athena&artemis による xafs データ解析 - pf · xafs講習会資料 - athena&artemis...
TRANSCRIPT
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XAFS Athena&Artemis XAFS
2010 10
KEK-PF
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1. Athena&Artemis .......................................................................... 4
1.1. ........................................................................................... 4
1.2. ( 2010 10 2) .................. 4
1.2.1. Horae ........................................................................... 5
1.2.2. Ifeffit ........................................................................... 5
1.3. ............................................................................. 5
1.4. (2010 10 2) ...................... 6
1.4.1. Windows ............................................................................... 6
1.4.2. Mac ...................................................................................... 7
1.4.3. LinuxBSDSolarisUNIX ............................................. 8
1.5. ................................................................................ 10
1.5.1. Horae ........................................................ 10
1.5.2. Ifeffit ........................................................ 10
1.5.3. FEFF ....................................................................... 11
1.6. ......................................................................................... 11
2. Athena .......................................................................... 11
2.1. Athena ...................................................... 12
2.1.1. .......................................................... 15
2.1.2. Ifeffit ..................................................... 17
2.1.3. ........................................................................... 17
2.1.4. ........................................................................ 18
2.2. ............................................................................. 18
2.2.1. ......................................... 18
2.2.2. .................................................................. 20
2.2.3. ............................................................................. 20
2.2.4. ........................................................................... 20
2.3. ............................................................................. 21
2.3.1. ........................................................................... 21
2.3.2. ................................................................................ 21
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2.3.3. ............................................................................. 21
2.3.4. ........................................................................... 21
2.3.5. ............................................................................. 21
2.3.6. ..................................................................... 21
2.3.7. ............................................................................. 21
2.3.8. ................................................................................ 22
2.4. ............................................................................. 22
2.4.1. ............................................................... 22
2.4.2. .................................................................. 22
2.4.3. Log-Ratio ............................................................................ 22
2.4.4. ........................................................................ 22
2.5. ........................................................................................... 22
2.5.1. ............................................................... 22
3. Artemis ......................................................................... 23
3.1. Artemis ..................................................... 23
3.2. ...................................................................................... 26
3.2.1. ........................................................................ 26
3.2.2. ............................................................ 27
3.2.3. EXAFS .................................................................. 27
3.2.4. .................................................................. 29
3.2.5. Fit .................................................................. 31
3.2.6. ........................................................................ 32
3.3. Artemis ...................................................................... 32
3.3.1. SUM ................................................................................... 32
3.3.2. GDS .................................................................. 32
3.3.3. Atoms ............................................................. 32
3.3.4. Quick first shell theory(QFS) ............................................... 33
3.3.5. FEFF(Version6L) .......................................................... 33
4. Hephaestus ............................................................................... 33
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1. Athena&Artemis 1.1.
AthenaArtemisIfeffitGUI
Windows MAC IfeffitAthenaArtemis
Ifeffit
Athena Artemis Athena Artemis
Horae Ifeffit UWXAFS
Feffit AutobkAthena Artemis
XAFS UWXAFS
XAFSUWXAFS
(CUI) GUI
(XAFS
)
Perl
(GUI)TkPGPLOT
WindowsMacLinuxBSDSolarisUNIX
OS
Athena Artemis GUI
Ifeffit
Ifeffit XAFS Athena ArtemisGUI
Athena Artemis GUI
Perl(
) PC
Athena Artemis GUI
Ifeffit
1.2. ( 2010 10 2)
HoraeIfeffitWindows MAC
Ifeffit Horae
-
Artemis FEFF GUI Ifeffit FEFF6L
7 FEFF()
1.2.1. Horae
070(WindowsMAC Ifeffit)
Athena 0.8.061
Artemis 0.8.014
Hephaestus 0.18
SixPack 0.67
1.2.2. Ifeffit
1.2.11 or 1.2.12
Ifeffit 1.2.11
Feff 6.02L
Feffit 2.984
Autobk 2.941
1.3.
Horae()
http://cars9.uchicago.edu/~ravel/software/
Downloads
Ifeffit
http://cars9.uchicago.edu/ifeffit/
Downloads
FEFF
http://leonardo.phys.washington.edu/feff/
9.03beta
8.4
Ifeffit FEFF6L EXAFS FEFF8
FEFF9 XANES
http://cars9.uchicago.edu/~ravel/software/http://cars9.uchicago.edu/ifeffit/http://leonardo.phys.washington.edu/feff/
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FEFF
FEFF
FEFF9 $500$250$250
FEFF8$400$200$200
FEFF7$350$175$175
FEFF9 $3000$1500$1500
FEFF8$2400$1200$1200
FEFF7$2100$1050$1050
1.4. (2010 10 2)
1.4.1. Windows
Windows NT, 2000, XP, VISTA, 7 (XP 64bit OK) Windows (95), 98, Mehttp://cars9.uchicago.edu/ifeffit/FAQ/Installing_Ifeffit#line-114 http://cars9.uchicago.edu/ifeffit/
win32 1.2.11 ifeffit-1.2.11.exe
2()
C:\Program Files\Ifeffit(
)
IfeffitAthenaArtemis
TIPS Athena Artemis runner.exe
runner.exe
Athena Artemisathena.exe
http://cars9.uchicago.edu/ifeffit/FAQ/Installing_Ifeffit#line-114http://cars9.uchicago.edu/ifeffit/
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1.4.2. Mac
Mac OS 10.2 PPC Intel CPU
http://cars9.uchicago.edu/ifeffit/
OS ver. CPU type Installer File
10.6, 10.5 Intel or PPC IXAFS_3.0.3 / iXAFS_211b1 (Universal)
10.4, 10.5 Intel or PPC iXAFS (Universal)
10.4 PPC ifeffit-1.2.10-Mac10.4_PPC_horae66.dmg
10.4 Intel ifeffit-1.2.10-Mac10.4_Intel_horae66.dmg
10.4 Intel iXAFSinstall.tar.gz
10.3 PPC ifeffit-1.2.8_Mac10.3.dmg
10.2 PPC ifeffit-1.2.4.dmg
Mac OS X CPU
Snow Leopard
http://cars9.uchicago.edu/ifeffit/
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perl(ver 5.8.9
ver 5.10.0)GUI perl/tk
(ifeffit)
SorceForge http://cars9.uchicago.edu/~ravel/software/downloads.html
Matt Newville
#Mac OS X PGPLOT ifeffit
(Mac OS X 10.6)PGPLOT
ifeffit
//////
1.4.3. LinuxBSDSolarisUNIX
PerlTkPGPLOTFortran
http://cars9.uchicago.edu/ifeffit/
Source Kit ifeffit-1.2.11c.tar.gz
PGPLOT
Windows Mac Horae
http://cars9.uchicago.edu/~ravel/software/downloads.html
horae-070.tar.gz
PGPLOTIfeffitHorae
Ifeffit
Ifeffit http://cars9.uchicago.edu/ifeffit/Mailing_List
Web Public archive
http://cars9.uchicago.edu/ifeffit/http://cars9.uchicago.edu/~ravel/software/downloads.htmlhttp://cars9.uchicago.edu/ifeffit/Mailing_List
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(
OSOpenSUSE 11.3 x86_64
Linux Kernel2.6.34.7-0.3.1
OS
C/C++
Perl
Tcl/Tk
gcc-fortran
Ifeffit(PGPLOT + Ifeffit)
./PGPLOT_install gidriv.f--no-gif
./PGPLOT_install --no-gif --with-64bit
PGPLOT Ifeffit
./configure
make
make install
Ifeffit
Horae
perl -MCPAN -e 'install Bundle::XasPerlBundle'
Perl
YES
sh build
Horae 1
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Athena Can't locate Tk/Splashscreen.pm
CPAN Tk::Splashscreen
cpan
CPAN
install Tk::Splashscreen
quit
/usr/bin/ifeffit_shell.pl
/usr/bin/lsprj
/usr/bin/rdaj
/usr/bin/artemis
/usr/bin/hephaestus
/usr/bin/atoms
/usr/bin/athena
1.5.
UWXAFS
AthenaArtemis GUI
Feffit Autobk
1.5.1. Horae
AthenaArtemisHephaestusAtoms http://cars9.uchicago.edu/~ravel/software/docs.html
1.5.2. Ifeffit
IfeffitAutobkFeffit http://cars9.uchicago.edu/ifeffit/Documentation
http://cars9.uchicago.edu/~ravel/software/docs.htmlhttp://cars9.uchicago.edu/ifeffit/Documentation
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Athena
1.5.3. FEFF
FEFFWeb
http://leonardo.phys.washington.edu/feff/html/documentation.html
XAFS FEFF8
http://msmd.ims.ac.jp/jxs/feff82j.pdf
XAFSWeb
1.6.
(Bruce Ravel)
"IFEFFIT: interactive EXAFS analysis and FEFF fitting" M. Newville, J.
Synchrotron Rad. 8, pp 322-324 (2001).
"ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption
spectroscopy using IFEFFIT" , B. Ravel and M. Newville, J. Synchrotron Rad. 12,
pp 537-541 (2005).
"ATOMS: crystallography for the X-ray absorption spectroscopist", B. Ravel J.
Synchrotron Rad. 8, pp. 314-316 (2001) .
2. Athena Athna
XANES
Athena
http://leonardo.phys.washington.edu/feff/html/documentation.htmlhttp://msmd.ims.ac.jp/jxs/feff82j.pdfhttp://cars9.uchicago.edu/~newville/Papers/JSR_PH5149.pdfhttp://dx.doi.org/10.1107/S0909049505012719http://dx.doi.org/10.1107/S0909049505012719http://dx.doi.org/10.1107/S090904950001493X
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2.1. Athena
UI
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File Edit
Group Values
-
Plot Mark
Data Merge
Analysis Settings
-
Help
2.1.1.
Athena
Athena(.prj)
Athena(.norm.chi)
()
#
()
OS
data.dat OK
data - .dat NG
data - copy.dat OK
Windows
Windows7
Windows7
-
Windows
File Open Files
Athena
X
GraphicsWindow
OK
ln(I0/I)
-
(I1+I2++In)/I0
Group
Data TypeEnergy Units
PreprocessBinReference
Athena
(.prj)
ArtemisAthena
Artemis EXAFS
2.1.2. Ifeffit
Athena Ifeffit Ifeffit
Athena PalettesIfeffit
Athena PalettesTitles#
Data
Echo AthenaMacro Ifeffit
Journal
2.1.3.
Athena Group
Athena()
Group
Group (Mark) ON
GroupGroup
-
GroupAlt+k
GroupAlt+j
Group()Alt+l
2.1.4.
Athena
Group
GroupGroup
ValuesGroup
(E0:)
()
GroupMark
2.2.
Artemis EXAFS
2.2.1.
PF SPring-8(9809
)
Athena(I0 I)
PF XAFS Athena
2010 6 Bruce Ravel PF SPring-8
Athena
-
http://cars9.uchicago.edu/ifeffit/BruceRavel/PhotonFactorySpring8
PFBL12C.pm
Web
C:\Documents and Settings\UserName\Application Data\horae\Ifeffit\Plugins\F
iletype\Athena\
(WindowsXP)
C:\Users\UserName\AppData\Roaming\horae\Ifeffit\Plugins\Filetype\Athena
(Windows7)
PC
C:\Program Files\Ifeffit\share\perl\Ifeffit\Plugins\Filetype\Athena
PFBL12C.pm
2010 10 6
PFBL12C.pm ()142
$list[2+$i] = $list[2+$i] - $offsets[2+$i];
$list[2+$i] = $list[2+$i]
OK
AthenaSetting Plugin Registry
PFBL12CONReturn to the main
window
E = hc2d sin
hc=12398.52
PFBL12C.pm
d
Z Edge
http://cars9.uchicago.edu/ifeffit/BruceRavel/PhotonFactorySpring8
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2.2.2.
E0Athena E0
Pre-edge
range Group
Autobk
k-weightPre-edgeNormalizationSpline
Pre-edgeNormalization
Spline
k
S/N k-weightRbkgSpline clamps
2.2.3.
Phase correction ONR
R Artemis
Off
Arbitrary k-weight 123
dkdr
2.2.4.
Group Mark
EkRqWindow
Stack
Ind(Windows)
PF X Y
-
Plotting parameters plot multiplier
2.3.
Athena
2.3.1.
2.3.2.
2.3.3.
2.3.4.
QuickScan
2.3.5.
2.3.6.
Lorentzian Gaussian
2.3.7.
-
2.3.8.
Group
2.4.
Athena
XANES
2.4.1.
GroupGroup
2.4.2.
XANES
2.4.3. Log-Ratio
2.4.4.
2 Group Group
2.5.
2.5.1.
Setting Edit Preferences
athena.ini
OK
Plot Window
Athena Plot Window
-
Athena
3. Artemis ArtemisEXAFS
Feffit Feffit
Artemis FEFF
Atoms FEFF
FEFF
EXAFS
3.1. Artemis
UI
-
File Edit GDS
Data Sum
-
Fits Theory
Paths Plot
-
Help
3.2.
AthenaArtemis
1. Athena
2.
3. Atoms
4. FEFF
5.
6.
3.2.1.
FEFF
Athena ()
Athena(.prj)OpenFile
Artemis
2
1
Athena chi.dat
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3.2.2.
Athena
Fitting SpaceFit k-weights
Fit k-weights
k-weight
Independent PointsData
How Many Independent Points?
Athena
3.2.3. EXAFS
Artemis(Ifeffit)
EXAFS
3 FEFF
FEFF
Atoms
Artemis
Atoms TheoryNew Atoms PageBlank Page
Atoms( Atoms
)
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Atoms Au
()
Cluster Size EdgeCore
Cluster Size
6 EXAFS 6
VESTA
VESTA http://www.geocities.jp/kmo_mma/crystal/jp/vesta.html
Edge Core X ()
CuOCu EXAFS
CuO O
FEFF
http://www.geocities.jp/kmo_mma/crystal/jp/vesta.html
-
Run AtomsAtomsFEFF
Run FEFF FEFF
FEFF FEFF
NLEG 2
Run FEFF
FEFF FEFF
FEFF
Just the first
No paths
3.2.4.
Add
Add Paths
-
Artemis(Ifeffit) EXAFS
model(k) = path(k, Amp(k), Phase(k), PathParameters)Paths
Amp(k)Phase(k) FEFF
S02 amp
N:S02 N
N:=1 S02=amp*n 2
delR Reff
-
Guess, Def, Set
Guess Set
Def reff
1 2
12 n1 Guess
2 n2 Def n2=12-n1
3.2.5. Fit
Fit
R-factor
2
-
1
3.2.6.
Plot after the fit ON
3.3. Artemis
3.3.1. SUM
EXAFS
3.3.2. GDS
Skip Artemis
GDS
Restrain
After
3.3.3. Atoms
Ifeffit
C:\Program Files\Ifeffit\share\atomsdb
TheoryNew atoms pageImport atoms.inp
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3.3.4. Quick first shell theory(QFS)
QFS
FEFF
3.3.5. FEFF(Version6L)
2
Artemis Preference feff
Value feff6l
FEFF
Atoms feff.inp
Preference atomsfeff_version
FEFF8 8
template feff.inp
C:\Program Files\Ifeffit\share\atp
Artemis FEFF
FEFF Print feffnnnn.dat
Theory Add a feff path
4. Hephaestus Horae Hephaestus
1. Athena&Artemis1.1. 1.2. (2010102)1.2.1. Horae 1.2.2. Ifeffit
1.3. 1.4. (2010102)1.4.1. Windows1.4.2. Mac1.4.3. LinuxBSDSolarisUNIX
1.5. 1.5.1. Horae1.5.2. Ifeffit1.5.3. FEFF
1.6.
2. Athena2.1. Athena2.1.1. 2.1.2. Ifeffit2.1.3. 2.1.4.
2.2. 2.2.1. 2.2.2. 2.2.3. 2.2.4.
2.3. 2.3.1. 2.3.2. 2.3.3. 2.3.4. 2.3.5. 2.3.6. 2.3.7. 2.3.8.
2.4. 2.4.1. 2.4.2. 2.4.3. Log-Ratio2.4.4.
2.5. 2.5.1.
3. Artemis3.1. Artemis3.2. 3.2.1. 3.2.2. 3.2.3. EXAFS3.2.4. 3.2.5. Fit3.2.6.
3.3. Artemis3.3.1. SUM3.3.2. GDS3.3.3. Atoms3.3.4. Quick first shell theory(QFS)3.3.5. FEFF(Version6L)
4. Hephaestus