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

Re: question on Athena data import
by Jay Brandes 11 Dec '06

11 Dec '06

Ended up looking at the older threads and the fix posted a few months ago, to use the program textwrangler and save in UNIX text format, worked. The problem seems to be that the normal Mac text handling programs do not have this option and Athena requires it. Just looking at the files in another text editing program does not reveal the problem. Anyway, problem solved.

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Hack and slash
by Paul Fons 06 Dec '06

06 Dec '06

I hacked and slashed and have succeeded in building the wrapper and making a new version of horae. It is getting rather late here so I will have to turn in, but I think the idea of making a different Makefile for the wrapper is a good one. As it didn't seem to be particularly difficult, I assume that I will have no trouble putting one together. I will post a new tarball later tommorrow on sourceforge with a new Mac installer (power pc). This problem with the tarball was new -- there was no conflict before (or was there). The error associated warning message occurred when tar attempted to write the file "atoms" on top of the directory "Atoms". I wonder if the archive order was different before hiding the conflict? Paul On Dec 6, 2006, at 11:59 PM, Bruce Ravel wrote: > On Wednesday 06 December 2006 08:30, Paul Fons wrote: >> Alas Bruce, not everyone has a unix without training wheels. The >> darwin OS is case insensitive. Sort of a good thing in many ways. >> For instance take the example of "atoms" and "Atoms" in the horae-063 >> directory. This frozzed tar in the unpacking stage and I didn't >> realize the conflict until today (I was in Italy until last Friday so >> didn't get a chance to compile horae until today). > > Hmmm... not so trivial. But I'll try to have a trial tarball for you > later today. > >> Can you remove the conflict with uppercase and lowercase "atoms/ >> Atoms" in the horae directory so this doesn' happen every time. It >> would also be sort of neat if there were a some sort of "honest" way >> to compile the ifeffit_wrapper.c source without having to hack the >> ucky MakeMaker output (a switch perhaps). All this is of course, >> when you have time. Thanks for the new release. > > If I knew how to honestly compile the wrapper, I'd be happy to do so. > > Are you able to compile other C code from perl packages "out of the > box"? For example, if you downloaded (to suggest an example that > horae uses) Compress::Zlib and did the typical perl-y build > incantation, does it run to completion without further input? If so, > then I can simply remove all darwin-specific code from my > makefile.PL. If not, then you need to tell me what to do. > > One option is for you to provide me with a makefile that builds > ifeffit_wrapper. I'll add that to the tarball and simply have > Makefile.PL skip the compilation of ifeffit_wrapper. Then your > external makefile can be used to build ifeffit_wrapper. That adds a > step to the build incantation, but that's not so bad. > > Perhaps better, I can simply skip the build of ifeffit_wrapper for > darwin on the assuption that it is already installed or has been > installed some other way. That way, the wrapper can be part of the > installer package, not part of the tarball update for darwin. That > is, in fact, what my Makefile.PL does for debian. > > B > > > > > -- > Bruce Ravel ---------------------------------------------- > bravel(a)anl.gov > > Molecular Environmental Science Group, Building 203, Room E-165 > MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 > > Argonne National Laboratory phone and voice mail: (1) 630 > 252 5033 > Argonne IL 60439, USA fax: (1) 630 > 252 9793 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ >

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CN and bond distances in Artemis
by Juan Antonio Maciá Agulló 06 Dec '06

06 Dec '06

Hi all, I read your papers Anatoly. You fixed the value of S02 found in the Pt metal, and the expression in Artemis would be like this: N:1 x S02: amp·N, right?? I have a low value of S02 in the case of platinum (0.53), how can I solve the problem? Bond distances = delR + Reff (with phase correction)? Thank you very much, Best regards, JA

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RE: Ifeffit Digest, Vol 46, Issue 5
by Khalid, Syed 06 Dec '06

06 Dec '06

You can download Pt foil, L3 edge data from the following web data base: The energy range is -200 eV below to 1250 eV above the edge. Save it as txt file. Follow the instructions to save the data file as given on the main page. http://www.nsls.bnl.gov/beamlines/x18b/data.htm A quick fitting of first path gives Amp = SO2 = 0.77 Syed Khalid -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, December 06, 2006 8:12 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 46, Issue 5 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: CN and bond distances in Artemis (Juan Antonio Maci? Agull?) 2. RE: CN and bond distances in Artemis (Anatoly Frenkel) 3. Re: CN and bond distances in Artemis (Matthew Marcus) 4. Re: CN and bond distances in Artemis (Scott Calvin) 5. RE: CN and bond distances in Artemis (Anatoly Frenkel) 6. Re: CN and bond distances in Artemis (Bruce Ravel) 7. Re: Re: question on Athena data import (Gerrit Schmithals) ---------------------------------------------------------------------- Message: 1 Date: Tue, 05 Dec 2006 19:31:53 +0100 From: Juan Antonio Maci? Agull? <Juan.Macia(a)ua.es> Subject: Re: [Ifeffit] CN and bond distances in Artemis To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <4575BB18.4FA6855E(a)ua.es> Content-Type: text/plain; charset="us-ascii" Hi all, I did fits with self absorption corrected data (Fluo and Booth algorithms) and the value for S02 is 1.20 (0.30). It seems that I am not very lucky, if I take an average value (1.20 and 0.50), it should be ok (0.85) jeje, I am joking. Then...what can I do now? Thank you very much, Best regards, JA P.S. If I do not answer until Monday do not hate me, I will be on holidays.

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Re: [Ifeffit] Problem opening old artemis files
by Carlo Segre 01 Dec '06

01 Dec '06

Hi Igor: There are clearly issues with this file. I tried to use the "unzip -t" command to look inside it and the output is as follows: segre@id1:~$ unzip -t CdPer.apj Archive: CdPer.apj testing: HORAE OK testing: README OK tmp/: mismatching "local" filename (descriptions/), continuing with "central" filename version testing: tmp/ OK file #4: bad zipfile offset (local header sig): 2040 ... ... ... file #182: bad zipfile offset (local header sig): 257961 testing: data0.feff3/ OK testing: data0.feff3/feff0001.dat OK testing: data0.feff3/paths.dat OK testing: data0.feff3/feff.inp OK testing: data0.feff3/misc.dat OK testing: data0.feff3/files.dat OK testing: log_files/ OK testing: data0.feff6/ OK testing: data0.feff6/feff0001.dat OK testing: data0.feff6/paths.dat OK testing: data0.feff6/feff.inp OK testing: data0.feff6/misc.dat OK testing: data0.feff6/files.dat OK testing: descriptions/ OK testing: descriptions/artemis.bak OK testing: descriptions/journal.artemis OK testing: descriptions/artemis OK So there are errors in a number of the zipped up files inside the archive. I think we can rule out changes in format because some of the files are being found correctly, Bruce? Carlo On Fri, 1 Dec 2006, Igor Vasconcelos wrote: > Oi Carlo, > > This email was hiding somewhere and I just saw it. Here goes a project I am > having problems with. it is a simple Cd perchlorate solution. > > Thanks, > > Igor > > > > -- 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 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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OS X Mactel
by Carlo Segre 01 Dec '06

01 Dec '06

Hello All: Jeff Terry's tar archive with installable binaries of Ifeffit and horae for OS X Mactel has been put on the MRCAT web site http://mrcat.iit.edu/iXAFS.tar.gz Instructions for installation are in the tarball. An installer is being developed but please test this version. Cheers, 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 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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Problem opening old artemis files
by Igor Vasconcelos 30 Nov '06

30 Nov '06

Dear all, As I described in the previous email: >I installed the most recent "sarge" package in my Kubuntu box with no >problems. However, I haven't succeeded opening my Artemis files I created >about 5 months ago under Fedora 3. >I don't really know whether this comes >from a version incompatibility or it is a linux distribution related >problem. I am attaching a file with info trapped by Artemis. I'd appreciate if someone, most likely Bruce :-), could help me figure this out. Thanks, Igor _________________________________________________________________ Share your latest news with your friends with the Windows Live Spaces friends module. http://clk.atdmt.com/MSN/go/msnnkwsp0070000001msn/direct/01/?href=http://sp…

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Re: question on Athena data import
by Bruce Ravel 30 Nov '06

30 Nov '06

On Thursday 30 November 2006 10:09, Jay Brandes wrote: > Dear Dr Ravel- I have been using your program Athena for XANES and > EXAFS analysis and have liked it alot. I am having a very > frustrating problem, however. I have some older data that is in text > format and cannot get Athena to import it. I have tried taking the > data examples and replacing the data with my own and I only get the > error message "...has fewer than 10 data points. I have tried copying > the format exactly as far as I can see it in my text editing > programs, but no go. Tab delineated, space delineated, etc., don't > work either. This is very simple 2 column data. The documentation > doesn't seem to indicate that there should be any problems. I use Mac > OS X 10.4. Any advice would be greatly appreciated! Hi Jay, I am taking the liberty of CCing my answer to the mailing list. I am happy to answer this sort of question, but I prefer that it be asked on the mailing list so that others may benefit by the exchange. I have written some guidelines on how to report problems with the software: http://cars9.uchicago.edu/~ravel/software/bugs.html The reason I am pointing this out is that I am better able to help users who familiarize themselves with the suggestions on that page. Without an example of the troublesome data file, I cannot replicate the problem on my computer and therefore cannot offer reliable advice. All that said, the Ifeffit FAQ might be helpful to you. In particular, questions 3 and 4 on this page: http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions are probably directly relevant to your problem. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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new horae Debian packages
by Carlo Segre 30 Nov '06

30 Nov '06

Hello All: The horae-063 Debian packages have been built. For the "sarge" release, you can find it at my repository deb http://fermi.phys.iit.edu/debian/sarge binary/ For the "sid" (unstable) release, it has been uploaded to the Debian mirrors and should be available within 24 hours or so. For the "etch" (testing) release, I hope that it will make it into the contrib section before release at the end of December. It takes about 10 days. If you just can't wait, let me know. Finally, I know that the "etch" and "sid" Debian packages will not install in Ubuntu (along with ifeffit too). Is there any interest in getting these included in Ubuntu? If so, please let me know and I will see about it. I have not tried as of yet since I don't know any Ubuntu developers yet. Cheers, 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 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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OS X Mactel
by Magnus Bergknut 29 Nov '06

29 Nov '06

Hi ³If anyone would like to test the OS X Mactel version, please drop me an email and I will send you a link to it.² I would greatly appreciate a link in order to try the Mactel build. Best Regards /Magnus ---------------------------------------------------- Magnus Bergknut, PhD SLU Institutionen för Skogsekologi Petrus Laestadius väg 901 83 Umeå Swedish University of Agricultural Sciences, SLU Department of Forest Ecology Petrus Laestadius vag S-901 83 Umeå SWEDEN Phone: +46 90 786 8230 ---------------------------------------------------- ########################################### This message has been scanned by F-Secure Anti-Virus for Microsoft Exchange. For more information, connect to http://www.f-secure.com/

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