October 2004 - Ifeffit - millenia.cars.aps.anl.gov

Re: Ifeffit Digest, Vol 20, Issue 22
by Michel Jaouen 25 Oct '04

25 Oct '04

>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: Artimis (Matt Newville) > 2. RE: Artimis (Scott Calvin) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Sat, 23 Oct 2004 13:46:12 -0500 (CDT) >From: Matt Newville <newville(a)cars.uchicago.edu> >Subject: RE: [Ifeffit] Artimis >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <Pine.LNX.4.44.0410222107350.19561-100000@corvette> >Content-Type: TEXT/PLAIN; charset=US-ASCII > > >> I did encounter that "No absorbing atom (ipot=0) defined" error >> sometimes, but I run Artemis only after I have feff calculations >> done. > >I don't understand whether Feff ran to completion or not. Are you >saying that you made a successful run of Feff (including real >output files) but that Artemis still failed to read this >calculation? That seems pretty strange. > >> By the way, I use FEFF8. > >For Feff8, I believe you need to be much more careful about line >endings. It's not able to use Windows line-endings on unixes, for >example. > >But also: why would you use Feff8 for EXAFS analysis, as with >artemis?? Feff8 is a XANES code. As far as I know, it does not >give any improvements for EXAFS. > >--Matt > > > > > >------------------------------ > >Message: 2 >Date: Sun, 24 Oct 2004 11:23:03 -0400 >From: Scott Calvin <SCalvin(a)slc.edu> >Subject: RE: [Ifeffit] Artimis >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Cc: SCalvin(a)slc.edu >Message-ID: <a06010203bda178b3a7b7(a)[130.132.241.87]> >Content-Type: text/plain; charset="us-ascii" ; format="flowed" > >> >>But also: why would you use Feff8 for EXAFS analysis, as with >>artemis?? Feff8 is a XANES code. As far as I know, it does not >>give any improvements for EXAFS. > > >FEFF8 does give at least one improvement for EXAFS, which I've used >on occasion: the self-consistent field calculation can be used to >give an improved estimate of E0 prior to fitting. > >--Scott Calvin >Sarah Lawrence College > I agree with Scott: SCF calculation gives more reliable estimate of E0 because the Fermi level is more accurate. It makes that, when several atomic species are involved, you only need in principle one E0 for fitting (I have verified this point, at least for the case I'm presently working on). >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 20, Issue 22 >*************************************** -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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Re: Ifeffit Digest, Vol 20, Issue 22
by Michel Jaouen 25 Oct '04

25 Oct '04

Yongsheng, > > I did encounter that "No absorbing atom (ipot=0) defined" error >> sometimes, but I run Artemis only after I have feff calculations >> done. > >I don't understand whether Feff ran to completion or not. Are you >saying that you made a successful run of Feff (including real >output files) but that Artemis still failed to read this >calculation? That seems pretty strange. > >> By the way, I use FEFF8. > >For Feff8, I believe you need to be much more careful about line >endings. It's not able to use Windows line-endings on unixes, for >example. Artemis works fine for me (on a Mac) with feff8: just ask in the menu for Import feff calculation and choose the folder where is your feff8 calculation where you must have: feff.inp feffXXX.dat files files.dat paths.dat BUT ALL files must be Unix! Following Matt's advice, use BBEdit Lite (that's free or if you had some money buy BBEdit (the last vesrion is 8): that is really a very good Editor (the best for me) on Mac. Then open your files, check the option button and select Unix for Line Breaks. Best regards Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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RE: [Ifeffit] Artimis
by Chen, Yongsheng 23 Oct '04

23 Oct '04

Hi Bruce, Thanks for your advices. I did edit my Feff.inp in Word, but did not have any problems with the old version. I tried the cleaned up Feff.inp you sent me, it worked better in the sense that I could close Artemis after the warning appeared again, with my own version, I would have to use ForceQuit. I am a new mac user. I try to understand the message in the artemis.trap, although it's a text file, I do not understand too much. I sort of remember there is a notice about Perl version on some website. I have seen 'Perl' appearing in the trap file in many places, is this relative to the problem? Thanks for your help. Yongsheng > ---------- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Bruce Ravel > Reply To: ravel(a)phys.washington.edu;XAFS Analysis using Ifeffit > Sent: Friday, October 22, 2004 10:49 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Artimis > > <<File: feff.inp>><<File: ATT1852209.txt>> > On Friday 22 October 2004 12:30 pm, Chen, Yongsheng wrote: > > I installed the lastest version of Artemis, but met problems when trying to > > import FEFF calculations. The trap file and the feff input file are > > attached. The old version worked fine. I have a mac. > > Yongsheng, > > What is the history of the files you sent? The feff.inp file you > included in your email has a large number of non-printable chatracters > at the beginning of the file and all of the lines are terminated by > Macintosh end-of-line characters (that is, carriage return (ascii 13), > rather than line-feed (ascii 10)). Artemis currently makes no effort > to deal correctly with Mac EOL characters and Feff (as compiled on an > OSX, which is really a version of Unix under the hood) will not do so > either. Some quick tests suggested that is the case. > > So, there seems to be two problems with the feff.inp file you sent me > > 1. The junk characters at the beginning of the file. Those will > certainly confuse feff. > > 2. The end-ol-line characters. > > You can probably fix both by opening up the feff.inp file in any text > editor, stripping out the junk at the top of the file and explicitly > saving the file as a unix text file. I am sure that some of the Mac > users on the list can provide more details should you need it. > > I am suspicious that you might have edited the feff.inp file with a > word processor (such as MS Word). That is a very poor idea because it > can be hgard to avoid the situation where the word processor inserts > additional, not-for-display information in the file that neither > Artemis nor Feff will know how to deal with. If you create your > feff.inp files outside of Artemis, you must be careful not to do so in > a way that inserts additional stuff into the file. > > When I cleaned up the feff.inp file you sent, Artemis had no problem > with it. > > I suppose that another possibility is that the file became > "contaminated" after you tried it in Artemis but before I received > your email. If that is the case, it is really important that you fix > that and try submitting your question again. It is possible that you > are seeing some deeper problem in Artemis, but that I am focussing on > the ways in which the file became contaminated. That's a problem > because I am therefore not addressing the real issue. > > Attached is the cleaned up file, which works for me. > > 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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Athena
by Gael Poirier 22 Oct '04

22 Oct '04

Hi Bruce, I have a problem with Athena version 0.8.032. When I select several opened groups as marked groups and plot them in E (using plot marked groups in E), it doesn't work and only the last opened spectrum appears in the graphic window. The program gives an error message:"ERROR:the minimum value of the forward fourier transform range exceeds the maximum value". However, I've tried with Athena 0.8.024 (IFEFFIT 1.2.5) and it worked very well. How can I plot all the groups in the same graphic window using Athena 0.8.032? Thank you very much Gael

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Artimis
by Chen, Yongsheng 22 Oct '04

22 Oct '04

Hi Bruce, I installed the lastest version of Artemis, but met problems when trying to import FEFF calculations. The trap file and the feff input file are attached. The old version worked fine. I have a mac. Thanks a lot. Yongsheng <<ARTEMIS.TRAP>> <<feff.inp>>

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RE : RE : [Ifeffit] Is artemis running on G5 Mac,
by POGER David 202545 21 Oct '04

21 Oct '04

Hello Thank you very much for your help Matt. Your advice was quite obvious in fact but I followed it to use horae_update properly. Thanks to that, I could see what was my first problem. I had an error about Aquaterm (the installation script couldn't find an Aquaterm library file (aquaterm.1.0.0.dylib I believe). So, I re-installed Aquaterm (the latest version found on SourceForge). And then, the installation was perfect, without any error anymore. And, here is now my second problem. When I open a project file (a '.chi' file) in Artemis, the program takes about 5s to try to open it (with the comment 'plotting in r space' at the bottom of the window), and then crashes down... I'm really sorry! Any other help or any idea? Thank you David > -----Message d'origine----- > De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] De la part de Matt Newville > Envoyé : jeudi 14 octobre 2004 23:54 > À : XAFS Analysis using Ifeffit > Objet : Re: RE : [Ifeffit] Is artemis running on G5 Mac, > > > On Thu, 14 Oct 2004, POGER David 202545 wrote: > > > I fear it doesn't work for me. I have untared the Horae-045.tar > > file in the Ifeffit directory. And when I type 'perl > > Makefile.PL', the installation script crashes and says 'Could > > not open /config/Config.mak file for reading'. The Greek gods > > may not be with me! I'll wait for the next tarball... Thanks a > > lot in adavance! > > This is probably still an issue with permissions, but I'm not sure > what you did exactly. It sounds like you tried to run horae_update > in the Applications/Ifeffit directory. If so, this probably won't > work, as you probably do NOT have write permissions to the > /Applications/Ifeffit directory, and horae_update creates a > folder (horae-045) to build the code it will install. > > Let me be more specific. Sorry if most of this is obvious! > 1. Open a Terminal > 2. move to your home directory: Type 'cd'. > 3. run horae_update with permission to write to the > /Library/Perl and /Applications/Ifeffit. Type > 'sudo horae_update'. When prompted for a password, > type the password for your user account (that is, > the same one you logged in as). > > 4. If you get a message that says 'command not found', then > read the message. > a) if the message begins 'bash: ... command not found' > then type '. /Applications/Ifeffit/bin/iff_init.sh' > Yes, that's a '.' followed by a space. > b) if the message begins 'tcsh: ... command not found' > then type 'source /Applications/Ifeffit/bin/iff_init.csh' > > Then do 'sudo horae_udate' again. > > If you already have the horae-045.tar.gz file, 'sudo horae_update' > is exactly the same as: > tar xvzf horae-045.tar.gz > cd horae-045 > perl Makefile.PL > sudo make install > > Once the installation is successful, you can remove the > 'horae-045' folder. > > --Matt > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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(no subject)
by Gael Poirier 19 Oct '04

19 Oct '04

Hello, I'm a new user of FEFFIT programs and actually I have some problems with Athena (version 0.8.032). In fact, when I try to import data files, the program apparently identificate the commas (,) as a column separator. I think that my input file is correct: ASCII data and each column separated by a space. What can I do to resolve it?? Thank you very much for your help Gaël Poirier Universidade Estadual Paulista (UNESP) Brazil

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RE : [Ifeffit] Is artemis running on G5 Mac,
by POGER David 202545 14 Oct '04

14 Oct '04

Hi I fear it doesn't work for me. I have untared the Horae-045.tar file in the Ifeffit directory. And when I type 'perl Makefile.PL', the installation script crashes and says 'Could not open /config/Config.mak file for reading'. The Greek gods may not be with me! I'll wait for the next tarball... Thanks a lot in adavance! David > -----Message d'origine----- > De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] De la part de Bruce Ravel > Envoyé : mercredi 13 octobre 2004 19:23 > À : XAFS Analysis using Ifeffit > Objet : Re: [Ifeffit] Is artemis running on G5 Mac, > > On Wednesday 13 October 2004 12:49 pm, Matt Newville wrote: > > Hi, > > > > OK, I agree that a simple 'horae_update' also did not work to > > update thes for me. It appears that the new codes are built > > but not installed. This definitely did work for me: > > tar xvzf horae-045.tar.gz > > cd horae-045 > > perl Makefile.PL > > make > > sudo make install > > > > I believe that 'sudo horae_update' will also work. > > > > --Matt > > > > PS: Oddly, without the 'sudo', horae_update did not give a > > warning about installing as root. I got largely the same log file > > as Stefano, and also got this on the screen: > > > > print() on closed filehandle OUT at /Applications/Ifeffit/bin/horae_update > > line 263. > > > > perhaps this is printed to STDERR not STDOUT?? it's not in > > horae_update.log. Anyway, this is where the warning about > > trying to install as someone other than root is. > > > > The horae_update could probably use other improvements, as > > horae_update --force --file=horae-045.tar.gz > > > > still attempts to download the tarball, requires it to > > be named 'horae-045.tar.gz' and then deletes it. > > What you said is exactly right. There was a problem that had > horae_update complain about a closed file handle and exit just before > doing the "make install" step. I think I fixed it and asked Stefano > to give it a try. > > I'll post a fix tomorrow (I hope) and the fix will be included in the > next tarball. > > 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/ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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RE: [Ifeffit] delR and delE
by Kelly, Shelly D. 14 Oct '04

14 Oct '04

Ritika, delr and Eo are correlated. So you can (1) force delr to the same for two paths with different Eo-values, or (2) use two different delr-values with one Eo-value. Most prefer the second choice over the second choice. Also, Eo is important at low k-values. If you move your k-range that you use in the FT of your data you might find a different Eo value, or that only one Eo is needed with a shorter k-range than with a longer k-range. I do not think that you model is "okay" with three Eo values. How much does EO differ? Usually Eo is the last button I turn on when I try to make a model fit the data. Large Ezero values (> 10 eV) are common if you have a poor model. So use only one Eo at the beginning. Often I just set it to zero, and then when the model gets close, try to add one or two more to really get it right on. I would try only one Eo first. Let delr vary for all the paths and change the k-range. See how small the k-range needs to be before you can fit the data with only one E0 value. 1.9 Angstroms is a short distance. It would seem more reasonable to me that you might need two Eo values. One for this short shell and then one more for all the other shells. Give these things a try and tell us how it goes. Shelly > -----Original Message----- > From: ritika.uppal(a)yale.edu [mailto:ritika.uppal@yale.edu] > Sent: Wednesday, October 13, 2004 2:50 PM > To: Segre, Carlo U.; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] delR and delE > > > > I have 3 different values of Eo for the fit. 2 for the first > shell and > the 3rd for the rest of the paths. Actually the bond distance > of the 6 > oxygens in the first shell differs. 3 of them have a bond length of > around 1.9 A and the other 3 around 2.2 A. So using one value of Eo > does not fit the second peak very well. > > Ritika > > > Quoting "Carlo U. Segre" <segre(a)iit.edu>: > > > > > delR is just the deviation from the distance you used in > the feff.inp > > file to generate the paths. It can be positive or negative > depending > > on > > > > whether these atoms are closer or further away from the > central atom. > > > > By delE, do you mean Eo? When you say two values, do you mean > > different values for two different shells? > > Carlo > > > > > > On Wed, 13 Oct 2004, ritika.uppal(a)yale.edu wrote: > > > > > Hi guys, > > > I have a few questions about the fitting parameters. the delR for > > my > > > fit has a negative value. Is that wrong or its possible to have a > > > negative value?? and also for the first shell, I have 2 values of > > del > > > E. Does that mean that the model I am using is not a good one?? > > > > > > Thanks for all your help > > > Ritika > > > _______________________________________________ > > > 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 > > _______________________________________________ > > 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 >

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RE: [Ifeffit] delR and delE
by Kelly, Shelly D. 13 Oct '04

13 Oct '04

See below for clarification.. > -----Original Message----- > From: Kelly, Shelly D. > Sent: Wednesday, October 13, 2004 3:10 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] delR and delE > > > Ritika, > > delr and Eo are correlated. So you can (1) force delr to the > same for two paths with different Eo-values, or (2) use two > different delr-values with one Eo-value. Most prefer the > second choice over the second choice. This should read "Most prefer the second choice over the first." > > Also, Eo is important at low k-values. If you move your > k-range that you use in the FT of your data you might find a > different Eo value, or that only one Eo is needed with a > shorter k-range than with a longer k-range. > > I do not think that you model is "okay" with three Eo values. > How much does EO differ? Usually Eo is the last button I > turn on when I try to make a model fit the data. Large Ezero > values (> 10 eV) are common if you have a poor model. So use > only one Eo at the beginning. Often I just set it to zero, > and then when the model gets close, try to add one or two > more to really get it right on. > > I would try only one Eo first. Let delr vary for all the > paths and change the k-range. See how small the k-range > needs to be before you can fit the data with only one E0 value. > > 1.9 Angstroms is a short distance. It would seem more > reasonable to me that you might need two Eo values. One for > this short shell and then one more for all the other shells. > > Give these things a try and tell us how it goes. > > Shelly > > > -----Original Message----- > > From: ritika.uppal(a)yale.edu [mailto:ritika.uppal@yale.edu] > > Sent: Wednesday, October 13, 2004 2:50 PM > > To: Segre, Carlo U.; XAFS Analysis using Ifeffit > > Subject: Re: [Ifeffit] delR and delE > > > > > > > > I have 3 different values of Eo for the fit. 2 for the first > > shell and > > the 3rd for the rest of the paths. Actually the bond distance > > of the 6 > > oxygens in the first shell differs. 3 of them have a bond length of > > around 1.9 A and the other 3 around 2.2 A. So using one value of Eo > > does not fit the second peak very well. > > > > Ritika > > > > > > Quoting "Carlo U. Segre" <segre(a)iit.edu>: > > > > > > > > delR is just the deviation from the distance you used in > > the feff.inp > > > file to generate the paths. It can be positive or negative > > depending > > > on > > > > > > whether these atoms are closer or further away from the > > central atom. > > > > > > By delE, do you mean Eo? When you say two values, do you mean > > > different values for two different shells? > > > Carlo > > > > > > > > > On Wed, 13 Oct 2004, ritika.uppal(a)yale.edu wrote: > > > > > > > Hi guys, > > > > I have a few questions about the fitting parameters. > the delR for > > > my > > > > fit has a negative value. Is that wrong or its possible > to have a > > > > negative value?? and also for the first shell, I have 2 > values of > > > del > > > > E. Does that mean that the model I am using is not a good one?? > > > > > > > > Thanks for all your help > > > > Ritika > > > > _______________________________________________ > > > > 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 > > > _______________________________________________ > > > 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 > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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