Forum: Forums peak shapes RSS
Peak shape
Peak shape in Pawley fitting
mariahovhannesian #1
User title: mariahovhannesian
Member for a month · 3 posts
Group memberships: Members
Show profile · Link to this post
Subject: Peak shape
Hi,
I am a quite new user of Topas and your answer will be very appreciated. I am using Topas 6 academic version.
To train myself I calculated an xrd pattern from a .cif file. I wanted to realize indexing, pawley fitting and eventually structure solution. I generated the xrd pattern by using 1.54056 Å wavelength.

I determined the space group and lattice parameters by indexing but when I do a Pawley fit I am getting a very low Rwp value. The peak positions are metching but the peak shape is not. Is it because I used the wrong instrumental parameters, which one would be the correct choice? Or do I need to change peak shape parameters in Pawley fit? Unfortunetly I have very limited understanding about peak shapes therefore I cannot ask more spesific questions.
AlanCoelho #2
Member since Aug 2011 · 274 posts
Group memberships: Members
Show profile · Link to this post
Its not possible to see what is happening without the iNP file. Can you post it please
mariahovhannesian #3
User title: mariahovhannesian
Member for a month · 3 posts
Group memberships: Members
Show profile · Link to this post
Thank you, here is the input file. I was thinking that I will havea better Pwp value since I calculated the pattern.

cif: http://www.crystallography.net/cod/1516287.cif

r_wp  16.1414871 r_exp  12.2328729 r_p  9.98837614 r_wp_dash  15.8278194 r_p_dash  9.83134636 r_exp_dash  11.9951589 weighted_Durbin_Watson  0.268498376 gof  1.31951727

'--------------------------------------------------------------
'General information about refinement here
'Remove comments as required
'--------------------------------------------------------------

iters 100000
chi2_convergence_criteria 0.001
'do_errors
                                                                                 
'--------------------------------------------------------------
'Information on datafile etc here
'Check that default weighting is appropriate for your data
'--------------------------------------------------------------
xdd mof-5.raw
    start_X 0
    finish_X 45
    x_calculation_step = Yobs_dx_at(Xo); convolution_step 4
    bkg @ -1.65132376`  1.98711337` -1.81129057`  0.800973428` -0.507475166`  0.0156892834`
   lam
       ymin_on_ymax 0.0001
      la 1 lo 1.540596 lh 0.5     
    Zero_Error(zero, 0.03184`)

    hkl_Is   
                'circles_conv @   -0.18561
                'gauss_fwhm @  0.105703184
                'lor_fwhm @  0.0518812716
                'one_on_x_conv @  0.1
                'prm u  0.19774
                'prm v  0.04069
                'prm w  0.08299
                'peak_type pv pv_lor @  0.955696792 pv_fwhm = u * Tan(Th)^2 + v * Tan(Th) + w;
                                          
        TCHZ_Peak_Type(pku,-0.05244`,pkv,  0.01217`,pkw, -0.00088`,pkz, 0.00052`,pky, 0.06371`,pkxz, 0.07720`)
        Simple_Axial_Model(axial, 3.81348`)
        Cubic(25.8680)
        space_group "Fm-3m"
This post was edited on 2019-05-25, 22:05 by mariahovhannesian.
AlanCoelho #4
Member since Aug 2011 · 274 posts
Group memberships: Members
Show profile · Link to this post
Is this what you did:

1) calculate the mof-5.raw pattern
2) Pawley fit to the calculated pattern

How did you calculate the mof-5.raw pattern
mariahovhannesian #5
User title: mariahovhannesian
Member for a month · 3 posts
Group memberships: Members
Show profile · Link to this post
I used a software (Mercury) to calculate the xrd pattern from a cif (mof-5) that I found online. Then I indexed it to find the space group and lattice parameters of it as if it is an experimental data. When I was indexing, from the instrument/corrections I select cuKa1 emission profile (because in Mercury the pattern was calculated using 1.54056 Å wavelength. After I found the space group and lattice parameters I wanted to do pawley fit to see if the space group and lattice parameters are matching well with my data. Here I got a lower rwp than I expected. I thought I got a low rwp because I didnt adjust the peak shape parameters or I entered the wrong instrument settings (since there is no real instrument). I post this question to figure out where I made a mistake that I didn't get a perfect fit.
AlanCoelho #6
Member since Aug 2011 · 274 posts
Group memberships: Members
Show profile · Link to this post
The peak shapes from Mercury probably does not use the Simple_Axial_Model. For a description of what TOPAS is doing in regards to peak shapes then see:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849620/
Close Smaller – Larger + Reply to this post:
Verification code: VeriCode Please enter the word from the image into the text field below. (Type the letters only, lower case is okay.)
Smileys: :-) ;-) :-D :-p :blush: :cool: :rolleyes: :huh: :-/ <_< :-( :'( :#: :scared: 8-( :nuts: :-O
Special characters:
Go to forum
Not logged in. · Lost password · Register
This board is powered by the Unclassified NewsBoard software, 20120620-dev, © 2003-2011 by Yves Goergen
Current time: 2019-06-26, 06:54:29 (UTC +00:00)