RE: [Ifeffit] Artimis
Hi Matt, I did encounter that "No absorbing atom (ipot=0) defined" error sometimes, but I run Artemis only after I have feff calculations done. By the way, I use FEFF8. Thanks everybody for your kind help. I am afraid I can not do more test now since I am leaving tomorrow for Argonne for more XAFS experiments. Will check back if the problem remains after I have tried what you have suggested. Have a good weekend. Yongsheng
---------- From: ifeffit-bounces@millenia.cars.aps.anl.gov on behalf of Matt Newville Reply To: XAFS Analysis using Ifeffit Sent: Friday, October 22, 2004 2:20 PM To: ravel@phys.washington.edu; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Artimis
Hi,
On Friday 22 October 2004 4:38 pm, Chen, Yongsheng wrote:
Thanks for your advices. I did edit my Feff.inp in Word, but did not have any problems with the old version.
It is certainly possible to do so, but you MUST be careful to save the file as text. Because it is so easy to forget and just save in whatever format Word decides to use, I always discourage people from using Word for that purpose.
Actually, Feff6 (and ifeffit) handle Unix and Windows line endings just fine, but do have a harder time with Mac line-endings. I'm not sure I know how to fix this: As far as I can tell it's at the level of the fortran's read() statement. Sorry.
One thing that confuses me is that Feff6 *should* have reported a Feff 6L.02 Fatal Error: No absorbing atom (ipot=0) defined
which could have been used as a clue that something went wrong. I don't know how artemis checks if a feff run went OK.
Hey Mac users! Could someone suggest a simple editor that Yongsheng, a new Mac user, should consider for the task of editing the kinds of text files that Feff and similar programs work with?
TextEdit can save file with Unix-style line endings, especially if you set the default to using 'Plain text' in the Preferences menu.
BBedit is a popular and very good editor for Mac OS X.
--Matt
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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
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
Scott, Michel, Scott Calvin wrote:
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.
Michel Jauoen wrote:
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).
Interesting -- I haven't seen this effect, but I probably haven't looked very hard either. I don't think that having an E0 'closer to the experiment' is a significant gain, as it still is relative to the experimental E0 (which is usually the fairly ad-hoc max-of-derivative) and has to be refined in the fit. But if it can reduce the number of situations where you need 2 E0's, that could be important. I think it's still not well understood when multiple E0's are needed, but having some insight on where Feff8's SCF is noticeably better might be a good start. Would one of you be willing to send an example, and/or maybe give some indication of what sort of systems would need 2 E0's with Feff6 and 1 E0 with Feff8? Thanks, --Matt
Hi Bruce, I seem to be encountering a bug in adding paths to a FEFF calculation with Artemis. To see this bug, follow these steps: 1) open the Artemis project that comes with the distribution under ifeffit/examples/Artemis/ybco/cu.apj (that's the YBCO copper edge project) 2) Discard a path (#4 is what I just tried) under the FEFF1 calculation. Make sure it's the one under FEFF1, and not FEFF0. 3) Click on FEFF1 under the Data & Paths pane, so that the interpretation of that calculation shows. Right click on path 4 in the interpretation, and choose "Add feff0004.dat to path list." When I do this, it adds to the FEFF0 calculation, rather than the FEFF1 calculation as it should. Or, try this instead for step 3: 3) Click on FEFF1 under the Data & Paths pane. Go to the "theory" menu at the top, and choose "Add a feff path." Then select feff0004.dat from the list. When I do it this way, it ends up as a totally new FEFF calculation, rather than as part of FEFF1. I am using Windows XP and Artemis 0.7.010. --Scott Calvin Sarah Lawrence College P.S. Do you prefer me to identify bugs the way I did here, by telling you how to reproduce it using an example file, or by sending you a project file myself? It makes sense to me that I refer it to an example file that you more or less know the history of, but if you'd rather I send project files myself, I'm happy to do that.
On Tuesday 26 October 2004 6:15 pm, Scott Calvin wrote:
Hi Bruce,
I seem to be encountering a bug in adding paths to a FEFF calculation with Artemis. To see this bug, follow these steps:
<snip>
P.S. Do you prefer me to identify bugs the way I did here, by telling you how to reproduce it using an example file, or by sending you a project file myself? It makes sense to me that I refer it to an example file that you more or less know the history of, but if you'd rather I send project files myself, I'm happy to do that.
Actually a clear recipe is my favorite kind of bug report. A project file should be sent if it serves to clarify the recipe. It's on my list of things to do. Thanks, B -- Bruce Ravel ----------------------------------- ravel@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/
participants (4)
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Bruce Ravel -
Chen, Yongsheng -
Matt Newville -
Scott Calvin