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Update *.nff file in '/ssf' folder
kipil #1
Member since Jul 2018 · 8 posts
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Subject: Update *.nff file in '/ssf' folder
Hi all,

I prepared new '*.nff' with more details, and would like to update in the '/ssf' folder. I replaced an old file 'nff' file to the new 'nff' file, but the TOPAS6 program (academic version) still use the old 'nff' file, even though I moved it to the other folder.

Is there a way to make the program recognize new 'nff' file?

Thanks,
Kipil
AlanCoelho #2
Member since Aug 2011 · 256 posts
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If the program can't find the NFF file then it uses fixed wavelength coefficients corresponding to the nearest energy; a message, similar to the following,  is displayed:

   Using fixed wavelength dispersion coefficients for atom…

The ‘str’ dependent keyword ‘report_on_str’ can be used to display the f’ and f’’ used for all atoms in the structure.

If you get stuck then send me your INP and data file and I will have a look.
kipil #3
Member since Jul 2018 · 8 posts
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Thanks for your reply!

Yes, I had that message. The format of my new nff file was wrong, and the program calculate coefficients rather than reading the new nff file. Now I solve the problem.

I have one more question. I am using absorption correction function in the resonant diffraction refinement. I found that 'mixture_MAC' value is not calculated by new nff file. I found that it is calculated from the file in '/mac' folder.
 Is there a way to report f' and f'' value from the given wavelength? Then I can calculate correct 'mixture_MAC' value from those.

Thanks,
Kipil
This post was edited on 2018-07-27, 05:22 by kipil.
rowlesmr #4
Member since Oct 2011 · 181 posts
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Hi Kipil


You can also set the f' and f'' values in the input file.

Look up the f0_f1_f11_atom, f0, f1, and f11 keywords in the TechRef.

Matthew
--
Matthew
kipil #5
Member since Jul 2018 · 8 posts
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Hi Matthew,

Thanks for your comment. My refinement has another issue. I know the exact lattice parameter of my material, but the energy is not defined. So I refine the energy of the X-ray to the lattice parameter. The f' and f'' are so sensitive to the energy as I measured several diffraction patterns across the edge, for the resonant diffraction. This is a reason why I want to get the f' and f'' value from the Topas program rather than giving the value.

Kipil
AlanCoelho #6
Member since Aug 2011 · 256 posts
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Hi Kipil

The report_on_str keyword outputs the f' and f'' (for version 6). Including the keyword for CeO2 gives:


      • f1 and f11 values for CeO2 ***
   Ce+4 -1.81997611 10.0820179
   O-2 0.0523209357 0.0337069703


cheers
alan
kipil #7
Member since Jul 2018 · 8 posts
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Thanks Alan,

I would like to use those value (f1 and f11) during the refinement, using f11 value for absorption calibration instead of 'mixture_MAC' value. Can you please let me know if there is a way to call those value in the .inp file?

To be clear, what I would like to know is whether I can record f11 value to other parameters for additional calculation.
Ex) prm !absorption =Get(f11);

Thanks,
Kipil
AlanCoelho #8
Member since Aug 2011 · 256 posts
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>what I would like to know is whether I can record f11 value to other
>parameters for additional calculation.
>Ex) prm !absorption =Get(f11);

You would need to explicitly define f11 and then give it a parameter name; ie.

   load f0_f1_f11_atom f11 {
          Pb+2
       pb_f11 5 ' this is f11 for Pb
   }

The parameter name pb_f11 can then be used in equations.
kipil #9
Member since Jul 2018 · 8 posts
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Thanks so much Alan!
kipil #10
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Hi Alan,

Thanks for your previous response. I tried that command, but that command refines f1 and f11 of Ni instead of importing those values from the 'ni.nff' file from 'C:\Topas6\ssf' folder. Is there a way to only read the f1 and f11 values at specific energy instead of refining them? To be more clear, I attach a screenshot. In the screenshot, I loaded f1 and f11 curve (as function of energy) in the TOPAS program. I indicated two lines at ~7.6 keV and ~8.2 keV. For example, I would like to import f1 and f11 values from those two specific energies in my script. Then it would be helpful to calculate absorption correction factor for resonant diffraction.

[I attach a link of the screenshot]
https://www.dropbox.com/s/rdmvwbz6ull1nl3/f1f11.png?dl=0

Thanks,
Kipil
rowlesmr #11
Member since Oct 2011 · 181 posts
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maybe try

   load f0_f1_f11_atom f11 {
          Pb+2
       !pb_f11 5 ' this is f11 for Pb
   }
--
Matthew
kipil #12
Member since Jul 2018 · 8 posts
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Hi Matthew,

Thanks for suggesting. Unfortunately, it does not work. I think that function apply a fixed value of Pb_f11 as 5. For example, if I use really big vale like '!ni_f11 10000', the refinement diverge.

Thanks,
Kipil
AlanCoelho #13
Member since Aug 2011 · 256 posts
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In reply to post #11
Hi Kipil

>Is there a way to only read the f1 and f11 values at specific energy instead of refining them

There isn’t; what I think you want is a phase dependent function that looks something like:

   str
      prm = Get_f1(Al); 0
      prm = Get_f11(Al); 0
      etc…

I will try and put this in for the next version.

cheers
alan
kipil #14
Member since Jul 2018 · 8 posts
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Yes, that kind of function is what I want to use.
Thanks for your reply, and I am looking forward to using it in the next version!

Best,
Kipil
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