[Ifeffit] iron carbide fitting with Artemis
Yunyun Zhou
yyzhouzhou at gmail.com
Fri Oct 27 19:50:37 CDT 2017
Hello Mike,
Thank you so much for your detailed explanation. I do appreciate your help.
I agree with you that walking through these steps with an expert will be
much helpful. I should attend some XAFS workshop in the future. Thanks
again for your help.
Have a great weekend!
Best,
Yunyun
On Thu, Oct 26, 2017 at 6:17 PM, Mike Massey <mmassey at gmail.com> wrote:
> The way I usually do it is to just pick one of the FEFF paths (instead of
> both) corresponding to the distance you care about. I actually haven't used
> the latest version of Artemis to do any fitting recently, but I assume it
> is still similar.
>
> In your list of FEFF paths, pick C1.1, right-click and "include C1.1 in
> the fit." Then you define your fitting parameters for that atom at that
> distance, one of which should be the coordination number of the atom (I
> typically might define amplitude as S02*CN and put path degeneracy at 1,
> but there are probably other, better ways to do this — I hope someone more
> knowledgeable might correct me if this is a poor approach).
>
> So then your amplitude fitting parameter, "amp_C1," basically becomes a
> proxy for the coordination number of that atom at that distance, and
> "ss_C1" is your measure of disorder. So instead of trying to fit two C at
> 1.94 and 1.99 Angstroms individually, you model that with a single path of
> C at around 1.97 Angstroms (or whatever FEFF's R plus your fit's delr is)
> with disorder ss_C1, and you either set the coordination number to 2, or
> you guess it in the fit and hope it comes out to around 2, since it
> probably should.
>
> There are probably a lot of ways to approach this, every person seems to
> have their preferred method. You might consider setting up a screen-sharing
> videoconference with someone and get them to walk you through their process
> for fitting. It seems to be something that is effectively learned through
> apprenticeship. Another possibility is attending an EXAFS fitting workshop,
> if any are coming up.
>
> I recommend getting a really good handle on single-phase fitting before
> even attempting multi-phase fits. If appropriate, you can even just do LCF
> for the multi-phase system.
>
>
> Just my two cents, hope my thoughts are helpful and not grossly wrong (if
> wrong, hopefully someone will correct me — thanks in advance).
>
> Cheers,
>
>
> Mike
>
>
>
>
>
> On Oct 26, 2017, at 2:06 PM, Yunyun Zhou <yyzhouzhou at gmail.com> wrote:
>
> Hello Mike,
>
> Thank you very much for your help. I have a question about combining
> different atoms in a shell. For example, in the Fe5C2 model,
> ATOMS * this list contains 221 atoms
> * x y z ipot tag distance
> 0.00000 0.00000 0.00000 0 Fe1 0.00000
> -0.19385 1.76888 -0.78107 4 C1.1 1.94335
> -0.19385 -0.94552 1.72493 4 C1.2 1.97661
>
> If I am going to combine C1.1 and C1.2, shall I set them the cartisian
> coordinate as in FEFF file?
>
> ATOMS * this list contains 221 atoms
> * x y z ipot tag distance
> 0.00000 0.00000 0.00000 0 Fe1 0.00000
> 0.00000 0.00000 1.94335 4 C1.1 1.94335
>
> Thanks a lot for your help again!
>
> Best,
>
> Yunyun
>
>
> On Thu, Oct 26, 2017 at 4:40 PM, Mike Massey <mmassey at gmail.com> wrote:
>
>> I definitely recommend combining multiple atoms of similar distances into
>> the same path. That's what you end up with anyway if you use multiple
>> paths, with a lot more potential problems in the software.
>>
>> Sometimes it is beneficial to split a shell of of atoms into two, to
>> capture some physical behavior (for example, 2 atoms at 3 Angstroms and 4
>> atoms at 3.3 Angstroms, instead of one very disordered shell of 6 atoms at
>> 3.2 Angstroms).
>>
>> Depending on your data quality, I recommend building a fitting model with
>> maybe 2-8 total "shells" of atoms at different distances.
>>
>>
>>
>> Mike
>>
>>
>> > On Oct 26, 2017, at 12:52 PM, Yunyun Zhou <yyzhouzhou at gmail.com> wrote:
>> >
>> > Hello All,
>> >
>> > I am having trouble fitting my sample with both Fe5C2 and Fe3O4 as
>> standards. Hopefully somebody could help me out and I really appreciate it.
>> >
>> > My iron sample was mainly iron carbide in the core and iron oxide on
>> the shell. Fe5C2 has a monoclinic structure and generated complicated FEFF
>> paths. Many of the paths have similar distances. I have found some paper
>> reported their results as follows, which apparently combined several paths
>> together and assume they have similar path length. My first question is
>> does someone know how they did it? It seems that combing similar paths
>> makes fitting much easier, but I am not sure whether this is a correct way
>> to do the fitting.
>> >
>> > My second question is regarding fitting with the two combined models of
>> Fe5C2 and Fe3O4. I haven't fit with two models before. Is it just like what
>> I did in the attached Artemis file? Shall there be any restrictions between
>> the two models and do I have to fix some of the parameters?
>> >
>> > Thank you very much in advance for your help!
>> >
>> > Best,
>> >
>> > Yunyun Zhou
>> >
>> > Fe5C2 FEff paths:
>> > <image.png>
>> >
>> > Literature reported results:
>> > <image.png>
>> > <artemis_CWV 130 spent_example.fpj>
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