Matt:
I am running into a somewhat annoying problem with continuous scan data
imports into athena where there are many datapoints before the edge (I
think > 400 or so). With these files, the location of the edge (and
element identification as well) using the first derivative does not work.
The edge is identified as being somewhere in the pre-edge. As I reduce
the number of data points in the pre-edge, the edge identification moves
closer to the true edge and then locks in correctly when the number of
data points in the pre-edge is small enough (again, I think this is less
than 400 points).
I can address this problem by running these data through a rebinning
process in the pre-edge but I think that if it is possible to handle this
in ifeffit, that would be a good idea.
On a second note, would you tell me whether you or Bruce is planning to
maintain the ifeffit perl wrapper? At this time, ifeffit 1.2.6a and horae
046 have different versions of the Ifeffit.pm script (1.3 and 1.301
respectively). I recently ran into a problem because I had the ifeffit
version and horae 046.
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
Hi, Bruce - Ge crystals certainly are a must. Shouldn't forget that people
use Si monochromator crystals at different temps also. Instead of making
a list of d spacings for each reflection, I would just keep values of the
lattice constants at a few reference temps and interpolate the lattice
constant a for the temp of interest, then any of the d spacings can be
calculated as d[hkl]=a/Sqrt[h^2+k^2+l^2] (if memory serves me correctly)
Same for Ge and Diamond since they are the same structure. That way it's
just a handful of numbers, no big deal.
Matt's point as to whether it really should be athena's job to read in all
file formats is a good one. Mostly you want to make it easy for a
new format to be added by the end user. A scripting language would
suffice although perl might be difficult for most people to deal with.
Perhaps the equation parser used in ifeffit could be deployed as end-user
configurable preprocessor for massaging beamline data into the right
form. If those were saveable as templates for different types of data it
would be convenient.
thanks -grant
On Wed, 1 Dec 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote:
> 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. common mono crystals (Bruce Ravel)
> 2. Re: common mono crystals (Matt Newville)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 1 Dec 2004 10:24:17 -0500
> From: Bruce Ravel <ravel(a)phys.washington.edu>
> Subject: [Ifeffit] common mono crystals
> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov>
> Message-ID: <200412011024.17160.ravel(a)phys.washington.edu>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Hi folks,
>
> One of my chores for today is to implement a utility in Athena for
> converting encoder readings in a raw data file into energy. This will
> make some of the data in the Lytle database a bit easier to use. One
> of the things that the user must specify is the d-spacing of the mono
> crystal. I want to provide a menu of common crystals.
>
> The orange book is kind enough to provide an exhaustive list -- but
> it's kind of overkill. Somehow I doubt if many people are using a
> sucrose 001 monochromator even though that d-spacing is given in the
> orange book ;-) (Really! It's on page 4-12!)
>
> I want to do an informal survey of what crystals the ifeffit crowd
> regularly uses. I am certainly going to include Si111, Si311, and
> Si200 in the list, so I don't need to hear from people who use those
> crystals. What others should go in the list? Beryl? Germanium?
> Graphite? Let me know....
>
> Thanks,
> 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/
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 1 Dec 2004 09:58:12 -0600 (CST)
> From: Matt Newville <newville(a)cars.uchicago.edu>
> Subject: Re: [Ifeffit] common mono crystals
> To: ravel(a)phys.washington.edu, XAFS Analysis using Ifeffit
> <ifeffit(a)millenia.cars.aps.anl.gov>
> Message-ID:
> <Pine.LNX.4.44.0412010940170.26700-100000(a)millenia.cars.aps.anl.gov>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
> Bruce,
>
> Diamond 111 is fairly common (I'd guess more common than anything
> but Si), and you probably meant Si(220) instead of (200). InSb is
> probably the next most common for the 1 to 2 keV range. I think
> the others are not so common for XAFS as the energy bandpass is
> too wide. Also, Si at room temperature is slightly different than
> at LN2 temperature....
>
> But also needed for that calculation is the number of motor steps
> or encoder steps per angular unit. OK, angular unit is probably
> most commonly in degrees, but I wouldn't assume that it's never in
> radians. For steps per angular unit, it's usually a many thousand
> steps per degree but it can be pretty much any number.
>
> So, it's complicated to convert 'steps' to eV. Personally, I'm
> comfortable insisting that the beamline/facility provide energy in
> eV, keV, Angstroms. or at least angle in degrees with the
> monochromator lattice constant clearly given.
>
> That is, I don't think this should be athena's job. I think it
> would be better to have more support for beamline-specific
> formats. Then, if some particular beamline saves the "energy"
> in nanoJoules or milliradians that could be marked and
> auto-converted, but I don't think athena should worry about what
> kind of monochromator was used or steps-per-degree.
>
> The data in the Lytle archive is possibly a special case, because
> it's commonly available. It's usually well marked for conversion
> to energy, but the data is poorly documented and spotty in quality
> and it's often hard to tell what exactly the columns are (e-yield
> v. fluorescence, for example). That can make it hard to asses the
> quality of the data (is self-absorption a problem, etc). I do use
> it sometimes, but the data is not all that reliable.
>
> Having a more complete and well-maintained database of data,
> including some of the data from the Lytle database would be nice.
> Any volunteers to work on that?
>
> --Matt
>
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit(a)millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 22, Issue 1
> **************************************
>
Hi folks,
One of my chores for today is to implement a utility in Athena for
converting encoder readings in a raw data file into energy. This will
make some of the data in the Lytle database a bit easier to use. One
of the things that the user must specify is the d-spacing of the mono
crystal. I want to provide a menu of common crystals.
The orange book is kind enough to provide an exhaustive list -- but
it's kind of overkill. Somehow I doubt if many people are using a
sucrose 001 monochromator even though that d-spacing is given in the
orange book ;-) (Really! It's on page 4-12!)
I want to do an informal survey of what crystals the ifeffit crowd
regularly uses. I am certainly going to include Si111, Si311, and
Si200 in the list, so I don't need to hear from people who use those
crystals. What others should go in the list? Beryl? Germanium?
Graphite? Let me know....
Thanks,
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/
