hands-on tutorial on fdmnes and fitit · nazarenko elena postdoc. gothenburg university. sweden....
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![Page 1: Hands-on tutorial on FDMNES and FitIt · Nazarenko Elena PostDoc. Gothenburg University. Sweden. Outline FDMNES (XANES simulations)-program description-example FeO6 FitIt (XANES fitting](https://reader033.vdocuments.mx/reader033/viewer/2022052007/601c40f629538662776b9dfc/html5/thumbnails/1.jpg)
Hands-on tutorial on FDMNES and FitIt
Nazarenko Elena
PostDoc. Gothenburg University. Sweden
![Page 2: Hands-on tutorial on FDMNES and FitIt · Nazarenko Elena PostDoc. Gothenburg University. Sweden. Outline FDMNES (XANES simulations)-program description-example FeO6 FitIt (XANES fitting](https://reader033.vdocuments.mx/reader033/viewer/2022052007/601c40f629538662776b9dfc/html5/thumbnails/2.jpg)
Outline
� FDMNES (XANES simulations)
- program description
- example FeO6- example FeO6
� FitIt (XANES fitting program)
- short program description
- example protein PerR
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Basis of XAS
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FDMNES. Author
Yves Joly [email protected] Néel, CNRS, Grenoble, France
Y. Joly "X-ray absorption near edge structure calculations beyond the muffin-tin approximation"
Phys. Rev. B 63, 125120 (2001)
Institut Néel, CNRS, Grenoble, Francehttp://www.neel.cnrs.fr/fdmnes
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FDMNES. Short description
� XANES (mostly K-, L- edges), DAFS or RXD or RXS� Full relativistic monoelectronic calculations (DFT-
LSDA)Finite Difference Method (FDM) to solve the � Finite Difference Method (FDM) to solve the Schrödinger equation. The shape of the potential is free (non muffin-tin approximation)
� Green formalism (multiple scattering) on a muffin-tin potential
� Now. Multi-electronic extension using the “Time-Dependant DFT” and self-consistant potential
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Muffin-tin approximation
0
1
2
-30.00
-27.00
-24.00
-21.00
-18.00
-15.00Zn
N2
C2
Coo
rdin
ate
(Ang
.)
0 1 2 3 4 5
-2
-1-12.00
-9.000
-6.000
-3.000
0
N1 C1 Coo
rdin
ate
(Ang
.)
Coordinate (Ang.)
0 1 2 3 4 5
-2
-1
0
1
2-30.00
-27.00
-24.00
-21.00
-18.00
-15.00
-12.00
-9.000
-6.000
-3.000
0
C2Zn
Zn
N1
N2
C1
C2
Coordinate (Ang)
Coo
rdin
ate
(Ang
)
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FDMNES. Example: FeO6
Fe-O distance: 2.16 Å
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FDMNES. Input file. The first part
fdmnes/entree/test_stand/feo6_inp.txt ! Main indata file for fdmnes to simulate FeO6 molecule! Calculation on FeO6 using the multiple scattering approch! with convolution, comparison with an experimental spectra and fit.
Filoutxanout/test_stand/feo6 / name of output file and directory
Range-6. 0.1 -3. 0.2 0. 0.5 20. 1. 40. 2. 60. / energy range
Radius / radius of calculated cluster, Å3.0
Green /multiple scattering aproach/ by defaut: finite difference method
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FDMNES. Input file. The second part
Molecule /molecule or crystal2.16 2.16 2.16 90. 90. 90. = a, b, c, alpha, beta, gamma
26 0.0 0.0 0.0 = Z, x, y, z / atomic number and position8 1.0 0.0 0.0 8 -1.0 0.0 0.0 8 0.0 1.0 0.0 8 0.0 1.0 0.0 8 0.0 -1.0 0.0 8 0.0 0.0 1.0 8 0.0 0.0 -1.0
! keywords for the convolution / convolution of the spectrum. Might beConvolution / done separately. “arctangeant” shape for
/the broadeningEfermi /cutting of the occupated states-4.8Estart-10.End
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FDMNES running. Step-by-step
� Prepare or modify the input file. For FeO6 example go to fdmnes/entree/test_stand/feo6_inp.txt
� Go to the mail folder with the fdmnes.exe ->/fdmnes/
� Modify the file fdmfile.txt ->
1entree/test_stand/feo6_inp.txtentree/test_stand/cu_inp.txt
� Run fdmnes.exe
� Trace the output files with calculated spectra -> fdmnes/xanout/test_stand/
feo6.txt – without convolutionfeo6_conv.txt – with convolution
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FitIt. Athours
http://www.nano.sfedu.ru/fitit.html
Grigory Smolentsev and Alexandre SoldatovSouthern Federal University &Lund University
G. Smolentsev, A. Soldatov, Journal of Synchrotron Radiation 2006, 13, 19-29G. Smolentsev and A.V. Soldatov, Comp. Matter. Science 39 (2007) 569.
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FitIt. GUI
� Multidimensional interpolation approximation.
� Quantitative determination of the local atomic of the local atomic structure
� Use external programs as FEFF and FDMNES
� It allows to minimize the number of time-consuming XANES calculations required to find optimal values of the parameters.
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New FitIt project. Step-by-step. Part 1
� Install FitIt package. Tick FDMNES during the installation process
� Prepare a work folder with files (see for example PerR_Madrid folder): in.pdb - PDB file with initial structure
fdmnes.inp – input fdmnes file without atomic coordinates
File with experiment – should consist number of energy points of and two coulumns with File with experiment – should consist number of energy points of and two coulumns with energy and absorption signal (see PerR_Madrid/FePerR.dat)
� Run FitIt for example from the ”Start menu”
� Press the first button ”New project”
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New FitIt project. Step-by-step. Part 2
� Specify your working folder and file with experiment pressing the buttons to open files
� Make a programm configuration. Tip: Open in the configuration. Tip: Open in the executable list the fdmnes template /Program
files/FitIt/fdmnes.wrk
� Leave empty the field with theoretical spectra if you don’t have them
� Specify the Energy range for experiment
� Press ”OK”
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Simulations of Fe-edge PerR protein
0.04
0.05 Full potential Muffin-tin approximation
-10 0 10 20 30 40 50 600.00
0.01
0.02
0.03
Photoelectron Energy (eV)
- Strong non muffin tin effects - Full potential (beyond the muffin tin approximation) calculations using FDMNES code.
- Cluster 4.5 Ă- Quantitative XANES fitting using FitIt package
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What kind of structural information we can see from XANES?
1.0
1.5
XA
NE
S (
arb.
un.
)
PerR protein
7120 7140 7160
0.0
0.5
Experiment
XA
NE
S (
arb.
un.
)
Energy (eV)
Starting model
� Distances Fe-His&Fe-Asp (1.9-2.1A)� Angle between Asp changes from 120º to 180º� In plane rotation of aspartates� Axial rotations of aspartates - influence very slightly
influence significantly
Fe
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FitIt. PerR example. Step-by-step
� Go to the folder /PerR Madrid/
� Run fit_PerR.fbf
� Play with the parameters on the slider bar
� Look on the table with calculated spectra. Look how are different � Look on the table with calculated spectra. Look how are different the calculated (blue one) and interpolated spectra (green one).
� Remember the spectra with the big difference which you should include in the polinomial.
� Press the button ”auto polynomial” and tick these spectra.
� Play with the parameters on the slider again.
� Try to find the combination of parameters wich gives the best fit results
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Structural model of iron binding site
Trigonal dipyramid
Bestfit model:square pyramid
Molecular Microbiology (2009) 73(1), 20–31
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Thank you for your attention!
Poster MS42.P01(C516). X-ray absorption spectroscopy studies of copper site in
the ubiquinol oxidase
August 25-26