Windows Vista

newer
conversion to Artemis k^0*chi(k)...

snnn01ag＠uniba.it

7 Nov 2007 7 Nov '07

9:22 a.m.

Hi, I want only to inform Bruce and all the ifeffit´s users that I downloaded the ifeffit 1.2.10 version on my new computer that uses Window Vista software! After trying several times to load it from your site (and this is a problem of Vista!), now I have my athena, artemis and hephaestus. I must admit the program works a quite good. Ok, somethimes it crashes by itself, but you have only to close and reopen it (so, save all every 5 minutes). I hope no other problems emerge! Anna. ------------------------------------------------------- Questo messaggio e' protetto da un sistema di cifratura

Show replies by date

Bruce Ravel

7 Nov 7 Nov

1:40 p.m.

On Wednesday 07 November 2007 04:22:23 snnn01ag@uniba.it wrote:

...

Hi, I want only to inform Bruce and all the ifeffit´s users that I downloaded the ifeffit 1.2.10 version on my new computer that uses Window Vista software! After trying several times to load it from your site (and this is a problem of Vista!), now I have my athena, artemis and hephaestus. I must admit the program works a quite good. Ok, somethimes it crashes by itself, but you have only to close and reopen it (so, save all every 5 minutes). I hope no other problems emerge!

Hi Anna, Thanks for the information. In my (very limited) experience, it helps to install Ifeffit into your personal space rather that its default location. That way you do not need admin priviledge to run it. I am unaware of a new problem resulting in such frequent crashes. It seems highly likely that you are running into this well-known issue: http://cars9.uchicago.edu/~ravel/software/windows_crash.html If so, the work-around is quite simple ;-) There is some more information about installing our software on Vista and other operating systems at http://cars9.uchicago.edu/iffwiki/FAQ/Installing_Ifeffit Regards, B -- Bruce Ravel ----------------------------------- bravel@bnl.gov National Institute of Standards and Technology Building 535A, Room M7 c/o Brookhaven National Laboratory Upton NY, 11973, USA My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

Matt Newville

3:32 p.m.

Hi, The windows installer for Ifeffit 1.2.10 was changed for (and tested on!!) Vista. The main issue was with privilege for installing (to C:\Program Files) and where to store temporary data ('stashes') for horae projects, which now defaults to be in the user's HOME folder instead of into the more restricted C:\Program Files\Ifeffit folder. I updated the FAQ entry on Vista. --Matt

Richard Mayes

3:39 p.m.

New subject: Self absorption questions

Greetings all! I'm trying to explain self absorption for our group's guide to EXAFS and I need some help understanding some of the finer details of self absorption. In the realm of fluorescence EXAFS, am I correct in that at a given energy there is a certain penetration depth of the X-rays that is expected (in a thick, dilute sample), but in a thick, concentrated sample, the penetration depth is actually less than the expected depth in thick, dilute samples (causing the decrease in the amplitude of the oscillation peak in Bruce's "wiggle up" of the XAFS oscillation)? Then, in the "wiggle down" of the XAFS oscillation, the penetration depth is actually more than what would be expected so the depth of the oscillation valley decreases. As a result, for thick concentrated samples like a metal foil, in the "wiggle up," the fluorescence accounts for fewer than expected absorbing atoms and in the "wiggle down" the fluorescence accounts for more than expected absorbing atoms. Next, in our amorphous silicates (doped with Ti, V, Cr, W, or Sn), is the self absorption effect greater in the lower Z elements (like titanium) than in the higher Z elements (like tin)? Does the high background due to the silicon at the lower energies (4.9 keV) in relation to the higher energies (29.2 keV) have an effect or is it just an underlying, independent issue that is more pronounced with the lower Z elements when self absorption occurs? Thanks! -Richard -- Richard Mayes Graduate Research Assistant Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

Bruce Ravel

4:07 p.m.

New subject: Self absorption questions

Hi Richard, I'll take a quick stab at this.

...

I'm trying to explain self absorption for our group's guide to EXAFS and I need some help understanding some of the finer details of self absorption. In the realm of fluorescence EXAFS, am I correct in that at a given energy there is a certain penetration depth of the X-rays that is expected (in a thick, dilute sample), but in a thick, concentrated sample, the penetration depth is actually less than the expected depth in thick, dilute samples (causing the decrease in the amplitude of the oscillation peak in Bruce's "wiggle up" of the XAFS oscillation)? Then, in the "wiggle down" of the XAFS oscillation, the penetration depth is actually more than what would be expected so the depth of the oscillation valley decreases. As a result, for thick concentrated samples like a metal foil, in the "wiggle up," the fluorescence accounts for fewer than expected absorbing atoms and in the "wiggle down" the fluorescence accounts for more than expected absorbing atoms.

So, why is "wiggling up" attributed to me? I don't think I wiggle up any more than anyone else in the XAS community! ;-) Dani Haskel and I wrote up a decent explanation of this some years ago. Look at chapter 2 of this: http://www.aps.anl.gov/xfd/people/haskel/FLUO/fluo.ps When you work out the math, you end up with a term that depends on mu(E) in the numerator *and* the denominator of the expression. Bepending on the reltive sizes of the absorption of the absorber and the matrix, you get more or less attenuation due to the presence of the mu(E) term in the denominator. (If someone wanted to replicate the discussion in that link in the FAQ, that would be a valuable addition.)

...

Next, in our amorphous silicates (doped with Ti, V, Cr, W, or Sn), is the self absorption effect greater in the lower Z elements (like titanium) than in the higher Z elements (like tin)? Does the high background due to the silicon at the lower energies (4.9 keV) in relation to the higher energies (29.2 keV) have an effect or is it just an underlying, independent issue that is more pronounced with the lower Z elements when self absorption occurs?

I think the best way to look at this is to consider what is meant when you call an XAS sample "thin". That is, what we consider thin at the Ti edge is very differnet from thin at the Sn edge. So, yes, self-absortion tends to be more of an issue at the Ti edge. But I am uncomfortable making a blanket statement because self-absorption depends on the details. One can certainly make a Sn edge sample that will have self-absorption. Again, it has to do with the relative amount of absorption of the absorber compared to the matrix. Follow the math in that link above, and it should be quite clear. You didn't ask about this, but it always seems worth repeating. Self-absorption is an amplitude problem. You can still measure distances accurately even in a severely attenuated data set. Sometimes transmission is not possible and your choices are fluorescence with attenuation or going home. Obviously, fluo with attenuation is the better choice. ;-) HTH, B -- Bruce Ravel ----------------------------------- bravel@bnl.gov National Institute of Standards and Technology Building 535A, Room M7 c/o Brookhaven National Laboratory Upton NY, 11973, USA My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

Matthew Marcus

4:30 p.m.

New subject: Self absorption questions

You can find a writeup which explains overabsorption in great and gory detail at http://xraysweb.lbl.gov/uxas/Beamline/Operation/Operation.htm . mam ----- Original Message ----- From: "Richard Mayes" To: "XAFS Analysis using Ifeffit" Sent: Wednesday, November 07, 2007 7:39 AM Subject: [Ifeffit] Self absorption questions

...

Greetings all!

I'm trying to explain self absorption for our group's guide to EXAFS and I need some help understanding some of the finer details of self absorption. In the realm of fluorescence EXAFS, am I correct in that at a given energy there is a certain penetration depth of the X-rays that is expected (in a thick, dilute sample), but in a thick, concentrated sample, the penetration depth is actually less than the expected depth in thick, dilute samples (causing the decrease in the amplitude of the oscillation peak in Bruce's "wiggle up" of the XAFS oscillation)? Then, in the "wiggle down" of the XAFS oscillation, the penetration depth is actually more than what would be expected so the depth of the oscillation valley decreases. As a result, for thick concentrated samples like a metal foil, in the "wiggle up," the fluorescence accounts for fewer than expected absorbing atoms and in the "wiggle down" the fluorescence accounts for more than expected absorbing atoms.

Next, in our amorphous silicates (doped with Ti, V, Cr, W, or Sn), is the self absorption effect greater in the lower Z elements (like titanium) than in the higher Z elements (like tin)? Does the high background due to the silicon at the lower energies (4.9 keV) in relation to the higher energies (29.2 keV) have an effect or is it just an underlying, independent issue that is more pronounced with the lower Z elements when self absorption occurs?

Thanks!

-Richard

-- Richard Mayes

Graduate Research Assistant Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Bruce Ravel

4:43 p.m.

New subject: Self absorption questions

On Wednesday 07 November 2007 11:30:59 Matthew Marcus wrote:

...

You can find a writeup which explains overabsorption in great and gory detail at http://xraysweb.lbl.gov/uxas/Beamline/Operation/Operation.htm .

Matthew, That Java-rich page is fairly broken, at least on Firefox on my linux machine. But I am interested in reading what you wrote. Can you post a direct link to the content about overabsorption? Thanks, B -- Bruce Ravel ----------------------------------- bravel@bnl.gov National Institute of Standards and Technology Building 535A, Room M7 c/o Brookhaven National Laboratory Upton NY, 11973, USA My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

Bruce Ravel

10:11 p.m.

New subject: Self absorption questions

On Wednesday 07 November 2007 11:30:59 Matthew Marcus wrote:

...

You can find a writeup which explains overabsorption in great and gory detail at http://xraysweb.lbl.gov/uxas/Beamline/Operation/Operation.htm .

For those of you who, like me, could not read Matthew's write-up, I posted a PDF file that Matthew sent me to http://xafs.org/Tutorials. It's the fourth link under the "XAFS Tutorials and Overviews" heading. B -- Bruce Ravel ----------------------------------- bravel@bnl.gov National Institute of Standards and Technology Building 535A, Room M7 c/o Brookhaven National Laboratory Upton NY, 11973, USA My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

Anatoly Frenkel

8 Nov 8 Nov

1:56 a.m.

New subject: Self absorption questions

Matthew: It is a beautiful summary. Thanks for putting it together. Here is another reference, for your collection: A. Ryazhkin, Y. Babanov, M. Takafumi "Thickness inhomogeneity and fluorescence effects in EXAFS spectroscopy for powder samples: solution of the inverse problem". J. Synchrotron Rad. (2001), 8, 291-293. as well as the earlier one: D. L. Brewe, D. M. Pease, J. I. Budnick, "Corrections of residual fluorescence distortions for a glancing-emergence-angle x-ray-absorption technique " Phys. Rev. B 50, 9025-9030 (1994). and the later one: A. I. Frenkel, D. M. Pease, J. I. Budnick, P. Shanthakumar, T. Huang Application of Glancing Emergent Angle Flourescence for Polarized XAFS Studies of Single Crystals J. Synchrotron Rad. 14, 272-275 (2007) Anatoly -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Matthew Marcus Sent: Wednesday, November 07, 2007 11:31 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Self absorption questions You can find a writeup which explains overabsorption in great and gory detail at http://xraysweb.lbl.gov/uxas/Beamline/Operation/Operation.htm . mam ----- Original Message ----- From: "Richard Mayes" To: "XAFS Analysis using Ifeffit" Sent: Wednesday, November 07, 2007 7:39 AM Subject: [Ifeffit] Self absorption questions

...

Greetings all!

I'm trying to explain self absorption for our group's guide to EXAFS

...

need some help understanding some of the finer details of self absorption. In the realm of fluorescence EXAFS, am I correct in that at a given energy there is a certain penetration depth of the X-rays that is expected (in a thick, dilute sample), but in a thick, concentrated sample, the penetration depth is actually less than the expected depth in thick, dilute samples (causing the decrease in the amplitude of the oscillation peak in Bruce's "wiggle up" of the XAFS oscillation)? Then, in the "wiggle down" of the XAFS oscillation, the penetration depth is actually more than what would be expected so the depth of the oscillation valley decreases. As a result, for thick concentrated samples like a metal foil, in the "wiggle up," the fluorescence accounts for fewer than expected absorbing atoms and in the "wiggle down" the fluorescence accounts for more than expected absorbing atoms.

Next, in our amorphous silicates (doped with Ti, V, Cr, W, or Sn), is

and I the

...

self absorption effect greater in the lower Z elements (like titanium) than in the higher Z elements (like tin)? Does the high background due to the silicon at the lower energies (4.9 keV) in relation to the higher energies (29.2 keV) have an effect or is it just an underlying, independent issue that is more pronounced with the lower Z elements when self absorption occurs?

Thanks!

-Richard

-- Richard Mayes

Graduate Research Assistant Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Matthew Marcus

5:23 a.m.

New subject: Self absorption questions

MessageThanks. It was never intended as a comprehensive review. It was intended to be what you described it as, a summary. It's actually part of a larger review article on microprobe for soil science. I broke it out for users to read because all too many of them haven't a clue about this stuff. In my work, samples are generally inhomogeneous and of unknown composition, so inverse methods don't work. What I do in XANES fitting is to use the simplest model of overabsorption and have the one parameter that results be a fitting parameter. This works better than it has any right to. Inverse methods might, however, be useful for standards. What I do now is to map a sample which has been ground fine and deposited on tape or similar and look for small particles on which to do fluorescence. The sneaky thing about overabsorption is that even if you look at transmission, you can get fooled by hole effect, which distorts the transmission signal in a way very similar to what overabsorption does to a fluorescence signal. Thus, you might think you're OK because the transmission edge jump is small and the fluorescence looks just like the transmission when both modes have been compromised by the same amount. I'll look at the papers you cite. mam ----- Original Message ----- From: Anatoly Frenkel To: 'XAFS Analysis using Ifeffit' Sent: Wednesday, November 07, 2007 5:56 PM Subject: Re: [Ifeffit] Self absorption questions Matthew: It is a beautiful summary. Thanks for putting it together. Here is another reference, for your collection: A. Ryazhkin, Y. Babanov, M. Takafumi "Thickness inhomogeneity and fluorescence effects in EXAFS spectroscopy for powder samples: solution of the inverse problem". J. Synchrotron Rad. (2001), 8, 291-293. as well as the earlier one: D. L. Brewe, D. M. Pease, J. I. Budnick, "Corrections of residual fluorescence distortions for a glancing-emergence-angle x-ray-absorption technique " Phys. Rev. B 50, 9025-9030 (1994). and the later one: A. I. Frenkel, D. M. Pease, J. I. Budnick, P. Shanthakumar, T. Huang Application of Glancing Emergent Angle Flourescence for Polarized XAFS Studies of Single Crystals J. Synchrotron Rad. 14, 272-275 (2007) Anatoly -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Matthew Marcus Sent: Wednesday, November 07, 2007 11:31 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Self absorption questions You can find a writeup which explains overabsorption in great and gory detail at http://xraysweb.lbl.gov/uxas/Beamline/Operation/Operation.htm . mam ----- Original Message ----- From: "Richard Mayes" To: "XAFS Analysis using Ifeffit" Sent: Wednesday, November 07, 2007 7:39 AM Subject: [Ifeffit] Self absorption questions > > Greetings all! > > I'm trying to explain self absorption for our group's guide to EXAFS and I > need some help understanding some of the finer details of self absorption. > In the realm of fluorescence EXAFS, am I correct in that at a given > energy there is a certain penetration depth of the X-rays that is expected > (in a thick, dilute sample), but in a thick, concentrated sample, the > penetration depth is actually less than the expected depth in thick, > dilute samples (causing the decrease in the amplitude of the oscillation > peak in Bruce's "wiggle up" of the XAFS oscillation)? Then, in the > "wiggle down" of the XAFS oscillation, the penetration depth is actually > more than what would be expected so the depth of the oscillation valley > decreases. As a result, for thick concentrated samples like a metal foil, > in the "wiggle up," the fluorescence accounts for fewer than expected > absorbing atoms and in the "wiggle down" the fluorescence accounts for > more than expected absorbing atoms. > > Next, in our amorphous silicates (doped with Ti, V, Cr, W, or Sn), is the > self absorption effect greater in the lower Z elements (like titanium) > than in the higher Z elements (like tin)? Does the high background due to > the silicon at the lower energies (4.9 keV) in relation to the higher > energies (29.2 keV) have an effect or is it just an underlying, > independent issue that is more pronounced with the lower Z elements when > self absorption occurs? > > Thanks! > > -Richard > > -- > Richard Mayes > > Graduate Research Assistant > Barnes Group > 450/452 Buehler Hall > Department of Chemistry > University of Tennessee > Knoxville, TN 37996 > > _______________________________________________ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------------------------------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Bruce Ravel

1:43 p.m.

New subject: Self absorption questions

Hi gang, I started a new page at xafs.org devoted to this topic. Please add new information, relevant literature references, and other resources to the wiki page. http://xafs.org/Experiment/OverAbsorption B On Wednesday 07 November 2007 20:56:54 Anatoly Frenkel wrote:

...

Matthew:

It is a beautiful summary. Thanks for putting it together.

Here is another reference, for your collection:

A. Ryazhkin, Y. Babanov, M. Takafumi "Thickness inhomogeneity and fluorescence effects in EXAFS spectroscopy for powder samples: solution of the inverse problem". J. Synchrotron Rad. (2001), 8, 291-293.

as well as the earlier one:

D. L. Brewe, D. M. Pease, J. I. Budnick, "Corrections of residual fluorescence distortions for a glancing-emergence-angle x-ray-absorption technique " Phys. Rev. B 50, 9025-9030 (1994).

and the later one:

A. I. Frenkel, D. M. Pease, J. I. Budnick, P. Shanthakumar, T. Huang Application of Glancing Emergent Angle Flourescence for Polarized XAFS Studies of Single Crystals J. Synchrotron Rad. 14, 272-275 (2007)

Anatoly

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Matthew Marcus Sent: Wednesday, November 07, 2007 11:31 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Self absorption questions

You can find a writeup which explains overabsorption in great and gory detail at http://xraysweb.lbl.gov/uxas/Beamline/Operation/Operation.htm . mam ----- Original Message ----- From: "Richard Mayes" To: "XAFS Analysis using Ifeffit" Sent: Wednesday, November 07, 2007 7:39 AM Subject: [Ifeffit] Self absorption questions

...
Greetings all!

I'm trying to explain self absorption for our group's guide to EXAFS

and I

...
need some help understanding some of the finer details of self

absorption.

...
In the realm of fluorescence EXAFS, am I correct in that at a given energy there is a certain penetration depth of the X-rays that is

expected

...
(in a thick, dilute sample), but in a thick, concentrated sample, the penetration depth is actually less than the expected depth in thick, dilute samples (causing the decrease in the amplitude of the

oscillation

...
peak in Bruce's "wiggle up" of the XAFS oscillation)? Then, in the "wiggle down" of the XAFS oscillation, the penetration depth is

actually

...
more than what would be expected so the depth of the oscillation

valley

...
decreases. As a result, for thick concentrated samples like a metal

foil,

...
in the "wiggle up," the fluorescence accounts for fewer than expected absorbing atoms and in the "wiggle down" the fluorescence accounts for more than expected absorbing atoms.

Next, in our amorphous silicates (doped with Ti, V, Cr, W, or Sn), is

the

...
self absorption effect greater in the lower Z elements (like titanium) than in the higher Z elements (like tin)? Does the high background

due to

...
the silicon at the lower energies (4.9 keV) in relation to the higher energies (29.2 keV) have an effect or is it just an underlying, independent issue that is more pronounced with the lower Z elements

when

...
self absorption occurs?

Thanks!

-Richard

-- Richard Mayes

Graduate Research Assistant Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Bruce Ravel ----------------------------------- bravel@bnl.gov National Institute of Standards and Technology Building 535A, Room M7 c/o Brookhaven National Laboratory Upton NY, 11973, USA My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

Richard Mayes

9 Nov 9 Nov

5:09 p.m.

New subject: SA and issue with importing into Artemis

Everyone, thanks for the info on self absorption! I'm currently working on writing a short summary for our group based on the information everyone shared. Bruce, I'm having an issue importing a k3-weighted project into Artemis from Athena. (I looked on the mail list and your webpage for a bug report and couldn't find one, my apologies if I missed it.) The problem: I'm trying to import a k3-weighted spectrum into Artemis, but it appears to be importing the k2-weighted spectrum instead. I don't know if this is related or a change between versions of Artemis, but the k-weight used in Athena isn't being carried over into Artemis as the fit k-weight as well. Attached is the Athena and Artemis projects showing this and a pdf with pics of the 2 spectra I'm seeing (in case this is an issue only on my computer). I tried changing the group name and deleting all the groups in Athena except the one I wanted and this still occurs. Any ideas on how to get around this? FYI: I'm running Athena (0.8.054) and Artemis (0.8.011) on a laptop (1.7 GHz Pentium M processor & 2 GB RAM) with Windows XP Pro. Thanks!! -Richard -- Richard Mayes Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

Richard Mayes

5:13 p.m.

New subject: SA and issue with importing into Artemis

Oops! Forgot the attachments. Sorry about that. I should also add, the file I'm trying to import into Artemis is "k_3.191_13.860". -Richard

...

Everyone, thanks for the info on self absorption! I'm currently working on writing a short summary for our group based on the information everyone shared.

Bruce, I'm having an issue importing a k3-weighted project into Artemis from Athena. (I looked on the mail list and your webpage for a bug report and couldn't find one, my apologies if I missed it.)

The problem: I'm trying to import a k3-weighted spectrum into Artemis, but it appears to be importing the k2-weighted spectrum instead. I don't know if this is related or a change between versions of Artemis, but the k-weight used in Athena isn't being carried over into Artemis as the fit k-weight as well. Attached is the Athena and Artemis projects showing this and a pdf with pics of the 2 spectra I'm seeing (in case this is an issue only on my computer). I tried changing the group name and deleting all the groups in Athena except the one I wanted and this still occurs.

Any ideas on how to get around this?

FYI: I'm running Athena (0.8.054) and Artemis (0.8.011) on a laptop (1.7 GHz Pentium M processor & 2 GB RAM) with Windows XP Pro.

Thanks!! -Richard

-- Richard Mayes

Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

-- Richard Mayes Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

Anatoly Frenkel

5:26 p.m.

New subject: SA and issue with importing into Artemis

...

Everyone, thanks for the info on self absorption! I'm currently working on writing a short summary for our group based on the information everyone shared.

Bruce, I'm having an issue importing a k3-weighted project into Artemis from Athena. (I looked on the mail list and your webpage for a bug report and couldn't find one, my apologies if I missed it.)

The problem: I'm trying to import a k3-weighted spectrum into Artemis, but it appears to be importing the k2-weighted spectrum instead. I don't know if this is related or a change between versions of Artemis, but

Richard, I tried with Athena v50 and Artemis v007 and it worked (the data were ported correctly). I do not think it is version dependent. The data that you save in Athena are ported to Artemis with 0 k-weighting, so you have to manually set your k-weighting in artemis if you want to match the same k-weighting that you liked in athena. As you know, there is k-weighting for FT and k-weigthting for plotting data in k-space, which have nothing to do with each other. Note that the vertical axis in the bottom figure of your PDF file has unit of A^-3 which means it was indeed k2-weighting in FT in Artemis. You just have to make it k3 weighting in FT and it will give you the same plot as the top figure (and the unit will be A^-4). Anatoly -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Richard Mayes Sent: Friday, November 09, 2007 12:13 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] SA and issue with importing into Artemis Oops! Forgot the attachments. Sorry about that. I should also add, the file I'm trying to import into Artemis is "k_3.191_13.860". -Richard the

...

k-weight used in Athena isn't being carried over into Artemis as the fit k-weight as well. Attached is the Athena and Artemis projects showing this and a pdf with pics of the 2 spectra I'm seeing (in case this is an issue only on my computer). I tried changing the group name and deleting all the groups in Athena except the one I wanted and this still occurs.

Any ideas on how to get around this?

FYI: I'm running Athena (0.8.054) and Artemis (0.8.011) on a laptop (1.7 GHz Pentium M processor & 2 GB RAM) with Windows XP Pro.

Thanks!! -Richard

-- Richard Mayes

Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

-- Richard Mayes Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

Richard Mayes

5:34 p.m.

New subject: SA and issue with importing into Artemis

DO'OH! Thanks Anatoly! I must be blind. I totally missed that. -Richard

...

Richard,

I tried with Athena v50 and Artemis v007 and it worked (the data were ported correctly). I do not think it is version dependent.

The data that you save in Athena are ported to Artemis with 0 k-weighting, so you have to manually set your k-weighting in artemis if you want to match the same k-weighting that you liked in athena. As you know, there is k-weighting for FT and k-weigthting for plotting data in k-space, which have nothing to do with each other.

Note that the vertical axis in the bottom figure of your PDF file has unit of A^-3 which means it was indeed k2-weighting in FT in Artemis. You just have to make it k3 weighting in FT and it will give you the same plot as the top figure (and the unit will be A^-4).

Anatoly

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Richard Mayes Sent: Friday, November 09, 2007 12:13 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] SA and issue with importing into Artemis

Oops! Forgot the attachments. Sorry about that.

I should also add, the file I'm trying to import into Artemis is "k_3.191_13.860".

-Richard

...
Everyone, thanks for the info on self absorption! I'm currently working on writing a short summary for our group based on the information everyone shared.

Bruce, I'm having an issue importing a k3-weighted project into Artemis from Athena. (I looked on the mail list and your webpage for a bug report and couldn't find one, my apologies if I missed it.)

The problem: I'm trying to import a k3-weighted spectrum into Artemis, but it appears to be importing the k2-weighted spectrum instead. I don't know if this is related or a change between versions of Artemis, but the k-weight used in Athena isn't being carried over into Artemis as the fit k-weight as well. Attached is the Athena and Artemis projects showing this and a pdf with pics of the 2 spectra I'm seeing (in case this is an issue only on my computer). I tried changing the group name and deleting all the groups in Athena except the one I wanted and this still occurs.

Any ideas on how to get around this?

FYI: I'm running Athena (0.8.054) and Artemis (0.8.011) on a laptop (1.7 GHz Pentium M processor & 2 GB RAM) with Windows XP Pro.

Thanks!! -Richard

-- Richard Mayes

Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

-- Richard Mayes

Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Richard Mayes Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

Bruce Ravel

5:39 p.m.

New subject: SA and issue with importing into Artemis

On Friday 09 November 2007 12:26:33 Anatoly Frenkel wrote:

...

I tried with Athena v50 and Artemis v007 and it worked

You should consider updating. ;-) B -- Bruce Ravel ----------------------------------- bravel@bnl.gov National Institute of Standards and Technology Building 535A, Room M7 c/o Brookhaven National Laboratory Upton NY, 11973, USA My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

Anatoly Frenkel

5:42 p.m.

New subject: SA and issue with importing into Artemis

...and send you bug reports every day? :(((((((((( A. -----Original Message----- From: Ravel, Bruce [mailto:bravel@bnl.gov] Sent: Friday, November 09, 2007 12:39 PM To: anatoly.frenkel@yu.edu; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] SA and issue with importing into Artemis On Friday 09 November 2007 12:26:33 Anatoly Frenkel wrote:

...

I tried with Athena v50 and Artemis v007 and it worked

Bruce Ravel

5:34 p.m.

New subject: SA and issue with importing into Artemis

On Friday 09 November 2007 12:13:01 Richard Mayes wrote:

...

Oops! Forgot the attachments. Sorry about that.

I should also add, the file I'm trying to import into Artemis is "k_3.191_13.860".

Richard, I don't think there is a problem. Athena stores the un-k-weighted data internally and applies the k-weight when you request a plot in k or R space. Similarly, Artemis imports the un-k-weighted data from the Athena project file. When Artemis plots the data in k or R space, the k-weighting selected in those little radio buttons in the upper right hand corner of the Artemis window, just beneath the label that says "Plotting options". If you click on the "3" button, then k^3 weighted data is plotted. I am looking at k^3 weighted plots of your data from Athena and Artemis as I write this. I don't see a difference. I suspect that you are just being surprised by the details of how Artemis decides what to plot. See page 8 of this document: http://cars9.uchicago.edu/~ravel/talks/artemis.methyltin.pdf Or am I not understanding your problem? B

...

-Richard

...
Everyone, thanks for the info on self absorption! I'm currently working on writing a short summary for our group based on the information everyone shared.

Bruce, I'm having an issue importing a k3-weighted project into Artemis from Athena. (I looked on the mail list and your webpage for a bug report and couldn't find one, my apologies if I missed it.)

The problem: I'm trying to import a k3-weighted spectrum into Artemis, but it appears to be importing the k2-weighted spectrum instead. I don't know if this is related or a change between versions of Artemis, but the k-weight used in Athena isn't being carried over into Artemis as the fit k-weight as well. Attached is the Athena and Artemis projects showing this and a pdf with pics of the 2 spectra I'm seeing (in case this is an issue only on my computer). I tried changing the group name and deleting all the groups in Athena except the one I wanted and this still occurs.

Any ideas on how to get around this?

FYI: I'm running Athena (0.8.054) and Artemis (0.8.011) on a laptop (1.7 GHz Pentium M processor & 2 GB RAM) with Windows XP Pro.

Thanks!! -Richard

-- Richard Mayes

Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996

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