Re: [Ifeffit] How to input atoms in solid solution for Artemis

[Fuxiang Zhang]

Thank you all for the help.

Fuxiang

On Thu, Jun 23, 2016 at 10:19 PM, Matt Newville 
wrote:

> Fuxiang,
>
>
> On Thu, Jun 23, 2016 at 4:47 PM, Fuxiang Zhang  wrote:
>
>> Hi, Scott,
>>
>> In fact, I have a series of single crystal Ni-Fe alloys (Fm-3m) with
>> known atomic ratio, and measured both Fe and Ni edges for samples and
>> standards. I just want to see if there's any difference between the local
>> bonding environment of Fe and Ni, such as R, N and sigma2. Now using the
>> suggested method by Matt by changing atoms in FEFF.inp file, I can only
>> get ss, deltr and E0 from fitting (I don't know how to refine N and R).
>>
>
> You can refine N and deltaR for any scattering path.  R is Reff + deltaR,
> so that *is* refining R.   When you say "I don't know how to refine N and
> R", I'm left unsure what part you do and do not know. There are lots of
> on-line examples and documentation.  If you're having trouble, it might
> help to ask a specific question.
>
>
>> But the fitting with Ni (or Fe) edge can only generate the same R and
>> deltr for Ni-Ni and Ni-Fe pairs.
>>
>
> I'm sorry, I don't understand.  In principle, the Ni-Ni distance and Ni-Fe
> distances can be different, of course.
>
> Fitting the edges of Ni and Fe will yield a little difference in the R and
>> deltr. Which results should I believe, or something wrong I am using the
>> program because I cannot generate different R for Ni-Ni and Ni-Fe pairs
>> with the same data set.
>> Many thanks for your suggestions and helps.
>>
>
> I can't tell whether you're saying you do not know how to tell Artemis to
> refine different distances for Ni-Ni and Ni-Fe, or that when you do tell it
> to do this that the result is that the two distances are the same.
>
> As said earlier, unless you're looking at some weird situation, I would
> expect measuring distances and coordination numbers separately for Ni-Ni,
> Ni-Fe, Fe-Fe, and Fe-Ni to be very, very hard.   My recollection (could be
> wrong) is that the nominal near-neighbor distances for fcc Ni and bcc Fe
> are both around 2.48 Ang.  With Z different by only 2, I would not expect
> these to be distinguishable.
>
> But the program definitely allow you to try
>
> --Matt Newville
>
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Re: [Ifeffit] How to input atoms in solid solution for Artemis

[Matt Newville]

Fuxiang,


On Thu, Jun 23, 2016 at 4:47 PM, Fuxiang Zhang  wrote:

> Hi, Scott,
>
> In fact, I have a series of single crystal Ni-Fe alloys (Fm-3m) with known
> atomic ratio, and measured both Fe and Ni edges for samples and standards.
> I just want to see if there's any difference between the local bonding
> environment of Fe and Ni, such as R, N and sigma2. Now using the suggested
> method by Matt by changing atoms in FEFF.inp file, I can only get ss, deltr
> and E0 from fitting (I don't know how to refine N and R).
>

You can refine N and deltaR for any scattering path.  R is Reff + deltaR,
so that *is* refining R.   When you say "I don't know how to refine N and
R", I'm left unsure what part you do and do not know. There are lots of
on-line examples and documentation.  If you're having trouble, it might
help to ask a specific question.


> But the fitting with Ni (or Fe) edge can only generate the same R and
> deltr for Ni-Ni and Ni-Fe pairs.
>

I'm sorry, I don't understand.  In principle, the Ni-Ni distance and Ni-Fe
distances can be different, of course.

Fitting the edges of Ni and Fe will yield a little difference in the R and
> deltr. Which results should I believe, or something wrong I am using the
> program because I cannot generate different R for Ni-Ni and Ni-Fe pairs
> with the same data set.
> Many thanks for your suggestions and helps.
>

I can't tell whether you're saying you do not know how to tell Artemis to
refine different distances for Ni-Ni and Ni-Fe, or that when you do tell it
to do this that the result is that the two distances are the same.

As said earlier, unless you're looking at some weird situation, I would
expect measuring distances and coordination numbers separately for Ni-Ni,
Ni-Fe, Fe-Fe, and Fe-Ni to be very, very hard.   My recollection (could be
wrong) is that the nominal near-neighbor distances for fcc Ni and bcc Fe
are both around 2.48 Ang.  With Z different by only 2, I would not expect
these to be distinguishable.

But the program definitely allow you to try

--Matt Newville
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Re: [Ifeffit] How to input atoms in solid solution for Artemis

[Anatoly I Frenkel]

You definitely will see the difference (sorry that I am replying instead of 
Scott who will not mind of course) because from Ni edge the result means an 
effective mixture of Ni-Ni and Ni-Fe bond lengths, and for edge - the effective 
mixture of Fe-Ni and Fe-Fe bonds. That's why you get different results. If you 
could measure separately Fe-Ni and Ni-Fe (you can't ) their lengths should have 
been the same, of course, but in your case you are not doing that, hence the 
difference.

It could have been caused by a million other reasons, e.g. the correlation with 
other parameters or bad data quality or mistakes in the model or how you 
constructed the fitting procedure, but it is besides the point.

Anatoly

Sent from my iPhone

On Jun 23, 2016, at 5:51 PM, Fuxiang Zhang 
> wrote:

Hi, Scott,

In fact, I have a series of single crystal Ni-Fe alloys (Fm-3m) with known 
atomic ratio, and measured both Fe and Ni edges for samples and standards. I 
just want to see if there's any difference between the local bonding 
environment of Fe and Ni, such as R, N and sigma2. Now using the suggested 
method by Matt by changing atoms in FEFF.inp file, I can only get ss, deltr and 
E0 from fitting (I don't know how to refine N and R). But the fitting with Ni 
(or Fe) edge can only generate the same R and deltr for Ni-Ni and Ni-Fe pairs. 
Fitting the edges of Ni and Fe will yield a little difference in the R and 
deltr. Which results should I believe, or something wrong I am using the 
program because I cannot generate different R for Ni-Ni and Ni-Fe pairs with 
the same data set.
Many thanks for your suggestions and helps.

Fuxiang Zhang

On Thu, Jun 23, 2016 at 4:23 PM, Scott Calvin 
> wrote:
One additional thought:

Distinguishing Ni-Ni and Ni-Fe by creating two different feff paths and fitting 
the spectrum as a mixture of the two is very difficult, to put it mildly, as 
both Anatoly and Matt indicated.

But the bond length determined by your fit may be able to give you a clue, 
particularly when compared to appropriate standards. Depending on the details 
of your structure, the average bond length may depend on the fraction of sites 
occupied by iron to a degree which is measurable by EXAFS. Even if you simply 
use a nickel-nickel scattering path in feff to model your structure, 
differences in bond length could be indicative of changes in site occupancy.

Ideally, this could be done by creating a series of standards with known 
iron-nickel ratios, fitting the bond length for each, and then comparing a fit 
of a sample with a similar structure but unknown iron-nickel ratio to the 
results for the standards.

—Scott Calvin
Sarah Lawrence College

On Jun 23, 2016, at 3:41 PM, Fuxiang Zhang 
> wrote:

Hi, Matt and Anayoly,
Thank you very much for the help.

Fuxiang

On Thu, Jun 23, 2016 at 1:51 PM, Anatoly I Frenkel 
> wrote:
Whatever you decide to do, remember that Ni Ni and Ni Fe pairs look very 
similar by EXAFS, so it does not matter how you end up doing it.
You can as well use pure Ni but you may want to consider both fcc and bcc 
structure for making the model because the alloy may end up to be either that 
or that, especially if it is a nanoalloy.

Anayoly



Sent from my Verizon Wireless 4G LTE Tablet


 Original message 
From: Fuxiang Zhang >
Date: 6/23/2016 12:51 PM (GMT-05:00)
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] How to input atoms in solid solution for Artemis

Hi, All,
I am new in using EXAFS techniques. Just wondering how to input atomic 
structure of NiFe solid solution to Artemis. It has a simple Ni-structure, but 
both Ni and Fe occupy the same site. If I use partial occupancy, Artemis 
program does not allow. Anyone can give me an ideal?
Also the coordination number N cannot be refined in this simple system (12), is 
that right? In fact I just want to get the N through the fitting of EXAFS 
because of the partial occupancy.
Thank you very much

Fuxiang Zhang

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Re: [Ifeffit] How to input atoms in solid solution for Artemis

[Fuxiang Zhang]

Hi, Scott,

In fact, I have a series of single crystal Ni-Fe alloys (Fm-3m) with known
atomic ratio, and measured both Fe and Ni edges for samples and standards.
I just want to see if there's any difference between the local bonding
environment of Fe and Ni, such as R, N and sigma2. Now using the suggested
method by Matt by changing atoms in FEFF.inp file, I can only get ss, deltr
and E0 from fitting (I don't know how to refine N and R). But the fitting
with Ni (or Fe) edge can only generate the same R and deltr for Ni-Ni and
Ni-Fe pairs. Fitting the edges of Ni and Fe will yield a little difference
in the R and deltr. Which results should I believe, or something wrong I am
using the program because I cannot generate different R for Ni-Ni and Ni-Fe
pairs with the same data set.
Many thanks for your suggestions and helps.

Fuxiang Zhang

On Thu, Jun 23, 2016 at 4:23 PM, Scott Calvin 
wrote:

> One additional thought:
>
> Distinguishing Ni-Ni and Ni-Fe by creating two different feff paths and
> fitting the spectrum as a mixture of the two is very difficult, to put it
> mildly, as both Anatoly and Matt indicated.
>
> But the bond length determined by your fit *may* be able to give you a
> clue, particularly when compared to appropriate standards. Depending on the
> details of your structure, the average bond length may depend on the
> fraction of sites occupied by iron to a degree which is measurable by
> EXAFS. Even if you simply use a nickel-nickel scattering path in feff to
> model your structure, differences in bond length could be indicative of
> changes in site occupancy.
>
> Ideally, this could be done by creating a series of standards with known
> iron-nickel ratios, fitting the bond length for each, and then comparing a
> fit of a sample with a similar structure but unknown iron-nickel ratio to
> the results for the standards.
>
> —Scott Calvin
> Sarah Lawrence College
>
> On Jun 23, 2016, at 3:41 PM, Fuxiang Zhang  wrote:
>
> Hi, Matt and Anayoly,
> Thank you very much for the help.
>
> Fuxiang
>
> On Thu, Jun 23, 2016 at 1:51 PM, Anatoly I Frenkel 
> wrote:
>
>> Whatever you decide to do, remember that Ni Ni and Ni Fe pairs look very
>> similar by EXAFS, so it does not matter how you end up doing it.
>> You can as well use pure Ni but you may want to consider both fcc and bcc
>> structure for making the model because the alloy may end up to be either
>> that or that, especially if it is a nanoalloy.
>>
>> Anayoly
>>
>>
>>
>> Sent from my Verizon Wireless 4G LTE Tablet
>>
>>
>>  Original message 
>> From: Fuxiang Zhang 
>> Date: 6/23/2016 12:51 PM (GMT-05:00)
>> To: ifeffit@millenia.cars.aps.anl.gov
>> Subject: [Ifeffit] How to input atoms in solid solution for Artemis
>>
>> Hi, All,
>> I am new in using EXAFS techniques. Just wondering how to input atomic
>> structure of NiFe solid solution to Artemis. It has a simple Ni-structure,
>> but both Ni and Fe occupy the same site. If I use partial occupancy,
>> Artemis program does not allow. Anyone can give me an ideal?
>> Also the coordination number N cannot be refined in this simple system
>> (12), is that right? In fact I just want to get the N through the fitting
>> of EXAFS because of the partial occupancy.
>> Thank you very much
>>
>> Fuxiang Zhang
>>
>> ___
>> Ifeffit mailing list
>> Ifeffit@millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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>>
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Re: [Ifeffit] How to input atoms in solid solution for Artemis

[Scott Calvin]

One additional thought:

Distinguishing Ni-Ni and Ni-Fe by creating two different feff paths and fitting 
the spectrum as a mixture of the two is very difficult, to put it mildly, as 
both Anatoly and Matt indicated.

But the bond length determined by your fit may be able to give you a clue, 
particularly when compared to appropriate standards. Depending on the details 
of your structure, the average bond length may depend on the fraction of sites 
occupied by iron to a degree which is measurable by EXAFS. Even if you simply 
use a nickel-nickel scattering path in feff to model your structure, 
differences in bond length could be indicative of changes in site occupancy.

Ideally, this could be done by creating a series of standards with known 
iron-nickel ratios, fitting the bond length for each, and then comparing a fit 
of a sample with a similar structure but unknown iron-nickel ratio to the 
results for the standards.

—Scott Calvin
Sarah Lawrence College

> On Jun 23, 2016, at 3:41 PM, Fuxiang Zhang  wrote:
> 
> Hi, Matt and Anayoly,
> Thank you very much for the help.
> 
> Fuxiang
> 
> On Thu, Jun 23, 2016 at 1:51 PM, Anatoly I Frenkel  > wrote:
> Whatever you decide to do, remember that Ni Ni and Ni Fe pairs look very 
> similar by EXAFS, so it does not matter how you end up doing it.
> You can as well use pure Ni but you may want to consider both fcc and bcc 
> structure for making the model because the alloy may end up to be either that 
> or that, especially if it is a nanoalloy.
> 
> Anayoly
> 
> 
> 
> Sent from my Verizon Wireless 4G LTE Tablet
> 
> 
>  Original message 
> From: Fuxiang Zhang > 
> Date: 6/23/2016 12:51 PM (GMT-05:00) 
> To: ifeffit@millenia.cars.aps.anl.gov 
>  
> Subject: [Ifeffit] How to input atoms in solid solution for Artemis 
> 
> Hi, All,
> I am new in using EXAFS techniques. Just wondering how to input atomic 
> structure of NiFe solid solution to Artemis. It has a simple Ni-structure, 
> but both Ni and Fe occupy the same site. If I use partial occupancy, Artemis 
> program does not allow. Anyone can give me an ideal?
> Also the coordination number N cannot be refined in this simple system (12), 
> is that right? In fact I just want to get the N through the fitting of EXAFS 
> because of the partial occupancy.
> Thank you very much
> 
> Fuxiang Zhang 
> 
> ___
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> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit 
> 
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit 
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> 
> 
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Re: [Ifeffit] How to input atoms in solid solution for Artemis

[Fuxiang Zhang]

Hi, Matt and Anayoly,
Thank you very much for the help.

Fuxiang

On Thu, Jun 23, 2016 at 1:51 PM, Anatoly I Frenkel  wrote:

> Whatever you decide to do, remember that Ni Ni and Ni Fe pairs look very
> similar by EXAFS, so it does not matter how you end up doing it.
> You can as well use pure Ni but you may want to consider both fcc and bcc
> structure for making the model because the alloy may end up to be either
> that or that, especially if it is a nanoalloy.
>
> Anayoly
>
>
>
> Sent from my Verizon Wireless 4G LTE Tablet
>
>
>  Original message 
> From: Fuxiang Zhang 
> Date: 6/23/2016 12:51 PM (GMT-05:00)
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: [Ifeffit] How to input atoms in solid solution for Artemis
>
> Hi, All,
> I am new in using EXAFS techniques. Just wondering how to input atomic
> structure of NiFe solid solution to Artemis. It has a simple Ni-structure,
> but both Ni and Fe occupy the same site. If I use partial occupancy,
> Artemis program does not allow. Anyone can give me an ideal?
> Also the coordination number N cannot be refined in this simple system
> (12), is that right? In fact I just want to get the N through the fitting
> of EXAFS because of the partial occupancy.
> Thank you very much
>
> Fuxiang Zhang
>
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> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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Re: [Ifeffit] How to input atoms in solid solution for Artemis

[Matt Newville]

Hi Fuxiang,

On Thu, Jun 23, 2016 at 11:38 AM, Fuxiang Zhang  wrote:

> Hi, All,
> I am new in using EXAFS techniques. Just wondering how to input atomic
> structure of NiFe solid solution to Artemis. It has a simple Ni-structure,
> but both Ni and Fe occupy the same site. If I use partial occupancy,
> Artemis program does not allow. Anyone can give me an ideal?
>

The concept of "partial occupancy" for a representation of a crystal does
not really work for modeling EXAFS.   Instead, to model EXAFS, you make a
cluster of atoms, each of which has X, Y, Z positions and a fully
determined atomic number -- an atom cannot be half Fe and half Ni.

You can start with a crystal structure of a full occupancy crystal and
create a cluster of atoms from that, then EDIT this representation of that
cluster (held in feff.inp) to build a cluster with some atoms moved,
replaced by other species, etc.Editing feff.inp is sort of a common
answer on this list, and I'm sure that an internet search will give you
directions.   You may even find

   https://bruceravel.github.io/demeter/artug/extended/dopants.html

from the Artemis documentation helpful. ;).

Also the coordination number N cannot be refined in this simple system
> (12), is that right?
>

No, that is not right.


> In fact I just want to get the N through the fitting of EXAFS because of
> the partial occupancy.
>

One can get partial coordination numbers from EXAFS analysis.

As Anatoly points out, distinguishing "Ni-Ni" from "Ni-Fe" or "Fe-Fe" will
be extremely difficult.

Hope that helps,

--Matt
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Re: [Ifeffit] How to input atoms in solid solution for Artemis

[Anatoly I Frenkel]

Whatever you decide to do, remember that Ni Ni and Ni Fe pairs look very 
similar by EXAFS, so it does not matter how you end up doing it.
You can as well use pure Ni but you may want to consider both fcc and bcc 
structure for making the model because the alloy may end up to be either that 
or that, especially if it is a nanoalloy.

Anayoly



Sent from my Verizon Wireless 4G LTE Tablet


 Original message 
From: Fuxiang Zhang 
Date: 6/23/2016 12:51 PM (GMT-05:00)
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] How to input atoms in solid solution for Artemis

Hi, All,
I am new in using EXAFS techniques. Just wondering how to input atomic 
structure of NiFe solid solution to Artemis. It has a simple Ni-structure, but 
both Ni and Fe occupy the same site. If I use partial occupancy, Artemis 
program does not allow. Anyone can give me an ideal?
Also the coordination number N cannot be refined in this simple system (12), is 
that right? In fact I just want to get the N through the fitting of EXAFS 
because of the partial occupancy.
Thank you very much

Fuxiang Zhang
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