Hi All, Since this is my first message to the mailing list, I`d like to say thanks very much to Bruce, Matt and everyone else who is involved for this great piece of software. It makes life in the EXAFS world so much easier. I am working with metal clusters and would like to do some FEFF calculations on icosahedral clusters. Is there anyone out there who has a FEFF input file (or equivalently a list of coordinates) for an icosahedral cluster (147 atoms is probably sufficient for my purpuses). Thanks Patrick --------------------------------------------------------------------------------- Dr. Patrick Kluth ARC Australian Postdoctoral Fellow Department of Electronic Materials Engineering Research School of Physical Sciences and Engineering The Australian National University Canberra, ACT 0200 AUSTRALIA Phone: +61 2 6125 0358 Fax: +61 2 6125 0511 Mobile: +61 408 66 31 04 Email: Patrick.Kluth@anu.edu.au http://www.rsphysse.anu.edu.au/eme ---------------------------------------------------------------------------------
Hi Patrick, Hopefully this will do it. A disclaimer: I never actually tested this on an icosahedral material, and I did the coordinates by hand, so I can't guarantee it. --Scott Calvin Sarah Lawrence College
I am working with metal clusters and would like to do some FEFF calculations on icosahedral clusters. Is there anyone out there who has a FEFF input file (or equivalently a list of coordinates) for an icosahedral cluster (147 atoms is probably sufficient for my purpuses).
That was quick! Thanks very much. Patrick At 08:06 PM 19/07/2005 -0400, you wrote:
Hi Patrick,
Hopefully this will do it. A disclaimer: I never actually tested this on an icosahedral material, and I did the coordinates by hand, so I can't guarantee it.
--Scott Calvin Sarah Lawrence College
I am working with metal clusters and would like to do some FEFF calculations on icosahedral clusters. Is there anyone out there who has a FEFF input file (or equivalently a list of coordinates) for an icosahedral cluster (147 atoms is probably sufficient for my purpuses).
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--------------------------------------------------------------------------------- Dr. Patrick Kluth ARC Australian Postdoctoral Fellow Department of Electronic Materials Engineering Research School of Physical Sciences and Engineering The Australian National University Canberra, ACT 0200 AUSTRALIA Phone: +61 2 6125 0358 Fax: +61 2 6125 0511 Mobile: +61 408 66 31 04 Email: Patrick.Kluth@anu.edu.au http://www.rsphysse.anu.edu.au/eme ---------------------------------------------------------------------------------
Hi Bruce, Two issues I've found with the latest Artemis release; one is a bug, and one is undesirable behavior (at least to me!). My specs: Running Artemis 0.8.000 under Windows XP Professional. The bug: To see this bug, open examples/Artemis/EuTiO3/eto.apj. Click Fit and let it use the default options for naming. Now un-include the Ti edge from the fit. Change amp_ti, e0_ti, and sso_ti to "set." Run a new fit (so that it saves the old one). Change the k-range on Eu and run a new fit again (#3). Now highlight fits 1 and 2 under the Eu edge and try to "discard selected fits." For me, it deletes fit 1, but not fit 2. It also dumps an error to the screen, which I'll send to you separately as an rtf file. (Incidentally, Artemis used to put these error messages in a file somewhere--does it still do that? It seems silly to have to do a screen capture to send it to you.) This behavior seems to be associated with multi-edge fits where some of the edges are turned off for some of the fits, but I wouldn't swear to it. The undesirable feature: This one is easy to see; even the plain vanilla copper project will do it. Basically, restoring a fit model tends to take subsequent journal entries with it. That is not how a journal should work--if I try five fits and take notes along the way, and then decide to return to the second fit, the notes I've written since the second fit (including, say, the formula for the potion which will allow cats to recite Shakespeare) shouldn't vanish. --Scott Calvin Sarah Lawrence College
On Sunday 07 August 2005 21:19, Scott Calvin wrote:
This one is easy to see; even the plain vanilla copper project will do it. Basically, restoring a fit model tends to take subsequent journal entries with it. That is not how a journal should work--if I try five fits and take notes along the way, and then decide to return to the second fit, the notes I've written since the second fit (including, say, the formula for the potion which will allow cats to recite Shakespeare) shouldn't vanish.
I'm normally not much of a cat person, but I want to meet *your* cats. This is a good point. I currently treat the journal as part of the data associated with a fit. As you point out, the journal should be associated with the project as a whole. I'll put fixing this high on the to do list. Thanks, B -- Bruce Ravel ----------------------------------- bravel@anl.gov -or- ravel@phys.washington.edu Environmental Research Division, Bldg 203, Room E165 Argonne National Laboratory phone: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
On Sunday 07 August 2005 21:19, Scott Calvin wrote:
(Incidentally, Artemis used to put these error messages in a file somewhere--does it still do that? It seems silly to have to do a screen capture to send it to you.)
I concur. It is silly. Capturing the messages to a file was a great idea -- in theory. In practice, however, it didn't work so well. You may also remember that the period in which I was trapping error messages to a file was also a period where A&A were prone to hang in those situations, requiring the process manager to kill them. If you are so inclined, you can read up on signal catching in perl: http://www.perldoc.com/perl5.8.4/pod/perlipc.html#Signals The bit beneath the first example box is the relevant part. It would seem that catching signals would be safe, given that the current version of perl is greater than the version mentioned on that man page. However, I am still using perl 5.6 to build the windows executables, so the problem with undeferred signals persists and will do so until I upgrade to 5.8 on my windows machine. (I have a compelling reason for not doing so at this time...) That said, I could put a check in the code to see if a version of perl is running that could safely generate the trap files.... B -- Bruce Ravel ----------------------------------- bravel@anl.gov -or- ravel@phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi all: Is there anyway to include the spatial group F4-3m in the Atoms or Tkatoms list? Could you please let me know how to introduce the flatten option using the Ifeffit command line? Is there a way that I can write the fitting errors to a file using the Ifeffit command line?. For the fitting parameters I usually do write_data (......,path1_s02,path1_e0,...) but I would also like to write the errors from each fitted value. Thanks a lot! Angela -- Dr Angela M. Beesley School of Chemical Engineering and Analytical Science The University of Manchester PO Box 88 Sackville Street Manchester M60 1QD United Kingdom Tel: +44 (161) 306 4468 Fax: +44 (161) 306 4399 Mob: 07811143510
On Wednesday 17 August 2005 11:37, Angela Beesley wrote:
Is there anyway to include the spatial group F4-3m in the Atoms or Tkatoms list?
Do you mean the space group for the zincblende structure, number 216? My copy of the international tables says that the symbol for that one is "F -4 3 m". I don't see an "F 4 -3 m" in the tables.
Could you please let me know how to introduce the flatten option using the Ifeffit command line?
The following was harvested from Athena's ifeffit buffer. The macro is used to make an array with a step function. The flat_c? parameters are the difference between the pre- and post-edge line parameters. ## making a step function macro step x.array x a.step "Return A.STEP function centered at STEP with X.ARRAY as the x-axis" n___step = nofx($1, $2) n___points = npts($1) set t___oss.zeros = zeros(n___step-1) set t___oss.ones = ones(n___points-n___step+1) set $3 = join(t___oss.zeros, t___oss.ones) erase n___step n___points erase @group t___oss end macro ## make the flattened, normalized spectrum ... step udvl.energy 8332.7 udvl.theta set flat_c0=-21.5995647811943 - 1.46770521905781 set flat_c1=0.00579640154058703 - -0.00023480310579162 set flat_c2=-3.65584986262377e-07 set udvl.line = (flat_c0 + flat_c1*(udvl.energy+0) + flat_c2*(udvl.energy+0)**2) set udvl.flat = (udvl.pre + (1.8050 - udvl.line)*udvl.theta) / 1.8050 set udvl.fbkg = (udvl.bkg-udvl.preline+(1.8050-udvl.line)*udvl.theta)/1.8050 newplot(udvl.energy+0, "udvl.bkg+0", xlabel="E (eV)", ylabel="x\gm(E)", fg=black, bg=white, grid, gridcolor="grey82" , xmin=8132.7, xmax=9132.7, style=lines, color="red", key=bkg, title="x10c.xfs") plot(udvl.energy+0, "udvl.xmu+0" , xmin=8132.7, xmax=9132.7, style=lines, color="blue", key="\gm")
Is there a way that I can write the fitting errors to a file using the Ifeffit command line?. For the fitting parameters I usually do write_data (......,path1_s02,path1_e0,...) but I would also like to write the errors from each fitted value.
The uncertainty in a guess parameter, call it foo, is the scalar "delta_foo", which you can query ifeffit for. Uncertainties are not propagated through the path parameters in ifeffit. HTH, B -- Bruce Ravel ----------------------------------- bravel@anl.gov -or- ravel@phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
participants (6)
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Angela Beesley -
Bruce Ravel -
Bruce Ravel -
Patrick Kluth -
Scott Calvin -
Scott Calvin