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

RE: [Ifeffit] feff doesn't like cluster
by Kelly, Shelly D. 21 Jul '05

21 Jul '05

Oh well, I guess that could be fixed. Atoms assumes that the absorbing atom will also be a scattering atom, hence ipot 0 and ipot 1 are always defined with the same atom type. SK > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan > Sent: Thursday, July 21, 2005 10:14 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] feff doesn't like cluster > > Shelly, > > but why did ATOMS generate an ipot that doesn't exist? > > Juro > > On Jul 21, 2005, at 4:59 PM, Kelly, Shelly D. wrote: > > > > > Hi Juro, > > > > Feff is old fasioned. It requires that all ipot numbers are in order > > and that they exist, otherwise it just quits. In your example below > > ipot number 1 was not defined. > > > > Shelly > > > >> -----Original Message----- > >> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > >> bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan > >> Sent: Thursday, July 21, 2005 9:51 AM > >> To: XAFS Analysis using Ifeffit > >> Subject: Re: [Ifeffit] feff doesn't like cluster > >> > >> Hello, > >> > >> thank you for the fast response. According to Norbert's > >> suggestion, I looked in the feff file. The problem seems to > >> be with the potential 1, assigned to As. Removing this line > >> and rewriting all potentials in the list makes feff like > >> the input. However, I don't understand why ATOMS has > >> generated these ipot values. The atoms.inp is below. > >> > >> Juro > >> > >> ----------------------------------part of feff.inp > >> POTENTIALS > >> * ipot Z element > >> 0 33 As > >> 1 33 As > >> 2 8 O > >> 3 26 Fe > >> > >> ATOMS * this list contains 24 > >> atoms > >> * x y z ipot tag > >> distance > >> 0.00000 0.00000 0.00000 0 As > >> 0.00000 > >> -1.40201 0.76410 -0.53997 2 O3_1 > >> 1.68554 > >> 0.00000 -1.59002 -0.56202 2 O4_1 > >> 1.68643 > >> 0.00000 -0.00003 1.68705 2 O1_1 > >> 1.68705 > >> 1.37801 0.79495 -0.56207 2 O2_1 > >> 1.68724 > >> -2.86303 -0.03582 -1.71095 3 Fe2_1 > >> 3.33550 > >> -1.39501 -2.50095 -1.71100 3 Fe3_1 > >> 3.33591 > >> -1.46101 -0.86989 -2.91804 2 O13_1 > >> 3.37731 > >> -2.86203 -1.70487 -0.55592 2 O12_1 > >> 3.37740 > >> 0.00000 -0.69408 3.59511 3 Fe1_1 > >> 3.66150 > >> 0.00000 -2.60210 2.90109 2 O7_1 > >> 3.89708 > >> 2.03002 -0.69418 3.59504 2 O9_1 > >> 4.18655 > >> -2.03002 -0.69397 3.59518 2 O8_1 > >> 4.18663 > >> -2.86503 1.63323 -2.86599 2 O11_1 > >> 4.36918 > >> 0.07200 -3.29702 -2.86609 2 O15_1 > >> 4.36921 > >> -4.26604 0.79825 -0.50387 2 O10_1 > >> 4.36923 > >> -1.32901 -4.13200 -0.50397 2 O14_1 > >> 4.36963 > >> 0.00000 1.21295 4.28913 2 O6_1 > >> 4.45734 > >> 0.00000 -1.38895 -4.49813 2 O5_1 > >> 4.70769 > >> -2.79603 -3.41087 -2.86399 2 O17_1 > >> 5.25873 > >> -4.33104 -0.83474 -2.86393 2 O16_1 > >> 5.25897 > >> 0.00000 -1.38912 5.50217 2 O5_2 > >> 5.67482 > >> 5.73406 0.79772 -0.50422 2 O10_2 > >> 5.81120 > >> 0.00000 1.21312 -5.71117 2 O6_2 > >> 5.83859 > >> END > >> > >> > >> ----------------------------------atoms.inp > >> title model6 > >> space P 1 > >> rmax=6.0 a=10.0001 b=10.0002 c=10.0003 alpha=90.001 > >> beta=90.002 gamma=90.003 > >> core=As > >> atom > >> ! At.type x y z tag > >> As 0.00000 0.00000 0.00000 As > >> Fe 0.00000 -0.06940 0.35950 Fe1 > >> Fe -0.28630 -0.00360 -0.17110 Fe2 > >> Fe -0.13950 -0.25010 -0.17110 Fe3 > >> O 0.00000 0.00000 0.16870 O1 > >> O 0.13780 0.07950 -0.05620 O2 > >> O -0.14020 0.07640 -0.05400 O3 > >> O 0.00000 -0.15900 -0.05620 O4 > >> O 0.00000 -0.13890 0.55020 O5 > >> O 0.00000 0.12130 0.42890 O6 > >> O 0.00000 -0.26020 0.29010 O7 > >> O -0.20300 -0.06940 0.35950 O8 > >> O 0.20300 -0.06940 0.35950 O9 > >> O -0.42660 0.07980 -0.05040 O10 > >> O -0.28650 0.16330 -0.28660 O11 > >> O -0.28620 -0.17050 -0.05560 O12 > >> O -0.14610 -0.08700 -0.29180 O13 > >> O -0.13290 -0.41320 -0.05040 O14 > >> O 0.00720 -0.32970 -0.28660 O15 > >> O -0.43310 -0.08350 -0.28640 O16 > >> O -0.27960 -0.34110 -0.28640 O17 > >> > >> > >> On Thu, 21 Jul 2005 08:53:27 -0500 (CDT) > >> Matt Newville <newville(a)cars.uchicago.edu> wrote: > >>> Juraj, > >>> > >>> Please post the feff.inp file. You might also > >>> send the atoms.inp file. > >>> > >>> -Matt > >>> > >>> On Thu, 21 Jul 2005, Juraj Majzlan wrote: > >>> > >>>> Hello, > >>>> > >>>> I collected As K EXAFS data and created a cluster which > >>>> could represent the "probable geometry". I have an > >>> ATOMS > >>>> file with coordinates of the atoms in a triclinic unit > >>>> cell. ATOMS did its thing but FEFF refused to process > >>> the > >>>> data and generated an error: > >>>> Feff 6L.02 > >>>> No atoms or overlap cards for unique pot 1 > >>>> Cannot calculate potentials, etc. > >>>> Fatal Error: at RDINP > >>>> > >>>> Then I filled the empty space around the cluster with > >>>> hydrogen atoms on a grid, hoping that FEFF would like > >>> it > >>>> more, but the same error came. > >>>> > >>>> Short of creating a complete structure (of some sort) > >>> with > >>>> the cluster embedded in it, what can I do to make this > >>>> work? > >>> > >>> > >>> _______________________________________________ > >>> Ifeffit mailing list > >>> Ifeffit(a)millenia.cars.aps.anl.gov > >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > >> > >> > >> ---------------------------------- > >> Juraj Majzlan > >> Institute of Mineralogy and Petrology > >> Albert-Ludwig-University of Freiburg > >> Albertstrasse 23b > >> Freiburg, D-79104, Germany > >> telephone +49-761-203-6416 > >> fax +49-761-203-6407 > >> http://www.minpet.uni-freiburg.de > >> _______________________________________________ > >> 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 > > > > ---------------------------------------------------------------------- > Juraj Majzlan > Institute of Mineralogy and Geochemistry > Albert-Ludwig-University of Freiburg > Albertstrasse 23b > D-79104 Germany > telephone +49-761-203-6416 > fax +49-761-203-6407 > http://www.minpet.uni-freiburg.de/Majzlan.html > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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RE: [Ifeffit] feff doesn't like cluster
by Kelly, Shelly D. 21 Jul '05

21 Jul '05

Hi Juro, Feff is old fasioned. It requires that all ipot numbers are in order and that they exist, otherwise it just quits. In your example below ipot number 1 was not defined. Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan > Sent: Thursday, July 21, 2005 9:51 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] feff doesn't like cluster > > Hello, > > thank you for the fast response. According to Norbert's > suggestion, I looked in the feff file. The problem seems to > be with the potential 1, assigned to As. Removing this line > and rewriting all potentials in the list makes feff like > the input. However, I don't understand why ATOMS has > generated these ipot values. The atoms.inp is below. > > Juro > > ----------------------------------part of feff.inp > POTENTIALS > * ipot Z element > 0 33 As > 1 33 As > 2 8 O > 3 26 Fe > > ATOMS * this list contains 24 > atoms > * x y z ipot tag > distance > 0.00000 0.00000 0.00000 0 As > 0.00000 > -1.40201 0.76410 -0.53997 2 O3_1 > 1.68554 > 0.00000 -1.59002 -0.56202 2 O4_1 > 1.68643 > 0.00000 -0.00003 1.68705 2 O1_1 > 1.68705 > 1.37801 0.79495 -0.56207 2 O2_1 > 1.68724 > -2.86303 -0.03582 -1.71095 3 Fe2_1 > 3.33550 > -1.39501 -2.50095 -1.71100 3 Fe3_1 > 3.33591 > -1.46101 -0.86989 -2.91804 2 O13_1 > 3.37731 > -2.86203 -1.70487 -0.55592 2 O12_1 > 3.37740 > 0.00000 -0.69408 3.59511 3 Fe1_1 > 3.66150 > 0.00000 -2.60210 2.90109 2 O7_1 > 3.89708 > 2.03002 -0.69418 3.59504 2 O9_1 > 4.18655 > -2.03002 -0.69397 3.59518 2 O8_1 > 4.18663 > -2.86503 1.63323 -2.86599 2 O11_1 > 4.36918 > 0.07200 -3.29702 -2.86609 2 O15_1 > 4.36921 > -4.26604 0.79825 -0.50387 2 O10_1 > 4.36923 > -1.32901 -4.13200 -0.50397 2 O14_1 > 4.36963 > 0.00000 1.21295 4.28913 2 O6_1 > 4.45734 > 0.00000 -1.38895 -4.49813 2 O5_1 > 4.70769 > -2.79603 -3.41087 -2.86399 2 O17_1 > 5.25873 > -4.33104 -0.83474 -2.86393 2 O16_1 > 5.25897 > 0.00000 -1.38912 5.50217 2 O5_2 > 5.67482 > 5.73406 0.79772 -0.50422 2 O10_2 > 5.81120 > 0.00000 1.21312 -5.71117 2 O6_2 > 5.83859 > END > > > ----------------------------------atoms.inp > title model6 > space P 1 > rmax=6.0 a=10.0001 b=10.0002 c=10.0003 alpha=90.001 > beta=90.002 gamma=90.003 > core=As > atom > ! At.type x y z tag > As 0.00000 0.00000 0.00000 As > Fe 0.00000 -0.06940 0.35950 Fe1 > Fe -0.28630 -0.00360 -0.17110 Fe2 > Fe -0.13950 -0.25010 -0.17110 Fe3 > O 0.00000 0.00000 0.16870 O1 > O 0.13780 0.07950 -0.05620 O2 > O -0.14020 0.07640 -0.05400 O3 > O 0.00000 -0.15900 -0.05620 O4 > O 0.00000 -0.13890 0.55020 O5 > O 0.00000 0.12130 0.42890 O6 > O 0.00000 -0.26020 0.29010 O7 > O -0.20300 -0.06940 0.35950 O8 > O 0.20300 -0.06940 0.35950 O9 > O -0.42660 0.07980 -0.05040 O10 > O -0.28650 0.16330 -0.28660 O11 > O -0.28620 -0.17050 -0.05560 O12 > O -0.14610 -0.08700 -0.29180 O13 > O -0.13290 -0.41320 -0.05040 O14 > O 0.00720 -0.32970 -0.28660 O15 > O -0.43310 -0.08350 -0.28640 O16 > O -0.27960 -0.34110 -0.28640 O17 > > > On Thu, 21 Jul 2005 08:53:27 -0500 (CDT) > Matt Newville <newville(a)cars.uchicago.edu> wrote: > > Juraj, > > > > Please post the feff.inp file. You might also > > send the atoms.inp file. > > > > -Matt > > > > On Thu, 21 Jul 2005, Juraj Majzlan wrote: > > > > > Hello, > > > > > > I collected As K EXAFS data and created a cluster which > > > could represent the "probable geometry". I have an > > ATOMS > > > file with coordinates of the atoms in a triclinic unit > > > cell. ATOMS did its thing but FEFF refused to process > > the > > > data and generated an error: > > > Feff 6L.02 > > > No atoms or overlap cards for unique pot 1 > > > Cannot calculate potentials, etc. > > > Fatal Error: at RDINP > > > > > > Then I filled the empty space around the cluster with > > > hydrogen atoms on a grid, hoping that FEFF would like > > it > > > more, but the same error came. > > > > > > Short of creating a complete structure (of some sort) > > with > > > the cluster embedded in it, what can I do to make this > > > work? > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > ---------------------------------- > Juraj Majzlan > Institute of Mineralogy and Petrology > Albert-Ludwig-University of Freiburg > Albertstrasse 23b > Freiburg, D-79104, Germany > telephone +49-761-203-6416 > fax +49-761-203-6407 > http://www.minpet.uni-freiburg.de > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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file type plug-ins
by Bruce Ravel 17 Jul '05

17 Jul '05

Hi, One of the new features in Athena 0.8.041 is a plug-in architecture for processing data files that are not recognized by Ifeffit. Ifeffit and Athena are pretty successful at importing data from many of the beam-lines around the world that do XAS, but there are a number of beam-lines whose data requires either special, hardwired code in Athena or intervention by the user before importing into Athena. Neither of these solutions is particularly satisfying. Here I describe my latest attempt to address this recurring problem. It is now possible to write a short perl Module and drop it in the correct location. Athena will find and load that module and use it to recognize and reformat data that could otherwise not be imported. Currently, Athena ships with three such plug-ins, one for NSLS X10C, one for APS 12BM, and one for NSLS X15B. The NSLS X10C plug-in is extensively documented and explains how to write other plug-ins. This means that any time a user runs into trouble importing data into Athena, a plug-in can be written and dropped into place. Athena will then be able to import that data. No upgrade required. How cool is that? So, if you have data that Athena has trouble with, you can take a stab at writing a plug-in. Or the beam-line scientist can do so. Or I can. Indeed, I encourage users and beam-line scientists from beam-lines that use formats that give trouble to Athena to contact me with examples of those data files. Or, even better, write a plug-in, send it to me, and I'll distribute it with my codes. B P.S. Some beam-lines that generate data that cannot immediately be read by Ifeffit include: * X10C at NSLS (Athena has for some time included special code for dealing with these data -- this chore has been moved to a plug-in) * 12BM at the APS (the header contains a line that confuses Ifeffit) * X15B at NSLS (uses a legacy binary format) * the XAS beam-line at the LNLS, (see http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-August/001335.html for that discussion) * At least one of the XAS BLs at SPring8 uses a confusing multi-column format and mono angle instead of energy * Any BL using Spec is likely to generate data files that Ifeffit cannot read * Much of the data in the Ferrel Lytle Database at IIT is in formats that cannot be directly imported into Athena Athena currently includes plug-ins for the first three BLs on this list, each involving less than 50 lines of code. These are easy things to write! The one for NSLS X15B, however, does not yet work on Windows. It works great on my Linux boxes, but I have yet to get it to work on Windows. Stay tuned. -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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new release of Athena, artemis, and Hephaestus
by Bruce Ravel 17 Jul '05

17 Jul '05

Hi everyone, I have put a new version of the source code for my programs at SourceForge and on my web site. The new tarball is version 053. Unix and Mac OSX users can download and install the latest tarball or use the horae_update script at any time. A new windows update will be coming out shortly, as will debian packages. The biggest feature of this release is that I have retired version 0.7 of Artemis and released the development version as Artemis 0.8. >From this point on, all development and most support for 0.7 will stop and I will be developing and supporting 0.8. I have said a lot about the new features in recent months, but for those unfamiliar with all the changes, there are links on my EXAFS software page and on the Artemis page to a PDF file with an overview of the new features. I look forward to receiving comments, suggestions, and bug reports. I will be particularly eager to hear of any problems importing project files from 0.7 into 0.8. I will try to give bug reports of that sort my speedy attention. There are new features in Hephaestus' ion chamber and formula utilities that I hope you will find helpful. Athena has many new features, including improvements to the linear combination fitting dialog, some new plotting options, and a number of bug fixes and user interface improvements. The most important new feature in Athena is a plug-in architecture for processing file types that Ifeffit is unable to read. I plan to describe that in a separate post to the mailing list. Have fun, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu *** My cell phone number has changed. Please ask if you need the new number Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Re: compilation problem under MAC OS X - all ok now!
by Brugger, Joel (SAM) 17 Jul '05

17 Jul '05

Thanks Matt - installing g77 and then recompiling perl/Tk and horae did the trick! Bruce - sorry, I meant Perl/Tk... Paul, you may want to upgrade the installation notes to mention that g77 has to be installed first. Installion with Fink was a pleasure. Thanks again guys! JOEL -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: 7/12/2005 12:30 PM Subject: Ifeffit Digest, Vol 29, Issue 8 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: A question (Scott Calvin) 2. RE: A question (Frenkel, Anatoly) 3. Re: A question (Bruce Ravel) 4. rbkg (Silvio Levy) 5. compilation problem under MAC OS X (Brugger, Joel (SAM)) 6. Re: rbkg (Bruce Ravel) 7. Re: compilation problem under MAC OS X (Bruce Ravel) 8. Re: compilation problem under MAC OS X (Paul Fons) 9. Re: compilation problem under MAC OS X (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Mon, 11 Jul 2005 14:24:33 -0400 From: Scott Calvin <scalvin(a)slc.edu> Subject: Re: [Ifeffit] A question To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: SCalvin(a)slc.edu Message-ID: <3.0.1.32.20050711142433.00c35ca0(a)mail.slc.edu> Content-Type: text/plain; charset="us-ascii" At 11:45 AM 7/11/2005 -0500, Bruce wrote: >On Monday 11 July 2005 10:39, Mark Mark wrote: >> Hi >> Thank you all for the help. I wonder if I have to use X,Y, and Z parameters >> while originating a feff input file from ATOM or I can use X/a, Y/b, and >> Z/c parameters. I appreciate all the help. > >I don't quite understand the question, but perhaps an example of an >atoms input file would help clarify. This is taken from the examples >that come with the software: >> I would add to Bruce's comment that the FEFF.INP file then gives coords in terms of angstroms, rather than the cell coordinates ATOMS uses. So if you create or modify a FEFF.INP file directly, use angstroms. For an ATOM.INP file use cell coordinates. --Scott Calvin Sarah Lawrence College ------------------------------ Message: 2 Date: Mon, 11 Jul 2005 15:47:56 -0400 From: "Frenkel, Anatoly" <frenkel(a)bnl.gov> Subject: RE: [Ifeffit] A question To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <2332D75C71E72E4CBDFC8100FB054FE3793C3F(a)exchange2000-02.b459.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" ...... and if you use SS and OVERLAP cards in FEFF, use Bohr's units, which is cute but I hope they will convert this units to Angstroms some day. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Scott Calvin Sent: Monday, July 11, 2005 2:25 PM To: XAFS Analysis using Ifeffit Cc: SCalvin(a)slc.edu Subject: Re: [Ifeffit] A question At 11:45 AM 7/11/2005 -0500, Bruce wrote: >On Monday 11 July 2005 10:39, Mark Mark wrote: >> Hi >> Thank you all for the help. I wonder if I have to use X,Y, and Z parameters >> while originating a feff input file from ATOM or I can use X/a, Y/b, and >> Z/c parameters. I appreciate all the help. > >I don't quite understand the question, but perhaps an example of an >atoms input file would help clarify. This is taken from the examples >that come with the software: >> I would add to Bruce's comment that the FEFF.INP file then gives coords in terms of angstroms, rather than the cell coordinates ATOMS uses. So if you create or modify a FEFF.INP file directly, use angstroms. For an ATOM.INP file use cell coordinates. --Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------ Message: 3 Date: Mon, 11 Jul 2005 15:01:16 -0500 From: Bruce Ravel <bravel(a)anl.gov> Subject: Re: [Ifeffit] A question To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200507111501.16792.bravel(a)anl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 11 July 2005 14:47, Frenkel, Anatoly wrote: > ..... and if you use SS and OVERLAP cards in FEFF, use Bohr's units, which > is cute but I hope they will convert this units to Angstroms some day. Hmm... weird. I did not know that. I feel compelled to point out that anyone -- Anatoly, Mark Mark, *anyone* -- can change the source to feff6L, the version that ships with Ifeffit, to fix this or any other user interface shortcoming. If you do so, let us know about it here on the list so the change (if it's a good one) can be rolled back into the Ifeffit distribution. "And that," he pontificates, "is the beauty of open source...." B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu *** My cell phone number has changed. Please ask if you need the new number Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ ------------------------------ Message: 4 Date: Mon, 11 Jul 2005 15:28:09 -0700 From: Silvio Levy <levy(a)msri.org> Subject: [Ifeffit] rbkg To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <E1Ds6kz-0001Ls-00(a)pinch.msri.org> Hi, I'm a new reader of the list. Thanks for all this very useful software and impressive documentation. I'm having trouble understanding the role of rbkg in spline (or autobk). Ravel's Exafs Analysis with FEFF and FEFFIT describes it as "the cutoff between the portion of the Fourier transformed spectrum dominated by the background function and the portion containing information about the local structure". This would seem to imply that after removal of the background spline, the signal will have NO frequencies below rbkg -- that is, in the R domain, it would be 0 (or close to 0) for R < Rbkg. But this is not quite what I see; varying Rbkg has a large effect throughout the plot of chir_mag versus R. In particular I observe sometimes that with Rbkg = 1.3 (say) I get a very different R-plot than with either Rbkg = .9 or 1.5 -- not just at low R but throughout. And yet the Rbkg = .9 and 1.5 R-plots look similar to one another, much more than to R-plot for the intermediate value of R. Moreover changing Rbkg shifts the peaks in the R-plot noticeably. What does the algorithm actually do with this parameter? It would be nice to understand that without having to decipher the code. Forgive me if this information is given somewhere, but I couldn't find it. Note: I'm working with compounds for which I don't yet have a good theoretical model, so I don't know how to choose between Rbkg values based on the position of the peaks. Thanks Silvio Levy ------------------------------ Message: 5 Date: Tue, 12 Jul 2005 08:39:57 +0930 From: "Brugger, Joel (SAM)" <Brugger.Joel(a)saugov.sa.gov.au> Subject: [Ifeffit] compilation problem under MAC OS X To: "'ifeffit(a)millenia.cars.aps.anl.gov'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <5801DF3664AC854AA3CC2DB83E718D30030C0CBF(a)sagemsg0006.sagemsmrd01.sa.gov ...au> Content-Type: text/plain Hi, While I had no problem following Matt's instructions to get Ifeffit working on my desktop after upgrading to 10.4, I'm still stuggling to install ifeffit on the new laptop. I've tried different combinations of the binary installer and manual compilations of Tcl/TK and horae, but I run into this error: %JoelG4:/Applications/Ifeffit/bin joelb$ ./hephaestus %dyld: lazy symbol binding failed: Symbol not found: _s_copy % Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bund le % Expected in: dynamic lookup % %dyld: Symbol not found: _s_copy % Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bund le % Expected in: dynamic lookup % %Trace/BPT trap Only thing I can think of at this stage is reinstalling the OS! Thanks! JOEL ------------------------------ Message: 6 Date: Mon, 11 Jul 2005 18:28:18 -0500 From: Bruce Ravel <bravel(a)anl.gov> Subject: Re: [Ifeffit] rbkg To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200507111828.18498.bravel(a)anl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 11 July 2005 17:28, Silvio Levy wrote: > Hi, I'm a new reader of the list. Thanks for all this very useful > software and impressive documentation. Thanks for the kind words. > I'm having trouble understanding the role of rbkg in spline (or > autobk). Ravel's Exafs Analysis with FEFF and FEFFIT describes it as > "the cutoff between the portion of the Fourier transformed spectrum > dominated by the background function and the portion containing > information about the local structure". > > This would seem to imply that after removal of the background spline, > the signal will have NO frequencies below rbkg -- that is, in the R > domain, it would be 0 (or close to 0) for R < Rbkg. That would be true if an infinite Fourier transform were possible. Alas, our FT is finite (no negative values of k and positive values only go out to 12 or so). Since the FT is finite, the Fourier components leak to the left and to the right. In practice, this means that our signal has non-zero spectral weight below Rbkg and our background has non-zero spectral weight above that value. Thus, in practice, the background spline and the parameters we eventually use to fit the data are correlated. Although there are many things in that document that I would state differently today, the language I used to describe Rbkg is valid. Rbkg *is* the frequency we choose as that cutoff, but the cutoff is never as clear as you anticipated. All the details of the Autobk algorithm are in Physical Review B47:21 (1993) p. 14126. See page 30 in this PDF file http://cars9.uchicago.edu/xafs/NSLS_2003/Kelly.pdf for a nice graphical demonstration of what Rbkg means. (The rest of that document is pretty useful, as well.) HTH, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu *** My cell phone number has changed. Please ask if you need the new number Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ ------------------------------ Message: 7 Date: Mon, 11 Jul 2005 18:33:29 -0500 From: Bruce Ravel <bravel(a)anl.gov> Subject: Re: [Ifeffit] compilation problem under MAC OS X To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200507111833.29175.bravel(a)anl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 11 July 2005 18:09, Brugger, Joel (SAM) wrote: > While I had no problem following Matt's instructions to get Ifeffit working > on my desktop after upgrading to 10.4, I'm still stuggling to install > ifeffit on the new laptop. I've tried different combinations of the binary > installer and manual compilations of Tcl/TK and horae, but I run into this > error: A caveat: I do not own a Mac and have not tried to install the codes on 10.4. That said, I wanted to point out that Tcl/Tk has *nothing* to do with installing my codes on a computer. My codes use Tcl/Tk in no way whatsoever. Perl/Tk, on the other hand, is essential to the story. See http://search.cpan.org/~ni-s/Tk-804.027/ The Perl bindings to the Tk toolkit come with its own, modified version of Tk. You must install Perl/Tk to get my codes to work. Installing Tcl/Tk just ain't part of the deal. HTH, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu *** My cell phone number has changed. Please ask if you need the new number Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ ------------------------------ Message: 8 Date: Mon, 11 Jul 2005 15:04:21 -1000 From: Paul Fons <paul-fons(a)aist.go.jp> Subject: Re: [Ifeffit] compilation problem under MAC OS X To: bravel(a)anl.gov, XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <C8746064-01D5-4B97-B565-4E4E45EFE69E(a)aist.go.jp> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed I thought I would bring up the Wiki entry regarding installation on Tiger 10.4 at (http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz? req=all#2.12). If there is a problem, I would like to modify the text. In short, I have (re)installed horae on two 10.4 systems upgraded from 10.3 as well as on a brand spanking new dual G5. It works without error on each. For the G5, I installed the new version of Tk (as explained in the Wiki entry) and then just ran the binary installer (as I recall). I don't recall having any problems with the installation and it works fine on all three machines. Please excuse me for mentioning the obvious, but if this a new machine with the OS pre-installed, it is necessary to install X11 which is an optionally install on the included installation DVD's. Once this is installed, download Tk (tcl is included and does not require reinstallation) and install it, and then the binary installer for ifeffit. I don't recall if the binary installer has the latest version of horae and ifeffit, but once the base installation is in place, you can upgrade any time from terminal by typing "sudo horae_update". Paul On Jul 11, 2005, at 13:33 PM, Bruce Ravel wrote: > On Monday 11 July 2005 18:09, Brugger, Joel (SAM) wrote: > >> While I had no problem following Matt's instructions to get >> Ifeffit working >> on my desktop after upgrading to 10.4, I'm still stuggling to install >> ifeffit on the new laptop. I've tried different combinations of >> the binary >> installer and manual compilations of Tcl/TK and horae, but I run >> into this >> error: >> > > A caveat: I do not own a Mac and have not tried to install the > codes on > 10.4. > > That said, I wanted to point out that Tcl/Tk has *nothing* to do with > installing my codes on a computer. My codes use Tcl/Tk in no way > whatsoever. > > Perl/Tk, on the other hand, is essential to the story. See > http://search.cpan.org/~ni-s/Tk-804.027/ > > The Perl bindings to the Tk toolkit come with its own, modified > version of > Tk. You must install Perl/Tk to get my codes to work. Installing > Tcl/Tk just > ain't part of the deal. > > HTH, > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > > ravel(a)phys.washington.edu > > *** My cell phone number has changed. Please ask if you need the > new number > > Environmental Research Division, Building 203, Room E-165 > Argonne National Laboratory phone and voice mail: (1) 630 > 252 5033 > Argonne IL 60439, USA fax: (1) 630 > 252 9793 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: http://feff.phys.washington.edu/~ravel/software/ > exafs/ > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 9 Date: Mon, 11 Jul 2005 21:57:13 -0500 (CDT) From: Matt Newville <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] compilation problem under MAC OS X To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <Pine.LNX.4.44.0507112144331.24556-100000@corvette> Content-Type: TEXT/PLAIN; charset=US-ASCII Joel, > %dyld: Symbol not found: _s_copy > %Trace/BPT trap > > Only thing I can think of at this stage is reinstalling the OS! No, you don't need to do that!! What's missing (and we forgot to put it in the instructions) is that you need Fink's g77 installed as well as the new version of perl/Tk and the "developers disk", including the X11 libraries -- I hear these are labelled differently for 10.4, and that installing XCode might be the best approach. For Fink, see http://fink.sourceforge.net/. Using Fink is not always easy (and requires root access, which for most Mac users means using 'sudo'). There are reasonable instructions for Fink, and FinkCommander is a very nice front end to use. I'm pretty sure you won't need anything besides g77 from Fink. It should be that after installing Fink you can open a Terminal and do: ~> . /sw/bin/init.sh ~> sudo apt-get -f install g77 Sorry for the confusion, --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 29, Issue 8 **************************************

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RE: [Ifeffit] multielectron transition
by Jensen, Mark P. 13 Jul '05

13 Jul '05

I am aware of two examples in the literature where EXAFS have been fit without and with consideration of multielectron excitation. Both Found a 0.01 - 0.02 A contraction in the first shell scattering pathlength when the multielectron effects were removed. The relevant papers are: P. D'Angelo, H.-F. Nolting, and N. V. Pavel, Phys. Rev. A, 53 (1996) 798 J.A. Solera, J. Garcia, and M. G. Proietti, Phys. Rev. B, 51 (1995) 2678 In the second paper they show that the effect of multielectron excitations for the lanthanide-aquo ions is unimportant in the fitting of the EXAFS for lanthanides heavier than samarium, and that the multielectron excitations are not even visible by the time one reaches dysprosium. ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Barton, David G. > Sent: Wednesday, July 13, 2005 9:30 AM > To: 'XAFS Analysis using Ifeffit' > Subject: RE: [Ifeffit] multielectron transition > > Iztok, > > This is good stuff. Mulitelectron features definitely throw > at least a small wrench in a typical background substraction > routines that only substract smooth, broad features using splines. > > My naïve questions are: > 1) What chemical elements show a sizable contribution from a > multielectron feature that could skew spline based EXAFS data > analysis routines? > 2) Are there any examples in the literature where a > spline-based EXAFS analysis (i.e. bond lengths, coordination > numbers with statistics) is performed on a more complex > system than with and without the removal of these > multielectron features as a comparison. > > > Dave > > > -----Original Message----- > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > > Iztok.Arcon(a)p-ng.si > > Sent: Wednesday, July 13, 2005 10:21 AM > > To: bravel(a)anl.gov; XAFS Analysis? using Ifeffit? > > Cc: QY ZML; XAFSA Analysis usingI Ifeffit > > Subject: Re: [Ifeffit] multielectron transition > > Importance: Low > > > > > > Dear Bruce > > > > An example of treating atomic absorption background > including large > > multielectron features in L edge spectra of Ce is given in the > > attached paper. Full atomic absorption background for > nearby elements > > Cs and Xe can be seen in the second attached paper. Some > other useful > > references on this topic are given below: > > > > > > J. A. Solera, J. Garcia, M. G. Proietti, Phys. Rev. B 1995, > > 51, 2678–2686. > > > > A. Kodre, I. Arčon, M. Hribar, M. Štuhec, F. Villain, W. > > Drube, L. Troeger, Physica B 1995,208&209, 379–380. > > > > J. Padežnik Gomilšek, I. Kozjek Škofic, N. Bukovec, A. Kodre, > > Thin Solid Films 2004, 446, 117–123. > > > > E. Fonda, D. Andreatta, P. E. Colavita, G. Vlaic, J. > > Synchrotron Rad. 1999, 6, 34–42. > > > > > > also some our references for atomic absorption spectra of K > > edge exafs: > > > > A. Kodre, I. Arčon, J. Padežnik Gomilšek, R. Frahm > > Multielectron excitations in x-ray absorption spectra of Rb > > and Kr J. Phys. B: At. Mol. Opt. Phys. 35 (2002) 3497-3513 > > > > A. Kodre, I. Arčon, J. Padežnik Gomilšek, A. Mihelič > > Atomic absorption background in EXAFS spectra of Rb in > > inter-alkaline alloys Physica Scripta. Vol, T115, (2005) 218-220 > > > > A. Kodre, R. Prešeren, I. Arčon, J. Padeznik Gomilšek, M.. > > Borowski, A study of transferability of atomic background on > > EXAFS spectra of simple gaseous compounds of As, J. Synch. > > Radiation 8 (2001) 282-284 > > > > R. Prešeren, A. Kodre, I. Arčon, M. Borowski, > > Atomic background and EXAFS of gaseous hydrides of Ge, As, > > Se, and Br, J. Synch. Radiation 8 (2001) 279-281 > > > > There are many other papers of different authors on the > > multielectron photoexcitations (see references in above > > papers). Additional information on multielectron > > photoexcitations in exafs spectra of L and K edges of > > different elements and some subtraction procedures can be > > found also on the dedicated web site of our group: > > > http://www.p-ng.si/~arcon/xas/mpe/mpe5.htm > > best regards and congratulations for well supported > program packages for > exafs analysis. > > Iztok Arcon > > > > On Tuesday 12 July 2005 11:18, QY ZML wrote: > >> I am analyzing EXAFS of some rare earth systems. It is known that > >> there are ?multielectron transitions in these systems. So, > I want to > >> know how to subtract multielectron process contribution > generally and > >> if ATHENA has a feature to do this. ?Thank you very much. > > > > Athena does not currently have a feature for doing this. Drat! > > > > I would be willing to implement something empirical for > doing this. I > > would like to see a discussion here on the mailing list of > the merits > > of different > > approaches. Since I have never given this very much > thought, I am not > > with > > any strong opinions for how it should (or should not) be > done. But I can > > certainly consider implementing it. > > > > B > > > > -- > > Bruce Ravel ----------------------------------- > bravel(a)anl.gov -or- > > > > ravel@phys.washington...edu > > > > *** My cell phone number has changed. Please ask if you > need the new > > number > > > > Environmental Research Division, Building 203, Room E-165 > > Argonne National Laboratory phone and voice mail: > (1) 630 252 > > 5033 > > Argonne IL 60439, USA fax: > (1) 630 252 > > 9793 > > > > My homepage: http://feff.phys.washington.edu/~ravel > > EXAFS software: > > http://feff.phys.washington.edu/~ravel/software/exafs/ > > > > > > _______________________________________________ > > 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 >

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RE: [Ifeffit] multielectron transition
by Barton, David (DG) 13 Jul '05

13 Jul '05

Iztok, This is good stuff. Mulitelectron features definitely throw at least a small wrench in a typical background substraction routines that only substract smooth, broad features using splines. My naïve questions are: 1) What chemical elements show a sizable contribution from a multielectron feature that could skew spline based EXAFS data analysis routines? 2) Are there any examples in the literature where a spline-based EXAFS analysis (i.e. bond lengths, coordination numbers with statistics) is performed on a more complex system than with and without the removal of these multielectron features as a comparison. Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Iztok.Arcon(a)p-ng.si > Sent: Wednesday, July 13, 2005 10:21 AM > To: bravel(a)anl.gov; XAFS Analysis? using Ifeffit? > Cc: QY ZML; XAFSA Analysis usingI Ifeffit > Subject: Re: [Ifeffit] multielectron transition > Importance: Low > > > Dear Bruce > > An example of treating atomic absorption background > including large multielectron features in L edge spectra of > Ce is given in the attached paper. Full atomic absorption > background for nearby elements Cs and Xe can be seen in the > second attached paper. Some other useful references on this > topic are given below: > > > J. A. Solera, J. Garcia, M. G. Proietti, Phys. Rev. B 1995, > 51, 2678–2686. > > A. Kodre, I. Arčon, M. Hribar, M. Štuhec, F. Villain, W. > Drube, L. Troeger, Physica B 1995,208&209, 379–380. > > J. Padežnik Gomilšek, I. Kozjek Škofic, N. Bukovec, A. Kodre, > Thin Solid Films 2004, 446, 117–123. > > E. Fonda, D. Andreatta, P. E. Colavita, G. Vlaic, J. > Synchrotron Rad. 1999, 6, 34–42. > > > also some our references for atomic absorption spectra of K > edge exafs: > > A. Kodre, I. Arčon, J. Padežnik Gomilšek, R. Frahm > Multielectron excitations in x-ray absorption spectra of Rb > and Kr J. Phys. B: At. Mol. Opt. Phys. 35 (2002) 3497-3513 > > A. Kodre, I. Arčon, J. Padežnik Gomilšek, A. Mihelič > Atomic absorption background in EXAFS spectra of Rb in > inter-alkaline alloys Physica Scripta. Vol, T115, (2005) 218-220 > > A. Kodre, R. Prešeren, I. Arčon, J. Padeznik Gomilšek, M. > Borowski, A study of transferability of atomic background on > EXAFS spectra of simple gaseous compounds of As, J. Synch. > Radiation 8 (2001) 282-284 > > R. Prešeren, A. Kodre, I. Arčon, M. Borowski, > Atomic background and EXAFS of gaseous hydrides of Ge, As, > Se, and Br, J. Synch. Radiation 8 (2001) 279-281 > > There are many other papers of different authors on the > multielectron photoexcitations (see references in above > papers). Additional information on multielectron > photoexcitations in exafs spectra of L and K edges of > different elements and some subtraction procedures can be > found also on the dedicated web site of our group: > http://www.p-ng.si/~arcon/xas/mpe/mpe5.htm best regards and congratulations for well supported program packages for exafs analysis. Iztok Arcon > On Tuesday 12 July 2005 11:18, QY ZML wrote: >> I am analyzing EXAFS of some rare earth systems. It is known that >> there are ?multielectron transitions in these systems. So, I want to >> know how to subtract multielectron process contribution generally and >> if ATHENA has a feature to do this. ?Thank you very much. > > Athena does not currently have a feature for doing this. Drat! > > I would be willing to implement something empirical for doing this. I > would like to see a discussion here on the mailing list of the merits > of different > approaches. Since I have never given this very much thought, I am not > with > any strong opinions for how it should (or should not) be done. But I can > certainly consider implementing it. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > > ravel@phys.washington...edu > > *** My cell phone number has changed. Please ask if you need the new > number > > Environmental Research Division, Building 203, Room E-165 > Argonne National Laboratory phone and voice mail: (1) 630 252 > 5033 > Argonne IL 60439, USA fax: (1) 630 252 > 9793 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: > http://feff.phys.washington.edu/~ravel/software/exafs/ > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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multielectron transition
by QY ZML 13 Jul '05

13 Jul '05

Hello all, I am analyzing EXAFS of some rare earth systems. It is known that there are multielectron transitions in these systems. So, I want to know how to subtract multielectron process contribution generally and if ATHENA has a feature to do this. Thank you very much. ZM

3 2

(no subject)
by Dr. K.R.S. Priolkar 12 Jul '05

12 Jul '05

Hi I wouldlike to know if it is possible to refine Ce L1 edge EXAFS using Artemis wherein there is a contribution of Ce L2 EXAFS. If yes, how to go about it? Thanks in advance Kaustubh -- Dr. Kaustubh R. S. Priolkar Tel:(O): 91-832-2451245-8 Department of Physics : 2456480-85 Extn: 351 Goa University (R): 91-832-2412235 Taleigao Plateau Fax: 91-832-2451184/2452889 Goa 403 206 India Cell: 9890357378

2 1

Re: [Ifeffit] rbkg
by Silvio Levy 12 Jul '05

12 Jul '05

Matt - thank you very much for the detailed explanation. Silvio

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