Re: [Ifeffit] XasPerlBundle problems

17 Sep 2010

      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:
...
Send Ifeffit mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Ifeffit digest..."
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:
...
Send Ifeffit mailing list submissions to
      ifeffit@millenia.cars.aps.anl.gov
To subscribe or unsubscribe via the World Wide Web, visit
      http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
or, via email, send a message with subject or body 'help' to
      ifeffit-request@millenia.cars.aps.anl.gov
You can reach the person managing the list at
      ifeffit-owner@millenia.cars.aps.anl.gov
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Ifeffit digest..."
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
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
------------------------------
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
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
_______________________________________________
Ifeffit mailing list
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http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] XasPerlBundle problems

Matt Newville