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

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 30 Nov '03

30 Nov '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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