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

Re: Ifeffit Digest, Vol 10, Issue 2
by Zhan Zhang 05 Dec '03

05 Dec '03

Matt, One thing I noticed is that the link below does not work on my computer. Both Netscape and IE have trouble to find the file. However, if the filename removed from the link, the correct directory showed and the file can be found there. I am not sure what is wrong but it seems the browsers do not like the filename (or something else). Once the file downloaded, and installed, it is relatively smooth-going. But I first did that a strange way: I freshly install the Iffefit 1.2.4 downloaded Nov. 9th 03. And I run the updater came with the version (dated Oct-12, 03). I was told two updates available and I decide to go with it. It seems working ok. Athena was launched. Then I quit Athena and install the updater-1.1. And it seems messed things up. First I noticed the new updater was named updater_old.exe (with a recent date). Then when I launched Athena, the old updater run again and did the two updates without progress bar. Upon finishing, Athena launched fine. Next I quit and tried to relaunch Athena--only found out the Path for the '.bat' files were all changed to C:\Program Files\Iffefit instead of my installation directory C:\Iffefit. I did not pursue this too far believing I was doing it wrong way. I deleted (rather rudely) all files in the installation directory and reinstalled Iffefit and then installed the new updater before launching any program. Everything is fine now and no weird thing happened. I would guess no one else will do it my way. But just let you know things might go out of control if run in wrong order. Thanks. Zhan >Hi Everyone, > >I've posted a new version of the Updater program for windows -- >the program that automatically looks for updates to the Ifeffit++ >distribution for Windows. This is distributed in the form of an >installer program, and can be downloaded from > > http://cars.uchicago.edu/ifeffit/src/ifeffit_updater-1.1.exe > >or from the Sourceforge.net site (see the Ifeffit Download page). > >Installing this (to the same directory as Ifeffit is installed in!) >will upgrade versions 1.2.1 and higher of Ifeffit to "the latest", >including a new version of the updater program and the latest >versions of athena and artemis. > >The new updater shows progress for downloading uppdate files so it >shouldn't appear to "just sit there and do nothing", and should have >a much better chance at successful downloads. This updater also >"remembers" the last time it looked for updates. Once it has looked >for an update, it won't even look for another day (and this 'wait >time' can be increased). > >I recommend all Windows users to install this updater. In a few >minutes I'll post a new 'update' as well. This should test wether >the new updater is working. Please do NOT install this with the old >updater, but rather install the new updater first, which should make >the updater should run the first time you run an Ifeffit program. > >Please let me know if there are problems!! > >--Matt > > > -- -------------------------- Zhan Zhang Northwestern University Argonne National Laboratory Materials Science & Engineering Dept. Environmental Research Division MLSB 1058 Building 203, C-137 2220 N. Campus Drive 9700 Cass Ave. Evanston, IL 60208 Argonne, IL 60439 U.S.A U.S.A. Email address: zhanzhang(a)northwestern.edu Office: (630) 252-8629 Fax: (630) 252-5498 --------------------------

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Windows updates
by Matt Newville 05 Dec '03

05 Dec '03

Hi Everyone, I've posted a new version of the Updater program for windows -- the program that automatically looks for updates to the Ifeffit++ distribution for Windows. This is distributed in the form of an installer program, and can be downloaded from http://cars.uchicago.edu/ifeffit/src/ifeffit_updater-1.1.exe or from the Sourceforge.net site (see the Ifeffit Download page). Installing this (to the same directory as Ifeffit is installed in!) will upgrade versions 1.2.1 and higher of Ifeffit to "the latest", including a new version of the updater program and the latest versions of athena and artemis. The new updater shows progress for downloading uppdate files so it shouldn't appear to "just sit there and do nothing", and should have a much better chance at successful downloads. This updater also "remembers" the last time it looked for updates. Once it has looked for an update, it won't even look for another day (and this 'wait time' can be increased). I recommend all Windows users to install this updater. In a few minutes I'll post a new 'update' as well. This should test wether the new updater is working. Please do NOT install this with the old updater, but rather install the new updater first, which should make the updater should run the first time you run an Ifeffit program. Please let me know if there are problems!! --Matt PS: next up is a "real" installer for Mac OS 10.3. If there are any people who need or want to use Ifeffit with Mac OS 10.2, please let me know.

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Re: [Ifeffit] stability of athena
by SCalvin100＠aol.com 02 Dec '03

02 Dec '03

In a message dated 12/2/03 9:34:37 AM Eastern Standard Time, mjensen(a)anl.gov writes: the only time I can recall having trouble with crashes is when I have closed (not just minimized) the PGPlot window that pops up once the data is imported. If you close that window Artemis will crash. Well at least it used to crash, maybe Bruce has "fixed" that I just try to remember not to close the Graphics window. Closing the graphics window still causes a crash, as far as I know. It's a problem with the software Bruce uses to write his software, and thus difficult for him to address. --Scott

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stability of athena
by atkwong＠umich.edu 02 Dec '03

02 Dec '03

I was hoping to get some help on the use of Athena. Iam new to XAFS, and I just installed the latest version of the ifeffit staller (1.2.4) on my pc running windows 200 professional. i can read my raw data, but once this is done, the program crashes when I try to manipulate it. Does anyone have any suggestions? Thank you in advance for your help. -Antek Wong-Foy University of Michigan Chemical Engineering 3230 HH Dow 2300 Hayward Ann Arbor, MI 48104

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stability of athena
by atkwong＠umich.edu 02 Dec '03

02 Dec '03

I was hoping to get some help on the use of Athena. Iam new to XAFS, and I just installed the latest version of the ifeffit staller (1.2.4) on my pc running windows 200 professional. i can read my raw data, but once this is done, the program crashes when I try to manipulate it. Does anyone have any suggestions? Thank you in advance for your help. -Antek Wong-Foy University of Michigan Chemical Engineering 3230 HH Dow 2300 Hayward Ann Arbor, MI 48104

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wiki or similar for IXS
by Grant Bunker 01 Dec '03

01 Dec '03

Greetings, all - for a while now I have been considering setting up a wiki or slash driven site for the IXS education stuff. I haven't so far, mostly because The ifeffit mailing list seems to fill much of the need, at least as far as data analysis is concerned. My question is similar to Matt's: would people use it? If so, Carlo and I will set one up. Comments would be appreciated. thanks - grant On Wed, 26 Nov 2003 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. Re: new user contributions page (Dean Hesterberg) > 2. Re: new user contributions page (Matt Newville) > 3. Re: new user contributions page (Carlo U. Segre) > 4. Re: new user contributions page (Bruce Ravel) > 5. Scott's tutorial (Tamas Varga) > 6. Re: new user contributions page (Matt Newville) > 7. Re: new user contributions page (Carlo U. Segre) > 8. FBox in newest horae (Carlo U. Segre) > 9. Cu / CuO References? (Norbert Weiher) > 10. Re: Cu / CuO References? (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 26 Nov 2003 14:13:18 -0500 > From: Dean Hesterberg <dean_hesterberg(a)ncsu.edu> > Subject: Re: [Ifeffit] new user contributions page > To: ravel(a)phys.washington.edu, XAFS Analysis using Ifeffit > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <a05210605bbeaab7912c0(a)[152.1.121.24]> > Content-Type: text/plain; charset="us-ascii" ; format="flowed" > > Hi Bruce, > > I thought you were on vacation - get the heck out of there!! > > Best wishes for your trip to Nepal if that happens. > > Dean > > > PS: I have noted to send you some files for Linear combination > fitting testing - will do so in December. > > ------------------------------ > > Message: 2 > Date: Wed, 26 Nov 2003 13:49:51 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] new user contributions page > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.44.0311261317490.2817-100000@corvette> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Bruce and Everyone, > > > I have started a page of user contributed materials. Here's the URL: > > > > http://leonardo.phys.washington.edu/~ravel/software/exafs/contrib.html > > > > Scott's tutorial is there. > > > > I'd certainly enjoy having more things to put on that page.... > > First, thanks for the contribution, Scott! That's really great. > > Another approach might be to make a set of web pages that many users > could directly contribute to, using a wiki or other web-based > content-management software that doesn't require direct intervention > to the web-server machine (that is, content is edited and saved > solely through web pages). This could have the potential advantages > of letting Scott (and/or anyone else) update tutorials and docs at > their discretion and of allowing one to make contributions from an > internet cafe in Nepal (without loss of generality!). > > Such things are certainly possible: I think I could set something > like this on our web server. If so, I'd hope to dedicate it to XAFS > in general rather than just Athena/Artemis/Ifeffit. It might be > nice to coordinate this with the International XAFS Society. > > Is this worth doing?? Would people take advantage of it? > > --Matt > > > > ------------------------------ > > Message: 3 > Date: Wed, 26 Nov 2003 14:14:11 -0600 (CST) > From: "Carlo U. Segre" <segre(a)iit.edu> > Subject: Re: [Ifeffit] new user contributions page > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.58.0311261411110.29475(a)oxide.phys.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > > Matt: > > Since I am effectively the sysadmin for the International Xafs Society > server, I would be happy to coordinate. We are in the process of > migrating the server to a pair of "new" machines and this should be taken > care of within a few weeks. These are not really state of the art > machines but much better than the one that is currently there. > > Whatever I can do to help (including setting up a wiki if that is what is > best) pelase let me know. > > Carlo > > > On Wed, 26 Nov 2003, Matt Newville wrote: > > >Hi Bruce and Everyone, > > > >> I have started a page of user contributed materials. Here's the URL: > >> > >> http://leonardo.phys.washington.edu/~ravel/software/exafs/contrib.html > >> > >> Scott's tutorial is there. > >> > >> I'd certainly enjoy having more things to put on that page.... > > > >First, thanks for the contribution, Scott! That's really great. > > > >Another approach might be to make a set of web pages that many users > >could directly contribute to, using a wiki or other web-based > >content-management software that doesn't require direct intervention > >to the web-server machine (that is, content is edited and saved > >solely through web pages). This could have the potential advantages > >of letting Scott (and/or anyone else) update tutorials and docs at > >their discretion and of allowing one to make contributions from an > >internet cafe in Nepal (without loss of generality!). > > > >Such things are certainly possible: I think I could set something > >like this on our web server. If so, I'd hope to dedicate it to XAFS > >in general rather than just Athena/Artemis/Ifeffit. It might be > >nice to coordinate this with the International XAFS Society. > > > >Is this worth doing?? Would people take advantage of it? > > > >--Matt > > > > > >_______________________________________________ > >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 > > ------------------------------ > > Message: 4 > Date: Wed, 26 Nov 2003 15:29:58 -0500 > From: Bruce Ravel <ravel(a)phys.washington.edu> > Subject: Re: [Ifeffit] new user contributions page > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200311261529.58106.ravel(a)phys.washington.edu> > Content-Type: text/plain; charset="iso-8859-1" > > On Wednesday 26 November 2003 02:49 pm, Matt Newville wrote: > > Such things are certainly possible: I think I could set something > > like this on our web server. If so, I'd hope to dedicate it to XAFS > > in general rather than just Athena/Artemis/Ifeffit. It might be > > nice to coordinate this with the International XAFS Society. > > > > Is this worth doing?? Would people take advantage of it? > > A wiki is definately an excellent tool for documentation. > > I think a site using Slash (the engine used by slashdot.org and other > sites) or some similar discussion and content management system would > be an excellent idea and could serve most every function currently > served by the IXS, but in a much more dynamic and interactive fashion. > > Slash can have many topics, so one could imagine WinXAS and GNXAS > topics as well as Ifeffit, Feff, and general XAS topics. It's > configurable for the user, so each person can look at as many or as > few topics as he finds interesting. Content can be presented and > dicussions can be carried out. It would really be quite a remarkable > resource for the XAS community. > > Of course, I think it would be nice if someone other than Matt or I > volunteered to set up and administer a discussion and content > management system ...... > > B > > -- > Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu > Code 6134, Building 3, Room 222 > Naval Research Laboratory phone: (1) 202 767 5947 > Washington DC 20375, USA fax: (1) 202 767 1697 > > 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: 5 > Date: Wed, 26 Nov 2003 16:27:13 -0500 > From: Tamas Varga <tamas.varga(a)chemistry.gatech.edu> > Subject: [Ifeffit] Scott's tutorial > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <5.0.0.25.2.20031126161549.00a6cd30(a)chem-mail.chemistry.gatech.edu> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20031126/8f1… > > ------------------------------ > > Message: 6 > Date: Wed, 26 Nov 2003 15:34:46 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] new user contributions page > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.44.0311261433570.3598-100000@corvette> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Bruce, Carlo, > > Thanks for the immediate feedback. On the technical side, I run the > web pages for CARS on a dual Xeon server - it seems pretty fast. > I've played with Zope/Plone a little: it's a very nice 'content > management' tool. I've been thinking about setting this up on the > CARS machines for awhile, and would be willing to use this an excuse > to really try to get it to work. > > Then again, this might be an ideal job for the IXS (The user info, > software catalog, and error analysis pages would benefit from having > outside people directly edit their own info). I'm willing to try > this here at CARS, but I'm happy to have someone else do it too! > > My main question has been would such a thing get used? I guess one > way to find out is to set it up and see if it gets used. My sense > is now that it would get used (especially with Scott's zip file of > ZnO examples, and remembering that Francois sent wavelet software > and Corwin Booth sent self-absorption software earlier this year > too). OK, I will put this on my to-do list. > > Somewhat unrelated (but since I'm clogging your mailbox), I should > have a much better 'Windows Updater' with Bruce's latest programs > ready in a week or so, and a "real installer" for Mac OS X 10.3 > sometime in the next few weeks as well. > > --Matt > > > > ------------------------------ > > Message: 7 > Date: Wed, 26 Nov 2003 15:42:40 -0600 (CST) > From: "Carlo U. Segre" <segre(a)iit.edu> > Subject: Re: [Ifeffit] new user contributions page > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.58.0311261540450.29475(a)oxide.phys.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Matt: > > I have an interest in trying out zope as well for other IIT uses. I have > not yet spent much time figuring out how to set it up and make it work > effectivley though. > > Although the IXS server will not be as good as the CARS one, I believe > that it could handle the load. > > One possibility is that Matt and I get together and discuss it, then come > up with a reasonable plan. > > Carlo > > > On Wed, 26 Nov 2003, Matt Newville wrote: > > >Bruce, Carlo, > > > >Thanks for the immediate feedback. On the technical side, I run the > >web pages for CARS on a dual Xeon server - it seems pretty fast. > >I've played with Zope/Plone a little: it's a very nice 'content > >management' tool. I've been thinking about setting this up on the > >CARS machines for awhile, and would be willing to use this an excuse > >to really try to get it to work. > > > >Then again, this might be an ideal job for the IXS (The user info, > >software catalog, and error analysis pages would benefit from having > >outside people directly edit their own info). I'm willing to try > >this here at CARS, but I'm happy to have someone else do it too! > > > >My main question has been would such a thing get used? I guess one > >way to find out is to set it up and see if it gets used. My sense > >is now that it would get used (especially with Scott's zip file of > >ZnO examples, and remembering that Francois sent wavelet software > >and Corwin Booth sent self-absorption software earlier this year > >too). OK, I will put this on my to-do list. > > > >Somewhat unrelated (but since I'm clogging your mailbox), I should > >have a much better 'Windows Updater' with Bruce's latest programs > >ready in a week or so, and a "real installer" for Mac OS X 10.3 > >sometime in the next few weeks as well. > > > >--Matt > > > > > >_______________________________________________ > >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 > > ------------------------------ > > Message: 8 > Date: Wed, 26 Nov 2003 16:41:25 -0600 (CST) > From: "Carlo U. Segre" <segre(a)iit.edu> > Subject: [Ifeffit] FBox in newest horae > To: IFEFFIT Mailing List <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.58.0311261637390.30108(a)oxide.phys.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > > Bruce: > > I have made a quick stab at packaging the newest version of horae. I > noticed that FBox.pm is no longer included, however, the error in the ope > file dialog now reappears. That is, the second time the open dialog > routine is used, it begins at the root directory. I think that this was > the reason you used a patched version of FBox. I think that I will > re-include FBox.pm in my Debian packages. > > For documentation purposes, I am using perl-tk 800.024. > > 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 > > ------------------------------ > > Message: 9 > Date: Thu, 27 Nov 2003 00:07:39 +0100 > From: Norbert Weiher <weiher(a)tech.chem.ethz.ch> > Subject: [Ifeffit] Cu / CuO References? > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <200311270007.39565.weiher(a)tech.chem.ethz.ch> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Friends, > > I am doing an XAS lecture and as example I would like to present Cu and CuO... > Data for Cu I have - but not for CuO :( Can anyone give me Cu K edge spectra > from this one? The Farrel Lytle DB is somehow down... > > Thanks for helping - and Bruce: Wish you a nice vacation if you still read > this... > > Cheers, > > Norbert > -- > Dr. rer. nat. Norbert Weiher (weiher(a)tech.chem.ethz.ch) > Institute for Chemical and Bioengineering - ETH Hönggerberg > HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32 > > > ------------------------------ > > Message: 10 > Date: Wed, 26 Nov 2003 17:23:23 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] Cu / CuO References? > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.44.0311261719080.3997-200000@corvette> > Content-Type: text/plain; charset="us-ascii" > > Hi Norbert, > > A CuO spectra is attached. It's from > http:/cars9.uchicago.edu/~newville/ModelLib/search.html > > It may not be the best data, but it should be OK for an example. > There are a few other spectra for model data there, but it's hard > to keep it up-to-date. > > Good luck on the lecture!! > > --Matt >

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Re: [Ifeffit] Scott's tutorial
by SCalvin100＠aol.com 28 Nov '03

28 Nov '03

Hi Tamas, You have a rather old version of Artemis (the current version is 0.6.009, and I wrote the tutorial with 0.6.008). Download the new version and you'll find that Artemis automatically generates a set of "Guess" variables that are reasonable to start with (unless someone changes the option described in your second paragraph.) Also, this is a good time to mention something Bruce pointed out to me. He said: "2. The first project is nice because it starts blank and walks the user through importing data and feff paths. The second project is a bit confusing because the data and feff path have to be changed from what they were on your computer to what they are on the users computer. It would be useful to start the journal with a note about that." To do this, highlight the FEFF calculation in the "Data & Paths" panel and use the option under the FEFF menu to "Change Path to FEFF", then highlight ZnO.chi and use the option under Data to "Change data file." --Scott In a message dated 11/26/03 4:29:53 PM, tamas.varga(a)chemistry.gatech.edu writes: > I'm doing Scott's posted tutorial on ZnO and found that the step-by-step > instructions in the journal for the first project part (very first fitting) > don't contain the step of creating guess parameters (amp, E0, etc.) and giving a > value to them. After selecting the R range, the tutorial goes right to > hitting the "Fit" button. I think this step (defining guess and path parameters) > is imporant to indicate for beginners. > Also, the tutorial says: > "If the fit does not appear to match what is described below, go to > Settings, then Edit Preferences, autoparams, do_autoparams, and check the red box. > Save changes for future sessions, then Quit Artemis without saving the project > and start again. If you are using a copy of Artemis which belongs to someone > else, change it back later so they don't yell at you." > I could not find the Edit Preferences option under Settings at all. Is this > a problem with my version (0.6.005)/copy? >

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Cu / CuO References?
by Norbert Weiher 26 Nov '03

26 Nov '03

Dear Friends, I am doing an XAS lecture and as example I would like to present Cu and CuO... Data for Cu I have - but not for CuO :( Can anyone give me Cu K edge spectra from this one? The Farrel Lytle DB is somehow down... Thanks for helping - and Bruce: Wish you a nice vacation if you still read this... Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (weiher(a)tech.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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FBox in newest horae
by Carlo U. Segre 26 Nov '03

26 Nov '03

Bruce: I have made a quick stab at packaging the newest version of horae. I noticed that FBox.pm is no longer included, however, the error in the ope file dialog now reappears. That is, the second time the open dialog routine is used, it begins at the root directory. I think that this was the reason you used a patched version of FBox. I think that I will re-include FBox.pm in my Debian packages. For documentation purposes, I am using perl-tk 800.024. 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 user contributions page
by Bruce Ravel 26 Nov '03

26 Nov '03

Hi folks, A couple weeks ago, Scott sent me a wonderful collection of Artemis project files which serve as a nifty tutorial on how to use Artemis. To quote from Scott's README file: "The tutorial is meant for people who understand the rudiments of EXAFS analysis, but have little practical experience. In other words, I assume you know what a "path" is, but are unsure of how to know what paths to include in a fit." For anyone just starting out using Artemis or anyone who would like some tips and hints from an expert user, Scott's tutorial should prove very helpful, indeed. I have started a page of user contributed materials. Here's the URL: http://leonardo.phys.washington.edu/~ravel/software/exafs/contrib.html Scott's tutorial is there. I'd certainly enjoy having more things to put on that page.... Regards, Bruce -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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Scott's tutorial
by Tamas Varga 26 Nov '03

26 Nov '03

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vacation time!
by Bruce Ravel 25 Nov '03

25 Nov '03

Hi! This is my last message of the day to the mailing list. I promise! I wanted to let you all know that I will be taking some vacation time starting on Friday. I will not be near computers while I am gone (that's what makes it a vacation ;-) so I will not be responding to any email. Don't stop sending in bug reports and feature suggestions while I am away! I will read them all upon my return in mid-December. Regards, Bruce -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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phase corrections and saving files
by Bruce Ravel 25 Nov '03

25 Nov '03

Hi folks, I have received a few questions recently on the topic of saving data to column data files after doing a phase corrected Fourier transform. Both Athena and Artemis will do this. Let me explain how it works. ** In Athena, when you save chi(R) as a column data file for the current group it will save the phase corrected chi(R) if the button for central atom phase corrections is checked for that group. ** In Artemis, you can save chi(R) for the data, the fit, or any part of the fit. If a path has been chosen for the phase correction on the data page, then the Fourier transform will be done using that path's phase correction before writing out chi(R). ** Thus the rule for both programs is simple. If you select a phase correction, it will be applied before writing out chi(R). ** For both programs, chi(q) will likewise be written out with the phase correction is the phase correction is chosen. That is, if the phase correction is chosen, it will be applied to the forward transform and the backward transform will be done on that spectrum. ** Neither program writes out a phase corrected chi(k). ** Athena uses a central atom phase correction and no scattering atom correction. Artemis uses both a central and scattering atom phase correction, but only that of the path selected for the correction. The fit in Artemis is *always* done using the non-phase-corrected data and the non-phase-corrected feffNNNN.dat files. ** There was a recent discussion on the mailing list about doing phase *and* amplitude corrections. Neither Athena nor Artemis does that at this time. If you observe a situation where either program does not behave as advertised, let me know so I can fix it for the next release. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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Fwd: athena - Win 98 and Win NT
by Bruce Ravel 25 Nov '03

25 Nov '03

Brad, I am passing this along to the mailing list to see if anyone else has any better wisdom for you. But I'll take a stab. Win98: did you put "SHELL=C:\COMMAND.COM /E:4096 /P" into `config.sys', as the Win98 instructions on my and Matt's web sites suggest? Otherwise I am not familiar enough with Win98 to provide better guidance. WinNT: I have never seen the message you described and don't quite know what it means. What happens on NT if you install the stuff in to C:\Program Files\ rather than onto the F: disk? Again, I am not very familiar with NT (I've never actually haad it on a machine that I own.) Win2K: Whew! Using this seems like the path of least resistance. Anyone else have any wisdom? B ---------- Forwarded Message ---------- Subject: athena - Win 98 and Win NT Date: Tue, 25 Nov 2003 14:32:31 -0600 (CST) From: Brad Lindseth <bjl(a)ccrc.wustl.edu> To: ravel(a)phys.washington.edu Hi, We took some XAFS data a week ago at the APS. I installed athena to look at the data. Here is my report: 1. installed on Win 98: athena runs, but says "Error: Runtime exception" in the DOS window. And then a Microsoft Visual C++ Runtime library box says: Runtime Error! Program c:\ifeffit\grwnd.exe abnormal program termination. 2. installed on WinNT 4.0: in the DOS window it says: F:\PROGRA~1\Ifeffit>athena Can't load 'C:\TEMP\athena\{62B3D752-A76A-4C15-B621-8205B2665DBC}\/auto/Ifeffit/ Ifeffit.dll' for module Ifeffit: load_file:The paging file is too small for this operation to complete at DynaLoader.pm line 206. BEGIN failed--compilation aborted at athena line 59. 3. windows 2000 installation works just fine. Should I just use the win 2000 installation, or is there a simple fix for the other two? Thanks, Brad Lindseth # Brad Lindseth # Graduate Student # Washington University # Phone: (314) 977-0283 # E-mail: bjl1(a)cec.wustl.edu # Web: http://clarion.cec.wustl.edu/~bjl1/ ------------------------------------------------------- -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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new release of Athena and Artemis
by Bruce Ravel 25 Nov '03

25 Nov '03

Hi folks, I just posted a new tarball containing the source code for Athena 0.8.024 and Artemis 0.6.009. The Windows updater is not quite ready yet, but as soon as it is, Windows users will be able to update their computer. This is mostly a bug fix release, but I did add a new feature to Athena last week while I was at NSLS. You can now align data using a reference channel. The documentation has not yet been updated to reflect this new feature, but I describe it briefly on the News page for the latest release: http://leonardo.phys.washington.edu/~ravel/software/exafs/NEWS Alignment to a reference channel should work equally well if the reference spectrum is of the same edge as the data or of another element with a nearby edge. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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Fwd: Line stlye in Artemis
by Bruce Ravel 24 Nov '03

24 Nov '03

> I am using Athena and Artemis to analysis my EXAFS data. I want to > plot the raw data in dashed line and the fitting in solid line. I > tried "settings","plot" selections in Artemis(version 1.2.4), but no > line style choice is available. Can you please tell me how to change > the settings? > -Chuanyong Jing Chuanyong, I am taking the liberty of replying to your email via the Ifeffit mailing list. There is currently no ability to change the linestyle in Artemis. Sorry. It would be resonable to have separate linestyles for the data, the fit, and the other components of the fit (i.e. background and paths). I will put that on the list of things to do. I should point out that I consider the graphics in Artemis and Athena (that is the pgplot graphics that are provided via ifeffit) to be for quick-n-dirty, on screen plotting. I don't make any great effort to provide graphics that are beautiful enough for publication. For that, I think it is better to export the components of the desired plot to column data files and use a program (Origin, Kaleidagraph, Igor, XMGrace, SciGraphica, or whatever) that is intended for making beautiful, publication-quality plots. The level of graphical sophistication that one expects for publication is beyond the scope of what Artemis and Athena are intended to do. Still, your request for different line types is a reasonable one and I will implement it eventually. Ragards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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Some direction
by H H 23 Nov '03

23 Nov '03

Since, I am new in doing XAFS fitting, I hope some one just direct me little bit. In order to my fitting, I always filter each individual shell and then fit the back scattering. When I do that I get a good result. However, after I fit each individual shell and get R and Sigma^2, then I try to combine the shells together. The resultant spectrum does not match the fit. Do I have to combine the shells together after I fit each one individually or it is possible to do each one by its own? __________________________________ Do you Yahoo!? Free Pop-Up Blocker - Get it now http://companion.yahoo.com/

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Re: [Ifeffit] Re: a question about EXAFS fitting result
by SCalvin100＠aol.com 12 Nov '03

12 Nov '03

My two cents (understanding that we have no specifics on Steven's particular sample): This particular comparison to a standard would make me exceedingly nervous as a general rule. Any sample which has a coordination 5/9 of the empirical standard is hardly a minor variation on the standard. And since the DW factor is likely to correlate highly to coordination number for a single-shell fit, part of an apparent change in coordination number might actually be due to a change in DW factor. Again, without knowing the details of the project, or even Bruce's reply as to what happened with the cobalt foil, I highly recommend analyzing more than just the nearest neighbor when trying to determine coordination number. For example, average coordination number for the first shell is theoretically reduced in nanoparticles, but due to other effects this is a highly unreliable measure of particle size. When the effect of scattering off of neighbors beyond the nearest is included, however, Anatoly Frenkel (among others) has demonstrated that particle size can often be determined with reasonable accuracy. --Scott Calvin Sarah Lawrence College In a message dated 11/12/03 8:45:45 AM Eastern Standard Time, ravel(a)phys.washington.edu writes: > I am analyzing cobalt. As I spoke with you before, I got the > coordination number of cobalt foil as around 9 instead of 12. You > explained me why it can happen. What I want to know is If we got > coordination number as 5 for a sample we are interested in and got > the cobalt foil coordination number as 9, can I proportionally > correct the value? (Consider 9 as 12 and multiply 5 by the ratio) Or > just disregard the foil's coordination number? Could you please let > me know what would be the better way to get the correct value? Steven, This is the sort of question for which we created the mailing list, so I am forwarding it and my brief answer there. If you are not already subscribed, you might find it useful to do so. The simple answer is "probably". The point of measuring a standard under identical conditions to the sample is to recognize any systematic effects in the measurement, the smaple, the detectors, or the theory. If all else besides the sample is equal, then you can probably make the argument you suggest above. It will be, of course, incumbant upon you to convince your reader that what you did was reasonable when you publish. You most certainly CANNOT cite "Bruce Ravel, private communication" as your justification!!! That said, if you want more specific help from the crowd on the mailing list, you may wish to provide some more specifics about the details of your problem.

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RE: [Ifeffit] testing ravelware
by Kelly, Shelly D. 12 Nov '03

12 Nov '03

Hi Matt, > Hi Shelly, > > > > Bruce says: > > > P.S. Once again, on the topic of how people can contribute to the > > > ifeffit project without writing code, volunteering > to conceive of > > > a battery of tests and then actually running them would be an > > > excellent contribution. Any takers? > > > > I would think that someone would want to write a perl script to > > execute a bunch of Athena/Artimis commands and then check > the results. > > Then have the script write out a report. (Kind of like what tkperl > > does when you do install the software?) Can Athena/Airtimes > commands > > be executed from a script? If someone was willing to > figure out how > > to do this for one or two of the commands, I would be > willing to extend it to the rest. > > Testing ifeffit commands with the Ifeffit perl module is > definitely possible. That may miss some artemis/athena > capabilities and potential problems, but would still be > useful. You could certainly emulate much of athena's > functionality into perl scripts to do background subtraction, > FFTs, and merging of data with a wide range of parameters and > data sets. > > A script like the simple one below might be pretty good place > to start. (This could be done in languages other than perl > and English). There is also a test.pl with the ifeffit > source perl module (I think it's called t/ifeffit.t in > horae), which mostly tests passing of data between perl and > Ifeffit. Since the script below essentially runs an ifeffit > script, there are several test/example scripts in the > examples/ folder that could be used as the basis of other tests. > > The main difficulty is deciding when the analysis or > calculated values are "right", which makes detecting problems > hard to automate. > > If anyone wants more pointers on how to use the ifeffit from > scripts (perl, python, tcl, ...), please let us know. > > --Matt > > #! /usr/bin/perl > use Ifeffit; > use Ifeffit qw(get_scalar); > > my $xmu_file = "a.xmu"; > my $expected_e0 = 8980.0; > my $toler = 0.5; > > print "Test Finding E0 for $xmu_file: "; > > my $script =<<"END"; > read_data(file = $xmu_file, prefix = my, type = xmu) > pre_edge(my.energy, my.xmu) > END > > $ret = ifeffit($script); # should test $ret for errors. > $e0 = get_scalar("e0"); > print " found $e0, which is "; > > if ( abs($e0 - $expected_e0) le $toler) { > print "ok\n"; > } else { > print "outside of expected range\n"; > } > > ##---- end test_e0.pl This is the kind of script is what I had in mind. As you mentioned this script checks ifeffit directly. I would like to extend it so that Athena is checked. Does anyone know how to do that? This makes me think that if one was cleaver about the way that the test is written that it could be done to check both Athena and/or Ifeffit. That would make the tests more general diagnostic tools. Shelly

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Re: a question about EXAFS fitting result
by Bruce Ravel 12 Nov '03

12 Nov '03

On Tuesday 11 November 2003 04:21 pm, Steven Sangyun Lim wrote: > I am analyzing cobalt. As I spoke with you before, I got the > coordination number of cobalt foil as around 9 instead of 12. You > explained me why it can happen. What I want to know is If we got > coordination number as 5 for a sample we are interested in and got > the cobalt foil coordination number as 9, can I proportionally > correct the value? (Consider 9 as 12 and multiply 5 by the ratio) Or > just disregard the foil's coordination number? Could you please let > me know what would be the better way to get the correct value? Steven, This is the sort of question for which we created the mailing list, so I am forwarding it and my brief answer there. If you are not already subscribed, you might find it useful to do so. The simple answer is "probably". The point of measuring a standard under identical conditions to the sample is to recognize any systematic effects in the measurement, the smaple, the detectors, or the theory. If all else besides the sample is equal, then you can probably make the argument you suggest above. It will be, of course, incumbant upon you to convince your reader that what you did was reasonable when you publish. You most certainly CANNOT cite "Bruce Ravel, private communication" as your justification!!! That said, if you want more specific help from the crowd on the mailing list, you may wish to provide some more specifics about the details of your problem. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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] testing ravelware
by Kelly, Shelly D. 10 Nov '03

10 Nov '03

Bruce writes: If enough people volunteered to check out some aspect of the code each time a new release comes out, then no one would actually have to do that much work [5]. Indeed, a network of use testing volunteers could be incorporated into the release process such that a version does not get released until the problems the testers uncover get fixed. Okay Bruce, I will volunteer to test part of Athena. I will work on whatever part you think would be the most helpful, assuming [5] from your previous message. Shelly

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Tk804.025_beta, update
by Bruce Ravel 08 Nov '03

08 Nov '03

Hi folks, I just wanted to leave you all with an update as to the issue raised earlier this week by Joon and Paul regarding the use of perl/Tk 804.025. This message concerns linux and unix users and OSX users who know how to build everything from source. This is not an issue for Windows users because I have built the executables for the programs using an version of perl/Tk taht is not effected by the problems I will discuss below. The version of perl/Tk currently being distributed at www.cpan.org is version number 804.025_beta5. If you go to the CPAN website or use the CPAN interface to install perl/Tk from the command line, you will end up downloading that version of perl/Tk. In response to mail from Joon and Paul, I downloaded and installed that version of perl/Tk and have come to the conclusion that it is too unstable to be reliably used with Athena and Artemis. One of the problems raised by Joon and Paul was, in fact, my own bug. However, there are several other serious problems that are bugs in perl/Tk 804.025 and so are out of my control. For the foreseeable future, I urge everyone to use an older version of perl/Tk -- 800.024. I keep a copy at my web site: http://leonardo.phys.washington.edu/~ravel/misc/Tk-800.024.tar.gz Athena and Artemis are very well tested against this version and do not require any of the functionality offered by the more recent version of perl/Tk. I will keep my eye on the development of perl/Tk and let people know when I think it is acceptible to upgrade to the more recent version (which will have some nice features, such as unicode support allowing e.g. Japanese speakers to keep their project journals in Japanese). I hope this hasn't been too confusing for anyone and I want to again thank Joon and Paul for their input as I worked through this issue. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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] testing ravelware
by Kelly, Shelly D. 07 Nov '03

07 Nov '03

> Bruce says: > P.S. Once again, on the topic of how people can contribute to the > ifeffit project without writing code, volunteering to conceive of > a battery of tests and then actually running them would be an > excellent contribution. Any takers? I would think that someone would want to write a perl script to execute a bunch of Athena/Artimis commands and then check the results. Then have the script write out a report. (Kind of like what tkperl does when you do install the software?) Can Athena/Artimis commands be executed from a script? If someone was willing to figure out how to do this for one or two of the commands, I would be willing to extend it to the rest. Shelly

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Carlo's problem with wurtzite
by Bruce Ravel 07 Nov '03

07 Nov '03

Hi folks, Last week Carlo posted a problem he was having with a hexagonal space group. He was getting different results when entering data directly into TkAtoms than when he saved the input data and reread it into TkAtoms. I finally found the source of the problem. All output files in TkAtoms are formatted according to "template files". The reason these template files exist is to make it easy for the user to tweak the appearence and content of the files Atoms writes out. Unfortunately there is a bug in the template that is used to save the input data to an atoms.inp file. In Carlo's example, one of the atoms was at the position (1/3,2/3,0). When Atoms save the data, it saved that position as (0.3333,0.3333,0), i.e. with four digits of precision. It turns out that Atoms considers *five* digits of precision, so it was not recognizing that 0.3333 was meant to represent 1/3. This lead directly to the problem that Carlo reported. Eventually Carlo was able to explain this to me in a way that made it into my very dense skull! ;-) This problem will be fixed in the next release of Atoms. Anyone who wants to fix this problem beforehand, here are the simple instructions: unix people: 1. Copy the atoms.atp file to your ~/.atoms/ directory. (Create it if it does not already exist.) The atoms.atp file will be found in someplace like /usr/lib/perl5/site_perl/5.8.0/Xray/atp/ 2. Edit ~/.atoms/atoms.atp and change the precision in the first non-comment line from 8.4 to 9.5. 3. Save the file and fire up TkAtoms. Should work now. windows people: 1. Using WordPad or NotePad, edit the file C:\Program Files\Ifeffit\perl\Xray\atp\atoms.atp 2. Change the precision in the first non-comment line from 8.4 to 9.5. 3. Save the file and fire up TkAtoms. Should work now. There is a moral to this story. Atoms handles numerical precision in a quirky manner. If it is possible to use a factional representation of a number, do so. (I.e. always use "1/3" rather than 0.33, 0.333, 0.3333, or 0.33333 -- even though the last one will, in fact, work correctly.) Thanks to Carlo for finding this problem and to Peter for a valient if unsuccessful stab at solving the problem. Thanks guys! B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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Carlo's problem with wurtzite
by John J. Rehr 06 Nov '03

06 Nov '03

Hi everyone, We encountered a similar problem with the default atoms precision of 5 digits for the Ti-omega phase structure. For that structure atoms gave different results for the Wyckoff coordinates: 1/3 2/3 1/2 and ..3333 .6666 .5 This (apparently) confused the degeneracy checker in atoms causing atoms to print out pairs atoms at nearly identical points. Although there may be cases where a difference between say 0.67 and 2/3 is a significant distortion, I think it's very rare that crystallographic parameters are known to better to 4 digits. Thus I'm wondering whether reducing the precision that atoms demands of a user might be advantageous. J. Rehr

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