Nanonis STM Simulator Tutorial - SPM Controller - … · be used to change the configuration...

Nanonis STM Simulator Tutorial

Software Version 4

Manual Version 4.0

NANONIS | STM Simulator | 2

Contents Introduction ............................................................................................................................................................................... 4

Minimum System Requirements and Installation ..................................................................................................... 5

Getting Started .......................................................................................................................................................................... 6

Session Directories ............................................................................................................................................................. 6

Online Help ............................................................................................................................................................................ 6

System Startup ..................................................................................................................................................................... 6

Running the Z-Feedback .................................................................................................................................................. 7

Tip Home Position, TipLift™ ........................................................................................................................................... 8

Scan Control ............................................................................................................................................................................... 9

Setting the scan parameters ......................................................................................................................................... 10

Saving parameters with an Image ............................................................................................................................. 10

Global Counter............................................................................................................................................................... 11

Cross sectioning Scan Data ........................................................................................................................................... 12

Advanced Scan Options .................................................................................................................................................. 12

Changing the View of an Image ................................................................................................................................... 14

Using the Mouse ................................................................................................................................................................ 14

Choosing the Data to Display ....................................................................................................................................... 14

Online Image Processing ............................................................................................................................................... 14

Pasting Data into the Background ............................................................................................................................. 15

Changing the Color Scale ............................................................................................................................................... 15

Color Palettes ................................................................................................................................................................. 16

Saving an Image ................................................................................................................................................................. 16

Viewing Several Channels in Parallel ....................................................................................................................... 17

Quad-Scan Monitor – four Views in one Window ............................................................................................... 18

Line Monitor ....................................................................................................................................................................... 19

2D Plot Controls ................................................................................................................................................................ 19

Bias Module ......................................................................................................................................................................... 21

Understanding the Feedback Loop ................................................................................................................................ 23

Purpose of feedback ........................................................................................................................................................ 23

Working Principle............................................................................................................................................................. 23

Bandwidth Considerations ........................................................................................................................................... 24


Signal Oversampling ........................................................................................................................................................ 27

Spectroscopy ........................................................................................................................................................................... 28

Bias Spectroscopy ............................................................................................................................................................. 28

Z Spectroscopy ................................................................................................................................................................... 31

Spectroscopy Locations ................................................................................................................................................. 31

Grid .................................................................................................................................................................................... 32

Line .................................................................................................................................................................................... 33

Cloud ................................................................................................................................................................................. 33

Coarse Approach .................................................................................................................................................................... 35

Automatic approach ........................................................................................................................................................ 35

Advanced automatic approach parameters ........................................................................................................... 36

Displaying Data in Graphs .................................................................................................................................................. 37

Time domain display ....................................................................................................................................................... 37

Frequency domain display ............................................................................................................................................ 39

Long Term Spectrum ....................................................................................................................................................... 40

Sample tilt correction .......................................................................................................................................................... 41

Thermal Drift ........................................................................................................................................................................... 43

Drift Compensation .......................................................................................................................................................... 43

Atom Tracking.................................................................................................................................................................... 43

Contact AFM ............................................................................................................................................................................. 45

Defining a new Z Controller.......................................................................................................................................... 45

Detector calibration using Force Distance curves .............................................................................................. 46

Detector calibration using lockin module .............................................................................................................. 48

Atomic Manipulation ............................................................................................................................................................ 50

Diagnostics and Analysis .................................................................................................................................................... 52

TCP Receiver ....................................................................................................................................................................... 52

Diving deeper .......................................................................................................................................................................... 54


Introduction Thank you for downloading the SPM Simulator package from Nanonis. This program has many

powerful features that provide benefits in a variety of situations.

It can be used to learn about the capabilities of the Nanonis controller before one is

purchased.

It can also be used to teach other people how to use the software without the presence of

the hardware. This can be particularly useful as a presentation tool in a group meeting or

anytime you are separated from the hardware.

A third application is as a general purpose SPM teaching tool. Because of the accuracy and

depth of the simulated microscope backend, fundamental principles such as feedback

optimization, important operating parameters, and data acquisition modes can be learned

when first starting out in the field of SPM.

Lastly, existing Nanonis customers find the simulator an invaluable tool to debug and

troubleshoot LabVIEW development using the programming interface because it does not

tie up the PC used to operate the microscope but still provides the full capabilities of the

environment to make sure the new program works as intended before it is placed into

service on the main PC.

The document is not meant as an introduction into scanning tunneling microscope, the reader is

expected to be already familiar with the basic working principle of an STM.


Minimum System Requirements and Installation Please make sure your computer meets the following requirements:

Windows XP/Vista or Windows 2000 operating system.

Minimum of 1 GB RAM

Minimum of 1.5 GHz processor

Screen resolution of at least 1280x1024 pixels is recommended. With a lower resolution

some windows will be partly hidden and you will not be able to use them.

In the case that your computer does not fulfill these requirements, you might experience sluggish

behavior.

The installer is a regular Windows Installer, available at http://sim.nanonis.com. The installer will

guide you through the installation procedure. If you have a previous version of the Demo software

installed, the installer will uninstall that version first.

http://sim.nanonis.com/


Getting Started The first time the program is started a message may appear warning you a program is trying to

access a port blocked via a firewall. This port must be unblocked in order for the main program to

communicate with the background process that is simulating the actual Nanonis hardware. This

communication is through the internal loopback device present in all network protocol

implementations. No external communication outside of the computer takes place. When operating

host PC and the Nanonis standard controller connected via a network cable. Once communication is

established, you will next be asked to accept the license agreement. Click the Accept button to then

launch the main program.

Session Directories A dialog will appear asking to define a session

directory. The concept of sessions can be very

powerful in a multi-user or multi-microscope

situation. Sessions allow the isolation of experimental

conditions, screen layouts, microscope calibration

factors, etc. to be easily organized. A great example is

a low temperature microscope that has different piezo

calibrations at room temperature and low

temperature. Instead of entering the new piezo factors when the temperature changes, everything

can be updated by simply saving one session file and opening a different one. To get started in the

tutorial, browse into a specific directory and then click the Choose Curr Directory button in the

window to place all session information in this folder.

Online Help There is a great deal of online help available throughout the program. Almost every button and

entry box has a tip strip associated with it. By leaving the mouse cursor over the item, a small box

appears with a short text description of the item. Context help is available within each window by

pressing F1. A separate window will open with a detailed discussion about every item contained

within a particular window.

System Startup When the program is launched, the main window will appear as shown in Figure 1. To get started

with the program the most important modules to open are under the Modules menu. Three to open

right away are Z Controller, Bias, and Scan Control.

Figure 1: Main Window

A Nanonis Session enables you to

have measurement data and the

corresponding configuration

parameters in one single place.


Running the Z-Feedback The next window to introduce is the Z Controller window shown in Figure 2. This is used to control

the feedback bandwidth, control the working setpoint, monitor the instantaneous z piezo position,

and configure the SafeTip feature. When the program is started, the feedback loop is deactivated

and the tip is held fully retracted. To start with a known set of working parameters, choose

File/Load Program Defaults. The setpoint, proportional gain, and integral response are all set to

values that are known to work for stable control of the simulated microscope.

Figure 2: Z-Controller window.

Once the parameters are set, the tip can be engaged. Since the simulator is built to behave like the

tip is just above the surface, there is no need for a coarse approach to occur. The steps required to

configure coarse approach will be covered later. For now, simply click the large engage button on

the right side of the window. The red pointer on the

scale moves downward as the tip is ramped towards

the surface. It will reach feedback around zero. The

current will change from almost zero to the requested

setpoint value and then be reasonably steady. At this

point the tip height is actively controlled by the

feedback loop. The digital readout of the z position

will start to fluctuate and you may also see small

motion of the blue indicator. Similar to the other

controls, the dynamic range of the z scale can be

changed to cover a small part of the full z piezo range

for sensitivity or it can be left at the default scale

where the entire z range is displayed.

The digital feedback loop of the system has

proportional (P) and integral (I) gain. The speed of the loop response to a deviation from the

setpoint is determined by the combination of the P and I factors. The larger the P value the faster

the loop will respond. For integral gain the units can be time constant or the inverse of the time

constant. If you feel more comfortable working in the units of a time constant flip the toggle switch

Things you can do with a digital

feedback: stop the feedback

instantaneously, keep the tip at

a constant height without

droop, lift the tip by an exactly

defined amount, withdraw

without delay in case a signal

reaches a certain threshold or

control on combinations of

signals.


on the left side of the integral control. Similar to the other controls in the program, the range of the

P and I gain can be changed using the arrow buttons at the end of the scale. Use this to either

increase the sensitivity so small changes are possible or to provide more dynamic range for large

adjustments. More details about the feedback system will be presented later. For now, the default

values of the simulator will provide reasonable imaging performance.

Any time while the loop is active or inactive, the Setpoint can be changed using the appropriate

control. It has both a slider control and number entry box available. In the slider control is a yellow

bar graph that fills to indicate the instantaneous value of the current. The scale of the bar graph is

logarithmic so be sure to properly interpret the graph. The range of the bar graph is controlled

using the set of buttons above the indicator. The + and – buttons decrease and increase the range of

the bar graph limits, the fs buttons automatically changes the scale to range from 0 to the maximum

current (when using an STM feedback signal) as determined by the preamplifier gain. The 0 button

places 0 in the middle of the range and the C button places the measured value when the button is

pressed in the center of the range.

Tip Home Position, TipLift™ Another important term to understand is the concept of the Home position for the tip. To park the

tip at a fixed position and have the digital feedback loop then hold it there, define the location using

the Home Position setting and then click the Home button. Keep in mind the defined position is on

an absolute scale. To hold the tip a specific height over the surface it is preferable to use the Tip Lift

feature instead of the Home button. For example, if the z position is +50 nm and you want to hold

the tip 8 Angstrom away from its current position, the Home Position should be defined as 49.2 nm.

If the current z position drifts to 20 nm, the Home Position would have to be redefined to be 19.2

nm. It is far easier to define the Tip Lift distance to be 8 Angstrom and for any position, the tip will

be pulled back that distance from the present position when the loop is disabled. With the

simulated STM, the current will drop to zero if the tip is pulled back more than a few Angstroms

from its tunneling position.


Scan Control Once tunneling has been achieved, a scan can be started and images will be obtained. The image

configuration is contained in the Scan Control window shown in Figure 3.

There are three main groups of controls in the window. The Scan, Follow Me, and Grid buttons can

be used to change the configuration display on the left side of the window. Note these can be

changed while acquisition or other function is taking place without interrupting the current mode.

This provides a chance to make changes to various sets of parameters in anticipation of the current

operation completing and starting the next operation right away instead of waiting to configure it

and then starting.

Figure 3: Scan Control, all the activity that involve moving the tip like scanning, spectroscopy or manipulation are done from within this module.

The most commonly used group is the Scan set of tabs. They will be used for image acquisition and

scanning. The first step should be to activate the imaging channels to be acquired at each pixel

location. The list is contained in the Scan tab. Click on the name of each channel to highlight it for

activation. To acquire multiple channels during the scan, hold the Ctrl key and click on each channel

to highlight it. By default the Topography (Z(m)) and Current channels are active. The pixel density

is also configured in the same area of the tab. By clicking the link control next to the window, the

Pixels and Lines can be forced to always equal each other for ease of configuration (only one needs


to be changed), but they can also be made independent to have a different number of pixels and

lines if desired.

To begin a scan, click the button with the downward facing arrow. This will commence a scan from

the top of the frame towards the

bottom. The image will appear on a

line by line basis and a two

dimensional image will be built up

as shown in Figure 4.

Setting the scan parameters The position and size of the scan

frame is set in the top of the tab.

Values can be entered directly here

or the mouse can be used to

determine the size as described

below and when that is done, these

values will be updated to show the

new settings. Next to the Size

parameters is a control that can be set to lock the X and Y axis to be equal at all times (scanned

region will be a square) or unlocked so the region will be

rectangular in shape. The speed of the tip as it scans over the

surface is determined by the parameters in the Speed section.

The time required for one line can be fixed (Time/line) which

means the actual velocity of the tip over the surface will change

as the scan size is changed. Alternatively, the tip velocity can be

fixed which means the time required for each scan line will

vary as the scan frame size is changed. Click on the lock icon to

toggle which parameter is fixed and which one varies. Note

that either parameter can be changed to change the acquisition

speed, the lock merely determines which is fixed as the frame

is changed. As any of the parameters that effect the total time

to acquire one frame are changed, the Time/frame is updated

to reflect the amount of time that each image will require. Also,

on the right side of the window is a countdown timer that

displays the amount of time left to complete the currently

acquired image.

Saving parameters with an Image To automatically form the name of a file as data is saved, the

Save tab (Figure 5) should be configured next. The Basename is

the text string that every fill will begin with. The Image number

is then the value incremented for each file as it is saved to

insure the files are uniquely named and also sequentially numbered for easy browsing later.

Figure 5: Save tab in the Scan Control window. Choose a basename for automatic filename generation, add a comment to each file, and choose the parameters to save in each file header

Figure 4: The image starts to appear as each linescan is acquired


There is now a long list of special codes that can be entered as part of the basename to help

uniquely identify files and provide more functionality in the naming convention. Special codes that

can be entered are the following

%a abbreviated weekday name

%b abbreviated month

name

%c locale-specific date

and time

%d day of month

%H hour of current time

(in 24 hour format)

%I hour of current time

(in 12 hour format)

%m month number

%M minute of current

time

%p am/pm designation

%S second of current time

%x locale-specific date

%X locale-specific time

%y last two digits of year

%Y four digits of year

So, using the code %Y-%m-%d would produce something like 2008-09-05 and %H%M%S would

produce something like 022405 (somebody is

working late in the lab).

Global Counter

The code %N translates into a number which is

given by a global counter. The counter can be set

and reset in the Options window available from

the main window menu. The global counter will

increase by 1 every time it is accessed. For

example, if you want to sort your files in the order

Figure 6: Use the analyze tab to measure features in the image while data is still being acquired

With the global counter you can

generate filenames that can

easily be sorted chronologically

without relying on the time

stamp to be handled correctly by

the operating system.


you acquired them, you could name them %N-ScanData, %N-BiasSpec and %N-ZSpec, which would

generate a list of file with a running counter for all three file types.

Cross sectioning Scan Data The third tab present when the Scan grouping is active is the new Analyze tab (Figure 6). This can

be used to take cross sections and

also measure distances and

angles on the surface while

acquisition continues. There is no

longer a need to wait for an

image to be finished and saved in

order to open it in a separate

module that has measurement

tools. When the Analyze tab is

selected a line appears on the

image. Click on either endpoint to

drag it to a new location. As the

line gets longer or shorter the total length of it is displayed in the information window. This can be

used as a ruler to measure features in the image. By grabbing in the middle of the line with the

mouse, the line can be shifted laterally while maintaining its length and angle orientation. To view a

cross section of the data covered by the line, click the Cross Section button and a separate graph

window will open to display the data (Figure 7). As the line is then moved around the plot will

update in real time. To determine the angle between two crystallographic axes on the surface, the

angle button should be clicked. This adds a dashed line to the image area. Both of them can be

moved around and the display will show the length of each one as well as the angle between them.

Advanced Scan Options Less frequently changed parameters related to scanning are contained in the Options window

(Figure 8) opened from the Tools dropdown menu. Scanning can always be in the same slow

direction (from the top each time or from the bottom each time) or it can alternate between

scanning from top to bottom and then bottom to top.

This will save the time required to return to the origin

each time and also remove piezo creep from the image

resulting from the quick motion back to the origin. To

activate this mode, check the Bounce Scan box so the

tip “bounces” off the bottom of the frame when it is

reached. When the Stop button is pressed and

scanning stops, the tip can be moved to a fixed

location every time for consistency. To use this, check

the Custom end of scan position box and enter the

percentage of full piezo range to place the tip. Values

of 0,0 would place the high voltage outputs to zero

and center the tip in the middle of the scanable area. If

Figure 7: Cross section of data extracted from the Scan Control window

Under Advanced Scan Options

you find many things like where

the tip should stay at the end of

a scan, whether the last image

should be pasted automatically

in the background, or if the

forward and backward speed of

a scan should be the same or

different.


the box is not checked, the tip motion is halted immediately and the tip remains fixed at the

position when the scan is stopped until moved again. The tip position can always be determined by

locating the blue dot in the viewing area.

Other options in this window are

used to determine the image

painting of the data when various

processes occur. Since the data will

appear in the window, the

preceding data can be erased when

moving or rotating the frame to

avoid confusion. If the frame is

moved partway through an image a

split will be evident since the frame

will shift over the surface thereby

producing an offset of the features.

There are times where this is

helpful to see but other instances

where it will create confusion.

Turn the feature on or off using

this checkbox. It is also possible to

choose to have the frame erased

when the next frame starts. This

can be activated by checking the box labeled starting a new scan. The data can also be pasted into

the viewing area to compare to future images or also to be used as a navigational aid as the frame is

zoomed and moved over the surface. To automatically paste the last image into the area choose the

condition with the next set of boxes. The final parameter related to scanning in this window is the

Backward linear speed. By default the reverse scan takes the same amount of time as the forward

scan. This can be changed to be faster or slower using the ratio parameter or entering a fixed speed

with the Custom box. This can be helpful to speed up total acquisition if the image in one direction is

sufficient and the tip can be rapidly returned to start the next line. Be careful about maintaining

feedback control of the tip height when using a fast return speed though.

When the end of the frame is reached, the next scan

will start if the adjacent Continuous Scan button is

activated. This scan will either proceed in the same

direction as the previous one or reverse the slow scan

direction depending on the status of the Bounce Scan

check box discussed above. The next button in the row

can be used to pause the scan and hold the tip at the

position when the button was pressed. Any number of

functions can then be performed exactly at that spot

(voltage pulse, spectroscopy, external equipment acquisition, etc.) and when finished the button

can be released and the image acquisition will continue. The next button will halt the slow scan

Figure 8: Less frequently used parameters are contained in the Options window accessed from the tools menu

While a scan is paused, you can

use follow me to move the tip to

a new position, do spectroscope

there and then resume the scan

from where you paused.


increment and continue to raster the tip back and forth at the same line position. This can be very

handy to alter other conditions and check the response to the change using the line scan monitor

window. The final button stops the scan.

Changing the View of an Image Above the image viewing area in the right corner are a set of buttons used to change the view of the

image. The paradigm used in this control is a camera floating over the image area which can be

panned, zoomed, and rotated. The mouse icon changes as a visual reminder of what camera

parameter will be changed. To pan (shift laterally) the view, click the hand icon. Choosing the next

magnifying glass icon allows the zoom factor of the view to be altered using the scroll wheel of the

mouse. The next two icons zoom in our out a fixed amount each time one of them is clicked. The

next icon adjusts the view so the current scan frame exactly fills the window. Keep in mind if the

frame is rotated with respect to the normal X and Y axes, the camera angle will be rotated to match

the frame axes so it will no longer look rotated, but the actual scan will still be occurring at the

designated angle. Any image can be pasted into the background of the area to be preserved as a

navigational aid. The details of pasting an image will be covered below. The next button in the row

adjusts the view to exactly coincide with the presently pasted image. The final button goes to a full

scale view equal to the maximum reachable area given the current piezo calibration factors.

Using the Mouse The row of buttons on the left side above the viewing

area are used to adjust the scan frame parameters

using the mouse instead of entering numbers in the

entry boxes. When the button on the left side is picked,

the scan frame can be grabbed and shifted laterally.

This physically moves the frame to a different part of

the surface. Clicking the next button will allow the

operator to rotate the frame using the mouse. The next button can be used to grab the corner of the

frame and resize it to scan over a larger/smaller portion of the surface. The final button is used to

also change the size, but in this case the center of the frame remains fixed and the image size

increases or decreases symmetrically about the center of the current frame. When right-clicking the

mouse before depressing the left button, any action is canceled. The mouse wheel zooms in and out

in the viewer. The size of the scan frame of course stays constant.

Choosing the Data to Display On the right side of the window is the Scan Display section. This is used to determine what data

channel is displayed in the area, which direction to display, what processing to apply to the data

before showing it, and the controls to paste and image into the window. If more than one channel is

acquired, all available image channels are displayed in a list when clicking the Channel control.

Directly below that is a toggle switch to determine if the forward or reverse image is displayed.

Online Image Processing The data can also be processed before being displayed to remove any slope or offsets due to tip

changes. Since the color map continuously adjusts to always span the largest and smallest values,

The mouse wheel works in the

scan control window to zoom in

and out!


contrast might be lost if the data spreads over a large range due to artificial reasons. The

preprocessing steps that can be applied are Subtract Average, Subtract Slope, Subtract Average and

Slope, and Differentiate. The first choice will set the average value of each line scan to zero. This is

very helpful to remove offset of scan lines due to tip changes or slow thermal drift in the

microscope. Subtract Slope will fit the best line to each individual line scan and then subtract this

from the data and display the result. This is most useful to remove slope along the fast scan

direction and allow the color scale to be used over the small variations on the surface instead of the

larger range covered by the slope. Subtract Average and Slope removes the slope of each line and

also sets the average value to zero for each line. Differentiate will calculate the derivative of the line

scan and display the result. This can be useful to accentuate small changes in the data which might

be relevant in determining if the experiment is working as expected. The finals set of controls will

place an image into the window.

Pasting Data into the Background Pressing the stamp icon copies the currently acquired

data frame into the window which will remain visible

as subsequent frames are acquired. This provides a

very convenient way to leave a large area view of the

surface on the screen while zooming and moving

around to concentrate on specific features of the

surface. To have a complete image pasted into the

window, click the Next button. It will change color to

highlight that the current frame will be pasted into the window when it is completed. Pressing the

All toggle button will paste every frame into the window upon completion and erase the previous

one.

Changing the Color Scale The color scale and appearance of the image can be changed using the controls in the Color Scale

section of the window. The sliders can be moved to determine the physical value that corresponds

to the highest color and the lowest color. Try manually adjusting their position and note their effect

on the data. The small buttons next to the sliders determine the total range of the scale that the

sliders can be set to. For example if the data values exceed the upper end of the scale, the upper

slider will not be able to reach the value so all data above the slider position will be the same color.

The scale should be reduced to access larger physical values to remove the color saturation. This is

achieved using the minus button. Once the scale is changed, adjust the sliders to better use all of the

colors over the entire data range. If the scale is large and the data range is very small, there will be

poor control when trying to make adjustments. Use the plus button to zoom the scale so the sliders

can be accurately adjusted over a small range of

values to an appealing appearance of the image.

To automatically have the slider range adjust to

the maximum and minimum physical values

currently displayed, use the as button. To have

the slider range be set to the absolute maximum

You can automatically paste

every scan in the background by

pressing the All button next to

the stamp icon

The color scale as well as the

color palette can be changed

even while scanning.


and minimum values (+/- 10 V for example) use the fs button. To set the center of the slider range

to the center of the physical values, press the C button. To pick a new color palette for the image

click the Palette control and select a new one from the list.

Color Palettes

Color Palettes can be added or

changed using the palette control

window accessed from the

Tools/Options menu. The tool used

to define and create palettes is

shown in Figure 9. The buttons

along the bottom can be used to

add new palettes, clone an existing

palette as a starting point, delete a

palette, or save a redefined palette

into the settings file. The small

markers next to the color scale can

be dragged to change the mapping

and linearity of the map. New ones

can be added by right clicking

when over the scale and choosing

New Marker. Right click when the

cursor is over a marker and choose

Marker color to redefine the color at this position.

Saving an Image To permanently save a set of images, use the save buttons at the top of the window. The main save

icon looks like a floppy disk. Pressing it will write the data to the file immediately, but keep in mind

this will be only a partial image. This can then be opened for analysis while the rest of the image

finishes which can be helpful in determining if an experiment is working properly without waiting

for the entire scan to finish which often can be a long time with slow scans. To save a complete

image when the scan completes, click the Next button which will change its appearance to indicate

the current frame will be written to a file when the scan

reaches the end. To save all images after each frame

completes, depress the All button. When combined with

the autonaming scheme configured in the Save tab, each

file will be written to the disk and will have a unique

name sequentially numbered.

Figure 9: With the color palette designer, new palettes can be created, stored and loaded.

Images can be saved individually

or automatically at the end of

every scan.


Viewing Several Channels in Parallel The Scan Control window is the main

navigational tool used to set the scan

parameters and view the data as it is acquired.

If more than one channel is acquired during

the scan the image to display in the control

window can be changed. This can be useful if

the acquisition conditions are such that an

important feature is visible in one channel but

not others. The relevant channel can be loaded

and the scan frame moved around relative to

this visible feature instead of driving blindly

and hoping to locate the frame in the correct

region. To change the displayed channel,

switch to the Display tab and pick the new

display channel from the Channels dropdown

list. All active data buffers will be present in

the list and after a new one is picked, the

image changes immediately to the new

channel.

Viewing more than one data channel during

acquisition is a simple task. Additional

windows can be opened to view other

channels, but these are view only and cannot

be used for navigation. It is usually a good idea

to open the images of a channel formed by both scan directions to check for reproducibility and that

no scan artifacts are present. At the top of the Scan Control window is the Tools menu which can be

used to open multiple image window. These are called Scan Monitor A and Scan Monitor B. An

example is shown in Figure 10. Note the window looks similar to the Scan Control window with the

color mapping tools. There are controls to change the active color map as well as the auxiliary

colors for text, labels, etc. Once a window is opened the displayed channel can be changed using the

dropdown menu similar to the Scan Control window. The same processing can also be applied to

each line scan before display just like the scan control window. Images can also be pasted into these

windows for storage and comparison to later scans using the Paste button as described above for

the Scan Control window.

Along the top of the viewing area the name of the

channel and the total range of the data currently are

displayed. This information can be turned on and off

using the check boxes in the upper right corner. The

bottom part of the viewing area also contains a scale

bar to be used for estimating feature sizes as they

Figure 10: The scan monitor lets you view a second data channel, independent of what is display in the scan control window.

You can fix the camera of the

scan monitor to the main camera

or the scan frame.


appear in an image.

The color mapping of the data is automatically adjusted after each line of data is displayed in the

image. Occasionally, a glitch or excessive noise will skew the color mapping and it will not be

optimal. The high and low color values can be manually adjusted for a better image appearance

using the controls. The data values that correspond to color 0 and color 256 are shown in the top of

the window. A slider is also presented that contains a green bar to represent the range of the data.

The two small red controls can be used to adjust the physical value of color zero and color 256. If

the color map is automatically adjusted, the sliders will be at the end of the green bar as shown in

the figure. Similar to other parts of the program, there are a set of buttons to control the range of

the displayed data values. Use this to gain finer control of the slider limits or to allow the sliders to

be adjusted over a very large range of values.

Quad-Scan Monitor – four Views in one Window One additional window that can be opened to view multiple data channels is the Quad Scan Monitor

which is also accessed from the

Tools menu. This window has four

small panels which can be

individually configured to show

other channels or the same data

channel but with a different color

map or processing applied. An

example with the forward and

reverse Current channel and

forward and reverse Topography

channel is shown Figure 11. Each

panel has its own set of controls.

To change the settings for any

pane, click on it so the border is

highlighted in red and then use the

three tabs at the top of the window

to change the settings and colors

for this pane. Each pane can also

have an image pasted into the

background similar to the monitor

windows.

One camera angle is applied to all

four panes. Use the controls on the

right side of the window to change

this view point for all panes

simultaneously. Figure 11: The Quad Scan Monitor is particularly useful in NC AFM to view Topography, Amplitude, Phase, and Dissipation all at once


Line Monitor Once the scan is set up, it may also

be useful to open a graph window to

display each line scan as it is

acquired. This is accomplished by

choosing Line Monitor A from the

Tools menu in the Scan Control

window. A window as shown in

Figure 12 will appear. Up to four sets

of line scans can be shown in the

window. It is very helpful to display

the last 1, 2, 3, or 4 line scan on the

same graph to compare their

appearance as the feedback loop

parameters are adjusted. Features

may appear sharper or more

rounded and noise may appear or

disappear. This information is very

valuable in deciding the optimal

feedback settings. Each line scan is

offset along the y axis by the amount

selected in the lower left corner. The

closer together they are, the smaller the total y range so features can be seen easier.

However, confusion can occur if the line scans overlap. Do not offset the lines by a large amount in

an attempt to avoid overlap as this will create a y scale with such a large dynamic range that the

plots will appear almost flat and little structure will be visible. Notice there is a small triangle

symbol in the upper left corner of the entry box. Whenever this symbol is present, right clicking on

the box will open a quick access menu to change the value by a fixed percentage instead of absolute

numerical values. Often this is a quicker and easier adjustment to make rather than entering

numbers.

2D Plot Controls The forward or backward scan display can be turned off by unchecking the box in the lower right

corner next to the line. Next to each direction name is a small icon showing the currently selected

color and background. Click this icon for a menu which allows a great deal of configurability for the

graph window. The graph style can be changed from the Common Plots menu. The plot can be lines

only, data points only, points and lines combined, bar graphs, etc. Experiment with different plot

styles for each type of data plot as some can provide

more insight into the data compared to other styles.

The color is changed in the next menu item, and the

third one on the list is used to select the line type when

a line plot is used. The line thickness can also be

Figure 12: Successive scan lines displayed in the Line Monitor while the tip moves over a step edge

The controls for graphs and plots

are taken right from LabVIEW.


changed for each plot and the graphs can also be displayed using smoother lines by choosing the

anti-aliased option. Note this effects display of the screen resolution pixels only and is not the same

as processing of the actual data points to change the underlying data. For bar plots, a variety of

choices exist to determine how the bars are drawn. If a bar plot is chosen, the baseline of the bars is

determined by the next setting called Fill Base Line. The Interpolation option is used to decide how

the actual data points are connected with a line. Direct segments, right angle segments, right angle

segments with the real data in the center are all choices under this menu. When the data points are

displayed, the symbol for the points is chosen from the point style menu item. Finally, the axis title

for the x and y axes can be turned on or off using the last items.

Along the top of the plot window is a control used to choose what active channels are displayed in

the window as well as the processing to apply to each

line plot before it is graphed. On the right side at the

top of the window are a set of buttons used to change

the x and y axes. The number of significant digits, the

display units, and the choice of logarithmic and linear

axis can be made using these buttons. The color of the

plot grid can also be changed using these buttons.

There are a set of buttons for each axis. If the first button in the group shows a closed lock, the other

controls are disabled and cannot be changed. To manually adjust the axis first click the icon to open

the lock and then make any changes desired. To prevent accidental changing of the display, the lock

can be clicked again to close it and prevent additional changes.

Along the left side of the screen is a collection of buttons known as QuickScale which can be used to

make changes to the range of the axis. Clicking the fs (full scale) button makes the plot

automatically scale from the minimum physical value to the maximum physical value. Using the as

(auto scale) button scales the range to fit the currently displayed plot in the window. The + and –

buttons can be used to increase or decrease the dynamic range of the axis for each button click. The

lower set of buttons adjust the DC offset of the plot. It can shift the plots within the window up or

down each time the arrow buttons are clicked or

the 0 button can set the center of the axis to zero.

The C button is used to set the average value of

the currently displayed data to be the center of

the y axis.

You can edit the number of digits

displayed at an axis as well as the

display format of the numbers.

QuickScale buttons are an easy

way to adjust the axes of a plot.


Bias Module The bias module is used to set the tunneling bias. This can be done by typing a value in the display

window or using the slider. The parameter entry window can have values entered in multiple ways.

The cursor can be placed in any digit location and new

values typed. Alternatively, the cursor can be placed in

any digit location and the up and down arrow keys on the

keyboard can be pressed to increase/decrease the value of

that number. Normally, it is the digit to the left of the

cursor that is changed. Be careful when the cursor is next

to the left-most digit. As the number changes and a new

place value digit is added or one is taken away (think

about what happens when the up key is pressed when

the current value is 9 or the down button is pressed when the digit is 0), the amount the number

changes for each key press may change.

The slider control has many extra tools that can help its usefulness. On each end of the slider is an

arrow button. This can be used to increase or decrease the endpoints of the slider range which can

help with fine control of the bias output if the slider is

used instead of trying to enter values directly. There

are a series of buttons above the slider that can also be

used to help set the slider endpoints. The 0 button is

used to set the center of the slider range to zero. The C

button is used to set the center of the slider range to

the current value of the bias. In effect, a DC offset is

added to the slider range. The + button will decrease

the range of the slider (zoom in) and the – button will increase the range of the control (zoom out).

After making changes to the slider control, the fs button can be used to return the range to its full

maximum/minimum value. In the case of the bias this would be +/- 10 V by default.

The Tools menu can expand the window to include two extra sections. One is used to change the

calibration of the bias output DAC. For example, if a voltage divider is installed between the bias

output and the sample which attenuates the bias output, the attenuation factor can be entered here

so the software can adjust for this. If the output is divided by ten so 1 V out is actually a 100 mV tip-

sample bias, the user would have to mentally take this into account when setting this bias. It is far

easier to enter the 0.1 adjustment factor and the values entered in the software can be the real

tunneling bias. If the bias output DAC is not used to control a tip-sample bias and instead controls

some other signal, the units can be changed to reflect the new meaning of the Bias DAC.

Many times a good way to improve the performance of the tip is to apply a high voltage bias pulse

of a short duration. To perform this, the window can be expanded to open the pulse control section.

A duration, peak value, and feedback on/off control are included. After setting the values to the

desired amount, press the Pulse button to immediately produce a single pulse from the Bias DAC.

After the pulse is done, the bias returns to its nominal tunneling value.

Figure 13: The bias pulse and calibration is hidden and can be accessed through the tools menu.

You can change the calibration

of the bias to reflect an external

divider which you might have put

in the signal path.


One point to note is the simulated microscope image does not accurately reflect the bias behavior of

the real Si(111) surface. The image does not switch between the filled and empty state views when

the bias polarity is reversed.


Understanding the Feedback Loop Once the image display and line scan graph are opened and configured, a deeper investigation of

imaging techniques can be explored. The simulator provides a nearly ideal platform for learning

basic SPM principles because complicated interactions due to poorly formed tips or sample

preparation techniques are eliminated. When the image quality changes, it is due to fundamental

control issues and not uncontrollable changes in the tip or sample surface.

Purpose of feedback The prime determining factor of the image quality is the feedback loop. The purpose of the loop is

to maintain a constant feedback signal. This is done by moving the tip up or down to control the

tunneling gap width in STM, the cantilever deflection in contact AFM, or the tip-sample separation

in non-contact AFM. An STM traces out contours of constant density of electronic states which in

the most basic approximation is equal to the surface. Because of the sharp tip in an STM, these

contours can be localized to the orbitals of each atomic site which gives rise to its incredible

resolution.

Working Principle The feedback loop is always working in the background whether the tip is stationary or scanning. It

measures the feedback signal (current in this case) and compares the value to the predetermined

setpoint. If the current is not equal, an error signal (current – setpoint) is calculated. If the current

is larger than the setpoint, the tip is too close and needs to be pulled away from the surface. If the

current is less than the setpoint, the tip is too far away

and needs to be pushed towards the surface. The tip is

moved by changing the voltage applied to the z piezo.

When the tip is stationary over the surface, once it is

adjusted to the correct height in an ideal world it would

not need to be moved again because the position would

then be fixed. However, there are many factors

conspiring to move the tip and sample relative to each other. The various parts of the microscope

may have small temperature fluctuations and this will cause them to thermally expand and contract

which will produce relative motion. The ambient vibrations in the environment will be oscillating

the tip back and forth with respect to the sample which will produce fluctuations in the current as

the gap distance oscillates. The electronics of the system will have a noise level both in the current

conversion circuit and the high voltage amplifier circuit driving the z piezo. This noise will also

create small fluctuations in the input signal. Therefore, the feedback loop has to constantly be

watching the input current and making small adjustments to the tip height to maintain a constant

input signal.

The key factor in the feedback loop's ability to maintain a constant input signal is the system

bandwidth. The faster the system can respond to changes, the more “up to date” the control voltage

will be kept and the closer the input signal will remain when compared to the setpoint. However,

there is an upper limit to the bandwidth and once that is exceeded the system will cross a

resonance and become unstable. The simulator will also be able to demonstrate this concept.

No instrument is ever this perfect

and the simulator can even

demonstrate this.


Bandwidth Considerations The loop bandwidth is determined by the P and I settings of the feedback loop. A higher P leads to

faster response and a slower Time Constant will slow the response down. The I factor can be

entered as time by flipping the toggle switch next to the I control to the down position so the units

of the I factor is seconds. This means there are two factors to control the bandwidth and learning

how to fine tune both of them will take some time. Both can be used to achieve roughly the same

effect as demonstrated in Figure 14. In the left line scan plot, the P gain was increased during the

scan to change from stable feedback to oscillation. Since the graph shows the last three pairs of scan

lines, the older ones show nice control and the atomically resolved lattice. The most recent ones

show a large, unstable oscillation. On the right side of the figure, the Time Constant was decreased

until the loop started to oscillate which results in the same appearance in the line scans. Try to vary

the factors to cause oscillations or stabilize the loop and see how much each needs changed to have

an effect on the image.

Figure 14: Line Monitor showing how the feedback changes from stable to unstable due to a change in the proportional gain (left) or integral time constant (right).

At the other end of the possible operating conditions is having a loop response that is too slow. In

this case, the loop will not respond to deviations from the setpoint so the tip will glide over the

surface at approximately the same mean height. As it goes over features of various heights, the tip

sample junction will change which means the tunneling current will change. When this occurs,

features will be visible in the current image instead of the topography image. This condition is

sometimes referred to as constant height mode as opposed to the more conventional constant

current mode. Constant height mode does not need to be operated with the loop explicitly disabled.

As long as the loop response is slow enough to no longer follow the small surface variations, the

small scale surface features will then appear in the current image instead of the topography image.

A nice illustration of this mode is illustrated in Figure 15. During the scan the Time Constant was

increased dramatically so the loop cannot react as quickly. There is a very clear transition in the

behavior of the two data channels visible in the graphs. As the loop slows down, the atomic

resolution in the topography channel disappears and the newest line scans appear relatively

featureless except for the very deep corner holes in the lattice. As the corrugation disappears in the

topography channel, the variations visible in the current channel increase dramatically. In the


oldest line scan (top of the graph) the current is almost completely flat because the loop is doing an

excellent job of maintaining the input signal at the setpoint value. In the newest line scans (lower

plots) the current channel shows fluctuations of a few hundred picoamps.

Since the loop is always active, there is a final important factor that determines the accuracy of the

loop when following the surface. This is the scan speed. As the tip moves across the surface and the

loop adjusts the height, it is a good idea to give the loop enough time to update the z piezo voltage at

each position in order to be confident the surface is tracking correctly. As the scan speed is

increased, the loop bandwidth should be increased to maintain good surface reproduction. An

example of image quality suffering as the speed is changed without adjusting the loop bandwidth is

shown in Figure 16. The line time was changed from almost 700 ms/line to less than 100 ms/line

during the second line. The oldest line (top) still shows very nice topography with little variations i

n the current channel. The newest pair of lines shows a dramatic increase in the fluctuations on the

current channel which is interpreted as meaning the surface is not being followed as accurately and

the loop is no longer maintaining a constant current. The topography data still shows reasonably

good representation of the surface, but the data is not as high quality as when scanning slower. In

most real world cases there is some variation in the feedback channel. The idea is to minimize this

as best as possible so the topography channel can be interpreted as being acquired at a steady

feedback condition.

These three interrelated factors need to be considered at all times when trying to achieve nice

images that can also be interpreted properly. The interplay between them can be a bit complicated,

but mastery of it can be achieved with practice and patience.

Figure 15: The Time Constant was increased during the scan to reduce the loop bandwidth. The atomic corrugation disappears from the topography channel (left) and begins to appear in the current channel (right).


Based on the illustrations discussed above, it would seem a slower scan speed is better because it

gives the loop a better chance of following the surface reliably. However, scanning slow is not a

panacea for all problems and introduces a number of points to consider. The most important one is

drift. Usually, the system has slow lateral motion caused by pieces expanding and contracting due

to temperature changes. On an atomic scale, this drift can cause the surface to appear skewed when

it is a substantial amount compared to the total time required to take an image. Other points to

consider when selecting a scan speed include the surface dynamics. If the system being studied

changes over time, the data needs to be acquired quickly to capture the changes in time over the

course of multiple images instead of the evolution occurring within a single, slowly acquired image.

Once a good understanding of the feedback control is gained,

a good exercise to pursue is to add noise to the system and

use the feedback parameters and scan speed to improve the

image quality and remove the noise from the system. Noise

can be added into the simulated microscope by opening the

Nanonis STM Simulator background process. The window

should be present in the Task Manager toolbar. Clicking this

button will open a window as shown in Figure 17. Increase

or decrease the noise in the z channel or the noise on the

inputs so the feedback loop see a change in noise on the

input channel. There should be a noticeable difference in the

line scans as the noise is changed. Once a change can be seen,

alter the feedback settings to improve the image quality.

More advanced feedback loop control exercises will be

presented in later chapters.

Figure 16: The scan speed was increased during the scan without changing the loop parameters. The decrease in quality in the topography (left) and current (right) indicates the loop cannot follow the surface as accurately

Figure 17: The simulated microscope background process configuration window


Signal Oversampling With increased noise in the system, this is a good time to investigate the signal averaging

algorithms in the system. As everyone knows, taking more readings and averaging them together

will effectively increase the resolution past the limit normally set by the 16 bit ADCs. The

underlying acquisition rate of the input channels occurs at a fixed rate. As the scan timing slows

down, more readings can be taken and averaged together so the resolution increases. Change the

noise level in the z direction by a factor of ten or more and look at the effect on the topography

channel. The line scans should be noticeably noisier and the image quality degraded. Instead of

changing the feedback loop bandwidth of the system to help clean up the line scans, slow the scan

down so more readings are averaged together at each pixel. This will also decrease the noise on the

topography channel and help improve image quality. The same averaging can be done for

spectroscopy data, time domain oscilloscope traces, and noise power spectra introduced later.


Spectroscopy

Bias Spectroscopy Point spectroscopy is a very powerful technique used to probe the state of a surface and acquire

interesting information besides the simple topographic shape of the surface. In most cases the

feedback loop is switched off and a voltage

ramped while recording the response of

various input signals. When operating an STM,

the most common technique is to ramp the

bias voltage while recording the current. This

can be used to determine the density of states

of the surface under study. When a

spectroscopy routine disables the feedback

loop, the green button in the Z Controller

window will turn off to indicate the loop is

disabled. One of the important factors in

acquiring good spectroscopic results is to open

the loop at the correct time. Since the current depends exponentially on the tip-sample separation,

a small deviation can have a large effect on

the acquired current. The Nanonis

software and controller addresses this

situation using averaging. The noise in the

system on the topography signal will have

a certain peak-to-peak value and when the

loop is opened, the tip can be held at any

position within the range of the noise. To

reduce the spread in value when feedback

is disabled, the system will acquire

readings for a fixed amount of time and

calculate the average z output value over

this interval. When the loop is disabled,

the tip is fixed to this specific average z

value. The longer the time, the closer

together the grouping of the tip-sample

separation each time the loop is opened.

The downside of this is that the total

amount of time required for a set of

measurements is increased since this

averaging will take place each time the

loop is disabled. Be careful to not use too

large of a value or the actual acquisition

time might become unreasonably long given other factors. If manually switching off the feedback

Figure 18: Bias spectroscopy configuration window

An inherent assumption is that

the tip is the same height over

the surface whenever the

spectroscopy is performed. This

is not true and therefore

switching off the feedback has to

be treated carefully.


the parameter that determines the averaging time is Switch off Delay in the lower right corner of the

window. When disabling the loop through spectroscopy, the Switch off Delay is configured in the

individual spectroscopy parameter window.

The window to configure bias spectroscopy is accessed using the Experiments menu and is shown in

Figure 18. The first step is selecting what input channel to acquire as the voltage is swept. Any

channel listed in the window can be activated and recorded. The parameters next to the channel list

determine how many steps will be in the voltage sweep and how many curves to acquire. If more

than one sweep is to be obtained, the second sweep can be acquired from the final value back to the

initial value. This saves time since the bias does not have to be reset to the initial value. It can also

help remove anomalous current induced by capacitive

coupling between the tip and sample. Since I=C(dV/dt)

there will be a current offset induced by the voltage

ramp. If the output is ramped in both directions, in one

direction the offset will be positive and in the other

direction it will be negative. If this behavior is

observed when plotting the spectroscopy curves, they

should be averaged together to cancel the two offset

signals and leave purely the current due to the tip-

sample bias. The loop will be disabled during the

sweep if the Z controller hold checkbox is marked.

When disabling the loop, the output can be averaged

for a fixed amount of time and the digital output set to the average value instead of the

simultaneous value just as the loop is disabled. The appropriate length of time will depend on the

noise fluctuations present in the feedback loop output as well as the desired accuracy in holding the

tip over the surface the same distance each time the loop is opened. After the loop is opened, the tip

can be moved a fixed amount closer or further from the surface by setting the Z Offset parameter to

a non-zero value. Negative values will move the tip closer to the surface and positive values will

move the tip away from the surface. By combining this feature with a programming loop using the

LabVIEW interface it is possible to perform a

series of spectroscopy measurements at various

heights over the surface. This can be used to

increase the dynamic range of the spectroscopic

data by pushing the tip closer to the surface

after each curve and exploiting the increase in

tunneling current as the tip-sample distance

decreases. Dividing by the amplification due to

the smaller gap will produce normalized data as

if it was taken at a fixed distance over the

surface, but with better resolution. This method

allows as many as 7 orders of magnitude in dynamic range to be measured on the current channel.

After the voltage has been ramped to the initial value, it is usually a good idea to wait a fixed

amount of time for the system to reach a new equilibrium. Since this jump to the initial value may

The Switch-off Delay lets you

average the z position over some

time before switching off the

feedback and holding the tip at

the averaged position: You will

get a reproducible tip-height,

and reproducible spectroscopy

results.

The spectroscopy module can be

combined with the LabVIEW

Programming Interface to

perform a series of

measurements at various heights

above the surface.


be quite large, it may take some time to stabilize. By looking at the signal using an oscilloscope, a

good measurement of the required time can be obtained. This delay should be entered in the Initial

Settling Time box.

Once the output is ramped, the sweep timing

determines the acquisition during the ramp. The

Slew Rate will be used to move the voltage from one

output value to the next. A higher rate will move the

voltage quicker, but is more likely to induce artifacts

unless sufficient time is provided for them to

disappear. When each output voltage is reached, the

system waits for Settling Time before starting to

sample the input channels in order for the system to

equilibrate. Two common examples of when this is

needed is the capacitive coupling which induces a DC offset on the current channel proportional to

the dV/dt rate and also if a lockin amplifier is in use it will require a few time constant intervals to

reach its equilibrium output each time the voltage is changed. The number of readings to average

together to form the data point is

determined by the Integration Time

parameter. A higher number reduces

noise, but will increase the amount of

time the acquisition requires.

Once the ramp is complete, the output

returns to its normal value (in the case of

bias, it is returned to the tunneling bias

value) and the loop is re-enabled. When

acquiring spectroscopy during image

acquisition, it is a good idea to let the

feedback loop adjust the tip height before

starting to move the tip to the next image

pixel. The amount of time to wait is set by

the Z Control Time parameter. Any time a

parameter is changed that effects the

amount of time required to measure a

complete curve, the Sweep time box is

updated.

The upper and lower limits of the

measurement are set in the Limits

section. Values can be typed in the entry

boxes or the slider control can be used to

move the endpoints. To start a

measurement at the current location of the Figure 19: Generic Sweep module used for I(z) spectroscopy

The generic sweeper lets you

sweep setpoints, lockin

parameters like phase,

amplitude and frequency, or

simple things as the bias or a

generic output.


tip, press the Start button in the Control section. A sweep can be interrupted once started using the

Stop button. Each graph will appear in the lower part of the display after it is finished. Various

smoothing algorithms can be applied using the Filter type drop down. After choosing a filter type

the parameters of the function are controlled by the Order and Cutoff frq controls directly below the

drop down list. To show/hide/delete curves from the graph change to the Display and Save tab. The

check box on the far right side can be used to hide or show curves. Clicking a line in the list will

allow that curve to be written to a file or deleted. All of the plots can be deleted using the Delete All

button. The plots can also be changed to display the numerical derivative of the data by choosing

dY/dV from the Function list. Also, the density of states plot can be displayed when plotting I-V data

by choosing (dY/dV)/(Y/V) entry from the list.

Z Spectroscopy Another common STM experiment is Z spectroscopy

also located under the Experiments section. The

interface is identical to the Bias Spectroscopy window,

the only difference is the loop is opened and the z piezo

is ramped instead of the bias. This produces a curve

with an exponential shape due to the nature of the

current-z dependence in STM.

When the spectroscopy data is acquired very slowly

and the data needs to be displayed as it is acquired instead of at the end as with normal

spectroscopy, the Approach-Retract module should be used. This was originally created to ramp the

z piezo and record the cantilever deflection at each point. It is commonly used to measure the

surface adhesion and elasticity and to also calibrate the detector when operating in contact AFM

mode.

To sweep any signal and record the response of other channels, the Generic Sweep (Figure 19) can

be used. This module has more timing parameters at your disposal and can be more effective for I-z

curves in most cases. First, choose an output channel to be swept and select which channels to

record. Then pick an upper and lower limit and after this is done, set the number of points in the

curve or the step size. Since one determines the other, choose the parameter to set using the toggle

switch on the right side of the control. As one is changed, the grayed out one will be calculated and

displayed. The Measurement period determines the number of points averaged together at each step

and the Settling time is the interval to wait after the ramp reaches the next step level before data is

measured. This provides ample time for any slowly responding signal to reach its new equilibrium

value.

This module has nearly unlimited potential, bounded only by the imagination of the user. Since

there are undedicated outputs, they can be connected to external equipment to ramp any

controllable signal (temperature, magnetic field, frequency, etc.) and record a response.

Spectroscopy Locations

The Z Spectroscopy module

allows you to quickly sweep the

tip position and simultaneously

acquire spectroscopy data.


The spectroscopy measurements discussed up to now

have all occurred wherever the tip happens to be when

the acquisition is started. Many times it is desirable to

acquire spectroscopic maps over the surface to

investigate the spatial dependency of the electronic

states. For this application the Experiments on a Grid

module should be used. The tip is moved across the

surface and when it reaches a predefined location the

motion is stopped and spectroscopic sweeps are

performed. The curves acquired at each pixel are

indexed so after the complete acquisition is finished they can be individually viewed and associated

with the correct location. Additionally, slices can be taken across the three dimensional data to form

images at a specific step along the sweep. The first step in setting up the experiment is to determine

the size of the grid and the pixel spacing. This is done in the Scan Control window.

Grid

When the Grid button is first clicked, a grid is overlaid on the currently configured scan area, the

size and location of the grid can be changed by typing values into the parameter entry boxes or by

using the mouse. Similar to resizing the scan frame in the Scan Control window, the mouse action

can be defined to be Scale, Rotate, Move, or Resize. The same buttons are used as when the Scan

button is active, but when the Grid button is active the mouse is used to change the size of the grid

instead of the image frame. Keep in mind in the new software, the grid can be changed while image

acquisition is still going on. Once this is done, click the mouse anywhere in the image area and drag

the cursor to perform the desired action. Change the number of pixels within the grid using the X

and Y Points control. If the pixel density becomes too large, the individual grid lines disappear and

all that remains is the outer border of the grid. Also, note it is possible to have the pixels along the

line not be equal to the lines in the frame. An example of a configured grid is shown in Figure 20.

After configuring the grid,

the spectroscopic

experiment to perform at

each location must be

chosen. This is done using

the drop down list in the

Experiment section of the

window. Be sure the sweep

is properly configured in its

respective module window

before starting the scan.

When the start button in the

Experiment section is

pressed, the software checks

the configuration of that

module and pulls the Figure 20: Grid of spectroscopy locations

In grid spectroscopy mode you

can run all of the spectroscopy

experiments automatically on

multiple locations: on a grid,

along a line or at arbitrary

locations n the sample.


parameters from there to acquire the data. Be sure to understand the spectroscopy experiment is

started using the Start button in the lower left corner of the Grid section and NOT using the Start

button at the top of the window. It is also possible to call an external VI at each location which again

provides an unparalleled amount of experimental flexibility and control limited only by creativity

and imagination. The external VI can communicate with an external piece of equipment for

sophisticated integration of other techniques with SPM or it can be a VI written using the

programming interface to perform a specialized acquisition not provided by the base package.

Unless the spectroscopy is very fast, the total amount

of time required to finish one image may be quite long.

There is an obvious tradeoff between the pixel density

and total time required. As the number of pixels is

increased to get better spatial resolution the

acquisition time also grows. Try using a sufficient

density to have resolution of the silicon lattice and

acquire a full set of data running over night if required.

Once this completes and the data is saved, investigate it with the data browser and slice the curves

to form images at a specific value along the sweep. Be sure to activate autosave within the

spectroscopy module used so all of the data is saved as it is acquired, otherwise it will be lost when

the scan is done.

Line

Instead of performing spectroscopy on a grid of points, it can be very interesting to acquire a family

of curves along a line. This provides a nice way to study the spatial dependence of electronic states

with respect to a feature on the surface such as a step edge or defect. To choose this, click the Line

radio button in the window and then a pattern of x symbols will appear on the image. The number

of locations, length of the line, and orientation can all be changed to match the desired spatial

location.

Cloud

The third option for defining

spectroscopy locations is the

Cloud option. When this is chosen,

an arbitrary set of points can be

defined by clicking in the viewing

area. Each click adds an

additional spectroscopy location.

This can be particularly useful is

there is only a specific region of

the surface where spectroscopy is

important. Instead of acquiring

data over the entire image which

would waste quite a bit of time

and acquire extra curves, the tip Figure 21: A cloud of arbitrary spectroscopy locations

Be sure to activate autosave

within the spectroscopy module

used so all of the data is saved as

it is acquired


will stop when it reaches the configure location so the curves are concentrated only in the area of

interest on the surface. When the Cloud option is picked three new tools appear in the tool bar

above the viewing area. These are used to determine if mouse clicks add points remove already

present points or laterally shift an already present point. Also, the section on the left side of the

window will present a numerical list of X,Y point pairs as each one is added. An example with a set

of points along the step edge is shown in Figure 21.


Coarse Approach When starting the simulator for the first time, the tip was already close enough to the surface that

activating the feedback loop created feedback. In a real microscope, of course, this is not usually the

case. After placing a tip and sample in the system some means must be available to close the

macroscopic gap and get the tip and sample microscopically close. This is achieved many different

ways, but usually involves some type of motor that can create very tiny steps in a controlled

fashion. In order to avoid tip damage the control software must be able to induce individual steps in

the motor and test for a feedback condition between steps. To

exercise more caution, the z piezo can be fully retracted before

each step and then slowly extended after the step to see if it

can reach the surface. If it cannot achieve a feedback signal,

the tip is pulled back again and the cycle repeated. The specific

interface to drive the motor does not matter for the purposes

of this simulator, but most of the time this is achieved by

toggling one or more digital TTL lines which communicate

with an external piece of equipment.

To practice a real-life coarse approach it is necessary to first

retract the tip from the surface. Before performing this step,

stop any data acquisition that may be taking place. Open the

motor control window using the menu item Modules/Motor

Control which is shown in Figure 22. Use the Z retract button a

few times to fully disengage from the surface.

Automatic approach Once the gap is large enough that the feedback controller has the tip fully extended, a coarse

approach can be started to simulate the real situation. Open the

automatic approach control from the tools menu of the Z

Controller window. The window is shown in Figure 23. The first

time it is opened, only part of it will be visible. Use the checkbox

to view the full size. If the motor takes extremely small steps

relative to the full z piezo range (step size ~1/100 of the z piezo

range), there is no need to test for a stop condition after each

step. Multiple steps can be taken between each testing cycle to

speed up the entire approach time required. This is controlled by

the Number of Pulses parameter. After each step it is usually a

good idea to wait a short amount of time for any large mechanical

vibrations caused by the coarse motion to decay away before

ramping the tip towards the surface. The interval is set by the

Delay after moving parameter. The shorter this time, the faster the approach can be. Use an

oscilloscope to look for transients on the feedback signal after each step and use a delay longer than

the transient.

Figure 23: Computer controlled approach window

Figure 22: Manual control of the coarse approach motor is in the Motor Control window


Advanced automatic approach parameters The Stop Condition is what z position should be considered in range. It makes little sense to stop the

approach the first time the surface is reached because this usually occurs with the z piezo still

substantially extended. The first action a user will take after this is to step the motor forward a few

more times so the z piezo is in the middle of its range. This manual adjustment can be performed

automatically by the software by having it not stop the approach until the z piezo is approximately

centered. How closely the condition can be set to zero depends on the coarse step size compared to

the z piezo range. The approach stops when the feedback loop output crosses this threshold. If the

condition is zero and the n-1 step placed the z piezo at -5 nm so one more step is needed whatever

the distance covered by one motor step will be the z position when the approach is stopped after

the next step. It is best to have this threshold set to a slightly negative value so when it is crossed

the tip may end very close to zero.

For unattended approach with some measure of safety, it is recommended to pull the tip back from

the surface after the approach is done. This reduces the risk of damage to the tip if an adverse event

occurs that would cause tip-sample contact when it is in feedback just above the surface. For

example, if the approach occurs during lunch break or class and the tip would be left over the

surface for an hour or two with nobody around it is far safer to fully retract the z piezo so nothing

bad can happen while nobody is around using the microscope. To utilize this feature make sure the

Withdraw when tip is landed box is checked.


Displaying Data in Graphs In effect, there are two distinct types of diagnostic and analysis tools available: a set that displays

the data in the time domain and a set that displays the data in the frequency domain. They each

have their strengths and appropriate applications. To view a signal in the time domain for a quick

measurement of its amplitude there are four different graph modules which are accessed via the

Graphs menu. In order of decreasing time resolution the choices are Oscilloscope, Signal Chart,

History, and Long Term Signal Chart. The oscilloscope can be used to capture transients, etc.

because it features a real triggering function

comparable to modern oscilloscopes. Interestingly, all

of these modules can be opened and acquiring data at

the same time to provide a view of the same signal on

different time scales. All data channels are always

acquired at a steady rate and what it is processed and

displayed is simply a matter of which windows are

opened and how they are configured.

Time domain display The oscilloscope is shown in Figure 24. The controls specific to it are located on the right side of the

window. The triggering can be configured along with the time base of the display. Note that

changing the Time Base also alters the sampling rate of the data. The Time Base can be changed

from 256 ms to a maximum of 12.8 seconds in power of 2 increments. If the length of data displayed

is more than desired, the plot can be zoomed into a smaller section using the standard tools

discussed above, but keep in mind the time resolution will still be determined by the sampling rate

of the original time base.

There are three triggering modes, Immediate, Level, and Auto. Use level mode to pick a signal value

that should trigger the acquisition to occur and the time trace to be displayed. Use this to capture an

event that is known to occur at a specific value. If the trigger occurs and it is to be analyzed and

saved, a subsequent event will be

ignored if the Hold button is

depressed. Auto triggering will

continually update the display,

but the software will adjust the

trigger level to accomplish this.

Immediate is more like free

running mode where the latest

data is always displayed with no

trigger taken into account. At any

time (whether a trace is held or

the scope is in free run mode, the

Save Trace button can be pushed

to save the data that is displayed Figure 24: Oscilloscope window

The system has various

possibilities to display data in

both the time and frequency

domain.


on the screen to a file.

The time domain display with the next best resolution is the Signal Chart shown in Figure 25. It can

show two channels and also contains a

control for additional averaging to be

performed. As the Averaging parameter is

increased, the time resolution will

decrease because more readings from the

FPGA card are averaged together by the

program, but the rms noise level of the

channel will decrease. To change the

channel displayed in each pane, click the

channel name to produce a list with all

available signals.

The third display is the History graph

which also has two panes for

simultaneous display of two signals. At

any time the record shown in the window

can be saved by clicking the Save button.

It can also be cleared and started over

again by pressing the Clear button.

The final display which can acquire a signal over the longest time interval is the Long Term Chart as

shown in Figure 26. This will record 10000 data points so the total length of time is determined by

the sampling rate. If a signal changes very slowly and needs to be recorded this is the best choice of

the four modules. Examples where this could be useful are a temperature or pressure input to an

open analog channel, the z controller output to record thermal drift of the head in the z direction, or

the X and Y output signals if tracking is activated to record the lateral drift as a function of time. As

the points are acquired, the display counts down the remaining time before the buffer fills up. The

interval entered in the Delay box determines the spacing between readings.

Figure 25: Signal chart window

Figure 26: The Long Term Chart can act as a strip chart recorder and acquire data over a lengthy period of time.


Frequency domain display When searching for noise sources, many times it is advantageous to study the signal in Fourier

space (frequency domain) instead of the time domain so the precise frequency components can be

seen. This can provide strong clues to their origin. For example, if the peaks are at harmonics of the

power line (60 Hz in USA and some other parts of the world, 50 Hz in much of Europe) this

indicates grounding or shielding issues that should be investigated. If peaks in the feedback signal

are nonexistent when out of range, but appear when in range this is usually caused by vibrations

reaching the tip-sample junction.

The bandwidth of the spectrum is determined by the sampling range. In the case of the realtime

system this depends on the RT

Engine Frequency and the

Oversampling in use. For

example, using the default values

of 10 kHz and oversampling ten

times means the overall

sampling rate is 1 kHz. Since this

is reduced by a factor of 2 due to

the nature of the FFT algorithm

the maximum detectable

frequency is 500 Hz. To increase

the bandwidth of the

measurement either increase the

engine frequency or decrease the

sampling rate. An example of a spectrum from the simulator (and therefore devoid of any specific

peaks) is shown in Figure 27. The maximum frequency is 500 Hz due to the default conditions. Feel

free to alter the engine frequency and oversampling and note the difference in the spectrum.

A very useful feature for comparing before and after data is to use the Paste function. When this

button is clicked the current data is stored in memory and left on the graph using a red line. As the

acquisition continues, differences between the previous data and the instantaneously acquired data

can be easily seen when comparing the two graphs. Use this to test a set of conditions and then

make changes and see if things improve. When testing the simulator, acquire a spectrum and then

increase the noise level of the simulated

microscope by using the simulator configuration

window in the toolbar discussed earlier. As the

noise level is increased or decreased the

baseline of the spectrum will rise or fall. An

example of this is also seen in the figure.

Figure 27: The fully functional spectrum analyzer can help pinpoint noise sources

The spectrum analyer is ideal to

find ground loops and 50/60Hz

noise in your system. Any glitch

becomes immediately visible.


Long Term Spectrum The spectrum graph can only display two curves at once, a pasted one and the actively acquired

one. To look at the spectrum over a longer time scale and notice trends in peak location and peak

height, the Long Term Spectrum should be employed. This unique presentation of noise power

displays the last 50 curves acquired. The total length of time covered by these curves depends on

the bandwidth of the measurement.

The longer the time required to

obtain one curve, the longer the time

covered by the display.

An example from the simulator is

shown in Figure 28. The bright streak

shows a noise peak at 50 Hz that was

eliminated about 2/3 of the way into

acquisition. If a peak shifted to a

different frequency, the band would

not be horizontal and instead the

bright spots corresponding to the

peaks would shift up and down in the

image. To see more distinctly the

peaks compared to the background

level the spectra can be averaged

together before presenting. This is

determined by the parameters in the

Averaging section. There is even a

peak hold mode that can be quite

interesting and help locate

transients that otherwise may be

averaged away and lost.

Figure 28: Long term spectrum view can be used to observe the evolution of a signal over time


Sample tilt correction Another feature that is useful in some cases is the sample tilt correction. Under normal

circumstances when scanning with feedback on, this has no real benefit. If the sample and tip are

misaligned, the overall surface slope will be followed by the feedback loop just like it follows the

small variations in surface height. If scanning or tip motion will take place with the feedback loop

disabled, then it is important to remove the sample tilt in order to minimize the possibility of tip

damage. When the sample tilt is corrected, a ratio of the x and y position is digitally added to the z

output piezo. For any given position the tip will also be pulled back or pushed forward as it moves

in order to follow the first order tilt. When the tip is moved without feedback control and no tilt

correction, it will contact the surface as demonstrated in Figure 29. Both the feedback and the tilt

correction produce the same tip trajectory (assuming reasonable feedback parameters) so it does

not matter which accomplishes the task of following the linear tilt unless one is missing and then

the other must be present to avoid tip-surface contact. Two good examples of scanning with the

loop open are multi-pass mode where the tip is

lifted when the line is repeated in order to study

electrical or magnetic effects and lithography

routines which require a disabled loop for proper

conditions.

To understand the process of correcting for sample

tilt using the simulator it is necessary to first

introduce tilt into the ideal surface produced by

the virtual STM. This is accomplished by opening

the Simulator window as shown in Figure 31 which

is present in the taskbar at the bottom of the

screen. Change the Plane x and Plane y values from

zero to any arbitrary amount and start a scan. The

images will now appear to have slope from one

side to the other. Be sure to have the preprocessing

mode set to Raw in order to see this. If the

preprocessing is set to Slope Subtract, the slope

that is present in the real data will be subtracted

before display and therefore hidden. It will be in

the actual data, but not the displayed images. This

is why it is usually a good idea to use either the

Raw display mode or only subtract the average z value from each line in order to avoid missing an

important point that should be realized about the data. Once the slope is visible in the line scans

and the images, start removing the slope by opening the window using Modules/Piezo Calibration

(Figure 31). As the scan progresses adjust the Tilt X and Tilt Y parameters until the image looks flat.

The best method to do this is use the standard data entry method of placing the cursor next to a

digit and use the up/down arrow keys to increase/decrease the value until it is optimized. An

example of how it should appear is shown in Figure 30. It is usually easier to only adjust the x factor

Figure 29: Removing the sample slope automatically allows trouble free scanning with feedback disabled


and when done, rotate the scan by 90 degrees and

now perform the correction for the y axis. The

best display to use when judging the removal of

tilt is the Line Scan Monitor. Each scan line will

appear flatter and flatter as the slope is removed

and at some point it will start to tilt the other way

indicating overcompensation. Find the values

which make the scans appear as horizontal as

possible.

The top part of the image shows a gradient from

one side to the other since the color scale is

showing the large change in z value over the width of the scan area due to the tilt. As the scan

progressed, the correction parameters were changed and at the bottom of the image it appears to

be one uniform color because the feedback loop values are now approximately the same value since

there is little variation other than

the small atomic corrugation. In

subsequent images the automatic

color optimization will narrow the

range of the color scale to span

the smaller z values and a high

contrast image will appear.

Figure 31: Automatic sample tilt correction

Figure 30: Image appearance with tilt removed automatically (middle section) compared to using the feedback loop to correct the tilt


Thermal Drift The materials used when building a microscope will expand and contract when the temperature of

the system changes. Because data acquisition takes place on the nanometer scale, small changes in

temperature will be visible in the images by

the slow shift in the lateral position of

features. If the lateral drift rate is constant,

this can be nullified by adding a small

correction voltage to the x and y voltages at

a constant rate. The simulator can provide

experience with this technique.

Drift Compensation Since the simulated microscope works as an

ideal system there will be no lateral drift

present. By adding a compensating voltage

to the scan signals, this will introduce drift

into the system. The compensating voltage

can be entered by using the Atom Tracking

module shown in Figure 32. Begin by

setting the Drift X and Drift Y parameters to

non-zero values and clicking the activate

button. When this is done, the lattice will

immediately appear distorted as seen in

Figure 33. The observed effect is symmetric

to not compensating for drift that is present

in a microscope. Try changing the amount

of drift and notice the skewing of the lattice

increases or decreases. When using a

physical microscope, if the lattice appears

distorted then the most likely cause is

lateral drift that should be compensated.

Atom Tracking The drift can also be measured by the

acquisition software. Place the tip directly

over an atom on the simulated surface. In a

real microscope it is better to choose a more

distinct feature than an atomic lattice site. Something like a vacancy or an adsorbate will provide an

easier feature to follow because the local gradient is much larger. That type of site is relatively

steeper given its lateral dimensions are about one atomic space, but it will appear taller or deeper

than an atom within the lattice.

Figure 32: Atom tracking module to null drift


The tracking works by orbiting the tip over a site and measuring the derivative of the signal. When

the tip encounters a locally steep location it knows it is falling off the atom and moves in the

opposite direction in an effort to stay on top of a local maxima (when on top of an atom or

adsorbate) or minima (when in a hole). Enter an orbit frequency of a few Hz up to maybe 100 Hz.

Given a single atomic site is tracked the orbiting radius

should not be very large, a value of 200 pm will work well

on the silicon surface. The time constant of the gradient

measurement should be slow enough to average over a few

oscillations, but not so slow as to not update the tip

location very often. This can cause the tip not follow the

feature very accurately if it is moving rather quickly. An

Integral value of 10 pm/deg/sec is a good starting point.

Start the orbit and then adjust the phase until the

measurement seems to be tracking well. This can be judged

using the red cross in the lower graph. When the phase is

well tuned, it will move only along the x axis back and forth.

As the tracking proceeds it will update the measured rate of

motion along the x and y axis. After some time when small

variations have been averaged away, the measured drift

should be equal to the value entered above which artificially introduced drift.

If this was an actual working microscope that had no drift rate entered in the software to begin

with, the measured rate would be entered and the skewed lattice appear like more of the expected

result from crystallographic considerations. In the exercise here, drift was introduced artificially

and the software was then used to measure the

drift rate. The values should match when the

measurement was done properly. To return to a

proper lattice appearance, set the drift rates

back to zero or simply disable drift

compensation by turning off the activate button

on the left side of the section.

Figure 33: The upper part of the image shows lattice distortion due to drift turned on as the scan was acquired from the bottom towards the top

The atom tracking lets you

automatically compensate for

drift and sample tilt!


Contact AFM The controller is flexible enough to operate any microscope in any mode. Another popular mode is

contact AFM. A cantilever touches the surface and its deflection measured by a laser beam bouncing

off the back of it into a position detector. This mode can also be simulated in the existing software.

The back end produces signals like a cantilever is touching the surface at the same time as the STM

tip is tunneling. The signal related to this deflection is Input 3 and can be seen in all channel lists. To

be convinced it simulates a cantilever signal, retract the tip from the surface and note the

magnitude of the signal. Then

approach again and notice the signal

level changes due to the cantilever

contacting the surface and being

bent up.

Defining a new Z Controller

Create a new feedback signal by

opening the Controller Configuration

window using the tools menu of the

Z controller window. The window is

displayed in Figure 34. First enter an

arbitrary string for the controller

name. In the example shown, it has

been named Contact AFM. The

control signal should also be named

using a meaningful string; this was

given the name Force Error in the

example. The deflection of the

cantilever can be both a positive and

negative voltage so it has to be

redefined to bipolar using the

dropdown list. With the window

open, it is also evident the control

signal does not have to be a single

analog input. Instead, it can be a complicated mathematical expression derived from two inputs and

adding, subtracting, multiplying, or dividing them and using the feedback loop to maintain this

relationship constant.

A SafeTip condition can also be defined for each controller. This feature allows the system to

monitor a second signal from any source and if this signal meets some predefined condition,

corrective action is automatically taken to avoid possible tip damage. For example, if the total signal

from the quadrant photodiode falls below a certain threshold this usually means the cantilever

alignment has developed a problem and the system should pull the tip back because it is no longer

correcting to a reliable deflection signal. Another example would be the excitation signal required

Figure 34: Configuration of a new feedback source for contact AFM operation


to drive the cantilever at its resonance. If this increases substantially this means a large amount of

energy is injected into the system to maintain the cantilever resonance which should not be

necessary. This probably indicates something else has happened to the oscillating system and it

should be investigated because the validity of the acquired data is questionable.

Once the new controller has been configured close the window and change the Z Controller to the

new choice. The change takes effect immediately so it is a good idea to have the tip retracted when

making the change.

After the approach is finished make

sure the feedback loop is stable and

under control. This can be judged

by the stability of the Force Error

bar graph in the Z Controller

section, or by using one of the time

domain graphs. A set of parameters

that provide pretty good control are

a P gain of 35 nm/V and an I Time

Constant of 43 msec.

An image can be acquired that will

show atomic resolution on silicon

though this is impossible in contact

mode with a real microscope. If

everything appears to be working

stably, force distance curves should

be acquired as the next step. The tip

can be pulled back while recording

the deflection signal. As a bonus,

the current will also be acquired to

illustrate the simulator works like a

simultaneous STM and contact

AFM.

Detector calibration using

Force Distance curves The Generic Sweeper module found

under the Experiment menu will

work very well for this acquisition.

It is shown in Figure 35 with

reasonable parameters set. Choose appropriate limits for the minimum and maximum z values

keeping in mind these are relative to the feedback loop position when the loop is opened. A

negative value pushes the tip closer to the surface and a positive value pulls the tip away. The step

size from the minimum to maximum can be determined by choosing how many points to acquire

Figure 35: Generic sweeper module configured for Force-distance curves


along the curve. When any of the three parameters are changed (min, max, and # of points) the

increment is recalculated and displayed. The speed of the sweep is entered using the Measurement

Period parameter and the slew rate. The period determines how many readings to acquire and

average together at each voltage step and the slew rate determines how quickly to change the

voltage from one step to the next. When using the generic sweeper any output signal can be swept

and any input signal can be measured. There may be some experiments where the loop should

remain on during the acquisition. This is set using the Z Controller off check box.

Once everything is set, start the measurement by clicking one of the two start buttons in the control

section. The data can be acquired from the minimum to maximum or vice versa. The direction of the

sweep is selected by the start button. When the sweep starts, the slider in the middle section will

move to illustrate the progression of the measurement. The actual output value will also be

displayed numerically in the window.

Data similar to the graphs of Figure 35 should be seen. The sloped part of the curve is produced by

the z piezo moving the cantilever when in contact with the surface. Since the surface is modeled as

infinitely hard, as it moves the cantilever must bend to accommodate the push. This bending

produces motion of the reflected laser spot across the PSD which produces a change in the voltage

signal out of the detector. This linear

relationship can be used to determine the

detector sensitivity which is the change in

voltage from the detector for a given

displacement of the cantilever. The flat part of

the curve is because after the cantilever loses

contact with the surface, it returns to its

equilibrium deflection and maintains that for

the rest of the acquisition. In this simulated

microscope there is no adhesion, so the large

v-shaped part of the curve commonly seen

when the cantilever sticks to the surface in an

actual microscope is absent. Note that just

about when the cantilever loses contact with

the surface and the force error becomes flat,

the current rapidly drops from a saturated

value to zero. The decrease in current does

indeed follow an exponential shape as

expected for a tunneling gap simulator.

With Input 3 recorded as volts, the detector

sensitivity can be measured. This is the

overall amplifier gain in the circuit to convert

motion of the reflected laser spot into a

voltage. Once the voltage change as a function

of calibrated cantilever deflection is known,

Figure 36: Beam deflection window to enter the calibration values of the AFM detector system


the overall conversion from voltage out of the PSD to applied force can be determined. When

performing the spectroscopy outlined above, the cantilever is moved a specific amount and

assuming an infinitely stiff material means the distance the z piezo moves is identical to the

distance the cantilever is deflected. The linear slope of the Input 3 curve supports this assumption.

Measure the slope of the curve to obtain the output volts per unit distance factor (Volts/meter).

Divide the known cantilever spring constant (Newton/meter) by this factor to obtain the

conversion of how many volts correspond to a given applied force (Newtons/Volt). This can be

entered in the Beam Deflection window so the force setpoint and all measured data have the

physically meaningful units of force. The label can be changed to Force or something similar. The

units should be changed to N for Newtons and then the appropriate calibration factor entered in the

box below the label.

Detector calibration using lockin module Another method to calibrate the AFM

detector is to use the internal lockin detector

module. Once the cantilever is in contact with

the surface the z piezo can be modulated a

small amount. This will modulate the

cantilever deflection up and down (keep in

mind we assume the surface is infinitely

hard) which will appear as a modulation on

Input 3. By using the lockin to measure the

amplitude of the voltage swing for a given z

modulation the conversion factor of voltage

output as a function of cantilever

displacement can be determined.

The lockin module is shown in Figure 37

configured for the experiment. The output is

applied to the z channel which simply means

the z DAC is not only outputting the feedback

loop response, but internally the controller is

also mathematically adding a dither to the

DAC value before it is actually set. This

mathematical summation should produce a far cleaner signal than outputting the z signal on a DAC

and then using analog circuitry to sum it with the analog output of an external lockin as

conventionally done. Choose the signal to be modulated from the dropdown list. Note the flexibility

provided by the Nanonis system. Virtually any input or output can be modulated. This makes a wide

variety of experiments possible that previously would have been much more difficult (consider

modulating the setpoint to measure the response of the feedback loop in the time domain or

modulating the bias to determine dI/dV during spectroscopy ramps). Then choose a frequency for

the excitation signal and the amplitude. The signal to measure as the response is chosen using the

Demodulate list. The Harmonic control can be set to look at the fundamental frequency or higher

order harmonics.

Figure 37: Lockin amplifier module for AFM detector calibration


Once everything is

configured, click the green

square next to the

modulate list to activate

the output. By opening one

of the time domain graph

windows, the modulation

output and its response

should be visible as shown

in Figure 38. As the piezo

is moved, the cantilever is

clearly also moving up and

down as expected. Instead

of trying to measure the

peak to peak variation on

the force as the piezo is

moved, let the lockin

module measure the amplitude. Click the Auto button to be sure the lockin has the correct phase

and the actual response measured in volts is then displayed in the lower window. This can be

divided by the z amplitude to obtain the voltage change from the PSD for a given displacement of

the cantilever.

Figure 38: Modulating the z voltage while in contact with the surface


Atomic Manipulation A very popular technique used with SPMs is to manipulate atoms or small molecules and build

structures on a surface to study their properties. The functionality to draw features on the surface

or move items around is shown accesses by the Follow Me button. The window is shown in Figure

39. There are two ways to designate a destination for the tip. Either enter an X,Y coordinate pair

and click the Move button or use

the mouse to point to a spot and

click and the tip will start to move

as soon as the mouse is clicked. A

small red circle will indicate the

destination of the tip.

A particularly powerful feature of

the software is the ability to

record a signal on two channels

while the tip is in motion. This

can be used to capture changes in

the signals as the tip moves. The

acquisition is configured in the

Data acquisition section. Choose

the amount of oversampling to

apply for smoother traces but a loss of time resolution when capturing transient events. Click the

Show Graph button to open the time

domain window shown in Figure 40.

The number of samples to collect can

be set as well as the two channels to

display.

To apply different feedback conditions

during the motion activate the

Alternate settings section by clicking

the button. There are two choices that

can be made here. A different feedback

condition can be used to move the tip

closer or farther away (if needed clone

the existing controller and simply

change the setpoint or use a totally

different control signal during motion)

and a different bias condition can also

be used.

The second tab under the Follow Me

family is for Lithography. A series of lines can be drawn in the window and overlaid on an image. If

Figure 39: Follow Me group of controls in the Scan Control window

Figure 40: Tip move recorder can acquire data as the tip moves along an arbitrary path


they are saved, they can be recalled at any point in time. There is also the possibility of using the

script language itself to type in a series of movements instead of drawing the figure. Once the

pattern has been drawn, the Execute button can be clicked to perform the routine. The pattern can

be erased using the Delete button and they can also be saved and recalled using the Save and Load

button respectively.

Keep in mind, as

stated earlier, the

patterns and

lithography recipes

can be created and

arranged while

scanning is active in

preparation for the

completion of the

frame. This saves

valuable time

compared to a

system where the

mouse can only

perform one

function at a time

and one

experimental step has to finish before preparation for the next thing can start.

Figure 41: Lithography can draw features on the surface by connecting a set of straight line segments


Diagnostics and Analysis

TCP Receiver The next step is to explore the diagnostics included in the program. Some of these features can also

be used for clever experimental data acquisition but primarily they are meant to be used for

monitoring signals and diagnosing possible issues. One item that can be varied to check its effect on

acquisition is the overall data acquisition

rate. This is determined by a group of

parameters in the TCP Receiver shown in

Figure 42. It can be opened by choosing

System/TCP Receiver from the main window.

The large green LED indicator is lit when

there is a connection established between

the software and the electronics (a

simulated controller in this software). The

RT Engine Frequency and Signals

Oversampling couple together to determine

the overall acquisition rate of the software.

The frequency setting determines the rate of

the control loops inside the real time

hardware or simulated hardware. By default

the engine runs at 10 kHz, for STM it is

usually safe to increase this to 20 kHz or

even 30 kHz with no adverse effects. If an

AFM is operated especially in non-contact mode it is advisable to leave this at 10 kHz to not

overload the system. Increasing this will speed up the system and let everything run faster and the

maximum acquisition speed limit will also be raised. In thorough testing of the simulator package it

was routinely operated at 30 kHz and no problems were ever experienced. The RT-sampling Period

displays the inverse of the RT Engine frequency. The Signals Oversampling is used to determine how

many readings are averaged together in the real time controller before sending the measurement

value to the software. Lowering the sampling will

increase the noise of the data, but allow it to be

acquired faster. It can also be used to raise the

frequency window of the spectrum analyzer

discussed below. This should be investigated to

understand the effect between noise level of the

data and getting the data as quickly as possible.

All of the sliders, limits on controls, and graphs

are updated at a rate determined by the

Animations period. There is little benefit to

increasing this to a rapid value because the eye

Figure 42: The TCP Receiver window determines the sampling rate and averaging of the realtime engine

Oversampling is an important

concept used in the Nanonis

system. Every signal goes

through one or more stages or

oversampling to achieve the best

possible resolution require at

that point.


will not be able to read the display anyway if it updates too quickly. The default is 20 msec which

means the values are updated 50 times/second. The Indicators period determines the update of the

numerical display boxes. This should be slow enough so the eye can process the readings and make

decisions based on them. The default is 200 msec which is 5 updates/second. Measurements period

is the time to average readings together for very precise measurements where low noise is desired.

By averaging together more readings, the noise decreases by the square root of the number of

readings (assuming broadband noise) so the sensitivity improves. This needs to be adjusted

depending on the nature of the experiment being performed.

The activity graph helps diagnose communication problems. The white line is the current time

difference between a pair of packets and the red line is the moving average. This time difference

should be equal to the Signals Period discussed above. In the example shown in Figure 42, the

average is very close to 1.0 msec as expected. The white graph shows large fluctuations because of

the speed of the graph update. If the average is not equal to the expected period, this would usually

indicate an overloaded RC4 and the RT Frequency should be decreased or too much data is trying to

be acquired.


Diving deeper After following this tutorial there are many ideas you probably thought of as modules were

unveiled and discussed. Feel free to return to those parts of the software and explore them deeper

to gain a better appreciation for the freedom of creativity the software permits. A variety of

experiments can be tried and meaningful results can be obtained given the depth of the simulated

STM background process. Here are some ideas for learning sections that were not covered in detail.

Configure a SafeTip condition for the Z feedback and see if you can trigger it and if the

software takes the correct action.

Experiment with different layouts and microscope parameters to simulate a multi-user,

multi- scan head environment and see how the sessions feature takes care of this.

The TCP Received window has a large number of parameters. How do they effect the data

appearance in various display windows?

Try using atomic manipulation with varying conditions and use the time domain tools to see

if the change in conditions occurs during motion as expected. (What channel can you look at

to detect when the tip is in motion?)

Look into the Piezo Calibration window and artificially add drift to the microscope. What

does it do to the images? Have you seen this before when using a real microscope?

Use the Atom Tracking window to try to measure the drift and then compensate for it. Can

you return the image to the expected result?

Add noise to the system in the STM Controller background process trying some of the other

parameters in the window. What does it do to the data? What are various techniques you

can use to reduce its appearance in the images? Does the best technique for removing the

noise depend on which parameter was changed to introduce the noise?

Work with the spectrum analyzer and long term spectrum and see how the noise appears as

well as when a signal is modulated using the lock in amplifier module operating

independently.

Measure dI/dV(V) with the spectroscopy module.

Measure the transfer function of the z-feedback (dZ/dI as a function of the modulation

frequency while the feedback is running). There is a special module available in the tools

menu of the Lock-In detector – or you can use the generic sweeper to do this – What are the

differences?

Explore the possibilities of a second controller in the Follow-Me mode.

Look at the spectrum of a modulated signal in the Long Term Spectrum chart.

Learn what is behind the scaling icons that can be found next to almost every graph.

Listen to the topography of your sample with the Signal-to-Sound graph.

Let your imagination run wild and enjoy investigating the software, but also enjoy having a

“perfect” microscope that acquires very beautiful data day after day. It is also nice to know it has a

tip resilient enough to withstand unimagined abuse!

Nanonis STM Simulator Tutorial - SPM Controller - … · be used to change the configuration...

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