RHK Technology R9 User manual

R9 Control System User Guide v5.5

R9 Control System User Guide v5.5
RHK Technology
Publication date 13 October 2015
Copyright © 2012-2015 RHK Technology, Inc

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Table of Contents
About This Quick Start Guide .....................................................................................................................xiv
Significant Changes in R9s 3.0...................................................................................................................xvi
Significant Changes in R9s 4.0.................................................................................................................xviii
Significant Changes in R9s 4.2................................................................................................................... xx
Significant Changes in R9s 5.0..................................................................................................................xxii
Significant Changes in R9s 5.2.................................................................................................................xxiv
Chapter 1. Prepare Your SPM System.........................................................................................................1
1.1 Check the Hardware for Damage..................................................................................................1
1.2 Configure the Power .....................................................................................................................1
1.3 Connecting the Ethernet ...............................................................................................................2
1.3.1 Ethernet Connection .............................................................................................................3
1.3.2 Using more than one Ethernet Communications Link...........................................................3
1.4 Start and try the R9 Control System Software (R9s) ....................................................................3
1.4.1 Opening R9 Software (R9s)..................................................................................................4
1.4.2 Understand IHDL™ and the R9 Software Components .......................................................4
1.4.3 Open a Preconfigured IHDL™ File .......................................................................................5
1.4.4 Workbench User Interface Component Overview.................................................................8
1.4.5 Components of Interest.........................................................................................................9
1.5 Initial Testing of the R9 Controller...............................................................................................11
1.5.1 Initial Tests ..........................................................................................................................14
1.5.2 Measuring Preamplifier Noise and Adjusting Input Circuit Parameters..............................16
1.5.3 Adjusting Bias Voltage Parameters.....................................................................................19
1.5.4 Further Testing....................................................................................................................22
Chapter 2. Connect Your Microscope.........................................................................................................23
Chapter 3. Approach...................................................................................................................................24
3.1 Approach Settings.......................................................................................................................24
3.2 Feedback Settings ......................................................................................................................25
3.3 Fast In .........................................................................................................................................27
3.4 Slow Approach............................................................................................................................27
3.5 Adjusting the Position with Single Steps.....................................................................................28
3.6 Operating Mode Switching..........................................................................................................29
Chapter 4. Acquire an Image......................................................................................................................31
4.1 Verify the Available Signals.........................................................................................................31
4.2 Configure Scan Settings .............................................................................................................32
4.2.1Multi-height Imaging............................................................................................................35
4.3 Begin Image Acquisition..............................................................................................................36
4.4 Optimizing Feedback and Scanning Parameters........................................................................38
4.5 Drift Correction............................................................................................................................39
4.5.1 Automatic Drift Correction...................................................................................................41
4.5.2 Manual Drift Correction .......................................................................................................41
4.6 Image+Spectroscopy Mode ........................................................................................................41
4.6.1 Points ..................................................................................................................................41
4.6.2 Line......................................................................................................................................42
4.6.3 Region.................................................................................................................................43
4.6.4 Line Spectroscopy with Image Line Verification .................................................................43
Chapter 5. Display and Analyze your Image...............................................................................................44
5.1 Browser.......................................................................................................................................44
5.2 Basic Image Processing..............................................................................................................45
5.2.1 Background Removal..........................................................................................................45
5.2.2 Filtering................................................................................................................................46
5.3 Displaying SPM Images..............................................................................................................46
5.3.1 Image Manipulation.............................................................................................................46

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5.3.2 Display Image in 3D Format................................................................................................47
5.3.3 Export the SPM Image........................................................................................................48
5.4 Displaying Spectral Data on an Image........................................................................................48
5.5 Locating SM4 Data Files.............................................................................................................50
Chapter 6. Acquire Spectroscopy Data.......................................................................................................51
6.1 Configuring the I/V Ramp Spectroscopy Settings.......................................................................51
6.2 Starting an IV Spectroscopy Procedure......................................................................................54
6.3 dI/dV Spectroscopy Measurements............................................................................................56
6.3.1 Background for dI/dV measurement ...................................................................................59
Chapter 7. Analyze Spectroscopy Data......................................................................................................63
7.1 Analyzing Spectroscopy Data.....................................................................................................63
7.1.1 Display and Analyze your Spectroscopy Data....................................................................63
7.1.2 Exporting your Spectroscopy Data......................................................................................64
Appendix A. IHDL Element Details .............................................................................................................66
A.1. Overview of a Hardware Item..........................................................................................................66
A.2. Hiding Dashboard Panels to Ribbon ...............................................................................................67
A.3. Overview of an R9 Control ..............................................................................................................68
A.4. User-Configurable Max/Min Ranges on Data Entry........................................................................70
A.5. Adding Procedure Panel to Hardware Composites on the Dashboard...........................................71
A.6. Configure Measure Items ................................................................................................................71
Appendix B. Hardware Space Components ...............................................................................................73
B.1. Channel 1 Drive and Channel 2 Drive.............................................................................................73
B.1.1. Hardware Space.......................................................................................................................73
B.1.2. Block Diagram of Output Circuitry............................................................................................74
B.1.3. Property Panel in Hardware Space..........................................................................................74
B.2. Channel 1 Input and Channel 2 Input..............................................................................................77
B.2.1. Hardware Space.......................................................................................................................77
B.2.2. Block Diagram of Input Circuitry...............................................................................................78
B.2.3. Property Panel in Hardware Space..........................................................................................78
B.3. Channel 3 Input and Channel 4 Input..............................................................................................80
B.3.1. Hardware Space.......................................................................................................................80
B.3.2. Block Diagram of Input Circuitry...............................................................................................80
B.3.3. Property Panel in Hardware Space..........................................................................................81
B.4. CH5 Input.........................................................................................................................................82
B.5. STM Bias .........................................................................................................................................82
B.6. Lock-in Amplifiers ............................................................................................................................83
B.6.1. Hardware Space.......................................................................................................................83
B.6.2. Using the Lock-in Amplifier as a Low Pass Filter.....................................................................84
B.6.3. Using the Lock-in Amplifier for dI/dV Measurements...............................................................85
B.6.4. Lock-in Amplifiers Operating Independent of the High Speed Inputs ......................................85
B.7. Feedback Loops..............................................................................................................................86
B.7.1. Auxiliary PI Feedback Controller ..............................................................................................89
B.7.2. Kelvin PI Feedback Controller..................................................................................................90
B.8. Filters for High Speed Inputs...........................................................................................................91
91
B.9. Transient Recorder..........................................................................................................................91
B.10. Scan Processor .............................................................................................................................92
B.10.1. Slope Compensation Range...................................................................................................93
B.11. Internal Piezo Modulation..............................................................................................................93
B.12. High Voltage Amplifiers .................................................................................................................95
B.13. Status ADCs ..................................................................................................................................98
B.14. Pulse Counting ..............................................................................................................................98
B.15. TTL Inputs and Outputs.................................................................................................................99
B.16. Forth Scripts ................................................................................................................................100
B.17. Description...................................................................................................................................100
B.18. Measure Item...............................................................................................................................101

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B.18.1. Data Channels have User-Configurable Names..................................................................102
B.19. External Hardware Devices.........................................................................................................102
B.19.1. Preamps ...............................................................................................................................102
B.19.1.1. External Control Support for FEMTO Preamps.............................................................103
B.19.2. PMC100 (Piezo Motor Controller) ........................................................................................104
B.19.3. PPC200 Approach Interface Module....................................................................................104
B.19.4. Z Scan Input added to the Piezo Tube Item.........................................................................105
B.19.5. External Hardware Item for AFM Cantilevers.......................................................................105
B.20. Microscopes.................................................................................................................................106
Appendix C. Connecting the Microscope..................................................................................................108
C.1. RHK UHV300/700 - STM Beetle ...................................................................................................108
C.2. RHK UHV350/750 - AFM/STM Beetle...........................................................................................110
C.3. RHK UHV900 - Pan STM..............................................................................................................111
Appendix D. R9 Connector Pinouts ..........................................................................................................114
D.1. R9 Preamp I/O 44-Pin Female Connector ....................................................................................114
D.2. R9 DC Power Output 9-Pin Female Connector ............................................................................115
D.3. R9 Laser I/O 26-Pin Female Connector........................................................................................116
D.4. R9 High Voltage Output 10-Pin Female Connector ......................................................................117
D.5. R9 Rear Panel BNCs.....................................................................................................................118
D.6. R9 Low Voltage Outputs 15-Pin Female Connector.....................................................................119
D.7. R9 Digital I/O 25-Pin Female Connectors (2)................................................................................120
D.8. R9 Preamp I/O Cable 44-pin to 15-pin..........................................................................................121
Appendix E. Configuring the High Voltage Block......................................................................................122
E.1. RHK UHV300/700 STM Beetle......................................................................................................123
E.2. RHK UHV350/750 AFM/STM Beetle.............................................................................................123
E.3. RHK UHV900 STM Pan.................................................................................................................124
Appendix F. Approach...............................................................................................................................125
F.1. RHK STM Beetle - UHV300/700....................................................................................................126
F.1.1. Confirm Connections to Microscope.......................................................................................126
F.1.2. Check Approach and Feedback Settings ...............................................................................127
F.2. RHK AFM/STM Beetle - UHV350/750...........................................................................................127
F.2.1. Confirm Connections to Microscope.......................................................................................127
F.2.2. Check Approach and Feedback Settings ...............................................................................127
F.2.2.1. Beetle Single Step In .......................................................................................................128
F.2.2.2. Beetle Single Step Out.....................................................................................................129
F.2.2.3. Beetle Fast In...................................................................................................................129
F.2.2.4. Beetle Fast Out................................................................................................................130
F.2.2.5. *Z Beetle Approach Slow* ...............................................................................................130
F.3. RHK Pan - UHV900.......................................................................................................................130
F.3.1. Confirm Connections to Microscope.......................................................................................130
F.3.2. Check Approach and Feedback Settings ...............................................................................131
Appendix G. Feedback Modes..................................................................................................................132
G.1. PI Controller Gain Values..............................................................................................................132
G.2. Z PI Controller Linearization..........................................................................................................132
G.3. STM Mode.....................................................................................................................................133
Appendix H. Helpful Hints.........................................................................................................................134
Appendix I. Details on an IHL File's Construction.....................................................................................135
I.1. Scan Processor...............................................................................................................................135
I.2. Scan Heads.....................................................................................................................................137
I.3. Preamplifiers ...................................................................................................................................137
I.4. Input Channels................................................................................................................................137
I.5. Lock-in Amplifiers............................................................................................................................137
I.6. Z PI Loop.........................................................................................................................................138
I.6.1. Each Feedback Mode Remembers Gain.................................................................................138
I.7. Channel 1 Drive ..............................................................................................................................139

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I.8. Bias Setting.....................................................................................................................................139
I.9. Z Offset............................................................................................................................................139
I.10. PPC200.........................................................................................................................................139
I.11. Measure Items ..............................................................................................................................139
I.12. Scan Area Window........................................................................................................................140
I.13. Ramp Spectroscopy Settings........................................................................................................140
I.14. Hardware Watchers ......................................................................................................................140
I.15. Fast Sweep Aborts........................................................................................................................141
I.15.1. Fast Sweep Abort Setup........................................................................................................141
7.1.3 ...........................................................................................................................................141
I.16. ‘Yes/No’ Message Box ..................................................................................................................142
I.17. Multiple R9 Controls in a State .....................................................................................................143
I.17.1. Sweep Options in R9 Controls...............................................................................................143
Appendix J. Details on Procedure Space Constructions ..........................................................................145
J.1. Constructing Procedures................................................................................................................145
J.2. Connecting Components in Hardware Space and Procedure Space............................................147
J.3. Rearranging Connecting Lines.......................................................................................................147
J.4. Deleting a Connecting Line............................................................................................................148
J.5. Example Procedure........................................................................................................................149
J.6. Setting Parameters as Reference or Value....................................................................................153
J.7. Naming a Procedure ......................................................................................................................154
J.8. Validating the Procedure................................................................................................................155
J.9. Running the Procedure ..................................................................................................................159
J.9.1. From Hardware Space............................................................................................................159
J.9.2. From a Procedure Panel.........................................................................................................160
J.10. Stopping the Procedure................................................................................................................160
J.11. Adding Loops to Procedures........................................................................................................161
J.11.1. Accidental Deletion of a State or Loop..................................................................................165
J.12. Adding Conditionals to Procedures..............................................................................................165
J.12.1. A “Script Conditional” Item ....................................................................................................166
J.13. Configuring Startup and Shutdown Procedures...........................................................................166
Appendix K. Reference Guide ..................................................................................................................168
K.1. Scan Area Window........................................................................................................................168
K.1.1. Main Panel..............................................................................................................................168
K.1.2. Advanced Panel .....................................................................................................................172
K.1.3. Save Panel .............................................................................................................................174
K.1.4. Save - dataSAFE....................................................................................................................176
K.1.5. Navigation Config. ..................................................................................................................176
K.2. XY Graph Windows .......................................................................................................................178
K.2.1. XY Graph Toolbar ......................................178
K.2.1.1. Select Curve ....................................................................................................178
K.2.1.2. Zoom ........................................................................................................................179
K.2.1.3. Cursor Mode .............................................................................................................180
K.2.1.3.1 Statistics ...............................................................................................181
K.2.1.4. Autoscale ..................................................................................................................181
K.2.1.5. Pan ...........................................................................................................................182
K.2.1.6. Curve Groups ............................................................................182
K.2.2. Settings Tab ....................................................................................................................183

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K.2.2.1. Curves Tab ........................................................................................................183
K.2.2.1.1 Show..........................................................................................................................184
K.2.2.1.2 Preprocessing Modes................................................................................................184
K.2.2.1.3 Display Modes...........................................................................................................185
K.2.2.1.4 Curve Attributes .............................................................................................185
K.2.2.2. Layout Tab .........................................................................................................186
K.2.2.3. Cursor Mode Tab .......................................................................................187
K.2.3. Context Menu .........................................................................................................................187
K.3. Oscilloscope ...........................................................................................................................188
K.3.1. Settings...................................................................................................................................188
K.4. Spectrum Analyzer .................................................................................................................189
K.4.1. Settings...................................................................................................................................190
K.4.2. Common Usage......................................................................................................................190
K.5. Monitor ...................................................................................................................................191
K.5.1. Controls ..................................................................................................................................192
K.6. Transient Recorder and Transient Recorder FFT .........................................................................193
Appendix L. Power Supply Wiring.............................................................................................................196
Appendix M. Graphically Configured Oscillators and Lock-in Amplifiers..................................................197
M.1. Typical Example............................................................................................................................197
M.2. Advanced Example.......................................................................................................................198
Appendix N. Phase-Locked Loop (PLL)....................................................................................................200
N.1. PSD Alignment Window ................................................................................................................200
N.2. Frequency Sweeps........................................................................................................................201
N.2.1. Coarse Sweep........................................................................................................................202
N.2.2. Measure Peak ........................................................................................................................203
N.2.3. Set Frequency........................................................................................................................203
N.2.4. Unwrap Phase........................................................................................................................203
N.2.5. Procedures.............................................................................................................................204
Appendix O. Inventor SDK........................................................................................................................204

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List of Figures
Figure 1.1. Check the R9 for damage...........................................................................................................1
Figure 1.2. Location of Power, Frequency, Voltage and Serial Number Information ...................................2
Figure 1.3. Ethernet Connection Diagram ....................................................................................................3
Figure 1.4. R9 Dashboard.............................................................................................................................4
Figure 1.5. Opening a preconfigured IHDL™ ...............................................................................................6
Figure 1.6. Selecting the Workbench tab......................................................................................................6
Figure 1.7. RHK UHV300 Preconfigured STM Hardware Workbench..........................................................7
Figure 1.8. UHV 300 STM Hardware Workbench Overview.........................................................................8
Figure 1.9. Hardware Space.......................................................................................................................10
Figure 1.10. Save the IHDL with a New Name...........................................................................................12
Figure 1.11. Auto-backup IHDL Files..........................................................................................................12
Figure 1.12. Workbench - Testing UHV 300.ihl ..........................................................................................13
Figure 1.13. R9s Testing Screen using the Testing UHV 300 ihl ...............................................................14
Figure 1.14. Oscilloscope - Topography and Current.................................................................................16
Figure 1.15. Testing the Input Offset ..........................................................................................................17
Figure 1.16. Spectrum Analyzer Result at Full Bandwidth .........................................................................18
Figure 1.17. Spectrum Analyzer Result with 2 kHz Filter with 48 dB rolloff................................................19
Figure 1.18. Bias Voltage and CH1 Drive Settings.....................................................................................20
Figure 1.19. Bias Modulation through the Tunneling Gap Simulator..........................................................21
Figure 3.1. Open the Approach Procedures Panel.....................................................................................25
Figure 3.2. Typical Dashboard for STM......................................................................................................26
Figure 3.3. Camera View of the Tip and Sample........................................................................................27
Figure 3.4. Z Feedback Bar ........................................................................................................................29
Figure 3.5. Mode Switching.........................................................................................................................29
Figure 4.1. Checking the Available Signals ................................................................................................31
Figure 4.2. Scan Area Window Main Panel ................................................................................................32
Figure 4.3. Scan Area Window - Advanced, Save......................................................................................34
Figure 4.4. Scan Area Window –Tip Standby Position..............................................................................34
Figure 4.5. Scan Area Window - Nav Config., Image Settings...................................................................35
Figure 4.6. Multi-height Imaging .................................................................................................................36
Figure 4.7. Open an Image Window...........................................................................................................37
Figure 4.8. Open an Image Line .................................................................................................................37
Figure 4.9. Scan Area Window - Drift Settings ...........................................................................................39
Figure 4.10. Automatic Drift Correction.......................................................................................................40
Figure 4.11. Image+Spectroscopy - Points.................................................................................................42
Figure 4.12. Image+Spectroscopy - Line....................................................................................................42
Figure 4.13. Image+Spectroscopy - Region ...............................................................................................43
Figure 5.1. File Explorer View.....................................................................................................................44
Figure 5.2. Shadow style Artifact from X Offset Subtract ...........................................................................45
Figure 5.3. Image Manipulation ..................................................................................................................46
Figure 5.4. Pre-processing Data Mode and Color Map Mode....................................................................47
Figure 5.5. Interactive 3D............................................................................................................................48
Figure 5.6. Image+Spectroscopy - Display Spectral Data..........................................................................49
Figure 5.7. Locating SM4 Data Files...........................................................................................................50
Figure 6.1. Dashboard View of the IV Ramp Spectroscopy Settings .........................................................52
Figure 6.2. Spectroscopy - Alternate Scan Direction: Disabled..................................................................53
Figure 6.3. Spectroscopy - Alternate Scan Direction: Enabled...................................................................53
Figure 6.4. Graphical Representation of Ramp Spectroscopy Timings......................................................54
Figure 6.5. Scan Area Window access to Spectroscopy Procedures.........................................................55
Figure 6.6. The Preconfigured UHV300 ihl.................................................................................................56
Figure 6.7. Dashboard for UHV300.ihl........................................................................................................57

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Figure 6.8. Example I/V Spectroscopy Measurement on a Pair of Back to Back FETs.............................57
Figure 6.9. Spectroscopy Settings and Circuit Diagram for the Trial dI/dV Spectroscopy .........................58
Figure 6.10. Modification to Pre-configured UHV300 Dashboard...............................................................58
Figure 6.11. The 'dI' Oscilloscope Trace for 2mV Oscillation Amplitude shown above and a series
resistance of 200 Meg Ohms...............................................................................................................59
Figure 6.12. I/V and dI/dV Spectroscopy Plots...........................................................................................60
Figure 6.13. Pictorial representation of dI/dV..............................................................................................61
Figure 6.14. Interferometer Feedback ........................................................................................................62
Figure 7.1. Spectroscopy............................................................................................................................64
Figure 7.2. Two different kinds of file export format, picture file and ASCII file..........................................65
Figure A.1. Hardware Space Properties .....................................................................................................66
Figure A.2. Hiding Dashboard Controls ......................................................................................................67
Figure A.3. Hiding Dashboard Panels to Ribbon........................................................................................68
Figure A.4. Showing Panels on the Ribbon ................................................................................................68
Figure A.5. R9 Controls...............................................................................................................................69
Figure A.6. Ramping R9 Controls...............................................................................................................69
Figure A.7. User-Configurable Limits on Data Entry...................................................................................70
Figure A.8. Settings for User-configurable Limits .......................................................................................70
Figure A.9. Adding Procedure Panels to composites on the Dashboard ...................................................71
Figure A.10. Preconfigured STM Measure Items........................................................................................72
Figure B.1. Channel 1 Drive - Hardware Space..........................................................................................73
Figure B.2. Block Diagram of Drive 1 and Drive 2 Output Circuitry............................................................74
Figure B.3. Channel 1 Drive - Property Panel in Hardware Space.............................................................74
Figure B.4. Hardware Space - Channel 1 Input..........................................................................................77
Figure B.5. Block Diagram of Channel 1 and Channel 2 Input Circuitry.....................................................78
Figure B.6. Property Panel in Hardware Space..........................................................................................78
Figure B.7. Hardware Space - Channel 3 Input..........................................................................................80
Figure B.8. Block Diagram of Channel 3 and Channel 4 Input Circuitry.....................................................80
Figure B.9. Property Panel in Hardware Space..........................................................................................81
Figure B.10. CH5 input in Hardware Space................................................................................................82
Figure B.11. STM Bias................................................................................................................................82
Figure B.12. Lock-in Amplifier - Hardware Space.......................................................................................83
Figure B.13. Lock-in Amplifier - Low Pass Filter.........................................................................................84
Figure B.14. Lock-in Amplifier used for dI/dV .............................................................................................85
Figure B.15. Lock-in Amplifier operating independent of the inputs...........................................................86
Figure B.16. Feedback Loop Controllers ....................................................................................................87
Figure B.17. Feedback Loop Connections..................................................................................................87
Figure B.18. Auxillary PI Feedback Controller............................................................................................89
Figure B.19. Aux PI Input in Hardware Space............................................................................................89
Figure B.20. Aux PI Input Settings..............................................................................................................90
Figure B.21. Kelvin PI Feedback Controller................................................................................................90
Figure B.22. Kelvin PI input in Hardware Space.........................................................................................90
Figure B.23. Kelvin PI input Settings ..........................................................................................................91
Figure B.24. Filters for High Speed Inputs..................................................................................................91
Figure B.25. Transient Recorder.................................................................................................................92
Figure B.26. Scan Processor......................................................................................................................93
Figure B.27. Slope Compensation..............................................................................................................93
Figure B.28. Internal Piezo Modulation.......................................................................................................94
Figure B.29. Internal Piezo Modulation Output...........................................................................................95
Figure B.30. High Voltage Amplifiers..........................................................................................................95
Figure B.31. High Voltage X Scan Signal Output Examples ......................................................................96
Figure B.32. Status A/D Inputs....................................................................................................................98
Figure B.33. Pulse Counting.......................................................................................................................98
Figure B.34. TTL Output .............................................................................................................................99
Figure B.35. Forth Scripts.........................................................................................................................100
Figure B.36. Description............................................................................................................................100

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Figure B.37. Measure Item........................................................................................................................101
Figure B.38. Property Panel Configuration...............................................................................................102
Figure B.39. External Hardware Devices - Preamps................................................................................102
Figure B.40. External Control Support for FEMTO Preamps....................................................................103
Figure B.41. PMC100................................................................................................................................104
Figure B.42. PPC200................................................................................................................................105
Figure B.43. A –Z Scan Added to the Piezo Tube Item............................................................................105
Figure B.44. External Hardware Item for AFM Cantilevers.......................................................................105
Figure B.45. Microscopes .........................................................................................................................106
Figure B.46. Piezo Sensitivity Selector.....................................................................................................106
Figure B.47. Show/Hide Items from Hardware Composites .....................................................................107
Figure C.1. RHK STM Beetle - Connections Block Diagram....................................................................108
Figure C.2. R9 Connection Diagram for the RHK UHV300 Beetle STM ..................................................108
Figure C.3. Combined Bias and Preamp Cable........................................................................................109
Figure C.4. RHK AFM/STM Beetle - Connections Block Diagram ...........................................................110
Figure C.5. RHK STM Pan - Connections Block Diagram........................................................................111
Figure C.6. Combined Bias and Preamp Cable........................................................................................112
Figure D.1. R9 Preamp I/O 44-Pin Female Connector.............................................................................114
Figure D.2. DC Power Output 9-Pin Female Connector...........................................................................115
Figure D.3. R9 Laser I/O 26-Pin Female Connector.................................................................................116
Figure D.4. R9 High Voltage Output 10-Pin Female Connector...............................................................117
Figure D.5. R9 High Voltage Output Defaults for RHK Microscopes........................................................117
Figure D.6. R9 Rear Panel BNCs .............................................................................................................118
Figure D.7. R9 Low Voltage Outputs 15-Pin Female Connector..............................................................119
Figure D.8. R9 Digital I/O 25-Pin Connectors...........................................................................................120
Figure D.9. R9 Preamp I/O Cable 44-pin to 15-pin...................................................................................121
Figure E.1. Common Scan Head Designs................................................................................................122
Figure E.2. RHK UHV300/700 High Voltage Block...................................................................................123
Figure E.3. RHK UHV350/750 High Voltage Block...................................................................................123
Figure E.4. RHK UHV900 High Voltage Block..........................................................................................124
Figure F.1. The Approach Procedure Panel .............................................................................................126
Figure F.2. STM Beetle Approach Procedure Panel ................................................................................127
Figure F.3. AFM/STM Beetle Approach Procedure Panel........................................................................128
Figure F.4. Beetle Single Step In Procedure ............................................................................................129
Figure F.5. Beetle Slow Approach Procedure...........................................................................................130
Figure I.1. RHK UHV300 STM IHL ...........................................................................................................135
Figure I.2. Scan Processor Connection to High Voltage Block.................................................................136
Figure I.3. Setting Gain in Feedback Mode ..............................................................................................138
Figure I.4. Hardware Watcher in PLL........................................................................................................140
Figure I.5. Fast Sweep Abort ....................................................................................................................141
Figure I.6. Settings for Fast Sweep Abort.................................................................................................141
Figure I.7. 'Yes/No' Message Box.............................................................................................................142
Figure I.8. Play a Sound with Message Box Notification ..........................................................................143
Figure I.9. Simplified R9 Controls .............................................................................................................144
Figure J.1. Creating a Procedure..............................................................................................................145
Figure J.2. New Procedure Space............................................................................................................146
Figure J.3. Connecting Components in Hardware Space and Procedure Space.....................................147
Figure J.4. Selecting a Wire......................................................................................................................148
Figure J.5. Using the Arranging Pins ........................................................................................................148
Figure J.6. Deleting a Wire........................................................................................................................149
Figure J.7. Pulse Tip template ..................................................................................................................149
Figure J.8. Pulse Tip - set first Activate to CH1 Drive...............................................................................149
Figure J.9. Pulse Tip - CH1 Drive Properties............................................................................................150
Figure J.10. Pulse Tip - Hiding CH1 Drive Properties ..............................................................................151
Figure J.11. Pulse Tip - Setting the CH1 Drive Pulse Rise.......................................................................152
Figure J.12. Pulse Tip - Setting the Pulse Duration..................................................................................152

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Figure J.13. Pulse Tip - Setting the CH1 Drive Pulse Fall........................................................................153
Figure J.14. Pulse Tip - Setting a Reference............................................................................................153
Figure J.15. Pulse Tip - Setting a Name...................................................................................................155
Figure J.16. Validating a Procedure..........................................................................................................156
Figure J.17. Results of Validation .............................................................................................................157
Figure J.18. Real-time Wiring Validation...................................................................................................157
Figure J.19. Validation Status Indicators ..................................................................................................158
Figure J.20. Initialization Progress Bar .....................................................................................................158
Figure J.21. Compile on Initialize..............................................................................................................159
Figure J.22. Opening a Procedure from Hardware Space........................................................................160
Figure J.23. Running a Procedure from Hardware Space........................................................................160
Figure J.24. Tip Pulse - Original Procedure..............................................................................................161
Figure J.25. Tip Pulse - Adding a Loop.....................................................................................................161
Figure J.26. Selecting Multiple Objects.....................................................................................................162
Figure J.27. Cutting and Pasting Objects in Procedure Space.................................................................163
Figure J.28. Cutting and Pasting States and Loops inside Procedure Space..........................................164
Figure J.29. Setting the Loop Count .........................................................................................................164
Figure J.30. Tip Pulses inside a Loop.......................................................................................................165
Figure J.31. Protection against Accidentally Delecting a State or Loop...................................................165
Figure J.32. Conditional Inside Procedure Space ....................................................................................166
Figure J.33. Script Condition in Procedure Space....................................................................................166
Figure J.34. Configure Post-Initialize and Pre-Shutdown Procedures .....................................................167
Figure K.1. Scan Area Window Main Panel..............................................................................................168
Figure K.2. Toggle Zoom ..........................................................................................................................169
Figure K.3. Procedure Panels...................................................................................................................170
Figure K.4. Configuring Procedure Panels ...............................................................................................171
Figure K.5. Z Feedback Meter Set Range ................................................................................................171
Figure K.6. Z Feedback Bar......................................................................................................................172
Figure K.7. Scan Area Window Advanced Panel .....................................................................................172
Figure K.8. Scan Area Window Save Panel .............................................................................................174
Figure K.9. SM4 File names......................................................................................................................174
Figure K.10. Parameters Changed During Image Acquisition..................................................................175
Figure K.11. Scan Area Window dataSAFE Panel...................................................................................176
Figure K.12. Scan Area Window Navigation Config. Panel......................................................................177
Figure K.13. XY Graph Window................................................................................................................178
Figure K.14. XY Graph Toolbar - Select Curve.........................................................................................178
Figure K.15. XY Graph Toolbar - Zoom....................................................................................................179
Figure K.16. XY Graph Toolbar - Cursor Mode ........................................................................................181
Figure K.17. Cursor Mode Statistics Dialog Box.......................................................................................181
Figure K.18. XY Graph Toolbar - Autoscale .............................................................................................182
Figure K.19. XY Graph Toolbar - Pan.......................................................................................................182
Figure K.20. XY Graph Toolbar - Curve Groups.......................................................................................182
Figure K.21. XY Graph Settings................................................................................................................183
Figure K.22. XY Graph Settings - Curves.................................................................................................183
Figure K.23. XY Graph Settings - Panes ..................................................................................................184
Figure K.24. XY Graph Settings - Preprocessing Modes .........................................................................184
Figure K.25. XY Graph Settings - Display Modes.....................................................................................185
Figure K.26. XY Graph Settings - Curve Attributes...................................................................................185
Figure K.27. XY Graph Settings - Layout..................................................................................................186
Figure K.28. XY Graph Layout Settings....................................................................................................187
Figure K.29. XY Graph Context Menu ......................................................................................................187
Figure K.30. XY Graph Oscilloscope ........................................................................................................188
Figure K.31. XY Graph Oscilloscope Settings ..........................................................................................188
Figure K.32. XY Graph Spectrum Analyzer ..............................................................................................189
Figure K.33. Spectrum Analyzer Settings.................................................................................................190
Figure K.34. Monitor Controls...................................................................................................................192

R9 Control System User Guide v5.5
xii
Figure K.35. Transient Recorder Output...................................................................................................193
Figure K.36. Transient Recorder FFT Output...........................................................................................194
Figure L.1. Power Supply Terminal Wiring ...............................................................................................196
Figure M.1. Typical reference setup in Hardware Space..........................................................................197
Figure M.2. Typical reference setup on the Dashboard............................................................................198
Figure M.3. Advanced reference setup in Hardware Space.....................................................................198
Figure M.4. Advanced reference setup on the Dashboard.......................................................................199
Figure N.1. Phase-Locked Loop ...............................................................................................................200
Figure N.2. PSD Alignment Window.........................................................................................................201
Figure N.3. Frequency Sweep ..................................................................................................................202
Figure N.4. Unwrap Phase Procedure in Frequency Sweep....................................................................203

R9 Control System User Guide v5.5
xiii
List of Tables
Table 4.1. Z Bar Zoom Ranges................................................................................................................33
Table B.1. Channel 1 Drive Output...........................................................................................................74
Table F.1. Preconfigured Approach Systems.........................................................................................126
Table K.1. Types of Monitors..................................................................................................................191
Table L.1. R9 Input Fuses......................................................................................................................196

xiv
About This Quick Start Guide
Important
Before handling your instrument, please go through this Quick Start guide thoroughly.
Skipping any of the installation, configuration or testing steps will result in it taking longer
for you to learn to use the R9 components and may lead to abuse of your equipment.
Since this is a Quick Start Guide, you may have questions about using your R9 Controller System that
this Guide does not answer. Please email, Skype, call or fax us with your questions. We will be happy to
provide you with the service and information you need to help you get your R9 system operational. We
also look forward to assisting you in customizing your system to perform new tasks. The open
architecture, flexible design and customization possibilities afforded by our Iconic Hardware Description
Language (IHDL™) will often make seemingly difficult hardware and/or procedural enhancements both
easy and effective.
The R9 Section [http://www.rhk-tech.com/the-r9-spm-control-system.php] of the RHK website at www.rhk-
tech.com will be updated with new applications, user contributed IHDL™ solutions, bug-fixes, and new
options to make your research more productive.
This Guide covers information needed to quickly become familiar with the R9 Control System
environment. To reduce the learning curve and minimize the potential for damaging expensive
equipment, some content will cover simple testing of the R9 Controller without connecting to your
microscope. You will simultaneously confirm that your R9 Control System components are working while
getting a hands-on walkthrough. Do not skip the testing: Everyone learns faster and better this way.
This guide assumes you have an RHK Beetle UHV300 STM scan head operating at atmospheric
pressure or in an ultra-high-vacuum (UHV) environment. It also assumes that you will be using tunneling
current as the feedback signal to perform topographic imaging and I/V spectroscopic measurements. This
assumption is for illustration purposes only. The settings for most operations will be the same for other
types of scan heads.
The Chapters are arranged according to the sequence of steps you will take to get your first topographic
images and spectroscopic curves with your new system. The steps are:
1. Prepare your system
•Unpack and inspect the R9 Control System.
•Configure the Power
•Connect the Ethernet communications links between the R9 Control System Computer and the R9
Control System Hardware (R9h) components and the Computer and the user's Local Area Network
(LAN).
•Start the R9 Control System Software (R9s) and become familiar with its operation.
•Turn on and set up the R9 Controller, perform simple tests before connecting your microscope
2. Connect your microscope
•Cable connections
•Complete R9h testing
3. Approach sample
4. Take an image
•Re-check hardware configuration
•Configure image settings
•Take image

About This Quick Start Guide
xv
•Refine settings and repeat image
5. Analyze your image
6. Perform spectroscopy measurements
•Spectroscopy at a selected point on your image
•Spectroscopy at every point on an image
7. Analyze your spectroscopy measurements

xvi
Significant Changes in R9s 3.0
Below is a summary of the significant software changes in R9s 3.0.
1. High Voltage Amplifiers: New options have been added including:
a. Output voltage limits of the HV Amplifiers now automatically scale the full range of the signal
connected to the amplifier's input to the limited output range. Previous versions clipped the voltage
output without scaling the signals.
b. Output limit settings have been simplified.
c. Sine and Cosine outputs of the internal NCO (Numerically Controlled Oscillator) can be digitally
summed into each HV Amplifier.
d. The Value of the R9 Controls connected to High Voltage Amplifiers are now displayed in physical
units of the output, such as 'nm', instead of volts.
2. Synchronization of Oscillators and Lock-in Amplifiers: Oscillation reference frequencies can be
configured graphically.
3. Dashboard Panels can be Minimized: The Dashboard Panels can now be minimized to the ribbon bar
In order to maximize the use of space. This is useful when a Panel is used infrequently, such as the
Current Input and Current Filter (in the case of STM).
4. Spectroscopy: The spectroscopy routines have been improved to allow bias modulation to be disabled
during topographic portions of measurements. Feedback loop parameters can now be separately set
for topographic imaging and to set tunnel gap resistance for spectroscopic measurements.
5. Piezo Sensitivity Selector: Up to four different temperature calibrations can be stored in an IHL file.
These calibrations can be changed when the controller is not initialized.
6. Z Position feedback indicator range can be automatically set from the Scan Area Window.
7. Scan Offset and Rotation buttons on the Scan Area Window have customizable behavior.
8. Automatic Startup and Shutdown Procedures: Added the ability to have a procedure automatically
launch after the software has been initialized and before the software has been shutdown.
9. Image Counter: Added a counter for the number of images scanned.
10. Dashboard controls, such as the PI Tip Control (freeze/retract/unlimit) are automatically updated
when changed by a procedure. Previously, these settings were not updated in the Dashboard when
changed by a Procedure.
11. Ramping a Dashboard Control will cause it to turn yellow for the duration of the ramping cycle (e.g. if
the bias voltage were ramped from 1 V to 5 V at a rate of 1 V/s, the bias field will turn yellow for the four
seconds during the ramp).
12. Custom Procedure Panels can now be added to Hardware Composites such that the controls and
input parameters appear on the Dashboard rather than having to go into the hardware space to change
them.This allows much greater flexibility for user configurable custom procedures.
13. Data Analysis (Browser) split into a separate program. The program is automatically assigned to a
separate processor core so processing large amounts of data will not interfere with the acquisition
software. Additionally, memory used in the image processing application is not shared with the data
acquisition application so more memory is available to each process.

What’s New
xvii
14. Improved Graph Windows: The XY Graph Windows have been improved. Additional Cursor options
are now available: Two vertical cursors, one diagonal cursor, and horizontal cursors. Cursors now move
on all graph panes to help lineup features.
15. Improved Monitor Items: Improved precision on the monitor items make for a more steady reading.
16. Improved Transient Recorder: The Transient Recorder can be armed and triggered in a procedure.
The FFT of the Transient Recorder's data is also computed.

xviii
Significant Changes in R9s 4.0
1. The Z-PI Feedback Type Logarithmic and Divide modes have changed greatly in scaling from
previous versions. This should be checked prior to initializing in v4.0 if these modes were being used
previously. The following table provides a guide for how the new values should scale.
EXAMPLE #1
EXAMPLE #1
EXAMPLE #2
EXAMPLE #2
Old Setting
New Setting
Old Setting
New Setting
Software
R9s 3.0
R9s 4.0
R9s 3.0
R9s 4.0
Feedback Type
Logarithmic
Logarithmic
Divide
Divide
Integral Gain
100 m/s
10 um/s
10 m/s
1.00 um/s
2. Addition of the Phase-Locked Loop (PLL): see the PLL section below and PLL Setup Guide for
detailed instruction on using the PLL. The PLL uses lock-in 0 for demodulation and CH2 Drive for a
master oscillator (e.g. probe drive and its own internal reference). So when the PLL is placed on the
hardware space these items are appropriately made unavailable from the hardware drawers.
3. Addition of the Photo-Sensitive Detector (PSD) Alignment Window: this tool was added which allows
the tracking of the laser intensity on the PSD quadrants for an AFM with beam deflection based feedback.
4. Addition of Frequency Sweeps Window: The basic window for looking at the resonance of a cantilever
or tuning fork where a range of drive frequencies is swept with some defined interval and the
corresponding lock-in is referenced to the frequency at each step.
5. Measure Peak: Allows the outer cursors to be dragged with the mouse and they automatically set to
the Start and Stop values on the panel, which are then used in a subsequent sweep.
6. Set Frequency: The middle cursor will automatically be positioned at the frequency where the lock-in
amplitude was maximum. Pressing Set Frequency will drive the resonator at that frequency.
7. Unwrap Phase: Automatically fixes phase wrapping; pressing set frequency after using the Unwrap
Phase procedure is necessary to store the new phase information.
8. Addition of Inteferometric Feedback Module: A panel was added to allow sweeping of the high voltage
DAC associated with controlling the Fabry-Perot cavity length of the etalon (distance between fiber and
cantilever) while monitoring the DC input into the ADC, such that the quadrature point can be chosen and
put under feedback.

What’s New
xix
9. Increased Slope Compensation Range: The sensitivity of X and Y slope compensation has been
greatly increased. The controls still accept a decimal value between -1.000 and 1.000.
10. Z Piezo Sensitivity Polarity Controls Z Output Polarity: The Z Output Polarity is now controlled by the
Z Piezo Sensitivity Polarity. Rather than setting the Z to Invert and not Sum, it’s simpler to put in a
negative piezo sensitivity, if it is so required.
11. Calibrations Can be Configured on the Fly: now the piezo calibration factors may be changed while
initialized; previously it was necessary to shut down first. Note: the Z-PI Tip Control must be set to
Freeze or Center such that a large fast voltage swing is not applied to the Z-scan.
12. New Filters for High Speed Inputs: Low Pass Filters 0 and 1 were added, which are one-pole
Butterworth filters that are configurable at 250, 500, 1000, 2000, and 4000 Hz. Simply connect in
hardware space the ADC to the Low Pass Filter (CH1 LP0) and (CH2 LP1) and a dropdown box
may be selected at the desired cutoff frequency.
13. Untangled Lock-ins from Inputs: previously Lock-in 0 was tied to ADC CH1 and Lock-in 1 to CH2.
Now CH1 or CH2 can feed either of the lock-ins, or one channel can feed both (for example looking at
multiple harmonics).
14. New CH5 ADC: The CH5 input can accept +/- 10 V signals. It has no offset DAC and no Dashboard
controls.
15. New Status ADCs: Four status ADC inputs have been added, which are useful for reading segment
voltages on a PSD. They can also be used like any other ADC or as general purpose differential inputs
with a range of +/- 0.5 V.
16. Additional Feedback Loops: Aux and Kelvin. The Aux PI Loop is typically used for inteferometric
feedback, but can be used for general purposes as well. The Aux can vary high voltage DACs to
maintain setpoint of the ADC, but the Kelvin can only vary the CH1 and CH2 Drive signals for its setpoint
(as Kelvin Force is typically varying the bias voltage, which is on one of these channels).
17. Added Pulse Counting Inputs: 100 MHz pulse counters were added that can accept an input of 0.0-
3.3 V; pulse inputs are 50-Ohm terminated.
18. Added Hardware Watchers: The Hardware watcher allows the R9 to monitor many of the internal
signals and anticipate potential problems. An example of this being Lockguard, which can be set to
retract the tip if the PLL loses lock for any reason. The time constant associated with Lockguard making
this ‘decision’ would be 10 nanoseconds and not limited by the much slower filters of the PLL.
19. Fast Sweep Aborts: this uses a Hardware Watcher to monitor an input channel and abort if a
specified threshold range is exceeded.
20. Yes/No Message Boxes: Allows procedures to message the user for a real-time decision.
21. Feedback Mode Switching now remembers the previous Integral and Proportional gains that were
used. This is convenient and a nice safety feature because the different feedback modalities typically
have gains that are orders of magnitude different from one another.
22. Multiple R9 Controls in a State: IHL construction is much easier due to changes in the ways that the
IHLs can be wired. Now, any number of different R9 controls can be ramped in a given state.

xx
Significant Changes in R9s 4.2
1. Multi-height Imaging: sometimes referred to as “lift mode,” this is the surface is scanned, the trace is
‘memorized’ and repeated at a given height above the surface. Up to 3 different heights may be chosen
and the retrace height is configurable by the user. This is particularly useful for MFM.
2. Parameter Changes During Acquistion are Recorded: The Data Browser can now display notifications
on the images that indicate where parameter changes occurred (e.g. set point changes or scan speed,
etc.).
3. New Image + Spectroscopy Modes have been Added; Points, Line Grid: The R9 software can now
take topography and pause to take spectroscopic data in a set of selected points, along a line, or in an
array of points, user configurable within the image area. The locations of where the spectroscopic data
acquisitions were recorded can be toggled on and off to display on the image.
4. Line Spectroscopy with Image Line Verification: The software can be configured to take spectroscopy
at locations along a defined line. Before and after acquire the spectral data, the software will perform 4
line scans along that line to confirm the location and check for stability. Then the software can display
this spectral data using the same method as the Image + Spectroscopy files.
5. More Friendly SM4 File Naming: Index-based file names will append the 4 digit Index to the Root of
the file name. Time based is also selectable if this is preferred over sequential index.
6. Press ESC to Stop a Procedure: a running procedure will be stopped by using the ESC key, provided
that the procedure has the Stop condition implemented.
7. Composites: Individual hardware space components contained in Hardware Composites can now be
shown or hidden from the Dashboard. Previously, the item could only be hidden from Hardware Space
after opening the hardware composite.
8. Composite Nesting now Possible: Composites can now contain other composites. Useful for object-
oriented Procedure programming. Examples are the various spectroscopies, which are doing the same
core thing, but a set of points different based on which procedure was chosen (e.g. grid or line). They all
can contain the same core composite though, even though the outer shells of the procedures are
different.
9. Protection Against Accidentally Deleting a State or a Loop: a message box will warn that the object
has multiple sub-items and ask for confirmation that you want to delete it.
10. Message Boxes will Beep on Popup: this can be useful to notify the a user of an event while the user
may not be directly watching the software.
11. New Method to Locate SM4 Data Files: Right-clicking an open image or spectroscopy data file and
selecting Show SM4 in Windows Explorer will open an explorer window with the SM4 file highlighted.
This allows for much more convenient moving, copying, renaming, etc.
12. IHL Configuration Files will Backup Automatically: IHL files will create a backup file automatically
when the save button is pressed. Up to 2 backup files will be kept for each IHL file.