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

RE: [Ifeffit] database
by Michel Schlegel 22 Aug '05

22 Aug '05

Le 21:18 19/08/2005, vous avez écrit: >Carlo, Thanks for the offer of help! > >Dave, thanks for the suggestions, I think those are all good. > >In fact, I think none of this is that hard to do, but it will >take some time. For what it's worth, I think the data should be >stored in a 'proper' relational database, if for no other reason >than to make it easier and faster to search. It will also make >many of the 'fancier' features (user comments) easier to >implement. I may be just a nuisance, but wouldn't it be interesting to contact people currently developping mineralogical databases (e.g., from the Mineralogical Society of America) to have some insight on how their database is organized? That may save a lot of time. >At this point, I think the most immediate need is (as Dave >mentioned yesterday) to identify a reasonable format for the >data at both upload time and at download time. For upload, we'd >certainly want a web form where fields could be filled in or >parsed from a file following a 'Standard Data File Format'. I think the simplest way is to separate the "general information" field from the "data field". The general information may be entered as a standard fill-in submission page, and this information would then be entered as commented lines (e;g., startting with "#") at the beginning of the download files (pardon me if you think this is obvious!). Among the information to be added, I suggest a few more technical hints, like: - Synchrotron/beamline/station (or "calculated") - Crystal (e;g., Si(111)) - detection mode - raw spectrum/average of xxx spectra Other questions: - Is it advisable to accept only "raw" data (including glitches), or will some kind of preprocessing be allowed? - Would it be advisable to rank the spectra according to their quality (as for the powder diffraction files)? Best regards, Michel -- Michel Schlegel Commissariat à l'énergie atomique CEN de Saclay, DEN/DPC/SCP/LRSI Bat 391 - Piece 205B F91 191 Gif-sur-Yvette Cedex, France Ph: +33 (0)1 69 08 93 84 Fax: +33 (0)1 69 08 54 11

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RE: [Ifeffit] Cu oxides spectra
by Barton, David (DG) 22 Aug '05

22 Aug '05

Matt, As you know I am a strong supporter of such a model compound database. I am fairly certain that most people that have collected an XAFS spectra have at some point wanted to compare their data with a model compound or two that they didn't have on hand when they collected their data at the beamline. Not only would such a database help those that need a spectra that they didn't collect, but it would also help those that are attempting to collect model spectra and would like a comparison of data quality with others that have collected spectra on the same compound. > I think there are a few important features for such a database: > - through-the-web uploading and annotating of data, probably > after 'logging on' (as with the FAQ). > - simple visualization, even if just plotting mu(E). > - link to crystallographic info. Say, an atoms.inp. > - easy searching. > - either "user comments" added by others (aka Amazon-style > reviews) or some way to indicate that the data is "good". These are all excellent features to add to the database. I especially like the "user comments"/rating feature, this would be very helpful as the database grows and some spectra are collected on similar compounds. This would help users find the spectra with the highest data quality as determined by the community. Other fields that I believe would be of some value in your current model database would be: - add separate fields for compound name and elemental composition (should make searching easier for elements) - add fields for source of model compound (i.e. purchased from vendor {vendor name, purity, etc} or if synthesized {give journal reference to synthesis procedure}) - add check box if phase purity has been checked by other analytical methods and add a text field where the user could describe what other techniques were used. - add field for which edge was collected (k-edge, L1-edge, etc). - under link to crystallographic info you could add a field for Journal Reference to crystal structure. Hope this helps, Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Matt Newville > Sent: Friday, August 19, 2005 12:04 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Cu oxides spectra > > > Hi Dave, > > > Excellent start to a Model compounds XAFS library. > > Well, actually it's close to a decade old. But it *is* still > only a start. ;) > > > How can I add data to this collection? I have collected > ~50 reference > > spectra and would like to donate them to the world. > > I believe everyone in the XAFS community could benefit by > > sharing of reference spectra with one another and I would like > > to do my part. > > > Do you have a page that I could enter the spectra info and > upload the > > data? Or would it be better to create a spreadsheet with > the spectra > > info and zip up all raw spectra data? I am willing to format it in > > any form that works for you. > > Right now, you can just mail me the spectra and any > information you have on them. I'd prefer them as column data > of energy, xmu, and any other channels you might have (i0, a > reference foil, etc), and in individual files rather than a > spreadsheet. > > I think it's definitely worth looking into re-implementing > this Model Data database. Looking at the code and data I > have, I think this is definitely possible, and it does seem > like it is time to revisit this idea. > > I think there are a few important features for such a database: > - through-the-web uploading and annotaing of data, probably > after 'logging on' (as with the FAQ). > - simple visualization, even if just plotting mu(E). > - link to crystallographic info. Say, an atoms.inp. > - easy searching. > - either "user comments" added by others (aka Amazon-style > reviews) or some way to indicate that the data is "good". > > Does anyone else have thoughts or suggestions for such a > database of model compound data? Is a database like this > worth doing? > > Thanks, > > --Matt > > > > _______________________________________________ > 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] Cu oxides spectra
by Barton, David (DG) 19 Aug '05

19 Aug '05

Matt, Excellent start to a Model compounds XAFS library. How can I add data to this collection? I have collected ~50 reference spectra and would like to donate them to the world. I believe everyone in the XAFS community could benefit by sharing of reference spectra with one another and I would like to do my part. Do you have a page that I could enter the spectra info and upload the data? Or would it be better to create a spreadsheet with the spectra info and zip up all raw spectra data? I am willing to format it in any form that works for you. Regards, Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Matt Newville > Sent: Wednesday, August 17, 2005 10:27 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Cu oxides spectra > > > Marco (Scott), > > There's CuO and Cu2O (and azurite) data available: > http://cars9.uchicago.edu/~newville/ModelLib/search.html > > The Cu2O there is from the Lytle database. > > Reading data from the Lytle database is not always easy, > but there is a FAQ entry about how to do this: > > http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=show&file =faq03.004.htp Hope that helps, --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Cu oxides spectra
by marco antoni alsina corvalan 17 Aug '05

17 Aug '05

Hi all, My name is Marco, and I´m currently attempting to identify mixed phases of copper oxides through XANES. Searching for standards I visited the XAFS Database, however I was not able to read the Farrel Lytle database, and I mean I don't fully understand whow to extract the energy and absorption from the data (I also think that there is not a standard along with the data). If anyone knows how to read this Database or better yet, if anyone has measure copper oxides standards I would be very greatful if you would let me use that data for XANES comparisons. Thanks Marco Alsina Estudiante de Magister Departamento de Ingeniería Hidráulica y Ambiental Pontificia Universidad Católica de Chile

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Icosahedral cluster coordinates
by Patrick Kluth 17 Aug '05

17 Aug '05

Hi All, Since this is my first message to the mailing list, I`d like to say thanks very much to Bruce, Matt and everyone else who is involved for this great piece of software. It makes life in the EXAFS world so much easier. I am working with metal clusters and would like to do some FEFF calculations on icosahedral clusters. Is there anyone out there who has a FEFF input file (or equivalently a list of coordinates) for an icosahedral cluster (147 atoms is probably sufficient for my purpuses). Thanks Patrick --------------------------------------------------------------------------------- Dr. Patrick Kluth ARC Australian Postdoctoral Fellow Department of Electronic Materials Engineering Research School of Physical Sciences and Engineering The Australian National University Canberra, ACT 0200 AUSTRALIA Phone: +61 2 6125 0358 Fax: +61 2 6125 0511 Mobile: +61 408 66 31 04 Email: Patrick.Kluth(a)anu.edu.au http://www.rsphysse.anu.edu.au/eme ---------------------------------------------------------------------------------

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Bug in artemis of horae-053
by Paul Fons 16 Aug '05

16 Aug '05

I have had been bitten by surprisingly few bugs in the latest version of artemis, but I thought I would pass along an observation of one that should be easy to confirm. I am doing multiple edge fits and have in the past imported new data by using the project data item in the file menu. Selecting this brings up a dialog which asks if the new (path) data should replace the old data or should it be new (e.g. a new feff calculation). It doesn't appear to make any difference which option is selected, it always replaces the existing data. I seem to remember that this used to work in earlier versions... In any case, a work around is just to use the open item under the file menu which then does generate a new feff calculation entry. Oh, one more thing, as I recall Calculation is misspelled in the theory menu (it hurts to look at it as I live in a land with a lot of broken English (Japan))! Paul

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RE: [Ifeffit] Athena plotting multiple k-weights; confusion about "k" and "k-weight"
by Kelly, Shelly D. 15 Aug '05

15 Aug '05

Hi Charles, I think that you understand correctly and that Athena doesn't label the axis correctly when multiple k-weights are being plotted. The FT are different when different k-weights are used because different regions of chi(k) are emphasized differently. Shelly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Charles Chusuei Sent: Mon 8/15/2005 12:23 PM To: 'XAFS Analysis using Ifeffit' Subject: [Ifeffit] Athena plotting multiple k-weights; confusion about "k" and "k-weight" Hello all: I'm confused about what is meant by "k-weight" and "k" and how they are used in the Athena plotting. As I understand it, "k" refers to the photo-electron wavenumber, k = [2m(E-E0)]/(h/2pi)^2]^ 0.5. A "k-weight" is the degree that chi(k) can be amplified. For instance k-weight of "2" in the Athena program plots a k^2*chi(k) versus k. A k-weight of "3" plots a k^3*chi(k) versus k, etc. However, in plotting multiple "spectra" using the same data file of different k-weighting one can see the different lineshapes for each k-weight [for instance assigning k-weights = 1,2 and 3]. Yet, the Athena output has the labels of "k^2*chi(k)" versus "k" even though there are multiple k-weights used. Is this a typo in the ordinate label where it would be more appropriately labeled as "k^n*chi(k)" versus "k" where n = weight, or am I fundamentally misunderstanding the relationship between "k" and "k-weight"? I'd appreciate assistance in understanding if the latter is the case. Thank you for your thoughts. Charles _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Athena plotting multiple k-weights; confusion about "k" and "k-weight"
by Charles Chusuei 15 Aug '05

15 Aug '05

Hello all: I'm confused about what is meant by "k-weight" and "k" and how they are used in the Athena plotting. As I understand it, "k" refers to the photo-electron wavenumber, k = [2m(E-E0)]/(h/2pi)^2]^ 0.5. A "k-weight" is the degree that chi(k) can be amplified. For instance k-weight of "2" in the Athena program plots a k^2*chi(k) versus k. A k-weight of "3" plots a k^3*chi(k) versus k, etc. However, in plotting multiple "spectra" using the same data file of different k-weighting one can see the different lineshapes for each k-weight [for instance assigning k-weights = 1,2 and 3]. Yet, the Athena output has the labels of "k^2*chi(k)" versus "k" even though there are multiple k-weights used. Is this a typo in the ordinate label where it would be more appropriately labeled as "k^n*chi(k)" versus "k" where n = weight, or am I fundamentally misunderstanding the relationship between "k" and "k-weight"? I'd appreciate assistance in understanding if the latter is the case. Thank you for your thoughts. Charles

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problem with the new version of athena
by Carmelo Prestipino 11 Aug '05

11 Aug '05

Hi I have a really strange problem with the new version of athena. After updating to iffefit 1.2.7 I lose the possibility to use athena, but the rest of the package works well. I already try do deinstall everything and install ifeffit again but nothing changed. This problem is present only on my computer while in the computer of my colleagues athena works well. The file 1.txt is the answer of calling from the shell "athena.exe" the file 2.txt is the answer of calling from the shell "athena.bat" I'm using a windows 2000 sistem Any idea? Bye Carmelo -- ************************************************************************ Carmelo Prestipino(*) Department of Inorganic, Physical and Material Chemistry Via P. Giuria 7 I-10125 Torino Italy Tel +39011-6707841> Fax +39011-6707855 E-mail carmelo.prestipino(a)unito.it (*) also with INFM UdR di Torino Universita' ************************************************************************* C:\Programmi\Ifeffit>athena.bat Ifeffit checked for updates recently. Untagged opnames: recv i_predec localtime sassign rewinddir untie sockpair scope seekdir ucfirst fteowned i_negate rv2cv leave accept ge redo stringify substcont index right_shift aelem hex sservent send gt multiply bit_or unlink gv wantarray i_ne exi t lcfirst semctl open rv2sv gprotoent backtick syswrite getlogin grepstart subtract ftsize eof warn ehostent nextstate dofile aassign ftatime gvsv null gmtime shift stat flip substr postinc open_dir cond_expr atan2 left_shift time hslice leaveeval ret urn grepwhile socket preinc telldir seq link ftfile setstate sysread chdir each av2arylen ioctl reset ftewrite refgen gpwuid ord join modulo chown pop padav shmread ftsvtx pos and pow sgrent oct rindex chr sge aelemfast regcomp andassign fteexec rv2gv ftpipe ftsuid sort i_divide sprotoent fork entersub sgt ftbinary chmod unpack fteread bind tell eservent entertry semop push getpriority flock rv2hv lc ftrowned gpwnam system le gsbyport dump concat pushmark ftctime lt mapstart i_postdec repeat pack leaveloop stub exists sin threadsv syscall utime quotemeta ftchr padsv bit_xor log mapwhile rcatline sysopen readdir alarm truncate seek const padany sselect entereval abs ftzero ne helem close ftblk i_eq gpwent gpbynumber values pushre leavesub proto type die dbmclose aslice binmode wait complement list reverse flop snetent gsbyname fttty ftrexec leavetry match unstack eprotoent i_preinc gpbyname shutdown ftrwrite crypt postdec iter listen anoncode trans lineseq ftrread length ftsgid sprintf print chomp or add enter predec lock epwent tie fttext chop i_ge sle schop umask closedir gnetent subst tied i_add setpgrp i_modulo defined scmp negate getpeername undef rmdir ftlink slt regcreset i_gt rename ghostent msgsnd method_named kill orassign requ ire sqrt method ftis lstat splice mkdir leavesublv gsockopt ftdir i_ncmp scalar getpgrp chroot padhv ncmp vec exp unshift caller qr dbstate ggrnam cos sne ftmtime symlink srefgen ftsock enterloop schomp keys msgrcv msgget shmget anonhash exec waitpid xor sleep read range goto getppid delete prtf shostent int next fcntl getsockname shmwrite i_multiply setpriority gelem sysseek regcmaybe getc enterwrite semget not gservent ggrent anonlist formline glob fileno ssockopt rv2av spwent i_subtract ggrgid tms gnbyname rand divide srand enteriter bit_and study eq dbmopen gnbyaddr leavewrite i_le pipe_op ghbyname connect ref lslice bless uc readline enetent select readlink msgctl i_lt i_postinc split last egrent ghbyaddr shmctl Can't locate Tk/Popup.pm in @INC (@INC contains: C:\DOCUME~1\lello\IMPOST~1\Temp\par-lello\cache-5d90d4330465c124b0c34b24a7275a8a36486b2a/inc/lib C:\DOCUME~1\lello\IMPOST~1\Temp\par-lello\cache-5d90d4330465c124b0c34b24a7275a8a36486b2a/inc CODE(0x12d32 6c) .) at Tk/Widget.pm line 259. BEGIN failed--compilation aborted at -e line 835. C:\Programmi\Ifeffit> C:\Programmi\Ifeffit>athena.exe can't open \perl\Xray\space_groups.db: No such file or directory at Xray/Xtal.pm line 115 Compilation failed in require at Ifeffit/Files.pm line 50. BEGIN failed--compilation aborted at Ifeffit/Files.pm line 50. Compilation failed in require at script/athena line 86. BEGIN failed--compilation aborted at script/athena line 86. BEGIN failed--compilation aborted at -e line 835. C:\Programmi\Ifeffit>

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Athena
by gfabbris＠lnls.br 09 Aug '05

09 Aug '05

Hi! My name is Gilberto Fabbris, I`m from LNLS, that stay in Campinas-SP, Brazil. I installed the Ifeffit (the last version) today. I runned the Athena, but when I tried to align, or calibrate energy, the Windows (XP) accused a error in the program and closed it. How can I fix it? Thank you! Gilberto Fabbris

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ifeffit 1.2.7
by Matt Newville 25 Jul '05

25 Jul '05

Hi Folks, I've posted Ifeffit 1.2.7, including a new Windows installer, source code, and a Mac Binary installer (currently OS 10.3 only) on the IFeffit Web Page. I'll post these to sourceforge.net as soon as I can. For Windows users, there is also an automatic update that may be downloaded and installed. The changes to the ifeffit library are small: a few bugfixes, added a 'penalty()' math function (as per a discussion on this list about restraints) and an improved mechanism for ifeffit to report its status to a calling program like Athena and Artemis. The Windows and Mac installers also include the latest versions of Bruce's Athena, Artemis, and Hephaestus. There are still some known issues with "PAR-" files from Bruce's codes on Windows. Bruce and I think we can solve this, and are aiming to release a new Windows installer sometime in the next month (or so) that fixes this and cleans up some of the messiness of the Windows installer. --Matt

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RE: [Ifeffit] surface EXAFS
by Kelly, Shelly D. 21 Jul '05

21 Jul '05

Hi Matt, I should have given these details right away. My trick is to parameterize the feff paths in terms of an x, y, z coordinate for the atom on the surface. Then I refine three different polarization dependent data sets to find the best x, y, and z position of the atom on the surface. Thanks for the references! Shelly > -----Original Message----- > From: Matt Newville [mailto:newville@cars.uchicago.edu] > Sent: Thursday, July 21, 2005 11:13 AM > To: Kelly, Shelly D.; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] surface EXAFS > > Hi Shelly, > > > I am working on a project were I trick feffit into moving an > > atom around on the surface of a plane to refine polarization > > dependent surface EXAFS data. I made a quick literature > > search and have not found any other EXAFS papers that do such > > a thing. Are you aware of similar work? I would like to give > > credit in our manuscript. > > I know of other work in progress (some in progress for a pretty > long time!!). I also believe there are a few surface XAFS > papers that used feffit. I think these may count, though I > don't have a copy of any of these in front of me: > > L. Y. Zhao et al, Applied Surface Science 228, p 257 (2004) > P. Luches et al, Surface Science 566, p 84 (2004) > L. Damoc, et al J. Applied Physics 92, p 1862 (2002) > S. K. Kim, et al, PRB 62, p 3025 (2000). > > I think there are probably others. > > I'm not sure what the 'trick' you're using is. Doing a polarized > calculation (with feff or in feffit) for an atom on a surface > doesn't seem like such a big deal, but maybe you're doing > something fancier. > > One paper that I know is in progress (and a just-completed > thesis) measures the 'height above the surface' of a sorbed atom > by defining several different distances in terms of this height. > > --Matt

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surface EXAFS
by Kelly, Shelly D. 21 Jul '05

21 Jul '05

Hello all, I am working on a project were I trick feffit into moving an atom around on the surface of a plane to refine polarization dependent surface EXAFS data. I made a quick literature search and have not found any other EXAFS papers that do such a thing. Are you aware of similar work? I would like to give credit in our manuscript. Shelly

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feff doesn't like cluster
by Juraj Majzlan 21 Jul '05

21 Jul '05

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? Thank you, Juro Majzlan ---------------------------------- 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

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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/

2 1

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 >

1 0

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 >

1 0

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

1 0

rbkg
by Silvio Levy 11 Jul '05

11 Jul '05

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

3 2

compilation problem under MAC OS X
by Brugger, Joel (SAM) 11 Jul '05

11 Jul '05

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.bundle % Expected in: dynamic lookup % %dyld: Symbol not found: _s_copy % Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle % Expected in: dynamic lookup % %Trace/BPT trap Only thing I can think of at this stage is reinstalling the OS! Thanks! JOEL

4 3

RE: [Ifeffit] A question
by Frenkel, Anatoly 11 Jul '05

11 Jul '05

.... 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

2 1

A question
by Mark Mark 11 Jul '05

11 Jul '05

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. Mark __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

3 2

Missing ipot problem
by rvv052＠mail.usask.ca 09 Jul '05

09 Jul '05

I was able to fix the problem with too many atoms, but then I get another error. It says: No atoms or overlap cards for unique pot 1 Cannot calculate potentials, etc. I know that this problem occurs because potentials 0, 2, 3, 4, 5, and 7 exist in the ipot coloumn, but I do not have a 1 potential (or a 6 potential as I found out by assigning a 1 potential to one of the other atoms). I never encountered this problem with ifeffit during my other calculations, so I am wondering what it means and what I can do about it. Remko van den Hurk

2 1

Exit wavefunctions as f(incoming planewave)
by Schiros, Theanne 07 Jul '05

07 Jul '05

Hello- I'm forwarding a question from a colleague outside the EXAFS community for which I don't have a good answer in hopes that some of you will... "Thinking about EXAFS, I was recently involved in an attempt to analyse TEM images. There are now effective ways to get the complete exit electronic vawefunction as a function of the incoming planewave. It would be quite interesting to be able to get the atomic potentials from the plane wave. This seems to me an inverse problem quite similar to that of the EXAFS you are working on. Do you know of any attempt in that direction? Do you think the softwares you use for solving EXAFS could be used/adapted in this way?" Thanks! theanne

1 0

RE: [Ifeffit] R-factor
by Frenkel, Anatoly 06 Jul '05

06 Jul '05

Victor raised a very good point. To extend his suggestion, I would find the best fit parameters by fitting the original data. Then, I would fit the back-Fourier-transformed data in the same exactly r-range as before, using the same q-range as the k-range used in the first fit. All fit parameters should be fixed to the best fit values found earlier and run the "fit" again (nothing is going to be varied). This will assure that you are varying only one factor in this comparison: the spectral content. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of vikrai(a)comcast.net Sent: Wed 7/6/2005 12:22 PM To: XAFS Analysis using Ifeffit Cc: Subject: Re: [Ifeffit] R-factor Alison, I don't think that the difference of R-factors you mention is a big deal. You did not mention in your message more important thing. Did you get the same values of parameters? Besides, it is hardly to expect to find a signal caused by photoelectron backscattering at R<1 A. So the lower limit in R-space fitting equal to 0.1 A is too small probably. As well as the lower limit in q-space fitting because in proteins in this momentum region only full multiple scattering approach should work correct. Victor Krayzman -------------- Original message -------------- > Bruce, > > I've looked, and my R-factors for the back-transformed > space are not necessarily twice the value of the R-factors > for the k-space fits. In fact, they are often quite > close. For example, just recently I had a k-space > R-factor of 0.102 and a q-space R-factor of 0.113. Now, I > realize those numbers are very close, but I'm afraid if I > try to publish this, then I will get criticism for the > q-space R-factors being larger. If I can explain it, then > maybe it won't be a problem. > > I do see what you're saying about the complex vs. real > function, and that definately makes sense, but they don't > differ by a factor of 2. Hmmm. > > alison > > On Wed, 6 Jul 2005 09:43:03 -0500 > Bruc! e Ravel wrote: > > On Tuesday 05 July 2005 18:39, Alison Costello wrote: > >> I have a question regarding the calculation of the > >>R-factor. I am > >> currently using SIXPACK to process my protein EXAFS > >>data, and I fit the > >> data in both k-space and in q-space (back-transformed > >>k-space). I > >> typically will use k-ranges = [1-13.6] and for > >>multiple-scattering fits, > >> will use an R-range of 0.1 - 4.5. Sometimes, the > >>R-factor for the q-space > >> fit is greater than the R-factor for the k-space fit, > >>which should not be > >> true, as the back-transformed space filters out noise. > >> I am confused as to > >> why this occurs, and am wondering if the R-factor for > >>the back-transformed > >> space is calculated differently than for k-space f! its. > > > > A lison, > > > > I would expect the R factor to be bigger in k space due > >to the high frequency > > portions of the data that get filtered out of the q > >space data. That is what > > happened in the one example I just tried. > > > > What are some example values of the R-factors? Do they > >differ by about a > > factor of 2? > > > > One thing that occurs to me is that chi(q) is a complex > >function while chi(k) > > is a real function. In Ifeffit those two functions > >should have the same > > number of points, but the R factor in q is computed > >using both parts of the > > complex function. Thus it would seem reasonable if they > >differed by about 2 > > and there were no significant Fourier components in the > >data beyond your rmax. > > > > B > > > > -- & gt; > Bruce Ravel ----------------------------------- > >bravel(a)anl.gov -or- > > ravel(a)phys.washington.edu > > Environmental Research Division, Building 203, Room > >E-165 > > Argonne National Laboratory > > phone: (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] R-factor
by vikrai＠comcast.net 06 Jul '05

06 Jul '05

Alison, I don't think that the difference of R-factors you mention is a big deal. You did not mention in your message more important thing. Did you get the same values of parameters? Besides, it is hardly to expect to find a signal caused by photoelectron backscattering at R<1 A. So the lower limit in R-space fitting equal to 0.1 A is too small probably. As well as the lower limit in q-space fitting because in proteins in this momentum region only full multiple scattering approach should work correct. Victor Krayzman -------------- Original message -------------- > Bruce, > > I've looked, and my R-factors for the back-transformed > space are not necessarily twice the value of the R-factors > for the k-space fits. In fact, they are often quite > close. For example, just recently I had a k-space > R-factor of 0.102 and a q-space R-factor of 0.113. Now, I > realize those numbers are very close, but I'm afraid if I > try to publish this, then I will get criticism for the > q-space R-factors being larger. If I can explain it, then > maybe it won't be a problem. > > I do see what you're saying about the complex vs. real > function, and that definately makes sense, but they don't > differ by a factor of 2. Hmmm. > > alison > > On Wed, 6 Jul 2005 09:43:03 -0500 > Bruce Ravel wrote: > > On Tuesday 05 July 2005 18:39, Alison Costello wrote: > >> I have a question regarding the calculation of the > >>R-factor. I am > >> currently using SIXPACK to process my protein EXAFS > >>data, and I fit the > >> data in both k-space and in q-space (back-transformed > >>k-space). I > >> typically will use k-ranges = [1-13.6] and for > >>multiple-scattering fits, > >> will use an R-range of 0.1 - 4.5. Sometimes, the > >>R-factor for the q-space > >> fit is greater than the R-factor for the k-space fit, > >>which should not be > >> true, as the back-transformed space filters out noise. > >> I am confused as to > >> why this occurs, and am wondering if the R-factor for > >>the back-transformed > >> space is calculated differently than for k-space fits. > > > > Alison, > > > > I would expect the R factor to be bigger in k space due > >to the high frequency > > portions of the data that get filtered out of the q > >space data. That is what > > happened in the one example I just tried. > > > > What are some example values of the R-factors? Do they > >differ by about a > > factor of 2? > > > > One thing that occurs to me is that chi(q) is a complex > >function while chi(k) > > is a real function. In Ifeffit those two functions > >should have the same > > number of points, but the R factor in q is computed > >using both parts of the > > complex function. Thus it would seem reasonable if they > >differed by about 2 > > and there were no significant Fourier components in the > >data beyond your rmax. > > > > B > > > > -- > > Bruce Ravel ----------------------------------- > >bravel(a)anl.gov -or- > > ravel(a)phys.washington.edu > > Environmental Research Division, Building 203, Room > >E-165 > > Argonne National Laboratory > > phone: (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

1 0

R-factor
by Alison Costello 06 Jul '05

06 Jul '05

I have a question regarding the calculation of the R-factor. I am currently using SIXPACK to process my protein EXAFS data, and I fit the data in both k-space and in q-space (back-transformed k-space). I typically will use k-ranges = [1-13.6] and for multiple-scattering fits, will use an R-range of 0.1 - 4.5. Sometimes, the R-factor for the q-space fit is greater than the R-factor for the k-space fit, which should not be true, as the back-transformed space filters out noise. I am confused as to why this occurs, and am wondering if the R-factor for the back-transformed space is calculated differently than for k-space fits. Thank you. alison

3 2

Too Many Atoms
by rvv052＠mail.usask.ca 30 Jun '05

30 Jun '05

The problem that I have is that with 141 crystallographic sites for a DNA molecule and a space group p 4 2 2, I end up with 611 atoms after running ATOMS. This gives me the error: Feff 6L.02 Fatal Error: Too many atoms in ATOMS list. Maximum is 500. I tries decreasing the number of crystalographic sites by removing hydrogen atoms, but then I got another error: Feff 6L.02 No atoms or overlap cards for unique pot 1 Cannot calculate potentials, etc. Fatal Error: at RDINP. I tried increasing the Rmax as indicated, but this only served to increase the number of atomes, leading me to the error given above. I was hoping that someone could help me with this problem. Remko van den Hurk

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RE: [Ifeffit] feff data
by Barton, David (DG) 23 Jun '05

23 Jun '05

Steven, Sorry for the duplicate....I sent the previous message as HTML (shame on me) beta-Ga2O3 files are attached. I attached the CIF (crystallographic information file) and an Artemis project that has the FEFF.inp inside it. CIF files can be opened directly in Artemis by choosing the File option, Import ATOMS files, and then select *.CIF in drop down box. If you need just the FEFF.inp for another purpose you can just cut it out of Artemis project and paste it to a text file. Dave Barton -------------------------- Dear all, Does anyone out there, by any chance, have feff data or .inp file of Gallium oxide (any of GaO, Ga2O, and Ga2O3)? I tried to create an .inp file but it was out of my ability. If somebody has one or can give me an information where or how to get, I will do appreciate it. Thank you. Steven Steven Sangyun Lim Associate Research Scientist Dept. of Chem. Eng., Yale University Tel : 203-432-4365

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RE: [Ifeffit] feff data
by Barton, David (DG) 22 Jun '05

22 Jun '05

Steven, beta-Ga2O3 files are attached. I attached the CIF (crystallographic information file) and an Artemis project that has the FEFF.inp inside it. CIF files can be opened directly in Artemis by choosing the File option, Import ATOMS files, and then select *.CIF in drop down box. If you need just the FEFF.inp for another purpose you can just cut it out of Artemis project and paste it to a text file. Dave Barton _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Steven S. Lim Sent: Wednesday, June 22, 2005 10:14 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] feff data Dear all, Does anyone out there, by any chance, have feff data or .inp file of Gallium oxide (any of GaO, Ga2O, and Ga2O3)? I tried to create an .inp file but it was out of my ability. If somebody has one or can give me an information where or how to get, I will do appreciate it. Thank you. Steven Steven Sangyun Lim Associate Research Scientist Dept. of Chem. Eng., Yale University Tel : 203-432-4365

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feff data
by Steven S. Lim 22 Jun '05

22 Jun '05

Dear all, Does anyone out there, by any chance, have feff data or .inp file of Gallium oxide (any of GaO, Ga2O, and Ga2O3)? I tried to create an .inp file but it was out of my ability. If somebody has one or can give me an information where or how to get, I will do appreciate it. Thank you. Steven Steven Sangyun Lim Associate Research Scientist Dept. of Chem. Eng., Yale University Tel : 203-432-4365

1 0

IFEFFIT for OS X 10.4
by Ann Liang 21 Jun '05

21 Jun '05

Hi all, I just recently upgraded my computer from Mac OS X 10.3 to 10.4 (Tiger). I was not able to open programs in the IFEFFIT package. Please help. Thanks, Ann -- ANN LIANG Bruce. C. Gates Catalysis Research Group Chemical Engineering & Materials Science University of California at Davis One Shields Ave. Davis, CA 95616 530-752-3544 (office) 530-752-1031 (fax)

5 6

EXAFS mean free path in small particles
by Laurent Menard 21 Jun '05

21 Jun '05

Disclaimer: I'm an experimentalist and not a theorist. I'm not sure that Zhao and Montano's calculations are correct. I think their calculation for the transition probability assumes that the electron density is constant when, in actuality, there is a spatial dependence resulting from quantum confinement effects. As a result, the energy of the surface plasmon peak as calculated by Zhao and Montano is constant for all cluster sizes at approximately the classical value of omega(bulk plasmon)/3^0.5 and shows an increase with decreasing particle size. Including quantum confinement results in a blue shift of the surface plasmon resonance with decreasing particle size and a decrease in transition probability for decreasing particle sizes (as suggested by Anatoly). This change in the calculation will also impact the bulk plasmon and I don't know what that trend will be. As far as their experimental demonstration with Fe nanoparticles is concerned, I really can't make an assessment about the experiment since they don't indicate how the nanoparticle size was determined and I'm not familiar with their preparation of the nanoparticles. I'm not sure from this paper what the impact on the MFP will be although there very well could be some effect on the EXAFS. Personally, when I began working on EXAFS of nanoparticles and small clusters (Au13), I was leery of using the bulk phase and amplitudes to fit the data. My experience to this point has been that there have not been observable deviations of coordination numbers for nanoparticle systems using these FEFF inputs. That being said, I tend to agree with Matt that this is something that people working in this area need to think about a bit more than it seems they have judging by the literature. I would like to see some (correct) theoretical assessments that support the assertion that bulk phases and amplitudes are ok for nanoparticles that I think has been demonstrated by validating EXAFS results with other techniques (mostly electron microscopy). -Laurent

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EXAFS mean free path in small particles
by matthew marcus 20 Jun '05

20 Jun '05

I'm working on a couple of projects involving nanoparticles, and a collaborator pointed out an old paper by Zhao and Montano (PRB 40,3401(1989)) which claimed theoretical reasons why the electron mean free path in nanos should be smaller than in bulk. This would cause coordination numbers to be underestimated. The effect is supposedly due to a surface plasmon which grows in importance as particle size shrinks. I have reasons why I think this paper exaggerates the possible effects, but I'm posting this to see what other people think about this effect. The paper seems to have gone down into obscurity, but that doesn't mean it isn't right. Thanks. Matthew Marcus

4 6

EXAFS mean free path in small particles
by Matthew 17 Jun '05

17 Jun '05

A couple of notes on this group treat the Zhao&Montano Al-plasmon results as if they were experimental truth. They are in fact theoretical, based on what I think is a jellium model, though that word isn't used. Their only experimental data is on matrix-isolated Fe particles. mam

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RE: [Ifeffit] EXAFS mean free path in small particles
by Frenkel, Anatoly 17 Jun '05

17 Jun '05

Matt, In their paper, Zhao and Montano studied Al particles that showed surface plasmon activity for sizes as small as 10 A. I had no idea that Al does it, and it is very peculiar. However, I have been dealing most heavily with gold nanoparticles. According to literature (here is another article: Sarathy et al, J.Phys.Chem. B, 1997, v. 101 pp. 9876-9880, and ref. 14 within), Au nanoparticles show no surface plasmon activity below 20 A. Our recent experiment, where we have taken UV-vis. measurements of several samples of Au nanoparticles that were very small (13 to 100 atoms) and monodisperse, did not show any surface plasmon band around 525 nm where it appears at larger particles. In fact, Zhao and Montano say in p. 3403: "we would like to point out that based on the experimental results for noble metals [Cu, Au, and Ag] no evidence of a substantial change in the electron MFP value between bulk and small particles was found". That, to my mind, is an indirect but a fair reason to reuse bulk amplitudes, at least for Cu, Au and Ag. I also think, if HRTEM and EXAFS agree, it says for itself (that bulk FEFF amplitudes are correct). If they do not agree, AND if other reasons for discrepancy can be ruled out (e.g., broad size distribution, or electron-beam caused growth of particles), AND if the discrepancy is in the right direction (EXAFS-determined size is smaller than the HRTEM-determined size), then surface plasmon and other losses should be looked into. And, I agree, it is an important issue to be aware about. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Matt Newville Sent: Tuesday, June 14, 2005 9:47 PM To: XAFS Analysis using Ifeffit Subject: RE: [Ifeffit] EXAFS mean free path in small particles Anatoly, > The point is, to my opinion, that since In the most > interesting range, below 2nm, the plasmon activity decreases, > therefore its effect on EXAFS interpretation, if any, should > be negligible. I think I may not understand your point. The Zhao and Montano paper shows very pronounced changes in the plasmon spectra between each of 10,3,2, and 1 nm for Al. At 1 nm, the surface plasmon is definitely dominating -- not going away. So their conclusion, that lambda changes substantially below 10 nm due to the changing relative importance of surface-to-bulk plasmons seems well-argued to me (not to say its correct). I agree (I think) with Matthew that the Zhao and Montano work shouldn't be too easily dismissed, though it might not be completely correct. I don't know of any other work on how lambda might depend on particle size, and never really thought about this. The Rao paper seems broader in scope and not necessarily addressing plasmons and mean free path, but I only skimmed it, so maybe I missed something. Their fig 8 definitely shows a size dependence of O K-edge, though I didn't immediately see a clear interpretation for this -- it could have several explanations. Again, I only skimmed this paper, so maybe I missed something: perhaps the electron diffraction literature has more information?? > ... There are other evidences that small particles have DOS > similar to molecules, not typical metals. Most notable is the > evidence that HOMO-LUMO band grows to more than 1 eV at sizes > of 1 nm range. Hmm, I'm not sure I see that becoming more molecular and less metallic indicates that using the bulk mean-free-path is OK. . The 'universal mean free path' that Feff uses and the fact that S02 is still has to be a fitting parameter even for excellent data with Feff8 suggests to me that there may be many hidden sins in Feff's mean-free-path calculation. Sadly, we seem to be a little short on theorists these days. --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

2 1

EXAFS course at Brookhaven
by Anatoly Frenkel 16 Jun '05

16 Jun '05

Hello IFEFFIT subscribers: In September 28-30, 2005, National Synchrotron Light Source at Brookhaven National Laboratory will host a short course: "EXAFS Course: Theory, Experiment, and Advanced Applications" This hands-on course is aimed to help design, perform and analyze EXAFS experiments, and to learn about some of the potential pitfalls that must be avoided. The course will be self-contained, starting with the fundamentals and proceeding to the more advanced topics, including recent theoretical developments, data analysis techniques and specific applications of EXAFS. More information is available at the course web page: http://www.nsls.bnl.gov/newsroom/events/workshops/exafs/Default.htm Please pass it along to all who may be interested. Anatoly Anatoly Frenkel Yeshiva University

1 0

Athena and Artemis reference
by Bruce Ravel 15 Jun '05

15 Jun '05

Hi folks, I just got word today that my and Matt's submission to Journal of Synchrotron Radiation has been published and is available on-line. Here is the citation: ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT B. Ravel and M. Newville Journal of Synchrotron Radiation, Volume 12, Part 4, pages 537---541. Here's a link: http://www.iucr.org/cgi-bin/paper?ph5155 This reference is more up-to-date and reflective of the current state of the codes than the reference in Physica Scripta from the Malmo EXAFS conference, so it is my preference that you use it. B -- 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/

1 0

odd feff6 behavior
by Bruce Ravel 13 Jun '05

13 Jun '05

Hi, Here's a feff6 curiosity. Take this atoms.inp file: title = TiN space = 225 a = 4.24173 b = 4.24173 c = 4.24173 core = Ti edge = K rmax = 7.0 atoms ! elem x y z Ti 0.00000 0.00000 0.00000 N 0.50000 0.50000 0.50000 Run atoms, then run feff6l (the one that comes with Ifeffit, it's the only version I've tried this with). Feff ends with this error message: Eliminating path degeneracies... Plane wave chi amplitude filter 2.50% np, np1x= 12001 12000 Fatal Error: at PATHSD: np > np1x This message comes from pathsd.f, but I don't understand either the message or the part of the code it comes from. Does anyone else have a hint as to the problem? One more datum. If you reduce rmax to 6.7 in the atoms.inp file, the problme persists. If you make rmax 6.6, feff6l is happy. Thanks, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone: (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/

4 5

IFEFFIT on Tiger - confusion between Perl 5.8.1 and 5.8.6
by Brugger, Joel (SAM) 11 Jun '05

11 Jun '05

I lost IFEFFIT after upgrading to MAC OS X 10.4 (Tiger). Apparently, this is due to the fact that the upgrade replaced Perl 5.8.1 by Perl 5.8.6. I redid the IFEFFIT installation (for 10.3), which created a Perl5.8.1 folder with all the goodies. However, as the following error message shows, the system is not happy and is looking for some stuff in the new PERL. And does not find it. I'm not sure how to revert to 5.8.1, or alternatively more everything to the new 5.8.6. Hopefully this is a trivial question :-) Thanks for any help, JOEL [JoelG5:/Applications/Ifeffit/bin] joelb% ./hephaestus Can't load '/Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/Event/Event.bundle' for module Tk::Event: dlopen(/Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/Event/Event.bu ndle, 1): Library not loaded: /System/Library/Perl/5.8.1/darwin-thread-multi-2level/CORE/libperl.dylib Referenced from: /Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/Event/Event.bundle Reason: image not found at /System/Library/Perl/5.8.6/darwin-thread-multi-2level/XSLoader.pm line 68. at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/Event.pm line 10Compilation failed in require at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 13.BEGIN failed--compilation aborted at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 13.Compilation failed in require at ./hephaestus line 54.BEGIN failed--compilation aborted at ./hephaestus line 54.Undefined subroutine &Tk::Event::CleanupGlue called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/Event.pm line 3.END failed--call queue aborted at ./hephaestus line 54.

3 2

Importance and Edge Step
by Barton, David (DG) 08 Jun '05

08 Jun '05

Hello, I noticed two new features in Athena 0.8.040 and am unsure of how to use them. The new features are "Importance" and "Edge Step". I attempted to use the Edge Step feature by checking "Fix Step" and then entering a value, but the Edge Step always reverts back to the automated value. However, when I use the Increase/Decrease buttons (Left/Right arrow in Edge Step window) the edge step does change, but it only changes in increments of 0.01 which is much too large for my datasets. Is there something I am missing here? Also, I couldn't locate Bruce's changelog for Athena so I am unsure of what the new "Importance" feature does. Anyone used this new feature yet? Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA

3 11

Re: Ifeffit Digest, Vol 28, Issue 6
by Satyender Goel 07 Jun '05

07 Jun '05

Hi Matt, I have managed to get everything up and running. Thank you so much for your patience and help without which it wouldn't have been possible. I appreciate your effort and the interest taken in helping me solve my problem. Sorry for the trouble. Regards, Satyender Goel Quoting ifeffit-request(a)millenia.cars.aps.anl.gov: > 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: Re: Ifeffit Digest, Vol 28, Issue 4 (Matt Newville) > 2. Re: Bug report (Scott Calvin) > 3. Re: Importance and Edge Step (Gerrit Schmithals) > 4. Re: Bug report (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 7 Jun 2005 10:18:24 -0500 (CDT) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] Re: Ifeffit Digest, Vol 28, Issue 4 > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0506070933460.14613-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Satyender, > >> Finally i got my Perl script running using, >> >> BEGIN { >> $ENV{IFEFFIT_DIR} = 'C:\Program Files\Ifeffit\'; >> } >> >> at the begining of my program.... > > If your perl scripts are running, you must have the Ifeffit > modules installed, no??? If it's working, then it's probably > not necessary to rebuild the perl module. But if you're going > to be using it heavily, it might be worth figuring out how to do > build it anyway. > >> I have added the environment variable IFEFFIT_DIR, but it does >> not seem to make a difference. > > Hmm, that's really strange, but maybe I'm not understanding? > It should definitely work to set IFEFFIT_DIR as an environmental > variable and run perl in that environment without having BEGIN { > $ENV{IFEFFIT_DIR}='...';} in the script. Well, the BEGIN {} > block in the script is really setting the environmental > variable, so if that works, setting it from the Control Panel > should work to. Are you should the command shell you're using > has this environmental variable set? Try typing > C:\> set > to see a list of environmental variables. > >> I have tried.......... >> >> "C:\Program Files\Ifeffit\wrappers\perl\build, and do >> perl Makefile.PL >> nmake install" >> >> after editing makefile.pl as per... >> >> "'LIBS' => [' -LC:\"Program Files"\Ifeffit ifeffit_10 ']," >> and also copied ifeffit.pm to C:\perl\site\lib... >> >> I have visual studio installed on my computer, however the nmake command >> does not seem to be working. >> >> SCREEN DISPLAY AFTER THE CHANGES: >> >> C:\Program Files\Ifeffit\wrappers\perl\build>perl makefile.pl >> Note (probably harmless): No library found for oldnames.lib >> Note (probably harmless): No library found for kernel32.lib >> <snip> > > This is probably because the VC/Visual Studio stuff isn't in > your path, and since perl is going to try to run 'cl' and > 'nmake' from the command line, the command shell needs to find > them from the environmental variables. The details of how to do > this depends on how your compiler was installed. You can > probably start with and edit the batch file below. > > Please give more details and a better sense of what does and > doesn't work. Like, what does > > C:\> perl -e "use Ifeffit;" > > report? If it reports "cant find Ifeffit.pm in @INC ....", you > don't have the Ifeffit module installed. If it reports nothing, > it is installed, and you're ready to go. If it reports messages > about PGPLOT, you'll be fine once the environmental variables > for PGPLOT_DIR and PGPLOT_DEV are set. > > Hope that helps, > > --Matt > > REM ---- > REM sample settings for VC,NMAKE, etc > REM probably have to reset BASE_DIR > set BASE_DIR=C:\Program Files\Microsoft Visual Studio > set CPU=i386 > set INCLUDE=%BASE_DIR%\VC98\INCLUDE > set LIB=%BASE_DIR%\VC98\LIB > set > PATH=%BASE_DIR%\Common\Msdev98\BIN;%BASE_DIR%\VC98\BIN;%BASE_DIR%\Common\Tools;%BASE_DIR%\Common\Tools\WINNT;%PATH% > > REM ---- > > > > > ------------------------------ > > Message: 2 > Date: Tue, 07 Jun 2005 12:13:59 -0400 > From: Scott Calvin <scalvin(a)slc.edu> > Subject: Re: [Ifeffit] Bug report > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <3.0.1.32.20050607121359.00b15540(a)mail.slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Thanks, Matt. > > Yes, I've been working around it by just adding "+0" to path expressions > that end in a parentheses. I hadn't quite figured out that it required > starting with a non-matched parentheses to trigger the error; it's good to > know exactly what circumstances cause it to arise. > > A suggestion for Bruce--ifeffit flags these kinds of syntax errors pretty > well. Is it possible for Artemis to look at the ifeffit output and alert > the user to examine the iffefit output if there is an error? > > --Scott Calvin > Sarah Lawrence College > > At 09:33 AM 6/7/2005 -0500, you wrote: >> Hi Scott, >> >> Yep, that is an ifeffit error. It turns out to be specific to >> math expressions in path() commands, but it is definitely a bug. >> It seems that a math expression for a path parameter that starts >> with '(' and ends with ')' and for which these '(' and ')' are >> not a matched pair will incorrectly raise a syntax error. This >> doesn't happen for set() or def(). >>> > > > ------------------------------ > > Message: 3 > Date: Tue, 07 Jun 2005 18:57:01 +0200 > From: Gerrit Schmithals <schmithals(a)hmi.de> > Subject: Re: [Ifeffit] Importance and Edge Step > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <42A5D1DD.6090603(a)hmi.de> > Content-Type: text/plain; charset=ISO-8859-1 > > On Monday 06 June 2005 09:27, Gerrit Schmithals wrote: > >>> How do I implement more than 4 references? There is a box for entering >>> the number but it does not enlarge the reference-list as I expected it >>> to do. >>> >>> > Bruce Ravel schrieb: > >> All of this is explained in the doc page for the LCF dialog. (That >> is, I think I explained it all there. It may be [is?] poorly >> explained ....;-) >> >> The length of the standards list is set in the preferences dialog. >> The relevant parameter is linearcombo->maxspectra. >> >> >> > Thanks for that hint. I really should have found that setting by myself. > > I did not use the combinatorical fitting so far, but concerning the > normal linear fitting I observed two issues: > > I had an Athena project with some references loaded as chi(k)-data and > some unknown samples as chi(k) as well. Athena won't let me start the > Linear Fit-Dialog stating that it (she) needs at least three > xmu-spectra. Changing the preference to "standard fit in k-space" does > not help. Workaround: I just loaded some dummy xmu-Spektra and can now > work with the dialog. > > Also, only these xmu-spectra can be selected from the "standards pluck > boxes", the only way to insert the chi(k)-references is to use "use > marked groups". That is a bit of a problem when you have to move one of > the groups up because its value is negative. Workaround is to move up > the groups in in Data group section. > > Some other issues came into my mind while working with the dialog but > they are really of minor importance: > - Is there any possibility to plot the linear fit and the data in > R-space right away? (without first saving it as a datagroup) > - It would be nice to be able to store the relative weigths together > with the newly created dataset. > > Cheers, > Gerrit > > > > > ------------------------------ > > Message: 4 > Date: Tue, 7 Jun 2005 12:01:02 -0500 > From: Bruce Ravel <bravel(a)anl.gov> > Subject: Re: [Ifeffit] Bug report > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200506071201.02798.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > On Tuesday 07 June 2005 11:13, Scott Calvin wrote: >> A suggestion for Bruce--ifeffit flags these kinds of syntax errors pretty >> well. Is it possible for Artemis to look at the ifeffit output and alert >> the user to examine the iffefit output if there is an error? > > One of the features new to ifeffit 1.2.7 is a scalar flag, &status, that gets > set to something other than 0 when something bad happens. Matt added this so > there would be an easy way for A&A to know when an error was encountered. > > I have not yet implemented any functionality surrounding &status, but it's on > the list of things to do. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > ravel(a)phys.washington.edu > Environmental Research Division, Building 203, Room E-165 > Argonne National Laboratory phone: (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 > > > End of Ifeffit Digest, Vol 28, Issue 6 > ************************************** >

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Athena Problems
by McCready, Alistair 07 Jun '05

07 Jun '05

Hi, I am having some problems with Athena. I reformatted my hard drive the other day (windows XP Pro), and downloaded Athena etc. After installing the programs, they work fine. However, once I download the updates, Athena refuses to work. I try to open the program and all I get a black command-style box filled with odd words/text. I do not have a virus (first thing I checked), and all the updated versions of the other programs all work fine (e.g. Artemis, Hephaestus). I just wanted to check if anyone else has ever had this problem? Alistair "SRC provides Smart Science Solutions" This e-mail and any files transmitted with it are intended only for the named recipients and may contain legally privileged and/or confidential information. If you are not the intended recipient please do not disseminate, distribute or copy this e-mail without the consent of the sender.

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Re: Ifeffit Digest, Vol 28, Issue 4
by Satyender Goel 07 Jun '05

07 Jun '05

Thanks a lot Dear Matt and Bruce, Finally i got my Perl script running using, BEGIN { $ENV{IFEFFIT_DIR} = 'C:\Program Files\Ifeffit\'; } at the begining of my program.... I have added the environment variable IFEFFIT_DIR, but it does not seem to make a difference. I have tried.......... "C:\Program Files\Ifeffit\wrappers\perl\build, and do perl Makefile.PL nmake install" after editing makefile.pl as per... "'LIBS' => [' -LC:\"Program Files"\Ifeffit ifeffit_10 ']," and also copied ifeffit.pm to C:\perl\site\lib... I have visual studio installed on my computer, however the nmake command does not seem to be working. SCREEN DISPLAY AFTER THE CHANGES: C:\Program Files\Ifeffit\wrappers\perl\build>perl makefile.pl Note (probably harmless): No library found for oldnames.lib Note (probably harmless): No library found for kernel32.lib Note (probably harmless): No library found for user32.lib Note (probably harmless): No library found for gdi32.lib Note (probably harmless): No library found for winspool.lib Note (probably harmless): No library found for comdlg32.lib Note (probably harmless): No library found for advapi32.lib Note (probably harmless): No library found for shell32.lib Note (probably harmless): No library found for ole32.lib Note (probably harmless): No library found for oleaut32.lib Note (probably harmless): No library found for netapi32.lib Note (probably harmless): No library found for uuid.lib Note (probably harmless): No library found for ws2_32.lib Note (probably harmless): No library found for mpr.lib Note (probably harmless): No library found for winmm.lib Note (probably harmless): No library found for version.lib Note (probably harmless): No library found for odbc32.lib Note (probably harmless): No library found for odbccp32.lib Note (probably harmless): No library found for msvcrt.lib Writing Makefile for Ifeffit C:\Program Files\Ifeffit\wrappers\perl\build>nmake 'nmake' is not recognized as an internal or external command, operable program or batch file. Regards, Satyender Goel

2 1

ifeffit module for perl
by Satyender Goel 06 Jun '05

06 Jun '05

Hi, I am developing algorithms for Automation of "DATA MINING FOR HIGH THROUGHPUT SYNCROTRON SPECTROSCOPIES" with Dr. S L M Schroeder group. I have come across a problem in accessing IFEFFIT libraries through Perl on WINDOWS Platform. I have installed latest version of IFEFFIT as well as PERL. Evertime i try accessing IFEFFIT Through Perl it gives the error like: c:\work>perl -w trial.pl Can't locate loadable object for module ifeffitin @INC <@INC contains: C:/Perl/lib c:/Perl/site/lib .> at trial.pl line 2. Compilation failed in require at trial.pl line 2. BEGIN failed--conpliation aborted at trial.pl line 2. I have trying putting 'Perl folder from wrappers of IFEFFIT' to Perl/site/lib, but no success so far. I am stuck with my work. Any solution to get Access of IFEFFIT libraries through Perl? Cheers!!! Satyender Goel MSc 'Cheminformatics'

4 3

E0 limit
by alita＠chemmail.chem.fsu.edu 03 Jun '05

03 Jun '05

When I fit some Cr compound in Artemis I obtain a e0 for each path around 6.68 . In " Using Artemis" by dr. Bruce Ravel page 49 there is a example where he is also obtaing a 6.59 value for e0. Is there a limit for this e0? I must restrain this value to be under 5? How can I calculate this value? Thanks, Adrian Lita

2 1

RE: [Ifeffit] Importance and Edge Step
by Barton, David (DG) 02 Jun '05

02 Jun '05

Bruce, thanks for the info.. When referring to the Edge Step feature you mentioned that: "You can type in a number, as before" This does not appear to be working, if I check "Fix Step", enter a value into the edge step window, and then recompute the background, the value of the edge step reverts back to the automatic value. Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Bruce Ravel > Sent: Thursday, June 02, 2005 3:00 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Importance and Edge Step > > > On Thursday 02 June 2005 13:06, Barton, David (DG) wrote: > > I noticed two new features in Athena 0.8.040 and am unsure > of how to > > use them. The new features are "Importance" and "Edge Step". I > > attempted to use the Edge Step feature by checking "Fix > Step" and then > > entering a value, but the Edge Step always reverts back to the > > automated value. However, when I use the Increase/Decrease buttons > > (Left/Right arrow in Edge Step > > window) the edge step does change, but it only changes in > increments of > > 0.01 which is much too large for my datasets. Is there > something I am > > missing here? > > > > Also, I couldn't locate Bruce's changelog for Athena so I > am unsure of > > what the new "Importance" feature does. Anyone used this > new feature > > yet? > > > Importance: > This number is used only in a merge and only when the > "Weight by importance" > button in the Merge menu is checked. It's intention is to allow > user-specified weights in a merge. If you trust one data > set twice as much > as another, the more trusted one might be given an > importance of 2 while the > other is given an importance of 1. This was in response to > a feature > request -- personally I am not clear how would know how to > weight different > data sets. > > Edge step: > I got a request for a quick way to play around with the > size of the edge > step. When the "fix step" button is checked, you can then > specify an edge > step which will then be used to normalize the data. You > can type in a > number, as before, or you can tweak the edge step up or > down. You can set > the size of the tweak in the preferences using > bkg->step_increment. Note > that if the "fix step" button is not checked, the edge step will be > recomputed every time the background is recalculated. > > And I do need to be more conscientious about updating the > change logs. Sorry. > > B > > -- > 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/ > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

1 0

idealized 95-atom Pt cluster
by Charles Chusuei 30 May '05

30 May '05

Hi,,, I'm a new user to Artemis and Atoms. I would like to generate a simulated EXAFS spectrum of an idealized bare 95-atom cluster of Pt (with no ligands attached to it). Looking at Cambridge data files, the largest cluster documented is 18, so I would have to make one up. I would like to arrange the 95 atoms into an idealized sphere with the standard geometry for bulk Pt-Pt bonding that can be predicted from the crystal structure (e.g. metallic radius = 139nm, metallic separation = 277.5nm separation, etc.) I understand this can be done using Artemis and Atoms. I'm relatively new to using the software (prodominantly know how to use Athena for plotting the experimental EXAFS data , not much more). Could anyone provide suggestions on how to get started on this task? E.g. Generating the crystal data and displaying the EXAFS of the resulting bare cluster? Charles

6 10

new windows updater
by Matt Newville 27 May '05

27 May '05

Hi Folks, There's a new Windows updater available (this is #15) with new versions of Athena, Artemis, and Diana that address some of the problems people have reported. Please give them a spin! --Matt

1 0

RE: [Ifeffit] Least Squares Fitting in Athena
by Ravel, Bruce D. 25 May '05

25 May '05

> I have a couple of comments about LSF in Athena and I would like to hear > other people's opinions on the matter. > Also, it would be interesting to know: are there > many people who use Athena to do LSF? > I found that there is some inconsistency with plotting after > the fit is done. In my case nonzero energy shifts are applied to > the fitted data and the standards. The resulting linear combination fit > doesn't look shifted in energy appropriately - visually there is a > mismatch between the data and the fit. On the other hand, R-factor and > Chi^2 are very reasonable. This looks somewhat confusing. > Also, in my experience the obtained fractions in Athena come out slightly > different from those I could get using Sixpack LSF software. In my fits I > used the same constrains/options, same data and references and same data > range. What can be the cause of this? Hi, I have recently seem similar behavior. There are several possible causes for what you are seeing -- the most likely being an error in how the standards are interpolated onto the grid of the unknown data. I have been working hard on the LCF features in Athena recently and have fixed several bugs and added lots of new features. Rather than try particularly hard to address your questions now, I am going to wait and see if they persist after I release the next version of Athena (which will be soon). B

1 0

Least Squares Fitting in Athena
by Stanislav Stoupin 24 May '05

24 May '05

Hello all, I have a couple of comments about LSF in Athena and I would like to hear other people's opinions on the matter. Also, it would be interesting to know: are there many people who use Athena to do LSF? I found that there is some inconsistency with plotting after the fit is done. In my case nonzero energy shifts are applied to the fitted data and the standards. The resulting linear combination fit doesn't look shifted in energy appropriately - visually there is a mismatch between the data and the fit. On the other hand, R-factor and Chi^2 are very reasonable. This looks somewhat confusing. Also, in my experience the obtained fractions in Athena come out slightly different from those I could get using Sixpack LSF software. In my fits I used the same constrains/options, same data and references and same data range. What can be the cause of this? Stanislav Stanislav Stoupin ----------------------------- Research Assistant/PhD student BCPS department Illinois Institute of Technology email: stousta(a)iit.edu voice: 312-567-7983

2 1

Propagation of uncertanties
by Kelly, Shelly D. 17 May '05

17 May '05

Hi Matt and Bruce, I request that Athena reports the uncertainty in the basic EXAFS parameters and not just the fitted variables. For example, the uncertainty in the optimized debye temperature is reported, but the uncertainty in sigma2 value is not currently reported. I could see how this could be done by Athena or by including a new function in IFEFFIT. -What do you think? Thanks Shelly

3 2

Contribution of multiple scattering paths - basic question
by Gerrit Schmithals 13 May '05

13 May '05

Hello, I want to fit a cobalt-porphyrin for which I have an atom.inp-file and EXAFS experimental data at Co K-edge . I started with a simple sum of paths for all paths with a distance below 5 A and an amplitude above 10 (see attachment). If one compares experiment (black curve) with this first fit (red curve) the first shell peaks overlap quite nicely but not the second and third (fourier transforms of the single paths are also drawn as blue and red curves). Then I excluded four paths (the red ones) and did a second sum of path. Now the other shell peaks overlap as well (green curve). The four exluded paths are multiple scattering paths via one nitrogen and one carbon atom. I conclude that the extinction of the second shell peak in the first simulation is due to the fact that these paths have a different phase shift than the other paths with a similar frequency. Do I make a simple error (adjustments of the fitting parameters necessary?) or does that tell me something about the system? I appreciate any help. Regards, Gerrit

3 5

XAFS Summer Schools
by Matt Newville 09 May '05

09 May '05

Hi Folks, I thought I'd mention a couple of summer schools and XAFS courses that are happening this summer. I know many of you have attended summer schools or XAFS workshops in the past, and there are many people on this list who are fairly new to XAFS and synchrotron work in general. First, there will be a four-day XAFS school at Advanced Photon Source, Argonne, IL from July 26 to 30. More Information is at http://cars.uchicago.edu/xafs_school/ (Both Bruce and I will be involved with this). The application deadline for this is June 10, 2005. I believe there will also be an EXAFS Course at NSLS, Brookhaven Lab, NY in October, 2005: http://www.nsls.bnl.gov/newsroom/events/workshops/exafs/ In addition, there are also annual synchrotron based summer schools covering a range of techniques at Argonne National Lab, and a joint summer school between SSRL (Stanford) and ALS (Berkeley). I think the deadline for these may have passed. But there are quite a few other workshops, courses, and summer schools, including outside the US. A more complete list is at http://lightsources.org/cms/?pid=1000510 Cheers, --Matt PS: If you know of other courses, etc feel free to advertise them here.

1 0

Re: athena for OSX.4
by Paul Fons 09 May '05

09 May '05

Please excuse me for forwarding a copy to the list in case there are others out there that have run into the same problem. For all those who want to be Tigers (Mac OS 10.4), here is a brief summary of the installation procedure. I should add that there is not an installer that will do everything at once, but the procedure is really pretty easy. I have not tried installing horae on a brand new system, I have only tried (and succeeded) in making a previously functional horae-051 under Mac OS 10.3 work properly under Mac OS (Tiger) 10.4. The errors you see are generated because there is a new version of perl installed (5.8.6) which doesn't know about Perl/Tk, the graphics system that Bruce uses for all of his packages. The solution is simple, you must download and install Perl/Tk and then reinstall horae. After that everything just works again. The build procedure is nearly automatic, but you need to have installed the developer tools (which are included on the Tiger installation DVD). First you need to download Tk from CPAN (the server where free Perl software is hosted). Here is the procedure. 0. I assume you had an installed and functional horae running under 10.3 and did an upgrade to 10.4 1. Download the source for Tk by a. make a new (temporary) scratch directory mkdir temp; cd temp b. download Tk going in your browser of choice go to the web page: http://search.cpan.org/~ni-s/Tk-804.027/ and hitting the download button on that page (the file will be named Tk-804-2.027.tar.gz) c. uncompress the file in your scratch directory tar zxf /the-path-to-your-download-directory/ Tk-804-2.027.tar.gz d. change to the Tk directory, compile, and install the new Tk cd Tk-804.027 perl Makefile.PL make sudo make install e. now you must download and install the latest version of horae via Bruce's web page go to the site http://leonardo.phys.washington.edu/~ravel/ software/downloads.html#unix and use the download link for horae-051.tar.gz f. decompress and install the new horae source cd ../temp (move up from the Tk directory to the top level of your new temporary directory) tar zxf /the-path-to-your-download-directory/ horae-051.tar.gz cd horae-051 perl Makefile.PL make sudo make install That's it. You are done. I just popped up a X11 window (you did remember to install the X11 program which is an optional install on the Tiger DVD accessible using the "Customize" button in the installer, right?) and typed artemis & and poof, artemis appeared. Note that if you did a clean install you should still be able to get everything working by downloading Matt's installer and installing the 10.3 copy (it won't work out of the box) and then following the above procedure. I have not verified this, however, so caveat empor as the Romans said... Hope this helps. Paul On May 10, 2005, at 3:08 AM, denauwer(a)tele2.fr wrote: > Dear Paul, > > We have contacted Bruce because we want to use Athena on Mac OSX.4 > and it is not working. We have tried from the terminal and we got > the following message: > > "Can't load '/Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/ > Event/Event.b > undle' for module Tk::Event: dlopen(/Library/Perl/5.8.1/darwin- > thread-multi-2lev > el/auto/Tk/Event/Event.bundle, 1): Library not loaded: /System/ > Library/Perl/5.8. > 1/darwin-thread-multi-2level/CORE/libperl.dylib > Referenced from: /Library/Perl/5.8.1/darwin-thread-multi-2level/ > auto/Tk/Event/ > Event.bundle > Reason: image not found at /System/Library/Perl/5.8.6/darwin- > thread-multi-2lev > el/XSLoader.pm line 68. > at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/Event.pm line 10 > Compilation failed in require at /Library/Perl/5.8.1/darwin-thread- > multi-2level/ > Tk.pm line 13. > BEGIN failed--compilation aborted at /Library/Perl/5.8.1/darwin- > thread-multi-2le > vel/Tk.pm line 13. > Compilation failed in require at /Applications/Ifeffit/bin/athena > line 53. > BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/ > athena line 53. > Undefined subroutine &Tk::Event::CleanupGlue called at /Library/ > Perl/5.8.1/darwi > n-thread-multi-2level/Tk/Event.pm line 3. > END failed--call queue aborted at /Applications/Ifeffit/bin/athena > line 53." > > Could you if you have time, please, explain what we have to do to > fix this problem? > > Thank you for your help, > Christophe Den Auwer > > > Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

1 0

Re: athena for OSX.4
by Paul Fons 09 May '05

09 May '05

Please excuse me for forwarding a copy to the list in case there are others out there that have run into the same problem. For all those who want to be Tigers (Mac OS 10.4), here is a brief summary of the installation procedure. I should add that there is not an installer that will do everything at once, but the procedure is really pretty easy. I have not tried installing horae on a brand new system, I have only tried (and succeeded) in making a previously functional horae-051 under Mac OS 10.3 work properly under Mac OS (Tiger) 10.4. The errors you see are generated because there is a new version of perl installed (5.8.6) which doesn't know about Perl/Tk, the graphics system that Bruce uses for all of his packages. The solution is simple, you must download and install Perl/Tk and then reinstall horae. After that everything just works again. The build procedure is nearly automatic, but you need to have installed the developer tools (which are included on the Tiger installation DVD). First you need to download Tk from CPAN (the server where free Perl software is hosted). Here is the procedure. 0. I assume you had an installed and functional horae running under 10.3 and did an upgrade to 10.4 1. Download the source for Tk by a. make a new (temporary) scratch directory mkdir temp; cd temp b. download Tk going in your browser of choice go to the web page: http://search.cpan.org/~ni-s/Tk-804.027/ and hitting the download button on that page (the file will be named Tk-804-2.027.tar.gz) c. uncompress the file in your scratch directory tar zxf /the-path-to-your-download-directory/ Tk-804-2.027.tar.gz d. change to the Tk directory, compile, and install the new Tk cd Tk-804.027 perl Makefile.PL make sudo make install e. now you must download and install the latest version of horae via Bruce's web page go to the site http://leonardo.phys.washington.edu/~ravel/ software/downloads.html#unix and use the download link for horae-051.tar.gz f. decompress and install the new horae source cd ../temp (move up from the Tk directory to the top level of your new temporary directory) tar zxf /the-path-to-your-download-directory/ horae-051.tar.gz cd horae-051 perl Makefile.PL make sudo make install That's it. You are done. I just popped up a X11 window (you did remember to install the X11 program which is an optional install on the Tiger DVD accessible using the "Customize" button in the installer, right?) and typed artemis & and poof, artemis appeared. Note that if you did a clean install you should still be able to get everything working by downloading Matt's installer and installing the 10.3 copy (it won't work out of the box) and then following the above procedure. I have not verified this, however, so caveat empor as the Romans said... Hope this helps. Paul On May 10, 2005, at 3:08 AM, denauwer(a)tele2.fr wrote: > Dear Paul, > > We have contacted Bruce because we want to use Athena on Mac OSX.4 > and it is not working. We have tried from the terminal and we got > the following message: > > "Can't load '/Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/ > Event/Event.b > undle' for module Tk::Event: dlopen(/Library/Perl/5.8.1/darwin- > thread-multi-2lev > el/auto/Tk/Event/Event.bundle, 1): Library not loaded: /System/ > Library/Perl/5.8. > 1/darwin-thread-multi-2level/CORE/libperl.dylib > Referenced from: /Library/Perl/5.8.1/darwin-thread-multi-2level/ > auto/Tk/Event/ > Event.bundle > Reason: image not found at /System/Library/Perl/5.8.6/darwin- > thread-multi-2lev > el/XSLoader.pm line 68. > at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/Event.pm line 10 > Compilation failed in require at /Library/Perl/5.8.1/darwin-thread- > multi-2level/ > Tk.pm line 13. > BEGIN failed--compilation aborted at /Library/Perl/5.8.1/darwin- > thread-multi-2le > vel/Tk.pm line 13. > Compilation failed in require at /Applications/Ifeffit/bin/athena > line 53. > BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/ > athena line 53. > Undefined subroutine &Tk::Event::CleanupGlue called at /Library/ > Perl/5.8.1/darwi > n-thread-multi-2level/Tk/Event.pm line 3. > END failed--call queue aborted at /Applications/Ifeffit/bin/athena > line 53." > > Could you if you have time, please, explain what we have to do to > fix this problem? > > Thank you for your help, > Christophe Den Auwer > >

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Horae in Mac OS 10.4 (Tiger)
by Paul Fons 09 May '05

09 May '05

Being one who likes going where few have gone before, I went and installed Tiger (which has perl 5.8.6 installed by default by the way). I then installed the latest Tk and followed that up by the usual incantations for the horae-051 and all was well. It works without trouble. This just in case anyone else out there wants to use the new search feature spotlight (very handy for those pdfs, source code etc.) I can search my 20 gigabyte home directory in about 10 seconds for content (not just filename). Neat stuff. Paul

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Comments on the new version
by Gerrit Schmithals 06 May '05

06 May '05

Hello Bruce, thank you for your constant efforts on improving this great analysis software. I just want to report a few observations on the new versions of Athena and Artemis. I use Windows 2000, Ifeffit + Update 014. - The file http://cars9.uchicago.edu/ifeffit/updates/update.dat still indicates an update level of 012. As discussed before it is easy to update the windows version by downloading the updater zip-files and extract them to the program folder. - The csv-file exported from Athena as two extra commas in the title lines so that title and data is misaligned. - When exporting data from Artemis choosing "Save selected group as" the x-value column is only exported if the original dataset is also selected. - I was often not able to export data via File | Save Data/Fit/Residual As | chi(k) (Artemis message below). I figured out, that it works when the group of the original chi-data is selected in the Data & Paths-window, but not when Fit or Residual is chosen. Another bug: if one of the FEFF-paths is selected while exporting via "Save data as" then the values of the original chi-data will be exported, but the filename and header will reflect the chosen path. I was initially trying to export some FEFF-paths using this method and was quite confused that they all look the same :). A tip that I can give to other users: it something seems to be wrong with the exported data, it is always possible to extract the correct data by saving the project to disc and opening it with an unzip program. Cheers, Gerrit Artemis message: Ifeffit checked for updates recently. Tk::Error: Can't call method "param_summary" on unblessed reference at script/ar temis line 7878. [\&main::save_data,fit,k] (menu invoke) main::__ANON__('Tk::Error: Can\'t call method "param_summary" on unbless ed refer...') called at blib\lib\Tk.pm (autosplit into blib\lib\auto\Tk\Error.al ) line 402 Tk::Error('MainWindow=HASH(0x219c69fc)', 'Can\'t call method "param_summ ary" on unblessed reference at scr...', '[\&main::save_data,fit,k]', '(menu invo ke)') called at Tk.pm line 340 eval {...} called at Tk.pm line 340 Tk::MainLoop() called at script/artemis line 1798 require main called at ../blib/lib/PAR.pm line 260 PAR::_run_member('Archive::Zip::ZipFileMember=HASH(0x11c0104)', 1) calle d at script/main.pl line 4 require main called at ../blib/lib/PAR.pm line 260 PAR::_run_member('Archive::Zip::ZipFileMember=HASH(0x11c0254)') called a t ../blib/lib/PAR.pm line 226 PAR::import('PAR') called at -e line 824 __par_pl::BEGIN() called at script/artemis line 0 eval {...} called at script/artemis line 0

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Need an advice
by Steven S. Lim 06 May '05

06 May '05

Dear all, I have a question to ask all of you as follows. We have been investigating the EXAFS of some partially reduced Co materials (by Co EXFAS) and would wish to obtain some qualitative information on the Co metal particles. If, in fact, the Co had some average coordination environment because we have a distribution of Co particle sizes with oxygen adsorption, analyzing the windowed Co-O and Co-Co peaks together as a linear combination and assessing the average oxygen and Co coordination from the Co edge absorption (what we do with Athena) would appear to give a useful answer. However, if what we have is closer to a physical mixture of small Co metal particles and Co oxide particles, it would seem that it would be more appropriate to analyze separately the windowed Co-O and Co-Co peaks in R-space, to somehow normalize the Co-Co to the fraction of metal in the sample and use this as a qualitative measure of metal particle size. Is there a way to do this with Athena or other method? Or do you know of a reference where this has been discussed? Of course, we can (and will) make experimental mixtures as references but wonder if there is a different way of doing the analysis or if there is some literature on this problem (which we have not been able to locate). Thank you. Steven

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new updates for windows
by Matt Newville 05 May '05

05 May '05

Hi Folks, As Gerrit S mentioned earlier, there is now a new updater for Windows that will install the latest versions of Athena, Artemis, Diana, and Hephaestus. In addition, there is an upgrade of the Ifeffit library to 1.2.7... a source release will be available soon -- if you're interested, it's already under http://cars.uchicago.edu/ifeffit/src/ but I haven't updated all the web pages or sourceforge yet. I think Bruce has discussed most of the new features in his programs. One thing that we should warn you about is that these versions of Bruce's programs use a new method to make Windows executables. Really, this is better for many reasons, but it currently means a noticeable lag in startup time, even before a splash screen pops up. We're looking into this, but please be patient! Thanks, --Matt

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How is the path data exported?
by Gerrit Schmithals 03 May '05

03 May '05

Hello, I just started to use Artemis again and at the moment I am a bit confused about the results. In one Artemis experiment I just select two FEFF-paths and choose a "sum of paths" which produces the result shown in the appended picture (SumOfPaths2). Shouldn't the fit be more or less look like the sum of the two paths? I also exported both paths as chi(k)-data and manually added them which produced the same result as the chi(k) of the fit. But when I use more paths I get a different result: the manually summed chi has a greater amplitude (see chi.png). Could that be related to the fact that the fit parameters are applied to the sum of path but not to the exported paths? Cheers Gerrit

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Reporting math expressions in scientific papers
by MauRo 02 May '05

02 May '05

Hi folks, I would like to ask you if it exist one common convention, apart the XAFS society one, to report IFEFFIT results when you have unusual math expressions. In particular, I have used a two-phase model (two FEFF calculations) to fit my sample and for the amplitude variable I have these math expressions: amp_feff1 = amp * x amp_feff2 = amp * y = amp * (1-x) In this way I can estimate the global amplitude variable and introduce a "percentage" of the two chemical compounds (correlation is kept under control). How to explain what I have done to a non-ifeffiter? Mauro --- Mauro Rovezzi <laluvedda(a)gmail.com> Physics student @ GILDA BM08 c/o ESRF (Grenoble, France)

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???
by Elena Ion 02 May '05

02 May '05

Hello, Questions from a beginner in EXAFS...using Athena and Arthemis >From where to get the error bars for number of neighbours, distance and sigsqr (ss)? What are Chi-square,Reduced Chi-square and R-factor and how should be their values in a fit? Sometimes it happen that "R-factor for this data set" does not have the same value as the first R-factor from results. Why? many thanks, Elena

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Fwd: help about Arthemis
by Bruce Ravel 30 Apr '05

30 Apr '05

Mahendra, I am forwarding your question and my answer to the Ifeffit mailing list. I recommend that you make use of that resource for your EXAFS and analysis software questions. Once you make the sum of paths, you should find that, in the File menu, the menu item for "Save fit as" is enabled. I acknowledge that is somewhat confusing -- you made a summation, not a fit. But as far as Artemis is concerned, summations and fits are very similar. In any case, you can use that item in the File menu to save your summation in k, R, or q space. There is a small bug in there. If you have not imported data yet, you can still save the summation in the manner I described, but the information written to the header will be incorrect. That will not preclude using the file, however. Hope that helps, B ---------- Forwarded Message ---------- Subject: help about Arthemis Date: Friday 29 April 2005 15:19 From: koppolu uma mahendra kumar <mahixs(a)gmail.com> To: ravel(a)phys.washington.edu Dear Dr.Bruce Ravel, i am a new user of Arthemis. i calculated an exafs signal using phase and amplitudes calculated from Feff. i used the option "sum of paths(no fit)" in Arthemis. i am not able to save this as an ascii file. Please help me to go ahead. thanking you mahendra kumar ------------------------------------------------------- -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone: (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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horae-051 debian packages
by Carlo Segre 28 Apr '05

28 Apr '05

I have built and uploaded the 051 version for Debian. I will convert to rpms as soon as I have time. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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new tarbell, again
by Bruce Ravel 28 Apr '05

28 Apr '05

The 051 release is up on my website and on SourceForge. Carlo, Paul, Stefano, and Matt helped iron out all the problems in Athena and horae_update. Thanks guys! B -- 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 27 Apr '05

27 Apr '05

Hi folks! After a rather long hiatus, I have finally released a new source code tarball for my codes. You can grab it from SourceForge or from my web site. The linux, unix, and Max OSX users can run the horae_update script at any time. If history is any guide, Carlo will have new debian packages on SourceForge lickedysplit ;-) I plan to build new Windows executables on Monday morning. Hopefully there will be a Windows updater package soon after that. The list of new features, improvements, and bug fixes is quite long. Here is a summary of the most important new developments: Athena: ** You can now rebin your data using Ifeffit's rebin() function. Rebinning can be done on the fly in the column selection dialog as the data is imported or you can use the rebinning dialog which is found under the Data menu to rebin data already imported into Athena. ** After editing a parameter in one of the little text entry boxes, you can hit "enter" or "return" and the data will be replotted. This is a keyboard shortcut for the red plot buttons. ** There are several cosmetic changes on the main page intended to convey more information about the state of a data group. The large blue text in each section on the main page changes its shade of blue depending on whether the group is "up to date" with respect to that group of parameters. This will make sense when you see it! Artemis: ** This is almost certainly the last release for which there will be distinct stable and development versions of Artemis. Very soon I will be retiring the 0.7 branch of Artemis and renumbering the development branch as Artemis 0.8. For now the "artemis" program still refers to Artemis 0.7 and the "diana" program still refers to the development version. Soon, there will be no "diana" and "artemis" will refer to version 0.8. Here is a short PDF document with lots of pictures describing the major changes between 0.7 and 0.8: http://leonardo.phys.washington.edu/~ravel/misc/artemis0.8.pdf Hephaestus: ** I added a fluorescence line finder which works almost exactly like the current edge finder. I hope everyone enjoys the latest versions. I encourage everyone to try out the development version of Artemis. Have fun! Bruce -- 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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this time for sure!
by Bruce Ravel 25 Apr '05

25 Apr '05

Hi! I just uploaded release 050 of the source code tarball for Athena, Artemis, and Hephaestus to SourceForge and my web site. This version fixes some problems related to perl/Tk 804 that surfaced after the previous release two days ago. I think that this version should work well. I'm keeping my fingers crossed! Unfortunately, the horae_updater script that you linux and Mac users have on your computers will not work due to some changes at SourceForge. Grrrr! You can grab an updated version of the updater here: http://leonardo.phys.washington.edu/~ravel/software/packages/horae_update That version should work around the new changes at SF. I built and tested the codes on Windows today. I am using a new system for building Windows executables. Athena and Artemis worked fine, but there was a problem with Hephaestus. Hopefully I'll get that problem solved and a new Windows updater will become available soon. I'm really excited about this release -- Athena has seen lots of improvements and the development version of Artemis is almost ready for widespread use -- so I am eager to get over these hurdles. Regards, B -- 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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an interesting Atoms problem
by Bruce Ravel 22 Apr '05

22 Apr '05

Hi! This week I received an interesting question about Atoms whose answer will, I think, be of wide interest to the denizens of this list. The fellow who started the discussion had an atoms.inp file for ammonium tetraoxorhenate, (NH4)ReO4. Here is the input data: space = I 41/a a = 5.995 c = 12.440 rmax=10 core = Re1 atoms # elem. x y z tag Re 0.00000 0.00000 0.00000 Re1 O 0.20450 0.37860 0.17020 O1 N 0.00000 0.00000 0.50000 N1 These data ran atoms to completion, but then Feff stopped after issuing the statement about computing the "muffin tin radii and interstitial parameters" with this error message: WARNING: NO ATOMS CLOSE ENOUGH TO OVERLAP ATOM 10, UNIQUE POT 3!! My correspondant found this message a little cryptic and asked for advice. You will notice that the input data for atoms did not specify the hydrogen positions. Often it is fine with both Atoms and Feff to neglect the positions of the hydrogen atoms. For example, in a mineral phase with water molecules in the crystal structure, one can often just specify the positions of the water oxygens and neglect the water hydrogens. Doing so will still let both Atoms and Feff run to completion and leave you with a Feff calculation that is quite useful in analysis. So what happened here? Apparently my correspondent presumed that ammonium is like water in that specifying the locations of the hydrogens is not essential to the Feff calculation. Like in water, the hydrogens are fairly tightly bound to the nitrogen -- less than an Angstrom away -- so it might be ok. In this case, however, the hydrogens are essential. Adding the hydrogen position H 0.37200 0.45600 0.03300 H1 avoids the problem during the Feff run. Feff finishes and the analysis can proceed. It turns out that, while the N and the H are, indeed, quite close together, the N is quite a long way away from its next nearest neighbor, which is oxygen. The oxygen shell is split into two subshells, the closer of which is at about 2.85 Angstroms from the N. When Feff goes to compute the muffin tin potential, a near neighbor separation of 2.85 Angstroms is too large and it is unable to determine the radii of the atoms. That is the meaning of Feff's slightly cryptic error message. With the intervening hydrogen atoms, Feff's algorithm for constructing the muffin tins is no longer ill-defined -- the separation between atoms is no longer too large. To conclude, while it is probably unlikely that the hydrogen locations can be well measured by the EXAFS experiment, it is quite important to include the hydrogens in the theory. The rule of thumb that says that hydrogens in hydrated crystal structures can be neglected is not a very good general rule. This is certainly a case where the hydrogens cannot be ignored. Well, *I* thought it was interesting. Hopefully you did too! B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone: (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: [Ifeffit] Estimation of Pt and Au particle size
by Barton, David (DG) 19 Apr '05

19 Apr '05

Scott: Thank you for your detailed and prompt response. I look forward to testing out your example file of fitting Pt particle size, it should be a good starting point to begin this type of "rough" analysis. After working though this "rough" analysis we will then consider if our data quality will allow for a more detailed analysis of particle shape or distribution. Where we want to eventually take this analysis is to determine if we can measure differences in the particle size distribution in a series of samples. Ifeffit Community: I am still open to additional example Artemis files, especially if someone has a file that they would want to share related to fitting Gold particle sizes. Regards, Dave > -----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: Tuesday, April 19, 2005 9:29 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Estimation of Pt and Au particle size > > > Hi David, > > Sure thing. I'll send you a Pt file as a separate email; I'll also > send you a copy of the paper we're currently preparing for > publication. The final versions we used we're big Ifeffit scripts > rather than Artemis files, but I'm sure I can scare up a > representative Artemis file from earlier in the process. > > Just a brief comparison of the two methods I've seen out there: > > 1) Fit the coordination number of each shell. Anatoly Frenkel has > several publication related to this. > > 2) Assume the crystallites are "roughly" spherical and constrain the > coordination numbers in a fit to reflect this. The only size-related > fitting parameter is then R, the radius of the crystallite. I have > written a few papers related to this method. > > Method 1 has the advantage that it can in principle handle any > morphology; Anatoly has used it with supported catalysts (they may > even have been Pt, but I don't recall offhand) and distinguished > between shapes like rafts, hemispheres, etc.. > > Method 2 has the advantage that is uses only 1 size-related > parameter. For a complicated fit or one with limited data quality, > that's nice. On the other hand, if the morphology is far from > spherical (e.g. needles), then it doesn't work very well. This method > can even be used with an empirical standard (as opposed to a > theoretical standard like FEFF) to give a (rough) model-independent > estimate of size. > > So I tend to think method 1 is better when you have a very uniform > sample, as can happen with supported catalysts, while method 2 is > often appropriate when you have a "messier" sample with roughly > spherical particles, as is often the case when wet chemical methods > are used. > > It should also be noted thatusing both techniques there have been > many reports that for polydispersed samples EXAFS yields a mean > smaller than that found by other methods (e.g. Scherrer analysis). > Part of that can be explained by the different weightings inherent in > the different techniques (EXAFS reads a 10 nm and 10 micron > crystallite as essentially identical, but "notices" a 1 nm > crystallite, while XRD would find the 10 micron signal dominant), but > I am not yet convinced that there isn't something else at work as > well. My group is currently planning a follow-up study of Pt to > resolve this question. > > --Scott Calvin > Sarah Lawrence College > > >Ifeffit Community: > > > >Over the past year or so I have seen several discussions of > >estimation of metal cluster size (collections of several to hundreds > >of metal atoms) using coordination numbers derived from EXAFS > >fitting. I was wondering if anyone on the list would be willing to > >share an example of their Artemis project file where this analysis > >was done successfully for Pt and/or Au particle sizes. As a first > >pass I am just interested in roughly estimating an average particle > >size with future considerations for estimations of particle size > >distributions if data quality and theory allows. > > > >Thanks in advance to anyone willing to share their project files. > >Given the number of experts in the field reading this list it just > >seemed to make sense to build upon the back giants. > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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Estimation of Pt and Au particle size
by Barton, David (DG) 19 Apr '05

19 Apr '05

Ifeffit Community: Over the past year or so I have seen several discussions of estimation of metal cluster size (collections of several to hundreds of metal atoms) using coordination numbers derived from EXAFS fitting. I was wondering if anyone on the list would be willing to share an example of their Artemis project file where this analysis was done successfully for Pt and/or Au particle sizes. As a first pass I am just interested in roughly estimating an average particle size with future considerations for estimations of particle size distributions if data quality and theory allows. Thanks in advance to anyone willing to share their project files. Given the number of experts in the field reading this list it just seemed to make sense to build upon the back giants. Regards, Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA

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a basic (?) EXAFS question
by Juraj Majzlan 18 Apr '05

18 Apr '05

Hello, I have a question about fitting an EXAFS dataset. The compound is FeAs2, crystalline, and will be used as a model for further study. I was able to fit the first three shells very well. However, when I try to fit the fourth shell, I either get amplitude that is too high (> 2, with large errors), or 0.0. There are several single-scattering and several multiple-scattering paths in that region. Sometimes, only excluding one of the MS paths leads immediately from amplitude of >2 to 0.0. I'd appreciate any advise about what is the meaning of these changes and the inability to fix the spectrum. Attached are few pictures from Artemis. Thank you, Juro Majzlan ---------------------------------- 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

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RE: [Ifeffit] a basic (?) EXAFS question
by Kelly, Shelly D. 18 Apr '05

18 Apr '05

Hi Juro, Another thing to try, is to simply sum up all the paths from the crystal structure. Then compare the chi(k), and real and mag of the FT. Then plot the individual contriubtions from each of the paths to see how many are significant and how the different paths are contibuting to the overall model. If the model with all the paths is way different from the data then there may be a problem with the structure. SK ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Matt Newville Sent: Sun 4/17/2005 2:52 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] a basic (?) EXAFS question Hi Juro, I think you'd have to give us more information about how you did the fits. A few obvious questions are: what R range did you use for the fit? what was floated and what was fixed in the fit? how far out does the data go in k-space? I'm afraid that I don't know the crystallographic details of loellingite, but the EXAFS for many crystal structures get very complex by the fourth shell. This is especially true in slightly disordered structures where multiple-scattering and single paths nearly overlap. Part of the reason for this is that multiple-scattering paths can "spread out" in R-space, making it difficult to know where to stop including paths. --Matt On Sun, 17 Apr 2005, Juraj Majzlan wrote: > Hello, > > I have a question about fitting an EXAFS dataset. The > compound is FeAs2, crystalline, and will be used as a model > for further study. I was able to fit the first three shells > very well. However, when I try to fit the fourth shell, I > either get amplitude that is too high (> 2, with large > errors), or 0.0. There are several single-scattering and > several multiple-scattering paths in that region. > Sometimes, only excluding one of the MS paths leads > immediately from amplitude of >2 to 0.0. > > I'd appreciate any advise about what is the meaning of > these changes and the inability to fix the spectrum. > > Attached are few pictures from Artemis. > > Thank you, > > Juro Majzlan > > > ---------------------------------- > 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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Problems running Adobe Illustrator and IFFEFFIT package programs
by Matthew Ginder-Vogel 14 Apr '05

14 Apr '05

Hello, I was running Adobe Illustrator and then started up Hephaestus and Illustrator immediately crashed. For the sake of science I tried a couple other programs (sixpack and Athena) with similar results. Another person in my research group has also experienced these problems. I just wanted to alert other people to the perils of running Illustrator with one of the other programs. thanks, matt -- ******************************************** Matthew Ginder-Vogel Doctoral Student Department of Geological and Environmental Sciences Stanford University Soil and Environmental Biogeochemistry Group gindervm(a)pangea.stanford.edu ********************************************

1 0

Fwd: Re: Wrong window project file
by Scott Calvin 01 Apr '05

01 Apr '05

Thanks, Bruce. I'm moving this thread back to the ifeffit board: > >On Thursday 31 March 2005 18:41, you wrote: >> Incidentally, trying to shrink down the file has made me notice there's a >> lot of leftover stuff in the zip file--it looks like every data file I've >> ever used for chi data is still in there, as well as an old fit for each of >> those. Artemis almost never crashes any more (yay!), so those aren't a >> legacy of crashes--it just appears that every time I change data files it >> leaves the old one (and the associated fit) sitting in the project file. >> Since I sometimes use the same model with lots of different data, that >> starts to add up. > >Before I actually split Artemis into two branches, I was already starting to >think about the concept of maintaining a history of all fits done. The >presence of all that stuff makes no sense in the context of the stable >branch, but it is much more sensible in the development branch. > >The data should all be chi(k) data -- not so big and it compresses well. >Project files are big because the feff calc, not because of the data. The example I sent you had about 300 k of the zipped project file in old chi data, and the total file is 3 M, so yes, most of it in this case is FEFF calculations. I'm concerned, though, that the former number can only go up. Here's what I think is a reasonable hypothetical: someone has a really stable Artemis model that they like for their materials, and they use it over and over again on various samples. Unlike the file I sent you, it might also use a fairly small number of FEFF paths. Combine that with the fact that the time used by Autosaves is of course quite dependent on the size of the project file (and maybe the number of files in it? I'm not sure how the zipping algorithm works in that respect), and it becomes potentially annoying. I don't consider this a high priority issue, but it seems like something worth thinking about. >Another future reason for hanging onto all the data is batch functions. >Suppose you had a temperature series and wanted to fit each of the scans with >the same model. Wouldn't it be cool to tell artemis-of-tomorrow to fit all >the data and then show the temperature dependence of one of the sigma^2s? Yes, it would be very cool. I guess I'm just asking for a "clear history" option or something like that. In the mean time, I'm happy to do this manually if I know it won't confuse Artemis. If I just root around in the zipped project file and remove the old .chi and .fit files, will that confuse Artemis in any way? --Scott Calvin Sarah Lawrence College

2 1

Re: sigma squared
by Bruce Ravel 01 Apr '05

01 Apr '05

Hi Karla, These are excellent questions for the mailing list, so I am taking the liberty of CCing my answers to the list. That way, other people can have a chance to answer your excellent questions. On Thursday 31 March 2005 14:10, you wrote: > Hello, > I am fairly new to EXAFS data analysis. I am currently working on > data that I collected from 10-ID at the APS. Aha! My new home! I just collected my first spectra from that beamline a couple of weeks ago. ;-) > I have a couple of questions. First, in Artemis, when I click on > the "x" buttons to select my k- and r-ranges, the window never seems > to correspond to where I clicked. Is this a bug? Probably not. The default in Artemis is use a Kaiser-Bessel window. The various strange words to describe FT windows ("Kaiser-Bessel", "Hanning", "Welch", and so on) refer to different functional forms for the window. None of the functional forms will be 0 at the specified boundary -- instead they all have window sills that extend a bit below the boundary. Thus, if you use the Kaiser-Bessel window, set kmin=2, and dk=1, the window will become non-zero at about 1.5. In short, it's not a bug. It's an unexpected (for you, at least ;-) feature of the functional form of the window. Try setting dk or dr to 0 then replotting. The FT may not look good, but the window plotted by Artemis will be what I think you were expecting. > Second, why does Artemis allow a physical parameter like sigma > squared to be negative? There are a few ways I could answer this question. I could talk about how Artemis allows arbitrarily sophisticated fitting models where the sophisticated user needs complete freedom to specify the fitting model. But that's a little abstract, so let's consider a slightly more concrete example. Suppose that your sample has some kind of oxygen-coordinated iron atom and you have reason to believe that there is a high level of disorder in the first coordination shell. So you choose to run Feff using some model compound that itself has much disorder in the first shell. You then use the first shell paths that came from the Feff calculation to model your unknown data. In this case a negative sigma^2 might be telling you that your unknown has *less* disorder than you model compound. In more general terms, the negative sigma^2 is probably trying to tell you something. You should remember that sigma^2 is correlated to other terms in the fit, most importantly to the various amplitude terms, such as coordination number and S02. If sigma^2 is negative, then the fitten value for amplitude is probably to small. A negative sigma^2 will puff up the signal to compensate for the amplitude term being rather too small. If Artemis did not allow sigma^2 to go negative, you might never know about this kind of problem. So I would say that this too is a feature of the program and not a bug. > Lastly, I have had a hard time figuring out these math expressions > despite reading over the mailing lists. Can you use the ">" sign so > that sigma squared is always greater than 0? How else can I write a > math expression so that the fitting never gives me a sigma squared > that is less than 0? Any help would be greatly appreciated! Using ">" won't work. ">" is not a symbol in Ifeffit's math parser. This is a topic that has come up many times over the past few years on the mailing list. In fact, I think that someone should write a FAQ entry on this topic. Here are a few suggestions: 1. Guess a parameter like this: "guess ss 0.003", then use it on the sigma^2 line of the path page like this: "abs(ss)". 2. A very similar approach is to use the max function. In the sigma^2 line of the path page, say this: "min(ss, 0)". This can be improved slightly. Doing this: "min(ss, 0.001)" constrains the sigma^2 for the path to be no smaller than 0.001. 3. If you start reading the mailing list archives here: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-February/001650.html you will find a conversation between Matt and Scott about a way to impose a penalty for a sigma^2 being too small rather than forcing to be above a hard boundary. Matt's scheme is kind of involved... If you use any of these approaches, I would encourage you to do so with hesitation. As I mentioned above, the negative sigma^2 is not a short coming of Ifeffit or Artemis. Much more likely, it is useful information that you should heed and use to figure out what shortcoming in your fitting model is leading that to happen. HTH, B -- 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/

9 16

installation of horae in fedora2
by ynliu＠eps.mcgill.ca 22 Mar '05

22 Mar '05

Hello,all We finally succeeded in installing horae-048 in Fedora 2! It took us a long time to figure out why Tk could not be detected, but it turned out that the right version of Tk is the key. We found Tk-804.027 working in our Fedora2 system. The right order of installation is also important. We had to restart everything in installing horae after we set up Tk.If you are using this Tk-804.027, you don't need to look for unix folder as said on some web,just simply gunzip tar -xvf finename.tar (enter the new folder Tk-804.027) make make install(after this,you can make test if you want) And then the installation of horae will jsut go fluently following the instructions! To use athena or artemis, you need to enter the fold where athena.pl and artemis.pl are,and then "perl athena.pl". cheers Yanan ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

4 5

file causing trouble creating chis
by Daniel Carter 15 Mar '05

15 Mar '05

Ok Matt, I thought you might have a general idea for how I could gather more info for you about the problem. I did mention previously this weekend to you that I am using windows XP. I also had thought I'd posted a file, but I'd just sent it to Adam. From now on I will send a file every time I have a problem. This is with athena version 8.034. Matts theory that there is not enough of a Mu(E) range sounds good to me so far. --Dan

3 3

Re: [Ifeffit] file causing trouble creating chis
by Adam Webb 15 Mar '05

15 Mar '05

Hi, I looked at the file. But as with your first file, I have no trouble saving chi files. I used athena 0.8.34 on Windows 2000. You should not have any trouble with XP. BTW the file you sent says it was created with Athena 0.8.30. I think it should still work but it might indicate a problem with your installation. You could try unistalling and re-install and get the updates when the updater runs. I hope this helps, Adam > Ok Matt, > > I thought you might have a general idea for how I could > gather more info for you about the problem. I did mention previously > this weekend to you that I am using windows XP. I also had thought > I'd posted a file, but I'd just sent it to Adam. From now on I will > send a file every time I have a problem. This is with athena version > 8.034. Matts theory that there is not enough of a Mu(E) range sounds > good to me so far. > > --Dan ------------------------------------------------------ M. Adam Webb Ph.D., MCIC Alberta Synchrotron Institute (http://www.asi-cls.ca/) 8308 - 114 Street, Suite 2080 Edmonton, Alberta, T6G 2E1, Canada Phone: (780)492-5464 Fax: (780)492-6160 Email: adam.webb(a)asi-cls.ca

1 0

blank chi files still
by Daniel Carter 15 Mar '05

15 Mar '05

Bruce, Matt, Adam, others, I'm still having this problem with Athena where I try to save data as a chi file and the file is created, but empty. The chi files should be several killobytes large, but mine are 0 KB. I've just upgraded to the newest version of Athena 8.037. I wonder, is it my data or my operating system? No one else seems to be having these sorts of problems. --Dan

2 1

Athena functionality report
by Raul Barrea 14 Mar '05

14 Mar '05

Hi Bruce, I found a difference in functionality in Athena when I tried to use "open file" or "open many files" in the main menu . When using the many files option I found this message: Athena trapped a warning! The following message was trapped by Athena: Athena0.8.034warnC:\Program Files\Ifeffit\horae\stash\ATHENA.TRAPCODE(0x21a5d800 ) at athena line 1363 main::__ANON__('Tk::Error: Can\'t call method "lower" without a package or objec...') called at blib\lib\Tk.pm (autosplit into blib\lib\auto\Tk\Error.al ) line 402 Tk::Error('MainWindow=HASH(0x21072a84)', 'Can\'t call method "lower" wit hout a package or object reference...', '[\&main::read_file,1]', '(menu invoke)' ) called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at athena line 1419 When I opened the same file alone using the "open file" option , Athena says the file is not monotonically sorted and it cannot be opened. So, that's the problem with the file. Then, Athena offers to sort the data and continue loading the file. Why this message is not shown when I opened multiple files? I tried to open only one file (the one that is not monotonically sorted) using the "open many files" option and the message was the same as the "open file"option. When using the "many files" option with many files, Athena does not show that message window and stays partially inactive (menu options are active but plot options are not active). A few sample file are atached. Thanks, Raul -- Raul Barrea, Ph.D. Assistant Research Professor of Physics, Associate Director Biophysics Collaborative Access Team (BioCAT) CSRRI, Dept. BCPS, Illinois Institute of Technology BioCAT/APS/435B/Sector 18 Argonne National Laboratory 9700 South Cass Avenue, Argonne, IL 60439 Tel.: (630) 252-0541 Fax: (630) 252-0545 Email: barrea(a)bio.aps.anl.gov Email: barrea(a)iit.edu pager: barrea-pager(a)bio.aps.anl.gov # File header: # Date and time: Sun Feb 20 23:25:41 2005 # Original name of the file: whiteCuscan.154 # Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -74.0000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. 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Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.7000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. 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Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.8000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. Motor 2 position: 6.2000 # Scaler channel_number/column_name/dark_current: # ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0 # Dark current last measurement: Sun Feb 20 20:17:51 2005 # # # # # # # # # # Energy I0, I1, CuKalfa # 8779.02544 433951.11893 132784.30641 183.33786 8779.17763 436815.36667 133447.63333 141.66667 8779.81082 439482.03333 134747.63333 216.66667 8780.76531 440382.03333 134464.30000 141.66667 8781.71088 438232.03333 134530.96667 216.66667 8782.65665 440173.70000 134480.96667 225.00000 8783.60264 440082.03333 134664.30000 208.33333 8784.54883 441157.03333 135155.96667 216.66667 8785.49371 438932.03333 134080.96667 200.00000 8786.43880 439473.70000 134630.96667 208.33333 8787.38714 438398.70000 133797.63333 200.00000 8788.33417 438715.36667 134355.96667 183.33333 8789.27989 437207.03333 133639.30000 191.66667 8790.22734 437015.36667 134147.63333 241.66667 8791.17653 424165.36667 129697.63333 216.66667 8792.12439 433532.03333 132714.30000 208.33333 8793.07095 439940.36667 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Original name of the file: whiteCuscan.153 # Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.9000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. Motor 2 position: 6.2000 # Scaler channel_number/column_name/dark_current: # ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0 # Dark current last measurement: Sun Feb 20 20:17:51 2005 # # # # # # # # # # Energy I0, I1, CuKalfa # 8779.02544 433634.44445 133059.31319 166.67078 8779.17459 437473.70000 133564.30000 191.66667 8779.80625 440073.70000 134939.30000 266.66667 8780.76227 440582.03333 134755.96667 175.00000 8781.70631 439757.03333 134755.96667 150.00000 8782.65056 438990.36667 134322.63333 191.66667 8783.59807 439523.70000 134147.63333 191.66667 8784.54426 439682.03333 134864.30000 158.33333 8785.48914 439732.03333 134214.30000 225.00000 8786.43575 438548.70000 134097.63333 175.00000 8787.38257 439715.36667 134189.30000 266.66667 8788.32807 437440.36667 133664.30000 208.33333 8789.27531 437715.36667 134005.96667 241.66667 8790.22276 435532.03333 133222.63333 158.33333 8791.17042 424065.36667 130064.30000 158.33333 8792.11982 431790.36667 131622.63333 233.33333 8793.06637 439115.36667 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Original name of the file: whiteCuscan.150 # Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.6000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. Motor 2 position: 6.2000 # Scaler channel_number/column_name/dark_current: # ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0 # Dark current last measurement: Sun Feb 20 20:17:51 2005 # # # # # # # # # # Energy I0, I1, CuKalfa # 8779.02544 432592.75209 132475.96547 175.00432 8779.20655 435715.36667 133297.63333 233.33333 8779.86866 436465.36667 133597.63333 183.33333 8780.82316 437198.70000 133547.63333 233.33333 8781.76874 438007.03333 134439.30000 175.00000 8782.71301 437823.70000 133214.30000 66.66667 8783.66053 438132.03333 134872.63333 183.33333 8784.60826 437873.70000 133439.30000 125.00000 8785.55315 437923.70000 134372.63333 141.66667 8786.49825 437890.36667 133622.63333 191.66667 8787.44509 436590.36667 133614.30000 208.33333 8788.39213 435848.70000 133114.30000 166.66667 8789.33938 436748.70000 133489.30000 158.33333 8790.28685 434573.70000 133222.63333 141.66667 8791.23452 420948.70000 128247.63333 183.33333 8792.18240 431765.36667 132214.30000 183.33333 8793.12897 437840.36667 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2 1

Residual
by yetao＠chem.uga.edu 11 Mar '05

11 Mar '05

Hi, Is there anyone who can tell me how to view the residual in Artemis? Every time I checked the residual, only got the data curve. Best, Ye

4 5

back to work....
by Bruce Ravel 10 Mar '05

10 Mar '05

Hi everyone! I am back from vacation and (on March 7th) started my new position here in Argonne's Environmental Research Division. I had a splendid vacation and am very excited about my new position. For those of you who are APS users, I'll be spending a good fraction of my time at sector 10 (MR-CAT). Stop by and say hi -- especially those of you that I have met in person! I have to confess that I have not been following the discussions on the mailing list very closely in the last several weeks, but I see that there have been a number of bug reports and other problems that people have encountered with the software. I am still settling into my new job and my new home, but I hope to get back to work on the codes real soon. And I will certainly resume active participation in the discussions on the list. Regards, Bruce -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Environmental Research Division, Bldg 203, Room E165 Argonne National Laboratory phone: (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/

3 2

Re: [Ifeffit] Athena Chi file created, but nothing there
by Adam Webb 08 Mar '05

08 Mar '05

Dan, I think the problem was when you first imported the data. When you import the data, Athena tries to figure out what type it is. In your case the first file is very short and Athena probably selected XANES data. This disables the k,q etc since they don't apply. Re-import your data but be sure to select mu(E) as the Data Type in the import window. The rest of your problems should go away. Cheers, Adam > Dear mailing list -- > > I'm having difficulty creating a chi file. First off I cannot > plot my data files in k, q , etc. The files can only be plotted in E > or merged and plotted in k, q, etc. > > Second, when I go to the file menu to create a chi(k) from the > marked original text file, Athena won't let me. That is to say the > only option is create to Save Mu(E) and when I do that a file is > created with nothing in it. > > When I merge 2 data files and create a chi(k) file from that, > again, a file is created and named, but nothing is there. Is there > something wrong with my data files? I don't see any error messages. > Let me know if you need more info. > > I'll also attach my athena file. > > Thanks, Dan ------------------------------------------------------ M. Adam Webb Ph.D., MCIC Alberta Synchrotron Institute (http://www.asi-cls.ca/) 8308 - 114 Street, Suite 2080 Edmonton, Alberta, T6G 2E1, Canada Phone: (780)492-5464 Fax: (780)492-6160 Email: adam.webb(a)asi-cls.ca

2 1

Athena Chi file created, but nothing there
by Daniel Carter 04 Mar '05

04 Mar '05

Dear mailing list -- I'm having difficulty creating a chi file. First off I cannot plot my data files in k, q , etc. The files can only be plotted in E or merged and plotted in k, q, etc. Second, when I go to the file menu to create a chi(k) from the marked original text file, Athena won't let me. That is to say the only option is create to Save Mu(E) and when I do that a file is created with nothing in it. When I merge 2 data files and create a chi(k) file from that, again, a file is created and named, but nothing is there. Is there something wrong with my data files? I don't see any error messages. Let me know if you need more info. I'll also attach my athena file. Thanks, Dan

1 0

Re: uncertainties in "relative" values (Josh Kas)
by joshua jason kas 27 Feb '05

27 Feb '05

Hi Scott, if I understand correctly, the absolute uncertainties in the sizes are still large when you fit sizA and delta_size=(sizeB-sizeA), but I think that the uncertainty in the parameter delta_size showing the difference between the two could be very small, showing that there is a correlation between sizeA and sizeB. In order get this behavior I think you have to leave sizeA unconstrained when you do the multiple-dataset fit. If the uncertainty in delta_size is small, then the absolute uncertainties will be approximately sizeA +- ds_a, sizeB +- ds_a, more or less the same as before, but the uncertainty in sizeB given sizeA is much smaller sizeB = sizeA + delta_size +- dds. -Josh Kas > Hi Matt, > > I tried that, before realizing it didn't really do anything. > Performing a multi-dataset fit with two guessed variables, say size_A > and sizeA_v_sizeB, is of course completely equivalent to just having > the two sizes as guessed variables. And if size_A is set to some > arbitrary (but reasonable) value, sizeA_v_sizeB is equivalent to just > fitting size_B, and produces the "absolute" uncertainty again. This > would be different if the fit were truly multi-dataset in the sense > that we had parameters in common between samples, so that > constraining the size of A had some effect on the fit for B. But the > parameters that are in common, like S02, we constrained to a standard > rather than refining through a multi-dataset fit. > > I like your analogy to airline tickets...that is something like the > situation we seem to have. > > --Scott Calvin > Sarah Lawrence College > >> Hi Scott, >> >> Would it make sense to define a factor between the size of the >> two (or more) particles, say "sizeA_v_sizeB" and vary *that* in >> a fit of the two particles, keeping all the other things >> (k-weight, ranges, etc) the same for the two fits? That is, >> instead of asking "what is the size of particle A and what is >> the size of particle B?", ask "what is the size of particle A >> and how much bigger is particle B?". If you're observations are >> right, sizeA_v_sizeB should be statistically different from 1. >> >> --Matt >> >> PS: The price of airline tickets vary widely with many factors, >> but for any given flight, the price (starting "retail" price) of >> a first class ticket is always higher than a coach ticket. Of >> course, the coach ticket on some flights can easily be twice the >> price of a first class ticket on other flights. But everyone >> knows first class is always more expensive than coach. ;). > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 24, Issue 11 > *************************************** >

1 0

[Fwd: FEFF Q]
by Bruce Ravel 27 Feb '05

27 Feb '05

Ryan, I am on vacation right now, so I have taken the liberty of forwarding your mail to the Ifeffit mailing list. Hopefully someone there will offer up an answer to your questions. Regards, B ---------------------------- Original Message ---------------------------- Subject: FEFF Q From: "R Tappero" <rtappero(a)udel.edu> Date: Fri, February 25, 2005 5:55 pm To: ravel(a)phys.washington.edu -------------------------------------------------------------------------- Hello Dr. Ravel, My name is Ryan Tappero and I am a graduate student in Dr. Sparks Env. Soil Chem research group. I am preparing for an XAFS experiment with M. Newville at APS. I read a recent paper (attached) where the authors used FEFF7 to generate theoretical phase and amplitude functions for cluster models (density functional theory/ DFT optimized structures). I am collaborating with one of my group members on this project, and he has completed the molecular orbital calcs for our proposed clusters. He has provided me with a set of coordinates for the optimized sorption complexes. I can not figure out how to input the x,y,z, coordinates into FEFF in order to generate the dominant scattering paths (for use with theoretical fitting of the XAFS data). Can you point me in the right direction? Sincere Thanks, Ryan Tappero Env. Soil Chem. U of DE, PLSC rtappero(a)udel.edu 410-996-9819 ravel <mailto:ravel@phys.washington.edu> @phys.washington.edu

2 1

Postdoc position at HASYLAB
by Edmund Welter 15 Feb '05

15 Feb '05

Dear colleagues, at the Hamburger Synchrotron Strahlungslabor (HASYLAB) is a postdoc position in the XAFS business available. For more information please follow: http://www.desy.de/v2/docs/1107528217-e.pdf The main tasks of the succesfull applicant will be the operation of the X1 XAFS-beamline, to take care of the industrial XAFS users (This gives ample opportunities to use all the very nice programs which are topic of this list...) and last but not least HASYLAB strongly encourages postdocs to work in their own field of science. If you have questions about this mail or the available position please do not reply to the mailing list, but contact me directly instead. Best regards, Edmund Welter -- Dr. Edmund Welter HASYLAB at DESY e-mail : edmund.welter(a)desy.de Notkestr. 85 fon : (+49)-40-8998-4510 D-22603 HAMBURG fax : -2787 GERMANY secretary : -2304

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RE: About Cu2+ xafs
by Anatoly Frenkel 13 Feb '05

13 Feb '05

Dear Igor, Your problem is very interesting: the dependance of EXAFS analysis results on the FEFF model, and I am cc'ing my response to the group. Obviously, there does not exist a unique way to solve it. It is also true that it is important to know which set of results to choose because if you apply s02 to analyze your unknown compounds, whether it is 0.8 or 1.0 matters. There are several approaches that keep you from breaking your head trying to understand the underlying physics between SCF and nSCF and which of the two values of E0 are better . To choose which model is better, you have to approach it systematically by applying these models (SCF, nSCF and SS) to different systems where you know what debye waller factors should be (e.g., by performing temperature-dependent studies and comparing the resuls you obtained for DWF against those predicted by Einstein or Debye models. This has been done by many and it is a foolproof method. However, it is hard to do temperature dependent studies in solutions, and thus your options may be limited. You can also analyze pure Cu foil data measured in the same conditions at the same beamline, and obtian its S02 (it should be about 0.95 as I remember) and then impose it on your Cu2+ complex. However, this procedure does not allow the S02 in aqueous solutions to be slightly different than in the bulk Cu compounds, and we know that they may be different because the chemistry is strongly different, chemical potentials are discontinuous, and the argument of chemical transferrability of amplitudes and phases may not work. Also, it doesn't answer the question which FEFF calculation to prefer for the analysis of the complexes, but it helps a bit because it gives you some ballpark estimate what S02 should be. So, the first approach is to take S02 from Cu foil or Cu oxide data and impose it on the Cu in solution data. It may be a good start. By the way, in your case, both answers deviate by 10% from the average value: S02 = 0.9. That means, if you do not know which model is more reliable, pick 0.9 and your coordination numbers will be defined with 10% accuracy. It is a good accuracy in case of solutions. The second important question is what to do with E0 and distances. They do correlate, as your results show, and they should. However, the first nearest neighbor (equatorial) distances are identical between the two models. The second, axial, distances are different but overlap within the uncertainties. May be that one should be preferred that gives more realistic E0? Unfortunately, E0 is loosely defined in XAFS analysis (FEFF sets it at the muffin tin level) and it can be within 10-20 eV above Fermi energy. Since Fermi energy must be below 1s-3d transition energy, both of your results are, technically, legitimate. Unfortunately, there is no way to tell what should be the r_axial - partly, because it depends on pH and other factors, but it looks like both your models do give good agreement with expectations. What all these models have in common is that they are all based on theoretical calculations which means that they contain a black box and are hard to check experimentally. Some time ago, I adjusted FEFFIT to solve these problems by "bypassing" the black box part of them. I used an old-fashioned way of EXAFS analysis by using experimental standards instead of theoretical standards. For example, if you are certain that Cu2+ in aqueous solution is octahedrally coordinated, you can use this data set as experimental standard. If you extract the scattering amplitude and phase from this data set, the amplitude function will contain f(k) and S02 in it, and thus it spares you from trying obtaining it from the fit unambigously. Moreover, the phase function will have E0 and delta(k) informations in it as well, and if you align your standard and unknown in energy, the best results for delta r will be less model dependent if you relied on E0 obtained by FEFF. Here is a short paper where this method is explained in detail. http://pubweb.bnl.gov/people/frenkel/EXP-FEFF/thiols.pdf Regards, Anatoly Anatoly Frenkel Yeshiva University anatoly.frenkel(a)yu.edu -----Original Message----- From: Igor Frota de Vasconcelos [mailto:idevasco@nd.edu] Sent: Tuesday, February 08, 2005 9:39 AM To: Frenkel, Anatoly Subject: Re: About Cu2+ xafs Dear Dr. Frenkel, Thanks for your message! I will try put the whole story in a nut shell without leaving important details out! I am working with two different models for my hydrated Cu2+. The first one is a simple one with four water molecules on the equatorial plane, and two in the z axis. The four equatorial O's are 2 A away from the central Cu while the two axial O's are 2.29 A. I positioned the hydrogen atoms according to some molecular dynamics simulations of hydrated Cs and Pb (MD simulation of hydrated Cu2+ is harder because of the Jahn-Teller distortion). I also put eight water molecules in a second shell at 3.95 A to try to minimize truncation effects in the self-consistent calculation. I then used feff8.20 to calculate paths self-consistently (I will call this SCF) and not self-consistently (nSCF). The other model is the one you suggested in the mailing list (I'll call this one SS). The results using the latest linux based horae package are (the subscripts e and a denote equatorial and axial O's (I did not include results from multiple-scattering and hydrogen paths): 1) SCF: S02 = 0.9982900 +/- 0.0616710 E0 = -7.5800660 +/- 0.5694190 dr_e = -0.0443480 +/- 0.0034370 => r_e = 1.955652 +/- 0.0034370 ss_e = 0.0069170 +/- 0.0004820 dr_a = -0.0760780 +/- 0.0346330 => r_a = 2.213922 +/- 0.0346330 ss_a = 0.0320830 +/- 0.0076460 Reduced chi-square : 466.198889482 R-factor : 0.000652086 Measurement uncertainty (R) : 0.000306860 2) nSCF: S02 = 0.7977480 +/- 0.0758730 d_E0 = 1.1833490 +/- 0.8799960 dr_e = -0.0448740 +/- 0.0057950 => r_e = 1.955126 +/- 0.0057950 ss_e = 0.0051430 +/- 0.0008710 dr_a = -0.0107380 +/- 0.0451450 => r_a = 2.279262 +/- 0.0451450 ss_a = 0.0338300 +/- 0.0138210 Reduced chi-square : 2078.758619285 R-factor : 0.003396526 Measurement uncertainty (R) : 0.000306860 3) SS: S02 = 0.8082010 +/- 0.0866670 d_E0 = 1.1847890 +/- 1.6045490 dr_e = -0.0329940 +/- 0.0067630 => r_e = 1.957006 +/- 0.0067630 ss_e = 0.0049640 +/- 0.0008280 dr_a = -0.0959300 +/- 0.1364220 => r_a = 2.194070 +/- 0.1364220 ss_a = 0.0460070 +/- 0.0358600 The nSCF and SS results are very similar but some SS errors are significantly larger. Therefore I will base my comments and comparisons on the SCF and nSCF results. As you can see, the structural parameters are pretty much within error! S02 and d_E0 however, differ quite a lot. Although the d_E0 of 1.18 from the nSCF seems more reasonable than the -7.58 value from the SCF, the SCF fit is much better (lower reduced chi-square and R-factor). The S02 values are not within error. My problems are, then, two-folded: The first is a practical one: I don't know which S02 and d_E0 to pick and it is really bad because nailing them down (specially S02) is the whole purpose of the analysis of this standard. The second problem is of philosophical nature and more important than the first one because its clarification will provide the answer for the first problem and also some peace of mind. I do not understand why the E0 corrections (d_E0's) are so different. The fact that the correction obtained from SCF calculation is larger (and apparently worse) than that obtained from the nSCF calculation (absolute values) seems counter intuitive to me. The E0 value I picked for background subtraction is 8989 eV, and applying the corrections, I find an edge energy of 8990.1 eV and 8981.5 eV respectively. This second value falls in the pre-edge region, pretty much on the 1s-3d transition bump. Despite the evidences, I tend to trust the SCF's d_E0 value the most but would like to understand the physics (or lack of) behind the different feff calculations! I apologize if I bored you with unecessary details! Thank you very much for your attention and willingness to help! I really appreciate it! Best regards, Igor Anatoly Frenkel wrote: Dear Igor, I am getting back to your question now. It would help if I knew what E0 value you are getting. What is the value of s02 that you are obtaining? How are you modeling the Cu2+ standard compound? Are you using a bulk reference of a Cu-O bond (e.g., by using CuO oxide, or you are using a method in one of the IFEFFIT posts that I suggested (by using SS and OVERLAP cards)? If you tried one but not another, it is important that you compare them because the small clusters have all sort of truncation effects that cumulatively change photoelectron scattering amplitude and phase from those in the bulk. If both models produce similar FEFF paths for the first nearest Cu-O distance, it does not matter which one to choose in order to fit the standard compound. If they are different, use them separately when you fit the EXAFS data, and see which one gives you a more reasonable values of s02 and E0. I'll wait until I have a feedback from you because without knowing exactly what you are doing it is hard to give advice on what to do. From my experience with different Cu2+ complexes, these systems can be reliably analyzed. Let me know where you are getting stuck. Regards, Anatoly [Anatoly Frenkel] From: Igor Frota de Vasconcelos [mailto:idevasco@nd.edu] Sent: Wednesday, January 26, 2005 12:16 PM To: Frenkel, Anatoly Subject: About Cu2+ xafs Dear Dr. Frenkel, I am Igor Vasconcelos and I work under the supervision of Dr. Bruce Bunker at the University of Notre Dame's Physics department. I am currently working with some XAFS data on Cu(II) adsorbed on bacterial cell walls. I started out with (Cu(H2O)6)+2 standard to have a better feeling about the Cu+2 systems and to obtain a reliable estimate of S02 to use in the samples' fits. I am using SCF FEFF8.20 paths to fit the data and, although structural parameters make sense, I have exhausted my resources and still haven't understood a rather strange Eo value I am getting. I suspect it has to do with the way feff performs the calculations. I understand you have an extensive knowlegde on this system and I am hopeful you will be willing to provide me some help. I have followed recent posts in the ifeffit mailing list from you and I have two of your papers (Env. Science Tech. 1998 and 2000) on the subject as references. I would be very grateful if you would take the time to receive my question and answer it, in case you have the time and the inclination. I am looking forward to hearing from you. Thank you in advance for your attention, Igor -- IGOR F. VASCONCELOS Department of Physics University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556 USA phone: (1 574) 631 5650 fax: (1 574) 631 5952 e-mail: idevasco(a)nd.edu www.nd.edu/~idevasco -- IGOR F. VASCONCELOS Department of Physics University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556 USA phone: (1 574) 631 5650 fax: (1 574) 631 5952 e-mail: idevasco(a)nd.edu www.nd.edu/~idevasco

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Debye-Waller factors for metal oxides ?
by TAO,Ye 09 Feb '05

09 Feb '05

Dr.Rehr mentioned the calculation of DWs using spring constants with the equation-of-motion method(EM) and the recursion method(RM). I wonder if these two methods can be incorporated into ifeffit like Debye and Enstein model. I use EM to calculate the DWs for metal complex molecules, and they work pretty well for a preliminary analysis, but I have to input the calculated DW factors into Artemis one by one manually :-( Ye

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DW Factor follow up
by Ian James Drake 07 Feb '05

07 Feb '05

> Hi, > > Thank you for all this valuable information. > > Can I make a general statement in comparing the DW of metal and its crystalline oxide at a given >temperature? For example, I find the DW for Al metal to be 0.015A in the first scattering path >(Al-Al) at 25C (using correlated Debye model). However, the fitted value of the DW for Al oxide >in the first path (Al-O) was 0.001 A. In both fits, the CN was set to a constant since it is >known from other techniques. Can a general statement be made comparing relative magnitudes of >metal-metal DW and metal-oxygen DW-factors? > > Is there a good general resource for the Debye temperatures of metal oxides, like zeolite or >Al2O3? > > Thank you again for all your guidance. > > Ian Drake

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RE: [Ifeffit] Debye-Waller factors for metal oxides ?
by Kelly, Shelly D. 07 Feb '05

07 Feb '05

I agree with John Rehr. With a temperature dependent data set, the best model that I have found is to allow each atom pair to have a thermal and static disorder component. Sigma2 = debye(Temp,Td_O1) + stat_O1 (This example is for the first oxygen (O1) shell of the metal oxide) The static disorder component should be the same for all data sets from the same sample at the different temperatures. The thermal component should increase as the temperature increases. If you are lucky a Debye or Einstein model will work well enough. You will have to test both. In addition, the thermal change in sigma2 should be about the same for different samples that are closely related. (We could argue about this last point. The best thing to do is to test this constraint by first not imposing it and determine within the uncertainties in the measurement, if it is true. I have found that it usually is an okay constraint.) In the end, you simultaneously model the temperature dependence and the sample dependence spectra all together. You constrain the static disorder term to be independent of temperature, and you constrain the debye temperature to be independent of sample change. This should impose enough constraints on sigma2 values to accurately look at changes in coordination number. Of course the coordination numbers do not change as a function of temperature but only as a function of sample changes. HTH Shelly Shelly Kelly ---------------------------- skelly(a)anl.gov Bldg 203, RM E113 phone: (1) 630-252-7376 Argonne National Laboratory fax: (1) 630-252-9793 Argonne, IL 60439 www.mesg.anl.gov > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of John J. Rehr > Sent: Monday, February 07, 2005 10:07 AM > To: XAFS Analysis using Ifeffit > Cc: John J. Rehr > Subject: Re: [Ifeffit] Debye-Waller factors for metal oxides ? > > > > The lack of accurate Debye-Waller factors in complex materials, like > metal oxides, can be a real problem. In my view, simple phenomenological > methods like correlated Debye and Einstein models can't always be trusted. > > There is an alternative approach to fitting DW factors in such systems > which might be useful. The idea is to fit a few spring constants k_ij > between > the atoms, rather than the DW factors themselves, e.g., for the most > important > sites. This is efficient since the spring constants are temperture > independent. This has been tested by Rossner et al. using their Bayesian > approach [Rossner, H. H. and Krappe, H. J., (2004). Phys. Rev. B 70, > 104102] > The fitting is does via an analytical formula for the Debye-Waller factors > based on a fast recursion method [Poiarkova, A. V. & Rehr, J. J. (1998). > Phys. Rev. B 59, 948]. > > Of course, such an approach still misses contributions to the DW factors > due to structural disorder, which are addititive. > > J. Rehr > > > > On Sun, 6 Feb 2005, Ian James Drake wrote: > > > Hi, > > > > There is little discussion over the significance of fitted Debye-Waller > > factors (ss2) found for metal centers in metal oxides of heterogeneous > > catalysts. I am searching for a better way of determining how > reasonable > > these values are in the fits I get. > > > > 1. Are phenomenological models like the correlated Debye model and > Einstein > > model appropriate? It seems that Debye temperatures are hard to find for > > oxides. > > > > 2. Is there an equivalent value for ss2 in x-ray crystallography data > that I > > can refer to for comparison in these materials? What should I look for > in > > reviewing published x-ray crystallographic data? > > > > 3. Is the temperature dependence reported for the ss2 for some metals > (like > > Cu and Al) similar to their respective oxides? For example, in Debye- > Waller > > factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: > > Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three > > between 25C and 300C. Would I expect a factor of three increase in > > crystalline zeolites (AlO4 structural units). > > > > 4. Specific to my work: I have studied Al containing oxides at > temperatures > > between 25 and 300 C. I would like to quantify coordination changes > by > > doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at > temperature > > and I observe no change in the broadening of the data. Likewise, the > fitting > > shows no sensitivity in the Debye-Waller factor. It is nearly constant > at > > 0.001 A over the temperatures of interest. Since ss2 and the > coordination > > number (CN) are correlated, I would like a way to bind the error on the > > fitted CN by modeling real physical changes in the Debye-Waller factors. > Do > > you have any suggestions? > > > > Looking forward to your thoughts. > > > > Ian Drake > > Graduate Student > > UC Berkeley > > _______________________________________________ > > 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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EXAFS sample prep
by Kelly, Shelly D. 02 Feb '05

02 Feb '05

Hi Ritika, I hope you do not mind, I'm sending this to the Ifeffit mailing list since others might be interested as well. This email message is about how to prepare an EXAFS sample. We are talking about measuring a Ti-edge from some sample in solution. But any edge and any sample in any matrix will also work just file. You want to set-up your sample so that you have a lot of Ti atoms in the path of the x-ray beam. This is because the EXAFS signal comes from the adsorption from the Ti atoms. Hence more Ti atoms give more adsorption events resulting in a smaller statistical error in the EXAFS spectra. BUT..... In transmission mode the EXAFS signal comes measuring the number of x-rays incident on the sample and transmitted through the sample. If all the x-rays are adsorbed by the Ti atoms in the sample then you do not have any transmitted x-ray signal. Hence you get really noise data because you have no statistically significantly transmitted x-ray signal. So you need your sample to be thin so that a lot of the x-rays pass through the sample such that you have something to measure. In fluorescence mode the EXAFS signal comes from the x-rays emitted by the Ti atoms as the core hole is re-filled. These emitted x-rays need to escape the sample without being re-adsorbed by the sample. Hence the sample needs to be dilute for fluorescence mode measurements. When you make a measurement in fluorescence mode it is always best to collect the transmitted x-ray signal as well. Then you can make a comparison to see if "self adsorption effects" are small. Transmission measurements typically have better signal to noise ratio than fluorescence measurements. So if you can, make your measurements in transmission mode. You can use Tkatoms or Artemis to calculate the best sample thickness and the best concentration to use for the measurements and which EXAFS mode will work best for your samples. >From the components of your sample you can calculate the thickness of the sample that will give 2.5 adsorption lengths. The transmitted x-ray intensity is given by the incident x-ray intensity multiplied by the exponential of the absorption coefficient times the sample thickness. I = I0 * exp(-mu(E) * x) Where I is the transmitted x-ray intensity I0 is the initial x-ray intensity Mu(E) is the absorption coefficient = weighted sum of absorption coefficient from each atom in the beam. X is the thickness of the sample. IF mu(E) * x = 2.5 then the percent of transmitted x-rays is about 10% of the incident x-ray intensity. This is just enough at NSLS where the incident x-ray intensity will be about 10^6 x-rays per second. This means that 10^4 x-rays per second will hit your transmitted Ion chamber. You want to make the transmitted ion chamber adsorb all (99%) of theses x-rays. Then your statistical error in the measurement will be 1/sqrt(N) or 1/sqrt(10^4) or 1%. You need to have at least this many x-rays to measure. At the beam line you measure the total absorption edge. The EXAFS signal, if you are lucky, makes up about 10% of the absorption edge. Hence you need to have a statistical error of no more than 1% to make a measurement. If you can make the sample thinner then you do even better. Now for the other problem: You want to get as many Ti atoms into the sample with a total sample thickness of 2.5 absorption lengths. To do this part you need to calculate the absorption of just the Ti atoms in the sample. I call this delta_mu(E). If you can get the delta_mu(E) * x to be between 0.1 and 1.0 with the total absorption of the sample below 2.5 then you can make the measurement in transmission mode. This means that between 10% and 70% of the absorption in the sample will be due to the Ti atoms. This is enough to get a good transmission signal. If you adsorption from the Ti atoms in the sample is between 1% and 10% then you will hope to make the measurement in fluorescence mode. Now for the practical part: Say you have a solution with 1% Ti-stuff in water by NUMBER of atoms. If you usually work by weight then you need to convert to number for this calculation. Take the feff.inp file for Ti-stuff. Look at the top of the file. You should find total_mu(E) (absorption of the entire sample at the Ti edge), and delta_mu(E) (absorption of Ti atoms at the Ti-edge). Then use Hephaestus to calculate the total_mu(E) for water at the Ti edge energy. To get the total absorption you need to calculate the weighted average for water and Ti-stuff. See how thick you can make your sample and satisfy the criteria for less than a total absorption length of 2.5. (99%_by_number_water_atoms * total_mu(E)_for_water + 1%_by_number_Ti-stuff * total_mu(E)_for_Ti-stuff ) * sample_thickness = 2.5 Once you have that thickness then you can see what the absorption for just the Ti atoms is. 1%_by_number_Ti-Stuff*delta_mu(E)_for_Ti * sample_thickness = absorption_length_for_Ti And then you can figure out if you have a fluorescence or transmission experiment. Absorption_length = 0.1 to 1.0 you have transmission. Absorption_length=0.01 to 0.1 you have fluorescence. Usually you have to go around and around with this sort of calculation to optimize the conditions for the measurements. Hope that Helps Shelly

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RE: [Ifeffit] Two edge problem (in the same scan)
by Kelly, Shelly D. 26 Jan '05

26 Jan '05

> -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel > Sent: Wednesday, January 26, 2005 1:30 PM > To: asg2(a)lehigh.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Two edge problem (in the same scan) > > > Hello everybody, > > I have a question/problem. Last year during the EXAFS course at NSLS, I > > had requested Bruce if it is possible to analyze the data with two > > edges. For example, I have the data for As and Se K-edges, which I > > collect in the same scan. In WinXAS program, I can section the edges and > > analyze them separately. At that time, the program was not able to > > perform these edges or the sectioning. Have we reached this possibility. > > I tried again using the latest updated Athena, but it seems not to be > > working. Can you please tell me whether the sectioning or dealing with > > two edges in the same spectra can be done > > I don't unfderstand why "sectioning" is necessary. What precludes you > from reading the data set a second time and setting e0 to be appropriate > for the second edge? Then your pre- and post-edge lines will be made > using the second e0 and everything else should just follow normally. > > I understand that Athena does not have a way to specify the second edge in > the column selection dialog, but that seems to me like an inconvenience > more than a real limitation. It is an inconvenience because you then have > to specify the second e0 by hand rather than have Athena's magic find it > for you, but is that really so hard? > > B > [Kelly, Shelly D.] Another feature that I have found useful for data with multiple edges is the truncate function. Once you read the data set into Arthena. Make a copy of the data set. Choose your e-zero for each data set. And then truncate the data sets to the "normal" range. This will help with some of the automatic presets, which use the full data range by default, and can give you a very scary initial background function. SK

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Two edge problem (in the same scan)
by Ashtosh Ganjoo 26 Jan '05

26 Jan '05

Hello everybody, I have a question/problem. Last year during the EXAFS course at NSLS, I had requested Bruce if it is possible to analyze the data with two edges. For example, I have the data for As and Se K-edges, which I collect in the same scan. In WinXAS program, I can section the edges and analyze them separately. At that time, the program was not able to perform these edges or the sectioning. Have we reached this possibility. I tried again using the latest updated Athena, but it seems not to be working. Can you please tell me whether the sectioning or dealing with two edges in the same spectra can be done Ashtosh

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[DATA-REQUEST] Platinum standards
by MauRo 24 Jan '05

24 Jan '05

Hi to all, I'm looking forward for some EXAFS (transmission or fluorescence) spectra of Platinum oxide and Platinum carbide at L_III and/or L_I edge. Is there anyone who has taken this data and is so kind to send them to me? Thanks, Mauro

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Increase NOVP error message meaning
by Paul Fons 23 Jan '05

23 Jan '05

I am trying to run feff on some chalcogenide structures that have rather nearest-neighbor long bond lengths, e.g. > Bond search from target site: Te1 > ...found 6 atoms within 0.00 - 3.20 A of this site > > ------------------------ > dist [Å] atoms > ------------------------ > 1. 3.0488 6 > ------------------------ > Bond search complete When I use this structure in feff82, I get the rather mysterious error INCREASE NOVP: > > Calculating potentials ... > free atom potential and density for atom type 0 > free atom potential and density for atom type 1 > free atom potential and density for atom type 2 > free atom potential and density for atom type 3 > initial state energy > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > tell authors to INCREASE NOVP Being an experimentalist, I did increase novp until the previous error message stopped, however this resulted in a core dump: > Calculating potentials ... > free atom potential and density for atom type 0 > free atom potential and density for atom type 1 > free atom potential and density for atom type 2 > free atom potential and density for atom type 3 > initial state energy > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > iph, rnrm(iph)*bohr, rmt(iph)*bohr, folp(iph) > 0 1.76126E+00 1.74898E+00 1.01667E+00 > 1 1.71891E+00 1.63874E+00 1.12886E+00 > 2 1.35785E+00 8.69242E-01 1.15000E+00 > 3 1.78418E+00 1.76792E+00 1.02193E+00 > mu_old= nan > Done with module 1: potentials. > Calculating LDOS ... > LDOS calculation for specified grid > Calculating energy and space dependent l-DOS. > It takes time ... > potential type 0 > Segmentation fault (core dumped) When running the equivalent file in feff6, I get the > Calculating potentials and phases... > free atom potential and density for atom type 0 > free atom potential and density for atom type 1 > free atom potential and density for atom type 2 > free atom potential and density for atom type 3 > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > phase shifts for unique potential 0 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > phase shifts for unique potential 1 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > phase shifts for unique potential 2 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > phase shifts for unique potential 3 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > Preparing plane wave scattering amplitudes... > nncrit in prcrit 9 This message seems similar to the troubleshooting section in feff8 for which it states: • Non-physical, widely spaced distributions of atoms. Symptoms of this common problem are very large muffin-tin radii (see the header of any ‘.dat’ file) and possibly a failure of the phase-shift program to converge. This gives error message hard test fails in fovrg. How to I avoid this problem (obviously the crystal structure is a given!). I tried the INTERSTITIAL card, but to no avail. Any suggestions are welcome. Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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Windows update for athena/artemis
by Matt Newville 18 Jan '05

18 Jan '05

Hi, I've built a Windows update file to upgrade to the latest versions of Athena and Artemis. Since Bruce is off-line for a while and since there is no easy way for us to make these executables, there is not much we'll be able to do if there is a problem with this version. Because of this, I am NOT releasing this as a normal update yet, but would like the braver of you to download and install this update by hand and give the new versions of Athena and Artemis a test drive. The update file is at http://cars9.uchicago.edu/ifeffit/updates/ifup_013.zip which is just a simple zip file that can be unpacked in your Ifeffit folder. (Probably C:/Program Files/Ifeffit). If you're willing to try these versions, please let me know how it goes. I'll wait until I hear some positive responses before I make a general update release that would automatically update everyone to these versions. Thanks, --Matt

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RE: [Ifeffit] Some questions about ATOMS and FEFF
by Barton, David (DG) 16 Jan '05

16 Jan '05

Patrick, Welcome to the mailing list! This list is an excellent forum for newcomers and veterans alike. > 2) Running the FEFF6 software directly or through the Artemis > bundle, I never get any "chi.dat" output file as a weighted sum of the > individual This feature is built into Artemis. After you run the FEFF calculation with Artemis and choose which paths to import, just highlight the paths in the DATA & PATHS window that you would like to sum and then choose DATA-->SUM OF PATHS-->SELECTED DATA PATHS from the menu. This will produce the chi(k) sum which can be plotted along with your data set. A shortcut to this menu item can also be found by right-clicking on the selected paths and choosing DATA-->SUM OF PATHS-->SELECTED DATA PATHS. I often use this feature to get a rough feeling for the relative contributions of each path in the calculation by plotting the SUM along with all of the individual paths. Have Fun, Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Ph: (989) 636-4753 Fax: (989) 638-6225 Email: dgbarton_remove_me(a)dow.com > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Patoo > Sent: Sunday, January 16, 2005 9:07 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Some questions about ATOMS and FEFF > > > Hi, > > I am just starting to work with the ARTEMIS/ATHENA software suite for > EXAFS data processing and analysis and a newcomer in this > mailing list. This project is really very nice and useful for > the EXAFS community and > I really enjoy to learn how to use it. > I read most of the documents which are available on the website and > around, but I have already two questions : > 1) in the "feff.inp" command file, what are the options of the cards > CONTROL and PRINTS > 2) Running the FEFF6 software directly or through the Artemis > bundle, I > never get any "chi.dat" output file as a weighted sum of the > individual > "feffNNNN.dat" individual path contribution. Is there any forgotten > option to get it ? > > Thanks in advance for your help > > Patrick > > -- > *********************************************************** > Dr. Patrick Judeinstein > R.M.N. en Milieu Orienté, (UMR 8074), Bâtiment 410 > I C M M O (Institut de Chimie Moléculaire et des Matériaux d'Orsay) > Université Paris-Sud, 91405 Orsay Cedex - France > Tel : +33 (0)1 69 15 70 17 ou ++ 33 (0)1 69 15 47 68 ; Fax + > 33 (0)1 69 15 81 05 > > e-mail : pjudeins(a)icmo.u-psud.fr > web site : http://patoo.hope.free.fr > > *********************************************************** > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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Some questions about ATOMS and FEFF
by Patoo 16 Jan '05

16 Jan '05

Hi, I am just starting to work with the ARTEMIS/ATHENA software suite for EXAFS data processing and analysis and a newcomer in this mailing list. This project is really very nice and useful for the EXAFS community and I really enjoy to learn how to use it. I read most of the documents which are available on the website and around, but I have already two questions : 1) in the "feff.inp" command file, what are the options of the cards CONTROL and PRINTS 2) Running the FEFF6 software directly or through the Artemis bundle, I never get any "chi.dat" output file as a weighted sum of the individual "feffNNNN.dat" individual path contribution. Is there any forgotten option to get it ? Thanks in advance for your help Patrick -- *********************************************************** Dr. Patrick Judeinstein R.M.N. en Milieu Orienté, (UMR 8074), Bâtiment 410 I C M M O (Institut de Chimie Moléculaire et des Matériaux d'Orsay) Université Paris-Sud, 91405 Orsay Cedex - France Tel : +33 (0)1 69 15 70 17 ou ++ 33 (0)1 69 15 47 68 ; Fax + 33 (0)1 69 15 81 05 e-mail : pjudeins(a)icmo.u-psud.fr web site : http://patoo.hope.free.fr ***********************************************************

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re:fits
by k-kupiecki＠northwestern.edu 15 Jan '05

15 Jan '05

Thank you Bruce and Shelley! I just wanted to thank Matt, Bruce and everyone involved with IFEFFIT/Artemis/Athena... it has been a Godsend.... I couldn't have stumbled on it at a better time (I'm frantically trying to analyze about 4 beamtimes worth of SEXAFS data for papers and my thesis and WINXAS wasn't really working out for me)!!!!! Does anyone have any suggestions for additional literature in regards to better understanding the quality of fits and the parameters involved?.... or perhaps know when we might be able to expect a updated version of the Artemis literature? (What is currently there has helped me sooo much that I've been checking for an update every couple of weeks hoping to get see sections 2.2-3.2..... ) Also.... I guess I've realized that only knowing IFEFFIT with Artemis I kinda take things for granted (like I didn't know that IFEFFIT was having problems, in certain cases since I had only been checking the "Results" and the error messages on the bottom of the window....) which meant I missed errors like this in the IFEFFIT (since I didn't notice anything unusual in the "Results"): ............ # Do the fit! ## fitting difference of Cov_0_06ML_bl1435_111703.chi and one or more paths ... ## === data set #1 of 1 feffit(1-8, group=data0_fit, chi=data0.chi, k=data0.k, kweight=2.00, rmin=1, rmax=4, kmin=2.5, kmax=15, dk=2, kwindow=kaiser-bessel, fit_space=R, do_bkg=no, data_set=1, data_total=1) feffit fitting 1 data sets fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... no uncertainties estimated! fit gave a warning message: too many fit iterations. try again with better guesses or a simpler problem. ............................................... I guess my question is.... is there anything else I should be looking for in the IFEFFIT printout that I might not otherwise notice by just using Artemis and looking at the error messages and "Results"? Thanks for the input! Sincerely, Kristine Witkowski Northwestern University

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another bug
by Norbert Weiher 13 Jan '05

13 Jan '05

Hi Bruce, sorry to bother again - here's the issue: I fit a given spectrum say in kw=2, choose as plotting option "kw". If I plot the fit and the data, only the data gets the correct kw, the fit is displayed with kw=1. If I select kw=1,2 or 3, everything is fine. The problem exists also when exporting the fits to a file... I noticed this in diana and artemis... Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (norbert.weiher(a)manchester.ac.uk) School of Chemical Engineering and Analytical Science Sackville Street, Manchester, M60 1QD - Phone: +44 161 306 4468

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horae-048 with Athena 0.8.037 and Artemis 0.7.014/DR008
by Bruce Ravel 13 Jan '05

13 Jan '05

Hi folks, I just released the latest source tarball for linux, unix, and Mac OSX. Copies can be found on SourceForge and on my web site. A windows updater and Carlo's debian packages should follow soon. A new windows executable of the development version of Artemis can be found along with some notes on its use at http://leonardo.phys.washington.edu/~ravel/software/exafs/diana/ This is mostly a bug fix release. I have addressed almost all of the problems reported in the last 10 days on the mailing list. (I think the lone exception is the control-click problem Paul reported yesterday.) Additionally, I have added a new feature to the development version of Artemis. In the Theory menu, you can now find an entry that reads "Quick first shell theory". This is in response to the thread started by Carlo the other day. This prompts you for a concise description of a single shell scattering problem -- absorber and scatterer species, distance, coordination geometry, edge -- and produces a quick-n-dirty feff calculation suitable for a quick-n-dirty first shell fit. I wrote a document page -- just click on the document button at the bottom of the quick first shell theory dialog. Try it out -- it should make sense once you poke at it a bit. As I said yesterday, this release is probably the last one for at least a couple of months. There is some chance that I might update the source code tarball in that time, but I lose my ability to make windows executables tomorrow. I am keeping my fingers crossed that the windows executables that I just built and that will be in the next updater will prove to be solid. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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personal news
by Bruce Ravel 12 Jan '05

12 Jan '05

Hi! I wanted to let all the good folks on the mailing list know about an imminent change in my life. This coming Friday will be my last day with my current employer, the Naval Research Lab. I will be taking a 7-week vacation, then starting a new position at Argonne working in the Environmental Research Division. My responsibilities there will include helping to build an XAS station on the Sector 10 bending magnet. My new boss knows all about the software and has encouraged me to continue working on it. Yay! For the coming 7 weeks, I'll only be posting to the mailing list sporadically. For two of those weeks, I will be traveling for fun outside of North America and I have no intention of looking at a computer during that time! Before the end of the week I intend to have a new source code tarball and new Windows executables of Athena and both versions of Artemis. Until I am settled in at the new job, it is unlikely I will update the codes, even in the event of a serious problem. Once I get to Argonne in early March, I look forward to meeting all of you whom I do not know and who pass through the APS. A period of transition is an excellent opportunity to look back upon and evaluate recent times. The last three years in which I have been working on the programs have been some of the most rewarding of my career. It has been enormously gratifying to see so many people get involved in my efforts at the level of sending me bug reports and feature suggestions and working with me to improve the quality of the codes. And it has been enormously fun to see this mailing list grow into a real community populated by some of the friendliest, smartest, and most helpful people that I know. Many of you have made a real impact on the product of my three years of labor. I am thankful for that and I hope that you see a bit of yourselves every time you fire up the codes. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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look what happens when you go away for a day!
by Bruce Ravel 12 Jan '05

12 Jan '05

Hi! Yesterday I spent the day away from the office. This morning I saw an impressive number of bugs and other issues reported in the short span that I wasn't paying attention. ;-) ** Mauro mentioned a problem changing between the raw and column views of a log file. I cannot reproduce this behavior. Mauro, can you send me a project file that demonstrates this? ** Paul mentioned a number of problems regarding data import. At least one of them seems to be the same problem Michel Jaouen mentioned in private email the day before. Matt, in his response, explained the problem exactly. Silly bug by me. ** Chachi mentioned a confusing error message from Feff. Matt explained the situation. The next versions of both the stable and development branch of Artemis will issue a much clearer error message in the situation Chachi reported. I will make a new release of the source code tarball this week. A windows updater package will follow shortly. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Bug in Artemis Rename horae-047
by Paul Fons 12 Jan '05

12 Jan '05

Thanks for the new version Bruce -- here is a quick bug report: I was bitten by a rename bug in diana (not carefully documented yet) so I tried artemis thinking things would be smoother. Upon renaming a feff calculation in artemis (horae-047), the rename window opens (I used the control key to make the pop up menu appear and chose the rename this feff calculation from there), and I enter the new name. Good. Wait, the rename window opens again (with the default name FEFFx -- where x is the original name of the calculation). I get an error when I try entering the name again (noted below). The changed name is already reflected in the list on the right after the first renaming. Something similar happened in diana as well. This should be easy to reproduce, let me know if you need more details. Paul <Key-Return> (command bound to event) at /Applications/Ifeffit/bin/artemis line 1586 main::__ANON__('Tk::Error: Can\'t call method "focus" on an undefined value a...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) line 488 Tk::Error('MainWindow=HASH(0x1e04a58)', 'Can\'t call method "focus" on an undefined value at /Applicat...', '<Key-Return>', '(command bound to event)') called at /Applications/Ifeffit/bin/artemis line 13619 eval {...} called at /Applications/Ifeffit/bin/artemis line 13619 main::Echo('There is already a Feff calculation named "Sbcore"!') called at /Applications/Ifeffit/bin/artemis line 13631 main::Error('There is already a Feff calculation named "Sbcore"!') called at /Applications/Ifeffit/bin/artemis line 4673 main::rename_feff() called at /usr/local/lib/perl5/site_perl/5.8.6/darwin-2level/Tk.pm line 247 eval {...} called at /usr/local/lib/perl5/site_perl/5.8.6/darwin-2level/Tk.pm line 247 Tk::__ANON__('Tk::Menu=HASH(0x1ea6660)', 'active') called at /usr/local/lib/perl5/site_perl/5.8.6/darwin-2level/Tk/Menu.pm line 531 Tk::Menu::Invoke('Tk::Menu=HASH(0x1ea6660)', 1) called at /usr/local/lib/perl5/site_perl/5.8.6/darwin-2level/Tk.pm line 406 eval {...} called at /usr/local/lib/perl5/site_perl/5.8.6/darwin-2level/Tk.pm line 406 Tk::MainLoop() called at /Applications/Ifeffit/bin/artemis line 1796 Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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ARTEMIS export error
by Norbert Weiher 12 Jan '05

12 Jan '05

Dear Bruce, just tried to export some data to a file using the "save selected groups as" command. He gives me the message "You cannot save more than -2 groups to a single file". That's a step back compared to the limit of 15 I we had before :) Went quickly through some of my fits - but it is the same everywhere. I attached an example file. Hope it helps... Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (norbert.weiher(a)manchester.ac.uk) School of Chemical Engineering and Analytical Science Sackville Street, Manchester, M60 1QD - Phone: +44 161 306 4468

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RE: Ifeffit Digest, Vol 21, Issue 17
by crojasa＠unmsm.edu.pe 11 Jan '05

11 Jan '05

Hello. When i run feff on artemis, for a FeCo system , It appears a error message: Feff 6L.02 Fatal error : To many atoms in ATOMS list . Maximum is 5000 Which is the problem, Feff6 not support above 500 atoms?? wait your replys Chachi

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How does AUTOBK handle the pre-edge background removal?
by hsnuboy＠ksu.edu 11 Jan '05

11 Jan '05

Dear Ifeffit list, There is one question I don't understand very well. How does AUTOBK algorithm handle the pre-edge background removal? I check the mannual of using ATHENA and the paper, "Near-edge x-ray-absorption fine strructure of Pb: A comparison of theory and experiment", M. Newville, et al., Phys. Rev., B47:21 (1993), 14126. Both of them have no information about dealing pre-edge background removal with AutoBK and how is it work within Athena? Hence, I ask this qustion for all the experts on the list. Thank you for your help. Sincerely, Yu-Chuan Lin Research Assistant Dept. of Chemical Engineering Kansas State University

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new release of Athena and Artemis
by Bruce Ravel 11 Jan '05

11 Jan '05

Happy New Year everyone! To welcome in the new year, I have made a new release of my codes. There are several changes in Athena, some improvement to the development branch of Artemis, and a few bug fixes to the stable branch of Artemis. Source code tarballs are now available at SourceForge and on my website. Complete lists of changes are available at http://leonardo.phys.washington.edu/~ravel/software/exafs/notes/ A Windows updater package will be available soon. The biggest new feature in Athena is a dialog for doing self absorption corrections. I coded up four different algorithms and made it easy to switch between them so you can compare different approaches to the problem. The document page built into Athena has all the details. Among the other new features are linear combination fits of standards to data using chi(k) spectra, an option for using the smoothed derivative to align or calibrate data, and lots of bug fixes and minor improvements to the user interface. The new releases of Artemis are all about bug fixes. Several recently reported problems were fixed in the stable branch and many lingering problems from the previous release of the development branch have been fixed. I wrote a few short web pages introducing all the new features in the development version of Artemis. Here's the link: http://leonardo.phys.washington.edu/~ravel/software/exafs/diana/ It's mostly screenshots and terse descriptions, but hopefully you'll find it useful. For the Windows users out there, I built a Windows executable of the development version for the first time. There is a link to it on that web page along with instructions for how to install it. I am eager to get more feedback from users about the development version so I can start thinking about moving it back down to the stable branch. Special thanks this time to all the people who were at my class at the Canadian Light Source User's Meeting in November. Many of the improvements to this release of Athena were suggested or inspired by Canucks. Thanks! B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Postdoctoral position
by Matt Newville 07 Jan '05

07 Jan '05

OK, here's another postdoc opening, this from Tom Trainor at University of Alaska, Fairbanks (fftpt(a)uaf.edu) ------------------------------------------------------------ A Postdoctoral Position is available in the Department of Chemistry and Biochemistry, University of Alaska Fairbanks, to study the structure and reactivity of hydrated metal-oxide surfaces. The successful candidate will be part of ongoing studies focused on understanding the structure of metal-oxide surfaces and the relationship between structure and reactivity in aquatic environments using synchrotron based x-ray scattering/spectroscopy (surface diffraction, x-ray absorption fine structure and x-ray standing waves) and complimentary scanning probe microscopy and computational techniques. The position involves close collaboration with members of a diverse research group emphasizing the connection between experimental studies and theoretical simulations. A strong background in mineral/fluid interface chemistry or metal-oxide surface chemistry and previous experience with synchrotron based x-ray methods is desired. Application details can be found at http://www.uaf.edu/uafhr/Employment/Job1204-477.html . Please contact Tom Trainor (fftpt(a)uaf.edu) for additional information. The University of Alaska Fairbanks is an Equal Opportunity /Affirmative Action Employer. ------------------------------------------------------------ --Matt

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Re: postdoc opening
by Matt Newville 07 Jan '05

07 Jan '05

Hi Folks, I get a fair number of questions and notices about jobs and post-doc opportunities related to XAFS. So far, I've been reluctant to use this list for that purpose, but since there are many grad students and post-docs on this list, it seems that posting these to the mailing list could help everyone. So, here's a notice for a post-doc fellowship at LBNL, sent to me from Corwin Booth (chbooth(a)lbl.gov) http://actinide.lbl.gov/gtsc/JobDetails.htm Corwin also wrote: > The final candidate will work closely with one or more group > members on something related to actinide research. The group is > an actinide chemistry group, however there are opportunities to > work in solid state physics. Somebody interested in x-ray > absorption spectroscopy, x-ray scattering and/or magnetism of > f-electron systems would obviously be great for me, and I am > starting to focus on measurements in diamond anvil cells. We > have high-radioactivity labs, as well, so someone interested in > synthesis of actinide intermetallics could also make big > contributions. There are other opportunities, so an interested > person could contact me. If you know of any potential > candidates I would appreciate you forwarding them the ad or this > email. We plan on filling this position ASAP. Good luck!! --Matt PS: if anyone else would like to post job notices here, feel free.

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Fwd: News
by Bruce Ravel 07 Jan '05

07 Jan '05

Hi Folks, Can anyone here help Michel with his problems installing the latest horae on his Mac? Thanks, B ---------- Forwarded Message ---------- Subject: News Date: Friday 07 January 2005 06:11 am From: Michel Jaouen <Michel.Jaouen(a)univ-poitiers.fr> To: ravel(a)phys.washington.edu Previously I have updated all using sudo horea_update. At that date (september 2004) it creates a folder horae-042 with the attached log file. It fixes the problems I have mentionned previously: all run fine (artemis version number 07.013, athena version number 08.035). I have seen your mail concerning a new update (horae-047). So I do as previously: sudo horea_update. I receive in the terminal window a lot of informations related to the instal and at the end all seems OK. But when I run artemis in a terminal X window, I have the same version as previously. Looking in the Ifeffit folder I don't see an horea-047 folder nor a log file. The only change I found are in the bin folder where I have new artemis and athena files that are labelled as executable unix files but I can open by clicing on them as text files! So what happens here: I miss something I guess, but what? Any hints? Cheers Michel PS I don't obtain the new interface as quoted on your web server, so I suspect I have some install to do "by hands", but why it is different from the previous update? ------------------------------------------------------- -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Generating single scattering paths in Artemis
by Carlo U. Segre 06 Jan '05

06 Jan '05

Bruce: Occasionally, I don't know or don't care what the extended crystallographic environment of the absorber. All I want to do is apply single scattering analysis and I need some simple paths from FEFF. At this time, I can't see how to do this within Artemis since the Atoms page requires a space group and more information than I have available. Would it be possible to have the option for a simpler interface which just allows me to generate single scattering paths between two atoms at a specific distance from each other? Perhaps, I could even specify a coordination geometry (tetrahedral, octahedral, etc.)? Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Re: [Ifeffit] Generating single scattering paths in Artemis
by Frenkel, Anatoly 06 Jan '05

06 Jan '05

<<feff.inp>> Hello Carlo et al, FEFF6 allows to use SS cards that were specifically designed to calculate single-scattering paths in the case the structural details are not known, as in Carlo's case. I am attaching a working example where I used to calculate single scattering FEFF in Cu-O in octahedral coordination in Cu2+[H2O]6 complex. I included hydrogen in the input file since it affects charge on oxygen, but in principle it works. Some details are given in this article: http://pubweb.bnl.gov/people/frenkel/HUMIC-EXAFS/est.pdf You can run FEFF6 using attached file and note that it produces three files, each corresponds to the single shell of Cu-O atoms. Note the use of the OVERLAP card in the attached file, as well as the use of Bohr's radius to work around the bug in FEFF6 that uses distances in OVERLAP as multiples of Bohr's radius instead of Angstrems, while the units in SS card are in Angstrems. Regards, Anatoly Anatoly Frenkel, Ph.D. Associate Professor Department of Physics Yeshiva University 245 Lexington Avenue New York, NY 10016 http://www.yu.edu/faculty/afrenkel Office: tel. (212) 340-7827 fax (212) 340-7788 anatoly.frenkel(a)yu.edu Laboratory: tel. (631) 344-3013 frenkel(a)bnl.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 (DG) Sent: Wednesday, January 05, 2005 4:46 PM To: 'XAFS Analysis using Ifeffit' Subject: RE: [Ifeffit] Generating single scattering paths in Artemis Scott, > This can be fixed by editing the feff.inp file to remove the > Fe potential 1, but that's not enough--the oxygen scatterers > then have to have their potential renumbered to 1 to make > things work. That's a lot of work to do what should be simple. > > So I vote for changing the way Artemis works in such > circumstances so that less editing is needed: if the > absorbing atom is not present in the scattering list, then it > shouldn't have a second entry in the potential list. > I second this vote, since I also have had this same problem. New users could become quickly disgruntled by the Fatal Error message when attempting to put in simple systems or just by choosing a short cluster distance to only include the first shell in the FEFF calculation. At a minimum, it would be nice if Artemis trapped this error and reported a more friendly popup error message. Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit <<feff.inp>>

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Re: Generating single scattering paths in Artemis
by Webb, Samuel M. 05 Jan '05

05 Jan '05

Hi all... I know that this isn't necessarily an Artemis solution, but there is an option/module in SIXPACK (that other IFEFFIT interface) to do just what you've been asking about -- create simple single scattering paths between two atoms in a variety of coordination environments (tetrahedral, octahedral, etc). It has a nice periodic table interface to boot. I use it occasionally to do some quick and dirty fitting -- I do agree with Scott that its not always the most accurate way to go about things. The resulting FEFF file is placed in a FEFF folder in the sixpack root directory. Hope that helps some. Sam

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RE: [Ifeffit] Generating single scattering paths in Artemis
by Barton, David (DG) 05 Jan '05

05 Jan '05

Scott, > This can be fixed by editing the feff.inp file to remove the > Fe potential 1, but that's not enough--the oxygen scatterers > then have to have their potential renumbered to 1 to make > things work. That's a lot of work to do what should be simple. > > So I vote for changing the way Artemis works in such > circumstances so that less editing is needed: if the > absorbing atom is not present in the scattering list, then it > shouldn't have a second entry in the potential list. > I second this vote, since I also have had this same problem. New users could become quickly disgruntled by the Fatal Error message when attempting to put in simple systems or just by choosing a short cluster distance to only include the first shell in the FEFF calculation. At a minimum, it would be nice if Artemis trapped this error and reported a more friendly popup error message. Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D

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Athena & Artemis in Windows
by Peter Southon 22 Dec '04

22 Dec '04

Hello Windows people A few days ago Shelly suggested that Athena and Artemis don't work when installed in the directory "C:/program files/ifeffit/". This has always worked for me using XP, though I wouldn't be surprised if it caused problems in some earlier versions of Windows. Regarding Poorani's question about TRAP files, I have found it useful to put a shortcut to "C:/program files/ifeffit/horae/stash/ARTEMIS.TRAP" on my desktop or wherever for easy access. Cheers, Peter >Date: Fri, 11 Jun 2004 08:36:32 -0500 >From: "Kelly, Shelly D." <SKelly(a)anl.gov> >Subject: RE: [Ifeffit] Running FEFF >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <1C1577844A0BDF448E14E8CCB2F74424015A1B6D(a)ANLMAIL.anl.gov> >Content-Type: text/plain; charset="us-ascii" > >Hi Poorani, > >I believe that Athena and Artemis do not work properly when installed in >the C:/program files/ifeffit directory. The installation proceedures >say to specify C:/ifeffit instead. To fix if, but all of C:/program >files/ifeffit into the trash and then re-install. > >Shelly Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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RE: [Ifeffit] Using more than one E0
by Kelly, Shelly D. 15 Dec '04

15 Dec '04

Hey Scott, One correction, I botched this part: > -----Original Message----- > From: Kelly, Shelly D. > Sent: Wednesday, December 15, 2004 10:06 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Using more than one E0 > > Hi Scott, > > See below: > > The MS scheme you outline below seems to treat the E0 due to the > scattering species (I'll call that the "bonus" E0 for lack of a better > term) as being the average of the bonus E0's for all the scattering > atoms > in the path. Thus you give the Cu-O1-Cu1-Cu path as using the average of > the O1 and the Cu1 bonus E0's, while the Cu-O1-Cu-O1 path uses just the > O1 bonus E0. I would naively expect we should be using the sum, rather > than the average. After all, if this bonus E0 is a correction to the > shift caused by the muffin-tin potential FEFF has calculated, shouldn't > a > MS path that bounces off the same atom twice have to use twice the > correction? I feel like there's something basic I'm missing here... > > [Kelly, Shelly D.] The energy shift applies to the entire scattering > event. The scattering event can not be broken down into the sum of the > legs. [Kelly, Shelly D.] Most of the time, it is good to think about the scattering event as being a sum of the legs. If you follow this through you can see why the energy shift is an average rather than a sum. Take two sine waves and displace one from the other by a few eV. Then add them up. The total will have an energy shift that is in between the two that you started out with. --Hence an average rather than a sum. Hence the energy shift for the entire scattering event can be > approximated as an average of the energy shift from each leg. I have > used the average energy shift a lot and found that it works well. I > have never tried using a sum of the energy shifts... I think that in > an extreme limit you can convince yourself that the sum will break down > for an 8 legged paths. The energy shifts are "never" greater than 10 > eV. "never" in my experience. -Hence the answer to your next question. > > Also, what is your experience as to the actual differences in bonus E0's > that you get in ionic compounds? Right now one of my students is working > with Sr(NO3)2... should we really expect the difference in bonus E0's > between the Sr2+ and the oxygen atoms to be more than 12 eV, or does > some > kind of charge overlap from the nitrate ions actually make the strontium > ions behave as if they are less than +2? > > [Kelly, Shelly D.] One full electron of ionic bonding gives about 6 eV. > So that is about the most you would expect from different ions in a > solid. Usually, I have found 3 to 4 eV. You make up most of the > valence state change from the shift in the edge position. I have found > unrealistic energy shifts when I try to use too much chi(k) data at low > k. I'd look there first for you 12 eV shift. > > HTH > Shelly > > > _______________________________________________ > 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] Using more than one E0
by Kelly, Shelly D. 15 Dec '04

15 Dec '04

Hi Scott, See below: The MS scheme you outline below seems to treat the E0 due to the scattering species (I'll call that the "bonus" E0 for lack of a better term) as being the average of the bonus E0's for all the scattering atoms in the path. Thus you give the Cu-O1-Cu1-Cu path as using the average of the O1 and the Cu1 bonus E0's, while the Cu-O1-Cu-O1 path uses just the O1 bonus E0. I would naively expect we should be using the sum, rather than the average. After all, if this bonus E0 is a correction to the shift caused by the muffin-tin potential FEFF has calculated, shouldn't a MS path that bounces off the same atom twice have to use twice the correction? I feel like there's something basic I'm missing here... [Kelly, Shelly D.] The energy shift applies to the entire scattering event. The scattering event can not be broken down into the sum of the legs. Hence the energy shift for the entire scattering event can be approximated as an average of the energy shift from each leg. I have used the average energy shift a lot and found that it works well. I have never tried using a sum of the energy shifts... I think that in an extreme limit you can convince yourself that the sum will break down for an 8 legged paths. The energy shifts are "never" greater than 10 eV. "never" in my experience. -Hence the answer to your next question. Also, what is your experience as to the actual differences in bonus E0's that you get in ionic compounds? Right now one of my students is working with Sr(NO3)2... should we really expect the difference in bonus E0's between the Sr2+ and the oxygen atoms to be more than 12 eV, or does some kind of charge overlap from the nitrate ions actually make the strontium ions behave as if they are less than +2? [Kelly, Shelly D.] One full electron of ionic bonding gives about 6 eV. So that is about the most you would expect from different ions in a solid. Usually, I have found 3 to 4 eV. You make up most of the valence state change from the shift in the edge position. I have found unrealistic energy shifts when I try to use too much chi(k) data at low k. I'd look there first for you 12 eV shift. HTH Shelly

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RE: [Ifeffit] Using more than one E0
by Kelly, Shelly D. 14 Dec '04

14 Dec '04

Hi Guys, I wanted to add another comment about using multiple E0's. One of the best formulas that I have found involves assigning different atom types different E0's. This method seems to work well for M.S. paths. Here is an example of how it goes. I think that Daniel Haskel was the first to publish this type of E0 stuff. "Single and multiple scattering XAFS in BaZrO3: a comparison between theory and experiment" D. Haskel, B. Ravel, M. Newville and E. A. Stern Physica B 208&209 (1995) 151 Lets pretend that we have a copper oxide that we want to model. First shell Oxygen called O1, Second shell Cu called Cu1, Third shell Oxygen called O2. This method would use three E0's. One for the first shell oxygen atoms, Eo1. One for all the Cu atoms Ecu. and one for all other oxygen atoms Eo2. The Cu-O1 path has E0=Eo1. The Cu-Cu1 path has E0=Ecu. The Cu-O2 path has E0=Eo2. The Cu-O1-Cu-O1 path has E0=Eo1, (only scattering from O1 atom). The Cu-O1-Cu1-Cu path has E0=0.5*Eo1+0.5*Ecu. (scattering once from O1 and once from Cu1) ... And so forth and so on. Now if you set something like this up. You need to look at the results carefully and see if it works. Generally, scattering from an atom that has lost an electron due to an ionic bond will have a positive deltaE, and scattering from an atom that has gained an electron will have a negative deltaE. Of course this negative/positive deltaE is added to the alignment deltaE. If the values for Eo2 and Ecu are the same within the uncertainties of the measurement then you need to make them the same variable, so then you will only have two energy shifts, but you can still use it. This is most often the case as Matt mentioned but I always like to test it out. In addition, one electron transfer is about a shift by 6 eV, so if these values differ by more than say 10 eV something is not right. Since the shift is generally smallish, say 2 eV, your fit has to be really accurate to "see" these shifts. In particular they seem to be most important when you have all the deltaR values constrained in some way so that the error in deltaR is really really small. For example all deltaR values are related to unit cell parameters and atomic positions or and overall expansion term. HTH Shelly -----Original Message----- From: Wojciech Gawelda [mailto:wojciech.gawelda@epfl.ch] Sent: Thursday, May 27, 2004 1:18 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Using more than one E0 Hi everybody, I would like to address a couple of questions which are partially related to my recent struggles in fitting some EXAFS data. I'm trying to fit my data using several shells of different neighbors including a few single scattering paths and also so multiple scattering contributions (mainly collinear multiple scattering paths) all calculated with the help of FEFF 8.20. Now, I found once in the FEFFIT manual the following suggestion: one might consider using several different E0's for different paths in order to improve the fit. Ok, the explanation was based on some approximations coming from FEFF code which include incomplete core-hole shielding, lack of angular variations of the valence charge distribution and charge transfer between atoms in polar materials. My question is the following: does anyone of you have some experience with such procedure? And if yes, shall than distinguish between the first shell of nearest neighbors and the rest of the atoms in terms of their E0 corrections (using 2 parameters)? Or perhaps one can use separate E0's for each path? That's one thing... The second question concerns the background correction in Artemis: I was trying to find an easy explanation of what this procedure does during the fit but I guess I'm still somewhat confused...how one can judge whether the spline co-refinement does the right job? Some people on this mailing list underline that one should avoid high correlations between fitting parameters and background parameters in order to make sure that the fit is correct. But is it the only criterion? In some of my fits background line looks kind of constant over the entire R-range which was taken into the fit. Sometimes it becomes like a modulation peaking underneath some scattering paths...even if the background parameters don't correlate significantly with fitting parameters I have my doubts whether the result is trustful. Any hints about this procedure? Well, I'll greatly appreciate any comments and feedback from all you guys. I hope I'll be able to share some of my own soon :-) Cheers, Wojciech ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: <mailto:wojciech.gawelda@epfl.ch> wojciech.gawelda(a)epfl.ch WWW: <http://lsu.epfl.ch> http://lsu.epfl.ch *********************************************************************

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RE: [Ifeffit] a question about the white line
by Kelly, Shelly D. 14 Dec '04

14 Dec '04

I just put a background tutorial on my web page. Complete with project files and a pdf showing screen shots and some instructions. It used MoO3 which I found to have a particularly tough background. I used a theory to remove the background and then showed how to reproduced the "same" chi(k) data without the theory. If anyone wants to play with the background and add suggestions I will incorporate more info. Here is a link to the tutorial: www.mesg.anl.gov/skelly.html Shelly > -----Original Message----- > From: Newville, Matthew G. > Sent: Sunday, December 12, 2004 11:03 PM > To: XAFS Analysis using Ifeffit > Cc: John J. Rehr; Joshua Kas > Subject: RE: [Ifeffit] a question about the white line > > Hi John, Josh, > > > Certainly if a spline can do a good job of fitting the mu_0, then the > current > > approach is more or less ok. However in systems with strong white lines > > mu_0 can be strongly peaked and hence very difficult to fit with a few > > spline points. The broadening function lamda(E) can be constrained to be > small. > > Also, for cases with large whitelines, the location of e0 is difficult > to > > fit - the true e0 can lie well below the edge jump. > > Oh, maybe I misunderstood. Is lambda(E) in > > mu_0 = mu^thy_0(E,E_0,Gamma)[1 + lambda(E)] > > just a broadening term or a highly adjustable spline?? I guess > the whole question is how much freedom this function has. > > It definitely sounds interesting to use a theoretical mu_0, > especially for challenging white lines, but it's not clear how to > best make this accessible to users. I'll probably have to think > about this some more, but it would be nice to know the mechanics > of how you're doing it, and how well you need to know the > structure before you start. > > > In our view, mu0 does not depend very much on structure, since it's > > mostly determined by the local embedded atom potential. For this reason > > it's calculation would also be quite fast (only phase shifts and the > > cross-section are needed) compared to a calculation of chi(k) which > > requires multiple scattering paths. > > Well, usually a standard for autobk only needs a decent guess of > the first shell. Getting a standard does require some prior > knowledge of the system and calculation time, but I don't know > that it would be a lot more knowledge and time than would be > needed for a mu^thy_0(E). Anyway, it would still be interesting > to compare these two (autobk using calculated chi(k) v. starting > with a mu^thy_0 and massaging it to match data). > > On the other hand, it sounds as if the mu^thy_0(E) for a few dozen > (or few hundreds) challenging systems could be tabulated. That > would make it very fast and very simple to use! > > --Matt > > _______________________________________________ > 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] a question about the white line
by John J. Rehr 12 Dec '04

12 Dec '04

We very much appreciate Matt's comments on our suggestion suggestion on using a priori theory in fitting the background XAS: >> Thus we have attempted to use the theoretical mu_0 from FEFF as >> an a priori, and spline corrections on top of that. Thus the form >> of mu_0 would be: >> >> mu_0 = mu^thy_0(E,E_0,Gamma)[1 + lambda(E)] >> >> where the theoretical mu^thy_0 has an adjustable edge position >> (E_0) and broadening (Gamma), and lambda(E) is the spline correction >> which includes both instrumental variations with E and theoretical >> errors. Matt Newville makes the following observation: > That sounds interesting. But if you include a spline with the > calculated mu0(E), how important is the mu^thy_0(E)? Like, how > much work do you need to put into mu^thy_0 if you have lambda to > pick up the slack? Certainly if a spline can do a good job of fitting the mu_0, then the current approach is more or less ok. However in systems with strong white lines mu_0 can be strongly peaked and hence very difficult to fit with a few spline points. The broadening function lamda(E) can be constrained to be small. Also, for cases with large whitelines, the location of e0 is difficult to fit - the true e0 can lie well below the edge jump. For example, FEFF8 calculations show that the Re whiteline is almost completely due to the local embedded atomic absorption, whereas the large whiteline in SF6 has a different origin. The difference between these cases is not something that can be determined without the use of a theoretical mu0. Likewise the determination of E0 cannot be done well without theory in such cases. > On the one hand, since a spline is needed, it might imply that you > don't really gain much. On the other hand, it might also imply > that you could calculate and tabulate a reasonable 'universal > background function' for any given absorber-scatterern pair as a > starting background curve. Otherwise, it seems to me that the > prior information that goes into getting mu0(E) might be roughly > equivalent to using Feff to generate a standard chi(k) for autobk. In our view, mu0 does not depend very much on structure, since it's mostly determined by the local embedded atom potential. For this reason it's calculation would also be quite fast (only phase shifts and the cross-section are needed) compared to a calculation of chi(k) which requires multiple scattering paths. > Anyway, I'd be interested in comparisons of this with autobk > with/without a standard chi(k). And, of course, code donations > for improved algorithms are always welcome. ;). Us too! We would also be interested in sharing our code developments, e.g., eventually integrating them into ifeffit if appropriate. Josh Kas John Rehr

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RE: [Ifeffit] Re: EXAFS-Question concerning \delta(k)
by Kelly, Shelly D. 10 Dec '04

10 Dec '04

Hi, > -----Original Message----- > From: Newville, Matthew G. > Sent: Wednesday, December 08, 2004 11:27 PM > To: XAFS Analysis using Ifeffit > Cc: Frank Haaß > Subject: Re: [Ifeffit] Re: EXAFS-Question concerning \delta(k) > > Hi, > > Bruce summarized Frank's questions about phase shifts as: > > > If I understand your question, there are two parts. (1) Why is > > the shift due to the phase correction always negative (i.e. > > always to a smaller value in FT[chi(R)])? And (2) Why is the > > shift always in the neighborhood of 1/2 angstrom? > > I think there is a simple way to picture why the phase shift is > negative in terms of the quantum mechanical 'scattering from a > potential' problem -- the one where you usually end up talking > about tunneling through a barrier. I'll give it a try: > > ____ ~~~~~~~> ____ > ~~~~~~>| | E<V0 | | E>V0 > __| |__ __| |__ > > > Here we're in the E>V0 regime (on the left). We normally think of > the photoelectron as having energy E= hbar^2k^2/2m, where k is the > wavenumber for the 'free' photoelectron (that is, having escaped > the central atom and far from the scattering atom). But to > participate in the EXAFS, it does leave the absorbing atom and > scatter from the neighbor. When it is near the strong potentials > of the central and scattering atom, the wavenumber would be better > written like > k = sqrt[ 2m * (E-V0)] / hbar > > as for the barrier above (where V0 is the potential energy). > That is, k is lower (the electron wavelength is longer) in the > presence of a strong potential: kinetic energy being traded for > potential energy. > > To describe the EXAFS, we use only k with V0=0, which overestimate > the average kinetic energy of the photoelectron. That means we get > fewer periods of oscillations for a given R than 2*k*R would > suggest, which leads to the negative direction of the phase shift. > [Kelly, Shelly D.] I think that my explanation for a negative phase shift is just the same, but slightly easier for my brain to comprehend. Which means that I'll make some mistakes but it works for me..:) The photoelectron is negative and it scatters off of the electrons from the surrounding atoms. Hence the photoelectron is slowed down when it gets close to the other electrons. Negative and Negative repel, giving rise to fewer periods of oscillations, and a negative phase shift. As for the magnitude of the shift, lighter elements have a larger shift than the heaver elements. You can think about that by remembering that lighter elements scatter more at low k. If you have a photoelectron that scatters with very little energy (moving slowly) it will be slowed down more by the electrons. Heaver elements scatter more at high k. So, a photoelectron that scatters with a lot of energy will not get slowed down as much, hence a smaller phase shift. HTH Shelly

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Compiling Ifeffit wrapper, Athena, etc on AMD64 Linux Box
by mjpushie＠ucalgary.ca 09 Dec '04

09 Dec '04

I've been running in to some problems getting Athena, Artemis, and the other add-on packages to ifeffit, compiled on my AMD Athlon-64 Linux box (running Fedora Core 3, 64-bit version). I can run "perl Makefile.PL" without any problems and get the message: Yay! Now type "make" then "make install" to finish ... Once I run "make" it gets to the point of putting everything together and I get the following message (after the rest of it appears to run successfully): gcc -shared ifeffit_wrap.o -o blib/arch/auto/Ifeffit/Ifeffit.so -L/usr/local/lib -lifeffit -L/usr/local/pgplot -lpgplot -lpng -lz -L/usr/X11R6/lib -lX11 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.2 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm -lgcc_s /usr/bin/ld: /usr/local/lib/libifeffit.a(ifeffit.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libifeffit.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [blib/arch/auto/Ifeffit/Ifeffit.so] Error Thus far I have: 1) Successfully installed PGPLOT-5.2.0, editing the makefile to read: LIBS=-L/usr/X11R6/lib64 -lX11 `$(SRC)/cpg/libgcc_path.sh` -lgcc -lm -lc instead of ... -L/usr/X11R6/lib -lX11 ... 2) Successfully installed ifeffit-1.2.6 after editing: src/Makefile src/cmdline/Makefile src/test/Makefile to contain: PGPLOT_LIBS = -L/usr/local/pgplot -lpgplot -lpng -lz -L/usr/X11R6/lib64 -lX11 instead of ... -L/usr/X11R6/lib -lX11 ... 3) Successfully installed Tk-804.027 after editing Makefile.PL to read: X11LIB=/usr/X11R6/lib64 4) began installing the ifeffit wrapper, athena and artemis with $ perl Makefile.PL (which completed successfully) $ make (gives errors) I've edited the Makefile in the horae-046 directory where ifeffit_wrap.c and ifeffit_wrap.o are located to append -fPIC following the call to gcc, producing: gcc -shared ifeffit_wrap.o -fPIC -o blib/arch/auto/Ifeffit/Ifeffit.so -L/usr/local/lib -lifeffit -L/usr/local/pgplot -lpgplot -lpng -lz -L/usr/X11R6/lib -lX11 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.2 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm -lgcc_s /usr/bin/ld: /usr/local/lib/libifeffit.a(ifeffit.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libifeffit.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [blib/arch/auto/Ifeffit/Ifeffit.so] Error 1 I'm no compiling wizard, and I'm not even certain that -fPIC is supposed to be passed to gcc in this manner. Is there some other way around the whole shared/static thing, or is this not even the real issue? If anyone on the list has any suggestions, by all means please send them along. I'd like to get some work done!! Sorry for the length of the post. Jake

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Re: EXAFS-Question concerning \delta(k)
by Bruce Ravel 08 Dec '04

08 Dec '04

Frank, I am taking the liberty of forwarding my answer to the Ifeffit mailing list. I am not sure that I can answer your question entirely to your satisfaction and thought it would be useful to offer it up to the list for more commentary. > It is well known that there is a difference in the peak maxima of the > Fourier transformed EXAFS, G(r), and the "real" pair distribution function, > say F(r). As I have observed in spectra taken on pure metals, the maxima of > G(r) and the calculated core-shell-distances (calculated out of the crystal > structure) coincide pretty good. On oxidic samples, this is not the case, > G(r) is always shifted to lower r-values, about 0.5 \AA, sometimes even > almost 1 \AA. I agree that the shift due to the phase might be smaller for a pure metal than for an oxide, but it isn't 0. For copper, for instance, the highest point of the first peak is about 1/4 angstrom lower than the distance to the first shell. > It is always said that this difference is due to the phase shift \delta(k) > in the EXAFS equation, but I have not found a reasonable explanation, WHY > \delta(k) is influenced in this way! What are the parameters "behind" > \delta(k)? > > Maybe you have a little time to answer my question, because I am really not > satisfied with the explanations I found in literature. If I understand your question, there are two parts. (1) Why is the shift due to the phase correction always negative (i.e. always to a smaller value in FT[chi(R)])? And (2) Why is the shift always in the neighborhood of 1/2 angstrom? This is one of those things that I take for granted and rarely think too hard about. Here are my stabs at decent answers to your questions. I'll try the second part first. I wnet all the way back to the Lee and Beni paper from 1977 (Phys Rev B v.15 #6, p. 2862) which shows some plane wave calculations of the various central atom phase shifts. (There are lots of reasons to look at later papers as we now know that curved wave effects are very important, but for motivating a quick 'n' dirty understanding, it is useful to think about plane waves.) These are shown in Fig. 5 on page 2868. There is a Z dependence -- Rh is very different from Mg in the plot -- but all of them have essentially the same k dependence. That is, the traces in that plot are roughly parallel. We can approximate those phase shifts as linear -- 2delta = a*k + b. (They are obviously not linear but the quadratic term isn't huge, and it's helpful to keep the argument simple.) With this assumption, we are Fourier transforming an exafs function with a sine term like this: sin( 2kR + a*k + b) = sin( (2R+a)*k + b ) When you Fourier transform this, the peak will be shifted away from the "correct" R value by a/2. As you can see in the figure in Lee&Beni, all these functions are downward-sloping. Thus a is a negative number, resulting in an inward shift of the peak. All the central atoms have about the same slope, so they are all shifted by about the same amount. Any variation would have to do with the phase shift of the scatterer. So why is the slope of the central atom phase shift always negative and never positive? I think I am going to be less helpful for this question, but maybe someone else can pick up the slack. When you solve the problem of scattering of partial waves off a hard sphere, you find that each partial wave has a phase shift of -pi/2 times the angular momentum of the partial wave. That is, the effect of the scattering is to *decrease* the phase of the particle scattered in a way that is dependent on the angular momentum. An atom isn't a hard sphere and the calculation is a lot harder than for a hard sphere, but the essential physics is the same. Of course, this discussion has been hand-waving. For a proper understanding of all this stuff, I recommend the important Rehr-Albers review of XAS in Rev. Mod. Phys. v.72 #3 (2000) pp 621-654. Indeed, anyone who does XAS regularly should probably keep a copy of that paper on the desk. HTH, B > Thanks!! > > Yours, > > Frank > > --- > Dipl.-Ing. Frank Haass > Darmstadt University of Technology > Institute for Materials Science / Structure Research > Petersenstrasse 23 > D-64287 Darmstadt > > Tel.: +49 (0) 6151 16-2697 > Fax: +49 (0) 6151 16-6023 > > eMail: haass(a)tu-darmstadt.de -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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RE: [Ifeffit] a question about the white line
by Kelly, Shelly D. 08 Dec '04

08 Dec '04

Hi Bruce, I have worked with tough background removals. They are particularly difficult the first time you encounter each one. My methodology goes something like this. It isn't easy and sometimes very frustrating. 1) Determine how broad the rise in the adsorption edge. How many eV is it from the bottom to the flat part above the edge. If you edge is broad > 10 eV then Ezero will be somewhere high on the adsorption edge. If you edge is sharp then Ezero will be somewhere low on the adsorption edge. 2) Remove the background. Look at the FT with all three k-weights. Determine if Rbkg is reasonable. 3) You must have a good idea about the first shell. Run Feff and look at the theory with all variables set to zero, Ezero =0, sigma2=0 and delr=0. If you have a split shell be sure to include all the paths that make up the first peak in the FT of the data. 4) Compare theory to data using a well padded k-range. Leave out the first two oscillations in k, starting around 4 to 5 inverse angstroms. Set Ezero equal to zero. Run a fit, determine delr for the paths and sigma2. Look at the fit and the data in k-space with all three k-weights. Check to see if delr and sigma2 are reasonable. See if you think that moving Ezero around in Athena will help line things up at low k. 5) Import the "fit" into Athena and use it as the theory. Remove the background moving Ezero to line up the data and the theory at low k. And then start all over. 6) This procedure will not work if you use the wrong theory hence the frustrating part. HTH - If someone on the list is willing to try this procedure out and gets stuck and you are willing to share all. I will continue to help on the mailing list. Shelly Shelly Kelly ---------------------------- skelly(a)anl.gov Bldg 203, RM E113 phone: (1) 630-252-7376 Argonne National Laboratory fax: (1) 630-252-9793 Argonne, IL 60439 www.mesg.anl.gov > -----Original Message----- > From: Bruce Ravel [mailto:ravel@phys.washington.edu] > Sent: Tuesday, December 07, 2004 3:00 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] a question about the white line > > On Tuesday 07 December 2004 03:47 pm, you wrote: > > Hi Bruce, > > > > Feel free to have them contact me. I have done a lot of Re compounds. > > > > Jeff > > Hmmm.... The point of a mailing list is to have a public, searchable > archive where useful information can be discussed and shared in an > open manner. > > I could have just answered the question myself, but I thought that it > was one of broad interest. Thus I had hoped to solicit discussion on > the mailing list. > > B > > -- > Bruce Ravel ----------------------------------- > ravel(a)phys.washington.edu > Code 6134, Building 3, Room 405 > Naval Research Laboratory phone: (1) 202 767 > 2268 > Washington DC 20375, USA fax: (1) 202 767 > 4642 > > NRL Synchrotron Radiation Consortium (NRL-SRC) > Beamlines X11a, X11b, X23b > National Synchrotron Light Source > Brookhaven National Laboratory, Upton, NY 11973 > > 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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Frustrating monochromator glitch
by m.bondin＠pgrad.unimelb.edu.au 08 Dec '04

08 Dec '04

Dear mailing list - my last round of EXAFS experiments performed on the Fe-K edge in fluorescence mode gave data extending nicely to 15 in k. One problem was a nasty monochromator glitch at approx 13.5 in k which is so great in some cases it causes sufficient distortion to the data that even upon deglitching I must cut back the data to 13 in order to gain a good fit using my models. Firstly I was wondering if someone here could describe to me how a monochromator glitch arises (some systematic defect in the monochromator crystal or more? - the only problem with this explanation is that some data sets seem more affected than others and it has not manifested itself as badly in previous trips). Also is there any other way to handle the removal of a monochromator glitch besides deglitching? My supervisor seems to think that there must be a scale factor or offset in the I0 monitor counts which could be corrected in order to overcome a glitch in the existing data - has anyone ever ! thought of other ways to salvage data in this way? Regards, Mark -- Mark Bondin PhD student School of Chemistry, University of Melbourne (03) 8344 7015 (Tower lab) 0409 252 983 (mobile)

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RE: [Ifeffit] a question about the white line
by Barton, David (DG) 08 Dec '04

08 Dec '04

Friends, Thanks Bruce for forwarding the question to the Ifeffit mailing list regarding background subtraction for samples with strong white lines. The Re sample that sparked the question is attached (white line >3mu). The data is not perfect, but it is good enough for discussion. My first approach to subtracting the background was similar to what Matt mentioned (Matt said: "I know others regularly use kmin >1"), this method seemed to work fairly well using kmin= 1.5 and Rbkg = 1.0. I then used Matt's suggestion to shift the Eo and keep kmin = 0.5, this method ultimately gave a similar subtraction albeit with a phase shift that should be taken care of when the data is fit to theory. It will be interesting to compare the results of the fit using these two methods of background subtraction, especially the first shell which is a Re-CO that has a short distance and is sensitive to background subtraction. Thanks, Dave _________________________________ David Barton, PhD The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Ph: (989) 636-4753 Fax: (989) 638-6225 Email: dgbarton(a)dow.com

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RE: [Ifeffit] a question about the white line
by Kelly, Shelly D. 08 Dec '04

08 Dec '04

> -----Original Message----- > From: Newville, Matthew G. > Sent: Tuesday, December 07, 2004 11:17 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] a question about the white line > > Shelly, > > That seems like a lot of steps to me, and it almost seems like > you're mimicking by hand the use of a standard chi(k) with > autobk/spline(). Do you find very different results using a > standard chi(k) with autobk/spline()? If so, do you have any > suggestions for how the more automated version could be improved? > [Kelly, Shelly D.] Hi Matt, You are right. My method does use a lot of steps. I have seen "large" differences in the background removal for the first two full cycles in k-space. I will show a figure, soon. But often what happens is the default spline cuts the EXAFS data too many times through the edge. Your suggestion for an automated approach is a good one. Here is an idea. (1) Set kmin high in the spline range, so that you do not use the first two oscillations in k. (2) Fit the first shell, in a way that makes sense. (3) Use the theory to remove the background using kmin=0 in the spline range. As Matt points out you can tell if the theory is reasonable by the shape through the white line region. You will get to the same place as before. -Assuming that you use a reasonable theory and your original choice of Ezero is not too far off. I will try it out on some tough data and let you know how it goes. Shelly

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Exporting data to Igor
by Gerrit Schmithals 08 Dec '04

08 Dec '04

Hello, I now frequently use the possibility of exporting data from Athena to my analysis software Igor Pro 5. I have a few suggestions on the exporting behaviour: - The abscissa-column of exported BFT data (q-space) is wrong when using File | Save marked group as data | ... This applies to the magnitude, real and imaginary part. Obviously the R-space values are used instead of q-space as can be seen from the column header. When using File | Save chi(q) no problems occur. (see Data.zip, Athena 0.8.034, Ifeffit 1.2.6a) - Along with exporting the data I also use Edit | Write a report | CSV report (marked groups) to get a printout of all parameter values with which the data was processed. I have written a small script for Igor to read that data into a text wave from where it can be displayed or used in further routines e.g. to automatically be displayed in a graph. If anyone is interested I can post that script. Bruce, if there is time left for it, could you also include the value of the check button 'Phase correction' along with the exported data? (BTW: The unchecked button displays either 'No' or 'Off' but it seems irrelevant) Cheers, Gerrit

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a question about the white line
by Bruce Ravel 07 Dec '04

07 Dec '04

Hi, Last week I was asked an interesting question. A long-time ifeffit user was showing A&A to some grad students new to the XAS biz: [An] issue that came up with them as they began to use the software was: Dealing with background substraction from compounds with enormous white lines (Re data). I thought it would be useful to hear comments from people on the mailing list. Any takers? B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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RE: [Ifeffit] Re: Ifeffit Digest, Vol 22, Issue 1
by SCHLEGEL Michel 177447 06 Dec '04

06 Dec '04

> > But: I'm not aware of any beamline saving data in mono steps. > > AFAIK, only the old Lytle data is in this format. We should not > > do anything to encourage this very bad practice. For the record, > > it's bad because it assumes you know: 1) steps per degree, 2) > > value of steps at angle=0, and 3) lattice spacing of crystal. If > > you don't know all three values, you have nothing. > > > > So, I agree it would be foolish to try to support every beamline > > format, and not likely to be successful. I also think putting in > > the lattice constant for YB66 or polynomial coefficients for the > > thermal expansion curve of Si is a similarly doomed. > > > > I think that Matt is right. > > It is a shame to waste the old Lytle data, but let us not > allow that to continue. If someone really wants the data > from that old Lytle data bank then there are inconvenient > ways to extract the information, just as it should be. Would it be advisable - realistic to convert once and for all the old Lytle data from the mono step scale to the energy scale? (I mean, by wirtue of a well-hacked perl macro). Is there any scientific reason why the old mono step scale should be kept? > I second the "Athena test". As such, spec files with all scans cannot be read by Athena, but you can copy out individual "scans" in separate files, for which comment lines all start with "#", the last line given the name of the motors and detectors ("energy", "IO"...) and the data is then ordered as an array. The promblems are (1) usually all scans (table, slits...) are collected in one file, and (2) the column ordering varies from file to file (a problem which is already wonderfully addressed by Athena, though). So maybe a separate splitting macro to take out the do the job would be more convenient than asking athena to do all theis work. Granted it's tedious, but compared to the time needed to correctly extract, interpret & fit the data... Michel

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Re: differential evolution algorithm (fwd)
by Grant Bunker 02 Dec '04

02 Dec '04

Carlo suggested that I submit this (edited) to the ifeffit list... gb ---------- Forwarded message ---------- Date: Thu, 2 Dec 2004 21:40:54 -0600 (CST) From: Grant Bunker <bunker(a)agni.phys.iit.edu> To: Carlo U. Segre <segre(a)iit.edu> Cc: Bruce Ravel <ravel(a)phys.washington.edu>, Grant Bunker <bunker(a)biocat1.iit.edu> Subject: Re: differential evolution algorithm Hi, Carlo - DE is a very nice and simple genetic algorithm for finding global minima. As far as I know I have been the only person applying it to XAFS. It might be overkill for the application though - is this just for finding maximum in the edge derivative? If it is, it's probably simpler just to smooth the data (e.g. with binomial smoothing which you can do by repeated convolution Y(n)=y(n+1)+2*y(n)+y(n-1))/4), followed by a derivative. I've done it that way before (or use smoothing splines) in the distant past and it worked fine. In the edge-finding hack in the mathematica notebook (for automated data reduction) I sent you I just used differential evolution out of laziness, but it's very good for more difficult fitting problems like the stuff we have been doing with the ab initio DWFs in enzymes. It's arguable whether using the max derivative is the best way to choose E0 anyway, but that's a different story. thanks - grant ps I googled "differential evolution" and uncovered a good web site at berkeley. Probably it has references to the original article by storn and price. A couple of years ago I implemented it in Mathematica code for global fitting calling feff as an external "function". The intrinsic NMinimize function in Mathematica also has it available as a minimization method in purely numerical (nonsymbolic) calculations. http://www.icsi.berkeley.edu/~storn/code.html On Thu, 2 Dec 2004, Carlo U. Segre wrote: > > I am somewhat ignorant. Grant uses the builtin function from Mathematica. > Perhaps he can give a bit more information. Grant? > > Carlo > > On Thu, 2 Dec 2004, Bruce Ravel wrote: > > > > >> Grant has been using a differential evolution algorithm to take case of > >> noisy data. Perhaps this could help? > > > > Carlo, > > > > Is there a reference for this in the exafs conmtext? I'd like to read > > up on it. > > > > B > > > > > > > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Special Projects, Graduate College > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > Carlo.Segre(a)iit.edu http://www.iit.edu/~segre >

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RE: [Ifeffit] Too many points in pre-edge
by Barton, David (DG) 02 Dec '04

02 Dec '04

Carlo and Matt: > With these files, the location of the edge (and element > identification as well) using the first derivative > does not work. I also had a similar problem when we had a somewhat noisy pre-edge and edge data. Often our analysis of the XANES requires high confidence in the edge energy to determine energy shifts and to accurately align our spectra using metal foil references. Of course, I can always manually assign the edge position in Athena, but it would be nice if Ifeffit was a bit smarter about how it chooses Eo since it is critical for Athena operation when a reference standard is used to calibrate a sample spectra. I would guess that there is some robust algorithm that one could implement which would more accurately determine either (1) the maximum in the first derivative or (2) the zero of the second derivative for data with any number of data points or noisy data. I imagine that such an algorithm would include some sort of adjustable "smoothing" parameter to filter the signal from noise. Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Ph: (989) 636-4753 Fax: (989) 638-9350 Email: dgbarton(a)dow.com > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On > Behalf Of Carlo U. Segre > Sent: Thursday, December 02, 2004 9:44 AM > To: IFEFFIT Mailing List > Subject: [Ifeffit] Too many points in pre-edge > > > > Matt: > > I am running into a somewhat annoying problem with > continuous scan data > imports into athena where there are many datapoints before > the edge (I > think > 400 or so). With these files, the location of the > edge (and > element identification as well) using the first derivative > does not work. > The edge is identified as being somewhere in the pre-edge. > As I reduce > the number of data points in the pre-edge, the edge > identification moves > closer to the true edge and then locks in correctly when > the number of > data points in the pre-edge is small enough (again, I think > this is less > than 400 points). > > I can address this problem by running these data through a > rebinning > process in the pre-edge but I think that if it is possible > to handle this > in ifeffit, that would be a good idea. > > On a second note, would you tell me whether you or Bruce is > planning to > maintain the ifeffit perl wrapper? At this time, ifeffit > 1.2.6a and horae > 046 have different versions of the Ifeffit.pm script (1.3 and 1.301 > respectively). I recently ran into a problem because I had > the ifeffit > version and horae 046. > > Carlo > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Special Projects, Graduate College > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > Carlo.Segre(a)iit.edu http://www.iit.edu/~segre > _______________________________________________ > 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] Re: Ifeffit Digest, Vol 22, Issue 1
by Kelly, Shelly D. 02 Dec '04

02 Dec '04

> > I want to go back a step. First, you asked what commonly used > crystals athena should know about. I think the answer should be > "None". Athena should not be the tool to convert mono steps to > energy. It should not know the thermal expansion curve for Si. > The beamline should supply values in units of energy or wavelength > or provide software to convert to such units. > > Then the discussion got to supporting data formats from different > beamlines. I don't disagree with your desired formatting rules. > For what it's worth, I think we (that is, those on this email > list) are as qualified to set such a standard as the IXS (or at > the very least, we're approximately a quorum of any such group of > the IXS). Here's a proposed draft 0.1 for a data format standard > for beamline collection software: > > The data can be read and used by Athena without modification. > > Whether any such standard is actually used is a different matter. > At the APS there are at least six different beamline data formats > used for XAFS (there might be more than that: I'm pretty sure > sectors 4, 5, 10, 12, 13, and 20 each use different formats). At > least 3 of these pass the athena standard. One of those formats > is spec, which does not meet this standard. I believe spec is > used widely at many other synchrotrons. At the APS, some data is > saved in HDF format. HDF may become more common as EPICS seems to > be moving this way. I don't know that any EXAFS data is currently > saved only as HDF, but I wouldn't be surprised if happens. If I'm > not mistaken, SSRL saves data in a binary format. It can be > converted to ASCII, but that still does not meet the 'read by > athena' rule. I believe we had a recent example where data from > SRS was close, but also did not quite meet this standard. > > But: I'm not aware of any beamline saving data in mono steps. > AFAIK, only the old Lytle data is in this format. We should not > do anything to encourage this very bad practice. For the record, > it's bad because it assumes you know: 1) steps per degree, 2) > value of steps at angle=0, and 3) lattice spacing of crystal. If > you don't know all three values, you have nothing. > > So, I agree it would be foolish to try to support every beamline > format, and not likely to be successful. I also think putting in > the lattice constant for YB66 or polynomial coefficients for the > thermal expansion curve of Si is a similarly doomed. > I think that Matt is right. It is a shame to waste the old Lytle data, but let us not allow that to continue. If someone really wants the data from that old Lytle data bank then there are inconvenient ways to extract the information, just as it should be. I second the "Athena test". Shelly

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Too many points in pre-edge
by Carlo U. Segre 02 Dec '04

02 Dec '04

Matt: I am running into a somewhat annoying problem with continuous scan data imports into athena where there are many datapoints before the edge (I think > 400 or so). With these files, the location of the edge (and element identification as well) using the first derivative does not work. The edge is identified as being somewhere in the pre-edge. As I reduce the number of data points in the pre-edge, the edge identification moves closer to the true edge and then locks in correctly when the number of data points in the pre-edge is small enough (again, I think this is less than 400 points). I can address this problem by running these data through a rebinning process in the pre-edge but I think that if it is possible to handle this in ifeffit, that would be a good idea. On a second note, would you tell me whether you or Bruce is planning to maintain the ifeffit perl wrapper? At this time, ifeffit 1.2.6a and horae 046 have different versions of the Ifeffit.pm script (1.3 and 1.301 respectively). I recently ran into a problem because I had the ifeffit version and horae 046. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Re: Ifeffit Digest, Vol 22, Issue 1
by Grant Bunker 01 Dec '04

01 Dec '04

Hi, Bruce - Ge crystals certainly are a must. Shouldn't forget that people use Si monochromator crystals at different temps also. Instead of making a list of d spacings for each reflection, I would just keep values of the lattice constants at a few reference temps and interpolate the lattice constant a for the temp of interest, then any of the d spacings can be calculated as d[hkl]=a/Sqrt[h^2+k^2+l^2] (if memory serves me correctly) Same for Ge and Diamond since they are the same structure. That way it's just a handful of numbers, no big deal. Matt's point as to whether it really should be athena's job to read in all file formats is a good one. Mostly you want to make it easy for a new format to be added by the end user. A scripting language would suffice although perl might be difficult for most people to deal with. Perhaps the equation parser used in ifeffit could be deployed as end-user configurable preprocessor for massaging beamline data into the right form. If those were saveable as templates for different types of data it would be convenient. thanks -grant On Wed, 1 Dec 2004 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. common mono crystals (Bruce Ravel) > 2. Re: common mono crystals (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 1 Dec 2004 10:24:17 -0500 > From: Bruce Ravel <ravel(a)phys.washington.edu> > Subject: [Ifeffit] common mono crystals > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200412011024.17160.ravel(a)phys.washington.edu> > Content-Type: text/plain; charset="us-ascii" > > > Hi folks, > > One of my chores for today is to implement a utility in Athena for > converting encoder readings in a raw data file into energy. This will > make some of the data in the Lytle database a bit easier to use. One > of the things that the user must specify is the d-spacing of the mono > crystal. I want to provide a menu of common crystals. > > The orange book is kind enough to provide an exhaustive list -- but > it's kind of overkill. Somehow I doubt if many people are using a > sucrose 001 monochromator even though that d-spacing is given in the > orange book ;-) (Really! It's on page 4-12!) > > I want to do an informal survey of what crystals the ifeffit crowd > regularly uses. I am certainly going to include Si111, Si311, and > Si200 in the list, so I don't need to hear from people who use those > crystals. What others should go in the list? Beryl? Germanium? > Graphite? Let me know.... > > Thanks, > B > > -- > Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu > Code 6134, Building 3, Room 405 > Naval Research Laboratory phone: (1) 202 767 2268 > Washington DC 20375, USA fax: (1) 202 767 4642 > > NRL Synchrotron Radiation Consortium (NRL-SRC) > Beamlines X11a, X11b, X23b > National Synchrotron Light Source > Brookhaven National Laboratory, Upton, NY 11973 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ > > > > ------------------------------ > > Message: 2 > Date: Wed, 1 Dec 2004 09:58:12 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] common mono crystals > To: ravel(a)phys.washington.edu, XAFS Analysis using Ifeffit > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0412010940170.26700-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Bruce, > > Diamond 111 is fairly common (I'd guess more common than anything > but Si), and you probably meant Si(220) instead of (200). InSb is > probably the next most common for the 1 to 2 keV range. I think > the others are not so common for XAFS as the energy bandpass is > too wide. Also, Si at room temperature is slightly different than > at LN2 temperature.... > > But also needed for that calculation is the number of motor steps > or encoder steps per angular unit. OK, angular unit is probably > most commonly in degrees, but I wouldn't assume that it's never in > radians. For steps per angular unit, it's usually a many thousand > steps per degree but it can be pretty much any number. > > So, it's complicated to convert 'steps' to eV. Personally, I'm > comfortable insisting that the beamline/facility provide energy in > eV, keV, Angstroms. or at least angle in degrees with the > monochromator lattice constant clearly given. > > That is, I don't think this should be athena's job. I think it > would be better to have more support for beamline-specific > formats. Then, if some particular beamline saves the "energy" > in nanoJoules or milliradians that could be marked and > auto-converted, but I don't think athena should worry about what > kind of monochromator was used or steps-per-degree. > > The data in the Lytle archive is possibly a special case, because > it's commonly available. It's usually well marked for conversion > to energy, but the data is poorly documented and spotty in quality > and it's often hard to tell what exactly the columns are (e-yield > v. fluorescence, for example). That can make it hard to asses the > quality of the data (is self-absorption a problem, etc). I do use > it sometimes, but the data is not all that reliable. > > Having a more complete and well-maintained database of data, > including some of the data from the Lytle database would be nice. > Any volunteers to work on that? > > --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 22, Issue 1 > ************************************** >

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common mono crystals
by Bruce Ravel 01 Dec '04

01 Dec '04

Hi folks, One of my chores for today is to implement a utility in Athena for converting encoder readings in a raw data file into energy. This will make some of the data in the Lytle database a bit easier to use. One of the things that the user must specify is the d-spacing of the mono crystal. I want to provide a menu of common crystals. The orange book is kind enough to provide an exhaustive list -- but it's kind of overkill. Somehow I doubt if many people are using a sucrose 001 monochromator even though that d-spacing is given in the orange book ;-) (Really! It's on page 4-12!) I want to do an informal survey of what crystals the ifeffit crowd regularly uses. I am certainly going to include Si111, Si311, and Si200 in the list, so I don't need to hear from people who use those crystals. What others should go in the list? Beryl? Germanium? Graphite? Let me know.... Thanks, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

2 1

Importing Athena data into Excel
by sej9＠cornell.edu 29 Nov '04

29 Nov '04

I can't remember how to import chi(r) data from a merged file in Athena into Excel. Sarah

2 1

formula checking
by Peter Southon 22 Nov '04

22 Nov '04

Hello all, I've got a quick question about the checking of formulas. I mistakenly typed "//" instead of "/" into several 'def' commands in my model. Unfortunately it took me a long time to find the mistake, since it was a complex model and by some fluke the equation gave almost (but not quite) the expected value. Since "//" doesn't seem to be a valid Ifeffit operator, why didn't either Ifeffit or Artemis pick it up? Regards, Peter Peter Southon Postdoctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 7482

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Rbkg value in Athena
by Ann Liang 18 Nov '04

18 Nov '04

Hi Bruce, I am a little bit confused on what the Rbkg value should be when I do the background subtraction. I have read some previous posts which stated that Rbkg can be determined after the fit. However, I always think that the fit depends strongly on how the background being subtracted. How does the initial spline value affect the background subtraction? Should it be 1eV or 25 eV above the edge? I appreciate your help. Thanks, Ann

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Re: [Ifeffit] formula checking
by Scott Calvin 17 Nov '04

17 Nov '04

Hi Matt, Bruce, etc., I think Matt's suggestion is a very good one. In the past, I have occasionally run into problems where Ifeffit flags a problem but Artemis doesn't check for the particular flag. Since when I'm rolling along using Artemis I don't alsays inspect the Iffefit messages, I didn't realize anything funny has happened immediately...it wasn't until I realized the fit didn't make sense that I checked if Ifeffit had correctly identified a typo or whatever. I've always alerted Bruce when these things have come up, and he's incorporated them into new releases, but it would be very good if Ifeffit had a couple of generic warning flags that Artemis could grab on to and thus prominently alert the user that something went wrong... --Scott Calvin Sarah Lawrence College At 11:08 AM 11/17/2004 -0600, you wrote: >Hi Bruce, Peter, > >Ifeffit does print a warning message about a syntax error on using >'//'. But it's completely believable and forgivable that Artemis >doesn't catch this. > >Bruce, would it help if a flag was set indicating 'syntax error' >in addition to printing the warning message? That way you could >wrap each of the definitions with a perl function that did the >ifeffit command and check for syntax errors, doing something >sensible (popping up a warning dialog box, for example) on a >syntax error. That might be better than checking for '//' itself, >because it would detect other syntax errors as well. > >A flag meaning 'math error' (as on divide-by-zero or sqrt(-1)) >might be useful too, I suppose.... >

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Re: strange distance obtained using atoms
by Bruce Ravel 15 Nov '04

15 Nov '04

On Thursday 11 November 2004 9:11 am, Valmor Mastelaro wrote: > Bruce, I´m using the atoms program to obtain the feff.inp file for a PZT > compound. when I introduced the crystallographic informations on the atoms, > I obtained only one distance that is too short to be true, Ti-Zr = 0.483 > > I verify all the crystallographic parameters in the literature and they > seens to be correct. (Journal of Physics: condensed matter 10, 6251-6269 > (1998). Hi Valmor. I am taking the liberty of forwarding my answer to the Ifeffit mailing list as well as the feffusers list. Here is the Atoms input file that Valmor sent: space = R 3 c a = 5.78510 c = 14.2880 core = Ti edge = K rmax = 9.0 atoms ! elem x y z tag occ. Pb 0.00000 0.00000 0.27170 1.00000 Ti 0.00000 0.00000 0.03590 1.00000 Zr 0.00000 0.00000 0.00210 1.00000 O 0.16321 0.34281 0.08333 1.00000 Actually, the one very short atom was only the most obvious of a host of problems with this input data. Look also at the Zr/Ti coordination shell. There are far too many atoms and they are much too close (about 0.483 AA apart -- imagine that!) to one another. Reading the paper that he cited, I see that coordinates are given for the anion and cation positions by parameterized deviations from the symmetry positions of the space group. It's really a very clever paper -- the parameters of the structure are things like cation displacement and octahedral tilt. Very cool stuff, all of which is explained abstractly in Table 1. Then in Table 3, the authors give the actual values of the parameters for each of the anions and cations. Among the data in this table are the fractional occupancies of Zr and Ti along with separate displacement parameters for those two cations. Before I go on, you need to read this old entry to the Ifeffit mailing list: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2002-July/000092.html That entry actually answers your question about why Atoms isn't working as you anticipated, but I'll expand on a few points here. Feff (and therefore Atoms) presumes that you have one entire atoms at any given site. Feff does not allow you to fractionally occupy a location in space. This may be a shortcoming of Feff, but there are good reasons why Feff behaves that way. Since Feff does not know how to compute a cluster with fractional atoms, Atoms does attempt to write fractional atoms to the cluster. Thus, when you put *both* Ti and Zr in the atoms.inp file, Atoms put six of each in the unit cell. (This crystal has six formula units in each unit cell.) That's obviously incorrect. The paper you cite clearly states that the samples have between 13 and 40% Ti according to the stoichiometry Pb Zr_{1-x} Ti_x O_3. So it is simply incorrect to have both the Ti and Zr entries in your atoms input file. As I explain in the link above, you generally cannot solve a problem like this with a single Feff calculation. You simply must consider an analysis strategy which involves at least 2 and possibly many more Feff calculation. Are you doing EXAFS analysis? If so, then you should consider running Feff once without the Ti site and using the parameter given in the cited paper for the Zr site. Then run Feff again with the Zr site and using the parameters given for the Ti site. Then, when you do your analysis, you will need to multiply the amplitude terms for the paths from the Zr calculation by (to use the example of one end member) 0.87 and multiply the amplitudes of the paths from the Ti calculation by 0.13. Or are you doing XANES calculations? In that case, you will need to run many Feff calculations with the Ti and Zr sites randomly populated following the modle of the Au2O3 that I discuss in the link above. In any case, the bottom line that you have to remember when using Atoms and Feff is that these programs do not and cannot treat occupancy in the same manner as is discussed in a paper on Reitveld refinement. (That is true at least in the context of running a *single* Feff calculation.) You have to understand and think hard about how Atoms works and how Feff works and how they should be used for your specific analysis problem -- this is particularly true in a problem like this, which involves a rather complicated scheme for treating the relationship between stoichiometry and structure. Hope that helps, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Please accept my apology
by Firouzeh Tannazi 11 Nov '04

11 Nov '04

Dear Ifeffit Mailing-List Members; Please accept my apology for accidentally sending a personal message to the ifeffit mailing list. Best Regards, Firouzeh Tannazi.

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Thesis Correction
by Firouzeh Tannazi 11 Nov '04

11 Nov '04

Hi Dr. Bunker; Let me at first thank you very much for the corrections and edition that you have made on the dissertation. I just want to remind you those sections that need more corrections. First the Introduction section which is very disperse! As we have "Abstract" part and any chapter has introduction we may eliminate the introduction chapter and add its stuff to other introduction parts or if you think it is better to keep it, I really appreciate if you write it in the way that more emphasize will be on last part . The next part is section 2.6, "X-ray Fluorescence Spectroscopy" which I want to talk about the differences and similarities between that method and XAFS. Regards, Firouzeh.

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new update for Windows
by Matt Newville 11 Nov '04

11 Nov '04

Hi I just posted a new update to Ifeffit for Windows. This includes the recent changes to Athena, Artemis, and Hephaestus that Bruce mentioned recently (in http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-November/001487.html) It also includes a new base Ifeffit library (1.2.6a) that can now write up to 99 array columns to output files, to fix the bug that Borbert Weiher and Bruce pointed out. In addition, the default Ifeffit library now allows for 1024 paths. If you have trouble running this (say, on an older machine), there is also a version of ifeffit_10.dll that supports up to 256 paths under the 'build_setup\dlls\IFF1.2.6a_MPATHS256' folder. --Matt

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MoS2 fit
by Grant Bunker 11 Nov '04

11 Nov '04

I haven't played with these data or this analysis, but the difficulty in fitting the known structure may suggest a problem with the data. One experimental problem that springs to mind, since MoS2 is a layered structure, is whether there might be a preferred orientation in the sample particles, i.e. the particles might not be randomly oriented. Since the x-ray beam is polarized this could cause some serious weirdness in the XAFS fitting (if the polarization weren't explicitly considered). grant On Thu, 11 Nov 2004 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. Commercial MoS2 fit (dmc(a)pdx.edu) > 2. Commercial MoS2 -- Correction (dmc(a)pdx.edu) > 3. Re: Commercial MoS2 -- Correction (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 11 Nov 2004 08:12:34 -0800 > From: dmc(a)pdx.edu > Subject: [Ifeffit] Commercial MoS2 fit > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <1100189554.41938f7244a49(a)webmail.pdx.edu> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi List, > > I have tried a variety of different things to get this fit to work. It > seems pretty decent now, although, for my two MS paths (4,5) I had to force the > sO^2's to be positive. In the process one of them is now zero. My > parameter 'amp' wants to be 0.5 so I had to set it to 0.7 because I know that > it shouldn't be as low as 1/2. Changing the k-weight doesn't seem to help. > Here's my Data: > > Thanks, Dan > > > > Project title : Fitting merge 10_15_04.chi > ============================================================ > > Independent points = 28.581054688 > Number of variables = 13.000000000 > Chi-square = 5995.284754934 > Reduced Chi-square = 384.780419245 > R-factor = 0.043668737 > Measurement uncertainty (k) = 0.000187262 > Measurement uncertainty (R) = 0.006509968 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0 = 0.8645560 +/- 1.2283680 (guessed as 0.864556 (1.228344)) > ss = 0.0041070 +/- 0.0005190 (guessed as 0.004107 (0.000519)) > ss2 = 0.0043590 +/- 0.0005200 (guessed as 0.004359 (0.000520)) > ss3 = 0.0217810 +/- 0.0333390 (guessed as 0.021781 (0.033341)) > ss4 = 0.0000000 +/- 0.0509500 (guessed as 0.000000 (0.050951)) > ss5 = 0.0000360 +/- 0.0063810 (guessed as 0.000036 (0.006382)) > ss6 = 0.0028730 +/- 0.0071340 (guessed as 0.002873 (0.007133)) > alpha = -0.0012530 +/- 0.0031940 (guessed as -0.001253 (0.003193)) > alpha2 = 0.0075160 +/- 0.0022250 (guessed as 0.007516 (0.002225)) > alpha3 = -0.0171580 +/- 0.0323200 (guessed as -0.017158 (0.032321)) > alpha4 = -0.0165410 +/- 0.1054840 (guessed as -0.016541 (0.105487)) > alpha5 = -0.0181860 +/- 0.0187940 (guessed as -0.018186 (0.018795)) > alpha6 = 0.0227330 +/- 0.0147690 (guessed as 0.022733 (0.014767)) > > Def parameters: > delr_1 = -0.0057180 > delr_2 = 0.0342980 > delr_3 = -0.0782970 > delr_4 = -0.0754820 > delr_5 = -0.0829880 > delr_6 = 0.1037370 > > Set parameters: > amp1 = .7 > > > Correlations between variables: > ss3 and alpha4 --> 0.8462 > e0 and alpha --> 0.8335 > ss4 and alpha3 --> -0.6693 > e0 and alpha2 --> 0.6159 > ss and ss2 --> 0.6114 > alpha5 and alpha6 --> -0.5959 > alpha4 and alpha5 --> -0.5821 > ss4 and ss5 --> -0.5505 > ss3 and alpha5 --> -0.5246 > alpha and alpha2 --> 0.5146 > ss5 and ss6 --> -0.4931 > ss2 and alpha5 --> 0.4681 > ss5 and alpha3 --> 0.3885 > ss6 and alpha6 --> 0.3700 > alpha2 and alpha5 --> 0.3208 > ss2 and alpha4 --> -0.2992 > ss4 and alpha5 --> 0.2955 > ss3 and ss4 --> 0.2923 > ss5 and alpha2 --> -0.2842 > e0 and alpha4 --> -0.2781 > ss2 and ss3 --> -0.2677 > alpha3 and alpha5 --> -0.2523 > All other correlations are below 0.25 > > > > ------------------------------ > > Message: 2 > Date: Thu, 11 Nov 2004 08:20:02 -0800 > From: dmc(a)pdx.edu > Subject: [Ifeffit] Commercial MoS2 -- Correction > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <1100190002.419391328eb1a(a)webmail.pdx.edu> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi List, > > It appears that changing the k-weight on my fit does improve the fit. > I still have the problem of forcing the sO^2's on the two MS paths to be > positive. Here's some new data with k-weight 3: > > Thanks, Dan > > Project title : Fitting merge 10_15_04.chi > ============================================================ > > Independent points = 28.581054688 > Number of variables = 13.000000000 > Chi-square = 1527.118835332 > Reduced Chi-square = 98.011262136 > R-factor = 0.025169471 > Measurement uncertainty (k) = 0.000185138 > Measurement uncertainty (R) = 0.081594539 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0 = 1.1335810 +/- 1.3393990 (guessed as 1.133581 (1.339426)) > ss = 0.0035870 +/- 0.0003110 (guessed as 0.003587 (0.000311)) > ss2 = 0.0042850 +/- 0.0002780 (guessed as 0.004285 (0.000278)) > ss3 = 0.0303100 +/- 0.0510420 (guessed as 0.030310 (0.051043)) > ss4 = 0.0000000 +/- 0.0303840 (guessed as 0.000000 (0.030385)) > ss5 = -0.0008090 +/- 0.0043530 (guessed as -0.000809 (0.004353)) > ss6 = 0.0059560 +/- 0.0089810 (guessed as 0.005956 (0.008981)) > alpha= -0.0006040 +/- 0.0023740 (guessed as -0.000604 (0.002374)) > alpha2= 0.0073900 +/- 0.0016520 (guessed as 0.007390 (0.001652)) > alpha3= -0.0167250 +/- 0.0535940 (guessed as -0.016725 (0.053595)) > alpha4= -0.0120340 +/- 0.0773040 (guessed as -0.012034 (0.077302)) > alpha5= -0.0216900 +/- 0.0127530 (guessed as -0.021690 (0.012751)) > alpha6= 0.0219980 +/- 0.0183950 (guessed as 0.021998 (0.018395)) > > Def parameters: > delr_1 = -0.0027560 > delr_2 = 0.0337230 > delr_3 = -0.0763210 > delr_4 = -0.0549150 > delr_5 = -0.0989780 > delr_6 = 0.1003830 > > Set parameters: > amp1 = .7 > > > Correlations between variables: > e0 and alpha --> 0.8490 > e0 and alpha2 --> 0.8006 > ss3 and alpha4 --> 0.7123 > alpha and alpha2 --> 0.6792 > ss4 and alpha5 --> 0.6298 > ss and ss2 --> 0.6114 > alpha5 and alpha6 --> -0.5959 > ss5 and alpha4 --> 0.5328 > ss3 and ss4 --> 0.5300 > ss5 and ss6 --> -0.4931 > ss4 and alpha3 --> -0.4617 > ss2 and alpha5 --> 0.3847 > ss6 and alpha6 --> 0.3700 > ss2 and alpha3 --> 0.3276 > ss4 and ss5 --> -0.2764 > alpha2 and alpha4 --> 0.2506 > All other correlations are below 0.25 > > > > > > ------------------------------ > > Message: 3 > Date: Thu, 11 Nov 2004 12:19:06 -0500 > From: Scott Calvin <scalvin(a)slc.edu> > Subject: Re: [Ifeffit] Commercial MoS2 -- Correction > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <3.0.1.32.20041111121906.00a657e0(a)mail.slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Dan, > > A couple of quick thoughts, that might also be helpful to people starting > out with EXAFS fitting. > > First of all, the good news is that changing the k-weight does not seem to > affect the values ifeffit finds for the parameters significantly (i.e. I > didn't see any that moved outside of their uncertainties). That's very > reassuring. The fact that the fit quality is noticeably better at k-wt 3 > suggests to me that you might try raising kmin a bit--maybe the k-wt 3 fit > works better because the fits are struggling at the low end of the k-range? > Sometimes it's hard to get the background to work right down at low k, and > it looks like you have plenty of data range based on the number of > independent points. > > Second, I don't like forcing S02 to 0.7 because 0.5 is too low very much. > An iffy sample or problems with normalization can both suppress S02 below > the nominally ideal value. Forcing the fit to adopt a higher S02 then just > has the effect of screwing up correlated variables, like the Debye-Waller > factors. I'd look for explanations for the low S02 rather than just > disallowing it. (I certainly have set S02 in some of my published work, but > those were cases of complex fits where it seemed to be a false minimum, > rather than a sample or normalization error.) > > Finally, I'd try some "reasonable" constraints on your MS paths. If they > are triangle paths, it is not possible to come up with a rigorous formula > for how to write the debye-waller factors and alpha's for MS paths in terms > of the direct scattering paths, because you don't know for sure how the > motions of nearby atoms correlate. But in my experience, which is mainly > with metals and transition metal oxides, fits are generally not > particularly sensitive to the details of MS path constraint strategies. > Here's a constraint strategy of medium complexity that I teach my > undergrads that you can try: > > Def the alpha's of the MS paths to be the average of the alpha's for the > direct scattering paths that make them up, weighted by the length of the > segment. It's quite probable in a material such as yours that some segment > will be a S-S path which you don't have available as a direct scattering > path. Maybe just leave that piece out of the average. > > Def the ss's of the MS paths to be the sum of the ss's for the direct > scattering paths that make them up, divided by 4. Why divided by 4? Because > the ss for a half-path is rigorously equal to 1/4 the ss for a whole path. > Why add them? If the ss of each segment is truly uncorrelated, then adding > them is statistically proper. Of course, this is a truly awful > approximation in some cases, notably as the paths come closer to being > focused (i.e. one of the angles of the triangle becomes large). In cases > where the biggest angle in the triangle is more than about 140 degrees, I > just treat it as a focused path, but I doubt that's true for your two MS's. > > Please understand that this constraint scheme is fairly arbitrary! When > working with a new material, I suggest trying a constraint scheme like > this, and then seeing how sensitive the fit is to this constraint. For > example, multiply all the ss's of the MS's paths by 2 and see how stable > the fit is. Go back to allowing the alpha for the MS paths to vary freely > and see again if the fit is stable. This kind of probing will tell you > whether the MS paths are something that have to be carefully considered, or > if they are just a small correction to your fit that should be included but > don't have to be included particularly carefully. It is my experience that > the latter is often the case, but you have to find out for yourself on this > material. > > --Scott Calvin > Sarah Lawrence College > > At 08:20 AM 11/11/2004 -0800, you wrote: > >Hi List, > > > > It appears that changing the k-weight on my fit does improve the fit. > >I still have the problem of forcing the sO^2's on the two MS paths to be > >positive. Here's some new data with k-weight 3: > >> > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 21, Issue 8 > ************************************** >

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Commercial MoS2 -- Correction
by dmc＠pdx.edu 11 Nov '04

11 Nov '04

Hi List, It appears that changing the k-weight on my fit does improve the fit. I still have the problem of forcing the sO^2's on the two MS paths to be positive. Here's some new data with k-weight 3: Thanks, Dan Project title : Fitting merge 10_15_04.chi ============================================================ Independent points = 28.581054688 Number of variables = 13.000000000 Chi-square = 1527.118835332 Reduced Chi-square = 98.011262136 R-factor = 0.025169471 Measurement uncertainty (k) = 0.000185138 Measurement uncertainty (R) = 0.081594539 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): e0 = 1.1335810 +/- 1.3393990 (guessed as 1.133581 (1.339426)) ss = 0.0035870 +/- 0.0003110 (guessed as 0.003587 (0.000311)) ss2 = 0.0042850 +/- 0.0002780 (guessed as 0.004285 (0.000278)) ss3 = 0.0303100 +/- 0.0510420 (guessed as 0.030310 (0.051043)) ss4 = 0.0000000 +/- 0.0303840 (guessed as 0.000000 (0.030385)) ss5 = -0.0008090 +/- 0.0043530 (guessed as -0.000809 (0.004353)) ss6 = 0.0059560 +/- 0.0089810 (guessed as 0.005956 (0.008981)) alpha= -0.0006040 +/- 0.0023740 (guessed as -0.000604 (0.002374)) alpha2= 0.0073900 +/- 0.0016520 (guessed as 0.007390 (0.001652)) alpha3= -0.0167250 +/- 0.0535940 (guessed as -0.016725 (0.053595)) alpha4= -0.0120340 +/- 0.0773040 (guessed as -0.012034 (0.077302)) alpha5= -0.0216900 +/- 0.0127530 (guessed as -0.021690 (0.012751)) alpha6= 0.0219980 +/- 0.0183950 (guessed as 0.021998 (0.018395)) Def parameters: delr_1 = -0.0027560 delr_2 = 0.0337230 delr_3 = -0.0763210 delr_4 = -0.0549150 delr_5 = -0.0989780 delr_6 = 0.1003830 Set parameters: amp1 = .7 Correlations between variables: e0 and alpha --> 0.8490 e0 and alpha2 --> 0.8006 ss3 and alpha4 --> 0.7123 alpha and alpha2 --> 0.6792 ss4 and alpha5 --> 0.6298 ss and ss2 --> 0.6114 alpha5 and alpha6 --> -0.5959 ss5 and alpha4 --> 0.5328 ss3 and ss4 --> 0.5300 ss5 and ss6 --> -0.4931 ss4 and alpha3 --> -0.4617 ss2 and alpha5 --> 0.3847 ss6 and alpha6 --> 0.3700 ss2 and alpha3 --> 0.3276 ss4 and ss5 --> -0.2764 alpha2 and alpha4 --> 0.2506 All other correlations are below 0.25

2 1

Commercial MoS2 fit
by dmc＠pdx.edu 11 Nov '04

11 Nov '04

Hi List, I have tried a variety of different things to get this fit to work. It seems pretty decent now, although, for my two MS paths (4,5) I had to force the sO^2's to be positive. In the process one of them is now zero. My parameter 'amp' wants to be 0.5 so I had to set it to 0.7 because I know that it shouldn't be as low as 1/2. Changing the k-weight doesn't seem to help. Here's my Data: Thanks, Dan Project title : Fitting merge 10_15_04.chi ============================================================ Independent points = 28.581054688 Number of variables = 13.000000000 Chi-square = 5995.284754934 Reduced Chi-square = 384.780419245 R-factor = 0.043668737 Measurement uncertainty (k) = 0.000187262 Measurement uncertainty (R) = 0.006509968 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): e0 = 0.8645560 +/- 1.2283680 (guessed as 0.864556 (1.228344)) ss = 0.0041070 +/- 0.0005190 (guessed as 0.004107 (0.000519)) ss2 = 0.0043590 +/- 0.0005200 (guessed as 0.004359 (0.000520)) ss3 = 0.0217810 +/- 0.0333390 (guessed as 0.021781 (0.033341)) ss4 = 0.0000000 +/- 0.0509500 (guessed as 0.000000 (0.050951)) ss5 = 0.0000360 +/- 0.0063810 (guessed as 0.000036 (0.006382)) ss6 = 0.0028730 +/- 0.0071340 (guessed as 0.002873 (0.007133)) alpha = -0.0012530 +/- 0.0031940 (guessed as -0.001253 (0.003193)) alpha2 = 0.0075160 +/- 0.0022250 (guessed as 0.007516 (0.002225)) alpha3 = -0.0171580 +/- 0.0323200 (guessed as -0.017158 (0.032321)) alpha4 = -0.0165410 +/- 0.1054840 (guessed as -0.016541 (0.105487)) alpha5 = -0.0181860 +/- 0.0187940 (guessed as -0.018186 (0.018795)) alpha6 = 0.0227330 +/- 0.0147690 (guessed as 0.022733 (0.014767)) Def parameters: delr_1 = -0.0057180 delr_2 = 0.0342980 delr_3 = -0.0782970 delr_4 = -0.0754820 delr_5 = -0.0829880 delr_6 = 0.1037370 Set parameters: amp1 = .7 Correlations between variables: ss3 and alpha4 --> 0.8462 e0 and alpha --> 0.8335 ss4 and alpha3 --> -0.6693 e0 and alpha2 --> 0.6159 ss and ss2 --> 0.6114 alpha5 and alpha6 --> -0.5959 alpha4 and alpha5 --> -0.5821 ss4 and ss5 --> -0.5505 ss3 and alpha5 --> -0.5246 alpha and alpha2 --> 0.5146 ss5 and ss6 --> -0.4931 ss2 and alpha5 --> 0.4681 ss5 and alpha3 --> 0.3885 ss6 and alpha6 --> 0.3700 alpha2 and alpha5 --> 0.3208 ss2 and alpha4 --> -0.2992 ss4 and alpha5 --> 0.2955 ss3 and ss4 --> 0.2923 ss5 and alpha2 --> -0.2842 e0 and alpha4 --> -0.2781 ss2 and ss3 --> -0.2677 alpha3 and alpha5 --> -0.2523 All other correlations are below 0.25

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new versions of my codes
by Bruce Ravel 05 Nov '04

05 Nov '04

Hi! I just posted new source code tarballs of my codes at my web site and at SourceForge. A while back, there were some problems with a bug in the updater script for unix. If you have problems using the updater, either download and install the tarball by hand or grab the latest copy of the updater script and run it instead: http://leonardo.phys.washington.edu/~ravel/software/exafs/utilities/horae_u… The fixed updater script will be installed once you get the new tarball installed. An updater package for windows users will hopefully be available next week, assuming no serious bugs are found in the new codes. For Athena and Artemis, this is mostly a bug fix release, although a lot of bugs were fixed. Athena has one new feature, which is an indicator at the top of the list of data groups which tells you when your project has been modified and needs to be saved. Clicking on this indicator is the same as choosing "File->Save project". For those people following the development version of Artemis, along with a number of important bug fixes there are two major new features: 1. In the Fits menu, there is a menu item for saving a "full data" file. This file records the data, the fit, the residual, the background (if appropriate), and the window as columns in a single file. If chi(R) or chi(q) is saved, the FT parameters appropriate to the chosen fit are used for all the columns. 2. You can now revert your project to a previous fitting model by selecting that fit from the Data and Paths List and selecting the restore option from the Fits menu. Fit model restoration can also be done with the right-click menu on the list on the log viewer page. I'll be eager to hear how well this works for others. This is a pretty exciting release of the development version for me because I have now completed all the features I was planning to add in this round of development. I am going to take a break from adding major new features to Artemis for a while to give people a chance to find the bugs. I am also planning to release a windows executable of the development version within the next few weeks to allow some more people to try out all the new features. As always, let me know what problems you run into. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide
by Kelly, Shelly D. 05 Nov '04

05 Nov '04

Hi Dan, Sigma2 can not be negative. It is the mean square displacement of the half path length. You can force it to be positive by using abs(ss) on the definition page for each path in the fit. Shelly > -----Original Message----- > From: dmc(a)pdx.edu [mailto:dmc@pdx.edu] > Sent: Thursday, November 04, 2004 10:19 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Fitting Commercial Molybdenum Disulfide > > Hi List, > > Here's my most recent data. I was able to look at the individual > paths > and changed my R-range to 2-4.5 angstroms on the first set of data, I set > the > second set of data to the same range, although 4 works better as a maximum > for > that set. The k-range on the second range had to be truncated though. > > Six paths are used for each fit, same parameters, except for amp (0.7 for > one > ~0.8 for the other). The seperate data sets still have a few parameters > that > are outside of the error bars of the other (ss2,ss3,ss4,alpha, > alpha2,alpha5). > What can I do to get these beamlines to agree? > > delr_# define alpha# * reff > all other parameters guessed. > ss for each path, only one e0 for all > > Thanks for the help, Dan > > > First Data set -- Full k-range works best, Full range used for fit. > Project title : Fitting merge 10_15_04.chi > > Guess parameters +/- uncertainties (initial guess): > e0 = 0.8686930 +/- 1.1038290 (guessed as 0.868694 > (1.103841)) > ss = 0.0041150 +/- 0.0004990 (guessed as 0.004115 > (0.000499)) > ss2 = 0.0044360 +/- 0.0004450 (guessed as 0.004436 > (0.000445)) > ss3 = 0.0243560 +/- 0.0201400 (guessed as 0.024368 > (0.020159)) > ss4 = -0.0065470 +/- 0.0047820 (guessed as -0.006545 > (0.004786)) > ss5 = -0.0016100 +/- 0.0050490 (guessed as -0.001611 > (0.005047)) > ss6 = 0.0059980 +/- 0.0139390 (guessed as 0.005996 > (0.013935)) > alpha = -0.0011360 +/- 0.0029380 (guessed as -0.001136 > (0.002938)) > alpha2 = 0.0071480 +/- 0.0019780 (guessed as 0.007148 > (0.001978)) > alpha3 = -0.0060900 +/- 0.0273580 (guessed as -0.006078 > (0.027378)) > alpha4 = -0.0198570 +/- 0.0154200 (guessed as -0.019851 > (0.015430)) > alpha5 = 0.1399050 +/- 0.0148530 (guessed as 0.139906 > (0.014848)) > alpha6 = 0.0199630 +/- 0.0268690 (guessed as 0.019961 > (0.026862)) > > Def parameters: > delr_1 = -0.0051820 > delr_2 = 0.0326180 > delr_3 = -0.0277930 > delr_4 = -0.0906110 > delr_5 = 0.6384270 > delr_6 = 0.0910950 > > Set parameters: > amp1 = .7 > > > Correlations between variables: > e0 and alpha --> 0.8170 > e0 and alpha2 --> 0.6726 > ss and ss2 --> 0.6591 > alpha and alpha2 --> 0.5516 > alpha5 and alpha6 --> -0.4856 > e0 and alpha3 --> 0.4083 > alpha3 and alpha4 --> 0.3588 > ss5 and ss6 --> -0.3581 > alpha and alpha3 --> 0.3100 > alpha2 and alpha3 --> 0.3045 > ss2 and alpha6 --> 0.2745 > e0 and ss3 --> 0.2649 > ss and ss3 --> 0.2627 > ss2 and ss3 --> 0.2626 > ss6 and alpha5 --> -0.2510 > All other correlations are below 0.25 > > > > > > > > > > > > Second Data Set -- Trucated k-range (2-13.5) > Project title : Fitting merge 10_15_04.chi > > Independent points = 25.270507813 > Number of variables = 14.000000000 > Chi-square = 1202.598221935 > Reduced Chi-square = 106.703108852 > R-factor = 0.057229121 > Measurement uncertainty (k) = 0.000827712 > Measurement uncertainty (R) = 0.022111003 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > amp = 0.7976070 +/- 0.1361170 (guessed as 0.776348 (0.139898)) > ss = 0.0037770 +/- 0.0015530 (guessed as 0.003589 > (0.001617)) > e0 = 0.5608430 +/- 1.8018380 (guessed as 0.642687 > (1.861307)) > alpha = -0.0061290 +/- 0.0049080 (guessed as -0.005966 > (0.005078)) > ss2 = 0.0029050 +/- 0.0009970 (guessed as 0.002686 > (0.001078)) > ss3 = 0.0075410 +/- 0.0094220 (guessed as 0.005992 > (0.008858)) > ss4 = -0.0110250 +/- 0.0035850 (guessed as -0.011776 > (0.004653)) > ss5 = -0.0042000 +/- 0.0078070 (guessed as -0.007610 > (0.005250)) > alpha2 = 0.0038110 +/- 0.0030450 (guessed as 0.003762 > (0.003187)) > alpha3 = -0.0037820 +/- 0.0145580 (guessed as 0.001200 > (0.015976)) > alpha4 = -0.0212550 +/- 0.0107080 (guessed as -0.011852 > (0.014417)) > alpha5 = 0.1151980 +/- 0.0236640 (guessed as 0.113430 > (0.014973)) > ss6 = 0.0028560 +/- 0.0166050 (guessed as -0.007250 > (0.003624)) > alpha6 = 0.0193530 +/- 0.0299640 (guessed as 0.001791 > (0.008195)) > > Def parameters: > delr_1 = -0.0279670 > delr_2 = 0.0173920 > delr_3 = -0.0172570 > delr_4 = -0.0969910 > delr_5 = 0.5256830 > delr_6 = 0.0883130 > > > Correlations between variables: > amp and ss --> 0.8382 > e0 and alpha --> 0.8048 > amp and ss2 --> 0.7964 > e0 and alpha2 --> 0.7533 > ss3 and alpha5 --> 0.7397 > ss5 and alpha4 --> -0.6999 > ss and ss2 --> 0.6591 > alpha and alpha2 --> 0.6159 > alpha5 and ss6 --> 0.6116 > ss5 and alpha3 --> -0.5790 > ss5 and alpha6 --> -0.5023 > ss3 and ss6 --> 0.4804 > alpha4 and alpha5 --> -0.4375 > e0 and alpha3 --> 0.4083 > ss4 and ss5 --> -0.4047 > ss3 and alpha4 --> -0.3972 > alpha5 and alpha6 --> 0.3827 > alpha3 and alpha6 --> 0.3498 > ss3 and ss5 --> -0.3278 > amp and ss3 --> 0.3209 > ss4 and ss6 --> 0.3181 > alpha and alpha3 --> 0.3100 > alpha2 and alpha3 --> 0.3045 > ss4 and alpha3 --> 0.2948 > amp and ss5 --> 0.2820 > ss2 and alpha6 --> 0.2745 > ss and ss3 --> 0.2627 > ss2 and ss3 --> 0.2626 > amp and alpha6 --> 0.2589 > alpha2 and alpha5 --> 0.2581 > All other correlations are below 0.25 > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Fitting Commercial Molybdenum Disulfide
by dmc＠pdx.edu 04 Nov '04

04 Nov '04

Hi Mailing list, I'm back at fitting commercial Molybdenum Disulfide to a Hexagonal p 63/m m c space group. Although my present fit is reasonable, thanks to the mailing list in August, I was hoping someone might have more suggestions to optimize it. Also, in order to better my fit, I still have seperate e0's, one for the first path, one for the remaining 2 paths. I haven't gotten a satisfactory physical explanation for this and I thought someone might have a good one. Also, the data on the same sample from two different beamlines seems to be somewhat different, namely the Reduced chi-square is very different (75.6 in one, 636.4 in the other). In both cases I use the first 3 single scattering paths. I may have included too much info, but better too much than too little. Thank You, Dan Carter Here are my parameters in both cases, values differ somewhat: Set: Amp = 0.7 guess: eO ~ 1.57 (1.52) (used for first path) guess: eO_1 ~ -4.77 (2.43) (used for remaining 2 paths) guess: ss ~ 0.0027 (0.000427) guess: alpha ~ -0.004 (0.003255) (positive for second fit) delr_1: alpha*reff First Fit: Project title : Fitting merge 10_15_04.chi Comment : Prepared by : Contact : Started : 11:49:36 on 22 October, 2004 This fit at : 11:10:57 on 28 October, 2004 Environment : Artemis 0.7.010 using Windows 2000, perl 5.006001, Tk 800.024, and Ifeffit 1.2.6 ============================================================ Independent points = 14.312500000 Number of variables = 4.000000000 Chi-square = 779.303886008 Reduced Chi-square = 75.568861674 R-factor = 0.041210572 Measurement uncertainty (k) = 0.000827712 Measurement uncertainty (R) = 0.022111003 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): e0_1 = -4.7737110 +/- 2.4268840 (guessed as -4.773687 (2.426889)) ss = 0.0027360 +/- 0.0004270 (guessed as 0.002736 (0.000427)) e0 = 1.5684690 +/- 1.5209160 (guessed as 1.568507 (1.520918)) alpha = -0.0040060 +/- 0.0032550 (guessed as -0.004006 (0.003255)) Def parameters: delr_1 = -0.0158980 Set parameters: amp = 0.7 Correlations between variables: e0_1 and alpha --> 0.8622 e0 and alpha --> 0.7870 e0_1 and e0 --> 0.7064 All other correlations are below 0.25 Project title : Fitting merge 10_15_04.chi Comment : Prepared by : Contact : Started : 11:49:36 on 22 October, 2004 This fit at : 11:10:57 on 28 October, 2004 Environment : Artemis 0.7.010 using Windows 2000, perl 5.006001, Tk 800.024, and Ifeffit 1.2.6 ============================================================ Independent points = 14.312500000 Number of variables = 4.000000000 Chi-square = 779.303886008 Reduced Chi-square = 75.568861674 R-factor = 0.041210572 Measurement uncertainty (k) = 0.000827712 Measurement uncertainty (R) = 0.022111003 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): e0_1 = -4.7737110 +/- 2.4268840 (guessed as -4.773687 (2.426889)) ss = 0.0027360 +/- 0.0004270 (guessed as 0.002736 (0.000427)) e0 = 1.5684690 +/- 1.5209160 (guessed as 1.568507 (1.520918)) alpha = -0.0040060 +/- 0.0032550 (guessed as -0.004006 (0.003255)) Def parameters: delr_1 = -0.0158980 Set parameters: amp = 0.7 Correlations between variables: e0_1 and alpha --> 0.8622 e0 and alpha --> 0.7870 e0_1 and e0 --> 0.7064 All other correlations are below 0.25 ===== Data set >>merge 6_17_04.chi<< ======================================== file: C:\Ifeffit\horae\stash\artemis.project.3\chi_data\merge 6_17_04.chi title lines: Athena data file -- Athena version 0.8.032 Saving merge 6_17_04 (group=merge) as chi(k) . Element=Mo Edge=K Background parameters . E0=20007.492 Eshift=0.000 Rbkg=1.000 . Standard=None . Kweight=2.0 Edge step=0.749 . Fixed step=no Flatten=yes . Pre-edge range: [ -150.000 : -75.000 ] . Normalization range: [ 150.000 : 895.199 ] . Spline range: [ 0.952 : 995.207 ] Clamps: None/Strong Foreward FT parameters . Kweight=2 Window=kaiser-bessel Phase correction=no . k-range: [ 2.000 : 16.100 ] dk=0.00 Backward FT parameters . R-range: [ 1.000 : 3.000 ] . dR=0.00 Window=kaiser-bessel Plotting parameters . Multiplier=1 Y-offset=0.000 . Merge in k space of: ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.101 (mos2_101) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.102 (mos2_102) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.103 (mos2_103) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.104 (mos2_104) k-range = 2.000 - 13.500 dk = 2.000 k-window = kaiser-bessel k-weight = 2 R-range = 1.000 - 3.000 dR = 0.100 R-window = kaiser-bessel fitting space = R background function = none phase correction = none R-factor for this data set = 0.74613 Second Fit: Project title : Fitting merge 10_15_04.chi Comment : Prepared by : Contact : Started : 11:49:36 on 22 October, 2004 This fit at : 11:23:36 on 28 October, 2004 Environment : Artemis 0.7.010 using Windows 2000, perl 5.006001, Tk 800.024, and Ifeffit 1.2.6 ============================================================ Independent points = 14.312500000 Number of variables = 4.000000000 Chi-square = 6562.747150466 Reduced Chi-square = 636.387602469 R-factor = 0.032979787 Measurement uncertainty (k) = 0.000181935 Measurement uncertainty (R) = 0.004860095 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): e0_1 = -4.0720090 +/- 1.9194040 (guessed as -4.773711 (2.426884)) ss = 0.0046360 +/- 0.0004110 (guessed as 0.002736 (0.000427)) e0 = 1.7659580 +/- 1.1543880 (guessed as 1.568469 (1.520916)) alpha = 0.0010900 +/- 0.0028430 (guessed as -0.004006 (0.003255)) Def parameters: delr_1 = 0.0043250 Set parameters: amp = 0.7 Correlations between variables: e0_1 and alpha --> 0.8416 e0 and alpha --> 0.8045 e0_1 and e0 --> 0.7141 All other correlations are below 0.25 ===== Data set >>merge 10_15_04.chi<< ======================================== file: C:\Ifeffit\horae\stash\artemis.project.3\chi_data\merge 10_15_04.chi title lines: Athena data file -- Athena version 0.8.032 Saving merge 6_17_04 (group=merge) as chi(k) . Element=Mo Edge=K Background parameters . E0=20007.492 Eshift=0.000 Rbkg=1.000 . Standard=None . Kweight=2.0 Edge step=0.749 . Fixed step=no Flatten=yes . Pre-edge range: [ -150.000 : -75.000 ] . Normalization range: [ 150.000 : 895.199 ] . Spline range: [ 0.952 : 995.207 ] Clamps: None/Strong Foreward FT parameters . Kweight=2 Window=kaiser-bessel Phase correction=no . k-range: [ 2.000 : 16.100 ] dk=0.00 Backward FT parameters . R-range: [ 1.000 : 3.000 ] . dR=0.00 Window=kaiser-bessel Plotting parameters . Multiplier=1 Y-offset=0.000 . Merge in k space of: ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.101 (mos2_101) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.102 (mos2_102) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.103 (mos2_103) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.104 (mos2_104) k-range = 2.000 - 13.500 dk = 2.000 k-window = kaiser-bessel k-weight = 2 R-range = 1.000 - 3.000 dR = 0.100 R-window = kaiser-bessel fitting space = R background function = none phase correction = none R-factor for this data set = 0.71585 Paths used to fit Both Data Sets, degen, s02 the same. other values different: F1 p 63/m m c: feff0001.dat .. feff = C:\Ifeffit\horae\stash\artemis.project.3\data0.feff2\feff0001.dat id = reff= 2.4135, nlegs= 2, path= Mo<->S label = r = 2.416130 degen = 6.000000 s02 = 0.700000 e0 = 1.765958 dr = 0.002630 ss2 = 0.004636 F1 p 63/m m c: feff0002.dat .. feff = C:\Ifeffit\horae\stash\artemis.project.3\data0.feff2\feff0002.dat id = reff= 3.1500, nlegs= 2, path= Mo<->Mo label = r = 3.153433 degen = 6.000000 s02 = 0.700000 e0 = -4.072009 dr = 0.003433 ss2 = 0.004636 F1 p 63/m m c: feff0003.dat .. feff = C:\Ifeffit\horae\stash\artemis.project.3\data0.feff2\feff0003.dat id = reff= 3.9683, nlegs= 2, path= Mo<->S label = r = 3.972625 degen = 6.000000 s02 = 0.700000 e0 = -4.072009 dr = 0.004325 ss2 = 0.004636

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IFEFFIT: Writing more than 16 arrays with write_data()
by Matt Newville 04 Nov '04

04 Nov '04

Hi Norbert, (Replying to the whole group this time....) On Wed, 3 Nov 2004, Norbert Weiher wrote: > Matt, > > I was just discussing with Bruce about exporting more than 15 sets with the > write_data() command. I am doing fits with lots of paths and like to have it > exported to one file... would it be difficult to increase the number of > arrays exportable by this command above 16 in IFEFFIT? It would not be difficult, and the current limit is definitely too low. I think it's a two line fix. But there will still be a finite limit of number of arrays. So: is 100 arrays enough? Do you need a fixed source kit or dll? And how quickly? This doesn't seem like a full release change to me. I haven't made any source changes to the stable distribution since July. So a question for Bruce and everyone else: Are there any other bug reports or suggestions for changes to the core? --Matt

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Problem exporting fit data with ARTEMIS
by Norbert Weiher 02 Nov '04

02 Nov '04

Dear Friends, I did a multi-dataset fit (9 data sets) and had the following problem: When trying to export all the fits to a single file (using save marked groups as), I got an empty file and artemis trapped a warning like the following. For sake of reproducing, I attached the file. My Tk version is the one which we should use (i.e. not the newest one) and saving just the experimental data in just the same fashion works... Any ideas why this happens? Regards, Norbert -- Error message follows -- Tk::Error: Can't call method "dispose" on unblessed reference at /usr/bin/artemi s line 7971. main::save_selected at /usr/bin/artemis line 7971 [\&main::save_selected,k] Tk callback for .menu1.menu.menu7 Tk::__ANON__ at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk.pm li ne 228 Tk::Menu::Invoke at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk/M enu.pm line 530 (command bound to event) main::__ANON__('Tk::Error: Can\'t call method "dispose" on unblessed ref erenc...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) l ine 402 Tk::Error('MainWindow=HASH(0x953f240)','Can\'t call method "dispose" on unblessed reference at /usr/b...','main::save_selected at /usr/bin/artemis line 7971','[\&main::save_selected,k]','Tk callback for .menu1.menu.menu7','Tk::__ANO N__ at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thr...','Tk::Menu::Invoke at /u sr/lib/perl5/site_perl/5.8.0/i586-linux...','(command bound to event)') called a t /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk.pm line 340 eval {...} called at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-mu lti/Tk.pm line 340 Tk::MainLoop() called at /usr/bin/artemis line 1785 -- Dr. rer. nat. Norbert Weiher (weiher(a)chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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RE: [Ifeffit] Artimis
by Chen, Yongsheng 02 Nov '04

02 Nov '04

Hi Matt, I did encounter that "No absorbing atom (ipot=0) defined" error sometimes, but I run Artemis only after I have feff calculations done. By the way, I use FEFF8. Thanks everybody for your kind help. I am afraid I can not do more test now since I am leaving tomorrow for Argonne for more XAFS experiments. Will check back if the problem remains after I have tried what you have suggested. Have a good weekend. Yongsheng > ---------- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Matt Newville > Reply To: XAFS Analysis using Ifeffit > Sent: Friday, October 22, 2004 2:20 PM > To: ravel(a)phys.washington.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Artimis > > Hi, > > > On Friday 22 October 2004 4:38 pm, Chen, Yongsheng wrote: > > > Thanks for your advices. I did edit my Feff.inp in Word, but did not have > > > any problems with the old version. > > > > It is certainly possible to do so, but you MUST be careful to save the > > file as text. Because it is so easy to forget and just save in > > whatever format Word decides to use, I always discourage people from > > using Word for that purpose. > > Actually, Feff6 (and ifeffit) handle Unix and Windows line endings > just fine, but do have a harder time with Mac line-endings. I'm > not sure I know how to fix this: As far as I can tell it's at the > level of the fortran's read() statement. Sorry. > > One thing that confuses me is that Feff6 *should* have reported a > Feff 6L.02 > Fatal Error: No absorbing atom (ipot=0) defined > > which could have been used as a clue that something went wrong. > I don't know how artemis checks if a feff run went OK. > > > Hey Mac users! Could someone suggest a simple editor that Yongsheng, > > a new Mac user, should consider for the task of editing the kinds of > > text files that Feff and similar programs work with? > > TextEdit can save file with Unix-style line endings, especially if > you set the default to using 'Plain text' in the Preferences menu. > > BBedit is a popular and very good editor for Mac OS X. > > --Matt > > _______________________________________________ > 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] choosing dk values
by Scott Calvin 01 Nov '04

01 Nov '04

Hi Mike, I would add to Matt's reply that it is sometimes quite important to realize that for a Hanning window and similar windows where there is a "sill" over which the window function goes from 0 to 1, the sill extends from kmin-dk/2 to kmin+dk/2 and from kmax-dk/2 to kmax+dk/2. This means that as you increase dk you actually sample more k-space, albeit in a suppressed way. Why is this important? Suppose you have something really screwy in your data at k=11.9 inverse angstroms...a second edge comes to mind as a possibility. You might then reasonably set kmax to 11 and think you're staying away from the problem. (Well, it might be messing up your background, but that's an issue for another day...) But suppose you make dk = 2. Now you are actually sampling data up to k = 12, which includes the really screwy bit. In some cases that can be a source of problems...it took me a long time to catch on to that particular wrinkle when I was starting out! Of course, with Artemis and Athena this is easy to catch, because you can plot the window function by checking the box marked "Window" (that Bruce is a clever dude). --Scott Calvin Sarah Lawrence College At 01:13 PM 11/1/2004 -0600, you wrote: >Hi Mike, > >On Mon, 1 Nov 2004, Michael A Groves wrote: > >> I'm doing some fitting with Artemis, and I noticed that, for >> different values of dk, I get better or worse fits. The only >> information I've gotten so far about dk was in the IFEFFIT >> documentation, and it basically said, "Don't mess with it." >> Can anyone give me more information on choosing a good dk value? >> Or, should I just stick with the default? >>

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choosing dk values
by Michael A Groves 01 Nov '04

01 Nov '04

Hi all, I'm doing some fitting with Artemis, and I noticed that, for different values of dk, I get better or worse fits. The only information I've gotten so far about dk was in the IFEFFIT documentation, and it basically said, "Don't mess with it." Can anyone give me more information on choosing a good dk value? Or, should I just stick with the default? Thanks, Mike Groves

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RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide
by Kelly, Shelly D. 29 Oct '04

29 Oct '04

Hi Dan, I would suggest using one ezero with three different delr values for these three paths. You are introducting only one more variable. delr and ezero are correlated so by constraining delr you need more ezero values or vise versa. Shelly > -----Original Message----- > From: dmc(a)pdx.edu [mailto:dmc@pdx.edu] > Sent: Friday, October 29, 2004 10:25 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Fitting Commercial Molybdenum Disulfide > > > Mike & list, > > Where can I find a reasonable model for my delr terms, > if I do assume > that the bond angles are changing/there is no isotropic > expansion? Is there a > description somewhere in the archives that I could look at? > > Creating different sigma squared parameters for each > path did help the R- Factor somewhat, but not the reduced > chi. Here's some data: > > > Fit with seperate sigma's: > > Independent points = 14.312500000 > Number of variables = 6.000000000 > Chi-square = 5778.957783654 > Reduced Chi-square = 695.212966455 > R-factor = 0.029041008 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0_1 = -4.0347670 +/- 2.9998980 > (guessed as -4.072009 > (1.919404)) > ss = 0.0042860 +/- 0.0005990 > (guessed as 0.004636 > (0.000411)) > e0 = 1.6770760 +/- 1.3230290 > (guessed as 1.765958 > (1.154388)) > alpha = 0.0009180 +/- 0.0034050 > (guessed as 0.001090 > (0.002843)) > ss2 = 0.0048160 +/- 0.0006910 (0.0000) > ss3 = 0.0225310 +/- 0.0657250 (0.0000) > Def parameters: > delr_1 = 0.0036440 > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0_1 and alpha --> 0.8542 > e0 and alpha --> 0.8470 > e0_1 and e0 --> 0.7407 > e0_1 and ss3 --> 0.7060 > alpha and ss3 --> 0.4715 > ss2 and ss3 --> -0.4214 > e0_1 and ss2 --> -0.3892 > e0 and ss3 --> 0.3772 > alpha and ss2 --> -0.2680 > All other correlations are below 0.25 > > > > > > > > > Fit without (original): > > > Independent points = 14.312500000 > Number of variables = 4.000000000 > Chi-square = 6562.747150128 > Reduced Chi-square = 636.387602437 > R-factor = 0.032979787 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0_1 = -4.0720130 +/- 1.9194050 > (guessed as -4.072009 > (1.919404)) > ss = 0.0046360 +/- 0.0004110 > (guessed as 0.004636 > (0.000411)) > e0 = 1.7659560 +/- 1.1543880 > (guessed as 1.765958 > (1.154388)) > alpha = 0.0010900 +/- 0.0028430 > (guessed as 0.001090 > (0.002843)) > > Def parameters: > delr_1 = 0.0043250 > > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0_1 and alpha --> 0.8416 > e0 and alpha --> 0.8045 > e0_1 and e0 --> 0.7141 > All other correlations are below 0.25 > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide
by Kelly, Shelly D. 29 Oct '04

29 Oct '04

Hi Dan, Take a look at the fit in q-space with the model below. I suspect that you have left out important Multiple scattering paths that would cause a miss-fit to the data at low k values. To test for this, change the fit range to something like 4.0 1/Anstroms for k-min value, and try again. Shelly > -----Original Message----- > From: dmc(a)pdx.edu [mailto:dmc@pdx.edu] > Sent: Friday, October 29, 2004 11:03 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide > > > Hi Shelly, > > I seperated the delr's with different alpha terms, but > Mike seems to think > that this is assuming isotropic expansion that isn't there. > Also, the reduced > chi-square has gone up 150 or so. > > delr# define: alpha# * reff > > > Thanks for the help, Dan > > > Results with 1 eO and differing delr's: > > Independent points = 14.312500000 > Number of variables = 7.000000000 > Chi-square = 6186.771083042 > Reduced Chi-square = 846.054165202 > R-factor = 0.031090393 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > ss = 0.0042720 +/- 0.0006590 > (guessed as 0.004636 > (0.000411)) > e0 = 1.3293700 +/- 1.4673640 > (guessed as 1.765958 > (1.154388)) > alpha = -0.0001750 +/- 0.0040010 > (guessed as 0.001090 > (0.002843)) > ss2 = 0.0043180 +/- 0.0007370 (0.0000) > ss3 = 0.0072300 +/- 0.0164390 (0.0000) > alpha2 = 0.0076940 +/- 0.0027880 (0.0000) > alpha3 = -0.0512670 +/- 0.0232140 (0.0000) > > Def parameters: > delr_1 = -0.0006930 > delr_2 = 0.0305320 > delr_3 = -0.2034430 > > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0 and alpha --> 0.8441 > ss3 and alpha2 --> 0.7651 > ss2 and alpha2 --> -0.6441 > e0 and alpha2 --> 0.5682 > ss2 and ss3 --> 0.4871 > alpha and alpha2 --> 0.4785 > ss3 and alpha3 --> 0.3825 > e0 and alpha3 --> -0.2743 > All other correlations are below 0.25 > > > > > > Original (2 e0s): > > > Independent points = 14.312500000 > Number of variables = 6.000000000 > Chi-square = 5778.957783654 > Reduced Chi-square = 695.212966455 > R-factor = 0.029041008 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0_1 = -4.0347670 +/- 2.9998980 > (guessed as -4.072009 > (1.919404)) > ss = 0.0042860 +/- 0.0005990 > (guessed as 0.004636 > (0.000411)) > e0 = 1.6770760 +/- 1.3230290 > (guessed as 1.765958 > (1.154388)) > alpha = 0.0009180 +/- 0.0034050 > (guessed as 0.001090 > (0.002843)) > ss2 = 0.0048160 +/- 0.0006910 (0.0000) > ss3 = 0.0225310 +/- 0.0657250 (0.0000) > > Def parameters: > delr_1 = 0.0036440 > > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0_1 and alpha --> 0.8542 > e0 and alpha --> 0.8470 > e0_1 and e0 --> 0.7407 > e0_1 and ss3 --> 0.7060 > alpha and ss3 --> 0.4715 > ss2 and ss3 --> -0.4214 > e0_1 and ss2 --> -0.3892 > e0 and ss3 --> 0.3772 > alpha and ss2 --> -0.2680 > All other correlations are below 0.25 > > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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to Gael Poirier
by Bruce Ravel 27 Oct '04

27 Oct '04

Hi folks, Recently Gael Poirier has been having a problem using Athena with some XANES data. For whatever reason, when I send mail to Gael it gets bounced back. But he seems to receive mail from the mailing list. Go figure. Sorry for filling up people mail boxes, but I am using the list to send this along... B =============================================================== Gael, Thanks for sending the data. It is now clear what went wrong. I recently made a change in how Athena tries to detect xanes data, that is data that does not extend very far into the extended region. The advantage of identifying data that is xanes and not exafs is that Athena then does not have to do a background removal, which saves a little bit of time doing chores like alignment and normalization. Sadly, you have uncovered a bug. That happens. Your bug is that the kmax for the fourier transform gets set to when the data are imported as xanes. Then Athena mistakenly aborts when it sees this, even though no FT will be performed. Oops! Fortunately there is an easy work-around. When you import the data, explicitly import them as mu(E) rather than xanes(E). The only draw-back of doing so is that Athena will do a background removal every time you change the normalization parameters. That's not a big loss. Thanks for pointing this out. I will certainly fix this in the next release. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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citing Artemis and Athena?
by k-kupiecki＠northwestern.edu 27 Oct '04

27 Oct '04

Hi everyone, I'm in the process of writing up my thesis and I've used Athena and Artemis quite a bit for the analysis of my SEXAFS data.... I was wondering what is the appropriate way to give references for this software and it's use? To my knowledge there are journal articles etc. regarding AUTOBK, FEFFIT, etc. Do I cite those? are there additional ways I should cite to give credit for Athena and Artemis too? Thanks for any suggestions you have! -Kristine Witkowski

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Re: Ifeffit Digest, Vol 20, Issue 22
by Michel Jaouen 25 Oct '04

25 Oct '04

>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: Artimis (Matt Newville) > 2. RE: Artimis (Scott Calvin) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Sat, 23 Oct 2004 13:46:12 -0500 (CDT) >From: Matt Newville <newville(a)cars.uchicago.edu> >Subject: RE: [Ifeffit] Artimis >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <Pine.LNX.4.44.0410222107350.19561-100000@corvette> >Content-Type: TEXT/PLAIN; charset=US-ASCII > > >> I did encounter that "No absorbing atom (ipot=0) defined" error >> sometimes, but I run Artemis only after I have feff calculations >> done. > >I don't understand whether Feff ran to completion or not. Are you >saying that you made a successful run of Feff (including real >output files) but that Artemis still failed to read this >calculation? That seems pretty strange. > >> By the way, I use FEFF8. > >For Feff8, I believe you need to be much more careful about line >endings. It's not able to use Windows line-endings on unixes, for >example. > >But also: why would you use Feff8 for EXAFS analysis, as with >artemis?? Feff8 is a XANES code. As far as I know, it does not >give any improvements for EXAFS. > >--Matt > > > > > >------------------------------ > >Message: 2 >Date: Sun, 24 Oct 2004 11:23:03 -0400 >From: Scott Calvin <SCalvin(a)slc.edu> >Subject: RE: [Ifeffit] Artimis >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Cc: SCalvin(a)slc.edu >Message-ID: <a06010203bda178b3a7b7(a)[130.132.241.87]> >Content-Type: text/plain; charset="us-ascii" ; format="flowed" > >> >>But also: why would you use Feff8 for EXAFS analysis, as with >>artemis?? Feff8 is a XANES code. As far as I know, it does not >>give any improvements for EXAFS. > > >FEFF8 does give at least one improvement for EXAFS, which I've used >on occasion: the self-consistent field calculation can be used to >give an improved estimate of E0 prior to fitting. > >--Scott Calvin >Sarah Lawrence College > I agree with Scott: SCF calculation gives more reliable estimate of E0 because the Fermi level is more accurate. It makes that, when several atomic species are involved, you only need in principle one E0 for fitting (I have verified this point, at least for the case I'm presently working on). >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 20, Issue 22 >*************************************** -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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Re: Ifeffit Digest, Vol 20, Issue 22
by Michel Jaouen 25 Oct '04

25 Oct '04

Yongsheng, > > I did encounter that "No absorbing atom (ipot=0) defined" error >> sometimes, but I run Artemis only after I have feff calculations >> done. > >I don't understand whether Feff ran to completion or not. Are you >saying that you made a successful run of Feff (including real >output files) but that Artemis still failed to read this >calculation? That seems pretty strange. > >> By the way, I use FEFF8. > >For Feff8, I believe you need to be much more careful about line >endings. It's not able to use Windows line-endings on unixes, for >example. Artemis works fine for me (on a Mac) with feff8: just ask in the menu for Import feff calculation and choose the folder where is your feff8 calculation where you must have: feff.inp feffXXX.dat files files.dat paths.dat BUT ALL files must be Unix! Following Matt's advice, use BBEdit Lite (that's free or if you had some money buy BBEdit (the last vesrion is 8): that is really a very good Editor (the best for me) on Mac. Then open your files, check the option button and select Unix for Line Breaks. Best regards Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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RE: [Ifeffit] Artimis
by Chen, Yongsheng 23 Oct '04

23 Oct '04

Hi Bruce, Thanks for your advices. I did edit my Feff.inp in Word, but did not have any problems with the old version. I tried the cleaned up Feff.inp you sent me, it worked better in the sense that I could close Artemis after the warning appeared again, with my own version, I would have to use ForceQuit. I am a new mac user. I try to understand the message in the artemis.trap, although it's a text file, I do not understand too much. I sort of remember there is a notice about Perl version on some website. I have seen 'Perl' appearing in the trap file in many places, is this relative to the problem? Thanks for your help. Yongsheng > ---------- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Bruce Ravel > Reply To: ravel(a)phys.washington.edu;XAFS Analysis using Ifeffit > Sent: Friday, October 22, 2004 10:49 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Artimis > > <<File: feff.inp>><<File: ATT1852209.txt>> > On Friday 22 October 2004 12:30 pm, Chen, Yongsheng wrote: > > I installed the lastest version of Artemis, but met problems when trying to > > import FEFF calculations. The trap file and the feff input file are > > attached. The old version worked fine. I have a mac. > > Yongsheng, > > What is the history of the files you sent? The feff.inp file you > included in your email has a large number of non-printable chatracters > at the beginning of the file and all of the lines are terminated by > Macintosh end-of-line characters (that is, carriage return (ascii 13), > rather than line-feed (ascii 10)). Artemis currently makes no effort > to deal correctly with Mac EOL characters and Feff (as compiled on an > OSX, which is really a version of Unix under the hood) will not do so > either. Some quick tests suggested that is the case. > > So, there seems to be two problems with the feff.inp file you sent me > > 1. The junk characters at the beginning of the file. Those will > certainly confuse feff. > > 2. The end-ol-line characters. > > You can probably fix both by opening up the feff.inp file in any text > editor, stripping out the junk at the top of the file and explicitly > saving the file as a unix text file. I am sure that some of the Mac > users on the list can provide more details should you need it. > > I am suspicious that you might have edited the feff.inp file with a > word processor (such as MS Word). That is a very poor idea because it > can be hgard to avoid the situation where the word processor inserts > additional, not-for-display information in the file that neither > Artemis nor Feff will know how to deal with. If you create your > feff.inp files outside of Artemis, you must be careful not to do so in > a way that inserts additional stuff into the file. > > When I cleaned up the feff.inp file you sent, Artemis had no problem > with it. > > I suppose that another possibility is that the file became > "contaminated" after you tried it in Artemis but before I received > your email. If that is the case, it is really important that you fix > that and try submitting your question again. It is possible that you > are seeing some deeper problem in Artemis, but that I am focussing on > the ways in which the file became contaminated. That's a problem > because I am therefore not addressing the real issue. > > Attached is the cleaned up file, which works for me. > > Regards, > B > > -- > Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu > Code 6134, Building 3, Room 405 > Naval Research Laboratory phone: (1) 202 767 2268 > Washington DC 20375, USA fax: (1) 202 767 4642 > > NRL Synchrotron Radiation Consortium (NRL-SRC) > Beamlines X11a, X11b, X23b > National Synchrotron Light Source > Brookhaven National Laboratory, Upton, NY 11973 > > My homepage: http://feff.phys.washington.edu/~ravel> > EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ > > >

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Athena
by Gael Poirier 22 Oct '04

22 Oct '04

Hi Bruce, I have a problem with Athena version 0.8.032. When I select several opened groups as marked groups and plot them in E (using plot marked groups in E), it doesn't work and only the last opened spectrum appears in the graphic window. The program gives an error message:"ERROR:the minimum value of the forward fourier transform range exceeds the maximum value". However, I've tried with Athena 0.8.024 (IFEFFIT 1.2.5) and it worked very well. How can I plot all the groups in the same graphic window using Athena 0.8.032? Thank you very much Gael

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Artimis
by Chen, Yongsheng 22 Oct '04

22 Oct '04

Hi Bruce, I installed the lastest version of Artemis, but met problems when trying to import FEFF calculations. The trap file and the feff input file are attached. The old version worked fine. I have a mac. Thanks a lot. Yongsheng <<ARTEMIS.TRAP>> <<feff.inp>>

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RE : RE : [Ifeffit] Is artemis running on G5 Mac,
by POGER David 202545 21 Oct '04

21 Oct '04

Hello Thank you very much for your help Matt. Your advice was quite obvious in fact but I followed it to use horae_update properly. Thanks to that, I could see what was my first problem. I had an error about Aquaterm (the installation script couldn't find an Aquaterm library file (aquaterm.1.0.0.dylib I believe). So, I re-installed Aquaterm (the latest version found on SourceForge). And then, the installation was perfect, without any error anymore. And, here is now my second problem. When I open a project file (a '.chi' file) in Artemis, the program takes about 5s to try to open it (with the comment 'plotting in r space' at the bottom of the window), and then crashes down... I'm really sorry! Any other help or any idea? Thank you David > -----Message d'origine----- > De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] De la part de Matt Newville > Envoyé : jeudi 14 octobre 2004 23:54 > À : XAFS Analysis using Ifeffit > Objet : Re: RE : [Ifeffit] Is artemis running on G5 Mac, > > > On Thu, 14 Oct 2004, POGER David 202545 wrote: > > > I fear it doesn't work for me. I have untared the Horae-045.tar > > file in the Ifeffit directory. And when I type 'perl > > Makefile.PL', the installation script crashes and says 'Could > > not open /config/Config.mak file for reading'. The Greek gods > > may not be with me! I'll wait for the next tarball... Thanks a > > lot in adavance! > > This is probably still an issue with permissions, but I'm not sure > what you did exactly. It sounds like you tried to run horae_update > in the Applications/Ifeffit directory. If so, this probably won't > work, as you probably do NOT have write permissions to the > /Applications/Ifeffit directory, and horae_update creates a > folder (horae-045) to build the code it will install. > > Let me be more specific. Sorry if most of this is obvious! > 1. Open a Terminal > 2. move to your home directory: Type 'cd'. > 3. run horae_update with permission to write to the > /Library/Perl and /Applications/Ifeffit. Type > 'sudo horae_update'. When prompted for a password, > type the password for your user account (that is, > the same one you logged in as). > > 4. If you get a message that says 'command not found', then > read the message. > a) if the message begins 'bash: ... command not found' > then type '. /Applications/Ifeffit/bin/iff_init.sh' > Yes, that's a '.' followed by a space. > b) if the message begins 'tcsh: ... command not found' > then type 'source /Applications/Ifeffit/bin/iff_init.csh' > > Then do 'sudo horae_udate' again. > > If you already have the horae-045.tar.gz file, 'sudo horae_update' > is exactly the same as: > tar xvzf horae-045.tar.gz > cd horae-045 > perl Makefile.PL > sudo make install > > Once the installation is successful, you can remove the > 'horae-045' folder. > > --Matt > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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(no subject)
by Gael Poirier 19 Oct '04

19 Oct '04

Hello, I'm a new user of FEFFIT programs and actually I have some problems with Athena (version 0.8.032). In fact, when I try to import data files, the program apparently identificate the commas (,) as a column separator. I think that my input file is correct: ASCII data and each column separated by a space. What can I do to resolve it?? Thank you very much for your help Gaël Poirier Universidade Estadual Paulista (UNESP) Brazil

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RE : [Ifeffit] Is artemis running on G5 Mac,
by POGER David 202545 14 Oct '04

14 Oct '04

Hi I fear it doesn't work for me. I have untared the Horae-045.tar file in the Ifeffit directory. And when I type 'perl Makefile.PL', the installation script crashes and says 'Could not open /config/Config.mak file for reading'. The Greek gods may not be with me! I'll wait for the next tarball... Thanks a lot in adavance! David > -----Message d'origine----- > De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] De la part de Bruce Ravel > Envoyé : mercredi 13 octobre 2004 19:23 > À : XAFS Analysis using Ifeffit > Objet : Re: [Ifeffit] Is artemis running on G5 Mac, > > On Wednesday 13 October 2004 12:49 pm, Matt Newville wrote: > > Hi, > > > > OK, I agree that a simple 'horae_update' also did not work to > > update thes for me. It appears that the new codes are built > > but not installed. This definitely did work for me: > > tar xvzf horae-045.tar.gz > > cd horae-045 > > perl Makefile.PL > > make > > sudo make install > > > > I believe that 'sudo horae_update' will also work. > > > > --Matt > > > > PS: Oddly, without the 'sudo', horae_update did not give a > > warning about installing as root. I got largely the same log file > > as Stefano, and also got this on the screen: > > > > print() on closed filehandle OUT at /Applications/Ifeffit/bin/horae_update > > line 263. > > > > perhaps this is printed to STDERR not STDOUT?? it's not in > > horae_update.log. Anyway, this is where the warning about > > trying to install as someone other than root is. > > > > The horae_update could probably use other improvements, as > > horae_update --force --file=horae-045.tar.gz > > > > still attempts to download the tarball, requires it to > > be named 'horae-045.tar.gz' and then deletes it. > > What you said is exactly right. There was a problem that had > horae_update complain about a closed file handle and exit just before > doing the "make install" step. I think I fixed it and asked Stefano > to give it a try. > > I'll post a fix tomorrow (I hope) and the fix will be included in the > next tarball. > > B > > > -- > Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu > Code 6134, Building 3, Room 405 > Naval Research Laboratory phone: (1) 202 767 2268 > Washington DC 20375, USA fax: (1) 202 767 4642 > > NRL Synchrotron Radiation Consortium (NRL-SRC) > Beamlines X11a, X11b, X23b > National Synchrotron Light Source > Brookhaven National Laboratory, Upton, NY 11973 > > 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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RE: [Ifeffit] delR and delE
by Kelly, Shelly D. 14 Oct '04

14 Oct '04

Ritika, delr and Eo are correlated. So you can (1) force delr to the same for two paths with different Eo-values, or (2) use two different delr-values with one Eo-value. Most prefer the second choice over the second choice. Also, Eo is important at low k-values. If you move your k-range that you use in the FT of your data you might find a different Eo value, or that only one Eo is needed with a shorter k-range than with a longer k-range. I do not think that you model is "okay" with three Eo values. How much does EO differ? Usually Eo is the last button I turn on when I try to make a model fit the data. Large Ezero values (> 10 eV) are common if you have a poor model. So use only one Eo at the beginning. Often I just set it to zero, and then when the model gets close, try to add one or two more to really get it right on. I would try only one Eo first. Let delr vary for all the paths and change the k-range. See how small the k-range needs to be before you can fit the data with only one E0 value. 1.9 Angstroms is a short distance. It would seem more reasonable to me that you might need two Eo values. One for this short shell and then one more for all the other shells. Give these things a try and tell us how it goes. Shelly > -----Original Message----- > From: ritika.uppal(a)yale.edu [mailto:ritika.uppal@yale.edu] > Sent: Wednesday, October 13, 2004 2:50 PM > To: Segre, Carlo U.; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] delR and delE > > > > I have 3 different values of Eo for the fit. 2 for the first > shell and > the 3rd for the rest of the paths. Actually the bond distance > of the 6 > oxygens in the first shell differs. 3 of them have a bond length of > around 1.9 A and the other 3 around 2.2 A. So using one value of Eo > does not fit the second peak very well. > > Ritika > > > Quoting "Carlo U. Segre" <segre(a)iit.edu>: > > > > > delR is just the deviation from the distance you used in > the feff.inp > > file to generate the paths. It can be positive or negative > depending > > on > > > > whether these atoms are closer or further away from the > central atom. > > > > By delE, do you mean Eo? When you say two values, do you mean > > different values for two different shells? > > Carlo > > > > > > On Wed, 13 Oct 2004, ritika.uppal(a)yale.edu wrote: > > > > > Hi guys, > > > I have a few questions about the fitting parameters. the delR for > > my > > > fit has a negative value. Is that wrong or its possible to have a > > > negative value?? and also for the first shell, I have 2 values of > > del > > > E. Does that mean that the model I am using is not a good one?? > > > > > > Thanks for all your help > > > Ritika > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > -- > > Carlo U. Segre -- Professor of Physics > > Associate Dean for Special Projects, Graduate College > > Illinois Institute of Technology > > Voice: 312.567.3498 Fax: 312.567.3494 > > Carlo.Segre(a)iit.edu http://www.iit.edu/~segre > > _______________________________________________ > > 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] delR and delE
by Kelly, Shelly D. 13 Oct '04

13 Oct '04

See below for clarification.. > -----Original Message----- > From: Kelly, Shelly D. > Sent: Wednesday, October 13, 2004 3:10 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] delR and delE > > > Ritika, > > delr and Eo are correlated. So you can (1) force delr to the > same for two paths with different Eo-values, or (2) use two > different delr-values with one Eo-value. Most prefer the > second choice over the second choice. This should read "Most prefer the second choice over the first." > > Also, Eo is important at low k-values. If you move your > k-range that you use in the FT of your data you might find a > different Eo value, or that only one Eo is needed with a > shorter k-range than with a longer k-range. > > I do not think that you model is "okay" with three Eo values. > How much does EO differ? Usually Eo is the last button I > turn on when I try to make a model fit the data. Large Ezero > values (> 10 eV) are common if you have a poor model. So use > only one Eo at the beginning. Often I just set it to zero, > and then when the model gets close, try to add one or two > more to really get it right on. > > I would try only one Eo first. Let delr vary for all the > paths and change the k-range. See how small the k-range > needs to be before you can fit the data with only one E0 value. > > 1.9 Angstroms is a short distance. It would seem more > reasonable to me that you might need two Eo values. One for > this short shell and then one more for all the other shells. > > Give these things a try and tell us how it goes. > > Shelly > > > -----Original Message----- > > From: ritika.uppal(a)yale.edu [mailto:ritika.uppal@yale.edu] > > Sent: Wednesday, October 13, 2004 2:50 PM > > To: Segre, Carlo U.; XAFS Analysis using Ifeffit > > Subject: Re: [Ifeffit] delR and delE > > > > > > > > I have 3 different values of Eo for the fit. 2 for the first > > shell and > > the 3rd for the rest of the paths. Actually the bond distance > > of the 6 > > oxygens in the first shell differs. 3 of them have a bond length of > > around 1.9 A and the other 3 around 2.2 A. So using one value of Eo > > does not fit the second peak very well. > > > > Ritika > > > > > > Quoting "Carlo U. Segre" <segre(a)iit.edu>: > > > > > > > > delR is just the deviation from the distance you used in > > the feff.inp > > > file to generate the paths. It can be positive or negative > > depending > > > on > > > > > > whether these atoms are closer or further away from the > > central atom. > > > > > > By delE, do you mean Eo? When you say two values, do you mean > > > different values for two different shells? > > > Carlo > > > > > > > > > On Wed, 13 Oct 2004, ritika.uppal(a)yale.edu wrote: > > > > > > > Hi guys, > > > > I have a few questions about the fitting parameters. > the delR for > > > my > > > > fit has a negative value. Is that wrong or its possible > to have a > > > > negative value?? and also for the first shell, I have 2 > values of > > > del > > > > E. Does that mean that the model I am using is not a good one?? > > > > > > > > Thanks for all your help > > > > Ritika > > > > _______________________________________________ > > > > Ifeffit mailing list > > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > > > > -- > > > Carlo U. Segre -- Professor of Physics > > > Associate Dean for Special Projects, Graduate College Illinois > > > Institute of Technology > > > Voice: 312.567.3498 Fax: 312.567.3494 > > > Carlo.Segre(a)iit.edu http://www.iit.edu/~segre > > > _______________________________________________ > > > 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 > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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RE: [Ifeffit] Is artemis running on G5 Mac,
by Stefano Luciano Ciurli 13 Oct '04

13 Oct '04

Hi all, sorry Bruce but I had to leave the office and have had no time to try your new script. I wil lgive it a try tomorrow afternoon (loaded with teaching around here). I'll let you know. Ciao, Stefano

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horae-045
by Bruce Ravel 13 Oct '04

13 Oct '04

Hey, It's been a busy week. I just posted another new tarball. This fixes: 1. The bug Norbert reported in Athena's file selection dialog (this bug does not exist in the current build of the windows executable, so there is not pressing need to update it) 2. The problem Igor reported with importing project files from the previous version of the development branch of Artemis 3. A bug in the build scripts that resulted in not being able to use the Atoms page in the development branch of Artemis. New tarballs are at SourceForge and at my web site. As before, this release is mostly intended for people following the development branch of Artemis. Thanks to Norbert, Igor, and Carlo for their help. Hopefully this one will work better than the last two...... ;-) B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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RE : [Ifeffit] Is artemis running on G5 Mac,
by POGER David 202545 13 Oct '04

13 Oct '04

Hi all I have tried horae_update... but it doesn't work... in fact, Artemis remains stuck to version 0.7.007, Athena to version 0.8.029 and so on. As if there was no update! I really don't know what I can do to make Artemis and Athena work. If anyone has any idea, one is welcome. David > -----Message d'origine----- > De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] De la part de Matt Newville > Envoyé : dimanche 3 octobre 2004 05:22 > À : XAFS Analysis using Ifeffit > Objet : Re: [Ifeffit] Is artemis running on G5 Mac, > > Michel, David, > > Have either of you tried upgrading Artemis using horae_update? I > don't know that it will help, but it might.... > > The message Michel sent looks like a Perl error that wouldn't be > processor dependent, so I'm not sure what's going on. All I can > say is that Artemis works for me on a G4. I'm perfectly willing > to believe that my system has something different from or not > included in the dmg (I try hard for this to not happen, but > realize that 'works for me' is not always sufficient). > > Can anyone else using a Mac report on how Artemis works for them? > Thanks, > > --Matt > > _______________________________________________ > 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 Digest, Vol 20, Issue 11
by Michel Jaouen 13 Oct '04

13 Oct '04

>On Wednesday 13 October 2004 10:15 am, Stefano Ciurli wrote: >> Hello David, >> >> >I have tried horae_update... but it doesn't work... in fact, Artemis >> > remains stuck to version 0.7.007, Athena to version 0.8.029 and so on.. As >> > if there was no update! I really don't know what I can do to make Artemis >> > and Athena work. >> >> i confirm that the horae_update script (run yesterday on my G4, not >> G5 - lucky you) yields the same versions of Artemis and Athena that >> you mention here. >> Stefano > >David, Stefano, > >What you guys say confuses me. When I run horae_update (not on a Mac, >but I don't see why that should make a difference) it downloads >horae-045, which contains athena 0.8.033 and artemis 0.7.011. The >horae-update script writes a log file which may be useful to me in >figuring out why it is behaving differently for you than it does does >for me. > >If it is behaving somehow wrong for you, you could always go to >SourceForge, download the package, unpack it, and do the "perl >Makefile.PL; make; sudo make install" incantation by hand. (The >script just automates those steps, it does not do anything different.) I confirm what Bruce says: running horae_update_042 (sudo horae_update) on my G5 (I haven't yet installed 045) fixes all my previously mentioned problems. All run smoothly. However, what makes me more puzzeling is that I don't obtain the same results (using of course all the same parameters) from Artemis compared to those I have found using Feffit in command line (Unix version). Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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rpm packages of horae, ifeffit, sixpack
by Carlo U. Segre 10 Oct '04

10 Oct '04

Hello All: I realized that there was a low cost method for me to generate *.rpm packages from my *.deb packages. I make no promises on how these will install or work and I really won't be able to do much to fix them since they are generated automatically but please let me know if they are useful or not working. You can get all the programs in my x-ray software archive at: http://fermi.phys.iit.edu/debian/rpm/ If anyone knows how best to make these available in an automated way please let me know and I will try to implement it. BTW: all these packages are comversions from the Debian "unstable" tree, which has the latest libraries and files. This is most likely the best version to work with Fedora. Cheers, Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Re: Iffefit for Mac OSX 10.3
by Matt Newville 08 Oct '04

08 Oct '04

Hi Ann, I think this should have been to the Ifeffit list: On Thu, 7 Oct 2004, Ann Liang wrote: > Hi Bruce or Matt, > > I encountered some problems with athena when I recently switched my > workstation from PC to Mac. The graphic window didn't show up at all which > made it impossible to process any data. Could you please provide me some > guidance on this issue? I assume you installed the Mac installer (ifeffit-1.2.6_Mac10.3.dmg). I'm not sure what the problem is, but I'd recommend these steps: First, install Aquaterm from http://aquaterm.sourceforge.net/ . That might 'just fix' the problem. If it doesn't, edit the file /Applications/Ifeffit/bin/iff_init.sh to read (line 7) export PGPLOT_DEV=/XS instead of export PGPLOT_DEV=/AQT (Make sure to leave no extra space around the = sign). That will tell Ifeffit to use X-Window graphics instead of Aquaterm. The Aquaterm device is a little bit nicer, but the X-Windows one should definitely work. If you're running athena by clicking the icon, that should be enough. If you're running athena by typing 'athena' in a Terminal, _and_ you're using the tcsh shell, you should also edit /Applications/Ifeffit/bin/iff_init.csh to read setenv PGPLOT_DEV /XS (Here, the space is necessary and there is no = sign!! The syntax for these two shells is different, but the meaning is the same). Hope that's enough, and sorry for the pain. If not let me know, --Matt

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New user to EXAFS
by William Bisson 07 Oct '04

07 Oct '04

Dear all, I am a new user to EXAFS and I am currently experimenting with the anaylsis software available. Does anyone know how to convert raw data collected from Daresbury, UK, station 7.1 to be read by IFEFFIT? I shall be grateful for any help Kind Regards William Bisson

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Athena bug?
by Carlo U. Segre 07 Oct '04

07 Oct '04

Bruce, Norbert: I tried to duplicate norbert's error with version 044 of horae. I used a multielement detector file frm MR-CAT and I noticed no problems or errors. I also tried Norbert's file and I noticed a couple of things. 1. Athena cannot find the column titles. In the MR-CAT data file, there is no problem with this. I tried removing the "#L " at the front of the title line in Norbert's file but still the titles cannot be parsed. 2. The first time I try to import the file, I have no errors apart form the warning that the data is not in order and must be sorted (the first line is the culprit). If I try to import the same file, the error occurs and the channel selection box is badly deformed (most buttons are missing and only 3 channels are noted). 3. I removed the out of order line (the first data line) and the imports worked fine more than once. There are still no titles. It looks like there are two issues here. One is that the out of order first line somehow messes up some internal variables in the program. In the past the "sort data" function seemed to work fine. The second issue is that Norbert's file is not compatible with Athena's parsing of column titles. I really don't know what the parameters are here so I can't say what the problem is but I will try to compare the MR-CAT multilelment files with this one to see what is going on. Norbert, it looks like you can prvent problems temporarily by jsut deleting the first data line. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Athena bug?
by Norbert Weiher 07 Oct '04

07 Oct '04

Bruce, I just upgraded to the newest package today - since then, athena does not like to import data files anymore... When I select a data set (which was possible to import with the older version), The "channel select" box appears totally small, and ATHENA dumps this error to the screen. I included a data file to test for your convenience. The channels to import are (10-22)/4 (fluorescence data). Hope its not a machine-typical thingie :) I still have the SuSE 8.2 installed and run on the latest IFEFFIT. Ah, sometimes importing the first set works (e.g. when reading multiple sets at once), but then it automatically crashes at the next set. Cheers, Norbert Nasty codebabbling follows... Athena0.8.033warn/home/weiher/.horae/stash/ATHENA.TRAPCODE(0x911ce90) at /usr/bin/athena line 1364 main::__ANON__('Tk::Error: Can\'t use string ("Sort data") as a HASH ref whil...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) line 402 Tk::Error('MainWindow=HASH(0x9c14628)','Can\'t use string ("Sort data") as a HASH ref while "strict r...','main::read_raw at /usr/bin/athena line 3786','main::read_file at /usr/bin/athena line 3537','main::__ANON__ at /usr/bin/athena line 453','(command bound to event)') called at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk.pm line 340 eval {...} called at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk.pm line 340 Tk::MainLoop() called at /usr/bin/athena line 1420 -- Dr. rer. nat. Norbert Weiher (weiher(a)chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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horae 043 tarball
by Bruce Ravel 06 Oct '04

06 Oct '04

Hi folks, I just put a new tarball on SourceForge and on my web site. This new tarball will be of interest to the people following the development version of Artemis. There are only small changes to the stable codes in this tarball and I will not be building new Windows executables. This new tarball is really only about the development version of Artemis. I am almost finished with the features I am planning for this round of development. (See the Artemis page on my web site for the complete list of features planned for this round of the development branch.) Once I polish off the last major feature, we will go into a testing period. Once I am content, I'll build some trial Windows executables. Once I am content with that, I'll merge the new feature back into the stable branch. Among the new features in the development branch: 1. A revamped feff interpretation page with new functionality 2. A revamped atoms page with new functionality 3. Major improvements to the fit history system 4. Direct import of data from Athena project files 5. A new type of parameter on the GDS page -- an "after" parameter is like a def in that it takes a math expression, but it is not part of the fit and is evaluated only after the fit finishes and then is recorded in the log file 6. Lots of bug fixes and minor feature enhancements. Lots of neat new stuff. Have fun and let me know what goes splat. B P.S. Carlo, FYI, two new files: Ifeffit/lib/artemis.doc/artemis_fitinfo.pod and Tk/TextUndoQuiet.pm. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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horae 044
by Bruce Ravel 06 Oct '04

06 Oct '04

Okee dokee. This time for sure! I fixed the bug in the install script. The TextUndoQuiet.pm file should end up in the right place now. New tarballs are at SF and on my web site. Let me know if it doesn't or if some other problem crops up. Thanks, Igor. Then... On Wednesday 06 October 2004 06:00 pm, Adam Webb wrote: > Bruce, > > FYI I get the same thing. Also the file permission is not set to > executable. I only mention it because the other files in the Tk directory > are set that way so TextUndoQuiet.pm stands out. That shouldn't matter, but thanks for letting me know, Adam. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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horae 043
by Igor Frota de Vasconcelos 06 Oct '04

06 Oct '04

Hi Bruce, I just installed the newest version of Horae and when I try to start Diana it complains that: Can't locate Tk/TextUndoQuiet.pm in @INC (@INC contains: /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Tk/widgets.pm line 14. at /usr/bin/diana line 61 BEGIN failed--compilation aborted at /usr/bin/diana line 67. I could a problem with my system but since the previous version was working fine, I thought I should report. I use Fedora Core 1 and Tk-800.024.tar.gz. Thanks, Igor -- IGOR F. VASCONCELOS Department of Physics University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556 USA phone: (1 574) 631 5650 fax: (1 574) 631 5952 e-mail: idevasco(a)nd.edu www.nd.edu/~idevasco

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Is artemis running on G5 Mac,
by Michel Jaouen 05 Oct '04

05 Oct '04

Hi, I'm trying to run artemis on my Mac on which one I have used Matt's installer (ifeffit-1.2.6_Mac10.3.dmg). Actually, I'm unable to run a two shells fit , even for Cu. Therefore, I go back to the 1st shell alone fit: it works (idem for Zr, a crazy stuff because for hcp we need two shells, but anyway. BUT EVEN for a ONE shell fit it returns an error: The following message was trapped by Artemis: Artemis0.7.007warn/Users/mjaouen/.horae/stash/ARTEMIS.TRAPCODE(0x1e3e9d4)/U sers/mjaouen/.horae/stash/artemis.pro ject.1/ at /Applications/Ifeffit/bin/artemis line 1564 main::__ANON__('Use of uninitialized value in numeric lt (<) at /Applications...') called at /Applicatio ns/Ifeffit/bin/artemis line 8988 main::check_path('HASH(0x1ddc568)') called at /Applications/Ifeffit/bin/artemis line 8861 main::write_paths('GLOB(0x140c07c8)','data0',1,'all','HASH(0x1de42e8)') called at /Applications/Ifeffit/ bin/artemis line 9602 main::generate_script(1) called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 247 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 247 Tk::__ANON__('Tk::Button=HASH(0x1eddaf4)') called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/B utton.pm line 111 Tk::Button::butUp('Tk::Button=HASH(0x1eddaf4)') called at /Library/Perl/5.8.1/darwin-thread-multi-2level /Tk.pm line 406 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 406 Tk::MainLoop() called at /Applications/Ifeffit/bin/artemis line 1766 This message was dumped to a file: /Users/mjaouen/.horae/stash/ARTEMIS.TRAP Please include that file along with your explanation when you make a bug report. What is strange is that I can save the project in such a condition, eg artemis behaves as if there is no error (the artemis palette is active while it is empty for a 2 shells fit and inactive, I cann't close it for exemple by cliquing on the red button: all windows are frozen)! Looking at the the monitor for activity, I see that Perl was using 99% of the CPU! In fact artemis crashes when trying to write the log file. The only way to go out from is to kill artemis in the X11 terminal window. I must say that I have asked to one of my friend in Paris (G. Hug) to make the install on his machine and he experienced exactely the same punition! Both we are using G5 based Mac. I suspect Perl and/or Tk to be not fully compatible with this CPU. Therefore my question is simple: has anybody been able to run artemis (version 0.7.007) on G5? Must I update horae and how to do it? Cheers Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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RE : [Ifeffit] Is artemis running on G5 Mac,
by POGER David 202545 01 Oct '04

01 Oct '04

Hi I use a Mac IBook and I have the same problem. I can't use the Mac version of Artemis (I use Matt's installer as well, ifeffit-1.2.6_Mac10.3.dmg). Artemis crashes and the only way to close it is killing the job in the X11 window. Cheers David -----Message d'origine----- De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] De la part de Michel Jaouen Envoyé : vendredi 1 octobre 2004 16:09 À : ifeffit(a)millenia.cars.aps.anl.gov Objet : [Ifeffit] Is artemis running on G5 Mac, Hi, I'm trying to run artemis on my Mac on which one I have used Matt's installer (ifeffit-1.2.6_Mac10.3.dmg). Actually, I'm unable to run a two shells fit , even for Cu. Therefore, I go back to the 1st shell alone fit: it works (idem for Zr, a crazy stuff because for hcp we need two shells, but anyway. BUT EVEN for a ONE shell fit it returns an error: The following message was trapped by Artemis: Artemis0.7.007warn/Users/mjaouen/.horae/stash/ARTEMIS.TRAPCODE(0x1e3e9d4)/U sers/mjaouen/.horae/stash/artemis.pro ject.1/ at /Applications/Ifeffit/bin/artemis line 1564 main::__ANON__('Use of uninitialized value in numeric lt (<) at /Applications...') called at /Applicatio ns/Ifeffit/bin/artemis line 8988 main::check_path('HASH(0x1ddc568)') called at /Applications/Ifeffit/bin/artemis line 8861 main::write_paths('GLOB(0x140c07c8)','data0',1,'all','HASH(0x1de42e8)') called at /Applications/Ifeffit/ bin/artemis line 9602 main::generate_script(1) called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 247 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 247 Tk::__ANON__('Tk::Button=HASH(0x1eddaf4)') called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/B utton.pm line 111 Tk::Button::butUp('Tk::Button=HASH(0x1eddaf4)') called at /Library/Perl/5.8.1/darwin-thread-multi-2level /Tk.pm line 406 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 406 Tk::MainLoop() called at /Applications/Ifeffit/bin/artemis line 1766 This message was dumped to a file: /Users/mjaouen/.horae/stash/ARTEMIS.TRAP Please include that file along with your explanation when you make a bug report. What is strange is that I can save the project in such a condition, eg artemis behaves as if there is no error (the artemis palette is active while it is empty for a 2 shells fit and inactive, I cann't close it for exemple by cliquing on the red button: all windows are frozen)! Looking at the the monitor for activity, I see that Perl was using 99% of the CPU! In fact artemis crashes when trying to write the log file. The only way to go out from is to kill artemis in the X11 terminal window. I must say that I have asked to one of my friend in Paris (G. Hug) to make the install on his machine and he experienced exactely the same punition! Both we are using G5 based Mac. I suspect Perl and/or Tk to be not fully compatible with this CPU. Therefore my question is simple: has anybody been able to run artemis (version 0.7.007) on G5? Must I update horae and how to do it? Cheers Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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Re: [Ifeffit] New user to EXAFS
by Bruce Ravel 30 Sep '04

30 Sep '04

On Thursday 30 September 2004 10:16 am, ritika.uppal(a)yale.edu wrote: > Hi Bruce, > Thanks for the reply. I have attached the artemis project file with > this email. Ritika, I'll add this to my list of things to look at today and get back to you when I have some information. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Fitting Problems via Artemis
by hsnuboy＠ksu.edu 27 Sep '04

27 Sep '04

Dear All, Greeting.This is Yu-Chuan. After struggling a long time, I just felt a little bit progress in the fitting program. However, there are still some questions confused me. 1. What's the meaning and purpose of "Fit Background" in Artemis? I know the backgound as "bare atom" in EXAFS theory. So, what kind of situation we need to use this function? 2. Is that possible for the Debye-Waller factor(sigma^2) be negative? Actually, I am not so sure about the physical meaning for that. Just know its a kind of thermal vibration. 3. Sometimes, The results obtained from Artemis seems not the same. Says, the guess parameters and uncertainties may be varied even if you input the same data for different time.Has anyone met this problem before? Sincerely yours, Yu-Chuan Lin Graduate Student and Reseach Assistant Kansas State University

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RE: [Ifeffit] Fitting Problems via Artemis
by hsnuboy＠ksu.edu 24 Sep '04

24 Sep '04

Dear Norbert, Thank you for your reply. About the DW factor, I think the problem may be another scatterer. Due to the self adsoption, I use Dr. Booth's correlation equation to correlate my data. Is that the way I obtain minus DW factor? The other parameters work great, except DW factor for about -0.001(the uncertainties is +/- 0.00094). Do you thinnk is that possible cause by self absorption or other effects? Thank you for your time. Sincerely, Yu-Chuan On Fri, 24 Sep 2004, nobert.weiher(a)chem.ethz.ch wrote: >Concerning the DW factor, you are right that it accounts for >vibrational disorder in the sample (in the ideal case). If, however, >your material has a high structural disorder by itself, DW factors >might become high due to this. The general behaviour is that they >should increase with temperature of the measurement. A negative value >is physically not possible, and usually means that something is wrong >with your fitting path. Possible things to check are >- did you use proper reference paths (i.e. were they correctly >computed by feff) >- is it maybe another scatterer which contributes to the EXAFS at this >part.

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RE: [Ifeffit] Fitting Problems via Artemis
by Weiher, Norbert 24 Sep '04

24 Sep '04

Dear Yu-Chuan, I quickly comment on the last two points you mentioned in your message. Concerning the DW factor, you are right that it accounts for vibrational disorder in the sample (in the ideal case). If, however, your material has a high structural disorder by itself, DW factors might become high due to this. The general behaviour is that they should increase with temperature of the measurement. A negative value is physically not possible, and usually means that something is wrong with your fitting path. Possible things to check are - did you use proper reference paths (i.e. were they correctly computed by feff) - is it maybe another scatterer which contributes to the EXAFS at this part. Concerning fit stabilities: I never encountered the problem you mentioned, i.e. when I use the same starting values for a fit (even for a bad one), the results are the same. A good fit should by definition converge to the same fitting parameters even when starting from slightly different points on the chi2 surface. However, it is possible that you obtain different results from different starting values. Possible things to do if your fit is not stable: - dont fit all parameters at one run (at least not in the first place) - start fitting all parameters independently, then grabbing the values of the former fits and slowly approach a stable point in the fit - if you have a stable result, try freeing all parameters and see if you reach the same point again. This is a quite good indication that you are on a good way. - if you include another shell, fix all first shell parameters and just fit the second one. Afterwards, vary all parameters again. Finally, the background refinement is a feature of ARTEMIS to correct the background spline you are using. Unfortunately, I have not much experience with it, so I leave it to the other IFEFFITers in the world to comment on this... Hope my suggestions help you to have more productive sessions with these great software packages. Cheers, Norbert

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Re: ? about l_scmt etc.
by k-kupiecki＠northwestern.edu 15 Sep '04

15 Sep '04

Matt & IFEFFIT group, This is actually a feff.inp question.... but I'm hoping someone might be able to clarify this for me... I was wondering what appropriate values are for l_scmt, l_fms, and stoichiometry for the feff.inp I'm working with regarding Au on a Ni surface (I'm fitting with feff calculations with either a single Au atom in the first Ni layer or two Au atoms in the first Ni layer)? Should they all be the same for each potential? I just wanted to check if my values were appropriate. I've used some values based off of an example file all along... but I'm not sure if I used them appropriately for my scenerio. I've read the FEFF8.10 manual but I'm still unclear as to the proper values... (i.e. in the past I have used the following for 2 Au's in the surface) POTENTIALS * ipot z element l_scmt l_fms stoichiometry 0 79 Au 3 3 0.001 1 28 Ni 2 2 4 2 79 Au2 3 3 4 Oh... one more question... I haven't been using the ellipticity card in the feff.inp file, even though I've been using "POLARIZATION 1 0 0"... is this OK? Thanks, Kristine

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Artemis and atoms.inp/feff.inp files
by Bruce Ravel 14 Sep '04

14 Sep '04

Hi folks, This morning, a user pointed out an interesting problem in any version of Artemis up to and including 0.7.010. I thought I should mention it on the list because I would be surprised if no one else runs into this particular issue. Artemis currently does no error checking to determine if an atoms.inp file is actually an atoms.inp file. Similarly Artemis does no error checking to confirm the feff-ness of a feff.inp file. This is a problem because there are separate menu entries in the File menu for importing atoms.inp and feff.inp file. Different things happen when you select these two items. If you choose the wrong kind of file, Artemis will get confused trying to read one file type as the other file type. This will lead to lots of error messages and may result in project files that cannot be saved and re-read by Artemis. Currently there is no better solution than to be sure that, when you intend to import a feff.inp file. you select a feff.inp file and, when you intend to import an atoms.inp file, you select an atoms.inp file. If you make this mistake, the best solution may be to quit Artemis and try again. Clearly this is an untenable situation. Building enough intelligence into Artemis to distinguish between atoms.inp and feff.inp files is now high on my to-do list. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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iPot Exceeded
by Barton, David (DG) 09 Sep '04

09 Sep '04

Thanks to Bruce for releasing the new versions. He has been extremely responsive to dealing with most of my bug reports and suggestions for change. The implementation of reading CIF files directly into Artemis and Atoms makes going from crystal structures in a database to simulated EXAFS patterns almost trivial. O.K. enough padding Bruce's ego...now for a question. Artemis 0.7.010, with FEFF6L on WinXP machine: What is the best way to deal with a crystalline compound in Artemis/FEFF that has 9 unique elements? Attached is a CIF file containing a Au cluster that has nine different elements, which is easily imported in to Artemis using Bruce's new import feature. When imported this compound has ~150 distinct atomic positions in the unit cell. Running FEFF within Artemis with this Atoms.inp file results in the error message: "Feff 6L.02 Unique potential 8 not allowed. Must be between 0 and 7 8 15 P Fatal Error: at RDINP" It appears that FEFF can only handle 8 unique elements at a time. No problem, I would like to ignore the H atoms anyway. Any suggestions on how to handle this within Artemis/FEFF? Otherwise, there is the obvious workaround, I can manually edit the CIF or Atoms.inp and eliminate the H atoms from one of those files and then run FEFF. It would be helpful if the Atoms input page would allow the user to sort the atomic positions by element and then select a range of these atomic positions and delete them all. Thanks Dave ipot Z element 0 79 Au 1 7 N 2 6 C 3 5 B 4 9 F 5 8 O 6 1 H 7 79 Au 8 15 P <<Au5N.cif>> David Barton The Dow Chemical Company Email: dgbarton(a)dow.com

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new development version of Artemis
by Bruce Ravel 07 Sep '04

07 Sep '04

Hi, For those interested in the development version of Artemis, I released a new source tarball this morning. It can be found on SourceForge or on my website. There are no changes to the stable version of Artemis or to the other programs. Here is a quick summary of the changes to the development version: http://sourceforge.net/project/shownotes.php?release_id=266237 Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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