Re: [Ifeffit] iron carbide fitting with Artemis

[Mike Massey]

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  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
> 0.00.00.0  0  Fe1   0.0
>-0.193851.76888   -0.78107  4  C1.1  1.94335
>-0.19385   -0.945521.72493  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
> 0.00.00.0  0  Fe1   0.0
>0.0 0.01.94335  4  C1.11.94335
> 
> Thanks a lot for your help again!
> 
> Best,
> 
> Yunyun
>  
> 
>> On Thu, Oct 26, 2017 at 4:40 PM, Mike Massey  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  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:
>> > 
>> >
>> > Literature reported results:
>> > 
>> > 
>> > 

Re: [Ifeffit] iron carbide fitting with Artemis

[Yunyun Zhou]

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
0.00.00.0  0  Fe1   0.0
   -0.193851.76888   -0.78107  4  C1.1  1.94335
   -0.19385   -0.945521.72493  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
0.00.00.0  0  Fe1   0.0
   0.0 0.01.94335  4  C1.11.94335

Thanks a lot for your help again!

Best,

Yunyun


On Thu, Oct 26, 2017 at 4:40 PM, Mike Massey  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  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:
> > 
> >
> > Literature reported results:
> > 
> > 
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Re: [Ifeffit] iron carbide fitting with Artemis

[Mike Massey]

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  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:
> 
> 
> Literature reported results:
> 
> 
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