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IMP Software Suite User Manual

1. mode Returns 1 strings as saved in ImageData 0 as mode 1 but empty strings automatic mode 1 as mode 1 but empty strings automatic mode 2 strings of karray_imp integers e g k 345 3 strings as defined in ScannerPannel e g To Do depreciate this function and have imp_str_list set by user in drive constructor or set to default value in auto setup get_input_ports Input port for each of the measured tones Returns array of port numbers 1 4 where tones are measured Return type np ndarray dtype np int64 See also mlaapi lockin Lockin get_port mlaapi lockin Lockin set_input_multiplexer get_invOLR mode_type flexural mode_nr 1 Get the inverse optical lever responsivity Parameters 4 9 ScanData 49 IMP Software Suite User Manual Release 4 0 2 e mode type str optional Name of mode i e flexural or torsional e mode nr int optional Mode number i e 1 2 3 Returns mode invOLR in m ADU Return type float Raises CalibrationError if the mode was not calibrated get_k mode_type flexural mode_nr 1 Get the cantilever stiffness Parameters e mode_type str optional Name of mode i e flexural or torsional e mode_nr int optional Mode number i e 1 2 3 Returns mode stiffness in N m Return type float Raises CalibrationError if the mode was not calibrated get_karray Frequencies of
2. MLA OUT 1 shaker IN 1 detector OUT A feedback TRIG IN 1 EOL A 2 a J TRIG IN 2 EOF Computer ETHERNET 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 M 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 AFM 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 The settings for the various AFM types are stored in the folder IMP Sessions and Settings settings configuration
3. 4 6 1 2 Built in functions The following built in functions are provided in all scripts tune_integer df takes the target value of df and returns a re defined value of df that is commensurate 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 4 6 Drive Constructor 39 IMP Software Suite User Manual Release 4 0 2 e 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 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 output port of the MLA M Configure Response adjusts the comb at the output port such that the synthesized comb appears at the input port The algo
4. Raises CalibrationError if the mode was not calibrated set_detector_noise p_detector_white mode_type flexural mode_nr 1 verbose True Set the detector noise floor for an existing calibration Parameters e p thermal float thermal noise force in ADU 2 Hz e mode type str optional Name of mode i e flexural or torsional e mode nr int optional Mode number i e 1 2 3 e verbose bool optional If True print a message to the console Raises CalibrationError if the mode was not calibrated set_df df Measurement bandwidth Parameters df float Hertz Hz See also set_samples_per_pixel set_endtime 10 Time at end of scan in seconds since the epoch Parameters t0 float seconds set_external_filename filename The filename of an external file associated with this scan Parameters filename st r filename Note Currently not implimented 54 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 set_ 0 f0 mode_type flexural mode_nr 1 verbose True Set the cantilever resonance frequency for an existing calibration Parameters e 0 float resonance frequency in Hz e mode_type str optional Name of mode i e flexural or torsional e mode_nr int optional Mode number i e 1 2 3 e verbose bool optional If True print a message to the console Raises CalibrationError if the mo
5. 3 1 2 3 Reconstructed force Sometimes refer to data analysis as inversion or reconstruction because it involves solving an inverse problem or reconstructing 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 physically well motivated we can find solutions 20 Chapter 3 Quantitative Analysis IMP Software Suite User Manual Release 4 0 2 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 3 1 2 3 1 Force Reconstruction Methods Force reconstruction can be perfor
6. Clear all No file saved Y Autosave Ready 2 2 4 Analyze Scan Data Raw ImAFM data the intermodulation spectrum at each pixel both trace and retrace are stored in one compact scan file The spectrum at each pixel is an highly compressed representation of the actual cantilever motion from which we reconstruct the tip surface force From the raw data 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 Intermodulation Products offers a Quantitative Analysis package with many methods of analysis and more are constantly being developed You can also use the ScanData python class to easily extract and analyze the data with your own analysis methods 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 same plot in the analysis view In the analysis view you will find the Image settings panel the Image Toolbar and the Color Bar With the Pixel inspector tool and Line inspector tool you can select individual pixels and lines for Quantitative Analysis as previously described 2 2 4 1 Image Smoothing The analysis panel is similar to the Image settings panel with an additional Smooth image button This button opens a dialog box where you can apply a Gaussian filter to your scan data Smoothing w
7. Lu Re A Re where L is the length of the beam and A Re is a dimensionless hydrodynamic function of the Reynolds number 2 pb wo Re Ti The Reynolds number is a dimensionless quantity which physically corresponds to the ratio of inertial forces to viscous forces in the hydrodynamic flow around the beam It is formed from the resonant frequency the fluid density p and viscosity jz and the width of the cantilever b which is the relevant length scale for desribing the flow The hydrodynamic function A Re has been calculated for beams of arbitrary cross section with length much larger than width either transverse dimension L gt b Sader 1998 However a generalization of the theory shows that the basic idea of desribing the damping in terms of a hydrodynamic function of a Reynolds number applies to an any elastic body of arbitrary shape which is damped by motion in a fliud Sader 2005 The beauty of this approach is that once the relevant hydrodynamic function A Re has been determined for a cantilever or plate of a particular shape as described by it s plan view dimensions effective length and width we can use this knowledge to calculate the fluctuation force on any cantilever of that shape simply by measuring the resonant frequency in the fluid Sader 2012 We measure the total noise which consists of two contributions the cantilever fluctuations Sqa nm Hz and the detector noise Sp p ADU Hz Since the cantileve
8. 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 reso nance to reconstruct the force between the tip and the surface Furthermore ImAFM 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 Quantita tive 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 static independent of time deflection of the cantilever Finding this one constant is sufficient to de
9. 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 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 detector 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 AFM 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
10. trace retrace e Zoom fixed in ImEFM e Improvements and fixes to Gwyddion loader e Can now load newer JPK files Installation notes e Application has been renamed from IMP Software Suite to IMP AFM Software Suite Manual unin stallation of previous version required to clean up start menu and desktop icon Version 2 4 1 Release date 2016 10 04 New features 78 Chapier 8 Changelog IMP Software Suite User Manual Release 4 0 2 e Frequency sweep reverse sweep direction e Manual setup panel for setting up the lockin e New ScanData file format version 9 keeping track of scan type ImAFM ImEFM etc e Model fit parameter maps additionally stored as ASCII files e Lifted motion displayed together with free motion in show meta data browser Bugfixes e ScanData fixed export to ascii and sampling frequency was not correct when using drive constructor e Easier to use binary Gwyddion loader for imp files Does not require any special version of or python Gwyddion for windows Note requires installation of Visual Studio 2015 redistributables from Microsoft Version 2 4 Release date 2016 06 30 New features e New MLA firmware MLA can measure DC component at all inputs simultaneously e Script to record ramps approach curves using DC signal e Support fo NT MDT triggers e New format for storing calibration in ScanData files Bugfixes e Improved interpretation of EOL and EOF signals from AFM Trace ret
11. 19 Simple Harmonic Oscillator Fit 8 Smooth image 15 Smoothing dialog 15 Spectrum fit 21 spring constant 8 Status Bar 14 subplots 13 Swap 12 swapping trace retrace 16 T Temperature 7 Thermal noise force 8 32 three dimensional parameter maps 17 three dimensional viewer 17 Time mode 30 tip surface forces 18 tip surface voltage 25 torsional calibration 10 Trace 12 triggering 65 U Use shading 19 user comments 17 V Vepd 27 W Width of resonance 8 88 Index
12. 55 set_invOLR afmapp Scanner ScanData ScanData method 56 set_k afmapp Scanner ScanData ScanData method 56 set_lift afmapp Scanner ScanData ScanData method 56 set_mla_all_settings afmapp Scanner ScanData ScanData method 56 a_calibration afmapp Scanner ScanData ScanData method 57 _mla_firmware_version afmapp Scanner ScanData ScanData method 57 set_output_mask afmapp Scanner ScanData ScanData set_ml method 57 set_phases afmapp Scanner ScanData ScanData method 57 set_Q afmapp Scanner ScanData ScanData method 53 set_resolution Index 87 IMP Software Suite User Manual Release 4 0 2 afmapp Scanner ScanData ScanData work 20 method 57 Work Flow 4 5 set_samples_per_pixel afmapp Scanner ScanData ScanData Z method 57 Zoom tool 13 set_scan_rate afmapp Scanner ScanData ScanData method 57 set_scan_size_x afmapp Scanner ScanData ScanData method 57 set_scan_size_y afmapp Scanner ScanData ScanData method 57 set_scan_subtype afmapp Scanner ScanData ScanData method 57 set_scan_type afmapp Scanner ScanData ScanData method 57 set_setpoint afmapp Scanner ScanData ScanData method 58 set_starttime afmapp Scanner ScanData ScanData method 58 set_tip_Vac afmapp Scanner ScanData ScanData method 58 set_tip_Vdc afmapp Scanner ScanData ScanData method 58 Setup 10 Signal Inspector panel
13. AFM or on a separate computer It is advantageous to run the AFM Suite on a modern computer with a multi core processor especially when analyzing full images to make Parameter Maps If the AFM 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 AFM Suite via Ethernet either the same computer used by the host AFM or a seperate computer 5 2 1 Connection to computer The AFM Suite will open analysis mode when it does not detect an MLA connected to the computer To establish 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
14. MLA button This will apply the tuning algorithm and configure the MLA In order to see what you actually got after the tuning you need to press Read from MLA and the table will show the values actually used by the MLA With so many tones at your disposal manual configuration of the MLA is obviously impractical when the measurement becomes more complex In this case you will want to use the Python scripting interface contained in the Drive Constructor 4 5 Advanced Setup 37 IMP Software Suite User Manual Release 4 0 2 4 5 6 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 an 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 intermodulation 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 harmon
15. Predefined vanables Iber ies eed dive o peek awe ed Hee ad 38 461 2 Built funcions osos amp ees be eR Ee we we eS ees 39 4 6 2 Synthesize and Configure z s e i e346 4 2h dd 244 40 46 3 Setting th feedback res a Sl eae Be ee ee A ae Oa 40 464 Debugging ascript 2 454564 wee ee See ee alae Se eal oS 40 465 Useful Python code blocks s risa 224 waa Se Baa a Be eo a 40 47 StreamRecord r o s sek ek eR ES a Ae we Ae Sad ee BA 41 474 Example script surcar a ec dost amp Gea Bee a el gS 42 4 3 Serpting Interface do eaeko te e ee Ra COA we ee a oS 43 AS RecorderAnalysisipy lt a Oe ie Bie a S ea 44 43 2 LiveParampeterMap pPy c ets fo Saw er Ge aa ee ee eo Ee Bos 44 49 wscanDatas ic 24 fo SK Rae Re ae Se BAe Boe ee a eee eee 2S A 44 4 91 ScanData Class xv c a e AS MRR ee E ROE Re ee Gs 44 4 10 FileManasement lt 5 e 2 4 9 4 betel Ge A Bee dee A e A 58 ANON Bile Typis lt 2 2065 bn 4 s Rp eh ee eR Pa ee ee oe eee BRS 59 4 11 Panels and VieWS eee eee ER OE He ee ee srs 59 Installation 61 Sel Install SoftWare oras dale EE Boe a HB DE a ES a ee a eS 61 3 2 Install Hardware sa cetaa di ss St Rp a et Pe ee ee 61 Jal Connection tocomputer 26 42205845 8480S di eS 61 32 2 Connection to host AFM s pe s oiea ae 6 BR BE Ae ROE OH ee 62 3 SEAEM TYDE 24 64 wars ds emai Gly Shwe wale aS d Ow e 62 5 3 1 Working without tippers e e sna a a ai a A A ae a ga a G 63 34 Common AFMS p lt saet eee
16. Strategy for all following data entries IDENTIFIER UNIT DATA get_mla_calibration The hardware calibration of the MLA Returns dict get_mla_firmware_version Version of the firmware loaded into the MLA Returns version number Return type int See also mlaapi hardware Hardware get_firmware_version get_original filename The file name when the data was first stored Returns filename Return type str get_output_mask Each bit in the mask determines weather the corresponing tone should be added to the output Returns a list of int with the mask for each of the two output ports Return type list See also mlaapi lockin Lockin set_output_mask mlaapi utils mask_to_int get_phases unit rad Drive phases for every tone Parameters unit str optional rad deg Raises ValueError if unknown unit is specified get_resolution Get the scan resolution Returns nx ny int number of pixels in fast scan direction int number of pixels in slow scan direction Return type tuple get_samples_per_pixel Number of samples in time window corresponding to one image pixel fs df Returns samples per pixel Return type float 4 9 ScanData 51 IMP Software Suite User Manual Release 4 0 2 get_scan_rate Number of scan lines per second trace retrace Returns Hertz Hz Return type float get_scan_size_x Returns scan size in the fast scan direct
17. 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 AFM 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 AFM Suite Your force model will be automatically loaded and it 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 th
18. a A e E e EA 63 SA Nanoscope M MMA TV cier o So eR ew OB aK ee HE 63 542 Nanoscope Y es ad ERRATA oe Re AS 63 AZ software senes 2 5 av eae Eye A PORES Sry oh Wee a8 64 543 Asylum NMPPSD on jek ra Roh EGER ES abe SR ES ees 64 SAA Asylum Cypher M pa oo 4 temi rria ea BEES BEE ERLE EE E 64 545 JPKNanowizard UT 65 NO NanoTec Electronica 24 4 onene A ER A e 65 5 4 6 1 Hardware Connection images s sess eos sa a e a a 65 5 4 6 1 1 SAM II connections ooa 65 5 4 6 1 2 Nanoscope Ill and Illa Trigger Access noaoo 65 5 4 6 1 3 Nanoscope V Connections lt o os c esere srn iresi crs 65 5 4 6 1 4 JPK Nanowizard III Connections 2 65 6 Multifrequency Lockin Amplifier 71 Gil Version UL 2 OS ae ee A A E E e AS 71 62 Version tl eci 524 4 oth ng BO pe eB Gees ae eH Be eee eee Shee woe 71 63 VERSION neco ses dle ok Saha ge le Ra eR eR eed eee eo A Ge ea a 71 6 3 1 Version Il Fitmwate saoe 56 be ke eee Ewe ew wae wee Ee be 72 7 Trouble Shooting 73 8 Changelog 75 9 References 81 Bibliography 83 Index 85 IMP Software Suite User Manual Release 4 0 2 Contents CONTENTS 1 IMP Software Suite User Manual Release 4 0 2 2 CONTENTS CHAPTER ONE INTRODUCTION The Intermodulation Products AFM Software Suite AFM Suite from Intermodulation Products AB is a col lection of software tools for performing Intermodulation Atomic Force Microscopy ImAFM a powerful quantitati
19. 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 _ 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 x cos 2 pix f_barxt x t x_hat fft rfft x 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 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 2 f_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 gt t delta_f 4 pixdf sin 2 pixdfx 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 operates in a different
20. 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 AFM 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 AFM Suite is platform independent running on Windows Macintosh or IMP Software Suite User Manual Release 4 0 2 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 as HTML or PDF The HTML version is linked with the help icons in the AFM 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 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 th
21. all image data in to a large array complex format untis ADU gt gt gt image_data sd get_data gt gt gt pick out the spectrm at one pixel x 100 y 99 and convert to units nm gt gt gt pixel image_data 99 100 sd get_invOLR gt gt gt convert from complex format to amplitude and phase gt gt gt amps np abs pixel gt gt gt phases np arctan2 np imag pixel np real pixel Note Functions in this class do not set or get the actual measurement conditions of the multi frequency lockin Setting data read from a file does not change the file on disk unless the data is written again with ScanData ScanData save_to_file get_Q mode_type flexural mode_nr 1 Get the cantilever quality factor Parameters e mode type str optional Name of mode i e flexural or torsional e mode_nr int optional Mode number i e 1 2 3 Returns mode quality factor Return type float Raises CalibrationError if the mode was not calibrated get_amplitudes unit digital Drive amplitudes for every tone Undriven tones have zero amplitude Parameters unit str optional digital ADU calibrated V percent Y Raises e CalibrationError if the specified units require conversion but no MLA cali bration was set e ValueError if unknown unit is specified get_calib_mode index mode_type None mode_nr 1 Fi
22. changing this DC offset Set point is the fraction of free oscillation amplitude in used as the set point for the scanning feedback Setting this this to a smaller value will cause the probe to oscillate closer to the surface To measure purely electrostatic force the tip should not come too close to the surface where other surface forces are much stronger than the electrostatic force A typical value for this parameter is 85 to 95 however you may want to use a smaller set point if the free oscillation is measured very far from the surface Pixel rate sets the measurement bandwidth or inverse the measurement time at each image pixel Making this smaller will improve the signal to noise ratio but it will also slow down the scan rate for a given image resolution number of pixels Setup executes an automatic routine to configure the MLA and software for the measurement After setup is executed the AC voltage will be applied to the tip ON OFF check box controls the tip sample voltage Checked means ON Uncheck and Check to see if anything changes in your image If not you may have a loose or incomplete electrical connection to the tip If you are using and ImEFM with front panel connections the tip sample voltage is applied from BNC port OUT 2 You can use a BNC T and oscilloscope in parallel to monitor this voltage e LED toggle check box controls the LED illumination when measuring surface photo voltage When unchecked there
23. convenient to use depends on the host AFM If you are using a Bruker NSV controller and Icon AFM the voltage that is applied between the tip and the sample comes from the MLA via the composite cable connected to the IMP Signal Access Module SAM Make sure that all switches on the SAM are in the IMP position and that the Bruker software is configured to apply voltage to the tip In the Bruker software enable advanced parameters click red puzzle icon and choose the option tip bias on the setting tip bias This setting should be effected if the ImAFM workspace is chosen in the Bruker software For other host AFMs you need to work through the signal path for the tip sample voltage which is applied from BNC port OUT 2 on the front panel of the MLA It can be a good idea to use a BNC Tee and look at this voltage with an oscilloscope in parallel so that you can actually see the applied signal A general connection scheme is given below ee me ae oee AFM controller AFM head borro rr rr Detector signal aq Cantilever drive Tip Sample Voltage Detector input Cantilever drive EOL trigger EOF trigger MLA OUT 2 OUT B LED TRIG IN 1 EOL TRIG IN 2 EOF ETHERNET Computer 3 3 1 1 Setting up the measurement Before you begin ImEFM you must first do the standard calibration procedure in the first two steps of the ImAFM Work Flow Finding the cantilever reson
24. 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 taken at one location center of the fast scan axis and the plot is updated at the line frequency 4 9 ScanData The AFM 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 analyze multifrequency data taken with the IMP Software Suite you will need to use the ScanData class Either copy the file from the IMP Software Suite default path C Program Files IMP Software Suite Scanner ScanData py and place in the directory of your own script or import it using the code below gt gt gt import sys gt gt gt suite_path r C Program F
25. data_format str optional IQreal complex amp phase speci fies data type e unit str optional ADU V m nm rad deg specifies units rad and deg only for phase Returns spectrum of free cantilever oscillation with required data format and units Return type np ndarray Raises e CalibrationError if the specified units require conversion but no MLA cali bration was set 48 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 e ValueError if the specified format and units are incompatible or the scan pass format or units are unknown See also get_lift Examples gt gt gt sd ScanData ScanData scan01612 imp gt gt gt get free response in nm gt gt gt data sd get_free unit nm gt gt gt freqs sd get_karray sd get_df gt gt gt plot amplitude vs frequency gt gt gt 1 plot freqs np abs data get_frequencies Frequencies of the measured tones Returns Hertz Hz Return type np ndarray dtype np float64 get_fs Lockin sampling frequency Returns samples second Hz Return type float get_imp str list mode 1 Function to create a string list to lable the tones Parameters mode int optional 1 0 1 2 3 Returns strings with names of imp s e g Drivel Drive2 IMP3L etc Return type list
26. e h 23 3 2 Analyzing lines dnd Surlaces ici sii Barca A ga e a GB Se aes A 24 3 2 1 Analyzing Linear Transects lt see e on a ee Ae Oe ee BS 24 3 2 2 Parameter Maps pa acids m Ge ee ws Boe A a Bd a He Ga as 24 3 3 Special Modes 2 2 9 ass we tp we old ORR eR ee ee ae De ee aS 25 3 3 1 Intermodulation Electrostatic Force Microscopy o 25 3 3 1 1 Setting Up the Measurement prosa pronta ae be ed 26 3 3 1 2 Analyzing and viewing the ImEFM data o 27 Advanced Topics 29 4 1 Intermodulation Measurement cs 0 026 528 ae nea rr a a 29 41 1 Time mode esmas ia e hee bes 30 412 Frequency mode comuna Bea a e e Be Ga we a S 30 ALS Feedback iio a a a ee a i ee al aS 30 4 2 Noise Calibration sos a miir a a ST Bal ea Rae eR eo 30 421 No teonsensitivity and accuracy s s geste ee a BP ee a 32 4 3 Programming your own Force Models e 33 44 Data Tree peacanna ke Re RR AR E RR 33 45 Advanced Setup seat e a e A Ee eee ea 35 45 1 Frequency imine 60464 dpb bee oe ae poe ee de a R 35 45 2 Setup Feedback i ec nt 644588 F444 04h e008 Hh soba kee ede ea 36 A 36 454 AI eal Re Be ale oe Be eal Ga S 37 ASD Manual Sepe ies a punice eer e ah ad ds Bae ee its G 37 45 6 Outoft Range ETOP cossens ea be ba eA hee we eA ad BA 38 46 Drive Constructor s sis 8 beg a Se Be By Sl eR dos eo oe Bw ee eS 38 46 1 Configure the MLAM Locuras cae A CR ee i 38 46
27. 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 61 IMP Software Suite User Manual Release 4 0 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 host AFM AFM controller AFM head Locc rr rr Detector signal Cantilever drive gt Detector input Cantilever drive EOL trigger EOF trigger
28. function to calculate the damping The calculation applies to a rectangular beam in the limit L gt gt b 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 Gg that are specific to the particular type of cantilever These constants have been measured and checked against other methods and according to theory they should apply to any can tilever 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 for a particular type of cantilever made with some other 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 Thermal tune responsivity brings up a field to enter the known stiffness of the cantilever fundamental eigenmode 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 thermal noise measurement is then applied to determine the cantile
29. 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 MLA Back side connections e 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 e 10 MHz OUT isa TTL sync signal for locking the MLA clock to external equipment 71 IMP Software Suite User Manual Release 4 0 2 6 3 1 Version Firmware Two basic firmware 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 72 Chapter 6 Multifrequency Lockin Amplifier 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 cr
30. 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 2 2 5 2 Import host AFM data The AFM height image is a record of the change of the probe height 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 scanning feedback and in most modern AFMs the height signal is measured using a linear sensor built in to the scanner When performing ImAFM M the height data is recorded by the host AFM To associate ImAFM M quantitative analysis with this height data 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 Mat
31. 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 do 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 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 s
32. manner it 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 stream 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 4 7 Stream Recorder 41 IMP Software Suite User Manual Release 4 0 2 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 exa
33. must be set up as usual with the Setup button in the Scanner or the Advanced setup perspectives This phase feedback is to be considered experimental e Gwyddion plug in to open ScanData files Instructions for how to install it in the folder C Program FilesIMP Software SuiteExtToolsGwyddion 79 IMP Software Suite User Manual Release 4 0 2 e New icon in the start menu to start the software in Debug mode Bugfixes e Better handling of unusual values of amplitude and df e The rotation of merged Asylum images is fixed e The data transfer speed is improved so it should be possible to scan faster Version 2 2 New features e Plot of free oscillation accessible from data tree e Many additional new features Bugfixes e Live parameter map works with half scan speed e Additional minor tweaks including description of units in imp files Version 2 1 New features e Improved smaller icon set white emblem on blue background e Many additional new features and bugfixes Version 2 0 New features e First version software to use the second generation multifrequency lockin amplifier MLA 80 Chapier 8 Changelog CHAPTER NINE REFERENCES 81 IMP Software Suite User Manual Release 4 0 2 82 Chapter 9 References BIBLIOGRAPHY Borgani 2014 Intermodulation electrostatic force microscopy for imaging surface photo voltage Riccardo Bor gani Daniel Forchheimer Jonas Bergqvist Per Anders Thor
34. n Olle Inganas and David B Haviland Applied Physics Letters 105 143113 2014 doi 10 1063 1 4897966 Borgani_2012 Borgani 2017 Background force compensation in dynamic atomic force microscopy Riccardo Borgani Per Anders Thor n Daniel Forchheimer Illia Dobryden Si Mohamed Sah Per Martin Claesson David B Haviland Borgani_2017 Forchheimer 2012 Model based extraction of material properties in multifrequency atomic force microscopy Daniel Forchheimer Daniel Platz Erik A Thol n 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 Thol n and David B Haviland Appl Phys Lett 103 013114 2013 Forchheier_2013 Green 2002 Torsional frequency response of cantilever beams immersed in viscous fluids with applications to the atomic force microscope Christopher P Green and John E Sader Jour Appl Phys 92 6262 2002 Haviland 2016 Quantitative force microscopy from a dynamic point of view David B Haviland Current Opin ion in Colloid amp Interface Science 27 74 81 2016 Haviland_2016 Higgins 2006 Noninvasive determination 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 Spectr
35. non zero Return type np ndarray dtype np int64 Examples gt gt gt sd ScanData ScanData scan01612 imp gt gt gt create frequency array for drive frequencies in Hz gt gt gt freqs sd get_drive_karray sd get_df 4 9 ScanData 47 IMP Software Suite User Manual Release 4 0 2 See also get_drive_amplitudes get_drive_phases get_drive phases Phases of driven tones Returns radians Return type np ndarray dtype np float64 See also get_drive_karray get_drive_amplitudes get_endtime Time at end of scan in seconds since the epoch Returns seconds Return type float get_external filename The filename of an external file associated with this scan Returns filename Return type str Note Currently not implimented get_f 0 mode_type flexural mode_nr 1 Get the cantilever resonance frequency Parameters e mode_type str optional Name of mode i e flexural or torsional e mode_nr int optional Mode number i e 1 2 3 Returns mode resonance frequency in Hz Return type float Raises CalibrationError if the mode was not calibrated get_feedback Feedback gains of the host AFM Returns i_gain p_gain of host AFM Will return zero if not implimented on host AFM Return type np ndarray dtype float64 get_free data_format complex unit ADU Spectrum of free cantilever oscillation Parameters e
36. not to exceed the max output out1_mask Boolean array with nfreq_out elements When the element is True False it will will not send the corresponding tone to port OUT 1 of the MLA The default value of this array is all True out2_mask Boolean array same as out1_mask but for port OUT 2 of the MLA Note that it is possible to send the same signal to both output ports The default value of this array is all False input_multiplex integer array with nfreq_in elements Each element can take on the values 1 2 3 or 4 When an element is 1 the corresponding tone will be measured at port IN 1 when the element is 2 the corresponding tone will be measured at port IN 2 etc Note that each tone can be measured at only one input port The default value is all elements 1 Note values can have any order but there is a correspondence between the first nfreq_out elements of the frequency array and the elements of the amplitude array a phase array p and the output mask arrays There is also a correspondence between all elements of the frequency array and input_multiplex array We access each element of these arrays with the tone index In summary The frequency array n or f does not have to be ordered in ascending frequency values The frequency MLA tones are specified by the indexed element of an array n drive tones 0 1 2 n m measurement tones 0 1 2 n m first n elements correspond n lt m and usually n m
37. 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 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 Spr 2kgTn 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 Fmin 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 VSpp 22 fN Hz The minimum detectable
38. possible values of df You should use this algorithm when the MLA is 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 AFM 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 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 surface The new
39. 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 additional forces on the tip which are not taken in to account in the reconstruction algorithms Hence overactive feedback means inaccurate forc
40. state is the normal and correct mode of operation When unchecked the free oscillation is not subtracted You can un check and check this box to test if something may be corrupt with your measurement of the free oscillation e Down sample will skip the given number of pixels in both X and Y directions reducing the number of calculations for ImEFM You may find the need to down sample if you have a slow computer and you are scanning with high speed and high pixel density In any case all raw data will be saved to file and a full resolution image can be calculated offline 28 Chapter 3 Quantitative Analysis CHAPTER FOUR ADVANCED TOPICS In order to comprehend some of the more advanced features in the AFM 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 arange the different Panels and Views and create your own custom screen layout Other advanced sections are given for the AFM scientist who want to experiment with different types of mul tifrequency measurement and analysis The AFM Suit
41. the Parameter map creator In this panel you may select the Mode1 to fit to the data and the initial values of all parametres as 24 Chapter 3 Quantitative Analysis IMP Software Suite User Manual Release 4 0 2 described in the Model Fit section Because the generation of parameter maps using Model Fit is computationally intensive it is often easire to use this interface off line so as not to overload the 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 coars
42. the data to generate force and parameter plots 2 2 3 6 1 X Pixel inspector tool A left click on the icon will activate this tool When the tool is activated a left 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 3 6 2 je Area inspector tool A left click on the icon will activate this tool When the tool is activated a left click and drag to form a loop in either the amplitude or phase image will select the data inside the loop marking it a transparent color All intermodulation spectral data will be averaged in the enclosed area if you have the Quantitative Analysis tools installed in your software this averaged data will be analyzed as one effective pixel Averaging over areas with the same response can give much lower noise and smoother force curves 2 2 3 6 3 NN Line inspector tool A left click on the icon will activate
43. the tool When active a left 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 2 2 3 6 4 X Clear pixels tool Removes all selected pixels from the image 2 2 3 6 5 a Level image tool Performs a plane fit to the amplitude and phase image data and subtracts off the plane thereby flattening the data 2 2 3 7 Status Banner The banner at the 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 14 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release 4 0 2 0 0 z o1 2 A utosave Current task and state OscillatioM mplitude nm 7 ol o mea sooi eies Settings
44. this upgrade we are simulatenously dropping support for MLA gen2 there will be no parallell releases of gen2 software Data obtained with MLA gen2 hardware can however still be opened and analysed in this and future versions to make use of the latest analysis techniques 75 IMP Software Suite User Manual Release 4 0 2 New features e Support for MLA gen3 1 serial numbers gt 3100 e Stream Recorder saves DC values of all four inputs with lockin data e Verbose flag added v to show more warnings and error messages Improvements e Model fit parameter maps speed up e New entry point to software with more obvious name start_afm py Bugfixes e Fix in Stream Recorder with low df Version 2 8 3 2 Release date 2019 02 22 New features e Moving surface model analysis plugin included by default e Linear Discriminant Analysis LDA included in Blackbox Analysis plugin Improvements e DMT_EXP model renamed DMT_ExpDamp to clarify exponential damping Bugfix e Fixed set new calibration from Session overview e Several fixes related to non square scans e Removed a lot of unecessary warnings when booting up start software with verbose to see more warnings Version 2 7 1 3 1 1 Release date 2018 09 05 Improvements e Frame title shows if we are in OFFLINE mode Bugfixes e Fix name collision version version dll which prevented software from starting on Window 10 e Fix some deprication warnings e Fi
45. 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 M 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 detector 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
46. 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 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 frequencies 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 f1 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 40 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 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 nfreg_out 2 findex of center of comb n mi n 0 afmi a l0 plmil p 0 n 0 n mil a 0 almil p 0 plmi Create an signal in the time domain consisting of
47. 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 2 2 2 3 Fitting noise data 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 actually exciting the cantilever i e present on the drive voltage then you can improve the calibration by simply removing it 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 gray and is not analyzed in the fit X clears the selected fit range W 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 2 2 2 4 Calibration R
48. you find corresponding tabs to control the different plots and the compensation for background forces You can also open this panel from the Advanced pull down menue e FI FQand Work tabs have options to Use shading which controls the plotting of the F7 A and Fg A curves When checked default case the lightest shade corresponds to the start of the pixel and the darker shade the end Use the Signal Inspector and select the Time tab to see the beat cycle for the selected pixel With the standard setup each pixel starts at close to zero amplitude with increasing amplitude followed by decreasing amplitude Thus the shading allows you to see how F7 A and FQ A differ from increasing to decreasing amplitude e Force tab contains several options explained in detail in Force Reconstruction Methods 3 1 2 5 Background force compensation The BG Comp tab in the Force Inspector Settings controls background force compensation The compensation requires measurement of the just lifted response see Measure just lifted If there is not a just lifted pixel mea sured you will get the same result as if None were selected The theory and application of background force compensation is described in Borgani 2017 e None turns off the compensation in which case all force curves will include background forces e Polynomial fits the linear response function of the background forces to a polynomial in frequency of the Polynomial degree given For standard
49. you scan so that you can view images of various quantities All raw intermodulation data and the processed image data will be stored in a the standard file type e g scan01234 imp You can view previous scans by pressing the Load _ imp button and navigating to the file 3 3 1 2 Analyzing and viewing the ImEFM data View group controls how the intermodulaiton spectral data is analyzed and what data is plotted You can select the following quantities to be shown in the image e Vcpd V the contact potential difference in Volts e Cz F m the tip surface capacitance gradient ge in F m 3 3 Special Modes 27 IMP Software Suite User Manual Release 4 0 2 2 e Czs F m2 the second derivative of the capacitance with respect to separation oe in F m e Trace or Ret race controls which scan to view The Difference between trace and retrace ofVcpd V gives the surface photo voltage when the LED toggle is activated i e change in contact potential between light and dark states e Horiz shift is the number of pixels to shift to compensate for offset between trace and retrace This offset arises if the scan overshoot factor or scan speed is not exactly correct e Vert shift is the number of pixels to shift to compensate for offset between trace and retrace This should always be zero but there maybe something funny with the host AFM e Swap diff changes the sign of the difference i e from trace retrace to
50. 4 2 2 3 0 1 Pixellanspectortool coe s ic scia ese ae eee eee ea 14 2 2 3 0 2 Area imspector tool sepii k ae ey Sede ee ee ee we 14 2 2 3 6 3 LIME Inspector tool ssa d sea ee we te al E 14 223 04 Clear pixels tool sa posea a AH gla Oh ea ROE a a a 14 2 2 3 63 Levelamagettodls s opa soe 2308 ben bea heed ee ed 14 2234 status Banners 2 4 6 4 2 22 bP esbhd A eS 14 224 Analyze Scan Data s sors gey a HA RAE AREY ORE VR OE ws 15 ZA A image Smoothing oe A ee A ds e E is 15 2 2 3 Session OVEFVIEW s ie Gok a ae edo da oes 15 A A A 16 2 25 2 Import host AFM datai socorro p e e a a e a A 16 22 95 Flipand swap scams lt s soua eg a a eie Ee e a we al EE 16 2 2 5 4 Batch process parameter maps and force volume data 16 225 5 Three dimensional viewer 6 4 20h ewe e a ee 17 2 2 6 Session Logbook secesie a s ia oe ed Qe pee we ede EA 18 3 Quantitative Analysis 19 3 1 Inspecting sinele pixels se serci ae bc o A BR A a Gl Be ga a kG 19 S31 Signal Inspector suk 4k eA de ROR A wae ed ee ES 19 SQ Force Inspector los er poi e Oe Se es a Sh eR ae ee let S 20 3 1 2 1 Dynamicforce quadratures scosse 6 64 ee ea oS Re ee E 20 3 1 2 2 Dassipated work and average potential 02202 20 3 1 2 3 Reconstructed force s sr es spei aap a a Ee eo 20 3 1 2 3 1 Force Reconstruction Methods ca ea ateei e ae EA E E A 21 3 1 2 4 Force Inspector Settings 44 pase da a e EE 23 3 125 Background force compensation aer Ged be
51. 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 dfxnp arange n_samples_beat 2 1 Frequency axis for plotting Index each beat in the stream ii_s np arange 0 sf n_samples n_samples_beat 1 remove last since it might not be complet 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 i 100 0 print Beat i i beat_i len ii_s Read data i_start ii_s beat_i continues on next page 42 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 continued from previous page 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 mus
52. Intermodulation products IMP Software Suite User Manual Release 4 0 2 Intermodulation Products AB Jan 09 2020 CONTENTS 1 Introduction 3 1 1 Conventions and useful tips e es cecek mameri ea ds ee ee aea 3 12 Sereen Layout e se 4 ee a RR ER AS Ae RR AE 3 L3 Pihon ae a A e A A AR A AA 3 2 The IMP Session and Work Flow 5 SS E ee EAs RRs 5 22 Work BIOW wu mea hate Poe ee eae ba Mal Boao Rew Gee eee Ye ee ba SE 5 221 Frequency SWeep a4 4 2053 be ek a Ra ae ES PRR Oe as ee aS 6 222 Calibration lt i gri bd eos bbe Ae ee kbd EGA eG De Ee bee 6 2 2 2 1 Choose Cantilever and Method 7 2222 Measure Noise ose e a a O ee ee E A 8 A RIMS MOISE AA ee es eae a gba aes Bik 8 2224 Calibration Result ses os prospere 8 2229 JCurrentCalabravion e A a a 9 2 2 26 Add Edit Remove cantilevers so ocs e 4 Se eae RE EA 10 2 2 2 7 Calibrating torsional eigenmodes ss s sos eo somar eii een 10 223 SCAMMMG 2er 4 Bac a a a a dde ae 10 22 3 1 Set pand SCA ri A a bow a ee ota bbe 11 2 232 Measurejustlitted ss osa a SE Se Oe ee 11 225 3 A A Be ee a ROR E a ew es ae al E 12 22 a ais Sg A ee atte el Bhs Bide oe Boe Gh dae wie ie Papen oe Bac 12 2239 Mage SENSES 003 6 e eae ESR Pa Ee ee eae E 12 alada Colon Bar 4 4 aa ete A Be A e et 12 22 3 5 2 Image Toolbar s ccu eo a RIE ON E E oe we 13 22 30 3 Mouse wheel zooming 2 5 s e rara eRe OS bw eA 13 22356 Selecting Dita dd Scam sye onee in le ok a ee ee A 1
53. 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 Polynomial degree is de scribed in Polynomial e ADFS Force Volume when checked will perform Amplitude 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 2 2 5 5 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 Left click and drag on the image to rotate the viewing angle Right click and drag to change the zoom The Viewer settings group allows for change of the 3D image properties including the Z scale which usually defaults to a factor larger than 1 in comparison to the X and Y scales Such scaling exaggerates the topography The Texture settings group controls which quantity is represented by the color p
54. 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 ImAFM 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 5 4 6 1 Hardware Connection images 5 4 6 1 1 SAM Ill connections 5 4 6 1 2 Nanoscope Ill and Illa Trigger Access 5 4 6 1 3 Nanoscope V Connections 5 4 6 1 4 JPK Nanowizard lll Connections 5 4 Common AFMs 65 IMP Software Suite User Manual Release 4 0 2 Fig 1 Typical connections for the SAM from Veeco Digital Instruments The images shows the SAM III con nected to a Dimension 3100 AFM These connections may be different depending on the controller AFM and SAM versions The switches in the image
55. a method 49 get_input_ports afmapp Scanner ScanData ScanData method 49 get_invOLR afmapp Scanner ScanData ScanData method 49 afmapp Scanner ScanData ScanData method 50 get_karray afmapp Scanner ScanData ScanData get_ get_k method 50 get_lift afmapp Scanner ScanData ScanData method 50 get_loaded_filename afmapp Scanner ScanData ScanData method 50 get_metadata_ascii afmapp Scanner ScanData ScanData method 51 get_mla_calibration afmapp Scanner ScanData ScanData method 51 get_mla_firmware_version afmapp Scanner ScanData ScanData method 51 get_original_filename afmapp Scanner ScanData ScanData method 51 get_output_mask afmapp Scanner ScanData ScanData method 51 get_phases afmapp Scanner ScanData ScanData method 51 get_0 afmapp Scanner ScanData ScanData method 45 get_resolution afmapp Scanner ScanData ScanData method 51 get_samples_per_pixel afmapp Scanner ScanData ScanData method 51 get_scan_rate afmapp Scanner ScanData ScanDaga method 51 get_scan_size_x afmapp Scanner ScanData ScanData method 52 get_scan_size_y afmapp Scanner ScanData ScanData method 52 get_scan_subtype afmapp Scanner ScanData ScanData method 52 get_scan_type afmapp Scanner ScanData ScanData method 52 get_setpoint afmapp Scanner ScanData ScanData method 52 get_starttime afmapp Scanner ScanD
56. a Current calibration in order to display in nanometers 4 5 5 Manual Setup The MLA allows for driving with more complex drive waveforms involving more than two tones and measuring with lockin schemes that do not simply measure closely spaced tones around one resonance The AFM Suite offers a few tools to aid in configuring the MLA for such measurements Select Manual setup from the Advanced pull down menu You can dock this panel for example in the Advanced Setup frame e Selecta Measurement time window or Measurement bandwidth These quantities are the in verse of one another and when you change only one of these the system will calculate the other to match your change e Input the frequencies of all tones where you either want to drive or listen for response These frequencies can be given as Freq kHz orasn the later being integer multiples of the measurement bandwidth see Intermodulation Measurement e Set the Amplitude and Phase of the tones only where you wish to drive If the amplitude is set to zero there is obviously no drive at that frequency Setting Phase does not effect the measurement of response phase regardless of the drive amplitude e The check boxes for Out 1 and Out 2 control the output mask When checked the drive will be applied at that output port e You can select which of the four input ports In 1 In 4 where the MLA will listen for response at any tone When you input all of your target values
57. ainted on the topography Default is the response phase at the first drive frequency You can choose to plot Amplitude or Phase of any frequency in the intermodulation spectrum If the imp file has an Add on image for example an IMEFM image or a parameter map these can also be painted on the topography You can also choose to a Parameter file consisting of 2D arrays the same size as the image stored as a numpy npz file Limits opens up a dialog box with a histogram of image pixels allowing you to set the upper and lower limits of the color scale The Camera position is shown in the boxes It is easiest to adjust this by left or right click and drag on the image If the Animate box is checked the image will rotate around the azimuth You can use screen capture programs to make a movie of this rotation The Plane fit group 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
58. al mode_nr 1 Check if a valid calibration is stored Parameters e mode type str optional type of cantilever mode flexural or torsional e mode_nr int optional mode number Returns True for a valid calibration Return type bool load_from file filename minimal False Summary Parameters e filename str filename to be opened e minimal bool optional if True only load parameters Raises FileVersionError if file version not supported reset_lift Empty previously stored lift data save_to ascii dirname 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 Parameters dirname str optional if None the directory is automatically named after the ScanData file save_to file filename Saves all data in the ScanData class to an hdf5 file Parameters filename str desired filename set_0 0 mode_type flexural mode_nr 1 verbose True Set the cantilever quality factor for an existing calibration Parameters e Q float quality factor e mode_type str optional Name of mode i e flexural or torsional e mode_nr int optional Mode number i e 1 2 3 e verbose bool optiona1 If True print a message to the console Raises CalibrationError if the mode was not calibrated set_ampl
59. ance with a Frequency Sweep and calibrating the cantilever using non invasive thermal noise Calibration Open the ImEFM panel by clicking on the ImEFM icon in the work flow or by selecting ImEFM from the Advanced pull down menu The ImEFM panel has the following controls Settings group controls the following e Osc amplitude is the desired amplitude of cantilever oscillation When Setup is executed the piezo drive voltage will be adjusted to achieve this value If you are using a standard EFM cantilever for example 26 Chapter 3 Quantitative Analysis IMP Software Suite User Manual Release 4 0 2 the HQ NSC15 Pt by micromash fo 325 kHz k 40 N m Pt front side coated you may want to use about 40 60 nm oscillation amplitude Tip AC voltage sets the amplitude of the low freqeucy AC voltage applied between the tip and sample This voltage induces a small electrostatic force on the cantilever which modulates of the cantilever oscilla tion The larger this voltage the larger the electrostatic force A typical value here is between and 6 Volts The maximum voltage that the MLA can apply is 7 Volts 14 volts by changing an internal jumper Tip DC offset sets a DC offset voltage between the tip and sample Often this can be set to zero but a small offset is useful when the contact actual potential is close to zero so that you measure some signal and not only noise You can also test for a change of potential by
60. are in the position for ImAFM M left for ImAFM M right for normal AFM Un screw x4 to open top lid Itt Hl TET t I Fig 2 Remove the 4 screws in each corner of the lid on the NS III or NS II a controler 66 Chapier 5 Installation IMP Software Suite User Manual Release 4 0 2 Fig 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 E NanoScope Illa x Se A Scanning Probe Microscope Controller ayr di Digital E Instruments Vecco Metrology Group Fig 4 BNC bulk head connectors giving access to EOL and EOF connectors on the front panel 5 4 Common AFMs 67 IMP Software Suite User Manual Release 4 0 2 Switches left for ImAFM right for normal AF a x from Feedback OU swircnes recut CU 205i mam pad from Signal OUT me Fig 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 6 The EOL and EOF triggers are on the front of the NS V controller Make the connections as labeled in the image 68 Chapter 5 Installation IMP Software Suite User Manual Release 4 0 2 5 4 Common AFMs 69 IMP Software Suite User Manual Release 4 0 2 70 C
61. 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 1f and when the scan size is imported together with height data from the host AFM see Import host AFM data 2 2 3 5 1 Color Bar The color bars have functionality for adjusting the images 12 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release 4 0 2 10 Histogram for IMP7L phase _ Set limits automatically excluding2 0 of the pixels right click click and drag double click 90 Phase deg a 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 plo
62. ashed but the process is still running in the computer and I can not stop it Solution In Windows start 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 position Problem I can not get a good fit to the noise calibration data Solution e There may be a spurious signal coming from your AFM 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 1s 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 of 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 73 IMP Software Suite User Manual Release 4 0 2 74 Chapter 7 Trouble Shooting CHAPTER EIGHT CHANGELOG This list oulines major new featur
63. asured You can also add your own 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 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 are interested in learning about the forces of interaction between the tip and surface 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 inertial force due to acceleration of the cantilever mass and the drive force that we apply by shaking of the cantilever base To properly separate out the tip surface force from all other contributions we require three things A good Calibration of the cantilever and a good measurement of the cantilevers free motion when it is far away from the surface and if you wish to compensate for background forces a good measurement of the cantilevers just lifted motion see Measure just lifted Calibration is performed at the outset of ImAFM M and the free motion is measured during Setup before scanning It is easy to lift well clear of the surface and re do either of thes
64. ata ScanData method 52 get_tip_Vac afmapp Scanner ScanData ScanData method 52 get_tip_Vadc afmapp Scanner ScanData ScanData method 52 given_list_is_empty afmapp Scanner ScanData ScanData method 52 has_calibration afmapp Scanner ScanData ScanData method 53 Home tool 13 host AFM files 15 Hydrodynamic function 7 hysteresis in FI FQ curves 19 Image Settings 12 image toolbar 13 ImEFM 25 ImLA 29 65 IMP Control 12 IMP Session 4 Import host AFM data 15 independent lockins 65 inputs 65 Intermodulation Lockin Analyzer 29 65 intermodulation measurement 29 inversion 18 invOLS 8 Line direction 12 Line Inspector 13 load_from_file afmapp Scanner ScanData ScanData method 53 Logbook 17 M asure lift 1l 86 Index IMP Software Suite User Manual Release 4 0 2 inimum detectabl LA 29 65 ode stiffness 8 odel Fit 22 Mouse wheel zooming 13 multifrequency lockin amplifier 29 65 N Noise calibration 30 noise floor 8 Noise measurement 8 noninvasive calibration 30 O optical lever sensitivity 8 3 force 8 32 oscillation range 11 oscillator approximation 30 outputs 65 P Pan Zoom tool 13 Parameter maps 24 Phase image 12 PID control 30 Pixel Inspector 13 plan view dimensions 7 Polynomial reconstruction 21 Q quadrature forces 19 Quality factor 8 Quantitativ
65. 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 kHz and Stop frequency kHz 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 kHz 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 The measurement time at each point is given by the inverse of the bandwidth You may need to adjust the Drive amplitude V in order to the right amount of excitation to excite the cantilever resonance Check boxes provide automatic features for finding the resonance and controlling the sweep Zoom peak performs a second 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 e Reverse sweep direction gives a sweep with increasing and then decreasing frequency over the range specified 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 sur
66. ced Topics IMP Software Suite User Manual Release 4 0 2 get_detector_noise mode_type flexural mode_nr 1 Get the detector noise floor Parameters e mode type str optional Name of mode i e flexural or torsional e mode nr int optional Mode number i e 1 2 3 Returns detector noise floor in ADU 2 Hz Return type float Raises CalibrationError if the mode was not calibrated Examples gt gt gt sd ScanData ScanData scan01612 imp gt gt gt psd np sqrt sd get_detector_noise sd get_invOLR lel5 gt gt gt print The detector noise floor is 2f fm sqrt Hz format psd The detector noise floor is 138 13 fm sqrt Hz gt gt gt psd np sqrt sd get_detector_noise sd get_invOLR sd get_k Sox lel5 gt gt gt print The equivalent noise force is 0f fN sqrt Hz format psd The equivalent noise force is 5013 fN sqrt Hz get_df Measurement bandwidth Returns Hertz Hz Return type float Examples gt gt gt sd ScanData ScanData scan01612 imp gt gt gt df sd get_df get_drive_amplitudes Amplitudes of driven tones Returns lockin output amplitude digital units LOA Return type np ndarray np int64 See also get_drive_karray get_drive_phases get_drive_karray Frequencies of driven tones as multiples of measurement bandwidth df Returns frequencies where drive amplitudes are
67. 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 F d Dyan 948 A further assumption is that the force is zero when the tip is sufficiently far from the surface Under these assump tions we can find the N polynomial coefficients g both odd and even coefficients from the measured spectrum of odd order intermodulation products The method is described in detail in Platz 201 2a Platz 2013b Polynomial reconstruction has the following options 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 3 1 Inspecting single pixels 21 IMP Software Suite User Manual Release 4 0 2 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
68. ched IMP images When the matching looks correct click OK and the AFM height data will be appended to the imp file Note In DI Veeco Nanoscope software version 5 there is a bug 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 2 2 5 3 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 sca
69. ctrostatic Force Microscopy The Intermodulation measurement concept can be applied to Electrostatic Force Microscopy EFM were a force on the cantilever is induced by a voltage applied between the tip and sample We call this method ImMEFM and its implementation requires the synchronous multi port capability of the Multifrequency Lockin Amplifier MLA Two output ports are used with ImEFM one port driving the tip sample voltage at a low frequency and the other port driving the cantilever via the shaker piezo near the cantilever resonance frequency The tip surface capacitance gradient is a nonlinear function of the tip surface separation and this nonlinearity causes intermodulation or frequency mixing between the electrostatic drive and the mechanical drive Measuring 4 intermodulation products near resonance and taking ratios of their amplitudes we extract the contact potential difference between the tip and surface The theory of the method and its validation was given by Borgani et al Borgani 2014 Here we describe the user interface in the AFM Software Suite ImEFM requires a conducting cantilever for example a Pt coating on the front side of the probe In the de scription given below a voltage is applied to the tip and the sample is grounded One can equally well apply the 3 3 Special Modes 25 IMP Software Suite User Manual Release 4 0 2 voltage to the sample and put the tip at at ground Which method is more
70. d Width b um in microm eters Make sure that you enter a Cantilever name and the Manufacturer Click Add and your cantilever will appear 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 Shape selector is used to specify that the cantilever is or is not rectangular e Click Add to create the new cantilever which will appear at the bottom of the cantilever selection list with the name user_cantilever name Creating a new cantilever does not effect the selected cantilever Close the dialog box and select the new 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 2 2 2 7 Calibrating torsional eigenmodes Torsional calibration uses the same principals as flexural calibration but the methods are not as well tested and established as flexural callibration We provide two methods for calibrating the lowest torsional eigenmode e Torsional Hydrodynamic Func
71. d pull down menu To removed 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 4 11 Panels and Views 59 IMP Software Suite User Manual Release 4 0 2 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 560 Scan direction Trace Retrace Swap Fip left right 279 8 KHz n 560 Phase deg cIx Ia Z E Autosave 4 60 Chapter 4 Advanced Topics CHAPTER FIVE INSTALLATION 5 1 Install Software The AFM Software 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
72. de darker shading This hysteresis can be related to the finite relaxation time of a visco elastic surface or plastic deformation of the surface However some measurement artifacts can also cause hysteresis such background forces that are not properly compensated for see Background force compensation over active feedback large error signal or excessive noise in the measured intermodulation spectrum If the hysteresis is small you can treat it as a weak effect in relation to the overall trend and in this case you can select mean curve when reconstructing the force vs deflection curve using Amplitude Dependent Force Spectroscopy ADFS 3 1 2 2 Dissipated work and average potential The Work tab brings up a double plot very similar to FI FQ We plot the product 2r A x F A vs the amplitude A We can regard this product as a work integral giving the work done by the tip surface force during the single oscillation cycle of amplitude A see Platz 2012b For a purely conservative interaction this work is zero at any amplitude Negative Fo means that energy in the cantilever was lost via the tip sample interaction for example via motion of a viscoelastic surface or irreversible deformation of the tip or the sample In contrast the quantity 27A x F A is not a work integral If the interaction were described by a conservative force this quantity is related to the average potential energy change in the oscillation cycle with the amplitude A
73. de to zero Test the system and if it works save this workspace as ImAFM For ImEFM you need to set the software as above and configure for connection for the tip voltage Go to the Advanced Settings menu red stop sign icon Under the group other go to tip bias control and select the option tip bias Also in this group go to sample bias control and select the option ground Test the system and if it works save this workspace as ImEFM 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 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 controller IN1 on the MLA lt gt Out 0 on the controller Signal routing is configured in the software cross point switch and these settings are most easily made by running a script o 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 t
74. de was not calibrated set_feedback array Feedback gains of the host AFM Parameters np ndarray dtype float 64 feedback parameters of host AFM i_gain p_gain Not implimented on all host AFMs set_free free data_format complex unit ADU Spectrum of free cantilever oscillation Parameters e free np ndarray spectrum of free cantilever oscillation with specified data format and units e data_format str optional IQreal complex specifies data type e unit str optional ADU V m nm rad deg specifies units rad and deg only for phase Raises e CalibrationError if the specified units require conversion but no MLA cali bration was set e ValueError if the specified format and units are incompatible or the scan pass format or units are unknown See also set_lift Examples gt gt gt sd ScanData ScanData scan01612 imp gt gt gt get free response in nm gt gt gt data sd get_free unit nm gt gt gt freqs sd get_karray sd get_af gt gt gt plot amplitude vs frequency gt gt gt 1 plot freqs np abs data set_frequencies freqs_Hz Frequencies of the measured tones Parameters freqs_Hz np ndarray dtype np float 64 Hertz Hz set_fs fs Lockin sampling frequency Parameters fs float samples second Hz set_input_ports
75. dex 0 set_starttime 10 Time at start of scan in seconds since the epoch Parameters t0 float seconds set_tip Vac value AC voltage applied to the tip in ImEFM Parameters value float Volts V set_tip Vdc value DC voltage applied to the tip in ImEFM Parameters value float Volts V 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 AFM 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 AFM Suite installed When you perform analysis on another computer all newly created analysis files will be added to the session folder sessions This folder contains session folders Each time you start the AFM 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
76. discussion of the torsional eigenmode Note For the calibration to be accurate is important that the calibration is performed when the cantilever is well free of the surface at least several cantilever widths or about 0 1 mm or more from the surface 2 2 2 1 Choose Cantilever and Method Calibration Parameters specifies the type of cantilever and calibration method e Temp C is the temperature of the damping medium which is in thermal equilibrium with the cantilever This temperature determines the magnitude of the thermal noise fluctuation force that is driving the can tilever e Fluid selects the density and viscosity of the damping medium surrounding the beam needed for calcula tion of hydrodynamic damping Noise calibration methods have not been tested thoroughly beyond studies in Air but we include to option to apply the theory in Water 20 C e Cantilever selects from a list of cantilevers for which calibration constants have been published If your cantilever is not on this list you can choose Arbitrary Rectangular and enter the cantilever Length L um andWidth b um of your rectangular beam cantilever You can edit the length and width fields for any chosen cantilever without changing the stored values for that cantilever Alterna tively 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
77. drag over the plot will zoom to the selected rectangle upon release 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 Gt Configure subplots opens up a dialog box to adjust the placement of the plot axes within the plot frame 2 2 3 5 3 Mouse wheel zooming In addition to the zoom tools in the image toolbar you can use the mouse wheel to rapidly zoom plots and images e Hover over the x or y axis of a plot just outside the plot frame and roll the mouse wheel Only that axis will zoom about the location of the mouse pointer Click the mouse wheel to auto scale the axis e Hower over any point in a plot or an image and roll the mouse wheel The plot or image will zoom about that point with equal zoom in the x and y directions Click the mouse wheel to auto scale the image or plot 2 2 Work Flow 13 IMP Software Suite User Manual Release 4 0 2 2 2 3 6 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
78. e Analysis 18 R Reconstruction Methods 21 Reference calibration 7 reset_lift afmapp Scanner ScanData ScanData method 53 Resonance frequency 8 responsivity 8 32 Ret race 12 Run calibration 8 S Sader constants 7 Save image tool 13 save_to_ascii afmapp Scanner ScanData ScanData method 53 save_to_file afmapp Scanner ScanData ScanData method 53 saving images 13 Scan rate 12 ScanData class in afmapp Scanner ScanData 44 scanner panel 10 Scanning 10 Select range 8 sensitivity 32 Session Logbook 17 Session Overview 15 Set point 11 set_amplitudes afmapp Scanner ScanData ScanData method 53 set_calibration afmapp Scanner ScanData ScanData method 53 set_cantilever_noise afmapp Scanner ScanData ScanData method 54 set_detector_noise afmapp Scanner ScanData ScanData method 54 set_df afmapp Scanner ScanData ScanData method 54 set_endtime afmapp Scanner ScanData ScanData method 54 set_external_filename afmapp Scanner ScanData ScanData method 54 set_f0 afmapp Scanner ScanData ScanData method 54 set_feedback afmapp Scanner ScanData ScanData method 55 set_free afmapp Scanner ScanData ScanData method 55 set_frequencies afmapp Scanner ScanData ScanData method 55 set_fs afmapp Scanner ScanData ScanData method 55 set_input_ports afmapp Scanner ScanData ScanData method
79. e at any time during the session We recommend that you check the calibration occasionally to see if the results are consistent with previous measurements After each re calibration you also need to re do Setup and make a new measuremnet of the just lifted response The most recently measured or Current calibration data free motion spectrum and lift motion spectrum are stored with each scan file These measurements are an important part of the analysis of the scan data and they can be viewed using the Data Tree 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 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 which puts the data in to the Data Tree allowing 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
80. e 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 AFM Software Suite A session folder named with the current date is automatically created where all your data will be stored 2 2 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 AFM Suite Click on these icons to open the different panels and views da Find the resonance by performing a Frequency Sweep x Calibrate the cantilever and detector using non invasive thermal noise Calibration N Setup and scan then engage the surface with the host AFM to start Scanning y Open previous scan files and use the pixel and line inspectors to Analyze Scan Data IMP Software Suite User Manual Release 4 0 2 View the session and import host AFM data batch process or 3D view in Session Overview Add comments to the automatic logging in the Session Logbook Each step in the work flow is described in detail in the following sections 2 2 1 Frequency Sweep SAS a After loading the cantilever and adjusting the detector find the cantilever resonance by sweeping the frequency of the
81. e 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 being 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 3 3 Special Modes The intermodulaiton measurement concept can be applied to the many different modes of AFM and several special modes are under development At present the following modes are available 3 3 1 Intermodulation Ele
82. e 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 Multifrequency Lockin Amplifier MLA also known as the Intermodulation Lockin Analyzer ImLA Tholen 2011 The instrument is specially designed to make a phase sensitive measurement of many intermodulation products generated by a nonlinear system that is driven by two or more tones Intermodulation should not occur when the cantilever is oscillating in air above a surface because the freely oscil lating 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 p
83. e 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 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 Show meta data to open a box to view the calibration data stored with this scan file i e the Current calibration at the time that the data file was closed as well as a time and frequency domain plot of the Free and Lfited motion 4 3 Programming your own Force Models 33 IMP Software Suite User Manual Release 4 0 2 8 Data Tree Y Scans Current Scan Y Users david_haviland Documents Anaysis 2014 03 31 to w M Pixel at 137 58 Trace Y inv ADFS v Inv poly 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
84. e 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 amplitude 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 36 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 4 5 4 Units You can select between displaying the cantilever response signal in Analog to Digital Units ADU or in nanometers nm You must have
85. e target IMD the response is measured and stored as the lift response You can Abort if something is not working If you did not measure just lifted during the scan it is possible to perform background force compensa tion if your scan file has a parachuting pixel in the image as described in Background force compensation 2 2 Work Flow 11 IMP Software Suite User Manual Release 4 0 2 2 2 3 3 Set point Amplitude set point is the set point for the AFM scanning feedback ImAFM M 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 If you are having trouble engaging the surface you can lower this set point Sometimes background forces cause drop in amplitude by as much as 75 at the surface This effect can cause a false engage at a position well lifted from the surface If Measure just lifted is performed amplitude change is calculated as a percent of the amplitude at the just lifted position 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 2 2 3 4 Scan rate Scan rate is the required rate of scanning determined by the chosen pixel rate measurement bandwidth df and number of pixels in the scan line x resolution You must set t
86. ed 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 2N Fourier sums in real time at user specified frequencies where N is the number of tones in your version or the firmware 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 250 times in the measurement time window Tm 1 0f 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 sensitivity of a high Q resonance to measure the thermal equilibrium fluctuations of cantilever deflection
87. erform 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 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
88. es and bug fixes between releases of the ImnAFM suite Each release typically also includes additional minor bugfixes and smaller new features Version 4 0 2 Release date 2019 11 07 Note see changenote for 4 0 1 regarding updating from earlier versions Improvements e ImEFM turns on output amplifiers if needed Bugfixes e Fixed exporting force curves from data tree e Fixed 3D viewer on Windows e Fix to ImFFM which could freeze Version 4 0 1 Release date 2019 09 09 Due to changes in the hardware bootup sequence the following commands must be run from the built in Python shell once for every MLA if it was shipped with an older version from mlaapi import setup setup upload_bootware mla hardware ip_address Additionally if the IP address has been changed from the default 192 168 42 50 you must also run setup set_ip_address mla hardware ip_address mla hardware ip_address Improvements e Various improvements to Frequency sweep voltage kept at zero after sweep individual curves can be shown hidden from toolbar Bugfixes e Removed transients appearing during startup e Fix bug in ADFS force volume export e Various bugfixes in cantilever calibrator allow lt 1kHz range allow user to re zoom while acquiring data Version 4 0 Release date 2019 07 24 We have made a major transition of the software under the hood It is now based on Python 3 instead of Python 2 and is therefor more future proof With
89. esult The Calibration Result is displayed in several ways including important figures of merit to judge the quality of the calibration It is useful to think of the calibration as having two parts The calibration of the cantilever the force transducer and the calibration of the detector the deflection sensor or optical lever Cantilever e Resonance frequency fo k m kHz of the simple harmonic oscillator model used to model the cantilever eigenmode with mode stiffness k and effective mass m 8 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release 4 0 2 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 2r fo y 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 Mode stiffness k N m is the eigenmode stiffness or dynamic spring constant which is the coeffi cient of the linear restoring force in the simple harmonic oscillator model describing the eigenmode 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 i
90. face The AFM 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 6 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release 4 0 2 The IMP Suite determines the parameters of the cantilever as a dynamic transducer of force ImAFM being a dynamic method of force measurement requires the stiffness of the beam in the frequency band of the mea surement near resonance which is not the same as the static bending stiffness of the beam The method works with the fundamental eigenmode of the cantilever or the resonance with lowest frequency 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 the Flexural or Torsional eigenmode The latter calibration is available if you have the Intermodulation Frictional Force Microscopy ImFFM option The cal ibration 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 the flexural eigenmode and end with a
91. 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 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 SS a Spp Here again we assume that the detector noise is independent of frequency in the band of interest If the pixel time is T 1 ms and oo 150 fm WHz the minimum detectable cantilever deflection at each pixel would be 32 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 dmin 4 SI B 4 7 pm It is also interesting to express the detector noise as an Equivalent force noise y Sppe ky Soa Ca 6 pN VHz which in a measurement time For the example given above and k 40 N m we find T 1 ms gives an equivalent minimum detectable force of ae ad kdmin 0 19nN This would be the minimum detectable force with the cantilever if the measurement were dominated by detector noise
92. from the assumption that it the the force can be written function of the tip position i e there exists a force curve F d It further assumes that the force is zero for positive deflection i e F d 0 for d gt 0 If these assumptions are valid the F d curve is extracted by performing an inverse Able Transform on the F A curve 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 Three features control ADFS e Reconstruct from FI A for is a pull down menu selector that allows you to select different regions of the F A curve that will be used for ADFS Usually best results are found for Longest monotonous amplitude increase which is the default selection However you can reconstruct for decreasing amplitude or for a mean curve which averages the increasing and decreasing amplitude Note that often with soft materials the F A and F A show hysteresis meaning that they are different for increasing or decreasing amplitude This can be a sign that the surface is not relaxing to its equilibrium position between successive taps of the tip In this case a force curve F d can not describe the interaction and ADFS gives only an approximate view of the force 22 Chapter 3 Quantitative Analysis IMP Software Suite User Manual Release 4 0 2 e Stavitzky Golay smooth
93. hapter 5 Installation CHAPTER SIX MULTIFREQUENCY LOCKIN AMPLIFIER 6 1 Version Ill For the MLA 3 please refer to the online manual at https intermodulation products com manuals IMP MLA _ user_manual mla html 6 2 Version ll For the MLA 2 please refer to the online manual at https intermodulation products com manuals IMP MLA_ user_manual mla_2 html 6 3 Version Version I of the MLA or ImLA has fewer connections and can handle fewer frequencies Front side connections e Signal OUT sends the drive frequency 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 e Feedback OUT delivers a error signal to the host AFM where zero volts corresponds to the set point in the AFM 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 e 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
94. he 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 e 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 e Output 0 on the Cypher backpack lt gt IN 1 on the MLA e Input 0 on the Cypher backpack lt gt OUT 1 on the MLA e Input 1 on the Cypher backpack lt gt OUT A on the MLA M 64 Chapter 5 Installation IMP Software Suite User Manual Release 4 0 2 The signal routing is made as for the MFP 3D as described above which is easily done by running the ImAFM_Cypheripf script 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 scrip
95. he atomic force microscope J E Sader et al Jour Appl Phys 97 124903 2005 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 Thol n C Hutter and D B Haviland Rev Sci Instr 82 026109 2011 Tholen_2011 Thoren 2017 Calibrating torsional eigenmodes of micro cantilevers for dynamic measurement of frictional forces P A Thor n et al to be published 2017 84 Bibliography A accuracy 32 Acquire noise data 8 ADFS 21 22 ADU 8 Amplitude Dependent Force Spectroscopy 22 Amplitude image 12 Analysis 15 Area inspector 14 B Back tool 13 back side connections 65 Background force compensation 23 Batch parameter maps 16 C Calibration 6 Calibration method 7 Calibration Result 8 Cantilever 7 Cantilever calibration 6 Color Bar 12 comments 17 connections 65 Contact potential difference 25 current calibration 9 Cz 27 D Data Acquisition 8 Detection noise floor 8 Detector noise floor 32 detector responsivity 8 detector sensitivity 8 dissipated energy 20 E Electrostatic Force Microscopy 25 Exclude data 8 F Feedback 30 FI FQ 19 file association 15 INDEX finding the resonance 6 Fitting noise data 8 Flip right left 12 Flip u
96. he 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 but it is not necessary that the scan rates match exactly A 1 deviation is not noticeable in the images and it is better that the host AFM scan rate be slightly smaller than the ImAFM M 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 half 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 2 2 3 5 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 direction 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
97. ic and intermodulation distortion of the free cantilever oscillation with harmonic and intermodulation due to a tip surface force Any output signal should also not exceed the maximum or be too small in order to avoid distortion in the MLA Often drive amplitudes are shown in percent of full output The drive waveform coming from an output port of the MLA can be conditioned with external amplifiers or attenuators to suit the application Internal 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 Drive Constructor is initially selected in the Advanced pull down menu The Python scripting in terface allows you configure the Multifrequency Lockin Analyzer MLA You can use the Drive Constructor to create a frequency comb of drive tones and to select the frequencies at which you want to perform lockin measurement Before attempting to use the Drive Constructor you should read the section on ntermodulation Measurement 4 6 1 Configuring the MLA The Python scripting interface has several pre defined variables and and built in functions to help in the con struction 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 IMP Sessions and Set tings settings drive_setups user_drive_scripts py These scripts are we
98. ided 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 running a Multimode AFM or Dimension AFM the IMP NS4 SAM gives you signal access If the NS V controller i
99. iles IMP Software Suite gt gt gt sys path append suite_path gt gt gt from Scanner import ScanData 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 IDE 4 9 1 ScanData Class class afmapp Scanner ScanData ScanData filename None This class handles the storage and retreval of data to and from a scan file e g scan01234 imp The class is designed to be easily extendable and new functions will be added as the IMP Suite grows Most functions set data in or get data from the containers provided in the class Units are specified in square brackets in the doc strings In additon to SI units e g Hz sec Volts some functions use the following native lockin or digital units e PCU phase counter units an integer number between 0 and 2 42 e ADU analog to digital units integer steps of an AD converter e DAU digital to analog units integer steps of a DA converter 44 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 Examples gt gt gt instanciate class and load data from file gt gt gt sd ScanData ScanData scan01612 imp gt gt gt get the frequency array units Hz gt gt gt freqs sd get_karray sd get_adf gt gt gt load
100. ill convolve the stored intermodulation data with a Gaussian function of width Sigma pixels in the x and y direction 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 and it lowers the 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 ratio by a factor of 3 This is a smart way to improve the signal quality without increasing the measurement time by exploiting the idea that neighboring pixels are more likely to have the same response Note however that smoothing does introduce a correlation length to your data which you can clearly see as a granularity in high 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 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 2 2 Work Flow 15 IMP Software Suite User Manual Release 4 0 2 2 2 5 1 Session Open IMP session and choose a session folder An overview
101. import height data from Nanoscope version 9 2 e Corrected scaling of Nanoscope height files when height sensor calibration existed but height sensor was not used e Tweaks to make measure just lifted more stable e Modified behaviour of session log book to reduce the risk of deleting log entry by mistake Version 2 5 Release date 2017 03 02 New features Background force compensation using new measure lift function Changes to force curve plotting ADFS default no longer polynomial plot only modulated range Stavitzky Golay smoothing of ADFS force curves Speed up of FI and FQ calculation Speed up of ADFS force curves force volume export almost 40x faster New Mode Intermodulation Frictional Force Microscopy ImFFM with torsional eigenmode calibration Support for input multiplexing feature of the MLA needed for ImFFM available from Drive Constructor Mouse wheel zoom features in all plots and images Drag and drop support for opening files and folder Graphs showing convergence of calibration Simplified ImAFM set up automatic modulation range Script for calculating True Topography using feature on FI FQ curves Level data tool in analysis pannel New scheme in ImEFM for improved surface tracking Improvements to Drive Constructor Improvements to 3D viewer use amplitude and phase images as texture Update and improvement of the User Manual Bugfixes e Lasso tool picks data from correct scan pass
102. in to the table select the tuning algorithm that you would like to apply see Frequency tuning e tune 0 no tuning will give you your target values but this tuning will suffer from Fourier leakage and it will not be possible to lock in on harmonics or intermodulation products without phase drift tune 1 prio f default will tune the measurement bandwidth and frequencies putting prior ity on getting as close as possible to the selected frequencies This is the default tuning scheme that works well for most applications e tune 1 prio df will tune the measurement bandwidth and frequencies putting priority on getting as close as possible to the selected measurement bandwidth tune 2 prio f perfect will tune the measurement bandwidth and frequencies putting prior ity on getting as close as possible to the selected frequencies In contrast to the tune 1 options the tune 2 options are perfect in that they create exact matches between bandwidth and frequencies tune 1 gets very close to a match but not exact so that there will be a very small and for most purposes negligible amount of Fourier leakage tune 1 options also use a periodic correction method to avoid phase drift The correction is not necessary fortune 2 options tune 2 prio df perfect will tune the measurement bandwidth and frequencies putting pri ority on getting as close as possible to the selected measurement bandwidth Finally press the Write to
103. inear 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 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 p
104. ing is a routine to smooth the ADFS force curves Smoothing su presses wiggles in the force curves caused by noise and limited spectral range of the cantilever Two num bers control the smoothing The smoothing window length is the precent of the total number of points in the full force curve over which the smoothing is made You can also choose the Smoothing polynomial degree The smoothing fits a polynomial over a sliding window to generate a smoothed point Fast Polynomial A computationally efficient method to determine the polynomial coefficients of the conservative tip surface force 1s 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 as scan data is acquired Live parameter mapping available as a script the pull down menu 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 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 1 2 4 Force Inspector settings The Settings button in the Force Inspector panel opens a separate panel where
105. ion x in meters Return type float Note Scan size is determined by the host AFM It is either entered manually in the GUI or au tomaically when reading in height data Automatic over writes manual get_scan_size_y Returns scan size in the slow scan direction y in meters Return type float Note Scan size is determined by the host AFM It is either entered manually in the GUI or au tomaically when reading in height data Automatic over writes manual get_scan_subtype Additional scan sub type identifier Returns str get_scan_type Scan type identifier e g ImAFM ImEFM ImFFM Returns str get_setpoint Amplitude setpoint Returns value of setpoint at end of scan Value between 0 and 1 is the fraction of free oscil lation amplitude at the feedback tone with index On i e first element of frequency array and response arrays Return type float get_starttime Time at start of scan in seconds since the epoch Returns seconds Return type float get_tip Vac AC voltage applied to the tip in ImEFM Returns Volts V Return type float get_tip_Vdc DC voltage applied to the tip in ImEFM Returns Volts V Return type float given_list_is_empty Ist 52 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 Returns True if list is or only has elements of type otherwise False Return type bool has_calibration mode_type flexur
106. ith a slowly varying amplitude envelope Zoom 1s required to see the individual oscillation cycles 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 19 IMP Software Suite User Manual Release 4 0 2 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 or atto Joules aJ nN nm versus nanometers nm as determined in the Calibration step The Force Inspector panel has three tabs FI FQ Work Force which control the display of the different different plots as described in detail below You can control the plots and analysis presented in there three different tabs by opening the Force Inspector settings panel 3 1 2 1 Dynamic force quadratures The FI FO tab brings up a double plot of two integral quantities plotted versus the oscillation amplitude not cantilever deflection The plot F A is a weighted average of the f
107. itudes amps_digital Drive amplitudes for every tone Undriven tones have zero amplitude Parameters amps_digital np ndarray dtype np int64 digital units ADU set_calibration mode_type mode_nr file_name f0 O k invOLR cantilever_noise detec tor_noise Set calibration based on mode_type and mode_nr Parameters e mode type st r Name of mode i e flexural or torsional 4 9 ScanData 53 IMP Software Suite User Manual Release 4 0 2 e mode_nr int Mode number i e 1 2 3 e file name st 1 Name of calibration file belonging to this calibration e 0 float Mode resonance frequency in Hz e Q float Mode quality factor e k float Mode stiffness in N m e invOLR float Inverse optical lever responsitivy in m ADU e cantilever_noise float Cantilever noise in ADU 2 Hz e detector_noise float Detector noise in ADU 2 Hz Note If mode is already calibrated overwrite current calibration If it doesn t exist add it to self calib_list set_cantilever_noise p_thermal mode_type flexural mode_nr 1 verbose True Set the thermal noise force for an existing calibration Parameters e p thermal float thermal noise force in ADU 2 Hz e mode_type str optional Name of mode i e flexural or torsional e mode_nr int optional Mode number i e 1 2 3 e verbose bool optional If True print a message to the console
108. le contains several different classes each containing a different 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 so that parameters can be input and output on the screen Alterntively you can simply edit the values in the Python code reload the script and run it again These scripts serve as a starting point to develop your own measurement methods Some useful scripts currently available are described below 4 8 Scripting Interface 43 IMP Software Suite User Manual Release 4 0 2 4 8 1 RecorderAnalysis py PlotTimeMode opens a GUI for viewing and extracting sections 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 seript will parse the time stream to a series of beats or time windows T given by the inverse of the measurement bandwidth T 1 Af 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
109. ll 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 1 1 Pre defined variables The following variables are defined in all scripts For some of these variables you will want to change their values or re define them but do not change their shape or data type Other variables should not be changed but you will want to use their values 38 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 f0 real Hz and Q real are the measured resonant frequency and quality factor stored in the Current calibration If you have not run a calibration these will be zero and your drive script may give an error if you do not set them to a reasonable value in your script nfreq_out integer and nfreq_in integer are the number of drive frequencies and response frequencies respectively These numbers will depend on the MLA firmware that you are running In the most common configurations nfreq_out freq_in and in any case nfreq_out lt nfreq_in Do not re define these values f_sample samples per second is the sampling frequenc
110. measured tones as multiples of measurement bandwidth df Returns Return type np ndarray dtype np int64 Examples gt gt gt sd ScanData ScanData scan01612 imp gt gt gt create array of frequencies in Hz where response was measured gt gt gt freqs sd get_karray sd get_df get_lift data_format complex unit ADU Spectrum of cantilever oscillation at the lifted scanner position Parameters e data_format str optional IQreal complex amp phase speci fies data type e unit str optional ADU V m nm rad deg specifies units rad and deg only for phase Returns spectrum of lifted cantilever oscillation with required data format and units Return type np ndarray Raises e CalibrationError if the specified units require conversion but no MLA cali bration was set e ValueError if the specified format and units are incompatible or the scan pass format or units are unknown Note Used for separating background forces from nonlinear forces See also get_free 50 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 get_loaded filename The filename used when loading ScanData from disk Returns filename Return type str get_metadata_ascii Return all metadata as a string new line separated string Returns str
111. med 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 ImAFM M 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 actually 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 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
112. mined 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 parses 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 AFM 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 Path to AFM 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
113. n 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 la um 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 re sponsivity see Note on sensitivity and accuracy for further discussion Actually the calibration internally in the software does not rely on a calibrated measurement of Volts by the MLA nor does it rely on the calibration of the AFM scanner to determine detector responsivity The software uses the noise measure ment 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 comprise a more primary form of calibration All force and distance data given by the AFM Software Suite are derived from this calibration independent of calibration error in the measurement of detector signal in Volts or movement of the scanner in nm The thermal noise method does however depend weakly on a calibrated measurement of temperature e Noise floor fm WHz is the detector noise expressed as an equivalent deflection noise of the cantile
114. nce problems keeping track of your files if you remove or modify this number or the type name before it The following files are generated by the IMP Suite and stored in a session folder e 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 e 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 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 Work Flow Icons for the advanced panels appear when selected in the advance
115. nd the index of calibration if exist in self calib_list Else return False and index None Parameters e mode type str optional type of cantilever mode flexural or torsional e mode nr int optional mode number Returns cal_exists mode_index bool True if the calibration was found False otherwise int the index of the required calibration None if not found Return type tuple get_cantilever_noise mode_type flexural mode_nr 1 Get the thermal noise force Parameters e mode type str optional Name of mode i e flexural or torsional 4 9 ScanData 45 IMP Software Suite User Manual Release 4 0 2 e mode nr int optional Mode number i e 1 2 3 Returns cantilever thermal noise force in ADU 2 Hz Return type float Raises CalibrationError if the mode was not calibrated Examples gt gt gt sd ScanData ScanData scan01612 imp gt gt gt psd np sqrt sd get_cantilever_noise sd get_k sd get_ gt invOLR lel5 gt gt gt print Cantilever thermal noise force is 2f fN sqrt Hz format psd Cantilever thermal noise force is 21 90 fN sqrt Hz get_data data_slice slice None None None slice None None None slice None None None scan_pass trace data_format complex unit ADU The data measured during the scan Parameters e data_slice tuple optional tuple of Python slice objects tone_slice
116. ns Toggle will switch checked to unchecked and unchecked to checked Apply to checked 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 2 2 5 4 Batch process parameter maps and force volume data Analyze checked scans selects which type of Parameter Maps will be made on the checked scans in a batch process As parameter maps are computationally demanding it is very useful to set up and run batch processes 16 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release 4 0 2 e Parameter 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 Parameter Map Polynomial when checked will perform the analysis described in Fast
117. nt 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 10 Chapter 2 The IMP Session and Work Flow IMP Software Suite User Manual Release 4 0 2 2 2 3 1 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 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 AFM 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 Setup runs a routine to determine
118. o fake EOL signal to be generated and in this case the AFM 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 Ill 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 M 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 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 the microscope before the controller or any other ancillary equipment You can also use the SAM prov
119. orce which is in phase with the sinusoidal cantilever motion determined over a single oscillation cycle of the cantilever Similarly the quadrature force FQ A is a weighted average of the force 90 degree phase shifted from the harmonic motion in phase with the velocity It is important to note that F A and F 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 Every single point on the Fr A and Fo A plots represents an integral of the tip sruface interaction force over one single oscillation cycle see Platz 2012b The force quadratures are special in that they are a direct transformations of the intermodulation spectral data They are simply another way of looking at the spectral data without making any assumptions as to the nature of the tip surface force They tell us something fundamental about the tip surface force as it is experienced by the cantilever in the reference frame of the oscillating cantilever F A is a conservative force e g due to elastic interaction and FQ A is a dissipative force e g resulting from the viscous nature of a moving surface You can read more about force quadratures and their interpretation in Haviland 2016 You may notice hysteresis in the F A and Fo A curves where the integrated force on the up beat increasing amplitude lighter shading is different from that on the down beat decreasing amplitu
120. oscopy C Hutter D Platz E A Thol n 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 Thol n 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 Thol n and D B Haviland Nanotechnology 23 265705 2012 Platz_2012a Platz 2012b Interaction imaging with amplitude dependence force spectroscopy Daniel Platz Daniel Forchheimer Erik A Thol n 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 Thol n 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 Thol n and David B Haviland Beilstein J Nanotechnol 4 352 2013 Platz_2013b 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 83 IMP Software Suite User Manual Release 4 0 2 Sader 2005 General scaling law for stiffness measurement of small bodies with applications to t
121. ould be added to the output Parameters mask 1ist a list of int with the mask for each of the two output ports See also mlaapi lockin Lockin set_output_mask mlaapi utils mask_to_int set_phases phases_rad Drive phases for every tone Parameters phases_rad np ndarray dtype np float 64 radians rad set_resolution nx ny Set the scan resolution Parameters e nx int number of pixels in fast scan direction e ny int number of pixels in slow scan direction set_samples_per_pixel samples_per_pixel Number of samples in time window corresponding to one image pixel fs df Parameters samples_per_pixel float samples per pixel set_scan_rate scan_rate Number of scan lines per second trace retrace Parameters scan_rate float Hertz Hz set_scan_size_x value Parameters value float scan size in the fast scan direction x in meters set_scan_size y value Parameters value f1oat scan size in the slow scan diretion y in meters set_scan_subtype scan_subtype Additional scan sub type identifier Parameters scan_subtype st r set_scan type scan_type Scan type identifier e g ImAFM ImEFM ImFFM ScanData 57 IMP Software Suite User Manual Release 4 0 2 Parameters scan_type st r set_setpoint value Amplitude setpoint Parameters value float between 0 and 1 is the fraction of free oscillation amplitude at the feedback tone with in
122. p dpwn 12 flipping images l6 Fluid 7 Force 19 Force curves 19 Force Inspector 19 Force Inspector settings 23 Force Reconstruction 21 force sensitivity 8 Forward tool 13 Frequency Mode 30 Frequency mode 30 Frequency Sweep 6 front side connections 65 G Gaussian filter 15 get_amplitudes afmapp Scanner ScanData ScanData method 45 get_calib_mode_index afmapp Scanner ScanData ScanData method 45 get_cantilever_noise afmapp Scanner ScanData ScanData method 45 get_data afmapp Scanner ScanData ScanData method 46 get_detector_noise afmapp Scanner ScanData ScanData method 46 get_df afmapp Scanner ScanData ScanData method 47 get_drive_amplitudes afmapp Scanner ScanData ScanData method 47 get_drive_karray afmapp Scanner ScanData ScanData method 47 get_drive_phases afmapp Scanner ScanData ScanData method 48 get_endtime afmapp Scanner ScanData ScanData 85 IMP Software Suite User Manual Release 4 0 2 method 48 get_external_filename afmapp Scanner ScanData ScanData method 48 get_f0 afmapp Scanner ScanData ScanData method 48 get_feedback afmapp Scanner ScanData ScanData method 48 get_free afmapp Scanner ScanData ScanData method 48 get_frequencies afmapp Scanner ScanData ScanData method 49 Es afmapp Scanner ScanData ScanData method 49 get_imp_str_list afmapp Scanner ScanData ScanDat
123. pecified data format and units e data_format str optional IQreal complex specifies data type e unit str optional ADU V m nm specifies units Raises e CalibrationError if the specified units require conversion but no MLA cali bration was set e ValueError if the specified format and units are incompatible or the scan pass format or units are unknown Note Used for separating background forces from nonlinear forces See also set_free set_mla_all_settings mla Convenience function to set all MLA related settings from a mla instance Parameters mla mlaapi mla_suite MLA object instance of MLA 56 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 Note This method will set self nr_input_freq self nr_output_freq and call the methods listed in See also See also set_fs set_mla_calibration set_mla firmware _version set_samples per pixel set_output_mask set_input_ports set_amplitudes set_phases set_frequencies set_mla_calibration cal The hardware calibration of the MLA Parameters cal dict set_mla firmware version ver Version of the firmware loaded into the MLA Parameters ver int version number See also mlaapi hardware Hardware get_firmware_version set_output_mask mask Each bit in the mask determines weather the corresponing tone sh
124. ports Input port for each of the measured tones 4 9 ScanData 55 IMP Software Suite User Manual Release 4 0 2 Parameters np ndarray dtype np int 64 array of port numbers 1 4 where tones are measured See also mlaapi lockin Lockin get_port mlaapi lockin Lockin set_input_multiplexer set_invoOLR invOLR mode_type flexural mode_nr 1 verbose True Set the inverse optical lever reposponsivity for an existing calibration Parameters e invOLR float inverse optical lever reposponsivity in m ADU e mode_type str optional Name of mode i e flexural or torsional e mode_nr int optional Mode number i e 1 2 3 e verbose bool optional If True print a message to the console Raises CalibrationError if the mode was not calibrated set_k k mode_type flexural mode_nr 1 verbose True Set the cantilever stiffness for an existing calibration Parameters e k float stiffness in N m e mode_type str optional Name of mode i e flexural or torsional e mode_nr int optional Mode number i e 1 2 3 e verbose bool optional If True print a message to the console Raises CalibrationError if the mode was not calibrated set_1ift lift data_format complex unit ADU Spectrum of cantilever oscillation at the lifted scanner position Parameters e lift np ndarray spectrum of lift cantilever oscillation with s
125. r noise is statistically independent from the detector 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 4 2 Noise Calibration 31 IMP Software Suite User Manual Release 4 0 2 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 7 This coefficient together with the value of wo 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 thereby the theoretical value of the damp ing coefficient 7 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 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
126. race and left right flipping is auto matically syncronized after EOF trigger First and last scan line of images now stored correctly e Fix model fit force curves not appearing when using area tool Version 2 3 Release date 2016 04 06 New features e Measure lift e When saving an image directly from the GUI you will now get a dialog box where you can type the res olution There is also a new option in the Save as type field named Native resolution png With this option pure png files will be saved with the same resolution as the data In addition separate files with the colorbars will be generated This could be practical if you want to assemble the figure yourself in for example powerpoint e There is a hold off time default 1 ms before a new trigger can be accepted to avoid bouncing e Phase feedback using port OUT C This is activated from the python shell with mla feedback activate_phase The full phase range of pi to pi corresponds to a voltage range of 1 V to 1 V You can offset the voltage with mla feedback set_phase_offset val when val is 32768 to 32767 A more convenient way to adjust the offset may be to use mla feedback set_current_phase_to_value V where V is a voltage 4 to 4 This will read the current phase value and adjust the offset of the phase feedback so that the resulting voltage on port OUT C is the specified value Before you can do anything with the phase feedback the normal feedback
127. requency tuning Frequency tuning is key to performing measurements 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 This interface offers three different tuning schemes e 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 4 5 Advanced Setup 35 IMP Software Suite User Manual Release 4 0 2 e Integer is a more 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
128. retace trace e Cz fit opens a dialog box Cz fit settings that allows you to control the intermodula tion frequencies an polynomial order used for calculating the capacitance gradient 90 Where a polynomial approximation of C z is assumed see Borgani 2014 You can see the result of the calculation at any pixel by clicking the blue pixel inspector icon x in the image tool bar The red pixel inspector icon clears all selected pixels This feature is in the experimental stage of development e Load imp will load a previous scan file with saved ImMEFM data If you load a file where ImEFM was not performed you will get a warning but your EFM images will show some thing that is not at all related to the electrostatic force e Save imp will save the currently analyzed raw data and EFM images If Autosave is checked each scan will automatically be saved upon completion Debug group contains some tools for trouble shooting the measurement checking to see if all connections are OK and that you are really measuring an electrostatic force e Set voltage When checked the Setup routine will apply the AC voltage between tip and sample When unchecked the tip sample voltage will not be applied and it will be held at ground In this case you are simply doing single freqeuncy dynamic AFM e Use Free When checked the free oscillation will be subtracted from the engaged oscillation to calculate the electrostatic force The checked
129. rithm that makes this adjustment assumes that a chain of linear systems e g actuator gt cantilever gt detector is connected between the output and input ports of the MLA and it will not work properly when nonlinearity is present in the chain If the drive voltage to the piezo shaker is not very high and the detector signal is not close to saturation the AFM is very close to a linear chain In this case after pressing Configure Response the actual cantilever motion have the frequency content given by the comb synthesized from your script 4 6 3 Setting the feedback Setup Feedback performs the necessary routines to make the free response at the tone index zero correspond to 100 set point value By convention the MLA calculates the feedback error signal from the amplitude of the response at the tone with index zero frequency specified 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 see useful code block below It is probably best to chose the frequency where you get the largest free response for feedback More information on feedback can be found in the section on Intermodulation Measurement Feedback and in the section on Advanced Setup Setup Feedback 4 6 4 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
130. roducts 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 looks 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 dri
131. s 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 62 Chapter 5 Installation eeee IMP Software Suite User Manual Release 4 0 2 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 it is also possible perform ImAFM 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 fake EOL trigger before it starts to record a scan line Setting both of these fields to zero causes n
132. s 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 2 2 3 2 Measure just lifted Measure just lifted starts a routine to measure the oscillating cantilever at a point where the tip just stops interacting with the surface The response at this just lifted position is needed for Background force compensation Dialog boxes open to explain what the routine is doing You can choose the Quick option to quickly extend the scanner to its full lift position and measure lift but for accurate measurement you should stop the scan while maintaining engagement with the surface e g temporarily set the scan size to zero and choose OK The feedback set point is slowly increased until the total Intermodulation Distortion IMD at the surface drops below a target value determined by the measured IMD at the full lift position where Set up was performed This full lift IMD is usually just noise as the cantilever response is linear meaning that there is no IMD far from the surface When the IMD falls below th
133. s 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 5 4 Common AFMs 63 IMP Software Suite User Manual Release 4 0 2 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 2 1 software settings With the NS V controller and software v8 and later it is also necessary to configure the software to make the connections required for ImAFM M In addition to setting the system to contact mode and setting the set point to 0 Volts you need do the following To get access to the shaker piezo when the Bruker is set to contact mode go to the Microscope pull down menu and select Generic Lockin Select the tab for Lockin 1 and enable this lockin Under drive routing select tapping piezo and set the amplitu
134. 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 and the calibration plot 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 well away from from the surface at least several cantilever widths at least 0 1 mm 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 scan with ImAFM 2 2 Work Flow 9 IMP Software Suite User Manual Release 4 0 2 2 2 2 6 Add Edit Remove cantilevers In the Calibration Parameters group the Cantilever selector has the option to Add Edit Remove cantilevers This option does not change the selected cantilever It opens a dialog box that allows you to change calibration parameters of the selected cantilever or create a new cantilever The Add tab has two options for creating a new cantilever e Basic is for rectangular cantilevers Enter the Length L um an
135. 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 Save as imp to open a dialog box where you can resave the entire scan file with all meta data to a new imp file This is usefull when you make changes to the scan data for example if you redefine the lift oscillation see below Right click on a pixel or patch and select 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 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
136. t be an interger data sf get_samples ii_s n n_samples_beat data_fft np fft rfft data len data Plot 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 AFM Suite comes with a python scripting interface with which you can develop you own multifrequency 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 Intermodulation Products provides a variety of example 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 AFM 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 demonstrates how scripts are constructed as a Python class This fi
137. t for each lockin time window e ScanData addon images can be viewed directly in the Session overview Improvements e A lot of stability fixes in the underlying MLA library e Significant speed up of noise calibration e Easier to integrate customized analysis in Session overview e ImEFM allow changing DC offset while scanning Bugfixes e Fixed a bugs which could prevent processing of retrace in AFMs with only one trigger per line such as Asylum Cypher e mla osc ad_is_in_safe_range was not properly detecting a clipped input e Fix resolution of non square images in Gwyddion loader e Frequency Sweep fixed limits for max V and frequency Version 2 5 2 Release date 2017 09 04 New features e Principal component analysis PCA added to black box model scripts e Smooth pixel tool calculate force curves from the avarage of several pixels e Physical ports for vertical and horizontal signal can be set from config ini e New panel Menu gt Advanced gt Message Log to see error messages and debug print outs Improvements e Improved interface for measure just lifted e Improved color scales with more linear lightness Bugfixes e reset_tones_on_new_pixel was set automatically when running start_lockin affecting some custom imaging modes 77 IMP Software Suite User Manual Release 4 0 2 e Software did not start after having reached 9999 measurement files Version 2 5 1 Release date 2017 04 04 Bugfixes e Ability to
138. t to open a small GUI which aids in setting all parameters in the JPK software Press Setup 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 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 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
139. termine a static force F which gives rise to the static deflection d 30 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 d LF 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 This linear relation between dynamic force and dynamic deflection is most easily expressed in the frequency domain d w G w F w The frequency dependence is contained in the dimensionless factor G called the transfer gain and the hat de notes a complex 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 func tion and it is usually denoted w For the simple harmonic motion of each eigenmode of the cantilever A A Y w X w FG w wo Q ll izg Gel Three parameters are needed to calibrate each eigenmode The mode stiffness k effective mass m and viscous damping coefficient 7 or alternatively the stiffness k resonant frequency w y k m and the quality factor Q Vmk n A complete calibra
140. the frequency and amplitude of the two drive tones You must be well above the surface when you perform setup several cantilever widths or at least 0 1 mm 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 scan 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 Use the host AFM software to engage the sample and start the scan When the end of line EOL triggers are detected the AFM 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 thi
141. 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 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 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 e Save Data to text file to export the force curve found using that reconstruction method 4 5 Advanced Setup The Advanced Setup view is initially selected in the Advanced pull down menu Here 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 e f1 kHz the frequency of drive 1 e 2 kHz the frequency of drive 2 e df the measurement bandwidth df abs f2 f1 n where n 1 2 3 e Al 5 the amplitude of drive 1 in percent of full output e 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 frequency tuning 4 5 1 F
142. tion requires a fourth constant that converts the detector signal as measured in the digital counting units used by the MLA or Analog to Digital Units ADU to the actual cantilever deflection in nanometers This fourth constant is called the detector responsivity a ADU m Note that here we could express the responsivity in SI units Volts m which would further require a calibration of the MLA against a voltage standard 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 27Im X w 2kgT 1 216 c0 1 bm Hz Ww 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 7 Hydrodynamic theory is used to calculate the damping due to the surrounding fluid air water etc Sader 1998 The result can be written as n
143. tion uses the analytical expression for the hydrodynamic func tion of a long rectangular beam calculated by Green and Sader Green 2002 This method calibrates the fundamental eigenmode using the length and width values given in the fields above e Torsional Flexural beam theory requires that you first calibrate the flexural eigenmode If this is done the mode stiffness k_flex and the resonant frequency 0_flex should appear in the fields below This method uses the ratio of resonant frequencies of the torsional and flexural modes to calibrate the torsional mode in reference to a calibrated flexural mode The method is explained in a paper by Thoren 2017 2 2 3 Scanning Before scanning the host AFM must be configured for ImAFM by simply putting it in contact mode with the feedback set point set to zero volts On some AFM s software scripts or special modes are provided to do this automatically Other AFM s require that you set the break out box switches in the correct position so that a fake deflection signal is fed from the MLA to the host AFM The host AFM can then 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 wa
144. 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 Dynamic force quadratures Redefine as lift oscillation is very usefull if you have a file with a pixel or group of pixels patch selected with the Area inspector tool where the cantelever has lost contact with the surface This parachuting pixel or patch can be used to redefine the just lift oscillation in the imp file see Measure just lifted Note that the redefinition is only valid in the loaded scan data It is not saved to disk unless you actively save a new version of the imp file 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 34 Chapter 4 Advanced Topics IMP Software Suite User Manual Release 4 0 2 Pixels selected in the current scan will not be removed when a new scan is generated When the scan moves passed a selected pixel
145. tted 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 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 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 2 2 3 5 2 Image Toolbar All plots and images have a toolbar with the following functions Home returns to the initial plot or the full image Pan Zoom when selected left click and drag will cause the plot to zoom starting from the point of click Dragging horizontally 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 A Zoom when selected a right click and
146. two drive frequency ImAFM M you want to choose the default value polynomial degree two points can only determine a straight line The polynomial of higher degree is only interesting if you use the Drive Constructor to create drive schemes with several drive tones e Harm Osc describes the effect of the background forces as a renormalization of the cantilever parame ters f0 and Q Note If you did not make a measurement of the just lifted response during the scan it is still possible to perform background compensation If the scan file has a parachuting pixel somewhere in the image you can use the 3 1 Inspecting single pixels 23 IMP Software Suite User Manual Release 4 0 2 response at this pixel as the just lifted response Select this pixel with the Pixel inspector tool Open the Data Tree and find the selected pixel in the tree Right click on that pixel in the tree and choose Redefine as lift oscillation This redefinition is only temporary To make it permanent you must save the imp file right click on the file in the tree possibly with a new file name 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 l
147. urface 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 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 parameter map as described in Batch process parameter maps and force volume data Amplitude Dependent Force Spectroscopy ADFS ADF S works
148. vanced Topics IMP Software Suite User Manual Release 4 0 2 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 AFM 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 AFM Suite A few examples are given in Examples py config ini This is the main configuration file which is dynamically changed by the AFM 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 If you run the MLA as a stand alone instruent independant of the AFM Software Suite for ImAFM M there will also be other files and folders in the main IMP sessions and settings folder These files and folders are described in a seperate manual dedicated to the MLA alone 4 10 1 File Types The AFM 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 experie
149. ve comb The underlying assumption is that the response is periodic on the long time scale T associated with the base tone 29 IMP Software Suite User Manual Release 4 0 2 The MLA has two different modes 4 1 1 Time mode Time mode sends all samples to the computer which can be a huge amount of data if the measurement time is long Therefore it is often favorable to down sample the response averaging sequential samples to give an effective lower sampling frequency Down sampling reduces the noise and it allows for the transfer to the computer of longer uninterrupted streams see Stream Recorder but it does reduce the maximum frequency that an be analyzed A DFT of a time mode data stream will give you the entire intermodulation spectrum up to the Nyquist frequency or half the sampling frequency This spectrum reveals all the mixing in your non linear system When finding intermodulation products in ths manner there is a latency between the end of the measurement time window Tm 1 6f 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 uses 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 acquir
150. ve surface analysis method 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 AFM 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 AFM 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 the 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 e Radio buttons e Control settings e output fields e 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
151. ver The noise floor is a good figure of merit for expressing the sensitivity of the opto electronic system which detects the cantilever deflection Note that this noise floor will depend on the type of cantilever in particular the length and on the adjustment of the detector location of laser spot 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 measurements with the same cantilever and two different detectors the larger this number the better the detector see Note on sensitivity and accuracy Finally the Calibration panel shows three plots of Stiffness Res freq and Q factor which are updated as the data is averaged and re anlayzed These plots allow you to judge how many measurements are required to converge to a stable value 2 2 2 5 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 calibration constants These constants define the current calibration After each scan all calibration constants from the current calibration are stored with the
152. ver mode stiffness 2 2 Work Flow 7 IMP Software Suite User Manual Release 4 0 2 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 2 2 2 2 Measure 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 on the bottom Status Banner of the main frame calibration files
153. 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 Save image as opens a save dialog so you can save to a desired location and choose between several different file formats Render movie will create a movie of a single rotation around the azimuthal angle as see in the viewer when the Animate box is checked The movie uses 3D ray tracing so it takes a rather long time to generate the movie This feature is experimental and it requires that you install Povray software Render 3D will use a 3D ray tracing program to create the same view seen in the viewer with shadows added It can take several seconds to render the image The image will be stored in your session folder in a sub folder called Povray This feature is experimental and it requires that you install Povray software 2 2 Work Flow 17 IMP Software Suite User Manual Release 4 0 2 2 2 6 Session Logbook The Intermodulation AFM Software Suite keeps a session log while you are working 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 This log is a text file formatted for easy reading so you can quickly see exactly what was measured and when it was me
154. will be no illumination on either trace or retrace When checked the LED will be on during trace and off during retrace You can check that this is actually the case by storing the LED voltage as a axillary signal image of your host AFM has this capability The LED voltage is applied from the MLA through port OUT B Scheme selector allows you to choose between ImEF the standard mode for measuring contact potential difference In this mode the measurement bandwidth is equal to the frequency of the applied tip sample AC voltage ImEFM_slow scans slower with better SNR In this mode the measurement bandwidth is half the frequency of the applied tip sample AC voltage After all settings have been adjusted press Set up to configure measurement press St art and then use the host AFM software to engage the sample The system will start to process triggers collect data and build an IMEFM image You must manually set the Scan Rate on the host AFM to the value given by the ImEFM M software at the bottom of the panel After you engage and get a stable scan it is a good idea to press Measure Free to make a new measurement of the free oscillation well above the sample The electrostatic force is determined from the difference between the engaged oscillation and the free oscillation and accurate reconstruction requires a good measurement of the free oscillation The intermodulation spectral data will be processed in real time as
155. x a connection time out error that effected some machines Version 2 7 3 1 Release date 2018 07 05 New features e Compatibility with MLA generation 3 version 3 1 e GUI to change config ini settings Advanced gt All settings e New menu MLA for to access additional lockin functionality e Fitted force model is now displayed also in the Fi and Fq plots e K means clustering ability to cluster either in force or deflection domain new gui to select file Improvements e GUI library updated to wxPython 4 76 Chapter 8 Changelog IMP Software Suite User Manual Release 4 0 2 e Message log does not pop up on every error instead a message is printed in the status bar in the bottom of the screen Double click to see whole message e Addonviewer colorscale selector right click on colorbar and scroll zoom implemented Bugfixes e PNG export from model fit did sometimes not work if no scan size had been set e New firmware for gen 3 205 fixes a small glitch in feedback output signal Version 2 6 Release date 2018 03 27 New features e Lockin monitor to easily view lockin values in Manual Setup panel e New Script Panel for scripts in the style of the IMP MLA software e Previous Scripts have been renamed into Plugins NOTE Old scripts have to be manually moved from IMP Sessions and settingssettingsscripts to settingsafm_plugins e Input and output port selector in Frequency Sweep e Ability to set a different DC offse
156. y of the MLA Do not re define this value df real Hz T real sec or samples_per_pixel integer The measurement bandwidth is set by assigning a value to one and only one of these variables df 1 T samples_per_pixel f_sample n integer array or f real array Hz The frequencies are set by assigning values to either of these arrays f n df The length of these arrays is nfreq_in and should not be changed The first nfreq_out entries are the frequencies at which it is possible to drive a real array arbitrary units The drive amplitudes are set by assigning values to this array The length of a is set to be nfreq_out and should not be changed Amplitudes are set relative to each other in arbitrary units The maximum or peak amplitude is then set with the amplitude scaling factor see below p real array Radians The drive phases are set by assigning values to this array The length of p is set to nfreq_out and should not be changed Phases are given in radians asf real is the amplitude scaling factor a real number between zero and one asf 1 gives maximum output voltage of the MLA at peak amplitude of the waveform 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 Advanced users only asf 1 overrides the scaling of amplitudes in which case the amplitude values must be given in ADU and care must be taken
157. y_slice x_slice e scan_pass str or int optional trace retrace interleave trace interleave retrace specifies scan pass e data_format str optional IQreal complex amp phase speci fies data type e unit str optional ADU V m nm rad deg specifies units rad and deg only for phase Returns slice of the 3D data set The data set has shape index of tone pixel y coord pixel x coord Return type np ndarray Examples gt gt gt sd ScanData ScanData scan01612 imp gt gt gt get engaged response at pixel x 99 y 88 trace complex values in onm gt gt gt data sd get_data unit nm gt gt gt pixel data 88 99 gt gt gt alternative way which avoids large object data gt gt gt data_slice np s_ 88 99 gt gt gt pixel sd get_data data_slice unit nm gt gt gt get phase image at tone number 15 retrace in degrees gt gt gt data_slice np s_ 15 gt gt gt phase_image sd get_data data_slice scan_pass retrace data_ o format phase unit deg Raises e CalibrationError if the specified units require conversion but no MLA cali bration was set e ValueError if the specified format and units are incompatible or the scan pass format or units are unknown 46 Chapter 4 Advan
158. 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 AFM 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 AFM 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 AFM Suite to work with your particular host AFM 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 58 Chapter 4 Ad

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