[Ifeffit] XasPerlBundle problems

Joshua Kas joshua.j.kas at gmail.com
Sat Sep 18 15:08:01 CDT 2010


Hi Matt,
Thanks for the quick response. I did run the command from within the horae
install directory, and the file XasPerlBundle.pm is in the Bundle directory,
i.e.,

verrocchio.phys #] pwd
/tmp/horae-070
verrocchio.phys #] ls
.   Bundle  INSTALL           aug    build_private  libperlxray
..  CPAN    INSTALL_not_root  build  horae
verrocchio.phys #] ls Bundle/
.  ..  XasPerlBundle.pm
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
CPAN: LWP::UserAgent loaded ok
Fetching with LWP:
  http://www.perl.com/CPAN/authors/01mailrc.txt.gz
Going to read /CPAN/source/authors/01mailrc.txt.gz
Fetching with LWP:
  http://www.perl.com/CPAN/modules/02packages.details.txt.gz
Going to read /CPAN/source/modules/02packages.details.txt.gz
  Database was generated on Sat, 18 Sep 2010 17:59:57 GMT

  There's a new CPAN.pm version (v1.9402) available!
  [Current version is v1.7602]
  You might want to try
    install Bundle::CPAN
    reload cpan
  without quitting the current session. It should be a seamless upgrade
  while we are running...

Fetching with LWP:
  http://www.perl.com/CPAN/modules/03modlist.data.gz
Going to read /CPAN/source/modules/03modlist.data.gz
Going to write /CPAN/Metadata
Warning: Cannot install Bundle::XasPerlBundle, don't know what it is.
Try the command

    i /Bundle::XasPerlBundle/

to find objects with matching identifiers.



Could there be something wrong with my installation of CPAN that would cause
this behavior?
Cheers,
Josh Kas

On Sat, Sep 18, 2010 at 10:00 AM, <ifeffit-request at millenia.cars.aps.anl.gov
> 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: XasPerlBundle problems (Matt Newville)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 17 Sep 2010 16:32:53 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] XasPerlBundle problems
> Message-ID:
>        <AANLkTi=tDjqnmBT8nhWZ0VtAMrvyZTSdvHLPePmR0iYu at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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:
> >>
> >> 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 (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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> >> Ifeffit at millenia.cars.aps.anl.gov
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