beq values being negative

suneetkale

Hi,

I get negative beq values when I run refinement of for a sample using LaB6 standard.
Even without the LaB6 are negative values for beq allowed? Should I stop the refinement and fix them to 1?

I am enclosing the cif and data file as well

lle27-lab6-12186-exported.txt

53kB

nb2snc.txt

5kB

lab6-nist.txt

3kB

Here is the code I used -

`'continue_after_convergence 'To continue refinement

'---------------------------- Weighted profile factors, expected R factors, and Goodness of fit values-------------------------------------------------------------------------------
r_p 16.9016764 r_p_dash 29.647421
r_wp 24.798923 r_wp_dash 36.0398251
r_exp 2.59190554 r_exp_dash 3.76676933
gof 9.5678344
weighted_Durbin_Watson 0.987039393 'autocorrelation in the residuals from the statistical regression analysis

'do_errors 'calculates the corelation matrix - last step

Backup_INP

'------------------------[File name & Location]---------------------------------------------------------------------------------------------------------------------------------------

xdd "C:\Users\sunee\OneDrive\Graduate_Studies\Birkel_Group\Processed_DATA\XRD_Analysis\D2_Phaser\LaB6_Refinement\Lin-LIn_D2\LLE27\Added\LLE27_LaB6_12186_exported.raw"

r_exp	2.59190554	r_exp_dash	3.76676933
r_wp	24.798923	r_wp_dash	36.0398251
r_p		16.9016764	r_p_dash	29.647421
weighted_Durbin_Watson	0.987039393	gof	9.5678344
'weighting = 1/Sqrt(Yobs);

start_X  10    'starting 2Th value for data
finish_X  90	'end 2Th value for data
x_calculation_step 0.001 'calculation step size for 2Th
bkg @  614.319855` -315.081606` -130.261592`  80.0577518` -5.41802902` '5 order polynamial background refinement

range 1
LP_Factor ( 0)
Specimen_Displacement ( ,-0.08930)

Rp	141
Rs	141
lam
	ymin_on_ymax	0.0001
	la  0.653817 lo  1.540596 lh  0.501844
	la  0.346183 lo  1.544493 lh  0.626579

'------------------------- [Strcutre_data_from_CIF_LaB6]-----------------------------------------------------------------------------------------------------------------------------------

str
local !CIF_PHASE_ID 1

'spherical_harmonics_hkl sh
'sh_order 4

TCHZ_Peak_Type(, 0.07128,,-0.00396,,-0.00689,, 0,, 0.08839,, 0)
'TCHZ_Peak_Type(@, 0.01,@, 0.01,@, 0.01,, 0,@, 0.01,, 0)


r_bragg	11.4594
phase_MAC	237.338517
phase_name	"LaB6"

MVW( 203.772, 71.827, 32.625`)
space_group 221
scale @  0.00896710325`

'scale_pks = Max (sh, 0); 

Phase_LAC_1_on_cm( 1118.08681)
Phase_Density_g_on_cm3( 4.71094)

Cubic( 4.1568260)
site La1	num_posns  1 x  0.0000 	y  0.000	z  0.000	occ La	1 beq  1
site B1		num_posns  6 x  0.1975	y  =1/2;	z  =1/2;	occ B	1 beq  1

'Out_CIF_STR ("LaB6.cif")

'------------------------------------------[Main_MAX_Phase - Nb2Sn0.6Zn0.4C]--------------------------------------------------------------------------------------------------------------------
str
local !CIF_PHASE_ID 2

'spherical_harmonics_hkl sh
'sh_order 4

'TCHZ_Peak_Type(, 0.01,, 0.01,, 0.01,, 0,, 0.01,, 0)
TCHZ_Peak_Type(@,-0.35594`,@, 0.33300`,@,-0.06891`,, 0,@, 0.36992`,, 0)

r_bragg	5.48051861
phase_MAC	155.845396
phase_name	"Nb2Sn0.6Zn0.4C"

MVW( 590.426, 121.612`, 67.375`)
space_group 194
scale @  0.00377479994`

'scale_pks = Max (sh, 0);

Hexagonal( @  3.167963`, @  13.992207`)


site	Nb	num_posns	4	x	!xNb	=1/3;	y	!yNb	=2/3;	z	zNb	0.58749`	occ	Nb	1	beq	@  1.96027`
site	Sn	num_posns	2	x	!xSN	=1/3;	y	!ySn	=2/3;	z	!zSn	=1/4;	occ Sn !a  0.600 beq b  3.17805` occ Zn =1-a; :  0.40000 beq =b; :  3.17805`
site	C	num_posns	2	x	!xC		0.00	y	!yC		0.00	z	!zC		0.00	occ	C	1	beq	@ -5.37254`

'Out_CIF_STR ("Nb2Sn0.6Zn0.4C.cif") 'creates CIF with all strcutre paramters

'------------------------------------------[Custom_Macros]----------------------------------------------------------------------------------------------------------------------------

'Graphical_Data (40Zn_Graphical_Data.txt)
'Two_Th_Data (2Th_data.txt)
'Editor (40Zn_Editor_Data.txt)

'---------------------------------[END]-----------------------------------------------------------------------------------------------------------------------------------------------`

rowlesmr

negative Beq values have no physical significance. Your data doesn't support the refinement of ADPs, as you don't have enough angular range.
Don't use 1, find a good single structure determination in the ICSD, or somewhere eles, and use that value. Does the NIST SRM660 certificate cite a crystal structure? See if that suits your purposes.

suneetkale

rowlesmr

Does that make it okay to accept refinements with negative beq values? What is a good practice here?

As far as the second question, Thank you. I refered to the structure from the certificate and it uses 0 for LaB6.

johnsoevans

You shouldn’t really accept a refinement with a model that’s not physically sensible unless you know why. Negative displacement parameters can arise for a number of reasons: absorption, surface roughness, wrong atom type, too low an occupancy, etc. Some of those might be an important part of your model and need to be correct. If, however, you’re only interested in cell
parameters then negative adps might not matter.

P.S. could you delete the attachments and the unnecessary INP file text from yout post so we can keep the forum condense and easy for others to follow? Thanks.

suneetkale

@johnsoevans Thank you.

Thank you for your insights. You're right about ensuring the model's physical sensibility before accepting refinements. For files with LaB6, I only need lattice parameters, and going forward, I will check for negative ADP values.

P.S. I will delete the attachments and the unnecessary INP file text from my post to keep the forum concise and easy to follow. Thanks for the reminder!