Instructions for using BL14B2 XAFS Standard Sample database (Ver. BENTEN)
11.24.2022 Hironori Ofuchi
1. Connecting to a database site(1)OpentheSPring-8

experimental

datatransfersystem

BENTEN(URL:

https://benten.spring8.or.jp/). When you open the URL, the top page (Fig. 1) is displayed.

Fig. 1(2)

UI site (SPring-8 / SACLA electronic application system (https://user.spring8.or.jp/)), Enter youruser name (SPring-8 ID) and password, and click the Login button. To log in with your personal
email address, click "Guest login with Email" under the Login button. The guest login screen
shown in Figure 2 will be displayed. Enter your email address and click the Login button. If youlog in normally, the screen (Fig. 3) related to email address authentication (two-factorauthentication) will be displayed.

*After creating a new UI site account, it will take about a day to log in to this database site.

1

Fig. 2

Fig. 3(3)

Click " Send Email" button. Following screen is displayed (Fig. 4).

2

Fig. 4
(4)

Check e-mail of subject “Guide for BENTEN authentication” in your e-mail software (Fig. 5)

Fig. 5 BENTEN authentication e-mail(5)When you click the link in the e-mail, a screen will be displayed to prompt for authentication(Fig.6).

3

Fig.6(6)

Click “Authenticate” button. The authentication completion screen is displayed (Fig. 7)

Fig. 7 Authentication completion screen(7)

The email sending screen in Fig. 4 is redirected to the data viewing screen (Fig. 8).

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Fig. 8 Data viewing screen52. Browsing standard sample data
2-1. Viewing data
(1) In the tree display on the left side of the screen, the screen shown in Fig. 9 (a) is displayed. Thefolder hierarchy of the tree is・root(Fig. 9 (a))
・SPring-8(Fig. 9 (b))
・BL14B2(Fig. 9 (c))
・XAFS_Standard (Registration folder for XAFS standard sample data、Fig. 9 (d))
・Element(Fig. 9 (e))
・Absorption edge(K,L3,2,1、Fig. 9 (f))
・Net plane(Si(111) or Si(311)、Fig. 9 (g))
・Name of standard sample(Fig. 9 (h))
It is in the order of. In the corresponding data field, the information of the folder one level below thefolder selected in the tree display (in the case of the lowest layer, the data file included in the folder) isdisplayed.

Select root

Tree display
Corresponding data

Corresponding data
thumbnail image

Fig.9 (a) Initial screen for tree display(select the top (root) of the tree display)6

Select SPring-8(b) Selecting SPring-8 folder

Select BL14B2(c) Selecting BL14B2folder

7Select XAFS_Standard(d) Selecting XAFS_Standard folder

Select Cu(e) Selecting element folder (ex. Cu folder)8Select K(f) Selecting absorption edge folder (ex. K)

Select 111(g) Selecting net plane folder (ex. 111)9

Cu-foil を選択(h) Selecting sample name folder (ex. Cu-foil)
2-2. Browsing experimental data information(1)

Select the folder of the sample you want to browse from the tree display and display thecorresponding data screen (Fig. 10).

Fig.10 Display of applicable data screen (selecting Cu-foil folder)(2)

Click any of the data in the corresponding data screen on the upper right. Click to display

experimental data information (Fig. 11 (a) thumbnail image, (b) simple information).

10Click one(a)

Scroll down(b)Fig.11 Experiment data information screen(a) Thumbnail image (b) Simple information(Scroll down the lower right screen)

2-3. Types of experimental data
(1) In the BL14B2 XAFS standard sample database, 3 types of experimental data (extensions dat, ex3,
txt ((5 types if fitted encoder processing is available)) for one registration number, and detailed
informationof

theexperimental

data.

metadata.data_format.yml, metadata.data_info.yml) is registered.

11(metadata.main.yml,

(a)

(b)

Figure 12 Database registration data ((a) Cu-foil, (b) Pd-foil)
The measurement information is described in the file name of the experimental data in the followingorder.
Element－Absorption edge－Sample name－Net plane－Dwell time－Measurement date－(fe).Extension
An example of the measurement information shown in the file name of each registered data in FIG. 12
is shown below.
(Example 1) Cu-K_Cu-foil_Si111_50ms_120613.dat
Element: Cu
Absorption edge: K-edge
Sample name: Cu-foil
Net plane: Si (111)
Dwell time: 50msec per point
Measurement date: June 13, 2012
Extension: dat (9809 format)(Example 2) Pd-K_Pd-foil_Si111_50ms_150511_fe.txt Element:
PdAbsorption edge: K-edge
Sample name: Pd-foil
Net plane: Si (111)
Dwell time: 50msec per point
Measurement date: May 11, 2015
fe: With fitted encoder processing (*)
Extension: Readable by XAFS analysis software Athena((*) Refer to Appendix I about fitted encoder processing )12

Table 1 shows the file formats of the experimental data extensions.
Table 1 Extension file format
Extension

File typedat

Measurement data (9809 format)

ex3

Readable by XAFS analysis software REX2000

txt

Readable by XAFS analysis software Athena

The file with the extension yml contains information such as standard samples, measurement
conditions, measurement data, and main items. These are YAML-formatted text files that can beviewed with a text editor or browser (Fig. 12). Currently, three types of metadata.main.yml,metadata.data_format.yml, and metadata.data_info.yml are registered. Table 2 shows the items in eachyml file.

Fig.1213

Table 2 Items listed in the yml file (a) metadata.main.yml
sample (Category of sample)
chemical_formula

Chemical formula of the sample

lot_number

Lot number of the sample

model_number

Model number of the sample

nameSubstance name of the sample

supplier

Supplier name of sample

tagThe sample (main, measured by I0-I1 detector) or
reference sample (reference, measured by I1-I2detector)

measurement (Category of measurement parameters)
category

Measurement method category

sub_category

Measurement method subcategory

absorption_edge

Measuring element and absorption edge

instrument (Category of measuring instrument)
vertical_size [mm]4D slit size ((W) width)

horizontal_size [mm]4D slit size ((H) height)

type

Types of I0, I1 and I2 detectors

gasType of gas used for I0, I1 and I2 detectors

HV [V]

Applicable voltage value to I0, I1 and I2 detectors

amp_gain [V / A]

Gain value of I0, I1 and I2 detectors

localmeasurement_time [sec]Time taken from the start to the end of measurement

xafs_filename_list

File name of experiment data (9809 format)(b) metadata.data_format.yml

xafs_raw_data_format (Category of measurement data)
extension

extension

nameitem nameunit

unit

additional_metadata

Additional information for each item

xafs_processed_data_format (Category of converted data)14

extension

extension

nameitem nameunitunit

formulaConversion formula from measurement data

additional_metadata

Additional information for each item(c) metadata.data_info.yml

proposal_number

proposal number

access_rights

Access rights

data_depositor (Category of data writer)
name

Name of the data writerorganization

Data writer's organization

contact_name (Category of data responsible)
name

Name of the data manager

organization

Data responsible organizationrole

The role of the data manager

4．Download experimental data
4-1 How to download data
(1) Check the experimental data of the sample you want to download (Fig. 14).

Put a check

Fig. 14 Experimental data information screen (Cu-foil)

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(2) Click the "DOWNLOAD CHECKED ITEMS" button on the screen. A zip file save message will
be displayed, so save it in any folder.

Fig. 15 Experiment data save screen (for Microsoft Edge)
4-3 How to download multiple data
(1) If you want to download multiple data at once, check the check box of the data you want todownload and click the "DOWNLOAD CHECKED ITEMS" button (Fig. 16 (a)-(c)).

Fig. 16 (a) Downloading for each sample folder

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(b)Downloading for each net plane folder(d)Downloading for each element folder

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Appendix
I.

Fitted encoder processing for Angle selection
In the beamline BL14B2, short-period vibrational components different from EXAFS vibrations
sometimes overlap on the high-energy side of XAFS spectra measured in the high-energy region. Asexample, the normalized EXAFS of Pd(NH3)4Cl2・H2O measured at the Pd-K edge and Si(111) net
plane is shown in Fig.17. As the wavenumber increases, the short-period vibrational component
becomes more pronounced. This short-period vibrational component is not due to the sample, but tothe encoder of the crystal monochromator.

Fig.17 Normalized EXAFS of Pd(NH3)4Cl2・H2O (Pd-K, Si(111) net plane)(Angle(o) is specified for Angle selection when converting data with XAFS_DataConverter.)Figure 18 shows the angles of the crystal monochromator (PC and encoder values) when the XAFS
spectrum in Fig. 17 was measured, and it can be seen that there is a periodic shift in the encoder values
with respect to the PC angle. Since the sample-derived vibrational component is larger at the low
wavenumber side of the normalized EXAFS, the effect of this periodic vibration is negligible.
However, at the high wavenumber side, where the amplitude of the vibration component becomes
smaller, the effect cannot be ignored, and a short periodic vibration component appears as shown inFig.17. This periodic vibration of encoder values is not a problem specific to the beamline BL14B2,
but is also seen in other beamlines. (This has been confirmed at the beamline BL19B2 and BL46XU.
However, the degree of periodic deviation and the energy region where the deviation occurs vary frombeamline to beamline. In most cases, the periodicity is much different compared to the EXAFS
oscillation component, so the measured data are not affected).

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系列14.75000
y = -4.77531E-02x2 + 1.41862E+00x - 9.14014E-01
多項…

4.70000
4.65000
4.60000
4.55000
4.50000
4.45000

expansio
n4.40000

4.35000
4.35000 4.40000 4.45000 4.50000 4.55000 4.60000 4.65000 4.70000 4.75000
系列14.45000
y = -4.77531E-02x2 + 1.41862E+00x - 9.14014E-01
多項…

4.44500
4.44000
4.43500
4.43000
4.42500
4.42000
4.41500
4.41000
4.40500
4.40000
4.40000

4.41000

4.42000

4.43000

4.44000

Fig.18 Angles of Spectroscopic Crystals(From the file created by "Output Excel file (for angle correction confirmation)" in
XAFS_DataConverter)

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4.45000

The XAFS data conversion program corrects for this periodic shift using a polynomial
approximation (red line in Fig. 18) by processing the fitted encoder. Figure 19 shows a comparison of
the normalized EXAFS spectral shape with and without the fitted encoder process, and it can be seenthat the fitted encoder process eliminates the short-period vibration component on the highwavenumber side.

Fig.19 Normalized EXAFS of Pd(NH3)4Cl2・H2O (Pd-K edge, Si(111) net plane)(Blue line: without fitted encoder processing, red line: with fitted encoder processing)
When fitted encoder processing is performed, the XANES spectrum is modulated from the original
data as shown in Fig.20. Therefore, when discussing XANES spectra, care should be taken not to mix
fitted encoder processed data with non-fitted encoder processed data.
In addition, not all encoder-derived vibration components appear on the high wavenumber side of
all EXAFS spectra in the high-energy region. Figure 21 shows the normalized EXAFS ofPd(NH3)4Cl2・H2O measured on the Si(311) net plane, and unlike the measurement on the Si(111) netplane, no short-period vibration component is observed on the high wavenumber side, and thespectrum shape is almost unchanged after fitted encoder processing. Therefore, it is possible todetermine whether the short-period vibration on the high wavenumber side originates from theencoder or not by comparing the spectrum without fitted encoder processing (Angle(o)) and with fittedencoder processing (Angle(fitted encoder)).

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Fig.20 XANES spectra of Pd(NH3)4Cl2・H2O (Pd-K edge, Si(111) net plane)(Blue line: without fitted encoder processing, red line: with fitted encoder processing)Fig.21 XANES spectra of Pd(NH3)4Cl2・H2O (Pd-K edge, Si(311) net plane)(Blue line: without fitted encoder processing, red line: with fitted encoder processing)21

Revision history
Revision dateReviser

3.31.2022

Hironori Ofuchi

11.24.2022

Hironori Ofuchi

22