2.3.3.1.46. NXsample

Status:

base class, extends NXobject

Description:

Any information on the sample. ...

Any information on the sample.

This could include scanned variables that are associated with one of the data dimensions, e.g. the magnetic field, or logged data, e.g. monitored temperature vs elapsed time.

Symbols:

symbolic array lengths to be coordinated between various fields

n_comp: number of compositions

n_Temp: number of temperatures

n_eField: number of values in applied electric field

n_mField: number of values in applied magnetic field

n_pField: number of values in applied pressure field

n_sField: number of values in applied stress field

Groups cited:

NXbeam, NXdata, NXenvironment, NXfabrication, NXgeometry, NXhistory, NXidentifier, NXlog, NXoff_geometry, NXpositioner, NXsample_component_set, NXsample_component, NXsingle_crystal, NXsubstance, NXtransformations

Structure:

@default: (optional) NX_CHAR

Declares which child group contains a path leading ...

Declares which child group contains a path leading to a NXdata group.

It is recommended (as of NIAC2014) to use this attribute to help define the path to the default dataset to be plotted. See https://www.nexusformat.org/2014_How_to_find_default_data.html for a summary of the discussion.

name: (optional) NX_CHAR

Descriptive name of sample

sample_id: (optional) NX_CHAR

Identification number or signatures of the sample used.

chemical_formula: (optional) NX_CHAR

The chemical formula specified using CIF conventions. ...

The chemical formula specified using CIF conventions. Abbreviated version of CIF standard:

  • Only recognized element symbols may be used.

  • Each element symbol is followed by a ‘count’ number. A count of ‘1’ may be omitted.

  • A space or parenthesis must separate each cluster of (element symbol + count).

  • Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parentheses. That is, all element and group multipliers are assumed to be printed as subscripted numbers.

  • Unless the elements are ordered in a manner that corresponds to their chemical structure, the order of the elements within any group or moiety depends on whether or not carbon is present.

  • If carbon is present, the order should be:

    • C, then H, then the other elements in alphabetical order of their symbol.

    • If carbon is not present, the elements are listed purely in alphabetic order of their symbol.

  • This is the Hill system used by Chemical Abstracts.

temperature: (optional) NX_FLOAT (Rank: anyRank, Dimensions: [n_Temp]) {units=NX_TEMPERATURE}

Sample temperature. This could be a scanned variable

electric_field: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_eField]) {units=NX_VOLTAGE}

Applied electric field

@direction: (optional) NX_CHAR

Any of these values: x | y | z

magnetic_field: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_mField]) {units=NX_ANY}

Applied magnetic field

@direction: (optional) NX_CHAR

Any of these values: x | y | z

stress_field: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_sField]) {units=NX_ANY}

Applied external stress field

@direction: (optional) NX_CHAR

Any of these values: x | y | z

pressure: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_pField]) {units=NX_PRESSURE}

Applied pressure

changer_position: (optional) NX_INT {units=NX_UNITLESS}

Sample changer position

unit_cell_abc: (optional) NX_FLOAT (Rank: 1, Dimensions: [3]) {units=NX_LENGTH}

Crystallography unit cell parameters a, b, and c

unit_cell_alphabetagamma: (optional) NX_FLOAT (Rank: 1, Dimensions: [3]) {units=NX_ANGLE}

Crystallography unit cell parameters alpha, beta, and gamma

unit_cell: (optional) NX_FLOAT (Rank: 2, Dimensions: [n_comp, 6]) {units=NX_LENGTH}

Unit cell parameters (lengths and angles)

unit_cell_volume: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_comp]) {units=NX_VOLUME}

Volume of the unit cell

sample_orientation: (optional) NX_FLOAT (Rank: 1, Dimensions: [3]) {units=NX_ANGLE}

orientation_matrix: (optional) NX_FLOAT (Rank: 3, Dimensions: [n_comp, 3, 3])

Orientation matrix of single crystal sample using Busing-Levy convention: ...

Orientation matrix of single crystal sample using Busing-Levy convention: W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464

ub_matrix: (optional) NX_FLOAT (Rank: 3, Dimensions: [n_comp, 3, 3])

UB matrix of single crystal sample using Busing-Levy convention: ...

UB matrix of single crystal sample using Busing-Levy convention: W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464. This is the multiplication of the orientation_matrix, given above, with the \(B\) matrix which can be derived from the lattice constants.

mass: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_comp]) {units=NX_MASS}

Mass of sample

density: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_comp]) {units=NX_MASS_DENSITY}

Density of sample

relative_molecular_mass: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_comp]) {units=NX_MASS}

Relative Molecular Mass of sample

type: (optional) NX_CHAR

Any of these values:

  • sample

  • sample+can

  • can

  • sample+buffer

  • buffer

  • calibration sample

  • normalisation sample

  • simulated data

  • none

  • sample environment

situation: (optional) NX_CHAR

The atmosphere will be one of the components, which is where ...

The atmosphere will be one of the components, which is where its details will be stored; the relevant components will be indicated by the entry in the sample_component member.

Any of these values:

  • air

  • vacuum

  • inert atmosphere

  • oxidising atmosphere

  • reducing atmosphere

  • sealed can

  • other

description: (optional) NX_CHAR

Description of the sample

preparation_date: (optional) NX_DATE_TIME

Date of preparation of the sample

component: (optional) NX_CHAR (Rank: 1, Dimensions: [n_comp])

Details of the component of the sample and/or can

sample_component: (optional) NX_CHAR (Rank: 1, Dimensions: [n_comp])

Type of component ...

Type of component

Any of these values: sample | can | atmosphere | kit

concentration: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_comp]) {units=NX_MASS_DENSITY}

Concentration of each component

volume_fraction: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_comp])

Volume fraction of each component

scattering_length_density: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_comp]) {units=NX_SCATTERING_LENGTH_DENSITY}

Scattering length density of each component

unit_cell_class: (optional) NX_CHAR

In case it is all we know and we want to record/document it ...

In case it is all we know and we want to record/document it

Any of these values:

  • triclinic

  • monoclinic

  • orthorhombic

  • tetragonal

  • rhombohedral

  • hexagonal

  • cubic

space_group: (optional) NX_CHAR (Rank: 1, Dimensions: [n_comp])

Crystallographic space group

point_group: (optional) NX_CHAR (Rank: 1, Dimensions: [n_comp])

Crystallographic point group, deprecated if space_group present

path_length: (optional) NX_FLOAT {units=NX_LENGTH}

Path length through sample/can for simple case when ...

Path length through sample/can for simple case when it does not vary with scattering direction

path_length_window: (optional) NX_FLOAT {units=NX_LENGTH}

Thickness of a beam entry/exit window on the can (mm) ...

Thickness of a beam entry/exit window on the can (mm) - assumed same for entry and exit

thickness: (optional) NX_FLOAT {units=NX_LENGTH}

sample thickness

external_DAC: (optional) NX_FLOAT {units=NX_ANY}

value sent to user’s sample setup

short_title: (optional) NX_CHAR

20 character fixed length sample description for legends

rotation_angle: (optional) NX_FLOAT {units=NX_ANGLE}

Optional rotation angle for the case when the powder diagram has ...

Optional rotation angle for the case when the powder diagram has been obtained through an omega-2theta scan like from a traditional single detector powder diffractometer. Note, it is recommended to use NXtransformations instead.

x_translation: (optional) NX_FLOAT {units=NX_LENGTH}

Translation of the sample along the X-direction of the laboratory coordinate s ...

Translation of the sample along the X-direction of the laboratory coordinate system Note, it is recommended to use NXtransformations instead.

distance: (optional) NX_FLOAT {units=NX_LENGTH}

Translation of the sample along the Z-direction of the laboratory coordinate s ...

Translation of the sample along the Z-direction of the laboratory coordinate system. Note, it is recommended to use NXtransformations instead.

physical_form: (optional) NX_CHAR

Physical form of the sample material. ...

Physical form of the sample material. Examples include single crystal, foil, pellet, powder, thin film, disc, foam, gas, liquid, amorphous.

depends_on: (optional) NX_CHAR

NeXus positions components by applying a set of translations and rotations ...

NeXus positions components by applying a set of translations and rotations to apply to the component starting from 0, 0, 0. The order of these operations is critical and forms what NeXus calls a dependency chain. The depends_on field defines the path to the top most operation of the dependency chain or the string “.” if located in the origin. Usually these operations are stored in a NXtransformations group. But NeXus allows them to be stored anywhere.

geometry: (optional) NXgeometry

DEPRECATED: Use the field depends_on and NXtransformations to position the sample and NXoff_geometry to describe its shape instead

The position and orientation of the center of mass of the sample

BEAM: (optional) NXbeam

Details of beam incident on sample - used to calculate sample/beam interaction ...

Details of beam incident on sample - used to calculate sample/beam interaction point

SAMPLE_COMPONENT: (optional) NXsample_component

One group per sample component ...

One group per sample component This is the perferred way of recording per component information over the n_comp arrays

transmission: (optional) NXdata

As a function of Wavelength

temperature_log: (optional) NXlog

DEPRECATED: use temperature, see: https://github.com/nexusformat/definitions/issues/816

temperature_log.value is a link to e.g. temperature_env.sensor1.value_log.value

temperature_env: (optional) NXenvironment

Additional sample temperature environment information

magnetic_field: (optional) NXlog

magnetic_field.value is a link to e.g. magnetic_field_env.sensor1.value

magnetic_field_log: (optional) NXlog

DEPRECATED: use magnetic_field, see: https://github.com/nexusformat/definitions/issues/816

magnetic_field_log.value is a link to e.g. ...

magnetic_field_log.value is a link to e.g. magnetic_field_env.sensor1.value_log.value

magnetic_field_env: (optional) NXenvironment

Additional sample magnetic environment information

external_ADC: (optional) NXlog

logged value (or logic state) read from user’s setup

POSITIONER: (optional) NXpositioner

Any positioner (motor, PZT, …) used to locate the sample

OFF_GEOMETRY: (optional) NXoff_geometry

This group describes the shape of the sample

SINGLE_CRYSTAL: (optional) NXsingle_crystal

If the sample is a single crystal, add description of single crystal and unit ...

If the sample is a single crystal, add description of single crystal and unit cell.

SAMPLE_COMPONENT_SET: (optional) NXsample_component_set

Set of sample components and their configuration. ...

Set of sample components and their configuration. There can only be one NXsample_component_set in one component.

SUBSTANCE: (optional) NXsubstance

If the sample is made from a pure substance and cannot be further divided usin ...

If the sample is made from a pure substance and cannot be further divided using NXsample_component.

FABRICATION: (optional) NXfabrication

Details about the sample vendor (company or research group)

identifier: (optional) NXidentifier

An (ideally) globally unique identifier for the sample.

ENVIRONMENT: (optional) NXenvironment

Any environmental or external stimuli/measurements. ...

Any environmental or external stimuli/measurements. These can include, among others: applied pressure, surrounding gas phase and gas pressure, external electric/magnetic/mechanical fields, temperature, …

history: (optional) NXhistory

A set of physical processes that occurred to the sample prior/during experiment.

TRANSFORMATIONS: (optional) NXtransformations

This is the group recommended for holding the chain of translation ...

This is the group recommended for holding the chain of translation and rotation operations necessary to position the component within the instrument. The dependency chain may however traverse similar groups in other component groups.

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/base_classes/NXsample.nxdl.xml