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Help with surface refinement
dlowry #1
Member since Aug 2016 · 6 posts
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Subject: Help with surface refinement
I have a 2 part (at least) issue I am trying to work through. I am using version 5 of TOPAS, with access to both the academic and commercial versions, in either case working with launch mode and jedit.

First off, I have been able to work through the WO3 surface refinement example and apply it to some of my data successfully. With patterns collected as a function of tempertature with a Bruker D8 XRD I have been able to create the range .raw file using Bruker.EVA and subsequently run the surface refinement inp file and everything works out. This has worked with simple systems, MgO, Al2O3, or Mullite all spiked with Pt powder for temperature calibration.

Now for my first problem, I am working with RENbO4  materials that are monoclinic at low temperature and tetragonal at high temperature. So far I have been unsuccessful in using the remove_phase macro for the automatic removal of phases. For example if I set the macro as:

Remove_Phase( 3.0, 0.1) my understanding is if the weight percent is <3.0 and the error greater than 0.1 the phase should be removed. Hopefully I am making a simple mistake for this portion.

My second problem is when I try to create a range.raw file for synchrotron data, currently I have ~15 different samples that I have collected HTXRD data for using the XPD beamline at NSLS-II. Each of these samples has between 200 and 700 individual patterns. To generate the .xye files from the .tiff images I used GSAS-II. If I try to use Bruker.EVA, it seems to break with more than ~350 patterns loaded simultaneously (not a big deal, just moderately annoying). However, when one of these .xye files is loaded to EVA the wavelength is set to Cu and when changed to the appropriate wavelength the 2theta values are changed, it is important to note that the 2theta values are "correct" when EVA thinks Cu wavelength should be used.

Does anyone have an idea on how to fix this is EVA (I know this may be the wrong place to ask) OR is there a better way to create a .raw file from .xye datasets for use in the surface refinement .inp.


All help will be appreciated, and I am sure I will have more related questions as I try to work through these datasets.


Dan
rowlesmr #2
Member since Oct 2011 · 174 posts
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Hi Dan

I can't answer you Remove_Phase questin, as I've never tried doing that, but one way to work around it might be something like

(pseudo-code)
prm sc 0.1
scale = If(Or(current_range < 10, current_range > 20, 0, sc);
which would make the scale factor for the phase be zero if the range number is ouside the values 10..20.

There is probably another way to do it with # commands too.
.

On making a ranged raw file.. WHy are you doing that? Why not just use the XYE files directly? I always use the xye files directly for my surface refinements.


Matthew
--
Matthew
johnsoevans (Administrator) #3
User title: John Evans
Member since Aug 2009 · 185 posts
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I'd also say that, unless there's a good reason not to, you probably want to do sequential rather than surface refinement.  As Matthew said there's no reason not to use .xye files directly.  The syntax is in the tutorial:
http://community.dur.ac.uk/john.evans/topas_workshop/tutor…
dlowry #4
Member since Aug 2016 · 6 posts
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Thank you both for the responses. To date I have used the sequential refinement method with a .bat file successfully. However, I would like to generate a d_hkl and cif file for each pattern refined and with the .bat method I was unable to do this since I could not get the name of the file to change to prevent overwriting it.

Also as you have both stated, yes I would prefer to use the .xye files without converting to .raw, I apologize for not being clear. To that point I was asking for help in bundling the files to a single where I can use the filename and range macros such as in the parametric/surface tutorial with WO3.

Again thank you for any assistance
rowlesmr #5
Member since Oct 2011 · 174 posts
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Hi Dan

With sequential refinements with a batch file, you can just feed in a macro for the file names of the files you're after.

In your input file, just have something like
Out_CIF(CIFFILENAME)
Out_d_hkl(DHKLFILENAME)

and then in your call to tc, do somthing like
tc inputfile1 "macro CIFFILENAME { cif1.cif } macro DHKLFILENAME { dhkl_1.hkl }"
tc inputfile2 "macro CIFFILENAME { cif2.cif } macro DHKLFILENAME { dhkl_2.hkl }"

.

With the xye files, just put the file names in the xdd call and don't use the range command

xdd file1.xye
   ...
   ...
xdd file2.xye
   ...
   ...
xdd file3.xye
   ...
   ...
--
Matthew
dlowry #6
Member since Aug 2016 · 6 posts
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Matthew,

I will give that a try tonight or tomorrow morning, I am really glad you guys are available to help.

Dan
dlowry #7
Member since Aug 2016 · 6 posts
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Matthew,

Making the adjustments to the tc line in the .bat file seems to be the solution. Thank you again for the assistance.

Dan
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