[Ifeffit] Save the date: SCC short course at BNL, Nov. 6-8, 2024

[Anatoly Frenkel]

Hello,

As a follow up on my previous "save the date" message, the dates of the
Synchrotron Catalysis Consortium short course have been finalized (they
changed from the previous dates in an attempt to resolve the conflict with
other meetings). The final dates are: Nov. 6 (Wed) through Nov. 8 (Fri),
2024. The course will be held at Brookhaven National Laboratory.

The course is in the final stage of approvals - after we have it officially
approved I will send another update with the course agenda and registration
details.

Regards,

Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering (primary
appointment)
Department of Chemistry (affiliate appointment)
*Stony Brook University*
Stony Brook, NY 11794
Email:  anatoly.fren...@stonybrook.edu
<https://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0ybKTBGBlALcrWeszTCA..=mailto*3ajgchen*40columbia.edu__;JSU!!G_uCfscf7eWS!cvLq3GV_uhOS3ByVkN7zR4TKuu8Sqx3cotRwlfAlSYbUs__wjM2ZSdQe2-G2EV7prWGoope8L5Pmr5MXHOf67kuChmeItnMDgt8AlYMqrK-Chw$
 >
https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7eWS!cvLq3GV_uhOS3ByVkN7zR4TKuu8Sqx3cotRwlfAlSYbUs__wjM2ZSdQe2-G2EV7prWGoope8L5Pmr5MXHOf67kuChmeItnMDgt8AlYP4mnnZ4A$
 
Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!cvLq3GV_uhOS3ByVkN7zR4TKuu8Sqx3cotRwlfAlSYbUs__wjM2ZSdQe2-G2EV7prWGoope8L5Pmr5MXHOf67kuChmeItnMDgt8AlYNhipbOqw$
 

Joint Appointment:
Senior Chemist
Chemistry Division, *Brookhaven National Laboratory*
Upton, NY 11973
Email: fren...@bnl.gov
https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7eWS!cvLq3GV_uhOS3ByVkN7zR4TKuu8Sqx3cotRwlfAlSYbUs__wjM2ZSdQe2-G2EV7prWGoope8L5Pmr5MXHOf67kuChmeItnMDgt8AlYOGgEx-Jg$
 
---


On Fri, May 3, 2024 at 10:58 AM Anatoly Frenkel <
anatoly.fren...@stonybrook.edu> wrote:

> Dear subscribers:
>
> Please pass it along to your group members who may be interested in this
> opportunity.
> In continuation of the annual tradition at the Synchrotron Catalysis
> Consortium (SCC) at Brookhaven National Laboratory to organize and run XAFS
> short courses there since 2005, we are planning a first specialized course
> targeting catalysis and electrocatalysis researchers. The course will
> follow a successful model of our XAFS courses: the lectures (on the topics
> ranging from in situ/operando characterization and multimodal
> instrumentation to data analysis) and software demonstrations on the first
> two days, followed by the hands-on data analysis session on the last day.
> The program is being finalized, and we are in the process of getting the
> necessary approvals from BNL and DOE. In the meantime, please, mark your
> calendars and contact me if you have any questions.
>
> Anatoly
> 
> On sabbatical leave at Weizmann Institute of Science, Israel
> 
> ---
> Anatoly I. Frenkel
> Professor
> Department of Materials Science and Chemical Engineering (primary
> appointment)
> Department of Chemistry (affiliate appointment)
> *Stony Brook University*
> Stony Brook, NY 11794
> Email:  anatoly.fren...@stonybrook.edu
> <https://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0ybKTBGBlALcrWeszTCA..=mailto*3ajgchen*40columbia.edu__;JSU!!G_uCfscf7eWS!cvLq3GV_uhOS3ByVkN7zR4TKuu8Sqx3cotRwlfAlSYbUs__wjM2ZSdQe2-G2EV7prWGoope8L5Pmr5MXHOf67kuChmeItnMDgt8AlYMqrK-Chw$
>  >
> https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7eWS!cvLq3GV_uhOS3ByVkN7zR4TKuu8Sqx3cotRwlfAlSYbUs__wjM2ZSdQe2-G2EV7prWGoope8L5Pmr5MXHOf67kuChmeItnMDgt8AlYP4mnnZ4A$
>  
> Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
> https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!cvLq3GV_uhOS3ByVkN7zR4TKuu8Sqx3cotRwlfAlSYbUs__wjM2ZSdQe2-G2EV7prWGoope8L5Pmr5MXHOf67kuChmeItnMDgt8AlYNhipbOqw$
>  
>
> Joint Appointment:
> Senior Chemist
> Chemistry Division, *Brookhaven National Laboratory*
> Upton, NY 11973
> Email: fren...@bnl.gov
> https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7eWS!cvLq3GV_uhOS3ByVkN7zR4TKuu8Sqx3cotRwlfAlSYbUs__wjM2ZSdQe2-G2EV7prWGoope8L5Pmr5MXHOf67kuChmeItnMDgt8AlYOGgEx-Jg$
>  
> ---
>

Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering (primary
appointment)
Department of Chemistry (affiliate appointment)
* Stony

[Ifeffit] Save the date: SCC short course at BNL, Oct. 29-31, 2024

[Anatoly Frenkel]

Dear subscribers:

Please pass it along to your group members who may be interested in this
opportunity.
In continuation of the annual tradition at the Synchrotron Catalysis
Consortium (SCC) at Brookhaven National Laboratory to organize and run XAFS
short courses there since 2005, we are planning a first specialized course
targeting catalysis and electrocatalysis researchers. The course will
follow a successful model of our XAFS courses: the lectures (on the topics
ranging from in situ/operando characterization and multimodal
instrumentation to data analysis) and software demonstrations on the first
two days, followed by the hands-on data analysis session on the last day.
The program is being finalized, and we are in the process of getting the
necessary approvals from BNL and DOE. In the meantime, please, mark your
calendars and contact me if you have any questions.

Anatoly

On sabbatical leave at Weizmann Institute of Science, Israel

---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering (primary
appointment)
Department of Chemistry (affiliate appointment)
* Stony Brook University *
Stony Brook, NY 11794
Email:  anatoly.fren...@stonybrook.edu

https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7eWS!YRLhoyvmIL5kwnoceiCV3eQ7wWX47aQ1k1y09Mpy-l8iqoMvWE3pcVCaAdewmf0nUQNXBOb6Ai7e5QVllMXYE-weOGhON0Yr-BF9R8xsfeJtWA$
 
Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!YRLhoyvmIL5kwnoceiCV3eQ7wWX47aQ1k1y09Mpy-l8iqoMvWE3pcVCaAdewmf0nUQNXBOb6Ai7e5QVllMXYE-weOGhON0Yr-BF9R8xq5qLZ6Q$
 

Joint Appointment:
Senior Chemist
Chemistry Division, *Brookhaven National Laboratory*
Upton, NY 11973
Email: fren...@bnl.gov
https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7eWS!YRLhoyvmIL5kwnoceiCV3eQ7wWX47aQ1k1y09Mpy-l8iqoMvWE3pcVCaAdewmf0nUQNXBOb6Ai7e5QVllMXYE-weOGhON0Yr-BF9R8yIHM21vA$
 
---
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Re: [Ifeffit] weak scattering from second-nearest neighbors for single atom catalysts

[Anatoly Frenkel]

Hi Qiang,

There are many papers analyzing Pt SACs on ceria and many of them are able
to provide good evidence of Pt-O-Ce coordination. See for example Fig. 5d
in this paper and the discussion of the model and fit results.

M. Kottwitz, Y. Li, R. M. Palomino, Z. Liu, Q. Wu, G. Wang, J. Huang, J.
Timoshenko, S. D. Senanayake, M. Balasubramanian, D. Lu, R. G. Nuzzo, A. I.
Frenkel
*Local structure and electronic state of atomically dispersed Pt on
nanosized CeO2 support*
ACS Catalysis *9*, 8738-8748 (2019)


Regards,
Anatoly

On sabbatical leave at PSI, Switzerland.

---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering (primary
appointment)
Department of Chemistry (affiliate appointment)
* Stony Brook University *
Stony Brook, NY 11794
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel
Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2

Joint Appointment:
Senior Chemist
Chemistry Division, *Brookhaven National Laboratory*
Upton, NY 11973
Email: fren...@bnl.gov
https://www.bnl.gov/staff/frenkel
---


On Thu, Feb 8, 2024 at 2:08 PM Qiang  wrote:

> Hi everyone,
>
> I would like to have a discussion about the common EXAFS for single atom
> catalysts. It is usually observed that there is only one strong peak around
> 1.5A in EXAFS, and it is attributed to the nearest neighbors of O or N.
> Take an example of Pt1/CeO2 catalyst. Pt single atom is coordinated with a
> few oxygens, i.e., PtOx. These oxygens constitute the first shell of Pt. It
> is supposed that these O should also attach to the metal element of the
> support (Ce here). So there is also Pt-O-Ce structure. Why it doesnot have
> strong scattering peak in EXAFS? Is it that because the Pt-O-Ce formed is
> not ordered, or it is actually not a bond just some weak contact?
>
> Thank you very much.
>
> Qiang
>
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Re: [Ifeffit] EXAFS-50 symposium and short course, Oct. 30-Nov. 3 at BNL

[Anatoly Frenkel]

Hello, all:

Registration deadline for the EXAFS-50 symposium (Sep. 10) is approaching.
Please see the announcement below.
Regards,

Anatoly

On Mon, Aug 21, 2023 at 10:58 AM Anatoly Frenkel <
anatoly.fren...@stonybrook.edu> wrote:

> Dear subscribers:
>
> Sharing here my Linkedin post:
>
> I am excited to share that Brookhaven National Laboratory will be hosting
> the Symposium ("EXAFS-50") that will mark the 50th anniversary of
> Stern-Sayers-Lytle team's introduction of the Extended X-ray Absorption
> Fine Structure (EXAFS) technique in early 1970s. The Symposium will open
> the week of events, hosted by Brookhaven National Laboratory, that will
> include the talks of the experts in the field on the past, present and
> future of the EXAFS technique on Oct. 30 and 31, and culminate by the
> three-day long short course on advanced data analysis methods of EXAFS,
> from Nov. 1 to 3. Both events will be in-person. The web sites below have
> all the information for registration for the symposium (registration begins
> on Aug. 21) and for application/registration for the short course
> (application deadline is Aug. 31). Although the Symposium and the Short
> course are organized and run as separate events, attending both of them
> will be ideal for graduate students and postdocs. No registration fee is
> charged for attending these events but registration is required.
>
> EXAFS-50: https://www.bnl.gov/exafs-50/
> XAFS short course: https://www.bnl.gov/xafscourse/
> ---
> Anatoly I. Frenkel
> Professor
> Department of Materials Science and Chemical Engineering (primary
> appointment)
> Department of Chemistry (affiliate appointment)
> * Stony Brook University *
> Stony Brook, NY 11794
> Email:  anatoly.fren...@stonybrook.edu
> <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0ybKTBGBlALcrWeszTCA..=mailto%3ajgchen%40columbia.edu>
> http://you.stonybrook.edu/frenkel
> Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
> http://you.stonybrook.edu/scc2
>
> Joint Appointment:
> Senior Chemist
> Chemistry Division, *Brookhaven National Laboratory*
> Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
> Email: fren...@bnl.gov
> https://www.bnl.gov/staff/frenkel
> ---
>
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[Ifeffit] EXAFS-50 symposium and short course, Oct. 30-Nov. 3 at BNL

[Anatoly Frenkel]

Dear subscribers:

Sharing here my Linkedin post:

I am excited to share that Brookhaven National Laboratory will be hosting
the Symposium ("EXAFS-50") that will mark the 50th anniversary of
Stern-Sayers-Lytle team's introduction of the Extended X-ray Absorption
Fine Structure (EXAFS) technique in early 1970s. The Symposium will open
the week of events, hosted by Brookhaven National Laboratory, that will
include the talks of the experts in the field on the past, present and
future of the EXAFS technique on Oct. 30 and 31, and culminate by the
three-day long short course on advanced data analysis methods of EXAFS,
from Nov. 1 to 3. Both events will be in-person. The web sites below have
all the information for registration for the symposium (registration begins
on Aug. 21) and for application/registration for the short course
(application deadline is Aug. 31). Although the Symposium and the Short
course are organized and run as separate events, attending both of them
will be ideal for graduate students and postdocs. No registration fee is
charged for attending these events but registration is required.

EXAFS-50: https://www.bnl.gov/exafs-50/
XAFS short course: https://www.bnl.gov/xafscourse/
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering (primary
appointment)
Department of Chemistry (affiliate appointment)
* Stony Brook University *
Stony Brook, NY 11794
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel
Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2

Joint Appointment:
Senior Chemist
Chemistry Division, *Brookhaven National Laboratory*
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/staff/frenkel
---
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[Ifeffit] Advanced EXAFS analysis course Nov. 1-3

[Anatoly Frenkel]

Dear colleagues:

Please share this info with your students and postdocs. The application
deadline is Aug. 31.

https://www.bnl.gov/xafscourse/
Remember to state your expertise with EXAFS data analysis and modeling in
the application.

Regards,
Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering (primary
appointment)
Department of Chemistry (affiliate appointment)
* Stony Brook University *
Stony Brook, NY 11794
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel
Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2

Joint Appointment:
Senior Chemist
Chemistry Division, *Brookhaven National Laboratory*
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/staff/frenkel
---
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[Ifeffit] EXAFS course at BNL: Nov. 1-3, 2023

[Anatoly Frenkel]

Dear subscribers:

The information about the upcoming XAFS short course is here:

https://www.bnl.gov/xafscourse/

The course will be taught in-person. The place in the course is limited,
and, due to the emphasis on advanced methods, the preference will be given
to those participants who have prior experience with EXAFS data modeling
and analysis.

The info about the past course topics (2005-2022) is at the SCC website:
https://you.stonybrook.edu/scc2/xafs-workshops/

Regards,
Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering (primary
appointment)
Department of Chemistry (affiliate appointment)
* Stony Brook University *
Stony Brook, NY 11794
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel
Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2

Joint Appointment:
Senior Chemist
Chemistry Division, *Brookhaven National Laboratory*
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/staff/frenkel
---
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Re: [Ifeffit] Brain teaser

[Anatoly Frenkel]

HI Mike, it is dilute Pd in Au nanoparticles deposited on SiO2 with about
5% metal weight loading.
In my view, the lack of curvature in transmission (the original problem in
my post) is a simple consequence of two opposite trends, 1) the curving up
of the transmission signal by the same reason (yet to be identified, which
is something I will try to, after getting useful hints from many people
here) as the curving up of the incident beam and 2) the opposite trend due
to the greater removal of the photons at higher energy by I0 detector. The
two opposite trends tend to cancel each other.

Anatoly



On Thu, Jun 15, 2023 at 4:14 PM Mike Massey  wrote:

> A question because I'm not really super clear on how harmonics work:
>
> (I'll get to the question in a moment...) I note that I0 starts to go
> non-linear around 12200-12400 eV and stays that way. So an increase
> (proportional?) in the amount of signal in It might be happening at around
> the same point.
>
> Could Pd fluorescence into It be impacting the signal in It? I realize
> that the Pd emission lines are very low in energy but they are around 3k eV.
>
> I'm not super familiar with alloy systems but I did have an issue once
> upon a time with back fluorescence into an ion chamber and things went a
> bit wonky. This wouldn't exactly be "back" fluorescence, but if the system
> is mostly Pd with a little bit of Au, I guess...? And it might be easy
> enough to test, just put a high-pass filter in front of It?
>
> I got nothin' but it's kinda fun to take a shot. Cheers,
>
>
>
> Mike
>
>
>
>
> On Jun 16, 2023, at 03:26, Matt Newville 
> wrote:
>
> 
> Hi Anatoly,
>
> I think Robert or Matthew made this point, but if set up for Pd, the
> mirror angle may have been chosen to reject ~70 keV, but possibly not 36
> keV -- the harmonic at the Au edge.  Do you know what the mirror angle
> was?
>
> The Ar-filled I0 would be very efficient at absorbing 12 keV, and only
> pretty efficient at absorbing 36 keV.   That would leave a more
> harmonic-rich beam exiting I0 and hitting the sample than entering I0.  The
> good news is that the dense Pd/Au sample would be efficient at absorbing 36
> keV too (but it was ~1 absorption length at 24 keV?) too.
>
> Mono reflectivity of 36 keV vs 12 keV might also factor in.  If you were
> not deliberately detuning but the crystals were slightly misaligned,  the
> harmonic content may change significantly over the scan range.   I would
> not guess that to dominate, but maybe it factors in.
>
>
> On Thu, Jun 15, 2023 at 9:54 AM Anatoly Frenkel <
> anatoly.fren...@stonybrook.edu> wrote:
>
>> Thank you, Matt.
>> Ion chambers were filled with 90% Ar, and Pt coating was used, because we
>> were measuring Pd K edge for the project, but we decided to look at the Au
>> edge for testing purposes.
>>
>> Anatoly
>>
>> On Jun 15, 2023, at 10:45 AM, Matt Newville 
>> wrote:
>>
>> 
>> I'm not sure why the intensity would go up unless the ion chamber was
>> poorly set up.   But, as others have pointed out, the mirror reflectivity
>> for a Pt mirror should not change significantly over this energy range -
>> the energy range is not that close to the Pt L3 or L2 edges.Depending
>> on where it was located, fluorescence from the Pt mirror might pollute the
>> signal in the I0 ion chamber, but that would also likely be a fairly
>> constant background.
>>
>> But, why would you fill the I0 ion chamber with Argon?  A 10-cm ion
>> chamber filled with Ar would absorb about 50% of the beam at 12 keV.   Even
>> at 24 keV, that would absorb 8% of the beam - not necessarily a problem but
>> also probably generating at least a micro-Amp, so way more signal than you
>> would need.
>>
>> For mirror reflectivity curves, allow me to humbly remind everyone of
>>
>> https://xraydb.xrayabsorption.org/reflectivity/Pt/21.45/2.5/10/s/1000/51000/50/platinum/linear
>>
>> which is both interactive and works with X-ray energies above 30 keV.
>>
>>
>> On Wed, Jun 14, 2023 at 7:28 PM Anatoly Frenkel <
>> anatoly.fren...@stonybrook.edu> wrote:
>>
>>> Hello, all. It is a low- to medium- level brain teaser.
>>>
>>> Pt-coated collimating mirror was in place for Pd K-edge measurement, but
>>> Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It
>>> detectors were both Ar filled ionization chambers. Because of the energy
>>> dependence of reflectivity of the Pt mirror, I0 intensity was strongly
>>> nonlinear (blue curve). However, the transmission intensity in the It
>>> detector was almost linear (red curv

Re: [Ifeffit] [Ext] Re: Brain teaser

[Anatoly Frenkel]

But collimating mirror is in the front end. AnatolyOn Jun 15, 2023, at 10:52 AM, Carlo Segre  wrote:I would have guessed that the increase in I0 is primarily due to Pt fluorescence.  The yield does increase as the energy rises.CarloOn Thu, Jun 15, 2023 at 9:45 AM Matt Newville <newvi...@cars.uchicago.edu> wrote:I'm not sure why the intensity would go up unless the ion chamber was poorly set up.   But, as others have pointed out, the mirror reflectivity for a Pt mirror should not change significantly over this energy range - the energy range is not that close to the Pt L3 or L2 edges.    Depending on where it was located, fluorescence from the Pt mirror might pollute the signal in the I0 ion chamber, but that would also likely be a fairly constant background. But, why would you fill the I0 ion chamber with Argon?  A 10-cm ion chamber filled with Ar would absorb about 50% of the beam at 12 keV.   Even at 24 keV, that would absorb 8% of the beam - not necessarily a problem but also probably generating at least a micro-Amp, so way more signal than you would need.For mirror reflectivity curves, allow me to humbly remind everyone of   https://xraydb.xrayabsorption.org/reflectivity/Pt/21.45/2.5/10/s/1000/51000/50/platinum/linearwhich is both interactive and works with X-ray energies above 30 keV.On Wed, Jun 14, 2023 at 7:28 PM Anatoly Frenkel <anatoly.fren...@stonybrook.edu> wrote:Hello, all. It is a low- to medium- level brain teaser.Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? Anatoly
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Re: [Ifeffit] Brain teaser

[Anatoly Frenkel]

Thank you, Matt. Ion chambers were filled with 90% Ar, and Pt coating was used, because we were measuring Pd K edge for the project, but we decided to look at the Au edge for testing purposes. AnatolyOn Jun 15, 2023, at 10:45 AM, Matt Newville  wrote:I'm not sure why the intensity would go up unless the ion chamber was poorly set up.   But, as others have pointed out, the mirror reflectivity for a Pt mirror should not change significantly over this energy range - the energy range is not that close to the Pt L3 or L2 edges.    Depending on where it was located, fluorescence from the Pt mirror might pollute the signal in the I0 ion chamber, but that would also likely be a fairly constant background. But, why would you fill the I0 ion chamber with Argon?  A 10-cm ion chamber filled with Ar would absorb about 50% of the beam at 12 keV.   Even at 24 keV, that would absorb 8% of the beam - not necessarily a problem but also probably generating at least a micro-Amp, so way more signal than you would need.For mirror reflectivity curves, allow me to humbly remind everyone of   https://xraydb.xrayabsorption.org/reflectivity/Pt/21.45/2.5/10/s/1000/51000/50/platinum/linearwhich is both interactive and works with X-ray energies above 30 keV.On Wed, Jun 14, 2023 at 7:28 PM Anatoly Frenkel <anatoly.fren...@stonybrook.edu> wrote:Hello, all. It is a low- to medium- level brain teaser.Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? Anatoly
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Re: [Ifeffit] [Ext] Brain teaser

[Anatoly Frenkel]

Thank you, Robert, Matthew, Jeff, Kirill, Terry and Sirine for great 
suggestions. 

I initially thought that the explanation for the linearity or the transmission 
signal is a superposition of two opposite trends: 1) increase of flux with 
energy due to the mirror effect and 2) similar decrease with energy due to the 
photon removal by first effect in the I0 detector. But I did not look into the 
main reason for the curving up of the I0 signal and I agree it is not a result 
of the reflectivity. I fill follow up on all suggestions, and, if something 
more definitive transpires, will report back. 

Thanks again for your time and advice!

Anatoly

> On Jun 15, 2023, at 2:10 AM, matthew marcus  wrote:
> The mirror was set up for a run at the Pd K-edge, according to the problem 
> statement.  Therefore, its nominal angle must be such as to put the critical 
> energy >25keV.  An angle of 3mrad would do it. At that angle, the 
> reflectivity (assuming  no roughness) goes up with energy in the relevant 
> range, but only by a few percent.
> 
> We're not told what the ratio of gains of the current amps is, or whether the 
> ion chambers have the same path length, so we can't tell whether the signals 
> are comparable, as shown on the graph, or orders of magnitude different.
>mam
> 
> On 6/14/2023 10:17 PM, Jeffrey Terry wrote:
>> Well, I’ll take a shot. Looks like the mirror angle is totally fubared, you 
>> are getting Bragg peaks from the coating or substrate that are giving you 
>> the peaks in Io. Since you have no idea what angle those are going through 
>> Io, they are unlikely to make it into either the sample or It. Since those 
>> photons are removed from the beam hitting the sample, they would show up as 
>> intensity dips in It. I’d bet that most (all?) of the reflected beam is not 
>> going into the sample. I’m kind of surprised It signal is as clean as it is, 
>> but then I don’t know the gains on either measurement amplifiers. I couldn’t 
>> find a flat mirror angle that would cause the cutoff at 12870? eV but since 
>> it is a collimating mirror who knows what range of angles were actually 
>> being hit.
>> Jeff Terry
>> Interim Chair, Department of Biology
>> Interim Chair, Department of Social Sciences
>> Professor of Physics
>> Professor of Mechanical, Materials, and Aerospace Engineering
>> Editor, Applied Surface Science
>> Illinois Institute of Technology
>> 3101 S. Dearborn St.
>> Chicago IL 60616
>> 630-252-9708
>>> On Jun 14, 2023, at 7:27 PM, Anatoly Frenkel 
>>> mailto:anatoly.fren...@stonybrook.edu>> 
>>> wrote:
>>> Hello, all. It is a low- to medium- level brain teaser.
>>> Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au 
>>> L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It 
>>> detectors were both Ar filled ionization chambers. Because of the energy 
>>> dependence of reflectivity of the Pt mirror, I0 intensity was strongly 
>>> nonlinear (blue curve). However, the transmission intensity in the It 
>>> detector was almost linear (red curve). Why?
>>> Anatoly
>>> 
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Re: [Ifeffit] Brain teaser

[Anatoly Frenkel]

Amazing idea. I thunk you were the only one who succeeded to use third harmonic 
of Si for taking EXAFS at high atomic number elements. But that does not 
explain the peaks and dips. 

Anatoly

> On Jun 15, 2023, at 12:22 AM, matthew marcus  wrote:
> 
> Suppose the mono is being used at the 333 reflection (for Si), intentionally 
> working at the 3rd harmonic.  In that case, if the fundamental isn't filtered 
> out, you could get just what we see, with the sample doing the filtering 
> before the beam gets to the transmission chamber.
>mam
> 
>> On 6/14/2023 9:16 PM, Anatoly Frenkel wrote:
>> Thank you, Matthew and Robert, but I think the explanation is more simplle. 
>> The fact that there are peaks in I0 and dips in transmission is a clue that 
>> explains why transmission is almost linear while I0 curves up.
>> Anatoly
>>>> On Jun 14, 2023, at 11:34 PM, matthew marcus  wrote:
>>> 
>>> One thing that's pretty odd is that the glitches are peaks in I0, and dips 
>>> in It.  It would be much easier to explain if It was the one that increased 
>>> steeply and I0 was more linear, but the presence of the edge in It shows 
>>> that you didn't switch them.  Red = It.  What's that sudden drop at the end?
>>> 
>>> Could it be that the I0 chamber is misaligned so that beam is scraping one 
>>> of the plates?  That could cause all sorts of odd things to happen.
>>>mam
>>> 
>>>> On 6/14/2023 5:27 PM, Anatoly Frenkel wrote:
>>>> Hello, all. It is a low- to medium- level brain teaser.
>>>> Pt-coated collimating mirror was in place for Pd K-edge measurement, but 
>>>> Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It 
>>>> detectors were both Ar filled ionization chambers. Because of the energy 
>>>> dependence of reflectivity of the Pt mirror, I0 intensity was strongly 
>>>> nonlinear (blue curve). However, the transmission intensity in the It 
>>>> detector was almost linear (red curve). Why?
>>>> Anatoly
>>>> image.png
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Re: [Ifeffit] Brain teaser

[Anatoly Frenkel]

Thank you, Matthew and Robert, but I think the explanation is more simplle. The 
fact that there are peaks in I0 and dips in transmission is a clue that 
explains why transmission is almost linear while I0 curves up. 

Anatoly

> On Jun 14, 2023, at 11:34 PM, matthew marcus  wrote:
> 
> One thing that's pretty odd is that the glitches are peaks in I0, and dips 
> in It.  It would be much easier to explain if It was the one that increased 
> steeply and I0 was more linear, but the presence of the edge in It shows that 
> you didn't switch them.  Red = It.  What's that sudden drop at the end?
> 
> Could it be that the I0 chamber is misaligned so that beam is scraping one of 
> the plates?  That could cause all sorts of odd things to happen.
>mam
> 
>> On 6/14/2023 5:27 PM, Anatoly Frenkel wrote:
>> Hello, all. It is a low- to medium- level brain teaser.
>> Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au 
>> L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It 
>> detectors were both Ar filled ionization chambers. Because of the energy 
>> dependence of reflectivity of the Pt mirror, I0 intensity was strongly 
>> nonlinear (blue curve). However, the transmission intensity in the It 
>> detector was almost linear (red curve). Why?
>> Anatoly
>> image.png
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[Ifeffit] Brain teaser

[Anatoly Frenkel]

Hello, all. It is a low- to medium- level brain teaser.

Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au
L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It
detectors were both Ar filled ionization chambers. Because of the energy
dependence of reflectivity of the Pt mirror, I0 intensity was strongly
nonlinear (blue curve). However, the transmission intensity in the It
detector was almost linear (red curve). Why?

Anatoly

[image: image.png]
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Re: [Ifeffit] Question about EXAFS fitting of mixtures

[Anatoly Frenkel]

That question reminds me of a Russian riddle:
In each corner of a room there is a cat. In the eyes of each cat there are 
three cats. On the tail of each cat there is a cat. How many cats are there?

Anatoly

> On May 15, 2023, at 7:09 PM, Soyoung Kim  wrote:
> 
> 
> Dear all,
> 
> While fitting EXAFS for tiny Pt nanoparticles, a simple question occurred to 
> me. For these two scenarios:
> 1. All Pt atoms are coordinated to 3 O atoms and 3 Pt atoms each.
> 2. Half of the Pt atoms are coordinated to 6 O atoms and half to 6 Pt atoms.
> 
> If we fit only single-scattering paths, would it be possible to tell apart 
> these two scenarios with EXAFS fitting? What about linear combination 
> analysis of the XANES?
> 
> Thank you,
> Soyoung
> 
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Re: [Ifeffit] (no subject)

[Anatoly Frenkel]

Joyti,

The coordination number of Rh-C bonds is defined as the total number of
Rh-C bonds in the sample divided by the total number of Rh atoms in the
sample.
Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering (primary
appointment)
Department of Chemistry (affiliate appointment)
Stony Brook University
Stony Brook, NY 11794
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel
Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2

Joint Appointment:
Senior Chemist
Chemistry Division, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/staff/frenkel
---


On Mon, Apr 24, 2023 at 12:25 PM Jyoti Pandey 
wrote:

> Hello everyone,
>
> I have a cluster of 13 Rh atoms above the graphene sheet. The first
> coordination number that I am getting is around 1.65 (which is obtained by
> choosing a Rh-C) path. I am curious to know whether this value is the
> "exact" or the "average" coordination number w.r.t all the Rh atoms.
>
> Thanks
>
> With Best Regards
>
> Dr. Jyoti Pandey, Ph.D.
> Postdoctoral Researcher
> Department of Physics
> Central Michigan University, MI, USA
> Mobile No. +1-928-265-0599
> .
>
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Re: [Ifeffit] SO2 for samples with non-planar geometry

[Anatoly Frenkel]

Capillary made or what?AnatolyOn Apr 21, 2023, at 9:52 PM, Joel Brugger  wrote:Fluo, 0.5 wt% Cu.
On 22 Apr 2023, at 11:41 am, Anatoly Frenkel <anatoly.fren...@stonybrook.edu> wrote:Fluorescence or transmission?What is the Cu concentration? Could be self absorption. AnatolyOn Apr 21, 2023, at 9:31 PM, Joel Brugger <joel.brug...@monash.edu> wrote:Dear list,We are trying to fit EXAFS from data collected on solutions within a capillary. The capillary has OD 1mm, ID 0.8mm, and was placed horizontally. The beam is 1x2 mm (VxH).Fitting the copper reference foil, we get the expected SO2 value of ~0.7.However, the solution containing the Cu(II) aqua ion gives a coordination of 2, instead of the expected 5-6. So our SO2 for this solution is apparently ~0.25. I couldn’t find a discussion of the effect of geometry (in our case cylindrical rather than planar) on SO2. Is it possible that the low SO2 is a result of the odd geometry?Confused as ever,JOEL
Joël BruggerProfessor of Synchrotron GeosciencesMonash UniversitySchool of Earth, Atmosphere and Environment Room 257A, Level 2, 9 Rainforest WalkClayton, Victoria 3800AustraliaT: +61 3 9905 4898E: joel.brug...@monash.edu Twitter: @JoelBrugger

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Re: [Ifeffit] SO2 for samples with non-planar geometry

[Anatoly Frenkel]

Fluorescence or transmission?What is the Cu concentration? Could be self absorption. AnatolyOn Apr 21, 2023, at 9:31 PM, Joel Brugger  wrote:Dear list,We are trying to fit EXAFS from data collected on solutions within a capillary. The capillary has OD 1mm, ID 0.8mm, and was placed horizontally. The beam is 1x2 mm (VxH).Fitting the copper reference foil, we get the expected SO2 value of ~0.7.However, the solution containing the Cu(II) aqua ion gives a coordination of 2, instead of the expected 5-6. So our SO2 for this solution is apparently ~0.25. I couldn’t find a discussion of the effect of geometry (in our case cylindrical rather than planar) on SO2. Is it possible that the low SO2 is a result of the odd geometry?Confused as ever,JOEL
Joël BruggerProfessor of Synchrotron GeosciencesMonash UniversitySchool of Earth, Atmosphere and Environment Room 257A, Level 2, 9 Rainforest WalkClayton, Victoria 3800AustraliaT: +61 3 9905 4898E: joel.brug...@monash.edu Twitter: @JoelBrugger

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[Ifeffit] Save the date: XAFS short course at BNL and EXAFS-50 symposium

[Anatoly Frenkel]

Dear subscribers,

Please save the date for the two back-to-back, *in-person*, events:
EXAFS-50 symposium (Oct. 30-31) and annual EXAFS short course (Nov. 1-3,
2023), both to be run at Brookhaven National Laboratory. While the usual
format of our short courses is Wednesday through Friday, this year we will
mark the 50th anniversary of discovery of EXAFS by organizing a two-day
symposium on Monday-Tuesday to celebrate it. The short course participants
will benefit from attending the symposium as well because they will be able
to learn from, and interact with, leading experts in the field, credited
for developing the foundations of the EXAFS experiments, theory, data
analysis and modeling. Brookhaven shares with other synchrotron facilities
good memories of developing new techniques and applications of EXAFS, and
other labs, as well as the International X-ray Absorption Society (IXAS),
are planning their own efforts to commemorate the 50th anniversary in the
coming years.

Regarding the short course: following up on the feedback we received after
the 2022 course, we are planning to teach advanced topics in 2023. They
will include but not limited to: Reverse Monte Carlo EXAFS, Molecular
Dynamics EXAFS, Machine Learning EXAFS, MCR-ALS and others. More
information will soon appear on the web site of the Synchrotron Catalysis
Consortium that co-sponsors the short course. The other sponsors are
National Laboratory and the Users Executive Committee at the National
Synchrotron Light Source-II (to be confirmed).

We are grateful to BNL and Stony Brook University, as well as NSLS-II UEC
(to be confirmed) for the support of the EXAFS-50 symposium that will
enable participants to attend it registration fee-free.

Stay tuned for further updates.
Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering (primary
appointment)
Department of Chemistry (affiliate appointment)
Stony Brook University
Stony Brook, NY 11794
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel
Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2

Joint Appointment:
Senior Chemist
Chemistry Division, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/staff/frenkel
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Re: [Ifeffit] XANES temperature estimation

[Anatoly Frenkel]

Only evaporation temperature, when XANES spectrum disappears…:)

Anatoly

> On Nov 21, 2022, at 10:20 AM, Gabriele GAROFALO  
> wrote:
> 
> Hi everyone,
> 
> I'd like to estimate the temperature of some samples from some XANES spectra, 
> is there a way to do that? I couldn't find an answer in the mailing list 
> archive.
> 
> Thanks!
> 
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Re: [Ifeffit] Bug report: Athena, multiple data export

[Anatoly Frenkel]

" But would it be difficult to program it so that it will export properly,
e.g., with multiple energy axes?"
- that is what saving as unique files means.
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu
<https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0ybKTBGBlALcrWeszTCA..=mailto%3ajgchen%40columbia.edu>
http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/staff/frenkel
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
---


On Fri, Oct 8, 2021 at 6:29 PM Soyoung Kim  wrote:

> I see. Thank you for the quick reply.
>
> But would it be difficult to program it so that it will export properly,
> e.g., with multiple energy axes? Because when the data is plotted as a
> graph, it is hard to tell whether or not the x-axes are the same... And if
> you are processing data from someone else, you may not know whether or not
> they were collected with the same energy step settings.
>
> Best,
> Soyoung
>
> On Fri, Oct 8, 2021 at 3:24 PM Anatoly Frenkel <
> anatoly.fren...@stonybrook.edu> wrote:
>
>> It is not a bug. When groups have unique energy axes they should be saved
>> in different files.
>>
>> Anatoly
>>
>> > On Oct 8, 2021, at 6:19 PM, Soyoung Kim  wrote:
>> >
>> > 
>> > Dear Bruce and IFEFFIT community,
>> >
>> > Hope all is well. I found a bug with Athena's file export function. I
>> had two normalized mu(E) data with very similar spectra but different
>> x-axis values (collected with different energy step settings).
>> > 
>> >
>> > When I batch exported them to a .dat file using the purple E button
>> while "Save next plot to a file" was turned on, the resulting data only had
>> a single x-axis column, which was taken from the first data. Hence, when I
>> plot the two spectra from this .dat file, they now look different:
>> > 
>> >
>> > If I export each data individually to .dat files, then they are correct.
>> > 
>> >
>> >
>> > I'm attaching the Athena project file containing the two data and the
>> .dat files I exported, both together and individually.
>> >
>> > Please let me know if anything is unclear. Thank you in advance for
>> your help.
>> >
>> > Best,
>> > Soyoung Kim
>> >
>> > 
>> > 
>> > 
>> > 
>> > ___
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Re: [Ifeffit] Bug report: Athena, multiple data export

[Anatoly Frenkel]

It is not a bug. When groups have unique energy axes they should be saved in 
different files. 

Anatoly

> On Oct 8, 2021, at 6:19 PM, Soyoung Kim  wrote:
> 
> 
> Dear Bruce and IFEFFIT community,
> 
> Hope all is well. I found a bug with Athena's file export function. I had two 
> normalized mu(E) data with very similar spectra but different x-axis values 
> (collected with different energy step settings).
> 
> 
> When I batch exported them to a .dat file using the purple E button while 
> "Save next plot to a file" was turned on, the resulting data only had a 
> single x-axis column, which was taken from the first data. Hence, when I plot 
> the two spectra from this .dat file, they now look different:
> 
> 
> If I export each data individually to .dat files, then they are correct.
> 
> 
> 
> I'm attaching the Athena project file containing the two data and the .dat 
> files I exported, both together and individually.
> 
> Please let me know if anything is unclear. Thank you in advance for your help.
> 
> Best,
> Soyoung Kim
> 
> 
> 
> 
> 
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Re: [Ifeffit] S02 selection from reviewer

[Anatoly Frenkel]

I think that the variability of S02 between different samples, detection
methods etc. may or may not be a big concern for you if 1) the error bars
in the CNs (that you are not reporting) are larger than the difference in
their mean values (that you are reporting), and/or 2) larger than the
difference between their mean values and the CN=6 that the reviewer is
asking about. If yes to either 1) or 2), then the variability in the S02
values for differently prepared samples may cause smaller variation in your
best fit values of CN than the error bars reported by your fitting program,
and your choice of fixing your S02 to be constant (0.85) may be justified.
You need to have a really bad non-uniformity or concentration problem so
that your effective S02 changed from the expected 0.85 (assuming it is what
a correctly performed measurement would give) to, say, 0.5 or 0.6 is my
thought.

Anatoly



On Sat, Oct 2, 2021 at 3:50 AM Peng Liu  wrote:

> Dear IFEFFIT members,
>
> I am sorry to bother you again. I asked about S02 selection for the first
> major revision. I just received the second revision. The reviewer is not
> satisfied with one S02 value for all our samples.
> "
>
> 1. I am still not satisfied with selected SO2 value (it is set to 0.85).
> SO2 is not transferable between different samples and detection methods. It
> is not possible to use a value obtained from different compound using
> transmission measurement mode to completely different other compound
> measured using fluorescence mode. One method to fix SO2 value is to measure
> diluted solution (to avoid self-absorption) of reference material in
> fluorescence mode. Other is to use multiple spectra fitting for all samples
> of interest (e.g. with Sb(V)) measured using fluorescence mode where SO2
> parameter is the same for all samples.
>
> At the same time I am confident that CN values 5.6, 7.1 and 6.9 correspond
> to CN(Sb-O)=6. I suggest reconsidering the SO2 value for measurements in
> fluorescence mode.
> "
>
> We do get the S02 from a similar reference material measured in
> transmission mode, and our samples were all measured in fluorescence mode.
> It is not possible to measure the diluted reference material in
> fluorescence mode in one or two months. If you could give me some
> suggestions, that would be great.
>
>
> --
> Best Regards,
>
> Peng Liu
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[Ifeffit] XAFS short course at BNL: Nov. 17-19

[Anatoly Frenkel]

Dear subscribers:

As it does every year in the Fall, Synchrotron Catalysis Consortium at
Brookhaven National Laboratory will run a short course from November 17 to
19 at BNL. As in the last year, when it gathered 80 participants, it will
be virtual, and the course will be limited to 80 registered participants
again. The course application deadline is August 15. It will be an
introductory course, gearing at the beginner level.

The link with the course information and application instructions is here:

https://www.bnl.gov/xafs2021/

Please share this information with your group members and anyone else who
may be interested.

Thank you very much,

Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/staff/frenkel
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
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Re: [Ifeffit] EXAFS fitting sum of all paths in R space

[Anatoly Frenkel]

...Basically, you need to sum different paths in k-space, save as chi(k),
then import to Athena, perform FT in the same range as your data, and then
the result should be the same as obtained in Artemis for the fit vs data.
That will preserve the phase relationships between different paths, while
your procedure does not have that information because you save magnitudes
of the paths.

Anatoly



On Wed, Sep 23, 2020 at 8:58 AM Ashwini Kumar Poswal <
poswalashw...@gmail.com> wrote:

> Dear All,
> I have one problem regarding the sum of all paths (R-space) after fitting.
> If we include many paths for the fitting, the fitting shows a good fit but
> after fitting, I select all paths and export (using Artemis [Data] window:
> save data + marked paths as |χ(R)|. I plotted all paths in origin as well
> as the sum of all paths. But when I add up all the contributions from all
> the paths, the deviation at larger paths is extraordinarily high and not
> equal to final fit. I am attaching a figure for illustration. It is clearly
> seen that the final fit is lesser compared to one of the path and the sum
> of all paths is quite high compared to fit (as shown in second figure. Can
> anybody suggest, how to sum different paths?
> [image: image.png]
> [image: image.png]
>
> Regards
> *Ashwini Kumar Poswal*
> *Mumbai*
> *Tel.-+91 (022) 25595081*
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Re: [Ifeffit] EXAFS fitting sum of all paths in R space

[Anatoly Frenkel]

It is a nice demonstration that |χ(R)| is not equal to |χ1(R)|+ |χ2(R)| +
...  |χn(R)|.
It is equal to: |χ1(R) +  χ2(R) + ... χn(R) |. The latter is most often
smaller than the former, according to the Cauchy-Schwarz inequality.
Anatoly



On Wed, Sep 23, 2020 at 8:58 AM Ashwini Kumar Poswal <
poswalashw...@gmail.com> wrote:

> Dear All,
> I have one problem regarding the sum of all paths (R-space) after fitting.
> If we include many paths for the fitting, the fitting shows a good fit but
> after fitting, I select all paths and export (using Artemis [Data] window:
> save data + marked paths as |χ(R)|. I plotted all paths in origin as well
> as the sum of all paths. But when I add up all the contributions from all
> the paths, the deviation at larger paths is extraordinarily high and not
> equal to final fit. I am attaching a figure for illustration. It is clearly
> seen that the final fit is lesser compared to one of the path and the sum
> of all paths is quite high compared to fit (as shown in second figure. Can
> anybody suggest, how to sum different paths?
> [image: image.png]
> [image: image.png]
>
> Regards
> *Ashwini Kumar Poswal*
> *Mumbai*
> *Tel.-+91 (022) 25595081*
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[Ifeffit] Postdoctoral fellowship in AI - related field

[Anatoly Frenkel]

Please pass this info to anyone interested in this opportunity,
particularly, those students who are about to obtain their PhD and looking
for postdoctoral fellowships. This one may be suitable for those who plan
to use data science approaches for interpreting XANES and EXAFS data and
apply them to interdisciplinary research projects.

https://www.stonybrook.edu/commcms/iacs/opportunities/fellowships/Postdoctoral-Fellowships

You are welcome to contact me if you are interested.
Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
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[Ifeffit] XAFS short course at BNL: Nov. 18-20, 2020

[Anatoly Frenkel]

Dear mailing list subscribers:

Please pass this information along to your group members or others who may
be interested in this.

As it has done every year since 2005, on* Nov. 18-20, 2020*, Synchrotron
Catalysis Consortium (SCC) will run an annual short course on X-ray
absorption fine structure techniques and applications.

*Date of Event:*  November 18-20, 2020
*Official Name of Event: * Short course on X-ray Absorption Fine Structure:
Application to Nanomaterials
*Description:  * Every year Synchrotron Catalysis Consortium, in
partnership with NSLS-II, organizes and runs a 3-day short course to those
interested in learning about the use of x-ray absorption spectroscopy
methods. This year, the course will be offered online from November 18–20,
2020. The course will be useful for those scientists' who already possess
basic experience with XANES and EXAFS methods, including experiment and
data analysis, and are interested in advanced analysis and modeling methods
applicable for nanomaterials research. The course will be run in a flip
classroom mode. Participants will study video-presentations of leading
experts in XAFS methods and applications in advance of the workshop. The
video-lectures will be assembled to follow the workshop agenda. During the
workshop, the instructors will divide participants in breakout sections for
in-depth problem solving, data analysis and modeling, to best match
participants and their research interests. There will be Q sessions on
the subject of the lectures, and in depth practicums of the EXAFS and XANES
analysis software programs.

The course will be open to 80 participants, selected based on their
application materials.

Further info about the course, including the application materials and the
deadlines, is available here:

https://www.bnl.gov/xafs2020/

Note the application deadline: September 27, 2020.

For past XAFS workshops, and information about the SCC-supported beamlines
and capabilities, please visit the SCC web sites:

https://you.stonybrook.edu/scc2/xafs-workshops/

For any questions, please contact me.

Best regards,
Anatoly

---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu


http://you.stonybrook.edu/frenkel


Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
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[Ifeffit] Cool math expression

[Anatoly Frenkel]

I thought I share a really good idea I found in someone's fit project that
was shared with me.
Instead of varying deltaR and then doing something like: "after R_final =
2.79 + deltaR" to have Artemis calculate the actual bond length (and then
looking for its uncertainty in the list of guess parameters in the log file
for the corresponding deltaR variable's uncertainty), it can be written in
the Artemis data window as:
[image: image.png]
where A_Cr is the bond length, and its uncertainty will be written in the
same place with the best fit value in the guess parameters list.

Probably I am the only one not using this trick, but I still thought it
would be good to share.
Anatoly
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Re: [Ifeffit] errors in bond lengths

[Anatoly Frenkel]

Matthew,

In the paper by Purans et al that George references, they showed that the
FEFF fitting method and ratio method agreed, and in the ratio method the
amplitudes and phases are extracted from experimental standards, just as in
your paper.

Anatoly




On Sat, Apr 11, 2020 at 2:21 PM Matthew Marcus  wrote:

> The uncertainties reported by Artemis include as 'noise' the systematic
> deviation of FEFF calculation from the real thing.  Even if FEFF were
> perfect, those FEFF calcs haven't been through the mutilations inflicted
> by data reduction, such as spline fitting.  What I've done when looking
> at closely-related systems such as the same thing at differing
> temperatures is shell-by-shell fitting with one of them as reference.
> For an example of this kind of thing, see:
>
> Aruguete, D. M., Marcus, M. A., Li, L.S., Williamson, A., Fakra, S.,
> Gygy, F., Galli, G, A, Alivisatos, A. P. (2007)  "Surface structure of
> CdSe nanorods revealed by combined X-ray absorption fine structure
> measurements and ab Initio calculations", J. Phys. Chem. C 111(1),75-79
> and supporting information
>
> The SI has details about how the fits were done.  In this case, the
> different spectra didn't refer to differing temperatures but rather
> different polarization directions.
> mam
>
> On 4/11/2020 10:40 AM, George Sterbinsky wrote:
> > Hello,
> >
> > As is well known, EXAFS is more accurate at determining relative changes
> > in bond lengths than absolute changes in bond lengths due to cancelation
> > of systematic errors in relative comparisons. When comparing the
> > relative changes in bond lengths determined from EXAFS fits, as one
> > might for a temperature series for example, is it appropriate to use the
> > uncertainties returned by Artemis?
> >
> > My question arises in part from Phys Rev Lett vol. 100 pg. 055901
> > (2008), where the authors state that errors for changes in bond length
> > in a temperature series were determined by empirical means rather than
> > statistical means. This then raises the question as to if the authors
> > believe that statistical means would overestimate the error. My
> > inclination is to think that the uncertainties reported by Artemis would
> > be appropriate because of the scaling by the square root of reduced chi
> > squared. However, I want to see what others think about this before
> > committing to it.
> >
> > Thank you,
> > George
> >
> >
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[Ifeffit] Chris Chantler, Re: XAFS conference proceedings

[Anatoly Frenkel]

Dear Chris (if you are reading this),

Do you know when the Rad. Phys. Chem. issue with the latest XAFS conference
proceedings will be finalized and published online? It currently shows
"corrected proofs" but not the articles with pages.

Perhaps, it is a bad time to follow up and I am sorry for bothering you.
Hope everyone is safe and well.

Best regards,
Anatoly
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Re: [Ifeffit] XAFS.ORG WEBSITE??

[Anatoly Frenkel]

And where is its treasurer? :)

Anatoly

> On Jan 29, 2020, at 7:59 PM, Bare, Simon R  wrote:
> 
> 
> Talking of websites does anyone know what happened to the International XAFS 
> website? I can’t access it. And what is going on with this organization?
> Thanks.
>  
> Simon
>  
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[Ifeffit] Postdoctoral position

[Anatoly Frenkel]

 Our group has an opening for a postdoctoral position in heterogeneous
catalysis. Expert knowledge of X-ray absorption spectroscopy and in
situ/operando characterization of catalysts are required. The postdoc will
be stationed at Brookhaven National Laboratory. For inquires, please email
me at my Stony Brook University address, with a subject line: Postdoc in
heterogeneous catalysis.

Thank you,
Anatoly Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu
<https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0ybKTBGBlALcrWeszTCA..=mailto%3ajgchen%40columbia.edu>
http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
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Re: [Ifeffit] Two analysts, one spectrum, similar outcome?

[Anatoly Frenkel]

Are they equally smart?

Anatoly

> On Aug 13, 2019, at 9:39 PM, Mike Massey  wrote:
> 
> Hi Everyone,
> 
> 
> I'm curious, has anyone ever tried turning two analysts loose on the same 
> unknown EXAFS spectrum to see if their fits come out with similar 
> conclusions? If you have tried it, how did it work out? Were the conclusions 
> indeed similar? If not, why not, and what did you end up doing about it?
> 
> I was talking with a colleague today about our plans for data analysis, and 
> we settled on this approach (since there are two interested parties willing 
> to try to fit a series of unknown EXAFS datasets).
> 
> The hope is, of course, that the two analysts will independently reach 
> similar conclusions with similar fits and structural models, but to my mind 
> that outcome is by no means guaranteed. Given the (presumably) wide variation 
> in fitting customs and procedures, I can envision a scenario in which there 
> are major differences.
> 
> This got me wondering, "Has anyone tried this?" So I thought I'd ask.
> 
> 
> Your thoughts and experiences would be welcome. Thanks!
> 
> 
> 
> Mike Massey
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[Ifeffit] XAFS short course in BNL Nov. 13-15

[Anatoly Frenkel]

Dear subscribers:

The info about the XAFS2019 short course at BNL is here:
https://www.bnl.gov/xafs2019/

The application page is open.
Best,

Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
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[Ifeffit] Postdoctoral position is available

[Anatoly Frenkel]

 Dear mailing list subscribers,

There is an opening for a postdoctoral research associate position,
described briefly below (for more details please contact me).

A postdoc will investigate novel electromechanical materials using NSLS-II
beamline facilities at Brookhaven National Laboratory, with primary
technique being X-ray absorption fine structure. This position will be in
Stony Brook University (located in close proximity to Brookhaven), under
the supervision of Prof. Anatoly Frenkel. Responsibilities will include
setting up new in situ operations for testing novel materials under applied
electric field, developing and applying fast timing methods (such as
modulation excitation spectroscopy), and collaborating with other
participants of the NSF-BSF funded US-Israel collaboration. Annual trips to
Israel for collaborative research will be required. Ph.D. in Physics,
Chemistry or Materials Science, and strong knowledge of XAFS experiment,
data analysis and modeling, documented in publications, are required.

Three names of professional references are required with the applications
that should include a cover letter describing relevant prior experience and
interest in the position, and a CV with a list of publications. These
materials should be emailed to anatoly.fren...@stonybrook.edu  with a
subject line: XAFS postdoc position.
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu
<https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0ybKTBGBlALcrWeszTCA..=mailto%3ajgchen%40columbia.edu>
http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
---
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[Ifeffit] Two postdoctoral openings at SBU and BNL

[Anatoly Frenkel]

Dear mailing list subscribers,

There are two openings for postdoctoral research associate positions,
described briefly below (for more details please contact me).

Position 1:
A postdoc will investigate novel electromechanical materials using NSLS-II
beamline facilities at Brookhaven National Laboratory, with primary
technique being X-ray absorption fine structure. This position will be in
Stony Brook University (located in close proximity to Brookhaven), under
the supervision of Prof. Anatoly Frenkel. Responsibilities will include
setting up new in situ operations for testing novel materials under applied
electric field, developing and applying fast timing methods (such as
modulation excitation spectroscopy), and collaborating with other
participants of the NSF-BSF funded US-Israel collaboration. Annual trips to
Israel for collaborative research will be required. Ph.D. in Physics,
Chemistry or Materials Science, and expert knowledge of XAFS experiment,
data analysis and modeling, documented in publications, are required.

Position 2:
Catalysis Center for Chemical Innovations (CCEI), an Energy Frontier
Research Center (EFRC) at the University of Delaware, is hiring a
postdoctoral research associate to work with multiple teams of catalysis
researchers of CCEI on XAFS projects. The postdoc will lead collaborative
efforts by helping develop synchrotron-based projects, plan experiments,
lead the visiting researchers in data collection, and work with CCEI groups
on subsequent publications. This position will be supervised jointly by
Profs. Anatoly Frenkel (Stony Brook U.) and Jingguang Chen (Columbia U.).
The postdoc will be stationed at Brookhaven National Laboratory and travel
several times a year to U. Delaware for collaborative meetings. The
background is recent Ph.D. in Chemistry or Materials Science. Strong
background in catalysis and XAFS measurements, data analysis and modeling
are expected.

Three names of professional references are required with the applications
that should include a cover letter describing prior experience and interest
in the position, and a CV with a list of publications. These materials
should be emailed to anatoly.fren...@stonybrook.edu  with a subject line:
XAFS postdoc position.
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu
<https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0ybKTBGBlALcrWeszTCA..=mailto%3ajgchen%40columbia.edu>
http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
---
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Re: [Ifeffit] Standard deviation of R value

[Anatoly Frenkel]

As an additional comment, it is a murky issue whether the reported thing
together with R is the standard deviation. It is not easy to find it in the
literature but there are some papers dating back to the 1990s that state
that the uncertainties reported in the EXAFS fitting results correspond to
the 95% confidence level which means 2 standard deviations for an
approximately normal data set. I don't think it is correct. Regardless
whether the distribution of some or all fitting variables are treated by
the Levenburg-Marquartd method as normal or not, the reported error is
really not a standard deviation but a square root of the element in a
covariance matrix. What is the relationship of that and the standard
deviation of the fitting variable is one of the few remaining unsolved
mysteries in EXAFS analysis.

Anatoly


On Fri, Jan 11, 2019 at 11:05 AM Matt Newville 
wrote:

> Hi Erin,
>
> On Fri, Jan 11, 2019 at 8:19 AM Erin Finley  wrote:
>
>> Hello, I see in many publications the R value reported with a standard
>> deviation. However, when I look at my resulting data from a fit I don't see
>> one listed. I am still new to EXAFS research and so I am wondering where I
>> can get this information. I am assuming I need to calculate it from another
>> parameter I am just not sure which one.
>>
>>
> The uncertainties in R are typically in the fit report.  But also, we
> typically refine a "delR" parameter that is R - Reff, where Reff is the
> distance (half path-lengh) for the scattering path.  So, if you don't see
> an uncertainty reported for R but do see an uncertainty for delR (or
> whatever parameter name you used), use that.  The uncertainty in R will
> (normally) be the uncertainty in delR.
>
> If I'm misunderstanding the question, pleas give more details about what
> you are doing.
>
> --Matt
>
>
>
>
>
>
> Thanks for your help!
>> Cheers,
>>
>> --
>> Erin Finley
>> PhD Candidate
>> Brgoch Research Group
>> Department of Chemistry
>> University of Houston
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>
>
> --
> --Matt Newville  630-252-0431
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Re: [Ifeffit] TiO2 XAS spectrum

[Anatoly Frenkel]

Enyuan,

Here are the rutile and anatase spectra with the corresponding Ti foil
spectrum.
I will send you the name of a student who collected the spectra for
acknowledgement when you need it.

Anatoly Frenkel


On Fri, Nov 23, 2018 at 10:08 PM Enyuan Hu  wrote:

> Hi all,
>
> Can anyone share an XAS spectrum of TiO2? it would be best if a Ti foil
> spectrum is also included for calibration. Your help is much appreciated!
>
> Enyuan
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Ti compounds.prj
Description: Binary data
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Re: [Ifeffit] data on CdS

[Anatoly Frenkel]

Thank you so much, Robert and Bruce!

Anatoly

> On Nov 17, 2018, at 12:12 PM, Robert Gordon  wrote:
> 
> CdS Mu(E) measured in FLY on 20BM in 2013...no simultaneous reference for 
> energy calibration through...sorry...
> 
>> On Sat, Nov 17, 2018 at 8:58 AM Anatoly Frenkel 
>>  wrote:
>> Dear all - if someone could share raw Cd K-edge data of CdS, it would be 
>> really helpful!
>> Thank you,
>> 
>> Anatoly Frenkel
>> 
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[Ifeffit] data on CdS

[Anatoly Frenkel]

Dear all - if someone could share raw Cd K-edge data of CdS, it would be
really helpful!
Thank you,

Anatoly Frenkel
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Re: [Ifeffit] Ifeffit Digest, Vol 189, Issue 2

[Anatoly Frenkel]

If the sample is not homogeneous, it doesn’t matter if you use EXAFS or XANES 
spectra, they originate from the same atoms. 

Anatoly

> On Nov 2, 2018, at 2:39 AM, Raj kumar  wrote:
> 
> Dear Anatoly and Marcus,
> 
> Thanks for your answers. So in this case, i understood, I shouldn't use the 
> extended XAFS region for the analysis. In the other hand, is it allowed to 
> cut the region till 9150 eV and use the data for the XANES analysis?
> 
> Regards,
> Raj
> 
> 
>> On Thu, Nov 1, 2018 at 11:37 PM  
>> wrote:
>> Send Ifeffit mailing list submissions to
>> ifeffit@millenia.cars.aps.anl.gov
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>> To subscribe or unsubscribe via the World Wide Web, visit
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>> or, via email, send a message with subject or body 'help' to
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>> 
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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: Bump/oscillating pattern at high energies of EXAFS
>>   (Anatoly Frenkel)
>>2. Re: Bump/oscillating pattern at high energies of EXAFS
>>   (Matthew Marcus)
>>3. EXAFS of wine (Anatoly Frenkel)
>> 
>> 
>> --
>> 
>> Message: 1
>> Date: Thu, 1 Nov 2018 17:47:56 -0400
>> From: Anatoly Frenkel 
>> To: XAFS Analysis using Ifeffit 
>> Subject: Re: [Ifeffit] Bump/oscillating pattern at high energies of
>> EXAFS
>> Message-ID:
>> 
>> Content-Type: text/plain; charset="utf-8"
>> 
>> It is an effect of inhomogeneity of the sample, that is, the variation in
>> the metal density throughout the X-ray beam footprint.
>> Anatoly
>> 
>> 
>> 
>> On Thu, Nov 1, 2018 at 5:34 PM Raj kumar  wrote:
>> 
>> > Dear All,
>> >
>> > I have monitored the growth process of YbVO4 nanoparticles using EXAFS.
>> > Here, nanoparticles were synthesized in water medium. Both initial and
>> > final products (EXAFS) of the synthesis were measured using the continuous
>> > flow approach whereas the intermediate products were recorded, in the glass
>> > capillary, using the stopped flow. In the attached figure, you can find the
>> > same (all products). At high energies of EXAFS, both initial and final
>> > measurements show smooth behavior whereas the oscillating pattern/bump was
>> > observed for the intermediate states.
>> >
>> > Here, my question is: Is the oscillating pattern appearing in the
>> > intermediate states due to the sedimentation/in-homogeneity of the product
>> > in the capillary or it is the characteristic of the synthesis?
>> >
>> > With regards,
>> > Raj
>> > ___
>> > Ifeffit mailing list
>> > Ifeffit@millenia.cars.aps.anl.gov
>> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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>> -- next part --
>> An HTML attachment was scrubbed...
>> URL: 
>> <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20181101/431f9b86/attachment-0001.html>
>> 
>> --
>> 
>> Message: 2
>> Date: Thu, 1 Nov 2018 14:55:12 -0700
>> From: Matthew Marcus 
>> To: ifeffit@millenia.cars.aps.anl.gov
>> Subject: Re: [Ifeffit] Bump/oscillating pattern at high energies of
>> EXAFS
>> Message-ID: 
>> Content-Type: text/plain; charset=utf-8; format=flowed
>> 
>> Agreed.  The low frequency and high amplitude at the end is implausible as 
>> EXAFS.
>> 
>> Sincerely,
>> Matthew Marcus
>> > It is an effect of inhomogeneity of the sample, that is, the variation in 
>> > the metal density throughout the X-ray beam footprint.
>> > Anatoly
>> > 
>> > 
>> > 
>> > On Thu, Nov 1, 2018 at 5:34 PM Raj kumar > > <mailto:rajr...@gmail.com>> wrote:
>> > 
>> > Dear All,
>> > 
>> > I have monitored the growth process of YbVO4 nanoparticles using 
>> > EXAFS. Here, nanoparticles were synthesized in water medium. Both initial 
>> > and final products (EXAFS) of the synthesis 

Re: [Ifeffit] EXAFS of wine

[Anatoly Frenkel]

John,

Since when theorists started to need real samples? I thought a simulation is 
equally enjoyable. 

Anatoly

> On Nov 2, 2018, at 12:17 AM, John J Rehr  wrote:
> 
> Hi everyone
> 
> The spectrum is pretty noisy with all the super Tuscano  grapes ( Alicante, 
> Merlot etc) in the mix to give it’s complex berry character and  the 2016 is 
> supposedly better.
> How about we take some samples to the lab ...  ?
> 
>  John   
>  
> 
>> On Thu, Nov 1, 2018 at 16:07 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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Re: [Ifeffit] EXAFS of wine

[Anatoly Frenkel]

Unexpectedly enthusiastic responses on the wine post... seriously, though, it 
reminded me on the times when I was an editorial board member of Journal of 
Spectroscopy. In a sincere attempt to help the journal raise its impact factor 
I rejected every proposal for an invited issue, except for one.  It was 
“Spectroscopy of wine”, of course. 

Anatoly

> On Nov 1, 2018, at 8:30 PM, Christopher Patridge  wrote:
> 
> Should probably collect the data in triplicate….  
> 
> Chris
> 
> **
> Dr Christopher Patridge
> Assistant Professor
> Department of Chemistry
> SASE 315
> D’Youville College
> 320 Porter Ave.
> Buffalo, NY 14201
> 716-829-8096 / 315-529-0501
> patri...@dyc.edu
> 
> 
> 
>> On Nov 1, 2018, at 7:34 PM, Simon James  wrote:
>> 
>> Thanks for sharing. Looks like pretty usable data.
>> 
>> -Saj
>> 
>> 
>> 
>> Simon James PhD
>> Senior Research Officer
>> NHMRC-ARC Dementia Research Development Fellow 
>> 
>> Molecular Gerontology Laboratory
>> 
>> Melbourne Dementia Research Centre
>> University of Melbourne
>> The Florey Institute of Neuroscience and Mental Health
>> 
>> Kenneth Myer Building
>> 30 Royal Parade
>> PARKVILLE VIC 3052, Australia
>> 
>> Office: +61 (3) 9035 6420
>> Mob: +61 (4) 3811 0982
>> Web: www.florey.edu.au
>> simon.ja...@florey.edu.au
>> 
>>> On 2 Nov 2018, at 10:11 am, Leandro Acu  wrote:
>>> 
>>> I want one! Nothing better for a long synchrotron night!
>>> 
>>> Enviado desde Yahoo Mail para Android
>>> 
>>> El jue., 1 de nov. de 2018 a la(s) 19:37, Anatoly Frenkel
>>>  escribió:
>>> 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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Re: [Ifeffit] Bump/oscillating pattern at high energies of EXAFS

[Anatoly Frenkel]

It is an effect of inhomogeneity of the sample, that is, the variation in
the metal density throughout the X-ray beam footprint.
Anatoly



On Thu, Nov 1, 2018 at 5:34 PM Raj kumar  wrote:

> Dear All,
>
> I have monitored the growth process of YbVO4 nanoparticles using EXAFS.
> Here, nanoparticles were synthesized in water medium. Both initial and
> final products (EXAFS) of the synthesis were measured using the continuous
> flow approach whereas the intermediate products were recorded, in the glass
> capillary, using the stopped flow. In the attached figure, you can find the
> same (all products). At high energies of EXAFS, both initial and final
> measurements show smooth behavior whereas the oscillating pattern/bump was
> observed for the intermediate states.
>
> Here, my question is: Is the oscillating pattern appearing in the
> intermediate states due to the sedimentation/in-homogeneity of the product
> in the capillary or it is the characteristic of the synthesis?
>
> With regards,
> Raj
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[Ifeffit] Better late than never

[Anatoly Frenkel]

After 15 years or so of using Athena, I just accidentally learned that the
vertical scale of the plot can be changed by simply turning the scroll
wheel of the mouse!

Anatoly
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Re: [Ifeffit] Making N (coordination number) a variable.

[Anatoly Frenkel]

Make it 1 in the N window and make amp*N expression in the S02 window
instead. Then use N as a coordination number (fix or vary it).
Anatoly

---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
---

On Wed, Aug 1, 2018 at 11:07 AM, M Solo  wrote:

> Hello
> Is there a way in artemis to make N, coordination number, a variable to be
> used in GDS window? I do realize that N and ss are closely linked and do
> very similar things in the fit, but it seems i may need fractional
> (average) coordination number for one of the paths, and am fine fixing ss
> to see where N levels off.
>
> Thank you very much.
>
> Alex Solov
>
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[Ifeffit] Postdoc position

[Anatoly Frenkel]

Please pass this info along to those who may be interested in this
opportunity:

There is an opening for a postdoctoral research associate in my group. The
postdoc will be stationed in Brookhaven National Laboratory and work as a
member of a multi-institution team to develop and apply new methods of
operando characterization of catalysts. Expert knowledge of XAFS, strong
publication record and strong background in condensed matter physics are
required. For inquiries please contact me.

Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
---
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Re: [Ifeffit] Interpreting old XANES data with missing standards

[Anatoly Frenkel]

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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Re: [Ifeffit] 4+2 model for distortion

[Anatoly Frenkel]

Cute animation. I will now think of dynamic Jan Teller distortion every
time I see a flying pigeon.
Anatoly



On Wed, May 9, 2018 at 10:41 AM, Abdul Ahad 
wrote:

> hi all
> How to include this model in atom that is 4+2 or 2+4 for 2short or 4 long
> bond length of octahedra
> thanks
>
>
> *A. Ahad*
> **
> *Abdul Ahad*
> Junior Research Fellow
> *Dept of Physics*
> *Aligarh Muslim University*
> *Aligarh 202002 (U.P.), India*
>
> *http://www.researcherid.com/rid/G-8198-2018
> *
> *Email: a_ahad...@amu.ac.in , a...@mailaps.org
>  *
>
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Re: [Ifeffit] FeSe2 Se K-edge XANES request

[Anatoly Frenkel]

Will the data from the compositions shown in this paper be useful?

https://cpb-us-east-1-juc1ugur1qwqqqo4.stackpathdns.com/you.stonybrook.edu/dist/b/1881/files/2016/10/BaFeSe-EXAFS-y9zet9.pdf

Anatoly

Hi Folks,
>
> Does anyone have a near-edge spectrum of FeSe2, Se K-edge, they could
> share?
> (Ideally with Se elemental reference measured simultaneous.)
>
> Thanks,
> -R.
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Re: [Ifeffit] XAFS short course in BNL: Nov 1-3, 2017

[Anatoly Frenkel]

Dear all:

Resending the previous message: we are still accepting applications through Sep 
8. 

Regards,

Anatoly 

> On Jul 28, 2017, at 3:43 PM, Anatoly Frenkel <anatoly.fren...@stonybrook.edu> 
> wrote:
> 
> Dear subscribers:
> 
> Please share with your group members or others, who may be interested, the 
> following information about the short course on XAFS spectroscopy: 
> 
> Title: Data Analysis and Modeling of XANES and EXAFS Spectra. Applications to 
> Nanomaterials
> Dates: November 1-3, 2017
> Location: Brookhaven National Laboratory
> 
> The course is open for applications at this web site: 
> https://www.bnl.gov/exafs2017/
> 
> The course will be useful for those scientists who are familiar with the 
> foundations of XAFS experiment, theory and data analysis, and seek training 
> in advanced methods. The course will include lectures, software 
> demonstrations, and data analysis sessions. The emphasis will be on 
> applications of XAFS to nanomaterials but we will welcome all participants 
> who are interested in modern analysis methods. The course instructors will 
> use examples from their research during presentations. The topics covered 
> will include:
> 
> -Theory of XANES, 
> -XANES data analysis, 
> -Structural refinement using XANES, with emphasis on the following methods:
> -Molecular dynamics, 
> -Reverse Monte Carlo. 
> -Machine Learning methods
> 
> During the data analysis practicum on November 3, participants will get an 
> opportunity to work with research projects with the help of the course 
> instructors.
> 
> The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC).
> 
> Best regards,
> 
> Anatoly
> ---
> Anatoly I. Frenkel 
> Professor
> Department of Materials Science and Chemical Engineering
> Stony Brook University 
> Stony Brook, NY 11794, Ph: 631-632-2751 
> Email:  anatoly.fren...@stonybrook.edu
> http://you.stonybrook.edu/frenkel
> 
> Joint Appointment:
> Chemistry Department, Brookhaven National Laboratory
> Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
> Email: fren...@bnl.gov
> https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp 
> Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
> http://you.stonybrook.edu/scc2
> ---
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Re: [Ifeffit] XAFS short course in BNL: Nov 1-3, 2017

[Anatoly Frenkel]

Dear Rohit,

It should work now. Can you please check and let me know by email if there is 
still a problem?

Thank you,

Anatoly

Sent from my iPhone

> On Aug 1, 2017, at 6:18 AM, Rohit Satish <rs.2...@gmail.com> wrote:
> 
> Dear Anatoly 
> I would be very much interested in applying for the school linked above. But 
> it seems that the form has no field for entering my email id could you let me 
> know where I can provide my contact details. 
> 
> Regards
> Dr Rohit Satish 
> Research Fellow 
> School of Materials Science and Engineering 
> Nanyang Technological University
> 
>> On Sat, Jul 29, 2017 at 3:43 AM, Anatoly Frenkel 
>> <anatoly.fren...@stonybrook.edu> wrote:
>> Dear subscribers:
>> 
>> Please share with your group members or others, who may be interested, the 
>> following information about the short course on XAFS spectroscopy: 
>> 
>> Title: Data Analysis and Modeling of XANES and EXAFS Spectra. Applications 
>> to Nanomaterials
>> Dates: November 1-3, 2017
>> Location: Brookhaven National Laboratory
>> 
>> The course is open for applications at this web site: 
>> https://www.bnl.gov/exafs2017/
>> 
>> The course will be useful for those scientists who are familiar with the 
>> foundations of XAFS experiment, theory and data analysis, and seek training 
>> in advanced methods. The course will include lectures, software 
>> demonstrations, and data analysis sessions. The emphasis will be on 
>> applications of XAFS to nanomaterials but we will welcome all participants 
>> who are interested in modern analysis methods. The course instructors will 
>> use examples from their research during presentations. The topics covered 
>> will include:
>> 
>> -Theory of XANES, 
>> -XANES data analysis, 
>> -Structural refinement using XANES, with emphasis on the following methods:
>> -Molecular dynamics, 
>> -Reverse Monte Carlo. 
>> -Machine Learning methods
>> 
>> During the data analysis practicum on November 3, participants will get an 
>> opportunity to work with research projects with the help of the course 
>> instructors.
>> 
>> The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC).
>> 
>> Best regards,
>> 
>> Anatoly
>> ---
>> Anatoly I. Frenkel 
>> Professor
>> Department of Materials Science and Chemical Engineering
>> Stony Brook University 
>> Stony Brook, NY 11794, Ph: 631-632-2751 
>> Email:  anatoly.fren...@stonybrook.edu
>> http://you.stonybrook.edu/frenkel
>> 
>> Joint Appointment:
>> Chemistry Department, Brookhaven National Laboratory
>> Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
>> Email: fren...@bnl.gov
>> https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp 
>> Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
>> http://you.stonybrook.edu/scc2
>> ---
>> 
>> ___
>> Ifeffit mailing list
>> Ifeffit@millenia.cars.aps.anl.gov
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>> 
> 
> 
> 
> -- 
> Rohit Satish
> Research Student 
> School of Material Science and Engineering
> Nanyang Technological University
> Singapore 
> 
> Phone Number :+65-94764056
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Re: [Ifeffit] XAFS short course in BNL: Nov 1-3, 2017

[Anatoly Frenkel]

Dear Matthew and all,

The link can be copied directly to the browser URL field and it will work:

https://www.bnl.gov/exafs2017/

If NEXAFS spectra in some materials can be theoretically modeled as reliably as 
some XANES spectra in some materials then most methods that we will present 
should work with soft x-rays, but we haven't tried.  

Anatoly

Sent from my iPhone

> On Jul 28, 2017, at 4:57 PM, Matthew Marcus  wrote:
> 
> Dear Anatoly.  Regarding yours of Fri, 28 Jul 2017 15:43:01 -0400:
> 
> The website doesn't work for non-BNL people.  It pops up a login/password 
> window for the BNL domain.  I'm assuming that you want people from elsewhere 
> to be able to take the course.
> 
> I don't know yet whether I'll be able to go.  It does sound interesting.  My 
> knowledge of XAS analysis has remained pretty static.  Will there be anything 
> that applies
> to soft X-rays?  I'm moving to STXM, so will be dealing with soft X-rays.
> 
> 
> 
> 
> Sincerely,
>   Matthew Marcus
>> Dear subscribers:
>> Please share with your group members or others, who may be interested, the 
>> following information about the short course on XAFS spectroscopy:
>> Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications 
>> to Nanomaterials*
>> Dates: *November 1-3, 2017*
>> Location: *Brookhaven National Laboratory**
>> **
>> *The course is open for applications at this web 
>> site:https://www.bnl.gov/exafs2017/ 
>> 
>> The course will be useful for those scientists who are familiar with the 
>> foundations of XAFS experiment, theory and data analysis, and seek training 
>> in advanced methods. The course will include lectures, software 
>> demonstrations, and data analysis sessions. The emphasis will be on 
>> applications of XAFS to nanomaterials but we will welcome all participants 
>> who are interested in modern analysis methods. The course instructors will 
>> use examples from their research during presentations. The topics covered 
>> will include:
>> -Theory of XANES,
>> -XANES data analysis,
>> -Structural refinement using XANES, with emphasis on the following methods:
>> -Molecular dynamics,
>> -Reverse Monte Carlo.
>> -Machine Learning methods*
>> *
>> During the data analysis practicum on November 3, participants will get an 
>> opportunity to work with research projects with the help of the course 
>> instructors.
>> The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC).
>> Best regards,
>> Anatoly*
>> *
>> ---
>> Anatoly I. Frenkel
>> Professor
>> Department of Materials Science and Chemical Engineering
>> Stony Brook University
>> Stony Brook, NY 11794, Ph: 631-632-2751
>> Email: anatoly.fren...@stonybrook.edu 
>> 
>> http://you.stonybrook.edu/frenkel
>> Joint Appointment:
>> Chemistry Department, Brookhaven National Laboratory
>> Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
>> Email: fren...@bnl.gov 
>> https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
>> Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
>> http://you.stonybrook.edu/scc2
>> ---
>> ___
>> Ifeffit mailing list
>> Ifeffit@millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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[Ifeffit] XAFS short course in BNL: Nov 1-3, 2017

[Anatoly Frenkel]

Dear subscribers:

Please share with your group members or others, who may be interested, the
following information about the short course on XAFS spectroscopy:

Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications
to Nanomaterials*
Dates: *November 1-3, 2017*
Location: *Brookhaven National Laboratory*

The course is open for applications at this web site:
https://www.bnl.gov/exafs2017/


The course will be useful for those scientists who are familiar with the
foundations of XAFS experiment, theory and data analysis, and seek training
in advanced methods. The course will include lectures, software
demonstrations, and data analysis sessions. The emphasis will be on
applications of XAFS to nanomaterials but we will welcome all participants
who are interested in modern analysis methods. The course instructors will
use examples from their research during presentations. The topics covered
will include:

-Theory of XANES,
-XANES data analysis,
-Structural refinement using XANES, with emphasis on the following methods:
-Molecular dynamics,
-Reverse Monte Carlo.
-Machine Learning methods

During the data analysis practicum on November 3, participants will get an
opportunity to work with research projects with the help of the course
instructors.

The course is co-sponsored by BNL and Synchrotron Catalysis Consortium
(SCC).

Best regards,

Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
---
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Re: [Ifeffit] Nearest neighbor statistics in a random alloy

[Anatoly Frenkel]

... and if the random alloy is a nanoparticle, the equations are modified
(they will be the same as in Qingying's email in the bulk alloy limit and
if the NPs are sufficiently large).
See here, Eq. (11), for more details:

Chem. Soc. Reviews *41*, 8163-8178 (2012)


Anatoly
---

On Fri, Jun 23, 2017 at 9:28 AM, Qingying Jia  wrote:

> Hi Felix,
>
>
> Your assumptions are not correct because the model you use is not a
> representative unit cluster model. Basically the following three equations
> are always correct for foil:
>
>  NPt-Pt+NPt-Co=12
>
> NCo-Co+NCo-Pt=12
>
> NCo-Pt/NPt-Co=9
>
> And the specific values for the coordination number can be determined if
> you know the orderness of the structure. As for the random distribution of
> Pt and Co in foil,
>
> NPt-Pt/NPt-Co=9
>
> or equivalently,
>
> NCo-Pt/NCo-Co=9,
>
> Then you can get
>
> NPt-Pt=10.8, and NPt-Co=1.2
>
> The results will be different if the structure is ordered.
>
>
>   Regards,
>
> On Fri, Jun 23, 2017 at 9:02 AM, Felix E. Feiten  > wrote:
>
>> Dear all,
>>
>> I am fitting a Pt9Co1 foil sample.
>> I assume the sample to be basically fcc platinum with every 10th atom
>> randomly replaced by cobalt.
>>
>> Here are the assumptions I make:
>>
>> 1. every atom has 12 nearest neighbors
>>
>> 2. every Pt atom has (on average) 10.7 Pt nearest neighbors and 1.3 Co
>> nearest neighbors
>>
>> 3. every Co atom has (on average) 11.7 Pt nearest neighbors and 0.3 Co
>> nearest neighbors
>>
>> I have been told that assumptions 2 and 3 are not precise. Here is what
>> I'm confused about:
>>
>> In order to determine the number of Pt or Co nearest neighbors I looked
>> at an ensemble of 13 atoms:
>> 1 absorber and 12 scatterers/nearest neighbors.
>> I assume that the Pt/Co ratio in this ensemble is 9/1 and therefor,
>> statistically, 1.3 out of those 13 atoms should be Co. That means that if
>> Co is the central atom only 0.3 Co atoms are remaining for the 12 nearest
>> neighbors. On the other hand, if Pt is the central atom, (all) 1.3 Co atoms
>> are remaining for the 12 nearest neighbors.
>>
>> I have been told that the ratio of Pt/Co should be 9/1 in the 12 nearest
>> neighbors, not in the 12 atoms including the central atom (quote: "because
>> we have a bulk sample").
>>
>> But I do not understand why.
>>
>> Can someone please explain the correct answer to me?
>>
>> With kind regards,
>>
>> Felix
>>
>>
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Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 15

[Anatoly Frenkel]

Weizi,

Self absorption occurs in the transmission measurement of the powder
because it is a concentrated sample and it has to be exceedingly well made
to eliminate the thickness effect. Because it was shown in your previous
email to be lower than the film that decrease in intensity was caused by
self-absorption (if I remember your old email correctly). The fact that
your new data shows such decrease (compared to the powder or compared to
other conditions, such as an angle or a graphite dome) it is likely the
same effect (because it is exactly what self absorption would do with Ce L3
edge).

. Thin films should not have it because 200 nm is much lower than one
absorption edge of Ceria at Ce L3 edge energy. The reason you see it in
your films is because you chose a strange geometry to fight self absorption
(which should not exist in thin films). You make your angle grazing
incidence angle and you are making it effectively a very thick sample, thus
you create a condition for over absorption. Instead, you should have used
normal incidence and grazing exit, which is what needs to be done to
eliminate self-absorption in concentrated sample (which is not the case
here).

Anatoly


On Thu, Jun 22, 2017 at 12:12 PM, Weizi Yuan <
weiziyuan2...@u.northwestern.edu> wrote:

> Hi Anatoly,
> Thanks for your quick response.
> Yes, I actually asked the self absorption question about CeO2 a few weeks
> ago. And your answer that it is due to self absorption leads me to study
> more about it and I appreciate it.
> In that last question, the strong attenuation of signal occurs in the
> incident angle = 0.6 o . However, when the incident angle is 3 o  under
> room temperature ,air, the peak intensity is stronger than the CeO2
> measured in  transmission mode, which leads me to think that no over
> absorption correction needed here. And I try to  conduct the correction
> which gives me crazily high (~9 after normalization) peak intensity.
> This makes me further confirm that no strong self absorption effect here.
> And if no strong self absorption in RT, air ,then why strong attenuation
> in RT, vacuum condition(case ii in my question)?
> For your answer,I am a little confused. Are you saying self absorption
> occurred in only case ii or in both cases, even though the result of case i
> spectrum has a higher signal than the transmission mode data?
> Thank you,
> Weizi
>
>
> On Thu, Jun 22, 2017 at 10:16 AM,  cars.aps.anl.gov> wrote:
>
>> Send Ifeffit mailing list submissions to
>> 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
>> or, via email, send a message with subject or body 'help' to
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>>
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>> ifeffit-ow...@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. Self absorption or Ce4+ reduction in the CeO2 film? (Weizi Yuan)
>>
>>
>> --
>>
>> Message: 1
>> Date: Thu, 22 Jun 2017 10:11:05 -0500
>> From: Weizi Yuan 
>> To: ifeffit@millenia.cars.aps.anl.gov
>> Subject: [Ifeffit] Self absorption or Ce4+ reduction in the CeO2 film?
>> Message-ID:
>> > ail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear all,
>> I have measured some spectra of a CeO2 film(~200nm) grown on Yittria
>> stablized Zirconia(YSZ) substrate under 2 conditions.
>> (i) room temperature, ambient atmosphere
>> (ii) room temperature, vacuum (pO2~1E-6 atm) inside a graphite dome of
>> the
>> DHS 1100 anton paar,
>> The spectra are collected in fluorescence mode. The incident angle is 3 o
>>  and the fluorescence collection angle is 90 o.
>>
>> My questions are:
>> (i) From the theory behind the FLUO program developed Dr. Daniel Haskel,
>> CeO2 spectra collected with a 3 o incident angle *would have a strong self
>> absorption effect and need*
>>
>>  correction , however, *the signal *is not attenuated compared with the
>> CeO2 powder taken in a transmission mode, shown in attached plot.
>> I've gone through many literature and people sometimes tell that whether
>>  they have a successful self absorption correction by comparing the
>> spectrum with a spectrum taken under a transmission mode.
>> So I'm wondering if I can say that I don't need a self absorption
>> correction in this case?
>> (ii)
>> The Ce4+ peak in the spectrum collected under condition (ii) has a much
>> lower intensity. I think it is due to the reduction of Ce 4+ under vacuum,
>> however, the Ce3+ peak does not show an increased signal here. Which makes
>> ma doubt whether this is simply reduction of Ce *or might be from over
>> 

Re: [Ifeffit] Self absorption or Ce4+ reduction in the CeO2 film?

[Anatoly Frenkel]

Self absorption. 
There was a similar question a few weeks ago. 

Anatoly

Sent from my iPhone

> On Jun 22, 2017, at 11:11 AM, Weizi Yuan  
> wrote:
> 
> Dear all,
> I have measured some spectra of a CeO2 film(~200nm) grown on Yittria 
> stablized Zirconia(YSZ) substrate under 2 conditions.
> (i) room temperature, ambient atmosphere
> (ii) room temperature, vacuum (pO2~1E-6 atm) inside a graphite dome of  the 
> DHS 1100 anton paar,
> The spectra are collected in fluorescence mode. The incident angle is 3 o  
> and the fluorescence collection angle is 90 o.
> 
> My questions are: 
> (i) From the theory behind the FLUO program developed Dr. Daniel Haskel, CeO2 
> spectra collected with a 3 o incident angle would have a strong self 
> absorption effect and need
> 
>  correction , however, the signal　is not attenuated compared with the CeO2 
> powder taken in a transmission mode, shown in attached plot.
> I've gone through many literature and people sometimes tell that whether  
> they have a successful self absorption correction by comparing the spectrum 
> with a spectrum taken under a transmission mode.
> So I'm wondering if I can say that I don't need a self absorption correction 
> in this case? 
> (ii) 
> The Ce4+ peak in the spectrum collected under condition (ii) has a much lower 
> intensity. I think it is due to the reduction of Ce 4+ under vacuum, however, 
> the Ce3+ peak does not show an increased signal here. Which makes ma doubt 
> whether this is simply reduction of Ce　or might be from over absorption?　
> 
> Thanks for any response. 
> 
>  
> -- 
> Regards,
> Weizi Yuan,
> Graduate Student,
> Northwestern University,
> Ph:(+1)312-560-9619
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Re: [Ifeffit] Self absorption in CeO2 spectrum

[Anatoly Frenkel]

It is all self-absorption (over-absorption) that explains the difference. Ce 3+ 
will appear as a separate shoulder below the first peak and there is no 
evidence of this contribution in the spectra. 

These effects, including the difference between the spectra of the powder and 
film CeO2 due to self-absorption, are extensively described in literature. 

Anatoly

Sent from my iPhone

> On May 19, 2017, at 5:37 PM, Weizi Yuan  
> wrote:
> 
> Dear all,
> I have measured some XANES spectra of CeO2 film(~220nm) in fluorescence mode 
> at Ce L3 edge with two incident angles of 0.6 degree and 3 degree. My goal is 
> to get relative surface sensitive (penetration depth~ 20 nm above edge) 
> information of [Ce3+] from 0.6 o  while bulk sensitive information at 3 o 
> (penetration depth~ 160 nm above edge). In the meantime, I also collected 
> CeO2 powder reference spectrum under transmission mode. The comparison is 
> shown in the graph.
> The film at 3 degree has a sharper white line than the powder while at 0.6 
> degree, it is the opposite. I think this might be because at the surface of 
> the film,it has more Ce3+ while when we detect the bulk it has more Ce4+. 
> My question  is how can I tell if I need self-absorption correction or not 
> for the films in this case? Can I say I do not need self absorption 
> correction because I have a higher normalized u for the film collected in the 
> fluorescence mode than powder collected in the transmission mode?
> Thanks a lot for your comments.
> Weizi
> 
> 
> 
> -- 
> Regards,
> Weizi Yuan,
> Graduate Student,
> Northwestern University,
> Ph:(+1)312-560-9619
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Re: [Ifeffit] E0 on linear combination fitting: fit or not?

[Anatoly Frenkel]

I think (in agreement with Matt's comment) that if the standards are not
known to be calibrated to the same energy scale then LCA may not be as
useful if done in energy space. But, depending on the problem of course,
there could be a good spectral contrast between the data not only in energy
but also in k-space. The choice of the energy origin in k-space does not
depend on the energy scale but on the position of the "E0" point within the
edge region. Hence, even if the standards and the experimental spectrum are
not known to be calibrated to the same energy scale, the LCA can be done
for the data in k-space.

Of course, the k-space analysis may not necessarily be possible (if the
data quality is poor or k-range is too short or the background removal
process affects the results too strongly etc etc) or meaningful (if the
experimental data are obtained at different temperature, for example, than
the standards - then XANES analysis will be more meaningful by LCA than
EXAFS...) but there are definitely many cases out there where XANES and
EXAFS analysis by LCA results in similar values of mixing fractions.

Anatoly


On Fri, May 12, 2017 at 11:42 AM, Matt Newville 
wrote:

> Hi Pamela,
>
>
> On Thu, May 11, 2017 at 12:19 PM, Carrillo Sanchez, Pamela <
> pcarri...@bnl.gov> wrote:
>
>>
>>
>>
>>
>> Hi all,
>>
>>
>>
>> I have gone through the mail archives as well as following the
>> instructions of Athena user’s manual as well as Scott Calvin’s book but
>> still I find myself with the doubt of how correctly “choose E0”. I have
>> aligned the data and standards with the merge of reference foils
>> measurements of the metal (Mn). We did not have a reference foil placed
>> while measuring the data so I used the merge of the references scans when
>> the standards were measured and they showed a consistent energy shift.
>>
>>  I have set the same E0 for all the data and standard to the same E0, I
>> chose the first peak of the derivative in the data (6MnRh_RED). When I do
>> the LCF analysis without ‘fitting E0’ ,  I get a worse fitting than when I
>> choose the fit E0 on Athena as well as different types of components on the
>> fitting. Which one is the best choice for it ? From what I have read I
>> think that without fitting E0 would be the proper one regardless of the
>> “worse fit”.
>>
>>
>>
>
>
> The recommendation to not fit E0 in linear combination fitting is
> generally preferred, but also assumes that you have all data calibrated to
> the same energy scale.  The concern for fitting E0 in such a linear
> analysis is that energy shifts are often a sign of real chemical effects,
> not an indication of a change in energy calibration.
>
> But, you can definitely use Athena's linear combination fitting to figure
> out what the energy shift is between two spectra on the same material
> measured with different calibrations.
>
> Generally, it's best to measure several standards at the same time, so as
> to be able to assert that their energy scales (and resolution) are
> consistent.   It's OK to measure some samples / standards at different
> beamlines or different sessions at the same beamline as long you're careful
> about calibrating energy consistently (say with the same sample such as
> metal foil or hard-to-alter metal oxide) and the resolutions are similar.
> These days most beamlines are pretty stable in energy calibration and
> resolution.
>
> If the standards are well-aligned internally, applying very different E0s
> to the standards is probably not what you want.   Your "fit E0" example
> shows E0 shifts varying between ~0 and -6 eV for the different standards.
> I think that's kind of large - it's possible the energy scales for the
> standards vary by that much, but you might want to double-check that too.
>
> But, if you don't have calibrated standards, I might suggest asking the
> beamline scientist if they have an idea what kinds of energy shifts they
> expect.
>
>
> Hope that helps,
>
> --Matt
>
>
>
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[Ifeffit] Save the date: Nov 1-3, 2017, XAFS short course at BNL

[Anatoly Frenkel]

Dear Colleagues:

Please share with your group members or others, who may be interested, the
following information about the short course on XAFS spectroscopy:

Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications
to Nanomaterials*

Dates: *November 1-3, 2017*

Location: *Brookhaven National Laboratory*



The course will continue the annual tradition of gathering a group of
scientists, active in the field, to share their expertise with those
interested in learning about the use of x-ray spectroscopy methods in their
research.  *The course will be useful for those scientists who are already
familiar with the foundations of XAFS experiment, theory and data analysis,
and seek training in advanced analysis and modeling methods*. The course
will include lectures, software demonstrations, and data analysis sessions.
The emphasis will be on applications of XAFS to nanomaterials but we will
welcome all participants who are interested in modern analysis techniques.
Course instructors will use examples from their research during
presentations. Topics covered will include theory of XANES and EXAFS,
direct modeling methods using Molecular Dynamics simulations and Reverse
Monte Carlo, multiple data set modeling and multiple-scattering analyses.
Other topics will include, but not limited to: chemometrics, bonding
dynamics and transformation kinetics. During the data analysis practicum on
Nov. 3 the course participants will get an opportunity to work with
demonstration examples and/or their research projects with the help of the
course instructors.



The course will be open to 30 participants, selected based on their
application materials.

The course web page will appear on BNL web site in near future, with
instructions how to apply. For any inquiries please contact me.

Best Regards,

Anatoly
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
---
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Re: [Ifeffit] Athena and "norm" file groups

[Anatoly Frenkel]

I would try to rename .norm by .xmu and see if it will be able to do what
you want.
I would still be cautious doing it because .norm means that the raw data
was already altered (pre-edge function was subtrated and slope changed).
Doing anything like that is possible but not wise because it is not
guaranteed that you would obtain the same result as when you start from the
raw data directly.

For example, suppose "norm1" is normalization operation with one set of
parameters, and "norm2" - with another. Xmu is the raw absorption
coefficient data (obtained from the ratio of detector signals).
It is not likely that norm2 (xmu) will give the same results as
norm2(norm1(xmu)), although the differences may be small. That is the
reason, I think, Athena does not allow any ex post factum normalization to
the normalized data.

Anatoly Frenkel
Stony Brook University

On Oct 15, 2016 4:10 PM, "Mike Massey" <mmas...@gmail.com> wrote:

> Hi everyone,
>
>
> Apologies if this has been covered before, I'm just getting around to
> upgrading to Demeter. I have a bunch of old project files with a mishmash
> of data from different sources, and I'm having trouble getting them to work
> fully with the new software.
>
> Any group with a data type of "xmu" (energy space) seems to work as
> expected, but any group with a data type of "norm" (normalized data)
> doesn't seem to work properly when it comes to spline or post-edge
> background subtraction (which is handy if I want to do LCF, for example).
> Is this a bug or a feature? Has anybody yet developed a workaround?
>
> Any thoughts or advice would be greatly appreciated. The ultimate
> workaround is to use different data, but I'd like to use existing projects
> if possible (saves a lot of time and brain damage).
>
>
> Cheers, and thanks!
>
>
> Mike
>
>
>
>
>
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Re: [Ifeffit] a big big thank-you

[Anatoly Frenkel]

Dear Echkard,

 

I wish your thesis has a smooth journey between the Scilla and Charybdis on
your committee,

 

Anatoly

 

 

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bosman,
Eckhard
Sent: Monday, November 03, 2008 12:05 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] a big big thank-you

 

 

Hi,
a few days ago I finished my diploma thesis (Modeling of XANES-Spectra).
Now,

the thesis is submitted and I want to thank you all very much for your great
and quick help over the past months. I bring the odysseus explanation well
to mind :-)

Thanks a lot,
Eckhard


---
Eckhard Bosman
[EMAIL PROTECTED]
[EMAIL PROTECTED]
+49 (0)551-39-14441
Raum: E0.104
Institut für Röntgenphysik
Friedrich-Hund-Platz 1
37077 Göttingen
Germany

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Re: [Ifeffit] enrgy-axis-expansion

[Anatoly Frenkel]

Khalid, what you can do is to note how much the higher energy (at energy E1)
feature is shifted from what you think it should be (let's say by the amount
of D eV), provided that you fixed the lower energy point to what you wanted
(say, E0). Then, you should transfer the data into a spreadsheet and apply
linear scaling:

 

E -- E0 + (E-E0)*D

 

It will ensure that in the range between E0 and E1 the data are linearly
stretched or compressed, depending on the sign of D.

 

Anatoly

 

=

  _  

From: Khalid, Syed [mailto:[EMAIL PROTECTED] 
Sent: Monday, September 08, 2008 12:21 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] enrgy-axis-expansion

 

Is it possible in Athena to change the y-axis (energy
scale) at two different energy points of an EXAFS scan?

I have a Ni foil spectrum as a function of time.
The edge can be set at 8333.0 eV, and I want to
to assign higher energy to a known feature in the Ni scan.


Syed Khalid
725D, National Synchrotron Light Source
Brookhaven National Laboratory
Upton, NY 11973

Ph: 631-344-7496
FAX: 631-344-3238
e-mail: [EMAIL PROTECTED]

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Re: [Ifeffit] Linear combination analysis

[Anatoly Frenkel]

Sebastiano:
 
Sounds like a martensitic transition since it depends on the annealing
time. Thus, as Bruce wrote, XANES and EXAFS may be expected to be
different, due to the different lengths scales - if the boundaries of
local fcc regions are small. Another origin of this discrepancy in x and
y between XANES and EXAFS fits, is Debye-Waller factor. Due to the extra
disorder caused by the interface between fcc and bcc region within the
sample, EXAFS in the fcc region in B is not equivalent to EXAFS in D.
Analogously, EXAFS in the bcc region in B is not equivalent to EXAFS in
A. Therefore, linear combination of A and D will not give you B at
correct mixing fractions (correct, meaning, real physical mixing
fraction). To compensate for that, linear combination problem will stil
try to get you the betst fit but by expense of changing the x and y from
their correct values. 
 
XANES is giving you a more accurate result in this sense since
Debye-Waller factor, even if different between the unknown (B) from A or
D, will not affect XANES that much as EXAFS.
 
Anatoly
 

-Original Message-
From: Ravel, Bruce [mailto:[EMAIL PROTECTED] 
Sent: Thursday, June 05, 2008 10:39 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Linear combination analysis




Hi Sebastiano,

 I study a binary alloy (Fe98.7Cu1.3) where a phase change from bcc to
fcc
 is evident (at the Cu K edge of course) and it depends on the
annealing
 time. I have 4 samples A,B,C,D,  where the A shows a perfect bcc
structure,
 while the D a clear fcc structure. B and C have structure that is a
mix
 between the fcc and bcc. I found very interesting to perform some
linear
 fit simulations using the A and D of the XANES and EXAFS of the
samples B
 and C. so  for instance it is possible to get the xanes of the B
sample as
 linear combinations of A and D according to

 BXANES = x*AXANES+(1-x)*DXANES  and for the EXAFS

 BEXAFS = y*AEXAFS+(1-y)*DEXAFS

 The simulations work perfectly but:

 1-   Of course I expect that x=y (am I wrong?). but this is not
true
 according to the values that the linear fit provide me. There is a
small
 but significant difference as x=48±2% and y=44±2%. Does this
difference
 have any physical meaning? Is the error a bit too small (so should I
 increase it?)


I don't think you are either wrong or right -- it depends upon the
details of the system.  Were your system a mixture of two powders in
the ratios you observe in sample B and C, then you would indeed expect
x=y.

If I understand your situation correctly, you have an alloy that
displays a local structure (FCC-like around the Cu atom) that is
different from the bulk structure (presumably BCC since this is mostly
Fe).  That means that, on some length scale, the correlations in the
material change from FCC-like to BCC-like.

Suppose that length scale at which the correlations change is 10s of
Angstroms.  That is too far for the EXAFS-with-an-E to see, but near
the edge the mean free path of the photoelectron might be long enough
to start seeing that effect.  Thus the structure probed by the XANES
portion of the spectrum might not, in that sense, be identical to the
structure probed by the EXAFS.  In that case, you might not expect
x=y.  The extent of their difference is an indication that the XANES
is probing the system on a longer length scale than the EXAFS.

I admit that what I just wrote is a bit half-baked -- it's just my
initial thought upon reading your email.  But it seems plausible.

 2-   For the sample C, I got an amazing simulation adding some
noise
 (0.001), but when I try to export the data (operation: Write a
report) I
 cannot get the data corrected with the noise (I can get only 6
columns: k,
 data, fit, residual, sample D, sample A). Is there any way to get the
data
 from the data+noise curve?

Hmmm... I need to look into the soruce code, but I would guess that I
just forgot to apply the noise when writing out the LCF fit results.
I doubt that it will be a difficult fix and I will let the list know
when I have checked the fix into the SVN repository.  It is unlikely
that I'll have a chance to make a new Windows executable before
August, however.

As a work-around, you could generate a noise spectrum yourself and add
it to the data outside of Athena.  It won't be the same noise spectrum
that was used in the fit, but I suspect it'll be hard to tell the
difference when you make a plot.  As I say in the document The noise
is randomly generated using an epsilon that is chosen as a fraction of
the size of the edge step.

B





--
 Bruce Ravel   [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 My homepage:HYPERLINK
http://xafs.org/BruceRavelhttp://xafs.org/BruceRavel
 EXAFS software: HYPERLINK
http://cars9.uchicago.edu/~ravel/software/exafs/http://cars9.uchicago.
edu/~ravel/software/exafs/

Re: [Ifeffit] 2008 APS XAFS School

[Anatoly Frenkel]

Bruce and all:
 
Congratulations on the funding!
 
Anatoly
 
  

-Original Message-
From: Ravel, Bruce [mailto:[EMAIL PROTECTED] 
Sent: Friday, May 16, 2008 10:08 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] 2008 APS XAFS School



On Wednesday 14 May 2008 13:39:48 Matt Newville wrote:
 The application form for the 2008 APS XAFS School is now open:
 HYPERLINK
http://cars9.uchicago.edu/xafs_school/2008http://cars9.uchicago.edu/xa
fs_school/2008

 Details about this year's APS XAFS School are at
 HYPERLINK
http://xafs.org/Workshops/APS2008http://xafs.org/Workshops/APS2008


Hi everyone!

This year, for the first time, we have obtained funding for a
scholarship from the American Physical Society Forum on international
Physics to bring one participant to the APS XAFS Summer School from a
nation designated by the World Bank as low or lower middle
income.  Here are the details:

   HYPERLINK
http://xafs.org/Workshops/APS2008/FIPhttp://xafs.org/Workshops/APS2008
/FIP

Only a small handful of the subscribers to this mailing list qualify
for the scholarship (the details are explained on that wiki page).  I
certainly want to bring this opportunity to their attention.  If any
of the rest of you have colleagues in developing nations who might
benefit by this opportunity, please let them know.

Sadly, we only have funding for a single scholarship this year, so I
anticipate the competition will be tight.

Regards,
B


--
 Bruce Ravel   [EMAIL PROTECTED]

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 My homepage:HYPERLINK
http://xafs.org/BruceRavelhttp://xafs.org/BruceRavel
 EXAFS software: HYPERLINK
http://cars9.uchicago.edu/~ravel/software/exafs/http://cars9.uchicago.
edu/~ravel/software/exafs/


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[Ifeffit] FW: Brainteaser

[Anatoly Frenkel]

I think this answer is as good as the correct one! Anatoly. 
 
 -Original Message-
From: Woicik, Joseph [mailto:[EMAIL PROTECTED] 
Sent: Friday, April 04, 2008 3:28 PM
To: [EMAIL PROTECTED]
Subject: RE: Brainteaser


oh, i got it, you right clicked when you should have left clicked.

  _  

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[Ifeffit] Brainteaser

[Anatoly Frenkel]

Attached is a brainteaser which I think is cute. Too late for the April
fool's day but still... 
Some comments: three consecutive scans of the same sample were taken in
this order: scan 1, 2 and 3. Duration: 30 minutes per scan.
 
If these data look unusual to you please tell us why and what could've
happened in this experiment. 
 
Those of you who send first three correct answers will be acknowledged!
 
Anatoly
 
 


bt.pdf
Description: Adobe PDF document
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Re: [Ifeffit] Brainteaser

[Anatoly Frenkel]

I apologize to everyone who Matthew did not even give a chance to think
but the excuse is that Matthew is really good! 
 
It was a saturation of the I_t current amplifier. Another sign of that
is too sharp a rise of the edge right after the pre-edge - it is when
the I_t signal  drops below the saturation limit.
 
A comment: the last time NSLS had 20h of stored beam lifetime was in the
20th century, I think, but it is besides the point.
Anatoly
 
 

-Original Message-
From: Matthew Marcus [mailto:[EMAIL PROTECTED] 
Sent: Thursday, April 03, 2008 9:30 PM
To: [EMAIL PROTECTED]; XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Brainteaser


The most obvious explanation for why the post-edge scans line up and the
pre-edges don't is that the transmission chamber
current amp or V/F is saturated and reads a fixed value below the edge.
As the ring current decays, I0 goes down while
It is fixed below the edge, so ln(I0/It) decreases as observed.  With
this explanation, and noting that ln(I0/It)
decreased by about 0.05 in an hour, I infer that the stored-beam
lifetime is ~20hr.
mam

- Original Message - 
From: Anatoly Frenkel mailto:[EMAIL PROTECTED]  
To: [EMAIL PROTECTED] ; 'XAFS Analysis using
mailto:ifeffit@millenia.cars.aps.anl.gov Ifeffit' 
Sent: Thursday, April 03, 2008 6:13 PM
Subject: [Ifeffit] Brainteaser

Attached is a brainteaser which I think is cute. Too late for the April
fool's day but still... 
Some comments: three consecutive scans of the same sample were taken in
this order: scan 1, 2 and 3. Duration: 30 minutes per scan.
 
If these data look unusual to you please tell us why and what could've
happened in this experiment. 
 
Those of you who send first three correct answers will be acknowledged!
 
Anatoly
 
 



  _  




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[Ifeffit] FW: Brainteaser

[Anatoly Frenkel]

-Original Message-
From: Matthew Marcus [mailto:[EMAIL PROTECTED] 
Sent: Thursday, April 03, 2008 9:57 PM
To: [EMAIL PROTECTED]
Subject: Re: [Ifeffit] Brainteaser


Sorry about jumping in too quickly.  I've had this very thing happen to
me so I recognize the sharp edge rise.  Maybe I should have
replied privately to give others a chance to weigh in, or put ***spoiler
warning - possible solution  in the subject line.  My
apologies to all!
mam

- Original Message - 
From: Anatoly Frenkel mailto:[EMAIL PROTECTED]  
To: 'Matthew Marcus' mailto:[EMAIL PROTECTED]  ; [EMAIL PROTECTED]
; 'XAFS Analysis using  mailto:ifeffit@millenia.cars.aps.anl.gov
Ifeffit' 
Sent: Thursday, April 03, 2008 6:52 PM
Subject: RE: [Ifeffit] Brainteaser

I apologize to everyone who Matthew did not even give a chance to think
but the excuse is that Matthew is really good! 
 
It was a saturation of the I_t current amplifier. Another sign of that
is too sharp a rise of the edge right after the pre-edge - it is when
the I_t signal  drops below the saturation limit.

 
A comment: the last time NSLS had 20h of stored beam lifetime was in the
20th century, I think, but it is besides the point.
Anatoly
 
 

-Original Message-
From: Matthew Marcus [mailto:[EMAIL PROTECTED] 
Sent: Thursday, April 03, 2008 9:30 PM
To: [EMAIL PROTECTED]; XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Brainteaser


The most obvious explanation for why the post-edge scans line up and the
pre-edges don't is that the transmission chamber
current amp or V/F is saturated and reads a fixed value below the edge.
As the ring current decays, I0 goes down while
It is fixed below the edge, so ln(I0/It) decreases as observed.  With
this explanation, and noting that ln(I0/It)
decreased by about 0.05 in an hour, I infer that the stored-beam
lifetime is ~20hr.
mam

- Original Message - 
From: Anatoly Frenkel mailto:[EMAIL PROTECTED]  
To: [EMAIL PROTECTED] ; 'XAFS Analysis using
mailto:ifeffit@millenia.cars.aps.anl.gov Ifeffit' 
Sent: Thursday, April 03, 2008 6:13 PM
Subject: [Ifeffit] Brainteaser

Attached is a brainteaser which I think is cute. Too late for the April
fool's day but still... 
Some comments: three consecutive scans of the same sample were taken in
this order: scan 1, 2 and 3. Duration: 30 minutes per scan.
 
If these data look unusual to you please tell us why and what could've
happened in this experiment. 
 
Those of you who send first three correct answers will be acknowledged!
 
Anatoly
 
 



  _  




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Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?

[Anatoly Frenkel]

What would be really useful is to make a searchable database with links
to original publications (many of them are more than 20 years old but
are still the best resources on many issues) on many subjects discussed
in this list. 
 
For example: 
 
Number of independent data points: see Stern and Heald arcticle in
Handbook on Synchrotron Radiation, Ed Stern PRB article, etc.
 
Thickness effects: Kim and Stern PRB
 
Cumulants: G. Bunker, Nucl. Instrum. Methods in 1980s
 
Background removal: Newville, Livins, PRB etc.
 
Multiple scattering collinear paths and angular dependence of f(k): Lee
and Pendry PRB (1975?)
 
Transferability of photoelectron phase: Citrin, Kincaid, et al, Phys Rev
B, 1970s
 
(I may be wrong in the years and order of authors, but this this the
idea).
 
It would be so useful if someone (I cannot do it but will be happy to
help) took care of putting together a backbone version of it and set it
up as, say, wiki (which is  Bruce's idea as I once brought it up to
him). I am sure most of us will be happy to contribute references that
we know. Thus, such database may become an exhaustive resource of
information that should be a primer for every XAFS user. 
 
Anatoly
 
 

  

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Richard
Mayes
Sent: Friday, December 14, 2007 11:02 AM
To: XAFS Analysis using Ifeffit
Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED]
Subject: Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?



Kefan,

As someone who was in your place 2 years ago, one thing Bruce mentioned
was reading the papers of people you find on the mail list, however he
didn't specifically mention searching the mail list.  When I had
questions, the answers were often already discussed on the mail-list.
If
you're not a member of the mail-list, I highly recommend you join.  As I
currently struggle writing a how-to manual that's supposed to shorten
the
XAFS learning curve for our group, I find myself searching the mail-list
archives often to see how different people approach different issues.

Good luck on your quest!
-Richard



 Hi Bruce

 I have spent 1 month to learn the Athena by using your ATHENA User's
 Guide
 updated at Aug. 31,2007. I am very satisfied with it and thank you
very
 much. Now I am learning the ARTEMIS. However, till now I can not find
a
 suitable guide for a beginner. The PPT wrote by Shelly is not
suitable
 for
 me. And the artemisdoc.pod is also puzzled me. Is there a Artemis
 User's
 Guide like the Athena?

 Thanks

 Kefan

 --
 Kefan Wang
 School of Physics and Electronics
 Henan University, 475004
 E-mail: [EMAIL PROTECTED]; [EMAIL PROTECTED]


 Hi Kefan,

 I suspect that my answer to this question will be of broad interest,
 so I am taking the liberty of CCing the Ifeffit mailing list.

 Thank you for the very kind words regaridng Athena.  I am pleased that
 you found the Athena User's Guide so helpful.  Sadly, I have not yet
 written a document of comparable extent for Artemis.  I certainly
 understand that there is a need for comparable user guide, but finding
 the time and energy to write one has not yet happened.  Writing the
 Athena User's Guide was fairly exhausting and I need to take a break
 before embarking on a similarly large document for Artemis.

 I have to defend Shelly's various presentations.  I think they have a
 lot of good information in them.  I think that using them along with
 other resources can give you enough of an overview of Artemis to get
 started.  I strongly recommend that you work through Scott Calvin's
 ZnO example, which can be foun at
http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib
 ZnO is somewhat of an idealized example -- many of us work on
 problems that are pretty far removed from a simple crystal like ZnO.
 However, Scott's example is quite thorough.  Working through it while
 carefully following his comments in the project journals will
 introduce many of Artemis' features.

 As for the pod file -- those are the files that get displayed when you
 click on one of the documentation buttons from within Artemis.  I
 acknowledge that they are thin on details and somewhat out of date.

 The last bit of advice I can give you is to read the papers written by
 the names you see on the Ifeffit mailing list.  The folks who offer
 answers to question on the list are also some of the best
 practitioners of EXAFS analysis using Feff.  Although it might seem
 funny to read papers by Anatoly Frenkel or Paul Fons if you are
 studying environmental science (or Shelly Kelly's if you are a
 materials scientist), I strongly recommend doing so anyway.  Their
 science might be pretty far away from what you do, but the EXAFS
 analysis strategies are quite instructive and are certainly
 transferable.

 I know that is not the answer you were hoping for, but it may be
 helpful nonetheless.

 Regards,
 B

 --
  Bruce Ravel  --- [EMAIL PROTECTED]

  National Institute

Re: [Ifeffit] SA and issue with importing into Artemis

[Anatoly Frenkel]

Richard,
 
I tried with Athena v50 and Artemis v007 and it worked (the data were
ported correctly). I do not think it is version dependent.
 
The data that you save in Athena are ported to Artemis with 0
k-weighting, so you have to manually set your k-weighting in artemis if
you want to match the same k-weighting that you liked in athena. As you
know, there is k-weighting for FT and k-weigthting for plotting data in
k-space, which have nothing to do with each other. 
 
Note that the vertical axis in the bottom figure of your PDF file has
unit of A^-3 which means it was indeed k2-weighting in FT in Artemis.
You just have to make it k3 weighting in FT and it will give you the
same plot as the top figure (and the unit will be A^-4).
 
Anatoly

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



Oops!  Forgot the attachments.  Sorry about that.

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

-Richard


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

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

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

 Any ideas on how to get around this?

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

 Thanks!!
 -Richard

 --
 Richard Mayes

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



--
Richard Mayes

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


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[Ifeffit] SCC Mailing List

[Anatoly Frenkel]

Hello all:



Our group, Synchrotron Catalysis Consortium, or SCC, at the NSLS has started
a mailing list (SCC-Forum) to provide our users with an opportunity to
discuss problems that are specific to nanocatalysis science. Most of our
users come to SCC to perform in situ XAFS in catalysis  reactors, collect
time-resolved data, analyze low dimensional systems (e.g., nanoparticles,
monolayers, nanorods, and their real time reactivity, as just a few
examples) and thus may benefit from a specialized forum where these issues
are addressed in depth.



Postings by our list members would facilitate discussions of experimental
setups needed to study a specific catalysis problem, experimental regimes,
typical experimental pitfalls in these type of measurements and how to avoid
them, data modeling tricks and know-how, etc. The purpose of the list is to
help each other and the SCC group here at the NSLS by sharing your
experience and stimulate further development of catalysis science done by
XAFS and other synchrotron techniques.



For those who are not familiar with SCC, a good starting point describing
our activities is: http://www.yu.edu/scc.



To subscribe to the SCC mailing list, and start receiving and sending
postings, use   as the entry point the main SCC web page:
http://www.yu.edu/scc and click at the SCC Discussion Forum link in the
bottom right. Note that you may choose to receive daily digests of the
postings; regardless of your choice, you can access the message archives by
logging in to the list using the main entry point above. The interface is
the same as IFEFFIT; in fact, Matt kindly helped me to configure it to have
the same settings as IFEFFIT, to make it easier for those who wants to
subscribe to the both lists.



Perhaps, such “specialized” lists could be set up in the future by other
groups using XAFS, say, life sciences and environmental sciences, who will
continue using IFEFFIT  as a fantastic resource for general XAFS analysis
advice but have their own list themes, as does SCC-Forum. Regardless of
whether it may or may not be a good idea in general, I hope the SCC-Forum
list will be a useful resource for you. Any comments, please let me know.



Anatoly



Anatoly Frenkel, Professor

Department of Physics, Yeshiva University

245 Lexington Avenue, New York, NY 10016

http://www.yu.edu/faculty/afrenkel



Spokesperson, Synchrotron Catalysis Consortium

http://www.yu.edu/scc



Office: (212) 340-7827, Lab: (631) 344-3013, Fax: (212) 340-7868

Email: [EMAIL PROTECTED]
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Re: [Ifeffit] help with CoCr bimetallic catalyst

[Anatoly Frenkel]

Codruta - it's better off if you have someone walk you through this type of
analysis for the very first time, as it is somewhat involved. You may decide
to come to one of the short courses (the nearest ones will be at the APS in
the end of July, and the NSLS in October - the dates are still being
finalized), or collaborate with someone experienced on the list. As Scott
Calvin is reasonably close to Yale, he may be your best bet. If you are
willing to expand your radius and travel to Brookhaven for a few days, my
postdoc Adele Wang could help too.

Regards,

Anatoly

Anatoly Frenkel
Yeshiva University


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
[EMAIL PROTECTED]
Sent: Wednesday, June 06, 2007 11:45 AM
To: Ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] help with CoCr bimetallic catalyst

I have been, working with a bimetallic Co/Cr catalyst supported on a silica
template for synthesis of single wall carbon nanotubes. Recently I have
performed some analysis at the NSLS. It is clear from the spectra in R space
that the interatomic distances are modified compared to the monometallic
catalyst therefore I am dealing with an alloy.
Does anyone have or know about a model that would allow me to get a
coordination
nomber using Artemis.
Thank you,
Codruta.
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Re: [Ifeffit] Coordination of ball-milled alloys

[Anatoly Frenkel]

Have you measured Fe edge in this alloy, and if yes, have you tried to fit
the data measured from both Fe and Cr edges simultaneously? I would do it
first, without varying the mean free path. It will definitely reduce
correlations between N and ss2, which seems to be a problem here. Whether or
not it works, your method of imposing a lower bound for the EXAFS DWF using
a twice the XRD DWF is a great idea.

What is also missing in your story is the knowledge of the alloy structure
and homogeneity - are these random, substitutional alloys at this
concentration? A strongly distorted hcp (non closed packed) metal will have
a splite of 6 and 6 neighbors in the first shell - and you may not get the
coordination number right if you model it as a single shell of 12 neighbors.
Just a food for thought.

Anatoly


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Alejandro
Fernandez-Martinez
Sent: Friday, May 04, 2007 2:18 PM
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] Coordination of ball-milled alloys


Dear all,

I am quite new to XAS data analysis, maybe you can help me with a little
problem I have.

I am trying to fit EXAFS data at Cr K-edge of a bcc Fe30Cr70 alloy
synthesized by ball-milling. For those who don't know it, this technique
is very effective in alloying metals but introduces a lot of structural
defects in the structure. This is clearly seen in neutron diffraction
data (with DW 2 times larger than DWs of a Cr reference and larger FWHMs).

When fitting the EXAFS data without any specific constrain (only for
distances) I get DWs on the same order of magnitude for the Cr-foil than
for the alloy, and a very reduced coordination of N1=2.3 (compare with
N1=8 for the Cr-foil) for the first neighbour (without physical sense?).

In order to take into account the larger DWs for the alloyed sample (as
found in diffraction data) I have constrained the minimum value of the
DWs to a value double than the DWs of the Cr-foil. This gives me an
increase of the N for the first shell, but at the same time, I have to
refine lambda (photoelectron mean free path) in order to correct the
excesive decay introduced by the DW exponential in the EXAFS formula,
and to get a good fit. Then I get a more physically understandable N1=5.5.

- The 1st question is: do you think the logical discourse that I have
followed until now is correct? I don't have idea on how much some
quantities as lambda should or not be refined.
- 2nd question: what dou you think about the use of diffraction data as
constraint for EXAFS data analysis?

Many thanks in advance!

cheers,
Alex

--
Alejandro Fernandez-Martinez
Institut Laue-Langevin
6, rue Jules Horowitz - B.P. 156
38042 Grenoble Cedex 9, France

Tel: +33 (0)4.76.20.75.71
Fax: +33 (0)4 76.20.76.48
[EMAIL PROTECTED]

--
Geochimie de l'Environnement
LGIT - UJF
BP 53
38041 Grenoble Cedex
France

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Re: [Ifeffit] large Eo's and neg. D-W factors

[Anatoly Frenkel]

My observation (not rigorously tested though): the longer it takes to get a
good fit, the more suspicious are the results!

Anatoly


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Richard
Mayes
Sent: Wednesday, May 02, 2007 8:56 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] large Eo's and neg. D-W factors


Scott,

Thanks for the clues!  The restraints seem to be working to get the DW
factors positive.  I'm still battling Ifeffit reversing the paths, but
things are getting slowly better.

Rich

 Hi Rich,

 I know you posted this a while ago, so you may have gotten other
 answers, but I don't see them in my overflowing inbox. :)

 Years ago, I did some work with V2O3, and it was a very stubborn
 system to get a good fit on. Other people I knew who were working on
 the system have also had some trouble. This and other evidence led to
 some people publishing speculations on local distortions that get
 averaged out in XRD but show up in EXAFS. I also recall people
 talking about similar difficulties with other vanadium oxide systems.
 (Sorry; I don't have those references handy anymore, but searches
 should locate them).

 As far as the second issue you mention, with Ifeffit reversing the
 position of two atoms of the same species, it does happen some times.
 Why not? A V-O path is basically a V-O path to FEFF; it doesn't know
 that one's a single bond and one's a double bond. But since moving a
 path by more than about 0.1 Angstrom in Ifeffit starts to reduce the
 accuracy of the FEFF calculation, it's something you do want to try
 to prevent. One way to do that is with restraints; it shouldn't take
 much incentive for Ifeffit to refrain from switching the paths.

 --Scott Calvin
 Sarah Lawrence College


 At 05:02 PM 4/18/2007, you wrote:
Greetings!

I have inherited a vanadium EXAFS data set (due to a group member
graduating - lucky dog!) that is giving me major fits.  I am getting
consistent numbers with all my fits which visually look fantastic,
that is until I look at the numbers...one Debye-Waller factor is
negative (a V-O path) and the Eo's are large, the V-Cl path is on
the order of -20 eV, the V=O path is on the order of 17 eV, and the
V-O path falling at -11 eV.  ARe there any tricks outside of
restraints or constraints that I can attempt to get more realistic
values?  (I understand that a large Eo can be realistic, but a
negative Debye-Waller factor doesn't make sense.)  I can restrain
the V-O Debye-Waller factor and get a positive value, but then the
V=O D-W factor is negative.  If I restrain both D-W factors, the fit
falls apart, suggesting something else is wrong that I just can't find.

Another issue I'm having involves something in Artemis that's
confusing me.  Sometimes after a fit, the Artemis Pallet shows the
V=O feature as the one at 1.8 Angstroms and the V-O feature at 1.6
Angstroms, completely reversed to the FEFF model.  I have seen this
when I separated the chlorides as well (I attempted to model the Cl
at different distances as reported by Deguns, et. al. (attached) due
to the immediate environment around the V in our sample being
similar to the one they report in scheme 1-(I), p5008).  Attached is
a text file that shows an Artemis Pallet output illustrating what
I'm trying to describe for the V=O and V-O paths.  The Artemis
project that generated the output is also attached.


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Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

[Anatoly Frenkel]

Since I like the sound of my voice too, I will translate the zeitgeist
from Bruce's email. According to Wikipedia, It is originally a German
expression that means the spirit (Geist) of the time (Zeit). Can it be
loosely translate here as poltergeist?

Anatoly



-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bruce Ravel
Sent: Wednesday, March 28, 2007 3:41 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

On Wednesday 28 March 2007 13:15, Mario Gomez wrote:
 Hi Bruce my name is Mario and I was just wondering if your program can fir
 the EXAFS spectra without any atomic positions. Obviously the answer is no
 if you use atoms to create the FEFF file but what does one do when we have
 a semi-crystalline material for which no one has attempted the fractional
 coordinates.

 I mean the XRD pattern shows some crystalline but due to the high
 background I would think it would be very hard to do the Rietveld
analysis.

 So what can one do, can we fit the EXAFS spectra knowing only the chemical
 composition and perhaps the lattice geometry(orthorhombic or hexagonal)?

Mario,

Scott's answer was excellent, but I like the sound of my own voice so
I thought I'd answer as well ;-)

The Feff+Ifeffit+Artemis zeitgeist requires a list of atomic
coordinates to begin analysis.  Except in the rare situations, we
don't know the actual arrangement of atoms.  Indeed, to find out is
one of the reasons we might do EXAFS.

As Scott suggested, thinking about what you sample resembles is
usually a good place to start.  Consider amorphous germanium as an
example.  aGe is typically described as a continuous random network of
bonds which are about the same length as the bonds in crystalline Ge.
Because of that, crystalline Ge is a good place to start.  In fact, I
suspect that you could make considerable progress in analyzing aGe
data with that one Feff calculation on the well-ordered material.

EXAFS analysis is something of a creative endeavor -- the trick is to
figure out how to use things that you know to model things that you
don't know.  Reading papers by the folks who answer questions on this
list (Scott Calvin, Shelly Kelly, Anatoly Frenkel, Paul Fons) is a
really good source of ideas for your own work with IfeffitArtemis.

B

-- 
 Bruce Ravel  -- [EMAIL PROTECTED]

 Molecular Environmental Science Group, Building 203, Room E-165
 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007

 Argonne National Laboratory phone and voice mail: (1) 630 252 5033
 Argonne IL 60439, USAfax: (1) 630 252 9793

 My homepage:http://cars9.uchicago.edu/~ravel 
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Re: [Ifeffit] FEFF 6L.02

[Anatoly Frenkel]

It is probably because I know Bruce for so long that I give almost identical
replies to my students who email me: Dr. Frenkel, I tried to solve a
homework problem but it did not work. What did I do wrong?

Anatoly


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bruce Ravel
Sent: Monday, February 26, 2007 12:33 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] FEFF 6L.02

On Monday 26 February 2007 10:29, Roque, J (Josep) wrote:
 I am trying to run FEFF 6L.02 from  version of IFEFFIT 1.2.9 on a
 Windows platform but it doesn't seems to work.. How can I fix this
 problem??

That's not a bug report in that it provides no actionable information.

The statement Feff 6.02L doesn't work is demonstrably false.  People
use it on their windows machines all the time.  The statement Feff
6.02L does not work on Josep's machine might be true, however.

If you expect to get help from this mailing list, you need to provide
something: a screenshot demonstrating the problem, a transcription of
the error messages it generates, a description of any problems you had
installing the software, something

B

-- 
 Bruce Ravel  -- [EMAIL PROTECTED]

 Molecular Environmental Science Group, Building 203, Room E-165
 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007

 Argonne National Laboratory phone and voice mail: (1) 630 252 5033
 Argonne IL 60439, USAfax: (1) 630 252 9793

 My homepage:http://cars9.uchicago.edu/~ravel 
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/


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Re: [Ifeffit] question about Eo and simultaneous fitting

[Anatoly Frenkel]

It is true that in many cases oxidation/reduction affects the low k-range
behavior in chi(k), but if the second shell (metal-metal) frequency is not
affected, the data can still be aligned by focusing at the high k-portion of
the data, so what Shelly suggested, may be, in principle, done.

Anatoly


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Scott Calvin
Sent: Wednesday, February 14, 2007 10:55 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] question about Eo and simultaneous fitting

Hi Shelly,

Interesting--I've never tried that method with samples that I expect 
to differ in oxidation state. If it's differing in oxidation state, 
the local environment is probably different too...particularly, 
nearest-neighbor distances should be changed significantly. So how do 
you align the chi(k) data with each other, when they oscillate at a 
different frequency?

--Scott Calvin
Sarah Lawrence College

At 10:38 AM 2/14/2007, you wrote:

The approach that I like to take, is to vary the choice of E0 in the
background subtraction step so that the chi(k) spectra are well aligned
with each other and the theory.  Then only one Ezero parameter is
needed.

Cheers,
Shelly

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RE: [Ifeffit] Is there a physical meaning to a negative SO2

[Anatoly Frenkel]

A totally unrelated joke: If anyone ever watched Da Ali G show on HBO,
there was an episode, when Ali G interviews a famous economics professor.
The first question was: Professor, what is a PIN code?

A.

  -Original Message-
  From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Todd Luxton
  Sent: Tuesday, January 09, 2007 10:41 AM
  To: 'XAFS Analysis using Ifeffit'
  Subject: [Ifeffit] Is there a physical meaning to a negative SO2


  I am very new to XAFS analysis, I am wondering if there is a physical
meaning to a negative value for SO2.  Based on the XAFS equation I can't
understand what the physical significance of a negative SO2 value would be,
therefore I am assuming that my modeling results using Athena are not
representative of a physically realistic model due to the negative value
calculated fro SO2 or more specifically the amp variable in the guess set.
Any insight would be greatly appreciated.



  thanks
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RE: [Ifeffit] CN and bond distances in Artemis

[Anatoly Frenkel]

Dear JA,

For the record, I don't recall saying anything to the effect that S02 =
0.2 is close to the case of Pt nanoparticles - which would be wrong since
the smallest number for 13 atom particles is that of the cuboctahedron:
5.54. Thus, the ratio of 5.54 and 12 makes it 0.46. That means, if S02 in
the foil is 0.85, and in the nanoparticle it is 0.2 (I assume your
degeneracy is 12 as in the foil), it corresponds to the coord. number of
(0.2/0.85)*12 = 2.8 which is too small to correspond to a sample with the
majority of well defined nanoparticles in it.

I can only assume (because it is not clear) that your 0.2 was obtained by
assuming 12 neighbors as in the foil, instead of doing what Matt suggested
to do (amp = S02*N, where N is variable).

Anatoly



-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Juan
Antonio Macia Agullo
Sent: Tuesday, December 12, 2006 12:25 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] CN and bond distances in Artemis



Hi Matt,

Thank you very much for your comments. S02 is a variable for me and it gives
information about the size of the particles (related to coordination
number). For
instance, in the case of Pt foil it should be close to 0.85, however it is
much
smaller (0.20) in the case of platinum nanoparticles (size  2nm), Anatoly
commented
that it is normal this low value in the case of nanoparticles. Probably,
what you
purposed it has more sense than what I did. Then, as I understand, I have to
suppose
reasonable value of S02, lets say 0.85, or shall I have to use S02 from Pt
foil?
Secondly, I define the variable amp = S02*N and, shall I write a value of
one in the
box corresponding to N? I mean, the sight in Artemis shows like this: N:1 X
S02:amp.

Talking about the Nyquist theorem, a higher number of independent points
implies a
higher number of variables that can be used and it is especially useful for
me when
I fit only the first shell (R-range is small) due to the low number of
independent
points obtained. If I use the formula +2, I can define more variables. I
usually
use the crude rule: number of variables  2/3 Nip. I read this +2 formula
described by D.C. Koningsberger et al (Topics in Catalysis 10 (2000)
143-155) and I
though that was ok. What is the origin of this +2?

I have obtained a value of 0.53 for S02 in the case of Pt foil, it suggests
(as
people from this e-mailing list said) that a correction of self absorption
should be
used until reaching a reasonable value for S02 (0.85). After this, I will
apply the
same correction to the samples because they were measured in fluorescence
way too.
My samples contain less than 1% of platinum in weight (about 0.80%) and I do
not
know if there will be self-absorption.

Finally, I would like to ask about the detection of low Z scatterers
(usually O or C
from the support). I read in the aforementioned paper the difference file
technique,  Artemis includes this possibility? How can low Z scatterers be
detected?

Thanks a lot

Best regards,
JA


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RE: [Ifeffit] CN and bond distances in Artemis

[Anatoly Frenkel]

I would remeasure Pt foil in transmission, by all means.

Anatoly



-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Juan
Antonio Macia Agullo
Sent: Tuesday, December 05, 2006 1:32 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] CN and bond distances in Artemis



Hi all,

I did fits with self absorption corrected data (Fluo and Booth algorithms)
and the
value for S02 is 1.20 (0.30). It seems that I am not very lucky, if I take
an
average value (1.20 and 0.50), it should be ok (0.85) jeje, I am joking.

Then...what can I do now?

Thank you very much,

Best regards,
JA

P.S. If I do not answer until Monday do not hate me, I will be on holidays.

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RE: [Ifeffit] CN and bond distances in Artemis

[Anatoly Frenkel]

Hi Matthew,

It should be very easy to send to him Pt foil data, especially because,
based on my and others' tests, Pt data collected at different beamlines are
identical and thus transferable, but what if the beamline settings
(detuning, slit size, gases, etc.) were not optimized for his experiment? To
make sure everything is tuned up correctly, he should take his own Pt foil
data and compare with theory other other people standards (good idea!).
Alternatively, he will have to operate under assumption that everything was
tuned up correctly and his NP data are perfect, but why to take chances?

Anatoly


-Original Message-
From: Matthew Marcus [mailto:[EMAIL PROTECTED]
Sent: Tuesday, December 05, 2006 1:54 PM
To: [EMAIL PROTECTED]; XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] CN and bond distances in Artemis


I imagine somebody has done so and would be willing to provide that data.
Unfortunately, the Newville database doesn't have it,
and I don't think I do.  Anatoly, surely you must have done Pt foil?  Yes, I
know it's best to measure everything on the same
beamline, but it's
not essential.
mam
- Original Message -
From: Anatoly Frenkel [EMAIL PROTECTED]
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
Sent: Tuesday, December 05, 2006 10:37 AM
Subject: RE: [Ifeffit] CN and bond distances in Artemis


I would remeasure Pt foil in transmission, by all means.

 Anatoly



 -Original Message-
 From: [EMAIL PROTECTED]
 [mailto:[EMAIL PROTECTED] Behalf Of Juan
 Antonio Macia Agullo
 Sent: Tuesday, December 05, 2006 1:32 PM
 To: XAFS Analysis using Ifeffit
 Subject: Re: [Ifeffit] CN and bond distances in Artemis



 Hi all,

 I did fits with self absorption corrected data (Fluo and Booth algorithms)
 and the
 value for S02 is 1.20 (0.30). It seems that I am not very lucky, if I take
 an
 average value (1.20 and 0.50), it should be ok (0.85) jeje, I am joking.

 Then...what can I do now?

 Thank you very much,

 Best regards,
 JA

 P.S. If I do not answer until Monday do not hate me, I will be on
holidays.

 ___
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 http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit





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RE: [Ifeffit] CN and bond distances in Artemis

[Anatoly Frenkel]

If you mean that your S02 value for platinum foil is 0.53 instead of the
expected 0.85 or so, you have to first find out why that happened. There are
too many (for a quick list) setup-related and sample-related reasons that
can explain why it happened. You should be careful with your NP data
analysis, since your foil EXAFS acts up.

Anatoly


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Juan Antonio
Maciá Agulló
Sent: Monday, December 04, 2006 2:03 PM
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] CN and bond distances in Artemis


Hi all,

I read your papers Anatoly. You fixed the value of S02 found in the Pt
metal, and the expression in Artemis would be like this: N:1 x S02:
amp·N, right??
I have a low value of S02 in the case of platinum (0.53), how can I
solve the problem?
Bond distances = delR + Reff (with phase correction)?

Thank you very much,

Best regards,
JA




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RE: [Ifeffit] Coordination number

[Anatoly Frenkel]

These references may be useful as the answers to both why and how.

http://pubweb.bnl.gov/users/frenkel/www/PTRU/ptru.pdf

http://pubweb.bnl.gov/users/frenkel/www/PTRU/evolution.pdf

By average, do you mean average betwee the A-B and A-A first nearest
neighbor coordination numbers? They should not be averaged unless A and B
are similar elements, like Cu and Ni. If they have good Z-contrast, EXAFS
can count them separately, see refs above.

Anatoly


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Juan
Antonio Macia Agullo
Sent: Thursday, November 23, 2006 1:16 PM
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] Coordination number



Hi all,

I have a simple question but I am afraid it is polemic. Why people
always calculate coordination numbers and bond distances and how?
I have an e-mail where Bruce described perfectly how to calculate the
coordiantion number for the first shell. But,...if I have bimetallic
catalysts or/and a mixture of structures with several close paths
(similar Reff), then coordination number is an average number? I am not
very sure how to calculate them in Artemis with SO2 and standards.

Thank you very much

Best regards,
JA

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RE: [Ifeffit] Phase corrected Fourier transforms

[Anatoly Frenkel]

My 0.533 Rouble: In my experience with some Mn oxides, the Mn-O FT magnitude
peak's position is 0.5 A lower its corresponding 1NN bond length, while the
Mn-Mn are 0.3 A lower than their bond lenghts. Thus, it would be misleading
for this and other similar compounds to apply theoretical phase correction
of the 1NN to the entire data, as it will shift only one peak correctly.

Anatoly

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Matthew
Marcus
Sent: Saturday, September 23, 2006 4:14 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Phase corrected Fourier transforms


OK, I have to put in my US$0.02/e0.02.  The phase correction can't mean much
if the scattering atoms are different, which is usually
the case.  If the scattering atoms are very heavy, then the phase correction
has a kink in it which could cause strange shapes if applied
to light-atom shells.  I've played with this phase correction and amplitude
correction, while I was at it, and not been very impressed.
One place where it might be useful is in the aforementioned case of heavy
and light scatterers.  If you use the correction for one of
these, then the corresponding shells sharpen and the other ones blur out, so
you can get a rough idea of who's who.  I suspect
this works better if you do the amplitude as well.

A related technique is to use model compounds+FEFF to get 'semi-empirical'
amps and phases which include all the artifacts
of the experiment.  Suppose, for instance, that you're looking at Cu in a
matrix of Fe, and you have data for Cu metal but
not for any known Cu-Fe scattering pair.  You can synthesize a
'semi-empirical' Cu-Fe phase and amp like this:

phi(Cu-Fe) = phi_exp(Cu-Cu)+(phi_theor(Cu-Fe)-phi_theor(Cu-Cu))
amp(Cu-Fe) = amp_exp(Cu-Cu)*amp_theor(Cu-Fe)/amp_theor(Cu-Cu)

If you don't want to do this for modeling, you can use this method for
comparing two spectra which you think might
be alike except for the central atom, by correcting one spectrum with the
difference to make it comparable to the other.

Another aspect to this whole thing is that people are very used to
uncorrected FT's and are aware that you have to add 0.3-0.4A
to the distances.  If you show only corrected FT's, I wonder if that will be
satisfying to the audience.
mam

- Original Message -
From: John J. Rehr [EMAIL PROTECTED]
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
Cc: John J. Rehr [EMAIL PROTECTED]
Sent: Saturday, September 23, 2006 7:18 AM
Subject: Re: [Ifeffit] Phase corrected Fourier transforms



Dear Juan Antonio,

  I personally feel that adding phase correction to the XAFS FT is
highly desirable, and I encouraged its implementation in Athena.
The reasons are the following:

1) Peaks in  non-phase corrected FT are substantially in error.
2) The non-linearity of the phase shifts in high-Z materials leads
to multiple-peaks, thus blurring the FT.
3) Theoretical phase shifts are good enough that adding phase correction
tends to correct the peak positions and the problems due to non-linearities.
4) Adding phase correction does no-harm to the fits. That is, one gets
the same results whether or not phase correction is included.
5) Adding phase correction gives a FT which can be more easily
interpreted by eye, that is the peaks have a more physical interpretation.
On the contrary, non-phase corrected FTs can be mis-interpreted.

Overall, my view is that the phase correction is like a prescription
lens which gives a sharper image. While the image may not be perfect,
at least it's generally much superior to the non-phase corrected FT.

  J. Rehr

On Fri, 22 Sep 2006, Juan Antonio [iso-8859-1] Maciá Agulló wrote:



 Hi all,

 I have read Phase corrected Fourier transforms in Athena manual and now
 I have a big doubt, ¿phase correction or not in a publication?

 I have read also that this correction is different (more complete) in
 Artemis and I am not sure if I should correct also in Artemis and which
 path should I use and why.

 I saw many papers dealing with EXAFS fits and they showed a calculated
 bond distance, I think it is: d = Reff + deltaR, right?

 I also ask for a paper where I can find that deltaE is ok (even for
 high-Z backscatterers) if deltaE  10eV.

 I have high correlations between ss and SO2, and deltaR and deltaE. I
 tried different fits but I can not eliminate them, then...is the fit
 wrong?

 Sorry for these easy questions but I am a novice in XAFS.

 Thank you very much.

 Best regards,
 JA







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