2.3.3.3.47. NXatom_set¶
Status:
base class, extends NXobject
Description:
Base class for documenting a set of atoms.
Symbols:
The symbols used in the schema to specify e.g. dimensions of arrays.
n_ivec_max: Maximum number of atoms/isotopes allowed per (molecular) ion (fragment).
n_ranges: Number of mass-to-charge-state-ratio range intervals for ion type.
- Groups cited:
none
Structure:
identifier: (optional) NX_CHAR
A unique identifier whereby such an ion can be referred to ...
A unique identifier whereby such an ion can be referred to via the service offered as described in identifier_type.
identifier_type: (optional) NX_CHAR
How can the identifier be resolved? ...
How can the identifier be resolved?
Obligatory value:
inchiion_type: (optional) NX_UINT {units=NX_UNITLESS}
Ion type (ion species) identifier. ...
Ion type (ion species) identifier.
The identifier zero is reserved for the special unknown ion type.
nuclide_hash: (optional) NX_UINT (Rank: 1, Dimensions: [n_ivec_max]) {units=NX_UNITLESS}
Vector of nuclide hash values. ...
Vector of nuclide hash values.
Individual hash values \(H\) is \(H = Z + N \cdot 256\) with \(Z\) encode the number of protons \(Z\) and the number of neutrons \(N\) of each nuclide respectively. \(Z\) and \(N\) have to be 8-bit unsigned integers.
The array is sorted in decreasing order. For the rationale behind this see M. Kühbach et al. (2021)
nuclide_list: (optional) NX_UINT (Rank: 2, Dimensions: [n_ivecmax, 2]) {units=NX_UNITLESS}
Table which decodes the entries in nuclide_hash into a human-readable matrix o ...
Table which decodes the entries in nuclide_hash into a human-readable matrix of instances. The first column specifies the nuclide mass number, i.e. using the hashvalues from the isotope_vector this is \(Z + N\) or 0. The value 0 documents that no isotope-specific information about the element encoded is relevant. The second row specifies the number of protons \(Z\) or 0. The value 0 in this case documents a placeholder or that no element-specific information is relevant. Taking a carbon-14 nuclide as an example the mass number is 14. That is encoded as a value pair (14, 6) as one row of the table.
Therefore, this notation is the typical superscribed nuclide mass number and subscripted number of protons element notation e.g. \(^{14}C\). The array is stored matching the order of nuclide_hash.
volume: (optional) NX_NUMBER {units=NX_VOLUME}
Assumed volume of the ion. ...
Assumed volume of the ion.
In atom probe microscopy this field can be used to store the reconstructed volume per ion (average) which is typically stored alongside ranging definitions.
charge: (optional) NX_NUMBER {units=NX_CHARGE}
Charge of the ion.
charge_state: (optional) NX_NUMBER {units=NX_UNITLESS}
Signed charge state if the atoms form an ion reported in multiples of electron ...
Signed charge state if the atoms form an ion reported in multiples of electron charge.
In the example of atom probe microscopy, only positive values will be measured as the ions are accelerated by a negatively signed bias electric field. In the case that the charge state is not explicitly recoverable, the value should be set to zero.
In atom probe microscopy this is for example the case when using classical ranging definition files in formats like RNG, RRNG. These file formats do not document the charge state explicitly but the number of atoms of each element per molecular ion surplus the mass-to-charge-state-ratio interval. Details on ranging definition files can be found in the literature: M. K. Miller
name: (optional) NX_CHAR
Human-readable name (e.g. Al +++) of the atom set, the atom group, or ion type ...
Human-readable name (e.g. Al +++) of the atom set, the atom group, or ion type. The string should consists of UTF-8 characters, ideally using LaTeX notation to specify the isotopes, ions, and charge state. Examples are 12C + or Al +++.
To ease automated parsing, isotope_vector should be the preferred machine-readable information used.
mass_to_charge_range: (optional) NX_NUMBER (Rank: 2, Dimensions: [n_ranges, 2]) {units=NX_ANY}
Associated lower (mqmin) and upper (mqmax) bounds of the ...
Associated lower (mqmin) and upper (mqmax) bounds of the mass-to-charge-state ratio interval(s) [mqmin, mqmax] (boundaries inclusive). This field is primarily of interest for documenting NXprocess steps of indexing a ToF/mass-to-charge state histogram.
Hypertext Anchors¶
List of hypertext anchors for all groups, fields, attributes, and links defined in this class.
