.. auto-generated by dev_tools.docs.nxdl from the NXDL source base_classes/NXsample.nxdl.xml -- DO NOT EDIT .. index:: ! NXsample (base class) ! sample (base class) see: sample (base class); NXsample .. _NXsample: ======== NXsample ======== .. Contributors List .. |contrib_name| replace:: Aaron Brewster|phyy-nx|https://avatars.githubusercontent.com/u/13471434?v=4|2022-06-15 .. |contrib_name| replace:: Russ Berg|RussBerg|https://avatars.githubusercontent.com/u/4698891?v=4|2022-06-13 .. |contrib_name| replace:: Pete R Jemian|prjemian|https://avatars.githubusercontent.com/u/2279984?v=4|2022-01-28 .. |contrib_name| replace:: Peter Chang|PeterC-DLS|https://avatars.githubusercontent.com/u/1381719?v=4|2020-10-20 .. |contrib_name| replace:: Tobias Richter|zjttoefs|https://avatars.githubusercontent.com/u/856440?v=4|2018-05-15 .. |contrib_name| replace:: Mark Koennecke|mkoennecke|https://avatars.githubusercontent.com/u/5029850?v=4|2017-04-27 **Status**: base class, extends :ref:`NXobject` **Description**: .. collapse:: 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**: :ref:`NXbeam`, :ref:`NXdata`, :ref:`NXenvironment`, :ref:`NXgeometry`, :ref:`NXlog`, :ref:`NXoff_geometry`, :ref:`NXpositioner`, :ref:`NXsample_component`, :ref:`NXtransformations` .. index:: NXgeometry (base class); used in base class, NXbeam (base class); used in base class, NXsample_component (base class); used in base class, NXdata (base class); used in base class, NXlog (base class); used in base class, NXenvironment (base class); used in base class, NXpositioner (base class); used in base class, NXoff_geometry (base class); used in base class, NXtransformations (base class); used in base class **Structure**: .. _/NXsample@default-attribute: .. index:: default (file attribute) **@default**: (optional) :ref:`NX_CHAR ` .. collapse:: Declares which child group contains a path leading ... .. index:: plotting Declares which child group contains a path leading to a :ref:`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. .. _/NXsample/name-field: .. index:: name (field) **name**: (optional) :ref:`NX_CHAR ` Descriptive name of sample .. _/NXsample/chemical_formula-field: .. index:: chemical_formula (field) **chemical_formula**: (optional) :ref:`NX_CHAR ` .. collapse:: 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. .. _/NXsample/temperature-field: .. index:: temperature (field) **temperature**: (optional) :ref:`NX_FLOAT ` (Rank: anyRank, Dimensions: [n_Temp]) {units=\ :ref:`NX_TEMPERATURE `} Sample temperature. This could be a scanned variable .. _/NXsample/electric_field-field: .. index:: electric_field (field) **electric_field**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [n_eField]) {units=\ :ref:`NX_VOLTAGE `} Applied electric field .. _/NXsample/electric_field@direction-attribute: .. index:: direction (field attribute) **@direction**: (optional) :ref:`NX_CHAR ` Any of these values: ``x`` | ``y`` | ``z`` .. _/NXsample/magnetic_field-field: .. index:: magnetic_field (field) **magnetic_field**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [n_mField]) {units=\ :ref:`NX_ANY `} Applied magnetic field .. _/NXsample/magnetic_field@direction-attribute: .. index:: direction (field attribute) **@direction**: (optional) :ref:`NX_CHAR ` Any of these values: ``x`` | ``y`` | ``z`` .. _/NXsample/stress_field-field: .. index:: stress_field (field) **stress_field**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [n_sField]) {units=\ :ref:`NX_ANY `} Applied external stress field .. _/NXsample/stress_field@direction-attribute: .. index:: direction (field attribute) **@direction**: (optional) :ref:`NX_CHAR ` Any of these values: ``x`` | ``y`` | ``z`` .. _/NXsample/pressure-field: .. index:: pressure (field) **pressure**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [n_pField]) {units=\ :ref:`NX_PRESSURE `} Applied pressure .. _/NXsample/changer_position-field: .. index:: changer_position (field) **changer_position**: (optional) :ref:`NX_INT ` {units=\ :ref:`NX_UNITLESS `} Sample changer position .. _/NXsample/unit_cell_abc-field: .. index:: unit_cell_abc (field) **unit_cell_abc**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [3]) {units=\ :ref:`NX_LENGTH `} Crystallography unit cell parameters a, b, and c .. _/NXsample/unit_cell_alphabetagamma-field: .. index:: unit_cell_alphabetagamma (field) **unit_cell_alphabetagamma**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [3]) {units=\ :ref:`NX_ANGLE `} Crystallography unit cell parameters alpha, beta, and gamma .. _/NXsample/unit_cell-field: .. index:: unit_cell (field) **unit_cell**: (optional) :ref:`NX_FLOAT ` (Rank: 2, Dimensions: [n_comp, 6]) {units=\ :ref:`NX_LENGTH `} Unit cell parameters (lengths and angles) .. _/NXsample/unit_cell_volume-field: .. index:: unit_cell_volume (field) **unit_cell_volume**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [n_comp]) {units=\ :ref:`NX_VOLUME `} Volume of the unit cell .. _/NXsample/sample_orientation-field: .. index:: sample_orientation (field) **sample_orientation**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [3]) {units=\ :ref:`NX_ANGLE `} .. collapse:: This will follow the Busing-Levy convention: ... This will follow the Busing-Levy convention: W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464 .. _/NXsample/orientation_matrix-field: .. index:: orientation_matrix (field) **orientation_matrix**: (optional) :ref:`NX_FLOAT ` (Rank: 3, Dimensions: [n_comp, 3, 3]) .. collapse:: 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 .. _/NXsample/ub_matrix-field: .. index:: ub_matrix (field) **ub_matrix**: (optional) :ref:`NX_FLOAT ` (Rank: 3, Dimensions: [n_comp, 3, 3]) .. collapse:: 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 :math:`B` matrix which can be derived from the lattice constants. .. _/NXsample/mass-field: .. index:: mass (field) **mass**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [n_comp]) {units=\ :ref:`NX_MASS `} Mass of sample .. _/NXsample/density-field: .. index:: density (field) **density**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [n_comp]) {units=\ :ref:`NX_MASS_DENSITY `} Density of sample .. _/NXsample/relative_molecular_mass-field: .. index:: relative_molecular_mass (field) **relative_molecular_mass**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [n_comp]) {units=\ :ref:`NX_MASS `} Relative Molecular Mass of sample .. _/NXsample/type-field: .. index:: type (field) **type**: (optional) :ref:`NX_CHAR ` Any of these values: * ``sample`` * ``sample+can`` * ``can`` * ``sample+buffer`` * ``buffer`` * ``calibration sample`` * ``normalisation sample`` * ``simulated data`` * ``none`` * ``sample environment`` .. _/NXsample/situation-field: .. index:: situation (field) **situation**: (optional) :ref:`NX_CHAR ` .. collapse:: 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`` .. _/NXsample/description-field: .. index:: description (field) **description**: (optional) :ref:`NX_CHAR ` Description of the sample .. _/NXsample/preparation_date-field: .. index:: preparation_date (field) **preparation_date**: (optional) :ref:`NX_DATE_TIME ` Date of preparation of the sample .. _/NXsample/component-field: .. index:: component (field) **component**: (optional) :ref:`NX_CHAR ` (Rank: 1, Dimensions: [n_comp]) Details of the component of the sample and/or can .. _/NXsample/sample_component-field: .. index:: sample_component (field) **sample_component**: (optional) :ref:`NX_CHAR ` (Rank: 1, Dimensions: [n_comp]) .. collapse:: Type of component ... Type of component Any of these values: ``sample`` | ``can`` | ``atmosphere`` | ``kit`` .. _/NXsample/concentration-field: .. index:: concentration (field) **concentration**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [n_comp]) {units=\ :ref:`NX_MASS_DENSITY `} Concentration of each component .. _/NXsample/volume_fraction-field: .. index:: volume_fraction (field) **volume_fraction**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [n_comp]) Volume fraction of each component .. _/NXsample/scattering_length_density-field: .. index:: scattering_length_density (field) **scattering_length_density**: (optional) :ref:`NX_FLOAT ` (Rank: 1, Dimensions: [n_comp]) {units=\ :ref:`NX_SCATTERING_LENGTH_DENSITY `} Scattering length density of each component .. _/NXsample/unit_cell_class-field: .. index:: unit_cell_class (field) **unit_cell_class**: (optional) :ref:`NX_CHAR ` .. collapse:: 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`` .. _/NXsample/space_group-field: .. index:: space_group (field) **space_group**: (optional) :ref:`NX_CHAR ` (Rank: 1, Dimensions: [n_comp]) Crystallographic space group .. _/NXsample/point_group-field: .. index:: point_group (field) **point_group**: (optional) :ref:`NX_CHAR ` (Rank: 1, Dimensions: [n_comp]) Crystallographic point group, deprecated if space_group present .. _/NXsample/path_length-field: .. index:: path_length (field) **path_length**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_LENGTH `} .. collapse:: 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 .. _/NXsample/path_length_window-field: .. index:: path_length_window (field) **path_length_window**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_LENGTH `} .. collapse:: 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 .. _/NXsample/thickness-field: .. index:: thickness (field) **thickness**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_LENGTH `} sample thickness .. _/NXsample/external_DAC-field: .. index:: external_DAC (field) **external_DAC**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_ANY `} value sent to user's sample setup .. _/NXsample/short_title-field: .. index:: short_title (field) **short_title**: (optional) :ref:`NX_CHAR ` 20 character fixed length sample description for legends .. _/NXsample/rotation_angle-field: .. index:: rotation_angle (field) **rotation_angle**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_ANGLE `} .. collapse:: 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. .. _/NXsample/x_translation-field: .. index:: x_translation (field) **x_translation**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_LENGTH `} .. collapse:: 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. .. _/NXsample/distance-field: .. index:: distance (field) **distance**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_LENGTH `} .. collapse:: 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. .. _/NXsample/depends_on-field: .. index:: depends_on (field) **depends_on**: (optional) :ref:`NX_CHAR ` .. collapse:: 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. .. _/NXsample/geometry-group: **geometry**: (optional) :ref:`NXgeometry` .. index:: deprecated **DEPRECATED**: Use the field `depends_on` and :ref:`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 .. _/NXsample/BEAM-group: **BEAM**: (optional) :ref:`NXbeam` Details of beam incident on sample - used to calculate sample/beam interaction point .. _/NXsample/SAMPLE_COMPONENT-group: **SAMPLE_COMPONENT**: (optional) :ref:`NXsample_component` .. collapse:: 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 .. _/NXsample/transmission-group: **transmission**: (optional) :ref:`NXdata` As a function of Wavelength .. _/NXsample/temperature_log-group: **temperature_log**: (optional) :ref:`NXlog` .. index:: deprecated **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 .. _/NXsample/temperature_env-group: **temperature_env**: (optional) :ref:`NXenvironment` Additional sample temperature environment information .. _/NXsample/magnetic_field-group: **magnetic_field**: (optional) :ref:`NXlog` magnetic_field.value is a link to e.g. magnetic_field_env.sensor1.value .. _/NXsample/magnetic_field_log-group: **magnetic_field_log**: (optional) :ref:`NXlog` .. index:: deprecated **DEPRECATED**: use ``magnetic_field``, see: https://github.com/nexusformat/definitions/issues/816 magnetic_field_log.value is a link to e.g. magnetic_field_env.sensor1.value_log.value .. _/NXsample/magnetic_field_env-group: **magnetic_field_env**: (optional) :ref:`NXenvironment` Additional sample magnetic environment information .. _/NXsample/external_ADC-group: **external_ADC**: (optional) :ref:`NXlog` logged value (or logic state) read from user's setup .. _/NXsample/POSITIONER-group: **POSITIONER**: (optional) :ref:`NXpositioner` Any positioner (motor, PZT, ...) used to locate the sample .. _/NXsample/OFF_GEOMETRY-group: **OFF_GEOMETRY**: (optional) :ref:`NXoff_geometry` This group describes the shape of the sample .. _/NXsample/TRANSFORMATIONS-group: **TRANSFORMATIONS**: (optional) :ref:`NXtransformations` .. collapse:: 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. * :ref:`/NXsample/BEAM-group ` * :ref:`/NXsample/changer_position-field ` * :ref:`/NXsample/chemical_formula-field ` * :ref:`/NXsample/component-field ` * :ref:`/NXsample/concentration-field ` * :ref:`/NXsample/density-field ` * :ref:`/NXsample/depends_on-field ` * :ref:`/NXsample/description-field ` * :ref:`/NXsample/distance-field ` * :ref:`/NXsample/electric_field-field ` * :ref:`/NXsample/electric_field@direction-attribute ` * :ref:`/NXsample/external_ADC-group ` * :ref:`/NXsample/external_DAC-field ` * :ref:`/NXsample/geometry-group ` * :ref:`/NXsample/magnetic_field-field ` * :ref:`/NXsample/magnetic_field-group ` * :ref:`/NXsample/magnetic_field@direction-attribute ` * :ref:`/NXsample/magnetic_field_env-group ` * :ref:`/NXsample/magnetic_field_log-group ` * :ref:`/NXsample/mass-field ` * :ref:`/NXsample/name-field ` * :ref:`/NXsample/OFF_GEOMETRY-group ` * :ref:`/NXsample/orientation_matrix-field ` * :ref:`/NXsample/path_length-field ` * :ref:`/NXsample/path_length_window-field ` * :ref:`/NXsample/point_group-field ` * :ref:`/NXsample/POSITIONER-group ` * :ref:`/NXsample/preparation_date-field ` * :ref:`/NXsample/pressure-field ` * :ref:`/NXsample/relative_molecular_mass-field ` * :ref:`/NXsample/rotation_angle-field ` * :ref:`/NXsample/sample_component-field ` * :ref:`/NXsample/SAMPLE_COMPONENT-group ` * :ref:`/NXsample/sample_orientation-field ` * :ref:`/NXsample/scattering_length_density-field ` * :ref:`/NXsample/short_title-field ` * :ref:`/NXsample/situation-field ` * :ref:`/NXsample/space_group-field ` * :ref:`/NXsample/stress_field-field ` * :ref:`/NXsample/stress_field@direction-attribute ` * :ref:`/NXsample/temperature-field ` * :ref:`/NXsample/temperature_env-group ` * :ref:`/NXsample/temperature_log-group ` * :ref:`/NXsample/thickness-field ` * :ref:`/NXsample/TRANSFORMATIONS-group ` * :ref:`/NXsample/transmission-group ` * :ref:`/NXsample/type-field ` * :ref:`/NXsample/ub_matrix-field ` * :ref:`/NXsample/unit_cell-field ` * :ref:`/NXsample/unit_cell_abc-field ` * :ref:`/NXsample/unit_cell_alphabetagamma-field ` * :ref:`/NXsample/unit_cell_class-field ` * :ref:`/NXsample/unit_cell_volume-field ` * :ref:`/NXsample/volume_fraction-field ` * :ref:`/NXsample/x_translation-field ` * :ref:`/NXsample@default-attribute ` **NXDL Source**: https://github.com/nexusformat/definitions/blob/main/base_classes/NXsample.nxdl.xml