Re: [Ifeffit] iron carbide fitting with Artemis

[Yunyun Zhou]

Dear Fred,

Thank you very much for your help. Your explanation does help me understand
the theory behind. It also reminds me to be careful of using some
parameters for future fitting analysis. Thank you so much and have a great
weekend!

Best,

Yunyun

On Fri, Oct 27, 2017 at 2:24 AM,  wrote:

> Dear Yunyun,
> I don't think Mike has written anything particularly incorrect , but he
> didn't point out why this approach is necessary.
> I believe there are two things you should definitely be aware of.
> An EXAFS dataset has a very limited amount of information. Approximately
> deltak.deltaR no of variables can be fitted
> To any spectrum as an absolute maximum and preferably quite a lot fewer
> than this (where deltak and deltaR are your fitted data range in k and R
> space respectively.
> Because of this if say you know you have N C atoms at ca G angstroms
> around your central atom. It is best not to use a variable for fit the
> degeneracy for that path but set it at the number you know is correct.
>
> And secondly because an EXAFS spectrum is effectively a collection of Sine
> waves there is a limited resolution, i.e. you cannot resolve paths of the
> same atom type that are less then Pi/2k(max) A apart, where k(max) is the
> maximum range of your dataset in k space, and Pi is Pi. Hence to separate
> two paths of the same atom that are 0.1 A apart you need about 15k worth of
> data.
>
> Regards
> Fred
>
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or
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> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
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> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
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> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
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Re: [Ifeffit] iron carbide fitting with Artemis

[Yunyun Zhou]

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  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  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 

Re: [Ifeffit] iron carbide fitting with Artemis

[fred.mosselmans]

Dear Yunyun,
I don't think Mike has written anything particularly incorrect , but he didn't 
point out why this approach is necessary. 
I believe there are two things you should definitely be aware of.
An EXAFS dataset has a very limited amount of information. Approximately 
deltak.deltaR no of variables can be fitted 
To any spectrum as an absolute maximum and preferably quite a lot fewer than 
this (where deltak and deltaR are your fitted data range in k and R space 
respectively.
Because of this if say you know you have N C atoms at ca G angstroms around 
your central atom. It is best not to use a variable for fit the degeneracy for 
that path but set it at the number you know is correct.

And secondly because an EXAFS spectrum is effectively a collection of Sine 
waves there is a limited resolution, i.e. you cannot resolve paths of the same 
atom type that are less then Pi/2k(max) A apart, where k(max) is the maximum 
range of your dataset in k space, and Pi is Pi. Hence to separate two paths of 
the same atom that are 0.1 A apart you need about 15k worth of data. 

Regards
Fred



-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom


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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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