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

Another R-factor question
by Wayne Lukens 06 May '04

06 May '04

Hi Matt, Thanks again for clearing up my confusion over the origin of the R factor for fits in R-space. I now have a different and unrelated question about the R factor. From looking through the ifeffit code, it appears that the R factor is defined as sum(data-fit)/sum(data). Is this correct? The reason that I am asking is that I would like to use Hamilton's test (Acta Cryst 1965, V18, p.502) to determine whether adding additional shells to a fit actually results in a better fit. Hamilton's test uses the "crystallographic R factor", which is sqrt(sum(data-fit)/sum(data)), so I would like to know whether or not to take the square root of the R-factor ratios in Hamilton's test. Thanks again for the help! Sincerely, Wayne --- Wayne Lukens Scientist Lawrence Berkeley National Laboratory email: wwlukens(a)lbl.gov phone: (510) 486-4305 FAX: (510) 486-5596

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reporting bugs
by Bruce Ravel 04 May '04

04 May '04

Hi folks, Of late, I have received a large number of well-intentioned but incomplete bug reports. While I am always pleased when people let me know about the in my programs that need improvement, it seems prudent for me to spend a little bit of time educating all of you in the art of reporting bugs. The most important thing for you to remember is this: +------------------------------------------------------+ | If I cannot replicate the problem you are seeing, I | | will not be not be able to fix it. | +------------------------------------------------------+ I do not knowingly release software with show-stopping bugs (i.e. bugs that cause crashes or generate trap files). Thus, if you do see such an event, it is likely that I am not aware of it. You need not only to tell me *that* it happened, but to show me *how* to make it happen. Often showing me involves sending the data or project file that triggers the problem. Other times it involves sending me an explicit "recipe" of steps to take which demonstrate the problem. Sometimes both. When I receive a bug report with insufficient information, I cannot do anything until we have exchanged email a few more times. By sending me what I need to replicate the problem, you may reduce the amount of communication required and speed up the response. I have a somewhat long list of suggestions for reporting bugs at this web page: http://leonardo.phys.washington.edu/~ravel/software/exafs/bugs.html If you have not read that page recently, please take a few minutes to do so again. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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New binary installer for testing on Mac OS X
by Matt Newville 03 May '04

03 May '04

Hi Folks, There's a new version of a Mac Binary Disk image for testing at http://cars9.uchicago.edu/ifeffit/downloads Currently labeled ifeffit-1.2.5a-Mac10.3.dmg. This include horae-033, and uses the Aquaterm Plotting terminal by default, but supports the X-window plotting as well. This version is also ready for horae-update to work if Fink and Fink's g77 are installed on your system. This has been tested on exactly one machine and will require small changes to horae by Bruce, so we won't know how it really works until horae-034 is ready. Please try this out and let me know how it works. I have not yet put this version on Sourceforge.net, and will wait to do so until I hear a few positive responses that it works ok. --Matt

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Re: A question about the new Artemis version
by Peter Southon 02 May '04

02 May '04

As Bruce and Matt already know, I also have been trying to get Artemis to use the same FEFF calculation set for multiple data sets (in my case fewer data sets than Scott but with more paths). I've been taking the 'bite the bullet' approach and re-entering all the path parameters for each sample, but the ability to clone the calculations would help me a lot as well. I came up against two limits. First there is Ifeffit's limit of 256 paths, so I think Scott's student will hit this in the project he described (11 x 25). Matt has kindly sent me a modified version of Ifeffit which should have an increased limit, but I haven't had the chance to test it yet (partly for reasons described below). The second limit is when Artemis checks that there are not more than 256 paths before running a fit. When I tried running one fit I found that Artemis counts all the files that are opened, not just those selected to be included in the fit, but Bruce is fixing this. However, I suspect that Artemis too will have to be modified before it will let you run a fit with more than 256 paths using a modified Ifeffit. This is where Bruce's suggestion of writing a Ifeffit script and then editing with cut & paste (and find & replace) becomes particularly useful. This is quite similar to what I did with Feffit and Ifeffit before I started using Artemis, and works well but is rather time consuming. I understand that an item on Bruce's (very long) 'to do' list is to allow Artemis to open a Ifeffit script into a project - so that once manually modified you could transfer the project back into Artemis. There is another thing to look out for when constructing very large or complex Artemis projects. I have found that very occasionally Artemis will save a project into Bruces' new zip file format, but neglect to actually add in some (or any) of the data and feff files. The first symptom is that the size of the saved project is much smaller than it should be. Thus when re-opened, the project looks fine, but Artemis cannot open any of the required files when a fit is attempted. The data can be replaced, but I can't find a way of replacing any feff calculations without re-entering all of the parameters. Anyway, the purpose of all that is that if you are putting a lot of work into your Artemis project, it may be worthwhile to back it up occasionally, or save under a new name. >P.S. Thanks to Matt and Bruce again for even making such a thing >conceivable. Hear hear Peter Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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RE: [Ifeffit] Substrate material question
by Kropf, Arthur Jeremy 29 Apr '04

29 Apr '04

Paul, Silicon is quite strong. However, it is also brittle. For detectors I have been able to bend 200 micron silicon to less than a 200mm radius. That should be plenty of strain. Virginia Semiconductor is great. Look at their double-side polished stock and you can typically find one or two batches with less than 200 micron thickness. Wafers thinner than 100 microns begin to get quite fragile. Jeremy Kropf Chemical Engineering Division Argonne National Laboratory -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Fons Sent: Tuesday, April 27, 2004 7:59 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Substrate material question I have still not decided on the final substrate material, but I have a couple of samples coming from Dupont of polyimide (same composition as Kapton) material called vespel. It is essentially inert as one would expect (like Kapton), but due to differences in manufacture I understand it is hydroscopic. From this I assume that the reaction for making Kapton is diffusion limited and Vespel is essentially a "polycrystalline" -- in the sense there are grains between which water can absorb -- form of Kapton. The energy in question is 11.6 keV (the Ge edge). Si is an interesting idea but the loss for a 200 micron thick substrate is essentially 1/e. It is certainly worth considering for higher energies though! The 1/e value for polyimide is about 3500 microns in contrast, while the 1/e value for MgO is about 300. As in my experiment I want to create biaxial stress in a thin film on the substrate, I worry that the stress/strain curves for MgO are too stiff. On the other hand, thin S! i is a real possibility (darn, Si technology is everywhere!). I like the Si idea and might try that in parallel. Has anyone tried using thinned Si wafers (Virginia Technology ? sells mechanically thinned wafers I think -- I saw them at a MRS booth a long time ago). How fragile are the wafers? On 2004/04/28, at 0:32, Jeff Terry wrote: Hi Matt, Both items are good to know. I didn't realize that the laminated kapton structures still had good heat resistance. Jeff On Apr 27, 2004, at 10:22 AM, Matt Newville wrote: Hi Paul, I think you can get polyimide thicker than 175 microns. It may not go as Kapton, but maybe as Cirlex or Torlon or something else. I think goodfellow.com carries these in millimeter thick sheets and rods, and that they're still radiation and heat resistant. Goodfellow tends to be pricey, but has excellent information on thermal and mechanical properties. Using MgO, sapphire, or even diamond might be reasonable too. --Matt PS: I have a working build of PGPLOT with all of Aquaterm, X11, Postscript, and Png devices on Mac OS X. I'm still tweaking the makefile so that it links directly to the png objects to avoid possible conflicts with dynamic png and zlib libraries, but I should have a working ifeffit binary using this in a matter of days, and then be ready to tweak horae's Makefile.PL so that horae_update works. _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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RE: [Ifeffit] Minor bugs in the new versions
by Jensen, Mark P. 29 Apr '04

29 Apr '04

Along the topic of not being able to run Artemis and Athena simultaneously under Windows. 1. Lack of complaints doesn't mean that he problem is rare. I have consistently seen this behavior (run either Artemis or Athena) on 3 different Windows NT/Win 2000 (incidently 128 Mb RAM) machines. I recall pointing it out to Bruce many moons ago, and just accepting it as the way things were. Matt and Bruce obviously spend a lot of time working on their programs to our benefit, and I didn't think it was worth Bruce's time to chase a small, possibly not fixable, problem like that down. Thus, I did not bug him about it after the first mention of it. I would just extract the EXFAS signal in Athena, save the file, close Athena, open Artemis, and fit. It seemed like a small price to pay for being able to use a great set of programs. 2. However, the recent exchanges on this matter got me to look closer. Now I see that I can run both programs simultaneously on my brand-spanking-new 1 Gb RAM Windows XP computer. I'll have to try it under WinXP and 512 Mb RAM at home this evening. Maybe this is indeed a memory size problem. 3. It seems like more and more of the posts to the Ifeffit list are about general EXAFS things like (for a recent example), what k-range to use. Bruce and Matt and others have been very helpful to the needy, and I can tell it has been much appreciated. (I think I already know the answer to my following question). Has it been considered to "split" the Iffefit list into 2 topics, 1 for general XAFS and 1 for Ifeffit and related programs. (Suspected answer.... "Great idea Mark, we've talked about this before, why don't you volunteer?") Mark J. ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov

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Re: Artemis Crashed too often
by Aria 29 Apr '04

29 Apr '04

After reading these days' discussion in 'minor bugs report' thread, it reminds me of keeping a track of memory usage in my case. Here is a detailed list. Artemis starts: 56,100 K Loads project file: 59,180 K Save: 65,256 K After 1st fit: 88,252 K 2nd fit: 88,824 K 3rd fit: 89,320 K Save: 98,160 K 4th fit: 97,840 K Save: 98,164 K 5th fit: 298,152 K Crash I have also noticed the CPU usage is normally 25% during the fit process. But in the 5th fit, it went up to 25% for first several seconds, then drops to 0% suddenly. The memory usage jumps to 298,152K at the same time, and stayed for a few seconds before it finally crashed. Meanwhile, another process called 'dwwin.exe' with memory usage of 248,016K appeared. After the error message showed up, and closed all the Artemis windows, both of those big memory consuming processes disappeared. This practice is reproducible. I hope it helps a little bit. Best regards, Aria

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RE: [Ifeffit] Minor bugs in the new versions
by Jensen, Mark P. 29 Apr '04

29 Apr '04

I agree with Gerrit on this. This morning I took a look at the two "nearly identical" computers and found that 1. Athena and Artemis each consume about 230 MB of memory to run on my Windows 2000 or XP computers. 2. That the computer that could run both Athena and Artemis with 128 MB RAM had a considerably larger maximum virtual memory setting (600 MB) than the computer that would not (300 MB). Increasing the size of the virtual memory on the latter computer allows both to run. Bruce, as long as that is the amount of memory the programs should use, I guess that means this is not a minor bug in your software. In my case, it's a user that was being miserly with hard drive space. Mark Jensen ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov -----Original Message----- From: Schmithals [mailto:schmithals@hmi.de] Sent: Thursday, April 29, 2004 3:06 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Minor bugs in the new versions Matt Newville schrieb: > 2 I can definitely run artemis and athena at the same on a Windows > machine, so I doubt there's a lock on Perl's Ifeffit.dll. I'd > assume that if other people could only run one of these at a > time there would be many complaints. > > 3 On my WinXP box, athena and artemis each use about 55Mb at > startup -- without reading in any data. That seems to be about > 50% Ifeffit / 50% Perl/Tk (the ifeffit shell takes ~24Mb). > I don't know enough about what changed to guess why the memory > usage would've changed between versions of artemis and athena, > but I think they should both be able to run in 256Mb. Anyway, > I'd suggest watching the memory usage in TaskManager as you > start athena and artemis to see if it really is a memory issue. I now think its a memory problem, too. My computer is running Win2000, 256 MB of RAM, virtual memory is fixed to 400 MB. I started the Windows Task manager to watch memory usage: - without any programs running (except virus scanner, ..) its 119 MB - After starting Artemis it goes up to 412 MB - Athena won't run Then I set the virtual memory to fixed 600 MB. - After starting Artemis it again takes ~400 MB - Athena now starts! Memory usage is ~700 MB. But shutting down one program before starting the other has been OK for me, too. Regards, Gerrit _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Minor bugs in the new versions
by Schmithals 29 Apr '04

29 Apr '04

Dear Bruce, I installed the new versions of the programs. Many thanks for your ongoing work and especially for the new feature of exporting parameter values in Athena. While working with the new versions I listed the problems that I still ran over (all just minor problems that are not critical or for which I figured out a workaround). Some of the bugs have already been mentioned, but I was not sure if they should already be fixed with this release - if not please just ignore these points. Hope it helps to improve the software. My System is Win2000. Artemis 0.7.003 - After the update the path to the stash-folder is set to the default path: "c:\Program Files\Ifeffit\horae\stash" although my Ifeffit is installed at "c:\Programme\Ifeffit" and previously the stash folder was "c:\Programme\Ifeffit\horae\stash". Is it possible to set the stash folder automatically to the subfolder in the installation directory? Obviously, this should be corrected via: Options | General | Workspace. But Artemis will not let me do that. I included the messages that Artemis gives when I change the path and press "Save changes to future sessions" and "return to main window". In the latter case Artemis will ask if I want to keep changes for future sessions (obviously it recognizes that changes have not been saved) but will not return to the main program (and not change the path). However, it does affect working with Artemis in any other way (as far as I can tell). - Atoms potential cards (in feff.inp) is sometimes wrong. (work-around: enlarge r_max in atoms.inp) - Artemis will stumple if I try to import 30 paths (my default) but feff generated less than that (no paths will be loaded and and error message generated, see ARTEMIS Import.TRAP). - If I run feff, import 30 paths and then do that a second time, Artemis does not delete the old entries in the "data&paths"-window but just append the new entries with names "feff0001.dat:2" etc., is that the intended behaviour? The problem is that if I decrease r_max in feff.inp before doing the second run (to a value so that feff produces less than 30 path-files) Artemis will generate error messages when trying to plot the first path entries (obviously because they dont exist anymore). - Function "discard this dataset" does not delete the main folder "data0.feff.0". Therefore, after deleting a few FEFF-datasets I end up with a lot of folders "data0.feff.x", because the empty ones are not reused. The function also does not delete the corresponding parameter values (which is probably better than deleting them). - Set-up of Atoms/Feff-page before loading a datafile will lead to errors (already discussed) Athena 0.8.027 - Athena does not start when Artemis is running. Two new Windows will show up for a moment in the taskbar and disappear again, no error logs are written to the stash-folder. No problems occur if Artemis is not running. Also Artemis will not start when Athena is running. - When using the export function via "File | Save marked groups as data" Athena will state that I may not export more than 15 datafiles. But it also produces errors with less files: it seems that the maximum line width is limited to 259 characters. The line with the names of the datagroups is usually longer and therefore gets truncated. - Access to last opened files is not released: it is not possible to rename/delete project files that just have been closed or data files that just have been read in. This is possible after a new project file is opened or a new data file imported. - Sometimes the selection of groups gets faulty: when clicking on one of the groups it will not be highlighted. Instead the previously selected group will be redisplayed (and remains highlighted). Sometimes a completly different group will be highlighted and displayed. Closing and reopening will not solve the problem, but restarting of Athena does. I could not figure out how to reproduce this error and nothing is written to the stash-folder. - Athena sometimes resizes the width of the right panel (Data groups) by itself. E.g. when exporting data via "File | Save chi(R)" the window becomes wider and gets small again when clicking on a datagroup afterwards (but not always ?!). Atoms ? - I am not sure about the version number because "Help"|"About Atoms" displays "left" (?!) instead of version number. - The "Browse Space Groups" will still invoke the browser only once. Hephaestus 0.01 - Multiple choosing of Settings | Energies will TOGGLE between display in energies/wavelengths (instead of just keeping displaying in terms of energy). Moreover, the checkmark in the Settings-Dialog will stay at "Energies", even when displaying in wavelengts. Despite of this I would propose to display the unit on the main page anyway. - On my machine the checkmarks are hard to recognize as they only shown up as two tiny red dots. But they will show up as checkmarks when I hover over them with the mouse. (This behaviour is common to all the programs, also in previous versions). I also have some general question: - Is it possible to do an offline installation on a computer not connected to the internet? (e.g. by manually loading the updates-files and changing "update_site" in updater.ini) - Is there a way in Athena to display the raw data of a group as a text file? Athena will not allow to edit this data via "Edit | Edit data as text". I only had the idea of saving the group and looking at the resulting text file. - This raised another point: if I compare the file I read into Athena with the file I exported then I notice that they have a different scaling (abszissae values) - does Athena automatically change the scaling when importing data files? I also noticed that when exporting multiple groups then all groups are scaled to the same abszissae values which is not the case when I export them separately. Regards, Gerrit

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RE: [Ifeffit] Minor bugs in the new versions
by Jensen, Mark P. 28 Apr '04

28 Apr '04

Ifeffit friends, I have done several test with Athena and Artemis this afternoon, and the problem of running Athena and Artemis at the same time does not seem to be solely memory related. On two similar Win2000 machines, my old one with 128 Mb behaved as usual, only Artemis or Athena would run at one time. The first "program box" for Aretmis representing the text window would appear in the task bar, the updater program box would appear and then both would disappear instantly. I do not observe the Aretmis splash screen and she never really starts. It happens so fast that I can't read anything in the text window. This was it's "usual" behavior on the 3 computers I mentioned in the previous e-mail. This happens right from the get-go. Nothing else, other than the manditory windows services and the lab mandated anti-virus software was running. On the other machine, with 256 Mb, I could run both simultaneously. Aha! I'm on to something! When I took 128 Mb out of this 2nd computer, though, I could still start Athena and Artemis simultaneously! Rats, foiled again! Unfortunatley, I couldn't bump up that 1st computer to 256 Mb to see if that would enable both to run simultaneously on that computer. In the past, on the first computer, I have had to shut down other programs to get enough memory to run either Athena or Artemis. Maybe, people with this problem will just have to adopt my old approach and put up with this glitch. Mark ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov

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