Re: [Ifeffit] Questions for Artemis fit
Hi Dr. Newville,
I had similar situation and questions as with choosing Path
Parameters. My goal is to identify the occupancy sites for a doped
element in my sample. We have a rough guess of two possible sites,
part of the doped atoms are filling a void site of the unit cell, the
other part is to substitute an existing atom sites.
I was being able to writing two ATOM files and run FEFF twice to
calculate all possible PATH. But when I was going to define/guess the
parameters ('N','amp', 'enot', 'delr','ss')for EACH path, I totally
lost idea how to group all those paths, or how to guess all those five
parameters for each path. Of course, I couldn't get a good fit as I
don't know how to build the model and to refine parameters in this step.
Here I post my understanding of the five parameters: 'N', path
degeneracy, or coordination number; 'amp', usually close to 1, but as
I have doping elements, I am expecting small partial numbers in some
of the 'amp' to adjust for partial occupancy; 'enot', I think it is
just the energy shift of your spectra, and as I believe my spectra are
well aligned, I will SET 'enot' to zero. 'delr' is the variation of
the real atom-atom distances from the calculated ones (I think I need
to group paths to refine 'delr' but I don't know what's the criteria
to group paths). 'ss' is to consider about the disorder effect and
typically I use the Debye model. Let me know if I am wrong in any way.
Could you please give me some suggestion how did you get started? I am
looking forward to hearing from you.
Best regards,
Yanyun
Quoting Matt Newville newvi...@cars.uchicago.edu:
On Mon, Aug 18, 2014 at 7:45 PM, 이국승 lks3...@postech.ac.kr wrote:
Dr Newville,
Thank you for your reply.
My first question is that I did not find the atoms.inp file in the demeter
installer. If that is true, where can I get the atoms.inp file?
You might find what you're looking for at
http://cars9.uchicago.edu/~newville/adb/search.htmlMetallic Au (fcc) is
there.
Anyway, I did copy and paste the atoms.inp file of an old version of
Artemis from my colleague's PC. I followed the Artemis intruction video for
fitting Au foil data.
Hmm, it seems likely that you missed a step.
I filled the crystal lattice information, run atoms, and Feff calculation.
Did you import and define a Path after doing this calculation? Did you
define Path Parameters and variables for this fit?
Finally I clicked the Fit button and I got the error message that I
attached. Now here is my second question. What can I do to successfully Fit
without errors? Do you have any idea from the error message?
It indicates that you have defined variables to refine in the fit ('amp',
'enot', and so forth) but not explained how those variables should alter
the EXAFS signal. You'll probably want to use these in the Path
Parameters for the first shell Au-Au scattering. But, you are doing the
analysis, so the most important thing is that you understand how the
variables you are asking to be refined actually effect the EXAFS signal.
These error messages are a feature of the program to remind you that you
need to understand the model you are using for the EXAFS signal.
So, what do you intend 'amp', 'enot', 'delr', and 'ss' to do?If you
don't know, go back and review the tutorial information. The goal is not
to get a fit, the goal is to understand what the fit results mean.
Another question (it might seem random, but it is not): what is your
fitting range?
--Matt
PS: to be clear, these are not rhetorical questions. If you feel the need
to respond, please actually think about and answer all questions above.
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Re: [Ifeffit] Questions for Artemis fit
On Tue, Aug 19, 2014 at 9:55 AM, huyan...@physics.utoronto.ca wrote:
Hi Dr. Newville,
I had similar situation and questions as with choosing Path Parameters. My
goal is to identify the occupancy sites for a doped element in my sample.
We have a rough guess of two possible sites, part of the doped atoms are
filling a void site of the unit cell, the other part is to substitute an
existing atom sites.
I was being able to writing two ATOM files and run FEFF twice to calculate
all possible PATH. But when I was going to define/guess the parameters
('N','amp', 'enot', 'delr','ss')for EACH path, I totally lost idea how to
group all those paths, or how to guess all those five parameters for each
path. Of course, I couldn't get a good fit as I don't know how to build the
model and to refine parameters in this step.
Here I post my understanding of the five parameters: 'N', path degeneracy,
or coordination number; 'amp', usually close to 1, but as I have doping
elements, I am expecting small partial numbers in some of the 'amp' to
adjust for partial occupancy; 'enot', I think it is just the energy shift
of your spectra, and as I believe my spectra are well aligned, I will SET
'enot' to zero. 'delr' is the variation of the real atom-atom distances
from the calculated ones (I think I need to group paths to refine 'delr'
but I don't know what's the criteria to group paths). 'ss' is to consider
about the disorder effect and typically I use the Debye model. Let me know
if I am wrong in any way.
Could you please give me some suggestion how did you get started? I am
looking forward to hearing from you.
For each Path in a model, you need
a) a Feff.dat file -- this can be read from any Feff calculation, and
those can be generated from a crystal structure
b) a set of Path Parameters -- the physically meaningful quantities
N*S02, E0, deltaR, sigma2, etc from the EXAFS Equation.
Each of the Path Parameters is given as an equation in terms of the set of
Fit Parameters. Often times, the equations are very simple.That is,
sigma2 for Path1 may simply be defined to be evaluated from 'ss'. You
could make it 'ss*2', or something else.
There is also a set of Fit Parameters -- named quantities that may be
adjusted in the fit to make the sum of Paths best match your data. These
can be set, in which case they are frozen -- not varied in the fit.In
Artemis, the Fit Parameters are shown in the Guess/Set/Def page. The
quantities like enot, delr, ss, etc are Fit Parameters. You need to
fill out an expression for each Path Parameter you want changed in the fit
in terms of the set of Fit Parameters.
Artemis will help you by complaining if some of the Fit Parameters defined
are not used in any Path Parameters -- changing these values won't alter
the fit, so you should not have them defined as a variable Fit Parameter.
The system is designed to be very flexible. But this means that before you
do a fit you need to understand what each of the Fit Parameters does to the
Path Parameters for the Paths you are using in the fit. We could guess
that by enot, you mean the value for the Path Parameter 'E0', and that
you want to make sure that the E0 Path Parameter is given as enot for all
Paths. But this would be only a guess. You are setting up the model, so
you have to ask yourself why you have a variable 'enot', and what that
means for your model.
--Matt
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Re: [Ifeffit] Questions for Artemis fit
Hi Matt,
Thank you for your quick response. Your explanations of the Path
Parameter and Fit Parameter are very clear. Basically we have to guess
Fit parameters in GDS page and to know what a Fit Parameter does to
your Path Parameters by using math expression.
But my question is, for each path there are a set of Path Parameters,
does that mean we have to fit this set of path parameters independent
from those used in other paths? For instance, if I am going to
include 30 paths in my fitting, do I need to guess about 150
(30*5=150) parameters (except guess the same 'enot' for all paths)?
As shown on the fit Log file, the Correlation value between two fit
parameters is the bigger the better, or the smaller the better?
Thanks,
Yanyun
Quoting Matt Newville newvi...@cars.uchicago.edu:
On Tue, Aug 19, 2014 at 9:55 AM, huyan...@physics.utoronto.ca wrote:
Hi Dr. Newville,
I had similar situation and questions as with choosing Path Parameters. My
goal is to identify the occupancy sites for a doped element in my sample.
We have a rough guess of two possible sites, part of the doped atoms are
filling a void site of the unit cell, the other part is to substitute an
existing atom sites.
I was being able to writing two ATOM files and run FEFF twice to calculate
all possible PATH. But when I was going to define/guess the parameters
('N','amp', 'enot', 'delr','ss')for EACH path, I totally lost idea how to
group all those paths, or how to guess all those five parameters for each
path. Of course, I couldn't get a good fit as I don't know how to build the
model and to refine parameters in this step.
Here I post my understanding of the five parameters: 'N', path degeneracy,
or coordination number; 'amp', usually close to 1, but as I have doping
elements, I am expecting small partial numbers in some of the 'amp' to
adjust for partial occupancy; 'enot', I think it is just the energy shift
of your spectra, and as I believe my spectra are well aligned, I will SET
'enot' to zero. 'delr' is the variation of the real atom-atom distances
from the calculated ones (I think I need to group paths to refine 'delr'
but I don't know what's the criteria to group paths). 'ss' is to consider
about the disorder effect and typically I use the Debye model. Let me know
if I am wrong in any way.
Could you please give me some suggestion how did you get started? I am
looking forward to hearing from you.
For each Path in a model, you need
a) a Feff.dat file -- this can be read from any Feff calculation, and
those can be generated from a crystal structure
b) a set of Path Parameters -- the physically meaningful quantities
N*S02, E0, deltaR, sigma2, etc from the EXAFS Equation.
Each of the Path Parameters is given as an equation in terms of the set of
Fit Parameters. Often times, the equations are very simple.That is,
sigma2 for Path1 may simply be defined to be evaluated from 'ss'. You
could make it 'ss*2', or something else.
There is also a set of Fit Parameters -- named quantities that may be
adjusted in the fit to make the sum of Paths best match your data. These
can be set, in which case they are frozen -- not varied in the fit.In
Artemis, the Fit Parameters are shown in the Guess/Set/Def page. The
quantities like enot, delr, ss, etc are Fit Parameters. You need to
fill out an expression for each Path Parameter you want changed in the fit
in terms of the set of Fit Parameters.
Artemis will help you by complaining if some of the Fit Parameters defined
are not used in any Path Parameters -- changing these values won't alter
the fit, so you should not have them defined as a variable Fit Parameter.
The system is designed to be very flexible. But this means that before you
do a fit you need to understand what each of the Fit Parameters does to the
Path Parameters for the Paths you are using in the fit. We could guess
that by enot, you mean the value for the Path Parameter 'E0', and that
you want to make sure that the E0 Path Parameter is given as enot for all
Paths. But this would be only a guess. You are setting up the model, so
you have to ask yourself why you have a variable 'enot', and what that
means for your model.
--Matt
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Re: [Ifeffit] Questions for Artemis fit
Yanyun, Kug-Seung, Have you watched the videos that the folks at Diamond kindly host at http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html The ones titled Introduction to Artemis and EXAFS fitting and More Artemis and EXAFS fitting go a long way towards answering the questions you both are asking. Granted, you have to look at my ugly face for a long time, which is pretty horrifying. But I think you might find them helpful. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Questions for Artemis fit
Hi all, How would you deal with the case that the absorber atoms are occupying two different crystallography sites? Should I still use/guess the same 'S02' for paths calculated from two sites? Best, Yanyun Quoting huyan...@physics.utoronto.ca: Hi Scott, Thank you for giving me detailed examples. I will go with your suggestion and try to reduce free parameters. Best, Yanyun Quoting Scott Calvin scal...@sarahlawrence.edu: Hi Yanyun, On Aug 19, 2014, at 12:05 PM, huyan...@physics.utoronto.ca wrote: But my question is, for each path there are a set of Path Parameters, does that mean we have to fit this set of path parameters independent from those used in other paths? For instance, if I am going to include 30 paths in my fitting, do I need to guess about 150 (30*5=150) parameters (except guess the same 'enot' for all paths)? No. One of the great principles of Ifeffit (and thus Artemis) is that the path parameters do not have to be the same as the fit parameters. As a simple example, it's good to start with the model that all paths have the same value for E0. So you can guess a single parameter and then use that parameter for the E0 for all paths. As another simple example, a cubic crystal might be modelled as having a uniform thermal (or Vegard's law) expansion. Then there could be a single guessed parameter indicating the fractional expansion (called, for example, alpha) while the delr for each path could then be entered as alpha*reff. Much more complicated constraint schemes are possible, but for fits with large number of paths, the number of guessed parameters is almost always much much lower than the number of path parameters. As shown on the fit Log file, the Correlation value between two fit parameters is the bigger the better, or the smaller the better? Not necessarily. Correlations are provided to help understand the relationship between guessed parameters, but there's nothing inherently wrong with a high correlation...the uncertainty associated with that relationship is already represented in the uncertainties reported with the fit. In other words, it is more direct to focus on getting the uncertainties to be lower, rather than the correlations. --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Artemis and FEFF interaction in fit process
Artemis has a parameter, feff--executable, which identifies the Feff executable. Artemis runs this by a system call to create the potentials and phase shifts given the input structure. Artemis then runs its own version of the pathfinder. The results of those two calculations are stored in the project file. In an instance of Artemis, the Feff executable is run as needed to make the feff.dat files. That is, the first time you make a plot or a fit (there are a few other actions that will also trigger this), Artemis will run the Feff executable to make the path that is needed. Thus each path plotted or used in a fit requires a system call. The advantage of this is that project files remain relatively small because no data is saved for any path, only the metadata required to reproduce the path. This works because making a path is fast enough, certainly it is on the time scale that one spends staring at Artemis. All of that works with Feff6L. Given the limited amount of time that I can possibly spend on Demeter and the large number of things that need doing, making all that work with all other versions of Feff is not a priority for me. You could try pointing Demeter at whatever version of Feff you are using and seeing how it goes. I probably won't be in a position to do much if/when things don't go as hoped. That said, I am committed to making Artemis work with this version of Feff 8.5: https://github.com/xraypy/feff85exafs. In fact, I've been working on that for the last few weeks. There's a lot to do, so I don't have an ETA for when that version of Feff will be integrated into Artemis. If you have a compelling need to use some version of Feff other than the one we get to redistribute, then Artemis may not be the right tool for you. Of course there are things that you or anyone could do to help this along. We would welcome help with development of Feff 8.5 for EXAFS. I would welcome contributions to Demeter. Matt would be happy to see more people working with him on Larch. B On 08/19/2014 02:07 PM, Nate Turner wrote: Hello All, I have a question about Artemis' interaction with FEFF. I know you can either run FEFF6L in Artemis to populate a paths list or externally create the FEFF.dat files in FEFF and import them into Artemis. We currently do the later using FEFF9, the use of the SCF card gives a better Eo initial guess and our compound has fractional occupancy/disorder that requires us to do some altering of the atoms list after its populated in ATOMS, which we find best to do outside of Artemis. My question is once these external FEFF9 paths are brought in does Artemis use FEFF6L in the fit process or is FEFF in Artemis only to populate the paths list? If Artemis doesn't use FEFF in the fit process then there's no issue but while I've read the mailing list and seen that many do not believe there is any improvement in the EXAFS results from FEFF6L to FEFF9, I'd rather be consistent in which version of FEFF we use throughout the analysis. I would have Artemis calling to FEFF9 instead of FEFF6L if in fact Artemis does use FEFF in the fit. The reason I haven't gone ahead with having Artemis call to FEFF9 making this a non issue is I'm not sure how. I know you can direct Artemis to whatever version of FEFF you want under preferences, but then I'm not sure what file I need to direct to specifically for FEFF9. So to summarize, Does Artemis use FEFF in the fitting process or is its only function in Artemis to create the paths for the fit? If it does use FEFF in the fitting, how do you/is it possible to have Artemis call to FEFF9 instead of FEFF6L? Thanks all for your time, Nate Turner ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Artemis and FEFF interaction in fit process
On 08/19/2014 03:37 PM, Nate Turner wrote: In an instance of Artemis, the Feff executable is run as needed to make the feff.dat files. That is, the first time you make a plot or a fit (there are a few other actions that will also trigger this), Artemis will run the Feff executable to make the path that is needed. Thus each path plotted or used in a fit requires a system call. I see, so to be clear if I run FEFF9 and make the feff.dat paths through it, outside of Artemis, then import the feff.dat files into Artemis, FEFF6L is still called to when I want to plot or use a path in a fit? Technically speaking, the value of feff--executable is called to compute the contribution of each path. All the things that Artemis does behind the scenes to organize a Feff calculation and present it to the user of Artemis are guaranteed to work for the version of Feff6 that we can redistribute. I am working on making that same statement true for feff85exafs. I do not guarantee that statement to be true for other versions of Feff. It may work. It may not work. I have not tested what you want to do. I presume that this whole thread is in reference to the option in the File-import menu for importing an external Feff calculation. There is a reason that comes with a lengthy warning message before allowing you to do so. It's not a robust, well-tested part of Demeter. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
