and phase1 should be stored in the HDF5 file.

phase_name: (optional) NX_CHAR

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.

atom_identifier: (optional) NX_CHAR (Rank: 1, Dimensions: [n_pos])

Label for each atom position.

atom_type: (optional) NX_UINT (Rank: 1, Dimensions: [n_pos]) {units=NX_UNITLESS}

The hash value :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` ...

The hash value \(H\) is \(H = Z + N \cdot 256\) with \(Z\) the number of protons and \(N\) the number of neutrons of each isotope respectively. \(Z\) and \(N\) have to be 8-bit unsigned integers. For the rationale behind this M. Kühbach et al. (2021)

atom_position: (optional) NX_NUMBER (Rank: 2, Dimensions: [n_pos, d]) {units=NX_ANY}

Atom positions.

@depends_on: (optional) NX_CHAR

Details the reference frame in which the positions are defined.

atom_occupancy: (optional) NX_NUMBER (Rank: 1, Dimensions: [n_pos]) {units=NX_DIMENSIONLESS}

Relative occupancy of the atom position.

number_of_planes: (optional) NX_UINT {units=NX_UNITLESS}

How many reflectors are distinguished. ...

How many reflectors are distinguished.

Value has to match value for symbol n_hkl.

miller: (optional) NX_NUMBER (Rank: 2, Dimensions: [n_hkl, 6]) {units=NX_UNITLESS}

Miller indices :math:`(hkl)[uvw]` of the planes. ...

Miller indices \((hkl)[uvw]\) of the planes.

The first triplet specify \((hkl)\) the second triplet \([uvw]\). Miller indices refer to the Cartesian right-handed coordinate system of the unit cell.

dspacing: (optional) NX_NUMBER (Rank: 1, Dimensions: [n_hkl]) {units=NX_LENGTH}

Spacing between crystallographic planes as defined by field miller.

relative_intensity: (optional) NX_NUMBER (Rank: 1, Dimensions: [n_hkl]) {units=NX_DIMENSIONLESS}

Relative intensity of the signal for the plane.

number_of_scan_points: (optional) NX_UINT {units=NX_UNITLESS}

In case the :ref:`NXcrystal_structure` base class is used ...

In case the 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.

reference: (optional) NXidentifier

Reference to another resource that was used for ...

Reference to another resource that was used for instantiating this structure model.

ipfID: (optional) NXmicrostructure_ipf

pfID: (optional) NXmicrostructure_pf

odfID: (optional) NXmicrostructure_odf

Hypertext Anchors

List of hypertext anchors for all groups, fields, attributes, and links defined in this class.

NXDL Source:

https://github.com/FAIRmat-NFDI/nexus_definitions/tree/fairmat/contributed_definitions/NXcrystal_structure.nxdl.xml