[Ifeffit] Post-doc position at SSRL

[Ritimukta Sarangi]

Hello Folks,
We have an open post-doc position in XAS/EXAFS/advanced spectroscopy at SSRL. 
We are looking for someone with expertise in or  interest in 
biological/molecular applications of XAS.
Please see the job listing here:
https://careers.slac.stanford.edu/sites/default/files/SSRL_X-ray_Spectroscopy_Post_Doc_Announcement_0.pdf

If you have any questions, please do not hesitate to reach out. We are hoping 
to fill this position asap but can wait for for a few months for the right 
candidate!
Kind regards,
Riti Sarangi
SSRL



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[Ifeffit] Virtual SSRL Summer School on Synchrotron X-Ray Absorption Spectroscopy and Imaging Oct 25-28, 2022

[Ritimukta Sarangi]

Hello EXAFS enthusiasts,
We are hosting the SSRL "not quite summer" summer school at the end of
October this year (Oct 25-28). We wanted to include real experiments and
deferred the school to the start of operations at SSRL. The event is
virtual and all information (including registration details) can be found
at: https://conf.slac.stanford.edu/exafs-2022/
We recognize that there are several really good online resources for
learning about EXAFS and it has proved to be quite beneficial to the new
and experienced learners alike. We have changed our summer school format to
include additional teaching modules that can help participants learn
aspects of EXAFS data analysis that are beyond what we have typically
taught in the past. These new modules are especially helpful to the novice
user and include:
1) Opportunity to write a 1 to 1.5 page proposal to compete for
experimental time during the school.
2) A complete 1-day remote data measurement and hands-on demonstration of
beamline optimization and experiment setup during the live session.
3) Insights into becoming a user at SSRL, proposal writing and its review
process with examples of past successful proposals.

Looking forward to seeing some of you at the school.
Best Regards,
Riti Sarangi
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[Ifeffit] Postdoc announcement

[Ritimukta Sarangi]

Hello,
I apologize in advance for spamming everyone on the IFEFFIT site  with this
posting.

SSRL is currently looking to hire a two year post-doctoral fellow. The
successful candidate will utilize x-ray spectroscopic techniques (XAS and
EXAFS) to study the electronic and geometric structure of homogeneous
catalysis systems, including metalloprotein active sites and combine the
spectroscopic results with theoretical tools to gain insights into active
site structure and metalloprotein function correlations.

If you are interested or know of a candidate who will be interested, please
reach out to me and I can provide more information.

Best regards,
Riti Sarangi
Senior Scientist,
SSRL, SLAC
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[Ifeffit] Workshop Opportunity for XAS users in the field of Biogeochemistry.

[Ritimukta Sarangi]

Hello,
Apologies for the mass email.

SSRL, in conjunction with EMSL is organizing a Workshop titled
"Spectroscopy and Modeling for Molecular Insights into Environmental
Processes" on 26, Jan 2021. The main focus is to encourage and provide help
in getting started with the use of theory and modeling  (such as DFT and
MD) in the interpretation of EXAFS/XAS data.

Please find more information in the event flyer below:
https://www.dropbox.com/s/vvshxqpji4yok2s/SSRL_EMSL_Workshop_Flyer.pdf?dl=0

We encourage interested users and research groups to register and attend
the workshop. Looking forward to your participation.

Best regards,
Riti Sarangi
SSRL
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[Ifeffit] EXAFS, Spectroscopy and Imaging Summer School Youtube Page

[Ritimukta Sarangi]

Hello EXAFS enthusiasts,
We have uploaded our 2020 summer school material on the Youtube Channel :
https://www.youtube.com/channel/UC3sd8ZqQkNfDK11jM8cOWzw/videos
You may find useful material for your synchrotron XANES/EXAFS/Imaging
research. You can subscribe and share the page with colleagues as an
educational resource.
In the future (TBD), we plan to include recorded videos on advanced
spectroscopy techniques including soft and hard X-ray RIXS and XES methods.
If there are SSRL related material that you would like us to prepare,
please let us know and we can put it on the list.
Thank you for your time.
Best regards,
Riti Sarangi
SSRL.
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[Ifeffit] RE-REGISTRATION Request for SSRL Summer School

[Ritimukta Sarangi]

Hello everyone,
This message is going out at *11:23 AM PST on Aug 5, 2020*. Our
registration website for the summer school has been overwhelmed by requests
and we had to stop registration and fix some of the errors. I request that *if
you registered before that time, please go ahead and re-register* for the
summer school program. I apologize for the issues and request your
continued patience with us in determining the best way to support
smooth operations for this unprecedented amount of interest in the school.
Thank you,
Riti Sarangi
p.s -please email me at ri...@slac.stanford.edu, if you have any questions.
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Re: [Ifeffit] Wrong dates for the school in the Subject line of previous email! Correct dates: Sep 8-10, 2020

[Ritimukta Sarangi]

Hello folks,
If you have a question about the SSRL EXAFS summer school please email me
directly at ri...@slac.stanford.edu instead of emailing the feffit mailing
list.
Best.
-Riti


On Wed, Aug 5, 2020 at 7:54 AM Nirmalendu Patra 
wrote:

> Dear Riti,
>
> Thank you for the update. By the way I am unable to do the registration in
> the link that you shared.  It shows a message that " you may not submit
> another entry at this time". What does this mean? Kindly clarify this.
>
> Thank you
>
> Regards,
> *Nirmalendu Patra*
>
>
>
> On Wed, 5 Aug 2020 at 05:47, Ritimukta Sarangi 
> wrote:
>
>> Hello folks,
>> Please be advised that the dates in the subject line for the SSRL summer
>> school were incorrect. The school will be held from Sep 8-10, 2020.
>> Thank you,
>> Riti
>>
>> On Tue, Aug 4, 2020 at 5:05 PM Ritimukta Sarangi 
>> wrote:
>>
>>> Hello Folks,
>>> The registration page for the EXAFS Summer School at SSRL is now open.
>>> You can get more information at
>>> https://conf.slac.stanford.edu/exafs-2020/. The deadline to register is 
>>> *August
>>> 20, 2020. (*https://conf.slac.stanford.edu/exafs-2020/registration)
>>> Please note that the school is completely remote this year and will be
>>> conducted via zoom. Therefore, unlike previous years, we will not have a
>>> two step process (application/registration). Participants are only
>>> required to register. Once the information is confirmed, the participants
>>> will receive links to the zoom sessions.
>>> Please let me know if you have any questions or concerns. Looking
>>> forward to "seeing" you at the school!
>>> Best Wishes,
>>> Riti Sarangi
>>>
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[Ifeffit] Wrong dates for the school in the Subject line of previous email! Correct dates: Sep 8-10, 2020

[Ritimukta Sarangi]

Hello folks,
Please be advised that the dates in the subject line for the SSRL summer
school were incorrect. The school will be held from Sep 8-10, 2020.
Thank you,
Riti

On Tue, Aug 4, 2020 at 5:05 PM Ritimukta Sarangi 
wrote:

> Hello Folks,
> The registration page for the EXAFS Summer School at SSRL is now open. You
> can get more information at https://conf.slac.stanford.edu/exafs-2020/.
> The deadline to register is *August 20, 2020. (*
> https://conf.slac.stanford.edu/exafs-2020/registration) Please note that
> the school is completely remote this year and will be conducted via zoom.
> Therefore, unlike previous years, we will not have a two step process
> (application/registration). Participants are only required to register.
> Once the information is confirmed, the participants will receive links to
> the zoom sessions.
> Please let me know if you have any questions or concerns. Looking forward
> to "seeing" you at the school!
> Best Wishes,
> Riti Sarangi
>
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Re: [Ifeffit] Apply for SSRL EXAFS Summer School June 19-23

[Ritimukta Sarangi]

Hello Folks,
The registration page for the EXAFS Summer School at SSRL is now open. You
can get more information at https://conf.slac.stanford.edu/exafs-2020/. The
deadline to register is *August 20, 2020. (*
https://conf.slac.stanford.edu/exafs-2020/registration) Please note that
the school is completely remote this year and will be conducted via zoom.
Therefore, unlike previous years, we will not have a two step process
(application/registration). Participants are only required to register.
Once the information is confirmed, the participants will receive links to
the zoom sessions.
Please let me know if you have any questions or concerns. Looking forward
to "seeing" you at the school!
Best Wishes,
Riti Sarangi
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Re: [Ifeffit] Reported W L3-edge and L2-edge energy

[Ritimukta Sarangi]

Hello everyone,
In my experience, it is best to stay away from sulfate which has a hugely
intense peak subject to self absorption. At SSRL, we advice users to choose
Sodium Thiosulfate with the low lying and sharp S-S sigma star peak at
2472.02 eV and Tetraphenyl phosphonium bromide at 2146.96 eV for Phosphorus
(see Scott's paper at: J. Synchrotron Rad. 
 (2018). *25* ,
529-536)
Thanks,
Riti

On Thu, May 7, 2020 at 3:19 PM Matthew Marcus  wrote:

> For elements like P and S, people often use the energies of peaks.
> These are more immune to noise, energy-resolution effects and
> overabsorption than inflection points are.  For instance, on ALS 10.3.2,
> I used the sulfate peak of gypsum set at 2482.74eV.  I forget where I
> got that number.  Going down to soft X-rays, a common convention for the
> carbon edge is to use a pair of sharp peaks in CO2 gas at 292.74 and
> 294.96eV.
> mam
>
> On 5/7/2020 3:09 PM, Mike Massey wrote:
> > Hi Matt,
> >
> >
> > Indeed, in my experience (which is limited to one beamline at one
> > synchrotron facility for P XAS), once it is calibrated, the energy
> > selection tends to be quite stable, so I think you're on-target there.
> >
> > The trouble I still run into, though, is comparability of data between
> > studies. The difficulty is magnified by the fact that people tend to
> > identify certain near-edge features by the energy range at which they
> > occur. I do the same, of course, but I also try to carefully document
> > the material and energy I used to calibrate the monochromator.
> >
> > For the P K-edge, it doesn't really seem like people have settled on a
> > convention for calibrating the monochromator, unlike in the case of
> > iron, for example (where one just uses a foil and sets some feature of
> > that spectrum to their preferred value). If everyone was using the same
> > thing all would be happy, but most people use different materials and
> > different values. So datasets for P at the K-edge really aren't too
> > comparable just yet.
> >
> > Sorry to hijack the conversation, it's just an issue I've been mulling
> > over for a few years. The discussion of energy calibration values made
> > me think of it again.
> >
> >
> > Best,
> >
> >
> >
> > Mike
> >
> >
> >
> >
> >> On May 8, 2020, at 8:51 AM, Matt Newville 
> >> wrote:
> >>
> >> 
> >> Hi Mike,
> >>
> >>
> >> On Tue, May 5, 2020 at 10:56 PM Mike Massey  >> > wrote:
> >>
> >> On a tangentially related topic, I find that phosphorus K-edge XAS
> >> energy calibration conventions are still in a bit of a "Wild West"
> >> state, with a wide variety of materials and values in use for
> >> energy calibration. As an extreme example, one or two frequently
> >> cited papers in my field from the 2000s don't even report the
> >> material or value used for energy calibration, and only show
> >> portions of the spectra on an energy axis with values relative to
> >> an unknown E0.
> >>
> >>
> >> I have never measured a P K edge, or indeed any edge lower in energy
> >> than the S K edge (ignoring some X-ray raman work).  But if one is
> >> using a Si(111) double-crystal monochromator where P or S is
> >> approximately the low-energy (high-angle) limit, then it really should
> >> be that the calibration does not drift much and cannot be too wrong at
> >> low energies.
> >>
> >> That is, a mono calibration is controlled by a d-spacing and angular
> >> offset. Normally (or perhaps, in my experience), "re-calibrating" is
> >> done by changing the angular offset, leaving the d-spacing alone.
> >> That is, the d-spacing is presumably known, at least to within some
> >> thermal drift.
> >> If that is the case that the d-spacing really is not changing and what
> >> needs to be refined is the angular offset, then setting the offset at
> >> relatively high energy edges will be much more sensitive, and changing
> >> the angular offset to that a high-energy edge is correct should move
> >> lower energy edges by a smaller amount.   The corollary is that you
> >> have to move the offset a lot to move the P  K edge around, and that
> >> would have a larger (and ever-increasing) impact on higher energy
> >> edges such as Ca, Fe, Cu or Mo.
> >>
> >> The counter-argument is also true:  d-spacing has a bigger effect on
> >> the high-angle / low-energy edges.
> >>
> >> So, if you believe the mono d-spacing (or you believe the beamline
> >> scientist who believes it ;)) then calibrate at the highest energy you
> >> can.   The Kraft values don't go very low in energy.
> >>
> >> All that said, if using a different mono crystal such as InSb or more
> >> exotic crystals, I have no idea how stable those are.
> >>
> >>
> >> I too have picked my own material and value, and will be the first
> >> to acknowledge that I did so out of necessity and ease of
> >> comparison to other available data, 

Re: [Ifeffit] about the k-range choice

[Ritimukta Sarangi]

Hi Shaofeng,
Is there a reason not to use the highest k data? (You have really good data 
past k=14?). In general you should use as high of a k range as available unless 
the data are bad, compromised at high k and/or you want to compare to data of a 
certain k range. As you know, the shape of FT will look different as you 
increase k range for the transform. I suspect though that you would arrive at 
the same fit ( in this case) if you choose 12.4 or 13.4 data. 
Best Wishes,
Riti

Sent from my iPhone

> On Apr 28, 2020, at 7:56 AM, Shaofeng Wang  wrote:
> 
> 
> Dear all,
> I have a question about the k-range choice. I have a set of As K-edge XAS 
> spectrum and the k space is shown in following figure
> .
> <62CD6A1C65DE4791A677B8B96C5B567D.png>
> When I choose k-range=4-12.4 A-1, the shape of R space is like
> <284C723090C7429A9A9240868B20C63C.png>
> When I chose k-range=4-13.4 A-1, the R-space is like
> <2530E8F00B5E4A169C79D3230E58A885.png>
> The shape of second shell at approximately 2.8 A is obviously different. So, 
> my question is how to correctly choose k range?
>  
> 
> 祝
> 好运！
> Best regards,
> 
> 王少锋，Shaofeng Wang, Ph.D
> 中国科学院沈阳应用生态研究所，Institute of Applied Ecology, CAS
> Email: wangshaof...@iae.ac.cn; sf.w...@hotmail.com
> Address: Wenhua Road 72, Shenyang
> 
>  
> 发件人: George Sterbinsky
> 发送时间: 2020年4月14日 0:05
> 收件人: XAFS Analysis using Ifeffit
> 主题: [Ifeffit] Artemis crash upon empirical standard import.
>  
> Hello,
>  
> I am trying to import an empirical standard (.es file created in Athena) into 
> Artemis. Upon import, Artemis crashes. This occurs with both the latest mac 
> and windows releases (0.9.25 on mac and 0.9.26 on windows). I have attached 
> an Athena project file containing the data used to generate the .es file 
> (Co1-13C-std) and the data to be fit (Co1-57C-toFit). I have also attached 
> the .es file. Following the instructions at 
> https://bruceravel.github.io/demeter/documents/Artemis/extended/empirical.html,
>  I import Co1-57C-toFit into Artemis and the choose "import an empirical 
> standard" in the data window. When I choose the .es file from the file 
> selection dialog, Artemis crashes.
>  
> Thank you,
> George
>  
> <62CD6A1C65DE4791A677B8B96C5B567D.png>
> <284C723090C7429A9A9240868B20C63C.png>
> <2530E8F00B5E4A169C79D3230E58A885.png>
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Re: [Ifeffit] EXAFS of wine

[Ritimukta Sarangi]

Anatoly, 
If we digitize the picture and solve the structure, is the prize the bottle 
itself :-)
Best regards,
Riti

Sent from my iPhone

> On Nov 1, 2018, at 3:27 PM, Anatoly Frenkel  
> wrote:
> 
> I thought this mailing list is an appropriate venue to post a picture of the 
> bottle of wine I bought yesterday in a store on Long Island. 
> 
> 
> 
> 
> Anatoly
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[Ifeffit] micro-XAS Imaging Post-Doc Position

[Ritimukta Sarangi]

Hello,
Apologies for the spam email. We have a 3-year position available for
micro-XAS imaging for biological applications at SSRL, SLAC, Menlo Park, CA.
The details of the position are attached. Please contact me directly if you
or anyone you know might be interested.
Best Wishes,
Riti Sarangi
SSRL, SLAC


Post_doc position announcement.pdf
Description: Adobe PDF document
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Re: [Ifeffit] Interpreting old XANES data with missing standards

[Ritimukta Sarangi]

Hi  Don,
I am sure you are aware but I would like to remind you that the sulfides that 
you are working with have serious potential for self absorption. Most spectra 
out there have different degrees of self absorption which can really mess up 
LCA type analysis. This is not a quick solution, but you might consider 
remeasuring the standards following  a strict protocol of sample dilution, 
grinding and deposition on substrate to minimize any such artifacts.
Best,
Riti Sarangi


Sent from my iPhone

> On Jun 8, 2018, at 7:45 AM, Carlo Segre  wrote:
> 
> 
> You might also ask the beamline scientist at APS Sector 9, Tianpin Wu 
> 
> 
> carlo
> 
>> On Fri, 8 Jun 2018, Anatoly Frenkel wrote:
>> 
>> Don,
>> 
>> I am sure that Paul Northrup (north...@bnl.gov) will help - he was the
>> beamline scientist at X15B and is likely to have the standards you need.
>> 
>> Anatoly
>> 
>> 
>> ---
>> 
>>> On Fri, Jun 8, 2018 at 9:54 AM, Don Baker  wrote:
>>> 
>>> Hello All,
>>> 
>>> First let me apologize if the question below is inappropriate for this
>>> group, but I don't know of a better set of experts that I can ask.
>>> 
>>> So, here is some background:
>>> 
>>> I have some old S K-edge XANES data from NSLS X15B for S-bearing
>>> silicate glasses that was collected by a Ph.D. student who decided to
>>> leave for a good job rather than finishing their degree.  During my
>>> current sabbatical year I have been looking at the data and reading
>>> papers on the topic.  I think that I now understand, at least
>>> qualitatively, the changes in the spectra as a function of iron
>>> concentration in the glasses, but to perform quantitative modelling I
>>> need XANES spectra of MgS and CaS, which we did not think to collect all
>>> those years ago.  I have searched for XANES spectra of MgS and CaS on
>>> the CARS XAFS Data Library and on the XAFS Database at IIT without
>>> success.  I am unaware of other databases available.
>>> 
>>> Now for for my questions:
>>> 
>>> 1.  Does anyone know of a XANES database that contains MgS and CaS
>>> spectra?  (Or did I miss it in the databases I searched?)
>>> 
>>> 2.  If I cannot find measured MgS and CaS spectra, what do you think
>>> about using calculated spectra (e.g., Zheng et al.,2012, NPJ
>>> Computational Materials, 12 -- which uses FEFF) for quantitative
>>> modelling?
>>> 
>>> 
>>> And information, ideas, and suggestions that you may have will be
>>> appreciated.
>>> 
>>> 
>>> Wishing you all the best from a spring morning in Montreal,
>>> 
>>> Don
>>> 
>>> 
>>> 
>>> 
>>> --
>>> Melting rocks today for a better tomorrow . . .
>>> Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences,
>>> McGill University
>>> 
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>>> 
>> 
> 
> -- 
> Carlo U. Segre -- Duchossois Leadership Professor of Physics
> Interim Chair, Department of Chemistry
> Director, Center for Synchrotron Radiation Research and Instrumentation
> Illinois Institute of Technology
> Voice: 312.567.3498Fax: 312.567.3494
> se...@iit.edu   http://phys.iit.edu/~segre   se...@debian.org
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[Ifeffit] SSRL EXAFS School- Application Closing Soon!

[Ritimukta Sarangi]

Hello Friends,
This is a friendly reminder that applications will close on the 20th
(Sunday). Since we already have close to 150 applications(!!), we will not
be able to entertain late submissions. We will try to include as many
participants and we hope this will be a successful school.
Best Wishes and have nice weekend!
Riti Sarangi


On Mon, Apr 30, 2018 at 10:06 AM Ritimukta Sarangi 
wrote:

> Hello Friends,
> SSRL will host its annual summer school this year during the third week
> of August (13th-16th). The application page is now open. Please hit the
> "apply" button on:
>
> http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2018/index.html
>
> Note that seats are limited and we will have to choose from the
> application pool. Please apply soon to help us with the process. If
> selected, you will receive an email to register for the school. This year,
> we will drill down into Artemis based EXAFS analysis.
>
> Hope to see many of you here!
>
> Best Wishes,
> -Riti Sarangi
>
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[Ifeffit] SSRL EXAFS School- Application Open!

[Ritimukta Sarangi]

Hello Friends,
SSRL will host its annual summer school this year during the third week of
August (13th-16th). The application page is now open. Please hit the
"apply" button on:
http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2018/index.html

Note that seats are limited and we will have to choose from the application
pool. Please apply soon to help us with the process. If selected, you will
receive an email to register for the school. This year, we will drill down
into Artemis based EXAFS analysis.

Hope to see many of you here!

Best Wishes,
-Riti Sarangi
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[Ifeffit] SSRL XAFS Summer School

[Ritimukta Sarangi]

Hello,
SSRL will host its annual summer school this year during the third week of
August (13th-17th). The focus of the school will on EXAFS hands on data
analysis. In addition, electronic structure determination from the XAS
pre-edge analysis and advanced spectroscopies will be covered. Examples
from a wide range of scientific applications will be covered, including
metals in biology, chemical catalysis, heterogenous catalysis and materials.
I will post more information here, as and when it becomes available
(hopefully soon) and we hope that many of you can attend.
Best Wishes,
-Riti Sarangi
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[Ifeffit] SSRL EXAFS Summer School

[Ritimukta Sarangi]

Hello folks,
This is a reminder that today is the last day to apply for the summer school in 
April. I encourage you to visit the site at: 
http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2017/index.html 
.
Best Wishes,
-Riti Sarangi___
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[Ifeffit] Apply for SSRL EXAFS Summer School June 19-23

[Ritimukta Sarangi]

Hello Everyone,

The application page for the Summer School at SSRL  is up!
http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2017/index.html 


Please read through the text to understand the two-step process for coming to 
the school (application, followed by invitation to register). Although, we 
would love to accommodate everyone, we have personnel and beamline constraints 
that limit how many participants we can host. Please register by 10th April.

Thank you for your patience and all the emails (I might not have replied to 
everyone) about the school. I hope to see you at SSRL :-)

Best Wishes,
Riti Sarangi


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[Ifeffit] SSRL EXAFS Summer School 2017

[Ritimukta Sarangi]

Hello everyone,
Responding to popular demand, the SSRL summer school will be held during
the last week of June in 2017. More information will be available on the
SSRL website soon and I will send a link to the school webpage to this list
(when its available). Stay tuned!
Best,
-Riti Sarangi
SSRL
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[Ifeffit] EXAFS and XANES Summer School at SSRL

[Ritimukta Sarangi]

Hello folks,

I have received several queries over the last 6 months about hosting an
EXAFS Summer School in 2017 at SSRL. Typically we host it every other year,
so we would have offered the School in 2018. However, if there is very high
interest, we would certainly consider hosting a school in 2017. Please
reply to me directly at ri...@slac.stanford.edu if you or your group will
benefit from a school in 2017. Please note that we if go ahead with it, the
school will be in the June-July 2017 timeframe.

Best wishes,
-Riti Sarangi
SSRL
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Re: [Ifeffit] demeter installation in OSX El Capitan

[Ritimukta Sarangi]

I don't think it works on el capitan

Sent from my iPhone

> On Jul 20, 2016, at 22:37, Ping, Yuan  wrote:
> 
> Dear all,
> 
> I recently upgraded my mac to OSX El Capitan, and tried to install demeter 
> following the steps at http://bruceravel.github.io/demeter/
> 
> XQuartz 2.7.9 (xorg-server 1.17.4), Xcode 7.3.1, command line tools, “sudo 
> port -v self update”, “port upgrade outdated” were all OK. When I tried “sudo 
> port install xorg-server demeter”, it showed:
> 
> --->  Computing dependencies for xorg-server
> --->  Cleaning xorg-server
> --->  Computing dependencies for demeter
> --->  Dependencies to be installed: ifeffit libgcc cctools llvm-3.8 libcxx 
> libffi llvm_select gmp isl ld64 ld64-latest libmpc mpfr pgplot gcc5 ... (a 
> long list)
> 
> Then after many attempts to fetch libcxx-3.7.1_0.darwin_15.x86_64.tbz2 from 
> various websites, it showed:
> 
> Error: org.macports.archivefetch for port libcxx returned: archivefetch 
> failed for libcxx @3.7.1_0
> Error: Failed to install libcxx
> Please see the log file for port libcxx for details:
>
> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_libcxx/libcxx/main.log
> 
> The log file is attached. What should I do to fix it? Any suggestion will be 
> appreciated.
> 
> Thanks.
> Yuan
> 
> 
> 
> 
> 
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[Ifeffit] No Reference Foil

[Ritimukta Sarangi]

Hello Neil,
I guess you might have tried this already - do you have any signatures in the 
I0 data? Such as a glitch or any other edge absorption. Sometimes these can be 
used as “internal calibration”.
-Riti Sarangi


> On Jul 12, 2016, at 2:54 PM, Neil M Schweitzer 
>  wrote:
> 
> Hello,
> Long time follower/user and first time subscriber! I work at Northwestern 
> University, and one of the services I provide is analyzing XAS data for users 
> who collect data at APS. Generally, I am not at APS to help them collect 
> spectra, I help analyze the data afterwards. A user came to me recently with 
> some Ce L3 data that does not have reference foil data. If I am trying to 
> compare the EXAFS of several different samples (all which should be similar 
> oxidation state, and of which I have other references of similar oxidation 
> state). Does anyone have a suggestion how to work up the data if I can’t 
> calibrate it?
>  
> --
> Neil M. Schweitzer, Ph.D
> Operations Director, CleanCat Core Facility
> Research Assistant Professor
> Chemical and Biological Engineering
> Northwestern University
> 2137 Sheridan Road
> Evanston, IL 60208-3000
> Office: 847-491-2955
> http://cleancat.northwestern.edu 
>  
>  
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Re: [Ifeffit] Question about H scattering

[Ritimukta Sarangi]

Thank you Josh.

> On May 24, 2016, at 10:25 AM, Joshua Kas  wrote:
> 
> Hi Riti,
> You can change the muffin-tin radius using the FOLP card, which is available 
> in FEFF6 as well as later versions. For example, if the H atoms have the 
> potential index 1, then use
> 
> FOLP 1 0.8
> 
> to reduce the muffin tin radius of hydrogen.
> 
> FOLP 1 1.0
> 
> will have touching muffin tin potentials.
> 
> 
> Josh  
> 
> 
> On Tue, May 24, 2016 at 10:00 AM,  <mailto:ifeffit-requ...@millenia.cars.aps.anl.gov>> wrote:
> Send Ifeffit mailing list submissions to
> ifeffit@millenia.cars.aps.anl.gov 
> <mailto:ifeffit@millenia.cars.aps.anl.gov>
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit 
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> or, via email, send a message with subject or body 'help' to
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Ifeffit digest..."
> 
> 
> Today's Topics:
> 
>1. Re: Question about H scattering (Matt Newville)
> 
> 
> ------
> 
> Message: 1
> Date: Mon, 23 May 2016 15:44:20 -0500
> From: Matt Newville  <mailto:newvi...@cars.uchicago.edu>>
> To: Ritimukta Sarangi mailto:ritimu...@gmail.com>>, 
> XAFS Analysis using
> Ifeffit  <mailto:ifeffit@millenia.cars.aps.anl.gov>>
> Subject: Re: [Ifeffit] Question about H scattering
> Message-ID:
>  <mailto:xpmm...@mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Riti,
> 
> 
> On Mon, May 23, 2016 at 1:50 PM, Ritimukta Sarangi  <mailto:ritimu...@gmail.com>>
> wrote:
> 
> > Hi Matt,
> > I have a question about FEFF and I hope you can shed some light on it.
> > Several references point to the high muffin tin radius of H (0.77) in FEFF
> > and say that it should be closer to 0.2. Is there a way of changing the MT
> > radius of H in FEFF?
> > Thank you,
> > -Riti
> 
> 
> I'm CCing this to the Ifeffit mailing list, because there are probably many
> people with more experience with this than me.
> 
> I believe there is not a simple way to set the muffin tin radius for H or
> other atoms.  But, I think you can tweak this with the "FOLP" setting
> (usually a number between 1 and 1.25 or so, representing the amount of
> overlap between atoms).
> 
> My understanding is that Feff 9 handles hydrogen better than earlier
> versions, but I don't run very many calculations with H in the structures.
> Hopefully someone who does will share some insight.
> 
> --Matt
> -- next part --
> An HTML attachment was scrubbed...
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> --
> 
> Subject: Digest Footer
> 
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> 
> --
> 
> End of Ifeffit Digest, Vol 159, Issue 12
> 
> 
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[Ifeffit] Co(IV)oxide

[Ritimukta Sarangi]

Hello Ifeffit users,
We in the biomimetic community are having a heated discussion about the XAS 
(pre-edge and edge) data of Co(IV)=O molecular complexes. Turns out that there 
are very few bonafide complexes that can be used as a standard for Co(IV) and 
they are rather difficult to obtain. I would like to turn to the 
materials/geological community here and request the XANES data for CoO2, which 
is an unstable Co(IV)oxide mineral. I am hoping someone might have collected 
these data sets. If you have other opinion or thoughts on Co(IV) XANES in 
general, I would be thankful if you can spare the time to share it with me.
Thank you for your assistance,
Best Wishes,
-Riti Sarangi


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[Ifeffit] SSRL XAS Summer School 2016 - update

[Ritimukta Sarangi]

Hello Everyone,
The agenda and application pages are online for the XAS summer school at SSRL 
in July. Please note that there are two hands-on tracks and you can choose to 
attend one of either XAS-imaging or EXAFS sessions. The lecture part is the 
same for both the sessions and both sessions will benefit from the XANES and 
advanced spectroscopy lectures on the final day of the summer school. Note that 
the deadline for application is May10th. Accepted participants will be emailed 
before the 20th of May.

http://ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html 
<http://ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html>

Best Wishes,
-Riti Sarangi
Staff Scientist
SSRL, SLAC






> On Apr 4, 2016, at 12:32 PM, Ritimukta Sarangi  wrote:
> 
> Hello Everyone,
> This is an announcement for the XAS summer school to be held at SSRL between 
> July 18-22, 2016. We will cover XAS, EXAFS and Imaging beamlines with hands 
> on data collection sessions at beamlines, followed by in-depth data analysis 
> in a classroom setting. You can find more information at 
> :http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html 
> <http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html>.
>  The agenda and application pages will be finalized within a week and I will 
> post an update once it is up and running. But I wanted interested users and 
> participants to get a heads up.
> 
> 
> 
> 
> 

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[Ifeffit] SSRL XAS Summer School 2016

[Ritimukta Sarangi]

Hello Everyone,
This is an announcement for the XAS summer school to be held at SSRL between 
July 18-22, 2016. We will cover XAS, EXAFS and Imaging beamlines with hands on 
data collection sessions at beamlines, followed by in-depth data analysis in a 
classroom setting. You can find more information at 
:http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html 
<http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html>. 
The agenda and application pages will be finalized within a week and I will 
post an update once it is up and running. But I wanted interested users and 
participants to get a heads up.
Best Wishes,
Ritimukta Sarangi
SSRL






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Re: [Ifeffit] Any XAFS schools in North America this year?

[Ritimukta Sarangi]

We at SSRL will host an exafs summer school in July 3rd week. I can post more 
about it here next week when we finalize the format.

Sent from my iPhone

> On Feb 28, 2016, at 08:05, Robert Gordon  wrote:
> 
> 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] Feature near edge of Ni XANES spectrum

[Ritimukta Sarangi]

Hello Aditya,
If I understand correctly, the nomenclature you are using is a little
misleading. The sharp feature that you are referring to is a rising-edge
feature and is not after the edge. The is a classic feature for square
planar complexes and Ni does form a lot of those. The origin of this
feature has been argued (in molecular systems) to be either:

1) Valence bond configuration interaction feature (VBCI), which is a
formally forbidden 2 -electron transfer process. It gains intensity with
covalent overlap of metal with ligands and has been shown (in the case of
Cu(III) which is isoelectronic to Ni(II)) to increase with metal-ligand
bond strength.

2) It has also been attributed to longer-range multiple scattering.

It is important to realize that both effect increase in square planar
systems and usually such a feature is the hallmark of a square planar
molecule.
Best,
Riti

On Tue, Feb 9, 2016 at 6:19 PM, Aditya Shivprasad  wrote:

> Dear list,
>
> I have obtained nickel XANES spectra (attached) from metallic Zircaloy-2
> nuclear fuel cladding (Zr, 1.5% Sn, 0.15% Fe,  0.1% Cr, 0.05% Ni).
>
> In the spectrum, I identify the edge as being approximately 8331-8332 eV
> (based on maximum of first derivative), as it is for pure Ni. However, I
> also identify a sharp feature at less than 1 eV past the edge. If anyone on
> the list could help me to understand the origin of this feature, that would
> be very helpful.
>
> Thanks
> --
> Aditya Shivprasad
>
> aps...@psu.edu
> Ph.D Candidate
> Nuclear Engineering Department
> Pennsylvania State University
>
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Re: [Ifeffit] pi/2deltak

[Ritimukta Sarangi]

Thank you very much for the explanations and your time.
Best Wishes,
-Riti



> On Feb 1, 2016, at 9:16 AM, Robert Gordon  wrote:
> 
> Hi Riti,
> 
> A couple of caveats to Matt's answer:
> 
> The EXAFS equation is not simply a sum of sine functions. I can think of two 
> ways that the resolution criteria
> can be worked around:
> 
> 1. Consider the case of two close near neighbours in a single-crystal 
> environment whose close distances are 
> geometrically distinct such that, if one were to conduct 
> polarisation-dependent measurements, one
> could turn off one of the distances in one orientation (and perhaps the other 
> in another), one could fit the
> two sets to extract the two close distances. (i.e. you aren't trying to 
> resolve the two distances in one measurement)
> 
> 2. If there is a pronounced chemical difference between the neighbours, they 
> can be resolved even if the 
> distance separation is small, provided the  k-space range being used provides 
> enough independent parameters
> to conduct the fit.
> 
> If you wish to convince yourself that these two caveats work, I suggest 
> creating a model using the AuCu
> structure. If you contract or expand the c-axis, and substitute either Cu for 
> Au (i.e. make Cu but in lower symmetry)
> or substitute a different atom on one of the Cu sites, you can test both 
> Matt's explanation and my caveats above.
> 
> cheers,
> Robert
> 
> On 1/31/2016 6:33 PM, Matt Newville wrote:
>> Hi Riti, 
>> 
>> On Sat, Jan 30, 2016 at 7:35 PM, Ritimukta Sarangi < 
>> <mailto:ritimu...@gmail.com>ritimu...@gmail.com 
>> <mailto:ritimu...@gmail.com>> wrote:
>> Hello,
>> 
>> I was recently asked about the accuracy of this formulation for obtaining 
>> EXAFS resolution and I did not have a good answer. Can someone point to a 
>> reference or explain here? 
>> Thank you for your time,
>> Best,
>> -Riti
>> 
>> 
>> The deltaR = pi / 2DeltaK  follows from general Fourier analysis and 
>> formulas like it can be found in many signal processing textbooks.For 
>> on-line resources, googling "Frequency resolution Fourier transform" gives 
>> several good references.
>> 
>> The idea is that (using sound-waves as an example) in order to distinguish 
>> two close frequencies (say 440 Hz from 441 Hz, so a different of 1 Hz), you 
>> have to sample many periods (pi seconds) to be able to do this.
>> 
>> For EXAFS, if there are contributions from two neighbors that are very 
>> closely spaced, you would have to sample enough oscillations (go high enough 
>> in k) to see the effect of these two different distances beating against 
>> each other.   If you don't go out far enough in k,  you can't tell that 
>> these two contributions are actually from different distances.
>> 
>> Hope that helps, 
>> 
>> --Matt
>> 
>> 
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[Ifeffit] pi/2deltak

[Ritimukta Sarangi]

Hello,

I was recently asked about the accuracy of this formulation for obtaining
EXAFS resolution and I did not have a good answer. Can someone point to a
reference or explain here?
Thank you for your time,
Best,
-Riti
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Re: [Ifeffit] CuO XAS spectrum

[Ritimukta Sarangi]

Have you tried the Farrel Lytle Database?
-Riti

On Dec 2, 2015, at 3:32 PM, Enyuan Hu  wrote:

> Dear all,
> 
> I'm analyzing some Cu compounds spectra and was wondering if anyone has the 
> CuO XAS spectrum and is willing to share. Thanks.
> 
> best regards,
> Enyuan
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[Ifeffit] Hello

[Ritimukta Sarangi]

Hi Bruce and Matt,
Are there any obvious examples of where Sterns criteria is shown to be 
incorrect? Meaning that 2delkdelR/pi +2 has been shown to over predict the 
number of available independent parameters? I have often been asked this by 
students/users and failed to explain it well, except for taking of talking 
sources or error such as systematic, spline, etc.
Thanks!
-Riti



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Re: [Ifeffit] XANES fitting

[Ritimukta Sarangi]

Hi Matt,
Thank you. I am looking forward to comments from members from the forum. Yes, I 
have found some of Corwin's references. Perhaps it might help current and 
future EXAFS folks to have a page on the Ifeffit website discussing the causes 
of such systematic and random errors that you point out and listing some of 
these references?
Best,
-Riti


On Oct 12, 2011, at 11:35 AM, Matt Newville wrote:

> Hi Riti,
> 
> I hope it's OK that I'm sending this to the ifeffit mailing list, as
> there might be other interesting perspectives on your questions.
> 
> On Tue, Oct 11, 2011 at 3:47 PM, Ritimukta Sarangi  wrote:
>> Hi Matt,
>> This is Riti again. This time I have a question about EXAFS, which you are 
>> an expert on :-) I would like to get your view on
>> systematic errors in EXAFS. Say the data were collected on a standard EXAFS 
>> beamline like 7-3 at SSRL. The data have
>> been collected using fluorescence mode and a 30 element Ge detector. The 
>> data are modest, between k=2-15 A.
>> 
>> I used to quote in my papers that typical statistical and systematic errors 
>> lead to a total error in first shell distances of
>> +-0.02 A.  I know it can be more than that in some circumstances but then I 
>> tried to look at it a little more closely to
>> separate out the systematic error from all sources (instrument, measurement, 
>> detector, Analysis), but I could not find a
>> good reference. I understand that this is a difficult number to estimate. I 
>> was hoping that you could shed some light on it.
>> Thanks!
>> -Riti
>> 
> 
> I'm not sure of a good general reference for that either, though
> perhaps some of the papers from Corwin Booth are a good place to
> start?   Quoting +/- 0.02 Ang seems like a reasonable estimate for a
> typical value, but that's hardly rigorous.
> 
> My sense is that it's pretty challenging to separate "systematic" and
> "random" noise for most data sets.  Fluorescence data from a
> solid-state detector is probably the best-case for such a separation,
> because you have multiple detector elements or repeated scans,  and
> usually the individual detectors or scans really are dominated by
> statistical fluctuations.   If you add detector elements or scans
> together until the noise in the data (or variations in estimated
> parameters or estimated error bars)   stops getting better,
> systematic errors are starting to be noticeable. Eventually, as you
> increase the fluorescence counts, the fits will stop improving, which
> should be when systematic errors dominate.
> 
> --Matt


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