[Ifeffit] XasPerlBundle problems

Matt Newville newville at cars.uchicago.edu
Fri Sep 17 16:32:53 CDT 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 <joshua.j.kas at gmail.com> 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,
> <ifeffit-request at millenia.cars.aps.anl.gov> wrote:
>>
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>> than "Re: Contents of Ifeffit digest..."
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>>
>> Today's Topics:
>>
>>   1. Re: Bkg removal problem (Alfred Hummer)
>>   2. Mathematical expressions for the path parameters in       Fitting
>>      (sumitk at 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 <alfred.hummer at univie.ac.at>
>> To: ifeffit at millenia.cars.aps.anl.gov
>> Subject: Re: [Ifeffit] Bkg removal problem
>> Message-ID: <4C925ADD.90306 at 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 at millenia.cars.aps.anl.gov:
>> > Send Ifeffit mailing list submissions to
>> >       ifeffit at 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 at millenia.cars.aps.anl.gov
>> >
>> > You can reach the person managing the list at
>> >       ifeffit-owner at 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<bravel at bnl.gov>
>> > To: XAFS Analysis using Ifeffit<ifeffit at millenia.cars.aps.anl.gov>
>> > Subject: Re: [Ifeffit] Bkg removal problem
>> > Message-ID:<201009141407.55193.bravel at 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 at netzero.com
>> >>
>> >> On Fri, Sep 10, 2010 at 8:42 AM, Alfred Hummer
>> >>
>> >> <alfred.hummer at univie.ac.at>  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
>> >>>
>> >>>
>> >>> _______________________________________________
>> >>> Ifeffit mailing list
>> >>> Ifeffit at millenia.cars.aps.anl.gov
>> >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> >>
>> >> _______________________________________________
>> >> Ifeffit mailing list
>> >> Ifeffit at millenia.cars.aps.anl.gov
>> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> >>
>> >
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Fri, 17 Sep 2010 11:31:34 +0530
>> From: sumitk at barc.gov.in
>> To: ifeffit at millenia.cars.aps.anl.gov
>> Subject: [Ifeffit] Mathematical expressions for the path parameters in
>>        Fitting
>> Message-ID:
>>        <edb6390523394cc867a1b7e12aa03d81.squirrel at bts.barc.gov.in>
>> 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 <dr.sdkelly at gmail.com>
>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> Subject: Re: [Ifeffit] Mathematical expressions for the path
>>        parameters in   Fitting
>> Message-ID:
>>        <AANLkTim40RLMwFRFm1JN0becDx7MM7Lthqmw_xu=Jsk- at mail.gmail.com>
>> 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,  <sumitk at barc.gov.in> 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 at 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 <bjreese at gmail.com>
>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> Subject: Re: [Ifeffit] Mathematical expressions for the path
>>        parameters in   Fitting
>> Message-ID:
>>        <AANLkTikQG0L=-QWp_EX51XSuOYvN7_JZvESh5o9LSDp6 at mail.gmail.com>
>> 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 <dr.sdkelly at gmail.com>
>> 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,  <sumitk at barc.gov.in> 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 at millenia.cars.aps.anl.gov
>> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> > >
>> >
>> > _______________________________________________
>> > Ifeffit mailing list
>> > Ifeffit at millenia.cars.aps.anl.gov
>> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> >
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