Yun Xu | 18 Nov 23:32 2014
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experimental standard

Hi all
I have a complex oxide BaTi8-xGaxO16. What standards I should run?
Ga is the dopant. I guess I should run the sample without dopant BaTi8O16 as standard, or the simple oxide as BaO, TiO2 Ga2O3?  or is the standard necessary?
Also, I have colleage working on DFT, I assume the theoretical standard is the result from the DFT calculation, and by using the coordinates of the atoms, I can run FEFF and fit the data.
Thanks
Yun
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Bruce Ravel | 11 Nov 16:49 2014

Re: Fwd: Re: Re: problem about negative

On 11/11/2014 10:19 AM, Bruce Ravel wrote:
> Rbkg>1.1 can avoid the first peak,but the remaining curve is somewhat
> not smooth.How to distinguish whether a long wavelength oscillation
> appear as a real peak or false one?I am confused about it.
>         I find when I avoid the first scattering peak after white
> line(kmin=4.8 maybe too large),the first peak of R space
> disappeared.Because usually the first scatering peak is related to the
> first coordiantion shell,can I think the first peak in R space less 1A
> is a real peak instead of noise?

Zhanfei,

As I said yesterday, I don't know anything about your sample, so it is 
hard for me to know what the "right" answer is to your problem.  But I 
can make some observations and some suggestions.

  * Your data range is really short.  As you seem to have noticed 
(judging from the very short k-range in your project file), your data 
has serious systematic problems starting at 9 or 10 inverse Angstroms. 
I cannot quite tell, but your data appear to be transmission data.  Well 
it is possible that you have some instability or nonlinearity at the 
beamline, I would guess that your sample is not very homogeneous.  It is 
possible that more disciplined sample preparation might help extend that 
range of the interpretable data.

  * You are right that slightly increasing the Rbkg value seems to make 
a positive difference in the extracted chi(k) data.  Your data seem to 
be an example of the sort of data I was alluding to yesterday.  The 
background subtraction is difficult because it is difficult to 
distinguish the Fourier components of the background function from the 
Fourier components of the data.  I think that the background subtraction 
with Rbkg=1.1 looks much better than with Rbkg=1.0, but given how 
different they are, you have to be concerned about the correlations 
between the background and the parameters of the data.

It is clear that your data are of the sort for which background 
subtraction is difficult.  So how do you know what is an acceptable 
background subtraction?

Well, using only Fourier methods, I think we have demonstrated that you 
cannot know the right answer without some kind of prior knowledge.

So, how do you get that prior knowledge?

Well, my advice is to first solve some simpler problems.  Measure your 
standards.

Measure the common forms of moly oxide and moly sulfide.  Measure moly 
metal.  Analyze all of them.  The advantage of the standards is that you 
know what the answer should be.  Do the data processing and data 
analysis.  Make sure that, when you do the analysis, you get the right 
answers.

Having done that exercise, you will then have a lot more knowledge about 
what the various forms of moly oxide look like and what the challenges 
are when doing the data processing and data analysis.

Some questions:

   - Are there any forms of moly oxide for which the bond length is as 
short as 1.6?  If so, do the conditions of formation exist in your 
system?  Is your sample of a valence consistent with the valence of the 
Mo when it has such a short bond?

  - If you convince yourself that it is possible for moly to have an 
oxygen atom at 1.6 or 1.7, what did you have to do with your standard to 
get a sensible analysis of the EXAFS data?  Hopefully, that will guide 
you to doing a sensible analysis of your unknown sample.

  - If none of your moly oxide standards have an O atom at 1.6 or 1.7, 
why do you think it is chemically reasonable for your unknown sample to 
have such a short bond?  If, in fact, that short bond doesn't exist 
elsewhere in nature, why would your sample magically have such a short bond?

  - If you do not believe in such a short bond, then does your 
experience with the standards give you the confidence to increase Rbkg 
such that the low-R signal is removed by the background function?

I completely understand that you have a compelling reason to understand 
your unknown sample and that I am suggesting that you spend a good chunk 
of time measuring and analyzing a bunch of standards that are not your 
actual research project.  That might seem like time that takes you away 
from your real goal, but you have already demonstrated that you are 
stumped by your real goal.  I am saying the only way to get over your 
current hurdle is to take a step back and gain a deeper understanding of 
the data, the physics of EXAFS, the methods of EXAFS analysis, and the 
intricacies of your current problem.

B

--

-- 
  Bruce Ravel  ------------------------------------ bravel <at> bnl.gov

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

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/
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Katherine M. Davis | 10 Nov 15:34 2014
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installing Demeter on Yosemite

Dear all,

I was wondering whether anyone had tried installing the software on the new Mac OS (10.10 Yosemite)? Everything seems to work fine initially. I installed Macports and checked it installed correctly. At least when I test various commands, it seems to work. The sudo port install xorg-server demeter-devel command ran for about 3 hours until it quit. I tried restarting, but whenever I run the command, the following error message appears:

--->  Computing dependencies for xorg-server

--->  Cleaning xorg-server

--->  Computing dependencies for demeter-devel

--->  Configuring demeter-devel

Error: org.macports.configure for port demeter-devel returned: configure failure: command execution failed

Please see the log file for port demeter-devel for details:

    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_demeter/demeter-devel/main.log

To report a bug, follow the instructions in the guide:

    http://guide.macports.org/#project.tickets

Error: Processing of port demeter-devel failed


I will post the log file at the bottom of the email. The last 8 lines are as follows:

portbuild::add_automatic_buildsystem_dependencies
:debug:clean No need to upgrade! p5.16-term-twiddle 2.730.0_1 >= p5.16-term-twiddle 2.730.0_1
:debug:clean epoch: in tree: 0 installed: 0
:debug:clean p5.16-text-template 1.460.0_1 exists in the ports tree
:debug:clean p5.16-text-template 1.460.0_1  is the latest installed
:debug:clean p5.16-text-template 1.460.0_1  is active
:debug:clean Merging existing variants '' int 

Would anyone be able to help me with this? Any advice would be useful. Thanks for your time.

Best,
Kate Davis



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ZHAN Fei | 9 Nov 07:54 2014
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too small bond length in R space

Dear all:
  I encounter a problem of exafs fit in an example of Mo which have Mo-O Mo-S Mo-Mo bond.The problem is that the Mo-O peak in R space has too small bond length (less than 1.4A(+0.5A for phase correction) ).Because when 1.2>rbkg>0.68 there is little change in spectrum of R and k space,and when I increase the value of rmin of forward Fourier transform the peak changes little,so I think it's not a noise.But when I try to fit it use the 1.35A path of Mo-O,I can't fit it well.
Could you give me some advise about fit too small bond length,or recommend papers of similar situation?
picture of R space is attached.
Thanks
Sincerely,
zhanfei
ihep of China








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kaziz sameh | 4 Nov 12:29 2014
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Structure of Au2O3

Hi all,

I need the structure of Au2O3.

if you can help me I would be very grateful.

Kaziz


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Matthias Filez | 4 Nov 11:39 2014
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Larch-0.9.24 with Python2

Dear mailing list user,
 
When running an example file of Larch-0.9.24 with Python2 on Ubuntu x86_64, the following error was reported.
  File "Py_usinglarch.py", line 32, in <module>
    autobk(xafsdat.energy, xafsdat.mu, rbkg=1.0, _larch=my_larch)
  File "/usr/local/lib/python2.7/dist-packages/larch/__init__.py", line 37, in wrapper
    return fcn(*args, **keywords)
  File "/usr/share/larch/plugins/xafs/autobk.py", line 187, in autobk
    fit.leastsq()
  File "/usr/local/lib/python2.7/dist-packages/larch/fitting/minimizer.py", line 395, in leastsq
    lsout = leastsq(self.__residual, self.vars, **lskws)
  File "/usr/local/lib/python2.7/dist-packages/larch/fitting/minimizer.py", line 222, in leastsq
    shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
ValueError: need more than 1 value to unpack

Is Larch-0.9.24 compatible with Python2 on Ubuntu x86_64? If not, what packages and dependencies could we install to make it work on Python2? Or is Larch-0.9.24 only compatible with Python3?
 
Many thanks in advance,
Matthias
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pushkar shejwalkar | 4 Nov 10:22 2014
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Reporting the fitting data (uncertainty associated with N)

Dear All, 
          I have seen and also been told by few professors that when you report the fitting you must report the uncertainty associated with the measurement as evaluated by the program used for the fitting. 
Now, When I do the fitting I typically get the +/- values for E0, delR, ss and SO2. However, the N value we always put either 1,2 or such whole integers. Is there any way to find out the uncertainty associated with the coordination number (N used in XAFS equation)? 
If so how to find such uncertainty? can we see this in the log file generated after the fitting is over? 
Thank you very much for the help

Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,JSPS Fellow
Hokkaido University,
Sapporo,
Japan

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stephen.parry | 3 Nov 16:41 2014
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inp file - artemis crashing when running feff calc on manually generated inp file

Can someone spot the problem with the attached inp file?

 

I have manually reduced a cif file to remove multiple occupancy sites and cut down the unit cell from a large structure. I should be left with the first shell as Cartesian co-ords. I have then overwritten the co-ords and ipots into an old atoms generated inp file.

 

I can't spot any formatting problems but when I run the feff calculation in artemis the program crashes.

 

The feff.run error log file contains nothing obvious.

 

 

"Feff 6L.02

TITLE Ga_c6h5f

TITLE Ga

TITLE S

TITLE Gallium

TITLE Note: mixed occ removed manually SP

Calculating potentials and phases...

     free atom potential and density for atom type    0

     free atom potential and density for atom type    1

     free atom potential and density for atom type    2

     overlapped potential and density for unique potential    0

     overlapped potential and density for unique potential    1

     overlapped potential and density for unique potential    2

     muffin tin radii and interstitial parameters

"

 

 

 

Any help appreciated.

 

Regards,

Steve

 

 

 

 

=================

Dr Stephen Parry

Support Scientist, B18

Diamond Light Source Ltd.


 

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Attachment (ga_Feff.inp): application/octet-stream, 3303 bytes
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Bruce Ravel | 28 Oct 22:00 2014

Mac support for Demeter


Hi gang,

I just heard from Frank Schima, the fellow who kindly provided
packaging of Demeter via MacPorts.  Frank is moving to a new position
at NIST Boulder and will no longer be providing IT support for the
group out there that does some XAS.  That means his availability to
maintain and update the MacPorts package will be somewhere between
slim and non-existent.  Here is what he said:

    I am no longer working for Quantum Devices as of Friday,
    10/31/2014. So I will no longer be involved in updating Demeter and
    will be unsubscribing from the Ifeffit mailing list. For updates
    please follow the Macports procedures to request an update in
    Macports by opening a Trac ticket [1]. I may actually be able to
    perform the update but I cannot guarantee anything.

    [1] <https://trac.macports.org/newticket>

I know that this support for the Mac was valued by many people in our
community, so Frank will be missed.

I am not able to provide packaging support for Mac users.  Even if I
had the time or energy to take on a new packaging responsibility, I
simply don't own a Mac.

This would be a good time for someone to step up and take over
responsibility for the Mac package.  It seems that Frank has done the
bulk of the work.  The MacPort ecosystem seems to be well supported
and well documented, so I would think that someone else could readily
step into that role.

B

--

-- 
  Bruce Ravel  ------------------------------------ bravel@...

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 535A
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/
Karina Mathisen | 28 Oct 17:06 2014
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Saving data as chi(E) from Athena?

To whom it might concern

 

 

The older version of Athena had the possibility to save the data as chi(E), which is sorely missed in the newer version. Is there an easy fix for this?

 

Best regards

 

Karina Mathisen

 

 -------------------------------------------------------------------------------

Karina Mathisen, PhD

Deputy Head for teaching, Department of Chemistry

NTNU - Norwegian University of Science and Technology

Associate professor

Karina.Mathisen-XuRWurlvMDs@public.gmane.org

+47 735 96218

Realfagbygget E2-106, Høgskoleringen 5, Trondheim, Norway

--------------------------------------------------------------------------------

 

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Scott Bechler | 27 Oct 22:08 2014
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Setting E0 for imported data

Hello,

I am trying to compare a sample with unknown lead bonding with some lead standards. After entering in all of the data and standard scans with reference channels, I aligned the reference channels, which shifted the data scans as well. 

My question regards the E0 of the data and standard scans. Even though the scan itself shifted, the E0 still remains where it was when I imported it, prior to aligning the reference channels. The peak itself shifted, but the program still marks the E0 at the previous peak position. Is this an issue? If so, how do I adjust the E0 of the scans the same amount that the reference channels shifted?

It does say how much the scan shifted, so I went in and manually changed the E0 of each scan so that it correlated with this shift. Would this be an effective solution? If this does solve my problem, is there a less labor-intensive way to solve it in the program?

Thanks so much for your help!
-Scott
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