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

Re: [Ifeffit] Ifeffit Digest, Vol 157, Issue 9
by Matteo Busi 14 Mar '16

14 Mar '16

Hi Bruce, Sorry if I insisted, didn't mean to be rude. By the way the solution you proposed is exactly what I meant and I thank you. Anyways if you're going to implement this in the new release, personally I would prefer to have the mu(E) data in the .chi saved file as it simplifies my work. Don't know if it is the same to everybody. Thank you very much and have a good Easter Matteo Busi, UiS 2016-03-11 19:00 GMT+01:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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: Exporting Athena projects data (Bruce Ravel) > 2. Re: Exporting Athena projects data (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Mar 2016 08:57:50 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Exporting Athena projects data > Message-ID: <56E2CEDE.3040803(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2016 06:52 AM, Matteo Busi wrote: > > Hi Bruce I'm sending this again, probably the latest message was lost in > > the confusion. > > Or ... perhaps ... I've been really busy lately. > > I understand what you are looking for and will have a solution for you > soon, once I get some other, more pressing things done. > > B > > > I would like to have an output file containing chi(E) and mu(E) using the > > same energy (E) grid. > > If I export them separately ( the only available way I think right now) > > they have > > different energy grid. > > > > The previous messaging was: > >> Hi Mateo, > > > >> I'm not quite clear on what you are asking for. Do you want an ascii > >> output file that has a column containing chi(E) using the energy grid of > >> the original data? > > > >> If so, would it suffice to add a column to the mu(E) ascii output file? > >> That seems to me like a natural solution. > > > >>Cheers, > >>B > > > > Thanks and Regards > > Matteo, UiS > > > > > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 2 > Date: Fri, 11 Mar 2016 11:56:22 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Exporting Athena projects data > Message-ID: <56E2F8B6.7060508(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > Matteo, > > A fully correct solution to this will have to wait until the next > release, but I can offer a partial solution which you can implement > immediately. > > Locate the file > "perl\site\lib\Demeter\templates\process\ifeffit\save_xmu.tmpl" in > whatever location Demeter was installed on your computer. > > Grab this: > > > https://raw.githubusercontent.com/bruceravel/demeter/master/lib/Demeter/tem… > > and replace the previous "save_xmu.tmpl". When you download the > replacement, be sure that its filename is "save_xmu.tmpl" and that > your browser does not "helpfully" add a .txt extension. > > When you next save current group as mu(E), there will be an additional > column which contains the chi(E) on the grid of the original data. > That column will be 0 below the lower bound of the spline range and > above the upper bound of the spline range (i.e. in the energy range > over which chi is not defined). It is un-k-weighted. If you want to > look at k-weighted chi(E), /you/ will have to apply the k-weighting > /yourself/. > > I think that addresses your request. Let me know what you think. > > B > > > On 03/11/2016 06:52 AM, Matteo Busi wrote: > > Hi Bruce I'm sending this again, probably the latest message was lost in > > the confusion. > > > > I would like to have an output file containing chi(E) and mu(E) using the > > same energy (E) grid. > > If I export them separately ( the only available way I think right now) > > they have > > different energy grid. > > > > The previous messaging was: > >> Hi Mateo, > > > >> I'm not quite clear on what you are asking for. Do you want an ascii > >> output file that has a column containing chi(E) using the energy grid of > >> the original data? > > > >> If so, would it suffice to add a column to the mu(E) ascii output file? > >> That seems to me like a natural solution. > > > >>Cheers, > >>B > > > > Thanks and Regards > > Matteo, UiS > > > > > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ------------------------------ > > End of Ifeffit Digest, Vol 157, Issue 9 > *************************************** >

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Exporting Athena projects data
by Matteo Busi 11 Mar '16

11 Mar '16

Hi Bruce I'm sending this again, probably the latest message was lost in the confusion. I would like to have an output file containing chi(E) and mu(E) using the same energy (E) grid. If I export them separately ( the only available way I think right now) they have different energy grid. The previous messaging was: > Hi Mateo, > I'm not quite clear on what you are asking for. Do you want an ascii > output file that has a column containing chi(E) using the energy grid of > the original data? > If so, would it suffice to add a column to the mu(E) ascii output file? > That seems to me like a natural solution. >Cheers, >B Thanks and Regards Matteo, UiS

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Absorption length
by 이국승(에너지환경소재연구팀) 11 Mar '16

11 Mar '16

Dear members, I have seen many times the absorption length in materials for introduction of XAFS. The absorption length equals 1/mu, which is the thickness that I0 is attenuated to 1/e. But I do not understand why the absorption length is important. More importantly, I do not understand why the particle size in samples should be smaller than the absorption length. Could any one explain the absorption length including the question above and the relation between the absorption length and edge step calculations? Thanks in advance. Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Researcher ID: http://www.researcherid.com/rid/D-7088-2011

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Error in N (Number of Scatterers)
by Carolyn Carr 09 Mar '16

09 Mar '16

Hello Mailing List, I have read papers describing that EXAFS has an error regarding N the number of scatters of +/- 20%. The only original reference I can see to support this is "The effect of statistical noise on structural parameters in EXAFS data analysis" by L. Incoccia, S. Mobilio (1984, Il Nuovo Cimento D). However, in the more recent D. C. Koningsberger review "XAFS spectroscopy; fundamental principles and data analysis" (2000, Topics in Catalysis) he cites an error of 5% for N (although the paper cites slightly varying error for different absorber-scatterer pairs). Several months ago, I wrote to the mailing list regarding the difference of fitting in R- and k-space in Artemis and received several responses revealing that some comments made in the Koningsberger review are no longer valid in Artemis. In my literature search, I did not find additional papers describing the error inherent in N when fitting in Artemis. Since the paper cited by Koningsberger (X-ray-absorption fine-structure standards: A comparison of experiment and theory, G. G. Li, F. Bridges, and C. H. Booth, Physical Review B, 1995) utilized Feff6 for their theoretical standards and so does Artemis, is the error in N still the same? I was wondering if there is some literature that I have missed, or if the developers of the Demeter package can shed some light on this issue. Thank You, Carolyn Carr

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Path Missing Using Artemis
by lijuncha＠msu.edu 08 Mar '16

08 Mar '16

Hi all, During my use of Artemis, I found out that the FEEF paths finder had some problem with my atom, which is Cu12Sb4S13 in the attachment. I firstly ran atom on Cu12e, then ran the FEFF calculation. Then I found that the S24g.1 path was missing. Since S24g is near the core atom Cu12e and the path should exist, I was confused to send the message and hopefully get your response. Thanks, Junchao

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Any XAFS schools in North America this year?
by Robert Gordon 07 Mar '16

07 Mar '16

Hi All, I have a couple of students who are novices. I was hoping that one could go to a school to learn and perhaps get some hands-on experience before they get into the meat of their thesis work. I haven't seen any notices yet about schools taking place in the late spring or summer and was wondering if there are any plans to hold such. I am aware of the 1/2-day workshop planned for the DXC. Are there other options? Thanks, Robert

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Re: [Ifeffit] Ifeffit Digest, Vol 157, Issue 1
by Matteo Busi 07 Mar '16

07 Mar '16

> Hi Mateo, > I'm not quite clear on what you are asking for. Do you want an ascii > output file that has a column containing chi(E) using the energy grid of > the original data? > If so, would it suffice to add a column to the mu(E) ascii output file? > That seems to me like a natural solution. >Cheers, >B Hi Bruce I would like to have an output file containing chi(E) and mu(E) using the same energy (E) grid. If I export them separately ( the only available thing right now) they have different energy grid. Thanks and Regards 2016-03-04 15:18 GMT+01:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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. Exporting Athena projects data (Matteo Busi) > 2. Collected k-space and fitting range (Taehoon Kim) > 3. Re: Collected k-space and fitting range (Scott Calvin) > 4. Re: Exporting Athena projects data (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 Mar 2016 23:53:54 +0100 > From: Matteo Busi <basebush(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Exporting Athena projects data > Message-ID: > <CAOyEiGi7jNury5oTAostBixxinOF+Vxcg2= > 8Sf8VeM9rywEmrg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Bruce, hi mailing list readers. > With the project I'm working with, it came out that would be really useful > for me to export groups in both .xmu and .chi . > More in details I have to deal with a function that depends on both the chi > and xmu data. I tried to look at all the chances and through the guide but > I didn't find any function to do that. I was thinking of exporting > separately the .chi and .xmu data, but they have different point of the > Energy(eV) and that makes hard the programming of my evaluating scripts. > Should I use the spline function to estimate the .xmu data and use it > combined to the .chi data? > > Hope it's all clear. Thanks > Best Regards, > Matteo, UiS >

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Collected k-space and fitting range
by Taehoon Kim 04 Mar '16

04 Mar '16

Hello, I am a bit confused about the range of k-space, which may affect the quality of EXAFS fitting. I would like to understand whether there is a difference between the fitting using an identical fitting range of k-space obtained from different range of k-space collected. For example, is there a notable difference between a fitting of k = 2.3-11 which was deduced from a spectra data collected up to k=12 and a spectra data collected up to k=13 ? Kind regardsTerry

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Exporting Athena projects data
by Matteo Busi 04 Mar '16

04 Mar '16

Hi Bruce, hi mailing list readers. With the project I'm working with, it came out that would be really useful for me to export groups in both .xmu and .chi . More in details I have to deal with a function that depends on both the chi and xmu data. I tried to look at all the chances and through the guide but I didn't find any function to do that. I was thinking of exporting separately the .chi and .xmu data, but they have different point of the Energy(eV) and that makes hard the programming of my evaluating scripts. Should I use the spline function to estimate the .xmu data and use it combined to the .chi data? Hope it's all clear. Thanks Best Regards, Matteo, UiS

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Re: [Ifeffit] fluo_corr() script
by Matt Newville 26 Feb '16

26 Feb '16

Hi Gerome, (I'm CCing this to the Ifeffit mailing list) On Thu, Feb 25, 2016 at 9:30 PM, Gerome Melaet <gmelaet(a)lbl.gov> wrote: > Dear Dr. Newville, > I have tried to use the flu_corr() function to correct some of my recent > x-ray data on the cobalt K-edge. > Unfortunately, after multiple tryout I am unable to get it to work > properly. > I have received this error message a couple of time. > > > *File > "/Volumes/Python/anaconda/lib/python2.7/site-packages/larch/__init__.py", > line 37, in wrapper* > * return fcn(*args, **keywords)* > * File "/Volumes/Python/anaconda/share/larch/plugins/xafs/fluo.py", line > 57, in fluo_corr* > * muvals = material_mu(formula, energies, density=1, _larch=_larch)* > * File > "/Volumes/Python/anaconda/lib/python2.7/site-packages/larch/__init__.py", > line 37, in wrapper* > * return fcn(*args, **keywords)* > * File "/Volumes/Python/anaconda/share/larch/plugins/xray/materials.py", > line 68, in material_mu* > * mater = _materials.get(name.lower(), None)file <stdin>, line 0* > *AttributeError: ‘int' object has no attribute 'lower'* > > I have a .dat file two column with energy and normalized mu (I have done > most of the energy corrections during my shift at the synchrotron). > I am able to load both energy and mu, yet I am not sure I handle the > different args correctly in the fluo_corr() function. > > Here is how I tried: > > fluo_corr(dat.energy, dat.mu, formula=None, elem=‘Co’, edge=‘K’) > > Thanks in advance for your help, > > Best, > Gerome > Yes, you need to pass a valid (even if approximate) formula for the chemical composition of the material. See http://xraypy.github.io/xraylarch/xray/index.html#x-ray-properties-of-mater… for some further details. You might want to do something like fluo_corr(dat.energy, dat.mu, formula='Co0.5Fe0.5S04', elem=‘Co’, edge=‘K’) Perhaps obviously, getting the composition of light elements perfect is not critical. It's often noticed that one has to lower the concentration of the absorbing element some (perhaps even by half) to avoid over-correcting. As with many things, it's always good to practice on a system where you're pretty confident what the right answer should be. --Matt

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