xanes: mxan and fpms codes
TRANSCRIPT
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XANES: MXAN and FPMScodes
Keisuke Hatada1,2
Maurizio Benfatto21 Dipartimento di Fisica, Università Camerino
2 Laboratori Nazionali di Frascati - INFN
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Acknowledgement
• Isabella Ascone Grazie mille!• Joaquin García Ruiz ¡Muchas gracias!• Hiroyuki Oyanagi どうもありがとう御座います。
Many thanks!
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Recent active contributorsCalogero R. Natoli1
Maurizio Benfatto1
Stefano Della Longa2
Kuniko Hayakawa1,3
Keisuke Hatada1,4
1 INFN Laboratori Nazionali di Frascati2 Università L’Aquila3 Museo Storico della Fisica e Centro Studi e Ricerche ``Enrico Fermi”4 Università Camerino
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Multiple scattering approach
KKR (band): Korringa (1947), Kohn and Rostoker (1954)SCF-SW (Quantum Chemistry:MO): Slater and Johnson (1966), Smith and Johnosn (1969)
For spectroscopy,
LEED: PendryXPD : Rennert, Natoli & SebilleauXAFS: Natoli (1980), Rehr (FEFF code), Benfatto, Brouder, Foulis, Ebert, Fujikawa, Sipr, …
Also for ELNES, RXS
wide application of MS theoryK. Hatada, IXAS Web Magazine, 2nd issue, July (2010)
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4 atoms
Gii = G0
ii + G0inT nG0
ni
n! + G0
inT nG0nmT mG0
mi
nm! +!
lj
k
i
Obtain Gii:
G0ii :isolated
G0inT nG0
ni
n! :single scattering
G0inT nG0
nmT mG0mi
nm!
:double scattering
G0ij
G0ji
T j
G0ik G0
kl
G0li
T k
T l
Multiple scattering with Muffin-tin approximation :Green’s function picture
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Gii = G0
ii + G0inT nG0
ni
n! i" + G0
inT nG0nmT mG0
mi
n!m! i" +!
= [G0 (I !G0T )!1]ii
Full Multiple Scattering
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!(ri;k) = BLi (k)"L
i (ri )L#
!(rj ;k) = BLj (k)"L
j (rj )L#
!(rk ;k) = BLk (k)"L
k (rk )L#
!(rl ;k) = BLl (k)"L
l (rl )L#
lj
k
i
Site i:
Site j:
Site k:
Site l:
: local solution of SE
: amplitudeBLi (k)
!L (ri )
!(ri;k): global solution of SE
Matches WF and itsderivative on thesurface of cells!
WF is expanded by local solutions
Multiple scattering : wave function (WF) picture
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[T !1(I ! TG0 )]LL 'ij BL '
j
jL '" = IL
i (k)
This gives amplitudes on each sites. In other wordsmatching will be done implicitly by solving thisequation.
:Boundary condition of the cluster for the cite i centered.
ILi (k)
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Many applications have been done.
M. Benfatto and S. Della Longa, J. Synchrotron Rad., 8, 1087 (2001)
• XANES (X-ray Absorption Near Edge Structure) from edge to ~100 eV
• 3 dimensional information, sensitive to atomic species
MXAN code: fitting structural and electronic properties by XANES spectra for molecule, protein and amorphous. (disordered system)
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• S. Della Longa et al. Biophy. Jour. 85, 549 (2003)• P. Frank et al. Inorganic Chemistry 44, 1922 (2005)• C Monesi et al. PRB 72, 174104 (2005)• R. Sarangi et al. Inorganic Chemistry 44, 9652 (2005)• P. D’Angelo et al. JACS 128, 1853 (2006)• S. Marino et al. Biophy. Jour. 93, 2781 (2007)• ....• M. Bortolus et al. JACS 132, 18057 (2010)
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70
Two ways to calculate the scattering path operator Exactly: all MS
contributions are included
by series:
We have developed a new fitting method, called MXAN, that use the exact calculation of the scattering path operator
i) We work in the energy spaceii) We can start from the edgeiii) We can use polarization dependent spectra
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71
To perform structural fits
• Initial geometrical configurations• Exp. data
We generate hundred of theor. spectra by moving atomic coordinates
By comparison with exp. data we can fit relevant structural parameters
Minimization of error function
x
y
z
R
N
1iii
2i
2.expi
N
1inn
.thi
2sq w/w}/]y,..),r(..y{[R
The potential is calculated at each step – Norman criterion
M. Benfatto and S. Della Longa (2001) J. Synch. Rad. 8, 1087S. Della Longa et al. (2001) PRL 87, 155501 M. Benfatto et al. (2003) J. Synch. Rad. 10, 51
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72
(E) Behaves like the universal form and starts from energy Es with a jump As . Both Es , c and As are derived at each step of computation on the basis of Monte Carlo fit.
(E) contains all the intrinsic and extrinsic inelastic processes
Es
As
This jump is made via an arctang function
c
0
5
10
15
20
25
0 20 40 60 80 100
(E)
energy (eV)
To avoid the problems coming from the use of the full HL potential, the Exchange and Correlation part of the potential is calculated on the basis of a phenomenological approach real HL potential + convolution via a Lorentzian function with
tot (E)= c + (E)
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73
Transition metals in water solution
fits include fits include HydrogenHydrogen atomsatoms
R(Å) R(Å)
Co2+ 2.06(0.03) 2.092(0.002)
Ni2+ 2.04(0.03) 2.072(0.002)
Zn2+ 2.06(0.02) 2.078(0.002)
MXANGNXAS
P. D’Angelo et al. (2002) Phys. Rev B 66, 064209
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74
exp
best-fit
Fe (CN)6 in water
The bestThe best--fit condition corresponds to an octahedralfit condition corresponds to an octahedralsymmetry with Fesymmetry with Fe--C distance of 1.92(0.01) C distance of 1.92(0.01) ÅÅ and Cand C--N N distance of 1.21(0.01) distance of 1.21(0.01) ÅÅPrevious GNXAS analysis (Westre et al. JACS 117 (1995))reports Fe-C and Fe-N distances of 1.92 Å and 1.18 Å respectively
-50 0 50 100 150 2000
0,5
1
1,5
2
Energy(eV)
Fe K
-edg
e (a
rb. u
nits
)
Rsq =8.2
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75
0
0.5
1
1.5
2
0 20 40 60 80 100 120Energy(eV)
0
0.5
1
1.5
2
Rsq =28.78
Rsq =50.94
Fit with CO moleculesFe-C =1.94Å and C-O =1.11Å
Fit with NO moleculesFe-N =1.91Å and N-O =1.16Å
Chemical sensitivity
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76
just an increase of the error bar in the structural numbers
Three key points:
The use of a phenomenological dampingThe use of a phenomenological damping
The potential is calculated at each step of the The potential is calculated at each step of the atomic movement keeping the same Norman atomic movement keeping the same Norman criterioncriterionThe used energy range is wide enough to The used energy range is wide enough to minimize errors in the potential determinationminimize errors in the potential determination
Test cases indicate a good structural reconstruction Test cases indicate a good structural reconstruction at the atomic resolutionat the atomic resolution
high sensitivity to the structural changeshigh sensitivity to the structural changes
the fit results are weakly affected by the errors the fit results are weakly affected by the errors in the potential determinationin the potential determination
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111
thermal and structural disorder
We use MD to generate thousands of geometrical configurations – each snapshot with a time step of 50 fs is used to generated one XANES spectrum – average using ~ 104 geometrical configuration
2/121 )]()([)( i
N
ii
Nf EENR
Merkling et al. JACS 124 (2002)Campbell et al. Jour.Synch.Rad. 6 (1999)
Incremental Average
Rf < 10-4 ?averaged XANES spectrum
Total MD trajectories
Sequential snapshot extraction around the absorber
MXAN run MXAN run ………… Parallel calculations
yes no
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112
average
Ni2+ in water – Ni Kedge
Calculations for some particular snapshots
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113
Comparison between the averaged theoretical spectrum and a single theoretical spectrum at the symmetrical first shell configuration
Arrows indicate the damping - very weak effect - it can be included in the phenomenological treatment of the inelastic losses in MXAN
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114
including the second shell
average
first shell average
first + second shells average
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115
one shell fit
two shells fit
sizeable effects in the energy range 0 - 30 eV
P. D’Angelo et al. JACS 128 (2006)
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116
The water solvation of I-
0
0,2
0,4
0,6
0,8
1
1,2
1,4
1,6
-20 0 20 40 60 80 100Energy (eV)
L1 - L3 XAS data
as in the previous case we analyze those data by MD snapshots generate by QM/MM and DFT methods
in collaboration with Chergui’s group
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117
I-O pair distribution function from MD
the calculated coordination number varies from 7 to 9.7 - difficulty to define a solvation shell
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We have used more than 1000 frames - three of them at L3 edge
Very disordered system!
The calculation includes atoms (H and O) up to 7 Å
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119
L3 Fits
DFT
QM/MM
0
0,5
1
1,5
2
-20 0 20 40 60 80 100 120
L3-QM/MM simulation
fit-l3-mm-4Angexp-l3-mm-4Angfit-l3-mm-5.5Angexp-l3-mm-5.5Ang
energy (eV)
0
0,5
1
1,5
2
-20 0 20 40 60 80 100 120
L3-DFT simulation
fit-l3-dft-4Angexp-l3-dft-4Angfit-l3-dft-5.5Angexp-l3-dft-5.5Ang
fit-l3
-dft-
4Ang
energy (eV)
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120
L1 Fits
0
0,5
1
,5
2
-20 0 20 40 60 80 100 120
fit-l1-mm-4Angexp-l1-mm-4Angfit-l1-mm-5.5Angexp-l1-mm-5.5Ang
energy (eV)
L1-QM/MM simulation
0
0,5
1
1,5
2
-20 0 20 40 60 80 100 120
fit-l1-dft-4Angexp-l1-dft-4Angfit-l1-dft-5.5Angexp-l1-dft-5.5Ang
fit-l1
-dft-
4Ang
L1-DFT-simulation
QM/MM
DFT
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121
The QM/MM calculations reproduces better than DFT the experimental data for both L1 and L3 edges - Increasing the cluster size DFT becomes worse than QM/MM
It seems that DFT introduces a partial order that is not verify in the reality
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some conclusions
It is possible to fit the XANES energy range It is possible to fit the XANES energy range starting from the edge to obtain quantitative starting from the edge to obtain quantitative structural informationstructural information
We can treat, although numerically, very We can treat, although numerically, very disorder systems disorder systems –– possible application on possible application on nanonano--materialsmaterials
Future: new MXAN using the non-MT theory - improvements for the exchange-correlation potential
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MT approximation (MXAN)
Use sphericalshaped andaveraged potential
outside the cellspotential is flat
Non-MT (FPMS)
No interstitial region!
Potential inside cell isanisotropic Empty Cells (EC)
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For discontinued functionspherical harmonicsexpansionnever converges inpractice.(Gibbs phenomenon)
Radial component oscillate!
V (r) = VL (r)YL (r̂)L! (L=(l,m))
So called moon region.In this regionexpansion byspherical harmonicsnever converges.
FPMS
There are two types of lmax in MS1. potential power2. anisotropy
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L2!(r) = l(l +1)RL (r)YL (r̂)L"
We treat it as inhomogeneus term in Schrödinger equation.
To solve the equation efficiently, we developed modifiedNumerov method.
Since the wave function and its first derivative are continuous,the series converges uniformly even with truncated potential.
=> We expand the wave function.
!(r) = RL (r)YL (r̂)L" (L=(l,m))
Kellog, potential theory (1967)
K. Hatada et al, PRB (2007)
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Multiple scattering : Green’s function picture
Gii = G0
ii + G0inT nG0
ni
n! i" + G0
inT nG0nmT mG0
mi
n!m! i" +!
1
2 3
4
56
7
8
9
10
11
12
13
14
15
16
17
18
19
Gii
:Green’s function on cite i
All cites have centers.
G0ii :isolated
G0inT nG0
ni
n!
:single scattering
G0inT nG0
nmT mG0mi
nm!
:double scattering
G012
G021
T 2
G01,9
T 9
G01,12
T 12
G012,1
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Missing!
Check Natoli’s predictionof 30 years ago.
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Ge K-edge of GeCl4
1 Ge + 4 Cl + 38 EC(Empty cells)
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Other spectroscopies
• Energy-Loss Near-Edge Structure(ELNES)
• Resonant X-ray Scattering (RXS)• X-ray Photoelectron Diffraction (XPD)
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ELNES (NMT vs MT)
K. Hatada et. al, J. Phys. Cond. (2008)
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PHD of Ge 1s of GeCl4
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• You can find MXAN and FPMSprograms at,
http://www.lnf.infn.it/theory/CondensedMatter/index.html
Programs are free, but registration isobligated.
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THE MXAN PROCEDURE
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How to runFlow diagram of MXAN
Exp. file Coordinate file Commands file
MXAN MINUIT
Select structure VGEN CONTINUUM !2 test
Best fit files
Recalculate potential
Potential fixed
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We need three inputs
Experimental data: two columns file with thenormalized experimental data
energy(eV) abs-10.00 0.034048-9.000 0.037412-8.000 0.043628-7.000 0.052225-6.000 0.068452-5.000 0.098043-4.000 0.14981-3.000 0.23317-2.000 0.35128-1.000 0.532140.0000 0.747631.0000 1.00092.0000 1.28783.0000 1.5565…….. ………
We can use anyenergy step
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Starting geometry file – The prototype isgenerated by MXAN – Users must change itfor own use
&JOBfname ='NiH2'nsca = 19lmax = 3absorber= 1outersph=.false.edge ='k 'emin = -3.000emax = 150.000delta = 0.200xscale = 1.400gamma = .000typot ='hlrel'charelx ='ex'norman ='extrad'ovlpfac = .120coor ='angs'potcalc ='Y'symcalc ='Y'parcalc ='Y'v0imp = .000rhoimp = .000&END
tit1tit2tit3tit4 iz x y z rad ilig ------- comm ----------
28 .00000 .00000 .00000 1.26000 0 .00000 Ni________000 8 .00000 -1.90711 .00000 .90000 1 2.02119 O_________eq1……………………………………………………………………………………….
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----------------------------------------------------------------- CuN square piramid with O ax with H and more N --------------------------------------------------------------- CuNH --parameter- in.deviat. - init.err. --- phys.limits --- 1 r001 0.0000 0.0200 -0.1000 0.1000 2 f001 0.0000 3.0000 -20.0000 20.0000 3 t001 0.0000 0.0000 -10.0000 10.0000 4 r002 0.0000 0.0200 -0.1000 0.1000…………34 r012 0.0000 0.0000 -0.1500 0.150035 f012 0.0000 0.0000 -10.0000 10.000036 t012 0.0000 0.0000 -10.0000 10.0000
--------- Control options --------- 36 ! n of parameters (fixed + variable)NORM 1SHE ! Mode(NORM,EXTE,RECO),Search(1SHE,CXYZ,OPTN)U ! U (Unpol) XY (PolarXY) Z (Pol.z) P (Pol.)1 ! not active... --------- INPUT files -------------CuNH3.exp ! EXP. FILE to fit 0.01000 ! EXP. ERRORDATA.CuN8OH ! Coords and options for potentialN 1 ! Other th. calc. sites? How many? 0.5 CuN2H-22.BEST 0.0 ! Fract,Input calc.othersite, Shift? -------- INTERMEDIATE files -------------CuNH.PARM ! params for MSCuNH.SYMM ! File with symmetry info and lmaxCuNH.XALP ! X-alpha potentialCuNH.COUL ! Coulomb potentialCuNH.RHOD ! Charge densities --------- OUTPUT PREFIX ------------CuN8OH-1 ! Output files prefix (MAX 8 CHAR) -------- PARAMETERS align, norm, broad -------------- 0.025 0.004 1.500 3.000 !norm,+/-,Exp.shift,+/- Y 45000 ! Broad? Tot trials -3.500 2.000 ! E.Fermi -- +/- 1.600 0.400 ! Broad -- +/- 0.800 0.600 ! Broad_Exp -- +/- Y ! mf ? 1 ! # plasmons 14.000 10.000 10.000 8.000 ! En. +/- , Ampl. +/- N 0.02 70.0 0.02 !Extra Exc? ampl,energy,width-------- OTHER OPTIONS -------------- Y 6 ! Correlation links? How many? 1 7 4 10 2 8 5 11 16 22 19 25 ! between which params ? Y N !Slope?,Concerted motions? N 30.000 10.000 !weight?(N,A,T,G) xcentr, width
SET PRINT 3 SEEK 90! SCAN 13 10 -.2 .2! FIX 2. SIMPLEX 100 0.03 CALL FCN -2 MIGRAD SET OUT 70 HESSE SET OUT 8 SAVECALL FCN 3! CALL FCN -1! CONTOUR 1 4 3
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Control file – general information – methodsfor fitting – It is always calledCOMMAND.MIN
We get several outputs, the most important isthe BEST file where you find all informationabout the fit
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FPMS
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• Input file must be named as "data.ms".
• In principle the way to use parameters arethe same as "data.ms" of program POTGENor "DATA.****" of MXAN.
• For non-MT calculation, you should add, NMT = "NM" truncate = .true. (voronoi)or truncate = .false. (ASA)