2.3.3.3.10. NXafm

Status:

application definition (contribution), extends NXspm

Description:

An application definition to describe atomic force microscopy (AFM). ...

An application definition to describe atomic force microscopy (AFM).

In AFM a sharp tip mounted on a flexible cantilever senses the tip-sample interaction force. This application definition covers two complementary classes of AFM experiments:

  1. Imaging (raster scan): the tip is scanned over the sample surface in a raster (mesh) pattern while a feedback loop keeps a chosen setpoint of the positioner constant. This yields maps of the surface topography together with the accompanying channels such as amplitude, phase, frequency shift or deflection error. Such experiments are described by the meshSCAN scan pattern group.

  2. Force spectroscopy (single point): the lateral position of the tip is kept fixed and the tip-sample distance is ramped along z while the cantilever deflection is recorded, giving a force-distance (force-versus-z) curve for the approach and the retract (retrace) segment. Such experiments are described by the point_forceSCAN scan pattern group.

Both classes can be combined within a single experiment, as in force-volume mapping or peak force tapping, where a force-distance curve is recorded at every point of a raster grid.

Symbols:

No symbol table

Groups cited:

NXcollection, NXdetector, NXentry, NXenvironment, NXinstrument, NXphase_lock_loop, NXpositioner, NXsensor, NXspm_cantilever_oscillator, NXspm_cantilever, NXspm_piezo_sensor, NXspm_scan_control, NXspm_scan_pattern, NXspm_scan_region

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: NXafm

experiment_technique: (required) NX_CHAR ⤆

The AFM technique. ...

The AFM technique.

Obligatory value: AFM

scan_mode: (required) NX_CHAR ⤆

The mode of the scan. ...

The mode of the scan.

contact mode: Cantilever attempts to move on the sample surface in very close contact with the sample.

The cantilever deflection is usually employed to control the cantilever position using a PID feedback loop.

non-contact mode: Cantilever attempts to oscillate above the sample surface. Cantilever attempts to stay in the

interaction (atomic force) zone therefore cantilever oscillator amplitude and frequency are deformed. The cantilever frequency or oscillation amplitude is usually employed to control the cantilever position using a PID feedback loop.

tapping mode: Resembles to the non-contact mode, but at every point of scan the cantilever tip comes closer

to the sample surface (“taps it”). The cantilever oscillation amplitude is usually employed to control the cantilever position using a PID feedback loop.

peak force tapping mode: Like the tapping mode, but at each point of the scan force-distance curve is recorded.

The maximum force is usually employed to control the cantilever position using a PID feedback loop.

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

  • contact mode

  • tapping mode

  • non-contact mode

  • peak force tapping mode

INSTRUMENT: (required) NXinstrument ⤆

photo_detector: (optional) NXdetector ⤆

Information about the quadrant photodiode deflection detector or interferometer.

SENSOR: (optional) NXsensor

The sensor information for the photodiode or interferometer.

SPM_CANTILEVER: (recommended) NXspm_cantilever

The cantilever information.

cantilever_oscillator: (recommended) NXspm_cantilever_oscillator ⤆

When a cantilever is oscillated close to its resonance, this describes t ...

When a cantilever is oscillated close to its resonance, this describes the oscillator properties.

A cantilever can be used in direct contact mode to detect interaction forces or oscillated close to its resonance frequency near to surface in non-contact mode or in tapping mode. Changes in the oscillation amplitude, phase (between oscillated tail and moving tip) or resonance frequency are very sensitive to changes in the interaction potential field, giving rise of various measurement modes, such as non-contact or intermittent-contact (tapping) modes.

reference_amplitude: (recommended) NX_NUMBER {units=NX_ANY} ⤆

reference_frequency: (recommended) NX_NUMBER {units=NX_FREQUENCY} ⤆

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

phase_positioner: (recommended) NXpositioner ⤆

The phase positioner of the cantilever.

amplitude_positioner: (recommended) NXpositioner ⤆

The amplitude positioner of the cantilever.

phase_lock_loop: (recommended) NXphase_lock_loop

Phase locked loop for cantilever lock-in device.

SCAN_ENVIRONMENT: (required) NXenvironment ⤆

The environment information.

SPM_SCAN_CONTROL: (required) NXspm_scan_control ⤆

The scan control information related to the scan pattern and scan area.

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

The start of the scan in x direction (for afm raster scan)

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

The start of the scan in y direction (for afm raster scan).

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

The start of the scan in z direction (for point force spectroscopy).

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

The end of the scan in x direction (for afm raster scan).

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

The end of the scan in y direction (for afm raster scan).

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

The end of the scan in z direction (for point force spectroscopy).

meshSCAN: (optional) NXspm_scan_pattern ⤆

The mesh scan is a common technique used in AFM for imaging of the sur ...

The mesh scan is a common technique used in AFM for imaging of the surface of given sample in a grid pattern.

This group is required to be present if the AFM experiment is associated with a raster scan, which includes contact mode, non-contact mode, tapping mode and peak force tapping mode.

point_forceSCAN: (optional) NXspm_scan_pattern

The scan data from point force spectroscopy, force between the tip and ...
The scan data from point force spectroscopy, force between the tip and the sample at a specific point:

  1. approach

  2. retrace.

This group is required to be present if the AFM experiment is associated with point force spectroscopy.

scan_points_z: (recommended) NX_NUMBER ⤆

The number of points scanned in z direction, approach and retrace are same.

scan_points_approach: (recommended) NX_NUMBER ⤆

The number of points scanned in approach.

scan_points_retrace: (recommended) NX_NUMBER ⤆

The number of points scanned in retrace.

forward_speed_approach: (recommended) NX_NUMBER {units=NX_ANY} ⤆

The speed of the cantilever tip during approach in point force spectroscopy.

backward_speed_retrace: (recommended) NX_NUMBER {units=NX_ANY} ⤆

The speed of the cantilever tip during retract in point force spectroscopy.

XYpiezo_sensor: (optional) NXspm_piezo_sensor ⤆

This should be a link to the concept ...

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

head_temperature_sensor: (optional) NXsensor ⤆

This should be a link to the concept ...

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

head_temperature_sensor: (optional) NXsensor

The temperature of the scan environment or head of the cantilever.

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.

head_temperature: (optional) NX_NUMBER

This should be a link to ...

This should be a link to /entry/instrument/scan_environment/head_temperature

cryo_bottom_temperature: (optional) NX_NUMBER

This should be a link to ...

This should be a link to /entry/instrument/scan_environment/cryo_bottom_temperature

cryo_shield_temperature: (optional) NX_NUMBER

This should be a link to ...

This should be a link to /entry/instrument/scan_environment/cryo_shield_temperature

cantilever_oscillator: (optional) NXspm_cantilever_oscillator

This should be a link to ...

This should be a link to /entry/instrument/cantilever_spm/cantilever_oscillator

resolution_indicators: (optional) NXcollection ⤆

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

head_temperature: (optional) NX_NUMBER

This should be a link to ...

This should be a link to /entry/instrument/scan_environment/head_temperature

cryo_bottom_temperature: (optional) NX_NUMBER

This should be a link to ...

This should be a link to /entry/instrument/scan_environment/cryo_bottom_temperature

cryo_shield_temperature: (optional) NX_NUMBER

This should be a link to ...

This should be a link to /entry/instrument/scan_environment/cryo_shield_temperature

cantilever_config: (optional) NX_NUMBER

This should be a link to ...

This should be a link to /entry/instrument/cantilever_spm/cantilever_config

amplitude_excitation: (optional) NX_NUMBER

This should be a link to ...

This should be a link to /entry/instrument/phase_lock_loop/amplitude_excitation

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/NXafm.nxdl.xml