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

RE: [Ifeffit] Fitting Problems via Artemis
by hsnuboy＠ksu.edu 24 Sep '04

24 Sep '04

Dear Norbert, Thank you for your reply. About the DW factor, I think the problem may be another scatterer. Due to the self adsoption, I use Dr. Booth's correlation equation to correlate my data. Is that the way I obtain minus DW factor? The other parameters work great, except DW factor for about -0.001(the uncertainties is +/- 0.00094). Do you thinnk is that possible cause by self absorption or other effects? Thank you for your time. Sincerely, Yu-Chuan On Fri, 24 Sep 2004, nobert.weiher(a)chem.ethz.ch wrote: >Concerning the DW factor, you are right that it accounts for >vibrational disorder in the sample (in the ideal case). If, however, >your material has a high structural disorder by itself, DW factors >might become high due to this. The general behaviour is that they >should increase with temperature of the measurement. A negative value >is physically not possible, and usually means that something is wrong >with your fitting path. Possible things to check are >- did you use proper reference paths (i.e. were they correctly >computed by feff) >- is it maybe another scatterer which contributes to the EXAFS at this >part.

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RE: [Ifeffit] Fitting Problems via Artemis
by Weiher, Norbert 24 Sep '04

24 Sep '04

Dear Yu-Chuan, I quickly comment on the last two points you mentioned in your message. Concerning the DW factor, you are right that it accounts for vibrational disorder in the sample (in the ideal case). If, however, your material has a high structural disorder by itself, DW factors might become high due to this. The general behaviour is that they should increase with temperature of the measurement. A negative value is physically not possible, and usually means that something is wrong with your fitting path. Possible things to check are - did you use proper reference paths (i.e. were they correctly computed by feff) - is it maybe another scatterer which contributes to the EXAFS at this part. Concerning fit stabilities: I never encountered the problem you mentioned, i.e. when I use the same starting values for a fit (even for a bad one), the results are the same. A good fit should by definition converge to the same fitting parameters even when starting from slightly different points on the chi2 surface. However, it is possible that you obtain different results from different starting values. Possible things to do if your fit is not stable: - dont fit all parameters at one run (at least not in the first place) - start fitting all parameters independently, then grabbing the values of the former fits and slowly approach a stable point in the fit - if you have a stable result, try freeing all parameters and see if you reach the same point again. This is a quite good indication that you are on a good way. - if you include another shell, fix all first shell parameters and just fit the second one. Afterwards, vary all parameters again. Finally, the background refinement is a feature of ARTEMIS to correct the background spline you are using. Unfortunately, I have not much experience with it, so I leave it to the other IFEFFITers in the world to comment on this... Hope my suggestions help you to have more productive sessions with these great software packages. Cheers, Norbert

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Re: ? about l_scmt etc.
by k-kupiecki＠northwestern.edu 15 Sep '04

15 Sep '04

Matt & IFEFFIT group, This is actually a feff.inp question.... but I'm hoping someone might be able to clarify this for me... I was wondering what appropriate values are for l_scmt, l_fms, and stoichiometry for the feff.inp I'm working with regarding Au on a Ni surface (I'm fitting with feff calculations with either a single Au atom in the first Ni layer or two Au atoms in the first Ni layer)? Should they all be the same for each potential? I just wanted to check if my values were appropriate. I've used some values based off of an example file all along... but I'm not sure if I used them appropriately for my scenerio. I've read the FEFF8.10 manual but I'm still unclear as to the proper values... (i.e. in the past I have used the following for 2 Au's in the surface) POTENTIALS * ipot z element l_scmt l_fms stoichiometry 0 79 Au 3 3 0.001 1 28 Ni 2 2 4 2 79 Au2 3 3 4 Oh... one more question... I haven't been using the ellipticity card in the feff.inp file, even though I've been using "POLARIZATION 1 0 0"... is this OK? Thanks, Kristine

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Artemis and atoms.inp/feff.inp files
by Bruce Ravel 14 Sep '04

14 Sep '04

Hi folks, This morning, a user pointed out an interesting problem in any version of Artemis up to and including 0.7.010. I thought I should mention it on the list because I would be surprised if no one else runs into this particular issue. Artemis currently does no error checking to determine if an atoms.inp file is actually an atoms.inp file. Similarly Artemis does no error checking to confirm the feff-ness of a feff.inp file. This is a problem because there are separate menu entries in the File menu for importing atoms.inp and feff.inp file. Different things happen when you select these two items. If you choose the wrong kind of file, Artemis will get confused trying to read one file type as the other file type. This will lead to lots of error messages and may result in project files that cannot be saved and re-read by Artemis. Currently there is no better solution than to be sure that, when you intend to import a feff.inp file. you select a feff.inp file and, when you intend to import an atoms.inp file, you select an atoms.inp file. If you make this mistake, the best solution may be to quit Artemis and try again. Clearly this is an untenable situation. Building enough intelligence into Artemis to distinguish between atoms.inp and feff.inp files is now high on my to-do list. 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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iPot Exceeded
by Barton, David (DG) 09 Sep '04

09 Sep '04

Thanks to Bruce for releasing the new versions. He has been extremely responsive to dealing with most of my bug reports and suggestions for change. The implementation of reading CIF files directly into Artemis and Atoms makes going from crystal structures in a database to simulated EXAFS patterns almost trivial. O.K. enough padding Bruce's ego...now for a question. Artemis 0.7.010, with FEFF6L on WinXP machine: What is the best way to deal with a crystalline compound in Artemis/FEFF that has 9 unique elements? Attached is a CIF file containing a Au cluster that has nine different elements, which is easily imported in to Artemis using Bruce's new import feature. When imported this compound has ~150 distinct atomic positions in the unit cell. Running FEFF within Artemis with this Atoms.inp file results in the error message: "Feff 6L.02 Unique potential 8 not allowed. Must be between 0 and 7 8 15 P Fatal Error: at RDINP" It appears that FEFF can only handle 8 unique elements at a time. No problem, I would like to ignore the H atoms anyway. Any suggestions on how to handle this within Artemis/FEFF? Otherwise, there is the obvious workaround, I can manually edit the CIF or Atoms.inp and eliminate the H atoms from one of those files and then run FEFF. It would be helpful if the Atoms input page would allow the user to sort the atomic positions by element and then select a range of these atomic positions and delete them all. Thanks Dave ipot Z element 0 79 Au 1 7 N 2 6 C 3 5 B 4 9 F 5 8 O 6 1 H 7 79 Au 8 15 P <<Au5N.cif>> David Barton The Dow Chemical Company Email: dgbarton(a)dow.com

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new development version of Artemis
by Bruce Ravel 07 Sep '04

07 Sep '04

Hi, For those interested in the development version of Artemis, I released a new source tarball this morning. It can be found on SourceForge or on my website. There are no changes to the stable version of Artemis or to the other programs. Here is a quick summary of the changes to the development version: http://sourceforge.net/project/shownotes.php?release_id=266237 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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copy and paste
by Li Dangdang 07 Sep '04

07 Sep '04

Hi, I've a question: Is there copy/ paster function in parameters input? I want to copy and paste when i define the math expressions for many parameters, but it seems to me that i can only reinput the expression for every new parameters. It's kind of unconfortable if my definition is complexed. DD _________________________________________________________________ 享用世界上最大的电子邮件系统― MSN Hotmail。 http://www.hotmail.com

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debian packages of horae and sixpack
by Carlo U. Segre 01 Sep '04

01 Sep '04

Hello All: I just finished making Debian packages of horae-041 and the newest sixpack (0.52) the new horae includes the development release, diana, but does not yet make a menu entry for it. So far it is only available for sid (unstable). I plan to get it to woody by the end of the weekend if possible. A sarge package should be available on Saturday at teh latest. sixpack is only available for sid and sarge. woody does not have Tix8.1 which is required, so I cannot really make a woody package. I have not had time to make sure that these programs work completely, please send me bug reports off the list. 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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horae-041 ...
by Bruce Ravel 31 Aug '04

31 Aug '04

.... is on SF and my web site. http://sourceforge.net/project/shownotes.php?release_id=264607 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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RE: [Ifeffit] Artemis fit results question
by Kelly, Shelly D. 31 Aug '04

31 Aug '04

Hi Timm, You can use an expression that will return only positive values for you variables. sigma2 = abs(ss) guess ss This will force the model to use a positive values for sigma2. You can also use a penalty factor to keep the value inbetween a given range of values. I believe that there is an example of that in the Artemis or Ifeffit manual. -Most often negative values is a strong indication that something in the model is not quite right. Be sure to look at your data and fits showing the individual contribution from each path in the real or imaginary part of the FT. A negative sigma2 value or a really small sigma2 value usually indicates one of two different things. 1) You have included too much noise in the FT which is randomly adding signal all over in R-space hence your sigma2 values are unrealistically small to compensate. To check for this case, reduce the k-max value in the FT of the data by 1 1/angstrom and see what happens in the fit. 2) The path type is not right. sigma2 is small because you actually need more electron density for that scattering path. Hence try a path with larger Z. Negative values for the degeneracy would indicate that the path length and/or atom type is not correct. Set the degeneracy, sigma2, and delr to some reasonable values then look at the real/imaginary part of the FT for the data, fit and the contribution from the path of interest. Look to see if the signal from the path of interest has a positive contribution to the data before you try to optimize the parameters. Here is my rule of thumb for reasonable sigma2 (units= angstroms2) values sigma2 = 0.001 to 0.003 for double bonds that do not participate in binding to another atom. i.e. for the axial oxygen atoms of a uranyl moiety, UO2. sigma2 = 0.003 to 0.008 for "normal" well ordered shells. Like for Cu metal. This is the usual range. sigma2= 0.009 to 0.015 for disordered shells that are rather weekly bound. i.e. for the equatorial oxygen atom of the uranyl. There is usually 4 to 6 of them and they are not well ordered. Some times these shells can be split into two shells given enough data range in k-space. sigma2=0.015 to 0.025 for really soft bonds like solutions or squishy metals (AgCl) Sigma2 values also depend on the distance. The rules given above are for 1st and 2nd shells of atoms. HTH Shelly -----Original Message----- From: Strathmann, Timothy J. Sent: Monday, August 30, 2004 3:42 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Artemis fit results question This may be a question related to Artemis or to EXAFS fitting in general for a relative newcomer. Over the past months, when I've fit EXAFS data using Artemis and feff-derived single-scattering paths, I sometimes end up with best fit values for 2nd-shell coordination numbers or sigma squared values that are negative. Do these values have any meaning, or do they most likely signify that the chosen paths are not appropriate for fitting the spectral region in question? Also, is there a way to constrain the parameters to only consider positive values. Thanks. Timm Strathmann

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