Setting Limit on Phase 2th

suneetkale

Hi All,

I am trying to refine some synchrotron data for 47 multiphase samples from 8 different systems of elements. While I can refine the data and have all the parameters, I keep getting the same termination error for all files.
I had two questions:

How do I fix the error "Phase x-axis limits outside data x-axis limits"? To elaborate, I have high-res data, and I have set start_X 1.5 deg and finish_X 14 deg with a step size of 0.0001, with data ending at 15 deg. The 2th from .cif files show hkl markers in TOPAS beyond this limit, and TOPAS then terminates refinement. Is there a way to fix it?
Can I add all the structure data to one .inp file to go through all the data files for one system sequentially and output results in different folders? I am asking if I can avoid making 47 .inp files.

Thank you.

johnsoevans

I've never seen that error. TOPAS always calculates reflections beyond the maximum 2-theta as their profiles could potentially spread into the recorded range and contribute to intensity. I think the default is an extra 0.5 degrees. You can change this with extra_X_right (or extra_X_left for tof data). Your step size seems very small, maybe that is causing problems. Try rebin_with_dx_of 0.01 just to see if that fixes the problem.
Almost certainly yes. Search on the wiki for the #list command. Or look here. There have been some recent posts about ways to rename output files.

suneetkale

Thanks for replying, John. I have tried, but it didn't seem to fix the error completely. I took your suggestion and reduced the step size to 0.01, but now TOPAS keeps refining without doing anything to the calculated plot. It stays flat while RWP goes down to 34 and stops

I am enclosing the data file and code. I would appreciate it if you could comment.

motr-aadn-01-0002h52th-bkgd-subtracted.txt

220kB

------_Code-------
continue_after_convergence 'Comment out to stop

r_p 74.2758777 r_p_dash 92.9476929
r_wp 33.8144986 r_wp_dash 80.699339
r_exp 0.719803335 r_exp_dash 1.71783276
gof 46.9774131
weighted_Durbin_Watson 0.21349848

'do_errors

'-----------------[SK200_70Ge]-----------------------

xdd MOTR_AADN_01_0002.h5.2th_BKGD_SUBTRACTED.xye 'File name with extension

r_exp  0.719803335 r_exp_dash  1.71783276
r_wp  33.8144986 r_wp_dash  80.699339
r_p  74.2758777 r_p_dash  92.9476929
weighted_Durbin_Watson  0.21349848 gof  46.9774131
 
start_X  1.5   
finish_X  13.53 
x_calculation_step 0.01
bkg @  309.023647`  159.619286` 0 0


str
	r_bragg  76.2881301
	phase_MAC  0.942220333
	phase_name "Cr2Ga(0.3)Ge(0.7)C"
	MVW ( 167.551, 45.729`, 15.778`)
	space_group 194
	scale  @  1.40775053e-005`
	
	Phase_Density_g_on_cm3( 6.08421`)
	
	Hexagonal ( @  2.233438`,@  10.585572`)
	site Cr num_posns  2 x =1/3; y =2/3; z =0.586 occ Cr 1 beq =1
	site Ge num_posns 2 x =1/3; y =2/3; z =1/4; occ Ge !a 0.7 beq !b 1 occ Ga =1-a; :  0.30000 beq =b; :  1.00000
	site C num_posns  2 x  0 y  0 z  0 occ C  1 beq  1

Create_2Th_Ip_file(2Th_Cr2Ga(0.3)Ge(0.7)C.txt)
'--------------------------------------
str
r_bragg 81.0244325
phase_MAC 0.163790491
phase_name "C"
MVW ( 72.064, 32.430, 46.788)
space_group R-3mh
scale @ 0.000136866085`

	Phase_Density_g_on_cm3( 3.68996`)
	
	Trigonal( @  1.933574`, @  10.016008`)
	site C num_posns  6 x  0 y  0 z  0.16667 occ C  1 beq  1

Create_2Th_Ip_file(C.txt)
'--------------------------------------
str
r_bragg 74.0900105
phase_MAC 0.725902558
phase_name "Cr3Ge"
MVW ( 457.257, 80.030, 37.434)
space_group Pm-3n
scale @ 6.99326466e-006`

	Phase_Density_g_on_cm3( 9.48757`)
	
	Cubic(@  4.309413`)
	site Cr num_posns  6 x =1/4; y  0 z =1/2; occ Cr  1 beq  1
	site Ge num_posns  2 x  0 y  0 z  0 occ Ge  1 beq  1

Create_2Th_Ip_file(Cr3Ge.txt)

'------------------[Output-Graphical_Data]--------------------

Out_Yobs_Ycalc_and_Difference(SK200_70Ge_Graphical_Data.txt)

'--------------------------------------
for xdds
{
' Enter INP text
macro x_offset_eqtn_1 {a_coef_1((Rad 2Th)²) + b_coef_1((Rad 2Th)) + c_coef_1}
prm a_coef_1 -0.00001' 9.5598462e-06 '- prm b_coef_1 0.00008 ' -0.000101340104 '
prm c_coef_1 0

     GeometricIntensityFactorFlat2DDetector     
     ReflectionProbability     
     LorentzCorrection     
     th2_offset = x_offset_eqtn_1;   
   
    User_Defined_Dependence_Convolution(gauss_fwhm, , @, 0.00010`)   
    User_Defined_Dependence_Convolution(lor_fwhm,  , @, 1.53883`)   
    User_Defined_Dependence_Convolution(gauss_fwhm,  Tan(Th)    , @, 87.20613`)  
    User_Defined_Dependence_Convolution(lor_fwhm,  Tan(Th)    , @, 0.00191`) 
 lam   
    ymin_on_ymax  1e-06   
    la  1 lo !WavelengthID31 0.16531226319520955 min =0.164; max =0.167; lh  0.001   
	  
 convolution_step 4   
}

'----------------[MACROS]----------------------

macro vals_after_converg { val_on_continue = Val + Rand(-0.06Val, 0.06Val) } 'Simple macro used with the continue_after_convergence keyword above

macro GeometricIntensityFactorFlat2DDetector
{
'This includes the cosine dependance for longer transition through detecting layer (Cos(2Th) at higher angles
scale_pks = 1 / Cos(2 Th);
}
macro ReflectionProbability
{
' the probability of a reflection being in a scattering position. Usually bundled with the Lorentz correction
scale_pks = 1 / Sin(Th);
}
macro LorentzCorrection
{
' not sure this is perfectly correct for a 2D detector. Correction for the path taken through the Ewald sphere during the rotation of the crystallite in the primary beam
scale_pks = 1 / Sin(2 Th);
}

johnsoevans

Have your peaks just gone infinitely broad? You seem to have a fwhm of 87 degrees. Try making the peaks sharp again (reset to values from a standard). You might find that your cell parameters and scale factors have also refined to unreasonable values.

suneetkale

@johnsoevans No. I don't see any peaks at all. It stops refining, and there are no computational peaks. I will try that. Yes, all cell parameters and scales have gone to unreasonable values and hit limits.

suneetkale

suneetkale I have created the exact code with some other samples, which works very well. This happens only when I have a substitution in a structure at a particular site.

suneetkale

This is solved. I had incorrect instrument parameters.

Elena

Thank you, Suneet, for the update on the error. I came here after getting the same error and useless intentions to adjust the X-axis limits. In my case, the error was generated after the wrong assumption that RS can be 0 as the file was generated on the MP expert diffractometer using PIXcel 1D detector with no Receiving Slit.