Katy Wood 2008-08-29 16:47 Your local contact will train you in how to enter the enclosure and load samples. Before you do this independently you must sign the training form to acknowledge you have received the training. The following describes how to run the acquisition software. Login and password will be given to you by your local contact 1.2. Start gumtree Currently version 1.5.7, link on desktop Login and password will be given to you by your local contact. Normally gumtree would already be running. Caution – opening gumtree takes approximately 15 seconds Below describes starting an experiment with the 20 position sample changer at ambient temperature.

Click to start workflow

Fill in first four boxes with appropriate details. Ignore next three for now, then click

allows you to move the sample changer in the enclosure to a position where you can easily load your samples. Once in this position insert your sample blocks into the changer.

Tick the boxes corresponding to where you have put samples, and enter sample name, thickness and description. In the column Type the pull-down menu allows you to select either SAMPLE or EMPTY_BEAM. It’s best to treat your empty cell measurement as a SAMPLE. Making sure you have made the right selection simplifies data processing. Positions 19 and 20 on the sample changer are generally left with the SAMPLE (empty cell) and EMPTY_BEAM respectively. allows you to save a file with all sample names, thickness etc.. in the different positions. This can then be re-loaded at a later stage if you will be using similar sample names with The ‘Clear All’ and ‘Fill from Sample 1’ buttons are self-explanatory… Clicking brings up the following screen, where you can select your configurations:

Clicking under Configurations brings up the following:

Select the configuration then Your local contact will discuss suitable instrument configurations with you prior to commencing the experiment.

Several configurations can be selected in this way. deletes any you have added by mistake. Do not modify any configurations, only your local contact should do this. In the Transmission and Scattering boxes you enter the time the samples will be measured for. (If you would like to measure different samples for different amounts of time, you can change these values for individual samples later – only for the ‘scattering’ runs, not the transmissions). If you chose the Timer mode, enter the time you choose in seconds. In Counter mode, it will count to monitor and you should enter a monitor count rate. A table is given on the right of the computer with monitor counts, seconds etc… Enter counting times in all the different configurations. Once you are happy with configurations and counting times, brings up the following:

‘Normal’ environment is left selected if running with the 20 position sample changer at ambient temperatures. Click

A table now appears with your samples and configurations. (Scroll across to see all). If you do not with to measure all samples at all configurations, you can uncheck the appropriate boxes. If you wish to do absolute normalisation, always leave a transmission measurement of the empty beam as we use this. At this point the ‘preset’ column can be modified if you wish to count for different times. You do not need to measure the scattering from the empty camera (position 20) unless you are using this as a background (i.e. not using cuvette, solvent etc.). Underneath the table an estimated experimental time is given. If you change individual run times ‘Update’ will update this. If the runtime looks very long, you’ve probably made an error and selected to count to monitor counts but accidentally left the option selected as ‘time’. Click then starts the run you have setup. If you have not opened the shutter, you will see a prompt ‘shutter not open’. Check it’s open and then click to start your run! As per Section 1.3 except Instead of selecting 'Normal Environment, select ‘Controlled Environment’. Using the “Controlled Environment” option, you may then select a list of sample environment controllers for your experiment. Select dummy_motor if you would like to run the same series of samples multiple times.

In the example above, 3 steps will be generated on clicking on the ‘generate’ button, and the table will be updated as follows:

It is then possible to run the samples and configurations selected previously three times with a 2 second wait between each. Select /sample/tc1/setpoint to use temperature control (needs to be correctly set up first by your local contact).

To enter the preset values for the controller, type the numbers into the text boxes and press “Generate”. In the example above, the samples will be measured at 5 different temperatures, between 1 to 10 degrees. Insert a small wait in seconds at the beginning of each step. You may modify the preset values from the table if you do not wish to use the fixed step presets generated by GumTree. The multi sample workflow can support multiple sample environment controllers in an experiment. Press button under the controller to add more. Each additional controller simply adds a one more nested loop to your experiment sequence. As data is saved the run numbers appear in the table. It’s then particularly useful to save this table with . This button exports the table as a jpeg file, which can then be printed. Note that you only export what is visible on the screen. (If you wish to save all configurations you will have to scroll to the right). At the end of a multi sample workflow, a ‘report’ file is created. This file contains all the associations for the different configurations (which run numbers are scattering files, which are transmissions, empty beam etc…), and simplifies data reduction. If you’d like to treat your data before the end, you can create a report file by hitting . If you want to stop a multi-sample workflow early for some reason, make sure you first, as this is not done automatically. Data files are written and updated every minute in the directory in /experiments/quokka/data/current. This directory is read only. Report files are in /experiments/quokka/data/current/reports A read/write copy of the data is also copied to the directory named after the proposal number: /experiments/quokka/data/proposal/xxx. This data can be patched etc… and used to do data reduction (see section 3). It is updated approximately every 4 minutes. At the end of the cycle the read only copy of the data and report files will be moved into a directory named after the cycle number, eg. /experiments/quokka/data/cycle/030 Links to these directories can be found on the desktop. As the workflow moves through your run, messages will be displayed at the bottom in the ‘console’ indicating progress. Any errors will appear in red. Approximate counts/rates on ‘standard’ samples. A table is given in the log book with approximate count rates for some standard configurations measured on H2O, D2O samples. You should have similar values. Instrument dashboard: The dashboard displays a 2D image of the detector, most instrument settings and parameters such as L1 and L2. Do not modify anything from this dashboard. I have started a workflow, but would like to stop it. Click on the any of the ‘Interrupt buttons’. A report file will be saved. Multisample work flow will then go into ‘cleanup mode’, ie will drive the attenuation to a high value, protecting the detector from any possible over-exposure. By using , you can then modify the run and restart. I have started a workflow, but would like to pause it. The workflow can be paused if the acquisition is running in the monitor mode. You can press on the same button to resume from a paused acquisition. It is possible to look at data during collection, before the file is complete. Following the procedure below allows you to open the file and inspect the radial average, which will automatically be updated approximately every minute. Open “Igor with Quokka macros”, and in the macros menu select ‘Load Quokka Sans Reduction Macros’. Following yellow panel appears. Click on ‘Pick Path’ and navigate to /experiments/quokka/data/proposal/xxx In the ‘Reduction’ tab ‘Build protocol’. The following appears: Uncheck all except Sample and Average and ‘Save protocol’. Choose a name eg ‘on_line’. Note that it is not possible to put data on an absolute scale on the fly, as the transmission has not yet been calculated, you can however add in the other steps of the data reduction protocol if required. Select ‘Online Reduction’ on the ‘Raw Data’ tab The following appears: Select the file file you would like in top drop down menu. In the second window click ‘…’, The following appears: Select the protocol you have just built in the drop down menu, eg ‘on_line’ and ‘continue’. Then click ‘start’ on the pink ‘Online Reduction panel’. The radial average data will then be displayed and automatically updated. Before you leave the instrument, please: Clean and return your sample holders. Instructions in the ‘instructions’ section of the manual in the cabin. We will not lend sample holders to users who have a history of not returning them clean. Photocopy/scan the relevant pages of the logbook Take all raw and treated data either using a thumb drive, by burning the data to a CD/DVD (ask your local contact nicely) or using ANSTO sharefile (web-based system) at sharefile.ansto.gov.au.