March 2003 - Ifeffit - millenia.cars.aps.anl.gov

ifeffit and Mac OSX
by Matt Newville 04 Jul '04

04 Jul '04

Hi Raja, On Mon, 7 Oct 2002, rajasekaran swaminathan wrote: > Hi Matt, > > I tried again over the past few days to install the binary > installer on my mac (OS X.2). I couldn't find an attached aquaterm > / pgplot demo. The Aquaterm program opens, but I cannot see any > windows come out from that application. I mean, it is just like a > blank application. When I type ifeffit on Terminal app, it doesnt > recognise the presence of ifeffit in the ifeffitosx directory. i.e. > it says that the command is not found. The executable works > perfectly well on a Windows machine, and I was wondering whether > there are any such equivalents for a Macintosh machine. I also dont > think that the installer comes with athena/artemis/tkatoms etc.. Do > you have any other recommendations to resolve this issue? Also,if > it is possible, can I get a CD of these programs for a Macintosh > equivalent to an executable version for the Windows? > > I appreciate your help in this regard. I have used the binary installer once on a OS 10.1 system. It worked for me (after following the simple included instructions, of course) and plotting with Aquaterm did work. I haven't tried 10.2. I know the Mac binary installer does not include athena, artemis, or tkatoms. I believe it only provides the command-line ifeffit. I'm not sure I can answer many other questions about it. I don't know enough about it or 10.2 v. 10.1 issues to know how well it would work with 10.2. If the aquaterm/pgplot demos don't work, I'd guess it's a more serious problem and that the binary installer may not work. Is the Fink / X-Windows / PGPLOT installation procedure too big of a hassle? I know that can work, and that athena will work too. I also believe that the instructions are simpler for 10.2 than 10.1 (especially with respect to getting perl/Tk to work), but haven't tried this myself. I'm copying this message to the ifeffit mailing list, hoping that someone else may have better answers to these questions. How necessary is a complete binary installer for Mac OSX? Thanks, --Matt

4 4

athena 0.8.015 and artemis 0.5.008
by Bruce Ravel 27 Mar '03

27 Mar '03

Hi folks, I am releasing a new source tarball for Athena and Artemis today along with windows executables of both programs. They are available in their standard places on my web site. Athena: One small change in how title lines are handled. Other than that, this release is identical to the last. Artemis: Lots of small bug fixes and usability enhancements, including: 1. You can rearrange the order of the parameters on the Guess, Def, Set page. 2. You can rename data, feff calculations, and feff paths. This changes how they are displayed in the list, how paths are reported after a fit, and how legend strings are generated for plots. 3. Control-right-click or middle-click on an item in the Paths list will pop up a contextual menu. 4. A parameter can now be set as a "skip" parameter (as well as guess, def, or set). This means that Athena will ignore that parameter when building an ifeffit script for fitting. 5. You can now save multi-column data files where the columns contain the selected (i.e. highlighted in orange) items from the paths list I am hoping to start work on multiple data set fits in Artemis real soon. The next release will, I hope, have my first stab at that. Yay! Special thanks this time to Simon Bare for pointing out a very strange bug in Athena. Also I should point out that starting work on the Artemis document proved to be a good way to find bugs and other weird behavior in Artemis. Most of the changes this time are a direct result of stuff I found while trying to start the document! Peace, B P.S. The bug in how Athena handled titles is extremely specific. It was triggered by having a title line in a data file which had a percent sign (%), a hash (#), or an exclamation point (!) inside of matching parentheses somewhere on the line. Then, the problem was only triggered on Windows. I could not reproduce it on linux, only on Win2k. I also have not yet been able to reproduce it in a simpler context using the ifeffit command line. My temporary solution is to remove %, #, or ! from a title line if Athena is running on Windows. This is a bad solution because Athena should preserve the contents of the headers unaltered. However, it seems more important that Athena plot and remove backgrounds and do Fourier transforms. Thus, I decided to release this crude hack with a promise to return to the problem later. Also, I think that Athena's removing those three characters is only a small sin. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b 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/

1 0

Difference File Fits
by Norbert Weiher 19 Mar '03

19 Mar '03

Hi folks, I was just playing a bit around with some data and it sprang to my mind that sometimes the idea of doing difference file spectra fits would be a nice feature (like XDAP has it). This would be great to identify single contributions of certain scatterers that are close to each other or somehow other produce similar paths. How about including a feature which lets you extract a "new" chi.dat file from the original data minus some paths one has selected? This file could then be further processed. Finally something similar for EASE: I'm still one of those old-fashioned EMACS folks and would like to have something like this at my hands in EASE too. Bruce, what do you think about it? Would it be possible? I'm keen on hearing your ideas about this. Norbert -- Dr. rer. nat. Norbert Weiher (norbertweiher(a)yahoo.de) Laboratory for Technical Chemistry - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 2 3123

3 3

RE: [Ifeffit] A question for Windows users
by SCHLEGEL Michel 177447 17 Mar '03

17 Mar '03

Hello Bruce, everybody you wrote: > Athena is not always particularly creative about the names it suggests > for output files. For example, if you use the feature of saving > several marked groups to a single output file, Athena suggests that > the names be "marked.space". That is, if you save marked groups as > chi(k), the suggested file name is "marked.chi". If you save marked > groups as the real part of chi(R), the suggested file name is > "marked.chir_re". > > It is possible to configure Explorer such that it does not display > file extensions (i.e. the bit after the dot). That might make it hard > to tell different marked group output files apart if the suggested > names are used. > > Is this a problem for anyone? Should I change the suggested names > such that the suggestive part is not in the extension? That is, would > "chi.marked" and "chir_re.marked" be better names? Actually, as a Window user (booo! hisss!), my first move is to have all the extensions appearing in Explorer, a basic security move (e.g., to avoid clicking on a "picture.gif" that actually corresponds to a "picture.gif.exe", with all undesirable consequences). I also find it much easier to keep the pre-dot part of the data file for the sample name, and the post-dot part for the data type (and I'm eternally grateful to Ifeffit to provide us miscellaneous and yet distinct extensions; no joke). Therefore, I suggest NOT to change the current feature. Best regards, Michel Schlegel

3 2

Re: Ifeffit Digest, Vol 1, Issue 123
by Grant Bunker 14 Mar '03

14 Mar '03

HI, Irit - well, I'm sure the whole EXAFS community wishes you the best in delivery of your third child! And the whole world hopes the Bush/Saddam war will be short with minimum casualties on both sides. (I'll continue the conversation without the whole world listening) best wishes - grant ps congratulations on your Nature paper On Fri, 14 Mar 2003 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. Re: Ifeffit Digest, Vol 1, Issue 121 (Irit Sagi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 13 Mar 2003 21:07:04 +0200 > From: "Irit Sagi" <cssagi(a)wisemail.weizmann.ac.il> > Subject: [Ifeffit] Re: Ifeffit Digest, Vol 1, Issue 121 > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <se70f2fb.035(a)wisemail.weizmann.ac.il> > Content-Type: text/plain; charset=US-ASCII > > Oops, I see that the whole EXAFS community saw this mail.......Oh well, SHALOM from Israel. Irit. > > > > > > > > Dr. Irit Sagi > Department of structural Biology > The Weizmann Institute of Science > ISRAEL > Tel/Fax 972-8-9342130 > e-mail: irit.sagi(a)weizmann.ac.il > > >>> cssagi(a)wisemail.weizmann.ac.il 03/13/03 08:56pm >>> > Hi Grant > I read your e-mails regarding IFEFFIT and I could not help myself to ask how are you doing and how are things. > We are all OK here in Israel, as much as we can of course. I am pregnant with my third child and I am due by the end of the month. Besides this, we are well prepared for the USA-Iraq war. In fact we are expecting it to start on Monday. > I was invited to give a talk in the APS workshop this year but I will not be able to make due to the new baby. > I hope that everything is OK with you and your family. > All the best, Irit. > > Dr. Irit Sagi > Department of structural Biology > The Weizmann Institute of Science > ISRAEL > Tel/Fax 972-8-9342130 > e-mail: irit.sagi(a)weizmann.ac.il > > >>> bunker(a)biocat1.phys.iit.edu 03/13/03 08:38pm >>> > Matt - it might be sensible to just add a new function to do the > rebinning i.e. map mu(E)->mu'(E') on resampled grid (mu data around the > edge could be left unchanged). People could call the function ('rebin"?) > only they needed it; subsequent routines could be kept as they > are now. Anyone who doesn't like the rebinning wouldn't be obligated to > use it. > > thanks - grant > > On Thu, 13 Mar 2003 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. RE: Rebinning (Kelly, Shelly D.) > > 2. Rebinning (Bruce Ravel) > > 3. Re: Rebinning (Carlo U. Segre) > > 4. Re: Rebinning (Matt Newville) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 12 Mar 2003 13:52:45 -0600 > > From: "Kelly, Shelly D." <SKelly(a)anl.gov> > > Subject: RE: [Ifeffit] Rebinning > > To: "'XAFS Analysis using Ifeffit'" > > <ifeffit(a)millenia.cars.aps.anl.gov> > > Message-ID: > > <DC97518EF1B5E3418A86F59A9A58035D01D9A70A(a)ANLEXCH.CTD.ANL.GOV> > > Content-Type: text/plain; charset="us-ascii" > > > > Hello All, > > > > There seems to be a lot of interest in Rebinning data. I have a perl script > > that > > I've written to do the same thing. I thought it might be of interest. > > > > Shelly > > > > > -----Original Message----- > > > From: Newville, Matthew G. > > > Sent: Tuesday, March 11, 2003 2:08 PM > > > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > > > Subject: Re: [Ifeffit] Rebinning > > > > > > > > > Hi Carlo, > > > > > > Thanks!! That's wonderful. It seems like this should be an > > > option in spline() and bkg_cl(), and possibly in pre_edge(). I > > > admit to being still a little confused by the goal of the > > > rebinning, especially with respect to loss of resolution. It > > > seems like to use this script, you need to do two things: > > > 1. select an E0. The data will be put at energies that > > > will give an even k-grid with this e0. I think it's > > > inevitable that if e0 changes, you might want to re-bin. > > > > > > 2. assume that the k-grid is small enough that the > > > measurements at independent energies are within the > > > acceptable energy resolution that they can be > > > simply summed. > > > > > > Is that right? > > > > > > Would it be OK with you (and everyone else) to have a weighted > > > average replace the boxcar average? For example, at k=12, > > > [E(k+0.05) - E(k)] = 5eV, which is larger than normal energy > > > resolutions, so the boxcar average might wash out the high-k > > > EXAFS, no? It might be better to convolve the spectra with a > > > lorenztian reflecting the incident energy resolution (probably > > > defaulting to 1eV). Does that seem OK or is there something eles > > > going on? > > > > > > Anyway, thanks!! > > > > > > --Matt > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > >

1 0

Artemis document
by Bruce Ravel 14 Mar '03

14 Mar '03

Hi folks, I got mail this afternoon asking me about documentation for Artemis. That has, of course, been a long-standing shortcoming of the code. It turns out that I have spent a decent chunk of time in the last couple weeks working on the Artemis doc. It is only about 25% written, but the portions that I have written are introductory material. It should be useful even in its current, sparse form. Here's the URL: http://leonardo.phys.washington.edu/~ravel/software/exafs/docs.html I am only posting the PDF at this time. I'll be updating it frequently as I work on it, but I probably won't announce updates on this channel until it is a lot closer to finished. So check back often if you are interested. Please be aware that it is nowhere near finished. It is full of gaps, typos, suspicious statements, and dangling trains of thought. It is so far from finished that "documentation" may be too kind of a term. However, it seems that posting the unfinished doc on my web site is well within that open source spirit of "release early, release often" that I have adopted with my codes. If it proves useful to some of you -- super! B P.S. If anyone is interested in helping out with the doc, either by copy editing or by contributing text, let me know -- I'd be jumping- up-and-down happy if that happened. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b 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/

1 0

A question for Windows users
by Bruce Ravel 14 Mar '03

14 Mar '03

Hi folks, Athena is not always particularly creative about the names it suggests for output files. For example, if you use the feature of saving several marked groups to a single output file, Athena suggests that the names be "marked.space". That is, if you save marked groups as chi(k), the suggested file name is "marked.chi". If you save marked groups as the real part of chi(R), the suggested file name is "marked.chir_re". It is possible to configure Explorer such that it does not display file extensions (i.e. the bit after the dot). That might make it hard to tell different marked group output files apart if the suggested names are used. Is this a problem for anyone? Should I change the suggested names such that the suggestive part is not in the extension? That is, would "chi.marked" and "chir_re.marked" be better names? If no one pipes up, then I'll assume things are ok as they stand. If even one person makes a compelling argument, I'll probably change the suggested names throughout my programs to avoid this situation. Thanks. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b 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/

1 0

Re: Ifeffit Digest, Vol 1, Issue 121
by Irit Sagi 13 Mar '03

13 Mar '03

Oops, I see that the whole EXAFS community saw this mail.......Oh well, SHALOM from Israel. Irit. Dr. Irit Sagi Department of structural Biology The Weizmann Institute of Science ISRAEL Tel/Fax 972-8-9342130 e-mail: irit.sagi(a)weizmann.ac.il >>> cssagi(a)wisemail.weizmann.ac.il 03/13/03 08:56pm >>> Hi Grant I read your e-mails regarding IFEFFIT and I could not help myself to ask how are you doing and how are things. We are all OK here in Israel, as much as we can of course. I am pregnant with my third child and I am due by the end of the month. Besides this, we are well prepared for the USA-Iraq war. In fact we are expecting it to start on Monday. I was invited to give a talk in the APS workshop this year but I will not be able to make due to the new baby. I hope that everything is OK with you and your family. All the best, Irit. Dr. Irit Sagi Department of structural Biology The Weizmann Institute of Science ISRAEL Tel/Fax 972-8-9342130 e-mail: irit.sagi(a)weizmann.ac.il >>> bunker(a)biocat1.phys.iit.edu 03/13/03 08:38pm >>> Matt - it might be sensible to just add a new function to do the rebinning i.e. map mu(E)->mu'(E') on resampled grid (mu data around the edge could be left unchanged). People could call the function ('rebin"?) only they needed it; subsequent routines could be kept as they are now. Anyone who doesn't like the rebinning wouldn't be obligated to use it. thanks - grant On Thu, 13 Mar 2003 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. RE: Rebinning (Kelly, Shelly D.) > 2. Rebinning (Bruce Ravel) > 3. Re: Rebinning (Carlo U. Segre) > 4. Re: Rebinning (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Mar 2003 13:52:45 -0600 > From: "Kelly, Shelly D." <SKelly(a)anl.gov> > Subject: RE: [Ifeffit] Rebinning > To: "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <DC97518EF1B5E3418A86F59A9A58035D01D9A70A(a)ANLEXCH.CTD.ANL.GOV> > Content-Type: text/plain; charset="us-ascii" > > Hello All, > > There seems to be a lot of interest in Rebinning data. I have a perl script > that > I've written to do the same thing. I thought it might be of interest. > > Shelly > > > -----Original Message----- > > From: Newville, Matthew G. > > Sent: Tuesday, March 11, 2003 2:08 PM > > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > > Subject: Re: [Ifeffit] Rebinning > > > > > > Hi Carlo, > > > > Thanks!! That's wonderful. It seems like this should be an > > option in spline() and bkg_cl(), and possibly in pre_edge(). I > > admit to being still a little confused by the goal of the > > rebinning, especially with respect to loss of resolution. It > > seems like to use this script, you need to do two things: > > 1. select an E0. The data will be put at energies that > > will give an even k-grid with this e0. I think it's > > inevitable that if e0 changes, you might want to re-bin. > > > > 2. assume that the k-grid is small enough that the > > measurements at independent energies are within the > > acceptable energy resolution that they can be > > simply summed. > > > > Is that right? > > > > Would it be OK with you (and everyone else) to have a weighted > > average replace the boxcar average? For example, at k=12, > > [E(k+0.05) - E(k)] = 5eV, which is larger than normal energy > > resolutions, so the boxcar average might wash out the high-k > > EXAFS, no? It might be better to convolve the spectra with a > > lorenztian reflecting the incident energy resolution (probably > > defaulting to 1eV). Does that seem OK or is there something eles > > going on? > > > > Anyway, thanks!! > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > >

1 0

Re: Ifeffit Digest, Vol 1, Issue 121
by Irit Sagi 13 Mar '03

13 Mar '03

Hi Grant I read your e-mails regarding IFEFFIT and I could not help myself to ask how are you doing and how are things. We are all OK here in Israel, as much as we can of course. I am pregnant with my third child and I am due by the end of the month. Besides this, we are well prepared for the USA-Iraq war. In fact we are expecting it to start on Monday. I was invited to give a talk in the APS workshop this year but I will not be able to make due to the new baby. I hope that everything is OK with you and your family. All the best, Irit. Dr. Irit Sagi Department of structural Biology The Weizmann Institute of Science ISRAEL Tel/Fax 972-8-9342130 e-mail: irit.sagi(a)weizmann.ac.il >>> bunker(a)biocat1.phys.iit.edu 03/13/03 08:38pm >>> Matt - it might be sensible to just add a new function to do the rebinning i.e. map mu(E)->mu'(E') on resampled grid (mu data around the edge could be left unchanged). People could call the function ('rebin"?) only they needed it; subsequent routines could be kept as they are now. Anyone who doesn't like the rebinning wouldn't be obligated to use it. thanks - grant On Thu, 13 Mar 2003 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. RE: Rebinning (Kelly, Shelly D.) > 2. Rebinning (Bruce Ravel) > 3. Re: Rebinning (Carlo U. Segre) > 4. Re: Rebinning (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Mar 2003 13:52:45 -0600 > From: "Kelly, Shelly D." <SKelly(a)anl.gov> > Subject: RE: [Ifeffit] Rebinning > To: "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <DC97518EF1B5E3418A86F59A9A58035D01D9A70A(a)ANLEXCH.CTD.ANL.GOV> > Content-Type: text/plain; charset="us-ascii" > > Hello All, > > There seems to be a lot of interest in Rebinning data. I have a perl script > that > I've written to do the same thing. I thought it might be of interest. > > Shelly > > > -----Original Message----- > > From: Newville, Matthew G. > > Sent: Tuesday, March 11, 2003 2:08 PM > > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > > Subject: Re: [Ifeffit] Rebinning > > > > > > Hi Carlo, > > > > Thanks!! That's wonderful. It seems like this should be an > > option in spline() and bkg_cl(), and possibly in pre_edge(). I > > admit to being still a little confused by the goal of the > > rebinning, especially with respect to loss of resolution. It > > seems like to use this script, you need to do two things: > > 1. select an E0. The data will be put at energies that > > will give an even k-grid with this e0. I think it's > > inevitable that if e0 changes, you might want to re-bin. > > > > 2. assume that the k-grid is small enough that the > > measurements at independent energies are within the > > acceptable energy resolution that they can be > > simply summed. > > > > Is that right? > > > > Would it be OK with you (and everyone else) to have a weighted > > average replace the boxcar average? For example, at k=12, > > [E(k+0.05) - E(k)] = 5eV, which is larger than normal energy > > resolutions, so the boxcar average might wash out the high-k > > EXAFS, no? It might be better to convolve the spectra with a > > lorenztian reflecting the incident energy resolution (probably > > defaulting to 1eV). Does that seem OK or is there something eles > > going on? > > > > Anyway, thanks!! > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > >

1 0

Re: Ifeffit Digest, Vol 1, Issue 121
by Grant Bunker 13 Mar '03

13 Mar '03

Matt - it might be sensible to just add a new function to do the rebinning i.e. map mu(E)->mu'(E') on resampled grid (mu data around the edge could be left unchanged). People could call the function ('rebin"?) only they needed it; subsequent routines could be kept as they are now. Anyone who doesn't like the rebinning wouldn't be obligated to use it. thanks - grant On Thu, 13 Mar 2003 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. RE: Rebinning (Kelly, Shelly D.) > 2. Rebinning (Bruce Ravel) > 3. Re: Rebinning (Carlo U. Segre) > 4. Re: Rebinning (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Mar 2003 13:52:45 -0600 > From: "Kelly, Shelly D." <SKelly(a)anl.gov> > Subject: RE: [Ifeffit] Rebinning > To: "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <DC97518EF1B5E3418A86F59A9A58035D01D9A70A(a)ANLEXCH.CTD.ANL.GOV> > Content-Type: text/plain; charset="us-ascii" > > Hello All, > > There seems to be a lot of interest in Rebinning data. I have a perl script > that > I've written to do the same thing. I thought it might be of interest. > > Shelly > > > -----Original Message----- > > From: Newville, Matthew G. > > Sent: Tuesday, March 11, 2003 2:08 PM > > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > > Subject: Re: [Ifeffit] Rebinning > > > > > > Hi Carlo, > > > > Thanks!! That's wonderful. It seems like this should be an > > option in spline() and bkg_cl(), and possibly in pre_edge(). I > > admit to being still a little confused by the goal of the > > rebinning, especially with respect to loss of resolution. It > > seems like to use this script, you need to do two things: > > 1. select an E0. The data will be put at energies that > > will give an even k-grid with this e0. I think it's > > inevitable that if e0 changes, you might want to re-bin. > > > > 2. assume that the k-grid is small enough that the > > measurements at independent energies are within the > > acceptable energy resolution that they can be > > simply summed. > > > > Is that right? > > > > Would it be OK with you (and everyone else) to have a weighted > > average replace the boxcar average? For example, at k=12, > > [E(k+0.05) - E(k)] = 5eV, which is larger than normal energy > > resolutions, so the boxcar average might wash out the high-k > > EXAFS, no? It might be better to convolve the spectra with a > > lorenztian reflecting the incident energy resolution (probably > > defaulting to 1eV). Does that seem OK or is there something eles > > going on? > > > > Anyway, thanks!! > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > >

2 1