2.3.3.3.80. NXspm

Status:

application definition (contribution), extends NXsensor_scan

Description:

Scanning Probe Microscopy (SPM) is a branch of microscopy that utilizes a physic ...

Scanning Probe Microscopy (SPM) is a branch of microscopy that utilizes a physical probe to scan the surface of sample and image it at the atomic level.

The application class NXspm is designed as a skeleton and contains common technical concepts for specific SPM sub-techniques such as STM, STS, AFM etc. In addition, it can be utilized to describe the SPM experiments without further specialization for each sub-technique.

Symbols:

No symbol table

Groups cited:

NXamplifier, NXcalibration, NXcollection, NXdata, NXentry, NXenvironment, NXfabrication, NXhistory, NXinstrument, NXlockin, NXparameters, NXpid_controller, NXprocess, NXrcs, NXsample, NXsensor, NXspm_bias_spectroscopy, NXspm_piezo_sensor, NXspm_positioner, NXspm_scan_control, NXspm_scan_pattern, NXspm_scan_region, NXspm_temperature_sensor

Structure:

ENTRY: (required) NXentry ⤆

definition: (required) NX_CHAR ⤆

Name of the definition that is used for the application. ...

Name of the definition that is used for the application.

Obligatory value: NXspm

experiment_technique: (required) NX_CHAR

The technique of the experiment like STM, STS, AFM. ...

The technique of the experiment like STM, STS, AFM.

Any of these values: STM | STS | AFM

scan_mode: (optional) NX_CHAR

The mode of the scan. The possible options depend on the type of experiment. ...

The mode of the scan. The possible options depend on the type of experiment. For example, in STM, the scan mode could be constant height or constant current, in AFM, the scan mode could be contact mode, tapping mode or non-contact mode.

For general purpose usage, all scan modes from its sub-techniques are listed.

Any of these values or a custom value (if you use a custom value, also set @custom=True):

  • constant height

  • constant current

  • contact mode

  • tapping mode

  • peak force tapping mode

  • non-contact mode

scan_type: (recommended) NX_CHAR

The type of the scan. It mainly describes how scan probe moves in the scan r ...

The type of the scan. It mainly describes how scan probe moves in the scan region, e.g. forward, backward, or both (if scan is repeated). Any lab defined scan type

identifier_experiment: (recommended) NX_CHAR ⤆

The identifier for the experiment which should be unique at least in lab.

PROCESS: (optional) NXprocess ⤆

Define data processing (e.g., data analysis, image processing) program and ...

Define data processing (e.g., data analysis, image processing) program and associated workflow, software and store results.

INSTRUMENT: (required) NXinstrument ⤆

hardware: (required) NXfabrication ⤆

The hardware description of core instrument setup of experiment. ...

The hardware description of core instrument setup of experiment. Usually, the entire instrument is supplied by a single manufacturer. To describe the hardware from any sub-components, use the hardware group of that sub-component (child group of the NXinstrument group) group.

name: (recommended) NX_CHAR

Name of the hardware.

vendor: (required) NX_CHAR ⤆

Company name of the manufacturer.

model: (recommended) NX_CHAR ⤆

Version or model of the hardware setup provided by the manufacturer.

software: (required) NXfabrication ⤆

The software description of core instrument setup of experiment. ...

The software description of core instrument setup of experiment. Usually, the entire instrument is supplied by a single name/manufacturer/model/etc. To describe the software from any sub-components, use the software group of that component.

name: (optional) NX_CHAR

Name of the software.

vendor: (required) NX_CHAR ⤆

Company name of the manufacturer.

model: (recommended) NX_CHAR ⤆

Version or model of the component named by the manufacturer.

real_time_controller: (recommended) NXrcs

lockin_amplifier: (optional) NXlockin

The lock-in amplifier information.

flip_sign: (optional) NX_NUMBER

The sign (1 or -1) that renders the values of the lock-in current positi ...

The sign (1 or -1) that renders the values of the lock-in current positive. The calibration procedure with retracted tip is normally performed to compensate for the signal phase delay in SPM. The procedure yields two possible solutions corresponding to the chosen phase, this number should be equal to 1 or -1 depending on which solution is chosen (this concept mainly used in STS experiments).

active_channel: (recommended) NX_CHAR

The name of the active channel of the lock-in amplifier which is used fo ...

The name of the active channel of the lock-in amplifier which is used for the measurement.

SCAN_ENVIRONMENT: (required) NXenvironment ⤆

Information of the scan environment holding concept for ...

Information of the scan environment holding concept for temperature, setpoint (current or height), scan area and scan data.

Note: At least one field from head_temperature, cryo_bottom_temperature and cryo_shield_temperature must be provided.

head_temperature: (recommended) NX_NUMBER {units=NX_TEMPERATURE}

Temperature (stabilized or target value) of STM head. For array data of ...

Temperature (stabilized or target value) of STM head. For array data of head_temperature, use head_temperature_sensor group.

identifier_environment: (recommended) NX_CHAR ⤆

Unique identifier for the scan environment defined by the user or lab. W ...

Unique identifier for the scan environment defined by the user or lab. When multiple scans are performed in a single environment conditions or settings, the entire scan environment can be differentiated by this identifier. For example, scan on a sample of TiSe2 with layered of evaporated pyrene and annealed at 300K temperature for 5 min process.

cryo_bottom_temperature: (recommended) NX_NUMBER {units=NX_TEMPERATURE}

Temperature (stabilized or targeted single value) of the cold tail of th ...

Temperature (stabilized or targeted single value) of the cold tail of the cryostat. For array data of cryo_bottom_temperature, use cryo_bottom_temperature_sensor group.

cryo_shield_temperature: (recommended) NX_NUMBER {units=NX_TEMPERATURE}

Temperature (stabilized or targeted single value) of liquid nitrogen shi ...

Temperature (stabilized or targeted single value) of liquid nitrogen shield. For array data of cryo_shield_temperature, use cryo_shield_temperature_sensor group.

current_sensorTAG: (optional) NXsensor ⤆

This should be a link to ...

This should be a link to /entry/instrument/current_sensorTAG

voltage_sensorTAG: (optional) NXsensor ⤆

This should be a link to ...

This should be a link to /entry/instrument/voltage_sensorTAG

piezo_sensor: (optional) NXspm_piezo_sensor

This should be a link to ...

This should be a link to /entry/instrument/piezo_sensor.

XYZpiezo_sensor: (optional) NXspm_piezo_sensor

This should be a link to ...

This should be a link to /entry/instrument/XYZpiezo_sensor.

height_piezo_sensor: (optional) NXspm_piezo_sensor

This should be a link to the concept ...

This should be a link to the concept entry/instrument/height_piezo_sensor.

SPM_SCAN_CONTROL: (required) NXspm_scan_control

The scan control information like scan region or phase space, type of sc ...

The scan control information like scan region or phase space, type of scan (e.g. mesh, spiral, etc.), and scan speed, etc. This group mainly stores the scan settings data. For processed data or final experimental data would go to NXdata group.

scanTAG: (recommended) NX_CHAR

If there are multiple scans performed under the same environment, use ...

If there are multiple scans performed under the same environment, use this field to differentiate among them.

scan_region: (required) NXspm_scan_region ⤆

The scan region (phase space or sub-phase space) is the region where t ...

The scan region (phase space or sub-phase space) is the region where the scan is performed.

scan_range_x: (recommended) NX_NUMBER {units=NX_LENGTH} ⤆

The range of the scan in x direction.

scan_range_y: (recommended) NX_NUMBER {units=NX_LENGTH} ⤆

The range of the scan in y direction.

scan_offset_value_x: (recommended) NX_NUMBER {units=NX_LENGTH} ⤆

The offset of the scan in x direction.

scan_offset_value_y: (recommended) NX_NUMBER {units=NX_LENGTH} ⤆

The offset of the scan in y direction.

scan_angle_x: (recommended) NX_NUMBER {units=NX_ANGLE} ⤆

The angle of the scan region in x direction.

scan_angle_y: (recommended) NX_NUMBER {units=NX_ANGLE} ⤆

The angle of the scan region in y direction.

scan_start_x: (required) NX_NUMBER {units=NX_LENGTH} ⤆

The start of the scan in x direction.

scan_start_y: (required) NX_NUMBER {units=NX_LENGTH} ⤆

The start of the scan in y direction.

scan_end_x: (required) NX_NUMBER {units=NX_LENGTH} ⤆

The end of the scan in x direction.

scan_end_y: (required) NX_NUMBER {units=NX_LENGTH} ⤆

The end of the scan in y direction.

meshSCAN: (required) NXspm_scan_pattern ⤆

The mesh scan is a common technique used in SPM to scan the surface of ...

The mesh scan is a common technique used in SPM to scan the surface of the sample in a grid pattern.

scan_points_x: (required) NX_NUMBER ⤆

The number of points scanned in x direction.

scan_points_y: (required) NX_NUMBER ⤆

The number of points scanned in y direction.

step_size_x: (recommended) NX_NUMBER {units=NX_LENGTH} ⤆

The step size in x direction.

step_size_y: (recommended) NX_NUMBER {units=NX_LENGTH} ⤆

The step size in y direction.

current_sensorTAG: (optional) NXsensor ⤆

Information for current sensor. Any current sensor such as a current-volta ...

Information for current sensor. Any current sensor such as a current-voltage transimpedance amplifier involved in the experiment or in any special measurement or in any specialized experiment component can be registered under this group.

NAMEcurrent: (optional) NX_CHAR

The name of the current sensor used for specific measurement or in component.

current: (required) NX_NUMBER {units=NX_CURRENT}

Name of the current according to the purpose of the measurement. ...

Name of the current according to the purpose of the measurement. E.g., the field can be named as tip_current defining the current measured at the tip.

offset_value: (optional) NX_NUMBER {units=NX_CURRENT}

The offset in the tunneling current between tip and sample.

calibration: (optional) NXcalibration

Calibration data of the current sensor.

calibration_parameters: (optional) NXparameters ⤆

coefficient: (optional) NX_NUMBER {units=NX_ANY}

The coefficient of the calibration.

AMPLIFIER: (optional) NXamplifier

An amplifier information that amplifies the input signal.

current_gain: (optional) NX_NUMBER {units=NX_UNITLESS}

The gain of the current sensor.

voltage_sensorTAG: (optional) NXsensor ⤆

The sensor information for the voltage device. Any voltage sensor involved ...

The sensor information for the voltage device. Any voltage sensor involved in the experiment or in any special measurement or in any specialized experiment component can be registered under this group.

For this purpose, replace the TAG with the specific name or ID of the voltage sensor.

Do not register this group for sample bias voltage (DC), for that we have sample_bias_voltage group.

NAMEvoltage: (optional) NX_CHAR

The name of the voltage according to the purpose of the measurement. ...

The name of the voltage according to the purpose of the measurement. E.g., the field can be named as x_source_drain_bias_voltage defining the applied bias along the x-axis as source-drain channel, while current (tip current) will be measured along the z-axis.

voltage: (optional) NX_NUMBER {units=NX_VOLTAGE}

Voltage measured by sensor.

offset_value: (optional) NX_NUMBER {units=NX_VOLTAGE}

The offset voltage. The real voltage is the sum of the voltage and the o ...

The offset voltage. The real voltage is the sum of the voltage and the offset voltage.

calibration: (optional) NXcalibration

Calibration data of the voltage sensor.

calibration_parameters: (optional) NXparameters ⤆

coefficient: (optional) NX_NUMBER {units=NX_ANY}

The coefficient of the calibration.

AMPLIFIER: (optional) NXamplifier

An amplifier information that amplifies the input signal.

voltage_gain: (optional) NX_NUMBER {units=NX_UNITLESS}

The gain of the voltage sensor.

piezo_sensor: (optional) NXspm_piezo_sensor

This piezo sensor group refers to the XYZ (in all directions) piezo sensor.

x: (recommended) NX_NUMBER {units=NX_LENGTH} ⤆

The x position of the piezo.

y: (recommended) NX_NUMBER {units=NX_LENGTH} ⤆

The y position of the piezo.

z: (recommended) NX_NUMBER {units=NX_LENGTH} ⤆

The z position of the piezo.

height_piezo_sensor: (recommended) NXspm_piezo_sensor

The sensor information for the height (Z-axis) piezo device.

XYZpiezo_sensor: (optional) NXspm_piezo_sensor

For separate piezo sensors along X-, Y-, and Z-axis register this group, e ...

For separate piezo sensors along X-, Y-, and Z-axis register this group, e.g., x_piezo_sensor or height_piezo_sensor.

head_temperature_sensor: (recommended) NXspm_temperature_sensor

The temperature of the SPM measured near the sample or tip. This group is ...

The temperature of the SPM measured near the sample or tip. This group is intended to be used for an array data (e.g., time series).

cryo_bottom_temperature_sensor: (optional) NXspm_temperature_sensor

The temperature of the cold tail of the cryostat. This group is intended t ...

The temperature of the cold tail of the cryostat. This group is intended to be used for an array data (e.g., time series).

cryo_shield_temperature_sensor: (optional) NXspm_temperature_sensor

The temperature of the liquid nitrogen shield. This group is intended to b ...

The temperature of the liquid nitrogen shield. This group is intended to be used for an array data (e.g., time series).

sample_temperature_sensor: (optional) NXspm_temperature_sensor

The temperature of the sample. This group is intended to be used for ...

The temperature of the sample. This group is intended to be used for an array data (e.g., time series).

bias_spectroscopy_environment: (optional) NXenvironment ⤆

To explain bias and current behavior (sweep measurement especially in STS ...

To explain bias and current behavior (sweep measurement especially in STS experiment) due to voltage applied to the sample.

In some experiments, e.g., STM, bias spectroscopy could also be part of the measurement setup.

SPM_BIAS_SPECTROSCOPY: (required) NXspm_bias_spectroscopy

Setup and scan data for continuous measurement of bias voltage on the su ...

Setup and scan data for continuous measurement of bias voltage on the subject of experiment vs tunneling current from probe.

SPM_POSITIONER: (recommended) NXspm_positioner ⤆

Information about positioner used in STS scan settings, like PID contr ...

Information about positioner used in STS scan settings, like PID controller and offset.

Reuse, if needed, this group for positioners for multiple scans at different points on sample.

z_controller: (recommended) NXpid_controller ⤆

BIAS_SWEEP: (required) NXspm_scan_control ⤆

The bias voltage sweep is a common technique used to study properties ...

The bias voltage sweep is a common technique used to study properties (in this case current) in the sample or environment due to change in applied bias voltage.

scan_region: (required) NXspm_scan_region ⤆

The scan region (phase space or sub-phase space) is the region where ...

The scan region (phase space or sub-phase space) is the region where the scan is performed.

scan_start_bias: (required) NX_NUMBER {units=NX_VOLTAGE} ⤆

scan_end_bias: (required) NX_NUMBER {units=NX_VOLTAGE} ⤆

scan_offset_bias: (required) NX_NUMBER {units=NX_VOLTAGE} ⤆

The offset of the bias scan voltage.

scan_range_bias: (recommended) NX_NUMBER {units=NX_VOLTAGE} ⤆

linear_sweep: (required) NXspm_scan_pattern ⤆

The linear sweep is a common technique used on the substance or samp ...

The linear sweep is a common technique used on the substance or sample or environment to study the change in the behavior of the sample or substance or environment due to change in applied bias voltage.

scan_points_bias: (required) NX_NUMBER ⤆

step_size_bias: (required) NX_NUMBER ⤆

sample_bias_voltage: (optional) NXsensor ⤆

The DC bias voltage that is applied to the sample (for example in constant ...

The DC bias voltage that is applied to the sample (for example in constant- current mode in STM).

bias_voltage: (required) NX_NUMBER {units=NX_VOLTAGE}

The bias voltage (DC) applied to the sample.

bias_offset_value: (optional) NX_NUMBER {units=NX_VOLTAGE}

Offset value of the bias voltage.

calibration: (optional) NXcalibration

Calibration of the bias voltage measurement (V/V).

calibration_parameters: (optional) NXparameters ⤆

coefficient: (optional) NX_NUMBER {units=NX_ANY}

The coefficient of the calibration.

SAMPLE: (optional) NXsample ⤆

The sample information.

history: (recommended) NXhistory ⤆

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

sample_environment: (optional) NXenvironment ⤆

Information of environment around the sample.

temperature: (recommended) NX_NUMBER {units=NX_TEMPERATURE}

The single-valued temperature of the sample, also referred to as the tip ...

The single-valued temperature of the sample, also referred to as the tip temperature (not head temperature), since the tip and sample are in contact or in close proximity. For array like temperature data use sample_temperature_sensor group.

sample_bias_voltage: (optional) NXsensor ⤆

This should be a link to ...

This should be a link to

/entry/instrument/sample_bias_voltage sensor under instrument.

sample_temperature_sensor: (optional) NXspm_temperature_sensor

This should be a link to ...

This should be a link to

/entry/instrument/sample_temperature_sensor under instrument.

DATA: (required) NXdata ⤆

The data group.

DATA: (required) NX_NUMBER {units=NX_ANY} ⤆

The data (e.g. current, voltage, temperature) field that can be plotted ag ...

The data (e.g. current, voltage, temperature) field that can be plotted against the axes.

AXISNAME: (required) NX_CHAR_OR_NUMBER {units=NX_ANY} ⤆

The name of the axis that corresponds to the data field.

reproducibility_indicators: (optional) NXcollection ⤆

The group of indicators (links to the existing fields in different groups) t ...

The group of indicators (links to the existing fields in different groups) that measure the reproducibility of the experiment.

LINK_TO_FIELD: (optional) NX_CHAR

A place holder to create link to any field relevant considered as ...

A place holder to create link to any field relevant considered as reproducibility indicators (defined by laboratory).

LINK_TO_GROUP: (optional) NXcollection ⤆

A place holder to create link to any group relevant considered as ...

A place holder to create link to any group relevant considered as reproducibility indicators (defined by laboratory).

resolution_indicators: (optional) NXcollection ⤆

The group of indicators (links to the existing fields in different groups) t ...

The group of indicators (links to the existing fields in different groups) that are used to measure the resolution of the experiment results.

LINK_TO_FIELD: (optional) NX_CHAR

A place holder to create link to any field relevant considered as ...

A place holder to create link to any field relevant considered as reproducibility indicators (defined by laboratory).

LINK_TO_GROUP: (optional) NXcollection ⤆

A place holder to create link to any group relevant considered as ...

A place holder to create link to any group relevant considered as reproducibility indicators (defined by laboratory).

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/contributed_definitions/NXspm.nxdl.xml