Different behavior of "adps" in TOPAS 4.2 and TOPAS 5

metty

I am wondering about a different behavior of the adps macro in TOPAS 4.2 and TOPAS 5.
If I run the same input file in both programs, I get different results concerning the constraints of the anisotropic displacement parameters.

In TOPAS 4.2 I get:

ADPs { @ 0.01487`_0.00071 = Get(u11); @ 0.02211`_0.00128 = 0.5 Get(u11); 0 0 } ADPs_Keep_PD
ADPs { @ 0.03564`_0.00164 @ 0.03207`_0.00186 @ 0.02390`_0.00178 @ 0.01067`_0.00127 @ -0.01848`_0.00106_LIMIT_MIN_-0.0291853464 @ 0.00224`_0.00122 } ADPs_Keep_PD
ADPs { @ 0.03189`_0.00430_LIMIT_MIN_0 = Get(u11); @ 0.02271`_0.00666_LIMIT_MIN_0 = 0.5 Get(u11); 0 0 } ADPs_Keep_PD
ADPs { @ 0.04050`_0.00176 = Get(u11); @ 0.03010`_0.00349_LIMIT_MIN_0 = 0.5 Get(u11); 0 0 } ADPs_Keep_PD

whereas I get in TOPAS 5:

ADPs { @ 0.01512`_0.00188 @ 0.01448`_0.00148 @ 0.02520`_0.00241 @ 0.00574`_0.00174_LIMIT_MAX_0.0147976894 @ 0.00605`_0.00244_LIMIT_MAX_0.0195206012 @ -0.00028`_0.00192 } ADPs_Keep_PD
ADPs { @ 0.03200`_0.00171 @ 0.03354`_0.00198 @ 0.02116`_0.00187 @ 0.01051`_0.00130 @ -0.01635`_0.00107_LIMIT_MIN_-0.0260222577 @ 0.00111`_0.00130 } ADPs_Keep_PD
ADPs { @ 0.01846`_0.01278_LIMIT_MIN_0 @ 0.06854`_0.00993 @ 0.06737`_0.01742_LIMIT_MIN_0 @ 0.03557`_0.01086_LIMIT_MIN_-0.0355686291 @ 0.03526`_0.01470_LIMIT_MIN_-0.0352641578 @ -0.04143`_0.01339_LIMIT_MIN_-0.0679562909 } ADPs_Keep_PD
ADPs { @ 0.03447`_0.00867_LIMIT_MIN_0 @ 0.03433`_0.00539_LIMIT_MIN_0 @ 0.02919`_0.00474_LIMIT_MIN_0 @ -0.03440`_0.00880_LIMIT_MIN_-0.0344016692 @ 0.03172`_0.00897_LIMIT_MIN_-0.0317201503 @ -0.01777`_0.00567_LIMIT_MIN_-0.0316539587 } ADPs_Keep_PD

It is obvious that TOPAS 5 did not care about the symmetry constraints of the anisotropic displacement parameters.
The question is now why? I have used the exactly same input file for both programs with the command "adps ADPs_Keep_PD". Did I miss something new in the documentation?

johnsoevans

Dear Metty,

I think there was a bug in some intermediate versions of topas v5 which were later corrected (I'm afraid I forget the exact details now; it's mentioned in e.g. https://neutrons.ornl.gov/sites/default/files/Refining-POWGEN-data-TOPAS_040617.pdf).

If you want to check the values then try table 8.3.1.1 in International Tables or the table on P104 in Terry Willis' text “Thermal vibrations in crystallography”; both list the proper constraints.

Sorry it's not a more useful answer.

John

metty

Dear John,

thank you for sharing this information! I was just wondering that such a bug went into an official and commercial version of TOPAS 5 which is distribuited by Bruker. However, I guess Alan will fix this issue in the next Bruker version of TOPAS 6.

Many thanks and best wishes,

Metty

rowlesmr

I've currently got a requirement to see if I gan do some ADP refinements. As a workaround, I've written up some macros to do the constraints.

http://topas.dur.ac.uk/topaswiki/doku.php?id=adps_with_symmetry_constraints

I tried reading the International Tables, but couldn't understand it, so I got everything from “Thermal vibrations in crystallography”, as suggested by John.

You'll need the textbook or the original paper they took everything from to use them properly.

Matthew