Hi Josh, That cpan command should be done from the horae install directory. Saying perl -MCPAN -e 'install Bundle::XXX' is looking for the file named XXX.pm (which simply contains a list of Perl modules) in the directory Bundle/. I think that if it can't find that, then it goes to look on-line. Cheers, --Matt On Fri, Sep 17, 2010 at 3:24 PM, Joshua Kas wrote:

Hi, I'm trying to install horae on RHEL5 and I'm having trouble getting the prerequisites from CPAN. IFEFFIT installed fine, but when I try to install ARTEMIS/ATHENA I have the following problem:

verrocchio.phys #] perl -MCPAN -e 'install Bundle::XasPerlBundle' CPAN: Storable loaded ok Going to read /CPAN/Metadata   Database was generated on Fri, 17 Sep 2010 18:28:36 GMT Warning: Cannot install Bundle::XasPerlBundle, don't know what it is. Try the command

    i /Bundle::XasPerlBundle/

to find objects with matching identifiers.

This was after becoming root, then copying the CPAN/MyConfig.pm file to ~/.cpan/CPAN/. I am using the mose recent version of the horae tarball, i.e., horae-070. I'm out of ideas for now. Thanks very much for any help. Josh Kas

On Fri, Sep 17, 2010 at 10:00 AM, wrote:

...

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Today's Topics:

  1. Re: Bkg removal problem (Alfred Hummer)   2. Mathematical expressions for the path parameters in       Fitting      (sumitk@barc.gov.in)   3. Re: Mathematical expressions for the path parameters in      Fitting (Shelly Kelly)   4. Re: Mathematical expressions for the path parameters in      Fitting (Brandon Reese)

----------------------------------------------------------------------

Message: 1 Date: Thu, 16 Sep 2010 19:58:53 +0200 From: Alfred Hummer To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Bkg removal problem Message-ID: <4C925ADD.90306@univie.ac.at> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Thx for the detailed answer. Helped me a lot. Also tested it with other programs using smoothed splines, leading to similar results.

And you are right, I don't expect a peak at about 1A in the FT. The first peak at 1.5A in the FT should represent a mixed 1st shell of 3O/3N atoms at about 2A distance.

best regards Alfred

Am 15.09.2010 19:00, schrieb ifeffit-request@millenia.cars.aps.anl.gov:

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Today's Topics:

    1. Re: Bkg removal problem (Bruce Ravel)

----------------------------------------------------------------------

Message: 1 Date: Tue, 14 Sep 2010 14:07:55 -0400 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Bkg removal problem Message-ID:<201009141407.55193.bravel@bnl.gov> Content-Type: Text/Plain;  charset="iso-8859-1"

Alfred,

I certainly encourage you to look at Shelly's book chapter. It's very useful.

The question you ask is one that we hear frequently on this mailing list.  I don't mean anything bad by saying that -- in fact, it's an excellent question that every practitioner of XAS needs to come to terms with early on in his or her XAS career.  Indeed, I am pleased that you are insightful enough to recognize your confusion and wise enough to ask for help.

That said, I am a bit weary of answering questions about Rbkg on the mailing list.  Yours ain't the first! ;-)

Rather than answering here, I decided to write up a wiki page on the topic.  That way, I'll have something to point to the next time someone asks about Rbkg.

Here it is:    http://xafs.org/TheoryAnalysis/BackgroundRemovalWithAutobk

Hope it helps, B

On Friday 10 September 2010 10:25:50 am Shelly Kelly wrote:

...

Hi Alfred:

You should take a look at my book chapter. I go through a lot of details on how to remove the background. If you want a copy just send me an email directly and I'll send you a pdf.

Cheers, Shelly exafs@netzero.com

On Fri, Sep 10, 2010 at 8:42 AM, Alfred Hummer

 wrote:

...

Hello,

Currently I am working on a Ga XAS spectrum. I'm trying to extract the EXAFS data but I'm not sure if the background function is right, or how to set the right values.

I played around with different setting for kmin and Rbkg. So far I know that Rbkg defines the cutoff for the bkg frequencies in the FT optimization and setting it to high leads to loss in information, as more high frequencies are included in the bkg.

I also read that it is advisable to exclude strong white lines from the spline range (increasing kmin?). Would this a strategy in my case?

I attached the project file.

Maybe someone has a clue. The more I tried the bigger my uncertainty.

best regards

Alfred

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------------------------------

Message: 2 Date: Fri, 17 Sep 2010 11:31:34 +0530 From: sumitk@barc.gov.in To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Mathematical expressions for the path parameters in        Fitting Message-ID:         Content-Type: text/plain;charset=UTF-8

Hello, In EXAFS data modeling carried out by fitting excercise, we develop mathematical expressions for  different path parametrs as functions of a smaller set of fitting parameters that can be adjusted to achieve to best fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on different environmentally relevent mineral oxides. In conection of this i also analysed some reference standard compounds. In developing expression for different path parameters, though i developed the expressions using my own  understanding and taking help from one of Shelly's tutorial regarding SnO2 case, i am not confident. Basically SS2, and deltaE expressions puzzle me. Could someone help me in understanding basic approach in developing their expressions(for reference Eu2O3 structure could be taken). Regards, Sumit

------------------------------

Message: 3 Date: Fri, 17 Sep 2010 10:40:14 -0500 From: Shelly Kelly To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Mathematical expressions for the path        parameters in   Fitting Message-ID:         Content-Type: text/plain; charset=ISO-8859-1

Hi Sumit:

There are a lot of different ways to constrain the EXAFS parameters in a fitting model. Mostly they are determined by physically meaningful relationships or through trial and error of "what works". I just sent you my book chapter and you will find detailed discussion on many of the common constraints in there. Another good place to look is in the literature to find out what people have done for systems similar to yours.

HTH, Shelly

On Fri, Sep 17, 2010 at 1:01 AM,   wrote:

...

Hello, In EXAFS data modeling carried out by fitting excercise, we develop mathematical expressions for ?different path parametrs as functions of a smaller set of fitting parameters that can be adjusted to achieve to best fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on different environmentally relevent mineral oxides. In conection of this i also analysed some reference standard compounds. In developing expression for different path parameters, though i developed the expressions using my own ?understanding and taking help from one of Shelly's tutorial regarding SnO2 case, i am not confident. Basically SS2, and deltaE expressions puzzle me. Could someone help me in understanding basic approach in developing their expressions(for reference Eu2O3 structure could be taken). Regards, Sumit

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------------------------------

Message: 4 Date: Fri, 17 Sep 2010 10:54:21 -0600 From: Brandon Reese To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Mathematical expressions for the path        parameters in   Fitting Message-ID:         Content-Type: text/plain; charset="iso-8859-1"

Hi Shelly,

I am also looking into different ways to constrain my EXAFS fits.  If you wouldn't mind, I would also be very interested in a copy of your book chapter.

Thanks, Brandon

On Fri, Sep 17, 2010 at 9:40 AM, Shelly Kelly wrote:

...

Hi Sumit:

There are a lot of different ways to constrain the EXAFS parameters in a fitting model. Mostly they are determined by physically meaningful relationships or through trial and error of "what works". I just sent you my book chapter and you will find detailed discussion on many of the common constraints in there. Another good place to look is in the literature to find out what people have done for systems similar to yours.

HTH, Shelly

On Fri, Sep 17, 2010 at 1:01 AM,   wrote:

...

Hello, In EXAFS data modeling carried out by fitting excercise, we develop mathematical expressions for  different path parametrs as functions of a smaller set of fitting parameters that can be adjusted to achieve to best fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on different environmentally relevent mineral oxides. In conection of this i also analysed some reference standard compounds. In developing expression for different path parameters, though i developed the expressions using my own  understanding and taking help from one of Shelly's tutorial regarding SnO2 case, i am not confident. Basically SS2, and deltaE expressions puzzle me. Could someone help me in understanding basic approach in developing their expressions(for reference Eu2O3 structure could be taken). Regards, Sumit

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