2.3.3.3.42. NXatom¶
Status:
base class (contribution), extends NXobject
Description:
Base class for documenting a set of atoms. ...
Base class for documenting a set of atoms.
Atoms in the set may be bonded. The set may have a net charge to represent an ion. Ions can be molecular ions.
Symbols:
No symbol table
- Groups cited:
none
Structure:
name: (optional) NX_CHAR
Given name for the set. ...
Given name for the set.
This field could for example be used in the research field of atom probe tomography for storing a standardized human-readable name of the element or (molecular) ion like such as Al +++ or 12C +.
identifier_chemical: (optional) NX_CHAR ⤆
Identifier used to refer to if the set of atoms represents a substance. ...
Identifier used to refer to if the set of atoms represents a substance.
Obligatory value:
inchicharge: (optional) NX_NUMBER {units=NX_CHARGE}
Signed net (partial) charge of the (molecular) ion. ...
Signed net (partial) charge of the (molecular) ion.
Different methods for computing charge are in use. Care needs to be exercised with respect to the integration. T. A. Manz and N. G. Limas discuss computational details.
charge_state: (optional) NX_NUMBER {units=NX_UNITLESS}
Charge reported in multiples of the charge of an electron. ...
Charge reported in multiples of the charge of an electron.
For research using atom probe tomography the value should be set to zero if the charge_state is unknown and irrecoverable. This can happen when classical ranging definition files in formats like RNG, RRNG are used. These file formats do not document the charge state explicitly but only the number of atoms of each element per molecular ion surplus the respective mass-to-charge-state-ratio interval.
Details on ranging definition files in the literature are M. K. Miller.
volume: (optional) NX_NUMBER {units=NX_VOLUME}
Assumed volume affected by the set of atoms. ...
Assumed volume affected by the set of atoms.
Neither individual atoms nor a set of cluster of these have a volume that is unique as a some cut-off criterion is required.
identifier: (optional) NX_CHAR (Rank: 1, Dimensions: [n_pos]) ⤆
Identifier for each atom at locations as detailed by position.
type: (optional) NX_UINT (Rank: 1, Dimensions: [n_pos]) {units=NX_UNITLESS}
Nuclide information for each atom at locations as detailed by position. ...
Nuclide information for each atom at locations as detailed by position.
One approach for storing nuclide information efficiently is via hashing with the following formula
\(H\) is \(H = Z + N \cdot 256\) with \(Z\)
the number of protons and \(N\) the number of neutrons of each nuclide given as 8-bit unsigned integer values.
position: (optional) NX_NUMBER (Rank: 2, Dimensions: [n_pos, d]) {units=NX_ANY}
Position of each atom.
@reference_frame: (optional) NX_CHAR
Path to a reference frame in which positions are defined ...
Path to a reference frame in which positions are defined to resolve ambiguity when the reference frame is different to the NeXus default reference frame (McStas).
occupancy: (optional) NX_NUMBER (Rank: 1, Dimensions: [n_pos]) {units=NX_DIMENSIONLESS}
Relative occupancy of the atom position. ...
Relative occupancy of the atom position.
This field is useful for specifying the atomic motif in instances of NXunit_cell.
Hypertext Anchors¶
List of hypertext anchors for all groups, fields, attributes, and links defined in this class.
