Quantum Transport Measurement System Nanonis Tramea User Manual R6503

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Quantum Transport
Measurement System

User Manual

June 2016 (R6503)

Contents
Conventions

Safety information

About this Manual

Introduction

Instrument Overview

Front panel ......................................................................................................................... 10
Rear panel .......................................................................................................................... 11

Hardware Installation Guide

Setup .................................................................................................................................. 13
Interconnection of the instruments ..................................................................................... 13
Connection to host computer ............................................................................................. 15
Connection to computer screen .......................................................................................... 16
Powering ............................................................................................................................ 17

Software Installation Guide

Host computer requirements .............................................................................................. 19
Host computer network configuration ............................................................................... 20
Windows XP ........................................................................................................ 20
Windows Vista .................................................................................................... 22
Windows 7 and later ............................................................................................ 23
Nanonis software installation ............................................................................................. 28
License files ......................................................................................................... 30
Nanonis software startup.................................................................................................... 31
First time startup .................................................................................................. 31
Normal startup ..................................................................................................... 33
Quitting the software ........................................................................................... 34
Real-time software update ................................................................................... 35

Basic tutorials

Noise measurement ............................................................................................................ 39
DC measurement ................................................................................................................ 47
AC measurement ................................................................................................................ 51
Quantum dot simulator ...................................................................................................... 57

Troubleshooting

Network and software issues.............................................................................................. 63
License file issues .............................................................................................................. 64
Instrument doesn’t power up correctly .............................................................................. 65

Legal Information

Warranty ............................................................................................................................ 67
Copyright ........................................................................................................................... 67
Trademarks ........................................................................................................................ 67

Index

Quantum Transport Measurement System

Index • iii

Quantum Transport Measurement System

Conventions • 5

Conventions
The following signal words and symbols appear in this manual:
Warning: Indicates a potentially hazardous situation which, if not avoided, could result in a
malfunction of the instrument, damage to the instrument, injury, or death.

High voltage: Risk of electric shock. Lethal voltages present.

Note: Additional information to help you understand the internal functionality of the unit, or its
applications, but is not essential for general operation.

Italic

Commands, programs, menu items, functions, field names and product names are shown in italic
characters.

Quantum Transport Measurement System

Conventions • 6

Safety information
•

Carefully read this manual and all related documents before installing and using the instrument.

•

The safety notes and warnings have to be obeyed at all times.

•

Nanonis Tramea™ may only be installed and used by authorized and instructed personnel who have read this
manual.

•

Nanonis Tramea™ is designed for indoors dry laboratory use only.

•

Do not install substitute parts or perform modifications to this instrument. No user serviceable parts inside.

•

Do not operate the instruments if they are damaged or not functioning properly. Never use damaged accessories.

•

Do not operate the instruments during electrical storms, in order to avoid damaging the instrument.

•

Never use corrosive or abrasive cleaning agents or polishes. If necessary, clean the instrument with a soft and
dry cloth, and make sure that it is completely dry and free from contaminant before returning it to service.

Warning: Lethal voltages are present inside the instrument.

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Safety information • 7

About this Manual
This manual is intended as a reference tool for users of the Nanonis Tramea™ Quantum Transport Measurement
System, consisting of a real-time controller and one or more signal conversion interfaces. It explains installation and
operation of the instrument, focusing on its control software.
The Tramea quantum measurement system is based on the world-leading Nanonis SPM control system. Developed
more than ten years ago, it quickly gained a reputation for performance, stability, and modularity. The two core parts
of the system were the Realtime Controller which contained the CPU and FPGA processor and the Signal
Conditioning unit which had buffer amplifiers and filtering with a BNC interface. The Realtime Controller was
designated with the RC model name with the final number indicating the generation of the hardware and the Signal
Conditioning unit was given the model name starting with SC. Currently in its fifth generation the SC stands for
Signal Conversion instead of Signal Conditioning, and the latest modules are named RC5 and SC5. This hardware
foundation was designed for transport measurements, but the actual transport and SPM hardware are identical. The
Tramea system consists of two parts named the Tramea Signal Conversion (TSC) unit and the Tramea Realtime
Controller (TRC). In this manual there are references to both TRC and RC5 as well as TSC and SC5. These can be
used interchangeably from a hardware description standpoint since they are identical.
This manual is not a replacement for the RC5 and SC5 manuals. Technical information and installation guides for
the aforementioned instruments can be found in their respective user manuals.
Please make sure to have read the RC5 and SC5 user manuals before reading this manual and before operating the
instrument!
This manual is not a service manual for the RC5 or the SC5.

Revision history
June 2016 (R6503)

Initial release of the Nanonis Tramea™ manual

The SPECS order number for this manual is: 2100004181

Quantum Transport Measurement System

About this Manual • 8

Introduction
Nanonis Tramea™ is an advanced measurement solution, which combines the functionality of several different
single-purpose instruments into a single, high-performance, compact, fully software-controlled package.
Nanonis Tramea™ offers functionality of the following dedicated instruments:
•
•
•
•
•
•
•

Precision DC sources
Lock-in amplifiers
High-resolution data acquisition instruments
Oscilloscopes
Spectrum analyzers
Arbitrary waveform generators
Software measurement suites

The hardware provides up to 24 lowest noise 20-bit, 1 ppm precision outputs with 40 kHz bandwidth, up to 22-bit
output resolution, 120 dB dynamic range and temperature stabilization, and up to 24 inputs with 18-bit resolution,
adaptive oversampling and 100 kHz bandwidth. These features are rarely seen in other measurement systems and
never in models that also offer more than one channel.
Compared to measurement solutions based on a custom combination of the instruments listed above, Nanonis
Tramea™ offers several advantages going beyond pure hardware specifications. This section gives an overview of
the provided benefits, focusing on its software capabilities. Technical specifications and performance measurements
can be found in the RC5 and SC5 user manuals.
Nanonis Tramea is based on a FPGA- and real-time architecture allowing fast data generation and acquisition
speeds. It is possible to sweep and acquire up to 20’000 samples per second on multiple channels in parallel (up to
24), with intelligent algorithms controlling data acquisition timings. Experiment time can therefore be reduced by a
large amount, an advantage impossible to achieve in a multi-instrument environment typically controlled via lowspeed interfaces.
In order to handle the resulting large amount of high speed data, the software architecture is designed to constantly
give the user a full overview of the system, and at the same time full control of the signals and of the signal path. All
signals are processed in the digital domain, meaning that operations between signals are realized with just a few
mouse clicks. This allows e.g. differential measurements, symmetric biasing, AC+DC modulation schemes and
multi-frequency measurements. Signal analysis with oscilloscopes or FFT analyzers can be realized without any
change in wiring or addition of external hardware, taking full advantage of the exceptional performance of the
analog frontend and the signal handling flexibility. Extending the capabilities of the built-in software instruments
only requires software updates, in contrast to typical hardware instruments, which are limited by their hardware and
firmware specifications.
The Nanonis Tramea™ software architecture is based on the well proven and stable software platform of the
Nanonis SPM Control System, which is the result of several years of development and has an excellent track record
regarding reliability during years of laboratory operation around the world. Its capabilities make the programming
work required by the process of building a custom measurement suite no longer necessary, letting the user focus on
measurements rather than programming. If customization should be required, the programming options extend the
flexibility of the instrument even further and also easily integrate external instruments into the measurement set-up.
As experiments proceed with time, hardware and software requirements might grow as well. Nanonis Tramea™ uses
an industrial platform as a processing core, instead of a customized platform, and a modular concept for the
hardware frontends. The software is based on a widely used measurement and instrument control software suite.
New hardware and software modules can therefore be easily implemented, making the instrument adaptable to new
experimental requirements, should these appear.
For more detailed features of the RC5 and SC5 hardware, please refer to the RC5 and SC5 user manuals.
Quantum Transport Measurement System

Introduction • 9

Instrument Overview
Front panel

Figure 1: Nanonis Tramea front panel with one SC5/TSC.

1.
2.
3.
4.

Analog inputs: The eight BNC plugs AI1 to AI8 are the analog inputs of the SC5. All inputs can accept
voltages up to ±10 V and are differential. The analog bandwidth is 100 kHz (-3 dB).
Analog Outputs: The eight BNC plugs AO1 to AO8 are the analog outputs of the SC5. All outputs can deliver
voltages up to ±10 V and currents up to ±20 mA. The shields of the output BNCs are connected to the same
electrical ground. The analog bandwidth is 40 kHz (-3 dB).
SC5 Power LED (blue): Indicates that the SC5 is powered on.
RC5 Power LED (blue): Indicates that the RC5 is powered on.

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Instrument Overview • 10

Rear panel
5

9 10

NI PXIe-8840
Embedded Controller

18 19 20 21 22 23 24 25

Figure 2: Nanonis Tramea rear panel with one SC5. The interconnection between RC5 and SC5 is not shown.

SC5 Power switch: Turns the SC5 on and off.
SC5 Fuse holder: Contains two identical slow blowing fuses, each one connected to line and neutral of the
power supply transformer. Slow blowing 2A fuses (T2A, rated 250 VAC, 5×20 mm) should be used
independently from the line voltage.
7. SC5 IEC power socket.
8. GND BNC connector: The shield of this connector is connected to protection earth (PE), and therefore also
with the SC5 chassis. The inner conductor is connected to the GND reference of the analog electronics (AGND).
Please refer to the SC5 manual for more details.
9. Status LEDs (green): Indicate that the positive and negative rails of the auxiliary power supply are providing
the correct voltages (+15 V and -15 V respectively), and are not overloaded. If the external device connected to
the auxiliary power supply connector (10) is drawing too much current (more than 300 mA per rail), the LED of
the overloaded rail will start blinking with a frequency of 5-10 Hz. Please refer to the SC5 manual for more
details.
10. Auxiliary power supply connector: This connector supplies ±15 V with a maximum current of 300 mA per
rail. It can be used to power external devices like preamplifiers. Please refer to the SC5 manual for more details.
5.
6.

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Instrument Overview • 11

11. FAST AO: This BNC plug provides an additional analog output with a bandwidth of 1 MHz (-3dB). It can
deliver voltages up to ±10 V and currents up to ±20 mA. The shield of the BNC connector is connected to
AGND. Please refer to the SC5 manual for more details.
12. DEVICE SC 01/02/03: This connector is used for the communication between the SC5 and the RC5. The cable
for the connection between the two instruments is provided with the SC5.
13. RC5 Power switch: Turns the SC5 on and off.
14. RC5 Fuse holder: Contains two identical slow blowing fuses, each one connected to line and neutral of the
power supply transformer. Slow blowing 2A fuses (T2A, rated 250 VAC, 5×20 mm) should be used
independently from the line voltage.
15. RC5 IEC power socket.
16. Ethernet connector: This connector is used for TCP/IP communication with the host computer. The other
Ethernet port available should not be used. Please refer to the RC5 manual for more details.
17. DisplayPort connector: This connector is used for connecting a computer display to the RC5. The screen
displays the status information of the instrument. Please refer to the RC5 manual for more details.
18. OC4 device connectors: The Nanonis OC4 (optional instrument) is connected to these connectors using the
DEVICE RDIO cable supplied with the OC4. Do not connect a Nanonis SC5 to these connectors.
19. SC5 device connectors: The Nanonis SC5 is connected to these connectors using the DEVICE RDIO cable
supplied with the SC5. Do not connect a Nanonis OC4 to these connectors. Please refer to the Interconnection of
the instruments section for more details.
20. DIO Ports A-D: These four D-sub9 female connectors are used for communication and control of other
Nanonis instruments, as well as third party equipment. Please refer to the RC5 manual for more details.
21. High Speed Digital Input connectors: These four SMB connectors provide four inputs for high speed digital
communication. Please refer to the RC5 manual for more details.
22. Clock input: This SMB connector accepts a clock signal from an external 10 MHz clock source. Please refer to
the RC5 manual for more details.
23. Clock source LEDs (green): Indicate that the corresponding clock source is selected and that the RC5 digital
circuits are locked on that clock signal. Please refer to the RC5 manual for more details.
24. Clock output: This SMB connector outputs the 10 MHz clock signal of the clock source indicated by the Clock
source LEDs (23). Please refer to the RC5 manual for more details.
25. High Speed Digital Output connectors: These four SMB connectors provide four outputs for high speed
digital communication. Please refer to the RC5 manual for more details.

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Instrument Overview • 12

Hardware Installation Guide
This installation guide shows how to prepare and power-up Nanonis Tramea™. Following these instructions ensures
that the instrument is working correctly, and it can be connected to other instruments. Further steps will be explained
in detail in the chapters following this guide.
Please read the RC5 and SC5 user manuals carefully before proceeding.

Setup
When unpacking the RC5 and SC5 from their respective cardboard boxes, please make sure that all items listed in
the Content of delivery section of the RC5 and SC5 manuals are taken out of the boxes.
To properly set up the instrument, a square space of at least 40 cm × 45 cm × 35 cm (W × D × H) is required.
Additional SC5s or OC4s require an additional height of 10 cm for each instrument. The two instruments weigh
approximately 12 kg, and stability of their supporting table must be guaranteed. It must be possible to access the
hardware from the front and the rear in order to connect all necessary cables. The space has to be dry and kept within
the specified temperature range.
The RC5 is actively cooled, and the air intake is placed at the bottom of the instrument. The four plastic feet
supporting the instrument must not be removed, and no items should be placed between the supporting table and the
bottom of the instrument. The SC5 is passively cooled, and needs sufficient airflow around it for cooling.
Nanonis Tramea™ requires two power sockets (160 VA typical, 260 VA max at 100-230 V, 50-60 Hz for both
instruments) with proper grounding. Additional SC5s or OC4s require additional power sockets with 35 VA typical,
51 VA maximum.
Warning: The power cords must be connected to properly wired and earthed sockets.

Caution: Make sure that the air intake at the bottom of the RC5 is not obstructed; otherwise the RC5
might exceed its maximum operating temperature and shutdown.

Interconnection of the instruments
Only one single cable, supplied with the SC5, is needed as a connection between the SC5 and RC5. The DEVICE
RDIO cable is labelled as SHC68 – 68 – RDIO. Place the SC5 and RC5 at the desired location, and make sure that
the space requirements listed in the previous section are fulfilled.
Make sure that both the SC5 and the RC5 are switched off, but connected to the mains so they are earth grounded.
Connect the DEVICE RDIO cable to the DEVICE SC 01/02/03 port (12) of the SC5 first, then to the SC 01 port (19)
of the RC5, as shown in the figure below. Always tighten the screws on both sides of the connectors.

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Hardware Installation Guide • 13

NI PXIe-8840
Embedded Controller

Figure 3: Connection between the SC5 and the RC5. The power cords of both intsruments have to be connected to the
mains first.
Caution: Connect both the SC5 and the RC5 to the mains using the supplied power cords, before
connecting the instruments together!

Caution: Make sure that the screws of the DEVICE RDIO cable connectors are tightened; otherwise
the connectors might be damaged. Do not overtight the screws!

Caution: If a single SC5 is connected to the RC5, it must be connected to the SC 01 port at the back of
the RC5. Do not connect it to the SC 02 or SC 03 ports.

Multiple SC5 connection
Up to three Nanonis SC5s can be connected to a single RC5. Follow the instructions given in the previous section for
the connection of the additional SC5 units.
Since the different SC5s are addressed by their port number in the Nanonis software, make sure to label the
instruments in order to recognize which instrument is connected to which port. The figure below shows the
maximum configuration with three SC5s connected to the RC5.

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Hardware Installation Guide • 14

SC5 #1
SC5 #2
SC5 #3

NI PXIe-8840
Embedded Controller

Figure 4: Connection of three SC5s to a RC5. The SC5s are shown placed above the RC5, but they can be also placed
below the RC5.
Caution: If two SC5s are connected to the RC5, they must be connected to the SC 01 and SC 02 ports
at the back of the RC5. Do not connect the second SC5 to the SC 03 port.

Connection to host computer
The host computer running the control software is connected to the RC5 over a single Gigabit-Ethernet cable. A
crossover cable should be used if the RC5 is connected directly to the host computer, while a normal cable should be
used if the RC5 is connected over a switch. In both cases Cat-5e or Cat-6 cables should be used.
The cable should be connected to Ethernet connector 1 (16) at the back of the RC5, as shown in the picture below.
Ethernet connector 2 is disabled and should not be used.
For information about how to set-up the network adapter of the host computer, please refer to the Host computer
network configuration section below.

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Hardware Installation Guide • 15

NI PXIe-8840
Embedded Controller

CRS

Figure 5: The Ethernet cable for the connection of the RC5 with the host computer should be plugged into Ethernet
connector 1 as shown above.

Connection to computer screen
A computer screen connected to the DisplayPort connector (17) of the RC5 displays status information about the
instrument. Connecting a computer screen to Nanonis Tramea™ is not necessary during normal operation, but it can
help to detect the origin of a fault in case one of the following issues should appear:
•
•
•
•
•

A connection between host computer and the RC5 cannot be established and the RC5 does not respond to a
“ping” request.
The software does not detect the RC5
A Warning indicates a wrong real-time operating system release, and the update fails
A real-time operating system update fails
None of the instruments connected to the RC5 seems to be responding

A computer screen is connected using a DisplayPort cable as indicated in the figure below on the left. For computer
screens using a VGA input, the supplied DisplayPort to VGA adapter should be used, as shown below on the right.
For computer screens using DVI inputs, a DisplayPort to DVI adapter (not supplied) should be used.
Note: Certain computer screens connected over the DisplayPort to VGA adapter might not be recognized if
connected when the RC5 is already running. If nothing appears on the screen connected to the RC5, although the
RC5 is running, it is necessary to restart the RC5 by switching it off and then on again.

Quantum Transport Measurement System

Hardware Installation Guide • 16

NI PXIe-8840
Embedded Controller

Figure 6: Connection of a computer screen to the DisplayPort connector of the RC5 using a DisplayPort cable (left).
Connection to a computer screen using the supplied DisplayPort to VGA adapter (right). An adapter to DVI (not
supplied) must be used for computer screens with DVI input only.

Powering
Before powering the instruments, make sure that:
•
•

The SC5 or the SC5s are connected to the RC5 as explained above
If an external clock source is used as clock reference, that this source is connected and active (please refer to the
RC5 manual for details.)

Then turn on the SC5 first, followed by the RC5. The instruments are powered on with the power switches (5, 13) at
the back of the units (see below). The power LEDs (3, 4) will illuminate.

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Hardware Installation Guide • 17

Figure 7: Powering of Nanonis Tramea. Left side: Location of the power switches at the back of the SC5 and RC5. Right
side: LEDs which will illuminate after powering each instrument.

Nanonis Tramea™ is now ready for use. Should the RC5 or SC5 not turn on as described above, please refer to the
Troubleshooting section before proceeding. If a solution to the unexpected behavior is not listed there, please contact
SPECS before taking any further action.

How to proceed
•
•
•
•
•

Switch off the instruments
Make sure that all instruments are connected together, including external instruments connected to the DIO
ports (20), HS digital inputs or outputs (21, 25), and clock connectors (22, 24). For details about these ports,
please refer to the RC5 and SC5 manuals.
Make sure that the RC5 is connected to the host computer as described above.
Power on the instruments.
Follow the steps explained in the next sections for how to install and operate the Nanonis Tramea™ software.

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Hardware Installation Guide • 18

Software Installation Guide
Host computer requirements
The software running on the host computer is the control and visualization interface of a Nanonis system. The host
computer must therefore be able to handle and visualize all data transferred to/from the Nanonis system, translating
into the following basic requirements:
•
•
•

There should be sufficient screen space for the software modules and for data visualization. The use of two
screens is highly recommended.
CPU power should be sufficient for handling data transfers, processing data, and allowing a smooth user
interface operation.
There should be sufficient disk space for saving acquired data.

All real-time data processing is done on the RC5 CPU, meaning that it is not necessary to use the fastest computer
hardware available. However, using obsolete hardware might result in poor user interface performance, TCP
timeouts, or data losses.
The requirements for the host PC hardware are listed in the table below.
Parameter
CPU

Minimum requirements

Ideal configuration

Intel Core i3-4XXX 3 GHz or equivalent
or better

Intel Core i5-4XXX 3 GHz or equivalent
or better

RAM

4 GB

8 GB or better

Hard Drive

500 GB

2 TB 7200 rpm

Graphics card

Dual-head graphic card with digital
output (DVI or DisplayPort)
(no 3D acceleration required)

Network adapter

Gbit Ethernet

Screens

One screen:
21” 4:3, resolution 1600 × 1200
24”, 16:10, resolution 1920 × 1200
Two screens:
19” 5:4, resolution: 1280 × 1024
22” 16:10, resolution: 1680 × 1050

Two screens:
21” or 22” 4:3, resolution 1600 × 1200
24”, 16:10, resolution 1920 × 1200

Operating System

Windows 7 32-bit or higher

Windows 7 64-bit or higher

Note: Data streaming to disk into a database requires relatively high data transfer speeds. If this option is used, it is
recommended to use a dedicated hard drive for data storage (7200 rpm with large cache or SSD) and 16 GB RAM or
more.
Note: The number of software installations is not limited, meaning that the software can be installed in parallel on
different computers. However, only one software instance can connect to the RC5 at a time. If there are multiple
RC5 in use, the license file determines to which of the instruments the software will connect.
Note: The software runs under both 32-bit and 64-bit Windows operating systems. 64-bit operating systems are
recommended, since the software can allocate 2 GB of non-fragmented memory if sufficient RAM is installed (4 GB
or more).

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Software Installation Guide • 19

Note: A Laptop can be used for running the control software. However, due to limited screen resolution and physical
screen size only a limited number of software modules can be visible at the same time, and the workflow will be
considerably impaired.
Note: If an internet connection is necessary, two network adapters must be installed in the host computer, one for the
internet connection, and one for the connection to the RC5.

Host computer network configuration
This section describes how to configure the network adapter of the host computer. It is necessary to be logged on
with administrator rights, or at least to have a valid administrator password.
Configure the Network adapter of the host computer (the one connected to the RC5) using the following settings:
IP address:

192.168.236.X

Subnet mask:

255.255.255.0

With X being 1-99 and 111-255. Do not use IP addresses between 192.168.236.100 and 192.168.236.110, since
these IP addresses are reserved for the RC5. Do not use IP addresses already in use by other instruments, since this
will lead to an IP address conflict. In case the IP address of the RC5 needs to be changed (e.g. if the second network
adapter is in the same subnet), please contact SPECS. The following sections explain in detail the configuration for
each operating system. Please note that the appearance of dialog windows might be slightly different than shown in
the pictures below. The instructions refer to the Nanonis SPM Control System software, but the same procedures
apply also to the Nanonis Tramea™ software.

Windows XP
Note: Support and updates for Windows XP from Microsoft are not available anymore.
In the Start menu, open Settings, then Control Panel and choose Network Connections. Right-click on the network
adapter to which the RC5 is connected, and select Properties.

Select Internet Protocol (TCP/IP) and click on the Properties tab.

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Software Installation Guide • 20

In the configuration window, select Use the following IP address, and set the IP address to 192.168.236.X and the
subnet mask to 255.255.255.0, as shown below.

Click OK, then click OK again on the Local Area Network Properties window to close the window and apply the
new setting.

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Software Installation Guide • 21

Windows Vista
In the Start menu, open Control Panel and choose Network and sharing center (in classic view) or View network
status and tasks (normal view). Then select Manage network connections. Right click on the network adapter to
which the RC5 is connected and select Properties.

Select Internet Protocol Version 4 (TCP/IPv4) and click on the Properties tab.

In the configuration window, select Use the following IP address, and set the IP address to 192.168.236.X and the
Subnet mask to 255.255.255.0, as shown below.

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Software Installation Guide • 22

Click OK, then click OK again on the Local Area Network Properties window to close the window and apply the
new setting.

Windows 7 and later
Note: The procedure for Windows 7 is also valid for Windows 8 and Windows 10
In the Start menu, open Control Panel and choose Network and sharing center (in classic view) or View network
status and tasks (normal view). Then select Change adapter settings.

Right click on the network adapter to which the RC5 is connected (renamed to Nanonis LAN in this guide) and select
Properties.
Select Internet Protocol Version 4 (TCP/IPv4) and click on the Properties tab.

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Software Installation Guide • 23

In the configuration window, select Use the following IP address, and set the IP address to 192.168.236.X, the
Subnet mask to 255.255.255.0, and the Default gateway to 192.168.236.100 (the IP address of the RC5), as shown
below.

Click OK, then click OK again on the Nanonis LAN Properties window to close the window and apply the new
setting.
Make sure that the RC5 is switched on, and connect it to the host computer with a crossover Ethernet cable. Make
sure that it is connected to the correct network adapter! After connecting, the RC5 should be recognized, and the
following window will appear.

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Software Installation Guide • 24

Select Work network. Do not select Public network! The communication between RC5 and host PC might be
blocked if Public network is selected.

If you are not prompted to select the network location, it can be accessed from the Network and sharing center, as
shown below.

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Software Installation Guide • 25

Firewall configuration
In the Start menu, open Control Panel and choose Windows Firewall (in classic view) or System and Security and
then Windows Firewall (normal view). Then select Advanced settings, and select Inbound rules for the Nanonis SPM
controller.

Double-click on both Nanonis SPM Controller items, and make sure that the connection is enabled and allowed for
both items, as shown below.

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Software Installation Guide • 26

Switch to the Protocol and Ports tab for both Nanonis SPM Controller items and make sure that All ports is selected
for both the TCP and UDP tab (TCP shown below).

Switch to the Advanced tab, and verify that Private is checked.

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Software Installation Guide • 27

Note: As an alternative the firewall for the network adapter used by the Nanonis System can be disabled.

Nanonis software installation
Installation of the Nanonis software requires two files:
•
•

Nanonis SPM Controller Installer V5 RXXXX or Nanonis Tramea Installer V5 RXXXX
Nanonis license file

The Installer file has to be downloaded from the SPECS extranet website:
http://www.specs-zurich.com/en/extranetlogin.html
under the Software V5 SPM or Software V5 QT tab. The login credentials are provided by SPECS, and sent by email
after purchasing a Nanonis system.
The license file is also provided by SPECS. Make sure to have both files ready before starting the installation of the
Nanonis software.
Note: The license file determines which modules of the Nanonis software will be available once the software is
installed.
Note: The installer for Nanonis Tramea™ software found in the Software V5 QT tab does not contain any SPM
functionality. Therefore it is not possible to start the Nanonis Tramea™ software with a license file intended for a
Nanonis SPM Control System, or a Nanonis OC4.5-S. The installer for the Nanonis SPM Control System found in
the Software V5 SPM tab, on the other hand, contains both functionalities, meaning that it is possible to start the
Nanonis SPM Control System software with a Nanonis Tramea™ license file. Only quantum transport functionality
will be enabled in that case.
Note: The installation procedure described below is valid for both a first installation of the software, as well as for
an upgrade to a higher release.
Note: The appearance of dialog windows might be slightly different to those shown in the pictures below.

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Software Installation Guide • 28

For starting the installation process, double-click on the Nanonis SPM Controller Installer V5 RXXXX or Nanonis
Tramea Installer V5 RXXXX.exe file. The following message will appear:

Press OK to start the installation. After the installer has initialized, the following dialog window will appear:

If different installation directories compared to the ones shown are preferred, indicate a different directory in the
corresponding field. Otherwise press Next >>.

Read the license agreement and select I accept the License Agreement, then click Next >>. The following window
will appear. Depending on the installation type (first installation or upgrade), a different summary will be displayed.
The following picture is for an upgrade installation.

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Press Next >>, and the installation will start. Once the installation is finished, the following dialog window will
appear:

Press Next >> to finish the installation.

License files
Each RC5 is delivered with a license file. The license file is usually sent by email, together with the login credentials
to the extranet website http://www.specs-zurich.com/en/extranetlogin.html, and is required for the correct
functioning of the Nanonis hardware and software. The main functions of the license file are:
•
•

Ensure that the hardware is configured properly, according to the system configuration
Manage the software modules loaded when starting the Nanonis software

The license file is bound to the MAC address of the network adapter of the RC5, therefore each license file is
specific to a given RC5, and can’t be used with a different one. The license files are protected, meaning that by
changing entries, the license files become unusable.
Always keep the license file at a known location so it can be retrieved quickly. When contacting SPECS by email,
please always send the license file since this can contribute to speeding up the troubleshooting processes or facilitate
the addition of hardware and software modules.
Note that the license file needs to be changed if the real-time unit is replaced.

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Nanonis software startup
First time startup
In order to start the Nanonis software, double-click on the Nanonis software icon, or select the Nanonis software
from the Start Menu. The following startup screen appears:

Click on the No license file found! drop-down list and select Browse…. A dialog window appears, asking to specify
the license file to be used and its location. Select the correct license file (see the previous section for details about
license files) and click OK. Another dialog will appear, asking if the file should be copied into a directory where the
software can find it automatically, see below.

It is recommended to click Yes, since the license file will then be automatically selected at the next start of the
software. Note that it is possible to copy multiple license files to the Application Data directory. The files can then
be accessed directly from the software startup screen shown above, by clicking on the Available License Files dropdown list.
After clicking Yes the license file appears in the Available license files drop-down list, as shown below.

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All three indicators next to the License File data (License File valid, Not expired, Correct Version) should be green
indicating that no errors occurred.
Note that the file can be saved to a different location by clicking on the save icon, or can be deleted from the list by
clicking on the trash icon. The information icon provides information on the file when hovering the mouse over it.
In order to start the software for normal operation, click on the “Start” button.
Note: At this point a Windows Firewall warning might pop up, informing that the Firewall has blocked some
features of the program. Depending on the operating system, click on Unblock or Allow access in order to proceed.
This requires administrator privileges. If a different firewall is used, make sure that it also does not prevent the
Nanonis software from running. Antivirus software might also interfere with the startup process of the Nanonis
software. Please make sure that all antivirus software is deactivated at the first start of the Nanonis software. The
antivirus software then needs to be configured in such a way that the Nanonis software is not recognized as a threat
to the computer.
After clicking on the Start (Startup) button, the software will load the modules specified by the license file.
However, if the real-time software is outdated, it might be necessary to update it by following the on-screen
instructions explained in the Real-time software update section below. After that, the following information appears:

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Read the text, and if necessary click on Please refer to the online help for more information in order to access the
online help (does not require an internet connection). Then click on OK. In the next dialog window, browse for a
directory to be used as a session directory, then click on select current directory at the bottom right of the window.
Note that it is not possible to select cancel. All measured data will be saved in the session directory (for more details
please see the Session and Session Directory section).
The software is then ready to use.
Note: This procedure is necessary only during first time startup of the software or when using a new license file.
Otherwise the software automatically selects the last used session directory.
If the software should not start as described above, please refer to the Troubleshooting section.
There are three other options available in the startup screen: Cancel, hrDAC tuning, and Demo.
Cancel closes the startup screen without starting the software.
hrDAC tuning starts the hrDAC™ calibration procedure. Note that during calibration the analog outputs are
internally connected to the analog inputs. This means that output and input connectors will be electrically floating.
For more information about hrDAC™ and the calibration procedure, please refer to the SC5 user manual.
Demo starts the software in simulation mode and loads the quantum dot simulator model (see further below and the
Quantum Dot Simulator section for more details).

Normal startup
When starting the Nanonis software with the Start (Startup) button, the last session directory is retrieved from the
registry. This is user specific, i.e. different users may use separate session directories.
The software then loads and starts the modules. Each module loads its settings from the "Nanonis-Session.ini" file in
the session directory (session settings file). If a module can't find its stored settings in this file, it will load the
settings from the default settings file. The layout is then loaded from the session settings file. If no layout can be
found in the session settings file, it is loaded from the default settings file.
Note that it is possible to select a different settings file for startup from within the software (see the Options section
for more details). However, if the requirement is to start the instrument with safe settings in order to prevent sample
damage, it is recommended to use the safe start option explained below, rather than defining an additional safe
settings file just for startup (since this is exactly what the safe start option does).
Note that the software loads the last settings saved in the session settings file (or a different file if specified in the
Options, although not recommended). It means that output voltages as well as any other setting stored in this file will
be applied immediately after the software has finished loading. These settings might not be safe for the sample
connected to the instrument, and might also not be the settings which were active when the instrument was turned off
at the end of the previous measurement session. This is the case if the user did not store them in the session file when
closing the software. Therefore, it is recommended to use the safe start option if there is any doubt about what
settings would be applied when starting the software.

Safe Start options
By clicking on the three dots next to the Start (Startup) button, it is possible to select different settings to be loaded
during startup of the software. The two options, apart from the Startup settings option leading to a normal startup
are:
•
•

Safe Settings: The software loads the settings stored in the Safe Settings file. The Start button displays Start
(Safe)
Sync to RT (not available yet): The software stores the voltages set on the real-time system, and applies the
same voltages when initializing. The Start button displays Start (RT Sync)

The two safe start options should be used in different cases, depending on the reasons for choosing the safe start
option.
Safe settings should be used if:

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•
•
•
•

It is necessary to have 0 V on all analog outputs (Note: this assumes that the voltages stored in the safe settings
file are not modified from the default value of 0 V for all outputs and software modules controlling output
signals)
The instrument has been switched off and it is unclear what settings have been stored in the session settings file
(e.g. when a different user was operating the instrument).
There has been a power cut and both the host PC and Nanonis Tramea have switched off during the power cut.
It is not possible to disconnect the sample from the instrument during the start of the software

Sync to RT should be used if:
•
•
•

The Host PC has crashed while the real-time system is running or during a measurement
The Host PC has been switched off by mistake while the software is running
The Nanonis software stopped responding while the real-time system is running

Demo mode
When selecting Demo mode the software starts in simulation mode and loads the quantum dot simulator model (see
the Quantum Dot Simulator section for more details). This means that the software will launch and connect to a
simulator on the host computer instead of connecting to the hardware. The simulation mode can be used to gain
familiarity with the software without the risk of damaging samples, or for testing and debugging measurement
routines written in the Programming Interface, in the Scripting Module, or with the TCP Interface. Only the modules
licensed in the license file will be loaded, and a license file is necessary for starting the software in simulation mode.
It is not necessary to have the hardware connected to the host computer, and Demo mode will work on any computer
where the Nanonis software is installed and where a valid license file is available.
By clicking on the three dots next to the Demo (QD Sim) button, it is possible to select the settings loaded for the
simulation mode. The two available options are:
•

•

QD Simulator Settings (default): The software loads the default settings of the simulator model. This ensures
that signals are configured correctly and sets voltage ranges so that starting a simulated measurement will lead
to results. This option should be chosen for training the use of the instrument or if testing of customized routines
requires a meaningful measurement result.
Startup Settings: The software loads the settings of the normal startup. Signal configuration, voltage ranges
and other parameters are configured according to the last stored settings. These settings will probably not be
compatible with the simulator model and therefore starting a measurement will probably not lead to any
meaningful data. This option should be chosen when testing customized routines that require identical
conditions to normal operation of the instrument.

Quitting the software
Quitting the software is possible by selecting Quit in the File menu of the main window. After selecting Quit, a
window appears giving the possibility to save Settings, the Layout and the Signals Configuration, as shown below.
For more information about settings and layouts, please refer to the Multi-user approach: Sessions, settings and data
storage data storage section further below.

If any of the options is unchecked, the corresponding settings or configurations will be lost. Checking the options
results in the following:

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•
•
•

Save Settings to: stores all settings into the selected settings file. Press the configuration icon on the right to
open the Settings options in order to create new settings files or rename existing settings files
Save Layout to: stores the current layout to the selected layouts file. Press the configuration icon on the right to
open the Layouts options in order to create new layouts files or rename existing layouts files
Save Signals Configuration: Stores the configuration of the signals set in the signals manager in the presets
file. The configuration is automatically loaded during the following software startup.

Real-time software update
The Nanonis software running on the host computer requires a specific release of the real-time software installed on
the RC5. If the latter is older than the required release, a real-time software update is necessary. This is the case
when:
•
•

The Nanonis software has been updated between testing of the RC5 at SPECS and delivery of the instrument
A newer release of the Nanonis software has been downloaded and installed

If the update is necessary, a dialog window automatically appears after pressing the Start button in the startup screen:

Press Install new in order to install an updated release of the real-time software. The following information window
is displayed:

Click Next > in order to start the installation. The following two progress windows are displayed:

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The procedure takes approximately 2 minutes. Once the update process is completed, the following window appears:

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Press Finish to end the real-time update. The startup screen appears again, and the software can now be started
normally. If the update process should stop, please refer to the Troubleshooting section.

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Basic tutorials
Scope
The scope of the following tutorials is to provide basic instructions on how to perform the first measurements with
the instrument. A DUT (sample) or any external wiring is not required, since all measurements can be performed in
loop-back (calibration) mode. The tutorials provide step-by-step instructions which require no prior knowledge about
the functionality of the instrument.
Software modules and functionalities which are not strictly needed for the measurements are not described in this
section, and only a little background information is provided. Detailed information is provided in the Software
Operation Guide as well as in the Advanced Tutorials section.
The tutorials assume that the Host PC software has been installed as explained in the previous sections.
Note that the screenshots provided show the actual configuration explained in the text, and can therefore be used for
correctly configuring a module in case the written explanation is not clear.

Preparation
Please make sure that both the RC5 and SC5 are powered on and connected to the Host PC as explained in the
Hardware Installation Guide. Make sure that the Nanonis software is installed as explained in the Software
Installation Guide. Then start the Nanonis software (in normal mode) as explained in the Nanonis software startup
section.
Look for the Main Window shown in the picture below. All modules required for the tutorials can be accessed from
the menu in the Main Window.

Figure 8: Nanonis Tramea software Main Window

Depending on the measurement, it will be necessary to change the analog input mode of the SC5 in order to switch
between inputs connected to GND, inputs floating, or inputs connected to outputs (loop-back). The input mode is set
in the SC5 Control module shown below, which can be accessed from the Modules menu in the Main Window.

Figure 9: SC5 control module. The default setting with Input Mode set to Analog Inputs is shown.

The default setting is Analog inputs. With this setting the inputs are floating. Please select Ground (GND) if a
measurement has to be performed with inputs connected to GND, and Analog Output (Calibration Mode) if loopback mode with the inputs connected to the outputs is required.

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Noise measurement
This tutorial explains how to perform basic noise measurements, which will be useful when connecting the
instrument to the measurement set-up for the first time. The tutorial does not require any optional modules.

Preparation
Set the Analog input mode of the SC5 to GND in the SC5 Control module (shown above). Open the following
modules:
•
•
•
•

Signal Chart
History
Graphs/Oscilloscope 2T
Graphs/Spectrum Analyzer

Qualitative noise analysis with charts
Signal charts allow a qualitative estimate of the amount of noise on a signal. However, care has to be taken as signal
charts use significant averaging, meaning that frequencies above a certain limit will not be visible in the displayed
waveform. Additionally, due to the finite sampling rate, aliasing can lead to artefacts in the displayed signals. Signal
charts are therefore best used for low-frequency signals or drift. Please refer to the Signal Charts section for more
details on the effects of averaging.
Open the Signal Chart module and select AI1 and AI2 (Input 1 and Input 2) as signals to be displayed as shown
below. The chart will display approximately the same amount of noise on both input signals. Use the slider on the
upper right to change the oversampling and therefore the amount of averaging.

Figure 10: Signal Chart module showing input noise with inputs connected to GND and default averaging (10x).

Now change the Analog input mode in the SC5 Control module from GND to Analog Inputs. The signal chart will
show a periodic waveform with noise superimposed. By touching one of the shields of the AI1 or AI2 BNCs on the
SC5, the amplitude of the waveform will increase, as shown in the picture below for AI1.

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Figure 11: Signal Chart showing input noise with open connector (lower graph) and when touching the shield of an input
connector (upper graph). Default averaging (10x) is used.

By reducing averaging to 1x instead of 10x, the shape and amplitude of the waveform are displayed as shown below.

Figure 12: Same measurement as above but with averaging reduced to 1x showing the power line harmonic component of
the input noise.

Based on the chart, it is clear that there is a discrete noise source with an amplitude of about 500 mV p-p on input 1
and another noise source with identical frequency and an amplitude of about 300 µV p-p on input 2.
Repeat the same steps with the History module. Due to the larger default oversampling, the periodic waveform will
not be visible, as shown below.

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Figure 13: History module showing input noise with open connector (lower graph) and when touching the shield of an
input connector (upper graph). Note that the power line harmonic component of input noise is not visible due to the low
sampling rate being an integer multiple of the power line frequency.

The above examples show that signal charts can be conveniently used to get a quick impression of a signal. It also
shows the limits of signal charts: Determining the frequency of the AC power component, would it not be known in
advance, is difficult. Averaging and artefacts resulting from aliasing should always be considered carefully, since in
the above examples the power line harmonic component easily disappears from the plots with larger averaging even
if it is always present at the input.

Noise measurements with oscilloscopes
The oscilloscope modules offer a higher sampling rate and more sophisticated tools for quantitative noise analysis.
Despite being not as sensitive as a spectrum analyzer, they are well suited for a quick quantitative noise estimation.
This tutorial will discuss noise analysis with the dual-trace Oscilloscope 2T module, since the faster and generally
higher performance High Resolution Oscilloscope is an optional module. For the sake of simplicity only one trace
will be used.
Make sure that the inputs are set to GND in the SC5 Control module. Open the Oscilloscope 2T module
(Charts/Oscilloscope 2T) and select Input 1 as input signal for the upper trace as shown below. Press on the thin
double arrow pointing up and down on the left of and between the V/Div input fields (Autoscale). This will adjust
the units per division such that the signal will fill most of the vertical range.

Figure 14: Oscilloscope 2T module showing input noise with input 1 connected to GND and default settings.

In order to obtain quantitative data, press on the arrow pointing up (Increase) on the right of V/Div input field until
the signal becomes smaller than the full vertical range. Alternatively, insert a round number in the input field to the

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left of the arrows. In the image below the range has been set to 10 µV/Div. Right-click on the input field and select
Show scale. This will display a scale in the chart area and therefore facilitate an estimation of signal amplitudes.
Since the waveform is updated about 8 times per second, it makes sense to freeze the waveform in order to allow
better determination of waveform values. In order to do so, press the Hold button. Then, select the CHA tab at the
top right in order to display waveform parameters. Mark the checkboxes at the right of the Pk-Pk, AC, and DC fields
in order to display guide lines in the chart area. The module should look as shown in the picture below:

Figure 15: Oscilloscope 2T module showing input noise with input 1 connected to GND and configured for noise
amplitude measurements.

From the above screenshot it is possible to see that the input signal has a DC offset of -4.396 µV, an RMS amplitude
of 6.715 µV and a peak-peak amplitude of 36.47 µV. The orange guide line shows the DC offset, the grey line shows
the RMS amplitude with respect to the DC offset and the two blue lines show peak-peak amplitude.
Note that, as for any measurement in a limited time base and with a given sample rate, the numbers are valid only if
a frequency range is specified. In this case the frequency range is limited by the time base at the lower end and by
the sampling rate at the upper end. Therefore the noise has the amplitudes specified above in a frequency range from
about 8 Hz (1/time base) to 1 kHz (sampling rate/2). Extending the frequency to lower values requires an increase of
the time base or of the oversampling. Extending it to higher frequencies requires a reduction of signal oversampling
in the TCP Receiver module. For more details, please read the TCP Receiver and Oscilloscopes sections below, since
a detailed explanation goes beyond the scope of this section.
Now change the Analog input mode in the SC5 Control module from GND to Analog Inputs. The oscilloscope will
show a periodic waveform with noise superimposed. It is probably necessary to increase units per division in order
to display the full waveform, in the example below it was changed to 50 µV/Div. Note that you can use the C button
(located above te Pk-Pk display) to move the waveform to the center of the display area if no waveform appears.

Figure 16: Oscilloscope displaying input noise with open connector. A short BNC cable has been connected to the input in
order to enhance the power line component.

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Note that the noise is now dominated by one discrete frequency with a peak-to-peak amplitude of 498.2 µV and an
RMS amplitude of 142.3 µV.
If the waveform moves around in the display area it may be necessary to use triggering in order to lock the
waveform into a fixed position. In order to do so, change to the trigger tab, set the trigger to Level, and select a
suitable trigger level. The position on the time axis as well as the level can either be adjusted by inserting numbers in
the fields on the right, or by moving the grey arrow on top of the chart area and the green arrow at the right of the
chart area. In the figure below, triggering is set to a level of 50 µV and its position is in the middle of the time axis
(at 64.22 ms).
The frequency of the main AC component can be estimated with the use of cursors: The cursors are positioned with
the mouse on two peaks of the waveform. The difference in time between the cursor positions corresponds to the
period of the waveform (20 ms and therefore a frequency of 50 Hz).

Figure 17: Triggering of the waveform. The trigger position is marked by the arrows at the top and on the left of the
display area. Note that the cursors have been activated and allow an estimation of the frequency of the waveform.

Noise measurements often require a comparison between two different wiring configurations in order to determine
which one yields lower noise. The oscilloscope module allows pasting the trace into the display area, such that it can
be compared to a later measurement. In order to do so, change to the Traces tab and press CHA Paste. This will
paste the current waveform to the display area. If triggering is active, the pasted waveform might not be visible since
it is masked by the measured waveform.
Change the Analog input mode in the SC5 Control module from Analog Inputs to GND. In the Oscilloscope module
go to the trigger tab and set the trigger Mode to immediate. The amplitude of the waveform will drop to the level of
inputs connected to GND as shown below.

Figure 18: Waveform comparison with the paste function

The above examples demonstrate how to use an oscilloscope module for getting quantitative data about input noise
with acceptable precision in a short time. Despite not being as critical as for signal charts, measurement bandwidth

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should always be considered when trying to measure noise of broadband signals. Frequency resolution is also
relatively low due to the approximations occurring when using cursors. The use of a spectrum analyzer (see below)
is recommended for a precise frequency determination.
Note that the measurements displayed above can be performed identically with the single channel Oscilloscope
module or with the optional High Resolution Oscilloscope module.

Noise measurements with spectrum analyzers
Spectrum analyzers provide the highest frequency sensitivity for discrete signals, and also allow determining RMS
amplitude of a signal over a given frequency range (Band RMS). They are, however, a rather slow measurement tool
particularly when measuring at low frequencies. This tutorial will discuss noise analysis with the Spectrum Analyzer
module. Note that a more powerful spectrum analyzer is available with the optional High Resolution Oscilloscope
module.
Make sure that the inputs are set to GND in the SC5 Control module. Open the Spectrum Analyzer module
(Charts/Spectrum Analyzer) and select Input 1 for the input signal as shown below.
.

Figure 19: Spectrum Analyzer module showing input noise with input 1 connected to GND and default settings.

Note that it is possible to resize the window if a larger display area is required. This is particularly useful when
trying to minimize discrete noise sources, since the measurement set-up might be far away from the computer
screens and maximizing the display area significantly improves readability from larger distances.
Use the cursor to determine the power spectral density of the signal at a given frequency. In the above picture the
cursor is positioned at 801 Hz and the input noise equals 146 nV/√Hz at that frequency.
Note that the default resolution is chosen such that the update rate of the plot is sufficiently fast. The resolution can
be increased by a factor of 8 (by reducing the value in Hz) or by reducing the range. Both will result in a slower
update rate of the plot.
Now click on the three vertical dots next to the cursor position display on the lower right, and select Band RMS, df.
This will activate a second cursor, which can be used to determine band RMS noise in the frequency range between
the two cursors. Position one cursor at a frequency of 0 Hz and the other one at a frequency of 996 Hz as shown
below. The resulting band RMS is about 280 µV.

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Figure 20: Band RMS measurement with the spectrum analyzer module. Band RMS is measured in the frequency range
between the two cursors, in this case the full displayed frequency range between 0 Hz and 996 Hz.

This number is considerably larger than what was determined with the oscilloscope. The reason is that the frequency
range includes all frequency components from DC to 996 Hz, while the oscilloscope had a lower frequency limit of 8
Hz. In order to verify this, increase the resolution to 488 mHz, and position the two cursors at 8 Hz and 1 kHz. Since
the individual position of the left cursor is not displayed, it can be positioned at 8 Hz by moving it until df reaches
992 Hz. Now, the displayed band RMS is about 6.4 µV, as shown below, in agreement with the value measured with
the oscilloscope module.

Figure 21: Band RMS measurement in the same range as the oscilloscope measurement of the previous example.

Now change the Analog input mode in the SC5 Control module from GND to Analog Inputs, return the resolution to
the default value of 3.91 Hz and the cursor type to x,y.
Note that each time there is a large change in input signals it is recommended to press restart in order to restart
averaging of the spectrum and discard data which resulted from the large change of the signal.
The spectrum will show a series of peaks, the most prominent one being a 50 Hz peak (or 60 Hz, depending on the
country). Also in this case a short BNC cable has been connected to the input connector in order to increase the
amplitude of the 50 Hz component and its harmonics. Position the cursor on top of the 50 Hz peak, as shown below.
The peak amplitude is displayed as about 58 µV/√Hz.

Figure 22: Input spectrum with inputs floating. A short BNC cable was connected to the input in order to boost discrete
noise peaks.

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The measured amplitude is lower than the RMS amplitude measured with the oscilloscope (142.3 µV). The reason is
that the spectrum analyzer displays spectral density and not RMS amplitude, and the frequency resolution of the FFT
influences the result. RMS amplitude can be extracted from spectral density as follows:
𝑉𝑉 2
)) × 𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅 (𝐻𝐻𝐻𝐻)
𝑅𝑅𝑅𝑅𝑅𝑅 𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴 (𝑉𝑉) = �(𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠 𝑑𝑑𝑑𝑑𝑑𝑑𝑑𝑑𝑑𝑑𝑑𝑑𝑑𝑑 (
√𝐻𝐻𝐻𝐻

yielding 114.3 µV RMS. This number is lower than the oscilloscope amplitude since only the 50 Hz component is
considered. Note that the type of windowing function and the related spectral leakage have a significant influence for
amplitude determination. Additionally, the displayed amplitude will accurately reflect the real value the closer the
measured frequency lies to an FFT bin.
Alternatively, it is possible to make a band RMS measurement across a peak as shown below. The resulting band
RMS amplitude is now 143 µV, apparently in agreement with the Oscilloscope measurement. However, the
precision is limited by the FFT resolution and therefore the cursor positioning, leading to a larger band RMS
amplitude than the correct one. Increasing resolution will lead to a more precise band RMS measurement.

Figure 23: Using Band RMS for determining the RMS amplitude of a discrete signal with the Spectrum Analyzer module.
Note that it is recommended to use a much finer resolution than shown in the picture in order to improve band RMS
determination.

Similar to the oscilloscope, it is possible to paste a spectrum into the chart area in order to compare different spectra.
In order to do so, click on the paste tool on top of the chart area. Then, change the Analog input mode in the SC5
Control module from Analog Inputs to GND. Click Restart in the Spectrum Analyzer module in order to reset
averaging. The result is a comparison between the input spectrum with inputs connected to GND and floating.

Figure 24: Spectrum comparison with the paste function.

The above examples demonstrate how to use a spectrum analyzer module for frequency and noise determination.
The advantage of precise frequency determination comes at the cost of longer averaging time. Also, amplitude
determination of discrete frequency components always requires taking into account the FFT resolution and is
dependent on windowing and sampling frequency. The user should be aware that the amplitude of a peak in the FFT
spectrum resulting from a single discrete frequency does not translate directly into the RMS amplitude seen in the
oscilloscope.

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DC measurement
Preparation
Set the Analog input mode of the SC5 to Calibration mode in the SC5 Control module. This will connect each
output AOj to an input AIj, with j=1…8. Open the following modules:
•
•
•
•
•

User channels: Input 1 and Output 1
Signal Chart
History
1D Sweeper
3D sweeper

The two main tools used are the 1D sweeper and the 3D sweeper. There are two important differences between these
two tools: The 1D sweeper only sweeps one parameter, while the 3D sweeper can sweep and step up to 3 parameters
against each other, two of which must be analog outputs. The second difference is that the 1D sweeper performs
measurements with a point by point type acquisition, while the 3D sweeper runs data acquisition on the real-time
system for two of the three parameters, acquiring a complete trace at a much higher speed and in a time-deterministic
manner.

Point by point measurement
Open the Input 1 and Output 1 modules from the User Channels menu. Open the 1D sweeper and select Output 1 as
the sweep signal in the upper left side of the module. In the Channels table below the output selector, highlight Input
1 and Input 2 as the channels to be acquired. In order to select both, press Ctrl when clicking on the channel names.
Select the sweep range by typing a number into the Lower limit and Upper limit fields, e.g. -10 V and +10 V (full
range). Set the desired number of Steps (e.g. 200 resulting in a step size of 100 mV) and the Period (e.g. 100 ms).
Note that the period defines the integration time for each point, and also sets the settling time before each step to the
same amount. A period of 100 ms means a settling time of 100 ms and an integration time of 100 ms. Enter an Initial
settling time (e.g. 500 ms) which will define the waiting time at the beginning of the sweep. Larger settling times are
required for example when high gain preamplifiers or steep lock-in filters are used, since in that case it takes a
significant amount of time until the signal settles to the initial value of the measurement. The 1D sweeper module
should appear as shown below.
Note that it is possible to resize the module by dragging the border of the window in order to obtain a larger display
area for the chart.

Figure 25: 1D sweeper module configured for a sweep where the voltage of Output 1 is swept over its full range and
recorded on inputs 1 and 2.

Now open the Signal chart module and select Input 1 and Input 2 as the signals to be displayed. Open the History
module and also select Input 1 and Input 2 as chart signals.
Start a measurement by pressing the start button in the 1D sweeper (the triangle pointing to the right). During the
measurement the Signal Chart and History modules should display signals as shown below:

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Figure 26: Signal Chart and History display during the measurement. Note the irregular step pattern due to the nature of
the host-based point by point measurement.

Input 1 shows the signal of Output 1 (since they are connected together), while Input 2 shows only its own input
noise (which is larger than the output noise of Output 2 to which it is connected).
Note that the duration of data shown in the Signal Chart and History modules can be adapted by adjusting the
averaging (Signal Chart) or the number of displayed points (History).
As an illustration for the working principle of calibrations, assume that a 1/10 voltage divider is connected in series
to Output 1, that the sample outputs a current proportional to the applied voltage, and that a current to voltage
converter with a gain of 109 is connected between the sample and the input. While it would be possible to keep the
calibration as above and correct data in post processing, it is much more convenient to take these two elements into
account from the beginning.
In order to do so, open the Output 1 User channel module, change the Channel Name to “sample bias” and change
the Calibration to 0.1V/V by typing “0.1” or “100m”. The limits of the slider will now change to -1 V and +1V
indicating the maximum voltage applied to the sample after the voltage divider. Note that the voltage applied at the
SC5 output connector will still be in the range from -10 V to +10 V, but the software displays the actual voltage
applied to the sample. Change the Slew Rate to 0.1 V/s, which will limit the maximum speed of the change of
voltage (applied to the sample) to 0.1V/s. Note that the voltage at the output connector of the SC5 will change with a
maximum of 1 V/s, since the slew rate limitation takes into account the voltage change at the sample.
Open the Input 1 User channel module, change the Channel Name to “sample current”, change the SI-Unit to “A”
(since the sample outputs a current), and change the calibration to 1nA/V by typing “1n” (this takes into account the
gain of the current to voltage converter which outputs 1 V for 1 nA input current).
Now drag the slider in the Output 1 module (which is now called “sample bias”) completely to the left. The Input 1
module (now called “sample current”) will display a sample current of -10 nA (since the input still sees the full -10
V applied to the SC5 output, and -10 V correspond to -10 nA with a current gain of 1 nA/V), but it will take several
seconds to get to that value due to the slew rate limit.
Go back to the 1D sweeper, and note that the module has done a reset due to the change in signal name and
calibration. Select sample bias as Sweep Signal and sample bias as well as sample current as Channels to be
acquired. If a measurement is now started, the 1D sweeper will show a straight line in each display area, from -1 to
+1 V for sample bias, and from -10 nA to +10 nA for sample current.

Figure 27: 1D sweeper with user-modified signal names and data display taking into account modified signal calibrations.

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Fast measurement
Fast measurements are done with the 3D sweeper, which allows significantly higher measurement speeds than the
1D sweeper of the previous tutorial. The module is also far more complex, but this tutorial will just make use of the
base functionality.
Open the Input 1, Input 2, Output 1 and Output 2 modules from the User Channels menu. Open the 3D sweeper and
select Output 1 as the Sweep Channel and Output 2 as the Step channel 1 in the Configure tab of the module. Select
Input 1 and Input 2 as the channels to be acquired in the table on the left. In order to select both, press Ctrl when
clicking on the channel names. Select the sweep range by typing a number into the Start and Stop fields, e.g. -10 V
and +10 V (full range) for the sweep channel and 0 V and 1 V for step channel 1. If the tutorials have been followed
in order up to this point, please set the calibrations and units of the Output 1 and Input 1 modules to default values
(Unit: V, Calibration: 1V/V).
Set the desired number of points for the sweep channel (e.g. 2001 resulting in a step size of 10 mV) and for step
channel 1 (e.g. 101 resulting in a stepsize of 10 mV). Settling times and Integration times can be configured in a
more flexible way in comparison to the 1D sweeper, but for this tutorial the idea is just to measure at maximum
speed. Therefore, the sweep channel should be configured for a settling time at the beginning of the sweep (Init.
Settl.) of 50 µs, the Settling time before each measured point (Settl.) to 0 s, the settling time at the end of the sweep
to 50 µs and the integration time for each point to 50 µs. For step channel 1, adjust the initial settling time to 50 µs
and the end settling time to 50 µs. The entire measurement should now last slightly more than 10 seconds (for
200’000 points).
Set the slew rate of both channels to Inf, meaning no slew rate limitation. If the input field has an orange color, it
means that the slew rate set in the corresponding user outputs is lower than what is set in the 3D sweeper. Since
highest speed is desired now, go to the Output 1 and Output 2 modules and type Inf into the Slew Rate (V/s) field.
Note that the slew rate limit set in the User Output module cannot be exceeded by the 3D sweeper module but it is of
course possible to choose a lower slew rate in the 3D sweeper compared to the setting in the User Output module.
The 3D sweeper module should now be configured as shown below:

Figure 28: 3D sweeper module configured for a sweep where the voltage of Output 1 is swept over its full range, the
voltage of Output 2 is stepped from 0 to 1 V and with inputs 1 and 2 being acquired. The timing parameters are set for
maximum measurement speed resulting in a total measurement time of about 10 s.

Click on the Monitor A and Monitor B buttons in order to open two monitor displays, showing a 2D representation of
measured data. Set the acquired channels of the Monitors to Input 1 for Monitor A and Input 2 for Monitor B. Open
the Signal Chart and History modules, and set the signals to be acquired to Input 1 and Input 2. Make sure that the
SC5 is set to Calibration mode in the SC5 Control module. Then start a measurement by pressing the start button in
the 3D sweeper (the triangle pointing to the right).
At the end of the measurement, the 3D sweeper will display a diagonal line going from -10 V to +10 V, which in
reality is the superposition of 101 measured traces of 2001 points each.
The Signal chart and history modules should look as shown below:

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Figure 29: Signal Chart and History display during the measurement. The upper plot displays the sweep channel, while
the lower plot displays step channel 1. The history displays the full 2D measurement.

Note that each sawtooth-like waveform represents a full sweep. Irregularities in the shape of the signal as well as the
fact that the voltage does not reach ±10 V are due to averaging of the chart. At the end of the measurements the
output voltages remain at the last value, it is however possible to configure the module such that the voltages are
reset to the start voltages.
The monitor displays for Input 1 (Monitor A) and Input 2 (Monitor B) will display the data as shown below:

Figure 30: Monitor A and B displays for the above measurement. Monitor A shows the -10 V to +10 V sweeps of Input 1,
while Monitor B shows the 101 steps from 0 to +1 V of Input 2.

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AC measurement
Preparation
Note: This tutorial requires one optional lock-in module.
Set the Analog input mode of the SC5 to Calibration mode in the SC5 Control module. This will connect each
output AOj to an input AIj, with j=1…8. Open the following modules:
•
•
•
•
•
•
•

Lock-in module
Signals Manager
Signals Chart
Oscilloscope 2T
Spectrum analyzer
3D sweeper
Lock-in transfer function

The goal of the first part of this tutorial is to understand the operation of the lock-in module. Please note that this is
not a tutorial on principles of lock-in measurements, therefore having a basic understanding of these principles
would be advantageous.

Setting-up the lock-in module
As a first step it is necessary to make the demodulated signals (X, Y or R, φ) of the lock-in module accessible to data
acquisition. For this purpose, open the lock-in module, and select if X and Y or R and φ should be used for data
acquisition. This is configured next to the Harmonic and Phase settings of both demodulators.
For this tutorial, please select R,phi for both demodulators, as shown below:

Figure 31: Lock-in module configured for data acquisition of R and phi signals.

After this it is necessary to assign the demodulated signals (R, φ ) to the 24 signals which can be displayed or
recorded, meaning those visible in the signal selection of e.g. signal charts or sweepers. In order to do so, open the
Signals Manager module which can be accessed from the System Menu in the Main Window. Click on the
Assignment tab on top of the module. At the bottom of the now editable list of signals, there are 8 signals marked by
Reserved 1 to Reserved 8. Click on each of the upper four of them, and configure the signals as described in the table
below:
Slot number
16
17
18
19

Default assignment
Reserved 1
Reserved 2
Reserved 3
Reserved 4

Assign to
LI Demod 1 R
LI Demod 1 phi
LI Demod 2 R
LI Demod 2 phi

For this tutorial only the R and φ components will be used. The Signals Manager module will be configured as
shown below:

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Figure 32: Signals manager with demodulated lock-in channels assigned to Slots 16 to 19. The R and phi components have
been chosen, but X and Y could be chosen instead.

Now open the Signal Chart, and select the now available channels LI Demod 1 R and LI Demod 1 phi from the list of
24 channels for display. Also open the Oscilloscope 2T Module and select Input 1 for display (see the above tutorial
about noise measurements for details about the configuration).
Open the lock-in module. The module should be configured so that the modulation signal is applied to Output 1 and
demodulated from Input 1. The modulation frequency should be low enough so that many periods can be displayed
on the Oscilloscope 2T module without any changes to the default oversampling parameters. The lock-in module
features two independent demodulators, meaning that it is possible to demodulate different harmonics, or the same
harmonic but with different demodulator filter settings. This tutorial will discuss the second option further below
since it offers more benefits for typical transport measurements. For this reason, the parameters of the lock-in should
be configured as summarized in the table below:
Section
Modulate
Modulate
Modulate
Modulate
Demodulate
Demodulate
Demodulate
Demodulate
Demodulate
Demodulate
Demodulate
Demodulate
Demodulate
Demodulate
Demodulate
Demodulate
Demodulate
Demodulate
Demodulate

Parameter
(Modulated signal)
(Modulation)
Frequency
Amplitude
(Demodulated signal)
Demodulator 1 harmonic
Demodulator 2 harmonic
Demodulator 1 Ref. Phase
Demodulator 2 Ref. Phase
Demodulator 1 HP Order
Demodulator 2 HP Order
Demodulator 1 HP Cutoff
Demodulator 2 HP Cutoff
Demodulator 1 LP Order
Demodulator 2 LP Order
Demodulator 1 LP Cutoff
Demodulator 2 LP Cutoff
Demodulator 1 Sync
Demodulator 2 Sync

Setting
Output 1
ON
100 Hz
10 mV
Input 1
1
1
0 deg
0 deg
off
off
*
*
4
off
9.71 Hz
*
OFF
ON

*Parameter is not relevant for this tutorial.

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Note that these settings are chosen for demonstration purposes only, they do not represent ideal measurement
settings.
The Lock-in module will therefore be configured as shown below:

Figure 33: Lock in module configured for the measurements discussed in this tutorial.

In the signal display area at the bottom of the module, select R, phi D1. The amplitude R should be 10 mV or around
10 mV as shown above.
Open the Oscilloscope 2T module, and select Input 1 as the signal for Channel A. Adjust the range so that the full
waveform is displayed. A 100 Hz waveform with a peak-to-peak amplitude of 20 mV should be displayed, as shown
in the picture below. This is the signal applied to the Lock-in input.

Figure 34: Input signal of the lock-in module measured with the Oscilloscope 2T module.

Please note that the Oscilloscope will display no waveform if Output 1 is selected as the signal to be displayed. This
is due to the fact that the lock-in modulation is applied on the RC5 FPGA while the oscilloscope module only
displays data available on the real-time system, which is located upstream for output signals with respect to the
FPGA.
The lock-in is now configured for an AC measurement.

Lock-in measurement with sweep modules
Acquiring data is now straightforward: Open the 3D sweeper module (the same procedure also applies to the 1D
sweeper) and select a sweep range from -5 V and +5 V for the Sweep Channel (Output 1) and 0 V and 1 V for Step
Channel 1 (Output 2).
Set the number of points for the Sweep Channel to 101 (resulting in a stepsize of 100 mV) and for Step Channel 1 to
6 (resulting in a stepsize of 200 mV). The reason for the lower number of points in comparison to the previous
tutorial is that here it is necessary to take into account the time response of the lock-in filters, meaning that the time
for each point is longer. Configure the settling time at the beginning of the sweep (Init. Settl.) to 100 ms, the Settling
time before each measured point (Settl.) to 25 ms, the settling time at the end of the sweep (End Settl.) to 100 ms and
the Integration time for each point to 100 ms. For Step Channel 1, adjust the initial settling time to 50 ms and the
end settling time to 50 ms. The entire measurement should now last about two minutes. Note that the optimal settling

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time for each point is dependent on the selected lock-in filter settings (for more details, please see the Lock-in signal
processing section below).
Then, in addition to Input 1 and Input 2, select also the demodulated lock-in channels LI Demod 1 R and LI Demod 1
phi in the table on the left for data acquisition (Press Ctrl before clicking on the signals in order to select multiple
signals). Select LI Demod 1 R as a signal to be displayed in the 3D sweeper module and start a measurement.
At the end of the measurement the Module should look like shown below:

Figure 35: 3D Sweeper module configured for a DC+AC measurement, displaying demodulated lock-in data. Since the AC
amplitude is constant over the whole sweep, the measured signal is constant.

Since the input amplitude is constant (10 mV), the measured data are flat lines with noise determined by the lock-in
filter settings and by the integration time of the 3D sweeper. The following section illustrates the effect of different
filter settings.

Using multiple demodulators
Using multiple demodulators at the same time is very useful not only for determining the optimal filter settings, but
also for acquiring data with different detail or noise levels at the same time.
Open the Signal Chart, and select LI Demod 1 R and LI Demod 2 R as signals to display. They both will show a DC
signal at 10 mV, but with different noise levels. This is due to the fact that the two plots show the output signals of
two demodulators which have different configurations: Demod 1 uses a 4th-order low-pass filter with a corner
frequency of 9.71 Hz, while Demod 2 uses only sync filtering (assuming that the module is configured as explained
above). The result is shown below. Note that the vertical scale has been adjusted so that both plots have the same
scale.

Figure 36: Signal chart displaying the R (amplitude) output of two lock-in demodulators. The upper trace is obtained by
setting a 4th order low-pass filter, the lower trace by enabling only sync filtering.

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Demodulator 1 (using a 4th-order low-pass filter) has significantly lower noise than demodulator 2 (which uses sync
filtering only), but it is also clearly visible that this comes at the expense of speed.
Now repeat the measurement of the previous section, but now select also add LI Demod 2 R and LI Demod 2 phi in
the list of signals to be acquired with the lock-in. All of the other settings can be kept as in the previous section.
Toggle between LI Demod 1 R and LI Demod 2 R in the signals to be displayed in the 3D sweeper module in order to
see the differences between the two traces. Alternatively, use the Monitor A and Monitor B displays for a comparison
of the data, although the differences might not be noticeable with the input signal and the low number of points used
for this demonstration.
In order to quantify the noise difference at the output of the lock-in demodulators, open the Oscilloscope 2T and
Spectrum Analyzer modules.
First configure the Oscilloscope 2T such that LI Demod 1 R and LI Demod 2 R are both selected as input signals, and
make sure that both are fully displayed in the display area (see the Noise measurement section above for how to
configure the module). Set both inputs to AC coupling, and set the Time Base to 1.28 s. Due to the low frequency of
the AC modulation and the low cut-off frequency of the low-pass filter, selecting this large of a timebase will not
affect the noise measurement. The result should look like shown below.

Figure 37: Output noise of the lock-in demodulators. The upper trace is for a 4th order low-pass filter, the lower sync
filtering only.

Alternately choose the CHA and CHB tabs, and compare the measured peak to peak and RMS noise values for the
two traces. Note that the LI Demod 1 R signal has a lower noise amplitude and also looks smoother than the signal of
LI Demod 2 R. This is due to the fact that the sync filter used by demodulator 2 generates 100 measured amplitude
values per second, which are displayed without any averaging, while the low-pass filter of demodulator 1 removes
noise with a frequency above its cut-off frequency (of 9.71 Hz) according to its filter transfer function. Note that as
soon as the sync filter is active the output signal of the demodulator behaves step-like with each step corresponding
to one period of the waveform. This is also the case when combining sync filtering with a low-pass filter since the
sync filter is applied downstream with respect to the low-pass filter.
Now configure the Spectrum Analyzer module and select LI Demod 1 R as the signal to be displayed. Reduce the
Range to 500 Hz, increase the Resolution to 488 mHz and wait for the spectrum to stabilize, then press the paste icon
in order to paste the spectrum into the display area. Then select LI Demod 2 R in order to obtain a situation like
shown below and compare the two spectra.

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Figure 38: Output spectrum of the two lock-in demodulators. The pasted trace (red) is for a 4th order low-pass filter with
a cut-off of 9.71 Hz, while the yellow trace is for sync filter only.

The lower noise of the pasted trace (in red), that of LI Demod 1 R can easily be seen confirming the peak to peak and
RMS values of the Oscilloscope 2T. The sync filter trace shows the characteristic notches at the modulation
frequency and its harmonics. Note that the low-pass filter trace shows residuals of the modulation frequency and its
second harmonic, which would require a steeper filter for better suppression, or combined with a sync filter, since
the latter dampens these components very effectively (as can be seen for the yellow trace).
Note how the cut-off frequency and filter response (4th order) can easily be recognized when changing the mapping
mode of the X axis to logarithmic (right-click in the chart area in order to open the graph functions menu).
Again select LI Demod 1 R as the signal to be displayed in the Spectrum Analyzer module, and change the filter
order and cut-off frequency of demodulator 1 in the lock-in module to see the effect on the spectrum of the
demodulated amplitude. The figure below shows a comparison between a 1st order filter with a cut-off of 1.21 Hz
and an 8th order filter with a cut-off of 155 Hz.

Figure 39: Comparison of demodulator output noise with a 1st order filter with low cut-off (1.21 Hz, red trace) and an
8th-order filter with higher cut-off (155 Hz, yellow trace). Note that neither setting would make sense in a typical
measurement situation and are used here solely for demonstration purposes.

Note that the same measurements can be done for the lock-in phase signals, LI Demod 1 phi and LI Demod 2 phi.
A better-suited filter setting for clean, albeit slow, measurements would be an 8th-order filter with a cut-off frequency
of 19.4 Hz.

Transfer function measurement
A transfer function measures the frequency response of a system. It can be extremely useful e.g. in the case of lowtemperature measurements of nanodevices, where various stages of filtering are installed in the cryostat inserts.
These filters often have different characteristics resulting in unknown maximum bandwidths for the measurements.
In the case of gated nanostructures a transfer function measurement immediately delivers the usable bandwidth of
both source-drain and gate electrodes. This is achieved by:
•

Modulating the source-drain voltage and demodulating the source-drain current

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•

Modulating a gate voltage and demodulating the source-drain current

In the case of a current-source and voltage output measurement, source-drain voltages and currents are exchanged.
Such a measurement is straightforward: Open the Lock-in Frequency Sweep module either from the Experiments
menu, or by clicking on the transfer function icon on the top right of the lock-in module. Configure the Sweep Range
so that the Lower frequency is 1 Hz and the Upper frequency is 50 kHz. Right-click in the Lower frequency input
field and select Set frequency to this value in order to adjust the lock-in modulation frequency to 1 Hz. Set the
number of Steps to 100, the Settling Time to 500 ms and the Integration Time to 5 periods.
Make sure that the lock-in is configured as described in the previous section, then select LI Demod 2 R as a signal to
be displayed in the upper plot of the Lock-in Frequency Sweep module, and LI Demod 2 phi for the lower plot. The
data will be measured with the sync filter only, which is convenient since the transfer function tool averages for a
certain number of modulation periods, and not over a fixed integration time. Configure the axes so that both use a
logarithmic scale (right-click in the chart area and select Logarithmic under Mapping Mode X and Y.
Start a measurement, and the following trace should appear in the module:

Figure 40: Transfer function measurement of the SC5 outputs and inputs.

The trace shows a constant amplitude and phase with a roll-off starting slightly below 40 kHz. This corresponds to a
convolution of the amplitude and phase responses of the output and input stages of the SC5, dominated by the lower
cut-off frequency (-3 dB at 40 kHz) of the outputs.

Quantum dot simulator
This tutorial explains how to operate the quantum dot simulator. Both the standalone quantum dot simulator and the
standard software in simulation mode can be used for this tutorial, although in the latter case a lock-in module needs
to be licensed in order to perform simulated AC measurements. Nanonis TrameaTM Hardware is not required for the
tutorial.
As the name suggests, the quantum dot simulator simulates a single quantum dot. The parameters of the model are
typical for a top-gate defined single quantum dot and two single-particle energy levels are simulated by the model.
Please refer to literature for more details about quantum dots and quantum dot physics.
The model plugs in between the user outputs and the user inputs and therefore behaves like a real sample, including
simulated noise. The following parameters can be modified during simulated measurements:

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Parameter

Range

Function

Plunger Gate

-5 mV to +20 mV

Tunes the energy levels in the quantum dot

Source-Drain

-2 mV to +2 mV

Adjusts the source-drain voltage of the quantum dot (biasing of the dot)

Left Gate

-20 mV to +20 mV

Adjusts the tunnel coupling between the left lead (source or drain) and the dot

Right Gate

-20 mV to +20 mV

Adjusts the tunnel coupling between the right lead (drain or source) and the dot

Please note that further simulated parameters could also be modified, but there is no need to do so for this tutorial.
For more details about the model, please see the quantum dot simulator section below.
The quantum dot simulator is an excellent tool for learning the operation of the software without the risk of
damaging a real sample. It is also a useful tool for testing custom programmed scripts or routines in the TCP
interface or programming interface, but this is not covered by this tutorial.

Preparation
Since no hardware is required, only the software needs to be started. Please make sure to select QD simulator
settings in the startup screen, since otherwise the simulated sample might be tuned outside its operating range. Open
the following modules:
•
•
•

3D sweeper
Signals Chart
Lock-in module

DC measurements
This section will consider only DC measurements and therefore a lock-in module for measuring differential
conductance is not required.
When starting the software in simulation mode (or when starting the standalone quantum dot simulator), the
following modules will appear:
•
•
•
•
•
•

Main Window
User Outputs 1-4
User Input 1
Signal Chart
Lock-in
3D sweeper

To start a measurement, just press the start button in the 3D sweeper. This will start a stability diagram measurement
by sweeping the source-drain voltage from -2 mV to +2 mV (with 201 points) and stepping the plunger gate voltage
from -5 mV to + 20 mV (with 21 points). All signals are already configured, therefore it’s not necessary to select
data acquisition channels or configure any sweep and step channels.
At the end of the measurement the 3D sweeper module should display a series of quantized conductance steps as
shown in the figure below. The traces display the current through the quantum dot as a function of source-drain
voltage, and each trace is measured at a different plunger gate voltage.

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Figure 41: 3D Sweeper module in simulation mode, displaying quantized conductance steps of a simulated quantum dot.

For displaying the complete measurement, open a monitor display (e.g. Monitor A) which should look as shown
below. It displays the complete measurement and shows one complete “Coulomb Diamond” in the center of the
display area. By default, the horizontal axis corresponds to the Sweep channel and the vertical axis to step channel 1.
The axes can be inverted by changing the X-axis Channel at the top left of the display area.

Figure 42: Simulated stability diagram measured with quantum dot simulator default settings.

The default settings allow a fast measurement with poor resolution on the plunger gate voltage axis. In order to
obtain better data, change the Integration time of the Sweep Channel in the 3D sweeper module to 500 µs, the
number of points in the Sweep Channel to 401 and the number of points in Step Channel 1 to 101 points. Then, start
a measurement again. The data displayed in one of the monitors should now be much smoother than in the previous
case.
Note that it is also possible to perform a left gate vs. right gate sweep. For this purpose, change the value of User
Output 2 (Source-drain) to 100 µV and that of User Output 1 (Plunger Gate) to 8 mV in the corresponding User
Output modules. Then, change the sweep parameters in the 3D sweeper such that the Sweep Channel is set to Left
Gate and Step Channel 1 is set to Right Gate. The Start and Stop voltages should be set to -20 mV and +20 mV for
both gates respectively. With 401 points for the sweep channel and 101 for step channel 1, as set above, the result in
Monitor A should look as shown below. Note that the color scale has been readjusted in order to make both peaks
visible.

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Figure 43: Simulated left gate vs. right gate measurement of the conductance through a quantum dot. The color scale has
been adjusted in order to visualize the lower conductance peak (see the color scale slider at the top).

Differential conductance
Differential conductance can be obtained either by mathematically differentiating a DC measurement, or by using a
lock-in and measuring differential conductance. The first method just requires switching the data processing in the
3D sweeper or one of the monitor windows. In order to measure differential conductance this way, configure the 3D
sweeper for a stability diagram measurement (Sweep Channel: Source-Drain from -2 mV to +2 mV, Step Channel 1:
Plunger Gate from -5 mV to +20 mV) with 401 points for the Sweep Channel and 101 points for Step Channel 1. In
the display area of the 3D sweeper, select a filtering function (e.g. 5th order FIR) in order to smooth the data, and also
select dY/dV under Function in order to calculate and display the derivative of the data. After running a
measurement, the 3D sweeper will look as shown below:

Figure 44: 3D Sweeper module in simulation mode, displaying mathematically differentiated conductance of a simulated
quantum dot.

Note that 50 traces are displayed in this example, meaning that if a different value for No Plots is selected, the result
will look different. The same data can be displayed in a Monitor window. After setting the Processing tab to
Differentiate, also the monitor window will display differential conductance, as depicted below.

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Figure 45: Simulated stability diagram with mathematically differentiated conductance.

The second method requires a lock-in module. The simulated lock-in module has significantly lower performance
than the real lock-in module and only allows measurements with sync filtering. Nevertheless, differential
conductance measurements can lead to the results expected from a real measurement. Before starting the
measurement, configure the lock-in module by setting a modulation amplitude of 50 µV and a modulation frequency
of 2 kHz. This frequency value is not a realistic choice but helps to keep measurement time low since it allows using
500 µs as the integration time in the 3D sweeper. Select R/phi as RT Signals. The module should be configured as
shown below:

Figure 46: Simulated lock-in module configured for a differential conductance measurement. Note that the demodulator
configuration is not available in the quantum dot simulator or in demo mode.

In the 3D sweeper module, select the LI Demod 1 R and LI Demod 1 Phi channels for data acquisition in addition to
Dot current (press and keep Ctrl pressed while selecting the channels in order to select multiple signals). Set the
settling and integration times for the sweep channel to 1 ms and 500 µs resp. while keeping all other settings as for
the case described above.
Select LI Demod 1 R as the Channel to be displayed in the 3D sweeper and start a measurement. The result should
look very similar to that of the mathematically differentiated data shown above. Open a monitor window to see the
full measurement and switch between the Dot Current, Dot Current (differentiated) and LI Demod 1 R signals. It is

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also possible to open two monitors and the Inspector and look at the three different signals at the same time. The
results should look as shown below:

Figure 47: Comparison of DC and AC measurements taken simultaneously. The left graph displays the DC conductance.
The graph in the middle shows the mathematically differentiated DC conductance. The graph on the right displays the
differential conductance measured by the lock-in module.

Note that during the measurement it is always possible to look at the signals being acquired with any of the available
charts, oscilloscopes or spectrum analyzers. The signal chart, for example, can be set to display the DC dot current
and at the same time the demodulated AC conductance of the lock-in module:

Figure 48: Using the signal chart to display DC and AC conductance measurement at the same time. The upper trace is
the DC trace through the (simulated) quantum dot, the lower trace is the AC conductance demodulated by the lock-in
module.

Quantum Transport Measurement System

Basic tutorials • 62

Troubleshooting
Network and software issues
SYMPTOM:

The instrument turns on, but does not respond when starting the software. There is no
indication of faults. The following window appears after starting the software.

Figure 49: This error window appears if no communication between the RC5 and the host computer is possible.

REASON:

The real-time controller has not finished booting.

SOLUTION:

Wait about 20 seconds and try again. It takes about 30 seconds for the RC5 to finish its boot
process.

REASON:

Missing Ethernet cable. In this case there is no entry in the “Available RT-Controllers” field.

SOLUTION:

Make sure that an Ethernet cable is connected to both the correct Ethernet connector (16) of the
RC5, and the correctly configured Ethernet port of the host computer.

REASON:

Wrong Ethernet cable. In this case there might be no entry in the “Available RT-Controllers” field.

SOLUTION:

Make sure that the RC5 is connected to the host computer with a crossed Ethernet cable. A crossed
cable is not necessary if the RC5 is connected to the host computer over a switch, hub, or router.

REASON:

The RC5 is connected to the host computer over a router with incorrect configuration. In this case
there is no entry in the “Available RT-Controllers” field.

SOLUTION:

Make sure that the router is not acting as a DHCP server. The RC5 has a fixed IP address. Also
make sure that all devices connected to the router have IP addresses in the range 192.168.236.X,
with X being 1-99 or 111-255. The IP addresses from 192.168.236.100 to 192.168.236.110 should
not be used. Please contact SPECS if the IP address of the RC5 needs to be changed.

REASON:

Firewall or antivirus software is blocking the communication between RC5 and host computer.

SOLUTION:

Disable the Windows firewall, or any other active firewall. If the RC5 is connected directly to the
host computer, a firewall is not necessary. Disable any active antivirus software installed on the
host computer. If this solves the issue, enable the antivirus software, but make sure to configure it
so that the communication is not blocked. Note that system dialog windows requesting an
authorization for connecting to the RC5 or for a firewall exception might be displayed behind
another window. Please make sure that no authorization request is pending.

Quantum Transport Measurement System

Troubleshooting • 63

NOTE:

Connection issues related to firewalls, or operating system TCP/IP issues can be solved by
entering the IP address of the RC5 (192.168.236.100, if it has not been previously changed
from the default value, otherwise the changed IP address) in the “check this IP address”
field, and then click “Connect”. If a connection is still not possible, please check all possible
reasons listed here.

REASON:

No software or corrupted software installed on real-time controller. A dialog window appears,
informing that the RT-Controller did not respond.

Figure 50: Dialog window informing that no connection to the real-time software is possible.

SOLUTION:

Click on “Install Software” to reinstall the real-time controller software. If the software has been
started less than 60 seconds before the RC5 has been powered on, please click on “Try again” first.

REASON:

Outdated software installed on real-time controller. The following dialog window appears.

Figure 51: Dialog window informing that the software installed on the real-time controller needs to be updated.

SOLUTION:

Please follow the instructions given in the Real-time software update section above.

REASON:

Wrong license file. The MAC addresses in the field “Licensed MAC address” and “Available RTControllers” (see above) are different.

SOLUTION:

Make sure that the correct license file has been selected. The license files are bound to a specific
RC5, therefore license files for other RC5s will not work.

License file issues
SYMPTOM:

The “License file valid” LED in the startup screen of the software is dark.

REASON:

The license file has been tampered with, or has been generated incorrectly.

SOLUTION:

Retrieve the original license file and try again. If this does not solve the issue, please contact
SPECS.

SYMPTOM:

The “Not Expired” LED in the startup screen of the software is dark.

REASON:

The license file has expired. This is the case for time-limited licenses.

SOLUTION:

Use a license file with no time limitation. If not available, please contact SPECS.

SYMPTOM:

The “Correct Version” LED in the startup screen of the software is dark.

REASON:

The license file is intended for a different version of the software.

SOLUTION:

Use the license file sent with the RC5. If the file cannot be found, please contact SPECS.

Quantum Transport Measurement System

Troubleshooting • 64

Instrument doesn’t power up correctly
SYMPTOM:

The Power LED (1) does not light up.

REASON:

Fuses blown.

SOLUTION:

Disconnect the RC5 from the mains. Remove and check the fuses (3). If the fuses are blown,
replace them with fuses of the same rating (T2A), and try powering up the RC5. Should the fuses
blow again, please contact SPECS.

REASON:

RC5 damaged.

SOLUTION:

Disconnect the RC5 from the mains. Remove and check the fuses (3). If the fuses are intact, but
the unit is still not working, please contact SPECS.

SYMPTOM:

The instrument turns on, but does not respond when starting the software. The “DRIVE”
LED (see picture below) at the back of the RT-unit does not light when powering the RC5.

REASON:

Hard drive failure.

SOLUTION:

A hard drive failure is very unlikely, but cannot be ruled out. In the case of a hard drive failure, the
“DRIVE” LED at the back of the RT-unit does not light up when powering the RC5 (see picture
below for the location of the LED). Please note that during normal operation the LED is always
off, therefore a hard drive failure can only be detected by observing the LED when powering the
RC5. If the hard drive has failed, please contact SPECS.

Figure 52: Location of the "DRIVE" LED indicating normal functioning of the hard drive during start-up of the RC5 (NI
PXIe-8115 version shown).

SYMPTOM:

The instrument turns on, but does not respond when starting the software. There is no
indication of faults.

REASON:

Corrupt file system, or network-related issue (see above).

SOLUTION:

Connect a computer screen to the DisplayPort connector as explained in the Connection to
computer screen section. The status information shown on the screen should appear as shown in
the picture below. If the displayed information should be different, please take a picture of the
screen and contact SPECS.

Quantum Transport Measurement System

Troubleshooting • 65

CPU#
CPU 0:

Total Load
82%

ISRs
0% |−−−−−−−−|

Dev Op M Link Driver MAC Address
* 1 Int U R i1000e XXXXXXXXXXXX
2 Int i1000e XXXXXXXXXXXX

Timed Structures
75% |−−−−−−−−|

Other Threads
5% |−−−−−−−−|

IP Address
/Mask Adapter Mode
192.168.236.X
/24 TCP/IP (static)
- Disabled

LabVIEW Real-Time Executive
Build Time: Month X YYYY hr:min:sec
(C) Copyright 2002-2016 National Instruments Corporation
MAX system identification name: RC5-XXXXX
LabVIEW Real-Time Single-Core Kernel
Initializing network...
System Web Server started
NI-RIO Server 15.1.0b4 started successfully.
Welcome to LabVIEW Real-Time 15.X.X
NI_VISA Server 15.0 started successfully.
Starting Nanonis RT Engine
MAC Address is XX:XX:XX:XX:XX:XX
loading FPGA...Version: Generic 5, RT Release: XXXX, RT Type: V5
is running now
connected to 192.168.236.Y

Figure 53: Status screen of the RC5 during normal operation. CPU load might be different than shown in the picture.
CPU#
CPU 0:

Total Load
82%

ISRs
0% |−−−−−−−−|

Timed Structures
75% |−−−−−−−−|

Other Threads
5% |−−−−−−−−|

Build Time: Month X YYYY hr:min:sec
(C) Copyright 2002-2012 National Instruments Corporation
MAX system identification name: RC5-XXX
LabVIEW Real-Time Single-Core Kernel
Initializing network...
Device 1 - MAC addr: XX:XX:XX:XX:XX:XX - 192.168.236.X
Device 2 - MAC addr: XX:XX:XX:XX:XX:XX - disabled
System Web Server started

/24

(primary - static)

Startup Application: c:\ startup.rtexe
NI-RIO Server 4.1 started successfully.
NI_VISA Server 5.1 started successfully.
Welcome to LabVIEW Real-Time 11.X.X
Starting Nanonis RT Engine
MAC Address is XX:XX:XX:XX:XX:XX
loading FPGA...Version: Generic 4, RT Release: XXXX, RT Type: V45
is running now
connected to 192.168.236.Y

Figure 54: Status screen of the RC5 during normal operation (NI PXIe-8115 version). CPU load might be different than
shown in the picture.

For further hardware-related issues, please refer to the Troubleshooting section of the RC5 user manual.

Quantum Transport Measurement System

Troubleshooting • 66

Legal Information
Warranty
SPECS acknowledges a warranty period of 12 months (EU: 24 months) from the date of delivery (if not otherwise
stated) on parts and labour, excluding explicitly any software and consumables.
EXCEPT AS SPECIFIED HEREIN, SPECS MAKES NO WARRANTIES, EXPRESS OR IMPLIED, AND
SPECIFICALLY DISCLAIMS ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A
PARTICULAR PURPOSE. CUSTOMER’S RIGHT TO RECOVER DAMAGES CAUSED BY FAULT OR
NEGLIGENCE ON THE PART OF SPECS SHALL BE LIMITED TO THE AMOUNT THERETOFORE PAID
BY THE CUSTOMER. SPECS WILL NOT BE LIABLE FOR DAMAGES RESULTING FROM LOSS OF DATA,
PROFITS, USE OF PRODUCTS, OR INCIDENTAL OR CONSEQUENTIAL DAMAGES, EVEN IF ADVISED
OF THE POSSIBILITY THEREOF.
This limitation of the liability of SPECS will apply regardless of the form of action, whether in contract or tort,
including negligence. Any action against SPECS must be brought within one year after the cause of action accrues.
SPECS shall not be liable for any delay in performance due to causes beyond its reasonable control. The warranty
provided herein does not cover damages, defects, malfunctions, or service failures caused by owner’s failure to
follow the SPECS installation, operation, or maintenance instructions; owner’s modification of the product; owner’s
abuse, misuse, or negligent acts; and power failure or surges, fire, flood, accident, actions of third parties, or other
events outside reasonable control.

Copyright
Under the copyright laws, this publication may not be reproduced or transmitted in any form, electronic or
mechanical, including photocopying, recording, storing in an information retrieval system, or translating, in whole or
in part, without the prior written consent of SPECS GmbH.

Trademarks
SPECS® is a registered trademark of SPECS Surface Nano Analysis GmbH. Nanonis® is a registered trademark of
SPECS Zurich GmbH. Product and company names mentioned herein are trademarks or trade names of their
respective owners.

Quantum Transport Measurement System

Legal Information • 67

Quantum Transport Measurement System

Legal Information • 68

Index
A

adaptive oversampling 9
aliasing 39
averaging 39

Nanonis OC4.5-S 28
Nanonis SPM Control System 9, 28
network adapter 15, 19, 20, 22, 23

band RMS 39

oversampling 39

calibration 47
CPU 19

peak-peak amplitude 39
power socket 13
power spectral density 39

D
demodulator 51
DEVICE RDIO cable 11, 13
disk space 19

R
RAM memory 19
RMS amplitude 39

ethernet cable 15, 23
extranet website 28

sampling rate 39
simulation mode 31, 33
slew rate 47
sync filter 51, 57

F
FFT windowing 39
filter cut-off 51
filter order 51
firewall 23, 31

G
graphics card 19

H
hard drive 19
hrDAC calibration 31

T
temperature stabilization 9
time determinism 47
triggering 39

U
units 47

V
voltage divider 47

I
I/V converter 47
IP address 20, 22, 23

L
login credentials 28, 30

Quantum Transport Measurement System

Index • 69

SPECS Surface Nano Analysis GmbH
Voltastrasse 5
13355 Berlin
Germany
Tel. : +49 30 46 78 24-0
Fax :
+49 30 46 42 083
Email : support@specs.com
Web : www.specs.com

Quantum Transport Measurement System

Index • 70

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