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

Re: [Ifeffit] Ifeffit Digest, Vol 54, Issue 5
by ssanche3＠uiuc.edu 13 Aug '07

13 Aug '07

Hello again, I removed the artemis projects and the autosave file from C:\Program Files\Ifeffit\horae\stash\. The problem still presists. Everytime the window opens to either save a project or open a new data set Artemis crashes. Is there anything else I can do? Sincerely, Sergio Sanchez ---- Original message ---- >Date: Mon, 13 Aug 2007 12:00:01 -0500 >From: ifeffit-request(a)millenia.cars.aps.anl.gov >Subject: Ifeffit Digest, Vol 54, Issue 5 >To: ifeffit(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: problems in the current version of Artemis for Windows > (scalvin(a)slc.edu) > 2. EXAFS Divination Set results (scalvin(a)slc.edu) > 3. xanes feff8 sulfur (s440697(a)stud.uni-goettingen.de) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Sun, 12 Aug 2007 21:50:30 -0400 (EDT) >From: scalvin(a)slc.edu >Subject: Re: [Ifeffit] problems in the current version of Artemis for > Windows >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <1443.69.124.51.122.1186969830.squirrel(a)mail.slc.edu> >Content-Type: text/plain;charset=iso-8859-1 > >Hi Bruce (and others, if the spam filter lets this through), > >At 10:36 AM 8/1/2007, you wrote: > > >1. The most serious bug is a scenario where Artemis simply hangs when > you start it. > In the current version, there is bug in the place where Artemis > checks for abandoned projects, resulting in the behavior described > above. For now, the work-around is to close the Artemis console > window then, using your file manager, look at this folder: > C:\Program Files\Ifeffit\horae\stash\ > In that folder you should find several folders with names like > artemis.project.0 > artemis.project.1 > and so on. Toss each of those folders into the recycling bin and > try starting Artemis. It should work now. > >I've found that I also have to remove the artemis.autosave file or it >still won't work. Rather than putting it in the recycle bin, I put it in >another folder, and then have Artemis open it as if it were a regular >project. Voila! I can still recover the project... > >--Scott Calvin >Sarah Lawrence College > > > > >------------------------------ > >Message: 2 >Date: Sun, 12 Aug 2007 22:00:56 -0400 (EDT) >From: scalvin(a)slc.edu >Subject: [Ifeffit] EXAFS Divination Set results >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <1481.69.124.51.122.1186970456.squirrel(a)mail.slc.edu> >Content-Type: text/plain;charset=iso-8859-1 > >Hi all, > >I thought you might want to know about the first results from the "EXAFS >Divination Set" project I've been plugging. I don't think the results will >be any surprised to the veterans on this list, but might give novices an >idea of what's possible. > >To briefly recap, my students made up mixtures of various iron compounds >in various proportions, and then I analyzed them "blind." The idea was to >see how well XAFS analysis as practiced by an "expert'" can do in that >kind of case. Unfortunately, unbeknownst to me, the standards were poorly >prepped (i.e. they were very uneven). So these results show what can be >done with poor samples. I'm planning a follow-up for this fall using an >entirely new set of samples and standards prepped as carefully as we can. >Presumably better samples will generate more accurate results. >Nonetheless, it's nice to know what can be done under conditions that are >far from ideal. > >The first two samples I analyzed were mixtures of known compounds in >unknown amounts (iron and hematite in one case; iron, goethite, and >humboltine in the other). My analysis gave the correct percent composition >to within 15 percentage points in all cases. > >The next four samples were mixtures of two or three compounds from a list >(iron, hematite, goethite, humboltine, FeO, lepidocrocite, and magnetite). >I didn't know which compounds were chosen, whether there were two or >three, and how much of each. In two of the four cases I correctly >identified the compounds present. In one case I identified two of the >three compounds, and noted that there might be a third present in a small >concentration but that I couldn't confirm that; the three compounds proved >to be present. In the last case I correctly identified the majority >compound but misidentified the minor contributor. In three cases I found >the correct percent compositions to within 10 percentage points; the last >was off badly. > >The next three samples involved a compound completely unknown to me mixed >with one or two compounds known to me. I correctly identified the class of >the completely unknown compound. In two cases the percent compositions I >found were correct within 10 percentage points; the other within 16. > >The last sample was a mixture of the complete unknown with one or two >compounds chosen from the list, but without me knowing which ones. As >already indicated, I correctly identified the class of the complete >unknown. I also identified one of the two other compounds as definitely >present and the other as most likely if there were a third compound >involved. Percent compositions for this sample were not accurate. > >You could therefore argue that this shows that bad data yields bad >results. But I'd tend to look at it another way--even questionable data >can yield pretty good results. In all cases but one the substances were >correctly identified (twice provisionally as a possible minor >contributor), despite the fact that many of the candidate substances are >structurally similar in that they involve octahedrally coordinated iron. >Percent compositions were usually good rough guides, although on occasion >they went astray. > >I'll leave these data up at > >http://xafs.org/EXAFS_Divination_Set > >and let you know when I get the high-quality follow-up project posted... > >--Scott Calvin >Sarah Lawrence College > > > >------------------------------ > >Message: 3 >Date: Mon, 13 Aug 2007 13:00:19 +0200 (CEST) >From: s440697(a)stud.uni-goettingen.de >Subject: [Ifeffit] xanes feff8 sulfur >To: ifeffit(a)millenia.cars.aps.anl.gov >Message-ID: > <51243.134.76.41.165.1187002819.squirrel(a)webmail.stud.uni-goettingen.de> > >Content-Type: text/plain;charset=iso-8859-1 > >Hello! > >Does anybody know a person, who has experience respective the topics >xanes+feff8 and sulfur K-Edges? >I would be very thankful for an answer :-) > >sincerely yours, >Eckhard Bosman > > >--------------------------------- >Eckhard Bosman >e.bosman(a)stud.uni-goettingen.de >+49 (0)551-39-14441 >Raum: E0.104 >Institut f?r R?ntgenphysik >Friedrich-Hund-Platz 1 >37077 G?ttingen >Germany > > > >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 54, Issue 5 >**************************************

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xanes feff8 sulfur
by s440697＠stud.uni-goettingen.de 13 Aug '07

13 Aug '07

Hello! Does anybody know a person, who has experience respective the topics xanes+feff8 and sulfur K-Edges? I would be very thankful for an answer :-) sincerely yours, Eckhard Bosman --------------------------------- Eckhard Bosman e.bosman(a)stud.uni-goettingen.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany

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k range in ARTEMIS fitting
by Yuan Ping 13 Aug '07

13 Aug '07

Hello Bruce, Thank you for sharing your software. I found IFEFFIT in google and installed it recently in my MAC OSX computer. Trying to learn how to use it, I took a sample chi_k data (Al, k-edge) and played with the fitting in Artemis. One problem I can't solve by myself is that no matter how I chose the k range, r range, dr, dk, the fitting always stops at k~ 3 even though the data covers k= 1-8. So in the plot, the fit curve is much shorter than the data. Is this a plotting problem or a fitting problem? I've saved and attached the project to this email. Thank you very much for your attention. Yuan

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Regarding dopant additions in ATOMS
by Andrew Campos 02 Aug '07

02 Aug '07

Hi everyone, I am having an issue trying to figure out a way to simulate the XANES environment using FEFF 8.4 for some catalyst we are working with. What I am trying to do is use different structures from a crystal database which are from the Rietveld Structure Refinement method from the XRD patterns. The issue I'm having is trying to account for vacancies, which when compiling the crystal structure in ATOMS I think I am allowed to have 9 dopants (from the ATOMS manual, however it is saying there is an error past five dopants, all of which are null, but that is irrelevant I guess) " *** Warning at line 13 You have exceeded the maximum number of dopants. ATOMS will ignore this and all further dopants.-" I'm wondering if there is a better way to account for site occupancies <1, or whether this is altogether a bad idea to try and simulate the XANES environment in the first place. ATOMS is a great program however I might be doing something wrong. I appreciate any insight anyone can give in this! Sincerely, Andrew Campos

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Iron(III) carboxylate structures
by Scott Calvin 01 Aug '07

01 Aug '07

Hi all, Anyone out there have a structure (or a reference to a structure) for a carboylate salt of iron(III), e.g. iron(III) acetate or iron(III) citrate? The closest I've found is a really short Nature article from 1965, but I'd like something more quantitative. I'm particularly interested in the Fe-Fe coordination and distance. --Scott Calvin Sarah Lawrence College P.S. The mailing list's spam filter has decided that when I send messages from home I am actually engaged in something shady and is blocking me. This is the last day I know I'll be at SLC for a while, so I'm likely to have a hard time responding via the list until this gets straightened out. It's just the Ifeffit list, though--I can still send to people inside the ANL firewall with no problems.

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problems in the current version of Artemis for Windows
by Bruce Ravel 01 Aug '07

01 Aug '07

Hi, I rolled out a new version of Artemis in time for last week's XAFS Summer School at the APS. Unsurprisingly, a few bugs cropped up during the course of the week. Three of them are serious enough that I wanted to offer some advice on how to work around them until I manage to fix them. All three of these problems affect Windows users and appear not to affect Mac or linux users. 1. The most serious bug is a scenario where Artemis simply hangs when you start it. The symptom is that the console window appears, followed by the splash screen. Then Artemis' main windows fails to appear. The bug involves how I attempt to clean up when Artemis finds evidence of a large number of abandoned projects. In normal operation, Artemis uses disk space in a special folder to organize the data, feff, and other files associated with a project. When you exit Artemis normally, that folder is zipped up into a project file and removed from disk. When Artemis exits abnormally, the folder can be left in place. When Artemis notices four such apparently abandoned folders, it posts a dialog box offering to clean up the mess before continuing. In the current version, there is bug in the place where Artemis checks for abandoned projects, resulting in the behavior described above. For now, the work-around is to close the Artemis console window then, using your file manager, look at this folder: C:\Program Files\Ifeffit\horae\stash\ In that folder you should find several folders with names like artemis.project.0 artemis.project.1 and so on. Toss each of those folders into the recycling bin and try starting Artemis. It should work now. 2. A problem with similar symptoms might happen on Vista. If you do not have sufficient privilege to write files to C:\Program Files\Ifeffit\ then Artemis' splashscreen will appear then disappear without Artemis' main window appearing. For the Vista user, the solution to this problem is either to run Artemis with higher privilege (which may be frowned upon by the people who administer your computer) or to reinstall Ifeffit into a location where you have write privilege. 3. Many people have noticed that, after using the "Write special output" item in the Theory menu (which can be used to save an atoms.inp file, a feff.inp file, or other kinds of files), you are unable to save the file by clicking the "Save" button. The work around is to select the entire contents of the palette using the mouse or Control-a and then to cut-and-paste the contents into Notepad or Wordpad. I am hard at work on these and many other problems (see http://cars9.uchicago.edu/iffwiki/HoraeToDoList) and am hoping to make an update of the windows package and a new release of the tarball next week. Until then, hopefully this message will help you work around the most serious problems in the current version of Artemis. Regards, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Bug in Artemis 0.8.010?
by Joji Kuniya 31 Jul '07

31 Jul '07

Hi Bruce Thank you for new version of Artemis. It works so good. But there is a problem on my PC working. Artemis makes feff.inp files on the screen, but I can not save it. When I click save button on the Artemis palette, my PC only says only "ping". And, in the Echo palette, there is a message that "Artemis trapped one or more errors! Error message dumped to screen". Is there some good idea to solve thins problem? Thank you Joji Kuniya

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Debye Waller factors for Water Molecules
by Paul Fons 30 Jul '07

30 Jul '07

I am analyzing some Zn organo-metallic protein complexes and have take EXAFS data at low temperature at the Zn edge. I am now in the midst of trying to fit the data. For the mean squared relative displacement terms, I am using Grant's DFT parameterizations for the Zn-cysteine system. This is working fine. In one of my complexes, I also have a water molecule within the "first shell". Does anyone have a suggestion for a reasonable MSRD term for this (at 20 K)? Paul Dr. Paul Fons Nano-Optics Reseach Team Team Leader 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 following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所近接場光応用工学研究センター近接場光基礎研究チーム　チーム長ポール・フォンス

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Basic question in XANES calculation
by Joji Kuniya 27 Jul '07

27 Jul '07

Dear Sirs I am a beginner in XANES analysis. I tried to XANES simulation of Pt by Artemis program. Artemis stopped the calculation by memory limitation. I tried to down cluster size and RMAX parameter, and added "NLEG 4" after FMS sentence on feff.inp. But Artemis stopped the calculation with the same warning again. Please teach me how to make a good feff.inp file for XANES analysis. My PC is a notebook type PC(ThinkPad T60 with 2G memory). Thnak you. Joji Kuniya

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PPC Macintosh version of Horae 65 on SourceForge
by Paul Fons 25 Jul '07

25 Jul '07

I have made a new Macintosh installer for the PPC version of Horae 065 available on sourceforge. It would be neat if it could be copied to the cars download list in the wiki as well. Let me know if there are any problems. It seems to work fine on my end. As there are now two versions, a PPC and an Intel version, I have included PPC in the installer name, e.g. Ifeffit-1.2.9-Mac10.4_PPC_horae65_pkg.dmg Paul p.s. perhaps we should put the Horae 065 installer for Intel on the SourceForge site as well?

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