Changeset 1739 for Tutorials/SAsize/Small Angle Size Distribution.htm

Ignore:
Timestamp:
Mar 18, 2015 12:24:28 PM (8 years ago)
Message:

update small angle size tutorial

File:
1 edited

Unmodified
Removed
• Tutorials/SAsize/Small Angle Size Distribution.htm

 r1705 Von DreeleVon Dreele1218971319162014-03-20T16:54:00Z2014-05-03T16:09:00Z7127772822015-03-18T17:22:00Z112727256Argonne National Laboratory6017854214.00851115.00 /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:-536870145 1107305727 0 0 415 0;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast;} mso-outline-level:1; font-size:24.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-outline-level:2; font-size:18.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-outline-level:3; font-size:13.5pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-outline-level:4; font-size:13.0pt; font-family:"Cambria","serif"; font-family:"Cambria",serif; mso-ascii-font-family:Cambria; mso-ascii-theme-font:major-latin; mso-outline-level:5; font-size:12.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-pagination:widow-orphan; font-size:8.0pt; font-family:"Tahoma","sans-serif"; font-family:"Tahoma",sans-serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast;} mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast;} mso-pagination:widow-orphan; font-size:8.0pt; font-family:"Tahoma","sans-serif"; font-family:"Tahoma",sans-serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast;} mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast;} mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast;} mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast;} mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast;} mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast;} mso-ansi-font-size:24.0pt; mso-bidi-font-size:24.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-ascii-font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman"; mso-ansi-font-size:18.0pt; mso-bidi-font-size:18.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-ascii-font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman"; mso-ansi-font-size:13.5pt; mso-bidi-font-size:13.5pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-ascii-font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman"; mso-ansi-font-size:13.0pt; mso-bidi-font-size:13.0pt; font-family:"Cambria","serif"; font-family:"Cambria",serif; mso-ascii-font-family:Cambria; mso-ascii-theme-font:major-latin; mso-ansi-font-size:12.0pt; mso-bidi-font-size:12.0pt; font-family:"Times New Roman","serif"; font-family:"Times New Roman",serif; mso-ascii-font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman"; mso-ansi-font-size:8.0pt; mso-bidi-font-size:8.0pt; font-family:"Tahoma","sans-serif"; font-family:"Tahoma",sans-serif; mso-ascii-font-family:Tahoma; mso-fareast-font-family:"Times New Roman"; mso-ansi-font-size:8.0pt; mso-bidi-font-size:8.0pt; font-family:"Tahoma","sans-serif"; font-family:"Tahoma",sans-serif; mso-ascii-font-family:Tahoma; mso-fareast-font-family:"Times New Roman"; mso-ansi-font-size:10.0pt; mso-bidi-font-size:10.0pt; font-family:"Calibri","sans-serif"; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Calibri","sans-serif"; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Calibri","sans-serif"; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin;

In this tutorial you will determine the size distribution of particles in an alumina polishing powder using data from a constant wavelength synchrotron X-ray USAXS instrument. You will use both Maximum Entropy (MaxEnt) alumina polishing powder using data from a constant wavelength synchrotron X-ray USAXS instrument. You will use both Maximum Entropy (MaxEnt) and Total Non-Negative Least Squares (TNNLS) methods assuming spherical particles. The data were collected from so the data are not calibrated on an absolute scale.

If you have not done so already, start GSAS-II.

If you have not done so already, start GSAS-II.

Step 1: read in the data file

style='mso-fareast-font-family:"Times New Roman"'>1.      Use the Import/Small Angle Data/from a q step QIE data file menu item to read the data file into GSAS-II. This read option is set to read three column small angle scattering data (SASD) as Q in Å-1, intensity and estimated standard deviation in intensity; there may be a header with metadata information in the front of this file.  Change the file directory to Import/Small Angle Data/from q (A-1) step X-ray QIE data file menu item to read the data file into GSAS-II. This read option is set to read three column small angle scattering data (SASD) as Q in Å-1, intensity and estimated standard deviation in intensity; there may be a header with metadata information in the front of this file.  Change the file directory to Exercises/Small angleexercises/SAsize to find the file; you will have to select the any file (*.*) filter to see it.

style='mso-fareast-font-family:"Times New Roman"'>2.      Select the alumina data.dat data file in the first dialog and press Open. There will be a Dialog box asking Is this the file you want? Press Yes button to

At this point the GSAS-II data tree window will have several entries and

Step 2: Set Limits

range scattering is from very large objects not readily described by the size distribution analysis and above the scattering is mostly background. Select Limits under SASD alumina data.dat from the GSAS-II tree. Then set changed to 0.001 for Tmin and 0.1 for Tmax. You can also set the limits using the cursor on the plot by either picking a point on the curve with

Step 3 Select the scattering substances for your sample

Two scsttering substances need to be defined for your sample to give the anticipated scattering contrast; in this case one is alumina and the other is vacuum (really air). Parameters for a number of substances are defined in the file Two scsttering substances need to be defined for your sample to give the anticipated scattering contrast; in this case one is alumina and the other is vacuum (really air). Parameters for a number of substances are defined in the file Substances.py. You can add your own substances to this or better put them in UserSubstances.py. You can add your own substances to this or better put them in UserSubstances.py; this is read after Substances.py when you load substances for your selection. Select Substances under SASD alumina data.dat from the GSAS-II tree. Then do Edit/Load substance normal'>Edit/Load substance from the menu; a popup window will appear with possible selections

Select Alumina and press OK; the relevant data for alumina (and vacuum) are displayed next

are given for each substance. These can each be edited; the other values will change accordingly. If your substance isnt in the list, you can Edit/Add substance to create a new one (you will be asked for a name and the scattering density and that as affected by resonant scattering for the listed wavelength is displayed (the wavelength can be changed in the Instrument Parameters GSAS-II tree item if needed). The resonant scattering

Two of the substances you have loaded into GSAS-II next need to be selected for this size distribution analysis; Select Sample Parameters under SASD alumina data.dat from the GSAS-II tree. Near the bottom of the window will be two rows marked Material; select Alumina from one of the pull downs (leave the other as vacuum). The window will show at the bottom the computed contrast between alumina and vacuum without and with consideration of resonant scattering effects; the latter is used in subsequent calculations.

without and with consideration of resonant scattering effects; the latter is used in subsequent calculations.

For experiments for which you know the transmission and the sample thickness, you can manipulate the volume fractions to make the calculated transmission match the observed one. Additionally, if you have absolute scaling information, you can rescale the data by adjusting the histogram scale factor; multiple data sets can be scaled together via the Command/Set scale menu item.

You are now ready to attempt a size distribution analysis using the maximum entropy method. Select Models under SASD alumina data.dat from the GSAS-II tree; the window will display

It is clear that the intensity levels off at an apparent background level of ~0.12; enter that into the appropriate place in the data window. The plot will be redrawn showing a horizontal red line for the background. All the other parameters seem reasonable for a 1st attempt at a MaxEnt solution. Do Models/Fit; the console window will show that the calculation did not converge and the Size Distribution plot has a choppy appearance.

This is not a satisfactory result, but the suggestion given in the console window is worth trying. Change the Error multiplier to 5 (notice the increased error bars on the data plot) and repeat Model/Fit. Convergence is now achieved in <10 cycles (see console window for details)

You may wish to explore the effect of some of the other parameters in the data window. Most are obvious but Log floor factor needs a bit of explanation. This is the log of the minimum size distribution (scaled by the histogram scale factor and the contrast). This size distribution minimum needs to be set within 1-2 orders of magnitude of the optimal value and

a gradient refinement method for the special case of all positive data and parameter values. To try it on this alumina data, select IPG from the Fitting method pull down. The data window will change to give

Reset the Error multiplier back to 1.0 and then do Models/Fit to run the IPG fitting. The IPG algorithm did not converge in 100 cycles and

This can be considerably improved by setting the Error multiplier to 2.0; the IPG fit converges in <20 cycles and gives a smoother size

You may wish to explore the other parameters for the IPG fitting. If Q power weight is set to 0-4, that changes the data weighting to Qp. This can change the convergence of the IPG method and yield improved results if one is unsuccessful with the default settings. I got a nice fit with a Q power weight of 3 and Error multiplier of 2.0.

You should save this GSAS-II project as it will be used in the tutorial for fitting small angle scattering data; I used alumina.gpx.

You should save this GSAS-II project as it will be used in the tutorial for fitting small angle scattering data; I used alumina.gpx.

Note: See TracChangeset for help on using the changeset viewer.