January 2005 - Ifeffit - millenia.cars.aps.anl.gov

Fwd: News
by Bruce Ravel 07 Jan '05

07 Jan '05

Hi Folks, Can anyone here help Michel with his problems installing the latest horae on his Mac? Thanks, B ---------- Forwarded Message ---------- Subject: News Date: Friday 07 January 2005 06:11 am From: Michel Jaouen <Michel.Jaouen(a)univ-poitiers.fr> To: ravel(a)phys.washington.edu Previously I have updated all using sudo horea_update. At that date (september 2004) it creates a folder horae-042 with the attached log file. It fixes the problems I have mentionned previously: all run fine (artemis version number 07.013, athena version number 08.035). I have seen your mail concerning a new update (horae-047). So I do as previously: sudo horea_update. I receive in the terminal window a lot of informations related to the instal and at the end all seems OK. But when I run artemis in a terminal X window, I have the same version as previously. Looking in the Ifeffit folder I don't see an horea-047 folder nor a log file. The only change I found are in the bin folder where I have new artemis and athena files that are labelled as executable unix files but I can open by clicing on them as text files! So what happens here: I miss something I guess, but what? Any hints? Cheers Michel PS I don't obtain the new interface as quoted on your web server, so I suspect I have some install to do "by hands", but why it is different from the previous update? ------------------------------------------------------- -- 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/

2 1

Generating single scattering paths in Artemis
by Carlo U. Segre 07 Jan '05

07 Jan '05

Bruce: Occasionally, I don't know or don't care what the extended crystallographic environment of the absorber. All I want to do is apply single scattering analysis and I need some simple paths from FEFF. At this time, I can't see how to do this within Artemis since the Atoms page requires a space group and more information than I have available. Would it be possible to have the option for a simpler interface which just allows me to generate single scattering paths between two atoms at a specific distance from each other? Perhaps, I could even specify a coordination geometry (tetrahedral, octahedral, etc.)? 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

6 17

Re: [Ifeffit] Generating single scattering paths in Artemis
by Frenkel, Anatoly 06 Jan '05

06 Jan '05

<<feff.inp>> Hello Carlo et al, FEFF6 allows to use SS cards that were specifically designed to calculate single-scattering paths in the case the structural details are not known, as in Carlo's case. I am attaching a working example where I used to calculate single scattering FEFF in Cu-O in octahedral coordination in Cu2+[H2O]6 complex. I included hydrogen in the input file since it affects charge on oxygen, but in principle it works. Some details are given in this article: http://pubweb.bnl.gov/people/frenkel/HUMIC-EXAFS/est.pdf You can run FEFF6 using attached file and note that it produces three files, each corresponds to the single shell of Cu-O atoms. Note the use of the OVERLAP card in the attached file, as well as the use of Bohr's radius to work around the bug in FEFF6 that uses distances in OVERLAP as multiples of Bohr's radius instead of Angstrems, while the units in SS card are in Angstrems. Regards, Anatoly Anatoly Frenkel, Ph.D. Associate Professor Department of Physics Yeshiva University 245 Lexington Avenue New York, NY 10016 http://www.yu.edu/faculty/afrenkel Office: tel. (212) 340-7827 fax (212) 340-7788 anatoly.frenkel(a)yu.edu Laboratory: tel. (631) 344-3013 frenkel(a)bnl.gov -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Barton, David (DG) Sent: Wednesday, January 05, 2005 4:46 PM To: 'XAFS Analysis using Ifeffit' Subject: RE: [Ifeffit] Generating single scattering paths in Artemis Scott, > This can be fixed by editing the feff.inp file to remove the > Fe potential 1, but that's not enough--the oxygen scatterers > then have to have their potential renumbered to 1 to make > things work. That's a lot of work to do what should be simple. > > So I vote for changing the way Artemis works in such > circumstances so that less editing is needed: if the > absorbing atom is not present in the scattering list, then it > shouldn't have a second entry in the potential list. > I second this vote, since I also have had this same problem. New users could become quickly disgruntled by the Fatal Error message when attempting to put in simple systems or just by choosing a short cluster distance to only include the first shell in the FEFF calculation. At a minimum, it would be nice if Artemis trapped this error and reported a more friendly popup error message. Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit <<feff.inp>>

2 1

Re: Generating single scattering paths in Artemis
by Webb, Samuel M. 06 Jan '05

06 Jan '05

Hi all... I know that this isn't necessarily an Artemis solution, but there is an option/module in SIXPACK (that other IFEFFIT interface) to do just what you've been asking about -- create simple single scattering paths between two atoms in a variety of coordination environments (tetrahedral, octahedral, etc). It has a nice periodic table interface to boot. I use it occasionally to do some quick and dirty fitting -- I do agree with Scott that its not always the most accurate way to go about things. The resulting FEFF file is placed in a FEFF folder in the sixpack root directory. Hope that helps some. Sam

1 0

RE: [Ifeffit] Generating single scattering paths in Artemis
by Barton, David (DG) 05 Jan '05

05 Jan '05

Scott, > This can be fixed by editing the feff.inp file to remove the > Fe potential 1, but that's not enough--the oxygen scatterers > then have to have their potential renumbered to 1 to make > things work. That's a lot of work to do what should be simple. > > So I vote for changing the way Artemis works in such > circumstances so that less editing is needed: if the > absorbing atom is not present in the scattering list, then it > shouldn't have a second entry in the potential list. > I second this vote, since I also have had this same problem. New users could become quickly disgruntled by the Fatal Error message when attempting to put in simple systems or just by choosing a short cluster distance to only include the first shell in the FEFF calculation. At a minimum, it would be nice if Artemis trapped this error and reported a more friendly popup error message. Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D

1 0