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All posts by johnsoevans (213)

topic: Distortion mode refinement, strain, lattice parameters  in the forum: Forums topas
johnsoevans (Administrator) #1
User title: John Evans
Member since Aug 2009 · 213 posts
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Chloe,

Do you really need to refine the strain directly?

You should just be able to refine a/b/c/al/be/ga in the same way as you would for a conventional refinement.  i.e. fix al/ga to 90.  Just check that the low symmetry description is in a standard b-unique monoclinic setting.

John
topic: How to Use remove_phase Keyword in TOPAS 6  in the forum: Forums topas
johnsoevans (Administrator) #2
User title: John Evans
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In reply to post ID 2057
I've never personally used the remove phase option.  I've always preferred to set the file up in such a way that if a phase disappears its scale factor refines to zero (within uncertainty).  This can be done parametrically or often more simply by equating peak shapes etc between phases (to stop peaks becoming extremely broad and correlating with scale factors).  There's a bit on this in chapter 12 of the Rietveld/Topas book.

You can also set up phases for different ranges manually.  e.g. the book has this example code in it:

' Phase boundaries
#prm t = 100 + (Run_Number 4);   ‘Temperature = 100 + Run_Number * 4
#if Or(t < 158, t > 226);
   #define Phase1
#elseif And(t > 158, t < 198);
   #define Phase1
   #define Phase2
#elseif And(t > 198, t < 226);  
   #define Phase2
#endif
...
#ifdef Phase1
          str
         ...
#endif
topic: Rietveld Refinement Negative Peak Value  in the forum: Forums topas
johnsoevans (Administrator) #3
User title: John Evans
Member since Aug 2009 · 213 posts
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In reply to post ID 2059
Do you really mean the calculated intensity of the peak is negative, or do you men the intensity is lower then observed?  The only way that calculated peaks can be negative is if you're applying a preferred orientation correction that has refined to extreme values.
topic: Topas 6, running tc via Python subprocess  in the forum: Forums topas
johnsoevans (Administrator) #4
User title: John Evans
Member since Aug 2009 · 213 posts
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In reply to post ID 2055
We've used python to control topas v6 in the past without issues, so I'm not aware of any fundamental issues.  The tutorial at http://community.dur.ac.uk/john.evans/topas_workshop/tutor… used this approach.
topic: Rwp lower than Rexp  in the forum: Forums topas
johnsoevans (Administrator) #5
User title: John Evans
Member since Aug 2009 · 213 posts
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In reply to post ID 2039
Some of the Rietveld texts discuss why you can sometimes get unusual Chi^2 values (either much greater than one or less than one).  Missing experimental uncertainties from the DAC data could be one cause.  Was your file initially an .xye file?
You might look at Lynn McCusker et al's Rietveld guidelines paper: J. Appl. Cryst. 1999, 32, 36-50.  It discusses some of the common issues with Rwp.
topic: Saving results using parametric refinement  in the forum: Forums topas
johnsoevans (Administrator) #6
User title: John Evans
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In reply to post ID 2043
Dear Florian,

It shouldn't take that long.  Do you have do_errors turned on?  You might try without errors.

John
topic: Distortion analysis  in the forum: Forums structure solution
johnsoevans (Administrator) #7
User title: John Evans
Member since Aug 2009 · 213 posts
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In reply to post ID 2030
Hi Matthew,

Three possibilities if it's not easy to spot by eye:

1. For most of the "classic" structure types the aristotype is normally well known.  If it's less obvious you could look in the icsd and find the highest symmetry report for your structure type.  e.g. try the ANX/AB type formula or structure type search.
2. You could try a routine like "findsym" (part of the ISODISTORT suite) or one of the Bilbao routines with a high tolerance.  You could try this after making some coordinates closer to special values.  e.g. if you had an O at 0.23 you might move it to 0.25.
3. Parents don't always have to be real or even realistic structures.  Sometimes it can be convenient to increase symmetry to something that no longer makes chemical sense.  I don't think there's a recipe for that other than intuition.
topic: Individual phase output for sequential refinement  in the forum: Forums topas
johnsoevans (Administrator) #8
User title: John Evans
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In reply to post ID 2027
The standard way is to redo the refinement with iters 0 and the scale factor of the phase you want to exclude set to 0.

It's obviously a pain to do this by hand in a sequential refinement. 

If you're doing the sequential from a .bat file you can easily do this with #ifdef #endif flags in the INP file.  Basic idea would be to do each refinement twice.  The first time you refine as normal.  The second time (iters 0) you do the outputting.  You'd tell topas what type of refinement to do using commands like the ones at:

http://topas.dur.ac.uk/topaswiki/doku.…?id=automating_mu…
topic: hkl dependent peak shift possible?  in the forum: Forums topas
johnsoevans (Administrator) #9
User title: John Evans
Member since Aug 2009 · 213 posts
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In reply to post ID 2025
:-)
topic: hkl dependent peak shift possible?  in the forum: Forums topas
johnsoevans (Administrator) #10
User title: John Evans
Member since Aug 2009 · 213 posts
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In reply to post ID 2023
Do a search for "th2_offset" in the topas tech ref pdf file.  P71 has some info.
topic: Crystal Density (Crystal Density error in TOPAS v.3)  in the forum: Forums topas
johnsoevans (Administrator) #11
User title: John Evans
Member since Aug 2009 · 213 posts
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In reply to post ID 2017
As in the previous post, type "=1/3;" not just "1/3".  The = and ; indicates a topas equation.
topic: Crystal Density (Crystal Density error in TOPAS v.3)  in the forum: Forums topas
johnsoevans (Administrator) #12
User title: John Evans
Member since Aug 2009 · 213 posts
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In reply to post ID 2015
v3 is a long time ago, but this should work.  Did you type "=1/3;" into the relevant box (if you're using the gui) or into the site line (if you're using an input file. 

What you show isn't a "bug".  You've told topas in this example that x=1 and y=2 so the refinement is correct under that information.
topic: Crystal Density (Crystal Density error in TOPAS v.3)  in the forum: Forums topas
johnsoevans (Administrator) #13
User title: John Evans
Member since Aug 2009 · 213 posts
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In reply to post ID 2013
You need to make your fractional coordinates for Ru1 exactly 1/3 and 2/3 instead of 0.3330 and 0.66670.  Use =1/3; and =2/3;.  The atom will then be on the multiplicity 2 site you expect and the density will come down.  The clue is in the "Np 6" entry in your post.
topic: Converting a molecular z-matrix output from DASH into Topas format  in the forum: Forums topas
johnsoevans (Administrator) #14
User title: John Evans
Member since Aug 2009 · 213 posts
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In reply to post ID 1094
Just so the link is on the same page as this thread, see also: https://github.com/mspillman/zmatrix-to-inp
topic: GSAS Functions In Topas  in the forum: Forums topas
johnsoevans (Administrator) #15
User title: John Evans
Member since Aug 2009 · 213 posts
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In reply to post ID 2004
Alan: it's a long time ago, but my recollection was the profile functions gsas vs topas were essentially identical but I didn't think there was a direct correspondence between the actual numerical values of the coefficients between topas and gsas.  I think Yuanpeng wanted exact equivalence (I'm guessing to tie in with rmcprofile?).
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