Peak shape

mariahovhannesian

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

Its not possible to see what is happening without the iNP file. Can you post it please

mariahovhannesian

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"

alancoelho

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

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

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/