September 2010 - Ifeffit - millenia.cars.aps.anl.gov

Interatomic distances from feff paths
by Elsa E. Sileo 01 Oct '10

01 Oct '10

I am trying to use the following CIF files to generate the feff path at the As edge: 1- 'Iron(III) arsenate(V) dihydrate', Scorodite, H4 As Fe O6'; space group P c a b; number 61; orthorhombic and 2. Iron(III) tris(dihydrogenarsenate) pentahydrate Kaatialaite, Fe (H2 As O4)3 (H2 O)5, P 1 21/n 1, number 14; monoclinic and in both cases, after running Feff, I obtain distances Fe-As that are not real. For instance in scorodite I find a distance As-Fe = 1,71 A. How can I overcome this problem? Thanks, Elsa At 14:00 30/09/2010, you wrote: >Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > >You can reach the person managing the list at > ifeffit-owner(a)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: Ifeffit Digest, Vol 91, Issue 28 (Matt Newville) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 30 Sep 2010 11:28:28 -0500 >From: Matt Newville <newville(a)cars.uchicago.edu> >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Subject: Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28 >Message-ID: > <AANLkTinRMxoi2ANd=H=a+Bir5FRG0rruw_UPYy53sfCE(a)mail.gmail.com> >Content-Type: text/plain; charset=ISO-8859-1 > >Hi Elsa, > >On Thu, Sep 30, 2010 at 10:33 AM, Elsa Sileo <e_sileo(a)yahoo.es> wrote: > > > > Dear Matt, > > > > I have to perform EXAFS analysis, and when I tried to fit the first > > shell, I found deltaE0 values of about 8 eV. Following the paper of > > Kelly et al (Analysis of soils and minerals using X-ray absorption > > spectroscopy. In Methods of soil analysis, Part 5: Mineralogical > > methods; 2008; pp 446) I fitted the first shell obtaining values for > > deltaE0, sigma^2; delta R and amplitude. Then, using the obtained > > values, and making deltaE0=0, I got the theoretical signal. > >Why is important to have a theoretical spectra with deltaE0=0? > > > When I compare the experimental and theoretical spectrum I see a mismatch > > between the position of the nodes at low wavenumbers. > >Yes, that is what E0 does. > > > Having done this, how I have to proceed to correct the experimental > > data in order to obtain smalller delta E0 values? > >I think what you are trying to do (though I don't understand why) is >to adjust E0 for the experimental data so that the fit to a particular >theoretical standard gives deltaE0 close to zero. If so, you want to >adjust E0 in the background subtraction. If you change E0 by 8eV >there, you should end up with a deltaE0 in the fit that is close to >zero. > >Hope that helps, > >--Matt > > >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 91, Issue 30 >*************************************** > > >No virus found in this incoming message. >Checked by AVG - www.avg.com >Version: 8.5.445 / Virus Database: 271.1.1/3168 >- Release Date: 09/30/10 06:34:00 Dra. Elsa E. Sileo Solidos Inorganicos INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA CABA - Argentina Tel: (54 11) 4576 3380 ext. 113 Fax: (54 11) 4576 3341 e-mail: sileo(a)qi.fcen.uba.ar

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Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 30
by Elsa E. Sileo 30 Sep '10

30 Sep '10

Thanks Matt, now I realize that I can directly change de Eo in the Athena window, Elsa At 14:00 30/09/2010, you wrote: >Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > >You can reach the person managing the list at > ifeffit-owner(a)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: Ifeffit Digest, Vol 91, Issue 28 (Matt Newville) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 30 Sep 2010 11:28:28 -0500 >From: Matt Newville <newville(a)cars.uchicago.edu> >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Subject: Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28 >Message-ID: > <AANLkTinRMxoi2ANd=H=a+Bir5FRG0rruw_UPYy53sfCE(a)mail.gmail.com> >Content-Type: text/plain; charset=ISO-8859-1 > >Hi Elsa, > >On Thu, Sep 30, 2010 at 10:33 AM, Elsa Sileo <e_sileo(a)yahoo.es> wrote: > > > > Dear Matt, > > > > I have to perform EXAFS analysis, and when I tried to fit the first > > shell, I found deltaE0 values of about 8 eV. Following the paper of > > Kelly et al (Analysis of soils and minerals using X-ray absorption > > spectroscopy. In Methods of soil analysis, Part 5: Mineralogical > > methods; 2008; pp 446) I fitted the first shell obtaining values for > > deltaE0, sigma^2; delta R and amplitude. Then, using the obtained > > values, and making deltaE0=0, I got the theoretical signal. > >Why is important to have a theoretical spectra with deltaE0=0? > > > When I compare the experimental and theoretical spectrum I see a mismatch > > between the position of the nodes at low wavenumbers. > >Yes, that is what E0 does. > > > Having done this, how I have to proceed to correct the experimental > > data in order to obtain smalller delta E0 values? > >I think what you are trying to do (though I don't understand why) is >to adjust E0 for the experimental data so that the fit to a particular >theoretical standard gives deltaE0 close to zero. If so, you want to >adjust E0 in the background subtraction. If you change E0 by 8eV >there, you should end up with a deltaE0 in the fit that is close to >zero. > >Hope that helps, > >--Matt > > >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 91, Issue 30 >*************************************** > > >No virus found in this incoming message. >Checked by AVG - www.avg.com >Version: 8.5.445 / Virus Database: 271.1.1/3168 >- Release Date: 09/30/10 06:34:00 Dra. Elsa E. Sileo Solidos Inorganicos INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA CABA - Argentina Tel: (54 11) 4576 3380 ext. 113 Fax: (54 11) 4576 3341 e-mail: sileo(a)qi.fcen.uba.ar

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Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28
by Elsa Sileo 30 Sep '10

30 Sep '10

Dear Matt, I have to perform EXAFS analysis, and when I tried to fit the first shell, I found deltaE0 values of about 8 eV. Following the paper of Kelly et al (Analysis of soils and minerals using X-ray absorption spectroscopy. In Methods of soil analysis, Part 5: Mineralogical methods; 2008; pp 446) I fitted the first shell obtaining values for deltaE0, sigma^2; delta R and amplitude. Then, using the obtained values, and making deltaE0=0, I got the theoretical signal. When I compare the experimental and theoretical spectrum I see a mismatch between the position of the nodes at low wavenumbers. Having done this, how I have to proceed to correct the experimental data in order to obtain smalller delta E0 values? Thanks in advance, Elsa --- El mié, 29/9/10, ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> escribió: De: ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Asunto: Ifeffit Digest, Vol 91, Issue 28 Para: ifeffit(a)millenia.cars.aps.anl.gov Fecha: miércoles, 29 de septiembre, 2010 14:00 Send Ifeffit mailing list submissions to ifeffit(a)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(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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: Aligning Energy scales (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 28 Sep 2010 12:55:15 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Aligning Energy scales Message-ID: <AANLkTima_bGt5OO=K-Vb-0aRGwb9AC_W6BcBLwgCAg4t(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear Elsa, It sounds like you want to adjust the data chi(k) so that deltaE0 is 0 in a fit. Is that correct, or are you trying to do something else (say, align the XANES)? If that assumption is correct, you want to change the E0 used to extract chi(k) from the experimental spectra -- the E0 of the background subtraction. That is what sets k for the data. If that's not clear or not the right question, let us know, --Matt On Mon, Sep 27, 2010 at 2:00 PM, Elsa E. Sileo <sileo(a)qi.fcen.uba.ar> wrote: > I need to align a measured spectra to a theoretically calculated spectra. > I fitted the first shell obtaining values for deltaE0, sigma^2; delta R and > amplitude. > Then, using the obtained values, and making deltaE0=0, I got the theoretical > signal. > But I do not know how to use this last theoretical fit to align the spectra. > Can somebody help me? > > Thanks, > > Elsa > > > Dra. Elsa E. Sileo > Solidos Inorganicos > INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA > Int. G?iraldes 2160, Pabell?n 2, Piso 3, Ciudad Universitaria - C1428EHA > CABA - Argentina > Tel: (54 11) 4576 3380 ext. 113 > Fax: (54 11) 4576 3341 > e-mail: sileo(a)qi.fcen.uba.ar > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 91, Issue 28 *************************************** ns

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EXAFS spectrum of Fe foil (fcc)
by KONG Quingyu 30 Sep '10

30 Sep '10

Dear All, Does anyone has an EXAFS spectrum of gama Fe foil, or Fe foil spectrum measured at high temperature (more than 1000 degree). If you have this measurement, would you please send me a copy of the data. I would like to compare with our recent measured EXAFS spectrum. Thanks a lot in advance, Sincerely, Qingyu Kong Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr ************************************

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Aligning Energy scales
by Elsa E. Sileo 28 Sep '10

28 Sep '10

I need to align a measured spectra to a theoretically calculated spectra. I fitted the first shell obtaining values for deltaE0, sigma^2; delta R and amplitude. Then, using the obtained values, and making deltaE0=0, I got the theoretical signal. But I do not know how to use this last theoretical fit to align the spectra. Can somebody help me? Thanks, Elsa Dra. Elsa E. Sileo Solidos Inorganicos INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA CABA - Argentina Tel: (54 11) 4576 3380 ext. 113 Fax: (54 11) 4576 3341 e-mail: sileo(a)qi.fcen.uba.ar

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Re: [Ifeffit] iXAFS 3.0.3 for Mac OS X (Brandon Reese)
by Brugger, Joel (SAM) 23 Sep '10

23 Sep '10

Hi Brandon, Did you actually test the python module (i.e. Use python scripting to control arthemis?) On 10.6.4, I've obtain the following error: bash-3.2$ python Python 2.6.1 (r261:67515, Dec 17 2009, 00:59:15) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import math >>> import Ifeffit >>> iff = Ifeffit.Ifeffit() failed to load ifeffit library libifeffit.dylib /usr/local/share/ifeffit/:/opt/intel/Compiler/11.1/089/bin/intel64:/opt/local/bin:/opt/local/sbin:/Volumes/iXAFS3.0/iXAFS.app/Contents/Resources/local/bin:/opt/intel/Compiler/11.1/089/bin/intel64:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/Applications/iXAFS.app/Contents/Resources/local/bin:/Users/joelb/Desktop/Molecular Dynamics/nwchem-5.1-MACX-Darwin-gfortran-i386/bin/:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/Users/joelb/Desktop/Molecular Dynamics/nwchem-5.1-MACX-Darwin-gfortran-i386/bin/:/Applications/iXAFS.app/Contents/Resources/local/lib:/Applications/iXAFS.app/Contents/Resources/local/bin Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py", line 80, in __init__ raise ImportError('Cannot load ifeffit library') ImportError: Cannot load ifeffit library . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh is in my .profile and is loaded. Indeed, invoking libifeffit.dylib from the command line 'works': bash-3.2$ libifeffit.dylib bash: /Applications/iXAFS.app/Contents/Resources/local/lib/libifeffit.dylib: cannot execute binary file bash-3.2$ ls -l libifeffit.dylib -rwxr-xr-x 1 joelb admin 1500676 12 Sep 00:07 libifeffit.dylib So close! Godd news last: we did not try python scripting on another machine, but IFEFFIT appears to run perfectly on 10.5 now - thanks Matt (champagne cork noise). Joel & Barbara

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iXAFS 3.0.3 for Mac OS X
by Matt Newville 21 Sep '10

21 Sep '10

Hi All, OK, sorry for the delay, but I think that http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.3.dmg should now work well for both Mac OS X 10.6 and 10.5. That is, all the applications launch for me on a 10.6.5 machine and a 10.5.8 machine, and seem to work as expected. I'll try this on a PowerPC machine within the next couple days. I didn't include the Python module in this installer (I forgot), but put it at http://cars9.uchicago.edu/~ifeffit/src/IfeffitPython-2.0.1.tar.gz This *should* work now, but then I thought the last one was going to work too. It might be best to run this through the Ifeffit Shell, or to be extra careful in setting the environment to source the /..../iXAFS.app/Contents/Resources/local/bin/iff_init.sh As always, any feedback on what works and what doesn't would be greatly appreciated. Cheers, --Matt

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Space group notation
by Abhijeet Gaur 21 Sep '10

21 Sep '10

Hi all, I am trying to generate the theoretical model of a compound in Artemis. The compound crystallizes in the triclinic space group I1ˉ. As superscript and subscript cannot be given, I tried the notations like I-1, I1-, I1_, but it is showing the message "Invalid space group". I read the tutorial on "Atoms", still not able to resolve the problem. Please help. With regards Abhijeet Gaur

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Re: [Ifeffit] XasPerlBundle problems
by Joshua Kas 20 Sep '10

20 Sep '10

Hi Matt, Thanks for the suggestion. I tried removing the file /usr/lib/perl5/5.10.X/CPAN/Config.pm, but no luck. Finally, I wrote my own bash script which just went through each of the modules listed in XasPerlBundle.pm and did cpan -i $module This seems to have worked fine, although I only tested startup of artemis/athena. Cheers, Josh Kas On Mon, Sep 20, 2010 at 10:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. iXAFS 3.0.3 for Mac OS X (Matt Newville) > 2. Re: XasPerlBundle problems (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 19 Sep 2010 12:46:31 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] iXAFS 3.0.3 for Mac OS X > Message-ID: > <AANLkTin2OXBe79nM8=gr7sFY2CBGT=o5y8UAvfxfVUNV(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi All, > > OK, sorry for the delay, but I think that > http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.3.dmg<http://cars9.uchicago.edu/%7Eifeffit/src/iXAFS3.0.3.dmg> > > should now work well for both Mac OS X 10.6 and 10.5. That is, all > the applications launch for me on a 10.6.5 machine and a 10.5.8 > machine, and seem to work as expected. I'll try this on a PowerPC > machine within the next couple days. > > I didn't include the Python module in this installer (I forgot), but put it > at > http://cars9.uchicago.edu/~ifeffit/src/IfeffitPython-2.0.1.tar.gz<http://cars9.uchicago.edu/%7Eifeffit/src/IfeffitPython-2.0.1.tar.gz> > > This *should* work now, but then I thought the last one was going to > work too. It might be best to run this through the Ifeffit Shell, or > to be extra careful in setting the environment to source the > /..../iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > As always, any feedback on what works and what doesn't would be > greatly appreciated. > > Cheers, > > --Matt > > > ------------------------------ > > Message: 2 > Date: Sun, 19 Sep 2010 19:58:04 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: joshua jason kas <hebhop(a)u.washington.edu>, Bruce Ravel > <bravel(a)bnl.gov>, XAFS Analysis using Ifeffit > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XasPerlBundle problems > Message-ID: > <AANLkTik7OwOBWoTb_V3GTG1i5sU+3_FLo+eicY5qP8aD(a)mail.gmail.com<AANLkTik7OwOBWoTb_V3GTG1i5sU%2B3_FLo%2BeicY5qP8aD(a)mail.gmail.com> > > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Josh, > > > 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. > > I had similar troubles on Mac OS X, I think possibly due to a bad > CPAN/Config.pm file (that is, /usr/lib/perl5/5.10.X/CPAN/Config.pm). > Among other things, I was also seeing CPAN trying to use /CPAN/ as its > root directory -- that can't be very good. > > I think this could be related to the MyConfig.pm in Bruce's > distribution, which has > 'cpan_home' => File::Spec->catfile($ENV{__INSTALLING_BRPERL}, "CPAN"), > > but I haven't tested this carefully. > > Anyway, I would suggest blowing away the CPAN/CONFIG.pm file and > starting over. I think that will use a '.cpan' folder in your home > directory for CPAN stuff, and that might fix it. > > If that doesn't help, hopefully Bruce will have more insight. > > --Matt > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 91, Issue 23 > *************************************** >

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Re: [Ifeffit] XasPerlBundle problems
by Matt Newville 20 Sep '10

20 Sep '10

Hi Josh, > 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. I had similar troubles on Mac OS X, I think possibly due to a bad CPAN/Config.pm file (that is, /usr/lib/perl5/5.10.X/CPAN/Config.pm). Among other things, I was also seeing CPAN trying to use /CPAN/ as its root directory -- that can't be very good. I think this could be related to the MyConfig.pm in Bruce's distribution, which has 'cpan_home' => File::Spec->catfile($ENV{__INSTALLING_BRPERL}, "CPAN"), but I haven't tested this carefully. Anyway, I would suggest blowing away the CPAN/CONFIG.pm file and starting over. I think that will use a '.cpan' folder in your home directory for CPAN stuff, and that might fix it. If that doesn't help, hopefully Bruce will have more insight. --Matt

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