ISIS Neutron Training Course - Soft Matter
SANS Practical Sessions Introduction In addition to the taught part of this course, you will do some practical sessions. One of these, called Neutron Interactions, will deal with some of the more fundamental aspects of the interaction between neutrons and matter and is detailed elsewhere. This document relates to the sessions LOQ Sample Changer Experiment and SANS Data Analysis Practicals. The purpose of these two sessions is three‐fold:  to show you how to conduct a SANS experiment at ISIS (including making the samples),  to demonstrate how SANS may be used to elucidate and follow changes in size and shape brought about by a chemical or physical stimulus, and  to introduce you to some different methods of SANS data analysis and interpretation using various pieces of software. You will look at selected data from surfactants, polymers and proteins. But these examples are illustrative, so if the systems we have selected are not in your particular field of interest, it doesn’t matter. The important point is that the techniques and principles you will learn are extendable to almost any area of science that can be investigated by SANS. Safety None of the compounds that you might use in these sessions are unduly harmful – most are found in everyday preparations such as shampoos, shower gels and toothpaste – but always exercise good laboratory practice when handling them. Use the protective clothing, gloves and other equipment that can be found in the Chemistry Laboratory. Contents Background Experiment 1 : AOT microemulsions Sample Preparation Experiment 2 : SDS micelles Sample Preparation LOQ Sample Set‐Up Writing a Script File and Making the Calibration and Sample Measurement Writing a Mask File Results Tables Appendix 1 ‐ Writing a Script File Appendix 2 ‐ Running MANTID Appendix 3 ‐ A Sample Mask File 1
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Background Surfactants (the name is a contraction of “surface‐active agent”) are molecules that are amphiphilic in nature; a single surfactant molecule comprises of both a lyophilic (solvent‐loving) and a lyophobic (solvent‐hating) part. Commonly, the lyophilic (or hydrophilic when the solvent used is water as in this practical) group is called the head‐group and the lyophobic/hydrophobic section called the tail‐group. Examples include soaps, detergents and many copolymers. This amphiphilic nature of surfactant molecules results in some rather unusual solution physical chemistry: ‘Tail-group’ - lyophobic
Osm o tic press ure
‘Head-group’ - lyophilic
M ag nit ud e of p ro p erty
Tu rb idity
S olu biliza ti o n
Ma gn etic
re s on an ce
Su rfa ce ten s ion
air
Equ i va len t
con du ctivity
Self- diffus i on
water
CMC
Co nc e n tration o f s urfac tan t
As you can see there is an abrupt transition in a number of different colligative properties at the point identified as the critical micellisation concentration (cmc). Below the cmc, only individual surfactant molecules exist in solution. Above the cmc individual molecules and self‐assembled surfactant micelles coexist. Each micelle may contain from a few tens to several hundreds of surfactant molecules. The self‐assembly process that results in micelle formation is moderated by a delicate interaction between four main contributions to the free energy of the system: a) that arising from the interactions between surfactant tails and solvent molecules, b) that arising from the interactions between the surfactant tails of different molecules, c) that arising from the interactions of surfactant head groups with the solvent molecules, and d) that arising from interactions between the head‐groups of different surfactant molecules. These interactions may, or may not, be mediated by the presence of an electrolyte. Anything that affects one or more of these contributions will affect the micellisation process. This can lead to a rich variety of micellar phase behaviour. Although many surfactant systems exhibit spherical micellar geometries, discs, ellipses, rods and lamellae are not uncommon. 2
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Experiment 1: AOT microemulsions In this experiment you will be examining the microemulsions formed from a surfactant‐water‐oil mixture. In contrast to ordinary emulsions, which require high shear to disperse the droplets, microemulsions are formed upon simple mixing of the components resulting in thermodynamically‐stable complex fluids composed of water and oil domains that are separated by a surfactant monolayer. The microemulsions can be either direct (oil dispersed in water) and reversed (water dispersed in oil), depending on, for example, the composition or temperature. One of the main strengths of using neutron scattering to study colloid and polymer systems is the ability to introduce contrast through selective deuteration of individual components. However, there are limitations (primarily availability and cost) on the use of deuterated materials which must be considered when choosing various contrasts. In the experiment proposed here, selective deuteration, as shown in the table below, will be used to highlight the different components in a core‐shell‐droplet microemulsion consisting of AOT, water, and cyclohexane in the region of the phase diagram where surfactant covered water droplets are formed. Available scattering contrasts Water Surfactant Oil Core D H H Shell D H D Drop H H D Using SANS we will determine the shape, size and polydispersity of the droplets and the thickness of their surfactant shell. The scattering data for the different contrasts are analyzed using a molecular constrained model for ellipsoidal droplets of water covered by AOT, interacting as polydisperse hard spheres. All contrasts are fitted simultaneously by taking the different contrast factors into account. The Sample You will be using the anionic surfactant AOT (Sodium 1,4‐bis(2‐ethylhexoxy)‐1,4‐dioxobutane‐2‐sulfonate, also known as Aerosol OT, sodium dioctyl sulfosuccinate, sodium di‐2‐ethylhexyl sulfosuccinate, docusate sodium) Notice that the outstanding charge on the sulfate group is balanced by a hydrated sodium counter‐ion, i.e. it is an anionic surfactant. Useful Formulae 1 M (molar) solution = (molecular weight) g of solute in 1000 ml of solvent volume = mass / density For water‐in‐oil microemulsions: w = [water]/[surfactant] 3
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Molecular weight (gmol‐1) Density (gcm‐3) AOT 444.56 H2O 18 D2O 20 h‐cyclohexane 0.779 d‐cyclohexane 0.89 Sample Preparation You will need to make up a 0.1M solution of AOT in cyclohexane and to this add sufficient water to surfactant to give a w‐ratio of 15 (mol water/mol AOT). It is best to use a balance with at least 3 decimal places. If you require any help, please ask. 1. First calculate the masses required to make two 2 ml solutions of 0.1M AOT, one in h‐cyclohexane and the other in d‐cyclohexane. g Mass of AOT required Mass of h‐cyclohexane required Mass of d‐cyclohexane required 2. Now calculate the mass of water and D2O to give a w‐ratio of 15 (w‐ratio = mol water/mol AOT). g Mass of H2O Mass of D2O 3. Based on the above calculations you will need to make up 3 solutions with the correct contrast. It is best to add the AOT to the cyclohexane first and allow it to dissolve. You may want to add the water or D2O using a syringe. The resulting solutions should be clear. Solution 1: Solution 2: Solution 3: Core contrast Shell contrast Drop contrast Mass of AOT Mass of d‐cyclohexane Mass of H2O Mass of h‐cyclohexane Mass of D2O 4. Once your solutions are prepared, you will need to pipette some of solution 1 into a 1 mm pathlength single‐
stoppered quartz cuvettes, solutions 2 and 3 should be loaded into the 2 mm pathlength single‐stoppered quartz cuvettes. You will only need to fill each cuvette up to the bottom of the unpolished top part. Seal the cuvette with a PTFE stopper and some PTFE tape (or parafilm) (just around the top). The cuvette should be labelled either on the PTFE stopper or with pencil on the edge of the cuvette. 4
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Experiment 2: SDS micelles The Sample In this experiment you will be working with the surfactant SDS (sodium dodecyl sulfate, also known as sodium lauryl sulfate). This has a straight‐chain C12 alkyl tail coupled to a sulfate head‐group: +
Na O
-
O
CH3
S
O
O
Notice that the outstanding charge on the sulfate group is balanced by a hydrated sodium counter‐ion. SDS is an example of an anionic surfactant (the charge on the molecule in the absence of the counter ion is negative). The cmc of SDS in water at room temperature is 8∙3 mM (milli‐molar). The formula weight of SDS is 288∙4 g. The density of D2O is 1∙1 g/ml. The density of H2O is 0.997 g/ml. The formula weight of salt (NaCl) is 58∙5 g. % w/w cmc of SDS in H2O cmc of SDS in D2O Sample Preparation Please note that most samples are to be made up in D2O but one is to be made in H2O. Prepare two 5 ml of a 2 % w/w stock solution of SDS, one in H2O and one in D2O. Solution (a) in H2O Solution (b) in D2O Mass of SDS (in grams to 4d.p.) When the SDS has fully dissolved, pipette some of the solution (a) into a 1mm pathlength and some of solution (b) into a 2 mm pathlength single‐stoppered quartz cuvette. You need only fill the cuvette up to the bottom of the unpolished top part. Prepare 4 ml of a 0∙5 % w/w solution of SDS in D2O from the stock solution. Dilute some of the remaining stock solution with pure D2O to reduce the concentration from 2% to 0∙5 % w/w. ml Volume of D2O Volume of 2% stock solution of SDS Pipette this solution into a 5 mm pathlength single‐stoppered quartz cuvette. Prepare approximately 2 ml of a solution 2 % w/w SDS + 0∙2 M salt (NaCl) in D2O from the stock solution by simply adding an appropriate mass of salt crystals to 2 ml of the stock solution. g Mass of NaCl 5
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When the salt has fully dissolved, pipette some of the solution into a 2 mm pathlength single‐stoppered quartz cuvette. Prepare three background samples. Fill both a 2 mm pathlength and a 5 mm pathlength double‐stoppered quartz cuvette with pure D2O and a 1 mm pathlength double‐stoppered quartz cuvette with pure H2O. What Should the Scattering Look Like and Why? You should find that the scattering from the 2 % SDS sample (i.e. above the cmc) displays a prominent peak with a hint of a bump (the 2nd order contribution) on the high‐Q side. This arises out of the S(Q) contribution to the scattering resulting from the electrostatic interactions between the head‐groups at the surface of neighbouring micelles. This peak should be considerably weaker and much broader in the 0.5 % SDS sample because there are fewer micelles and they are farther apart, so the strength of the interactions are reduced. The shape of the peak in the 2 % SDS sample with added salt should resemble the one in the dilute system because the electrolyte “screens” the charges on the micelles, though it will be more intense because of the higher concentration. For 2 % in H2O sample then you should see very little (if any!) scattering as the neutron contrast in the system will be minimal (H‐
surfactant and H‐solvent). 6
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LOQ Sample Set‐Up 




Place standards, samples and an empty cuvette (as the can) in the appropriate rack at the LOQ sample position (making a note of which sample is in which position) Make sure samples are aligned Check that the beam is collimated to 8 mm diameter Lock up LOQ and open the shutter The samples should be run at 25 °C, so ensure that the rack temperature is set appropriately Writing a Script File and Making the Calibration and Sample Measurement 


Program a Script file to measure the standards first and then the samples (see Appendix 1) Begin the Script file (see Appendix 1) Once the standards have run and the samples are running you can write the mask file Writing a Mask File The mask file is a computer command file consisting of instructions that establish the default conditions for the reduction of the raw time‐of‐flight data into SANS Cross‐section versus Scattering Vector data. An example of a mask file can be found in Appendix 3. Data reduction is a necessary step before any data analysis can take place. The mask file is created using the calibration sample data that you have just collected and a program called Mantid. Please refer to Appendix 2 for help using Mantid. To make a mask file it is necessary to:  Determine the beam centre coordinates.  Determine the intensity scaling factor. 7
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Results Table: Standards and direct beam Pathlength (mm) Sample Temperature
(C) SANS
Run # Duration (μAhrs) TRAN Run # Duration
(μAhrs) 8 mm Diameter Beam – Standard and direct beam Calibration Sample (Polymer Blend) Calibration Background (Empty can) Direct Beam 1.035 25 1.035 25 25 n/a Results Table: Experiment 1 Sample Pathlength (mm) Temperature
(C) SANS
Run # Duration (μAhrs) TRAN Run # Duration
(μAhrs) H‐cyclohexane 1.0 25 D‐cyclohexane 2.0 25 Solution 1: Core Contrast 1.0 25 Solution 2: Shell Contrast 2.0 25 Solution 3: Drop Contrast 2.0 25 Results Table: Experiment 2 Sample Pathlength (mm) Temperature
(C) SANS
Run # Duration (μAhrs) TRAN Run # Duration
(μAhrs) D2O 2.0 25 D2O 5.0 25 H2O 1.0 25 0.5 % SDS in D2O 5.0 25 2.0 % SDS in D2O 2.0 25 2.0 % SDS + 0.2M NaCl in D2O 2.0 25 2.0 % SDS in H2O 1.0 25 8
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Appendix 1 ‐ Writing A Script File What are Script Files? Scripts are computer command files that BEGIN runs, wait for a specified time period or number of incident neutrons or microamp‐hours of protons, and then END runs automatically. They are a particularly efficient method of controlling the sample changer on LOQ, although it is possible to write variants for other tasks (such as temperature scanning a single sample, for example). This description assumes that you are using the sample changer. Creating a script file involves writing a short computer program in a language called GCL (Genie Command Language). Although GCL is a fairly straightforward language to learn, to save time we have provided a ‘script generator’. This generator can be used to create a simple script which can be edited as required. The extension for all scripts is .gcl The Script Generator From one of the two PCs in the LOQ cabin (though not the one used to control the instrument) double click on the ‘LOQ_script’ icon which is found on the desktop. This should open up an application which should look very similar to the picture below: Allows you to open or create a new
spreadsheet (as shown to the right)
Allows you to choose if you do all
TRANS or SANS runs f irst or if you
alternate between the two
Def ines aperture 2 as large or medium:
DO_SANS / LARGE or
DO_SANS / MEDIUM
Allows you to preview or
save the script
9
Def ines size and shape of aperture
3 (the f inal aperture)
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Position of sample in changer
Length of TRANS/SANS run
Qualif ier f or length of TRANS/SANS run: can be
minutes, seconds, f rames or microamp-hours
Allows you to alter the number
of SANS and TRANS runs
Neutron pathlength through the sample
(normally sample thickness) in mm
Sample title
Temperature
changed here:
CSET TEMP=20
LOQ waits f or 300 s bef ore moving
onto the next line of a script
Press the ‘Create New Table’ button and edit the spreadsheet provided in this application as required to generate your script (as shown above). Once completed you can preview your script (Preview Script button) and save it (Write Script button) so it can be loaded and run on the instrument PC. Please do not include spaces in your script names as they will not load onto the PC. Editing a Script File If you need to edit a script you have generated then this can be done using a program such as Notepad++. This program can be downloaded from the internet and is available on all LOQ PCs. An example script (as seen in Notepad++) is shown below: 10
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Current number of times TRANS and
SANS sections have been run
Sets script name on LOQ
dashboard
Defines how many times the TRANS and
SANS sections of the script will be run
Def ines aperture 3 (the f inal aperture)
Sets LOQ to transmission mode
If this condition is met then LOQ will run the
f ollowing tranmissions
Sets sample temperature to
25/20 C
Adds 1 to the transCount
variable
Once the ‘IF’ condition above it met the script will move
onto the DO_SANS /LARGE line
Sets LOQ to SANS mode with a
large aperture 2
LOQ waits f or 300 s bef ore
moving onto the next line
Moves the sample changer to position A, changes
the thickness to 2 mm, waits f or 50 Ahrs and
changes the sample title to Sample 1_SANS
Adds 1 to the sansCount
variable
If this condition is met then the script exits the loop
Once the script is completed then “SCRIPT
COMPLETED” is printed in the OpenGenie window
The MOVE command is followed by 5 parameters. These parameters must be separated from one another, and from the MOVE command, by a space, and must be specified in the order shown. The parameters are: pos ‐ the sample changer position. This must be given as the code displayed on the sample rack (eg, “A”, “B”, etc). If an absolute distance in mm is required then the command CSET SAMPLE=#.# (#.#=position in mm) must be written before the ‘MOVE’ line (where CSET TEMP is in the example above) and then the position function set to not move using pos=”NONE” thick ‐ the neutron pathlength through the sample in mm. This will normally be the same as the sample thickness time ‐ the run length (as an integer value). This may be given as minutes (though this is only programmed for 1<minutes<60, i.e. 59 minutes is the maximum run time in this mode), frames (NB: if you use mins/frames the run will progress even if the beam is down!) or microamp‐hours (A‐hrs). A‐hrs are the product of the ISIS proton current and time (in hours). Thus, if the accelerator is operating at 200 A, and LOQ is at 25 Hz, there will be 100 A‐hours to the hour. In the script, minutes is written as min, frames as frame and microamp‐hours as uAhr title ‐ the title for the run. This will be displayed both on the LOQ dashboard status display and written into the raw data file Notice that the transmission runs are much shorter than the scattering runs. This is normal. As a general rule of thumb, transmission measurements only need to run for 5 ‐ 10 minutes (or 7 – 15 AHours); though the actual length of time will of course depend on the nature of the particular sample. Also note that the DO_SANS /LARGE command is placed above the ‘IF’ statement This is not critical, but there is no point in making the computer set 11
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LOQ up for scattering measurements when it is already in the correct configuration ‐ you would just be wasting valuable measuring time! NB: if you want a line to be ignored in a script then precede the line with a ‘#’. For example: # MOVE pos=”B” thick=1.0 uAhr=50 title=”Sample 2_SANS” Starting a Script File LOQ is run from the instrument PC using SECI (Sample Environment Control Interface). The SECI window should look something like: User details: important as
def ines ownership of data
Current run title
Current run number
Shows status of LOQ
Values (such as temperature,
shutter position) monitored by
LOQ
Shows conf iguration of LOQ
This panel allows the control
panels f or dif ferent aspects of the
instrument operation to be
viewed
An OpenGenie window can be
opened using this tab
Number of spectra: typically
should be 17792 when in SANS
mode and 8 in TRANS mode
Current LOQ/ISIS current
An OpenGenie window
Firstly, your script must be loaded. To do this gain input focus in the OpenGenie window on the control PC and type: >> setscriptdir “t:\\” You only have to type this line once (unless OpenGenie has closed or you need to change directory). All LOQ scripts should be saved to t:\\ ‐ this is set as default from all script generators. Then type: >> loadscript “scriptname.gcl” If the script has been accepted i.e. no errors contained in it, then the OpenGenie window should look as below: 12
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If errors are contained then red text will also appear informing you what the error is. If this occurs the script will need modifying appropriately and reloading before carrying on with the next step. Once a script as been accepted without error then you can start the script running by typing (once again in the OpenGenie window): >> scriptname You’re script should now start to run. Note you do not type the extension .gcl Interrupting and Restarting Script Files When you start a script file, the latest version is loaded into the computers memory. This means that you can generate a new version of the script file and save it whilst the old version is running, without affecting the operation of the instrument. To stop, or interrupt, the script that is running, highlight the OpenGenie window and type: {Ctrl}‐C The computer will beep and you should regain the prompt (this symbol >>) in the OpenGenie window. There will also be a warning in the OpenGenie window informing you that if a run was in progress when you interrupted the script this run will continue (even if the script has been stopped). You should terminate this run manually by typing END or ABORT followed by {Return} (NB: END will stop the run and save the data and ABORT will stop the run and NOT save the data). But what if you want to re‐start a slightly modified script file without stopping the run in progress? To do this it is necessary to edit your script (do this before you interrupt your running script) using # as described earlier to comment out unwanted lines and ensure that the first executable MOVE line that the computer encounters in the revised script file is the one for the run in progress. You can even change the length, title, pathlength and delay type but don’t under any circumstances change the sample changer position code! The use of # will vary depending on the circumstance of the script interruption. In all cases the logic of the script (for example IF statements) must be correct. For example, suppose that the original script file above was interrupted after all the transmission runs had been completed and that LOQ had been allowed to change to SANS mode and temperature changed to 25 °C. The changer has moved to position A but you need to shorten the run times down to 30Ahrs. Firstly, you would type {Ctrl}‐C in the OpenGenie window and allow the LOQ to keep running (don’t type END or ABORT). Then you would load you new script which as shown below (the script names have not been changed): 13
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As script name has remained the
same there is no need to set it
again
Note that the numTRANS has now been
set to 0 (previously 1) so that the f inal
condition (the EXITIF statement) is met
Final aperture has not changed
and so this line can be ignored
Transmission section of f ile has
been completed and so can be
ignored
LOQ is already in SANS mode
Temperature does not required
setting again
Finally, this script can now be started. Please note, only interrupt a script when LOQ is actually collecting data as in the example above (i.e. when the status at the top of the SECI display shows “LOQ in RUNNING”). Otherwise you may actually interrupt the script whilst it is doing something vital to the operation of the instrument, like moving motors, writing data, etc and this can lead to a loss of time and data (as the instrument may be ‘lost’ and need re‐aligning). 14
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Appendix 2 ‐ Running Mantid Running The Program The program you shall be using is called Mantid. There should be an icon on the desktop of the PCs in the LOQ cabin. After opening the program, you will need to select Interfaces and then SANS (ISIS). You should now see a screen as shown below displaying the SANS gui. Mask file path & name
Reduce a single or a batch set of data
Make sure directories for data & mask files are listed. The program will search the directories in the order listed
In this set of boxes, enter run numbers for SANS, TRANS & direct beam
Specify filename for outputting 1D reduced data in the selected format: RKH – 3 column ascii, CanSAS – xml
Click Load Data once run numbers have been entered
Once data has been loaded you will be able to click 1D Reduce (& Plot Result)
You must click here to save 1D reduced data
You should check that the relevant directories containing the raw data and a mask file for LOQ are listed under the Manage Directories button. Data is typically stored in a subdirectory of J, the name depending on the cycle number (e.g. the training course is being run during cycle 2011/1). You must also specify the mask directory K:/masks/. 15
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Now specify a suitable mask file and click Reload. (This needs to be done even if one is listed as the User file). Until you have created a mask file, you should use the most recent one from K:/masks/. They are named such that the name identifies it as a mask file for LOQ for Mantid, the first part of the extension tells you the cycle run, e.g. 103 for cycle 2010, run 3, and the letter identifies their sequence of creation. You are now ready to load the data into Mantid. Fill in the relevant run numbers for the TK49 standard and empty can into the GUI, e.g.: Once the run numbers have been entered, you should click on Load Data. After at least one data set has been loaded into Mantid, the tabs for Analysis Details, Geometry and Masking will become accessible. The Analysis Details should look like this: Radial limits on the detector, outside of which data is ignored
Wavelength range to use for data reduction
The range, step size and binning of the Q range for 1D (Qx) or 2D (Qxy) data reduction
Wavelength range over which the transmission is either fitted directly (Linear) or the logarithm of the Y values are fitted (Log). If not selected, defaults to the wavelength for the data reduction
The values shown above are typical for data reduction on LOQ. However, you may have to alter at least the step size and binning depending on your data. Linear binning means that the data points are spread evenly over the specified Q‐range, the number of data points depending on the step size specified. Logarithmic bins are spaced evenly in a geometric series; 0.05 means 5% bins and ideally should match the instrumental resolution. 16
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In addition, you may need to determine the beam centre from the standard polymer SANS run. Once that data is loaded into Mantid, go to the Geometry tab. Beam centre Sample thickness, beam determined from height and width and Z‐
standard sample. These values should be offset of sample from nominal position, as picked up from the specified in your script and mask file
the instrument set‐up
Radial search limits for finding the beam centre. Typically these will be sufficient for LOQ
The automatic beam centre search simply requires running a number of iterations starting from the default position which is typically that previously defined. It is best to limit the Qx range to a maximum of about 0.15 Å‐1 and increase the width of the Q bins slightly and/or use Linear rather than Log bins to improve the data quality (under the Analysis Details tab). You may need to run around 20 iterations to reach convergence, however, it is probably best to check that the search works with fewer iterations first. Once the beam centre has been found, you should edit the mask file to have these coordinates (see Appendix 3). You should make sure that you save the edited mask file with the file extension you have been assigned for your experiment. The next step is to reduce the standard SANS data, using the correct transmissions and removing the scattering from the standard’s sample holder, called the ‘can’. Enter the necessary run numbers into the SANS gui (page 12). You can now click Plot Result and 1D Reduce. You will see all the relevant data sets being loaded into the Workspace tab, as well as a sequence of temporary files used in the data reduction. Finally a plot of the 1D reduced data should appear. If it does not, you may see an error message which should help you work out what has gone wrong (typically this might be a missing mask file, the run numbers being incorrect or the directory in which the data is stored not being specified). If you forgot to click on Plot Result, you can replot it by selecting the correct file in the Workspace tab, right mouse clicking on it and selecting Plot spectrum. The naming convention is such that it will start with the SANS run number followed ‘MAIN_1D and then by the wavelength limits for the data reduction separated by underscores as shown below: Raw data
Fitted transmissions for sample and can
Raw transmissions for sample and can
1D reduced data
17
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It is also possible to plot the 2D pattern by right mouse clicking on the raw SANS run number and selecting Show Instrument. If everything has worked and you have a 1D plot you are happy with, you can output it by entering a filename, selecting the necessary file output format and clicking on Save Result within the Save tab. Finally, before being able to reduce all your data following the same procedure as outlined above, you will need to fit the 1D data for the standard to determine the scaling factor for conversion of your data into absolute intensities. For this you will use a program called FISH as described in the handout for Data Analysis. 18
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Appendix 3 - A Sample Mask File
LOQ
Identifies instrument as LOQ
PRINT This is a LOQ user file for Mantid
MASK/CLEAR
Clear any spectrum (detector pixel) masks
MASK/CLEAR/TIME
Clear any time channel masks
L/WAV 2.2 10.0 .035/LOG
Establish the default  range & binning (Å)
L/R 35 419 3
Establish the radial limit for the detector (mm)
L/Q .009 .285 .002/lin
Establish the default Q range & binning for 1D data reductions (Å-1)
L/QXY 0 0.1 .002/lin
-1
Establish the default QX , QY range & binning for 2D data reductions (Å )
BACK/MON/TIMES 31000 39000
Remove the “prompt” spike in monitor time-of-flight spectra (s)
FIT/TRANS/YLOG 2.2 10.0
Interpolate transmissions from fits to the measured transmission data over specified 
MON/DIRECT=DIRECT.041
Location of main detector efficiency vs  correction file
MON/HAB=DIRECTHAB.983
Location of high angle detector efficiency vs  correction file
MON/FLAT=MANTID_FLAT_CELL.061B
Location of pixel-to-pixel efficiency correction file
PRINT XCORR **is** implemented if using Mantid 1.1.9556 or later &
LOQ_Definition.xml valid from 2002-02-26
PRINT YCORR **is** implemented if using Mantid 1.1.9556 or later &
LOQ_Definition.xml valid from 2002-02-26
MASK H126>H127
“Mask out” (i.e. ignore) the top two rows of the detector
PRINT no box masks implemented because corners are masked by default
MASK/T 19711.5 21228.5
Remove the “prompt” spike in main detector time-of-flight spectra (s)
MASK/T 39354.5 41348.5
Remove the “prompt” spike in main detector time-of-flight spectra (s)
PRINT masking out hab spectra 16641 & 17341 which get double counts
MASK S16641
“Mask out” a high angle detector spectrum (pixel) that gets double counts
MASK S17341
“Mask out” a high angle detector spectrum (pixel) that gets double counts
! set offset value = (-11.0 + Lsm) x 1000
SAMPLE/OFFSET -21.0
Establish the detector offset from the nominal sample detector distance (mm)
SET CENTRE 322.57 327.07 5.00 5.00
Establish the detector centre coordinates and pixel dimensions (mm)
SET SCALES 1.5739 1.179 1.233 1.244 1.216
Establish the absolute intensity scaling factors for all detectors/modules
PRINT MON/HABEFF correction not yet implemented
Establish the efficiency of the high angle detector at 1Å and at large angles
PRINT MON/HABPATH correction not yet implemented
Enable the previous correction
PRINT
Centre
&
scales
(COLETTE)
with
17/05/11,
62916.RAW,
11mm,
Identifies the date, name and calibration sample run associated with this mask file
Durham Rack, Bucknall
PRINT Loaded: MASK_MAN.111A, This is COLETTE MASK.111A for Mantid
19
02/03/13