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R Bragg over 99%
Simultaneous Rietveld & PDF refinement in sequential mode of synchrotron data
Skoswas #1
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Subject: R Bragg over 99%
I am fitting in sequential mode (Rietveld and PDF simultaneously) a series of thirty-one diffraction
patterns collected at Diamond. Everything seems to go fine,
but in three data sets the R_Bragg indicator jumps to over 99 for no apparent
reason. The fitted parameters vary in a smooth fashion for the whole series,
even for the patterns that display this strange behaviour. Could anyone find
an explanation for this, or spot what I am doing wrong?

I am attaching a list of the most relevant parameters.

Thanks in advance.

Xabier Turrillas (ICMAB-CSIC)

Temp(K) Rwp_riet  Rwp_PDF    R_Brag      a          err              c             err          xy1          err          zy2           err           xf1           err            zf1            err           xf2           err           zf2            err            xf3           err          Y_biso     err            K_biso     err            F_biso     err           
104.6   6.68065  29.65662   2.37529   8.15456   0.00166  11.49200   0.00454  0.26397   0.00029   0.25364   0.00067   0.22258   0.00097   0.37732   0.00115   0.16681   0.00075   0.15832   0.00150   0.33362   0.00149   0.27743   0.02789   0.19779   0.12262   0.05013   0.07451 
158.3   6.53591  28.12024   2.26936   8.15614   0.00164  11.49656   0.00447  0.26384   0.00029   0.25330   0.00065   0.22318   0.00097   0.37713   0.00116   0.16680   0.00074   0.15811   0.00148   0.33361   0.00147   0.24534   0.02691   0.54997   0.13071   0.04463   0.07321 
210.7   6.56947  27.68444   2.29121   8.15677   0.00195  11.50711   0.00531  0.26390   0.00029   0.25320   0.00066   0.22340   0.00101   0.37732   0.00120   0.16673   0.00077   0.15821   0.00156   0.33345   0.00155   0.27142   0.02720   0.73892   0.13741   0.10457   0.07422 
262.2   6.65546  27.65978   2.36595   8.16273   0.00181  11.50712   0.00491  0.26389   0.00029   0.25323   0.00068   0.22329   0.00105   0.37780   0.00124   0.16679   0.00076   0.15814   0.00154   0.33358   0.00153   0.31547   0.02810   0.85696   0.14193   0.13084   0.07466 
312.9   6.53701  27.03154   2.31474   8.17172   0.00165  11.51066   0.00452  0.26369   0.00029   0.25306   0.00068   0.22325   0.00107   0.37793   0.00126   0.16678   0.00074   0.15787   0.00150   0.33356   0.00149   0.37914   0.02901   1.14370   0.14931   0.19785   0.07591 
362.5   6.75107  26.97486   2.49434   8.17714   0.00163  11.51745   0.00445  0.26385   0.00030   0.25312   0.00070   0.22319   0.00113   0.37845   0.00133   0.16676   0.00076   0.15777   0.00154   0.33352   0.00152   0.42976   0.03022   1.19773   0.15364   0.24784   0.07732 
411.3   6.69419  26.70483   2.48172   8.18230   0.00161  11.52071   0.00441  0.26371   0.00030   0.25304   0.00071   0.22322   0.00117   0.37875   0.00137   0.16670   0.00076   0.15761   0.00153   0.33340   0.00152   0.47667   0.03091   1.39545   0.15870   0.30950   0.07808 
460.0   5.89273  26.79748   2.24005   8.18331   0.00107  11.48815   0.00298  0.26261   0.00030   0.25239   0.00068   0.22673   0.00133   0.37936   0.00151   0.16622   0.00066   0.15556   0.00131   0.33244   0.00131   0.58719   0.03070   2.30040   0.16942   0.69948   0.07562 
469.4   6.42751  26.92994   2.57618   8.18177   0.00114  11.48873   0.00318  0.26274   0.00033   0.25322   0.00075   0.22635   0.00143   0.37963   0.00163   0.16595   0.00073   0.15653   0.00147   0.33190   0.00146   0.67678   0.03306   1.93220   0.16892   0.72008   0.07781 
478.1   6.25583  26.69004   2.46015   8.18149   0.00111  11.48672   0.00310  0.26265   0.00031   0.25286   0.00072   0.22680   0.00140   0.37950   0.00160   0.16600   0.00070   0.15593   0.00141   0.33199   0.00140   0.65468   0.03218   2.14714   0.17049   0.76769   0.07750 
487.3   5.97566  26.58332   2.28426   8.18183   0.00107  11.48469   0.00302  0.26219   0.00032   0.25279   0.00073   0.22778   0.00144   0.37930   0.00163   0.16565   0.00071   0.15597   0.00142   0.33131   0.00141   0.64399   0.03116   2.49326   0.17277   0.84357   0.07682 
496.8   5.80083  26.60054   2.19282   8.18222   0.00105  11.48292   0.00295  0.26190   0.00032   0.25262   0.00073   0.22815   0.00145   0.37929   0.00164   0.16564   0.00069   0.15578   0.00140   0.33129   0.00139   0.65122   0.03088   2.66497   0.17395   0.87035   0.07685 
506.0   5.76904  26.64563   2.19040   8.18229   0.00105  11.48292   0.00295  0.26178   0.00032   0.25256   0.00074   0.22826   0.00147   0.37934   0.00166   0.16548   0.00070   0.15576   0.00141   0.33096   0.00140   0.66180   0.03110   2.70730   0.17518   0.88333   0.07717 
515.5   5.46299  26.90586   1.93526   8.18267   0.00104  11.48349   0.00294  0.26121   0.00031   0.25192   0.00074   0.22971   0.00148   0.37848   0.00166   0.16528   0.00071   0.15545   0.00143   0.33055   0.00141   0.63080   0.02981   3.34567   0.18284   1.01360   0.07903 
524.5   5.34556  27.42264   1.86198   8.18279   0.00109  11.48562   0.00307  0.26071   0.00032   0.25136   0.00076   0.23062   0.00151   0.37752   0.00169   0.16514   0.00074   0.15525   0.00149   0.33029   0.00147   0.63597   0.03009   3.82219   0.19453   1.11695   0.08449 
533.7   5.34831  27.89207   1.84998   8.18305   0.00083  11.48965   0.00227  0.26019   0.00034   0.25100   0.00081   0.23216   0.00162   0.37682   0.00181   0.16473   0.00082   0.15552   0.00167   0.32945   0.00164   0.62160   0.02988   4.43761   0.21128   1.25838   0.08996 
543.1   6.19516  26.48954   2.54625   8.18272   0.00117  11.49276   0.00327  0.26228   0.00032   0.25220   0.00074   0.22667   0.00146   0.38002   0.00163   0.16591   0.00069   0.15467   0.00137   0.33183   0.00137   0.75263   0.03390   2.24422   0.17576   0.82287   0.08074 
552.1   6.38441  26.27536   2.65446   8.18458   0.00121  11.49270   0.00339  0.26214   0.00035   0.25317   0.00081   0.22636   0.00163   0.38094   0.00180   0.16549   0.00076   0.15600   0.00153   0.33099   0.00152   0.78580   0.03463   2.25398   0.17667   0.84011   0.07985 
561.4   6.55330  26.25395   2.77144   8.18713   0.00115  11.49128   0.00322  0.26230   0.00035   0.25320   0.00081   0.22571   0.00160   0.38116   0.00178   0.16567   0.00074   0.15592   0.00149   0.33133   0.00148   0.80421   0.03532   2.15512   0.17699   0.80988   0.08051 
570.8   7.07119  26.47107   3.19337   8.18870   0.00117  11.49230   0.00327  0.26270   0.00037   0.25359   0.00084   0.22456   0.00165   0.38204   0.00181   0.16597   0.00075   0.15597   0.00151   0.33194   0.00150   0.84759   0.03756   1.81216   0.17722   0.73596   0.08223 
579.2   6.82279  26.16836   2.96915   8.19083   0.00112  11.49205   0.00314  0.26251   0.00035   0.25331   0.00081   0.22499   0.00160   0.38177   0.00176   0.16590   0.00072   0.15575   0.00146   0.33179   0.00145   0.82821   0.03633   2.02281   0.17742   0.78258   0.08111 
588.1   6.97023  26.12191   3.10097   8.19239   0.00115  11.49429   0.00322  0.26261   0.00036   0.25341   0.00082   0.22454   0.00162   0.38193   0.00179   0.16583   0.00074   0.15587   0.00149   0.33167   0.00148   0.85144   0.03729   1.90169   0.17789   0.77666   0.08211 
597.2   7.44620  26.31384  99.84540   8.19322   0.00120  11.49875   0.00338  0.26296   0.00038   0.25378   0.00086   0.22336   0.00167   0.38256   0.00184   0.16610   0.00077   0.15615   0.00155   0.33220   0.00154   0.90965   0.03960   1.60768   0.17830   0.71367   0.08467 
606.1   7.30788  26.08231  99.25965   8.19542   0.00116  11.49919   0.00328  0.26288   0.00037   0.25370   0.00085   0.22338   0.00164   0.38249   0.00180   0.16610   0.00075   0.15606   0.00151   0.33220   0.00150   0.90283   0.03885   1.71308   0.17792   0.73959   0.08392 
614.7   7.14435  25.94753   3.39971   8.19672   0.00114  11.50242   0.00319  0.26277   0.00036   0.25345   0.00083   0.22357   0.00161   0.38226   0.00177   0.16603   0.00074   0.15597   0.00150   0.33207   0.00149   0.89707   0.03822   1.85946   0.17869   0.78348   0.08370 
623.7   6.59525  26.04390   2.92050   8.19611   0.00115  11.51099   0.00323  0.26246   0.00034   0.25264   0.00079   0.22373   0.00146   0.38103   0.00162   0.16598   0.00073   0.15554   0.00146   0.33197   0.00145   0.96010   0.03764   1.88980   0.17531   0.83512   0.08490 
632.6   6.73343  25.54420   2.97863   8.19744   0.00117  11.51414   0.00327  0.26261   0.00034   0.25301   0.00080   0.22417   0.00155   0.38155   0.00172   0.16585   0.00075   0.15583   0.00152   0.33169   0.00151   0.88990   0.03638   2.15915   0.17900   0.90559   0.08370 
641.2   6.43371  25.26453   2.77363   8.20023   0.00110  11.51362   0.00306  0.26241   0.00033   0.25264   0.00077   0.22441   0.00146   0.38095   0.00163   0.16580   0.00071   0.15557   0.00144   0.33159   0.00143   0.89732   0.03545   2.31532   0.17749   0.95903   0.08296 
684.7   6.44499  24.49716   2.82143   8.21056   0.00098  11.52013   0.00277  0.26247   0.00032   0.25258   0.00074   0.22361   0.00140   0.38105   0.00156   0.16588   0.00068   0.15571   0.00138   0.33177   0.00137   0.93081   0.03543   2.30843   0.17598   1.02438   0.08283 
727.0   6.74725  23.30142   3.20232   8.21893   0.00096  11.53620   0.00268  0.26266   0.00032   0.25290   0.00076   0.22215   0.00141   0.38186   0.00156   0.16602   0.00070   0.15616   0.00142   0.33205   0.00141   1.00519   0.03648   2.04645   0.17253   1.07963   0.08411 
768.3   6.89651  21.88400  99.89733   8.22730   0.00088  11.55461   0.00244  0.26277   0.00032   0.25325   0.00076   0.22084   0.00141   0.38272   0.00156   0.16610   0.00072   0.15673   0.00146   0.33220   0.00144   1.06207   0.03628   1.85865   0.16653   1.16653   0.08399
johnsoevans (Administrator) #2
User title: John Evans
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Nothing obvious springs to mind.
Do you get the same behaviour if you run one of the misbehaving refinements again?
What happens if you change the finish_X slightly?
AlanCoelho #3
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R-Bragg in terms of the observed intensity Io and calculated intensity Ic is defined as:

R-Bragg = Sum[ Abs(Io(hkl) - Ic(hkl)), hkl ] / Sum[Io(hkl), hkl ]

where

    Io(hkl) = Sum[ Peak(i) Yobs(i)/Yc(i), i]
   
    Peak(i) = a scaled hkl peak

        and the summations are over all hkls

To get high R-Bragg values then Sum[Io(hkl), hkl ] is probably close to zero. Which means that all of Peak(i) intensities are close to zero.

In other words the phase is non-existent. You may instead want to plot the scale parameter for that phase and see how that changes.

cheers
alan
Skoswas #4
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In reply to post #2
I have run the sequential procedure one hundred times, and the behaviour is absolutely the same.

Now I am going to modify the final 2theta, and also to check, as Alan suggests, the scale factor variations.

Thanks for your help

Cheers,
 Xavier
Skoswas #5
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By restricting the angular domain the thing has improved. From the initial range 1.2 to 17, now the computations were restricted to 1.2 to 12 2theta. This way only the last pattern exhibits a Rwp over 99.
 
I have checked the scale factors and remain within the same range, 2.8 10^-8. The phase did not vanish.

Still the fact is puzzling...

Thank you ver much for your help.
Skoswas #6
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Sorry for the mistake in previous post, I meant R Bragg instead of Rwp.
Skoswas #7
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In reply to post #2
One last observation. When restricting the angular domain to 1.3 to 17.0 instead of 1.2 to 17.0, all R Bragg factors are coherent except for the last pattern.

I am including a list of temperatures, R Bragg and scale factors. Th two previously problematic Rb are marked with ???
  Temp(k)  R Bragg    Scale factor
  104.5    2.33    2.889 x10-8   
  158.2    2.24    2.911 x10-8   
  210.6    2.27    2.852 x10-8   
  262.2    2.34    2.755 x10-8   
  312.9    2.31    2.794 x10-8   
  362.5    2.46    2.946 x10-8   
  411.3    2.46    3.008 x10-8   
  459.9    2.26    2.804 x10-8   
  469.4    2.56    2.749 x10-8   
  478.1    2.45    2.772 x10-8   
  487.3    2.31    2.871 x10-8   
  496.8    2.21    2.925 x10-8   
  505.9    2.22    2.915 x10-8   
  515.5    2.02    2.926 x10-8   
  524.4    1.94    2.905 x10-8   
  533.6    1.94    2.898 x10-8   
  543.1    2.55    2.819 x10-8   
  552.0    2.64    2.789 x10-8   
  561.4    2.75    2.762 x10-8   
  570.7    3.19    2.645 x10-8   
  579.2    2.95    2.673 x10-8   
  588.1    3.09    2.734 x10-8   
  597.2    4.46??? 2.644 x10-8   
  606.0    3.71??? 2.665 x10-8   
  614.6    3.42    2.699 x10-8   
  623.6    2.89    2.858 x10-8   
  632.5    2.95    2.818 x10-8   
  641.2    2.75    2.913 x10-8   
  684.6    2.80    2.928 x10-8   
  726.9    3.21    2.923 x10-8   
  768.2   99.94    2.911 x10-8
rowlesmr #8
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Can you provide the data and input files for

579.2    2.95    2.673 x10-8  
  588.1    3.09    2.734 x10-8  
  597.2    4.46??? 2.644 x10-8  
  606.0    3.71??? 2.665 x10-8  
  614.6    3.42    2.699 x10-8  
  623.6    2.89    2.858 x10-8  

?
--
Matthew
johnsoevans (Administrator) #9
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If changing 2theta or d range had an effect it might be worth plotting esd vs X. Are there any rogue data points or esds in the xye file?
Skoswas #10
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In reply to post #8
Dear Mattew,

I am attaching the inp file and the data in two compressed files.

Please let me know any improvement that could be introduced in the script. Also point out any possible mistake.

I would really appreciate it.
The author has attached one file to this post:
The file “RIE.zip” attached to this post was not found!
AlanCoelho #11
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Hi Xavier

I got the XY files but I don't see the INP file attached. Can you e-mail me the INP file please
cheers
alan
rowlesmr #12
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In reply to post #9
The data are all XY.

When I ran the data/file as-received, it all worked. (in TA6; it wouldn't run in TA7 - Not Responding)

If I changed the lower limit from 1.3 to 1.2, I duplicated the 99 Rbragg for the final dataset. There are negative intensities in that data from 1.02 -- 1.24. Maybe that triggered it? But there are also negative intensities from 1.90 -- 2.00...?

The peaks are most definitely there, and there is only one str.

.

Ha!

(I think) It's a bug triggered by having the initial intensities being negative. I can make Rbragg be 99 by making the initial intensities be negative.
--
Matthew
AlanCoelho #13
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Thanks for looking into that Matthew.

Negative intensities would play havoc in the Io formula:

   Io(hkl) = Sum[ Peak(i) Yobs(i)/Yc(i), i]

I think it would be best to set the intensities to zero.
Skoswas #14
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In reply to post #11
Dear Colleagues,

I am going to try to summarise the situation on the R Bragg higher than 99 issue.
Matthew Rowles kindly run the inp script with the whole series of data sets. He has a straight Windows machine to run Academic TOPAS v.6. First he run the script with angular domain set between 1.3 and 17. Everyting was fine; all R Bragg within bounds.
Then he decreased the angle, starting at 1.2 2theta, and when executed, the last pattern (#31 at 768 K) run astray. He examined the points and, indeed, found rogue intensities, as John pointed out: Negative values between 1.02 and 1.24 and also between 1.9 and 2.0 2theta. He simply removed the negative signs between 1.02 and 1.24 and run the script again. This time all diffraction patterns exhibited R Bragg within bounds and the presence of negative values between 1.9 and 2.0 didn´t seem to affect.
Matthew suggested that I tried to reproduce his findings, but I couldn´t. I always obtained Rb larger than 99 for the last pattern no matter I removed the negative signs. Now I have to explain that I use a Mac machine with MAC OS Catalina and Parallels emulation of Windows 7 64 bits to run Academic TOPAS v6.
So, the provisional conclusion is that there is no issue for an execution of the script in a straight Windows machine provided that the rogue points are duly corrected. 

Being aaware of this facts and noticing that the last pattern exhibited the lowest background of the series, I decided to attempt something weird. You may hit the rough though. I increased the background of last pattern by adding 100 units to all pints. Same thing to the two other problematic patterns but with 40 units. Notice that the highest intensity is higher than 3000 counts.
Then I run the script --between 1.2 and 17-- and presto! All Rb were within bounds as you can see below. 

 Temp(K)    Rwp Rie  Rwp PDF  R Bragg  Scale factor (x10^8)
  104.5     6.68622  29.82854   2.38        2.892
  158.2     6.53265  28.72710   2.28        2.910
  210.6     6.56902  27.71072   2.29        2.851
  262.2     6.65435  27.60508   2.36        2.753
  312.9     6.52946  26.97072   2.31        2.797
  362.5     6.75275  26.90068   2.48        2.947
  411.3     6.69387  26.74042   2.48        3.010
  459.9     5.89235  26.76382   2.23        2.804
  469.4     6.42861  26.94508   2.57        2.743
  478.1     6.25695  26.68817   2.45        2.766
  487.3     5.97527  26.58315   2.28        2.867
  496.8     5.80009  26.60056   2.19        2.925
  505.9     5.76818  26.64935   2.19        2.914
  515.5     5.46224  26.90207   1.93        2.924
  524.4     5.34491  27.42164   1.86        2.906
  533.6     5.35406  27.90878   1.84        2.894
  543.1     6.19468  26.49461   2.54        2.816
  552.0     6.38588  26.30064   2.65        2.793
  561.4     6.55292  26.24389   2.77        2.761
  570.7     7.07137  26.50039   3.19        2.645
  579.2     6.82192  26.16378   2.96        2.672
  588.1     6.96488  26.11820   3.09        2.733
  597.2     6.96411  26.29118   3.23        2.646
  606.0     6.83986  26.07572   3.13        2.665
  614.6     7.14681  26.07962   3.41        2.709
  623.6     6.59576  26.04801   2.92        2.857
  632.5     6.73250  25.53428   2.97        2.815
  641.2     6.43783  25.26765   2.77        2.914
  684.6     6.44327  24.50503   2.82        2.927
  726.9     6.74651  23.25795   3.20        2.910
  768.2     6.02061  22.06586   2.89        2.913
 
Perhaps this behaviour could provide clues of what is going on. Now the question is what is the "real" Rb value for sets at 597, 606 and 768 K?

In any case I would like to thank everyone for the contributions and hints provided. If Alan wishes to have a closer look into this issue I could furnish the patterns. Also, in due time (after being accepted for publication) you could use these results for teaching purposes if you want.
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