[Ifeffit] XANES and DOS calculations
Joanna Czapla
czapla.asia at gmail.com
Sat May 22 10:21:41 CDT 2010
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 <ifeffit-request at millenia.cars.aps.anl.gov>:
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> Today's Topics:
>
> 1. fitting (mohamed sobhy)
> 2. update error in Windows 7 (pkraal at 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 <bakhshwan1981 at yahoo.com>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] fitting
> Message-ID: <725080.73390.qm at 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
>
>
>
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 2
> Date: Fri, 21 May 2010 12:09:24 +0200
> From: pkraal at geo.uu.nl
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] update error in Windows 7
> Message-ID:
> <3ded096a7acb18ecc34d49196967ce21.squirrel at 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" <menard at email.unc.edu>
> To: "'XAFS Analysis using Ifeffit'"
> <ifeffit at millenia.cars.aps.anl.gov>
> 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 at millenia.cars.aps.anl.gov
> [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of
> pkraal at geo.uu.nl
> Sent: Friday, May 21, 2010 6:09 AM
> To: ifeffit at 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 at 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 <bdg160 at psu.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] update error in Windows 7
> Message-ID:
> <AANLkTikFXm8cspcd65cHnFcT7R9MN78Gf8gjwBAY6oWB at mail.gmail.com>
> 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, <pkraal at geo.uu.nl> 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 at 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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> Ifeffit at millenia.cars.aps.anl.gov
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>
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