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.