[RMCProfile-users] Quantifying mixed site occupancy

[Eric O'Quinn]

Hi Allan,

A method that is similar to what Bob suggested if you have CrystalMaker: you can /Transform/Unit Cell/Collapse Supercell to pile up all of the atoms to their equivalent positions. Then (1) select and (2) isolate all of those atoms on a particular site and (3) /File/Export Data/Coordinates. This will give you a list of only the selected atoms as well as the occupying atomic species. Simple spreadsheet analysis can then give you the fraction that you want to know.

Best,
Eric

> On Oct 14, 2020, at 8:41 AM, Eric O'Quinn <eoquinn1 at vols.utk.edu> wrote:
> 
> Hi Allan,
> 
> A method that is similar to what Bob suggested if you have CrystalMaker: you can /Transform/Unit Cell/Collapse Supercell to pile up all of the atoms to their equivalent positions. Then (1) select and (2) isolate all of those atoms on a particular site and (3) /File/Export Data/Coordinates. This will give you a list of only the selected atoms as well as the occupying atomic species. Simple spreadsheet analysis can then give you the fraction that you want to know.
> 
> Best,
> Eric
> 
>> On Oct 14, 2020, at 8:28 AM, Von Dreele, Robert B. via rmcprofile-users <rmcprofile-users at shadow.nd.rl.ac.uk <mailto:rmcprofile-users at shadow.nd.rl.ac.uk>> wrote:
>> 
>> [External Email]
>> 
>> Hi Allan,
>> You could import the rmc6f file as a new phase in GSAS-II. Then transform it back to the original subcell; that will pileup all the equivalent atoms/vacancies on each site. That might male the counting a bit easier. (If pressed, I could add a counting tool into GSAS-II).
>> 
>> As for weights & chi**2, the weight “ought” to be chosen/changed between RMCProfile runs to make the various chi*2 values similar & all approaching unity. That way the minimization will optimally balance the contributions from the various data sets & lead to a more global minimum. Having the chi**2 values wildly different risks a false minimum where one data set is satisfied but not others.
>> Best,
>> Bob
>> 
>> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986 <https://go.microsoft.com/fwlink/?LinkId=550986>> for Windows 10
>> 
>> From: Playford, Helen (STFC, RAL, ISIS) via rmcprofile-users<mailto:rmcprofile-users at shadow.nd.rl.ac.uk <mailto:rmcprofile-users at shadow.nd.rl.ac.uk>>
>> Sent: Wednesday, October 14, 2020 3:57 AM
>> To: rmcprofile-users at shadow.nd.rl.ac.uk <mailto:rmcprofile-users at shadow.nd.rl.ac.uk><mailto:rmcprofile-users at shadow.nd.rl.ac.uk <mailto:rmcprofile-users at shadow.nd.rl.ac.uk>>
>> Cc: Playford, Helen (STFC,RAL,ISIS)<mailto:helen.playford at stfc.ac.uk <mailto:helen.playford at stfc.ac.uk>>
>> Subject: Re: [RMCProfile-users] Quantifying mixed site occupancy
>> 
>> Hi Allan,
>> 
>> I don't know of a pre-existing tool for this, unfortunately. It is often very system specific so it would be challenging to make a generic tool. The simplest way is probably to go through and count the atoms as you have mentioned, but I appreciate that with a large configuration that may be rather onerous. I'd be happy to take a look at your rmc6f file if you'd like, in case I can think of a quicker way of doing it?
>> 
>> Regarding chi^2, the value will change depending on how you've weighted your different datasets, whether you have any constraints, etc, so it's not really possible to say what a "good" number is. If the fit is visually good, the partials look sensible and the model is chemically reasonable then you're in good shape.
>> 
>> Best wishes,
>> Helen
>> 
>> -----Original Message-----
>> From: rmcprofile-users <rmcprofile-users-bounces at shadow.nd.rl.ac.uk <mailto:rmcprofile-users-bounces at shadow.nd.rl.ac.uk>> On Behalf Of Allan He via rmcprofile-users
>> Sent: 13 October 2020 23:46
>> To: rmcprofile-users at rmcprofile.org <mailto:rmcprofile-users at rmcprofile.org>
>> Cc: Allan He <alnhe at ucdavis.edu <mailto:alnhe at ucdavis.edu>>
>> Subject: [RMCProfile-users] Quantifying mixed site occupancy
>> 
>> Hi all,
>> 
>> In my system there is some mixed occupancy which I have modelled accordingly using the SWAP command.  I am wondering if there is an easy way to quantify the amount of site occupancy on each crystallographic site after the RMC simulations on the final supercell from the rmc6f file or does one have to go through it manually?
>> 
>> Additionally, what is considered a "good" final chi^2 value?  Thanks in advance!
>> 
>> Allan
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