Changes between Version 1 and Version 2 of Tutorials/KU/SAS


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Aug 13, 2018 4:19:04 PM (3 years ago)
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ajj
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  • Tutorials/KU/SAS

    v1 v2  
    99||   [#section23 2.3 Polydispersity] || 
    1010||   [#section24 2.4 Resolution] || 
    11  
     11|| [#section3 3. Fitting SANS data] || 
     12||   [#section31 3.1 Background Information] || 
     13||   [#section32 3.2 Calculating Scattering Length Density] || 
     14||   [#section33 3.3 Loading and Plotting the data] || 
     15||   [#section34 3.4 Fitting the data] || 
     16|| [#resources Resources] || 
    1217 
    1318== [=#intro Introduction] == 
    14 This exercise will introduce you to analysing SANS data using geometrical models in !SasView. In the first lab session you will look at how different shapes produce different scattering patterns, and how the model parameters affect the scattering pattern. In the second lab session you will then load some real SANS data and attempt to fit models to the data in !SasView. 
     19This exercise will introduce you to analysing SANS data using geometrical models in !SasView. In the firstly you will look at how different shapes produce different scattering patterns, and how the model parameters affect the scattering pattern. You will then load some real SANS data and attempt to fit models to the data in !SasView. 
    1520 
    1621This first exercise is divided into 2 sections: 
     
    190195}}} 
    191196 
    192  
    193 == What's Next? == 
    194 You can now move on to the second lab session looking at fitting of data : [wiki:KEMM37/Lab1B Lab 1B Data Fitting] 
     197== [=#section3 3. Fitting SANS data] == 
     198 
     199This part of the exercise will use real SANS data taken from a study of surfactant self assembly in deep eutectic solvents (DES).  
     200 
     201{{{ 
     202#!div style="background: lightblue" 
     203[=#task10 **TASK 10:**] Restart !SasView 
     204 
     205Before starting this part of the exercise, you should have a clean !SasView instance. Quit !SasView and restart it. 
     206}}} 
     207 
     208=== [=#section31 3.1 Background Information] === 
     209Deep eutectic solvents are a class of ionic liquids formed from a hydrogen bond donor and a halide salt. At a certain mixture ratio, the eutectic mixture, the melting point is significantly depressed to values below room temperature. 
     210 
     211Here we will examine the self-assembly of a [https://en.wikipedia.org/wiki/Surfactant surfactant], [https://en.wikipedia.org/wiki/Sodium_dodecyl_sulfate sodium dodecyl sulfate (SDS)] in the deep eutectic solvent formed from a 1:2 molar ratio mixture of [https://en.wikipedia.org/wiki/Choline_chloride   choline chloride] and [https://en.wikipedia.org/wiki/Urea   urea]. 
     212 
     213||Sodium Dodecyl Sulfate||Choline Chloride||Urea|| 
     214||[[Image(kemm37_sds.png)]]||[[Image(kemm37_choline.png)]]||[[Image(kemm37_urea.png)]]|| 
     215 
     216{{{ 
     217#!div style="background: lightblue" 
     218[=#task11 **TASK 11:**] Download the SANS data :  [attachment:KEMM37SasViewTutorialData.zip​] and unzip the file in a known location on your filesystem. Note where you have placed the data. 
     219}}} 
     220 
     221You should now have a folder called "Subtracted" containing a set of files named as follows: 
     222 
     223[[Image(kemm37_datafileslist.png)]] 
     224 
     225The data are SANS curves collected on SANS2D at ISIS and D22 at ILL for samples of protonated (normal) SDS in 1:2 d9-choline chloride:d4-urea. This sample was chosen to give maximum contrast and minimum background signal from incoherent scattering. There were 7 samples with 0.2 wt%, 0.5 wt%, 1.0 wt%, 2.0 wt%, 5.0 wt%, 7.5 wt% and 10 wt% of SDS in the DES with the filenames corresponding to each sample given below: 
     226 
     227|| Surfactant Concentration (wt%) || Data File || 
     228|| 0.2 || 0p2hSDS_dChCldUrea_sub.txt || 
     229|| 0.5 || 0p5hSDS_dChCldUrea_sub.txt || 
     230|| 1.0 || 1hSDS_dChCldUrea_sub.txt || 
     231|| 2.0 || 2hSDS_dChCldUrea_sub.txt || 
     232|| 5.0 || 5hSDS_dChCldUrea_sub.txt || 
     233|| 7.5 || 7p5hSDS_dChCldUrea_sub.txt || 
     234|| 10.0 || 10hSDS_dChCldUrea_sub.txt || 
     235 
     236All the data files have been processed to 1D scattering curves with the solvent background subtracted to leave only the coherent scattering signal on absolute scale. 
     237 
     238Additionally there is a folder called "Not subtracted" containing the data for task 14. 
     239 
     240=== [=#section32 3.2 Calculating Scattering Length Density] === 
     241 
     242The scattering length density is given by  
     243 
     244[[Image(kemm37_sld.png, 100px)]] 
     245 
     246Scattering lengths of relevant elements: 
     247||= **Element** =||= **Scattering Length (fm)** =|| 
     248||C     ||6.646|| 
     249||H     ||-3.739|| 
     250||D     ||6.671|| 
     251||N     ||9.36|| 
     252||O     ||5.803|| 
     253||Cl    ||9.577|| 
     254 
     255 
     256Physical properties of the DES components: 
     257||= **Component**       =||= **Chemical Formula** =||=  **Molecular Volume (Å3)**       =||= **Density (g/cm3)** =|| 
     258||d9-Choline Chloride|| C5H5D9NOCl      ||  210.77||  1.17|| 
     259||d4-Urea||     CD4N2O  ||   75.55||    1.41|| 
     260 
     261 
     262{{{ 
     263#!div style="background: lightblue" 
     264[=#task12 **TASK 12:**] Calculate the scattering length density (SLD) of a 1:2 mole ratio mixture of choline chloride and urea. 
     265 
     266Use the information in the table above to calculate the SLD. There are multiple ways to do so, including: 
     267* Calculating by hand 
     268* Using a spreadsheet 
     269* Using the SLD calculator built in to !SasView (in the Tools menu). 
     270* Using online calculators e.g. [https://www.ncnr.nist.gov/resources/activation/] 
     271 
     272Try calculating by hand and one or more of the other ways and see if you get the same answer! 
     273 
     274Remember that in mixtures, we use the volume fraction of each component to calculate the overall scattering length density: 
     275 
     276[[Image(kemm37_volumefraction_sld.png, 200px)]] 
     277 
     278 
     279}}} 
     280 
     281=== [=#section33 3.5 Loading data and Subtracting a Solvent Background] === 
     282 
     283You will now load in the original reduced data for the 0.5 wt% concentration of SDS and subtract the solvent background from it. 
     284 
     285{{{ 
     286#!div style="background: lightblue" 
     287[=#task13 **TASK 13:**] Click on the "Load Data" button in the Data Explorer 
     288 
     289Locate the folder where you placed the data, select all the files in the "Not subtracted" folder and click "Open" in the dialog. 
     290}}} 
     291 
     292{{{ 
     293#!div style="background: lightblue" 
     294[=#task14 **TASK 14:**] Subtract the solvent background using the "Data Operation" Tool 
     295 
     296From the "Tools" menu, select "Data Operation". 
     297 
     298}}} 
     299 
     300You should have a window that looks something like this: 
     301 
     302[[Image(kemm37_dataoperation.png, 500px)]] 
     303 
     304 
     305{{{ 
     306#!div style="background: lightblue" 
     307 
     308Give your output data set a name of your choosing in the "Output Data Name" box 
     309 
     310In the "Data 1" drop down, select the sample data set "0p5hSDS_dChCldUrea.txt". 
     311 
     312In the "Operator" drop down, choose "-" (minus) 
     313 
     314In the "Data 2" drop down, select the solvent data set "dChCldUrea.txt". 
     315 
     316Click "Apply", then "Close" 
     317 
     318In the data explorer, there should now be a data set with the name you chose above. 
     319 
     320Make a plot of the original data sets and your subtracted one to compare them and check you did the subtraction correctly. Make sure that there are check marks next to "0p5hSDS_dChCldUrea.txt", "dChCldUrea.txt", and the dataset with the name you chose. Click on "New Plot" at the bottom of the Data Explorer. 
     321 
     322Does the result look reasonable? What effects have subtracting the solvent scattering from the sample scattering had on the scattering curve? What are possible sources of the background signal that you are removing? 
     323 
     324}}} 
     325 
     326 
     327 
     328=== [=#section34 3.4 Loading and Plotting the subtracted data] === 
     329 
     330You will now load the background subtracted data into !SasView and make a plot in order to visually inspect the scattering curves.  
     331 
     332{{{ 
     333#!div style="background: lightblue" 
     334[=#task15 **TASK 15:**] Restart !SasView 
     335 
     336Before starting this part of the exercise, you should have a clean !SasView instance. Quit !SasView and restart it. 
     337}}} 
     338 
     339{{{ 
     340#!div style="background: lightblue" 
     341[=#task16 **TASK 16:**] Click on the "Load Data" button in the Data Explorer 
     342 
     343Locate the folder where you placed the data, select all the files in the "subtracted" folder and click "Open" in the dialog. 
     344}}} 
     345 
     346The Available Data section of the Data Explorer should look something like: 
     347 
     348[[Image(kemm37_loaddata.png)]] 
     349 
     350 
     351{{{ 
     352#!div style="background: lightblue" 
     353[=#task17 **TASK 17:**] Plot the loaded data 
     354 
     355Make sure that all the datasets have check marks next to them in the Available Data section of the Data Explorer, as shown above. 
     356 
     357Click the "New Plot" button in the Data Explorer. 
     358}}} 
     359 
     360A new window should appear with a plot of the data that looks something like: 
     361 
     362[[Image(kemm37_dataplot.png)]] 
     363 
     364{{{ 
     365#!div style="background: lightblue" 
     366[=#task18 **TASK 18:**] Examining the Data. 
     367 
     368Visually inspect the data, zooming in and making additional plots as needed. 
     369 
     370* What trends do you notice? 
     371* What can you say about the possible solution structure from looking at the data? 
     372 
     373}}} 
     374 
     375 
     376=== [=#section35 3.5 Fitting the data] === 
     377{{{ 
     378#!div style="background: lightblue" 
     379[=#task19 **TASK 19:**] Fitting the lowest concentration data. 
     380 
     381Select the lowest concentration data only in the data explorer by ensuring only 0p2hSDS_dChCldUrea_sub.txt has a check mark next to it and click “Send to" fitting. 
     382 
     383* Select the model for the structure you predicted for this dataset.  
     384  * How does it compare to the data? 
     385* Fill in parameters you know and adjust the others to see how close you get to the data. 
     386* Select parameters to fit and run the fit by clicking "Fit" at the bottom of the fitting panel. 
     387  * Do you get a good fit? 
     388  * Are the parameters you get physically reasonable? 
     389 
     390}}} 
     391 
     392 
     393{{{ 
     394#!div style="background: lightblue" 
     395[=#task20 **TASK 20:**] Fitting the other data, starting with the 7.5 wt% data set. 
     396 
     397Repeat for other concentrations 
     398* Does the same model fit all data? 
     399* What is consistent between datasets? What is different?  
     400 
     401 
     402}}} 
     403 
     404{{{ 
     405#!div style="background: lightblue" 
     406[=#task21 **TASK 21:**] Summarising the results 
     407 
     408Having fitted all the data sets you can now summarise the results and comment on the trends you observe. 
     409 
     410}}} 
     411 
     412 
     413== [=#resources Resources] == 
     414 
     415* NIST SLD calculator [https://www.ncnr.nist.gov/resources/activation/] 
     416* NIST Scattering Length and Scattering Cross Section Database [https://www.ncnr.nist.gov/resources/n-lengths/]