Re: [Ifeffit] data point limits in Athena?

[Robert Gordon]

Hi Jorg,

Matt is on to the problem...Too many numbers... I deleted
columns 2 - 58. Working with columns labelled Ioni1,2 and 3
was ok, with little problem reading it in to Athena 0.9.17 even with the
2460
lines. I say "little" because it does take several seconds on my system
for Athena to read in the file so I can select columns. If I reduce it to
just the 4 columns that are of most value to an end user (E, and detectors),
it opens in about 1s. Notepad takes about that long to open the original
file.
So the problem seems to be not so much one of length, but girth - an obese
datafile trying to squeeze into a hefty array-size/memory limit.

I would not consider this an Athena issue. There are numerous columns
in the datafile that are constants, many zero. The number of lines could
also be improved.
The data was collected at 0.3 eV steps from 6932 to 7700 eV and that
certainly
oversamples for most of that range.

..and this is the second instance I have seen of obese datafiles...starting
to wonder how prevalent this issue is or will be, particularly when
beamlines
use large multi-element detectors.

regards,
Robert




On Sun, Aug 4, 2013 at 3:00 PM, Matt Newville wrote:

> Jorg,
>
> On Sun, Aug 4, 2013 at 12:49 PM, Göttlicher, Jörg
>  wrote:
> > Hello Bruce,
> >
> > thanks a lot for your fast reply.
> > I did not want to attach an example file immediately when submiting a
> question to the mailing list.
> > But there is no problem to send you some files. In the attachments you
> will now find the original data file for trying to reproduce my problems
> and hopefully to find a solution.
> >
> > I attach also the files reduced to 1711 and 1627 data points (just by
> trial and error. I checked 1711 (didn't work), and 1627 (worked). The limit
> might be somewhere inbetween.
> >
> > Attached is their read in in Athena, too.
> >
> > The counters are the following:
> > 1 Energy
> > Nominator 62 Absorption (Transmission), sample
> >
> > Reference
> > Nominator 63 Reference (Fe foil)
>
> If you're having difficulty reading these data files, I think you may
> want to convert them into a more sensible format with say two or three
> columns before trying to read it into athena.   That might help
> isolate where any problem might be.
>
> --Matt
>
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Re: [Ifeffit] (D) Atoms crashing while running feff

[Robert Gordon]

HI Matt,

That cif file is an old version of the structure. I can get DArtemis to
crash if I use it too, but if I
shift the origin by -1/8, -1/8, -1/8 it works. No crash when running Feff.

Some more recent references for the structure:
http://rruff.geo.arizona.edu/AMS/minerals/Hercynite

Fd-3m has two origin choices.
When you look at the Feff atoms list (in feff.inp or in the DArtemis Feff
window/tab),
the difference between the two calculations (your attached cif versus space
group origin shift/other
structure determination) is quite apparent.

As per cif:

ATOMS  * this list contains 257 atoms
 *   x  y  z ipot tag   distance
0.00.00.0  0  Fe1   0.0
2.030002.030000.0  2  Fe1.1 2.87085
   -2.03000   -2.030000.0  2  Fe1.1 2.87085
   -2.030000.02.03000  2  Fe1.1 2.87085
0.0   -2.030002.03000  2  Fe1.1 2.87085
2.030000.0   -2.03000  2  Fe1.1 2.87085
0.02.03000   -2.03000  2  Fe1.1 2.87085
etc...



With origin shift:
 ATOMS  * this list contains 245 atoms
 *   x  y  z ipot tag   distance
0.00.00.0  0  Fe1   0.0
   -1.055601.055601.05560  3  O1.1  1.82835
1.05560   -1.055601.05560  3  O1.1  1.82835
1.055601.05560   -1.05560  3  O1.1  1.82835
   -1.05560   -1.05560   -1.05560  3  O1.1  1.82835
etc.

regards,
Robert



On Sat, Aug 17, 2013 at 1:32 PM, Matt Frith  wrote:

> Dear All,
>
> I have been trying to run a feff calculation on FeAl2O4 with Fe as the
> absorbing atom.  Every time I attempt the calculation in Artemis crashes.
> Atoms also crashes if it is run independently.
>
> The dartemis and datoms log files both read:
>
> "At line 90 of file istprm.f Fortran runtime error: End of file Can't
> close(GLOB(0x931c6cc)) filehandle: '' at
> C:/strawberry/perl/site/lib/Demeter/Feff.pm line 1015"
>
>
> Can someone please tell me what I need to edit to solve this problem? Can
> editing something on the input file fix this problem?
>
> The cif file and datoms log file for the problem are attached.  Problem
> occurred on Win 7 32bit computer.
>
> Thank you for your time.
>
> Sincerely,
>
> Matt Frith
> Graduate Student
> Princeton University
>
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Re: [Ifeffit] modeling significant defects and molecules

[Robert Gordon]

Hi Carl,

You can always use symmetry P1 and specify every atom in the unit cell
in the atoms input.

That can be tedious for a large unit cell, but is achievable.

-R.

On 10/31/2013 11:09 AM, Carl Brozek wrote:

dear listhost,

I would like to use Artemis/Atoms to simulate EXAFS of a crystalline 
material with significant defects that include additional atoms to the 
unit cell.


Can I simulate this material without making a new cif file? Ideally, I 
would be able to input a DFT-optimized model cluster as xyz 
coordinates only -- no crystallographic information.


This problem seems analogous to modeling discrete molecules. Can 
molecules be simulated by atoms/artemis? I know FEFF is capable of 
this, but I would like to use atoms for making my input file for feff.


Carl



--
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SB | 2010 | University of Chicago


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Re: [Ifeffit] error in ATOMS

[Robert Gordon]

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Re: [Ifeffit] error in ATOMS

[Robert Gordon]

ing
and I badly need help on this to get going. Sorry to
bother everyone.

Thanks!

Julius


On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino
mailto:jcampec...@gmail.com>
<mailto:jcampec...@gmail.com
<mailto:jcampec...@gmail.com>>> wrote:

Hi Chris,

Yeah, I did try "add a site" but it is not
responding. Does anyone else experience this problem?
Thank you, Chris.

Julius


On Mon, Nov 11, 2013 at 9:51 AM, Christopher
Patridge mailto:patri...@buffalo.edu> <mailto:patri...@buffalo.edu
<mailto:patri...@buffalo.edu>>> wrote:

Julius,

While I am not certain what the error means,
there is a button displayed right above the atom list
which says "ADD A SITE."  I would suggest that having a
unit cell as large as you do, along with rather weak
scatterers such as N, C, O, and I assume H, it is probably
unnecessary to have sites beyond the 3rd shell or so since
these contribute negligibly to the EXAFS.

Chris


Dr. Christopher Patridge
Assistant Professor of Chemistry
Dept of Math and Natural Science
D'youville College
320 Porter Ave., Buffalo, NY 14201
Phone: 716-829-8096 
>
Email:_patri...@dyc.edu <mailto:email%3a_patri...@dyc.edu>
<mailto:patri...@dyc.edu <mailto:patri...@dyc.edu>>_




On Nov 10, 2013, at 1:26 PM, Julius Campecino
mailto:jcampec...@gmail.com>
<mailto:jcampec...@gmail.com
<mailto:jcampec...@gmail.com>>> wrote:

Hi Bruce,

Here's the screen shot of my work in
ATOMS. It's supposed to be more than 7 atoms in the
core column but that's also one thing I do not know
how to add change and add more atoms.

When I click "Run Atoms", it gives me this
error "Can't call method "tag" on an undefined value
at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line
668.'' I am using the recent version 0.9.18.2 of the
Demeter installer.

Thank you for your help!

Julius
   
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Re: [Ifeffit] Demeter not working on Windows 8.1 64bit

[Robert Gordon]

Hi Matt, Shoaib (and Bruce lurking in the luminiferous ether),

I have 8.1 x64 on my laptop and just upgraded to 0.9.19 - clean install.
I can offer some additional details on this problem.

I read in a file in DAthena, extracted the chi(k) and saved the project.
All buttons worked. When the file was read in, 4 mini-graphs displayed,
and I could select k, E, R as desired for full graph.

The second time I run it, reading in the exact same file, only the 
energy mini-graph

displays and the E,k and R buttons no longer produce any graphs.

From the clean install, I saved the DAthena.prj. I started DArtemis, 
read in the DAthena.prj

file, haven't tried fitting but saved the DArtemis fpj file.
If I try re-opening the fpj file I just saved in DArtemis, DArtemis crashes,
but re-opening the DAthena prj file after starting DArtemis is not a 
problem.


In DAthena, if I go to the appdata/roaming/demeter directory and delete 
the demeter.ini file,
DAthena will display all 4 mini-graphs when I open the prj file and the 
k,R,E buttons work.


I uninstalled and went back to 0.9.18.2. DAthena seems to work - all 4 
mini-graphs, and E,k,R work.
DArtemis still opens, reads DAthena.prj but crashes when trying to read 
fpj file created under 0.9.18.2.


Going back to the last 0.8.0nn versions, no crashes from Artemis or Athena.

Hope this helps.

-R.


On 1/14/2014 12:38 PM, Matt Newville wrote:

Hi Shoaib,

On Tue, Jan 14, 2014 at 10:46 AM, Shoaib Muhammad  wrote:

Hi,



I have recently upgraded my computer to Windows 8.1 Pro x64 and after this
upgrade I can’t run Athena and Artemis. The problem symptoms are:



1-  If I use Demeter version 0.9.13, Athena opens but when I try to open
previously saved file, Athena simply crashes without showing any error.
Artemis also shows similar behavior.

2-  By using latest build Demeter 0.9.19, Athena behavior is slightly
different it opens the files and show the plot. But pressing the E,k,R
buttons does not change the plot. Artemis still crashes by opening any
project file without any error.



I have tried following things, installed in compatibility mode of Windows7.
Athena worked fine only once after installing in compatibility mode.

Installed in different drives but situations remains the same. Tried to “run
as Admin” but no improvement.

Installed Demeter on three different computers running Windows 8.1 x64 but
similar behavior is received.



Kindly suggest me some work around because I have to use Demeter on almost
daily basis. I have attached log file obtained from Demeter 0.9.13 running
under Window 8.1 x64.



Thanks,

Shoaib Muhammad

Department of Energy Science

Sungkyunkwan University

South Korea


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I think you might be in mostly uncharted waters with 64-bit Windows 8.
  I have access to many Windows machines, but I don't know of any
64-bit Windows 8.1 machines in our group.

If you're up for it, it might be worth installing demeter from source
from the github repository, following
http://bruceravel.github.io/demeter/pods/installation.pod.html
and asking for help if you get stuck.

I'm sure it would be a great help to others if you did this

--Matt

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Re: [Ifeffit] Demeter not working on Windows 8.1 64bit

[Robert Gordon]

Installing 0.9.19 overtop of 0.9.18.2 and Athena works fine.

Installing 0.9.19 clean (deleting demeter directory under appdata/roaming)
2nd attempt to open file in DAthena results in only 1 mini-graph.

Ranges are 0 for Emin/max, kmin/max, Rmin/max - putting a valid range 
restores
full graph e.g. Rmin = 0 , Rmax = 6 gives full-size R-space 
graph...ditto for fixing other
ranges. Fixed 3 out of 4 and read in a new file...obtained 3 
mini-graphs...reset q range

as well and that one appears too.

Exited. Restarted. Read in file -
Show Command Buffer/Plot Buffer
## energy quadrant
set title "{/*1.6 Energy}"
set xlabel "{/*1.4 Energy&{aa}(eV)}"
set ylabel "{/*1.4 x{/Symbol m}(E)}"
#set xrange [ 11870.11617648 : 11870.11617648 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_vlxtfjcm' using 
1:2 with lines ls 2,\
 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_tfoziltm' 
using 1:2 with lines ls 1,\
 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_fthredqy' 
using 1:2 with lines ls 3,\
 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_iebbuian' 
using 1:2 with lines ls 4


## k quadrant
set title "{/*1.5 k-space}"
set xlabel "{/*1.2 Wavenumber&{aa}({\305}^{-1})}"
set ylabel "{/*1.2 k^{2} {\267} {/Symbol c}(k)&{aa}({\305}^{-2})}"
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_xizghpwm' using 
1:2 with lines ls 1


## R quadrant
set title "{/*1.5 R-space}"
set xlabel "{/*1.2 Radial distance&{aa}({\305})}"
set ylabel "{/*1.2 {/*1.25 |}{/Symbol c}(R){/*1.25 |}&{aa}({\305}^{-3})}"
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_nwtxpqxm' using 
1:2 with lines ls 1,\
 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_vysurgrh' 
using 1:2 with lines ls 2


## q quadrant
set title "{/*1.5 q-space}"
set xlabel "{/*1.2 Wavenumber&{aa}({\305}^{-1})}"
set ylabel "{/*1.2 {/*1.25 Re[}{/Symbol c}(q){/*1.25 ]}&{aa}({\305}^{-2})}"
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_hxroumyr' using 
1:2 with lines ls 1


unset multiplot



So, seems to be setting the xranges to zero for a clean install these 
plots, and gnuplot
doesn't plot if no xrange. If I reset, then I can move around and use 
DAthena 9.19

without issue...DArtemis is still an unhappy DHuntress with fpj files...


On 1/14/2014 3:28 PM, Bruce Ravel wrote:

On 01/14/2014 04:11 PM, Robert Gordon wrote:

Hi Matt, Shoaib (and Bruce lurking in the luminiferous ether),

I have 8.1 x64 on my laptop and just upgraded to 0.9.19 - clean install.
I can offer some additional details on this problem.

I read in a file in DAthena, extracted the chi(k) and saved the project.
All buttons worked. When the file was read in, 4 mini-graphs displayed,
and I could select k, E, R as desired for full graph.

The second time I run it, reading in the exact same file, only the
energy mini-graph
displays and the E,k and R buttons no longer produce any graphs.

 From the clean install, I saved the DAthena.prj. I started DArtemis,
read in the DAthena.prj
file, haven't tried fitting but saved the DArtemis fpj file.
If I try re-opening the fpj file I just saved in DArtemis, DArtemis
crashes,
but re-opening the DAthena prj file after starting DArtemis is not a
problem.

In DAthena, if I go to the appdata/roaming/demeter directory and delete
the demeter.ini file,
DAthena will display all 4 mini-graphs when I open the prj file and the
k,R,E buttons work.


Robert,

If you are inclined to help me with some troubleshooting, I have a 
request.


If you can recreate the situation where only the energy part of the
quad plot is displayed and the plot buttons stop working, could you
tell me a couple things:

  1. What are the values for the plotting ranges in E, k, R, and q?
 The reason I ask is that I stumbled upon a situation where Emin,
 Emax, kmin, etc all got set to zero (as did a bunch of other
 parameters).  I could not figure out how to reproduce that
 problem, but it would be helpful to know if it happened to
 someone else.

  2. In the Monitor menu, click on "Show command buffer".  In the
 "Plot buffer" at the bottom of the window scroll up just a little
 bit to where you'll see lines that say things like

plot '/home/bruce/.horae/stash/gp_vdnzxmxl' using 1:2 with 
lines ls 1,\
 '/home/bruce/.horae/stash/gp_wfaastqg' using 1:2 with 
lines ls 2


 What I want to know is if the 8 random characters after
 "stash/gp_" are the same or different (as in my example here).

In short, I want to know if you have seen some problems I have
observed by not been able to reproduce.


0.9.19 does not appear to be one of my better p

Re: [Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fitting in Artemis

[Robert Gordon]

Hi Satty,

The crystal data in your inp file came from the paper. I checked the 
International
Crystal Structure Database (ICSD) - printout attached. The structure 
data in the paper
are not in standard form - atoms might not give the correct results if 
the input is bad- and there

are typos for two of the O5 coordinates according to the ICSD warning.
Does your institution have access to the ICSD - Online or on disc? If you
are not familiar with it, try talking to one of your institution's 
reference librarians.


I'm not certain what you mean by the corner-corner Mn. You were choosing Mn1
as the core in your inp. When I look at the structure, Mn1 sits in the 
middle of
the set of 3 octahedra that make up a side of the tunnel. Where would 
the corner-corner
distance be relative to the middle of the chain? You have 4 different Mn 
sites.


Fitting in R-space is common.

As for learning about crystal structures, try sitting in on a 
coordination chemistry
or solid state chemistry course. For a basic learning book, I like 
West's "Basic Solid
State Chemistry" or Muller's "Inorganic Structural Chemistry" (again, 
try the library
 if you don't want to buy a copy). More recent books may be available. 
A bit of

googling may reveal some online lessons, like:
http://www.seas.upenn.edu/~chem101/sschem/solidstatechem.html


regards,
Robert


On 2/6/2014 3:16 AM, Sathish Mayanna wrote:

Hi

I am having some problem to get the real crystallographic parameters 
for Todorokite (I know there are many literature available) I used the 
parameters from Post et al 1988 (/Rietveld refinement of the 
Todorokite structure/) and others as well (*attached Todorokite.inp 
file*).


I except the corner corner Mn in Todorokite, since its a tunnel 
structure, but the Feff calculations do not provide any corner corner 
Mn, in addition I cannot fit exactly even Mn-O or Mn-Mn.


But If I use Ramsdellite (*attached Ramsdellite.inp file*), which is 
also a tunnel structure, I could get the Corner-Corner Mn and can fit 
perfectly the Mn-O, Mn-Mn, but cannot fit in K space.


It would be really great, if anyone could provide me the model Tunnel 
type-Mn oxide crystallographic parameters to fit the data *(attached 
Mn Spectra.prj)*


p.s: I tried my best to learn and understand the crystallographic 
parameters and miller indices, but still I feel that I am very poor, 
it would be nice, if someone suggest some good and basic source to 
learn more about pure mineralogy (which is crucial to know the basic 
parameters for fitting in Artemis).

--
Satty


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todorokite.pdf
Description: Adobe PDF document
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Re: [Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fit

[Robert Gordon]

Was there no attachment to my earlier response?
I printed out the ICSD page with the correct parameters
and attached it as a pdf. My outgoing message indicates
the attachment is there.

-R.

On 2/9/2014 7:40 AM, Sathish Mayanna wrote:

Dear Dr. Robert

Thanks a lot for your information that's very helpful.

I checked the ICSD, but unfortunately we don't have access to the 
crystal data. It would be great, if you or someone has the access to 
the crystal data to provide me the coordinates, the *collection code: 
202727, Author: Post, Year: 1988. *

*
*
*Please let me know, if someone has the access to the data.*
*
*
Regards
Sathish
*
*
**


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   1. Re: Correct Crystallographic parameters for Todorokite EXAFS
  fitting in Artemis (Robert Gordon)


--

Message: 1
    Date: Thu, 06 Feb 2014 16:05:30 -0600
From: Robert Gordon mailto:ragor...@alumni.sfu.ca>>
To: XAFS Analysis using Ifeffit mailto:ifeffit@millenia.cars.aps.anl.gov>>
Subject: Re: [Ifeffit] Correct Crystallographic parameters for
Todorokite EXAFS fitting in Artemis
Message-ID: <52f4072a.1070...@alumni.sfu.ca
<mailto:52f4072a.1070...@alumni.sfu.ca>>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

Hi Satty,

The crystal data in your inp file came from the paper. I checked the
International
Crystal Structure Database (ICSD) - printout attached. The structure
data in the paper
are not in standard form - atoms might not give the correct results if
the input is bad- and there
are typos for two of the O5 coordinates according to the ICSD warning.
Does your institution have access to the ICSD - Online or on disc?
If you
are not familiar with it, try talking to one of your institution's
reference librarians.

I'm not certain what you mean by the corner-corner Mn. You were
choosing Mn1
as the core in your inp. When I look at the structure, Mn1 sits in the
middle of
the set of 3 octahedra that make up a side of the tunnel. Where would
the corner-corner
distance be relative to the middle of the chain? You have 4
different Mn
sites.

Fitting in R-space is common.

As for learning about crystal structures, try sitting in on a
coordination chemistry
or solid state chemistry course. For a basic learning book, I like
West's "Basic Solid
State Chemistry" or Muller's "Inorganic Structural Chemistry" (again,
try the library
  if you don't want to buy a copy). More recent books may be
available.
A bit of
googling may reveal some online lessons, like:
http://www.seas.upenn.edu/~chem101/sschem/solidstatechem.html
<http://www.seas.upenn.edu/%7Echem101/sschem/solidstatechem.html>


regards,
Robert


On 2/6/2014 3:16 AM, Sathish Mayanna wrote:
> Hi
>
> I am having some problem to get the real crystallographic parameters
> for Todorokite (I know there are many literature available) I
used the
> parameters from Post et al 1988 (/Rietveld refinement of the
> Todorokite structure/) and others as well (*attached Todorokite.inp
> file*).
>
> I except the corner corner Mn in Todorokite, since its a tunnel
> structure, but the Feff calculations do not provide any corner
corner
> Mn, in addition I cannot fit exactly even Mn-O or Mn-Mn.
>
> But If I use Ramsdellite (*attached Ramsdellite.inp file*), which is
> also a tunnel structure, I could get the Corner-Corner Mn and
can fit
> perfectly the Mn-O, Mn-Mn, but cannot fit in K space.
>
> It would be really great, if anyone could provide me the model
Tunnel
> type-Mn oxide crystallographic parameters to fit the data *(attached
> Mn Spectra.prj)*
>
> p.s: I tried my best to learn and understand the crystallographic
> parameters and miller ind

Re: [Ifeffit] D-Atoms program, common positions and occupancies

[Robert Gordon]

Hi Moneed,

Bruce is a busy fellow. I doubt he has time to double-check every user's 
input file.


Let's go through some steps that might help you.

What reference are you using for CdSe crystal structure?
What are (is) the Se positions (position) supposed to be in that structure
with the P63mc symmetry?... the Cd positions (position)?
What are they in your input file?

Only one unique atom should be specified for a given symmetry position 
that has

more than one symmetry-related atom in the unit cell.

More generally, how much do you understand about crystal structures and
symmetry? If the answer is "not much", taking a course on such would be 
beneficial,
or even reading about it in some standard inorganic or solid state 
chemistry texts.


regards,
Robert




On 4/5/2014 4:54 AM, Moneeb Shatnawi wrote:

Dear Bruce Ravel,
Hello,
 I am Moneeb Shatnawi from the University of Jordan. I have a question 
and I appreciate your help in advance.
 I have installed the Demeter program (version 0.9.18) and I tried to 
use your (D)Atoms program using the attached input files.


When I try to run atoms, I get a warning message stating that two 
sites generate one or more common positions and their occupancies sum 
to more than 1. (attached also the warning message that I got).

If I ignore this warning message and try to run FEFF, the program crashes.
When I change the space group to P 1 (as indicated by the message) , 
the program runs well.
My question is, could you please figure out the problem with these 
input files, so that I can run them with the correct space group?

Thank you so much in advance,
 Moneeb


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APS Sector 20
9700 S. Cass Ave. 435E
Argonne, IL, USA 60439
630-252-0581 ph
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Re: [Ifeffit] non-standard space group P 21/n

[Robert Gordon]

HI Andrea,

My suggestion, if you know where all the atoms are in the unit cell, is to
use
space group P1. It may be tedious and brute force in nature, but you won't
have
to worry about origin choices or non-standard space groups. You will still
know
which atoms are equivalent and can pick an appropriate one as your target
atom.

regards,
Robert

On Fri, Dec 5, 2014 at 8:07 AM, Sanson Andrea 
wrote:

> Dear all
>
> does anyone know if is it possible to create with ATOMS
> the non-standard space group P 21/n ?
>
> Space group keywords are listed at the atoms website
> http://iffwww.iff.kfa-juelich.de/icp/atoms/atoms.sgml-7.html#ss7.4
> but no keyword for P 21/n group is available.
>
> Thanks for any suggestion.
> Best regards,
> AS
>
>
>
>
>
>
>
>
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Re: [Ifeffit] Exploring XANES data for getting EXAFS results

[Robert Gordon]

There is also Smolentsev and Soldatov's work using FitIT as well as 
FDMNES and FEFF


G. Smolentsev and A.V. Soldatov "FitIt: new software to extract 
structural information on the basis of XANES fitting 
<http://dx.doi.org/10.1016/j.commatsci.2006.08.007>" Comp. Matter. 
Science 39 (2007) 569.


http://journals.aps.org/prb/abstract/10.1103/PhysRevB.75.144106

http://www.nano.sfedu.ru/fitit.html

Though I haven't tried it myself, Grigory did give an interesting talk 
on to the APS XAFS

community some years ago.


On 1/16/2015 9:53 AM, Matt Newville wrote:



On Fri, Jan 16, 2015 at 9:21 AM, Marcelo Alves <mailto:meal...@gmail.com>> wrote:


Hi all,

I wonder if it is possible from XANES unusual data treatment to
get information such as number and distances of neigbhors in the
first and second shells.


There is an old-ish (like, from the 1950's I think) and fairly 
heuristic rule that the XANES edge energy shifts scale as 1/R^2 for 
the nearest neighbor.I think that Grant Bunker has a nice set of 
slides showing this, somewhere on the web.  For example, I think this 
explains well slight energy shifts in the peak energy of the sulfate 
resonance. My recollection is that it works pretty well for many 
well-constrained set of spectra, but isn't quite as quantitative and 
readily applicable to unknown systems as one might hope.


It's also sort of related to the idea of bond-valence that, for a 
given class of systems (say, oxides of a particular metal), R, N, and 
formal valence state are not independent quantities.


--Matt


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Dr. Robert Gordon
Staff Scientist, CLS@APS
APS Sector 20 (CLS/XSD)
9700 S. Cass Ave. 435E
Argonne, IL USA  60430
ph/fx 630-252-0581/0580

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Re: [Ifeffit] error message by import

[Robert Gordon]

Hi Anna,

It would be helpful to know a bit more about your problem.
What version are you running? Could you provide the file?
I have version 0.9.21x64 and encounter no difficulty importing a 2-column
text file such as the attached.

With regards to your other query, there is a stand-alone version of 
atoms that came with 0.9.21.
It is visible in the windows start menu for me and opens the same window 
that I get if I try

to import an atom.inp or feff.inp from D'Artemis.

best regards,
Robert

On 4/8/2015 4:47 AM, Zimina, Anna (IKFT) wrote:


I get the following error message when I read the txt file with two 
columns of data (energy and intensity):


“11:42:20: Use of uninitialized value $line in pattern match (m//) at 
C:/strawberry/perl/site/lib/Demeter/Files.pm line 188.”


Still the data can be read. What is the problem?

Thanks in advance,

Anna Zimina.

__

Karlsruhe Institute of Technology (KIT)

Institute of Catalysis Research and Technology (IKFT)

Dr. Anna Zimina

Beamline scientist

Hermann-von-Helmholtz-Platz 1

Building 345,  Office 108

76344 Eggenstein-Leopoldshafen

Phone: +49 721 608 28673

Fax: +49 721 608 26789

E-Mail anna.zim...@kit.edu <mailto:anna.zim...@kit.edu>

xasf16



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9700 S Cass Ave. 435E
Argonne, IL, USA  60439

630-252-0581
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# data  : Fe, using Feff standard
# chi: from skey ASCII of newfe.b
# using simple minimization
# e0 =  7110.98; pre-edge range =[  -200.0   -50.0]; edge step =  2.108
# k range=[  1.00 17.60]; k weight=  1.00; sills  dk1, dk2  =  0.00  0.00
# bkg r =[  0.00  0.98];   11 knots in spline
# inpdat: no document line found
# --
# k  chi(k)  
  0.500E-01   0.000E+00
  0.100E+00   0.000E+00
  0.150E+00   0.000E+00
  0.200E+00   0.000E+00
  0.250E+00   0.000E+00
  0.300E+00   0.000E+00
  0.350E+00   0.000E+00
  0.400E+00   0.000E+00
  0.450E+00   0.000E+00
  0.500E+00   0.000E+00
  0.550E+00   0.000E+00
  0.600E+00   0.000E+00
  0.650E+00   0.000E+00
  0.700E+00   0.000E+00
  0.750E+00   0.000E+00
  0.800E+00   0.000E+00
  0.850E+00   0.000E+00
  0.900E+00   0.000E+00
  0.950E+00   0.5655127E-01
  0.100E+01   0.2060084E+00
  0.105E+01   0.2808007E+00
  0.110E+01   0.2122846E+00
  0.115E+01   0.1469233E+00
  0.120E+01   0.8558236E-01
  0.125E+01   0.3885868E-01
  0.130E+01   -.3205625E-02
  0.135E+01   -.2988494E-01
  0.140E+01   -.5032800E-01
  0.145E+01   -.6352721E-01
  0.150E+01   -.6917974E-01
  0.155E+01   -.6984850E-01
  0.160E+01   -.6646661E-01
  0.165E+01   -.6563130E-01
  0.170E+01   -.6711814E-01
  0.175E+01   -.6834159E-01
  0.180E+01   -.6921581E-01
  0.185E+01   -.6814639E-01
  0.190E+01   -.6501906E-01
  0.195E+01   -.5765744E-01
  0.200E+01   -.4453135E-01
  0.205E+01   -.2401327E-01
  0.210E+01   0.7335357E-02
  0.215E+01   0.4488946E-01
  0.220E+01   0.7977872E-01
  0.225E+01   0.9853840E-01
  0.230E+01   0.9232492E-01
  0.235E+01   0.6178783E-01
  0.240E+01   0.2341145E-01
  0.245E+01   -.1390825E-01
  0.250E+01   -.3846206E-01
  0.255E+01   -.5195529E-01
  0.260E+01   -.5546389E-01
  0.265E+01   -.4779275E-01
  0.270E+01   -.3509258E-01
  0.275E+01   -.2234229E-01
  0.280E+01   -.1596326E-01
  0.285E+01   -.1899550E-01
  0.290E+01   -.2327369E-01
  0.295E+01   -.2792808E-01
  0.300E+01   -.2152839E-01
  0.305E+01   -.8976581E-02
  0.310E+01   0.9856174E-02
  0.315E+01   0.2660002E-01
  0.320E+01   0.3893804E-01
  0.325E+01   0.4660523E-01
  0.330E+01   0.5051752E-01
  0.335E+01   0.5078438E-01
  0.340E+01   0.4720417E-01
  0.345E+01   0.4192519E-01
  0.350E+01   0.3830658E-01
  0.355E+01   0.3661301E-01
  0.360E+01   0.3510318E-01
  0.365E+01   0.3195203E-01
  0.370E+01   0.2673356E-01
  0.375E+01   0.2157586E-01
  0.380E+01   0.1734317E-01
  0.385E+01   0.1420028E-01
  0.390E+01   0.1007945E-01
  0.395E+01   0.3650033E-02
  0.400E+01   -.5376017E-02
  0.405E+01   -.1947654E-01
  0.410E+01   -.3440827E-01
  0.415E+01   -.5013820E-01
  0.420E+01   -.6089725E-01
  0.425E+01   -.6645940E-01
  0.430E+01   -.6661560E-01
  0.435E+01   -.6047763E-01
  0.440E+01   -.5072961E-01
  0.445E+01   -.3719363E-01
  0.450E+01   -.1978667E-01
  0.455E+01   -.1746187E-02
  0.460E+01   0.1679161E-01
  0.465E+01   0.2691962E-01
  0.

Re: [Ifeffit] error message by import

[Robert Gordon]

Just opening the file.txt in wordpad, and saving is enough to avoid that 
message

when importing.

-R.

On 4/8/2015 9:43 AM, Bruce Ravel wrote:

On 04/08/2015 10:15 AM, Zimina, Anna (IKFT) wrote:

When I try to import the attached file.txt, the warning message appears
(see screenshot.png). After clicking OK the file is imported.

The log file (dathena.log) and the message (log.txt) are attached.



When Athena is given a file, it runs a sequence of tests to try to
figure out what kind of file it is looking.  For example, it tries to
recognize an Athena project file and interpret it as such before
trying to interpret the file as column data.  File name and extension
is not a reliable way to do this, so it examines the content of the
file.

Your file is confusing one of the tests.  It's easily fixable.  I will
push a solution to github shortly and include the fix in the next
installer release.

So, what's the problem with your file?  Well, yours is a rather
strange one for the year 2015.  The newline character used is CR,
which is what was used by Mac OS9 and a few operating systems that
were common in the 1980s.  Pretty uncommon kind of file these days.
To be honest, I am pleasantly surprised that Athena reads it correctly
at all.

In fact, the test that gives that error message is something I wrote a
few weeks ago.  I certainly did not test it against a file with CR
line termination.

Until I make a new installer (which won't be for several weeks -- I am
just about to go on travel), you have a couple of options.  One is to
simply live with the error message and click the box away. Annoying,
but serviceable.  The other is to run your data files through some
kind of filter that changes the end-of-line character.  Searching
Google for "convert CR to CRLF" turns up several possibilities.

HTH,
B




--
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9700 S Cass Ave. 435E
Argonne, IL, USA  60439

630-252-0581
630-252-0580 fax

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Re: [Ifeffit] FEFF calculation for two inequivalent absorbing sites

[Robert Gordon]

Hi Eugenio,

Quick question: Did you change the tags for the Co atoms so that they are
different?
If I do that, I get 4 and 6 coordinate results. you can import the cif file
twice, run atoms on both
sites (with tags different) and get the two feff inputs for running.

-R.

On Thu, Apr 9, 2015 at 5:01 AM, Eugenio Paris 
wrote:

> Hello everybody,
>
> I'm trying to make Co K-edge EXAFS fitting for the Co3O4 compound (*.cif
> file is attached). The nearest neighbour of Co is oxigen at about 1.93
> Angstrom distance.
> Cobalt sits in two inequivalent sites in the unit cell. When I perform the
> FEFF calculation in Artemis for either one or the other site i get the same
> path with Reff = 1.93 and degeneracy = 4.
> So i wonder what is the correct way to take account of the presence of
> both sites. At the beginning i was thinking to put 2*amp as S0^2 parameter
> to take account for twice the coordination number.
> Then i tried to use the "Aggregate" option in Artemis. When I use this
> option i get exactly the same result, i.e. a SS path with Reff = 1.92 and
> degeneracy = 4... I was expecting to get twice the degeneracy.. (the margin
> and beta parameters are set to default)
>
> My question is:
> Why do i get the same path list when I do use the "Aggregate" pathfinder
> and when I don't? What is wrong in my interpretation?
>
> Thank you in advance!
> Sincerely,
> Eugenio
>
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Re: [Ifeffit] Scatter Plot in Athena

[Robert Gordon]

Hi Shoaib,

Go to the preferences menu (I have version 0.9.21).
Under the gnuplot section, there is a datastyle entry.
You can select lines, points or linespoints.
I don't see how to change symbol type or size though.

cheers,
-R.



On 5/3/2015 2:02 AM, Shoaib Muhammad wrote:


Dear All,

In Athena documentation section I can see data plotted as scatter 
instead of line type plot (for example the plot shown in the attached 
file). This feature seems to be helpful in deglitching the bad data 
points but I could not figure out how to do it! Can anybody guide me 
how to plot data as scatter in Athena? My platform is Windows8 x64.


Thanks,

/Shoaib




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Re: [Ifeffit] Ca EXAFS with Ge220 or InSb111 (Lisa Bovenkamp)

[Robert Gordon]

Another possibility is that the L-edges of In and Sb are giving 
considerable energy-dependence to
the beam in the EXAFS region...any non-linearity between detectors will 
make extraction of the EXAFS

problematic. Looking at CAMD's XAS beamline mono specs
http://www.camd.lsu.edu/beamline_info/DCM_beamline_2008.pdf
Si111, Si220 and Ge220 will all cover the Ca K-edge range.

-R.

On 5/11/2015 3:46 PM, Matthew Marcus wrote:
I found Ca EXAFS files on my data directory which go out to 600eV 
above the edge, done using Si111.
What's the symptom of the failure with InSb?  Could harmonics be the 
problem?  If there's something
mechanical going on with the mono such that you go through the max of 
the rocking curve, then as
you go through that max, you get more harmonics, which cause 
normalization failure.

mam

On 5/11/2015 11:06 AM, Lisa Bovenkamp wrote:

Hello.

No, the resolution is fine. I can do XANES fine with InSb111. We use 
those for years.
Just had problems with EXAFS because for this long range the flux has 
to be more stable

from the crystals.

Lisa
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Re: [Ifeffit] Reference for Setting k range in EXAFS analysis

[Robert Gordon]

Hi Navneet,

You have asked a rather open-ended question.
There are numerable resources available for learning about XAFS analysis 
that are straightforward
to find. Setting the k-range is more specific and governed by several 
factors.


The range chosen affects resolution and precision. In general, you would 
like as large a k-range
as you can reasonably obtain. Practically, this is limited by the sample 
(order/disorder, mean-square-

relative-displacement, Debye-Waller term) and by finite limits on beamtime.

My suggestion, as a starting point, is to consider what type of 
materials you plan on studying,
then check the literature for similar systems to see what results others 
have been able to obtain.


-R.

On 6/18/2015 3:42 AM, Navneet Singh wrote:


Dear All

Can I get some study material mentioning how to set the K-range for 
EXAFS analysis.


With best regards

Navneet Singh



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Re: [Ifeffit] Issues with Athena on high-performance systems

[Robert Gordon]

HI Nils,

My laptop has i5 (2.4GHz)/Intel/16GB running win7prox64 and I have no 
issues, even with the first plot.
How many files are you trying to plot? I test with just one and 
everything works fine.


-R.

On 6/25/2015 9:06 AM, Nils Skoglund wrote:


Hi,

I’m curious if anyone else is experiencing issues with Athena in more 
high-end systems running Windows 7? While I am used to having to wait 
for the _first_ plot to show  up, the software is virtually unusable 
to me now where any slight change (e.g. modifying range for the 
spline) to already imported data takes up to over a minute to replot. 
This didn’t use to be the case for me. The system is a laptop running 
Win 7 Professional with 2.40 GHz i7 CPU/16 GB RAM with plenty of space 
on the hard drives and a dedicated Intel HD 4600 graphics circuit.


If anyone has a work-around for this problem or can suggest anything 
to make Athena usable again, it would be most appreciated. Has anyone 
noticed previous versions of Athena running more smoothly?


Best regards,

Nils

*--*

*Nils Skoglund, Ph.D.*
Post-doctoral researcher

Energy Science
Department of Engineering Sciences and Mathematics
Luleå University of Technology
SE-971 87 Luleå
Sweden

Cell   :  +46 (0)72 529 52 08

Web page: http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en

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Re: [Ifeffit] Deglitching

[Robert Gordon]

Hi Bruce,

Sorry..wrong button when replying.

Terminal
Your value qt

Demeter.ini says wxt

I change the Set value to wxt and apply & save. message at bottom of screen
says "Now using wxt for gnuplot --> terminal and an ini file was saved"

Plucked point is now consistent.

However, when I exit and re-start Athena, back to qt and problem re-appears.
In demeter.ini, [gnuplot] section, it still says terminal = wxt, but 
under preferences,gnuplot

terminal it is back to qt.

If I change to x11, and restart, x11 is remembered.
If I change to wxt from x11, apply and save, it resets to qt when 
restarting even though the ini file says wxt.


-R.


On 9/4/2015 11:06 AM, Bruce Ravel wrote:

On 09/04/2015 01:37 PM, Robert Gordon wrote:


I can confirm something funny is happening here. In 0.9.21, the deglitch
menu would not display
points. I upgraded to 0.9.22 today and deglitch now displays points, but
when I choose a point
in a test data file (As2O3) and double-click, the energy point removed
is 11804.228, regardless of where
I double-click. I reverted back to 0.9.21 and with the same dataset,
this did not occur. In 0.9.21,
double-click removed the closest point to where I clicked.

I have win10pro x64 and installed the 64-bit versions of 0.9.21, .22


Can we *please* use the mailing list for these things.  It is helpful 
to the next person who runs into these issues if a discoverable record 
is left behind.


Using the preference tool, can you tell me what the value for 
gnuplot->terminal is?  If it is something other than "wxt", try 
changing it to "wxt".  The interaction with the cursor does not work 
correctly on some terminals.


If that's not the problem, then I am at a loss.  I don't see this 
behavior on any of my computers.


B





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Re: [Ifeffit] problems with deglitching in D-Athena 0.9.22

[Robert Gordon]

Hi Eva,

I suspect, when searching the mailing list, the recent discussion on 
deglitching issues in 0.9.22

was overlooked.
e.g.
http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05193.html
or
http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05232.html
 or Bruce's suggestion to try a newer beta version:
http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05251.html

If you look in the preferenecs menu under gnuplot terminal (say Win8 
versioin)
what do you see? I can deglitch in 0.9.22 release if i change my 
terminal to wxt,
but Athena won't save that change, so I have to re-apply it the next 
time I run

0.9.22 (haven't tried newer beta yet).

-R.


On 10/3/2015 11:46 AM, bajnoczi wrote:

Dear Ifeffit Staff,


 I have just installed the most recent version of Demeter on my 
computer both on Windows 8 64-bit as well as on a Virtual (WMware 
Player) Ubuntu 14.04.3 64-bit machine.


 I have exactly the same problem with both versions when I try to 
deglitch my data. When I go to the Deglitch and Truncate window, and 
choose the option "Choose a point" the plot appears with dots. So far 
it seems ok. Initially the orange crosshair is on the first data 
point. When I try to double-click on the point to be removed happens 
nothing at all. I can do whatever I want, the crosshair stays on the 
first measured data point, and stays there, so I only can remove this 
one.


 I've already consulted with the mailing list, but none of the 
proposed solutions worked for me. I have downloaded the 
DeglitchTruncate.pm from Github and upgraded my version, as well as 
set the energy shift to 0, but nothing helped.


 Do you have any idea what can be the solution for this problem?

 Thank you for your answer and help in advance.

Regards:
Éva Bajnóczi

Hungary
Hungarian Academy of Sciences, Wigner Research Centre for Physics

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Re: [Ifeffit] Athena open data project but not shown the curve

[Robert Gordon]

Hi Carlos,

My previous exposure to MD for EXAFS was as part of a collaboration here:
J. Synchrotron Rad. (2013). 20, 555–566

There, to get estimates of energy shift and amplitude (So^2), a 
simplified model was used
to fit the experimental data. In your case, that could be done by 
performing a FEFF

calculation for an atom best representing the average.

The FEFF calculation won't include deviations in Eo or So^2 or even
temperature effects by default. DEBYE, s02 (or HOLE or EDGE), and 
CORRECTIONS cards

could be used in generating the FEFF chi.dat.

 If your MD simulation gives you N, R and sig^2
for each shell (and each atom) you wish to include in your comparison, then
you can implement the Eo-shift and amplitude values from the simplified 
fit in each shell
of a simulation (using the FEFF.dat files) up to whatever shell you 
have the energy to try

to include in the simulation...I would suggest starting with the first shell
and include the second once you get a good agreement with the first.

There may still be deviations in peak position between experiment and 
calculation.

That can be considered by examination of a known standard.

You should consider the same k-space ranges for experiment and theory 
when comparing
your own results...comparison itself would be done in R-space, 
particularly if only using

a few shells.

 For comparison with the results of others, it would depend on 
available data
ranges and quality as to how to proceed. e.g. If I analyse 3 to 18 A-1 
and want to compare to
someone else who analysed 3 to 10 A-1 due to their data limits, then I 
should also
look at my results over their range to give a fair comparison. If the 
reverse situation is present,

then the comparison is only within the limits of available data.

regards,
Robert

On 11/5/2015 10:31 AM, Carlos Triana Estupinan wrote:

Hello
ROBERT

Thanks for your kind answer
I have an amorphous structure with 216 atoms, 72 of them are absorbing 
atoms. So, I did FEFF calculation for each of those absorber to get 
individual EXAFS, and then I dis an average of them to get an averaged 
EXAFS (total EXAFS).
I don't want to refine a structural model, but I want to compare the 
experimental EXAFS data with the averaged EXAFS I got for my model.


My question is, if I get the EXAFS just from FEFF calculation (chi(k) 
or xmu.dat), then I can import it to artemis, and compare with the 
experimental (but without do any fiting), just to compare EXAFSs. From 
FEFF I can obtain chi(k), u, u0, and X as a function of energy. Which 
of those (chi(k), u, u0, and X) should I compare with the experimental 
data.


Also, if I compare mi experimental EXAFS with other EXAFS spectra 
already published in papers, should be the EXAFS the same or it 
depends on the range for the fourier transform.


regards.

2015-11-05 18:50 GMT+01:00 Robert Gordon <mailto:ragor...@alumni.sfu.ca>>:


Hi Carlos,

Please clarify somethings for me regarding your inquiry.
You have a structural model and you have data.
You calculated a FEFF simulation of your structural model.
You did not use the FEFF.dat files to try to fit the model to
your data,
but instead just did a comparison of the simulated chi(k), presumably
with just some default settings in FEFF.inp in addition to your
structural model.
Is that correct?

Generally, it is the fit to the data that gives one feedback on
the validity
of the structural model (GIGO rules apply).

If you have a model, then you have a model coordination number and
can use
a program (e.g. Artemis) to refine amplitude, distance,
mean-square-relative displacement
and energy shift. Do you need explanations of what these
parameters represent?

So, to address what you were wondering, I believe the answer is
yes...you need to actually
do a fit, and the goal isn't to get the obtained spectrum to look
like your simulation.
Data is sacred. The goal is find a model that best reproduces the
data (within a confidence
level governed by the goodness of fit).

regards,
Robert


On 11/5/2015 7:06 AM, Carlos Triana Estupinan wrote:

Dear
Bruce

I am doing calculation of EXFAS for a amorphous structure created
by molecular dynamics. I am using FEFE to obtain chi(k) and the
file xmu, however, when comparing with experimental data with the
calculated EXFAS I have the following problems.

1) The Fourier transform of the EXAFS calculated by FEFF has the
same shape that the experiment spectra, however it is higher in
amplitude.

2) The calculated EXFAS by FEFF has the same oscillation in
K-space, but it does not match the oscillation in K (both of them
are shifted to each other).

I am wondering if I need to do an extra correction to the
calculated EXAFS by FEFF in order to match the K-space and the
amplitude in R-sapace. Shall I change the ener

Re: [Ifeffit] Opening "older" data files in the latest Athena version

[Robert Gordon]

Hi Marcelo,

How did you save the data file?
I can open Fe.060 without  issue using 0.9.22 but in order to do so,
I clicked on the fe.060 link, then selected RAW and then saved as text.
If I just right-clicked and saved link as from the list page, I ended up 
with

some html document.

regards,
Robert

On 11/9/2015 9:46 AM, Marcelo Eduardo Alves wrote:
I have downloaded the worked examples available at 
https://github.com/bruceravel/XAS-Education


However, I am not being able to open them in the latest Athena version 
(0.9.24) (e.g., Fe.060 of Fe foil folder).


Could those files be opened in the last Athena version?

Thank you.

Marcelo.



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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 12

[Robert Gordon]

Ah, yes...special characters...çã...Athena does not seem to like those 
in file names
If I replace with Calibração with Calibracao in a test directory of my 
own, then the file opens without issue.


-R.

On 11/9/2015 11:01 AM, Marcelo Eduardo Alves wrote:
I have downloaded the zip-file containing the example files and 
extracted them into other subfolders 
(i.e. C:\Users\Marcelo\Documents\1.Athena Calibração e 
Alinhamento\Examples\Fe foil).

I think that this was my error.
When I use C:\Fe foil the file was opened in Athena without any issue.
Thank you Robert and Guanghui

2015-11-09 16:24 GMT-02:00 <mailto:ifeffit-requ...@millenia.cars.aps.anl.gov>>:


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Today's Topics:

   1. Opening "older" data files in the latest Athena version
  (Marcelo Eduardo Alves)
   2. Re: Opening "older" data files in the latest Athenaversion
  (Robert Gordon)
   3. Re: Opening "older" data files in the latest Athena  version
  (Guanghui Zhang)
   4. Problems with EXAFS Fitting of Metalloprotein Zinc Samples
  (Carolyn Carr)


--

Message: 1
Date: Mon, 9 Nov 2015 15:41:33 -0200
From: "Marcelo Eduardo Alves" mailto:mealves.es...@usp.br>>
To: mailto:ifeffit@millenia.cars.aps.anl.gov>>
Subject: [Ifeffit] Opening "older" data files in the latest Athena
version
Message-ID: <97FB7D67CF2142A48FA29F9776D0A164@MarceloPC>
Content-Type: text/plain; charset="iso-8859-1"

Dear all,

I am using the latest version of Demeter (0.9.24) and I have
downloaded the data files available at
https://github.com/bruceravel/XAS-Education.

However, I am not being able to open the example files in Athena
(e.g., Fe.060 of Fe foil folder).

Please, would it be possible to open those example files in the
latest Athena version.

Thank you.

Marcelo.


___
Marcelo Eduardo Alves
Departamento de Ci?ncias Exatas - ESALQ/USP
Avenida P?dua Dias, 11
13418-900 Piracicaba-SP
Fone: 19-3429-4151- RAMAL 26
Email: mealves.es...@usp.br <mailto:mealves.es...@usp.br>
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Message: 2
Date: Mon, 9 Nov 2015 10:05:45 -0800
From: Robert Gordon mailto:ragor...@alumni.sfu.ca>>
To: ifeffit@millenia.cars.aps.anl.gov
<mailto:ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Opening "older" data files in the latest Athena
version
Message-ID: <5640e079.8010...@alumni.sfu.ca
<mailto:5640e079.8010...@alumni.sfu.ca>>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"

Hi Marcelo,

How did you save the data file?
I can open Fe.060 without  issue using 0.9.22 but in order to do so,
I clicked on the fe.060 link, then selected RAW and then saved as
text.
If I just right-clicked and saved link as from the list page, I
ended up
with
some html document.

regards,
Robert

On 11/9/2015 9:46 AM, Marcelo Eduardo Alves wrote:
> I have downloaded the worked examples available at
> https://github.com/bruceravel/XAS-Education
>
> However, I am not being able to open them in the latest Athena
version
> (0.9.24) (e.g., Fe.060 of Fe foil folder).
>
> Could those files be opened in the last Athena version?
>
> Thank you.
>
> Marcelo.
>
>
>
> ___
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Re: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples

[Robert Gordon]

Hi Carolyn,

Do you see this behaviour even for standard samples, where the local 
co-odination of the
zinc is known? If this is only happening for unknowns, then it could be 
telling you
that you have heavier or more scatterers present than you have included 
in your fitting model.


So^2, N and sig^2 are strongly correlated (So^2 and N directly for a 
1-shell fit).
Have you tried breaking the correlation by measuring at different 
temperatures

(changes sig^2, not N)?

In the EXAFS section of the Encyclopaedia of Molecular Biology, it 
discusses difficulties
in analysing Zn metalloproteins due to not including 
multiple-scattering. If a MS peak
is leaking or lurking under the first shell peak(s), there is additional 
intensity that the fitting might
try to compensate for by increasing N (and would depend on the strength 
of the MS peak, which is,

in turn, dependent on local geometry).

...just some initial thoughts...

cheers,
Robert



On 11/9/2015 10:24 AM, Carolyn Carr wrote:

Hi,

I have a general question rather than specific. I have only ever fit 
XAS data on metalloproteins and one feature that I see is that when 
fitting Zinc samples in R-space there is no local minima. For Cobalt 
and Nickel samples I typically get one or a few fits that are 
obviously significantly better in R-factor (with reasonable distances, 
sigma^2, etc) but for Zinc this is not the case.


I can get many good fits and Zinc likes to increase the coordination 
up to 8 for all data sets I have ever fit, although there is obviously 
no physical basis in this. This is true of not just my own proteins 
but Zinc samples made by collaborators, and after looking through 
previous group members fit tables, they had similar issues.


My understanding is that one of the benefits of fitting in R-space is 
that there is a local minima, whereas in k-space there are many 
minima. I was wondering if there was a physical basis for this feature 
in Zinc samples, or if perhaps my group is not aware of some 
experimental setup that we should be doing for Zinc that would resolve 
this problem.


Thank you for any help regarding this matter,

Carolyn Carr

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Re: [Ifeffit] Deglitching issues on Athena on latest Mac versions

[Robert Gordon]

Hi Wuhib,

Many of the issues related to plotting and point picking with 0.9.22 
have been related to the terminal settings
used by gnuplot. Since you searched the list and read many of the mac 
and windows-related messages in this regard,
you likely know this, but just in case, have you checked what terminal 
setting you are using?
I believe x11 is the optimal choice for mac. That would be the first 
think I would check.


regards,
-R.



On 12/20/2015 4:45 AM, Wuhib Tamrat wrote:

Hi all,

This is about the repeated Deglitching issues on Athena but only for 
latest Mac versions.


I know it is frustrating to be asked the same question over and over 
again, so I checked the mailing list several times all the way to the 
oldest mail dated "August 15, 2010". And, to my searching ability, 
issues regarding deglitching on Athena on mac have not been addressed.


If it is already discussed, I apologise in advance and please kindly 
direct me to the discussion.


I am working on the latest Demeter for "Mac version 0.9.22" on "OS X 
El Capitan, version 10.11”.


The following discussion were the only ones that I could find. They 
are on exactly the same issues but on Windows [Sathish on Dec, 2013 / 
Shoaib May, 2015 / Martina or Robert Gordon Sep, 2015 / Eva October, 
2015].


The problem that I am facing is the same as issues described before 
but on Mac. So I will describe it below.


After moving to the "Deglitch and Truncate Data” window and choosing 
Chi(E) the data is plotted as “line plot” not the “blue dots”. I am 
assuming the second option is the proper one since that is how it 
appears in Windows or other working versions. That is the first issue.


After clicking “Choose point” and double clicking on the plot, the 
cross hair falls on the E0 value not on the data point (not on the 
glitch). That is the second issue. I have attached a screen shot 
image, if it will help to visualise the problem. Also project file 
with two data glitches is attached.


The closest information I got from the mailing list was from the 
conversation started by “Shoaib” on May 2015 for Windows versions. 
Bruce suggested a short work around fix by playing with the E0 value. 
I tried to make a bald trial of moving the E0 to the point where the 
glitch is, hoping the cross hair falls on the glitch data point. But 
that created unrealistic plots since the glitch was close to the end 
of the collected data points (in E). Altering the 
"DeglitchTruncate.pm" file in the installation directory was a clever 
solution by Shoaib but I am not sure how to do that on Mac.










Thanks
Wuhib

PS: I know some users are sending amateur emails with insufficient 
information but some of us are debutant researchers/students (not 
seasoned researchers) and will learn from our mistakes. Please be kind 
and polite when suggesting the correct way to do it even though it is 
already on http://bruceravel.github.io/demeter/pods/bugs.pod.html or 
other locations. Thank you.






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Re: [Ifeffit] Deglitching issues on Athena on latest Mac versions

[Robert Gordon]

Well, another possibility is wxt...Matt discusses using it in this thread:
http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05346.html

Sorry I couldn't be more help...

cheers,
-R.


On 12/20/2015 3:33 PM, Wuhib Tamrat wrote:

Hi Robert,
That was also on my mind. As you may know, X11 is no longer available. 
What is instead available from Mac support and installed on my OS is X 
Quartz. In cases other than this deglitching issue, plotting function 
on Athena is performing properly.
And also when Athena opens on Mac two windows work simultaneously. 
“perl5.16” and the plotting window “X11”. So I could be wrong but my 
understanding is, even though X Quartz was the one installed, Athena 
is utilising it as x11.


I thank you for your advice.
Wuhib


On 20 Dec 2015, at 21:01, Robert Gordon <mailto:ragor...@alumni.sfu.ca>> wrote:


Hi Wuhib,

Many of the issues related to plotting and point picking with 0.9.22 
have been related to the terminal settings
used by gnuplot. Since you searched the list and read many of the mac 
and windows-related messages in this regard,
you likely know this, but just in case, have you checked what 
terminal setting you are using?
I believe x11 is the optimal choice for mac. That would be the first 
think I would check.


regards,
-R.



On 12/20/2015 4:45 AM, Wuhib Tamrat wrote:

Hi all,

This is about the repeated Deglitching issues on Athena but only for 
latest Mac versions.


I know it is frustrating to be asked the same question over and over 
again, so I checked the mailing list several times all the way to 
the oldest mail dated "August 15, 2010". And, to my searching 
ability, issues regarding deglitching on Athena on mac have not been 
addressed.


If it is already discussed, I apologise in advance and please kindly 
direct me to the discussion.


I am working on the latest Demeter for "Mac version 0.9.22" on "OS X 
El Capitan, version 10.11”.


The following discussion were the only ones that I could find. They 
are on exactly the same issues but on Windows [Sathish on Dec, 2013 
/ Shoaib May, 2015 / Martina or Robert Gordon Sep, 2015 / Eva 
October, 2015].


The problem that I am facing is the same as issues described before 
but on Mac. So I will describe it below.


After moving to the "Deglitch and Truncate Data” window and choosing 
Chi(E) the data is plotted as “line plot” not the “blue dots”. I am 
assuming the second option is the proper one since that is how it 
appears in Windows or other working versions. That is the first issue.


After clicking “Choose point” and double clicking on the plot, the 
cross hair falls on the E0 value not on the data point (not on the 
glitch). That is the second issue. I have attached a screen shot 
image, if it will help to visualise the problem. Also project file 
with two data glitches is attached.


The closest information I got from the mailing list was from the 
conversation started by “Shoaib” on May 2015 for Windows versions. 
Bruce suggested a short work around fix by playing with the E0 
value. I tried to make a bald trial of moving the E0 to the point 
where the glitch is, hoping the cross hair falls on the glitch data 
point. But that created unrealistic plots since the glitch was close 
to the end of the collected data points (in E). Altering the 
"DeglitchTruncate.pm" file in the installation directory was a 
clever solution by Shoaib but I am not sure how to do that on Mac.










Thanks
Wuhib

PS: I know some users are sending amateur emails with insufficient 
information but some of us are debutant researchers/students (not 
seasoned researchers) and will learn from our mistakes. Please be 
kind and polite when suggesting the correct way to do it even though 
it is already on 
http://bruceravel.github.io/demeter/pods/bugs.pod.html or other 
locations. Thank you.






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Re: [Ifeffit] pi/2deltak

[Robert Gordon]

Hi Riti,

A couple of caveats to Matt's answer:

The EXAFS equation is not simply a sum of sine functions. I can think of 
two ways that the resolution criteria

can be worked around:

1. Consider the case of two close near neighbours in a single-crystal 
environment whose close distances are
geometrically distinct such that, if one were to conduct 
polarisation-dependent measurements, one
could turn off one of the distances in one orientation (and perhaps the 
other in another), one could fit the
two sets to extract the two close distances. (i.e. you aren't trying to 
resolve the two distances in one measurement)


2. If there is a pronounced chemical difference between the neighbours, 
they can be resolved even if the
distance separation is small, provided the  k-space range being used 
provides enough independent parameters

to conduct the fit.

If you wish to convince yourself that these two caveats work, I suggest 
creating a model using the AuCu
structure. If you contract or expand the c-axis, and substitute either 
Cu for Au (i.e. make Cu but in lower symmetry)
or substitute a different atom on one of the Cu sites, you can test both 
Matt's explanation and my caveats above.


cheers,
Robert

On 1/31/2016 6:33 PM, Matt Newville wrote:

Hi Riti,

On Sat, Jan 30, 2016 at 7:35 PM, Ritimukta Sarangi 
mailto:ritimu...@gmail.com>> wrote:


Hello,

I was recently asked about the accuracy of this formulation for
obtaining EXAFS resolution and I did not have a good answer. Can
someone point to a reference or explain here?

Thank you for your time,
Best,
-Riti


The deltaR = pi / 2DeltaK  follows from general Fourier analysis and 
formulas like it can be found in many signal processing textbooks.
For on-line resources, googling "Frequency resolution Fourier 
transform" gives several good references.


The idea is that (using sound-waves as an example) in order to 
distinguish two close frequencies (say 440 Hz from 441 Hz, so a 
different of 1 Hz), you have to sample many periods (pi seconds) to be 
able to do this.


For EXAFS, if there are contributions from two neighbors that are very 
closely spaced, you would have to sample enough oscillations (go high 
enough in k) to see the effect of these two different distances 
beating against each other.   If you don't go out far enough in k,  
you can't tell that these two contributions are actually from 
different distances.


Hope that helps,

--Matt


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

[Robert Gordon]

Hi All,

I have a couple of students who are novices. I was hoping that one could 
go to a school
to learn and perhaps get some hands-on experience before they get into 
the meat of
their thesis work. I haven't seen any notices yet about schools taking 
place in the late

spring or summer and was wondering if there are any plans to hold such.

I am aware of the 1/2-day workshop planned for the DXC. Are there other 
options?


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

[Robert Gordon]

Wonderful! Thanks!

-R.

On 2/28/2016 11:33 AM, Bruce Ravel wrote:

On 02/28/2016 01:19 PM, Ritimukta Sarangi wrote:
We at SSRL will host an exafs summer school in July 3rd week. I can 
post more about it here next week when we finalize the format.


Please do.  I get asked about courses fairly often.  I'd like to be 
able to direct people to yours.


Cheers,
B




Sent from my iPhone

On Feb 28, 2016, at 08:05, Robert Gordon  
wrote:


Hi All,

I have a couple of students who are novices. I was hoping that one 
could go to a school
to learn and perhaps get some hands-on experience before they get 
into the meat of
their thesis work. I haven't seen any notices yet about schools 
taking place in the late

spring or summer and was wondering if there are any plans to hold such.

I am aware of the 1/2-day workshop planned for the DXC. Are there 
other options?


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

[Robert Gordon]

Thanks Anatoly!

On 3/7/2016 10:14 AM, Anatoly I Frenkel wrote:

Here is the info about the upcoming XAFS short course at Brookhaven (Nov 2-4, 
2016):

http://workshops.ps.bnl.gov/default.aspx?w=XAFS2016

Regards,
Anatoly
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Re: [Ifeffit] Questions to Bruce

[Robert Gordon]

Hi Dien,

To perhaps forestall a scolding from Bruce, let me point out the 
following advice on

error reporting:
https://bruceravel.github.io/demeter/pods/bugs.pod.html

RE:1. I am able to import multiple scans with reference data. My test 
was to try 3 scans and
associated reference data. I am using version 0.9.24. How many scans did 
you try to import?
Is there a problem with one of the scans you tried to import? There is a 
memory limit.
More information is needed to diagnose the problem you are having. It 
does not seem to

be a bug in the software. Look for the log file
that may contain information on why the program crashed. What does it say?
"Each of the GUI programs (Athena, Artemis, and Hephaestus) writes its 
output messages to a log file.

In win 7 to 10, This can be found in C:\Users\\AppData\Roaming\

RE: 2. It opens fine for me. Win10pro x64 system using version 0.9.24 
with the SSRL plugin registry
entries selected. Did you activate the SSRLmicro plugin? If I deactivate 
it, I cannot read the file.


regards,
Robert

On 3/23/2016 2:51 PM, dien...@srs.gov wrote:

HI, Bruce and Matt

I have two questions for you, please help me.

1. I collected U EXAFS data on APS 10-ID, while I input a single data 
file with reference data in Athena, it was OK, however, when I input 
multiple data files (scans) also with reference data, it was crushed. 
I could input multiple data files without reference data, which Matt 
helped me trouble shoot. The Demeter 8.24 version is used on my 
computer, I believe. Matt suggested me to update to the current 
version. I do not know if other users have this problem.


2. I have a U EXAFS data file which was collected at SSRL, however, I 
could not input this data file using Athena, how to fix this? format? 
See the attachment. thanks you so much.





Dien Li, Ph.D.
Environmental Sciences and Biotechnology
Savannah River National Laboratory
Aiken, South Carolina, 29808
Tel: 803-725-7520


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Re: [Ifeffit] Bug report

[Robert Gordon]

Can you send the text file as well, please?

On 4/9/2016 12:43 PM, Lorenzo Stievano wrote:

Hi,

I have to report a bug on a computer where Demeter 0.9.24 is installed.

Athena worked fine until a few days ago, but from a certain point it 
started to crash when I try to import a simple text data file (which 
worked well before). I have tried reinstalling Demeter (I actually did 
it twice) but the problem persist. The computer works under WIndows 7 
Professional, SP1, 64 bits.


Can you help me?

Thank you in advance,

Lorenzo

PS: The athena log after the crash is attached.


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Re: [Ifeffit] Bug report

[Robert Gordon]

The data file?

On 4/9/2016 10:19 PM, Lorenzo Stievano wrote:

Here it is.

Le 09/04/2016 23:52, Robert Gordon a écrit :

Can you send the text file as well, please?

On 4/9/2016 12:43 PM, Lorenzo Stievano wrote:

Hi,

I have to report a bug on a computer where Demeter 0.9.24 is installed.

Athena worked fine until a few days ago, but from a certain point it 
started to crash when I try to import a simple text data file (which 
worked well before). I have tried reinstalling Demeter (I actually 
did it twice) but the problem persist. The computer works under 
WIndows 7 Professional, SP1, 64 bits.


Can you help me?

Thank you in advance,

Lorenzo

PS: The athena log after the crash is attached.


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Re: [Ifeffit] Bug report

[Robert Gordon]

Another thought: Does this crash happen with other data files, or just 
this one?


On 4/9/2016 10:19 PM, Lorenzo Stievano wrote:

Here it is.

Le 09/04/2016 23:52, Robert Gordon a écrit :

Can you send the text file as well, please?

On 4/9/2016 12:43 PM, Lorenzo Stievano wrote:

Hi,

I have to report a bug on a computer where Demeter 0.9.24 is installed.

Athena worked fine until a few days ago, but from a certain point it 
started to crash when I try to import a simple text data file (which 
worked well before). I have tried reinstalling Demeter (I actually 
did it twice) but the problem persist. The computer works under 
WIndows 7 Professional, SP1, 64 bits.


Can you help me?

Thank you in advance,

Lorenzo

PS: The athena log after the crash is attached.


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Re: [Ifeffit] Bug report

[Robert Gordon]

The log file was attached, not a data file.
I have attached a datafile that is just text. Try importing it, please. 
It imports without issue for me.


Another thought: When you uninstalled/reinstalled, did you delete the 
AppData\Roaming\Demeter directory?
This may not get removed when an uninstall occurs and if it has a 
corrupted setting somehow, then

deleting it before reinstall may clear that.


On 4/9/2016 11:04 PM, Lorenzo Stievano wrote:

It was actually attached... anyway, now I just paste it in the message:

--

Started at 2016-04-09T21:33:05
Win7Professional (64-bit) Service Pack 1Service Pack 16176012102561

PATH is:
C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program 
Files\DemeterPerl\c\bin;C:\Program 
Files\DemeterPerl\perl\site\bin;C:\Program 
Files\DemeterPerl\perl\bin;C:\Program Files\DemeterPerl\c\bin\gnuplot\bin


perl version: v5.18.2
backend: ifeffit

@INC:
C:/Program Files/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread
C:/Program Files/DemeterPerl/perl/site/lib
C:/Program Files/DemeterPerl/perl/vendor/lib
C:/Program Files/DemeterPerl/perl/lib
.
Demeter version 0.9.24

YAML::Tiny failed to classify line ' ' at C:/Program 
Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm line 783.
YAML::Tiny::_error(YAML::Tiny=ARRAY(0x10c7d818), "YAML::Tiny 
failed to classify line 
'\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm 
line 303
YAML::Tiny::_load_string("YAML::Tiny", 
"\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm 
line 37
YAML::Tiny::Load("\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm line 296
Demeter::UI::Athena::IO::_data(Demeter::UI::Athena=HASH(0x4bbae8), 
"C:\\Users\\Utilisateur\\Desktop\\Ge K-edge 
Operando_ROCK\\operando"..., "C:\\Users\\Utilisateur\\Desktop\\Ge 
K-edge Operando_ROCK\\operando"..., 1, 0) called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm line 165
Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x4bbae8)) 
called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 859
Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30), 
Demeter::UI::Athena=HASH(0x4bbae8)) called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 782
Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30)) called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47
eval {...} called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47



--

Le 10/04/2016 07:53, Robert Gordon a écrit :

The data file?

On 4/9/2016 10:19 PM, Lorenzo Stievano wrote:

Here it is.

Le 09/04/2016 23:52, Robert Gordon a écrit :

Can you send the text file as well, please?

On 4/9/2016 12:43 PM, Lorenzo Stievano wrote:

Hi,

I have to report a bug on a computer where Demeter 0.9.24 is 
installed.


Athena worked fine until a few days ago, but from a certain point 
it started to crash when I try to import a simple text data file 
(which worked well before). I have tried reinstalling Demeter (I 
actually did it twice) but the problem persist. The computer works 
under WIndows 7 Professional, SP1, 64 bits.


Can you help me?

Thank you in advance,

Lorenzo

PS: The athena log after the crash is attached.


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Re: [Ifeffit] Bug report

[Robert Gordon]

Hi Bruce,

Sorry...should have suggested he back up the directory first. To that 
end, how about adding a statement or two

to the faq along the lines of:

Make a copy of the files in the AppData\Roaming\Demeter directory for 
help in diagnosing what

caused a file corruption.

-R.

On 4/11/2016 8:23 AM, Bruce Ravel wrote:

On 04/11/2016 09:16 AM, Bruce Ravel wrote:

On 04/10/2016 03:38 AM, Lorenzo Stievano wrote:

There must have been something corrupted in the AppData\Roaming\Demeter
directory. It crachesd even with your data file (as for mine), but now
it works fine since I reinstalled it AFTER removing the Roaming
directory.


I don't suppose that you saved the old Roaming folder?  There is no way
for me to identify the cause of this problem if I cannot identify and
inspect the file that triggered the problem.


Lorenzo, Robert,

I added a question to the FAQ related to this thread.

http://bruceravel.github.io/demeter/documents/SinglePage/faq.html#questions-about-windows 



If either of you have a comment on the language of the question or the 
answer, let me know.


Again, it would be a more helpful FAQ entry if could understand the 
origin of the problem.


B



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Re: [Ifeffit] Artemis/FEFF question

[Robert Gordon]

The Sc atom does not go at 0,0,0 in hcp. That is site 2a and has another 
atom at 0,0,0.5  which
is what the calculation gave. If you use position 2c (0., 0.6667, 
0.2500), you get 6 nn

at 3.256A above and below the central atom.

regards,
Robert

On 5/3/2016 6:02 PM, Dimitar Popmintchev wrote:

Dear All,

The database at http://cars9.uchicago.edu/~newville/adb/search.html 
 is down and I 
am trying to create an input file (for feff calculation) for pure 
scandium ( http://www.periodni.com/sc.html ).


The problem is when the 'atoms', and 'feff' in Artemis calculate the 
scattering paths, they shows distances smaller than the expected 
3.256A nearest neighbor distance. What is the error in the input file 
attached below ?


Thank you.
Dimitar

 ATOMS  * this list contains 117 atoms
 *   x  y  z ipot tag   distance
0.00.00.0  0  Sc1   0.0
0.00.02.63650  1  Sc1.1 2.63650
0.00.0   -2.63650  1  Sc1.1 2.63650
2.865681.654500.0  1  Sc1.2 3.30900
   -2.865681.654500.0  1  Sc1.2 3.30900


Input file for scandium

## This Atoms file was generated by Demeter 0.9.22
## Demeter written by and copyright (c) Bruce Ravel, 2006-2015

title = name: scandium
title = formula:  Sc
title = sites:Sc1
title = refer1:   Kittel, ISSP
title = refer2:
title = schoen:
title = notes1:   metal, hcp
space = P63/mmc
a = 3.30900  c = 5.2730
rmax  =   9.0core  = Sc1
atoms
# el. x   y   ztag
  Sc 0.0 0.0 0.0   Sc1


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Re: [Ifeffit] Questions

[Robert Gordon]

Has it occurred to you to upgrade your version (and your colleague too)? 
Current version is 0.9.24.


-R.

On 6/6/2016 8:50 AM, dien...@srs.gov wrote:

Hi, All

I am using Demeter Artemis version 9.18, however, I could not open the 
Artemis file that was generated from Artemis Version 9.21 from my 
collaborator, anyone can instruct or help? Thanks.


Dien Li, Ph.D.
Environmental Sciences and Biotechnology
Savannah River National Laboratory
Aiken, South Carolina, 29808
Tel: 803-725-7520


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Re: [Ifeffit] report bugs

[Robert Gordon]

HI,

This was also reported earlier this month and Bruce has indicated it is 
on his .todo list.

http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05587.html

You can use the stand alone version to prepare and save the atoms.inp file.
This file can then be imported (Add) in the main Artemis window under 
Feff calculations

and run in the atoms window that appears when this is done.

regards,
Robert

On 6/22/2016 11:24 PM, Shaofeng Wang wrote:

Dr. Chu,

I met this program, too. The beta version of 0.9.25 is ok.

王少锋



--
Shaofeng Wang, Ph.D of Geochemistry
Environmental Molecular Science Group
Institute of Applied Ecology, Chinese Academy of Sciences
Shenyang, 110016, China
wangshaof...@iae.ac.cn
www.iae.cas.cn

-原始邮件- From: 储胜启
Sent: Thursday, June 23, 2016 10:09 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] report bugs

Hi, deal bruce,

I have found a bug. When I click the button ‘Run Atoms’ in Artemis 
program, it will crash suddenly. I have tried this in different OS, 
Windows XP and Win7, and got the same error. The log file said as 
follows:


Demeter version 0.9.24

Can't call method "workspace" on an undefined value at 
C:/MyProgramm/DemeterPerl/perl/site/lib/Demeter/UI/Atoms/Xtal.pm line 
1004.


Best wishes,

-Shengqi Chu

Beijing Synchrotron Radiation Facility, Beijing 100049，China

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Re: [Ifeffit] How to change the data file in Dartemis?

[Robert Gordon]

Hi Isabelle,

If I understand your emails correctly, you are trying to fit two 
variations of a dataset (with different normalisations)
to a given model FEFF calculation, yes? You have two different chi(k)'s. 
Rather than trying to replace.

have you tried:

Just fitting them one at a time in Artemis? i.e.  Import the first 
chi(k), set the FT parameters etc. Generate
the FEFF model. Pick paths.  Set the GDS values. Save the project file. 
Run fit. Discard first data, import second
set the FT parameters, select paths, enter the GDS values in the data 
window...(save again, perhaps as different

fpj) and fit again?  (OK...this is replace, but by brute force)

How about fitting both at the same time using the same FEFF model: 
Import both chi(k)'s and run two
independent fits (i.e. amp1 for 1st, amp2 for 2nd etc) with the same 
FEFF calculation?


I have tested both of these routes and they do work (though there is an 
issue with the Artemis [Plot] window

dropping one of the datasets if it isn't being fit).

regards,
-R.

On 7/7/2016 7:04 AM, Isabelle Kieffer wrote:

Dear Bruce, dear all,

Just to add some input and precise my question.

The problem I encounter with "replace this chi(k)" did not appear to 
me until I tried to fit a spectrum twice with two different 
normalisations. In this case, after a fit on the first spectrum, I 
"replace this chi" with another that is normalised differently, and 
when I try to fit, it stops with the following error message:


 This data came from the the same source as another
 data group. You seem to be trying to increase your
 number of independent points by fitting the same data
 more than once in a multiple data set fit.


Seeing that, I wondered whether "replace this chi" was doing what I 
thought. The upgrade did not change anything. I just tried with a 
colleague working under windows and the result is also the same.


Shall I do differently to fit those two really similar spectra?

Thank you for your help,

Isabelle




On 01/07/2016 21:08, Bruce Ravel wrote:

On 07/01/2016 01:57 PM, Isabelle Kieffer wrote:

You mean that when you "Replace this chi(k)", it asks what to do, or it
supposes that you want to fit new data with the same model?


What I mean is: upgrade.  Many of the problems you are reporting have 
been fixed already.  If you upgrade and still see these problems, 
make a bug report and I will look into it.


B






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Re: [Ifeffit] fitting of S XANES with arctans and gaussians

[Robert Gordon]

Hi Matthew,

WinXAS, (Commercial program by Thorsten Ressler) does possess the 
capabilities you are seeking

but it costs E$200 for an academic/gov't license.

-R.

On 7/19/2016 5:21 AM, Bruce Ravel wrote:

On 07/18/2016 11:10 PM, Matthew Marcus wrote:

I'm trying to fit 37 micro-XANES spectra taken at the S K-edge, using
the method discussed in the paper by Manceau and Nagy "Quantitative
analysis of sulfur functional groups
in natural organic matter by XANES spectroscopy", Geochimica et
Cosmochimica Acta 99 (2012) 206–223.  In this paper, they fit spectra to
two arctangents and 6 gaussians,
with widths of the arctans slaved together and widths of gaussians 1-3
and 4-6 slaved (or all 6 to one value).  I'm looking for recommendations
as to how to do the fit.
They give prescriptions for how to set the initial estimates to give
robust values.  Manceau has told me that 'Athena works quite well', but
I don't see any obvious way there
to do the parameter constraints called for, or to keep peak heights from
going negative.  Athena also has a habit of assuming you want it to do
the normalization
for you; I've already done that and need no further 'help'.  Any ideas?


Matthew,

As for the pre-normalized data, you are supposed to be able to tell 
Athena at the time of import that the data are normalized mu(E).


http://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units 



If that doesn't work, let me know.

As for constraints in the peak fitting, that is certainly not 
implemented in Athena.  I am not quite sure why Alain thinks otherwise.


HTH,
B





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Re: [Ifeffit] Bug Report importing file.

[Robert Gordon]

According to
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2013-August/006762.html
limit is 8192

It is possible to rebin the data in Athena...in multiple steps...what it 
first imports, then export, then
attach the missing higher E data, re-import, rebin...using a near edge 
step size of 0.2 eV, 0.05 invAng
in the EXAFS and 2 eV in the pre-edge, these two steps were sufficient 
to reduce the data size to 555 points.


The match between original and rebin does show some small differences 
but I didn't deglitch first.




I don't like the steps in the original mu(E) either - rounding off too soon,
or is it there at this level in the raw data?
...discrete noise/quantization error at the 1:800 level versus 
'traditional exafs' 10^6 counts (1:1000)


On 7/24/2016 1:15 AM, Samy Ould-Chikh wrote:

Just a quick idea on why I cannot import the .txt file attached with previous 
email.

I realized that the files contain 11948 points ! (it's QEXAFS data).
Athena might have an hard limit of 8200 points that may be imported in a single 
file.


Best Regards,
Samy Ould-Chikh

KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology
Thuwal 23955-6900
Kingdom of Saudi Arabia

Tel: +966 12 8084486
E-mail: samy.ouldch...@kaust.edu.sa
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx





-Original Message-
From: Samy Ould-Chikh
Sent: Sunday, July 24, 2016 10:56 AM
To: XAFS Analysis using Ifeffit 
Subject: Bug Report importing file.

Hello,

I have some issue to import a file in Athena: just a simple x-y column (.txt 
attached with this email).

Ti K-edge.
Data range in the file  : 4916.30 up to 5436.88 eV.
Issue: only data up to 5260 eV are imported (see screenshot: bug-importation).

Version: Demeter 0.9.24
System: Windows 7 Professional SP1

Well, I hope it's just not me not being able to find a proper way to import the 
file...


Best Regards,
Samy Ould-Chikh

KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom 
of Saudi Arabia

Tel: +966 12 8084486
E-mail: samy.ouldch...@kaust.edu.sa
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx





This message and its contents including attachments are intended solely for the 
original recipient. If you are not the intended recipient or have received this 
message in error, please notify me immediately and delete this message from 
your computer system. Any unauthorized use or distribution is prohibited. 
Please consider the environment before printing this email.

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Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Robert Gordon]

Hi Juan,

I just installed demeter and larch on an Ubuntu 16.04lts system today.
I can reproduce something like your error. I use the 10K Cu data in the 
examples

folder.

If I import it and don't select the numerator on import, the plot window 
has issues

(~10^307 axis limit), but the file gets listed in the data list.

I can get 10^9 for the energy axis by specifying keV instead of eV for 
the import energy.


i.e. Matt's question: Did you import the data correctly?
(and why 10^9 if it is supposedly multiplying by 1000?...would have 
thought 10^6...)


Did you import a number of datasets with mixed keV and eV energy scales? 
I did that once
where the first file was in keV and subsequent ones in eV and the energy 
scale was decidedly

off for the subsequent ones.

cheers,
Robert

On 11/23/2016 7:45 PM, Matt Newville wrote:

Hi Juan,

On Wed, Nov 23, 2016 at 12:43 PM, Juan de la figuera 
mailto:juan.delafigu...@gmail.com>> wrote:


Dear all,

I have been installing demeter from git under ubuntu 16.04 LTS,
following the non-root instructions from:
https://gist.github.com/waveform80/3959252


I also installed xraylarch from git. Xaylarch is only missing:
#=== Warning: Some recommended Python Packages are missing:
epics:  needed for using the EPICS control system
pyFAI:  needed for xrd modules

It seems to work, but when I try to open a file that can be open
properly from Athena installed on Windows, I get:

Trying Larch server:

/home/juan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.in
i
Trying Larch server:  larch_server -p 4968 start
larch_server port=4968: started

gnuplot> set xrange [ 690013 : 795561 ]
 ^
line 0: warning: integer overflow; changing to floating point

gnuplot> set xrange [ 690013 : 795561 ]
^
line 0: warning: integer overflow; changing to floating point


and although it opens the data in a gnuplot window, the scale is
off (7x10^9 instead of 7x10^3). I am assuming once it is confused
about the scale, it makes a mess with the data.



Did you import the data correctly?

Did you try this with more than one data file?

Why did you not include that data file in your request for help?

If you had included the (or a) file giving you trouble, it would allow 
someone else to try to reproduce the problem, which might actually 
lead to an answer.


--Matt

PS:  Athena version 0.8.061 is more than 5 years old and is not supported.



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Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

[Robert Gordon]

Hi Juan,

I can open your file. It displays without issue.
My system is amd64 with ubuntu 16.04 LTS.
The version of Demeter I cloned from git is 0.9.26 (using the git clone
instruction), mostly following the 'David Hughes' guide" from here
https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.html
which seems to be what you found elsewhere.
There were a couple of differences I had to work around:
libpng3-dev had libpng12-dev substituted for it by apt
libgif4 and libwxgtk2.8-dev were not found. I manually installed 
giflib-5.1.4 and apt installed gtk2.0


I had to ctrl-c out of a loop regarding "can't find apache" when doing 
./Build installdeps
(Googling suggests this might be due to perl/build/cpan trying to use 
mod_perl-1.31 instead of -2.0.4

since 1.31 is slightly newer).

I am still tweaking my system, so this is a fresh install of demeter 
this morning - no larch yet,

so I get a 'no larch_server' message, but your file displays without issue.

You indicated you have version 0.9.24. What other differences did you 
encounter?


-R.

On 11/25/2016 2:23 AM, Juan de la figuera wrote:

Hi,

I send one of the data files we are currently acquiring (SPLINE 
beamline at ESRF).


I have checked that my compiled 0.9.24 version works with the examples 
cu10k.dat file, but it is true, as Robert confirmed, that strange 
things happen if you mark ev instead of kev.


With our data files like the one enclosed, dathena chokes on the 
scale. Actually it opens the window but it has x10^9 scale. On the 
other hand, the 0.9.24 for Windows opens the files ok. Now, the files 
are MSDOS-ended files, I tried converting them to Linux-ending, but 
same result. I also tried putting a # comment on the first line.


I stress that Athena 0.8.061 (included in the horae package in ubuntu) 
opens the file like a charm.


One additional detail (just in case), I have Ubuntu 16.04 LTS 64-bit.

Best,
Juan


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Re: [Ifeffit] struggling to install demeter under ubuntu 16.04

[Robert Gordon]

Hi,

I installed demeter recently under 16.04 lts. In response to Juan's 
issues, I described what I did here:


http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-November/00.html

One additional deviation was that I had already installed gfortran and 
gunplot (sudo apt install)

beforehand.

Matt noted in the next message that a larch issue needs addressing when 
importing files


http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-November/008889.html

but the ifeffit backend works.

I haven't tried everything, but reading and processing a file in Athena 
works fine.


-R.

On 12/1/2016 6:21 AM, Bruce Ravel wrote:

On 12/01/2016 09:12 AM, mfehse wrote:

In my struggle to install demeter under ubuntu 16.04 I'm slowly
advancing. I think some of the packages that were supposed to be
installed following the first line of the protocol were incomplete. I
have redone this and have now managed to build the dathena and other
files, but when I want to start it I get the following error message:


"marquinhos@marquinhos-Lapi:~/demeter$ bin/dathena

Could not find Larch Server -- falling back to Ifeffit
Can't locate object method "new" via package "Graphics::GnuplotIF" at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter.pm 


line 239.
Compilation failed in require at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm 


line 24.
BEGIN failed--compilation aborted at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm 


line 24.
Compilation failed in require at bin/dathena line 27.
BEGIN failed--compilation aborted at bin/dathena line 27.
Can't exec "-p": No such file or directory at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Larch.pm 


line 270.
"

any ideas what might be the problem?



That seems to be saying that Graphics::GnuplotIF is not installed.

It should have been installed when you did the "./Build installdeps" 
step.


B




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Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

[Robert Gordon]

Hi Bruce,

What if one were to do this FEFF calculation using the POLARIZATION card?
1 0 0 means something different if the atom positions have been rotated
by 45 degrees relative to the crystal axes along which the polarization 
is defined.


-R.



On 12/16/2016 10:14 AM, Bruce Ravel wrote:

On 12/16/2016 12:55 PM, Raj kumar wrote:

Thanks for the explanation. Yes, both files are generating the same kind
of output but the positioning of atoms can mislead in the context of
structure. That's why i have raised the question.


Hi Raj,

But they are /the/ /same/ structure, so they give the same XAFS 
results, which is the problem that all the versions of Atoms intend to 
solve. Again, I don't think there is anything wrong that needs my 
attention.


Cheers,
B



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Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

[Robert Gordon]

Hi Bruce,

The atoms.inp file attached is for bct Fe. In symmetry I4/mmm, the 
resulting feff input has the coordinates
rotated, while in Immm the resulting coordinates are not rotated 
relative to the crystal axes (i.e. in Immm
the 2nd near neighbour is obvious as a lattice constant away in each 
direction).


So, with no polarization, the results for scattering paths are the same 
(using CRITERIA default), as expected

Path #
Degen
Reff
Scattering Path
Type
Rank I4/mmm
Rank Immm
1
8
2.48
fe1
ss
100
100
2
4
2.835
fe2
ss
37.56
37.56
3
2
2.92
fe3
ss
17.59
17.59
4
16
3.897
fe1-fe1
ms
3.42
3.42
5
32
3.897
fe1-fe2
ms
12.83
12.83
7
16
3.94
fe1-fe3
ms
6.37
6.37


Now consider with  POLARIZATION 1 0 0 (and 1 1 0 for I4/mmm)

#
Degen
Reff
Scatt. Path
Type
I4 1 0 0
I4 1 1 0
Im 1 0 0

4
2.48
fe1
ss
100



4
2.48
fe1
ss
7.89



8
2.48
fe1
ss

100
100

4
2.835
fe2
ss
55.45



2
2.835
fe2
ss

62.05
62.05

16
3.897
fe1-fe1
ms
4.41
9.90
15.43

16
3.897
fe1- fe2
ms
19.03
21.58
21.59



For that first multiple scattering path, the scattering angles are 
36.1/90 for I4(1 0 0), 55.1/55.1
for I4(110) and for Im(100) they are 55.1/124.9. The ranking of this 
path is not the same,

and the plots for this path differ as well - in shape as well as amplitude.

Conceptually, the Immm model calculation has the atoms aligned with the 
crystal lattice
and the I4/mmm has the atoms rotated. FEFF sees a difference, and I 
would take
the Immm result as the correct one based on the positions of the atoms 
in the cluster

relative to the axes.

-R.


On 12/21/2016 6:49 AM, Bruce Ravel wrote:

On 12/19/2016 11:01 PM, Robert Gordon wrote:
What if one were to do this FEFF calculation using the POLARIZATION 
card?

1 0 0 means something different if the atom positions have been rotated
by 45 degrees relative to the crystal axes along which the polarization
is defined.


Well ... you could rotate the polarization vector by 45 degrees ...

I guess I have always considered FEFF's polarization card to be an a 
posteriori addition to the feff.inp file -- i.e. a decision that the 
user makes after using Atoms to convert crystal data to a cluster in 
feff.inp.


B



## This Atoms file was generated by Demeter 0.9.25
## Demeter written by and copyright (c) Bruce Ravel, 2006-2016

title = fe foil
space = I m m m
a =   2.83500b=   2.83500c =   2.92000
alpha =  90.0beta =  90.0gamma =  90.0
rmax  =  10.0core  = fe
 # polarization = 0.0  0.0  0.0
shift = 0.00.00.0
atoms
# el. x   y   ztag
  Fe 0.0 0.0 0.0   fe
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Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

[Robert Gordon]

en 
using POLARIZATION

(issues in FEFF6 aside), confusion is less-likely?

-R.

On 12/21/2016 10:51 AM, Bruce Ravel wrote:


Robert,

You have me confused.  You seem to be saying that using the correct 
space group symbol is important.  I couldn't possibly disagree.


Raj's original question had to do with the fact that two different 
versions of atoms, which used different algorithms for interpreting 
the crystal data, resulted in clusters that were rotated relative to 
one another.  My answer, appropriate (I think) in that case, was to 
shrug.


You seem to be commenting on something unrelated to the original 
question, but I'm not understanding the point.


B

On 12/21/2016 01:13 PM, Robert Gordon wrote:

Hi Bruce,

The atoms.inp file attached is for bct Fe. In symmetry I4/mmm, the
resulting feff input has the coordinates
rotated, while in Immm the resulting coordinates are not rotated
relative to the crystal axes (i.e. in Immm
the 2nd near neighbour is obvious as a lattice constant away in each
direction).

So, with no polarization, the results for scattering paths are the same
(using CRITERIA default), as expected
Path #
Degen
Reff
Scattering Path
Type
Rank I4/mmm
Rank Immm
1
8
2.48
fe1
ss
100
100
2
4
2.835
fe2
ss
37.56
37.56
3
2
2.92
fe3
ss
17.59
17.59
4
16
3.897
fe1-fe1
ms
3.42
3.42
5
32
3.897
fe1-fe2
ms
12.83
12.83
7
16
3.94
fe1-fe3
ms
6.37
6.37


Now consider with  POLARIZATION 1 0 0 (and 1 1 0 for I4/mmm)

#
Degen
Reff
Scatt. Path
Type
I4 1 0 0
I4 1 1 0
Im 1 0 0

4
2.48
fe1
ss
100



4
2.48
fe1
ss
7.89



8
2.48
fe1
ss

100
100

4
2.835
fe2
ss
55.45



2
2.835
fe2
ss

62.05
62.05

16
3.897
fe1-fe1
ms
4.41
9.90
15.43

16
3.897
fe1- fe2
ms
19.03
21.58
21.59



For that first multiple scattering path, the scattering angles are
36.1/90 for I4(1 0 0), 55.1/55.1
for I4(110) and for Im(100) they are 55.1/124.9. The ranking of this
path is not the same,
and the plots for this path differ as well - in shape as well as 
amplitude.


Conceptually, the Immm model calculation has the atoms aligned with the
crystal lattice
and the I4/mmm has the atoms rotated. FEFF sees a difference, and I
would take
the Immm result as the correct one based on the positions of the atoms
in the cluster
relative to the axes.

-R.


On 12/21/2016 6:49 AM, Bruce Ravel wrote:

On 12/19/2016 11:01 PM, Robert Gordon wrote:

What if one were to do this FEFF calculation using the POLARIZATION
card?
1 0 0 means something different if the atom positions have been 
rotated
by 45 degrees relative to the crystal axes along which the 
polarization

is defined.


Well ... you could rotate the polarization vector by 45 degrees ...

I guess I have always considered FEFF's polarization card to be an a
posteriori addition to the feff.inp file -- i.e. a decision that the
user makes after using Atoms to convert crystal data to a cluster in
feff.inp.

B





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Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

[Robert Gordon]

Hi Bruce,

Has this changed since you wrote the dos variant of the program?
I still have atoms.exe version 2.46b that came with FEFF7
and when I try the same bcc-bct-bco calculations of the Fe cell
the results don't vary. Even the tetragonal version remains aligned to 
the axes.


-R.



On 12/21/2016 12:58 PM, Bruce Ravel wrote:

On 12/21/2016 02:50 PM, Robert Gordon wrote:

So, for all but tetragonal, the orientation of the cluster can be
identified with the
orientation of the crystal axes. Does it not seem more logical to
preserve the
apparent orientation with respect to the crystal axes so that, when
using POLARIZATION
(issues in FEFF6 aside), confusion is less-likely?


Hmm ... I think I understand your point.

I think you may be ascribing too much agency and intelligence to the 
the Atoms algorithm.  The way Atoms works these days is to use this 
tabulation of chapter 7 of volume A of the International Tables:


https://github.com/bruceravel/demeter/blob/master/lib/Xray/Crystal/share/space_groups.db.PL 



It selects the symmetry operations appropriate to the specified space 
group and applies them to the list of unique coordinates. In the case 
of a space group with multiple settings, it uses some heuristics to 
try to guess the correct setting.  (That's what things like "b_unique" 
and so on are all about.  Those heuristics often fail.)  It expands 
out a unit cell and weeds through the unit cell to identify duplicates 
(i.e. high symmetry positions that repeatedly generate the same 
location when the symmetry operations are applied).  It then stacks up 
enough unit cells to contain the cluster, then translates fractional 
coordinates to Cartesian coordinates.


At no point in that operation does the program make any decisions on 
the basis of the definitions of the Cartesian axes.


None of this is a value judgment on what you have said or on Raj's 
original question -- I'm simply explaining how the program works. 
There just isn't an obvious mechanism in the code to let the user 
orient the cluster in a certain way.  That's an interesting idea, but 
not something available at this time.


To use Feff's polarization, you have to choose a polarization vector 
appropriate to the cluster as written.  Or, I suppose, write your own 
tool to rotate the cluster to a more convenient orientation.


B





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Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

[Robert Gordon]

Hi Bruce,

I looked at Site.pm and Cell.pm as well (and I don't program in perl, so 
please forgive

any naivete).

In Site.pm, lines 188 - 191, it says:
#-- rotate from F or C settings to P or I
  if ($is_tetr) {
($x, $y) = ($x-$y, $x+$y);
  };

and this looks like a 45 degree rotation to me, and I can understand why if
someone specified a cell that was "c-centred tetragonal" which is really P
or face-centred tetragonal being I, but is it being applied to all 
tetragonal systems?


In Cell.pm, lines 516 - 521, it says:
  ## rotate a tetragonal group to the standard setting
  if (($crystal_class eq "tetragonal" ) and ($setting ne 'positions')) {
my ($a, $b) = $self->get(qw(a b));
$self->a($a/sqrt(2));
$self->b($b/sqrt(2));
  };

but I see a re-scaling, not a rotation.

Possibly related: When I look at Site.pm on my linux box, from line 134 
on, it is almost all
purple. z and utag are highlighted in red, as is $self on line 138. The 
file looks normal
on github, but if I copy it, these colour changes manifest. I normally 
associate

blue with comments, purple with text strings, green for $self...

thanks,
-R.

On 12/21/2016 12:58 PM, Bruce Ravel wrote:

On 12/21/2016 02:50 PM, Robert Gordon wrote:

So, for all but tetragonal, the orientation of the cluster can be
identified with the
orientation of the crystal axes. Does it not seem more logical to
preserve the
apparent orientation with respect to the crystal axes so that, when
using POLARIZATION
(issues in FEFF6 aside), confusion is less-likely?


Hmm ... I think I understand your point.

I think you may be ascribing too much agency and intelligence to the 
the Atoms algorithm.  The way Atoms works these days is to use this 
tabulation of chapter 7 of volume A of the International Tables:


https://github.com/bruceravel/demeter/blob/master/lib/Xray/Crystal/share/space_groups.db.PL 



It selects the symmetry operations appropriate to the specified space 
group and applies them to the list of unique coordinates. In the case 
of a space group with multiple settings, it uses some heuristics to 
try to guess the correct setting.  (That's what things like "b_unique" 
and so on are all about.  Those heuristics often fail.)  It expands 
out a unit cell and weeds through the unit cell to identify duplicates 
(i.e. high symmetry positions that repeatedly generate the same 
location when the symmetry operations are applied).  It then stacks up 
enough unit cells to contain the cluster, then translates fractional 
coordinates to Cartesian coordinates.


At no point in that operation does the program make any decisions on 
the basis of the definitions of the Cartesian axes.


None of this is a value judgment on what you have said or on Raj's 
original question -- I'm simply explaining how the program works. 
There just isn't an obvious mechanism in the code to let the user 
orient the cluster in a certain way.  That's an interesting idea, but 
not something available at this time.


To use Feff's polarization, you have to choose a polarization vector 
appropriate to the cluster as written.  Or, I suppose, write your own 
tool to rotate the cluster to a more convenient orientation.


B





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Re: [Ifeffit] error when fitting in Artemis

[Robert Gordon]

Hi George,

Your paths are not listed. I don't know why you cannot rerun FEFF 
directly, but
you can export the feff.inp, Add it back in as a new feff calculation, 
and then run it.
Discard the old path from the path list and drag the new path over to 
continue.


-R.

On 12/22/2016 9:11 AM, George Sterbinsky wrote:

Hello,

I have attached an Artemis project. Upon opening the project, and 
clicking the fit button the error in the attached log file is 
generated and the fit is not run. Looking at the history, fits have 
been run previously without error. The error message indicates Feff 
may need to be run again, but upon opening the Atoms and Feff window 
and then clicking on the Feff tab, I see the Run Feff button is grey 
and cannot be clicked. What steps are necessary in order to run a fit?


Thank you,
George


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Re: [Ifeffit] Bond length and Coordination number problems from EXAFS

[Robert Gordon]

Hi Fuxiang,

I tried fitting just the first shell in your data:
kmin 3.5  kmax 11.775
Rmin 1.25  Rmax 2.56

I used just Pd-Ni and Pd-Pd single scatter paths with one amplitude, one 
E, 2 delR's and 2 sigma-squareds

for a 6 parameter fit.

I didn't let Nni or Npd vary in a fit, but did change them between fits. 
I get what seems to be

a double minimum yielding similar chi values as I varied Nni+Npd = 12
i.e. Npd in the range 1.6 - 1.8   or Npd 2.0 - 2.2 yielded similar values
Another minimum occurs near 2.4 but sig^2-pd is getting larger than 
seems plausible.


I did not try changing Ranges or windows to see if that would smooth out 
the oscillations in the fit

versus relative N values

amp ~ 0.7 (ok...but I didn't normalise the data or compare with Pd or Ni 
foils)

delEo  -7 (which seems large)
Rni  2.54Rpd 2.68   (both a bit small but would need to 
compare to Ni and Pd foil fits for systematic error in fitting)
ssni  0.0050(2)sspd   0.010(3)   (error bars from correlation with 
changing N - strong correlation

between Npd and sspd)

This is not consistent with your model, since it has more than 1 Pd in 
the 1st shell.
The R-values (apart from not having checked reference foils) are within 
reason for what one

would expect from sums of atomic radii.

Hope this helps get you pointed in the right direction as you refine 
your model.


cheers,
Robert



On 2/20/2017 10:57 AM, Fuxiang Zhang wrote:

Dear All,
I met a problem in fitting my sample. The sample is a very 
simple crystalline Ni (fcc) with minor Pd. I measured both the K-edge 
of Ni and Pd and fit with a 55 randomly distributed cluster model 
(from calculations). The model suggested that there are 1 Pd in the 
first and second-shell, 6-Pd in the 3rd-shell and 2-Pd in the 4th 
shell. I have attached the FPJ file here, can anyone help me to have a 
look.


1. In fitting the K-edge of Pd, most paths are single scattering, but 
I always get a shorter Pd-Pd length than Pd-Ni, even I tried to 
include all the paths. Not sure if I made any mistakes in the path 
parameters settings.


2. If including the minor contribution paths, I use the same 
parameters for the path: @Ni1.1 Ni1.1@ (acute triangle) and the path: 
@N1.1 Ni1.1@ (obtuse triangle), as well as single scattering path 
@Ni1.1@. I know there's a problem (though no much effect on the 
results), but don't know how to set the first two paths' parameters


3. If the result is correct, which may suggest there is no Pd in the 
1st-shell, but how to fit the coordination number of Pd is a problem. 
Since Pd is only 1/12 in the first shell, while the uncertainty of CN 
from EXAFS fitting is pretty large. Does it make a sense to refine the CN?


FPJ file is attached

Thank you very much

Fuxiang Zhang


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Re: [Ifeffit] Bond length and Coordination number problems from EXAFS

[Robert Gordon]

Hi Fuxiang,

How much background do you have in EXAFS fitting? Have you taken a course?
Do you have access to a good EXAFS primer book (e.g. Grant Bunker's or 
Scott Calvin's)?


/1) Which is better, to refine only the first shell or more shells. /
/The results seems to be quite sensitive on the selection of 
kmin/kmax and Rmin/Rmax, I cannot judge when can get reliable results 
(base on chi?) /


In general, I would take a kmin that is above the edge and away from any 
white line because background
removal in those areas (white line, or on the rising edge) is suspect. I 
would take a kmax that avoids data that cannot be distinguished from 
noise. I picked Rmax on the high side to isolate the 1st peak in the FT. 
I picked Rmin based on the magnitude of the 1st Feff shell and a need to 
get enough R-range to do a 6
parameter fit. It was a nervous choice since too low an Rmin could bring 
in unwanted artifacts. What it
comes down to is: do the choices allow a sufficient amount of data for 
use in fitting; and are

they defensible in review.

What I considered good fits were based in part on looking for where 
chi^2 is a minimum and
in part from inspection of the results - were the results consistent 
with a basic understanding
of how atom-atom distances should manifest. You applied this as well 
when you initially wrote
and noted your fit was giving Pd-Pd distances shorter than Pd-Ni, and 
you questioned that.


As for fitting higher shells, what is the problem you are trying to 
answer? Is the Pd distribution
statistical or showing evidence of clustering? The higher shells are 
weak and have multiple scattering
as well as back-scattering paths. The error in just the first shell Pd 
content is large, owing to the
strong correlation with the mean-square-relative-displacement. I would 
expect this to also be
problematic in higher shells - more so. So, can you build a defensible 
argument based on a first
peak analysis? Is taking more data an option (going to higher k with 
less noise)? This was just

the Pd data. How consistent is the Ni data fit?

/2) You used Rmax=2.56, while Rpd is 2.68, not sure if there's 
any contradict /


The sine term in the EXAFS equation is sin(2kR+delta). What is delta?
Did you measure reference foils for Ni and Pd? Where does the first peak 
manifest
in the |FT(k^n * chi(k))| - at what R-value? By how much is the peak 
shifted from the

crystallographic distance for the different standards?
/
/
/3) For the Nni and Npd, you change them manually and check the chi 
values during fitting, is that right?/


Correct. Try this yourself. I suggest you tabulate and plot them so you 
can see
the different subsidiary minima and maxima and how the fit results vary 
between them. Perhaps use

a broad range to get a sense of what a global minimum might be.

Please note: The questions I have posed are intended to stimulate 
thinking and need not warrant

a response.

Another curious note: If you look at the chi(k)'s for the 1st shell Feff 
paths, they are almost
180 degrees out of phase at higher k...a suppressing effect that could 
make it difficult to

study higher concentration mixtures.




cheers,
-R.

On 2/21/2017 6:22 AM, Fuxiang Zhang wrote:

Hi, Robert,
Thank you very much for the help. Based on the nominal composition, 
there should have more than one Pd atoms in the 1st shell and both the 
R values you got are reasonable.

I still have some questions about the fitting
1) Which is better, to refine only the first shell or more shells.
The results seems to be quite sensitive on the selection of 
kmin/kmax and Rmin/Rmax, I cannot judge when can get reliable results 
(base on chi?)
2) You used Rmax=2.56, while Rpd is 2.68, not sure if there's 
any contradict
3) For the Nni and Npd, you change them manually and check the chi 
values during fitting, is that right?


Thanks again

Fuxiang



On Tue, Feb 21, 2017 at 3:30 AM, Robert Gordon <mailto:ragor...@alumni.sfu.ca>> wrote:


Hi Fuxiang,

I tried fitting just the first shell in your data:
kmin 3.5  kmax 11.775
Rmin 1.25  Rmax 2.56

I used just Pd-Ni and Pd-Pd single scatter paths with one
amplitude, one E, 2 delR's and 2 sigma-squareds
for a 6 parameter fit.

I didn't let Nni or Npd vary in a fit, but did change them between
fits. I get what seems to be
a double minimum yielding similar chi values as I varied Nni+Npd = 12
i.e. Npd in the range 1.6 - 1.8   or Npd 2.0 - 2.2 yielded similar
values
Another minimum occurs near 2.4 but sig^2-pd is getting larger
than seems plausible.

I did not try changing Ranges or windows to see if that would
smooth out the oscillations in the fit
versus relative N values

amp ~ 0.7 (ok...but I didn't normalise the data or compare with Pd
or Ni foils)
delEo  -7 (which seems large)
Rni  2.54Rpd 2.68   (both a bit small but would need
to compare to Ni

Re: [Ifeffit] Space group type in Artemis

[Robert Gordon]

B11b in an alternate form of space group #9 (Cc or C1c1)
Atoms does take Bb as the space group, but that could be Bb11
(which does not produce an error message) with unique x-axis instead
of the unique z-axis in B11b.

My suggestion: When I use a crystal structure in Atoms,
I prefer to check the Inorganic Crystal Structure Database (ICSD)
for a standard form of the structure (and a list of distances for 
comparision).

That should net a structure in Cc format.

Useful reference for space groups:
http://img.chem.ucl.ac.uk/sgp/mainmenu.htm

regards,
-R.

On 3/11/2017 2:56 AM, Abhinav Prabhakar wrote:

Hello,

I have a question about the working of Artemis as a new user.

Artemis does not recognize the space group B11b. When importing a cif 
file of a crystal with this symmetry, it sends a prompt message that 
the space group symbol cannot be recognized. As a result, I changed it 
to P11b and it works. But would this change any crystal information 
(for eg. Degen, Reff values) significantly?


Thank you.

Regards,
Abhinav Prabhakar (Mr)



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Re: [Ifeffit] Conflicting FEFF calculation

[Robert Gordon]

Hi Ashis,

I can reproduce what you are seeing.
I exported the atoms.inp's for your two structures.

If I import TAA first and run atoms, it looks ok. I then import TPA and 
run - ok.

I re-run Atoms on TAA, it changes.

In fact, from a clean start of Artemis 0.9.25 on win10pro/AMD64, if I 
import TAA's inp and run it, it looks ok.
I added it again, it still looks ok, even if I re-run Atoms. I add TPA 
and run it, it looks ok, but if I rerun

either of the TAA, they have changed. Changes persist even if TPA discarded.

From another clean start of Artemis, I import TAA and run Atoms - ok.
I import a different inp (ni metal) and run it - ok. Re-run TAA and it 
is ok.


From another clean start, I import Ni metal and run it...ok
Import TPA and run it...ok...Rerun Ni and Ni changes...definite symmetry 
change.
This symmetry change persists even if I discard TPA and import another 
copy of Ni.


Clean start, import Ni and run, then import another Rhombohedral 
structure (B phase)
and same problem...symmetry changes and I don't seem to be able to get 
it to change back,
even when I deliberately change the space group for Ni and it is the 
only calculation remaining.


Clean start...import Ni...okadd rhombohedral structure (B) but don't 
run it..rerun Ni and Ni changes.


Clean start, import hexagonal structure (in P6)...ok...import 
Ni...okchange hex to Rhomb indexed on hex

and Ni changes when rerun...

So...problem seems to be related to the symmetry - stuck in Rhombohedral 
once a R-structure

is added...or symmetry changed to R.

Haven't tried on Linux yet.

-R.





On 4/3/2017 1:46 PM, Ashis Biswas wrote:


Dear Bruce,

Sorry for late reply. I wanted to test in another computer before 
replying. Unfortunately, this time also I got different results for 
TAA. Following is the click by click description of what I am doing to 
arrive in this state:


Double click on “Atemis” shortcut on desktop => Click “add” in the 
Feff calculation tab => Open “TPP” Atom input file from desktop=> 
Click “Run Atom” => Click “Run Feff” => Click “add” in the Feff 
calculation tab => Open “TAA” CIF file from desktop=> Click “Run Atom” 
=> Click “Run Feff”


I am sorry for killing your time. Actually, I am very much new in this 
field and therefore I really want to be sure that what I am doing for 
importing object for feff calculation is correct or not. Thank you 
very much for your support.


With regards,

Ashis


On 2017-03-28 16:13, Bruce Ravel wrote:

On 03/27/2017 11:02 AM, Ashis Biswas wrote:

Thank you very much for your reply. Here I am attaching two Artemis
projects files (TAA_TPA and TPA_TAA), named according to their order of
import. In my computer the paths for *TAA* are different in two project
files. For example, i) in TAA_TPA project the Reff for three single
scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to 
that in
TPA_TAA project, ii) the single scattering path @C5.1 (path number 
6) at

Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and
so on.

I am also attaching the papers from where the coordinates for TAA and
TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and
TPA (Pappalardo et al., 1983: Table 1; Fig. 1).



I agree that the TPA_TAA.fpj project file that you sent me has 
incorrect data in the Feff tab for TAA.


I have not, however, been able to reproduce that here.  And not for 
want of trying -- I spent the last half hour trying to find a way to 
replicate what you are showing in the TPA_TAA file. Regardless of the 
order in which I import the two structures and regardless of whether 
I have discarded and reimported Feff calculations, when I click the 
"Run Atoms" button on the TAA cif file, I /always/ get the structure 
from Table 4 in the Kamenar paper.  I cannot reproduce the Feff tab 
that you show in your TPA_TAA project file.


I have no idea how you got into the state you show in the TPA_TAA 
project.  It is clear that something went awry, but I don't know if 
it is an error of the program or of the user.  I can't fix a problem 
I can't observe.


I understand that this is not the answer you were looking for. I am 
simply not seeing the problem you are reporting.


B







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Re: [Ifeffit] Conflicting FEFF calculation

[Robert Gordon]

Hi Bruce,

Issues with the pre-release. Log file attached.

Seems to be looking for gnuplot in the wrong location. Gnuplot was 
installed to:

C:\Users\ragordon\AppData\Roaming\DemeterPerl\c\bin\gnuplot
not
C:\Strawberry...


also, log has this:
C:/Users/ragordon/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm 
line 26


Which has the slashes in the wrong direction for windows...just 
something from the log writing

or a linux-typo in the program somewhere?


-R.


On 4/4/2017 7:07 AM, Bruce Ravel wrote:



Robert, thanks for doing so much work to verify what Ashis is seeing.

That said, I am still not seeing this problem.  My working notion is 
that it is a problem that somehow got fixed while I was doing some 
other work a few months ago.


This morning, I prepared and uploaded a new installer package as a 
pre-release of the upcoming version.  Here's the direct link.


https://s3.amazonaws.com/demeter4xas/Demeter_0.9.26_with_Strawberry_Perl_(64)_pre2.exe 



If one or both of you could install this and let me know if the 
problem persists, I would be grateful.



I did uncover a bunch of of problems with Demeter's crystallography 
bits while I was working on


   https://github.com/bruceravel/WebAtoms,
   http://millenia.cars.aps.anl.gov/webatoms

I don't really see the value of sifting through all that work to 
figure out what had an impact on Ashis' issue.  If the newer code 
works -- that seems good enough to me.


B


On 04/03/2017 06:08 PM, Robert Gordon wrote:

Hi Ashis,

I can reproduce what you are seeing.
I exported the atoms.inp's for your two structures.

If I import TAA first and run atoms, it looks ok. I then import TPA and
run - ok.
I re-run Atoms on TAA, it changes.

In fact, from a clean start of Artemis 0.9.25 on win10pro/AMD64, if I
import TAA's inp and run it, it looks ok.
I added it again, it still looks ok, even if I re-run Atoms. I add TPA
and run it, it looks ok, but if I rerun
either of the TAA, they have changed. Changes persist even if TPA 
discarded.


From another clean start of Artemis, I import TAA and run Atoms - ok.
I import a different inp (ni metal) and run it - ok. Re-run TAA and it
is ok.

From another clean start, I import Ni metal and run it...ok
Import TPA and run it...ok...Rerun Ni and Ni changes...definite symmetry
change.
This symmetry change persists even if I discard TPA and import another
copy of Ni.

Clean start, import Ni and run, then import another Rhombohedral
structure (B phase)
and same problem...symmetry changes and I don't seem to be able to get
it to change back,
even when I deliberately change the space group for Ni and it is the
only calculation remaining.

Clean start...import Ni...okadd rhombohedral structure (B) but don't
run it..rerun Ni and Ni changes.

Clean start, import hexagonal structure (in P6)...ok...import
Ni...okchange hex to Rhomb indexed on hex
and Ni changes when rerun...

So...problem seems to be related to the symmetry - stuck in Rhombohedral
once a R-structure
is added...or symmetry changed to R.

Haven't tried on Linux yet.

-R.





On 4/3/2017 1:46 PM, Ashis Biswas wrote:


Dear Bruce,

Sorry for late reply. I wanted to test in another computer before
replying. Unfortunately, this time also I got different results for
TAA. Following is the click by click description of what I am doing to
arrive in this state:

Double click on “Atemis” shortcut on desktop => Click “add” in the
Feff calculation tab => Open “TPP” Atom input file from desktop=>
Click “Run Atom” => Click “Run Feff” => Click “add” in the Feff
calculation tab => Open “TAA” CIF file from desktop=> Click “Run Atom”
=> Click “Run Feff”

I am sorry for killing your time. Actually, I am very much new in this
field and therefore I really want to be sure that what I am doing for
importing object for feff calculation is correct or not. Thank you
very much for your support.

With regards,

Ashis


On 2017-03-28 16:13, Bruce Ravel wrote:

On 03/27/2017 11:02 AM, Ashis Biswas wrote:

Thank you very much for your reply. Here I am attaching two Artemis
projects files (TAA_TPA and TPA_TAA), named according to their 
order of
import. In my computer the paths for *TAA* are different in two 
project

files. For example, i) in TAA_TPA project the Reff for three single
scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to
that in
TPA_TAA project, ii) the single scattering path @C5.1 (path number
6) at
Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, 
and

so on.

I am also attaching the papers from where the coordinates for TAA and
TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) 
and

TPA (Pappalardo et al., 1983: Table 1; Fig. 1).



I agree that the TPA_TAA.fpj project file that you sent me has
incorrect data in the Feff tab for TAA.

I have not, however, been able to reproduce that here.  And not for
want of trying -- I spent the las

Re: [Ifeffit] Conflicting FEFF calculation

[Robert Gordon]

Actually, I just created C:\Strawberry\c\bin and copied gnuplot 
directorythat worked 

Changing demeter.ini more elegant though, and starts just as happily...

Had to change the Feff6 path in the ini as well or program would crash 
on loading a project file

i.e. log stated :
The feff executable could not be found at your specified 
location(C:\Strawberry\c\bin\feff6.exe) nor at the system default 
location(C:\Strawberry\c\bin\feff6.exe)




No context other than what was written in the log...had the slashes for 
linux in the @inc section too...

Just a curiosity I suppose...

On 4/4/2017 11:23 AM, Bruce Ravel wrote:

On 04/04/2017 11:58 AM, Robert Gordon wrote:

Seems to be looking for gnuplot in the wrong location. Gnuplot was
installed to:
C:\Users\ragordon\AppData\Roaming\DemeterPerl\c\bin\gnuplot
not
C:\Strawberry...


Drat!  I thought I had that working correctly.

You can manually fix that in the preferences.  Change 
Gnuplot-->program the the fully resolved path where it is installed.




also, log has this:
C:/Users/ragordon/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm 


line 26

Which has the slashes in the wrong direction for windows...just
something from the log writing
or a linux-typo in the program somewhere?


Don't know.  Was there any context?

B




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Re: [Ifeffit] Silent Oxygen

[Robert Gordon]

Hi Fuxiang,

Further to Bruce's note, I looked at your file. Your model splits the 
nearest oxygens by only 0.01A.

Is that the magnitude of splitting you anticipate?
Are you familiar with the resolution criteria for EXAFS?
(k-range [deltak]) * (R-resolution [deltaR]) ~ pi/2 for identical near 
neighbours

This is also discussed in the archives, e.g.:
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2007-November/003414.html

Looking at your chi(k), it seems usable, charitably, up to about 8 A-1, 
not to 12 A-1 as your
window suggests you have used. Claims of being able to resolve small 
splittings

with this data will be viewed with skepticism.

-R.

On 4/18/2017 11:34 AM, Bruce Ravel wrote:

On 04/18/2017 11:10 AM, Fuxiang Zhang wrote:

Hi, all,
I am in studying the EXAFS of perovskite and clearly see the split of
the first peak after ion irradiation. It should come from a symmetry
change, so I use a tetragonal model (instead the original cubic) which
contains two independent O sites. However, after running Atoms and
Feff, all paths are contributed by only one O atom and nothing related
to another Oxygen atoms (see attached file). As a result it may
be difficult to get a good fit of the first split Ta-O peaks. I am not
sure if it is true or something wrong.
Thank you very much


A fairly common question here on the mailing list.  This is a 
*feature* of Artemis, not a bug.


http://bruceravel.github.io/demeter/documents/Artemis/extended/fuzzy.html

If you want to /model/ a split in distance, you can drag that path 
into the path list twice and adjust the delta R and amplitude 
parameters accordingly.


B




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Re: [Ifeffit] Error using Atoms

[Robert Gordon]

Hi Adam,

I opened the cif file you provided and Artemis/Atoms immediately gave the
atoms.inp file attached.
Running Atoms gave the feff.inpI don't see a problem.

Could you provide more detail on how you achieved this erroneous result?
i.e. step by step...
e.g. I opened Artemis v0.9.25
I clicked 'add' under Feff calculations
I selected Rh.cif and clicked open
et voila! Much humble praise to Bruce...

-R.



On Thu, Jun 8, 2017 at 5:50 AM, Clark, Adam  wrote:

> Dear Mailing List
>
>
> I have encountered an issue when using the version of Atoms within
> Artemis for the calculation of the scattering paths on metallic FCC
> systems. Attached are both the cif file and the generated feff.inp file
> from using Atoms from within Artemis. Here the problem that occurs is the
> generation of two short atoms at distances of 1.91 Å before the first shell
> atoms at distances of 2.70 Å for metallic Rh.
>
>  ATOMS  * this list contains 69 atoms
>  *   x  y  z ipot tag   distance
> 0.00.00.0  0  Rh1   0.0
> 1.654110.955000.0  1  Rh1.1 1.91000
>-1.65411   -0.955000.0  1  Rh1.1 1.91000
>-1.654110.955001.91000  1  Rh1.2 2.70115
> 0.01.910001.91000  1  Rh1.2 2.70115
> 1.65411   -0.955001.91000  1  Rh1.2 2.70115
> 0.0   -1.910001.91000  1  Rh1.2 2.70115
>-1.654110.95500   -1.91000  1  Rh1.2 2.70115
> 0.01.91000   -1.91000  1  Rh1.2 2.70115
> 1.65411   -0.95500   -1.91000  1  Rh1.2 2.70115
> 0.0   -1.91000   -1.91000  1  Rh1.2 2.70115
>
>
> Using the same input CIF file within WebAtoms does not produce these short
> distances.
>
>
> Adam Clark
>
>
> PhD Student
>
>
>
> Industrial Doctorate Centre in Molecular Modelling and Materials Science,
>
> Department of Chemistry,
>
> University College London
>
>
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atoms.inp
Description: Binary data


feff.inp
Description: Binary data
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Re: [Ifeffit] question about sigma2 and atomic distance

[Robert Gordon]

I imagine they could, yes. Motivation to do so is another question entirely.

Considering myself more of an experienced amateur, and a fan of the
Socratic Method, let me ask you a few questions:

What do you currently understand about the relationship between two atoms
in a material and the mean square relative displacement
(i.e. sigma^2) associated with the distance between them?
What does it mean to have a mean-square-displacement? ..and then a
mean-square-relative displacement?
How would correlated, anti-correlated and uncorrelated relative motion
affect the msrd?

Now extend this thinking to an ensemble of atoms.
What might you expect to be the source of a msrd in a perfect crystal at
finite temperature?
What additional contribution may result from imperfections?








On Wed, Jun 7, 2017 at 7:12 PM, Shaofeng Wang 
wrote:

> Dear everyone,
>
> Could experts explain the relationship between sigma2 and atomic distance
> of same two atoms?
>
>
> Best regards,
>
> Shaofeng
>
> --
> Shaofeng Wang, Ph.D of Geochemistry
> Environmental Molecular Science Group
> Institute of Applied Ecology, Chinese Academy of Sciences
> Shenyang, 110016, China
> wangshaof...@iae.ac.cn
> www.iae.cas.cn
>
>
> *From:* Shaofeng Wang 
> *Sent:* Friday, June 02, 2017 4:32 PM
> *To:* XAFS Analysis using Ifeffit 
> *Subject:* [Ifeffit] a question about S02
>
> Hi everyone,
>
> I am fitting a standard material scorodite. The fitting results are pretty
> good, but the S02 is around 1.2 when the k range = 4-13.5. Is this result
> reasonable? Please see the attached files.
>
>
>
> Best regards,
>
> Shaofeng
>
> --
> Shaofeng Wang, Ph.D of Geochemistry
> Environmental Molecular Science Group
> Institute of Applied Ecology, Chinese Academy of Sciences
> Shenyang, 110016, China
> wangshaof...@iae.ac.cn
> www.iae.cas.cn
>
> --
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Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 4

[Robert Gordon]

Hi Adam,

I think the problem you are seeing is related to one observed back in April.
The Rh2O3 crystal you also have in your project has trigonal symmetry, and
trigonal symmetry in 0.9.25
tends to override all others. This was discussed in this thread:
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009083.html
Bruce made a pre-release of 0.9.26 available at the time that fixed this
problem:
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009084.html

The pre_2 release of 0.9.26 is also available on the main Demeter page:
https://bruceravel.github.io/demeter/

-R.



On Fri, Jun 9, 2017 at 5:54 AM, Clark, Adam  wrote:

> Dear Robert
>
>
> Attached I have given the different feff.inp files generated from using
> Artemis and from WebAtoms (named accordingly) along with images showing the
> input screens using default parameters.
>
>
> The difference comes in the atoms list generated. Using artemis two short
> atoms are produced at 1.91 A which are not present when I use WebAtoms.
> Interestingly I have now discovered this does not happen with every artemis
> project. I have attached a project where I am getting the erroneous
> feff.inp file generation. To replicate the error it is possible to add
> another feff calculation into this artemis project with the attached cif.
>
>
> The attached project is an example where this error occurs but I have not
> been able thus far to make a new project that repeats this error.
>
>
> Adam
> --
> *From:* Ifeffit  on behalf of
> ifeffit-requ...@millenia.cars.aps.anl.gov  cars.aps.anl.gov>
> *Sent:* 08 June 2017 23:59:09
> *To:* ifeffit@millenia.cars.aps.anl.gov
> *Subject:* Ifeffit Digest, Vol 172, Issue 4
>
> 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
> ifeffit-requ...@millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
> 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. Re: Error using Atoms (Robert Gordon)
>2. Re: question about sigma2 and atomic distance (Robert Gordon)
>
>
> --
>
> Message: 1
> Date: Thu, 8 Jun 2017 15:33:55 -0700
> From: Robert Gordon 
> To: XAFS Analysis using Ifeffit 
> Subject: Re: [Ifeffit] Error using Atoms
> Message-ID:
>  com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Adam,
>
> I opened the cif file you provided and Artemis/Atoms immediately gave the
> atoms.inp file attached.
> Running Atoms gave the feff.inpI don't see a problem.
>
> Could you provide more detail on how you achieved this erroneous result?
> i.e. step by step...
> e.g. I opened Artemis v0.9.25
> I clicked 'add' under Feff calculations
> I selected Rh.cif and clicked open
> et voila! Much humble praise to Bruce...
>
> -R.
>
>
>
> On Thu, Jun 8, 2017 at 5:50 AM, Clark, Adam 
> wrote:
>
> > Dear Mailing List
> >
> >
> > I have encountered an issue when using the version of Atoms within
> > Artemis for the calculation of the scattering paths on metallic FCC
> > systems. Attached are both the cif file and the generated feff.inp file
> > from using Atoms from within Artemis. Here the problem that occurs is the
> > generation of two short atoms at distances of 1.91 ? before the first
> shell
> > atoms at distances of 2.70 ? for metallic Rh.
> >
> >  ATOMS  * this list contains 69 atoms
> >  *   x  y  z ipot tag   distance
> > 0.00.00.0  0  Rh1   0.0
> > 1.654110.955000.0  1  Rh1.1 1.91000
> >-1.65411   -0.955000.0  1  Rh1.1 1.91000
> >-1.654110.955001.91000  1  Rh1.2 2.70115
> > 0.01.910001.91000  1  Rh1.2 2.70115
> > 1.65411   -0.955001.91000  1  Rh1.2 2.70115
> > 0.0   -1.910001.91000  1  Rh1.2 2.70115
> >-1.654110.95500   -1.91000  1  Rh1.2 2.70115
> > 0.01.91000   -1.91000  1  Rh1.2 2.70115
> > 1.65411   -0.95500   -1.91000  1  Rh1.2 2.70115
> > 0.0   -1.91000   -1.91000  1  Rh1.2 2.70115
> >
> >
> > Using th

Re: [Ifeffit] FEFF8/FEFF9 in Demeter​

[Robert Gordon]

https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06059.html

-R.

On Wed, Jun 14, 2017 at 11:55 PM, 이국승(에너지환경소재연구팀) 
wrote:

> ​Dear Ifeffit users,
>
>
> I remember that one of you have posted the method how we can use
> FEFF8/FEFF9 in Demeter​ program.
>
> But I cannot find the posting in the archives.
>
> Could you please kindly  let me know how can I find it or directly write
> again?
>
>
> Best,
>
> Kug-Seung Lee
>
>
>
>
>
> Kug-Seung Lee, Ph.D.
> Staff Scientist
> Manager, 8C Nano Probe XAFS Beamline
> Pohang Accelerator Laboratory
>
> Pohang 790-784, Republic of Korea
>
> Office: +82-54-279-1522
> Fax: +82-54-279-1599
> C. P.: +82-10-6419-7801
> Researcher ID: http://www.researcherid.com/rid/D-7088-2011
>
>
>
>
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Re: [Ifeffit] Demeter on Windows with Inkscape (and possibly other programs)

[Robert Gordon]

Hi Bruce,

I am not experiencing this issue. I have Athena and Inkscape both open 
right now.
My environment variables list does not have FONTCONFIG_FILE in it. I 
have a vague
recollection of deleting that env var some time ago when changing 
versions of Demeter.


Regardless, Demeter is working for me without issue...Inkscape as 
well...so perhaps
a simple short-term fix is just to delete FONTCONFIG_FILE  from the env 
var list rather than

uninstalling Demeter.

Demeter 0.9.26 (pre 2)
Inkscape 0.92 (fresh install today)
win10x64, AMDx64

cheers,
Robert
On 8/10/2017 1:42 PM, Bruce Ravel wrote:


Windows users:

I got an interesting bug report today from a fellow who develops a 
popular open source program for vector graphics editing (Inkscape).


Apparently, there is a problem in Demeter's installer that has an 
impact on the ability of that program (and possibly others) in 
accessing system font files.  The issue with Inkscape is described 
here: https://github.com/bruceravel/demeter/issues/51


I mention this here on the mailing list in an effort to help the folks 
who maintain Inkscape.


If you use Demeter and Inkscape on your Windows machine, there is a 
problem and it is my fault :(


The simplest solution is to uninstall Demeter, then continue using 
Inkscape.


If that's not true or if someone needs a better solution right now, 
post here and I will help you work out a solution.


I think the real fix to the problem is simple and I will work on a new 
installer this month.


Cheers,
B





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Re: [Ifeffit] [IFEFIT]Chi(E) in version 0.9.25

[Robert Gordon]

This already happens in Athena. It was requested back in 2014:
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04747.html
and Bruce did include energy as a column in the exported chi file in a 
future release

(present in 0.9.26)...e.g.
# XDI/1.0 Athena/0.9.26
# Element.edge:  K
# Element.symbol:    Fe
# Column.1:  k inverse Angstrom
# Column.2:  chi
# Column.3:  chik
# Column.4:  chik2
# Column.5:  chik3
# Column.6:  window
# Column.7:  energy


-R.

On 9/15/2017 6:32 AM, Matt Newville wrote:

Hi Michael,

On Fri, Sep 15, 2017 at 8:21 AM, Michael Stockenhuber 
> wrote:


Dear mailing list,

Is there any way to save data as Chi( E),i.e., energy one column
and chi(E) in the 2^nd column? This was possible in the past and
it would be great to have that to be able to import into excurv.



Sure:

   ~> larch

   larch> dat = read_ascii(datafile_name)
   larch> # ... make sure you have mu(E) as  'dat.energy' and 'dat.mu 
'


   larch> autobk(dat, rbkg=1.0, kweight=1)  # may want other options

   larch> write_ascii('my_chie.txt', dat.energy, dat.chie)
   larch> plot(dat.energy, dat.chie, xlabel='E (eV)', ylabel=r'$\chi(E)$')

Hope that helps,

--Matt



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Re: [Ifeffit] Metal-Metal Peak Splitting in 5d Transition Metals

[Robert Gordon]

Ramsauer-Townsend effect
Bruce gives some references at the end of this talk:
https://speakerdeck.com/bruceravel/the-ramsauer-townsend-effect-in-x-ray-absorption-spectroscopy

-R.

On 9/19/2017 2:06 AM, Shoaib Muhammad wrote:


Dear All,

I have a question that is not directly related to Athena or Artemis 
but it is more related with EXAFS theory. I work on lithium metal 
oxides and sometimes measure their XAS data. XAS data show typical 
trend, i.e; first prominent peak related with metal-oxygen 
co-ordination shell and second prominent peak is associated with 
metal-metal co-ordination shell in my materials. I have noticed that 
in similar crystal structures Li2MO3-type (where M is transition 
metal), if metal belongs to 3d transition metal groups I get a single 
prominent metal-metal peak but for 5d transition metals, the 
metal-metal peak splits and its intensity also drops. I could not 
figure out the reason for the splitting of metal-metal peak in case of 
5d metals. I have attached a PDF file in which calculated EXAFS 
spectra for Li2RuO3 (4d transition metal) and Li2PtO3 (5d transition 
metal) are shown and metal-metal (Pt-Pt) peak in Li2PtO3 shows clear 
splitting whereas metal-metal peak for Li2RuO3 does not split even 
though their “ATOMS” input files are very similar.


I would appreciate if anybody could briefly explain the reason for 
metal-metal peak splitting in 5d metals or point me towards any 
literature. Attachment can be downloaded from the below link as well.


https://www.dropbox.com/s/1m3kf764junuukk/Metal-Metal%20Peak%20Splitting%20in%205d.pdf?dl=0 



Thanks,

*Shoaib Muhammad*

Department of Energy Science

Sungkyunkwan University (South Korea)



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[Ifeffit] space group 224 & Atoms

[Robert Gordon]

Hi,

I was trying to simulate Cu2O...cubic...O tetrahedrally coordinated by 
Cu...Cu linearly coordinated by O.

There are two origin choices for space group 224 (Pn-3m).
If using origin choice 1, then atom positions would be
O    0,0,0
Cu  0.25,0.25,0.25
If using origin choice 2, translate by -0.25,-0.25,-0.25 to get
O  0.75,0.75,0.75
Cu  0,0,0
(or use the shift vector in Atoms...)

My understanding is that Demeter defaults to the 2nd origin choice.

Problem I am having is that neither gives me linearly coordinated copper 
using current Atoms.
If I read in the attached atoms.inp (choice 2) and Run Atoms, the ATOMS 
list in the

Feff output begins with:

 ATOMS  * this list contains 87 atoms
 *   x  y  z ipot tag   distance
    0.0    0.0    0.0  0  cu1   0.0
   -1.06675    1.06675    1.06675  2  o1.1  1.84767
   -1.06675   -1.06675    1.06675  2  o1.1  1.84767
    1.06675    1.06675   -1.06675  2  o1.1  1.84767
   -1.06675   -1.06675   -1.06675  2  o1.1  1.84767
 2.13350    2.13350    0.0  1  cu1.1 3.01722

I get 4-coordinate instead of 2-coordinate.
If I try origin choice 1, almost the same result

 ATOMS  * this list contains 83 atoms
 *   x  y  z ipot tag   distance
    0.0    0.0    0.0  0  cu1   0.0
   -1.06675    1.06675    1.06675  2  o1.1  1.84767
    1.06675   -1.06675    1.06675  2  o1.1  1.84767
    1.06675    1.06675   -1.06675  2  o1.1  1.84767
   -1.06675   -1.06675   -1.06675  2  o1.1  1.84767
    2.13350    2.13350    0.0  1  cu1.1 3.01722

If I run choice 1 with the shift vector, I do reproduce the choice 2 result.


 If I use the old dos version of Atoms with origin choice 2,
I do get linearly coordinated copper:

 ATOMS
    .0  .0  .0    0   cu1   .0
  -1.06675    -1.06675    -1.06675    1   o1   1.84767
   1.06675 1.06675 1.06675    1   o1   1.84767
    .0    -2.13350 2.13350    2   cu1  3.01722



SPECS:

Demeter 0.9.26 (pre2)
Win10x64
AMD64


-R.


## This Atoms file was generated by Demeter 0.9.26
## Demeter written by and copyright (c) Bruce Ravel, 2006-2017

title = Cuprite
space = 224
a =   4.26700b=   4.26700c =   4.26700
alpha =  90.0beta =  90.0gamma =  90.0
rmax  =   6.0core  = cu1
polarization = 0.0  0.0  0.0
shift = 0.00.00.0
atoms
# el. x   y   ztag
  Cu 0.0 0.0 0.0   cu1   
  O  0.75000 0.75000 0.75000   o1
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[Ifeffit] flattened norm export issues

[Robert Gordon]

Hi,

Encountered a difference on export of normalised data. Flattening does 
not seem to be preserved when

saving current group as norm(E) but is when saving marked group.

Example in norm.prj attached.
original data set normalised and flattened...displaying "Normalized" as 
current group or as marked group looks

the same:

current:

marked:


On saving current or marked group as norm(E), re-importing and plotting 
as mu(E)




marked is still flattened, but the set exported using "save current 
group as" is not flattened.

Similar difference saving "marked" versus saving "each marked"


So it seems only "Save marked group as..." preserves flattening for norm(E).

-R.


norm.prj
Description: Binary data
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Re: [Ifeffit] Hephaestus: Absorption Data Source

[Robert Gordon]

Hi,

The documentation for Hephaestus lists the same paper as you indicated.
(Access by going to Help-Document in Heph.)

Another reference with values tabulated is:
http://aip.scitation.org/doi/10.1063/1.95

Natural widths of atomic K and L levels, Kα X‐ray lines and several KLL 
Auger lines

Journal of Physical and Chemical Reference Data 8, 329 (1979);
M. O. Krause and J. H. Oliver

But I have noticed the values differ between that work and those in 
Heph/earlier work.

Krause and Oliver did not even cite that earlier work.

-R.

On 11/12/2017 1:28 PM, Daniel Przyrembel wrote:

Dear All

This might be a stupid question, but I have not been able to track this
down myself:

What is the data source of the "core-hole lifetimes" (i.e. the energy
widths "gamma(ch)" in eV) of the "Absorption edges" in the "Absorption"
panel of Hephaestus?

As far as I could see these lifetimes/widths are not given in the 'Elam
database'. Other XAS data tools based on the Elam database (like e.g.
'XrayDB') claim to be using values from 'O. Keski-Rahkonen and M. O.
Krause, Atomic Data and Nuclear Data Tables 14, pp139-146 (1974)
(http://dx.doi.org/10.1016/S0092-640X(74)80020-3)' for this. Because that
reference does not give tabulated values but rough data plots only, it is
difficult to compare those with the values in Hephaestus.

If someone knows the respective data source used in Hephaestus, the
answer/information is deeply appreciated!

Best regards

Daniel

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Re: [Ifeffit] Hephaestus: Absorption Data Source

[Robert Gordon]

Another reference that might help:

https://journals.aps.org/pra/abstract/10.1103/PhysRevA.22.1615
Core-level lifetimes as determined by x-ray photoelectron spectroscopy 
measurements

John C. Fuggle and Santos F. Alvarado
Phys. Rev. A 22, 1615 – Published 1 October 1980

X-ray photoelectron spectroscopy (XPS) has been used to measure lifetime 
broadening of L, M, N, O, and P core levels with binding energies less 
than 1500 eV in approximately 25 elements. The results show that the 
framework provided by previously accepted theoretical estimates of 
lifetime broadening is sometimes misleading. Lifetimes derived from 
theory and experiment often differ by a factor of 2 or more. In the 
transition metals of the first period plots of measured widths of the 
L1(2s),L2(2p12), and L3(2p32) levels as a function of atomic number show 
broad maxima which are not adequately described by theory. The origin of 
this broadening is extensively discussed, as is the overestimation of 
lifetimes by theory in other areas of the periodic table.



Also check "Cited by" references for potentially updated information.

-R.

On 11/13/2017 8:34 AM, Bruce Ravel wrote:

On 11/13/2017 11:15 AM, Daniel Przyrembel wrote:

Still I can't see any reference to 'Keski-Rahkonen and Krause' in



http://bruceravel.github.io/demeter/documents/Athena/hephaestus.html#absorption 




Here is the relevant bit from Feff:

https://github.com/xraypy/feff85exafs/blob/master/src/COMMON/setgam.f

Note that that bit in Feff is less sophisticated than you might think. 
My memory (Matt or John might remember better) is that Steve Zabinski 
(main author of Feff6) "interpolated" those values from the plots in 
the K&R paper.  This was done with a ruler back in the days before we 
had software tools for such chores.  I am not saying that the values 
in setgam.f are wrong -- just not as precise as you might imagine.


B





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Re: [Ifeffit] Hephaestus: Absorption Data Source

[Robert Gordon]

Spreadsheet attached...Adobe did most of the work...

On 11/13/2017 11:13 AM, Matt Newville wrote:




Anyone up for scanning the PDF of Krause and Oliver and cleaning up 
the data into machine readable values like a spreadsheet?  If so, I'd 
be happy to add them to the database.


--Matt


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linewidths-K-n-O-1979.xlsx
Description: MS-Excel 2007 spreadsheet
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Re: [Ifeffit] Athena: Data cannot be imported by using plugin PFBL12C

[Robert Gordon]

Hi Yuri,

You are probably running into the memory limit. This has been discussed  
a number of times

on this mailing list, e.g.:

https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03931.html

https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05673.html

Bruce's answer in the 2nd link provides some suggestions.

Note, if I delete 1500 rows or so from your fail file, I am able to 
import it.
This seems to be similar to the success.dat file which also appears to 
be truncated.


Using a column labelled '20' as Io seems to work


-R.

On 11/14/2017 12:59 AM, 平岡　裕治 wrote:

Dear all,

I tried to import a data of multi-element detector at SPring-8 by using
plugin PFBL12C to Athena, but it was not successful.
if the number of rows in the file is about 2000[success.dat], it can be
successfully imported. But for the data over about 4000 rows[fail.dat],
it seems that several data at first of both converted energy and
intensity are substituted by 0. column6.png shows intensity of ch6 vs
energy_attained and I0.png shows intensity of I0 vs energy_attained. you
can see this behavior. As a result, intensity cannot divide by I0, and
data cannot be imported.

if someone knows approach to solve this, could you teach me.

Best regards,
Yuji Hiraoka



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Re: [Ifeffit] Demeter 0.9.26 launch faillure

[Robert Gordon]

Hi,

In case you don't know where you can make this change, if you can't 
start the program to edit
it via the preferences, it is in the [gnuplot] section of demeter.ini 
which is in the same

directory as the log. For me, the relevant line reads:

program = 
C:\Users\ragordon\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin\gnuplot.exe


Issue was known from:
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06034.html

-R.

On 12/6/2017 7:57 AM, Dardenne, Kathy (INE) wrote:

Hello,

I experienced the same problem but find out that in the ini file,  the 
wrong directory was used (strawberry as in older version) for locating 
the executables.

Once you correct it,  it will work.

Greetings

Kathy

Envoyé depuis mon HTC

- Message de réponse -
De : "Kirill Lomachenko" 
Pour : "ifeffit@millenia.cars.aps.anl.gov" 


Objet : [Ifeffit] Demeter 0.9.26 launch faillure
Date : mer., déc. 6, 2017 16:08

Dear Bruce,
I have trouble running the Demeter 0.9.26_pre2 (64bit). When I start
Artemis after installation of Demeter, it closes after showing nothing
but the usual temple picture. Logfile is attached. The problem is
analogous on both Win7 SP1 and Win8.1 and repeats also for Athena and
Hephaestus.  Could you please tell whether there is something I can do
to fix it? Versions 0.9.25 and 0.9.24 start without problems.

I know that 0.9.26 is a preview version, but I was installing it only to
get the possibility to actually use the user-supplied value of epsilon_k
for fitting multiple dataset. If it is difficult to make the version
0.9.26 available soon, maybe in 0.9.25 there is a possibility to set
R-factor as a figure of merit for fitting rather than chi^2? That might
also help.

Thank you

All the best,
Kirill Lomachenko

--
Dr. Kirill A. Lomachenko
Scientist at BM23/ID24 beamlines
European Synchrotron Radiation Facility (ESRF)
71 avenue des Martyrs
CS 40220
38043 Grenoble Cedex 9, France
Tel: +33 438 88 19 14
www.esrf.eu 



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Re: [Ifeffit] Artemis having trouble

[Robert Gordon]

Opens fine for me...



Have you tried the usual suspects? Accidentally minimised a 
window...Restarting the computer (or log off/on)...

or sending the log file to see if there is an error message...

not much to go on here...

On 2/3/2018 3:29 PM, Sheraz Gul wrote:
Can anyone please explain why Artemis is failing to open the fpj file 
I have attached? It doesn't respond anymore and screen look like the 
screenshot attached. It has happened to me multiple times now; I'm 
using Demeter version 0.9.25 on windows 10.

Best regards,

--
Sheraz Gul


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Re: [Ifeffit] Artemis having trouble

[Robert Gordon]

When you reinstalled, did you delete the Demeter-related directories 
before reinstalling?


does the log file say anything?

On 2/3/2018 4:10 PM, Sheraz Gul wrote:
Thanks Robert, I have tried all the usual suspects, even reinstalled 
Demeter, but nothing works.


On Sat, Feb 3, 2018 at 3:48 PM, Robert Gordon <mailto:ragor...@alumni.sfu.ca>> wrote:


Opens fine for me...



Have you tried the usual suspects? Accidentally minimised a
window...Restarting the computer (or log off/on)...
or sending the log file to see if there is an error message...

not much to go on here...


On 2/3/2018 3:29 PM, Sheraz Gul wrote:

Can anyone please explain why Artemis is failing to open the fpj
file I have attached? It doesn't respond anymore and screen look
like the screenshot attached. It has happened to me multiple
times now; I'm using Demeter version 0.9.25 on windows 10.
Best regards,

-- 
Sheraz Gul



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--
Sheraz Gul


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Re: [Ifeffit] Artemis having trouble

[Robert Gordon]

Changes to demeter.ini previously discussed in this thread...

https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06035.html

On 2/4/2018 11:03 AM, Matt Newville wrote:



On Sun, Feb 4, 2018 at 11:50 AM, Sheraz Gul <mailto:s...@lbl.gov>> wrote:


Hi Matt,
            Thank you for the suggestions. I have other project
files in the same folder and they open fine. Anyways, I  upgraded
to Demeter version 0.9.26 pre 2 and somehow every project file
opens fine now. Although, in the ini file,  I had to correct the
paths corresponding to exe files for gunplot and feff; otherwise,
Athena/Artemis will crash before opening.



OK, well that's good that it is now working!
For a hint to other people who might have similar problems, you're 
saying that you had to change the location of Feff and Gnuplot in 
artemis.ini ?   What were they, and what did you set them to be?


--Matt

Best regards,
Sheraz

On Sun, Feb 4, 2018 at 9:28 AM, Matt Newville
mailto:newvi...@cars.uchicago.edu>>
wrote:

Hi Sheraz,

Robert suggested "the usual suspects", but your log file makes
me suspicious that some of these suspects are still suspect
;).  A few things to try:

a)  Try moving or deleting the "stash" at 
C:\Users\sgshe\AppData\Roaming\demeter\stash, especially the
...\stash\_dem_dducbins folder.

 b) Your project file looks like it is at
C:\Sheraz\Berkeley\UC Berkeley\Paul Alivisatos\Myounghwan Oh
CoMn Oct17 73\Fitting\Mn3O4.fpj
Could that path have non-ASCII characters in it?  I don't know
that this will cause a problem, but people have seen problems
with such
things in the past, and if you opened it once, it may be OK.
Still, it would be easy to move that to a simpler path (say,
C:\Users\sgshe\Mn3O4.fpj)
and trying to load that.


On Sat, Feb 3, 2018 at 6:26 PM, Sheraz Gul mailto:s...@lbl.gov>> wrote:

Yes, I did clean everything before reinstalling. The log
file says, "You must define a method name at

C:\Users\sgshe\AppData\Roaming\DemeterPerl\perl\vendor\lib\Class\MOP\Mixin\HasMethods.pm
line 96"
Not sure what that mean.

On Sat, Feb 3, 2018 at 4:14 PM, Robert Gordon
mailto:ragor...@alumni.sfu.ca>>
wrote:

When you reinstalled, did you delete the
Demeter-related directories before reinstalling?

does the log file say anything?


On 2/3/2018 4:10 PM, Sheraz Gul wrote:

Thanks Robert, I have tried all the usual suspects,
even reinstalled Demeter, but nothing works.

On Sat, Feb 3, 2018 at 3:48 PM, Robert Gordon
mailto:ragor...@alumni.sfu.ca>> wrote:

Opens fine for me...



Have you tried the usual suspects? Accidentally
minimised a window...Restarting the computer (or
log off/on)...
or sending the log file to see if there is an
error message...

not much to go on here...


On 2/3/2018 3:29 PM, Sheraz Gul wrote:

Can anyone please explain why Artemis is failing
to open the fpj file I have attached? It doesn't
respond anymore and screen look like the
screenshot attached. It has happened to me
multiple times now; I'm using Demeter version
0.9.25 on windows 10.
Best regards,

-- 
Sheraz Gul



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[Ifeffit] FeSe2 Se K-edge XANES request

[Robert Gordon]

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] FeSe2 Se K-edge XANES request

[Robert Gordon]

Thank you, but we have measured an FeSe standard. We are seeing a small 
component in one sample
that may be FeSe2-related and are looking for something to which to 
compare and possibly include in

LCF.

best regards,
Robert

On 3/14/2018 10:34 AM, Yasin Deep wrote:
For Te doped FeSe we have this paper. If you have any questions do not 
hesitate to communicate.


With Bests,

Yasin

14 Mar 2018 Çar 20:17 tarihinde Anatoly Frenkel 
> şunu yazdı:


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] Sulfur EXAFS k oscillations

[Robert Gordon]

Large mono glitch around k ~ 13.8 A-1  (E~3200 eV) on 4-3   perhaps?

On 4/9/2018 11:04 AM, Miller, Elizabeth Christine wrote:


Hi all,

I am analyzing some sulfur K-edge EXAFS data taken at 4-3 at SSRL. 
When I use a k-weight of k^3 to plot, my oscillations at high k reach 
over 100, which doesn’t make sense to me. I have looked over the data 
with Riti, and it seems that while the XANES are rather self-absorbed 
due to high concentrations of sulfur-containing salt, the data can be 
normalized, and the EXAFS should contain some information. I’ve 
included screenshots in the attachment of plots of all of the 
k-weights as well as my parameters. The mixtures are solutions of 
organics (acetonitrile, 1,1,2,2-Tetrafluoroethyl 
2,2,3,3-tetrafluoropropyl ether) with bis(trifluoromethane)sulfonimide 
lithium salt. I am also not hitting any other edges, as sulfur is the 
highest Z element in the solution. Any thoughts would be greatly 
appreciated!


Thank you,

Beth

Elizabeth C. Miller, Ph.D.

Postdoctoral Scholar

Stanford Synchrotron Radiation Lightsource

SLAC National Accelerator Laboratory

E-mail: ecmil...@slac.stanford.edu 



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Re: [Ifeffit] Se reference XANES

[Robert Gordon]

Not personally, but there is a spectrum of it in these:
https://academic.oup.com/jxb/article/66/15/4795/484381
http://aem.asm.org/content/71/5/2331
2nd one gives white line positions for ease of comparison

On 5/1/2018 3:41 AM, desmau wrote:

Hello everyone,

would anybody have a reference XANES spectrum of Se in Selenocysteine 
or of Se in bacteria ?


Thanks a lot in advance for your help.

Best regards



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Re: [Ifeffit] Athena programm for XAS data analysis

[Robert Gordon]

changing colour:
Preferences --> gnuplot --> col7  and Set a desired colour
then apply and savedisplayed "your value" might not update
until you restart Athena, but the plot should.




On Tue, May 8, 2018 at 3:07 AM, Stoll, Andreas (HIU) 
wrote:

> Hi Jonas,
>
>
> first of all thank you very much for your quick answer!
>
>
> unfortunately your suggestion is not working for my version of Athena. It
> just worked for the older versions...
>
>
> Is there another possibility?
>
>
> Greetings
>
>
> Andi
> --
> *Von:* Ifeffit  im Auftrag von
> Wielinski, Jonas 
> *Gesendet:* Dienstag, 8. Mai 2018 18:40
> *An:* XAFS Analysis using Ifeffit
> *Betreff:* Re: [Ifeffit] Athena programm for XAS data analysis
>
>
> Hi Andi,
>
>
>
> Using Athena under Windows, “Alt + J” and “Alt + K” move data groups
> upwards and downwards. I hope that answers your question.
>
>
>
> Best,
>
> Jonas
>
>
>
> *From:* Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] *On
> Behalf Of *Stoll, Andreas (HIU)
> *Sent:* Dienstag, 8. Mai 2018 10:12
> *To:* ifeffit@millenia.cars.aps.anl.gov
> *Subject:* [Ifeffit] Athena programm for XAS data analysis
>
>
>
> Hi,
>
>
>
> I´m using Athena Version 0.9.26 to analyse my XAS data.
>
>
>
> Is it possible to change the order of the imported data in the list after
> importing them? Or at least change the colour of the plotted data?
> Currently one of my standards is plotted in yellow and that is not really
> good...
>
>
>
> Thanks in advance!
>
>
>
> Greetings
>
>
>
> Andi
>
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Re: [Ifeffit] Basic questions about the preliminary data processing in Athena

[Robert Gordon]

Hi Haifeng,

Here's my take on what you described:

Two sample to be studied at the same edge using the same reference. 
Three scans on A and three on

B are done with simultaneous reference.

First: compare the three reference scans for A. If they agree, then 
compare the data scans. If they also look
similar (i.e. no evidence of changing in the beam), you can merge the 
three data scans
on A right away. If the references don't agree, then you determine by 
how much they differ (how much a correction
would be needed to bring them into alignment) and apply that same 
correction to the data before merging.
It is not meaningful to merge data that is not aligned. (If the sample 
scans show changes from scans 1  to 3,

then you need to rethink how to do the measurements)

Repeat for B.

Now compare the merged (corrected beforehand if necessary) references 
for A and B. If they agree,
you can compare data for A and B (merged) directly. If they do not, 
determine how much one reference
differs from the other and apply that same correction to, say, B, that 
brings its reference into alignment with

A's reference, and then compare A and B

You align the references between samples to the same value in order to 
do a meaningful comparison
between them. If you report energy positions of features in your 
near-edge spectra, the reader

would need to know to what energy those positions are referenced.

When possible, I recommend references that have tabulated edge values 
(i.e. metal foils). A reference
need not be the same edge as the one being studied. For arsenic, as an 
example, the gold L3-edge is
quite close to the As K-edge and serves as a good reference. If not 
possible to use a metal foil, use a
reference that another interested researcher could readily obtain or has 
used. This allows for
comparison of reproducibility. If your reference looks nothing like 
literature, you may have a problem
with the beamline or in how you processed the data. This should be one 
of the first things you

check when you start taking data at the beamlne.

You should also note how the beamline was calibrated when you did the 
measurements.


regards,
Robert

On 2018-07-22 1:21 PM, Haifeng Li wrote:

Dear ALL,

I am a beginner in Athena. Recently I got the spectra and I am 
confusing about the data calibration and alignment. The manual shows 
that calibrate the reference data of one scan and align other 
reference data to that calibrated one.


Here I want to show examples. I have two samples A and B, Each sample 
has three scans with the corresponding reference data. For sample A, 
1st scan is calibrated and the other two scans are aligned to 1st 
scan. Then merge them into merged A. The same procedures for sample B 
and get merged B. If I want to compare XANES of sample A and B, do I 
need to align the merged reference data between A and B? If so, why? 
My understanding is that all scans (original data and merged data) in 
sample A and B are calibrated to standard edge energy. Why do they 
need to align?


I appreciate your help.

Thanks,

Haifeng


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Re: [Ifeffit] Basic questions about the preliminary data processing in Athena

[Robert Gordon]

HI Haifeng,

Suppose you measure Fe foil three times, and all three scans overlap. 
They are aligned.
But suppose the edge positions are at 7116 eV instead of 7112 eV. The 
calibration is off.
You can adjust to it, but, as Carlo mentioned, it is really an angle 
correction, not simply a
shift in energy. It is better to have an accurate calibration to begin 
with, then aligned and

calibrated would be the same.

Note: Choice of target calibration can differ - some use the X-ray data 
booklet values

http://xdb.lbl.gov/
and some use the Kraft  et al. values
https://aip.scitation.org/doi/abs/10.1063/1.1146657

Just state which calibration you are using when presenting/publishing.

-R.


On 2018-07-27 10:32 AM, Haifeng Li wrote:

Hi, Robert,

Thanks for your help.

One more question. What is the real difference between calibration and 
alignment? Do they have specific meaning?


Thanks,

Haifeng

On Sun, Jul 22, 2018 at 5:45 PM, Robert Gordon <mailto:ragor...@alumni.sfu.ca>> wrote:


Hi Haifeng,

Here's my take on what you described:

Two sample to be studied at the same edge using the same
reference. Three scans on A and three on
B are done with simultaneous reference.

First: compare the three reference scans for A. If they agree,
then compare the data scans. If they also look
similar (i.e. no evidence of changing in the beam), you can merge
the three data scans
on A right away. If the references don't agree, then you determine
by how much they differ (how much a correction
would be needed to bring them into alignment) and apply that same
correction to the data before merging.
It is not meaningful to merge data that is not aligned. (If the
sample scans show changes from scans 1  to 3,
then you need to rethink how to do the measurements)

Repeat for B.

Now compare the merged (corrected beforehand if necessary)
references for A and B. If they agree,
you can compare data for A and B (merged) directly. If they do
not, determine how much one reference
differs from the other and apply that same correction to, say, B,
that brings its reference into alignment with
A's reference, and then compare A and B

You align the references between samples to the same value in
order to do a meaningful comparison
between them. If you report energy positions of features in your
near-edge spectra, the reader
would need to know to what energy those positions are referenced.

When possible, I recommend references that have tabulated edge
values (i.e. metal foils). A reference
need not be the same edge as the one being studied. For arsenic,
as an example, the gold L3-edge is
quite close to the As K-edge and serves as a good reference. If
not possible to use a metal foil, use a
reference that another interested researcher could readily obtain
or has used. This allows for
comparison of reproducibility. If your reference looks nothing
like literature, you may have a problem
with the beamline or in how you processed the data. This should be
one of the first things you
check when you start taking data at the beamlne.

You should also note how the beamline was calibrated when you did
the measurements.

regards,
Robert


On 2018-07-22 1:21 PM, Haifeng Li wrote:

Dear ALL,

I am a beginner in Athena. Recently I got the spectra and I am
confusing about the data calibration and alignment. The manual
shows that calibrate the reference data of one scan and align
other reference data to that calibrated one.

Here I want to show examples. I have two samples A and B, Each
sample has three scans with the corresponding reference data. For
sample A, 1st scan is calibrated and the other two scans are
aligned to 1st scan. Then merge them into merged A. The same
procedures for sample B and get merged B. If I want to compare
XANES of sample A and B, do I need to align the merged reference
data between A and B? If so, why? My understanding is that all
scans (original data and merged data) in sample A and B are
calibrated to standard edge energy. Why do they need to align?

I appreciate your help.

Thanks,

Haifeng


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

[Robert Gordon]

Or just swap...set N's to be the So^2 from a known coordination standard 
and define an amp for each shell...
e.g. So^2 = 0.8 from standard so all N's set to 0.8, and shell 1 had 
amp1 in the So^2 position defined as guess,

shell2 has amp2, etc

On 2018-08-01 8:15 AM, Anatoly Frenkel wrote:
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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Re: [Ifeffit] Artemis problem

[Robert Gordon]

That is an old and no longer supported version. Have you tried upgrading 
to the latest

Demeter variant, 0.9.26?

http://bruceravel.github.io/demeter/


On 2018-08-04 3:58 PM, ParasMani Rajput wrote:

Dear All,
I am using windows 8 and running ARTEMIS (1.2.11) in my leptop. Today 
Ifound that Artemis not working properly. When I am opening my project 
files in Artemis then showing an error massage "Artemistrapped one or 
more errors! Error message dumped to the screen" where i fitted and 
saved the project file the day before.

Please let me know if some has seen this problem and how to resolve it.
Regards,
Parasmani
---
Dr. Parasmani Rajput

Atomic & Molecular Physics Division  BL-09, INDUS-2 complex
Bhabha Atomic Research Centre             Raja Ramanna Centre for 
Advanced Technology

Trombay, Mumbai-85, India  Indore, Madhya Pradesh 452013, India

E-mail: parasmaniraj...@gmail.com 
Phone: (+91) 731-2442509

Web page :https://sites.google.com/site/parasmanirajput/
orcid.org/-0003-0694-6756 
http://www.researcherid.com/rid/E-4783-2011
---


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Re: [Ifeffit] Demeter on ubuntu 14.04

[Robert Gordon]

Hi Edmund,

I installed on 16.04 LTS following this:
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05851.html
though this was 2 years ago. A more recent installation, I think, did not
involve manually installing giflib-5.1.4.

-R.

On 2018-08-08 7:07 AM, Edmund Welter wrote:

Dear all,
I am hitting a wall trying to install the latest Demeter version on my 
ubuntu laptop.

System: Ubuntu 14.04
Demeter: 0.9.26
perl: 5.18.2
pdl and pdl::stats from repositories. (I tried a newer versions from 
cpan, but ot no avail)

moose: initially from repositories, than vs. 2.2011  from cpan

I did follow the installation instructions on
https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.html 


and tried to install demeter in ~/perl5
and also the instructions in:
https://bruceravel.github.io/demeter/documents/SinglePage/installation.html 


to install Demeter as sudo

Both attempts ended with the same result when I start dathena in a 
terminal the image of the goddess appears briefly and I get the 
following error messages in the terminal:

-
Invalid version format (non-numeric data) at 
/usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11,  line 90.
BEGIN failed--compilation aborted at 
/usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11,  line 90.
Compilation failed in require at /usr/local/lib/perl/5.18.2/Moose.pm 
line 15,  line 90.
BEGIN failed--compilation aborted at 
/usr/local/lib/perl/5.18.2/Moose.pm line 15,  line 90.
Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter.pm 
line 123,  line 90.
BEGIN failed--compilation aborted at 
/usr/local/lib/perl/5.18.2/Demeter.pm line 123,  line 90.
Compilation failed in require at 
/usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24,  line 90.
BEGIN failed--compilation aborted at 
/usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24,  line 90.
Compilation failed in require at /usr/local/bin/dathena line 31, 
 line 90.
BEGIN failed--compilation aborted at /usr/local/bin/dathena line 31, 
 line 90.
Use of uninitialized value $Larch::larch_exe in concatenation (.) or 
string at /usr/local/lib/perl/5.18.2/Larch.pm line 288,  line 90.
Can't exec "-q": No such file or directory at 
/usr/local/lib/perl/5.18.2/Larch.pm line 288,  line 90.



When i try to start denv to create the nice overview of installed 
components I only get the following errors:


[PDL->Version: 10 PDL_CORE_VERSION: 8 XS_VERSION: ] PDL::Stats::Distr 
needs to be recompiled against the newly installed PDL at 
/usr/lib/perl/5.18/DynaLoader.pm line 207.

Compilation failed in require at (eval 1130) line 5.
BEGIN failed--compilation aborted at (eval 1130) line 5.
BEGIN failed--compilation aborted at /usr/local/bin/denv line 24.
Use of uninitialized value $Larch::larch_exe in concatenation (.) or 
string at /usr/local/lib/perl/5.18.2/Larch.pm line 288.
Can't exec "-q": No such file or directory at 
/usr/local/lib/perl/5.18.2/Larch.pm line 288.

--
This is insofar interesting as I got the same error about PDL when I 
tried to start dathena before I installed the pdl::stats module from 
cpan, that means when both, pdl and pdl::stats were installed from 
repositories.


Any hint would be welcome, upgrading ubuntu to a newer LTS version 
might be useful (It is absolutely possible that something is weird 
with this installation after a lot of playing around) but I am 
currently reluctant to do so, because it will for sure break other 
things...


Best regards,
Edmund
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Re: [Ifeffit] Problem with Athena - Weronica/difference

[Robert Gordon]

Hi Weronica,

I tested this using the same scan loaded 3 times and was able to switch 
without issue.
I tested this with a different additional scan on the same element, and 
was able to switch without issue.


Please provide more information.
https://bruceravel.github.io/demeter/documents/SinglePage/bugs.html

-R.

On 2018-10-30 6:47 AM, Weronica Linpé wrote:

Hi,

I have a problem when looking at the difference scan between two scans.

When I move from the start up site to the differnece everything works 
fine and I get a differnece spectra. Here I can do some changes, but 
if I want to change which scans I'm using for the difference the 
program chrashes. Any ideas on why the program chrashes?



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Re: [Ifeffit] data on CdS

[Robert Gordon]

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 <
anatoly.fren...@stonybrook.edu> 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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# created: Sat Nov 17 09:09:50 2018
# from file: CdS.0001
# No: 188  [E0: 0,0,0,-1]
#-
#   X  Y
2.6509967484E+001  8.1981685849E-002
2.6522966218E+001  8.2039334847E-002
2.6530709632E+001  8.2314242540E-002
2.6540937882E+001  8.2622455830E-002
2.6551174044E+001  8.2973458220E-002
2.6559710229E+001  8.3025571378E-002
2.6569184074E+001  8.3467073750E-002
2.6581774578E+001  8.3868808081E-002
2.6590330509E+001  8.4288477980E-002
2.6599203394E+001  8.4907020243E-002
2.6610731441E+001  8.5616716176E-002
2.6619150126E+001  8.6300952848E-002
2.6627262057E+001  8.6950411767E-002
2.6640064027E+001  8.8519836354E-002
2.6650377022E+001  9.0255058520E-002
2.6657413200E+001  9.1903286891E-002
2.6669618074E+001  9.5520286690E-002
2.6678857412E+001  1.0088238447E-001
2.6680110698E+001  1.0198841339E-001
2.6681364102E+001  1.0322150882E-001
2.6682460927E+001  1.0426791489E-001
2.6683244429E+001  1.0493911662E-001
2.6684654849E+001  1.0604903078E-001
2.6686065418E+001  1.0755723314E-001
2.6687476137E+001  1.0934065869E-001
2.6688573467E+001  1.1087268087E-001
2.6690611604E+001  1.1427757282E-001
2.6692493239E+001  1.1804216394E-001
2.6694845656E+001  1.2372363963E-001
2.6696727890E+001  1.2964421093E-001
2.6698296621E+001  1.3574892067E-001
2.6700179342E+001  1.4467003583E-001
2.6702533118E+001  1.5907707229E-001
2.6704259485E+001  1.7492482873E-001
2.6705829104E+001  1.9376857997E-001
2.6707555899E+001  2.2456050148E-001
2.6709282917E+001  2.7488813854E-001
2.6710539071E+001  3.2931696535E-001
2.6712109430E+001  4.3075370795E-001
2.6712580574E+001  4.6509710082E-001
2.6713837039E+001  5.5121353203E-001
2.6714936543E+001  6.1890272150E-001
2.6716036138E+001  6.5795641989E-001
2.6716664519E+001  6.6843613404E-001
2.6718235601E+001  6.7225107612E-001
2.6719649732E+001  6.6655205452E-001
2.6721535475E+001  6.6061722896E-001
2.6723421484E+001  6.5649047122E-001
2.6724993363E+001  6.5310683840E-001
2.6727351529E+001  6.4541413355E-001
2.6729238361E+001  6.3828502209E-001
2.6731282732E+001  6.333743E-001
2.6732226393E+001  6.3225437205E-001
2.6734428529E+001  6.3335050642E-001
2.6735687056E+001  6.3476376759E-001
2.6737260382E+001  6.3454468468E-001
2.6738047115E+001  6.3393243290E-001
2.6739620719E+001  6.3098467813E-001
2.6740879736E+001  6.2698790960E-001
2.6742296273E+001  6.2249491618E-001
2.6743398127E+001  6.1792551178E-001
2.6744500073E+001  6.1348949344E-001
2.6745759551E+001  6.0889801897E-001
2.6747019148E+001  6.0478409463E-001
2.6748121393E+001  6.0208260371E-001
2.6750011168E+001  6.0155902348E-001
2.6751428675E+001  6.0439296087E-001
2.6753633985E+001  6.1351230405E-001
2.6755997221E+001  6.2628389052E-001
2.6758360877E+001  6.3937595288E-001
2.6761355441E+001  6.5242180872E-001
2.6763720046E+001  6.5837225603E-001
2.6766085070E+001  6.6059608871E-001
2.6769081369E+001  6.6041714557E-001
2.6771289598E+001  6.6088373790E-001
2.6773340424E+001  6.6188678594E-001
2.6774918197E+001  6.6274593239E-001
2.6776653963E+001  6.6298172944E-001
2.6778232127E+001  6.6216000409E-001
2.6779652635E+001  6.5963284561E-001
2.6781389016E+001  6.5530383783E-001
2.6784388752E+001  6.4580959676E-001
2.6787073297E+001  6.3811933114E-001
2.6790232276E+001  6.3077951179E-001
2.6793392003E+001  6.2572489506E-001
2.6796078358E+001  6.2306216403E-001
2.6798765254E+001  6.2167471876E-001
2.6800820303E+001  6.2241307189E-001
2.6803191907E+001  6.2596301819E-001
2.6805722081E+001  6.3040575480E-001
2.6807620026E+001  6.3462053538E-001
2.6809834636E+001  6.3976111639E-001
2.6812524299E+001  6.4497026040E-001
2.6815689301E+001  6.5023435444E-001
2.6819646607E+001  6.5436640485E-001
2.6823288363E+001  6.5705648242E-001
2.6826614311E+001  6.5852209889E-001
2.6830416408E+001  6.5977256730E-001
2.6833744128E+001  6.5956529809E-001
2.6836755637E+001  6.5919095135E-001
2.6838975077E+001  6.5818621906E-001
2.6841194885E+001  6.5563669923E-001
2.6843256465E+001  6.5367315379E-001
2.6846270114E+001  6.5041510566E-001
2.6850395156E+001  6.4598020656E-001
2.6854521469E+001  6.4170329136E-001
2.6858172729E+001  6.3861638675E-001
2.6861507358E+001  6.3717631457E-001
2.6864683966E+001  6.3682696907E-001
2.6867543559E+001  6.3740348384E-001
2.6870403761E+001  6.3774856792E-001
2.6873105625E+001  6.3855983608E-001
2.6876125999E+001  6.3981492308E-001
2.6879942182E+001  6.4206780961E-001
2.6883918528E+001  6.44

Re: [Ifeffit] Looking of a K-edge spectrum of maghemite

[Robert Gordon]

Attached...foil measured simultaneously in transmission on 20BM at 
APS..only to about 12 invAng though.


On 2018-12-17 9:08 a.m., Lorenzo Stievano wrote:

Hi everybody,

daes anybody have in his repository a Fe K-edge XAS spectrum of 
maghemite (gamma-Fe2O3)? I would need it as a reference material in a 
study on doped iron oxides.


Thanks a lot in advance!

Lorenzo

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# created: Mon Dec 17 09:22:12 2018
# from file: r-Fe2O3.0013
# No: 284  [E0: 0,0,0,-1]
#-
#   X  Y
6.9122217890E+000  2.3873525979E-001
6.9223211954E+000  2.3164588825E-001
6.9323498145E+000  2.2456452215E-001
6.9423170573E+000  2.1756838970E-001
6.9522426850E+000  2.1084974252E-001
6.9621979893E+000  2.0396161597E-001
6.9722448309E+000  1.9706588090E-001
6.9821465592E+000  1.9041022419E-001
6.9921604797E+000  1.8361093435E-001
7.0020590912E+000  1.7700662132E-001
7.0121015120E+000  1.7041316226E-001
7.0220487198E+000  1.6366768794E-001
7.0318264240E+000  1.5727851308E-001
7.0417376019E+000  1.5080703027E-001
7.0516252875E+000  1.4423514799E-001
7.0615419695E+000  1.3804722093E-001
7.0713924093E+000  1.3202582731E-001
7.0813778086E+000  1.2597846037E-001
7.0912540883E+000  1.2053001376E-001
7.1010308547E+000  1.1590367809E-001
7.1013408400E+000  1.1589968477E-001
7.1016294723E+000  1.1583510450E-001
7.1019608951E+000  1.1565987866E-001
7.1022709650E+000  1.1554434955E-001
7.1025169025E+000  1.1538424881E-001
7.1027735520E+000  1.1555100474E-001
7.1030836958E+000  1.1545374436E-001
7.1034259562E+000  1.1541521173E-001
7.1037896456E+000  1.1530363057E-001
7.1041105801E+000  1.1524828928E-001
7.1043673496E+000  1.1522977858E-001
7.1045813389E+000  1.1512092756E-001
7.1048595451E+000  1.1516503432E-001
7.1052447911E+000  1.1513521085E-001
7.1055979716E+000  1.1511001667E-001
7.1059083725E+000  1.1513839530E-001
7.1062295066E+000  1.1516503197E-001
7.1065292590E+000  1.1508938873E-001
7.1067755040E+000  1.1507978146E-001
7.1070110592E+000  1.1508875333E-001
7.1072894637E+000  1.1519326810E-001
7.1076214373E+000  1.1524191334E-001
7.1079534431E+000  1.1552987263E-001
7.1082961927E+000  1.1568739364E-001
7.1085747021E+000  1.1582230181E-001
7.1087889556E+000  1.1592800053E-001
7.1090139362E+000  1.1621977383E-001
7.1093246482E+000  1.1648145453E-001
7.1096568198E+000  1.1701166512E-001
7.1099568736E+000  1.1766040524E-001
7.1102676715E+000  1.1839233016E-001
7.1105892162E+000  1.1959170496E-001
7.1108679129E+000  1.2092582368E-001
7.144712E+000  1.2270620833E-001
7.1114039320E+000  1.2640049179E-001
7.1117470284E+000  1.3347889216E-001
7.1121008827E+000  1.4273741451E-001
7.1124440492E+000  1.5252079218E-001
7.1127550736E+000  1.6114797293E-001
7.1129695898E+000  1.6519158796E-001
7.1132163000E+000  1.6632391267E-001
7.1135595786E+000  1.6256279491E-001
7.1139458084E+000  1.5601936956E-001
7.1142569696E+000  1.5117921038E-001
7.1145788905E+000  1.4857390028E-001
7.1148793773E+000  1.4784161489E-001
7.1151584245E+000  1.4790850735E-001
7.1154052929E+000  1.4813537325E-001
7.1156629138E+000  1.4873506660E-001
7.1159634960E+000  1.4956729975E-001
7.1162963143E+000  1.5001480637E-001
7.1166399028E+000  1.5045073929E-001
7.1169727871E+000  1.5085192857E-001
7.1172090472E+000  1.5133179336E-001
7.1174238433E+000  1.5211471063E-001
7.1177030984E+000  1.5359173100E-001
7.1180360863E+000  1.5618725710E-001
7.1183368775E+000  1.5963936461E-001
7.1186484391E+000  1.6442814068E-001
7.1189600292E+000  1.7077800608E-001
7.1192609017E+000  1.7787256993E-001
7.1195403070E+000  1.8564152048E-001
7.1198089876E+000  1.9616114036E-001
7.1201206835E+000  2.1284405772E-001
7.1204754065E+000  2.3381610544E-001
7.1207979139E+000  2.5527944114E-001
7.1211527072E+000  2.8026058695E-001
7.1214215146E+000  3.0283915988E-001
7.1216473291E+000  3.2329228273E-001
7.1219269296E+000  3.4640936257E-001
7.1223033511E+000  3.7239957189E-001
7.1226583007E+000  3.9426157067E-001
7.1229810141E+000  4.1405761106E-001
7.1232929994E+000  4.3130341011E-001
7.1236050132E+000  4.4704105483E-001
7.1238524926E+000  4.6086797009E-001
7.1241107512E+000  4.7753722548E-001
7.1243797912E+000  5.0043035550E-001
7.1247026672E+000  5.2979522382E-001
7.1250363377E+000  5.6109746713E-001
7.1253915712E+000  5.9642879581E-001
7.1256930103E+000  6.3034418185E-001
7.1259083403E+000  6.5623996300E-001
7.1261236838E+000  6.8026119714E-001
7.1264251874E+000  7.0727878132E-001
7.1267697956E+000  7.3274840198E-001
7.1270605858E+000  7.5167920707E-001
7.1273729435E+000  7.6917451151E-001
7.1276745573E+000  7.8352552028E-001
7.1279869710E+000  7.9623375190E-001
7.1282455419E+000  8.0759972760E-001
7.1285256825E+000  8.2293619248E-001
7.1288597261E+000  8.4453697362E-001
7.1292153569E+000  8.68

Re: [Ifeffit] regarding installation

[Robert Gordon]

Dear Prof. Gupta,

Could you provide more information, please? This is not a useful bug report.
https://bruceravel.github.io/demeter/documents/SinglePage/bugs.html
Many researchers use this software without issue.

I have attached a test file for you to try. When you import it, please 
ensure the

data type is set to mu(E) and units are keV.



On my system (Win10x64, Demeter 0.9.26), the derivative plots without issue.



-R.

On 2018-12-23 12:11 a.m., mona gupta wrote:


respected sir/ma'am
whenever I use Athena / Hephaestus on the time of plotting derivatives 
..its hangs and after some time it shows per interpreter is not 
responding,,, so it is not working properly, even I am puzzled.

please give me quick reply facing such problem ..even reinstalled it.


Regards

Mrs Mona Gupta
Assistant Professor
Department of Physics
Govt PG College Kotdwar
H N B Garhwal University
Uttarakhand (India)

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# created: Tue Jul 27 16:17:21 2010
# from file: fe-calib.0004
# No: 361  [E0: 0,0,0,-1]
#-
#   X  Y
6.9718271736E+000  3.1371008379E-001
6.9767479971E+000  3.1089126005E-001
6.9817070281E+000  3.0800422954E-001
6.9868284175E+000  3.0506005802E-001
6.9915954539E+000  3.0194161622E-001
6.9967838188E+000  2.9921853792E-001
7.0016584570E+000  2.9626333068E-001
7.0066337362E+000  2.9343282108E-001
7.0117413192E+000  2.9055511016E-001
7.0165230556E+000  2.8783869570E-001
7.0217083429E+000  2.8494935294E-001
7.0265565563E+000  2.8228425448E-001
7.0315478879E+000  2.7955754636E-001
7.0366410077E+000  2.7687430621E-001
7.0414057342E+000  2.7428782362E-001
7.0465873922E+000  2.7131936382E-001
7.0514609826E+000  2.6883049238E-001
7.0564259997E+000  2.6659333883E-001
7.0614933954E+000  2.6396043725E-001
7.0662509750E+000  2.6172804077E-001
7.0712801203E+000  2.5946781823E-001
7.0762848999E+000  2.5728522575E-001
7.0810739131E+000  2.5584019366E-001
7.0861995790E+000  2.5437853242E-001
7.0909706232E+000  2.5383549655E-001
7.0958230730E+000  2.5470401617E-001
7.1008427660E+000  2.5818736437E-001
7.1014627305E+000  2.5913177908E-001
7.1018903580E+000  2.5965634024E-001
7.1023180391E+000  2.6039780060E-001
7.1029810509E+000  2.6175073102E-001
7.1035051354E+000  2.6289777627E-001
7.1039223215E+000  2.6403034833E-001
7.1042753649E+000  2.6513646074E-001
7.1048531513E+000  2.6708010328E-001
7.1054096307E+000  2.6947603252E-001
7.1059340887E+000  2.7192789857E-001
7.1062873406E+000  2.7419920566E-001
7.1067584000E+000  2.7776045615E-001
7.1073580243E+000  2.8283240095E-001
7.1078399416E+000  2.8915370204E-001
7.1082255245E+000  2.9598783753E-001
7.1086647137E+000  3.0535218192E-001
7.1093075315E+000  3.3002287142E-001
7.1098433055E+000  3.7572547122E-001
7.1103148563E+000  4.3977409820E-001
7.110690E+000  5.2307263857E-001
7.1113653627E+000  6.6546372068E-001
7.1119550743E+000  7.5606007282E-001
7.1123411225E+000  8.0840376602E-001
7.1126950384E+000  8.4777597513E-001
7.1132742527E+000  8.9983522243E-001
7.1138428364E+000  9.4890783329E-001
7.1143578619E+000  9.7752460257E-001
7.1147441819E+000  9.9103474538E-001
7.1151627447E+000  1.0012998872E+000
7.1157423778E+000  1.0118808575E+000
7.1162791628E+000  1.0307006223E+000
7.1166764381E+000  1.0583958728E+000
7.1170737596E+000  1.0992506625E+000
7.1177289041E+000  1.1894179952E+000
7.1182874871E+000  1.2798210087E+000
7.1187602056E+000  1.3513886762E+000
7.1191470239E+000  1.4172003064E+000
7.1197595759E+000  1.5256612829E+000
7.1203829871E+000  1.6246744022E+000
7.1208129922E+000  1.6974329335E+000
7.1211462833E+000  1.7467592392E+000
7.1216839181E+000  1.8088548395E+000
7.1222754141E+000  1.8716538084E+000
7.1227809554E+000  1.9193897931E+000
7.1231897456E+000  1.9505895923E+000
7.1236093443E+000  1.9819634283E+000
7.1241581279E+000  2.0179380634E+000
7.1247392890E+000  2.0530396172E+000
7.1251267846E+000  2.0809974581E+000
7.1255358554E+000  2.1068251500E+000
7.1261710885E+000  2.1486339968E+000
7.1267310528E+000  2.1953239142E+000
7.1272157113E+000  2.2370843756E+000
7.1276250320E+000  2.2745127006E+000
7.1281852344E+000  2.3349195466E+000
7.1288209597E+000  2.3930144423E+000
7.1292843594E+000  2.4376982829E+000
7.1296184771E+000  2.4660964381E+000
7.1301035448E+000  2.4877520323E+000
7.1307072807E+000  2.4886506749E+000
7.1312248533E+000  2.4663537878E+000
7.1316777935E+000  2.4353787893E+000
7.1320660757E+000  2.4021833810E+000
7.1325946417E+000  2.3549922447E+000
7.1331772376E+000  2.3094991848E+000
7.1336304362E+000  2.2731038006E+000
7.1339757707E+000  2.2482955311E+000
7.1345693956E+000  2.2195051615E+000
7.1351523275E+000  2.1984424190E+000
7.1356381799E+000  2.1875126176E+000
7.1360809054E+000  2.1845602555E+000
7.1365992910E+000  2.1851676867E+000
7.137

Re: [Ifeffit] Unwanted rescaling of energy axis when importing ascii file into Athena (Demeter 0.9.26)

[Robert Gordon]

Hi,

I switched your data from keV to eV before importing, and that does not 
have the same issue.


-R.

On 2019-01-09 6:35 a.m., Lukas Grote wrote:


Hello,

I am reporting an apparent bug in Athena (Demeter 0.9.26, Windows 10). 
When I import high energy resolution XAS data from an ascii file, the 
energy axis is automatically rescaled to 1.2eV step size, thus 
drastically reducing the resolution of the data. When the imported 
data has energy steps larger than 1.2eV, no rescaling occurs.


This issue may be similar to the one reported in March 2018 under the 
topic "Athena (Demeter 0.9.26) does not import all datapoints from 
ascci file". However, the issue I am seeing always results in 1.2eV 
steps in the imported data. If my original file hast 0.3eV steps, the 
number of points is reduced by a factor of 4. If it has 0.6eV steps, 
the number of points is reduced by a factor of 2.


I couldn't find any option to switch this recaling on / off, or to 
change the target energy step size.


The problem does not occur with Demeter 0.9.25. Attached please find 
two screenshots of the data import dialog for both versions of 
Demeter. The plots show the difference in energy scale. I also 
attached the original data file "no_rebin.dat" as well as spectra 
exported from both Demeter versions, one of them showing the 1.2eV steps.


Thank you and all the best,
Lukas

--
Lukas Grote

University of Hamburg
Center for Hybrid Nanostructures
Institute for Nanostructures and Solid State Physics
Luruper Chaussee 149, Bld. 600, Room 2.62
22761 Hamburg
Germany

+49 40 42838 1614

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# created: Wed Jan 09 09:11:08 2019
# from file: no_rebin.dat
# No: 300  [E0: 0,0,0,-1]
#-
#   X  Y
7.695000E+003  1.627000E-003
7.695300E+003  0.00E+000
7.695600E+003  0.00E+000
7.695900E+003  4.00E-006
7.696200E+003  0.00E+000
7.696500E+003  0.00E+000
7.696800E+003  0.00E+000
7.697100E+003  0.00E+000
7.697400E+003  1.90E-004
7.697700E+003  2.23E-004
7.698000E+003  0.00E+000
7.698300E+003  9.50E-005
7.698600E+003  0.00E+000
7.698900E+003  0.00E+000
7.699200E+003  5.13E-004
7.699500E+003  0.00E+000
7.699800E+003  0.00E+000
7.700100E+003  0.00E+000
7.700400E+003  0.00E+000
7.700700E+003  6.85E-004
7.701000E+003  0.00E+000
7.701300E+003  0.00E+000
7.701600E+003  1.212000E-003
7.701900E+003  1.252000E-003
7.702200E+003  0.00E+000
7.702500E+003  0.00E+000
7.702800E+003  0.00E+000
7.703100E+003  5.85E-004
7.703400E+003  0.00E+000
7.703700E+003  2.23E-004
7.704000E+003  0.00E+000
7.704300E+003  0.00E+000
7.704600E+003  0.00E+000
7.704900E+003  0.00E+000
7.705200E+003  0.00E+000
7.705500E+003  1.051000E-003
7.705800E+003  1.505000E-003
7.706100E+003  2.867000E-003
7.706400E+003  3.234000E-003
7.706700E+003  5.987000E-003
7.707000E+003  8.759000E-003
7.707300E+003  1.104000E-002
7.707600E+003  2.154400E-002
7.707900E+003  2.419700E-002
7.708200E+003  2.729500E-002
7.708500E+003  2.545500E-002
7.708800E+003  2.622900E-002
7.709100E+003  2.878800E-002
7.709400E+003  2.186200E-002
7.709700E+003  2.149500E-002
7.71E+003  1.581100E-002
7.710300E+003  1.294700E-002
7.710600E+003  1.238100E-002
7.710900E+003  1.489500E-002
7.711200E+003  1.502200E-002
7.711500E+003  1.729100E-002
7.711800E+003  2.015100E-002
7.712100E+003  1.776100E-002
7.712400E+003  2.071600E-002
7.712700E+003  2.291100E-002
7.713000E+003  3.075600E-002
7.713300E+003  3.416500E-002
7.713600E+003  3.863900E-002
7.713900E+003  5.061300E-002
7.714200E+003  6.470600E-002
7.714500E+003  8.677800E-002
7.714800E+003  9.986700E-002
7.715100E+003  1.247660E-001
7.715400E+003  1.407220E-001
7.715700E+003  1.752550E-001
7.716000E+003  2.023000E-001
7.716300E+003  2.324820E-001
7.716600E+003  2.891990E-001
7.716900E+003  3.340320E-001
7.717200E+003  3.657970E-001
7.717500E+003  4.208820E-001
7.717800E+003  4.632890E-001
7.718100E+003  5.094680E-001
7.718400E+003  5.573840E-001
7.718700E+003  6.133690E-001
7.719000E+003  6.789910

Re: [Ifeffit] Dynamic XAFS Simulations?

[Robert Gordon]

Hi,

Welcome to XAFS and all the excitement, thrills and adventure that implies!

First, since you are new to the subject, I would strongly recommend you 
take a course
on XAFS. Many synchrotron facilities offer such - e.g. The APS/IIT 
Summer school was held
last July; the SSRL course was last August, and NSLS2 had theirs in 
November. Any schools
being held this year will likely also be announced on this iFeffit 
mailing list.


Some other resources for learning the basics can be found here:
https://www.ixasportal.net/ixas/index.php?option=com_content&view=article&id=46&Itemid=136
Matt's introduction is a good place to start.

For "dynamic XAFS" searches, you should consider "pump probe xafs" or 
"time-resolved xafs"
as search terms. Searching for pump probe xafs for me easily yielded 
this article

https://link.springer.com/chapter/10.1007/978-3-319-43866-5_9

As for simulation of XAFS, one program is FEFF, developed by the Rehr 
Group at the University of Washington

http://feff.phys.washington.edu/
FEFF9 (8, 7) requires a license and modest fee for academic use, and is 
widely used for simulating both the
near edge and extended fine structure. Bruce Ravel's Demeter suite of 
programs for XAFS processing and analysis
includes an earlier version (FEFF6). Demeter is free - mostly a labour 
of love by Bruce, and he likes beer and maple syrup if you happen to run 
into him at a conference.


FDMNES (Yves Joly group, Institut Neel) is another program for 
simulating the near-edge. I find it works
quite well. It allows for tweaking of the starting electronic 
configuration as well (with cautionary notes) that
might be useful for simulating excited systems (I haven't checked 
literature to see if anyone has done so).


An additional program of note for fitting and simulation is GNXAS 
(DiCicco group, U. Camerino) but I haven't

used it myself.

I am probably overlooking others, but these should get you going. I 
strongly recommend you take a course

on the basics before plunging into any of these.

cheers,
Robert

On 2019-01-23 1:26 p.m., Hunter Allison wrote:

Hi,

      I'm a graduate student at the University of California, Irvine. 
Firstly, thank you for all the copious resources. It is a treasure 
trove of information and a beacon of light for someone just starting out.


     Let's begin with some brief background. In my research group, we 
intend to perform pump-probe spectroscopy with attosecond x-ray 
probes. The Professor says that we can use XAFS to study how the 
electrons move on these very short timescales. While the system is 
being setup and other experiments are being conducted, my Professor 
wants me to figure out how to do simulations of XAFS. This is a bit of 
a daunting order, since I've never simulated anything before and only 
have basic programming knowledge. The only direction I have is, "Try 
Google.".


     So, today, I've been "trying Google" and found my way to here. 
Since, I don't really know what I'm doing, I thought I try asking and 
finding out if anyone else does this sort of thing:
How/where does one do simulations of dynamic XAFS? Where would I get 
started?
(Please forgive me if this question has been answered somewhere else 
or if it seems profoundly dumb or too broad. I'm really just looking 
for some more direction. Perhaps, it could be that nobody does this 
and, in that case, I need to figure out how to model this myself. Wow! 
That thought seems daunting.)


     For example, let's say I want to find out how the x-ray 
adsorption of a carbon foil like Graphene would change on attosecond 
time scales as it's heated by a femtosecond laser and electrons move. 
Is there a program or code out there that people use to model this 
sort of thing?


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Re: [Ifeffit] Unable to use 64-bit Demeter on Windows computer

[Robert Gordon]

Hi Brittaney,

I downloaded the installer (in case Bruce put out a new version) and 
checked. It started up fine for me.


Possible reasons why you may be having issues:
1. You might need to run the installer as administrator
2. Your antivirus program is blocking installation

good luck!

-R.

On 2019-08-21 8:29 a.m., Brittaney Courchesne wrote:

Hello,

I am just sending this email to see if anyone has encountered the 
following problem:
I downloaded the newest 64-bit version of Demeter on my Windows 
computer, and it downloaded successfully, but now when I double click 
on the program, a tiny window pops up for about 0.5 seconds and then 
disappears. I have tried redownloading twice.


Thank you very much,
Brittaney

--
*/Brittaney Courchesne, G.I.T./*
MSc Geology Candidate
Harquail School of Earth Sciences
Laurentian University
Sudbury, ON
/bcourche...@laurentian.ca /

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Re: [Ifeffit] XAFS detection limit

[Robert Gordon]

You might also take a look at Steve Heald's article in JSR:

https://dx.doi.org/10.1107%2FS1600577515001320

"Strategies and limitations for fluorescence detection of XAFS at high 
flux beamlines"


-R.



On 2020-02-09 8:00 a.m., Christian Wittee Lopes wrote:

Hi Chris and Matt,

Thank you for the complete information, this will help a lot. It is 
always good to have such experienced people contributing to someone 
else's growth.


Kind regards,

Christian

Em dom., 9 de fev. de 2020 às 11:50, Matt Newville 
mailto:newvi...@cars.uchicago.edu>> escreveu:


Hi Christian,

On Thu, Feb 6, 2020, 8:40 PM Christian Wittee Lopes
mailto:chriswit...@gmail.com>> wrote:

Dear all,

Recently I was questioned about the EXAFS detection limit when
describing different metal species in a bimetallic sample.

By checking Pd and Cu K-edges, for example, I found Pd metal
nanoparticles and CuO clusters, respectively. But additional
techniques tell me I can have copper atoms in intimate contact
with the Pd nanoparticles. What would be the minimum amount of
these "single atoms" needed to be detected by EXAFS? is there
a detection limit or it depends on several parameters?


As Chris Chantler says, there are a lot of things that can
influence this, so there really isn't one simple answer.  Also, as
Chris says, advances in analytic methods have been (mostly) been
improving the situation.

At my beamline, we often get asked questions about detection
limits.  We're typically working in a different context than
nanoparticles/catalysts, but I think the basic ideas are about the
same.

A good starting rule-of-thumb for absolute detection limits is 1
ppm by atomic weight.  You might be able to do better sometimes,
but there are situations where XANES at 10 ppm is very hard.   For
sure, a matrix of light elements is much better than a matrix of
heavy elements.

For very dilute samples, one will be using fluorescence XAFS
measurements with a solid-state detector or know very well why you
are doing something different.  These solid-state detectors and
electronics are fundamentally limited to have energy resolutions
of ~120 eV (often 250 eV) and maximum total count rates of 5 MHz
(often 0.5 MHz).   Many beamlines use "a handful" (2 to 16)
parallel detectors, and some have up to 100 (but often with each
having a lower individual maximum count rate, and perhaps
less-than-ideal energy resolution).
With a count rate of a few MHz total and a sample with 1ppm of
"element of interest", the elastic and Compton scattering and/or
fluorescence from other elements will dominate that total count
rate and the energy resolution will give non-zero background in
the fluorescence spectrum.  That means that even seeing a peak
from 1 ppm of an element in an X-ray fluorescence spectrum with a
solid-state detector is challenging.  Not impossible, but
definitely not routine.

For sure, adding more detectors or counting for a long time can
help.  But those are linear in time and the number of detectors
(and no beamline has 1000 parallel detectors).  Low Z matrices
like water, biological material, carbon-rich materials are
easier.  Samples with nearby or overlapping fluorescence lines are
much harder.   That is 10 ppm Zn in water: yes, 1 ppm Zn in water:
maybe, 10 ppm Zn in CaCO3: maybe, 100 ppm Zn in Cu metal: no.  For
sure, XANES at 1ppm is sometimes possible. Getting interpretable
XAFS would take a lot longer, perhaps days of counting.

Using filters and/or Bent Laue Analyzers in front of a solid-state
(or integrating) detector can sometimes help to eliminate the
unwanted scatter signals before they get to the solid-state
detector.  Using crystal analyzers ("wavelength" vs "energy"
dispersive fluorescence) can help - they have lower backgrounds
and are not limited by the total scatter - but the solid angle for
these tend to be small.  Using crystal analyzer arrays are
probably really needed to get the best detection limits.  A few
beamlines do regularly do HERFD analysis with arrays of crystal
analyzers, and many of the rest of us are trying to catch up. 
Still, I believe that "1 ppm" is around the state of the art, if
not "heroic".

All of that is for the detection limit of an atomic species.  If
you are asking about detecting Cu in/on/with Pd nanoparticles with
CuO also present, the answer is far worse.  Cu XAS measurements
will be an average of all Cu atoms in the illuminated volume --
you cannot avoid the CuO.  Seeing that 1% of the Cu atoms are
bound to Pd and not to oxygen would be very challenging.

Hope that helps,
--Matt

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Re: [Ifeffit] Writing a Script for MD Simulations / Scripting Atoms

[Robert Gordon]

Are you specifying arguments for datoms.bat?

 datoms [--output format] [--rmax #] [--cif --rec=#] [--wx] mydata.inp

If no input or CIF file is specified at the command line, F
in the current working directory will be used, if available.

If the C<--wx> flag for running the GUI is given, all other command
line arguments are ignored.


for cif input
.../datoms.bat --c "yourfile.cif"

 I put the cif file in the bin directory for testing...don't have the 
bin directory in my $path


The log file (datoms.log) in appdata/roaming/demeter indicates it did 
the calculation




On 2020-07-28 7:29 a.m., David Sprouster wrote:

Dear IFEFFIT Experts,

My colleagues and I are working on preparing Python scripts which:
1) run about 20,000 cif files from MD simulations through Atoms,
2) produce feff.inp files,
3) run feff.inp files through Feff (for XANES),
4) average all the XANES spectra.

We are having trouble opening the stand alone Atoms program through 
Python – we can get Athena and Artemis to open, but for some reason 
Atoms will not.


A snipet of our code which includes the file path is attached below.

*
*

*Code:*

###

def openAtoms():

    try:

subprocess.run([r"C:\Users\ADIAZ\AppData\Roaming\DemeterPerl\perl\site\bin\datoms.bat"])

    except:

    print('Error')

openAtoms()

###


We have searched the Ifeffit archive for some answers but came up 
short, and we were wondering if anybody on the list has any 
suggestions for a potential fix to this problem?


Additionally, has anybody prepared a similar series of scripts (in 
Python) to generate XANES spectra from MD simulations? We note that 
Marcus Karolewski did discuss something similar in a past post: 
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02744.html


Thanks in advance,

Dave


--
--
David J. Sprouster, Ph.D.
Assistant Research Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
222 Old Engineering
Stony Brook, NY 11794
Phone: (631) 294-8983
web: http://stonybrook.edu/emrel
--

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Re: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported data

[Robert Gordon]

Data is just XANES at Ru L2...be better if it went to higher E for 
normalisation purposes

Why are you trying to plot XANES data in k,q or R?




On 2020-12-07 7:38 a.m., Ravel, Bruce wrote:

Likeliest reason:

https://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units

Make sure "xmu" is selected in the indicated menu.

Good luck,
B




On 12/7/20 10:26 AM, Deka, N. wrote:

Dear all

I am a new student trying to work with Athena for XAS data processing.
Attached is a data file which when I import does not show the background
and also Athena cannot plot “k” , “q” , “R” plots for the data. Please
suggest me a possible solution.

Thank you

Best Regards,

Nipon Deka

Leiden University


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Re: [Ifeffit] How to perform normalisation and background removal of data containing L3 and L2 edges

[Robert Gordon]

In checking the literature, has anyone indicated what data collection 
ranges they used, and what pre- and post-edge

regions were selected for normalisation?


Do you have more data below 2800eV that you are not showing?
Starting data collection only 50 eV or so below the edge can be 
problematic for estimating background,

particularly so if a large feature (white line) is present at the edge.

Around 2810 eV, the step size has changed from coarser to finer steps in 
energy:




and that seems to be associated with a change in slope, but with more 
noise in the coarser step range.


If I had to pick something with just this data, I could tolerate using 
the first 10 eV of the scan for

the pre-edge...



If it is just this one sample, and you aren't trying to conclude 
anything from absolute intensities,
this could be reasonable. If you are comparing, be consistent in how you 
treat the data, and understand
(and admit in presenting the data) that there can be errors associated 
with normalisation.
If I vary the post-edge values a few eV to either direction, the edge 
step changes by +/- 0.03 (0.90+/-0.03).
The variation is even larger if I push the pre-edge upper limit to 
closer to the edge. (and I can convince myself
that the 1st ~15 eV of the scan are reasonable, for an edge step closer 
to 0.94)


Generally, for this and future reference, make sure you have sufficient 
data range for processing. This
will vary depending on what edge you are studying, but here, I would 
have started at least 100 eV below

the edge.

Understand that processing has an element of subjective interpretation 
to it - asking yourself what is reasonable.

Treat similar data consistently.

Probably paraphrasing Bruce a bit, but he has a mantra of "Data handling 
and interpretation should be done
in a manner that is reasonable, plausible, and defensible." Over time, 
through experience, you can gain
an understanding of what constitutes reasonable, plausible and 
defensible. Practice on some standards

at different edges to get a feel for it.

Some more unsolicited advice:
Avoid bias - let the data tell their story. Explain how the data were 
collected. Describe in detail how the spectra
were processed. Discuss the results - what you observe, how it compares 
to literature. If you see differences,

report differences, and consider what might be plausible explanations.




On 2020-12-07 8:55 a.m., Deka, N. wrote:


Dear all

I am a student trying to learn Athena for XAS data processing. 
Attached is a data file which contains L3 and L2 edge of Ru. What 
should be the right parameters for background removal and 
normalization of this data set? In the videos from Bruce Ravel, I 
could not find any example for such a data set containing two edges.


Thank you

Best Regards,

Nipon Deka

Leiden University


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Re: [Ifeffit] How do I create a histogram based on R-space values

[Robert Gordon]

When i look at the files you included, I see R-value in the first 
column, then what I am assuming are
the (magnitude of) Fourier transforms of different data sets selected 
for export, with vertical

displacements of 10 or 25 between each data set.

A histogram plot would involve extracting N and R values (and 
mean-square-relative-displacements and Eo-shift).


So, some questions:
Do these individual datasets comprise multiple scans for one sample?
If so, do you plan on merging this data (typically, I do this before 
removing background and extracting chi(k))?


else if they represent data that is to be kept separate (not to be 
merged)...


Have you fit this data to get N and R (and...)?

If you have a standard (e.g. only 1 target element), where you know N 
and R, and what a histogram
plot of N vs R would be, have you tried examining that first to get a 
feel for what you need to do

with your unknowns?



On 2020-12-09 10:38 a.m., Deepak Varanasi wrote:


Good afternoon

I hope that everyone is safe and healthy.

I am trying to create a histogram of Number of atoms vs. the radial 
distance between the central atoms and their neighbours  (in 
Angstroms). I have the R-space data for 3 of my “central atoms” but I 
do not know how to create a histogram using them as each of them has 8 
columns of data and I do not know which one(s) to use.


Hence, may I ask for your guidance please?

Yours Sincerely

Deepak Varanasi

P.S.: I have appended an example file of an R-space reading to 
demonstrate what I mean .



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Re: [Ifeffit] Bi L3 standards

[Robert Gordon]

I have Bi metal foil and Bi2O3 you are welcome to use. Data were published
in:
dx.doi.org/10.1021/jp502996t|J. Phys. Chem. C2014, 118, 9696−9705

Some other standards are visible in here:
*Journal of Nuclear Materials 420* (*2012*) *116*–122 ... *D.A. McKeown et
al*.


-R.

On Tue, Jun 29, 2021 at 7:58 AM Schlesinger, Danielle R. <
danielle.schlesin...@jhuapl.edu> wrote:

> Hi everyone,
>
>
>
> Does anyone have a set of Bi L3 edge standards that they would be willing
> to share?
>
>
>
> Thank you!
>
>
>
> Danielle
>
>
>
>
>
> Danielle R. Schlesinger, Ph.D.
>
> *Post Doctoral Fellow – AOS/QPC*
>
> *Johns Hopkins University – Applied Physics Laboratory*
>
> Tel: (240) 592-5243
>
>
> ___
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>
# created: Sun Feb 16 22:02:39 2014
# from file: bi2o3-feb14-n.txt
# No: 351  [E0: 0,0,0,-1]
#-
#   X  Y
1.3219592902E+001  4.5890220175E-004
1.3229174474E+001  4.0691451036E-004
1.3239497039E+001  1.2582100285E-004
1.3249567656E+001  -1.4629079436E-004
1.3259308369E+001  -6.5893934277E-005
1.3269524811E+001  -1.1653289611E-004
1.3279795683E+001  -2.4426041715E-004
1.3289504299E+001  -2.9765343527E-004
1.3299111446E+001  -1.7531106844E-004
1.3309815431E+001  -4.3799580029E-005
1.3319607230E+001  1.3636339206E-004
1.3329103301E+001  4.2109040498E-004
1.3339506532E+001  9.5014784401E-004
1.3349498198E+001  1.6585871147E-003
1.3359193285E+001  2.8790372368E-003
1.3369253827E+001  4.7340384029E-003
1.3379329701E+001  7.6636789910E-003
1.3389225229E+001  1.2598459865E-002
1.3398743572E+001  2.1950794804E-002
1.3399253170E+001  2.2626775656E-002
1.3399841216E+001  2.3491686455E-002
1.3400350897E+001  2.4396813249E-002
1.3400860618E+001  2.5145511242E-002
1.3401527236E+001  2.6333237889E-002
1.3402115483E+001  2.7429204412E-002
1.3402743005E+001  2.8543416761E-002
1.3403292135E+001  2.9638528017E-002
1.3403802082E+001  3.0728598588E-002
1.3404272837E+001  3.1909063115E-002
1.3404665159E+001  3.2953325798E-002
1.3405018268E+001  3.3886495328E-002
1.3405410634E+001  3.4949156852E-002
1.3405842263E+001  3.6193494869E-002
1.3406195435E+001  3.7202049475E-002
1.340361E+001  3.8560347640E-002
1.3407098071E+001  3.9878766896E-002
1.3407804568E+001  4.2127158073E-002
1.3408471884E+001  4.4589412757E-002
1.3409021489E+001  4.7022028354E-002
1.3409649664E+001  5.0171002671E-002
1.3410160101E+001  5.3228140009E-002
1.3410631308E+001  5.6109145239E-002
1.3411259636E+001  6.0459873653E-002
1.3411770196E+001  6.2431771942E-002
1.3412359353E+001  6.7902628961E-002
1.3412830716E+001  7.2092177048E-002
1.3413262829E+001  7.5885614845E-002
1.3413734256E+001  8.0721803123E-002
1.3414087849E+001  8.4968040768E-002
1.3414480751E+001  8.9957129065E-002
1.3414952265E+001  9.6969000843E-002
1.3415423813E+001  1.0587603327E-001
1.3415934694E+001  1.1670720908E-001
1.3416563524E+001  1.3153352034E-001
1.3417113800E+001  1.4545366493E-001
1.3417782053E+001  1.6377513137E-001
1.3418371744E+001  1.8071756994E-001
1.3418882852E+001  1.9702475706E-001
1.3419433320E+001  2.1581022727E-001
1.3419865863E+001  2.3121159465E-001
1.3420298433E+001  2.4637666254E-001
1.3420731032E+001  2.6090719649E-001
1.3421124329E+001  2.7351326373E-001
1.3421438982E+001  2.8377166783E-001
1.3421871656E+001  2.9771474237E-001
1.3422343695E+001  3.1265310347E-001
1.3422776427E+001  3.2728764061E-001
1.3423484596E+001  3.5349172640E-001
1.3424153491E+001  3.8253725317E-001
1.3424822453E+001  4.1987391844E-001
1.3425334058E+001  4.5589019808E-001
1.3425806343E+001  4.9359498676E-001
1.3426396748E+001  5.4138322804E-001
1.3426869109E+001  5.7875838803E-001
1.3427380871E+001  6.1736069459E-001
1.3427971416E+001  6.5795150031E-001
1.3428443889E+001  6.8767198396E-001
1.3428916396E+001  7.1423167502E-001
1.3429349557E+001  7.3848572443E-001
1.3429743364E+001  7.5887036087E-001
1.3430097810E+001  7.7720799528E-001
1.3430570435E+001  8.0098698198E-001
1.3431082483E+001  8.2468050416E-001
1.3431555177E+001  8.4532360117E-001
1.3432185489E+001  8.7028483739E-001
1.3432737061E+001  8.8948686393E-001
1.3433288679E+001  9.0690781049E-001
1.3433958562E+001  9.2678060098E-001
1.3434589102E+001  9.4430656483E-001
1.3435101459E+001  9.5904144381E-001
1.3435535024E+001  9.7121888638E-001
1.3435968616E+001  9.8232791198E-001
1.3436441659E+001  9.9334318744E-001
1.3436835886E+001  1.0014082220E+000
1.3437151285E+001  1.0071323785E+000
1.3437584983E+001  1.0145747761E+000
1.3437979279E+001  1.0206639981E+000
1.3438452464E+001  1.0271275113E+000
1.3439004557E+001  1.0346625357E+000
1.3440029993E+001  1.0482797343E+000
1.3441095036E+001  1.0616509157E+000
1.3442041884E+001  1.0713855967E+000
1.3443107250E+001  1.0769264510E+000
1.3444054385E+001  1.0766776187E+000
1.3445041128E+001  1

Re: [Ifeffit] how to learn wavelet analysis

[Robert Gordon]

Try starting here:
https://www.esrf.fr/UsersAndScience/Experiments/CRG/BM20/Software/Wavelets

On 2021-11-10 6:48 p.m., 罗昕宇 wrote:


Dear IFEFFIT members,

I'm a fresh graduate student majoring in chemical engineering. I began 
to learn XAFS by myself one month ago. I bought and read the book 
/XAFS for Everyone/ written by Dr. Calvin. I think I have got a clear 
image of how EXAFS works. Recently, I am attracted bythe technique 
called Wavelet Analysis from literatures. It seems pretty powerful to 
correlate both temporal and frequency information, but something just 
wentprobably beyond my current knowledge base. I understand that a 
changeable window should be adapted to a make a trade-off between time 
and frequency, but I don't understand the logic that good 
time-resolution in high frequency is preferred while in low frequency 
a good frequency-resolution is better. I would appreciate it very much 
if you could answer my half-baked question and offer me with some 
learning material.



Best regards

Xinyu


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