<div dir="ltr">Hey all, <div><br></div><div>This is for your EXAFS notes. Matt provided some really helpful tips on manipulating S0^2 and N in artemis to get fractional coordination numbers, and also just on the fitting process in general. </div><div><br></div><div>Macon<br><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">---------- Forwarded message ---------<br>From: <strong class="gmail_sendername" dir="auto">Matt Siebecker</strong> <span dir="auto"><<a href="mailto:matthew.siebecker@ttu.edu">matthew.siebecker@ttu.edu</a>></span><br>Date: Wed, Jul 29, 2020 at 3:09 PM<br>Subject: Re: Can you spare some exafs advice?<br>To: Macon Abernathy <<a href="mailto:maber001@ucr.edu">maber001@ucr.edu</a>><br></div><br><br>
<div>
<font face="Arial">Hi Macron,<br>
<br>
It's nice to hear from you. And I'm glad the tutorials are
helpful. Even with the wealth of information out there on EXAFS
fitting, when it comes to the details, it is hard to find a
specific answer.<br>
<br>
For coordination numbers of the higher shells (like 2nd and 3rd
shells), I would still employ the same approach (i.e., setting CN
to "guess" parameter in Artemis as you described and fixing SO2 to
some determined value or 0.9). I this method is appropriate for
all coordination shells because it lets the software do the heavy
lifting, in terms of determining if a CN for a particular
scattering path is significant or not. <br>
<br>
I also like this approach because it can help confirm a hypothesis
if the sorption complex is mononuclear or binuclear (which in this
case the CN of the second shell Fe or Mn would be close to 1 or
2). Or, if the CN is calculated to be considerably higher, then
perhaps a surface precipitate is forming. If the CN for those
shells is fixed, then that detail may be missed. </font><font face="Arial"><font face="Arial"><font face="Arial">Additionally,
manually iterating between 0.1 CN units to test for fit
improvement is tedious and you might not test all the
variations.</font></font><br>
</font><font face="Arial"><br>
That said, you could make the argument for not doing guessing CN
(i.e., fixing CN). </font><font face="Arial"><font face="Arial">You
will see many examples where people fix CN based on a structural
model (which can also be rationalized).</font> Say for example,
if you think that it is a nonnuclear complex where the second
shell would ideally be 1. Or, if it is a binuclear complex, where
the second shell would be 2. You could make the case to "set"
those to be 1 or 2 to see how the fit behaves. I think there have
also been attempts to assign a % of nonnuclear or % binuclear
complexes based on more complex fitting models with As on Fe or Mn
oxides. Often, as you know, sorption is not all entirely one
species, but a mix of those species.<br>
<br>
If you have a mixed system with Mn and Fe oxides, it will be very
challenging to distinguish between those two adsorbents.<br>
</font><br>
<font face="Arial"><font face="Arial">In general, I would advise to
fix all other paths in a fit to focus on one path at a time at a
time. Say, for example, fix the first shell entirely (after
obtaining a reasonable first shell fit) and if your second shell
has 2 or 3 paths, then work on them 1 at a time (i.e. fix them
so as to not have too many variables). Eventually, the goal is
to produce a stable fit while floating (i.e., guessing) as many
variables as possible. But, guessing them all at once (without
being close to the best fit) will often lead to strange fits and
errors that are unreasonable.<br>
<br>
</font>If you can rationalize the reason for a fitting method
(objectively), than it is worth a try.<br>
<br>
Best,<br>
Matt<br>
<br>
</font>
<pre cols="72">Matthew G. Siebecker, Ph.D.
Assistant Professor
Applied Environmental Soil Chemistry
Dept. Plant and Soil Science
Texas Tech University
Office +1-806-834-0266
<a href="http://www.depts.ttu.edu/pss/ESC" target="_blank">http://www.depts.ttu.edu/pss/ESC</a></pre>
<div>On 7/27/2020 7:13 PM, Macon Abernathy
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hey Dr. Siebecker,
<div><br>
</div>
<div>I'm a graduate student in Sam Ying's lab at UC Riverside,
We had a chance to meet briefly during ACS in San Diego last
August, and I've benefited greatly from your EXAFS tutorials
on youtube. </div>
<div><br>
</div>
<div>I was wondering if you'd be able to answer a question for
me that I've been having a hard time answering based on what I
can find in the ifeffit mailing list, or in resources like
Calvin's EXAFS for Everyone or Bunker's Intro to EXAFS. </div>
<div><br>
</div>
<div>Basically, how do you get fractional coordination numbers
out of Artemis, particularly for 2nd and 3rd shell atoms? (i.e
maybe a measurement support 5.6±0.4 oxygens in a first shell
rather than 6, and 1.6 ± 0.2 Fe in the second shell rather
than 2)</div>
<div><br>
</div>
<div>I've seen some answers for getting a fractional
coordination number for the first shell that involves setting
"N" to 1, and then setting "amp" to "0.9*CN", but have had a
hard time finding out if that's appropriate for 2nd and 3rd
shell atoms, which in my systems are the atoms of interest,
usually because I'm trying to figure out what types of
adsorption complexes form between my adsorbate (which I have
exafs on-often As, V, Cr, etc) and my sorbent surface (often
Mn or Fe oxides). </div>
<div><br>
</div>
<div>I'd really appreciate any advice you have. </div>
<div><br>
</div>
<div>Thanks for taking the time, </div>
<div><br>
</div>
<div>Macon</div>
<div><br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr" data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">Macon J. Abernathy
<div>Ph.D Candidate</div>
<div>Department of Environmental Toxicology</div>
<div>University of California, Riverside</div>
<div><a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fucrsoils.weebly.com%2F&data=02%7C01%7Cmatthew.siebecker%40ttu.edu%7Cddca640059fa487af02708d8328b2a2b%7C178a51bf8b2049ffb65556245d5c173c%7C0%7C1%7C637314920574274284&sdata=qa3yNDqePACN4qhZBPkUoL4uaIbpvBKinzKvutSbSO8%3D&reserved=0" target="_blank">https://ucrsoils.weebly.com/</a><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
</div>
</div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr">Macon J. Abernathy<div>Ph.D Candidate</div><div>Department of Environmental Toxicology</div><div>University of California, Riverside</div><div><a href="https://ucrsoils.weebly.com/" target="_blank">https://ucrsoils.weebly.com/</a><br></div><div><br></div><div><br></div></div></div></div></div></div></div></div></div>