NXsample

Status:

base class, extends NXobject

Description:

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, NXgeometry, NXlog, NXnote, NXpositioner, NXsample_component, NXtransformations

Structure:

@default: (optional) NX_CHAR

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

chemical_formula: (optional) NX_CHAR

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}

This will follow the Busing-Levy convention:

    1. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464

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

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

    1. 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:

    1. 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 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

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

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 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). It is assumed to be the same for entry and exit

thickness: (optional) NX_FLOAT {units=NX_LENGTH}

sample thickness

sample_id: (optional) NX_CHAR

Identification number or signatures of the sample used.

state: (optional) NX_CHAR

Physical state of the sample

purity: (optional) NX_FLOAT {units=NX_UNITLESS}

Chemical purity of the sample

orientation: (optional) NX_CHAR

Surface termination of the sample (if crystalline)

layer: (optional) NX_CHAR

Number of layers of the sample (e.g. bulk, monolayer, pentalayer, etc.)

chemical_name: (optional) NX_CHAR

Full chemical name of the sample

chem_id_cas: (optional) NX_CHAR

CAS registry number of the sample chemical content.

gas: (optional) NX_CHAR

Gases might be fluxed on the surface for various reasons. Chemical designation, or residual.

gas_pressure: (optional) NX_NUMBER {units=NX_PRESSURE}

In the case of a fixed pressure measurement this is the scalar pressure. In the case of an experiment in which pressure changes, or anyway is recorded, this is an array of length m of pressures.

surface_dopant: (optional) NX_CHAR

Element of evaporated surface dopant such as alkali or other

surface_dopant_coverage: (optional) NX_FLOAT {units=NX_LENGTH}

Nominal thickness of the evaporated dopant

bias: (optional) NX_FLOAT {units=NX_VOLTAGE}

Voltage applied to sample and sample holder.

growth_method: (optional) NX_CHAR

Sample growth method (e. g. molecular beam epitaxy, chemical vapor deposition etc.)

vendor: (optional) NX_CHAR

Name of the sample vendor (company or research group)

substrate_material: (optional) NX_CHAR

Material of the substrate in direct contact with the sample.

substrate_state: (optional) NX_CHAR

Physical state of the substrate, similar options to sample_state

drain_current: (optional) NX_FLOAT {units=NX_CURRENT}

Current to neutralize the photoemission current. This field may also be found in NXmanpulator if present.

bias_voltage: (optional) NX_FLOAT {units=NX_VOLTAGE}

Possible bias of the sample with respect to analyser ground. This field may also be found as sample_bias in NXmanipulator if present.

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 been obtained through an omega-2theta scan like from a traditional single detector powder diffractometer

x_translation: (optional) NX_FLOAT {units=NX_LENGTH}

Translation of the sample along the X-direction of the laboratory coordinate system

distance: (optional) NX_FLOAT {units=NX_LENGTH}

Translation of the sample along the Z-direction of the laboratory coordinate system

depends_on: (optional) NX_CHAR

Refers to the last transformation specifying the positon of the manipulator in the NXtransformations chain.

geometry: (optional) NXgeometry

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 point

SAMPLE_COMPONENT: (optional) NXsample_component

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

sample_history: (optional) NXnote

A descriptor to keep track of the treatment of the sample before entering the photoemission experiment. Ideally, a full report of the previous operations, in any format (NXnote allows to add pictures, audio, movies). Alternatively, a reference to the location or a unique identifier or other metadata file. In the case these are not available, free-text description

notes: (optional) NXnote

Further notes.

transmission: (optional) NXdata

As a function of Wavelength

temperature: (optional) NXlog

temperature.value is a link to e.g. temperature_env.sensor1.value

temperature_log: (optional) NXlog

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

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

TRANSFORMATIONS: (optional) NXtransformations

Collection of axis-based translations and rotations to describe the location and geometry of the manipulator as a component in the instrument. Conventions from the NXtransformations base class are used. In principle, the McStas coordinate system is used. The first transformation has to point either to another component of the system or . (for pointing to the reference frame) to relate it relative to the experimental setup. Typically, the components of a system should all be related relative to each other and only one component should relate to the reference coordinate system.

Hypertext Anchors

List of hypertext anchors for all groups, fields, attributes, and links defined in this class.

NXDL Source:

https://github.com/FAIRmat-Experimental/nexus_definitions/tree/fairmat/contributed_definitions/NXsample.nxdl.xml