System Installation

• 1: Installing Open VnmrJ (Bridge12 Version)
• 1.1: Installing OVJ-B12
• 2: Setting Up the Hardware
• 2.1: Connecting the NMR Probe
• 2.2: Connecting an External Amplifier
• 2.3: External Trigger

1 - Installing Open VnmrJ (Bridge12 Version)

The following pages provide a step-by-step guide how to install the Bridge12 version of OVJ and getting the computer ready for your first NMR experiment.

System Requirements

The following computer hardware will be required:

This installation guide assumes that you are installing OVJ_B12 on a clean installation of Ubuntu 20.04 LTS. To install OVJ, please create an user account called vnmr1 during the installation process. This should be an account with administrator rights.

Once the Ubuntu installation is finished, please log in as this user.

1.1 - Installing OVJ-B12

Bridge12 does not offer a pre-compiled version of OVJ-B12. Instead, the package has to be build on the computer that is used to operate the spectrometer. However, the installation process is streamlined and does not require any specific programming skills besides navigating through some terminal windows.

Preparing the System

1. Start by opening a terminal window and update all installed packages to the latest version:

   1 2	sudo apt-get update sudo apt upgrade

   The best way to install OVJ-B12 is by using the GitHub repository. Updates are pushed to the GitHub repository and can be installed by the user from there.

2. Install git and python3-pip

   1 2	sudo apt install python3-pip sudo apt install git

   To communicate with the NMR spectrometer and the Bridge12 MPS a serial connection to the periphery is required. OVJ-B12 uses Python and the pyserial Python package for this purpose, which can be installed through pip.

   1	sudo pip3 install pyserial==3.5

Cloning the Repository

3. To clone the GitHub repository, open a terminal window

   1	git clone git@github.com:Bridge12Technologies/OpenVnmrJ_B12T

   Once the repository is downloaded change into the directory …..

Building the OVJ-B12 Package

4. Build the package. As a first step in the installation, the OpenVnmrJ and ovjTools repositories will be automatically downloaded. The complete build processes takes about 10 minutes.

   1	sudo ./buildb12

   We recommend opening a new console tab in the terminal window to monitor the build process. To do this copy and paste the command (tail -f) with the corresponding file shown in the console after starting the build process into the new console tab of the terminal window.

   

5. Once the build is finished check the build process with

   1

   ./whatsin

   The output should report 0 Errors and 0 Build Terminations for a successful build.

   

   If the build succeeded the folder ~/ovjbuild/dvdimageB12 is created.

Install OVJ-B12

6. To install OVJ-B12 change to the dvdimageB12 directory and execute ./load.nmr

   1 2	cd ~/ovjbuild/dvdimageB12 ./load.nmr

   A popup window will appear, press install to continue with the installation.

   

7. When asked to update users start the vnmrjAdmin program located on the Desktop. The program should start automatically. In vnmrjAdmin go to Configure -> Users -> Update users …

   

   and add all users (vnmr1, service and walkup if they were created) to the right side. Then press “update users”

   

   Once all users are updated, the bottom status line in OpenVnmrJAdmin will show “Update User Completed All Requested Users”. Once you see this message, close OpenVnmrJAdmin.

8. After this, the system will open a new terminal window and the user has to answer a few questions. Please answer both questions with y(yes).

   1 2	Standard configurations include the walkup and service accounts. Would you like to make them now? (y/n)

   1 2	Shall this system be configured as a spectrometer (see image below). Would you like to configure it now? (y/n)

   

9. Installing NMRPipe is optional and can be answered with n(no).

10. We recommend to install the OVJ manuals. When asked to install the manuals please answer the question with y(yes).

    

Finish Installation

11. Once the load.nmr script has finished the upgrade.nmr script should be executed

    1	./upgrade.nmr

12. The installation scripts places two icons to the Desktop: vnmrj and vnmrjAdmin. vnmrj can either be launched by double-clicking on the desktop icon or from the command line:

    1

    vnmrj

    It is convenient to add Open VnmrJ to the quicklaunch menu. This can be done by by searching for “openvnmr” and then dragging the program icon to the quicklaunch bar.

    

OVJ-B12 is now installed and ready for its first experiment.

2 - Setting Up the Hardware

System Description

Front Panel Connectors

The NMR probe is connected to the Bridge12 SCN using the SMA connector located on the front panel of the system.

Back Panel Connectors

Most connections for the Bridge12 SCN are located on the back panel.

Fuse

A fuse holder is located on the back panel of the SCN. If necessary, the user can replace the fuse. The dimensions are 5x20mm and the fuse should have a rating of 1.25A.

Placing the System

• Place the Bridge12 SCN close to the EPR spectrometer. It is recommended to keep the length of the cable connecting the probe to the system at a minimum length.
• The system should rest on a stable surface.

TRIG/STAT Channel Explanations

• 1 - 10 MHz Reference:
  • The 10 MHz reference is the master oscillator output
• 4 - Hardware Trigger:
  • When this is pulled to GND an acquisition resumes or starts
• 5 - Hardware Reset:
  • When this is pulled to GND the pulse program is reset - as long as this is low no pulses are generated and sent out
• 6/7/8/9 - Ground

Connecting the System

Electrical Connections

To power the SCN connect the external power supply to the PWR connection. then connect the USB-C port to a PC. Connect the input of a bandpass filter corresponding to your NMR frequency to the ‘FILT OUT’ connector and the output of the bandpass filter to the ‘FILT IN’ connector. Connect a \(\lambda\)/4 filter (e.g. a cable with the correct length) for your NMR frequency to the \(\lambda\)/4 connectors.

Connecting the NMR Probe Circuit

Changing the RF Filters

Not sure if we need this right now.

2.1 - Connecting the NMR Probe

The connector to connect the NMR probe to the Bridge12 SCN spectrometer is located on the front panel. The input impedance is 50 Ω.

If your probe has a BNC connector please use a SMA-BNC Adpater and a BNC cable to connect the probe.

2.2 - Connecting an External Amplifier

The Bridge12 SCN has an internal RF power delivering up to 2 W output power. For many (low frequency) experiments this power is sufficient.

If the available power from the internal amplifier is not sufficient, an external high-power RF amplifier can be connected to the system.

To connect an external amplifier the input of the external device must be connected to the AMP OUT connection on the back panel of the SCN. The output of the external amplifier must be connected to the AMP IN connection located on the back panel.

To blank the external amplifier, connect the blanking gate to the AMP BLNK output of the SCN. The blanking gate is active low.

Specifying the Amplifier pre-Blanking Time rof1

To use an external amplifier with blanking, the amplifier needs to be unblanked before sending the RF pulse. Amplifiers typically require a short time unblank. This time can be specified using the OVJ parameter rof1. The value is typically given by the manufacturer in the data sheet of the amplifier.

The value can be set from the OVJ command line:

1

rof1=1000

If the required value is larger than the default value, for rof1 can be changed using the setlimit command as shown below.

1

setlimit('rof1',MAX_VALUE,MIN_VALUE,STEP)

Enabling the External Amplifier and Setting the Drive Level

OVJ needs to be connected to use the external amplifier. This is done from the OVJ command line:

1

B12SCNControl('extamp 1')

The B12SCNControl('state?) command can be used to query the state of the amplifier. If the system returns “extamp” the external amplifier is enabled.

1

B12SCNControl('state?')

The drive level (input power) of the external amplifier can be set using the OVJ command line by specifying the value stored by tpwrf.

1

tpwrf=1

To disable the internal amplifier from the OVJ command line enter this command:

1
2

B12SCNControl('extamp 0')
B12SCNControl('state?')

If the command B12SCNControl('state?) returns “intamp”, the internal amplifier is used. The tpwrf value is automatically set to 100 (the maximum).

2.3 - External Trigger

The acquisition of an NMR spectrum by the Bridge12 SCN system can be triggered using an external trigger. The external trigger is connected to the TRIG/STAT connector located on the back panel. The pinout for the connector is given in the section describing the Back Panel Connectors.

The trigger is active low on the falling edge. This means, pulling pin 7 on the TRIG/STAT connector to GND will start the acquisition of an NMR spectrum. By default every acquisition needs to be triggered. If you require a different behavior (e.g. trigger 4 acquisitions to complete a phase cycle) the pulse program need to be changed accordingly. For further information please contact Bridge12 at support@bridge12.com.

The system also has a hardware reset, accessible through pin 9 on the TRIG/STAT back panel connector. When this pin is pulled to GND, the pulse program will reset. As long as the hardware reset of the SCN (pin 9) is pulled to GND no RF pulses are generated and send to the amplifier. Acquisition of an NMR spectrum is not possible.

Enabling the External Trigger

The external trigger needs to be enabled in OVJ for the user to be used. This is done either:

1. from the OVJ command line:

   1	B12HWTriggerFlag=1

2. by setting the value in the Enable HW Trigger (in the Acquisition tab) to 1

3. or by activating the HW Trigger checkbox in the 1H tab

Disabling the External Trigger

To disable the external trigger use the command

1

B12HWTriggerFlag=0

or set the value in the Enable HW Trigger box to 0 (Acquisition tab) or disable the checkbox in the Default 1H tab.