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IMP Software Suite User Manual

1. take components of comb at frequencies given by n array a abs x_hat n asf 0 1 adjust peak amplitude p angle x_hat n 4 6 Drive Constructor 35 IMP Software Suite User Manual Release 1 2 Create an signal in the time domain consisting of a rapidly oscillating component with a slowly modulated fre quency f_bar mod t Fourier transform and pick out the nfreq_out components close to the center frequency f_bar and set the amplitudes a and phases p N 2xint 2 n_bar number of time samples so f_max 2xf_bar t 1 df arange 0 1 1 N construct signal x t in the time domains x cos 2 x pi x f_ bar x t delta_f 4 pixdf sin 2 pixdf t FFT to get frequency comb x_hat fft rfft x N 2 a abs x_hat n asf 0 1 adjust peak amplitude p angle x_hat n 4 7 Stream Recorder When scanning a sample the MLA process end of line EOL and end of file EOF triggers and lockin data is stored at pixel locations in a scan file The stream recorder ignores all triggers and stores data as one continuous uninterrupted stream This mode is quite useful for taking data when the AFM probe slowly approachs and retracts from a surface The data stream can be stored in either time mode or frequency mode see Intermodulation Measurement e Start will start the stream record Click again to Stop If the Autosave box is checked in the Status Banner each run of the strea
2. When the Enable Fit box is checked the fit is performed in real time and displayed in the plot as a solid blue line The noise contribution from the cantilever motion is shown with the yellow dash line For a full description of the theory and fit see Noise Calibration Sometimes very low level spurious signals can be picked up when measuring noise If the spurious signal is not driving the cantilever you can remove improve the calibration by removing them from the fit Select the following tools in the calibration plot toolbar gt right click and drag on the plot will select a range where the fit will be performed Data outside this range becomes grey and is not analyzed in the fit Xx clears the selected fit range HK right click and drag defines an area over which data points are ignored in the fit The removed data is marked with a red x x clears all ignored data Calibration Result The Calibration Result is displayed in several ways giving you important figures of merit It is useful to think of the calibration as having two parts The calibration of the cantilever the force transducer and the 8 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release 1 2 calibration of the detector the deflection sensor or optical lever Cantilever e Resonance frequency fo y k m kHz of the simple harmonic oscillator model used to model the cantilever eigenmode with mode stiffness k and ef
3. 5 5 The connections to the SAM V from Bruker are identical to the SAM modules from DI and Veeco However these SAM modules can not be used interchangably Fig 5 6 The EOL and EOF triggers are on the front of the NS V controller Make the connections as labeled in the image 54 Chapter 5 Installation IMP Software Suite User Manual Release 1 2 5 4 Common AFMs 55 IMP Software Suite User Manual Release 1 2 56 Chapier 5 Installation CHAPTER SIX THE MULTIFREQUENCY LOCKIN AMPLIFIER MLA The MLA also known as the Imtermodulation Lockin Analyzer InMLA is a unique measurement instrument which could be described as a synchronous multifrequency waveform generator digital oscilloscope and real time Fourier analyzing instrument It is particularly powerful for Intermodulation Measurement but it can be used equally well for studying harmonics of a single drive or any kind of multi frequency response The MLA can be configured in many different ways to perform many different measurements Here we give a brief and general description of the MLA focusing on a technical description of the ports and how they may be configured The MLA is constructed from precision low distortion high speed analog to digital converters ADC digital to analog converters DAC and a highly parallel logic circuit called a Field Programmable Gate Array FPGA Different configurations of the MLA are realized by
4. The settings for the various AFM types are stored in the folder IMP Sessions and Settings settings configurations These files contain information about triggers over scan factors and more Advanced users can use the files in this folder as a template to make their own custom_afm ini settings file When the software is restarted a new custom_afm settings will appear as a choice in the pull down menu If your AFM type does not have a configuration file contact Intermodulation Products for help in making a custom configuration file lt info intermodulation products com gt 5 3 1 Working without triggers Nearly all AFM s have some kind of access to the end of frame EOF and end of line EOL triggers If the EOF trigger does not exist it is still possible to manually start the ImAFM scan when the host AFM scan starts However after several scans a manual restart is needed to re sync the frames If the EOL trigger does not exist 48 Chapter 5 Installation IMP Software Suite User Manual Release 1 2 it is also possible perform InAFM but in this case one needs to accurately adjust the timing in order to keep ImAFM in sync with the host AFM Under the Advanced pull down menu select Setup AFM Two fields appear in the AFM Setup dialog The Line frequency should be set to the frequency at which you want fake EOL trigger signals to come The Delay is the number of pixel time intervals the MLA will wait after the fa
5. as scan data is acquired Live parameter mapping availabe as a script the pull down menue Advanced gt Scripts gt LiveParameterMap e Start will activate this feature and you can see the selected Parameter as a color map painted during the scan 22 Chapter 3 Quantitative Analysis IMP Software Suite User Manual Release 1 2 e Show force curve when activated will plot the polynomial force curve at the center pixel of every scan line The force plot displays the selected parameter with a line or point on the force curve This type of parameter map can also be applied to scan data file as described in Batch process parameter maps and force volume data 3 2 Analyzing lines and surfaces At one pixel we can analyze data and make a curve of force or interaction energies as a function of cantilever deflection or oscillation amplitude These curves can be parametrized for example by fitting the data to a particular model of the interaction force It is often very interesting to plot how the parameters change along a linear transect of the image This type of analysis can be made in real time with the Line inspector tool You can also run analysis of all pixels in a scan file to produce a color map image of each parameter This later analysis is time consuming and it can be run in a batch processing mode The creation of these different types of parameter plots and maps are described in the following sections 3 2 1 Analyzing Linear
6. 2 tion You must set the host AFM to scan at the given scan rate otherwise the images will not be synchronized Some host AFMs do not allow arbitrary scan rate and it is not necessary that the scan rates match exactly A 1 deviation is not noticeable in the images but one should set the host AFM scan rate slightly smaller than the ImAFM scan rate You can slow down the scan rate using the same measurement bandwidth and pixel rate to help track better on a rough surface normal means scanning at the maximum rate and you can choose hal f or quarter speed Making this choice will result in a new calculation of the scan rate which must be set in the host AFM Slowing down the scan will help to track the surface more closely making the force measurement more accurate You can also change to new values of Osc rangeandMod Range during a scan Input the new values ad press Setup The cantilever will lift and perform a new setup routine adjusting to the new parameters However you can not change the value of Pixel rate df without first stopping the scan and lifting away from the surface Image settings The panel Image Settings contains the controls for displaying which images are plotted e IMP Control lets you select the frequency at which the Amplitude and Phase images are plotted The frequencies are ordered from lowest to highest going from left to right The text below the slider displays which frequency is being plotted e Scan dir
7. Ampli tudes are given in DAU digital to analog units A helping function max_ampl is useful in setting the amplitude A real array p with the phases of all drive tones The length of the array p must be nfreq_out Phases are given in radians A real number asf between zero and one This amplitude scaling factor will set the peak amplitude of drive signal asf 1 corresponds to maximum output voltage of the MLA The default value that you get if you do not specify this variable is asf 0 1 An error will appear in the debug window if asf is out of the range 0 1 asf 1 it overrides this function advanced users only 4 6 2 Synthesize and Configure Synthesize Comb runs the script and plots the comb as an amplitude phase plot in the frequency domain and the waveform in the time domain The MLA can be configured with this comb in one of two ways Configure Drive causes a voltage signal described by the synthesized frequency comb to be put at the signal out port of the MLA Configure Response adjusts the comb at the signal out port such that the synthesized comb appears at the signal in port If the input signal is the detector of an AFM measuring the deflection of a cantilever the actual cantilever motion will be that given by synthesized frequency comb Configure Response assumes that a chain of linear systems actuator gt cantilever gt detector is connected between the output and input ports of the MLA and it wi
8. Transects If the Quantitative Analysis software is installed selecting a line with the Line inspector tool activated will open the Line Inspector panel You will see a plot the amplitude and phase the intermodulation product corresponding to the image showing when the line was selected All data in each pixel along the transect line is selected for analysis with the Model Fit method of force reconstruction e The Line Inspector panel gives a list of all selected lines in the left column The color of the word line in the list corresponds to the color of the linear transect in the Amplitude and Phase images e Right click on the word line and choose Fit model from the menue The currently active model will be fit to the intermodulation spectral data along the transect line and a plot will be generated showing how each parameter of the model changes along the transect Depending on the length of the line and the speed of your computer there may be some delay while the fitting is being performed at each pixel e You can automatically perform the fitting directly after the line is selected by checking the Fit model check box at the bottom of the list of lines e Settings will open the Line Inspector Settings panel where you can activated different force models specify which parameters to adjust and set the intial values of all parameters as described in the Model Fit section e You can test different models along the same linear transect Simply
9. When the tool is activated a right click on either the amplitude or phase image will select the data at the point of click mark it with an X and open the Signal Inspector panel If you have the Quantitative Analysis tools installed in your software the Force Inspector will also open and display a force curve When the pixel inspector tool is active left click on the plot will un select the X nearest to the point of click and remove the data from the Data Tree The Quantitative Analysis tools allow you to analyze the spectral data in many different ways to reveal tip surface interaction The Data Tree allows you to compare different pixels form the same scan or different scans in the same plot 2 2 The Work Flow 13 IMP Software Suite User Manual Release 1 2 N Line inspector tool A left click on the icon will activate the tool When active a right click and drag on either the amplitude or phase image will select a transect line upon release and a left click will un select the line nearest to the point of click The Line Inspector panel will open and a plot of the amplitude and phase of the currently viewed image will be shown All data along this line will be selected and available for analysis If you have the Quantitative Analysis tools installed in your software the line inspector will allow Analyzing Linear Transects and plot parameters of the tip surface interaction along the selected transect Status Banner The banner at the
10. arange the different Panels and Views and create your own custom screen layout Other advanced sections are given for the AFM scientist who wants to experiment with different types of mul tifrequency measurement and analysis The IMP Suite has an Advanced Setup panel and a Drive Constructor to configure the drive tones and measurement frequencies of the Multifrequency lockin Amplifier MLA TM A Stream Recorder is also included to record continuous streams of intermodulation data for analysis with your own software A Scripting Interface is also described which allows you to fully customize your multifrequency mea surements with scripts that run in the IMP suite We also document the ScanData python class which organizes the multi frequncy data With the functions in ScanData you can write Python scripts that analyze an plot the data stored in the scan files e g scan01234 imp 4 1 Intermodulation Measurement Intermodulation AFM ImAFM would not be possible without The Multifrequency Lockin Amplifier MLA also known as the Intermodulation Lockin Analyzer ImMLA see Tholen 2011 The MLA comes in different versions and it can be configured in many ways but a typical configuration for mAFM has the MLA is driving the AFM cantilever with two drive tones and analyzing the response at 32 intermodulation products of the two drive tones such that all frequencies in the response are located close to a high Q resonance Intermodulatio
11. been measured and checked against other methods and according to theory they should apply to any cantilever of the same shape see Sader 2012 For this method the length and width fields have no influence Reference calibration brings up three fields If you have one good calibration using another means such that you know all three constants the quality factor stiffness and resonant frequency or Q ref k ref and 0 ref respectively you can use this calibration as a reference for calibrating other cantilevers of the same shape see Sader 2012 For this method the length and width fields have no influence 2 2 The Work Flow 7 IMP Software Suite User Manual Release 1 2 Thermal tune responsivity brings up a field to enter the known stiffness of the cantilever fundamental eigen mode k N m The thermal noise measurement is then applied to determine the detectors inverse responsivity nm V Thermal tune stiffness brings up a field to enter the known detector inverse responsivity Inv resp nm V The therm noise measurement is then applied to determine the cantilever mode stiffness Manual overrides the thermal noise measurement and no hydrodynamic damping theory is applied All four calibration constants are entered in the fields given the eigenmodes resonance frequency fO Hz dimensionless quality factor Q mode stiffness k N m and the detectors inverse responsivity Inv resp nm V Meas
12. change the model in the Line Inspector Settings panel then right click on the word line and choose Fit Model A fresh plot of the parameters of the new force model will be made along this line A new item is added to the list with each fit that your perform You can always go back to your previous plots by double clicking on that item in the list e Right click on any an item in the list and chose Save to export the results of that fit to a text file You can also save the plot image by clicking the save icon in the Image Toolbar e Right click on any item and select Remove to take it away from the list e Click on the small triangles to expand and contract the list of fits for each line e Right click on either the Amplitude or Phase image with the Line inspector tool activated to remove the line nearest to the right click 3 2 2 Parameter Maps You can fit a force model to every pixel of a scan to create a parameter map or color coded image of the pa rameter values From the Advanced pull down menu select Parameter map to open the Parameter map creator In this panel you may select the Model to fit to the data and the initial values of all parametres as described in the Model Fit section Because the generation of parameter maps using Model Fit is computationally 3 2 Analyzing lines and surfaces 23 IMP Software Suite User Manual Release 1 2 intensive it is often easire to use this interface off line so as not to overload th
13. complete calibration requires a fourth constant that converts the measured detector signal in Analog to Digital Units ADU to actual cantilever deflection in nanometers This fourth constant is called the detector responsivity a ADU m All four constants can be determined from one thermal noise measurement as described in Higgins 2006 Here we give a somewhat different derivation of the method which is based on the idea that the cantilever is in thermal equilibrium with the damping medium at temperature T and that the damping can be calculated using hydro dynamic theory Thermal equilibrium and linear response allow us to use the fluctuation dissipation theorem to relate the power spectral density of fluctuations of cantilever deflection to the imaginary part the dissipative or damping part of the linear response function Saa w 27 Im X w 2kwT my 1G w 1 m Hz The simple harmonic motion gives us the functional form of G w We fit this function to the measured noise peak at resonance thus determining wo and Q To get the magnitude of Saa we require knowledge of the damping coefficient my Hydrodynamic theory and dimensional analysis is used to calculate the damping due to the surrounding fluid air water etc Sader 1997 my Lu Re A Re Here L is the length of the cantilever beam and A Re is a dimensionless hydrodynamic function of the Reynolds number 2 pb wo Re du which is a dimensionless combin
14. cycle see Platz 2012b You may notice hysteresis in the F A and Fo A curves where the integrated force on the up beat increasing amplitude is different from that on the down beat decreasing amplitude This hysteresis can be the result of several things and it is a subject of on going research Some candidate causes are motion of the cantilever base during the beat caused by over active feedback large error signal excessive noise in the measured intermodula tion spectrum plastic deformation of the surface during the up beat strong viscous or inertial forces which delay the recovery of the surface between single oscillation cycles If the hysteresis is small you can treat it as a weak effect in relation to the overall trend and in this case smooth single valued curves can be plotted by selecting mean curveinFI FQ display options Conserved and dissipated work The Work tab brings up a double plot very similar to FI FQ The Conserved Work is simply F A x A and it is that work done by the tip on the surface which is recovered during the full oscillation cycle for example due to a purely elastic interaction between the tip and surface The Dissipated Work is similarly Fg A x A and it represents that work which is lost to heat or irreversible deformation of the tip and sample 20 Chapter 3 Quantitative Analysis IMP Software Suite User Manual Release 1 2 The plots presented in FI FQ and Work are direct transformations of th
15. during the x y scan The probe height h is the position of the base or the fixed end not the position of the tip z at the free end of the flexing cantilever see drawing in the section Force Reconstruction Methods The probe height is controlled by the feedback while scanning and in most modern AFMs the height signal is measured using a linear sensor built in to the scanner When performing ImAFM the height data is recorded by the host AFM To associate ImAFM quantitative analysis with surface topography it is necessary to import the height data in to the IMP Software suite Associate host AFM files e Import height data Navigate to the folder on your host AFM computer network or storage device where the host AFM files are stored When you OK the selected folder the Match Images window opens Drag the image thumbnails from Unmatched IMP images at the bottom and drop them on the corresponding AFM images at the top When you have matched a few images click Match with timestamps and the computer will attempt to associate all remaining files If the matching is incorrect you can drag images away from middle group of Matched IMP images When the matching looks correct click OK and a copy of the AFM height data files will be stored in the ImAFM M session folder with the scan number i e scan01234_ prefixing the host AFM file name The AFM height data will remain in the same file format as the Host AFM Note In DI Veeco Nanoscope software v
16. from zero deflection up to the peak value of the cantilever deflection In this case you set the modulation range to one half of the oscillation range e Pixel rate df is the spacing Af between tones in the frequency comb see Intermodulation Mea surement The pixel rate together with the number of pixels per line determine the scan rate e Resolution x y Sets the number of pixels to acquire in the fast scan direction x and the slow scan direction y The x resolution does not depend on the host AFM setting of pixels per scan line The x resolution together with the pixel rate determines the Scan Rate given by the IMP Suite The scan rate must be set on the host AFM to the value given by the IMP Suite The y resolution must also be set to the same value on the host AFM which determines the number of scan lines at the given rate e Setup runs a routine to determine the frequency and amplitude of the two drive tones If you get an Out of Range Error message you may need to adjust the oscillation range or attenuate the input signal see Advanced Setup This automatic setup is designed for basic ImAFM with two drive tones close to resonance Much more complicated measurements and modulation schemes can be setup with the Drive Constructor When the setup is complete the Scan button will not have gray text indicating that you are ready to scan Scan makes the software ready to acquire measurement data After pressing Scan e Set the sca
17. is not zero The thermal noise force is the square root of the power spectral density of force fluctuations Spr w fN WHz The force noise power spectrum is independent of frequency Spy 2kgT my and this type of white noise arises whenever the damping force is simply proportional to velocity With this thermal noise force we can calculate a minimum detectable force Finin or the force measured with SNR 1 in a given measurement time T measurement bandwidth B 1 T For example The scan speed and image resolution dictate a pixel time of T 1 ms and the thermal noise force is Spr 22 fN VHz The minimum detectable force at each pixel is therefore Fmin VSrrB 696 fN This minimum force is the signal which just equals the noise A good measurement is typically characterized by a signal which is many times the noise level or SN R gt 1 Note that you must scan 4 times more slowly to decrease Fin by a factor of 2 The detector Noise floor is the second quantitative measure of sensitivity If the measurement time is short or if you measure at frequencies away from the high Q resonance SN R is typically not determined by the actual force noise of the cantilever in its damping medium but rather by the electronic noise of the detector Spp We express this detector noise as an equivalent deflection noise by dividing it with the detector responsivity ssa a Spp Here again we assume that the detector noise is independent o
18. it The following files are generated by the IMP Suite and stored in a session folder calib01234 txt noise data and fitted calibration parameters see Calibration calib01234 png image of plot in calibration view sweep01234 txt frequency sweep data see Frequency Sweep sweep01234 png image of the frequency sweep plot scan01234 imp data for one scan including the current calibration in HDF5 format recorder01234 imp continuous stream of data taken in frequency mode see Stream Recorder recorder01234 std continuous stream of data taken in time mode scan01234_model npz parameter map data for the fitted model see Parameter Maps scan01234_p name png color map image of the parameter p name sessionlog txt chronological session log see Session Logbook You can always export an image of any plot that you see on screen by clicking the save image icon in the Image Toolbar which will bring up a save dialog box with several file format options You can also export raw data and the results of analysis to a text file using the Data Tree 4 10 File Management 45 IMP Software Suite User Manual Release 1 2 4 11 Panels and Views All views or screen layouts have a main panel to which auxiliary panels can be docked Several views are pre defined and they appear when clicking icons in the left column symbolizing the The Work Flow Icons for the advanced panels appear when selected in the advanced pull down menu To removed
19. of the curve is due to the fact that the intermodulation spectrum of odd order products is only able to reconstruct the polyno mial coefficients gj with odd j see Platz 2013b If this odd F d curve shows a well developed zero force region for d gt do then we can safely neglect long range forces and the assumption that F d 0 for d gt dy is well motivated Move the slider to change do Model Fit The Model Fit method assumes that the tip surface force is described by a particular interaction model which has some number of parameters The method performs a numerical optimization adjusting the parameters of the model so as to best reproduce the measured frequency components of the tip surface force The method is described in detail in Forchheimer 2012 Forchheimer 2013 Platz 2012a Nearly any model can be fit to the experimental data so long as it can be coded on a computer However the solver will spit out a solution and the software will give you a plot which looks like your force model even if it is a lousy fit to your data Model Fit should always be used together with Polynomial or ADFS in order to independently check if the model makes sense Model Fit also requires reasonable initial conditions for the solver to converge to a good solution Model Fit reconstruction has the following options e line style gives some plotting options for line type and thickness Choose model selects the different force models that are
20. performed at the outset of ImAFM M and the free motion is measured before scanning It is easy to re do either of these at any time during the session We recommend that you check the calibration and perform a new measurement of free oscillation occasionally to see if the results are consistent with previous measurements The most recent calibration data and free motion spectrum are stored with each scan at the end of the scan These measurements are an important part of the analysis of the scan data The focuses in this chapter is on how to use the software to perform different methods of analysis References are given to the scientific literature where the fundamental physics and mathematics of the force reconstruction methods explained are explained in detail 3 1 Inspecting single pixels The intermodulation spectra at individual pixels can be analyzed by selecting the data with the Pixel inspector tool This puts the data in to a Data Tree and it allows you to examine it in the following panels 3 1 1 Signal Inspector Activate the Pixel inspector tool in the Image Toolbar and left click on a point in either the Amplitude or Phase image to select a pixel right click to de select The data from this pixel is moved to the Data Tree and the Signal Inspector panel opens where you can see the tip motion durring the selected pixel time You can display the motion in the following ways e Time signal shows a very dense plot of fast oscillations w
21. port C on the front side of the Dulcinea controller In the WXsM software open the Dulcinea BNC monitor and set C 800 kHz to Normal force in order to output the cantilever deflection signal The feedback signal generated by the MLA is put into channel 7 on the rear side of the controller Open the feedback panel in the WXsM software View gt Feedback and set the Feedback Channel to CH 7 Set the the setpoint in the scan control panel to 0 V To configure the trigger signals open the User Digital Signals panel View gt Digital Signals and choose the configuration lt Customize gt Set channel 0 to Image and channel 3 to X ramp Now the Dulcinea controller outputs an EOF trigger on channel 0 and an EOL trigger on channel 3 at the digital signals connector at the rear side of the controller Please note that channel 0 corresponds to pin 2 and channel 3 to pin 9 on the connector Before starting to scan the voltage offset of the feedback channel 7 has to be adjusted Proceed in the ImAFMTM work flow until you have setup the piezo drive and the feedback my clicking on Setup in the Scanner Panel Now open the Input menu in the WxSM software View gt Inputs select the tab for channel 7 and click on Tune offset If the signal in the scope view of channel 7 is now at 0 V the tip can be engaged Make sure that there is no offset filter active when looking at channel 7 in the WXsM software Hardwar
22. static independent of time deflection of the cantilever Finding this one constant is sufficient to determine a static force F which gives rise to the static deflection d d 2F 26 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 1 2 ImAFM is a dynamic method where force is determined from cantilever motion d t A linear relation be tween force and motion also exists for dynamic AFM if deflection is small in comparison to the cantilever length However due to inertia and damping the constant of proportionality is frequency dependent d w 1G w F w The frequency dependence is contained in the dimensionless factor G called the transfer gain and the hat denotes an imaginary quantity with the real part being the Fourier cosine component and the imaginary part the sine component at the angular frequency w The complex frequency dependent quantity which relates each frequency component of the force to the component of the motion at the same frequency is called the linear response function and it is usually denoted w For the simple harmonic motion of each eigenmode of the cantilever a A 25 X w LG uo 000 Q H 12 SI Three parameters are needed to calibrate each eigenmode The mode stiffness k resonant frequency wo y k m and the quality factor Q wp 7 or alternatively the mode stiffness effective mass m and viscous damping coefficient my where 27y is the width of the resonance in Hz A
23. the advanced icons select again in the pull down menu Different panels appear when you click Settings buttons or they can be chosen from the Analysis pull down menu You can add these panels to the views or rearrange the panels in a view according to your desire Movable panels have a shaded grab bar on top where the panel name is located These panels can be free floating or you can dock them to a particular view e To un dock a panel click and drag the panel bar Release when it is un docked and it will be free floating A double click on the panel bar will also un dock the panel e To dock a panel click and drag the panel bar of a free floating panel and panel position icons will appear Move your mouse cursor to the desired dock location on the icon and your screen will show a shaded area Upon release the panel will dock to the shaded area IMP Control 279 8 kHz n 5 Amplitude uncalibrated OE 279 8 kHz n 560 Scan direction 9 Trace JRetrace Swap Panel dock icons Flip left right Flip up down 279 8 KHz n 560 Phase deg Osc rang 60 0 nm Mod range 30 0 nm Pixel rate df 0 5 kHz Setup Scan Measure free Amplitude set 06 75 0 normal Scan Rate Hz Resolution y256 IX IB z Y Autosave F 46 Chapter 4 Advanced Topics CHAPTER FIVE INSTALLATION 5 1 Install Software The IMP Software
24. the feedback set point set to zero volts The MLA gener ates a fake deflection signal and the host AFM will preform scanning feedback on this signal see Connection to host AFM The feedback parameters integral and proportional gain are set in the host AFM software The default scanner view has three components The Scanner panel the Image Settings panel and the main view showing the Amplitude and Phase images More panels can be added for example when you want to perform analysis as you scan making force curves or analyzing transects These panels will be addressed in the section on Quantitative Analysis Here we describe how to setup and execute the first scan Setup and Scan Three controls in the Scanner panel specify the parameters for Setup There must be a Current calibration in order for the setup to function e Osc range is the desired maximum amplitude of oscillation peak to peak in nanometers of the can tilever when it is free from the surface When the surface is engaged the oscillation range will be somewhat reduced depending on the Amplitude set point 10 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release 1 2 e Mod range is the range over which you want to modulate the amplitude The amplitude will be modu lated from the minimum value Osc range Mod range toamaximum value Osc range The tip surface forces will be measured over this range Typically you want to measure
25. the image in pixels Resizing the viewer to changes these numbers and their aspect ratio Background color can be chosen to something other than the default gray e Text color will effect the X and Y size labels Sample settings e Z scale sets the aspect ratio of the Z scale in relation to the X and Y scales This aspect ratio is displayed below the image together with the Peak height in nanometers or the height of the tallest feature in the image e Parameter is pull down menu listing all parameters of the model which was fit to the scan data Here you select the parameter which you want to display as a color map on the 3D view of the height data Note that parameters which where were unchecked in the fit settings were not adjusted and will therefore show only one color corresponding to their fixed value e Limits opens up a window with a histogram of the parameter values The shaded region is that covered by the color bar Everything outside this region is displayed as white You can click and drag on the left and right edges of this region to adjust the color bar limits or input the Min and Max values manually The check box at the top allows you to activate an automatic routine to adjust the limits excluding the given percent of pixels in the upper and lower tails of the histogram Camera position e Azimuth and Polar angles can be entered as degrees or left click and drag on the 3D image e Distance is changed by adjusting the con
26. the microscope before the controller or any other ancillary equipment You can also use the SAM provided by DI Veeco Bruker which gives access to many other signals but has some cross talk between signals which degrades performance and it requires two switches to change between normal operation and ImAFM M The actual connections on the DI Veeco Bruker SAM depend on which version you have and which controller you are running Consult your DI Veeco Bruker manual when making these connections Contact Intermodulation Products if you have any troubles as we have found errors in some versions of these manuals See SAM II connections for an image showing a typical connection The trigger signals on the NS IV controller are accessible from BNC connectors on the back side of the controller On the NS III and NS Illa controllers they are accessible via BNC connectors located inside the controller box You need to remove the lid to access these connections If you would like a more clean solution you can install connectors on the front of the controller You need to remove the front panel and drill two holes for this installation Intermodulation Products can provide the necessary cables and advice See Nanoscope III and Illa Trigger Access for images and detailed instructions on accessing the trigger signals 5 4 2 Nanoscope V The NS V controller is currently sold by Bruker for most of their AFMs e g the Icon and Fast Scan AFMs If the NS V is runn
27. 0 kSam sec A standard configuration uses OUT A for AFM feedback Back side connections e POWER is supplied to the MLA via an external power supply Use only the power supply delivered from Intermodulation Products Using any other supply voids the warranty ETHERNET The MLA communicates with the computer via the Ethernet connection The MLA may be directly connected to the Ethernet connection on the computer or it may be be put behind an Ethernet router switch or gateway e RF CLOCK IN and RF CLOCK OUT connections are used for synchronizing the internal clock of the MLA with the clock of some other piece of measurement equipment They receive and send respectively a 10OMHz square waveform Furthermore they are AC coupled and have a voltage range of 2 Vpp Other frequencies and voltage levels are available upon request These ports are designed to connect to a 50 Ohm matching impedance and signal distortions may occur if the receiving or sending connection is not 50 Ohm on the other end e TRIG 3and TRIG 4 are additional trigger ports When running with an AFM using the composite con nection to the AUX port e g Bruker Icon or FastScan Trig 3 reads the EOL trigger and Trig 4 reads the EOF trigger e AUX is designed for a composite cable connection to certain AFMs e g Bruker Icon and FastScan This port may be empty with your version of the MLA 6 3 Firmware There many possibilities to configure the lo
28. 1 2 e Use Correction will correct the measurement for an arbitrary linear frequency dependant transfer function embedded between the output and the input points of the measurement chain e Set Correction stores the last measured transfer function to an internal file which is used for the correction 2 2 2 Calibration Quantitative AFM starts with a good calibration of the cantilever and ImAFM requires this calibration before you start to scan a surface The IMP Software Suite contains the latest methods for cantilever calibration based on the measurement of the thermal Brownian motion of the cantilever and a theory of hydrodynamic damping of the oscillating beam By fitting a theoretical model to the noise data we determine all constants necessary to the measure the cantilever deflection in meters and convert this deflection to force in Newtons The calibration procedure applies to a particular cantilever eigenmode resonance Details and references to the literature are given in the advanced section on Noise Calibration Here we describe how to perform the calibration The tab at the very top selects between calibration of a Flexural or Torsional eigenmode The procedure is very much the same for either type of mode but the underlying formulas and analysis are different We begin by describing calibration of flexural eigenmodes and end with a discussion of torsional eigenmodes Choose Cantilever and Method Calibration Parameters speci
29. CONNECHONS ense La eee eG SU Re eS es 63 Firmware lt 6 4i5 Be Poe Cedie A 6 4 MLA version I before 2015 7 Trouble Shooting 8 References Bibliography CONTENTS 57 E ek ee grat ek EE 57 ee ee 57 paced OG es Bee et uber e a 58 itt iey bo eM de ee wee 59 61 63 65 IMP Software Suite User Manual Release 1 2 Contents CONTENTS 1 IMP Software Suite User Manual Release 1 2 2 CONTENTS CHAPTER ONE INTRODUCTION The Intermodulation Products Software Suite IMP Suite from Intermodulation Products AB is a collection of software tools for performing Intermodulation Atomic Force Microscopy ImAFM a powerful surface analysis method based on multifrequency AFM This manual explains how to use the IMP Suite through its Graphical User Interface GUI The manual is used most effectively when the IMP Suite is open and running taking data with your host AFM or analyzing already scanned data 1 1 Conventions and useful tips D The IMP help icon appears at several places in the IMP Suite Clicking on this icon will open a browser and jump to the appropriate place in the manual Screen text is denoted with a shaded box and it should coincide exactly with text in the IMP Suite on a button or next to a check box or input field The genindex contains key words and important screen text Each entry is linked to the appropriate place in the manual If you are wondering about th
30. Digital Units ADU or in nanometers nm You must have a Current calibration in order to display in nanometers 32 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 1 2 4 5 5 Out of Range Error The MLA is designed to handle signals within a normal range for a typical AFM Depending on your AFM and our experiment these normal range settings may need to be adjusted When the input signal exceeds the maximum clipping occurs inside the MLA and this induces harmonic and intermodulation distortion in the spectrum One way to avoid this problem is to simply attenuate the input signal Intermodulation Products provides attenuators to place at the SIGNAL IN port for this purpose Note however that a large signal coming from an AFM detector may bring the detector close to saturation which also gives harmonic and intermodluation distortion of the spectrum Furthermore a cantilever will behave with a nonlinear restoring force when it is driven to very large response amplitude One should be careful not to confuse these sources of nonlinearity which result in harmonic and intermodulation distortion of the free cantilever oscillation with harmonic and intermodulation due to a tip surface force The output signal should also not exceed the maximum or be too small in order to avoid distortion in the MLA The requested drive amplitudes Al and A2 are given in percent of full output the actual values a
31. Dragging hori zontally will zoom only the x axis dragging vertically will zoom only the y axis Dragging at an angle controls the relative rate of zoom of each axis Right click and drag will grab the plot at the point of click and slide it in the direction of the drag Performing these actions while holding down the x y or ctrl keys will restrict the pan or zoom to occur only in the x axis y axis or preserving current aspect ratio respectively aP Zoom When selected a right click and drag over the plot will zoom to the selected rectangle upon release es Save image Opens a dialog box for saving the image in several formats png eps pdf and more Sometimes you would like to change the aspect ratio of the plot or the relative size of the frame and text in your saved image Simply rescale the entire suite click and drag on the lower right corner or re size a particular frame before you save This action will rescale the plot and axes while keeping the text and line size fixed E Configure subplots The subplots icon opens up a dialog box to adjust the placement of the plot axes within the plot frame Selecting Data in a Scan Two important tools in the image toolbar are the pixel inspector and line inspector tools These tools do more than simply controlling the plot They select data at pixels and analyze the data to generate force and parameter plots x Pixel inspector tool A left click on the icon will activate this tool
32. FM The normal user will not need to be concerned with these files drive_setups Contains the file user_drive_setups py which is a Python file containing the scripts for the Drive Constructor both example scripts and user constructed scripts force_models Contains Python files with the force models You can add your own force model files here by copying and modifying example py When you restart the IMP Suite this file will be re loaded and your model will appear as a new force model scripts Contains Python scripts which can be sued to control different measurement schemes and create different modes This is for advanced users who will require some knowledge of the basic Python objects in the IMP Suite A few examples are given in Examples py config ini This is the main configuration file which is dynamically changed by the IMP Suite The normal user will not need to be concerned with this file If it becomes corrupted it can be deleted and a new file will be created with default values upon restart of the IMP Suite 4 10 1 File Types The IMP Suite generates files with a name indicating the type of file followed by an automatically incremented 5 digit counting number denoted 01234 below You are free to append an underscore followed by any valid file text after this counting number e g scan01234_my file text imp You may experience problems keeping track of your files if you remove or modify this number or the type name before
33. Intermodulation products IMP Software Suite User Manual Release 1 2 Intermodulation Products AB May 26 2015 1 Introduction 1 1 Conventions and useful tips 1 2 Screen Layout sos es ae miopie som eee dd we iy k 13 Python e sie ee rt oe a ok ae Kea wa 2 The IMP Session and Work Flow 2 1 Quick Start 4444 hAa wee a Se Re PS A aS 22 The Work Flows 54 8 as ee oe A AS Sok ee eG 3 Quantitative Analysis 3 1 Inspecting single pixels 0 0 3 2 Analyzing lines and surfaces 4 Advanced Topics 4 1 Intermodulation Measurement 200 4 4 2 Noise Calibration s lt ss a 2 64 ce ede ends 4 3 Programming your own Force Models 44 Data Trees netos cs a a Ake S 45 Advanced Setup se e re dou pis geo bee ee EE 46 Drive Constructo cs os md bb A EEA 47 Steam Recorder silba ee dicho e e eek ore ha Beets 4 3 Scripting Interface vota Rea we ee q Scam Diao ia deck a gt aco Bee 2 ye Bp de GS Rg 4 10 FileManagement 0 4 11 Panels and Views 4 lt 5 24644 e08 44444414 5 Installation Sil Install Softwares nee 4 aoe aoe be Edo be Gee 4 5 2 Install Hardwate 2 2424 0 44 2 6e 44264 445 2445 9 Set AFMTYp ii es a See hk a ces rel hs Ee Sey ew 3 4 Common AFMS se esa te So a Meal a Sh aS 6 The Multifrequency Lockin Amplifier MLA Gil Capabilities o 00 54 244 e680 4 Abe Se ek Ae eR 6 2
34. M which happens to be close to resonance Change cantilever and avoid the frequency of the spurious signal e You can exclude data points to avoid frequency bands where spurious signals and additional noise is getting in to you measurement e There may be an extra not thermal source of noise which is driving your cantilever Make sure the drive from the host AFM is off and disconnected Try turning off the high voltage drive to the Z piezo in a tip scanning AFM Problem When I open the software only get the Analysis and Session Overview icons in the work flow Solution This means that the software can not find the MLA on the ether net Check that the MLA is connected to the ether net and verify that the computer has ether net connection to the MLA 61 IMP Software Suite User Manual Release 1 2 62 Chapter 7 Trouble Shooting CHAPTER EIGHT REFERENCES 63 IMP Software Suite User Manual Release 1 2 64 Chapter 8 References BIBLIOGRAPHY Forchheimer 2012 Model based extraction of material properties in multifrequency atomic force microscopy Daniel Forchheimer Daniel Platz Erik A Tholen and David B Haviland Phys Rev B 85 195449 2012 Forchheimer_2012 Forchheimer 2013 Simultaneous imaging of surface and magnetic forces Daniel Forchheimer Daniel Platz Erik A Tholen and David B Haviland Appl Phys Lett 103 013114 2013 Forchheier_2013 Higgins 2006 Noninvasive det
35. Suite is installed with a standard installer When you install the software you agree to the terms of the IMP license The IMP software Suite can be run on the same computer as the host AFM or on a separate computer It is advantageous to run the IMP Suite on a modern computer with a multi core processor especially when analyzing full images to make Parameter Maps If the IMP Suite does not detect the The Multifrequency Lockin Analyzer MLA upon starting it will open up in analysis mode In analysis mode you can plot and analyze data taken previously but you can not take data You are free to install the software on as many seperate computers needed to analyze your data To take data you mast start the IMP Suite when connected to the MLA and a host AFM as described below 5 2 Install Hardware Connecting the hardware the first time requires some effort However if things are configured nicely one or two hardware switches is all that is needed to switch between the normal configuration of your host AFM and the ImAFM configuration The MLA is connected to the host AFM via a signal access module SAM provide by Intermodulation Products or your AFM supplier The MLA is connected to a computer running the IMP Suite via Ethernet either the same computer used by the host AFM or a seperate computer 5 2 1 Connection to computer The IMP Suite will open analysis mode when it does not detect an MLA connected to the computer To es
36. The shell 1s for advanced users who will need the developer documentation to use this feature effectively Delete removes the pixel from the data tree The cross will also be removed from the image and the plots from the Fore Inspector panel You can also remove any pixel by right clicking close to that pixel in the image when the Pixel inspector tool is selected Save time data to text file to export the cantilever deflection vs time during the time window for this pixel This data is is actually the inverse FFT of the spectral data taken by the MLA with some zero padding to give appropriate sampling in the time domain Save spectrum data to text file to export create the raw spectral data measured by the MLA at this pixel Save FI FQ data to text file to export the FI A and FQ A data for this pixel see In phase and quadrature forces The check boxes at each pixel and each force reconstruction controls plotting Un check to remove the cross from the image or plot from the Force Inspector panel without actually removing the data from the data tree Checking the box will show the plots again Pixels selected in the current scan will not be removed when a new scan is generated When the scan moves passed a selected pixel the image no longer corresponds to the selected pixel Selected pixels must be removed manually in the current scan Clear Allinthe Force Inspector panel removes all selected pixels in all scans Right click on a
37. _freq values append_lo_scan_rates val Append the list of scan_rate values append_lo_tip Vac val Append the list of tip AC voltage values append_lo_tip Vdc val Append the list of tip DC offset values append_setpoint setpoint linenr 3 Append a setpoint to the setpoint history The optional linenumer argument can also be negative linenr 1 changed in last image linenr 2 during setup linenr 3 unknown point of time equal_array arl ar2 Checks to see 1f two arrays have equal length Parameters e arl np array e ar2 np array Returns True or False Return type bool get_Q Returns dimensionless quality factor Return type float64 get_change_linenr Return the current value of change_linenrs i e the last in the list get_delta_f Return the current value of delta f i e the last in the list get_drive_amplitudes return the current i e latest drive amplitudes get_drive_karray Return the current value of drive_karray i e the last in the list get_drive_phases return the current i e latest drive phases get_external_ filename get_feedback Return the current value of feedback i e the last in the list get_free_oscillation Return the current value of free_oscillation i e the last in the list get_free_oscillations_complex num 1 40 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 1 2 get_imp_karray Return the c
38. aken at one location center of the fast scan axis and the plot is updated at the line frequency 38 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 1 2 4 9 Scan Data The IMP Software Suite stores data from a scan including all relevant metadata in one compact file with the file extension imp e g scan01234 imp The ScanData class manages the storage and retrival of the data If you want to write your own Python scripts to analyize multifrequency data taken with the IMP Software Suite you will need to use the ScanData class The documentation below was auto generated from the doc strings in Python code at the time this manual was compiled You can always see the documentation of the actual class version that you are using in the Python code itself using auto complete with any good Python API Advanced Programming Interface 4 9 1 Using the ScanData class Below are some example scripts which demonstrate how to load the ScanData class and get at the data stored in the scan file Can we make some kind of structure like matplot lib to exand tp see soruce code or result of run example of how to imshow the phase of particular frequency example of how to exchange the free oscillation with a particular pixel 4 9 2 ScanData Class class Scanner ScanData ScanData args Handels the storage and retreval of data from the scan file e g scan01234 imp This class is designed to be easily extendable and new fu
39. ame plot in the analysis view In the analysis view you will find the Image settings panel the Image Toolbar and the Color Bar which have functions previously described With the Pixel inspector tool and Line inspector tool you can select individual pixels and lines for Quantitative Analysis Image Smoothing The analysis panel has an additional Smooth image button which opens a smoothing dialog box where you can apply a Gaussian filter to your scan data This filter will convolve the stored intermodulation data with a Gaussian function of width in x and y given by Sigma in pixels The result is a new image stored to the given File name Where each pixel of the new image is a weighted average of neighboring pixels in the raw scan data file Smoothing with one pixel results little loss of sharpness in the image but it lowers then noise considerably The Gaussian has 98 of the weight within 3 Sigma of the center so smoothing with one pixel essentially averages a block of 9 pixels giving an improvement in the signal to noise ration by a factor of 3 This is a smart way to improve the signal quality without increasing the measurement time based on the assumption that neighboring pixels are more likely to have the same response Note however that smoothing does introduce a correlation length 14 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release 1 2 to your data which you can clearly see as a grainularity in hig
40. are willing to reduce the number of drive frequencies Contact Intermodulation Products if your experiment needs custom firmware 6 2 Connections Your MLA may have a clean front panel with out any connections as is the case when it is configured to be used with some AFM s where all connections are made from the back side via a composite cable Consult the MLA configuration sheet delivered with your instrument to see the precise configuration of all connections for your instrument The standard connections are briefly described below Front side connections 57 IMP Software Suite User Manual Release 1 2 e TRIG 1and TRIG 2 are trigger ports In a standard configuration these are configured to receive End of Line EOL and End of Frame EOF trigger signals respectively e IN land IN 2 are fast inputs which can operate at a maximum of 250 Msam sec The exact speed of these ports can be configured from the software The frequencies analyzed at these inputs are set by your firmware configuration e IN 3and IN 4 operate at a maximum of 62 5 Msam sec The exact speed of these ports can be configured from the software The frequencies analyzed at these inputs are set by your firmware configuration e OUT landOUT 2 are fast output ports The user can specify at run time which drive frequencies are sent to which output ports e OUT A OUT Band OUT C are three slow output ports run time controllable by the user combined speed is 80
41. ation of the resonant frequency the fluid density p and viscosity u and the width of the cantilever b The hydrodynamic function A Re has been calculated for arbitrary rectangular beams with length much larger than width L gt b Sader 1998 However the general theory applies to thin cantilevers of ar bitrary shape and A Re has been determined experimentally for the fundamental eigenmode of some commercial cantilevers with non rectangular shape Sader 2012 The deflection noise of the cantilever must be multiplied by the detector responsivity a to convert it to the measured quantity ADU Since the cantilever noise is statistically independent from the detectors own noise we can simply add their noise powers to get the total noise power spectrum at the output of the detector Su w ADU Hz Spp a Saa w We fit this expression to the measured data with a wo Q and Spp as fitting parameters Using the value of wo determined from the fit we can calculate the Reynolds number Re and thereby the hydrodynamic function to determine the damping coefficient my This coefficient together with the value of w and Q determined from the fit give the mode stiffness k Thus thermal equilibrium linear response theory and the hydrodynamic damping theory together give us all quantities needed to determine the linear response function of the cantilever and the detector It is important to point out that the hydrodynamic damping function and the
42. ckin measurement by changing the firmware The standard firmware uses a naming convention where the number of frequencies analyzed at each of the input ports is specified as in the examples below for a 42 frequency lockin e IMP 42 0 0 0 Response is analyzed at IN 1 only e IMP 0 0 42 0 Response is analyzed at IN 3 only e IMP 21 21 0 0 Response is analyzed at both IN 1 and IN 2 with 22 frequencies at each input e IMP 11 11 10 10 Response is analyzed at all inputs IN 1 IN 2 1N 3and IN 4 with 11 11 10 and 10 frequencies respectively The 42 frequencies that are measured may also be chosen as drive frequencies An output mask controls which drive frequency is applied to the ports OUT 1 or OUT 2 or both If you do not want to drive and only analyze response at one frequency simply set the drive amplitude to zero and set the mask so that frequency is not applied to either port Contact Intermodulation Products if these standard versions do not meet your needs lt info intermodulation products com gt 58 Chapter 6 The Multifrequency Lockin Amplifier MLA IMP Software Suite User Manual Release 1 2 6 4 MLA version before 2015 The original version of the MLA has one input port and two output ports Contact Intermodulation Products lt info intermodulation products com gt if you would like to upgrade to the newer version 6 4 1 Version connections Front side connections Signal OUT sends the drive freque
43. cs IMP Software Suite User Manual Release 1 2 sessions This folder contains session folders Each time you start the IMP Suite a dialog box opens to create a new or add to an existing session folder The default name of the new session folder is the date but you have the option to append a session name to the date When Autosave is checked see Status Banner data is automatically stored in the session folder scan files calibration files stream files the session log etc When you analyze data to create new files or import host AFM data files the default behavior is to always store everything in the session folder settings This folder contains many files that are changed dynamically by the IMP Suite and configuration files for different AFMs Normal users do not need to work directly with these files but advanced users may want to modify them If these files become corrupt they can be discarded and the IMP Suite will automatically recreate the files with their default values on the next start of the IMP Suite The settings folder has several sub folders calibration Contains several text files with the calibration constants for each type of cantilever pro grammed in the IMP Suite including those created by a user There is also a file fluid txt containing the density and viscosity of the various fluids that you may want to work in configurations Contains files for configuring the IMP Suite to work with your particular host A
44. d drag 30 Phase deg Set limits manually by clicking and dragging in the histogram or use text boxes below Min 37 1 Max 139 e Right click on the color bar to see a histogram of the plotted values You can adjust the image contrast by left click and drag on the borders to the shaded region These borders mark the max and min values for 12 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release 1 2 the color map used Data outside the shaded region is forced to either min or max If the check box is activated the software will automatically choose the max and min excluding the given percent of outlying values You can also change the color map in the histogram window e Click and drag upward or downward on the color bar to adjust the minimum and maximum values re spectively The color value of the center will remain constant You can do this action with the histogram open e Double click on the color bar to return to the automatic setting settings Image Toolbar All plots and images have a toolbar with the following functions sal Q Home Forward and Back tools The home tool to returns to the initial plot or the full image The forward and back buttons move through the successive plot views which the software remembers after each zoom or pan action Pan Zoom When selected left click and drag will cause the plot to zoom starting from the point of click
45. d is described in detail in Platz 2012a Platz 2013b Polynomial reconstruction has the following options 3 1 Inspecting single pixels 21 IMP Software Suite User Manual Release 1 2 e line style gives some plotting options for line type and thickness e Maximum IMP order is largest order of intermodulation product used in the determination of the poly nomial coefficients High order intermodulation products have lower signal level and depending on your scanning conditions they will disappear into the noise at some maximum order The maximum order should be set to the largest order IMP which has a reasonable signal to noise ratio SNR You can judge the signal the SNR by simply looking for contrast in the amplitude and phase images of any order IMP Polynomial degree is the number of coefficients N in the polynomial approximation of the force This number can not be greater than the maximum order intermodulation product in your spectrum e Assume localized force check box activates the routine to determine the even polynomial coef ficients Zero force region sets the crossover deflection dy above which the tip surface force is assumed to be zero The range is given in normalized coordinates where 1 0 means closest to the surface and 1 0 means furthest from the surface If you uncheck this fitting option you will reconstruct a force curve which is an odd function of deflection F d lt 0 F d gt 0 The odd nature
46. different firmware running on the FPGA Contact In termodulaiton Products if your experiment needs custom firmware The different firmware configurations are accessed from the Advanced pull down menu Select Load configuration and choose the desired version After making this selection you must quit the software cycle the power on the MLA and restart the software in that order 6 1 Capabilities Triggering Up to 6 trigger ports are possible any of which can either input or output a trigger signal configurable to different voltage levels Inputs Total of 4 input ports The sampling rate is configurable Two high speed ADC are 14 bit maximum 250 MSam sec and the other two ports are 16 bit maximum 62 5 MSam sec Outputs Two output ports have 16 bit DAC running at 500 MSam sec Up to 4 additional slow output ports are also possible with 16 bit DAC having a combined speed of 800 KSam sec Lockins As many as 42 independent non interfering lockins can run simultaneously At run time the user can send a drive tone at each frequency to either or both of the two output ports The frequency amplitude and phase of each drive tone is selected by the user at run time Both quadratures of response are measured at the user selected frequencies Firmware controls the total number of frequencies and the firmware controls which of 4 inputs will analyze the user selected frequencies Analysis at more than 42 response frequencies is possible if you
47. e If you change the set point by a large amount for example from 95 to less than 50 it is a good idea to re run Setup feedback The new set point values are active as soon as they are entered in the field and you hit return or tab The feedback port sends out an error signal for PID control of the Z scanner This feedback error signal is put back in to the host AFM controller in the place of the cantilever deflection signal If the host AFM is set to contact mode with the feedback set point in the AFM software set at zero volts the AFM s PID control will adjust the Z piezo to keep the error signal at zero volts or the value of the set amplitude The feedback gains are adjusted in the host AFM which is actually performing the feedback using the error signal is calculated by the MLA For example If the set point is set to 85 the system will engage the sample until the response amplitude at the feedback frequency drops to 85 of its free value When this 85 condition is met the MLA will have zero volts at the feedback output In our experience this amplitude feedback scheme is sufficient for tracking most surfaces When scanning large areas on rough surfaces the feedback has to respond rapidly in order to track the surface and rapid adjustments of the cantilever base height are necessary Force measurement is very difficult when the cantilever base is rapidly accelerated by an over active feedback This acceleration gives rise to add
48. e Connection images SAM III connections Fig 5 1 Typical connections for the SAM from Veeco Digital Instruments The images shows the SAM III connected to a Dimension 3100 AFM These connections may be different depending on the controller AFM and SAM versions The switches in the image are in the position for ImAFM M left for ImAFM right for normal AFM 5 4 Common AFMs 51 IMP Software Suite User Manual Release 1 2 Nanoscope lll and Illa Trigger Access Fig 5 2 Remove the 4 screws in each corner of the lid on the NS III or NS Illa controler Nanoscope V Connections JPK Nanowizard Ill Connections 52 Chapter 5 Installation IMP Software Suite User Manual Release 1 2 AAO M SANV 0 9 LV DIAS LNALNO Al sa i Ror eo Fig 5 3 Connect the End of Line EOL and End of Frame EOF triggers to the BNC connectors on the circuit board as shown The images shows cables which bring the these connections to BNC bulk head connectors mounted on the front panel of the controler NanoScope Illa Scanning Probe Microscope Controller di Digital IE Instruments Veco Metrology Group Fig 5 4 BNC bulk head connectors giving access to EOL and EOF connectors on the front panel 5 4 Common AFMs 53 IMP Software Suite User Manual Release 1 2 Switches left for ImAFM right for normal AF UFT TOGGLE TO CHANGE smes macht SS poe unm pod from Signal OUT Fig
49. e Dependent Force Spectroscopy ADFS on each pixel of an image The sett ings button opens a dialog with options similar to that for Parameter Maps Save to HDF5 will create one file containing an ADFS force curve at each pixel whereas Save to ASCII will create a folder with one file for each pixel where the pixel coordinates are given in the file name e Start the batch processing for all checked scans A status bar tells you how far the batch process has progressed Abort will end the process storing the data analyzed thus far It is not possible to resume an aborted process Three dimensional viewer To generate a three dimensional view you must have imported the height data from your host AFM Double click on the height image to open the IMP 3D viewer If you have generated a parameter map for the scan in question the 3D viewer will paint a color map of a parameter on to a 3D projection of the height data In the Viewer settings group the check box Same color bar 16 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release 1 2 will force the 3D viewer to use the same limits for all parameter images of the same type This feature makes it much easier to compare parameter maps between different scans When the viewer is open you will see functionality for Save image as where you can save to a desired location and choose between several different file formats Image settings e Choose the Size of
50. e computer while scanning Pa rameter maps can be generated while scanning using a method based on Fast Polynomial You may PPLY either method to your scan data files from the Batch process parameter maps and force volume data where you can also display the maps as 3D images projected on to the height data Analysis is controlled with the following options scan direction allows you to choose either the trace or retrace data for analysis CPU processes controls how many cores are used when multi threading the fitting Fitting a large number of pixels will load the CPU and it may be too sluggish to use while scanning Adjust this parameter to find a good balance between time to output and response time of your computer e X Y coarse graining controls THE number of fits to be performed If this factor is set to n fitting will be performed on blocks of n x n pixels If it is set to 1 all pixels will be analyzed Increasing this factor reduces the number of calculations and thus the time to output by a factor n and it results coarse grained map e At the bottom is a list file names that are open in the Analyze Scan Data view All checked files will be analyzed with the same model and initial conditions The bar below each file indicates the status of the analysis e click Start to begin the analysis and Abort to end the analysis The results of the analysis up to the time of Abort will be saved in the same folder as the scan file that is b
51. e function of a button in the software use the help icon or search for the button name in the genindex Linked text e g The IMP Session and Work Flow cross references to different parts of the manual Use the back button on your browser or PDF viewer to return to the jump point Bullet lists are used to describe related items which appear in a group For example groups of radio buttons control settings or groups of output fields all related to a particular task 1 2 Screen Layout The screen layout in the software can be customized to suit the users needs and the actual appearance depends on the computer platform used Linux Windows Mac A detailed discussion of how to customize the screen layout is given in the advanced section on Panels and Views For this reason we do not make extensive use of pictures or screen shots in the manual but rather screen text and icons gt 1 3 Python The IMP Software Suite is written in the computer language called Python an open source language with many powerful tools for plotting image analysis and numerical calculation These are collected in a set of modules called SciPy Scientific Python The IMP Suite is platform independent running on Windows Macintosh or Linux Native graphics environments are used in the GUI which is written in wx Python so icons and panels may appear slightly different on different platforms This manual is written in restructured text language and is available a
52. e intermodulation spectral data No assumptions about the tip surface interaction have been made in this analysis These curves are simply another way of looking at the spectral data Reconstructed force The Force tab brings up a single plot of the effective conservative force vs cantilever deflection Zero deflection in this plot corresponds to the equilibrium position and negative deflection to the cantilever bending toward the surface In order to reconstruct the force some assumptions about the tip surface interaction must be made These assumptions and the different reconstruction methods are described on a separate page Force Reconstruction Methods Force reconstruction can be performed on individual pixels via the Force Inspector on selected lines in an image by Analyzing Linear Transects or on entire images via Batch process parameter maps and force volume data ImAFM reconstructs tip surface force F d as a function of cantilever deflection d z h where the probe height h and the tip position z are measured from a fixed position in the inertial reference frame where the sample is at rest the lab frame InAFM force measurement is fast enough such that one can assume constant probe height h at each pixel This assumption will however break down when the feedback error signal is large and the base is moving rapidly to compensate for a rapid change in surface topography ImnAFM makes no assumption about where the surface act
53. ear in the pull down list The calibration method will will be based on the theoretical expression for the hydrodynamic damping function valid for L gt gt b see Method above e Advanced is for cantilevers of arbitrary plan view dimensions Here you can enter the Sader Constants if they are known or the calibration parameters of a Reference calibration fora cantilever of the same plan view dimensions see Method above Length and Width are interpreted as effective values for a non rectangular cantilever The Edit tab allows you to change calibration parameters of the selected cantilever The Remove tab allows you to remove a user added cantilever from the selection list Calibrating torsional eigenmodes Torsional calibration uses the same principal flexural calibration It is currently under development and two methods are available e Hydrodynamic Function uses the analytical expression for the hydrodynamic function of a long rect angular beam calculated by Green and Sader Green This method calibrates the fundamental eigen mode and it uses length and width given in the fields above e Thermal tune stiffness brings up a field to enter the the height of the tip or the distance that the tip is offset from the principle axis of the cantilever beam 2 2 3 Scanning Before you begin the host AFM must be configured for ImAFM M If no special ImAFM M mode is provided on your host AFM simply put it in contact mode with
54. ection has two buttons which control whether the Trace or Ret race will be plotted Data is acquired and stored for both scan directions Note that both trace and retrace are always stored in every scan Flipping between trace and retrace can be a good way to see if feedback errors are affecting your image e Swap will exchange the data stored as trace and retrace The host AFM trigger signals do not distinguish between different scan directions and sometimes it is necessary to swap so that trace and retrace are the same as that in the host AFM Do not worry if you do not get this correct during the scan as it can be easily corrected after the scan session using the Session Overview e Flip right 1left and Flip up down do not exchange trace and retrace data This action can also be done later in the Session Overview e Scan size when checked will display axis labels with the image size which must be entered in the x and y data fields Units should be given in either nanometers or micrometers using the characters nm um or um u will be displayed as u Scan size values will be stored when the scan is saved and these values will be overwritten if and when the scan size is imported together with height data from the host AFM see Import host AFM data Color Bar The color bars have functionality for adjusting the images Mo Histogram for IMP7L phase Set limits automatically excluding2 0 of the pixels right click click an
55. ections of a Stream Recorder file Run the script press Open and select a previously recorded std file containing stream data taken in Time mode The script will parse the time stream to a series of beats or time windows T given by the inverse of the measurement bandwidth T 1 A f assigning a beat index to each window A plot shows the maximum value of the oscillation envelope in each beat You can adjust the time window to include more than one beat thereby reducing the measurement bandwidth and thus the noise The time window is shown in the lower plot Export A11 will export the entire recorder file and Export zoom will export only the selected window lower plot to an ASCII format file A Fast Fourier Transform e g FFT of this data will give the response spectrum at the selected time window 4 8 2 LiveParampeterMap py LiveParameterMap runs an experimental new method for extracting polynomial force curves which is com putationally very efficient so that the curves are analyzed and parameter maps are made in real time as the AFM scans The method was developed and implemented by Daniel Forchheimer starting from a theory worked out by Daniel Platz Platz 2013b Choosing this script opens a GUI which allows you to choose ways of parameterizing the conservative tip surface interaction force A map of these parameters is created in real time and a force curve showing the extracted parameter can be plotted The force curve is t
56. eing analyzed When the model fit is performed on a the scan file scan01234 imp several new fiels are created with the same filename The files scan01234_p_name png are image files with color coded images of the parameter values Such a file is created for each parameter p_name in your model The file scan01234 npz contains the numerical data of the parameter values stored in one numpy array This file can be loaded in to a Python script with the numpy function numpy load file_name Here is an example Python script for reading and replotting the parameter values load the npz file in to the object pmap pmap np load scan01234 npz extract and plot data for parampater 3 vmin and vmax are color bar limits imshow pmap data 3 vmin 0 vmax 5 display the colorbar plt colorbar 24 Chapter 3 Quantitative Analysis CHAPTER FOUR ADVANCED TOPICS In order to comprehend some of the more advanced features in the IMP Suite it is necessary to understand in more detail how ntermodulation Measurement and Noise Calibration work After this general discussion we continue with sections devoted Programming your own Force Models We explain how to use the the Data Tree which organizes the analysis and allows you to view spectral data and extract it to an external text file A section is included on File Management describing the different file types and where they are stored in the computer We describe how to move and re
57. ensitivity of a high Q resonance to measure the thermal equilibrium fluctuations of cantilever deflection and thereby extract the calibration constants of both the cantilever and the detector The method models the cantilever s free dynamics as a simple harmonic oscillator an accurate model for one cantilever eigenmode in a frequency band near resonance ImAFM also takes advantage of this enhanced sensitivity and high accuracy using only signals near resonance to reconstruct the force between the tip and the surface Furthermore ImnMAFM determines tip surface force as a function of the cantilever deflection at fixed probe height Thus both axes of the reconstructed force vs deflection curve or force quadrature vs amplitude curve rely on one and the same calibration Quantitative measurement with ImAFM is therefore completely independent of the scanner calibration Platz 2012a Forchheimer 2012 Noise calibration is performed for each cantilever at the start of the ImAFM session and it should be redone if any adjustments are made to the detector Calibration is easily done at any time during a session so it can be frequently redone to check for consistency Since the accuracy of quantitative ImAFM is traceable to this one measurement it is important to understand the physical ideas behind noise calibration Calibration in the field of AFM is traditionally discussed in terms of finding the spring constant k associated with the
58. er IN 1 on the MLA lt gt Out 0 on the controller Cross point connections are most easily made by running a script or Igor Procedure file ImAFM_MFP3D ipf supplied by I e user alias left column lt gt Deflection right column user alias d left column lt gt Input fast right column It is necessary to write the changes and Lock the cross point You can Read the changes in the All tab and check if Deflection is indeed connected to Input fast NOTE making these changes redefines the alias s for all modes and therefore Contact mode will not work as normal unless you switch back to the original settings or restart the Asylum software Make a note of what Deflection is set to before you make these changes manually The trigger connections require that you purchase a controller accessory from Asylum Research called the Digital Access Module DAM This module connects to a DIN connector on the front of the controller it has BNC connections for Port 2 LINE on the DAM lt gt TRIG 1 on the MLA e Port 3 FRAME on the DAM lt gt TRIG 2 on the MLA 5 4 4 Asylum Cypher The Cypher AFM runs the ARC or ARC2 controller The signal connections can be made as with the MFP 3D but it is preferable if they are made on the so called backpack of the Cypher itself The signal connections are Output 0 on the Cypher backpack lt gt IN 1 on the MLA e Input 0 on the Cypher backpack lt gt OUT 1 o
59. ermination of optical lever sensitivity in atomic force microscopy M J Higgins R Proksch J E Sader M Polcik S Mc Endoo J P Cleveland and S P Jarvis Rev Sci Instr 77 013701 2006 Hutter 2010 Reconstructing Nonlinearities with Intermodulation Spectroscopy C Hutter D Platz E A Tholen T H Hansson and D B Haviland Phys Rev Lett 104 050801 2010 Hutter_2010 Platz 2008 Intermodulation atomic force microscopy D Platz E A Tholen D Pessen and D B Haviland Appl Phys Lett 92 153106 2008 Platz_2008 Platz 2012a The role of nonlinear dynamics in quantitative atomic force microscopy D Platz D Forchheimer E A Tholen and D B Haviland Nanotechnology 23 265705 2012 Platz_2012a Platz 2012b Interaction imaging with amplitude dependence force spectroscopy Daniel Platz Daniel Forch heimer Erik A Tholen and David B Haviland Nature Commu 4 1360 2012 doi 10 1038 ncoms2365 Platz_2012b Platz 2013a Interpreting force and motion for narrow band intermodulation atomic force microscopy Daniel Platz Daniel Forchheimer Erik A Tholen and David B Haviland Beilstein J Nanotechnol 4 45 2013 Platz_2013a Platz 2013b Polynomial force approximations and multifrequency atomic force microscopy Daniel Platz Daniel Forchheimer Erik A Tholen and David B Haviland Beilstein J Nanotechnol 4 352 2013 Platz_2013b Sader 1997 General scaling law for stiffness measurement of s
60. ersion 5 there is a bug 2 2 The Work Flow 15 IMP Software Suite User Manual Release 1 2 which requires you to simply open and close the file in the DI software before you can import it to the IMP suite e Hide unchecked will move all the unchecked scans to a sub folder of the session folder called hid den_scans These scans will no longer be displayed in the session overview but they are not erased You can always use your computers file browser to move a file from the hidden_scans folder back to the session folder where it will again be displayed when you click Reload Unhide all brings all files from the hidden_scans sub folder up to the session folder Flip and swap scans Because the host AFM does not code the trigger signals for trace and retrace only for change of fast scan direc tion it may be necessary to left right flip the scan data or exchange the trace and re trace data in order to associate the ImAFM scan correctly with the host AFM scan Furthermore AFM triggers do not code for slow scan direction only end of frame so it may be required to exchange up down flip images All this is easily done in the Session Overview To perform these these flip and swap operations you first have to select the scans Checkmarks control which files will be flipped and swapped Check will select all scans Uncheck deselects all scans Toggle will switch checked to unchecked and unchecked to checked Apply to c
61. es it in to time windows or beats on which the signal is periodic Each time window is assigned an index the beat index and the terminal asks for the beat index on which you want to perform analysis The script extracts that beat from the data file and simply plots both time data and the frequency data Note that you must input the path to the IMP Suite on your computer and the path to the std file that you want to analyze import matplotlib pyplot as plt import numpy as np import sys 36 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 1 2 Path to IMP Suite suitepath Users david_haviland IntermodulatorSuite sys path append suitepath from StreamRecorder import stdfile Path to stream recorder file in time mode recorder_path path_to_file std full path to recorder file in std format print loading file recorder_path sf stdfile stdfile recorder_path b_raw False do_scale False Read metadata from file fs sf freq_samples Sampling frequency Hz fl sf f1 First drive frequency Hz f2 sf f2 Second drive frequency Hz Calculate number of samples to avoid Fourier leakage n_samples_beat int np round fs abs f2 f1 Number of samples in one beat t 1 fs np arange n_samples_beat Time axis for plotting df fs n_samples_beat Frequency resolution freqs df xnp arange n_samples_beat 2 1 Frequency axis for plotting Index each beat in
62. es_per_pixel i e the last in the list get_sampling_freq Return the current value of sampling_freq i e the last in the list get_scan_rate Return the current value of scan_rate i e the last in the list get_scan_size_x Returns scan size in the fast scan direction x Return type float64 meters 4 9 Scan Data 41 IMP Software Suite User Manual Release 1 2 Note The scan size is determined by the host AFM and must have been entered in manually in the IMP suite Automatic reading for some AFM s is under development get_scan_size y Returns scan size in the slow scan direction y Return type float64 meters Note The scan size is determined by the host AFM and must have been entered in manually in the IMP suite Automatic reading for some AFM s is under development get_setpoint Return the current value of setpoint i e the last in the list The linenumber of the setpoint chnage is not returned get_starttime get_tip Vac Return the current value of tip AC voltage i e the last in the list get_tip Vda Return the current value of tip DC offset 1 e the last in the list given_list_is_ empty Ist Returns True if list is or only has elements of type otherwise returns False has_calibration has_equal_params other isEqual other load_from_file filename load_h5_ file filename load_legacy_imp_file filename Loads data from binary file in imp format purge_
63. etector response function 4 2 1 Note on sensitivity and accuracy In the above text we emphasized that accuracy is higher when we base force reconstruction on the callibration of high Q resonance This notion of accuracy is rooted in physical understanding We are better able to model the force transducer and deflection detector in a narrow frequency band near a single eigenmode resonance and thus make a good calibration in this narrow band We also argued that sensitivity is higher near resonance Our notion of sensitivity is independent of that regarding accuracy and it does not originate from theoretical understanding of the physics of cantilever beams or opto electronic detection Sensitivity has to do with the signal to noise ratio SN R of measurement The field of AFM has unfortunately adopted the term inverse optical lever sensitivity or invOLS to describe the constant a which converts the measured detector signal e g Volts to nm of cantilever deflection We use the term responsivity for a because it is actually the magnitude of a linear response function and it does not tell us anything about the SN R of the measurement The sensitivity of the measurement is described by two quantities which are displayed in the Calibration Result panel Thermal noise force is the random force due to collisions of the molecules in the damping fluid with the cantilever This random force has zero average value but the average of the force squared
64. f frequency in the band of interest If the pixel time is T 1 ms and 4 or 150 fm 1 Hz the minimum detectable cantilever deflection at each pixel would be dmin oe 4 7 pm It is also interesting to express the detector noise as an Equivalent force noise q S98 ky Soy For the example given above and k 40 N m we find a 6 pN VHz which in a measurement time T 1 ms gives an equivalent minimum detectable force of pey kdmin 0 19 nN This would be the minimum detectable force with the cantilever if the measurement were dominated by detector noise as is often the case for quasi static force measurements Thus sensitivity of the measurement is characterized by two quantities The noise force of the cantilever which represents a fundamental limit and the noise of the detector One would like the detector noise to be as low as 28 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 1 2 possible and a very useful way to compare different detectors is to use the ImAFM system to perform thermal noise calibration on the same cantilever mounted in two different host AFMs Since the cantilever force noise is identical in each case we can compare the ratio of the thermal noise peak to the detector background noise or the Peak to flat ratio The larger this ratio the better your detection It is also interesting to track this number as you measure If this ratio becomes smaller it may mean that the detec
65. fective mass m e Width of resonance y Hz related to the damping coefficient of the simple harmonic oscillator model 1 y is the characteristic time for exponential decay of oscillation amplitude due to the damping of the surrounding medium e Quality factor Q 27 fo is the ratio of the energy stored in the oscillation to the energy lost per cycle of oscillation A freely oscillating cantilever will ring for Q cycles before the amplitude decays by a factor of 1 e or 37 e Cantilever stiffness k N m is the eigenmode stiffness or the coefficient of the linear restoring force in the simple harmonic oscillator model e Thermal noise force fN WHz is the fluctuation force associated with the linear viscous damping of the cantilever This frequency independent force noise gives rise to a peak in the deflection noise near a high Q resonance The thermal noise force represents a fundamental sensitivity limit for force measurement see Note on sensitivity and accuracy Detector e Inverse responsivity a wm V is the inverse magnitude of the detectors response function which converts the measured signal in Volts V to a deflection of the tip in meters m In the literature this constant is often referred to as the inverse optical lever sensitivity invOLS but we prefer the term responsivity see Note on sensitivity and accuracy for further discussion The calibration performed here actually does not rely on a calibra
66. fies the type of cantilever and calibration method e Temp C is the temperature of the damping medium in Celsius used to determine the magnitude of the thermal noise fluctuation force driving the cantilever e Fluid selects the density and viscosity of the medium surrounding the beam needed for calculation of hydrodynamic damping Noise calibration methods have not been tested thoroughly beyond studies in Air but we include to option to apply the theory inWater 20 C Cantilever selects from a list of pre programed cantilevers for which calibration constants have been published If your cantilever is not on this list you can choose Arbitrary Rectangular and enter the Length and Width or plan view dimensions of your rectangular beam cantilever You can edit the length and width fields for any chosen cantilever without changing the stored values for pre programed cantilevers Alternatively you can Add Edit Remove cantilevers as described below e Method selects between six methods of calibration Hydrodynamic function uses an analytic expression for the hydrodynamic function to calculate the damping The calculation applies to a rectangular beam in the limit length gt gt width see Sader 1998 This method uses length and width given in the fields above Sader constants uses a good approximation to the hydrodynamic function described with three parameters ao a1 a2 that are specific to a particular cantilever These constants have
67. force reconstruction and select e Open shell here to open a python shell with an object called force containing the result of the force reconstruction at this pixel The data id used by the data tree is given along with a couple of useful 30 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 1 2 4 5 commands The shell is for advanced users who will need the developer documentation to use this feature effectively Get fitted parameters to open a dialog box showing the fitted parameters when the Model Fit method is used Save Data to text file to export the force curve found using that reconstruction method Advanced Setup The Advanced Setup view is initially selected in the Advanced pull down menu Thereafter the icon appears on the right column below the work flow icons Selecting Advanced Setup again will uncheck the selection and hide the icon In this view you can control the drive for standard Intermodulation AFM using two drive tones set the feedback and measure the response in real time Requested fields are the desired or target values of f1 kHz the frequency of drive 1 f2 kHz the frequency of drive 2 df the measurement bandwidth df abs f2 f1 n where n 1 2 3 A1 the amplitude of drive 1 in percent of full output A2 the amplitude of drive 2 in percent of full output Actual show the values that you get which depends on which algorithm you choose for frequenc
68. g a Frequency Sweep E Calibrate the cantilever using non invasive thermal noise Calibration N Set up and start a scan then engage the surface with the host AFM to start Scanning E Open previous scan files and use the pixel and line inspectors to Analyze Scan Data IMP Software Suite User Manual Release 1 2 Add comments to the automatic logging in the Session Logbook View the session and import host AFM data batch process or view 3D parameters maps in Session Overview Each step in the work flow is described in detail in the following sections 2 2 1 Frequency Sweep After loading the cantilever and adjusting the detector we find the cantilever resonance by sweeping the frequency of the cantilever drive signal while measuring the detector response signal The Frequency Sweep panel opens when you click the top icon in the work flow Run sweep Starts the measurement between the Start frequency and Stop frequency Edit these fields to change the sweep range The sweep range should include the likely resonance frequency of the cantilever which should be provided by the probe manufacturer and is usually printed on the probe box Reducing the measurement Bandwidth causes the sweep to be slower and the measured response to be more accurate The sweep speed also depends on the Number of points recorded during the sweep Two check boxes provide automatic features for finding the resonance e Locate peak performs a second
69. h order IMP images which are often more noisy Be careful not to interpret these smoothing induced grains as features in your image 2 2 5 Session Logbook The Intermodulation AFM Software Suite keeps a session log while you are working This log file is a text file formatted for easy reading so you can quickly see exactly what was measured and when it was measured The software automatically logs all important activity in chronological order with a time stamp For example making a new calibration storing an image starting or stopping the scan and much more You can also add your own text comments to the log file Add your comment to text field at the bottom of the panel and finish with Ctr1 Return Your comment will be time stamped in inserted in to the log file 2 2 6 Session Overview This view shows all the scans in a session automatically imports data from the host AFM sorts out unwanted scans to a sub folder adjust images for synchronization problems with the host AFM and generates parameter maps on multiple scans in a batch processing mode Session Open IMP sessionand choose a session folder An overview is generated showing file info and image thumb nails where each row corresponds to one scan Reload causes the overview to be updated to the current state of the session folder View session log opens a window showing the session log file Import host AFM data The AFM height image is a record of the change of the probe height
70. hecked scans e Flip Left Right is performed on both trace and retrace data but trace and re trace are not exchanged e Flip Up Down is performed on both trace and retrace data but trace and re trace are not exchanged e Swap Trace Retrace will exchange trace and retrace with out performing any flip Note that left right flip does not necessarily imply that trace and retrace were stored incorrectly when scanning Depending on whether you selected the trace or retrace for storing the height data in the host AFM you may want to exchange trace an retrace to get correct association ImAFM always stores both trace and retrace Batch process parameter maps and force volume data Analyze checked scans in the Session Overview lets you set up and run a batch process to make parameter maps on several files e Paramter Map Model fit when checked will perform the analysis described in Model Fit gen erating parameter maps or color coded images of tip surface force parameters The settings button opens a panel for choosing the model and fit parameters as described in Parameter Maps e Paramter Map Polynomial when checked will perform the anaysis described in Fast Polyno mial based on the polynomial representation of the conservative force distance curve The settings button opens a dialog with options similar to that for Parameter Maps Polynomail degree is desribed in Polynomial e ADFS Force Volume when checked will perform Amplitud
71. host AFM AFM controller AFM head Detector input Cantilever drive EOL trigger EOF trigger Detector signal Cantilever drive MLA Signal OUT Signal IN Feedback OUT EOL trigger IN EOF trigger IN The general connection scheme is shown the diagram above The cantilever drive detector feedback and trigger signals must be routed through the MLA This routuing may be with with BNC cables to the font pannel of the MLA or with a composite cable to the AUX connection of the back panel of the MLA On some AFMs a separate Signal Access Module SAM is required Intermodulation Products provides dedicated SAMs for a few common AFMs to easily toggle between the normal function of your host AFM and ImAFM On other AFMs notably Asylum and JPK one connects BNC cables directly to the controller and changes signal routing using software activated switches You can get a script from Intermodulation Products to automatically perform the signal routing Detailed instructions are given below for different AFM s Contact Intermodulation Products to find out what solutions exist for your particular AFM lt info intermodulation products com gt 5 3 Set AFM Type In the IMP Suite under the Advanced pull down menu select Setup AFM A dialog box appears with a pull down menu to choose your AFM type This option will only appear when the IMP Suite detects the MLA and starts in full mode ready for taking data
72. ibration constants These constants define the current calibration After each scan all calibration constants from the current calibration are stored with the scan file together with the raw spectral data acquired by the MLA It is not necessary to store a calibration file in order to analyze the data in scan file The Store and Load features are there only if you want to store or view raw noise data for a particular run of the calibration The raw noise data will be saved for each run if Autosave is checked It is very easy to re calibrate during a scan session and thereby re define the current calibration Simply stop the scan retract the probe from the surface and re run the calibration We recommend that you re calibrate frequently to check if anything has changed with the cantilever and detector Calibration should also be re run if any adjustments have been made to the laser or the detector and it must be performed with every new cantilever before you start to perform ImAFM M 2 2 The Work Flow 9 IMP Software Suite User Manual Release 1 2 Add Edit Remove cantilevers Add Edit Remove opens a dialog box that allows you to change calibration parameters of one of the stored cantilevers or to create a new cantilever The Add tab has two options e Basic is for rectangular cantilevers Enter the Length L um and Width b um in microme ters and the cantilever name and manufacturer Click Add and your cantilever will app
73. inding the force which produced the measured motion as opposed to forward problem of finding the motion resulting from a given force As is often the case the inverse problem is ill posed The limited sensitivity of our measurement gives inadequate information for finding a unique solution to the inverse problem The very small force that we are trying to determine only gives measurable motion at frequencies in a narrow band close to the high Q cantilever resonance Our challenge is therefore to reconstruct the force from this partial spectrum or narrow band response Fortunately with enough intermodulation spectral data and with a few assumptions that are not so very restrictive we can find useful solutions We call the solution of this inverse problem force reconstruction or reconstructing the force from the intermodulation spectrum In dynamic AFM there are several forces giving rise to the cantilever motion The tip surface force cantilever bending forces viscous drag force on the cantilever body and the inertial forces due to acceleration of the can tilever mass including the drive force resulting from the shaking of the cantilever base To properly separate out the tip surface force from all other contributions we require two things A good calibration of the cantilever see Calibration and a good measurement of the cantilevers free motion when it is far away from the surface see Measure free set point scan rate Calibration is
74. ing a Multimode AFM or Dimension AFM the IMP NS4 SAM gives you signal access If the NS V controller is running on a Multimode or Dimension AFM you can use the same SAM as that for the NSHI and NSIV controller described above If you are running a Bruker Icon Fast Scan or other more recent AFM using the NSV controller Intermodulation Products has a low noise SAM with access the vertical and latteral detector signals as well as apply a voltage to the tip If these connections are sufficient you do not need the SAM V module from Bruker However if you have the SAM V you can use it to make the connections See Nanoscope V Connections for an image showing a typical connection Contact Intermodulation Products if you would like a dedicated ImAFM SAM for the NS V Icon or Fast Scan systems Access to the trigger signals is on the front panel of the NS IV controller See Nanoscope V Connections for an image showing the access to the trigger signals 5 4 Common AFMs 49 IMP Software Suite User Manual Release 1 2 5 4 3 Asylum MFP 3D These systems can be found with the older MFP 3D controller the ARC and ARC2 controller With all of these controllers signal access is via BNC connections on the front panel of the controller and signal routing is configured in the software cross point switch Hardware connections OUT A on the MLA lt gt In 1 on the controller e OUT 1 on the MLA lt gt In 0 on the controll
75. ith a slowly varying amplitude envelope Zoom is required to see the individual oscillation cycles 19 IMP Software Suite User Manual Release 1 2 e Spectrum shows only the amplitude of the individual intermodulation frequency components ploted on a log scale The component which is plotted with a thicker line corresponds to the amplitude and phase image displayed You can click on different componets in the plot and the amplitude and the images will change to the amplitude and phase of that frequency component e Phasor shows a plot where both amplitude and phase are plotted in a polar plot or as vectors in a complex plane 3 1 2 Force Inspector If the Quantitative Analysis software is installed selecting a pixel with the Pixel inspector tool will open the Force Inspector panel where you see plots of the analyzed spectral data giving information about the interaction forces at each pixel Note that the physical units in the plots are given in calibrated nano Newtons nN and atto Joules aJ nN nm vs nanometers nm as determined in the Calibration step The Force Inspector panel has three tabs FI FQ Work Force which select the different plots as described in detail below The Settings button opens a panel where you find three corresponding tabs to control the different plots e Force Inspector Settings panel FI FO and Work tabs display options are chosen through a pull down menu that allows you to select different regi
76. itional forces on the tip which are not taken in to account in the reconstruction algorithms Hence overactive feedback means inaccurate force measurement Improving feedback and actually incorporating the feedback signal in to the force reconstruction is a subject for future research and development 4 5 3 Measure You can measure and plot the response in real time using two different modes e Run time mode starts the measurement of the response in the Time mode and plots the sampled stream of data in the time domain and its discrete Fourier transform DFT in the frequency domain The discrete data is plotted with a connected blue line You will notice a jumping of the phase of the oscillation envelope in the time domain signal This is normal as the data are analyzed and plotted in asynchronous chunks and not as one continuous stream The DFT of the time sampled data is however stable as each chunk as the same sampling frequency and same number of samples Run freq mode starts the measurement of the response in the Frequency mode and plots the ampli tude at the measured frequencies vertical red bars in the frequency domain and the oscillation envelope in the time domain connected red lines Stop will terminate the measurement You must stop the measurement before you start other measure ments for example scanning a sample or taking stream data 4 5 4 Units You can select between displaying the cantilever response signal in Analog to
77. ke EOL trigger before it starts to record a scan line Setting both of these fields to zero causes no fake EOL signal to be generated and in this case the IMP Suite relies on the trigger signals recived by MLA These two fields should be set to zero when running with external triggers from the host AFM 5 4 Common AFMs 5 4 1 Nanoscope III Illa IV ImAFM works perfectly well with older Multimode and Dimension AFMs originally developed by Digital Instruments DI then sold by Veeco and currently by Bruker These are excellent AFM s and there are many good instruments still in service The upgrade to ImAFM is a good way to give these systems a second life and convert them to a modern AFM with the latest surface analysis capabilities You do not need to upgrade to a NS V controller and ImAFM performance is not compromised with the older NS II and NS IV controllers Access to the detector signal and cantilever drive are provided via a Signal Access Module SAM from Intermod ulation Products This gives you low noise and low cross talk connection with the host AFM and one switch is all that is required to toggle between normal use of your AFM and ImAFM M The SAM should be placed in between the microscope and the controller If there is a Phase Extender Module with the NSIlla controllers you should place the SAM in between the microscope and the phase extender module A general rule of thumb is Place the SAM directly after
78. ks like the teeth of a hair comb with sharp spectral lines equally separated by the base frequency Af In the time domain the frequency comb is simply a periodic waveform with period T 1 Af A general statement of the intermodulation measurement concept is the following Drive a system with a frequency comb and measure a response comb The nonlinearity can be reconstructed from the difference between the response and drive comb The underlying assumption is that the response is periodic on the long time scale T associated with the base tone 25 IMP Software Suite User Manual Release 1 2 The MLA has two different modes 4 1 1 Time mode Time mode down samples the response averaging sequential samples to give an effective lower sampling fre quency of This improves the resolution to 16 bit and it allows for the transfer of every sample to the computer in an uninterrupted stream see ref stream recorder label A DFT of this data stream will give you the entire inter modulation spectrum up to the Nyquist frequency This mode reveals all the mixing in your non linear system However the time mode has a latency between the end of the measurement period T 1 Af and finish of the calculation of the Fourier coefficients which is the time require to DFT the window of sampled data Even when using the Fast Fourier Transform FFT algorithm to execute the DFT this latency is too costly when scanning over a surface In such situations one u
79. list to new a new value val set_scan_size_ x value Parameters value float64 meters scan size in the fast scan direction x set_scan_size_y value Parameters value float64 meters scan size in the slow scan diretion y set_starttime val set_tip Vac val Set the current value of tip AC voltage i e the last in the list to new a new value val set_tip Vdc val Set the current value of tip DC offset i e the last in the list to new a new value val swap_calibration_parameters 4 10 File Management The IMP suite is kept in different places depending on your computer system In Windows it is installed in c Program Files IntermodulatorSuite Users do not need to care about this folder as it contains only static files which should be installed from an installer All dynamic files that are changed when you change settings in the IMP Suite store data save a script etc are stored in the folder c IMP sessions and settings This folder has the following sub folders Moving data to another computer To transport your data to another computer for analysis be sure to first import the host AFM data i e height image data in to your session folder using the Session Overview Then simply copy the entire session folder to another computer with the IMP Suite installed When you perform analysis on another computer all newly created analysis files will be added to the session folder 44 Chapter 4 Advanced Topi
80. ll not work properly when nonlinearity is present 34 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 1 2 4 6 3 Debugging a script The Debug window allows you to test what is happening with your script Error messages will appear in this window and you can print any variable here using the dprint var_name statement in your script The script automatically prints relevant data for your comb in the Debug window 4 6 4 Setting the feedback frequency By convention the MLA calculates the feedback error signal from the amplitude of the response at the frequency located in the zeroth position of the n array or f array You should make sure that your script puts the frequency at which you would like to run feedback in the zero position the n array Note that the arrays do not need to be sorted in any particular order for example from lowest to highest frequency but there must be a one to one correspondence between the elements of the arrays which set the frequencies n array amplitudes a array and phases p array More information on feedback can be found in the section on ntermodulation Measurement Feedback and in the section on Advanced Setup Setup Feedback 4 6 5 Useful Python code blocks Some useful blocks of code for making frequency combs are described below These code blocks are used in the example scripts You can copy and paste these in to your scripts Tune df close to 500 Hz and set the fre
81. m recorder will result in a file being saved in the session folder The file name has the form record01234 where the number is automatically incremented In Time mode the files will have the std extension and in Frequency mode the files will have the imp extension see the File Management section for more information on file types Unchecking the Autosave box will result in no data being saved e Mode selects weather the data is stored in Time mode or Frequency mode In either mode all data is saved as a continuous stream without any breaks or gaps in the data e Plot controls only which data is being plotted and does not effect the saving of data You can adjust the number of points to be plotted in the past number of seconds The check boxes enable plotting of the amplitudes or amplitude and phase in the polar plot at the different frequencies listed Note that in the Time mode the response at all frequencies in the comb can be examined by analyzing stream data with the Fast Fourier Transform A script called PlotTimeMode see Scripting Interface is provided which gives a simple GUI inteface for plotting and extracting time mode data taken with the stream recorder Below we give an example which can be a useful starting point for your own analysis scripts The script can be copied to a new filename py modified and run for example in the Python shell 4 7 1 Example script This script reads a time mode stream data file std file and pars
82. mall bodies with applications to the atomic force microscope J E Sader et al Jour Appl Phys 97 124903 2005 Sader 1998 Frequency response of cantilever beams immersed in viscous fluids with applications to the atomic force microscope J E Sader Jour Appl Phys 84 64 1998 Sader 2012 Spring constant calibration of atomic force microscope cantilevers of arbitrary shape J E Sader et al Rev Sci Instr 83 103705 2012 Tholen 2011 The intermodulation lockin analyzer E A Tholen D Platz D Forchheimer V Schuler M O Tholen C Hutter and D B Haviland Rev Sci Instr 82 026109 2011 Tholen_2011 65
83. n rate on the host AFM to the Scan rate given in the scanner panel e Make sure your host AFM is set to contact mode and the set point is set to zero volts e Engage the sample and start the scan in the host AFM software When the end of line EOL triggers are detected the IMP Suite will begin to collect and display the scan data After the last scan line when an end of frame EOF trigger is detected a scan file is stored see Status Banner However the EOL and EOF triggers do not code for the direction of the scan It may be necessary to sometimes Flip left right or Flip up down to make your image match that displayed on the host AFM On some AFM s you can move to the top or bottom of a frame to start a fresh scan without waiting for the current scan to finish If this action is performed on the host AFM and if the EOF trigger is sent the IMP will save a scan file and automatically start collecting a new scan Some AFM s notably Asylum do not send and EOF trigger when you move to the top or bottom of a frame When the IMP suite is configured for such an AFM two buttons appear which allow you to Move to toporMove to bottom to keep the synchronization with the host AFM scan During the scan you can at any time perform the following actions and set the following parameters Measure free set point scan rate Measure free causes the cantilever to be pulled away from the surface where a new measurement of the free response is made The
84. n response should be zero when the cantilever is oscillating in air above a surface because the freely oscillating cantilever is a linear system When the cantilever is oscillating close to a surface and the tip is interacting with the surface the cantilever oscillation becomes nonlinear causing the generation of intermodulation products of the two drive tones Measuring both the amplitude and phase of the intermodulation products allows one to reconstruct the nonlinearity or the tip surface force Different force reconstruction methods are described in the chapter on Quantitative Analysis The intermodulation measurement concept can be extended to multiple drive tones and the MLA can be con figured to drive with more than two tones A special Drive Constructor interface is provided for setting up the multi frequency drive and configuring the MLA to measure at the desired frequencies Through a process called tuning the MLA and its accompanying software force all drive frequencies to be integer multiples or very nearly integer multiples of one base frequency Af and this base frequency serves as a reference signal for lockin measurement of the response If all the drive tones are integer multiples of the base frequency all of their intermodulation products will also be at integer multiples of the base frequency Such multi frequency signals are called frequency combs because their frequency representation when plotted as a power spectrum loo
85. n the MLA e Input 1 on the Cypher backpack lt gt OUT A on the MLA M The trigger connections with the ARC and ARC2 controller are done exactly as with the MFP 3D controller via the Digital Access Module 5 4 5 JPK Nanowizard Ill The connections to the JPK Nanowizard III are shown here JPK Nanowizard III Connections As with other systems ImAFM is done with the JPK software in contact mode Run the IMP JPK script to open a small GUI which aids in setting all parameters in the JPK software Press Set up to make the JPK system ready for ImAFM M Note that when doing the noise calibration on a JPK system it is a good idea to turn off the high voltage to the Z piezo Press the button HV Z OFF to toggle on and off the high voltage 50 Chapier 5 Installation IMP Software Suite User Manual Release 1 2 5 4 6 NanoTec Electronica As with other systems you should set the Nanotec software to run contact mode In the DA data acquisition view set all other modes to no in the Scanning gt Scan Options panel The Nanotec Dulcinea SPM controller has various inputs and outputs which have to be configured in the Nanotech WSxM Software Please note that the cantilever drive signal output from the MLA requires a special connector at the AFM head or a specific signal routing in the Nanotech Dulcinea controller Please contact Nanotec for further details The signal in port of the MLA has to be connected to the BNC
86. nctions will be added as the IMP Suite grows Most functions in this class fall in to one of two groups e Use append_ and reset_ to prefix functions for managing data in a list Use when you want to save the history which changes during the scan The final member of the list is often called the current data append_ function adds to the end of a list reset_ function clears the list to length zero and adds a new initial element e Use get_ and set_ to prefix functions which get data and set data respecitvely in the ScanData class This can be the raw image data at any pixel or meta data such as the calibration or free oscillation To Do e clean our not used functions e change invOLS to invOLR everywhere append_lo_change_linenrs val Append the list of change_linenrs values append_lo_delta_f val Append the list of delta f values append_lo_drive_amplitudes ar Append the list of drive_amplitudes append_lo_drive_karray ar Append the list of drive_karray values append_lo_drive_phases ar Append the list of drive_phases append_lo_feedback ar Append the list of feedback 4 9 Scan Data 39 IMP Software Suite User Manual Release 1 2 append_lo_free_oscillations ar Append the list of free_oscillation append lo imp karray ar Append the list of imp_karray values append_lo_samples_per_ pixel val Append the list of samples_per_pixel values append_lo_sampling_fregs val Append the list of sampling
87. ncy comb to the shaker piezo of the AFM The system is configured to work nicely with standard AFMs Internal jumpers can be moved to change the output voltage range Contact Intermodulation Products if you want different output range Feedback OUT delivers a error signal to the host AFM where zero volts corresponds to the set point in the IMP Suite When the host AFM is set to contact mode with set point zero in the host AFM software The voltage sent by the Feedback Out port constitutes the error signal in the control of the AFM feedback The feedback gains are set on the host AFM Signal IN receives the detector signal from the AFM The system is configured to work nicely with standard AFMs Attenuators can be used to reduce the amplitude of the input signal if necessary Contact Intermodulation Products if you want a different input range e EOF TRIG INis the End Of Line signal which is generated by the host AFM and received by the MLA e EOL TRIG IN is the End of Frame signal which is generated by the host AFM and received by the MLAM Back side connections 5V DC powers the MLA One should always use the power supply delivered with MLA Using any other supply voids the warranty e Ethernet The MLA communicates with the computer via the Ethernet connection The MLA may be directly connected to the Ethernet connection on the computer or it may be be put behind an Ethernet router switch or gateway 10 MHz OUT i
88. ons of the curve for plotting Typically you want to choose multi valued curves which shows F A and FQ 4 for both increasing and decreasing oscillation amplitude in the beat cycle of one pixel Use shading check box will activate a shading of the Fr A and Fo A curves such that the lightest shade corresponds to the start of the pixel and the darker shade the end In the Signal Inspector select the Time tab to see the beat cycle for the selected pixel e Force Inspector Settings panel Force tab contains several options were are explained in detail in Force Reconstruction Methods In phase and quadrature forces The FI FO tab brings up a double plot of two integral quantities plotted versus the oscillation amplitude not static cantilever deflection The plot F 4 is the force which is in phase with the sinusoidal cantilever motion integrated over a single oscillation cycle of the cantilever motion Similarly the quadrature force Fg A is the force which is 90 degree phase shifted from the harmonic motion in phase with the velocity It is important to note that F 4 and Fo A are not traditional AFM force curves They should not be compared to plots of the instantaneous force vs distance between the tip and surface or plots of measured cantilever deflection vs the quasi static probe height Every single point on the F A and F 4 plots represents an integral of the tip sruface interaction force over one single oscillation
89. parameters Purges the parameter history lists All except for the last entries are removed from the parameter lists This is useful when a new image is saved then the parameter history of the previous image should be removed Only the last value in each list is kept as the initial parameter for the new image reset_lo_change_linenrs val Reset the list of change_linenrs values and initialize it with one element with value val reset_lo_delta_f val Reset the list of delta f values and initialize it with one element with value val reset_lo_drive_amplitudes ar Reset the list of feedback values and initialize it with one element with array ar reset_lo_drive_karray ar Reset the list of drive_karray values and initialize it with one element with karray ar reset_lo_drive_phases ar Reset the list of feedback values and initialize it with one element with array ar reset_lo_feedback ar Reset the list of feedback values and initialize it with one element with array ar reset_lo free oscillations ar Reset the list of free_oscillation values and initialize it with one element with array ar 42 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 1 2 reset_lo_imp_karray val Reset the list of imp_karray values and initialize it with one karray ar reset_lo_samples_per_pixel val Reset the list of samples_per_pixel values and initialize it with one element with value val reset_lo_sampling_fregs val Re
90. programed in the software You can also add your own models to the software as described in the advanced section on Programming your own Force Models The help icon 2 opens a window showing the functional form a list of parameters and plot of F d for each model e The table gives a listing of the parameters for each model and the initial value for the numerical solver If the check box is unchecked the solver will not adjust that parameter and it will be fixed at it s initial value Model Fit can be applied to every pixel in a scan to generate a paramter map as described in Batch process parameter maps and force volume data Amplitude Dependent Force Spectroscopy ADFS ADFS makes no assumptions about the particular form of the force curve F d other than the force being zero for positive deflection i e F d 0 for d gt 0 The method performs an inverse Able Transform on the F A curve to reconstruct the conservative force F d The method is described in detail in Platz 2012b Platz 2013a This method can be applied to create a force volume data set from a scan data file as described in Batch process parameter maps and force volume data Fast Polynomial A computationally efficient method to determine the polynomial coefficients of the conserva tive tip surface force is described in Platz 2013b The method is very fast compared to standard Polynomial and Model Fit The faster computation enables parameter mapping in real time
91. quencies to consecutive integer multiples of df centered as close as possible to the resonant frequency f0 df tune_integer 500 fl f0 nfreq_out 2 df start freq of comb nl round f1 df integer closest fl n np int_ arange nfreq_out nl integer array of frequencies Tune df closer to 500 Hz and set the frequencies to consecutive integer multiples of df centered as close as possible to the resonant frequency f0 df tune_round 500 f0 fl f0 nfreq_out 2 df start freq of comb nl round f1 df integer closest fl n np int_ arange nfreq_out nl integer array of frequencies Exchange the frequency with the index mi with the feedback frequency at position n 0 put frequency near resonance as first frequency for feedback mi nfreq_out 2 index of center of comb n mi n 0 afmi a l0 plmil p 0 n 0 n mil a 0 almi p 0 plmi Create an signal in the time domain consisting of a rapidly oscillating component at the frequency f_bar and a slowly modulated amplitude mod Fourier transform and pick out the nfreq_out components close to f_bar and set the amplitudes a and phases p N 2xint 2 f_bar df number of time samples so f_max 2xf_bar t arange 0 1 1 N df construct signal x t in the time domain and FFT to get comb mod 0 1l sin 2 pixarange N N the modulation function x 1 mod cos 2 pixf_bar t x t x_hat fft rfft x
92. quency thereby only measuring response at this frequency 4 6 1 Constructing a drive frequency comb A Python scripting interface is built in to the drive constructor to help in the construction of drive frequency combs Using the interface requires knowledge of the Python programming language A pull down menu lists the name of various Python scripts stored in impdata drive_setups user_drive_scripts py These scripts are well commented to help you understand how they work You create a new script by changing the name of an old script and pressing Save Similarly Delete will kill the currently selected script The scripting interface has some useful functionality e Change font size with ctrl Plus ctrl Minus or ctrl Mouse wheel e Hit ctrl Space for a list of reserved keywords e A quick help and link to this manual appears by clicking the IMP help icon gt 4 6 Drive Constructor 33 IMP Software Suite User Manual Release 1 2 Pre defined variables The following variables are defined in all scripts e f0 Hz and Q are the measured resonant frequency and quality factor stored in the Current calibration e nfreq_out and nfreq_in are the number of drive frequencies and response frequencies respectively These numbers will depend on the MLA firmware that you are running e f sample is the sampling frequency samples per second of the MLA Built in functions The following built in functions are provided in all scrip
93. re give in Digital to Analog units The drive waveform coming from SIGNAL OUT port of the MLA can be conditioned with external amplifiers or attenuators to suit the application Intermal adjustments can be made inside the MLA to give more or less output voltage Contact Intermodulation Products regarding these adjustments 4 6 Drive Constructor The multiple tones in a frequency comb represent a periodic waveform in the time domain The Drive Constructor interface lets you configure the Mutifrequency Lockin Analyzer MLA creating the drive comb and choosing the measurement frequencies If you have a version of the MLA with more than two drive tones for example the IMP 24 24 there are endless possibilities for different drive waveforms and the question of which drive waveform is optimal for a particular measurements is the subject of ongoing research Before attempting to use the Drive Constructor you should read the section on ntermodulation Measurement The MLA versions are denoted IMP X Y and they are constructed such that the X drive tones always overlap with the and Y frequencies where response is measured In other words response is always measured at the X drive frequencies and X lt Y If you have the IMP 24 24 you can work with up to 24 frequencies which are the same on both the drive and response sides You can always work with fewer frequencies on the drive side by simply setting the drive amplitude to zero at any drive fre
94. reby the theoretical value of the damp ing coefficient my depends on the mode shape and is therefore specific to the particular eigenmode Calculations show that the mode shape of the fundamental eigenmode of a long rectangular beam is particularly insensitive to the Reynolds number Higher eigenmode shapes are sensitive to Re Sader 1998 and the mass of the tip placed 4 2 Noise Calibration 27 IMP Software Suite User Manual Release 1 2 at the end of the cantilever This calibration method is therefore applicable to the fundamental eigenmode and we can expect it to be valid in different fluids but its applicability to higher eigenmodes is questionable We should also stress that reconstructing force from the measured deflection over a wide frequency band for example from many harmonics of a single drive frequency requires determination of the detector response function w An ideal detector should have a flat frequency independent response function up to it s cut off frequency where it it will start to roll off or decrease with frequency to some power However real detectors do not always behave in this ideal way and the detector electronics can introduce frequency dependent amplitude changes and phase shifts over a wide frequency band Since ImAFM works in a narrow band we escape this difficulty and we can expect accurate calibration and therefore accurate force reconstruction with the assumption of a frequency independent d
95. s HTML or PDF The HTML version is linked with the help icons in the IMP Suite and it is more easily used when working with the Suite online A separate software developer documentation describes the usage and function of the Python objects which make up IMP Software Suite User Manual Release 1 2 the IMP Suite The developmer documentation is designed for users who want to enhance the functionality of the software by modifying the source code and programming their own measurement and analysis methods 4 Chapter 1 Introduction CHAPTER TWO THE IMP SESSION AND WORK FLOW 2 1 Quick Start Connect the intermodulation lockin to your host AFM and make sure the switch s on your signal access module are in the correct position For details on connecting to your AFM please consult the Install Hardware section Start the host AFM and set it to Contact Mode with the feedback set point set to zero volts Here we assume that zero volts on the detector corresponds to the equilibrium position of the cantilever when it is free from the surface G Start IMP Software Suite A session folder named with the current date is automatically created where all your data will be stored 2 2 The Work Flow The work flow is symbolically represented by the left column of 6 Im icons From top to bottom these icons guide the work flow in the IMP Suite Click on these icons to open the different panels and views da Find the resonance by performin
96. s a TTL sync signal for locking the MLA clock to external equipment 6 4 2 Version Firmware Two basic versions are available e IMP 2 23 Two drive frequencies at the Signal Out port 32 frequencies analyzed at the Signal IN port e IMP 24 24 24 drive frequencies at the Signal Out port and the same 24 frequencies are analyzed at the Signal IN port 6 4 MLA version before 2015 59 IMP Software Suite User Manual Release 1 2 60 Chapter 6 The Multifrequency Lockin Amplifier MLA CHAPTER SEVEN TROUBLE SHOOTING Below is a list of problems that may arise and solutions Contact Intermodulation Products if you are having problems getting your system to operate lt info intermodulation products com gt There is a hidden program long file in each session folder internallog dat which the company representative may need to see if the problem can not be solved over the phone Problem The software crashed but the process is still running in the computer and I can not stop it Solution In Windows tart the task manager control shift escape Look for imp_suite exe and kill that process Problem I get only a very weak signal and I do not see any resonance when I do a frequency sweep Solution Did you make sure that the hardware switch on the signal access module in is the correct Problem I can not get a good fit to the noise calibration data Solution e There may be a spurious signal coming from your AF
97. s synchronized to external frequency generators To avoid phase drift you should make sure that the frequency of the external generator is an exact integer multiple of df given in the IMP Suite to as many significant figures as possible with your generator The exact properties of these different tuning options have to do with the way in which frequencies are synthesized and analyzed in the MLA which we do not discuss in detail here It suffices to say that the small errors induced in 4 5 Advanced Setup 31 IMP Software Suite User Manual Release 1 2 the Rounding algorithm are negligible for ImAFM and we recommend that you use this tuning The automatic setup uses this algorithm 4 5 2 Setup Feedback Before you engage a sample and after you have made any changes to the drive configuration you must setup the feedback Feedback for ImAFM is controlled by the amplitude of response at one of the frequencies measured by the MLA see Feedback section For the basic two frequency drive feedback is run at frequency f1 With the Drive Constructor you have more control over which frequency to set as the feedback frequency e Setup will adjust the feedback so that zero volts at the feedback output port corresponds to the given set point e Set point is the desired response amplitude given as a percentage of the free response amplitude Ad justing the set point to more than 100 will cause the probe to lift away from the surfac
98. ses the MLA in frequency mode 4 1 2 Frequency mode Frequency mode does the Fourier Analysis of many frequencies in parallel inside the MLA as the samples are acquired In frequency mode you get the full bandwidth of the MLA up to the Nyquist frequency set by the sampling freqeuncy of the A D converters in the MLA The MLA performs 2Y Fourier sums in real time at user specified frequencies These sums give you the Fourier cosine and sine coefficients or the in phase and quadrature response This response can be converted to amplitude and phase with some calculation but often the analysis of data is more conveniently done on complex numbers 4 1 3 Feedback The MLA has a feature specifically designed for AFM where feedback is required to track the surface when scanning The amplitude of response at one dedicated feedback frequency is calculated inside the MLA This amplitude is subtracted from a set point amplitude forming an error signal A voltage proportional to this error signal is sent to one of the output ports In order to make the feedback more responsive the MLA updates the error signal 24 times in the measurement period T 1 Af The sections on Setup Feedback and Drive Constructor give more information on how the configure the feedback and set point 4 2 Noise Calibration A quantitative measurement of tip surface force requires an accurate calibration of the cantilever Noise calibration uses the enhanced force s
99. set the list of sampling_freq values and initialize it with one element with value val reset_lo_scan_rates val Reset the list of scan_rate values and initialize it with one element with value val reset_lo_setpoints val Reset the list setpoints values and initialize it with one element a value val reset_lo_tip_Vac val Reset the list of tip AC voltage values and initialize it with one element with value val reset_lo_tip_Vdc val Reset the list of tip DC offset values and initialize it with one element with value val save_to_ascii filename None Export to a collection of generically named ascii files in the directory dirname Creates a separate subdirectory for the scan and separate files for each amplitude and phase image for easy import into Matlab or similar If dirname None default the directory is automatically named after the scanData file save_to_file filename save_to_h5 filename save_to_legacy_imp_ file filename Saves data as binary file in imp format set_Q Q Parameters Q float64 dimensionless quality factor set_calibration_flexural kwargs set_calibration_torsional kwargs set_change_linenr val Set the current value of change_linenr i e the last in the list to new a new value val set_delta_f val Set the current value of delta_f i e the last in the list to new a new value val set_drive_amplitudes ar resets the list of drive amplitudes and appends the given array set_dri
100. sis 2014 03 31 to v M Pixel at 137 58 Trace Y inv ADFS vi Inv poly e Save as ascii to open a dialog box where you can save all amplitude and phase data in ASCII format The save will create individual files in a new empty folder There will be one file for both amplitude and phase at each of the measured frequencies both trace and retrace For example when 32 frequencies are measured 128 data files will be created If the image is 256 x 256 pixels this corresponds to about 140Mbytes of data in tab delimited text with a carriage return at the end of each scan line The name of each file begins with a number which codes for the frequency The number corresponds to the index of the k array which stores the integers multiples of Af which give the frequency values where amplitude and phase is measured see ntermodulation Measurement In the folder there is also a file called metadata txt which contains a list of integers in the array LO_IMP_KARRAY The number at the beginning of each file corresponds to the index of this array zero being the first element The integer values stored in this array times LO_DELTA_F gives the frequency at which the amplitude and phase is measured Right click on a pixel and select e Open shell here to open a Python shell with an object called pixel containing the data relevant to this pixel The data id used by the data tree is given along with a couple of useful commands
101. sweep with finer detail zoomed in on the peak response found in the sweep range e Transfer results to noise calibration transfers the center frequency and estimated sweep range to the next stage in the work flow Correcting Driven Response Use Correction is an advanced function that can be left unchecked for simple resonance finding This function is used to de embedd linear response from the measurement chain Sometimes electronic equipment between the output or input of the Multifrequency Lockin Amplifier MLA see Intermodulation Mea surement and the host AFM can cause frequency dependent amplitude and phase shifts to the signals that are measured by the MLA Use Correction compensates for any undesirable linear transfer of the signal due to these compenents embedded in the measurement chain The compensation is made using a procedure called de embedding performed in two steps 1 A frequency sweep is performed while by passing the AFM insert a short in place of the AFM After this sweep press the Set Correction button which transfers the result of this sweep to an internal correction file 2 Put the AFM back in to the measurement chain and check the Use Correction check box All subse quent sweeps performed with this box checked will correct for the amplitude and phase shifts measured in the first step In summary 6 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release
102. tablish the connection between the computer and the MLA you must first perform the steps below After this procedure the detection will be automatic The instructions given below are for Windows 7 1 Connect a standard Ethernet cable between the MLA and the computer 2 Goto Control Panel gt Network and Internet gt Network and Sharing Center 3 Locate the network adapter In the left panel choose Change adapter settings To identify which adapter corresponds to the Ethernet card connected to the MLA turn off the MLA There should be a red cross on the adapter icon with the text Network cable unplugged About one minute after the MLA is turned on the red cross will disappear and the text changes to Unidentified network 4 Configure the MLA adapter Right click again on the MLA adapter and choose Properties Se lect Internet Protocol Version 4 TCP IPV4 and click Properties Click Use the following IP address and fill in the following IP address 192 168 42 1 Subnet mask 255 255 255 0 5 Check the adapter At this point the internet connection between the MLA and the computer should be established To test the connection you can ping the MLA In a Windows terminal window type ping 192 168 42 50 The MLA should respond with something like 47 IMP Software Suite User Manual Release 1 2 Pinging 192 168 42 50 with 32 bytes of data Reply from 192 168 42 50 bytes 32 time 1ms TTL 128 5 2 2 Connection to
103. ted measurement of voltage by the MLA nor does it rely on the cali bration of the AFM scanner to determine detector responsivity The software uses the noise measurement to determine cantilever deflection in the digital counting units of the MLA or Ananog to Digital units ADU Thus the noise measurement and hydrodynamic theory together become a primary form of calibra tion that does not depend on the calibration of any other equipment apart from the thermometer measuring temperature e Noise floor fm yHz is the detector noise expressed as an equivalent deflection noise of the cantilever This figure is the correct measure of the sensitivity of the opto electronic system which detects the cantilever deflection e Equivalent force fN yHz expresses the detector noise as and equivalent force noise acting on the cantilever This equivalent force noise gives the sensitivity of force measurement if the same cantilever were to measure force quasi statically or at low frequency well below resonance Peak to flat ratio dB is the ratio of the noise peak thermal noise to the flat background noise detector noise If you compare two measurements with the same cantilever the larger this number the better your detection see Note on sensitivity and accuracy Current calibration Running a new calibration loading a previous calibration selecting a new range or excluding points runs the fitting routine which determines all the cal
104. the stream ii_s np arange 0 sf n_samples n_samples_beat 1 remove last since it might not be complete Loop through all beats and read max value beats_to_plot 1000 if len ii_s lt beats_to_plot ii_plot ii_s else skip float len ii_s beats_to_plot ii_plot np int_ skip np arange beats_to_plot peak np zeros len ii_plot for i beat_i in enumerate ii_plot if i1 100 0 print Beat i i S beat_i len ii_s Read data i_start ii_s beat_i data sf get_samples i_start n_samples_beat peak i max data Plot plt figure 1 plt clf plt plot ii_plot peak plt xlabel Beat index plt ylabel Peak value ADU plt show Ask terminal for beat number then data from that beat n 1 while n 1 s raw_input Enter beat index to plot try n int s except ValueError print Input must be an interger data sf get_samples ii_s n n_samples_beat data_fft np fft rfft data len data Plot 4 7 Stream Recorder 37 IMP Software Suite User Manual Release 1 2 plt figure 2 plt subplot 211 plt plot t data plt xlabel Time s plt ylabel In ADU plt subplot 212 plt semilogy freqs le 3 2xabs data_fft plt xlabel Frequency kHz plt ylabel Amplitude ADU plt show 4 8 Scripting Interface The IMP Suite comes with a python scripting interface with which you can develop you own m
105. tip surface force is determined by subtracting the free response from the engaged response The free response is automatically measured durring Setup but not between continuously acquired scans The most recent measurement of the free response is stored with the scan file when it is saved at the end of the scan and this most recent measurement is used for subsequent analysis Often the cantilever needs to settle in after engaging a surface and a new measurement of the free response is required after some time of scanning We recomend that you press Measure free if your force curves appear strange to check and see if this makes a difference Amplitude set point is the set point for the AFM feedback Feedback is based on the response amplitude at one of the two drive frequencies Drive 1 and the set point is given as a percent of the free response amplitude at this drive frequency see Setup Feedback To engage the surface this set point must be below 100 Setting the set point to more than 100 will cause the probe to lift from the surface a useful way to lift away from the surface without stopping the scan if you want to check or adjust something Scan rate is the required rate of scanning as determined from the pixel rate and x resolution The scan rate is determined by the chosen pixel rate measurement bandwidth df and number of pixels in the scan line x resolu 2 2 The Work Flow 11 IMP Software Suite User Manual Release 1
106. tor is poorly adjusted or there may be some additional source of detector noise 4 3 Programming your own Force Models One powerful feature of ImAFM is the ability to test different tip surface interaction models on the same data set Data is stored as the raw intermodulation spectrum at each pixel which is a frequency domain representation of the tip motion The Model Fit section of Force Reconstruction Methods describes how to use the IMP Suite to fit this data to an a force model This fit can be done at an individual pixel see Force Inspector along a liner transect see Analyzing Linear Transects or on an entire image see Parameter Maps and Three dimensional viewer Several common force models are programed in the IMP Suite and it is very easy to program your own force model and have it appear in the IMP Suite Constructing a good and physically well motivated force model can be difficult However once you have a good force model programing it in the IMP Suite is simple Some knowledge of the Python language is necessary see Python Simply copy the examples py file and give it a new name e g my_force_model py keeping it in the force_models folder Edit the copy to create your own force model The example py file is well documented with comment lines to help you understand the idea behind the Python code After you have finished with my_force_model py restart the IMP Suite Your force model will be automatically loaded and it
107. trol or right click and vertical drag on the 3D image Plane fit has three different methods for flattening the image e None shows the height data as it is stored in the host AFM height image file e Average fits a plane over the entire image and offsets all height data so that this plane is flat e Selected points allows you to flatten on a selected region of the image With this option selected hover over the image with the mouse When you press the p key the point at the mouse arrow will be selected After selecting 3 points a plane can be calculated and the image will offset all height data so that this plane is flat You can continue to select more than 3 points and the image will be flattened with a best fit plane to all selected points The clear button removes all selected points A red frame appears when you select points To make this frame disappear hover outside the image and press the p key 2 2 The Work Flow 17 IMP Software Suite User Manual Release 1 2 18 Chapter 2 The IMP Session and Work Flow CHAPTER THREE QUANTITATIVE ANALYSIS The quantitative analysis tools allow you to analyze the measured intermodulation spectral data at each pixel in a variety of ways Each spectrum is a frequency domain representation of the tip motion at that pixel and from this motion we determine the tip surface force We may refer to this analysis as inversion because it involves solving an inverse problem or that of f
108. ts e tune_integer df takes one argument the target value of df It returns a re defined value of df that is com mensurate with divisions of the MLA clock frequency such that Fourier coefficients will be calculated for perfect integer multiples of df This function is equivalent to the integer button in the frequency tuning controls of Advanced Setup You should use this tuning if you are synchronizing the MLA with other instruments tune_round df f0 takes two arguments the target value of df and a desired frequency commensurate with df e g the resonant frequency of the cantilever It returns a re defined value of df such that Fourier coefficients will be calculated for near integer multiples of df This function is equivalent to the round button in the frequency tuning controls of Advanced Setup Required quantities The script must set the values of the following variables One and only one of the following which specifies the measurement bandwidth Either df Hz T sec or samples_per_pixel integer df 1 T samples_per_pixel f_sample An array of integers n giving the frequencies for both drive and response The length of the array n must be nfreq_in and the first nfreq_out entries are the drive frequencies Alternatively you can specify the frequencies in an array called f Set either n or f but not both f n df A real array a with the amplitude of all drive tones The length of the array a must be nfreq_in
109. ually is in relation to the probe height This is in stark contrast to quasi static force measurement methods where one must assume a rigid tip and surface when calibrating the measurement of d by moving h In fact ImAFM M allows you to unambiguously define the location of the surface relative to h by associating it with a distinct feature on the F d curve see Forchheimer 2012 lt reference position in lab frame x Fig 3 1 The AFM detector measures cantilever deflection d The probe height h is adjusted while scanning The tip position in the lab frame is z h d Three basic methods are available for reconstructing F d In the Force tab of the Force inspector settings panel check the box to activate the desired Reconstruction Method You can use any combination of methods and plot all results on the same plot Each method makes different assumptions described below Click the method name to highlight it and view the options for that method Polynomial The Polynomial method approximates the conservative tip surface force a function of tip surface separation only as a polynomial of finite degree N in the cantilever deflection d N F d Aj gjd A further assumption is that the force is zero when the tip is sufficiently far from the surface Under these assumptions we can find the N polynomial coefficients gj both odd and even coefficients from the measured spectrum of odd order intermodulation products The metho
110. ultifrequency AFM methods and customize the IMP Suite to your particular measurement needs From this interface you can access all the classes and functions used by the IMP Suite for data acquisition storage plotting and analysis To take full advantage of the possibilities that this interface allows and to develop your own measurements you will need to learn the Python programing language and become familiar with the structure and functionality of the IMP Suite as described in the developer documentation Intermodulation Products provides a variety of scripts which can be modified and saved with a new name All scripts stored in the folder IMP_sessions_and_settings settings scripts will be loaded when the IMP Suite starts and they will appear in Advanced pull down menu under Scripts To run the script simply select it from the menu Reload scripts will close all open scripts are reload the currently saved script The file Examples py contains several different classes each containing a script with different functionality These scripts demonstrate how to make a GUI or step a quantity while scanning You can expand on these scripts to add GUI elements and controls or simply edit the values in the Python code reload the script and run it These scripts serve as a starting point to develop your own measurement methods Some useful scripts currently available are 4 8 1 RecorderAnalysis py PlotTimeMode opens a GUI for viewing and extracting s
111. ure noise Acquire Data controls the start of measurement saves data or loads previous measurement data e Run calibration starts the averaging of many separate noise measurements to decrease the fluctua tions in the noise data If Frequency Sweep was used to find the resonance and Transfer results to noise calibration was activated the software will automatically analyze an appropriate frequency range around the resonance The Status Banner indicates the progress of the calibration e Settings opens an Acquisition Settings dialog box where you can select the total number of Measurements in the average the Center frequency kHz and Frequency span kHz to analyze and the Frequency resolution Hz between data points You can also give a Down sampling factor which averages the given number of samples before transferring to the computer for spectral analysis e Save As opens a dialog box to save the noise data to a txt file If Autosave is checked this file will be automatically saved The file is saved in the JSON format and it can easily be opened in many different programing languages Matlab Python Java etc It is not necessary to save the raw noise data for each calibration as the software automatically keeps track of the Current calibration or most recent fit of calibration data which is stored as the relevant calibration in the scan file e Load opens a dialog box to load a previously saved noise data Fitting noise data
112. urrent value of imp_karray i e the last in the list get_imp_str_list mode 1 Returns a list of imp strings containing e g Drivel Drive2 IMP3L etc Without further options the strings are returned as saved in the corresponding ImageData With mode 0 same as mode 1 but if strings are empty automatically mode 2 With mode 1 same as mode 1 but if strings are empty automatically mode 3 With mode 2 strings of the imp ks are returned e g k 345 With mode 3 strings as defined in ScannerPanel are returned depending on the lockin scheme get_internal_imp_str_list get_invOLS Returns resopnsivity of optical lever Return type float64 nm ADU get_k Returns catilever eigenmode stiffness Return type float64 N m get_loaded filename Filename that was used when loading the ScanData from disk get_lockin_ scheme Gets the lockin scheme used for scanning currently returning 0 1 or 2 get_metadata_ascii Return all metadata as a string new line separated string Strategy for all following data entries IDENTIFIER UNIT DATA get_original filename get_p detector_white Returns 2 what is detector white Return type float64 get_p_ thermal Returns what is p_thermal Return type float64 get_params_dict get_resolution get_resonance_frequency Returns resonance frequency Return type float64 Hz get_samples_per_pixel Return the current value of sampl
113. ve_karray ar Set the current value of drive_karray i e the last in the list to a new karray ar set_drive_phases ar resets the list of drive phases and appends the given array set_external filename str set_feedback ar Set the current value of feedback i e the last in the list to new a new array ar set_free_oscillation ar Set the current value of free_oscillation i e the last in the list to new a new array ar set_imp karray ar Set the current value of imp_karray i e the last in the list to new a new karray ar set_invoOLS invOLS 4 9 Scan Data 43 IMP Software Suite User Manual Release 1 2 Parameters invOLS float64 nm ADU responsivity of optical lever set_k k Parameters k float64 N m cantilever eigen mode stiffness set_nr drive _fregs nr set_original_ filename str set_p detector_white p_detector_white Parameters p detector white float64 what is detector white set_p_thermal p_thermal Parameters p_thermal float64 what is p_thermal set_resolution i_x i_y set_resonance_frequency f0 Parameters 0 float64 Hz resonance frequency set_samples_per_pixel val Set the current value of samples_per_pixel i e the last in the list to new a new value val set_sampling_freq val Set the current value of sampling_freq i e the last in the list to new a new value val set_scan_rate val Set the current value of scan_rate i e the last in the
114. very bottom of every view has text describing what task the software is currently performing sweeping calibrating scanning etc and a status bar that graphically shows the time required to finish the task If Autosave is checked data is continuously saved to file save when the task is finished The name of the most recent saved file is also given tr O Sf A y _ 00 p pi q Z a He x g CARE Ba 0 2 Autosave Current task E iis A and state Dias ee a y a eT ie OscillatioMamplitude nm e SET NT socireiss Settings Clear all No file saved Y Autosave Ready 2 2 4 Analyze Scan Data One aspect of ImAFM which makes it so powerful is that all raw data trace and retrace are stored in one compact scan file The intermodulation spectrum at each pixel is an optimally compressed representation of the cantilever motion from which we reconstruct the tip surface force With the raw data stored in the scan file the AFM scientist can go back and make a more careful study of each point on the surface analyzing it with different models and plotting it in different ways To fully appreciate the analytical power of Intermodulation AFM you should have the Quantitative Analysis package from Intermodulation Prodcuts In File pull down menu select Open ctr1 0 The Amplitude and Phase images appear in a new tab for each open scan file You can open multiple tabs and compare data from different scans on the s
115. will appear as an option in the Mode 1 pull down menu Note that any changes you may have made to the examples py file will not be saved and upon restart it will be returned to its original default state 4 4 Data Tree The Data Tree panel is available from the Advanced pull down menu The panel can be docked in either the scanning view or the analysis view or both This panel lists scans which are open in the analysis panel as well as the current scan Under each scan there is a list of all the pixels which have been selected with the Pixel inspector tool The color of the text for each pixel corresponds to the color of the cross marking the pixel in the image Under each pixel there is a list of the different force reconstructions done on that pixel Right click on a scan file name and select e Open shell here to open a Python shell with an object called image containing all the data stored in this scan file The data id of the scan used by the data tree is given along with a couple of useful commands The shell is for advanced users who will need the developer documentation to use this feature effectively e Get calibration to open a dialog box with the calibration data stored with this scan file or the Current calibration at the time that the data file was closed 4 3 Programming your own Force Models 29 IMP Software Suite User Manual Release 1 2 8 Data Tree Y Scans Current Scan Y Users david_haviland Documents Anay
116. y tuning 4 5 1 Frequency tuning Frequency tuning is key to performing measurmenets with the Multifrequency Lockin Amplifier MLA MLA Tuning is the process of selecting the base tone df and the actual drive tones so that they meet the criteria for ImAFM that all frequencies are integer multiples df see Intermodulation Measurement There are three different algorithms for tuning None takes the requested frequencies and does not tune them at all Without tuning multi frequency linear response will be corrupted by Fourier leakage between drive tones and it is not possible to get an accurate measurement of intermodulation Rounding selects the closest frequencies to the requested values such that all frequencies will be near integer multiples of one base frequency Rounding gives a very small amount of Fourier leakage between tones but in almost all cases this leakage is well below the dynamic range of the measurement and therefore considered negligible The phase error is corrected at the end of each measurement time T 1 df so there should be no noticeable phase drift With this algorithm there is considerable freedom in the choice of frequencies Integer is amore strict algorithm where the condition of integer multiples is met exactly This algorithm gives no Fourier leakage between tones and no phase error but it is more restrictive in the choice of the possible values of df You should use this algorithm when the MLA i

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