SANS Practical Sessions - isis.stfc.ac.uk

ISIS Neutron Training Course - Soft Matter

1 02/03/13

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 Page 2

Experiment 1 : AOT microemulsions Page 3

Sample Preparation Page 4

Experiment 2 : SDS micelles Page 5

Sample Preparation Page 5

LOQ Sample Set‐Up Page 7

Writing a Script File and Making the Calibration and Sample Measurement Page 7

Writing a Mask File Page 7

Results Tables Page 8

Appendix 1 ‐ Writing a Script File Page 9

Appendix 2 ‐ Running MANTID Page 15

Appendix 3 ‐ A Sample Mask File Page 19


2 02/03/13

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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:

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.

‘Head-group’ - lyophilic

‘Tail-group’ - lyophobic

air

water


3 02/03/13

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]


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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:

Core contrast

Solution 2:

Shell contrast

Solution 3:

Drop contrast

Mass of AOT

Mass of h‐cyclohexane

Mass of d‐cyclohexane

Mass of H2O

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.


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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:

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

SO

OO

CH3

Na+O

-


6 02/03/13

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).


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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.


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Results Table: Standards and direct beam

Sample Pathlength

(mm)

Temperature

(C) SANS

Run #

Duration

(μAhrs)

TRAN

Run #

Duration

(μAhrs)

8 mm Diameter Beam – Standard and direct beam

Calibration Sample

(Polymer Blend) 1.035 25

Calibration Background

(Empty can) 1.035 25

Direct Beam 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


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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 preview or save the script

Allows you to open or create a new spreadsheet (as shown to the right)

Def ines aperture 2 as large or medium: DO_SANS / LARGE or DO_SANS / MEDIUM

Def ines size and shape of aperture 3 (the f inal aperture)

Allows you to choose if you do all TRANS or SANS runs f irst or if you

alternate between the two


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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:

Allows you to alter the number of SANS and TRANS runs

Temperature changed here:

CSET TEMP=20

Neutron pathlength through the sample (normally sample thickness) in mm

Sample title

Position of sample in changer Length of TRANS/SANS run

Qualif ier for length of TRANS/SANS run: can be minutes, seconds, f rames or microamp-hours

LOQ waits for 300 s before moving onto the next line of a script


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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

Defines how many times the TRANS and SANS sections of the script will be run

Def ines aperture 3 (the f inal aperture)

Current number of times TRANS and SANS sections have been run

Sets script name on LOQ dashboard

Sets LOQ to transmission mode

Sets sample temperature to 25/20 C

Sets LOQ to SANS mode with a large aperture 2

Adds 1 to the transCountvariable

If this condition is met then LOQ will run the following tranmissions

If this condition is met then the script exits the loop

Adds 1 to the sansCountvariable

Moves the sample changer to position A, changes the thickness to 2 mm, waits for 50 Ahrs and changes the sample title to Sample 1_SANS

Once the ‘IF’ condition above it met the script will move onto the DO_SANS /LARGE line

Once the script is completed then “SCRIPT COMPLETED” is printed in the OpenGenie window

LOQ waits for 300 s before moving onto the next line


12 02/03/13

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:

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:

An OpenGenie window

Current LOQ/ISIS current

Number of spectra: typically should be 17792 when in SANS

mode and 8 in TRANS mode

Values (such as temperature, shutter position) monitored by

LOQ

An OpenGenie window can be opened using this tab

Current run numberCurrent run titleUser details: important as def ines ownership of data

Shows status of LOQ

Shows conf iguration of LOQ

This panel allows the control panels for dif ferent aspects of the

instrument operation to be viewed


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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 30Ahrs. 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):


14 02/03/13

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).

As script name has remained the same there is no need to set it

again

Final aperture has not changed and so this line can be ignored

Note that the numTRANS has now been set to 0 (previously 1) so that the f inal

condition (the EXITIF statement) is met

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


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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.

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/.

Mask file path & name

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

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

Specify filename for outputting 1D reduced data in the selected format: RKH – 3 column ascii, CanSAS – xml

Reduce a single or a batch set of data


16 02/03/13

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

Radial limits on the detector, outside of which data is ignored

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

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:

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.


17 02/03/13

Sample thickness, beam height and width and Z‐offset of sample from nominal position, as specified in your script and the instrument set‐up

Beam centre determined from standard sample. These values should be picked up from the mask file

Radial search limits for finding the beam centre. Typically these will be sufficient for LOQ

1D reduced data

Raw data

Raw transmissions for sample and can

Fitted transmissions for sample and can

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.

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:


18 02/03/13

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.


19 02/03/13

Appendix 3 - A Sample Mask File

LOQ

PRINT This is a LOQ user file for Mantid

MASK/CLEAR

MASK/CLEAR/TIME

L/WAV 2.2 10.0 .035/LOG

L/R 35 419 3

L/Q .009 .285 .002/lin

L/QXY 0 0.1 .002/lin

BACK/MON/TIMES 31000 39000

FIT/TRANS/YLOG 2.2 10.0

MON/DIRECT=DIRECT.041

MON/HAB=DIRECTHAB.983

MON/FLAT=MANTID_FLAT_CELL.061B

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

PRINT no box masks implemented because corners are masked by default

MASK/T 19711.5 21228.5

MASK/T 39354.5 41348.5

PRINT masking out hab spectra 16641 & 17341 which get double counts

MASK S16641

MASK S17341

! set offset value = (-11.0 + Lsm) x 1000

SAMPLE/OFFSET -21.0

SET CENTRE 322.57 327.07 5.00 5.00

SET SCALES 1.5739 1.179 1.233 1.244 1.216

PRINT MON/HABEFF correction not yet implemented

PRINT MON/HABPATH correction not yet implemented

PRINT Centre & scales (COLETTE) with 17/05/11, 62916.RAW, 11mm,

Durham Rack, Bucknall

PRINT Loaded: MASK_MAN.111A, This is COLETTE MASK.111A for Mantid

Identifies instrument as LOQ

Clear any spectrum (detector pixel) masks

Clear any time channel masks

Establish the default range & binning (Å)

Establish the radial limit for the detector (mm)

Establish the default Q range & binning for 1D data reductions (Å-1)

Establish the default QX , QY range & binning for 2D data reductions (Å-1)

Remove the “prompt” spike in monitor time-of-flight spectra (s)

Interpolate transmissions from fits to the measured transmission data over specified

Location of main detector efficiency vs correction file

Location of high angle detector efficiency vs correction file

Location of pixel-to-pixel efficiency correction file

“Mask out” (i.e. ignore) the top two rows of the detector

Remove the “prompt” spike in main detector time-of-flight spectra (s)

Remove the “prompt” spike in main detector time-of-flight spectra (s)

“Mask out” a high angle detector spectrum (pixel) that gets double counts

“Mask out” a high angle detector spectrum (pixel) that gets double counts

Establish the detector offset from the nominal sample detector distance (mm)

Establish the detector centre coordinates and pixel dimensions (mm)

Establish the absolute intensity scaling factors for all detectors/modules

Establish the efficiency of the high angle detector at 1Å and at large angles

Enable the previous correction

Identifies the date, name and calibration sample run associated with this mask file

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