[Ifeffit] Athena with IOS "El Capitan"

[Manuel Cossio Kohler]

Hello,

I am having some issues with the Athena software. After upgrading the OS of
the macbook pro to "El Capitan" Version 10.11.3, Athena stopped working
properly. Once the iXAFS icon was clicked nothing happened. I decided to do
a bit of research and installed the latest verion of XQuartz version 2.7.8.
I was able to launch athena by executting "athena" from the terminal. Up to
that point, I figured that everything was running smoothly until I realized
that I could prompt any plots. Something in the software or operating
system was not allowing Athena to display plots. I would be really grateful
if you could provide me with a solution to this problem (if there is any)
or any advice that would allow me to process XAS data again. Thank you

Regards,

Manuel Cossio
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Re: [Ifeffit] pi/2deltak

[Ritimukta Sarangi]

Thank you very much for the explanations and your time.
Best Wishes,
-Riti



> On Feb 1, 2016, at 9:16 AM, Robert Gordon  wrote:
> 
> Hi Riti,
> 
> A couple of caveats to Matt's answer:
> 
> The EXAFS equation is not simply a sum of sine functions. I can think of two 
> ways that the resolution criteria
> can be worked around:
> 
> 1. Consider the case of two close near neighbours in a single-crystal 
> environment whose close distances are 
> geometrically distinct such that, if one were to conduct 
> polarisation-dependent measurements, one
> could turn off one of the distances in one orientation (and perhaps the other 
> in another), one could fit the
> two sets to extract the two close distances. (i.e. you aren't trying to 
> resolve the two distances in one measurement)
> 
> 2. If there is a pronounced chemical difference between the neighbours, they 
> can be resolved even if the 
> distance separation is small, provided the  k-space range being used provides 
> enough independent parameters
> to conduct the fit.
> 
> If you wish to convince yourself that these two caveats work, I suggest 
> creating a model using the AuCu
> structure. If you contract or expand the c-axis, and substitute either Cu for 
> Au (i.e. make Cu but in lower symmetry)
> or substitute a different atom on one of the Cu sites, you can test both 
> Matt's explanation and my caveats above.
> 
> cheers,
> Robert
> 
> On 1/31/2016 6:33 PM, Matt Newville wrote:
>> Hi Riti, 
>> 
>> On Sat, Jan 30, 2016 at 7:35 PM, Ritimukta Sarangi < 
>> ritimu...@gmail.com 
>> > wrote:
>> Hello,
>> 
>> I was recently asked about the accuracy of this formulation for obtaining 
>> EXAFS resolution and I did not have a good answer. Can someone point to a 
>> reference or explain here? 
>> Thank you for your time,
>> Best,
>> -Riti
>> 
>> 
>> The deltaR = pi / 2DeltaK  follows from general Fourier analysis and 
>> formulas like it can be found in many signal processing textbooks.For 
>> on-line resources, googling "Frequency resolution Fourier transform" gives 
>> several good references.
>> 
>> The idea is that (using sound-waves as an example) in order to distinguish 
>> two close frequencies (say 440 Hz from 441 Hz, so a different of 1 Hz), you 
>> have to sample many periods (pi seconds) to be able to do this.
>> 
>> For EXAFS, if there are contributions from two neighbors that are very 
>> closely spaced, you would have to sample enough oscillations (go high enough 
>> in k) to see the effect of these two different distances beating against 
>> each other.   If you don't go out far enough in k,  you can't tell that 
>> these two contributions are actually from different distances.
>> 
>> Hope that helps, 
>> 
>> --Matt
>> 
>> 
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Re: [Ifeffit] pi/2deltak

[Robert Gordon]

Hi Riti,

A couple of caveats to Matt's answer:

The EXAFS equation is not simply a sum of sine functions. I can think of 
two ways that the resolution criteria

can be worked around:

1. Consider the case of two close near neighbours in a single-crystal 
environment whose close distances are
geometrically distinct such that, if one were to conduct 
polarisation-dependent measurements, one
could turn off one of the distances in one orientation (and perhaps the 
other in another), one could fit the
two sets to extract the two close distances. (i.e. you aren't trying to 
resolve the two distances in one measurement)


2. If there is a pronounced chemical difference between the neighbours, 
they can be resolved even if the
distance separation is small, provided the  k-space range being used 
provides enough independent parameters

to conduct the fit.

If you wish to convince yourself that these two caveats work, I suggest 
creating a model using the AuCu
structure. If you contract or expand the c-axis, and substitute either 
Cu for Au (i.e. make Cu but in lower symmetry)
or substitute a different atom on one of the Cu sites, you can test both 
Matt's explanation and my caveats above.


cheers,
Robert

On 1/31/2016 6:33 PM, Matt Newville wrote:

Hi Riti,

On Sat, Jan 30, 2016 at 7:35 PM, Ritimukta Sarangi 
mailto:ritimu...@gmail.com>> wrote:


Hello,

I was recently asked about the accuracy of this formulation for
obtaining EXAFS resolution and I did not have a good answer. Can
someone point to a reference or explain here?

Thank you for your time,
Best,
-Riti


The deltaR = pi / 2DeltaK  follows from general Fourier analysis and 
formulas like it can be found in many signal processing textbooks.
For on-line resources, googling "Frequency resolution Fourier 
transform" gives several good references.


The idea is that (using sound-waves as an example) in order to 
distinguish two close frequencies (say 440 Hz from 441 Hz, so a 
different of 1 Hz), you have to sample many periods (pi seconds) to be 
able to do this.


For EXAFS, if there are contributions from two neighbors that are very 
closely spaced, you would have to sample enough oscillations (go high 
enough in k) to see the effect of these two different distances 
beating against each other.   If you don't go out far enough in k,  
you can't tell that these two contributions are actually from 
different distances.


Hope that helps,

--Matt


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Re: [Ifeffit] FW: Data summation - missing groups

[Godfrey, Ian]

Works like a charm!

Thanks,

Ian

-Original Message-
From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of 
Bruce Ravel
Sent: 27 January 2016 18:13
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] FW: Data summation - missing groups

On 01/27/2016 11:24 AM, Godfrey, Ian wrote:
> Having said that, I've downloaded and applied the patches from github 
> and have found a slightly annoying behaviour. Everytime I use the the 
> buttons under the plotlist (both the orange ones and the purple ones) 
> the component lists reset.
>
> i.e. I set up a sum with component 1 as, say, HAuCl4 standard and 
> component 2 as, say, Au foil and plot it. I then plot a couple of 
> datasets using the buttons on the RHS. At this point all the component 
> lists reset themselve to blank. I can reselect the component from the 
> dropdown easily enough, but this is annoying if I have several 
> components set up with corresponding weightings in a summation.

Simple fix committed at

https://github.com/bruceravel/demeter/commit/9fa28926e5bd119d8d6574afa03b579647ab519b

Will be in the next release.  (Also easy to apply by hand, if you are so
motivated.)

B

--
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 535A
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/
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