Question about Io during data collection
All: Recently our group was at the APS collecting Pb L(III) spectra on an ID line using quick XAFS. Data was collected from -200 to +800 eV for Pb L(III) at 0.2 eV steps with a count rate of 0.025 seconds. Each scan took about 2.5 minutes to complete. During our measurements we began noting issues with the linearity of scans collected in the extended region of the same sample. After poking around in the data we noticed that Io was not linear throughout the measurement for a portion of the scans. This was not always the true (see Athena project attached to the email, and images attache to the email). I was always under the impression that Io should ideally remain linear throughout the energy region scanned, or at least remain unchanged between replicate scans. We worked with the beamline scientists to try alleviate/fix the issue, but it kept persisting. I realize this is not an IFEFFIT issue, but I was hoping someone might be able to help me understand what was going on and why this was happening? If I have not included enough information for the question please let me know. [cid:image001.jpg@01D18B37.F66BD820] [cid:image002.jpg@01D18B37.F66BD820] All the Best, todd All the Best, Todd Luxton, Ph.D. Office of Research and Development National Risk Management Research Laboratory Land Remediation and Pollution Control Division Waste Management Branch Mailing Address: 5995 Center Hill Ave Cincinnati, OH 45243 Phone: Office: (513) 569-7210 Cell: (513) 319-5104 Fax: (513) 569-7879 Email: Luxton.todd@epa.govmailto:Luxton.todd@epa.gov "A nation that destroys its soils destroys itself" Franklin D. Rosevelt
Hi Todd, I have some familiarity with the beamline where these data were collected so I will take a stab at what might have gone wrong and what you may be able to do to salvage some of the data. Ideally, you want an Io(E) that is as flat as possible over the scan range, or at least over the region where the amplitude of your EXAFS signal starts rapidly declining, say above 8 A-1. We typically try to get a 10-20% smooth variation in Io intensity over the scan range in our measurements, which works for the setup and the systems we are interested in. The reason for this "requirement" is that while normalization of If or It to Io should take care of all variations in your incident photon intensity, your detectors respond differently to large changes in intensity (even if your detectors were exact replicates, which they are not, they are still using different gases in Io, It, and If). This non-linearity in the detector responses will result in any noise and EXAFS-like variations present in Io to also show up in your normalized If/Io or log(Io/It) spectrum and to interfere with the EXAFS signal you are trying to analyze. The problem will be exacerbated for elements like Pb at the L3 edge, where the EXAFS signal is of smaller amplitude to begin with so the noise and features resulting from non-linearity will be a bigger proportion of your measured signal. What seems to have happened in your measurement is that vibrations or temperature drifts or other mechanical instability caused the second monochromator crystal to move away from the Bragg condition, so your Io was likely travelling randomly along the rocking curve, causing large changes in measured Io intensity and changes in Io(E) structure from scan to scan. This beamline has a feedback loop that attempts to keep the incident intensity at the top of the rocking curve, but it may not have been doing its job at the time of your measurement or it may have been turned off to reduce the noise in Io resulting from the induced oscillation in the second crystal that creates the difference signal used in the feedback loop. These problems in Io could then be transferred in your data due to non-linearities in your detectors' response. It is also possible that the harmonic rejection mirror was not set up ideally and allowed harmonics in the incident beam, which would also result in non-linear response and spectral artifacts, particularly when your beam travels up and down the rocking curve. I guess the bottom line is that you now have a data set with individual scans that appear different from each other. I took a look at the project file you sent and it seems that the data are relatively repeatable scan to scan when you normalize and extract the EXAFS, despite what you show as large variation in Io and in the un-normalized data in your email. For datasets like that, I would not use the scans that differ significantly from the others and the scans that show large noise at high k (e.g. 006, 008, 010). When you average the relatively repeatable remaining scans you should be able to get workable data up to 9-10 A-1 or so. Whether you can tackle the research question you set out to answer with data like those depends, of course, on the system and the question. Hope that helps, Max. From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Luxton, Todd Sent: Thursday, March 31, 2016 9:28 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Question about Io during data collection All: Recently our group was at the APS collecting Pb L(III) spectra on an ID line using quick XAFS. Data was collected from -200 to +800 eV for Pb L(III) at 0.2 eV steps with a count rate of 0.025 seconds. Each scan took about 2.5 minutes to complete. During our measurements we began noting issues with the linearity of scans collected in the extended region of the same sample. After poking around in the data we noticed that Io was not linear throughout the measurement for a portion of the scans. This was not always the true (see Athena project attached to the email, and images attache to the email). I was always under the impression that Io should ideally remain linear throughout the energy region scanned, or at least remain unchanged between replicate scans. We worked with the beamline scientists to try alleviate/fix the issue, but it kept persisting. I realize this is not an IFEFFIT issue, but I was hoping someone might be able to help me understand what was going on and why this was happening? If I have not included enough information for the question please let me know. All the Best, todd All the Best, Todd Luxton, Ph.D. Office of Research and Development National Risk Management Research Laboratory Land Remediation and Pollution Control Division Waste Management Branch Mailing Address: 5995 Center Hill Ave Cincinnati, OH 45243 Phone: Office: (513) 569-7210 Cell: (513) 319-5104 Fax: (513) 569-7879 Email: Luxton.todd@epa.gov mailto:Luxton.todd@epa.gov "A nation that destroys its soils destroys itself" Franklin D. Rosevelt
Hi Todd,
On Thu, Mar 31, 2016 at 9:27 AM, Luxton, Todd
All:
Recently our group was at the APS collecting Pb L(III) spectra on an ID line using quick XAFS. Data was collected from -200 to +800 eV for Pb L(III) at 0.2 eV steps with a count rate of 0.025 seconds. Each scan took about 2.5 minutes to complete. During our measurements we began noting issues with the linearity of scans collected in the extended region of the same sample. After poking around in the data we noticed that Io was not linear throughout the measurement for a portion of the scans. This was not always the true (see Athena project attached to the email, and images attache to the email). I was always under the impression that Io should ideally remain linear throughout the energy region scanned, or at least remain unchanged between replicate scans. We worked with the beamline scientists to try alleviate/fix the issue, but it kept persisting. I realize this is not an IFEFFIT issue, but I was hoping someone might be able to help me understand what was going on and why this was happening? If I have not included enough information for the question please let me know.
It's a little hard to see much detail from the blurry images, but I0 is definitely falling in dramatically different ways for the different scans. My guess (from similar experience trying to do continuous XAFS scans at another APS ID line) is that the undulator is not tracking with the monochromator correctly in some of the scans. This tracking is definitely challenging for us. I suspect MR-CAT does small, constant energy steps per time point, but I'm not sure of this. There is no way I can scan my undulator at 25 ms per energy point. What I see (and from talking to the undulator control folks at the APS), there is about a 0.5 second "settling time" for the devices during which time is pointless to ask for another move. So, when I do QXAFS at 13-ID-E, I set up "a normal XAFS scan", with 0.05 Ang^-1 steps and move the mono energy between these points in a fixed time -- so doing a ~4 eV move per time point at 10 Ang^-1. But I find that if I try to go faster than about 100 ms per point, I see oscillations in I0, as the undulator lags behind and then tries to catch up. That can put oscillations in I0, but what you're seeing is it just falling off, like the tracking just isn't working. For those not at the APS, the undulators cannot be hardware-synchronized (perhaps that is "yet", but we've been waiting a long time). One can move the undulator at a constant rate in gap (mm) velocity, and then try to synchronize the mono energy to that... I don't do that and I'm pretty sure that MR-CAT does not either. Anyway, I would suspect the tracking of the undulator. Hope that helps, --Matt
Matt and Max,
Thank you for your responses, the information was really helpful in trying to understand what would lead to the changes in Io between scans. My knowledge of the infrastructure and mechanics of the beamline in front of Io is limited, and this short discussion has been very insightful. I wanted to make clear I was not trying to call out a specific issue with a beamline, but rather better inform myself about the how beamlines in general are setup and the mechanics behind it.
It is hard to find a specific text or manuscript that covers topics along this line. Not just with XAFS, the same could be said about a number of other spectroscopy/analytical techniques. Being able to pose questions of this nature to the list is really helpful and provides an insight and source of information that is not readily available.
All the Best,
Todd Luxton, Ph.D.
Office of Research and Development
National Risk Management Research Laboratory
Land Remediation and Pollution Control Division
Waste Management Branch
Mailing Address:
5995 Center Hill Ave
Cincinnati, OH 45243
Phone:
Office: (513) 569-7210
Cell: (513) 319-5104
Fax: (513) 569-7879
Email: Luxton.todd@epa.govmailto:Luxton.todd@epa.gov
“A nation that destroys its soils destroys itself”
Franklin D. Rosevelt
From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Matt Newville
Sent: Thursday, March 31, 2016 6:41 PM
To: XAFS Analysis using Ifeffit
participants (3)
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Luxton, Todd
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Matt Newville
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Maxim Boyanov