How to input atoms in solid solution for Artemis

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Fuxiang Zhang

23 Jun 2016 23 Jun '16

4:38 p.m.

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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Anatoly I Frenkel

23 Jun 23 Jun

5:51 p.m.

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

Fuxiang Zhang

7:41 p.m.

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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Scott Calvin

8:23 p.m.

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 mailto:afrenke2@yu.edu> 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 mailto:zhangfx@umich.edu> Date: 6/23/2016 12:51 PM (GMT-05:00) To: ifeffit@millenia.cars.aps.anl.gov mailto: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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Fuxiang Zhang

9:47 p.m.

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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Anatoly I Frenkel

11:11 p.m.

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 mailto:zhangfx@umich.edu> 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 mailto:dr.scott.calvin@gmail.com> 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 mailto:zhangfx@umich.edu> 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 mailto:afrenke2@yu.edu> 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 mailto:zhangfx@umich.edu> Date: 6/23/2016 12:51 PM (GMT-05:00) To: ifeffit@millenia.cars.aps.anl.govmailto: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.govmailto: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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto: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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto: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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto: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

Matt Newville

24 Jun 24 Jun

2:19 a.m.

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

Fuxiang Zhang

11:50 a.m.

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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Matt Newville

23 Jun 23 Jun

6 p.m.

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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Anatoly I Frenkel
Fuxiang Zhang
Matt Newville
Scott Calvin