Re: [Ifeffit] Using Larix from Jupyter notebook

[Mauro ROVEZZI]

 Dear Yohei, The example you are looking for is here: https: //urldefense. us/v3/__https: //github. com/xraypy/xraylarch/blob/537aeae71f8e320713986242deae9e3598c4de21/examples/Jupyter/struct2xas_examples. ipynb__;!!G_uCfscf7eWS!elR-TJN7jCxKN75SBbpCnK0NZ9uP38uurIxRaRGkB8CM3Ma0zxJNpcEh2RM_YMJ_mNqxVi1IgY-XY90Yz8ZyDzGqDwBteYcNBSvx5g$




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Dear Yohei,

The example you are looking for is here:

https://urldefense.us/v3/__https://github.com/xraypy/xraylarch/blob/537aeae71f8e320713986242deae9e3598c4de21/examples/Jupyter/struct2xas_examples.ipynb__;!!G_uCfscf7eWS!elR-TJN7jCxKN75SBbpCnK0NZ9uP38uurIxRaRGkB8CM3Ma0zxJNpcEh2RM_YMJ_mNqxVi1IgY-XY90Yz8ZyDzGqDwBteYcNBSvx5g$

We are collecting Jupyter notebooks examples in `examples/Jupyter` and 
we will soon add a gallery of them directly in the documentation.

Mauro

On 24/03/2024 13:35, Yohei Uemura wrote:
> Hi all I read the documentation of Larch and Larix can generate a feff 
> input file from a xyz file. https: //cars. uchicago. 
>  edu/xraylarch/xasviewer/overview. html Does anyone have a python script 
> to generate a feff input file from a xyz file using
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
> This message came from outside your organization.
> ZjQcmQRYFpfptBannerEnd
> Hi all
> 
> I read the documentation of Larch and Larix can generate a feff input 
> file from a xyz file.
> https://urldefense.us/v3/__https://cars.uchicago.edu/xraylarch/xasviewer/overview.html__;!!G_uCfscf7eWS!elR-TJN7jCxKN75SBbpCnK0NZ9uP38uurIxRaRGkB8CM3Ma0zxJNpcEh2RM_YMJ_mNqxVi1IgY-XY90Yz8ZyDzGqDwBteYdOs-hh5A$ 
> 
>
> Does anyone have a python script to generate a feff input file from a 
> xyz file using Larix?
> 
> Best regards,
> Yohei
> -- 
> 
> Yohei Uemura (Ph.D)
> Instrument scientist
> FXE beamline, European XFEL GmbH
> Address : Holzkoppel 4, 22869 Schenefeld, Germany
> Phone: +49-40-8998-6006
> 
> 上村洋平
> 所属 : FXE beamline, European XFEL GmbH,
> 住所 : Holzkoppel 4, 22869 Schenefeld, Germany
> 電話 : +49-40-8998-6006
> 
> 
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Re: [Ifeffit] XAS viewer unit detection during data reading

[Mauro ROVEZZI]

Dear Edmund,

That's great that you have find why the ASCII data parser in Larch was 
not detecting automatically the energy column from the labels in the 
header. The current choice is to look for "energy" or "ene" in the 
header to identify a data column as energy array.


Please, if you are willing to publicly share and example data file from 
P65, we could include it in the xafsdata examples here:


https://github.com/xraypy/xraylarch/tree/master/examples/xafsdata/beamlines

Those files are used for running the automatic tests and permit us 
improving the quality of Larch's code.


This is valid for any beamline who wants to contribute, even if I 
strongly encourage distributing data in HDF5/NeXus format instead of 
ASCII files.


Best,
Mauro

On 01/03/2023 14:31, Edmund Welter wrote:

Dear Maurizio, Matt,

I just checked why some older files from my beamline work correctly 
while the newer ones are not identified as xas data. After your 
explanation the reason is quite simple. In the old format the last line 
of the header was


#enc_energy mono_energy mono_bragg Step_Pos mono_X1vert

After rewriting major parts of the beamline software among other things 
the last line of the header changed to:


# E_enc E_step Bragg_enc Bragg_step...

Once I replace E_enc with something like energy_enc or enc_energy the 
data is correctly identified as xas data.


So, the easiest solution for data taken at P65 is that I will change the 
header in the data file so that the first column has a name that 
contains "energy". I think i remember that Athena was looking for the 
first column were the value of every point n+1 is larger than the value 
of point n. it then usually correctly identified that column to be the 
energy axis. However, I think labeling the columns correctly, that means 
following common accepted conventions, is much easier than programming a 
bunch of complicated fail safe energy axis recognising procedures.


Cheers,

Edmund



On 28.02.23 18:16, Matt Newville wrote:

Hi Siebe,

Just to agree with Edmund and Mauro:  selecting "energy" and changing 
data type from "raw" to "XAS" should help.  But, you would have to do 
this for every file, which is not ideal.


The file reader is trying to guess whether data is in energy (and if 
so, what units are used) and whether it is really XAS data or some 
other kind of data. I suspect that it is defaulting to "raw" because 
the energy column is not labeled "energy", but "col1" -- it sort of 
looks like the reader is not doing a good job of guessing what the 
columns mean.


Posting a file would help diagnose why it is guessing wrong.  The file 
reading does try to guess what beamline a data file came from, so if 
you send a file, maybe we can add enough hints for files from that 
beamline to work more reliably.




On Tue, Feb 28, 2023 at 6:37 AM Welter, Edmund  
wrote:


Dear Siebe,

did you try to change the data type from "raw" to XAS. If you
click on the small arrow on the right you should have the choice
between xas and raw. On my computer that works and after that I
can choose the unit for the X-axis. For some reason "raw" seems to
be the preset choice. Maybe Matt could change that, I fell into
this trap several times.

Cheers,
Edmund


*From: *"van der Veer, Siebe" 
*To: *"XAFS Analysis using Ifeffit"

*Sent: *Tuesday, 28 February, 2023 13:16:18
*Subject: *[Ifeffit] XAS viewer unit detection during data reading

Dear all,
I am not sure if this mailing list is the correct medium for this
question. Apologies, if not.

I am looking to import files in XAS viewer, which worked fine in
ATHENA, but in XAS viewer the correct units of the data are not
detected and I cannot manually change them. I can get a plot of
the data, but the data is not recognized by the software as XAS
data, i.e. a lot of plotting/conversion options do not show.

I hope the following screenshots provide sufficient information to
illustrate my issue.

Reading in a .dat file of fluorescence data. I can't change the
units in the marked area.

image.png

The data can be read into the XAS viewer, but I don't have the
regular plotting options in these dropdown menus.

image.png

Any advice would be much appreciated.

Kind regards,


-- 
*Siebe van der Veer* | *PhD student*

Nanostructures of Functional Oxides | Zernike Institute for
Advanced Materials
University of Groningen | Nijenborgh 4, 9747 AG Groningen | The
Netherlands
Email: s.van.der.v...@rug.nl|

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Re: [Ifeffit] XAS viewer unit detection during data reading

[Mauro ROVEZZI]

Dear Siebe,

In addition to the quick workaround suggested by Edmund, if you could 
send your data file to me (here or by private email), I could have a 
look why xas_viewer is not detecting the energy scale automatically.


@Edmund, usually the "xas" file type is setted automatically when the 
x-axis is identified as energy scale in the `read_ascii` function. If 
you have data files that are not detected correctly as XAS data files, 
please, do not hesitate to send them to us.


Best,
Mauro

On 28/02/2023 13:37, Welter, Edmund wrote:

Dear Siebe,

did you try to change the data type from "raw" to XAS. If you click on 
the small arrow on the right you should have the choice between xas and 
raw. On my computer that works and after that I can choose the unit for 
the X-axis. For some reason "raw" seems to be the preset choice. Maybe 
Matt could change that, I fell into this trap several times.


Cheers,
Edmund


*From: *"van der Veer, Siebe" 
*To: *"XAFS Analysis using Ifeffit" 
*Sent: *Tuesday, 28 February, 2023 13:16:18
*Subject: *[Ifeffit] XAS viewer unit detection during data reading

Dear all,
I am not sure if this mailing list is the correct medium for this 
question. Apologies, if not.


I am looking to import files in XAS viewer, which worked fine in ATHENA, 
but in XAS viewer the correct units of the data are not detected and I 
cannot manually change them. I can get a plot of the data, but the data 
is not recognized by the software as XAS data, i.e. a lot of 
plotting/conversion options do not show.


I hope the following screenshots provide sufficient information to 
illustrate my issue.


Reading in a .dat file of fluorescence data. I can't change the units in 
the marked area.


image.png

The data can be read into the XAS viewer, but I don't have the regular 
plotting options in these dropdown menus.


image.png

Any advice would be much appreciated.

Kind regards,


--
*Siebe van der Veer* | *PhD student*
Nanostructures of Functional Oxides | Zernike Institute for Advanced 
Materials

University of Groningen | Nijenborgh 4, 9747 AG Groningen | The Netherlands
Email: s.van.der.v...@rug.nl |

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Re: [Ifeffit] FDMNES Simulation for ZnO

[Mauro ROVEZZI]

Dear Danting,

As suggested by Carlo, reducing the core-hole broadening in the 
convolution parameters will give sharper features in the simulation. 
After that, I would adjust the Fermi level (again, at the convolution 
step) to get a better agreement with the first shoulder below the white 
line. Furthermore, you may adjust the lattice parameter to get a better 
agreement with the fine structure. If the sample is single crystal and 
wurtzite, you should take into account the polarization too.


To get a more detailed feedback, it would be good practice to share the 
FDMNES input file (including the convolution parameters) and more 
details about the measurement (e.g. transmission mode or fluorescence?, 
which polarization?, geometry?, monochromator resolution?, etc.) and the 
sample (powder or single crystal? Zincblende or wurtzite?, etc.).


Best,
Mauro

On 03/02/2023 17:12, Chen, Danting wrote:

Dear All,

I tried to run some simulations through FDMNES about XANES of ZnO with 
the absorber of Zn, and there are the results for simulated ZnO (red) 
compared with the experimental one (Green curve).


The white line matches well but the two additional peaks are not shown 
in the spectrum of simulated ZnO. I attached the input file for FDMNES 
here. Do you have any idea to improve it? I am quite new to running the 
simulation and would appreciate if you can give me some directions to 
modify it.


Best Wishes,

Danting


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Re: [Ifeffit] found some issues found in larch (read-in issues)

[Mauro ROVEZZI]

Dear Stefan,

Thanks for reporting these issues. Some of them are already known to us, 
but require time for fixing and implementing new features.


I take the occasion to say that anybody with Python programming skills 
is welcome to contribute and help with the development of Larch. Having 
a community of developers instead of always asking to one single person 
should be strongly considered.


Going back to your specific questions, here my two cents contribution.

On 26/10/2022 11:46, Mangold, Stefan (IPS) wrote:

Dear All, dear Matt,

all tests were done on Macs (one M1 & one Intel) with the latest version your 
software & latest OS.

1. Read-In of spec files works, but only one file at once. Even if multiple 
files are selected

>

2. If one tries to load text-files it is possible to load data form multiple 
files as long as you don’t try to load also the reference spectra. If you load 
the reference  also the read-in stopps at the transmission/fluorescence 
spectrum of the second file selected.


These are related to:

https://github.com/xraypy/xraylarch/issues/367

Furthermore, with respect to an ASCII file, a Spec file may contain 
multiple scans, so it is impossible to know in advance which scan to 
select if one selects multiple Spec files to load.


To my opinion, when you need to read multiple data from many files, the 
simplest approach is to write a small python script (or Jupyter 
notebook) that reads the data and save them in an Athena project file or 
Larch session that you can then easily read back with xas_viewer.


I can further help with that.


3. Trouble, that I sometimes can’t unmount network volumes after reading from 
them, larch saved on local discs. MacOS claims that python has files open; no 
other python program running


I let Matt or somebody else reply on this point.


4. unable to save the data of one XAS-viewer while having two xas-viewer open.


This is related to:

https://github.com/xraypy/xraylarch/issues/410

Best,
Mauro
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Re: [Ifeffit] Larch install error on MacOS 12.2

[Mauro ROVEZZI]

Dear Stefan,

Please, follow the installation instructions here:

https://xraypy.github.io/xraylarch/installation.html

If the first way (via binary installers) does not work for you, you have 
two options:


a) make a clearer report of what is not working. "Larch didn't launch" 
does not help that much to understand what went wrong on your machine. 
You may open a shell and type "larch" or "xas_viewer" to get a more 
explicit error message.


b) install via the second way listed in the documentation, that is via 
the GetLarch.sh script.


Hope that this will fix your issue.

Best,
Mauro

On 09/02/2022 09:05, Mangold, Stefan (IPS) wrote:

Dear all,

I upgraded a machine to 12.2 (MacPro), Larch was installed via binary 
installer. Afterwards Larch didn’t launch. I did a re-install with the binary 
installer and this didn’t work, because already installed. deleted it, but this 
also didn’t work

tried

pip install xraylarch

stopped
with
ERROR: Failed building wheel for fabio
Failed to build fabio

also no director with XAS viewer created.


best regards

Stefan Mangold

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[Ifeffit] Post-doc in catalysis at the ESRF

[Mauro ROVEZZI]

Dear all,

I'd like to advertise for a post-doc position in catalysis at the French 
CRG spectroscopy beamlines at the ESRF:


https://bit.ly/32FaDCQ

Please, feel free to diffuse it.

Best,
Mauro

--
Mauro Rovezzi
CNRS-OSUG | French CRG @ ESRF
Beamlines FAME (BM30) & FAME-UHD (BM16)
71 Avenue des Martyrs, 38043 Grenoble, France
Tel: +33(0)47688 2963 | Office: LOB-2-50
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Re: [Ifeffit] Issues reinstalling Larch, error creating desktop shortcut for macOS

[Mauro Rovezzi]

Dear Lauren,

Sorry for the trouble, this is a known bug that shows up with the 
upgrade to `silx==1.0.0`, a dependency of Larch. We have fixed it in the 
master brach of Larch on Github, as discussed here:


https://github.com/xraypy/xraylarch/issues/332

The quick fix is to reinstall larch with:

GetLarch.sh --devel

This will install a development version that is currently equivalent to 
0.9.57 but with this bug fixed.


Best,
Mauro


On 2022-01-04 21:51, Lauren N. Pincus wrote:

Hi Matt,

I'm having an issue with reinstalling Larch. I'm using macOS Catalina 
10.15.7. I had Larch previously installed and it was working well, but 
found I was no longer able to open up XAS Viewer. The application would 
start and then quit.


So, I removed Larch from my system and tried to reinstall it. I first 
used the mac installer but would get an error that the "Installation 
failed. The installer encountered an error that caused the installation 
to fail."


I then tried the installation using the script in terminal. This 
appeared successful, but no desktop shortcut was created. I tried to 
create a desktop shortcut using larch -m but get the following error:


(base) laurenpincus@lnp24mbp2020 ~ % larch -m

Traceback (most recent call last):

File "/Users/laurenpincus/xraylarch/bin/larch", line 5, in 

from larch.apps import run_larch

File 
"/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/__init__.py", 
line 52, in 


from . import builtins

File 
"/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/builtins.py", 
line 22, in 


from . import io

File 
"/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/__init__.py", 
line 39, in 


from .specfile_reader import (str2rng_larch, read_specfile, open_specfile,

File 
"/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/specfile_reader.py", 
line 26, in 


from silx.io.convert import write_to_h5, _is_commonh5_group

ImportError: cannot import name '_is_commonh5_group' from 
'silx.io.convert' 
(/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/silx/io/convert.py)


(base) laurenpincus@lnp24mbp2020 ~ %


Thanks,
Lauren

Lauren Pincus, PhD
NSF Earth Sciences Postdoctoral Fellow
Princeton University
Department of Geosciences

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Re: [Ifeffit] Problem in xrayLarch installation

[Mauro Rovezzi]

Dear Latif,

Thanks for reporting this. Unfortunately `pip` is not able to correctly 
install all dependencies of Larch. The way to go is to install those 
dependencies via `conda`.


Under Windows, this is achieved by running the script `GetLarch.bat` 
(https://raw.githubusercontent.com/xraypy/xraylarch/master/installers/GetLarch.bat). 
This script will download and install a minconda distribution, plus 
install Larch in it.


Seen you already have Anaconda installed, you could simply run the 
following commands from your Anaconda prompt:


conda install -yc conda-forge wxpython tomopy scipy matplotlib 
scikit-image scikit-learn pymatgen pycifrw

pip install wxmplot wxutils lmfit asteval pyshortcuts pyfai xraylarch

If this does not work, please, let me know. I have created a related 
Github issue in order to avoid such troubles in the future:


https://github.com/xraypy/xraylarch/issues/333

Best,
Mauro

On 2021-12-15 08:20, Latif Ullah Khan wrote:

Dear Sir Madam,

   I hope you are doing well, I Latif Khan, working as a 
beamline scientist at XAFS beamline SESAME light source. I was using 
LARCH on my Anaconda python environment at window PC. Now I re-install 
and upgrade the Anaconda to python 3.9. I am trying to install the 
xrayLarch from Anaconda command prompt (python 3.9), using “pip install 
xraylarch” . However, it is not installing and give me an following error:


If you kindly help me in this regard, I will be grateful to you.

Thank you in advance

Best regards

Latif


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[Ifeffit] List of online XAS databases

[Mauro Rovezzi]

Dear all,

On 2021-10-25 04:53, Matthew Newville wrote:
This is not exactly an answer about the XAS data available with 
Hephaestus, but you might find some additional useful XAS spectra  at 
the following online XAS databases:


https://xaslib.xrayabsorption.org/elem/ 


http://ixs.iit.edu/database/ 
https://www-ssrl.slac.stanford.edu/mes/spectra/index.html 

https://www.esrf.fr/home/UsersAndScience/Experiments/XNP/ID21/php.html 

https://pfxafs.kek.jp/xafsdata/list.php 

https://www.cat.hokudai.ac.jp/catdb/index.php?action=xafs_dbinpbrowse=2=13 

https://mdr.nims.go.jp/catalog?f%5Bmember_of_collections_ssim%5D%5B%5D=MDR+XAFS+DB=en 



There may be others!



I would add to the list our SSHADE/FAME database too:

https://www.sshade.eu/db/fame

Please, feel free to extend the list if you are aware of others. I agree 
with Matt that an ad hoc Working Group of the IXAS on this topic is welcome.


Best,
Mauro
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Re: [Ifeffit] request help about Zn standard spectra

[Mauro Rovezzi]

Dear Qiang,

Here some Zn K-edge spectra from the SSHADE/FAME database:

https://www.sshade.eu/search?db=fame=%22Zn%20K%20edge%22

Best regards,
Mauro

On 2020-01-26 21:06, Qiang Chang wrote:

Hi all,

May I ask if you have some standard spectra for Zn elements, like 
metallic Zn, ZnO, ZnNx, etc. I am vey appreciative if you could send me 
some copies.


  Thank you very much.

Best regards,
Qiang

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[Ifeffit] [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source

[Mauro Rovezzi]

Dear all,

I decided to upgrade ifeffit-1.2.11 on my Ubuntu 8.10 (Intrepid Ibex) 
desktop machine. Well, up to now I have always worked with PGPLOT  
Ifeffit binaries from Carlo that are just working fine but seen that 
they are still not ready for the new version I decided to build them by 
source.

First of all let me say that Ifeffit builds fine if I use the pgplot5 
binary package, BUT, as stated by Matt in the README.PGPLOT, Ifeffit 
will compile without plotting support in this case.

So the only way is to build also PGPLOT from source. Unfortunately the 
experience has failed both with the PGPLOT_install script and 
following steps in the install-unix.txt.

I have tried many possibilities but the make process interrupts on the 
drivers compilations. Seen that following install-unix.txt gives the 
same error (but on another driver!) of PGPLOT_install, let's focus on 
this last procedure to try debugging the situation:

$sudo ./PGPLOT_install
...
[all fine until the PGPLOT make]
[long list of errors + warnings like:]
...
/home/mauro/local/ifeffit-1.2.11/pgplot/drivers/xwdriv_iff.c:4445: 
error: ‘XWdev’ has no member named ‘gc’
...
make: *** [xwdriv_iff.o] Error 1
...
[then the final error due to the bad compilation]
collect2: ld returned 1 exit status
make: *** [pgdemo1] Error 1

OK, I have described more or less the situation but I would not flood 
the list with technical mails, so if someone would help me with this 
issue we can continue in private and then send just the solution to the 
list.

Anyway, the problem is not urgent seen that I can work with the 1.2.10 
  binary installation.

Have a nice day!
Mauro

-- 
Mauro Rovezzi [EMAIL PROTECTED]
PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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Re: [Ifeffit] [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source

[Mauro Rovezzi]

Hi Gareth,

Thank you for the answer!

Gareth Jones wrote:
 Ifeffit ./configure --with-pgplot-link=-lpgplot using Ubuntu's
 PGPLOT package has always* worked for me, at least well enough for
 using Horae (I use gnuplot to save plots to files).  I don't know then
 what's broken in the binary packages from Ifeffit's point of view, so
 hopefully someone more knowledgeble can clarify that, but if you just
 want plots in Athena and Artemis the --with-pgplot-link method seems
 to work.

Your solution works! Now I have PGPLOT installed from the binary package 
pgplot5, Ifeffit 1.2.11b compiled using -lpgplot and everything seems 
to work fine.

M.

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PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)
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[Ifeffit] [ATOMS] supercell input file

[Mauro Rovezzi]

Dear all,

I would like to submit to your attention a problem with Atoms that I 
still do not understand. What I would like to do is to generate a FEFF 
input file starting from a supercell, that is repeating the unit cell 
NXxNYxNZ times and create the crystal with the resulting box.


An example is given in the attached _test-atoms.inp_ created following 
this procedure: from wurtzite GaN (a,c cell parameters) that we describe 
with 2 atoms I reduce the symmetry and I use 4 atoms, then I create a 72 
atoms supercell - 4*(3x3x2) - that has 3ax3ax2c dimensions and finally I 
tell atoms to use P1 space group in order to replicate the supercell 
in x,y,z space and shift at the center the absorbing atom.


Here the *problem*: the resulting _test-feff8.inp_ present good values 
of distances but strangely it has generated an additional Fe potential 
(there is just 1 Fe absorbing atom in the box/list). This is annoying 
because I have to remove manually the wrong ipot to run FEFF.


Is it a stupid mistake generating the Atoms input file or is it an odd 
behaviour?


Cheers,
Mauro

PS: Atoms 3.0.1 (linux) 05/08/15
PPS: Do not pay attention to coordinates and distances, these are just 
test-files!


--
Mauro Rovezzi [EMAIL PROTECTED]
PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)


test-atoms.inp
Description: chemical/gamess-input


test-feff8.inp
Description: chemical/gamess-input
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Re: [Ifeffit] [FEFF8.4] Re(x) is .le. zero in besjn ?

[Mauro Rovezzi]

Mauro Rovezzi wrote:
 Hi all,
 
 A little question about a FEFF8 error message I have and I cannot
 understand what it means :
 
 Re(x) is .le. zero in besjn
 
 This error is generated when I try to add the SCF to an EXAFS
 calculation on MnO (manganosite) and the SCF iteration is at step 9 of 30.
 
 Seen that the cards in the feff.inp file are properly used (I normally
 run SCF in EXAFS calculations) do you have any idea of what is going on?

[UPDATE]

I would like to add that the same input file *works fine* with FEFF8.2;
this means probably there is a problem in my compilation of the 8.4
version... strange (the same error on a 64 and 32 bit machines with
different compilers)!

Well, if I have more news about this issue I will post again.

Have a nice day,
M.

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PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)
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[Ifeffit] [FEFF8.4] Re(x) is .le. zero in besjn ?

[Mauro Rovezzi]

Hi all,

A little question about a FEFF8 error message I have and I cannot
understand what it means :

Re(x) is .le. zero in besjn

This error is generated when I try to add the SCF to an EXAFS
calculation on MnO (manganosite) and the SCF iteration is at step 9 of 30.

Seen that the cards in the feff.inp file are properly used (I normally
run SCF in EXAFS calculations) do you have any idea of what is going on?

Thanks for your help, as usual!

Mauro

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PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)
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Re: [Ifeffit] [howto] configurational average in EXAFS with FEFF

[Mauro Rovezzi]

Anatoly,

I don't quote your answer because I would like to add some more elements
to specify what I'm searching for.

In my previous post I have used the term cluster in a wrong way, that
is I was thinking at the crystal-box (normally less than 216 atoms) used
in the ab-initio density functional theory calculations and doped with
few percent ( 10%) of an absorbing atoms. For example, if we put 5
absorbing atoms in a box of 64 (that represent the crystal host) we have
5 possible configurations for our FEFF calculation and is impossible in
an EXAFS fit to include all the important paths (too many!).

My idea to take into account the numerical simulation and combine it
with the experimental EXAFS data could be to use the pair radial
distribution function extracted from the simulation, average the
configurations, recalculate paths and proceed in the fit.

Well, I hope now is more clear... In any case, thank you for the useful
article!

Mauro

Frenkel, Anatoly wrote:
 Mauro, 
  
 If I do understand your question correctly, you may be asking how to handle a 
 multiple of inequivalent sites in atomic clusters with N atoms, where each 
 atom generates a unique sequence of single- and multiple-scattering paths. A 
 possible solution is given in this article:
  
 D. Glasner and A. I. Frenkel 
 Geometrical characteristics of regular polyhedra: Application to EXAFS 
 studies of nanoclusters 
 AIP Conf. Proc. 882 , 746-748 (2007). 
 https://exchange2000.bnl.gov/exchange/frenkel/Drafts/RE:%20%5BIfeffit%5D%20%5Bhowto%5D%20configurational%20average%20in%20EXAFS%20with%20FEFF.EML/XAFS13-Proc/clusters-geometry.pdf
   
  
 The PDF is here:
  
 http://pubweb.bnl.gov/users/frenkel/www/XAFS13-Proc/clusters-geometry.pdf
  
 It is the same type of averaging and radial distribution analysis approach 
 that you are proposing unless I misunderstood your question.
  
 Anatoly

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PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)
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