Problems with fit in pyrite structure with Se substitution
Dear all, I am fitting a crystal pyrite structure with Se substitution in one of the sulphur atoms. I am sharing my projects in artemis. In the AMV1 project, all the parameters are sensible except for the large amplitude. I would like to know if that could be the effect of the substitution. In the second project AMV-2, I am finding large E0, which I tried to overcome by aligning the spectra with the theory in Athena. However, the fitting afterwards is worse than without such correction. https://docs.google.com/open?id=0B6dBCadbyZwFS0tDTmdDSXlWVVU (AMV-1) https://docs.google.com/open?id=0B6dBCadbyZwFYlc2c3FKT0YtbXc (AMV-2) Any ideas to help to solve these problems will be very much appreciated. Kind regards, Adriana Dr Adriana Matamoros-Veloza School of Earth and Environment University of Leeds Leeds, LS2 9JT
On Tuesday, June 26, 2012 03:51:59 PM Adriana Matamoros Veloza wrote:
I am fitting a crystal pyrite structure with Se substitution in one of the sulphur atoms. I am sharing my projects in artemis. In the AMV1 project, all the parameters are sensible except for the large amplitude. I would like to know if that could be the effect of the substitution.
In the second project AMV-2, I am finding large E0, which I tried to overcome by aligning the spectra with the theory in Athena. However, the fitting afterwards is worse than without such correction.
https://docs.google.com/open?id=0B6dBCadbyZwFS0tDTmdDSXlWVVU (AMV-1)
For me, this one came back as 404 Not found.
https://docs.google.com/open?id=0B6dBCadbyZwFYlc2c3FKT0YtbXc (AMV-2)
This one I downloaded and looked at.
Any ideas to help to solve these problems will be very much appreciated.
I don't think I have quite enough information to offer a specific suggestion, but I have several questions and comments. 1. Sulfer EXAFS is HARD! The big problem is that it can be quite challenging to select E0 sensibly unless the sample is purely of one valence. 2. Have you measured the Fe edge of these samples? The reason I ask is that being able to compare results between the two edge will certainly help. I would expect the Fe data to be easier to deal with than the S, so I suspect that the Fe results would be a useful guide here. 3. It seems plausible that all the Fe might be bound up in your pyrite, but that some S might be in different form. Are you XANES data consistent with a pure sulfide? Or might there be other S species? 4. I downloaded and looked at the second file. You are correct -- that's a poor fit :( The first thing I did was to reset the E0 parameter to 0 and then plot the data along with the three paths. I see that the Fe shell is completely out of phase with the data. That is troubling -- I would expect it to constitute the bulk of the first peak in chi(R). But it is way off. That casts doubt on your starting model. So, is that because the sample is not a pyrite (which could be the case is some portion of the S was not bound to the Fe)? Or is it because E0 in Athena was chosen poorly (which might be the case if there is more than one S valence state)? Either way, a cursory examination of your project file suggests you are off to a unlikely start. Good luck, B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel
Hi Bruce, Actually, these data correspond to Se edge measured on natural pyrite grains; we did not measure Fe edge. There are three possibilities of Se chemical environment in these samples: (1) replacement of S with Se in the pyrite structure, (2) Se is forming its own phase with iron (Se-Fe bonds), (3) it could be the combination of these two. The project AMV-1 contains data for Se edge in a different pyrite grain than the project AMV-2. So, data can be slightly different taking into account the two possibilities above. I found a better fit for AMV-1, which I will really appreciate if you can give me your comments about this project (link is working now). https://docs.google.com/open?id=0B6dBCadbyZwFS0tDTmdDSXlWVVU Kind regards, Adriana -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: 26 June 2012 16:14 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Problems with fit in pyrite structure with Se substitution On Tuesday, June 26, 2012 03:51:59 PM Adriana Matamoros Veloza wrote:
I am fitting a crystal pyrite structure with Se substitution in one of the sulphur atoms. I am sharing my projects in artemis. In the AMV1 project, all the parameters are sensible except for the large amplitude. I would like to know if that could be the effect of the substitution.
In the second project AMV-2, I am finding large E0, which I tried to overcome by aligning the spectra with the theory in Athena. However, the fitting afterwards is worse than without such correction.
https://docs.google.com/open?id=0B6dBCadbyZwFS0tDTmdDSXlWVVU (AMV-1)
For me, this one came back as 404 Not found.
https://docs.google.com/open?id=0B6dBCadbyZwFYlc2c3FKT0YtbXc (AMV-2)
This one I downloaded and looked at.
Any ideas to help to solve these problems will be very much appreciated.
I don't think I have quite enough information to offer a specific suggestion, but I have several questions and comments. 1. Sulfer EXAFS is HARD! The big problem is that it can be quite challenging to select E0 sensibly unless the sample is purely of one valence. 2. Have you measured the Fe edge of these samples? The reason I ask is that being able to compare results between the two edge will certainly help. I would expect the Fe data to be easier to deal with than the S, so I suspect that the Fe results would be a useful guide here. 3. It seems plausible that all the Fe might be bound up in your pyrite, but that some S might be in different form. Are you XANES data consistent with a pure sulfide? Or might there be other S species? 4. I downloaded and looked at the second file. You are correct -- that's a poor fit :( The first thing I did was to reset the E0 parameter to 0 and then plot the data along with the three paths. I see that the Fe shell is completely out of phase with the data. That is troubling -- I would expect it to constitute the bulk of the first peak in chi(R). But it is way off. That casts doubt on your starting model. So, is that because the sample is not a pyrite (which could be the case is some portion of the S was not bound to the Fe)? Or is it because E0 in Athena was chosen poorly (which might be the case if there is more than one S valence state)? Either way, a cursory examination of your project file suggests you are off to a unlikely start. Good luck, B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
On Wednesday, June 27, 2012 11:48:27 AM Adriana Matamoros Veloza wrote:
Actually, these data correspond to Se edge measured on natural pyrite grains; we did not measure Fe edge.
There are three possibilities of Se chemical environment in these samples: (1) replacement of S with Se in the pyrite structure, (2) Se is forming its own phase with iron (Se-Fe bonds), (3) it could be the combination of these two.
The project AMV-1 contains data for Se edge in a different pyrite grain than the project AMV-2. So, data can be slightly different taking into account the two possibilities above. I found a better fit for AMV-1, which I will really appreciate if you can give me your comments about this project (link is working now).
https://docs.google.com/open?id=0B6dBCadbyZwFS0tDTmdDSXlWVVU
Adriana, I'd love to try to help you, but this link also returns 404 not found. This Google Docs thing does not seem to be your friend. Why not just attach the project file to your email. They are usually not that big. The largest one on my computer is under 3 MB. Drat! B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel
Hi Bruce, Great, thanks a lot. The file is shared again now. https://docs.google.com/open?id=0B6dBCadbyZwFS0tDTmdDSXlWVVU Looking forward to hearing from you. Best wishes, Adriana -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: 29 June 2012 15:54 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Problems with fit in pyrite structure with Se substitution On Wednesday, June 27, 2012 11:48:27 AM Adriana Matamoros Veloza wrote:
Actually, these data correspond to Se edge measured on natural pyrite grains; we did not measure Fe edge.
There are three possibilities of Se chemical environment in these samples: (1) replacement of S with Se in the pyrite structure, (2) Se is forming its own phase with iron (Se-Fe bonds), (3) it could be the combination of these two.
The project AMV-1 contains data for Se edge in a different pyrite grain than the project AMV-2. So, data can be slightly different taking into account the two possibilities above. I found a better fit for AMV-1, which I will really appreciate if you can give me your comments about this project (link is working now).
https://docs.google.com/open?id=0B6dBCadbyZwFS0tDTmdDSXlWVVU
Adriana, I'd love to try to help you, but this link also returns 404 not found. This Google Docs thing does not seem to be your friend. Why not just attach the project file to your email. They are usually not that big. The largest one on my computer is under 3 MB. Drat! B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
On Wednesday, June 27, 2012 11:48:27 AM Adriana Matamoros Veloza wrote:
Actually, these data correspond to Se edge measured on natural pyrite grains; we did not measure Fe edge.
There are three possibilities of Se chemical environment in these samples: (1) replacement of S with Se in the pyrite structure, (2) Se is forming its own phase with iron (Se-Fe bonds), (3) it could be the combination of these two.
Wait a minute! Are the data in your first project measured at the Se edge? Or the S edge? In your second project? You keep talking about Se substitution, but the Feff calculations in your two project files have no Se atoms in them. So I am confused -- what you say you want to do is not consistent with what you have actually done in your project files. I am not sure how to advise you because I am not sure which is correct. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel
Hi Bruce, In both projects the data corresponds to Se edge (no sulphur). Selenium data was collected on natural pyrite grains. When Se associates to pyrite, it is normally inferred that Se substituted sulphur within the pyrite structure. Both elements are chemically very similar. Looking at selenium as the core atom, we want to see if it is possible to get the chemical environment related to pyrite (Se-S, Se-Fe bonds). In natural environments if substitution of sulphur with selenium occurs the proportion is rather than low (perhaps maximum 1% of the population of sulphur atoms). So, in that case we are expecting to get data that fit to the pyrite structure taking Se as the core atom. For that reason, the Feff calculations were made with the crystal structure of pyrite with sulphur as the core atom and used Se edge instead. Is that making any sense? These data are also being compared with selenium crystal structures (Se-Fe bonds only), where the abundance of Se atoms is higher. Thanks a lot for taking your time in looking at my data. Adriana -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: 02 July 2012 19:02 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Problems with fit in pyrite structure with Se substitution On Wednesday, June 27, 2012 11:48:27 AM Adriana Matamoros Veloza wrote:
Actually, these data correspond to Se edge measured on natural pyrite grains; we did not measure Fe edge.
There are three possibilities of Se chemical environment in these samples: (1) replacement of S with Se in the pyrite structure, (2) Se is forming its own phase with iron (Se-Fe bonds), (3) it could be the combination of these two.
Wait a minute! Are the data in your first project measured at the Se edge? Or the S edge? In your second project? You keep talking about Se substitution, but the Feff calculations in your two project files have no Se atoms in them. So I am confused -- what you say you want to do is not consistent with what you have actually done in your project files. I am not sure how to advise you because I am not sure which is correct. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Adriana,
On Tue, Jul 3, 2012 at 3:26 AM, Adriana Matamoros Veloza
Hi Bruce,
In both projects the data corresponds to Se edge (no sulphur). Selenium data was collected on natural pyrite grains. When Se associates to pyrite, it is normally inferred that Se substituted sulphur within the pyrite structure. Both elements are chemically very similar. Looking at selenium as the core atom, we want to see if it is possible to get the chemical environment related to pyrite (Se-S, Se-Fe bonds). In natural environments if substitution of sulphur with selenium occurs the proportion is rather than low (perhaps maximum 1% of the population of sulphur atoms). So, in that case we are expecting to get data that fit to the pyrite structure taking Se as the core atom. For that reason, the Feff calculations were made with the crystal structure of pyrite with sulphur as the core atom and used Se edge instead. Is that making any sense?
What you should do is create the feff input as you did, selecting S as the absorbing atom, but then change the absorbing atom from S to Se, That is where it says (approximately): POTENTIALS 0 16 S 1 26 Fe 2 16 S you should edit this, replacing the above with POTENTIALS 0 34 Se 1 26 Fe 2 16 S Note that 0 in the first column means 'absorbing atom'. Potential 2 is for the non-absorbing S atoms, which you probably want to leave alone, as the structure you want to model is one absorbing Se atom in pyrite. You can also edit the list of atomic coordinates (this is useful if you want to move atoms around). In your case, you might want to change the "tag" for the absorbing atom, from something like ATOMS 0.00000 0.00000 0.00000 0 S1 0.00000 to ATOMS 0.00000 0.00000 0.00000 0 Se1 0.00000 That part is optional. Changing the POTENTIALS is not. After these edits, running Feff will generate scattering paths for Se-Fe, Se-S, and so on. --Matt
On Tuesday, July 03, 2012 09:26:38 AM Adriana Matamoros Veloza wrote:
In both projects the data corresponds to Se edge (no sulphur). Selenium data was collected on natural pyrite grains. When Se associates to pyrite, it is normally inferred that Se substituted sulphur within the pyrite structure. Both elements are chemically very similar. Looking at selenium as the core atom, we want to see if it is possible to get the chemical environment related to pyrite (Se-S, Se-Fe bonds). In natural environments if substitution of sulphur with selenium occurs the proportion is rather than low (perhaps maximum 1% of the population of sulphur atoms). So, in that case we are expecting to get data that fit to the pyrite structure taking Se as the core atom. For that reason, the Feff calculations were made with the crystal structure of pyrite with sulphur as the core atom and used Se edge instead. Is that making any sense?
I understand what you are trying to do, but what you actually did isn't very sensible. If Se is the central atom in the experiment, Se must be the central atom in the Feff calculation. The central atom phase shift (see http://leonardo.phys.washington.edu/feff/wiki/index.php?title=FEFF_Variables) for Se is very different from S. If you get that so wrong, it will have a profound impact on the evaluation of E0 and DeltaR. Here's a snippet from the feff input that you used: POTENTIALS * ipot Z tag 0 16 S 1 26 Fe 2 16 S ATOMS * this list contains 170 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 S1 0.00000 1.25695 1.25695 1.25695 2 S1.1 2.17711 -2.08047 0.62848 0.62848 1 Fe1.1 2.26237 0.62848 -2.08047 0.62848 1 Fe1.1 2.26237 0.62848 0.62848 -2.08047 1 Fe1.1 2.26237 It needs to be edited to read POTENTIALS * ipot Z tag 0 34 Se 1 26 Fe 2 16 S ATOMS * this list contains 170 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Se 0.00000 1.25695 1.25695 1.25695 2 S1.1 2.17711 -2.08047 0.62848 0.62848 1 Fe1.1 2.26237 0.62848 -2.08047 0.62848 1 Fe1.1 2.26237 0.62848 0.62848 -2.08047 1 Fe1.1 2.26237 The truly important change was to change the Z for potential 0 from 16 to 34. That tells Feff that the central atom is Se. The other two edits help Artemis help you understand the calculation. This illustrates an aspect of how Artemis works. In principle, it should not be necessary to press the "Run Atoms" button then to press the "Run Feff" button in order to make a Feff calculation happen. In many situation, those two buttons are pushed in quick succession, making the second button press seemingly unnecessary. There are, however, many analysis situations where it is useful for the user to pause between the two button presses and ponder feff's input data. In this case, you need to change the absorber to deal with the situation of having measured XAS at the edge of the dopant. Try that. I suspect your analysis will make more sense. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel
Hi Bruce, Matt, Fantastic! Many thanks for your help, I will try that and will let you know. Best wishes, Adriana :) -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: 03 July 2012 13:55 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Problems with fit in pyrite structure with Se substitution On Tuesday, July 03, 2012 09:26:38 AM Adriana Matamoros Veloza wrote:
In both projects the data corresponds to Se edge (no sulphur). Selenium data was collected on natural pyrite grains. When Se associates to pyrite, it is normally inferred that Se substituted sulphur within the pyrite structure. Both elements are chemically very similar. Looking at selenium as the core atom, we want to see if it is possible to get the chemical environment related to pyrite (Se-S, Se-Fe bonds). In natural environments if substitution of sulphur with selenium occurs the proportion is rather than low (perhaps maximum 1% of the population of sulphur atoms). So, in that case we are expecting to get data that fit to the pyrite structure taking Se as the core atom. For that reason, the Feff calculations were made with the crystal structure of pyrite with sulphur as the core atom and used Se edge instead. Is that making any sense?
I understand what you are trying to do, but what you actually did isn't very sensible. If Se is the central atom in the experiment, Se must be the central atom in the Feff calculation. The central atom phase shift (see http://leonardo.phys.washington.edu/feff/wiki/index.php?title=FEFF_Variables) for Se is very different from S. If you get that so wrong, it will have a profound impact on the evaluation of E0 and DeltaR. Here's a snippet from the feff input that you used: POTENTIALS * ipot Z tag 0 16 S 1 26 Fe 2 16 S ATOMS * this list contains 170 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 S1 0.00000 1.25695 1.25695 1.25695 2 S1.1 2.17711 -2.08047 0.62848 0.62848 1 Fe1.1 2.26237 0.62848 -2.08047 0.62848 1 Fe1.1 2.26237 0.62848 0.62848 -2.08047 1 Fe1.1 2.26237 It needs to be edited to read POTENTIALS * ipot Z tag 0 34 Se 1 26 Fe 2 16 S ATOMS * this list contains 170 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Se 0.00000 1.25695 1.25695 1.25695 2 S1.1 2.17711 -2.08047 0.62848 0.62848 1 Fe1.1 2.26237 0.62848 -2.08047 0.62848 1 Fe1.1 2.26237 0.62848 0.62848 -2.08047 1 Fe1.1 2.26237 The truly important change was to change the Z for potential 0 from 16 to 34. That tells Feff that the central atom is Se. The other two edits help Artemis help you understand the calculation. This illustrates an aspect of how Artemis works. In principle, it should not be necessary to press the "Run Atoms" button then to press the "Run Feff" button in order to make a Feff calculation happen. In many situation, those two buttons are pushed in quick succession, making the second button press seemingly unnecessary. There are, however, many analysis situations where it is useful for the user to pause between the two button presses and ponder feff's input data. In this case, you need to change the absorber to deal with the situation of having measured XAS at the edge of the dopant. Try that. I suspect your analysis will make more sense. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (3)
-
Adriana Matamoros Veloza -
Bruce Ravel -
Matt Newville