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

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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