Re: [Ifeffit] calibrating and aligning samples for LCF

24 May 2010

      If you trust that the calibration did not change between when the nanoparticles and the Fe foils were run, then all you need to do is to align the
spectra so that the edge for Fe comes out at the same place as it did for the references.  The tricky bit is that if you have references from somewhere else,
you may not know what the energy basis was.  Some people take the Fe K-edge to be at 7112eV, some at 7110.75 (Kraft's paper), etc.  If all reference spectra
came from the same source, it may be reasonable to assume that they all had the same energy reference, so you could do your LCF with an e0 shift as an additional
parameter.

Now, suppose you don't trust the calibration.  There may be a monochromator glitch at a convenient energy.  These tend not to move very much, so if you
have the raw data for Fe foil, you can back out the energy of the glitch, then use that to calibrate the unknown, provided the data for it was taken at the
same beamline as the Fe, and not too long before or after.

We have a set of reference spectra, most of which were collected at 10.3.2, and done with consistent calibration: http://xraysweb.lbl.gov/uxas/Databases/Overview.htm .
	mam

On 5/24/2010 2:39 PM, Monson, Todd wrote:
...
I have XAFS data from several Fe nanoparticle samples as well as some Fe and Fe oxide standards collected during two different months.  I would like to fit the Fe nanoparticle data using LCF and the Fe & Fe oxide standards.  Data collected from Fe foil during the two months have been calibrated in energy.  What is the best way to calibrate or align the other nanoparticle samples and standards collected during both of these sessions prior to doing LCF?
Thanks,
Todd
-----Original Message-----
From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov
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Today's Topics:
1. XANES and DOS calculations (Joanna Czapla)
----------------------------------------------------------------------
Message: 1
Date: Sat, 22 May 2010 17:21:41 +0200
From: Joanna Czapla 
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] XANES and DOS calculations
Message-ID:

Content-Type: text/plain; charset=windows-1252
Dear Feff Users,
first of all I must admit that I am a total beginner and probably there are some things which I don?t understand very well.
I need to make XANES and DOS calculations for K-edge of sulfur and then compare them with experiment. I use feff 8.4.
First, I started from inorganic compounds such as CdS. I generated feff.inp file in ATOMS and first run feff with default values (generated by ATOMS). The fit wasn?t perfect so I started to change parameters-FMS and SCF but there was so significant improvement. I can only add that others fit are even worse. My question is which parameter I should change or which card should I add to make XANES calculations better? Maybe you can recommend any paper?
The second question is about DOS calculations. I took the pDOS functions for each atom, set Fermi level from ldosNN files, but the main peaks are below this level and I don?t have any correspondence with XANES spectrum. For other compounds I have the same problem.
Should I add any extra shift?
I will be grateful for your advice.
Regards
Joanna Czapla
I add the original feff.inp file generated by ATOMS:
* This feff8 input file was generated by WebAtoms 1.8 (Atoms 3.0beta10)
 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001
TITLE name:     CdS  (greenockite) (cubic zinc sulfide structure)
 TITLE formula:  CdS
 TITLE sites:    Cd1,S1
 TITLE refer1:   wyckoff 1,III,110
 TITLE refer2:
 TITLE schoen:
 TITLE notes1:   cubic zinc sulfide structure
*  S K edge energy = 2472.0 eV
 EDGE      K
 S02       1.0
*         pot    xsph  fms   paths genfmt ff2chi
 CONTROL   1      1     1     1     1      1
 PRINT     1      0     0     0     0      0
*** ixc=0 means to use Hedin-Lundqvist
 *         ixc  [ Vr  Vi ]
 EXCHANGE  0
*** Radius of small cluster for
                          *** self-consistency calculation
                          *** A sphere including 2 shells is
                          *** a good choice
                          *** l_scf = 0 for a solid, 1 for a molecule
 *         r_scf  [ l_scf   n_scf   ca ]
 SCF       4.0
*** Upper limit of XANES calculation.
                          *** This *must* be uncommented to
                          *** make Feff calculate full multiple
                          *** scattering rather than a path expansion
 *         kmax   [ delta_k  delta_e ]
 XANES     4.0
*** Radius of cluster for Full Multiple
                          *** Scattering calculation
                          *** l_fms = 0 for a solid, 1 for a molecule
 *         r_fms     l_fms
 FMS        5.54240  0
*** Energy grid over which to calculate
                          *** DOS functions
 *         emin  emax   eimag
 LDOS      -30   20     0.1
*** for EXAFS:  RMAX   8.0 and uncomment
                          *** the EXAFS card
 RPATH     0.1
 *EXAFS     20
POTENTIALS
 *    ipot   Z  element            l_scmt  l_fms   stoichiometry
        0   16   S                  2       2       0.001
        1   48   Cd                 3       3       4
        2   16   S                  2       2       4
ATOMS                          * this list contains 87 atoms
 *   x          y          z      ipot  tag           distance
    0.00000    0.00000    0.00000  0    S1            0.00000     0
   -1.45450    1.45450    1.45450  1    Cd1           2.51927     1
    1.45450   -1.45450    1.45450  1    Cd1           2.51927     2
    1.45450    1.45450   -1.45450  1    Cd1           2.51927     3
   -1.45450   -1.45450   -1.45450  1    Cd1           2.51927     4
    2.90900    2.90900    0.00000  2    S1            4.11395     5
   -2.90900    2.90900    0.00000  2    S1            4.11395     6
    2.90900   -2.90900    0.00000  2    S1            4.11395     7
   -2.90900   -2.90900    0.00000  2    S1            4.11395     8
    2.90900    0.00000    2.90900  2    S1            4.11395     9
   -2.90900    0.00000    2.90900  2    S1            4.11395    10
    0.00000    2.90900    2.90900  2    S1            4.11395    11
    0.00000   -2.90900    2.90900  2    S1            4.11395    12
    2.90900    0.00000   -2.90900  2    S1            4.11395    13
   -2.90900    0.00000   -2.90900  2    S1            4.11395    14
    0.00000    2.90900   -2.90900  2    S1            4.11395    15
    0.00000   -2.90900   -2.90900  2    S1            4.11395    16
    4.36350    1.45450    1.45450  1    Cd1           4.82403    17
    1.45450    4.36350    1.45450  1    Cd1           4.82403    18
   -4.36350   -1.45450    1.45450  1    Cd1           4.82403    19
   -1.45450   -4.36350    1.45450  1    Cd1           4.82403    20
    1.45450    1.45450    4.36350  1    Cd1           4.82403    21
   -1.45450   -1.45450    4.36350  1    Cd1           4.82403    22
   -4.36350    1.45450   -1.45450  1    Cd1           4.82403    23
   -1.45450    4.36350   -1.45450  1    Cd1           4.82403    24
    4.36350   -1.45450   -1.45450  1    Cd1           4.82403    25
    1.45450   -4.36350   -1.45450  1    Cd1           4.82403    26
   -1.45450    1.45450   -4.36350  1    Cd1           4.82403    27
    1.45450   -1.45450   -4.36350  1    Cd1           4.82403    28
    5.81800    0.00000    0.00000  2    S1            5.81800    29
   -5.81800    0.00000    0.00000  2    S1            5.81800    30
    0.00000    5.81800    0.00000  2    S1            5.81800    31
    0.00000   -5.81800    0.00000  2    S1            5.81800    32
    0.00000    0.00000    5.81800  2    S1            5.81800    33
    0.00000    0.00000   -5.81800  2    S1            5.81800    34
   -4.36350    4.36350    1.45450  1    Cd1           6.34002    35
    4.36350   -4.36350    1.45450  1    Cd1           6.34002    36
   -4.36350    1.45450    4.36350  1    Cd1           6.34002    37
   -1.45450    4.36350    4.36350  1    Cd1           6.34002    38
    4.36350   -1.45450    4.36350  1    Cd1           6.34002    39
    1.45450   -4.36350    4.36350  1    Cd1           6.34002    40
    4.36350    4.36350   -1.45450  1    Cd1           6.34002    41
   -4.36350   -4.36350   -1.45450  1    Cd1           6.34002    42
    4.36350    1.45450   -4.36350  1    Cd1           6.34002    43
    1.45450    4.36350   -4.36350  1    Cd1           6.34002    44
   -4.36350   -1.45450   -4.36350  1    Cd1           6.34002    45
   -1.45450   -4.36350   -4.36350  1    Cd1           6.34002    46
    5.81800    2.90900    2.90900  2    S1            7.12557    47
   -5.81800    2.90900    2.90900  2    S1            7.12557    48
    2.90900    5.81800    2.90900  2    S1            7.12557    49
   -2.90900    5.81800    2.90900  2    S1            7.12557    50
    5.81800   -2.90900    2.90900  2    S1            7.12557    51
   -5.81800   -2.90900    2.90900  2    S1            7.12557    52
    2.90900   -5.81800    2.90900  2    S1            7.12557    53
   -2.90900   -5.81800    2.90900  2    S1            7.12557    54
    2.90900    2.90900    5.81800  2    S1            7.12557    55
   -2.90900    2.90900    5.81800  2    S1            7.12557    56
    2.90900   -2.90900    5.81800  2    S1            7.12557    57
   -2.90900   -2.90900    5.81800  2    S1            7.12557    58
    5.81800    2.90900   -2.90900  2    S1            7.12557    59
   -5.81800    2.90900   -2.90900  2    S1            7.12557    60
    2.90900    5.81800   -2.90900  2    S1            7.12557    61
   -2.90900    5.81800   -2.90900  2    S1            7.12557    62
    5.81800   -2.90900   -2.90900  2    S1            7.12557    63
   -5.81800   -2.90900   -2.90900  2    S1            7.12557    64
    2.90900   -5.81800   -2.90900  2    S1            7.12557    65
   -2.90900   -5.81800   -2.90900  2    S1            7.12557    66
    2.90900    2.90900   -5.81800  2    S1            7.12557    67
   -2.90900    2.90900   -5.81800  2    S1            7.12557    68
    2.90900   -2.90900   -5.81800  2    S1            7.12557    69
   -2.90900   -2.90900   -5.81800  2    S1            7.12557    70
   -7.27250    1.45450    1.45450  1    Cd1           7.55780    71
   -1.45450    7.27250    1.45450  1    Cd1           7.55780    72
    7.27250   -1.45450    1.45450  1    Cd1           7.55780    73
    1.45450   -7.27250    1.45450  1    Cd1           7.55780    74
    4.36350    4.36350    4.36350  1    Cd1           7.55780    75
   -4.36350   -4.36350    4.36350  1    Cd1           7.55780    76
   -1.45450    1.45450    7.27250  1    Cd1           7.55780    77
    1.45450   -1.45450    7.27250  1    Cd1           7.55780    78
    7.27250    1.45450   -1.45450  1    Cd1           7.55780    79
    1.45450    7.27250   -1.45450  1    Cd1           7.55780    80
   -7.27250   -1.45450   -1.45450  1    Cd1           7.55780    81
   -1.45450   -7.27250   -1.45450  1    Cd1           7.55780    82
   -4.36350    4.36350   -4.36350  1    Cd1           7.55780    83
    4.36350   -4.36350   -4.36350  1    Cd1           7.55780    84
    1.45450    1.45450   -7.27250  1    Cd1           7.55780    85
   -1.45450   -1.45450   -7.27250  1    Cd1           7.55780    86
 END
2010/5/21  :
...
Send Ifeffit mailing list submissions to ? ? ?
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or, via email, send a message with subject or body 'help' to ? ? ?
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Today's Topics:
? 1. fitting (mohamed sobhy)
? 2. update error in Windows 7 (pkraal@geo.uu.nl) ? 3. Re: update
error in Windows 7 (Laurent Menard) ? 4. Re: update error in Windows 7
(Bryan Gauntt)
----------------------------------------------------------------------
Message: 1
Date: Thu, 20 May 2010 14:14:18 -0700 (PDT)
From: mohamed sobhy 
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] fitting
Message-ID: <725080.73390.qm@web50302.mail.re2.yahoo.com>
Content-Type: text/plain; charset="us-ascii"
Dear all thanks for your help and explanation about the background I
fitted my data after removing the background and in the attached file
I got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation.
So how can I get the right coordination number?
How to improve the fitting of second shell?
thanks
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Message: 2
Date: Fri, 21 May 2010 12:09:24 +0200
From: pkraal@geo.uu.nl
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] update error in Windows 7
Message-ID:
? ? ? ?<3ded096a7acb18ecc34d49196967ce21.squirrel@webmail.geo.uu.nl>
Content-Type: text/plain;charset=iso-8859-1
Dear sir or madam,
I am using IFEFFIT on a Windows 7 system. When the runner informs that
updates are available, I select to download and install them. Then,
the first package is downloaded, but during expanding and installation
of this package the update basically stops and the runner gives an
error associated with access to bin/athena.exe. Windows 7 (like Vista
pretty easily stressed when you try to change software) does not
inform me that a program is trying to change the system or whatever,
so I don't know what to do. Is there anybody out there with similar
problems and maybe, even better, a solution?
Regards and many thanks,
Peter Kraal.
------------------------------
Message: 3
Date: Fri, 21 May 2010 09:23:38 -0400
From: "Laurent Menard" 
To: "'XAFS Analysis using Ifeffit'"
? ? ? ?
Subject: Re: [Ifeffit] update error in Windows 7
Message-ID: <01cb01caf8e8$d2cc0e90$78642bb0$@unc.edu>
Content-Type: text/plain; ? ? ? charset="US-ASCII"
Peter,
You need to make sure you have permission in Windows to write to the
IFEFFIT folder. ?If I remember correctly all you have to do is right
click on the IFEFFIT folder, select Properties. ?Go to the Security
Tab and then select the Edit button. ?Make sure that under Users all
of the "allow" boxes are checked then click OK. ?IFEFFIT should
install the updates the next time it checks for updates.
Regards,
Laurent
-----Original Message-----
From: ifeffit-bounces@millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of
pkraal@geo.uu.nl
Sent: Friday, May 21, 2010 6:09 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] update error in Windows 7
Dear sir or madam,
I am using IFEFFIT on a Windows 7 system. When the runner informs that
updates are available, I select to download and install them. Then,
the first package is downloaded, but during expanding and installation
of this package the update basically stops and the runner gives an
error associated with access to bin/athena.exe. Windows 7 (like Vista
pretty easily stressed when you try to change software) does not
inform me that a program is trying to change the system or whatever,
so I don't know what to do. Is there anybody out there with similar
problems and maybe, even better, a solution?
Regards and many thanks,
Peter Kraal.
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
------------------------------
Message: 4
Date: Fri, 21 May 2010 09:26:01 -0400
From: Bryan Gauntt 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] update error in Windows 7
Message-ID:
? ? ? ?
Content-Type: text/plain; charset=ISO-8859-1
Dear Peter,
I found that setting both Artemis and Athena to run in compatibility
mode (XP Service Pack 3) did the trick for me. ?You can do this by
locating the executables in the start menu and right clicking them.
Select "properties" and then the "compatibility" tab. Under
"compatibility mode" select the box next to "Run this program in
compatibility mode," and then select Windows XP (Service Pack 3) from
the drop-down list.
Best of luck,
Bryan Gauntt
On Fri, May 21, 2010 at 6:09 AM, ? wrote:
...
Dear sir or madam,
I am using IFEFFIT on a Windows 7 system. When the runner informs
that updates are available, I select to download and install them.
Then, the first package is downloaded, but during expanding and
installation of this package the update basically stops and the
runner gives an error associated with access to bin/athena.exe.
Windows 7 (like Vista pretty easily stressed when you try to change
software) does not inform me that a program is trying to change the
system or whatever, so I don't know what to do. Is there anybody out
there with similar problems and maybe, even better, a solution?
Regards and many thanks,
Peter Kraal.
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
--
Bryan D. Gauntt
PhD Candidate
Department of Materials Science and Engineering
274 Materials Research Lab
Penn State University
(814) 574-2751
------------------------------
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Re: [Ifeffit] calibrating and aligning samples for LCF

Matthew Marcus