athena&artemis による xafs データ解析 - pf · xafs講習会資料－ athena&artemis...

XAFS Athena&Artemis XAFS

2010 10

KEK-PF

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

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

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/

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/

1.4.2. Mac

Mac OS 10.2 PPC Intel CPU


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


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


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

(

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

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

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

2.1. Athena

UI

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

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

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

)

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

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

athena&artemis による xafs データ解析 - pf · xafs講習会資料 － athena&artemis...

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athena&artemis による xafs データ解析 - pf · xafs講習会資料－ athena&artemis...