[Ifeffit] XasPerlBundle problems
Joshua Kas
joshua.j.kas at gmail.com
Fri Sep 17 15:24:53 CDT 2010
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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> 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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