diff --git a/contributed_definitions/NXafm.nxdl.xml b/contributed_definitions/NXafm.nxdl.xml index 2df73e8cc..5a0e8f5fd 100644 --- a/contributed_definitions/NXafm.nxdl.xml +++ b/contributed_definitions/NXafm.nxdl.xml @@ -23,7 +23,7 @@ --> - An application definition to describe Atomic Force Microscopy (AFM) scanning + An application definition to describe atomic force microscopy (AFM) scanning technique. @@ -43,6 +43,8 @@ + + @@ -52,20 +54,33 @@ - The photo detector instrument information. + Information about the quadrant photodiode deflection detector. The cantilever information. + + Generally speaking, the cantilever resembles a leaf spring, which behaves as a simple harmonic oscillator. + When the probe (tip or particle) on the end of the cantilever is close to the surface of the sample, + an attractive or repulsive force appears between the cantilever and the sample, deforming the cantilever. + The detector (typically a light pointer hitting a quadrant photodiode) measures this deformation and, therefore, + the force acting on the cantilever. + In a typical AFM scan cantilever moves toward the surface of the sample until a user-defined value of force acting + on the cantilever is reached. The measured force is used as an input of a PID feedback loop, and the output of + this loop controls the vertical position of the cantilever. - Generally speaking, the cantilever resembles a simple harmonic oscillator. - When the cantilever tip is close to the surface of the sample, an attractive or repulsive force appears between the cantilever and the sample, deforming the cantilever. The detector (typically a photodiode) measures this deformation and, therefore, the force acting on the cantilever. - In a typical AFM scan cantilever moves toward the surface of the sample until a user-defined value of force acting on the cantilever is reached. The measured force is used as an input of a PID feedback loop, and the output of this loop controls the vertical position of the cantilever. + 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. Changes in the oscillation amplitude, phase (between oscillated tail and moving tip) + or resonance frequency are very sensitive to changes in the interction potential field, giving rise of + various measurement modes, such as non-contact or intermittent-contact (tapping) modes. + The threshold voltage for oscillator excitation. @@ -141,7 +156,7 @@ - The positioner information like the position of the tip, the position of the + The positioner information like the position of the end of the cantilever, the position of the sample, PID loop feedback etc. diff --git a/contributed_definitions/NXbias_spectroscopy.nxdl.xml b/contributed_definitions/NXbias_spectroscopy.nxdl.xml index ab7c6ddd5..c67fcb6d6 100644 --- a/contributed_definitions/NXbias_spectroscopy.nxdl.xml +++ b/contributed_definitions/NXbias_spectroscopy.nxdl.xml @@ -25,14 +25,19 @@ A base class for bias spectroscopy to describe the change in the physical properties of the sample with respect to the sweep voltage applied on a sample of STM/AFM/... experiment. + + In these experiments an electric potential is applied between the (conductive) sample and the probe + (tip), and the physical properties (e.g. tunnelling current) is measured as the function of this + potential. The potential is varied in so-called voltage sweeps and the corresponding properties are + recorded accordingly. The measurement of the I(V) curve can come in two ways: - 1. Constant Spacing: The bias voltage is swept from the start to the end with a constant - spacing between the tip and surface. - 2. Variadic Spacing: The bias voltage is swept from the start to the end in a discretized + 1. Constant spacing: The bias voltage is swept from the start to the end with a constant spacing between the tip and surface. + 2. Variable spacing: The bias voltage is swept from the start to the end in a discretized + spacing between the tip and surface. (Either an array of voltages, or the steps are defined). @@ -41,33 +46,40 @@ - The pid positioner information while running bias voltage-tunneling current - measurement. + The PID (proportional, integral, differential feedback system) positioner information while running + bias voltage-tunneling current measurement. + + These components position the probe relative to the sample, thus help obtaining maps of the data + across the sample surface. - The z-offset is a starting tip position before the sweep starts. + The z-offset is a starting tip position before the sweep starts (typically the position of a + piezo element). + - + The time or period is taken by a bias sweep to acquire the data for - a single bias sweep point. + a single bias sweep point (when the given point or whole sweep is started.). - + The time or period is taken by a bias sweep to be displayed. - + The time or period is taken by the circuit to measure a full bias sweep voltage or - bias current. + bias current. (duration of the measurement) + The time or period is taken by the circuit to indicate the bias sweep voltage @@ -80,9 +92,17 @@ The bias sweep information. + - The type of scan like mesh, spiral, etc. For STS experiment, the scan type is - usually a single-point scan (trajectory scan). + The type of scan like mesh, spiral, etc. + + This combines not only how the voltages are changed, but how the voltage values are + correlated to a position across the sample surface, measuring sweeps are each spatial + coordinate or mapping the response at constant voltage, etc. + For STS experiment, the scan type is usually a single-point scan (trajectory scan). @@ -93,14 +113,14 @@ The number of sweeps taken during the bias spectroscopy. - + The initial time is taken to settle the bias voltage at the desired value. On each sweep usually, the system takes time to settle to the bias voltage at the next value. - + The time is taken to settle the bias voltage at the desired value. The time (at the last sweep) to settle for the last value of the sweep. @@ -118,7 +138,7 @@ The z position after the sweeps are done. - + The total time needed for the entire voltage sweep. @@ -145,15 +165,19 @@ + The linear scan information for scanning of a smaple. + + In this scan type the probe is scanned with a constant velocity across the surface, + and parameters are measured along the line. The speed of the scanner or the probe during the scan. - + The time taken by the scanner to scan the entire area. diff --git a/contributed_definitions/NXcalibration.nxdl.xml b/contributed_definitions/NXcalibration.nxdl.xml index a0284e350..782a3e457 100644 --- a/contributed_definitions/NXcalibration.nxdl.xml +++ b/contributed_definitions/NXcalibration.nxdl.xml @@ -50,12 +50,12 @@ A description of the procedures employed. - + The start time of the calibration. - + The end time of the calibration. diff --git a/contributed_definitions/NXcantilever_spm.nxdl.xml b/contributed_definitions/NXcantilever_spm.nxdl.xml index bdcb1b367..e6487341b 100644 --- a/contributed_definitions/NXcantilever_spm.nxdl.xml +++ b/contributed_definitions/NXcantilever_spm.nxdl.xml @@ -31,6 +31,7 @@ Generally speaking, the cantilever resembles a simple harmonic oscillator. When the cantilever tip is close to the surface of the sample, an attractive or repulsive force appears between the cantilever and the sample, deforming the cantilever. The detector (typically a photodiode) measures this deformation and, therefore, the force acting on the cantilever. In a typical AFM scan cantilever moves toward the surface of the sample until a user-defined value of force acting on the cantilever is reached. The measured force is used as an input of a PID feedback loop, and the output of this loop controls the vertical position of the cantilever. + This part describes the oscillator driving the oscillations of a cantilever in an AFM or other experiment. @@ -109,7 +110,7 @@ The configuration information of the cantilever such as calibration information, - material properties, etc. + material properties, size, resonance, etc. @@ -121,6 +122,31 @@ The radius of curvature of the cantilever tip. The (substring) N denotes X or Y. + + + The shape of the cantilever as a general text, such as A-shape, beam, or arrow. + + + + + Nominal length between base and end of the cantilever in micrometers. + + + + + Nominal width of the cantilever in microns. + + + + + Nominal thickness of the cantilever in microns. + + + + + Nominal free resonance frequency of the cantilever in air, in kHz. + + The calibration information of the cantilever. diff --git a/contributed_definitions/NXcircuit.nxdl.xml b/contributed_definitions/NXcircuit.nxdl.xml index 5213107fb..6865bf8ec 100644 --- a/contributed_definitions/NXcircuit.nxdl.xml +++ b/contributed_definitions/NXcircuit.nxdl.xml @@ -22,13 +22,29 @@ # For further information, see http://www.nexusformat.org --> + + + Constant to be used in the definition: the number of channels of the + circuit board. + + + + number of channels of the circuit board. + + + Application definition for circuit devices. + + Electronic circuits are hardware components connecting several electronic components to achieve + specific functionality, e.g. amplifying a voltage or convert a voltage to binary numbers, etc. - Hardware where the circuit is implanted; includes hardware manufacturers and - type + Hardware where the circuit is implanted; includes information about the hardware manufacturers and + type (e.g. part number) + All the elements below may be single numbers of an array of values with length N_channel + describing multiple input and output channels. @@ -55,11 +71,15 @@ digital, mixed-signal. + - The operating frequency range of the circuit. + The operating frequency of the circuit, see also bandwidth below, which is possibly + centered around this frequency. However, not necessarily (e.g. running a 100 kHz bandwidth + amplifier at low, audio frequencies 1 - 20,000 Hz) + Input impedance of the circuit. @@ -78,13 +98,12 @@ - Noise level (in current or voltage) in the circuit. + RMS noise level (in current or voltage) in the circuit in voltage or current. - If circuit handles AC current or signal it may have a band Bandwidth of the circuit to be - responded. + The bandwidth of the frequency response of the circuit. @@ -104,7 +123,7 @@ - Number of output channels collected to this circuit. + Number of output channels collected to this circuit. Most probably N_channel. diff --git a/contributed_definitions/NXlockin.nxdl.xml b/contributed_definitions/NXlockin.nxdl.xml index 2941aee35..06c656d9d 100644 --- a/contributed_definitions/NXlockin.nxdl.xml +++ b/contributed_definitions/NXlockin.nxdl.xml @@ -27,13 +27,14 @@ The lock-in amplifier information: the device is being used to extract a (potentially) very weak input signal buried in the noisy background, where the input signal has - the same frequency (or its harmonic) as a known reference signal. Additionally, - the phase shift between the input signal and the reference signal is measured. + the same frequency (or its harmonic) as a known reference signal, using heterodyne + detection. + This method extracts the amplitude and phase shift of the current signal to the reference. The reference signal might be created by a generator built-in into the lock-in amplifier. - Hardware manufacturers and type of lock-in amplifier. + Hardware manufacturers and type (product number) of lock-in amplifier. @@ -58,16 +59,19 @@ usually applied to a sample and used to create a reference signal for the detection of the input signal - + - The number that defines the sign of the lock-in current. The calibration procedure - with retracted tip is normally performed to compensate for the signal phase delay + The sign (1 or -1) that defines the sign of the lock-in current. + The calibration procedure with retracted tip is normally performed to compensate for the signal phase delay in SPM. The procedure yields two possible solutions, this number should be equal - to 1 or -1 depending on which solution is chosen. + to 1 or -1 depending on which solution is chosen (this concept mainly used in STS experiments, + e.g. in Nanonis machine). - + Amplitude of the reference signal for the lock-in amplifier. @@ -80,14 +84,12 @@ - Phase of the reference signal for the lock-in amplifier. + Phase of the reference signal set in the lock-in amplifier. - The modulated output signal will be demodulated, in order to determine the amplitude - and phase at the frequency set in the Frequency field or harmonics, such as current, - bias, et.al. + Type of the demodulated signal, current | voltage. @@ -107,23 +109,11 @@ The amplitude of the demodulated signal. - - - The bandwidth of the modulated signal that can be applied in amplitude - demodulation mechanism. - - The phase of the demodulated signal. - - - The bandwidth of the modulated signal that can be applied in phase demodulation - mechanism. - - List of the demodulator channels. @@ -157,7 +147,7 @@ - Reference phase of reference signal with respect to the demodulated signal + An extra reference phase offset of reference signal with respect to the demodulated signal (foreach Channels). diff --git a/contributed_definitions/NXpiezo_config_spm.nxdl.xml b/contributed_definitions/NXpiezo_config_spm.nxdl.xml index dee9b34cf..46666150e 100644 --- a/contributed_definitions/NXpiezo_config_spm.nxdl.xml +++ b/contributed_definitions/NXpiezo_config_spm.nxdl.xml @@ -25,10 +25,11 @@ Discussion: No need to create this base class rather we can define in spm application definition.--> - A base class describing piezo settings for scanning probe microscopy. + A base class describing piezo actuator settings for scanning probe microscopy. - The piezoelectric material of SPM actuators gets deformed due to the applied electric field. - Description below shows calibration coefficients and other configuration parameters of the piezo actuators. + Piezoelectric actuators work utilizing the inverse-piezoelectric effect, when a voltage + is applied on the material and it deforms proportional to the applied voltage. + Description below shows calibration coefficients and other configuration parameters of open loop piezo actuators (that is actuators without capacitive sensor feedback systems). @@ -106,6 +107,11 @@ Discussion: No need to create this base class rather we can define in spm applic such the second-order correction is (V/m^2). + + + The drift correction status (true / false) in calibration step of piezo. + + The N (substring) denotes X, Y and Z directions. Define the diff --git a/contributed_definitions/NXpiezoelectric_material.nxdl.xml b/contributed_definitions/NXpiezoelectric_material.nxdl.xml index 4bf1be011..6677f0db7 100644 --- a/contributed_definitions/NXpiezoelectric_material.nxdl.xml +++ b/contributed_definitions/NXpiezoelectric_material.nxdl.xml @@ -37,6 +37,16 @@ (PZTs). + + + The identifier of the piezo material. + + + + The identifier of the piezo material. + + + The chemical formula of the material of the piezo scanner such as Pb(Zr,Ti)O3. diff --git a/contributed_definitions/NXpositioner_spm.nxdl.xml b/contributed_definitions/NXpositioner_spm.nxdl.xml index e0ed367c6..3048b7c96 100644 --- a/contributed_definitions/NXpositioner_spm.nxdl.xml +++ b/contributed_definitions/NXpositioner_spm.nxdl.xml @@ -24,7 +24,7 @@ Extending positioner from NXpositioner to maintain a measurement signal through - a feedback loop. + a feedback loop, specialized for scanning probe microscopy applications. @@ -47,8 +47,8 @@ - Indicate the tip position Z between tip and sample. The tip position can also be varied when - the controller is not running. This is the final position after the tip reaches an equilibrium state. + Indicate the tip position Z. The tip position can also be varied when the controller is not running. + This is the final position after the tip reaches an equilibrium state. diff --git a/contributed_definitions/NXscan_control.nxdl.xml b/contributed_definitions/NXscan_control.nxdl.xml index 8ecd4a67e..015c240a7 100644 --- a/contributed_definitions/NXscan_control.nxdl.xml +++ b/contributed_definitions/NXscan_control.nxdl.xml @@ -82,8 +82,7 @@ - This group specifies whether there is any movement when a data point is - measured. + This strig describes how the scan was performed. @@ -99,9 +98,9 @@ - The offset of the scan region from the origin along the specific scan axis. + The offset of center of the scan region from the origin along the specific scan axis. - 'N' denotes the name of the specific scan axis. + 'N' denotes the name of the specific scan axis. (Offset, start and end positions are related) @@ -145,7 +144,8 @@ - Define the scan speed in the forward direction along the axis. + Define the scan speed in the forward direction along the axis if forward and backward + speeds below are not specified. If the scan goes in the negative direction, the speed should be negative. @@ -181,7 +181,8 @@ - The number of steps the probe jumps over the scan steps or points. + The number of steps the probe jumps over the scan steps or points. This describes when not + every point from the scan_points is measured along an axis. Rename the field, according to the name of the dimension (e.g. stepping_x, stepping_voltage). @@ -245,7 +246,8 @@ - Define the direction of the spiral scan. (e.g. clockwise, anticlockwise) + Define the direction of the spiral scan. (e.g. clockwise, anticlockwise from looking back + along the surface normal) diff --git a/contributed_definitions/NXsensor_scan.nxdl.xml b/contributed_definitions/NXsensor_scan.nxdl.xml index e884a399f..472d047e8 100644 --- a/contributed_definitions/NXsensor_scan.nxdl.xml +++ b/contributed_definitions/NXsensor_scan.nxdl.xml @@ -39,6 +39,19 @@ with an UTC offset. + + + .. 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 visualised upon entry. + See https://www.nexusformat.org/2014_How_to_find_default_data.html + for a summary of the discussion. + + @@ -52,15 +65,15 @@ (such as temperature) or instrument-generated unique identifier. - + The unique identifier for the collection. The identifier is used to group a number of the experiments run upon the same setup and/or same sample. - + - - + + Define the program that was used to generate the results file(s) @@ -183,7 +196,7 @@ - + ISO8601 datum when calibration was last performed before this measurement. UTC offset should be specified. diff --git a/contributed_definitions/NXspm.nxdl.xml b/contributed_definitions/NXspm.nxdl.xml index 0afdf28ab..079df9929 100644 --- a/contributed_definitions/NXspm.nxdl.xml +++ b/contributed_definitions/NXspm.nxdl.xml @@ -30,19 +30,6 @@ for specific SPM sub-techniques such as STM, STS, AFM etc. - - - .. 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 visualised upon entry. - See https://www.nexusformat.org/2014_How_to_find_default_data.html - for a summary of the discussion. - - Name of the definition that is used for the application. @@ -337,12 +324,12 @@ The PID controller information for the z-axis. - + The average time taken by the z-controller to stabilize the tip. - + The time taken by the z-controller to measure physical properties. @@ -443,7 +430,7 @@ Calibration of the bias voltage measurement (V/V). - + The time or period is taken by the calibration to setup to acquire the data for the calibration. @@ -483,7 +470,7 @@ the reproducibility of the experiment. - + The group of indicators (links to the existing fields in different groups) that are used to measure the resolution of the experiment results. diff --git a/contributed_definitions/NXstm.nxdl.xml b/contributed_definitions/NXstm.nxdl.xml index 741cfb042..eb8bbb85d 100644 --- a/contributed_definitions/NXstm.nxdl.xml +++ b/contributed_definitions/NXstm.nxdl.xml @@ -90,57 +90,6 @@ TODO: Replace rename NXenvironment to experiment_environment in NXstm, NXspm and - - - The region of the scan area. - - - - The range of the scan area. - - - - - The offset of the scan area in 2D (X and Y) space. - - - - - The N (substring) denotes the angle of the scan area with different physical - axes. - - - - - - The scan information for mesh scan type for STM experiment. - - - - The speed of the scanner or the tip during the scan. - - - - - The time taken by the scanner to scan the entire area. - - - - - The N (substring) denotes the forward speed of the scanner. - - - - - The N (substring) denotes the backward speed of the scanner. - - - - - The data that comes from scanning the area. - - - @@ -195,7 +144,7 @@ TODO: Replace rename NXenvironment to experiment_environment in NXstm, NXspm and Calibration of the current measurement. - + The time or period is taken by the calibration to setup to acquire the data for the calibration. @@ -235,23 +184,6 @@ TODO: Replace rename NXenvironment to experiment_environment in NXstm, NXspm and The sensor information for the piezo device. - - - The x position of the piezo. In STS experiment or at the starting, - the piezo stays fixed at x,y and z and the the tunneling current - is measured with respect to the bias voltage (sweep voltage). - - - - - The y position of the piezo. - - - - - The z position of the piezo. - - The piezo configuration information like piezoelectric device calibration and @@ -356,7 +288,7 @@ TODO: Replace rename NXenvironment to experiment_environment in NXstm, NXspm and - + The group's concepts hold the link to the related concepts that define the reproducibility of the STM experiment. @@ -399,29 +331,29 @@ TODO: Replace rename NXenvironment to experiment_environment in NXstm, NXspm and - + The group's concepts hold the link to the related concepts that define the resolution of the STM experiment. - + Link to target: /ENTRY[entry]/experiment_instrument/scan_environment/tip_temp - + Link to target: /ENTRY[entry]/experiment_instrument/scan_environment/cryo_bottom_temp - + Link to target: /ENTRY[entry]/experiment_instrument/scan_environment/cryo_shield_temperature - + Link to target: /ENTRY[entry]/experiment_instrument/bias_spectroscopy_environment/BIAS_SPECTROSCOPY[bias_spectroscopy]/BIAS_SWEEP[bias_sweep] diff --git a/contributed_definitions/nyaml/NXafm.yaml b/contributed_definitions/nyaml/NXafm.yaml index 53f4bfe30..dcb92f282 100644 --- a/contributed_definitions/nyaml/NXafm.yaml +++ b/contributed_definitions/nyaml/NXafm.yaml @@ -1,6 +1,6 @@ category: application doc: | - An application definition to describe Atomic Force Microscopy (AFM) scanning + An application definition to describe atomic force microscopy (AFM) scanning technique. type: group NXafm(NXspm): @@ -12,7 +12,7 @@ NXafm(NXspm): scan_mode: doc: | The mode of the scan. - enumeration: [contact mode, tapping mode, non-contact mode] + enumeration: [contact mode, tapping mode, non-contact mode, Kelvin probe, electric force] experiment_instrument(NXinstrument): doc: | The group explains the core instruments' setup of the AFM experiment as well as the environment of the corresponding @@ -20,20 +20,34 @@ NXafm(NXspm): photo_detector(NXdetector): exists: optional doc: | - The photo detector instrument information. + Information about the quadrant photodiode deflection detector. (NXcantilever_spm): exists: optional doc: | The cantilever information. + + Generally speaking, the cantilever resembles a leaf spring, which behaves as a simple harmonic oscillator. + When the probe (tip or particle) on the end of the cantilever is close to the surface of the sample, + an attractive or repulsive force appears between the cantilever and the sample, deforming the cantilever. + The detector (typically a light pointer hitting a quadrant photodiode) measures this deformation and, therefore, + the force acting on the cantilever. + In a typical AFM scan cantilever moves toward the surface of the sample until a user-defined value of force acting + on the cantilever is reached. The measured force is used as an input of a PID feedback loop, and the output of + this loop controls the vertical position of the cantilever. cantilever_oscillator(NXobject): exists: optional doc: | - Generally speaking, the cantilever resembles a simple harmonic oscillator. - When the cantilever tip is close to the surface of the sample, an attractive or repulsive force appears between the cantilever and the sample, deforming the cantilever. The detector (typically a photodiode) measures this deformation and, therefore, the force acting on the cantilever. - In a typical AFM scan cantilever moves toward the surface of the sample until a user-defined value of force acting on the cantilever is reached. The measured force is used as an input of a PID feedback loop, and the output of this loop controls the vertical position of the cantilever. + 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. Changes in the oscillation amplitude, phase (between oscillated tail and moving tip) + or resonance frequency are very sensitive to changes in the interction potential field, giving rise of + various measurement modes, such as non-contact or intermittent-contact (tapping) modes. oscillator_excitation(NX_NUMBER): exists: optional unit: NX_ANY + + # is this correct? I would expect a driving voltage... doc: | The threshold voltage for oscillator excitation. phase_lock_loop(NXlockin): @@ -87,7 +101,7 @@ NXafm(NXspm): The material description and properties of the piezoelectric scanner materials. (NXpositioner_spm): doc: | - The positioner information like the position of the tip, the position of the + The positioner information like the position of the end of the cantilever, the position of the sample, PID loop feedback etc. tip_temp_sensor(NXsensor): exists: optional @@ -95,7 +109,7 @@ NXafm(NXspm): The temperature of the scan environment or tip of the cantilever. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# fa4fba4dbdb47b6b13313bb2987b9130506b025dac0b45aacd9d586f9e5aa137 +# 5e6d35c0745060adc6707dfd9991c887a33b67ca2ed32ece1f7a00403906419f # # # # # -# An application definition to describe Atomic Force Microscopy (AFM) scanning +# An application definition to describe atomic force microscopy (AFM) scanning # technique. # # @@ -141,6 +155,8 @@ NXafm(NXspm): # # # +# +# # # # @@ -150,20 +166,33 @@ NXafm(NXspm): # # # -# The photo detector instrument information. +# Information about the quadrant photodiode deflection detector. # # # # # The cantilever information. +# +# Generally speaking, the cantilever resembles a leaf spring, which behaves as a simple harmonic oscillator. +# When the probe (tip or particle) on the end of the cantilever is close to the surface of the sample, +# an attractive or repulsive force appears between the cantilever and the sample, deforming the cantilever. +# The detector (typically a light pointer hitting a quadrant photodiode) measures this deformation and, therefore, +# the force acting on the cantilever. +# In a typical AFM scan cantilever moves toward the surface of the sample until a user-defined value of force acting +# on the cantilever is reached. The measured force is used as an input of a PID feedback loop, and the output of +# this loop controls the vertical position of the cantilever. # # # -# Generally speaking, the cantilever resembles a simple harmonic oscillator. -# When the cantilever tip is close to the surface of the sample, an attractive or repulsive force appears between the cantilever and the sample, deforming the cantilever. The detector (typically a photodiode) measures this deformation and, therefore, the force acting on the cantilever. -# In a typical AFM scan cantilever moves toward the surface of the sample until a user-defined value of force acting on the cantilever is reached. The measured force is used as an input of a PID feedback loop, and the output of this loop controls the vertical position of the cantilever. +# 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. Changes in the oscillation amplitude, phase (between oscillated tail and moving tip) +# or resonance frequency are very sensitive to changes in the interction potential field, giving rise of +# various measurement modes, such as non-contact or intermittent-contact (tapping) modes. # # +# # # The threshold voltage for oscillator excitation. # @@ -239,7 +268,7 @@ NXafm(NXspm): # # # -# The positioner information like the position of the tip, the position of the +# The positioner information like the position of the end of the cantilever, the position of the # sample, PID loop feedback etc. # # diff --git a/contributed_definitions/nyaml/NXbias_spectroscopy.yaml b/contributed_definitions/nyaml/NXbias_spectroscopy.yaml index d16ab3d3a..f1ba312ee 100644 --- a/contributed_definitions/nyaml/NXbias_spectroscopy.yaml +++ b/contributed_definitions/nyaml/NXbias_spectroscopy.yaml @@ -2,43 +2,57 @@ category: base doc: | A base class for bias spectroscopy to describe the change in the physical properties of the sample with respect to the sweep voltage applied on a sample of STM/AFM/... experiment. + + In these experiments an electric potential is applied between the (conductive) sample and the probe + (tip), and the physical properties (e.g. tunnelling current) is measured as the function of this + potential. The potential is varied in so-called voltage sweeps and the corresponding properties are + recorded accordingly. type: group NXbias_spectroscopy(NXobject): measurement_type: doc: | The measurement of the I(V) curve can come in two ways: - 1. Constant Spacing: The bias voltage is swept from the start to the end with a constant - spacing between the tip and surface. - 2. Variadic Spacing: The bias voltage is swept from the start to the end in a discretized + 1. Constant spacing: The bias voltage is swept from the start to the end with a constant spacing between the tip and surface. + 2. Variable spacing: The bias voltage is swept from the start to the end in a discretized + spacing between the tip and surface. (Either an array of voltages, or the steps are defined). enumeration: [constant_spacing, variadic_spacing] (NXpositioner_spm): doc: | - The pid positioner information while running bias voltage-tunneling current - measurement. + The PID (proportional, integral, differential feedback system) positioner information while running + bias voltage-tunneling current measurement. + + These components position the probe relative to the sample, thus help obtaining maps of the data + across the sample surface. z_offset(NX_NUMBER): unit: NX_LENGTH doc: | - The z-offset is a starting tip position before the sweep starts. + The z-offset is a starting tip position before the sweep starts (typically the position of a + piezo element). + + # how these time specifications relate to the later time values, like + # scan_time? (NXcircuit): exists: optional - acquisition_time(NX_DATE_TIME): + acquisition_time(NX_NUMBER): exists: optional unit: NX_TIME doc: | The time or period is taken by a bias sweep to acquire the data for - a single bias sweep point. - animation_time(NX_DATE_TIME): + a single bias sweep point (when the given point or whole sweep is started.). + animation_time(NX_NUMBER): exists: optional unit: NX_TIME doc: | The time or period is taken by a bias sweep to be displayed. - measurement_time(NX_DATE_TIME): + measurement_time(NX_NUMBER): exists: optional unit: NX_TIME doc: | The time or period is taken by the circuit to measure a full bias sweep voltage or - bias current. + bias current. (duration of the measurement) + + # how does this indicators_period differs from animation time? indicators_period(NX_DATE_TIME): exists: optional unit: NX_TIME @@ -49,21 +63,30 @@ NXbias_spectroscopy(NXobject): doc: | The bias sweep information. scan_type: + + # I modify this text, by I may be wrong T. + # key is: I can change X,Y location at constant voltage or do a sweep + # at every X,Y coordinate, and I can define patterns how X,Y values follow + # each other (e.g. spiral) doc: | - The type of scan like mesh, spiral, etc. For STS experiment, the scan type is - usually a single-point scan (trajectory scan). + The type of scan like mesh, spiral, etc. + + This combines not only how the voltages are changed, but how the voltage values are + correlated to a position across the sample surface, measuring sweeps are each spatial + coordinate or mapping the response at constant voltage, etc. + For STS experiment, the scan type is usually a single-point scan (trajectory scan). enumeration: [linear] sweep_number(NX_NUMBER): doc: | The number of sweeps taken during the bias spectroscopy. - first_settling_time(NX_DATE_TIME): + first_settling_time(NX_NUMBER): exists: optional unit: NX_TIME doc: | The initial time is taken to settle the bias voltage at the desired value. On each sweep usually, the system takes time to settle to the bias voltage at the next value. - end_settling_time(NX_DATE_TIME): + end_settling_time(NX_NUMBER): exists: optional unit: NX_TIME doc: | @@ -80,7 +103,7 @@ NXbias_spectroscopy(NXobject): exists: recommended doc: | The z position after the sweeps are done. - total_spectroscopy_time(NX_DATE_TIME): + total_spectroscopy_time(NX_NUMBER): exists: recommended unit: NX_TIME doc: | @@ -102,13 +125,18 @@ NXbias_spectroscopy(NXobject): The N (substring) denotes the angle of the scan area with different physical axes. linear_sweep(NXobject): + + # is this a special case of the scans described above? doc: | The linear scan information for scanning of a smaple. + + In this scan type the probe is scanned with a constant velocity across the surface, + and parameters are measured along the line. scan_speed(NX_NUMBER): unit: NX_ANY doc: | The speed of the scanner or the probe during the scan. - scan_time(NX_DATE_TIME): + scan_time(NX_NUMBER): unit: NX_TIME doc: | The time taken by the scanner to scan the entire area. @@ -125,7 +153,7 @@ NXbias_spectroscopy(NXobject): The data that comes from scanning the area. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 5b57b4e955019fabedb0a7fe4fc70a0626dce64f58aa542d7ab6d4161d0a0bdd +# 5b49dd5999a0c8838e232a3bfd90ce43f173d07395f56231de1be8e67bd7151b # # # # -# +# # # The time or period is taken by a bias sweep to acquire the data for -# a single bias sweep point. +# a single bias sweep point (when the given point or whole sweep is started.). # # -# +# # # The time or period is taken by a bias sweep to be displayed. # # -# +# # # The time or period is taken by the circuit to measure a full bias sweep voltage or -# bias current. +# bias current. (duration of the measurement) # # +# # # # The time or period is taken by the circuit to indicate the bias sweep voltage @@ -208,9 +248,17 @@ NXbias_spectroscopy(NXobject): # The bias sweep information. # # +# # -# The type of scan like mesh, spiral, etc. For STS experiment, the scan type is -# usually a single-point scan (trajectory scan). +# The type of scan like mesh, spiral, etc. +# +# This combines not only how the voltages are changed, but how the voltage values are +# correlated to a position across the sample surface, measuring sweeps are each spatial +# coordinate or mapping the response at constant voltage, etc. +# For STS experiment, the scan type is usually a single-point scan (trajectory scan). # # # @@ -221,14 +269,14 @@ NXbias_spectroscopy(NXobject): # The number of sweeps taken during the bias spectroscopy. # # -# +# # # The initial time is taken to settle the bias voltage at the desired value. # On each sweep usually, the system takes time to settle to the bias voltage # at the next value. # # -# +# # # The time is taken to settle the bias voltage at the desired value. # The time (at the last sweep) to settle for the last value of the sweep. @@ -246,7 +294,7 @@ NXbias_spectroscopy(NXobject): # The z position after the sweeps are done. # # -# +# # # The total time needed for the entire voltage sweep. # @@ -273,15 +321,19 @@ NXbias_spectroscopy(NXobject): # # # +# # # The linear scan information for scanning of a smaple. +# +# In this scan type the probe is scanned with a constant velocity across the surface, +# and parameters are measured along the line. # # # # The speed of the scanner or the probe during the scan. # # -# +# # # The time taken by the scanner to scan the entire area. # diff --git a/contributed_definitions/nyaml/NXcalibration.yaml b/contributed_definitions/nyaml/NXcalibration.yaml index e7e362caf..2c59fac02 100644 --- a/contributed_definitions/nyaml/NXcalibration.yaml +++ b/contributed_definitions/nyaml/NXcalibration.yaml @@ -13,10 +13,10 @@ NXcalibration(NXobject): description(NX_CHAR): doc: | A description of the procedures employed. - start_time(NX_DATE_TIME): + start_time(NX_NUMBER): doc: | The start time of the calibration. - end_time(NX_DATE_TIME): + end_time(NX_NUMBER): doc: | The end time of the calibration. calibration_interval(NX_FLOAT): @@ -168,7 +168,7 @@ NXcalibration(NXobject): for a summary of the discussion. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0637e042803449160e95d45786d186382342ce32958d181cfbd42830ffb145c2 +# 43ca2db5ea4eeb4af5d70b9d78e32cc291cf755de199c0cc2538369b87ebed91 # # # # +# +# +# Constant to be used in the definition: the number of channels of the +# circuit board. +# +# +# +# number of channels of the circuit board. +# +# +# # # Application definition for circuit devices. +# +# Electronic circuits are hardware components connecting several electronic components to achieve +# specific functionality, e.g. amplifying a voltage or convert a voltage to binary numbers, etc. # # # -# Hardware where the circuit is implanted; includes hardware manufacturers and -# type +# Hardware where the circuit is implanted; includes information about the hardware manufacturers and +# type (e.g. part number) +# All the elements below may be single numbers of an array of values with length N_channel +# describing multiple input and output channels. # # # @@ -147,11 +179,15 @@ NXcircuit(NXobject): # digital, mixed-signal. # # +# # # -# The operating frequency range of the circuit. +# The operating frequency of the circuit, see also bandwidth below, which is possibly +# centered around this frequency. However, not necessarily (e.g. running a 100 kHz bandwidth +# amplifier at low, audio frequencies 1 - 20,000 Hz) # # +# # # # Input impedance of the circuit. @@ -170,13 +206,12 @@ NXcircuit(NXobject): # # # -# Noise level (in current or voltage) in the circuit. +# RMS noise level (in current or voltage) in the circuit in voltage or current. # # # # -# If circuit handles AC current or signal it may have a band Bandwidth of the circuit to be -# responded. +# The bandwidth of the frequency response of the circuit. # # # @@ -196,7 +231,7 @@ NXcircuit(NXobject): # # # -# Number of output channels collected to this circuit. +# Number of output channels collected to this circuit. Most probably N_channel. # # # diff --git a/contributed_definitions/nyaml/NXlockin.yaml b/contributed_definitions/nyaml/NXlockin.yaml index 6f9b266d8..cc2257a6e 100644 --- a/contributed_definitions/nyaml/NXlockin.yaml +++ b/contributed_definitions/nyaml/NXlockin.yaml @@ -4,14 +4,15 @@ doc: | The lock-in amplifier information: the device is being used to extract a (potentially) very weak input signal buried in the noisy background, where the input signal has - the same frequency (or its harmonic) as a known reference signal. Additionally, - the phase shift between the input signal and the reference signal is measured. + the same frequency (or its harmonic) as a known reference signal, using heterodyne + detection. + This method extracts the amplitude and phase shift of the current signal to the reference. The reference signal might be created by a generator built-in into the lock-in amplifier. type: group NXlockin(NXobject): hardware(NXfabrication): doc: | - Hardware manufacturers and type of lock-in amplifier. + Hardware manufacturers and type (product number) of lock-in amplifier. (NXamplifier): doc: | Description of the amplifier (after detection of the signal from the noise) @@ -26,17 +27,20 @@ NXlockin(NXobject): doc: | A periodic voltage signal generated by the lock-in, usually applied to a sample and used to create a reference signal for the detection of the input signal - lockin_current_flip_value(NX_NUMBER): + lockin_current_flip_sign(NX_NUMBER): exists: optional doc: | - The number that defines the sign of the lock-in current. The calibration procedure - with retracted tip is normally performed to compensate for the signal phase delay + The sign (1 or -1) that defines the sign of the lock-in current. + The calibration procedure with retracted tip is normally performed to compensate for the signal phase delay in SPM. The procedure yields two possible solutions, this number should be equal - to 1 or -1 depending on which solution is chosen. + to 1 or -1 depending on which solution is chosen (this concept mainly used in STS experiments, + e.g. in Nanonis machine). # (For bais modulate signal, it depands on the modulate type) # unit could be NX_VOLTAGE or NX_CURRENT + # these (reference amplitude, frequency and phase) should be specivied on channel basis, + # even when common reference is sent to different channels reference_amplitude(NX_NUMBER): unit: NX_ANY doc: | @@ -48,12 +52,10 @@ NXlockin(NXobject): reference_phase(NX_NUMBER): unit: NX_ANGLE doc: | - Phase of the reference signal for the lock-in amplifier. + Phase of the reference signal set in the lock-in amplifier. demodulated_signal(NX_CHAR): doc: | - The modulated output signal will be demodulated, in order to determine the amplitude - and phase at the frequency set in the Frequency field or harmonics, such as current, - bias, et.al. + Type of the demodulated signal, current | voltage. demodulated_frequency(NX_NUMBER): unit: NX_FREQUENCY doc: | @@ -69,20 +71,10 @@ NXlockin(NXobject): unit: NX_ANY doc: | The amplitude of the demodulated signal. - amplitude_demodulation_bandwidth(NX_NUMBER): - unit: NX_ANY - doc: | - The bandwidth of the modulated signal that can be applied in amplitude - demodulation mechanism. demodulated_phase(NX_NUMBER): unit: NX_ANGLE doc: | The phase of the demodulated signal. - phase_demodulation_bandwidth(NX_NUMBER): - unit: NX_FREQUENCY - doc: | - The bandwidth of the modulated signal that can be applied in phase demodulation - mechanism. demodulator_channels(NX_CHAR): doc: | List of the demodulator channels. @@ -109,7 +101,7 @@ NXlockin(NXobject): ref_phase_N(NX_NUMBER): unit: NX_ANGLE doc: | - Reference phase of reference signal with respect to the demodulated signal + An extra reference phase offset of reference signal with respect to the demodulated signal (foreach Channels). integration_time(NX_NUMBER): unit: NX_TIME @@ -124,7 +116,7 @@ NXlockin(NXobject): Ratio of output signal amplitude to input signal amplitue (V/V). # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# c5a5794e8253813e28db0dbe2df778f6bffd00b2447d0488f665e5f89a9a669a +# 340ff0c78db623cc9da1e2fbb030f3c24cd1f514f6d5a410c310d9238449a7b1 # # # -# +# # # # Amplitude of the reference signal for the lock-in amplifier. @@ -207,14 +203,12 @@ NXlockin(NXobject): # # # -# Phase of the reference signal for the lock-in amplifier. +# Phase of the reference signal set in the lock-in amplifier. # # # # -# The modulated output signal will be demodulated, in order to determine the amplitude -# and phase at the frequency set in the Frequency field or harmonics, such as current, -# bias, et.al. +# Type of the demodulated signal, current | voltage. # # # @@ -234,23 +228,11 @@ NXlockin(NXobject): # The amplitude of the demodulated signal. # # -# -# -# The bandwidth of the modulated signal that can be applied in amplitude -# demodulation mechanism. -# -# # # # The phase of the demodulated signal. # # -# -# -# The bandwidth of the modulated signal that can be applied in phase demodulation -# mechanism. -# -# # # # List of the demodulator channels. @@ -284,7 +266,7 @@ NXlockin(NXobject): # # # -# Reference phase of reference signal with respect to the demodulated signal +# An extra reference phase offset of reference signal with respect to the demodulated signal # (foreach Channels). # # diff --git a/contributed_definitions/nyaml/NXpiezo_config_spm.yaml b/contributed_definitions/nyaml/NXpiezo_config_spm.yaml index f13dab1d7..78dd861a6 100644 --- a/contributed_definitions/nyaml/NXpiezo_config_spm.yaml +++ b/contributed_definitions/nyaml/NXpiezo_config_spm.yaml @@ -1,9 +1,10 @@ category: base doc: | - A base class describing piezo settings for scanning probe microscopy. + A base class describing piezo actuator settings for scanning probe microscopy. - The piezoelectric material of SPM actuators gets deformed due to the applied electric field. - Description below shows calibration coefficients and other configuration parameters of the piezo actuators. + Piezoelectric actuators work utilizing the inverse-piezoelectric effect, when a voltage + is applied on the material and it deforms proportional to the applied voltage. + Description below shows calibration coefficients and other configuration parameters of open loop piezo actuators (that is actuators without capacitive sensor feedback systems). # Discussion: No need to create this base class rather we can define in spm application definition. type: group @@ -64,6 +65,9 @@ NXpiezo_config_spm(NXobject): with units: "[V] = [V/m] · [m] + [V/m2] · [m2]" where cx is the calibration of the piezo X and cxx is the 2nd order correction. The unit for such the second-order correction is (V/m^2). + drift_correction_status(NX_BOOLEAN): + doc: | + The drift correction status (true / false) in calibration step of piezo. drift_N(NX_NUMBER): unit: NX_ANY doc: | @@ -72,7 +76,7 @@ NXpiezo_config_spm(NXobject): move at that speed. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 983ecbb63ca89b8133a7b671fba009b74498d7745d5b569592931cb2df75b49e +# 96e710da01fe879d6ab92e5a15bf41b9f916f75e23b1d254f36999406f0afa60 # # # # # -# A base class describing piezo settings for scanning probe microscopy. +# A base class describing piezo actuator settings for scanning probe microscopy. # -# The piezoelectric material of SPM actuators gets deformed due to the applied electric field. -# Description below shows calibration coefficients and other configuration parameters of the piezo actuators. +# Piezoelectric actuators work utilizing the inverse-piezoelectric effect, when a voltage +# is applied on the material and it deforms proportional to the applied voltage. +# Description below shows calibration coefficients and other configuration parameters of open loop piezo actuators (that is actuators without capacitive sensor feedback systems). # # # @@ -181,6 +186,11 @@ NXpiezo_config_spm(NXobject): # such the second-order correction is (V/m^2). # # +# +# +# The drift correction status (true / false) in calibration step of piezo. +# +# # # # The N (substring) denotes X, Y and Z directions. Define the diff --git a/contributed_definitions/nyaml/NXpiezoelectric_material.yaml b/contributed_definitions/nyaml/NXpiezoelectric_material.yaml index 7dc433a5b..0960a4033 100644 --- a/contributed_definitions/nyaml/NXpiezoelectric_material.yaml +++ b/contributed_definitions/nyaml/NXpiezoelectric_material.yaml @@ -14,6 +14,12 @@ NXpiezoelectric_material(NXobject): doc: | The name of the material of the piezo scanner such as Lead Zirconate Titanates (PZTs). + piezo_material_identifier(NXidentifier): + doc: | + The identifier of the piezo material. + identifier(NX_CHAR): + doc: | + The identifier of the piezo material. chemical_description(NXsubstance): doc: | The chemical formula of the material of the piezo scanner such as Pb(Zr,Ti)O3. @@ -75,7 +81,7 @@ NXpiezoelectric_material(NXobject): viscous state. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 39d5862b3a9e4f526a71d3a1ad2234a4f4de5b953ce08c21e47f8bd7a9670ed7 +# 0f228771942f8ad9c37ecfbdd4dc96d0193a3da548a401a92aec2d436caf26c6 # # # id22 id13 --> id23 id13 --> id24 - + ``` ## STM App Def diff --git a/contributed_definitions/nyaml/SPM/NXafm.yaml b/contributed_definitions/nyaml/SPM/NXafm.yaml index 53f4bfe30..dcb92f282 100644 --- a/contributed_definitions/nyaml/SPM/NXafm.yaml +++ b/contributed_definitions/nyaml/SPM/NXafm.yaml @@ -1,6 +1,6 @@ category: application doc: | - An application definition to describe Atomic Force Microscopy (AFM) scanning + An application definition to describe atomic force microscopy (AFM) scanning technique. type: group NXafm(NXspm): @@ -12,7 +12,7 @@ NXafm(NXspm): scan_mode: doc: | The mode of the scan. - enumeration: [contact mode, tapping mode, non-contact mode] + enumeration: [contact mode, tapping mode, non-contact mode, Kelvin probe, electric force] experiment_instrument(NXinstrument): doc: | The group explains the core instruments' setup of the AFM experiment as well as the environment of the corresponding @@ -20,20 +20,34 @@ NXafm(NXspm): photo_detector(NXdetector): exists: optional doc: | - The photo detector instrument information. + Information about the quadrant photodiode deflection detector. (NXcantilever_spm): exists: optional doc: | The cantilever information. + + Generally speaking, the cantilever resembles a leaf spring, which behaves as a simple harmonic oscillator. + When the probe (tip or particle) on the end of the cantilever is close to the surface of the sample, + an attractive or repulsive force appears between the cantilever and the sample, deforming the cantilever. + The detector (typically a light pointer hitting a quadrant photodiode) measures this deformation and, therefore, + the force acting on the cantilever. + In a typical AFM scan cantilever moves toward the surface of the sample until a user-defined value of force acting + on the cantilever is reached. The measured force is used as an input of a PID feedback loop, and the output of + this loop controls the vertical position of the cantilever. cantilever_oscillator(NXobject): exists: optional doc: | - Generally speaking, the cantilever resembles a simple harmonic oscillator. - When the cantilever tip is close to the surface of the sample, an attractive or repulsive force appears between the cantilever and the sample, deforming the cantilever. The detector (typically a photodiode) measures this deformation and, therefore, the force acting on the cantilever. - In a typical AFM scan cantilever moves toward the surface of the sample until a user-defined value of force acting on the cantilever is reached. The measured force is used as an input of a PID feedback loop, and the output of this loop controls the vertical position of the cantilever. + 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. Changes in the oscillation amplitude, phase (between oscillated tail and moving tip) + or resonance frequency are very sensitive to changes in the interction potential field, giving rise of + various measurement modes, such as non-contact or intermittent-contact (tapping) modes. oscillator_excitation(NX_NUMBER): exists: optional unit: NX_ANY + + # is this correct? I would expect a driving voltage... doc: | The threshold voltage for oscillator excitation. phase_lock_loop(NXlockin): @@ -87,7 +101,7 @@ NXafm(NXspm): The material description and properties of the piezoelectric scanner materials. (NXpositioner_spm): doc: | - The positioner information like the position of the tip, the position of the + The positioner information like the position of the end of the cantilever, the position of the sample, PID loop feedback etc. tip_temp_sensor(NXsensor): exists: optional @@ -95,7 +109,7 @@ NXafm(NXspm): The temperature of the scan environment or tip of the cantilever. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# fa4fba4dbdb47b6b13313bb2987b9130506b025dac0b45aacd9d586f9e5aa137 +# 5e6d35c0745060adc6707dfd9991c887a33b67ca2ed32ece1f7a00403906419f # # # # # -# An application definition to describe Atomic Force Microscopy (AFM) scanning +# An application definition to describe atomic force microscopy (AFM) scanning # technique. # # @@ -141,6 +155,8 @@ NXafm(NXspm): # # # +# +# # # # @@ -150,20 +166,33 @@ NXafm(NXspm): # # # -# The photo detector instrument information. +# Information about the quadrant photodiode deflection detector. # # # # # The cantilever information. +# +# Generally speaking, the cantilever resembles a leaf spring, which behaves as a simple harmonic oscillator. +# When the probe (tip or particle) on the end of the cantilever is close to the surface of the sample, +# an attractive or repulsive force appears between the cantilever and the sample, deforming the cantilever. +# The detector (typically a light pointer hitting a quadrant photodiode) measures this deformation and, therefore, +# the force acting on the cantilever. +# In a typical AFM scan cantilever moves toward the surface of the sample until a user-defined value of force acting +# on the cantilever is reached. The measured force is used as an input of a PID feedback loop, and the output of +# this loop controls the vertical position of the cantilever. # # # -# Generally speaking, the cantilever resembles a simple harmonic oscillator. -# When the cantilever tip is close to the surface of the sample, an attractive or repulsive force appears between the cantilever and the sample, deforming the cantilever. The detector (typically a photodiode) measures this deformation and, therefore, the force acting on the cantilever. -# In a typical AFM scan cantilever moves toward the surface of the sample until a user-defined value of force acting on the cantilever is reached. The measured force is used as an input of a PID feedback loop, and the output of this loop controls the vertical position of the cantilever. +# 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. Changes in the oscillation amplitude, phase (between oscillated tail and moving tip) +# or resonance frequency are very sensitive to changes in the interction potential field, giving rise of +# various measurement modes, such as non-contact or intermittent-contact (tapping) modes. # # +# # # The threshold voltage for oscillator excitation. # @@ -239,7 +268,7 @@ NXafm(NXspm): # # # -# The positioner information like the position of the tip, the position of the +# The positioner information like the position of the end of the cantilever, the position of the # sample, PID loop feedback etc. # # diff --git a/contributed_definitions/nyaml/SPM/NXbias_spectroscopy.yaml b/contributed_definitions/nyaml/SPM/NXbias_spectroscopy.yaml index d16ab3d3a..f1ba312ee 100644 --- a/contributed_definitions/nyaml/SPM/NXbias_spectroscopy.yaml +++ b/contributed_definitions/nyaml/SPM/NXbias_spectroscopy.yaml @@ -2,43 +2,57 @@ category: base doc: | A base class for bias spectroscopy to describe the change in the physical properties of the sample with respect to the sweep voltage applied on a sample of STM/AFM/... experiment. + + In these experiments an electric potential is applied between the (conductive) sample and the probe + (tip), and the physical properties (e.g. tunnelling current) is measured as the function of this + potential. The potential is varied in so-called voltage sweeps and the corresponding properties are + recorded accordingly. type: group NXbias_spectroscopy(NXobject): measurement_type: doc: | The measurement of the I(V) curve can come in two ways: - 1. Constant Spacing: The bias voltage is swept from the start to the end with a constant - spacing between the tip and surface. - 2. Variadic Spacing: The bias voltage is swept from the start to the end in a discretized + 1. Constant spacing: The bias voltage is swept from the start to the end with a constant spacing between the tip and surface. + 2. Variable spacing: The bias voltage is swept from the start to the end in a discretized + spacing between the tip and surface. (Either an array of voltages, or the steps are defined). enumeration: [constant_spacing, variadic_spacing] (NXpositioner_spm): doc: | - The pid positioner information while running bias voltage-tunneling current - measurement. + The PID (proportional, integral, differential feedback system) positioner information while running + bias voltage-tunneling current measurement. + + These components position the probe relative to the sample, thus help obtaining maps of the data + across the sample surface. z_offset(NX_NUMBER): unit: NX_LENGTH doc: | - The z-offset is a starting tip position before the sweep starts. + The z-offset is a starting tip position before the sweep starts (typically the position of a + piezo element). + + # how these time specifications relate to the later time values, like + # scan_time? (NXcircuit): exists: optional - acquisition_time(NX_DATE_TIME): + acquisition_time(NX_NUMBER): exists: optional unit: NX_TIME doc: | The time or period is taken by a bias sweep to acquire the data for - a single bias sweep point. - animation_time(NX_DATE_TIME): + a single bias sweep point (when the given point or whole sweep is started.). + animation_time(NX_NUMBER): exists: optional unit: NX_TIME doc: | The time or period is taken by a bias sweep to be displayed. - measurement_time(NX_DATE_TIME): + measurement_time(NX_NUMBER): exists: optional unit: NX_TIME doc: | The time or period is taken by the circuit to measure a full bias sweep voltage or - bias current. + bias current. (duration of the measurement) + + # how does this indicators_period differs from animation time? indicators_period(NX_DATE_TIME): exists: optional unit: NX_TIME @@ -49,21 +63,30 @@ NXbias_spectroscopy(NXobject): doc: | The bias sweep information. scan_type: + + # I modify this text, by I may be wrong T. + # key is: I can change X,Y location at constant voltage or do a sweep + # at every X,Y coordinate, and I can define patterns how X,Y values follow + # each other (e.g. spiral) doc: | - The type of scan like mesh, spiral, etc. For STS experiment, the scan type is - usually a single-point scan (trajectory scan). + The type of scan like mesh, spiral, etc. + + This combines not only how the voltages are changed, but how the voltage values are + correlated to a position across the sample surface, measuring sweeps are each spatial + coordinate or mapping the response at constant voltage, etc. + For STS experiment, the scan type is usually a single-point scan (trajectory scan). enumeration: [linear] sweep_number(NX_NUMBER): doc: | The number of sweeps taken during the bias spectroscopy. - first_settling_time(NX_DATE_TIME): + first_settling_time(NX_NUMBER): exists: optional unit: NX_TIME doc: | The initial time is taken to settle the bias voltage at the desired value. On each sweep usually, the system takes time to settle to the bias voltage at the next value. - end_settling_time(NX_DATE_TIME): + end_settling_time(NX_NUMBER): exists: optional unit: NX_TIME doc: | @@ -80,7 +103,7 @@ NXbias_spectroscopy(NXobject): exists: recommended doc: | The z position after the sweeps are done. - total_spectroscopy_time(NX_DATE_TIME): + total_spectroscopy_time(NX_NUMBER): exists: recommended unit: NX_TIME doc: | @@ -102,13 +125,18 @@ NXbias_spectroscopy(NXobject): The N (substring) denotes the angle of the scan area with different physical axes. linear_sweep(NXobject): + + # is this a special case of the scans described above? doc: | The linear scan information for scanning of a smaple. + + In this scan type the probe is scanned with a constant velocity across the surface, + and parameters are measured along the line. scan_speed(NX_NUMBER): unit: NX_ANY doc: | The speed of the scanner or the probe during the scan. - scan_time(NX_DATE_TIME): + scan_time(NX_NUMBER): unit: NX_TIME doc: | The time taken by the scanner to scan the entire area. @@ -125,7 +153,7 @@ NXbias_spectroscopy(NXobject): The data that comes from scanning the area. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 5b57b4e955019fabedb0a7fe4fc70a0626dce64f58aa542d7ab6d4161d0a0bdd +# 5b49dd5999a0c8838e232a3bfd90ce43f173d07395f56231de1be8e67bd7151b # # # # -# +# # # The time or period is taken by a bias sweep to acquire the data for -# a single bias sweep point. +# a single bias sweep point (when the given point or whole sweep is started.). # # -# +# # # The time or period is taken by a bias sweep to be displayed. # # -# +# # # The time or period is taken by the circuit to measure a full bias sweep voltage or -# bias current. +# bias current. (duration of the measurement) # # +# # # # The time or period is taken by the circuit to indicate the bias sweep voltage @@ -208,9 +248,17 @@ NXbias_spectroscopy(NXobject): # The bias sweep information. # # +# # -# The type of scan like mesh, spiral, etc. For STS experiment, the scan type is -# usually a single-point scan (trajectory scan). +# The type of scan like mesh, spiral, etc. +# +# This combines not only how the voltages are changed, but how the voltage values are +# correlated to a position across the sample surface, measuring sweeps are each spatial +# coordinate or mapping the response at constant voltage, etc. +# For STS experiment, the scan type is usually a single-point scan (trajectory scan). # # # @@ -221,14 +269,14 @@ NXbias_spectroscopy(NXobject): # The number of sweeps taken during the bias spectroscopy. # # -# +# # # The initial time is taken to settle the bias voltage at the desired value. # On each sweep usually, the system takes time to settle to the bias voltage # at the next value. # # -# +# # # The time is taken to settle the bias voltage at the desired value. # The time (at the last sweep) to settle for the last value of the sweep. @@ -246,7 +294,7 @@ NXbias_spectroscopy(NXobject): # The z position after the sweeps are done. # # -# +# # # The total time needed for the entire voltage sweep. # @@ -273,15 +321,19 @@ NXbias_spectroscopy(NXobject): # # # +# # # The linear scan information for scanning of a smaple. +# +# In this scan type the probe is scanned with a constant velocity across the surface, +# and parameters are measured along the line. # # # # The speed of the scanner or the probe during the scan. # # -# +# # # The time taken by the scanner to scan the entire area. # diff --git a/contributed_definitions/nyaml/SPM/NXcalibration.yaml b/contributed_definitions/nyaml/SPM/NXcalibration.yaml index e7e362caf..2c59fac02 100644 --- a/contributed_definitions/nyaml/SPM/NXcalibration.yaml +++ b/contributed_definitions/nyaml/SPM/NXcalibration.yaml @@ -13,10 +13,10 @@ NXcalibration(NXobject): description(NX_CHAR): doc: | A description of the procedures employed. - start_time(NX_DATE_TIME): + start_time(NX_NUMBER): doc: | The start time of the calibration. - end_time(NX_DATE_TIME): + end_time(NX_NUMBER): doc: | The end time of the calibration. calibration_interval(NX_FLOAT): @@ -168,7 +168,7 @@ NXcalibration(NXobject): for a summary of the discussion. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0637e042803449160e95d45786d186382342ce32958d181cfbd42830ffb145c2 +# 43ca2db5ea4eeb4af5d70b9d78e32cc291cf755de199c0cc2538369b87ebed91 # # # # +# +# +# Constant to be used in the definition: the number of channels of the +# circuit board. +# +# +# +# number of channels of the circuit board. +# +# +# # # Application definition for circuit devices. +# +# Electronic circuits are hardware components connecting several electronic components to achieve +# specific functionality, e.g. amplifying a voltage or convert a voltage to binary numbers, etc. # # # -# Hardware where the circuit is implanted; includes hardware manufacturers and -# type +# Hardware where the circuit is implanted; includes information about the hardware manufacturers and +# type (e.g. part number) +# All the elements below may be single numbers of an array of values with length N_channel +# describing multiple input and output channels. # # # @@ -147,11 +179,15 @@ NXcircuit(NXobject): # digital, mixed-signal. # # +# # # -# The operating frequency range of the circuit. +# The operating frequency of the circuit, see also bandwidth below, which is possibly +# centered around this frequency. However, not necessarily (e.g. running a 100 kHz bandwidth +# amplifier at low, audio frequencies 1 - 20,000 Hz) # # +# # # # Input impedance of the circuit. @@ -170,13 +206,12 @@ NXcircuit(NXobject): # # # -# Noise level (in current or voltage) in the circuit. +# RMS noise level (in current or voltage) in the circuit in voltage or current. # # # # -# If circuit handles AC current or signal it may have a band Bandwidth of the circuit to be -# responded. +# The bandwidth of the frequency response of the circuit. # # # @@ -196,7 +231,7 @@ NXcircuit(NXobject): # # # -# Number of output channels collected to this circuit. +# Number of output channels collected to this circuit. Most probably N_channel. # # # diff --git a/contributed_definitions/nyaml/SPM/NXlockin.yaml b/contributed_definitions/nyaml/SPM/NXlockin.yaml index 6f9b266d8..cc2257a6e 100644 --- a/contributed_definitions/nyaml/SPM/NXlockin.yaml +++ b/contributed_definitions/nyaml/SPM/NXlockin.yaml @@ -4,14 +4,15 @@ doc: | The lock-in amplifier information: the device is being used to extract a (potentially) very weak input signal buried in the noisy background, where the input signal has - the same frequency (or its harmonic) as a known reference signal. Additionally, - the phase shift between the input signal and the reference signal is measured. + the same frequency (or its harmonic) as a known reference signal, using heterodyne + detection. + This method extracts the amplitude and phase shift of the current signal to the reference. The reference signal might be created by a generator built-in into the lock-in amplifier. type: group NXlockin(NXobject): hardware(NXfabrication): doc: | - Hardware manufacturers and type of lock-in amplifier. + Hardware manufacturers and type (product number) of lock-in amplifier. (NXamplifier): doc: | Description of the amplifier (after detection of the signal from the noise) @@ -26,17 +27,20 @@ NXlockin(NXobject): doc: | A periodic voltage signal generated by the lock-in, usually applied to a sample and used to create a reference signal for the detection of the input signal - lockin_current_flip_value(NX_NUMBER): + lockin_current_flip_sign(NX_NUMBER): exists: optional doc: | - The number that defines the sign of the lock-in current. The calibration procedure - with retracted tip is normally performed to compensate for the signal phase delay + The sign (1 or -1) that defines the sign of the lock-in current. + The calibration procedure with retracted tip is normally performed to compensate for the signal phase delay in SPM. The procedure yields two possible solutions, this number should be equal - to 1 or -1 depending on which solution is chosen. + to 1 or -1 depending on which solution is chosen (this concept mainly used in STS experiments, + e.g. in Nanonis machine). # (For bais modulate signal, it depands on the modulate type) # unit could be NX_VOLTAGE or NX_CURRENT + # these (reference amplitude, frequency and phase) should be specivied on channel basis, + # even when common reference is sent to different channels reference_amplitude(NX_NUMBER): unit: NX_ANY doc: | @@ -48,12 +52,10 @@ NXlockin(NXobject): reference_phase(NX_NUMBER): unit: NX_ANGLE doc: | - Phase of the reference signal for the lock-in amplifier. + Phase of the reference signal set in the lock-in amplifier. demodulated_signal(NX_CHAR): doc: | - The modulated output signal will be demodulated, in order to determine the amplitude - and phase at the frequency set in the Frequency field or harmonics, such as current, - bias, et.al. + Type of the demodulated signal, current | voltage. demodulated_frequency(NX_NUMBER): unit: NX_FREQUENCY doc: | @@ -69,20 +71,10 @@ NXlockin(NXobject): unit: NX_ANY doc: | The amplitude of the demodulated signal. - amplitude_demodulation_bandwidth(NX_NUMBER): - unit: NX_ANY - doc: | - The bandwidth of the modulated signal that can be applied in amplitude - demodulation mechanism. demodulated_phase(NX_NUMBER): unit: NX_ANGLE doc: | The phase of the demodulated signal. - phase_demodulation_bandwidth(NX_NUMBER): - unit: NX_FREQUENCY - doc: | - The bandwidth of the modulated signal that can be applied in phase demodulation - mechanism. demodulator_channels(NX_CHAR): doc: | List of the demodulator channels. @@ -109,7 +101,7 @@ NXlockin(NXobject): ref_phase_N(NX_NUMBER): unit: NX_ANGLE doc: | - Reference phase of reference signal with respect to the demodulated signal + An extra reference phase offset of reference signal with respect to the demodulated signal (foreach Channels). integration_time(NX_NUMBER): unit: NX_TIME @@ -124,7 +116,7 @@ NXlockin(NXobject): Ratio of output signal amplitude to input signal amplitue (V/V). # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# c5a5794e8253813e28db0dbe2df778f6bffd00b2447d0488f665e5f89a9a669a +# 340ff0c78db623cc9da1e2fbb030f3c24cd1f514f6d5a410c310d9238449a7b1 # # # -# +# # # # Amplitude of the reference signal for the lock-in amplifier. @@ -207,14 +203,12 @@ NXlockin(NXobject): # # # -# Phase of the reference signal for the lock-in amplifier. +# Phase of the reference signal set in the lock-in amplifier. # # # # -# The modulated output signal will be demodulated, in order to determine the amplitude -# and phase at the frequency set in the Frequency field or harmonics, such as current, -# bias, et.al. +# Type of the demodulated signal, current | voltage. # # # @@ -234,23 +228,11 @@ NXlockin(NXobject): # The amplitude of the demodulated signal. # # -# -# -# The bandwidth of the modulated signal that can be applied in amplitude -# demodulation mechanism. -# -# # # # The phase of the demodulated signal. # # -# -# -# The bandwidth of the modulated signal that can be applied in phase demodulation -# mechanism. -# -# # # # List of the demodulator channels. @@ -284,7 +266,7 @@ NXlockin(NXobject): # # # -# Reference phase of reference signal with respect to the demodulated signal +# An extra reference phase offset of reference signal with respect to the demodulated signal # (foreach Channels). # # diff --git a/contributed_definitions/nyaml/SPM/NXpiezo_config_spm.yaml b/contributed_definitions/nyaml/SPM/NXpiezo_config_spm.yaml index f13dab1d7..78dd861a6 100644 --- a/contributed_definitions/nyaml/SPM/NXpiezo_config_spm.yaml +++ b/contributed_definitions/nyaml/SPM/NXpiezo_config_spm.yaml @@ -1,9 +1,10 @@ category: base doc: | - A base class describing piezo settings for scanning probe microscopy. + A base class describing piezo actuator settings for scanning probe microscopy. - The piezoelectric material of SPM actuators gets deformed due to the applied electric field. - Description below shows calibration coefficients and other configuration parameters of the piezo actuators. + Piezoelectric actuators work utilizing the inverse-piezoelectric effect, when a voltage + is applied on the material and it deforms proportional to the applied voltage. + Description below shows calibration coefficients and other configuration parameters of open loop piezo actuators (that is actuators without capacitive sensor feedback systems). # Discussion: No need to create this base class rather we can define in spm application definition. type: group @@ -64,6 +65,9 @@ NXpiezo_config_spm(NXobject): with units: "[V] = [V/m] · [m] + [V/m2] · [m2]" where cx is the calibration of the piezo X and cxx is the 2nd order correction. The unit for such the second-order correction is (V/m^2). + drift_correction_status(NX_BOOLEAN): + doc: | + The drift correction status (true / false) in calibration step of piezo. drift_N(NX_NUMBER): unit: NX_ANY doc: | @@ -72,7 +76,7 @@ NXpiezo_config_spm(NXobject): move at that speed. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 983ecbb63ca89b8133a7b671fba009b74498d7745d5b569592931cb2df75b49e +# 96e710da01fe879d6ab92e5a15bf41b9f916f75e23b1d254f36999406f0afa60 # # # # # -# A base class describing piezo settings for scanning probe microscopy. +# A base class describing piezo actuator settings for scanning probe microscopy. # -# The piezoelectric material of SPM actuators gets deformed due to the applied electric field. -# Description below shows calibration coefficients and other configuration parameters of the piezo actuators. +# Piezoelectric actuators work utilizing the inverse-piezoelectric effect, when a voltage +# is applied on the material and it deforms proportional to the applied voltage. +# Description below shows calibration coefficients and other configuration parameters of open loop piezo actuators (that is actuators without capacitive sensor feedback systems). # # # @@ -181,6 +186,11 @@ NXpiezo_config_spm(NXobject): # such the second-order correction is (V/m^2). # # +# +# +# The drift correction status (true / false) in calibration step of piezo. +# +# # # # The N (substring) denotes X, Y and Z directions. Define the diff --git a/contributed_definitions/nyaml/SPM/NXpiezoelectric_material.yaml b/contributed_definitions/nyaml/SPM/NXpiezoelectric_material.yaml index 7dc433a5b..0960a4033 100644 --- a/contributed_definitions/nyaml/SPM/NXpiezoelectric_material.yaml +++ b/contributed_definitions/nyaml/SPM/NXpiezoelectric_material.yaml @@ -14,6 +14,12 @@ NXpiezoelectric_material(NXobject): doc: | The name of the material of the piezo scanner such as Lead Zirconate Titanates (PZTs). + piezo_material_identifier(NXidentifier): + doc: | + The identifier of the piezo material. + identifier(NX_CHAR): + doc: | + The identifier of the piezo material. chemical_description(NXsubstance): doc: | The chemical formula of the material of the piezo scanner such as Pb(Zr,Ti)O3. @@ -75,7 +81,7 @@ NXpiezoelectric_material(NXobject): viscous state. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 39d5862b3a9e4f526a71d3a1ad2234a4f4de5b953ce08c21e47f8bd7a9670ed7 +# 0f228771942f8ad9c37ecfbdd4dc96d0193a3da548a401a92aec2d436caf26c6 # # #