2.3.3.3.88. 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:
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|3a_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
cubiclaue_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.
Hypertext Anchors¶
List of hypertext anchors for all groups, fields, attributes, and links defined in this class.
